diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS index b145a3178f..4f561a4c19 100644 --- a/.github/CODEOWNERS +++ b/.github/CODEOWNERS @@ -16,6 +16,9 @@ src/COMPRESS/* @akohlmey src/GPU/* @ndtrung81 src/KOKKOS/* @stanmoore1 src/KIM/* @ellio167 +src/LATTE/* @cnegre +src/MESSAGE/* @sjplimp +src/SPIN/* @julient31 src/USER-CGDNA/* @ohenrich src/USER-CGSDK/* @akohlmey src/USER-COLVARS/* @giacomofiorin @@ -30,19 +33,86 @@ src/USER-PHONON/* @lingtikong src/USER-OMP/* @akohlmey src/USER-QMMM/* @akohlmey src/USER-REAXC/* @hasanmetin +src/USER-SCAFACOS/* @rhalver src/USER-TALLY/* @akohlmey src/USER-UEF/* @danicholson src/USER-VTK/* @rbberger + # individual files in packages src/GPU/pair_vashishta_gpu.* @andeplane src/KOKKOS/pair_vashishta_kokkos.* @andeplane src/MANYBODY/pair_vashishta_table.* @andeplane +src/MANYBODY/pair_atm.* @sergeylishchuk src/USER-MISC/fix_bond_react.* @jrgissing src/USER-MISC/*_grem.* @dstelter92 +src/USER-MISC/compute_stress_mop*.* @RomainVermorel + +# core LAMMPS classes +src/lammps.* @sjplimp +src/pointers.h @sjplimp +src/atom.* @sjplimp +src/atom_vec.* @sjplimp +src/angle.* @sjplimp +src/bond.* @sjplimp +src/comm*.* @sjplimp +src/compute.* @sjplimp +src/dihedral.* @sjplimp +src/domain.* @sjplimp +src/dump*.* @sjplimp +src/error.* @sjplimp +src/finish.* @sjplimp +src/fix.* @sjplimp +src/force.* @sjplimp +src/group.* @sjplimp +src/improper.* @sjplimp +src/kspace.* @sjplimp +src/lmptyp.h @sjplimp +src/library.* @sjplimp +src/main.cpp @sjplimp +src/memory.* @sjplimp +src/modify.* @sjplimp +src/molecule.* @sjplimp +src/my_page.h @sjplimp +src/my_pool_chunk.h @sjplimp +src/npair*.* @sjplimp +src/ntopo*.* @sjplimp +src/nstencil*.* @sjplimp +src/neighbor.* @sjplimp +src/nbin*.* @sjplimp +src/neigh_*.* @sjplimp +src/output.* @sjplimp +src/pair.* @sjplimp +src/rcb.* @sjplimp +src/random_*.* @sjplimp +src/region*.* @sjplimp +src/rcb.* @sjplimp +src/read*.* @sjplimp +src/rerun.* @sjplimp +src/run.* @sjplimp +src/respa.* @sjplimp +src/set.* @sjplimp +src/special.* @sjplimp +src/suffix.h @sjplimp +src/thermo.* @sjplimp +src/universe.* @sjplimp +src/update.* @sjplimp +src/variable.* @sjplimp +src/verlet.* @sjplimp +src/velocity.* @sjplimp +src/write_data.* @sjplimp +src/write_restart.* @sjplimp + +# overrides for specific files +src/dump_movie.* @akohlmey +src/exceptions.h @rbberger +src/fix_nh.* @athomps +src/info.* @akohlmey @rbberger +src/timer.* @akohlmey # tools tools/msi2lmp/* @akohlmey +tools/emacs/* @HaoZeke # cmake cmake/* @junghans @rbberger diff --git a/.gitignore b/.gitignore index 50b970249a..1ce415678e 100644 --- a/.gitignore +++ b/.gitignore @@ -1,6 +1,7 @@ *~ *.o *.so +*.lo *.cu_o *.ptx *_ptx.h @@ -32,6 +33,7 @@ log.cite .Trashes ehthumbs.db Thumbs.db +.clang-format #cmake /build* diff --git a/README b/README index a258a335e9..680986bf61 100644 --- a/README +++ b/README @@ -25,7 +25,7 @@ The LAMMPS distribution includes the following files and directories: README this file LICENSE the GNU General Public License (GPL) bench benchmark problems -couple code coupling examples using LAMMPS as a library +cmake CMake build system doc documentation examples simple test problems lib libraries LAMMPS can be linked with @@ -36,7 +36,14 @@ tools pre- and post-processing tools Point your browser at any of these files to get started: -doc/Manual.html the LAMMPS manual -doc/Section_intro.html hi-level introduction to LAMMPS -doc/Section_start.html how to build and use LAMMPS -doc/Developer.pdf LAMMPS developer guide +http://lammps.sandia.gov/doc/Manual.html the LAMMPS manual +http://lammps.sandia.gov/doc/Intro.html hi-level introduction +http://lammps.sandia.gov/doc/Build.html how to build LAMMPS +http://lammps.sandia.gov/doc/Run_head.html how to run LAMMPS +http://lammps.sandia.gov/doc/Developer.pdf LAMMPS developer guide + +You can also create these doc pages locally: + +% cd doc +% make html # creates HTML pages in doc/html +% make pdf # creates Manual.pdf and Developer.pdf diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index 7e4fd690e9..ce8de0b501 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -6,15 +6,66 @@ cmake_minimum_required(VERSION 2.8.12) project(lammps CXX) set(SOVERSION 0) -set(LAMMPS_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../src) -set(LAMMPS_LIB_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../lib) -set(LAMMPS_LIB_BINARY_DIR ${CMAKE_BINARY_DIR}/lib) +get_filename_component(LAMMPS_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../src ABSOLUTE) +get_filename_component(LAMMPS_LIB_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../lib ABSOLUTE) +get_filename_component(LAMMPS_LIB_BINARY_DIR ${CMAKE_BINARY_DIR}/lib ABSOLUTE) +get_filename_component(LAMMPS_DOC_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../doc ABSOLUTE) -#To not conflict with old Makefile build system, we build everything here -file(GLOB LIB_SOURCES ${LAMMPS_SOURCE_DIR}/*.cpp) + +# To avoid conflicts with the conventional Makefile build system, we build everything here +file(GLOB LIB_SOURCES ${LAMMPS_SOURCE_DIR}/[^.]*.cpp) file(GLOB LMP_SOURCES ${LAMMPS_SOURCE_DIR}/main.cpp) list(REMOVE_ITEM LIB_SOURCES ${LMP_SOURCES}) +# Utility functions +function(list_to_bulletpoints result) + list(REMOVE_AT ARGV 0) + set(temp "") + foreach(item ${ARGV}) + set(temp "${temp}* ${item}\n") + endforeach() + set(${result} "${temp}" PARENT_SCOPE) +endfunction(list_to_bulletpoints) + +function(validate_option name values) + string(TOLOWER ${${name}} needle_lower) + string(TOUPPER ${${name}} needle_upper) + list(FIND ${values} ${needle_lower} IDX_LOWER) + list(FIND ${values} ${needle_upper} IDX_UPPER) + if(${IDX_LOWER} LESS 0 AND ${IDX_UPPER} LESS 0) + list_to_bulletpoints(POSSIBLE_VALUE_LIST ${${values}}) + message(FATAL_ERROR "\n########################################################################\n" + "Invalid value '${${name}}' for option ${name}\n" + "\n" + "Possible values are:\n" + "${POSSIBLE_VALUE_LIST}" + "########################################################################") + endif() +endfunction(validate_option) + +function(get_lammps_version version_header variable) + file(READ ${version_header} line) + set(MONTHS x Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec) + string(REGEX REPLACE "#define LAMMPS_VERSION \"([0-9]+) ([A-Za-z]+) ([0-9]+)\"" "\\1" day "${line}") + string(REGEX REPLACE "#define LAMMPS_VERSION \"([0-9]+) ([A-Za-z]+) ([0-9]+)\"" "\\2" month "${line}") + string(REGEX REPLACE "#define LAMMPS_VERSION \"([0-9]+) ([A-Za-z]+) ([0-9]+)\"" "\\3" year "${line}") + string(STRIP ${day} day) + string(STRIP ${month} month) + string(STRIP ${year} year) + list(FIND MONTHS "${month}" month) + string(LENGTH ${day} day_length) + string(LENGTH ${month} month_length) + if(day_length EQUAL 1) + set(day "0${day}") + endif() + if(month_length EQUAL 1) + set(month "0${month}") + endif() + set(${variable} "${year}${month}${day}" PARENT_SCOPE) +endfunction() + +get_lammps_version(${LAMMPS_SOURCE_DIR}/version.h LAMMPS_VERSION) + # Cmake modules/macros are in a subdirectory to keep this file cleaner set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/Modules) @@ -23,21 +74,23 @@ if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS) set(CMAKE_BUILD_TYPE Release CACHE STRING "Choose the type of build, options are: None Debug Release RelWithDebInfo MinSizeRel." FORCE) endif(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS) -file(GLOB SRC_FILES ${LAMMPS_SOURCE_DIR}/*.cpp) -list(SORT SRC_FILES) -# check for files installed by make-based buildsystem -# only run this time consuming check if there are new files -if(NOT SRC_FILES STREQUAL SRC_FILES_CACHED) - file(GLOB SRC_PKG_FILES ${LAMMPS_SOURCE_DIR}/*/*.cpp) - message(STATUS "Running check for installed package (this might take a while)") - foreach(_SRC SRC_PKG_FILES) - get_filename_component(FILENAME "${_SRC}" NAME) - if(EXISTS ${LAMMPS_SOURCE_DIR}/${FILENAME}) - message(FATAL_ERROR "Found packages installed by the make-based buildsystem, please run 'make -C ${LAMMPS_SOURCE_DIR} no-all purge'") - endif() - endforeach() - set(SRC_FILES_CACHED "${SRC_FILES}" CACHE INTERNAL "List of file in LAMMPS_SOURCE_DIR" FORCE) -endif() +# check for files auto-generated by make-based buildsystem +# this is fast, so check for it all the time +message(STATUS "Running check for auto-generated files from make-based build system") +file(GLOB SRC_AUTOGEN_FILES ${LAMMPS_SOURCE_DIR}/style_*.h) +list(APPEND SRC_AUTOGEN_FILES ${LAMMPS_SOURCE_DIR}/lmpinstalledpkgs.h) +foreach(_SRC ${SRC_AUTOGEN_FILES}) + get_filename_component(FILENAME "${_SRC}" NAME) + if(EXISTS ${LAMMPS_SOURCE_DIR}/${FILENAME}) + message(FATAL_ERROR "\n########################################################################\n" + "Found header file(s) generated by the make-based build system\n" + "\n" + "Please run\n" + "make -C ${LAMMPS_SOURCE_DIR} purge\n" + "to remove\n" + "########################################################################") + endif() +endforeach() ###################################################################### # compiler tests @@ -49,20 +102,60 @@ if (${CMAKE_CXX_COMPILER_ID} STREQUAL "Intel") set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict") endif() -option(ENABLE_COVERAGE "Enable code coverage" OFF) -if(ENABLE_COVERAGE) - set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} --coverage") +# GNU compiler features +if (${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU") + option(ENABLE_COVERAGE "Enable code coverage" OFF) + mark_as_advanced(ENABLE_COVERAGE) + if(ENABLE_COVERAGE) + set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} --coverage") + endif() + option(ENABLE_SANITIZE_ADDRESS "Enable address sanitizer" OFF) + mark_as_advanced(ENABLE_SANITIZE_ADDRESS) + if(ENABLE_SANITIZE_ADDRESS) + set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize=address") + endif() + option(ENABLE_SANITIZE_UNDEFINED "Enable undefined behavior sanitizer" OFF) + mark_as_advanced(ENABLE_SANITIZE_UNDEFINED) + if(ENABLE_SANITIZE_UNDEFINED) + set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize=undefined") + endif() + option(ENABLE_SANITIZE_THREAD "Enable thread sanitizer" OFF) + mark_as_advanced(ENABLE_SANITIZE_THREAD) + if(ENABLE_SANITIZE_THREAD) + set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize=thread") + endif() endif() ######################################################################## # User input options # ######################################################################## -option(BUILD_SHARED_LIBS "Build shared libs" OFF) -if(BUILD_SHARED_LIBS) # for all pkg libs, mpi_stubs and linalg - set(CMAKE_POSITION_INDEPENDENT_CODE ON) +option(BUILD_EXE "Build lmp binary" ON) +if(BUILD_EXE) + set(LAMMPS_MACHINE "" CACHE STRING "Suffix to append to lmp binary (WON'T enable any features automatically") + mark_as_advanced(LAMMPS_MACHINE) + if(LAMMPS_MACHINE) + set(LAMMPS_MACHINE "_${LAMMPS_MACHINE}") + endif() + set(LAMMPS_BINARY lmp${LAMMPS_MACHINE}) endif() -option(DEVELOPER_MODE "Enable developer mode" OFF) -mark_as_advanced(DEVELOPER_MODE) + +option(BUILD_LIB "Build LAMMPS library" OFF) +if(BUILD_LIB) + option(BUILD_SHARED_LIBS "Build shared library" OFF) + if(BUILD_SHARED_LIBS) # for all pkg libs, mpi_stubs and linalg + set(CMAKE_POSITION_INDEPENDENT_CODE ON) + endif() + set(LAMMPS_LIB_SUFFIX "" CACHE STRING "Suffix to append to liblammps and pkg-config file") + mark_as_advanced(LAMMPS_LIB_SUFFIX) + if(LAMMPS_LIB_SUFFIX) + set(LAMMPS_LIB_SUFFIX "_${LAMMPS_LIB_SUFFIX}") + endif() +endif() + +if(NOT BUILD_EXE AND NOT BUILD_LIB) + message(FATAL_ERROR "You need to at least enable one of two following options: BUILD_LIB or BUILD_EXE") +endif() + option(CMAKE_VERBOSE_MAKEFILE "Generate verbose Makefiles" OFF) include(GNUInstallDirs) @@ -70,6 +163,34 @@ set(LAMMPS_LINK_LIBS) set(LAMMPS_DEPS) set(LAMMPS_API_DEFINES) +set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE GRANULAR + KSPACE MANYBODY MC MEAM MESSAGE MISC MOLECULE PERI REAX REPLICA RIGID SHOCK SPIN SNAP + SRD KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE USER-ATC USER-AWPMD USER-BOCS + USER-CGDNA USER-MESO USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE + USER-EFF USER-FEP USER-H5MD USER-LB USER-MANIFOLD USER-MEAMC USER-MGPT USER-MISC + USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-QTB USER-REAXC USER-SCAFACOS + USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM) +set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU) +set(OTHER_PACKAGES CORESHELL QEQ) +foreach(PKG ${DEFAULT_PACKAGES}) + option(PKG_${PKG} "Build ${PKG} Package" OFF) +endforeach() +foreach(PKG ${ACCEL_PACKAGES} ${OTHER_PACKAGES}) + option(PKG_${PKG} "Build ${PKG} Package" OFF) +endforeach() + +###################################################### +# packages with special compiler needs or external libs +###################################################### +if(PKG_REAX OR PKG_MEAM OR PKG_USER-QUIP OR PKG_USER-QMMM OR PKG_LATTE OR PKG_USER-SCAFACOS) + enable_language(Fortran) +endif() + +if(PKG_MEAM OR PKG_USER-H5MD OR PKG_USER-QMMM OR PKG_USER-SCAFACOS) + enable_language(C) +endif() + +# do MPI detection after language activation, if MPI for these language is required find_package(MPI QUIET) option(BUILD_MPI "Build MPI version" ${MPI_FOUND}) if(BUILD_MPI) @@ -88,13 +209,22 @@ else() list(APPEND LAMMPS_LINK_LIBS mpi_stubs) endif() -set(LAMMPS_SIZE_LIMIT "LAMMPS_SMALLBIG" CACHE STRING "Lammps size limit") -set_property(CACHE LAMMPS_SIZE_LIMIT PROPERTY STRINGS LAMMPS_SMALLBIG LAMMPS_BIGBIG LAMMPS_SMALLSMALL) -add_definitions(-D${LAMMPS_SIZE_LIMIT}) -set(LAMMPS_API_DEFINES "${LAMMPS_API_DEFINES} -D${LAMMPS_SIZE_LIMIT}") -set(LAMMPS_MEMALIGN "64" CACHE STRING "enables the use of the posix_memalign() call instead of malloc() when large chunks or memory are allocated by LAMMPS") -add_definitions(-DLAMMPS_MEMALIGN=${LAMMPS_MEMALIGN}) +set(LAMMPS_SIZES "smallbig" CACHE STRING "LAMMPS size limit") +set(LAMMPS_SIZES_VALUES smallbig bigbig smallsmall) +set_property(CACHE LAMMPS_SIZES PROPERTY STRINGS ${LAMMPS_SIZES_VALUES}) +validate_option(LAMMPS_SIZES LAMMPS_SIZES_VALUES) +string(TOUPPER ${LAMMPS_SIZES} LAMMPS_SIZES) +add_definitions(-DLAMMPS_${LAMMPS_SIZES}) +set(LAMMPS_API_DEFINES "${LAMMPS_API_DEFINES} -DLAMMPS_${LAMMPS_SIZES}") + +# posix_memalign is not available on Windows +if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows") + set(LAMMPS_MEMALIGN "64" CACHE STRING "enables the use of the posix_memalign() call instead of malloc() when large chunks or memory are allocated by LAMMPS. Set to 0 to disable") + if(NOT ${LAMMPS_MEMALIGN} STREQUAL "0") + add_definitions(-DLAMMPS_MEMALIGN=${LAMMPS_MEMALIGN}) + endif() +endif() option(LAMMPS_EXCEPTIONS "enable the use of C++ exceptions for error messages (useful for library interface)" OFF) if(LAMMPS_EXCEPTIONS) @@ -102,36 +232,55 @@ if(LAMMPS_EXCEPTIONS) set(LAMMPS_API_DEFINES "${LAMMPS_API_DEFINES} -DLAMMPS_EXCEPTIONS") endif() -set(LAMMPS_MACHINE "" CACHE STRING "Suffix to append to lmp binary and liblammps (WON'T enable any features automatically") -mark_as_advanced(LAMMPS_MACHINE) -if(LAMMPS_MACHINE) - set(LAMMPS_MACHINE "_${LAMMPS_MACHINE}") -endif() - option(CMAKE_VERBOSE_MAKEFILE "Verbose makefile" OFF) option(ENABLE_TESTING "Enable testing" OFF) -if(ENABLE_TESTING) +if(ENABLE_TESTING AND BUILD_EXE) enable_testing() -endif(ENABLE_TESTING) + option(LAMMPS_TESTING_SOURCE_DIR "Location of lammps-testing source directory" "") + option(LAMMPS_TESTING_GIT_TAG "Git tag of lammps-testing" "master") + mark_as_advanced(LAMMPS_TESTING_SOURCE_DIR LAMMPS_TESTING_GIT_TAG) -option(ENABLE_ALL "Build all default packages" OFF) -set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GRANULAR - KSPACE MANYBODY MC MEAM MISC MOLECULE PERI QEQ - REAX REPLICA RIGID SHOCK SNAP SRD) -set(OTHER_PACKAGES KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE - USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESO - USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF - USER-FEP USER-H5MD USER-LB USER-MANIFOLD USER-MEAMC USER-MGPT USER-MISC - USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-QTB USER-REAXC USER-SMD - USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM) -set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU) -foreach(PKG ${DEFAULT_PACKAGES}) - option(PKG_${PKG} "Build ${PKG} Package" ${ENABLE_ALL}) -endforeach() -foreach(PKG ${ACCEL_PACKAGES} ${OTHER_PACKAGES}) - option(PKG_${PKG} "Build ${PKG} Package" OFF) -endforeach() + if (CMAKE_VERSION VERSION_GREATER "3.10.3" AND NOT LAMMPS_TESTING_SOURCE_DIR) + include(FetchContent) + + FetchContent_Declare(lammps-testing + GIT_REPOSITORY https://github.com/lammps/lammps-testing.git + GIT_TAG ${LAMMPS_TESTING_GIT_TAG} + ) + + FetchContent_GetProperties(lammps-testing) + if(NOT lammps-testing_POPULATED) + message(STATUS "Downloading tests...") + FetchContent_Populate(lammps-testing) + endif() + + set(LAMMPS_TESTING_SOURCE_DIR ${lammps-testing_SOURCE_DIR}) + elseif(NOT LAMMPS_TESTING_SOURCE_DIR) + message(WARNING "Full test-suite requires CMake >= 3.11 or copy of\n" + "https://github.com/lammps/lammps-testing in LAMMPS_TESTING_SOURCE_DIR") + endif() + + if(EXISTS ${LAMMPS_TESTING_SOURCE_DIR}) + message(STATUS "Running test discovery...") + + file(GLOB_RECURSE TEST_SCRIPTS ${LAMMPS_TESTING_SOURCE_DIR}/tests/core/*/in.*) + foreach(script_path ${TEST_SCRIPTS}) + get_filename_component(TEST_NAME ${script_path} EXT) + get_filename_component(SCRIPT_NAME ${script_path} NAME) + get_filename_component(PARENT_DIR ${script_path} DIRECTORY) + string(SUBSTRING ${TEST_NAME} 1 -1 TEST_NAME) + string(REPLACE "-" "_" TEST_NAME ${TEST_NAME}) + string(REPLACE "+" "_" TEST_NAME ${TEST_NAME}) + set(TEST_NAME "test_core_${TEST_NAME}_serial") + add_test(${TEST_NAME} ${CMAKE_BINARY_DIR}/${LAMMPS_BINARY} -in ${SCRIPT_NAME}) + set_tests_properties(${TEST_NAME} PROPERTIES WORKING_DIRECTORY ${PARENT_DIR}) + endforeach() + list(LENGTH TEST_SCRIPTS NUM_TESTS) + + message(STATUS "Found ${NUM_TESTS} tests.") + endif() +endif() macro(pkg_depends PKG1 PKG2) if(PKG_${PKG1} AND NOT (PKG_${PKG2} OR BUILD_${PKG2})) @@ -139,24 +288,13 @@ macro(pkg_depends PKG1 PKG2) endif() endmacro() +# "hard" dependencies between packages resulting +# in an error instead of skipping over files pkg_depends(MPIIO MPI) -pkg_depends(QEQ MANYBODY) pkg_depends(USER-ATC MANYBODY) pkg_depends(USER-LB MPI) -pkg_depends(USER-MISC MANYBODY) pkg_depends(USER-PHONON KSPACE) -pkg_depends(CORESHELL KSPACE) - -###################################################### -# packages with special compiler needs or external libs -###################################################### -if(PKG_REAX OR PKG_MEAM OR PKG_USER-QUIP OR PKG_USER-QMMM OR PKG_LATTE) - enable_language(Fortran) -endif() - -if(PKG_MEAM OR PKG_USER-H5MD OR PKG_USER-QMMM) - enable_language(C) -endif() +pkg_depends(USER-SCAFACOS MPI) find_package(OpenMP QUIET) option(BUILD_OMP "Build with OpenMP support" ${OpenMP_FOUND}) @@ -177,10 +315,13 @@ if(PKG_KSPACE) if(${FFTW}_FOUND) set(FFT "${FFTW}" CACHE STRING "FFT library for KSPACE package") else() - set(FFT "KISSFFT" CACHE STRING "FFT library for KSPACE package") + set(FFT "KISS" CACHE STRING "FFT library for KSPACE package") endif() - set_property(CACHE FFT PROPERTY STRINGS KISSFFT ${FFTW} MKL) - if(NOT FFT STREQUAL "KISSFFT") + set(FFT_VALUES KISS ${FFTW} MKL) + set_property(CACHE FFT PROPERTY STRINGS ${FFT_VALUES}) + validate_option(FFT FFT_VALUES) + string(TOUPPER ${FFT} FFT) + if(NOT FFT STREQUAL "KISS") find_package(${FFT} REQUIRED) if(NOT FFT STREQUAL "FFTW3F") add_definitions(-DFFT_FFTW) @@ -189,21 +330,29 @@ if(PKG_KSPACE) endif() include_directories(${${FFT}_INCLUDE_DIRS}) list(APPEND LAMMPS_LINK_LIBS ${${FFT}_LIBRARIES}) + else() + add_definitions(-DFFT_KISS) endif() - set(PACK_OPTIMIZATION "PACK_ARRAY" CACHE STRING "Optimization for FFT") - set_property(CACHE PACK_OPTIMIZATION PROPERTY STRINGS PACK_ARRAY PACK_POINTER PACK_MEMCPY) - if(NOT PACK_OPTIMIZATION STREQUAL "PACK_ARRAY") - add_definitions(-D${PACK_OPTIMIZATION}) + set(FFT_PACK "array" CACHE STRING "Optimization for FFT") + set(FFT_PACK_VALUES array pointer memcpy) + set_property(CACHE FFT_PACK PROPERTY STRINGS ${FFT_PACK_VALUES}) + validate_option(FFT_PACK FFT_PACK_VALUES) + if(NOT FFT_PACK STREQUAL "array") + string(TOUPPER ${FFT_PACK} FFT_PACK) + add_definitions(-DFFT_PACK_${FFT_PACK}) endif() endif() if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE) find_package(LAPACK) - if(NOT LAPACK_FOUND) + find_package(BLAS) + if(NOT LAPACK_FOUND OR NOT BLAS_FOUND) enable_language(Fortran) - file(GLOB LAPACK_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/linalg/*.[fF]) + file(GLOB LAPACK_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/linalg/[^.]*.[fF]) add_library(linalg STATIC ${LAPACK_SOURCES}) set(LAPACK_LIBRARIES linalg) + else() + list(APPEND LAPACK_LIBRARIES ${BLAS_LIBRARIES}) endif() endif() @@ -213,7 +362,7 @@ if(PKG_PYTHON) add_definitions(-DLMP_PYTHON) include_directories(${PYTHON_INCLUDE_DIR}) list(APPEND LAMMPS_LINK_LIBS ${PYTHON_LIBRARY}) - if(BUILD_SHARED_LIBS) + if(BUILD_LIB AND BUILD_SHARED_LIBS) if(NOT PYTHON_INSTDIR) execute_process(COMMAND ${PYTHON_EXECUTABLE} -c "import distutils.sysconfig as cg; print(cg.get_python_lib(1,0,prefix='${CMAKE_INSTALL_PREFIX}'))" @@ -271,10 +420,17 @@ if(PKG_VORONOI) option(DOWNLOAD_VORO "Download voro++ (instead of using the system's one)" OFF) if(DOWNLOAD_VORO) include(ExternalProject) + + if(BUILD_SHARED_LIBS) + set(VORO_BUILD_OPTIONS "CFLAGS=-fPIC") + else() + set(VORO_BUILD_OPTIONS) + endif() + ExternalProject_Add(voro_build URL http://math.lbl.gov/voro++/download/dir/voro++-0.4.6.tar.gz URL_MD5 2338b824c3b7b25590e18e8df5d68af9 - CONFIGURE_COMMAND "" BUILD_IN_SOURCE 1 INSTALL_COMMAND "" + CONFIGURE_COMMAND "" BUILD_COMMAND make ${VORO_BUILD_OPTIONS} BUILD_IN_SOURCE 1 INSTALL_COMMAND "" ) ExternalProject_get_property(voro_build SOURCE_DIR) set(VORO_LIBRARIES ${SOURCE_DIR}/src/libvoro++.a) @@ -293,11 +449,14 @@ endif() if(PKG_LATTE) option(DOWNLOAD_LATTE "Download latte (instead of using the system's one)" OFF) if(DOWNLOAD_LATTE) + if (CMAKE_VERSION VERSION_LESS "3.7") # due to SOURCE_SUBDIR + message(FATAL_ERROR "For downlading LATTE you need at least cmake-3.7") + endif() message(STATUS "LATTE not found - we will build our own") include(ExternalProject) ExternalProject_Add(latte_build URL https://github.com/lanl/LATTE/archive/v1.2.1.tar.gz - URL_MD5 bed76e7e76c545c36dd848a8f1fd35eb + URL_MD5 85ac414fdada2d04619c8f936344df14 SOURCE_SUBDIR cmake CMAKE_ARGS -DCMAKE_INSTALL_PREFIX= -DCMAKE_POSITION_INDEPENDENT_CODE=${CMAKE_POSITION_INDEPENDENT_CODE} ) @@ -313,6 +472,57 @@ if(PKG_LATTE) list(APPEND LAMMPS_LINK_LIBS ${LATTE_LIBRARIES} ${LAPACK_LIBRARIES}) endif() +if(PKG_USER-SCAFACOS) + find_package(GSL REQUIRED) + option(DOWNLOAD_SCAFACOS "Download ScaFaCoS (instead of using the system's one)" OFF) + if(DOWNLOAD_SCAFACOS) + include(ExternalProject) + ExternalProject_Add(scafacos_build + URL https://github.com/scafacos/scafacos/releases/download/v1.0.1/scafacos-1.0.1.tar.gz + URL_MD5 bd46d74e3296bd8a444d731bb10c1738 + CONFIGURE_COMMAND /configure --prefix= + --disable-doc + --enable-fcs-solvers=fmm,p2nfft,direct,ewald,p3m + --with-internal-fftw + --with-internal-pfft + --with-internal-pnfft + $<$:--with-pic> + FC=${CMAKE_MPI_Fortran_COMPILER} + CXX=${CMAKE_MPI_CXX_COMPILER} + CC=${CMAKE_MPI_C_COMPILER} + F77= + ) + ExternalProject_get_property(scafacos_build INSTALL_DIR) + set(SCAFACOS_BUILD_DIR ${INSTALL_DIR}) + set(SCAFACOS_INCLUDE_DIRS ${SCAFACOS_BUILD_DIR}/include) + list(APPEND LAMMPS_DEPS scafacos_build) + # list and order from pkg_config file of ScaFaCoS build + list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs.a) + list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_direct.a) + list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_ewald.a) + list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_fmm.a) + list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_p2nfft.a) + list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_p3m.a) + list(APPEND LAMMPS_LINK_LIBS ${GSL_LIBRARIES}) + list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_near.a) + list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_gridsort.a) + list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_resort.a) + list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_redist.a) + list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_common.a) + list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_pnfft.a) + list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_pfft.a) + list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_fftw3_mpi.a) + list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_fftw3.a) + list(APPEND LAMMPS_LINK_LIBS ${MPI_Fortran_LIBRARIES}) + list(APPEND LAMMPS_LINK_LIBS ${MPI_C_LIBRARIES}) + else() + FIND_PACKAGE(PkgConfig REQUIRED) + PKG_CHECK_MODULES(SCAFACOS scafacos REQUIRED) + list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_LDFLAGS}) + endif() + include_directories(${SCAFACOS_INCLUDE_DIRS}) +endif() + if(PKG_USER-MOLFILE) add_library(molfile INTERFACE) target_include_directories(molfile INTERFACE ${LAMMPS_LIB_SOURCE_DIR}/molfile) @@ -322,14 +532,14 @@ endif() if(PKG_USER-NETCDF) find_package(NetCDF REQUIRED) - include_directories(NETCDF_INCLUDE_DIR) - list(APPEND LAMMPS_LINK_LIBS ${NETCDF_LIBRARY}) + include_directories(${NETCDF_INCLUDE_DIRS}) + list(APPEND LAMMPS_LINK_LIBS ${NETCDF_LIBRARIES}) add_definitions(-DLMP_HAS_NETCDF -DNC_64BIT_DATA=0x0020) endif() if(PKG_USER-SMD) - option(DOWNLOAD_Eigen3 "Download Eigen3 (instead of using the system's one)" OFF) - if(DOWNLOAD_Eigen3) + option(DOWNLOAD_EIGEN3 "Download Eigen3 (instead of using the system's one)" OFF) + if(DOWNLOAD_EIGEN3) include(ExternalProject) ExternalProject_Add(Eigen3_build URL http://bitbucket.org/eigen/eigen/get/3.3.4.tar.gz @@ -340,9 +550,10 @@ if(PKG_USER-SMD) set(EIGEN3_INCLUDE_DIR ${SOURCE_DIR}) list(APPEND LAMMPS_DEPS Eigen3_build) else() - find_package(Eigen3) - if(NOT Eigen3_FOUND) - message(FATAL_ERROR "Eigen3 not found, help CMake to find it by setting EIGEN3_INCLUDE_DIR, or set DOWNLOAD_Eigen3=ON to download it") + find_package(Eigen3 NO_MODULE) + mark_as_advanced(Eigen3_DIR) + if(NOT EIGEN3_FOUND) + message(FATAL_ERROR "Eigen3 not found, help CMake to find it by setting EIGEN3_INCLUDE_DIR, or set DOWNLOAD_EIGEN3=ON to download it") endif() endif() include_directories(${EIGEN3_INCLUDE_DIR}) @@ -391,10 +602,47 @@ if(PKG_KIM) include_directories(${KIM_INCLUDE_DIRS}) endif() +if(PKG_MESSAGE) + option(MESSAGE_ZMQ "Use ZeroMQ in MESSAGE package" OFF) + file(GLOB_RECURSE cslib_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.F + ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.c + ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.cpp) + + if(BUILD_SHARED_LIBS) + add_library(cslib SHARED ${cslib_SOURCES}) + else() + add_library(cslib STATIC ${cslib_SOURCES}) + endif() + + if(BUILD_MPI) + target_compile_definitions(cslib PRIVATE -DMPI_YES) + set_target_properties(cslib PROPERTIES OUTPUT_NAME "csmpi") + else() + target_compile_definitions(cslib PRIVATE -DMPI_NO) + set_target_properties(cslib PROPERTIES OUTPUT_NAME "csnompi") + endif() + + if(MESSAGE_ZMQ) + target_compile_definitions(cslib PRIVATE -DZMQ_YES) + find_package(ZMQ REQUIRED) + target_include_directories(cslib PRIVATE ${ZMQ_INCLUDE_DIRS}) + target_link_libraries(cslib PUBLIC ${ZMQ_LIBRARIES}) + else() + target_compile_definitions(cslib PRIVATE -DZMQ_NO) + target_include_directories(cslib PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/src/STUBS_ZMQ) + endif() + + list(APPEND LAMMPS_LINK_LIBS cslib) + include_directories(${LAMMPS_LIB_SOURCE_DIR}/message/cslib/src) +endif() + if(PKG_MSCG) find_package(GSL REQUIRED) option(DOWNLOAD_MSCG "Download latte (instead of using the system's one)" OFF) if(DOWNLOAD_MSCG) + if (CMAKE_VERSION VERSION_LESS "3.7") # due to SOURCE_SUBDIR + message(FATAL_ERROR "For downlading LATTE you need at least cmake-3.7") + endif() include(ExternalProject) if(NOT LAPACK_FOUND) set(EXTRA_MSCG_OPTS "-DLAPACK_LIBRARIES=${CMAKE_CURRENT_BINARY_DIR}/liblinalg.a") @@ -431,6 +679,11 @@ if(PKG_COMPRESS) list(APPEND LAMMPS_LINK_LIBS ${ZLIB_LIBRARIES}) endif() +# the windows version of LAMMPS requires a couple extra libraries +if(${CMAKE_SYSTEM_NAME} STREQUAL "Windows") + list(APPEND LAMMPS_LINK_LIBS -lwsock32 -lpsapi) +endif() + ######################################################################## # Basic system tests (standard libraries, headers, functions, types) # ######################################################################## @@ -445,12 +698,16 @@ endforeach(HEADER) set(MATH_LIBRARIES "m" CACHE STRING "math library") mark_as_advanced( MATH_LIBRARIES ) include(CheckLibraryExists) -foreach(FUNC sin cos) - check_library_exists(${MATH_LIBRARIES} ${FUNC} "" FOUND_${FUNC}_${MATH_LIBRARIES}) - if(NOT FOUND_${FUNC}_${MATH_LIBRARIES}) - message(FATAL_ERROR "Could not find needed math function - ${FUNC}") - endif(NOT FOUND_${FUNC}_${MATH_LIBRARIES}) -endforeach(FUNC) +if (CMAKE_VERSION VERSION_LESS "3.4") + enable_language(C) # check_library_exists isn't supported without a c compiler before v3.4 +endif() +# RB: disabled this check because it breaks with KOKKOS CUDA enabled +#foreach(FUNC sin cos) +# check_library_exists(${MATH_LIBRARIES} ${FUNC} "" FOUND_${FUNC}_${MATH_LIBRARIES}) +# if(NOT FOUND_${FUNC}_${MATH_LIBRARIES}) +# message(FATAL_ERROR "Could not find needed math function - ${FUNC}") +# endif(NOT FOUND_${FUNC}_${MATH_LIBRARIES}) +#endforeach(FUNC) list(APPEND LAMMPS_LINK_LIBS ${MATH_LIBRARIES}) ###################################### @@ -462,23 +719,14 @@ RegisterStyles(${LAMMPS_SOURCE_DIR}) ############################################## # add sources of enabled packages ############################################ -foreach(PKG ${DEFAULT_PACKAGES} ${OTHER_PACKAGES}) +foreach(PKG ${DEFAULT_PACKAGES}) set(${PKG}_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/${PKG}) - # ignore PKG files which were manually installed in src folder - # headers are ignored during RegisterStyles - file(GLOB ${PKG}_SOURCES ${${PKG}_SOURCES_DIR}/*.cpp) - file(GLOB ${PKG}_HEADERS ${${PKG}_SOURCES_DIR}/*.h) + file(GLOB ${PKG}_SOURCES ${${PKG}_SOURCES_DIR}/[^.]*.cpp) + file(GLOB ${PKG}_HEADERS ${${PKG}_SOURCES_DIR}/[^.]*.h) - foreach(PKG_FILE in ${${PKG}_SOURCES}) - get_filename_component(FNAME ${PKG_FILE} NAME) - list(REMOVE_ITEM LIB_SOURCES ${LAMMPS_SOURCE_DIR}/${FNAME}) - endforeach() - - foreach(PKG_FILE in ${${PKG}_HEADERS}) - get_filename_component(FNAME ${PKG_FILE} NAME) - DetectAndRemovePackageHeader(${LAMMPS_SOURCE_DIR}/${FNAME}) - endforeach() + # check for package files in src directory due to old make system + DetectBuildSystemConflict(${LAMMPS_SOURCE_DIR} ${${PKG}_SOURCES} ${${PKG}_HEADERS}) if(PKG_${PKG}) # detects styles in package and adds them to global list @@ -489,6 +737,17 @@ foreach(PKG ${DEFAULT_PACKAGES} ${OTHER_PACKAGES}) endif() endforeach() +# dedicated check for entire contents of accelerator packages +foreach(PKG ${ACCEL_PACKAGES}) + set(${PKG}_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/${PKG}) + + file(GLOB ${PKG}_SOURCES ${${PKG}_SOURCES_DIR}/[^.]*.cpp) + file(GLOB ${PKG}_HEADERS ${${PKG}_SOURCES_DIR}/[^.]*.h) + + # check for package files in src directory due to old make system + DetectBuildSystemConflict(${LAMMPS_SOURCE_DIR} ${${PKG}_SOURCES} ${${PKG}_HEADERS}) +endforeach() + ############################################## # add lib sources of (simple) enabled packages ############################################ @@ -497,8 +756,10 @@ foreach(SIMPLE_LIB REAX MEAM POEMS USER-ATC USER-AWPMD USER-COLVARS USER-H5MD if(PKG_${SIMPLE_LIB}) string(REGEX REPLACE "^USER-" "" PKG_LIB "${SIMPLE_LIB}") string(TOLOWER "${PKG_LIB}" PKG_LIB) - file(GLOB_RECURSE ${PKG_LIB}_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/*.F - ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/*.c ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/*.cpp) + file(GLOB_RECURSE ${PKG_LIB}_SOURCES + ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.F + ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.c + ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.cpp) add_library(${PKG_LIB} STATIC ${${PKG_LIB}_SOURCES}) list(APPEND LAMMPS_LINK_LIBS ${PKG_LIB}) if(PKG_LIB STREQUAL awpmd) @@ -534,19 +795,80 @@ endif() # packages which selectively include variants based on enabled styles # e.g. accelerator packages ###################################################################### +if(PKG_CORESHELL) + set(CORESHELL_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/CORESHELL) + set(CORESHELL_SOURCES) + set_property(GLOBAL PROPERTY "CORESHELL_SOURCES" "${CORESHELL_SOURCES}") + + # detects styles which have a CORESHELL version + RegisterStylesExt(${CORESHELL_SOURCES_DIR} cs CORESHELL_SOURCES) + + get_property(CORESHELL_SOURCES GLOBAL PROPERTY CORESHELL_SOURCES) + + list(APPEND LIB_SOURCES ${CORESHELL_SOURCES}) + include_directories(${CORESHELL_SOURCES_DIR}) +endif() + +# Fix qeq/fire requires MANYBODY (i.e. COMB and COMB3) to be installed +if(PKG_QEQ) + set(QEQ_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/QEQ) + file(GLOB QEQ_HEADERS ${QEQ_SOURCES_DIR}/fix*.h) + file(GLOB QEQ_SOURCES ${QEQ_SOURCES_DIR}/fix*.cpp) + + if(NOT PKG_MANYBODY) + list(REMOVE_ITEM QEQ_HEADERS ${QEQ_SOURCES_DIR}/fix_qeq_fire.h) + list(REMOVE_ITEM QEQ_SOURCES ${QEQ_SOURCES_DIR}/fix_qeq_fire.cpp) + endif() + set_property(GLOBAL PROPERTY "QEQ_SOURCES" "${QEQ_SOURCES}") + + foreach(MY_HEADER ${QEQ_HEADERS}) + AddStyleHeader(${MY_HEADER} FIX) + endforeach() + + get_property(QEQ_SOURCES GLOBAL PROPERTY QEQ_SOURCES) + list(APPEND LIB_SOURCES ${QEQ_SOURCES}) + include_directories(${QEQ_SOURCES_DIR}) +endif() + if(PKG_USER-OMP) set(USER-OMP_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-OMP) set(USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/thr_data.cpp ${USER-OMP_SOURCES_DIR}/thr_omp.cpp + ${USER-OMP_SOURCES_DIR}/fix_omp.cpp ${USER-OMP_SOURCES_DIR}/fix_nh_omp.cpp - ${USER-OMP_SOURCES_DIR}/fix_nh_sphere_omp.cpp) + ${USER-OMP_SOURCES_DIR}/fix_nh_sphere_omp.cpp + ${USER-OMP_SOURCES_DIR}/domain_omp.cpp) + add_definitions(-DLMP_USER_OMP) set_property(GLOBAL PROPERTY "OMP_SOURCES" "${USER-OMP_SOURCES}") # detects styles which have USER-OMP version RegisterStylesExt(${USER-OMP_SOURCES_DIR} omp OMP_SOURCES) + RegisterFixStyle("${USER-OMP_SOURCES_DIR}/fix_omp.h") get_property(USER-OMP_SOURCES GLOBAL PROPERTY OMP_SOURCES) + # manually add package dependent source files from USER-OMP that do not provide styles + + if(PKG_ASPHERE) + list(APPEND USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/fix_nh_asphere_omp.cpp) + endif() + + if(PKG_RIGID) + list(APPEND USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/fix_rigid_nh_omp.cpp) + endif() + + if(PKG_USER-REAXC) + list(APPEND USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/reaxc_bond_orders_omp.cpp + ${USER-OMP_SOURCES_DIR}/reaxc_hydrogen_bonds_omp.cpp + ${USER-OMP_SOURCES_DIR}/reaxc_nonbonded_omp.cpp + ${USER-OMP_SOURCES_DIR}/reaxc_bonds_omp.cpp + ${USER-OMP_SOURCES_DIR}/reaxc_init_md_omp.cpp + ${USER-OMP_SOURCES_DIR}/reaxc_torsion_angles_omp.cpp + ${USER-OMP_SOURCES_DIR}/reaxc_forces_omp.cpp + ${USER-OMP_SOURCES_DIR}/reaxc_multi_body_omp.cpp + ${USER-OMP_SOURCES_DIR}/reaxc_valence_angles_omp.cpp) + endif() + list(APPEND LIB_SOURCES ${USER-OMP_SOURCES}) include_directories(${USER-OMP_SOURCES_DIR}) endif() @@ -578,6 +900,11 @@ if(PKG_KOKKOS) ${KOKKOS_PKG_SOURCES_DIR}/npair_kokkos.cpp ${KOKKOS_PKG_SOURCES_DIR}/domain_kokkos.cpp ${KOKKOS_PKG_SOURCES_DIR}/modify_kokkos.cpp) + + if(PKG_KSPACE) + list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/gridcomm_kokkos.cpp) + endif() + set_property(GLOBAL PROPERTY "KOKKOS_PKG_SOURCES" "${KOKKOS_PKG_SOURCES}") # detects styles which have KOKKOS version @@ -615,29 +942,55 @@ if(PKG_OPT) endif() if(PKG_USER-INTEL) - if(NOT DEVELOPER_MODE) - if(NOT CMAKE_CXX_COMPILER_ID STREQUAL "Intel") - message(FATAL_ERROR "USER-INTEL is only useful together with intel compiler") - endif() - if(CMAKE_CXX_COMPILER_VERSION VERSION_LESS 16) - message(FATAL_ERROR "USER-INTEL is needed at least 2016 intel compiler, found ${CMAKE_CXX_COMPILER_VERSION}") - endif() + find_package(TBB REQUIRED) + find_package(MKL REQUIRED) + + if(NOT CMAKE_CXX_COMPILER_ID STREQUAL "Intel") + message(FATAL_ERROR "USER-INTEL is only useful together with intel compiler") endif() - option(INJECT_INTEL_FLAG "Inject OMG fast flags for USER-INTEL" ON) - if(INJECT_INTEL_FLAG AND CMAKE_CXX_COMPILER_ID STREQUAL "Intel") + + if(CMAKE_CXX_COMPILER_VERSION VERSION_LESS 16) + message(FATAL_ERROR "USER-INTEL is needed at least 2016 intel compiler, found ${CMAKE_CXX_COMPILER_VERSION}") + endif() + + if(NOT BUILD_OMP) + message(FATAL_ERROR "USER-INTEL requires OpenMP") + endif() + + if(NOT ${LAMMPS_MEMALIGN} STREQUAL "64") + message(FATAL_ERROR "USER-INTEL is only useful with LAMMPS_MEMALIGN=64") + endif() + + set(INTEL_ARCH "cpu" CACHE STRING "Architectures used by USER-INTEL (cpu or knl)") + set(INTEL_ARCH_VALUES cpu knl) + set_property(CACHE INTEL_ARCH PROPERTY STRINGS ${INTEL_ARCH_VALUES}) + validate_option(INTEL_ARCH INTEL_ARCH_VALUES) + string(TOUPPER ${INTEL_ARCH} INTEL_ARCH) + + if(INTEL_ARCH STREQUAL "KNL") + set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -xHost -qopenmp -qoffload") + set(MIC_OPTIONS "-qoffload-option,mic,compiler,\"-fp-model fast=2 -mGLOB_default_function_attrs=\\\"gather_scatter_loop_unroll=4\\\"\"") + add_compile_options(-xMIC-AVX512 -qoffload -fno-alias -ansi-alias -restrict -qoverride-limits ${MIC_OPTIONS}) + add_definitions(-DLMP_INTEL_OFFLOAD) + else() if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4) set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -xCOMMON-AVX512") else() set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -xHost") endif() include(CheckCXXCompilerFlag) - foreach(_FLAG -qopenmp -qno-offload -fno-alias -ansi-alias -restrict -DLMP_INTEL_USELRT -DLMP_USE_MKL_RNG -O2 "-fp-model fast=2" -no-prec-div -qoverride-limits -qopt-zmm-usage=high) + foreach(_FLAG -O2 -fp-model fast=2 -no-prec-div -qoverride-limits -qopt-zmm-usage=high -qno-offload -fno-alias -ansi-alias -restrict) check_cxx_compiler_flag("${__FLAG}" COMPILER_SUPPORTS${_FLAG}) if(COMPILER_SUPPORTS${_FLAG}) - set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${_FLAG}") + add_compile_options(${_FLAG}) endif() endforeach() endif() + + add_definitions(-DLMP_INTEL_USELRT -DLMP_USE_MKL_RNG) + + list(APPEND LAMMPS_LINK_LIBS ${TBB_MALLOC_LIBRARIES} ${MKL_LIBRARIES}) + set(USER-INTEL_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-INTEL) set(USER-INTEL_SOURCES ${USER-INTEL_SOURCES_DIR}/intel_preprocess.h ${USER-INTEL_SOURCES_DIR}/intel_buffers.h @@ -670,13 +1023,27 @@ if(PKG_GPU) ${GPU_SOURCES_DIR}/fix_gpu.h ${GPU_SOURCES_DIR}/fix_gpu.cpp) - set(GPU_API "OpenCL" CACHE STRING "API used by GPU package") - set_property(CACHE GPU_API PROPERTY STRINGS OpenCL CUDA) + set(GPU_API "opencl" CACHE STRING "API used by GPU package") + set(GPU_API_VALUES opencl cuda) + set_property(CACHE GPU_API PROPERTY STRINGS ${GPU_API_VALUES}) + validate_option(GPU_API GPU_API_VALUES) + string(TOUPPER ${GPU_API} GPU_API) - set(GPU_PREC "SINGLE_DOUBLE" CACHE STRING "LAMMPS GPU precision size") - set_property(CACHE GPU_PREC PROPERTY STRINGS SINGLE_DOUBLE SINGLE_SINGLE DOUBLE_DOUBLE) + set(GPU_PREC "mixed" CACHE STRING "LAMMPS GPU precision") + set(GPU_PREC_VALUES double mixed single) + set_property(CACHE GPU_PREC PROPERTY STRINGS ${GPU_PREC_VALUES}) + validate_option(GPU_PREC GPU_PREC_VALUES) + string(TOUPPER ${GPU_PREC} GPU_PREC) - file(GLOB GPU_LIB_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/*.cpp) + if(GPU_PREC STREQUAL "DOUBLE") + set(GPU_PREC_SETTING "DOUBLE_DOUBLE") + elseif(GPU_PREC STREQUAL "MIXED") + set(GPU_PREC_SETTING "SINGLE_DOUBLE") + elseif(GPU_PREC STREQUAL "SINGLE") + set(GPU_PREC_SETTING "SINGLE_SINGLE") + endif() + + file(GLOB GPU_LIB_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cpp) file(MAKE_DIRECTORY ${LAMMPS_LIB_BINARY_DIR}/gpu) if(GPU_API STREQUAL "CUDA") @@ -687,25 +1054,24 @@ if(PKG_GPU) endif() option(CUDPP_OPT "Enable CUDPP_OPT" ON) - set(GPU_ARCH "sm_30" CACHE STRING "LAMMPS GPU CUDA SM architecture") - set_property(CACHE GPU_ARCH PROPERTY STRINGS sm_10 sm_20 sm_30 sm_60) + set(GPU_ARCH "sm_30" CACHE STRING "LAMMPS GPU CUDA SM architecture (e.g. sm_60)") - file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/*.cu ${CMAKE_CURRENT_SOURCE_DIR}/gpu/*.cu) + file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu ${CMAKE_CURRENT_SOURCE_DIR}/gpu/[^.]*.cu) list(REMOVE_ITEM GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_pppm.cu) cuda_include_directories(${LAMMPS_LIB_SOURCE_DIR}/gpu ${LAMMPS_LIB_BINARY_DIR}/gpu) if(CUDPP_OPT) cuda_include_directories(${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini) - file(GLOB GPU_LIB_CUDPP_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/*.cpp) - file(GLOB GPU_LIB_CUDPP_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/*.cu) + file(GLOB GPU_LIB_CUDPP_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/[^.]*.cpp) + file(GLOB GPU_LIB_CUDPP_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/[^.]*.cu) endif() cuda_compile_cubin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS - -DUNIX -O3 -Xptxas -v --use_fast_math -DNV_KERNEL -DUCL_CUDADR -arch=${GPU_ARCH} -D_${GPU_PREC}) + -DUNIX -O3 -Xptxas -v --use_fast_math -DNV_KERNEL -DUCL_CUDADR -arch=${GPU_ARCH} -D_${GPU_PREC_SETTING}) cuda_compile(GPU_OBJS ${GPU_LIB_CUDPP_CU} OPTIONS $<$:-Xcompiler=-fPIC> - -DUNIX -O3 -Xptxas -v --use_fast_math -DUCL_CUDADR -arch=${GPU_ARCH} -D_${GPU_PREC}) + -DUNIX -O3 -Xptxas -v --use_fast_math -DUCL_CUDADR -arch=${GPU_ARCH} -D_${GPU_PREC_SETTING}) foreach(CU_OBJ ${GPU_GEN_OBJS}) get_filename_component(CU_NAME ${CU_OBJ} NAME_WE) @@ -722,7 +1088,7 @@ if(PKG_GPU) add_library(gpu STATIC ${GPU_LIB_SOURCES} ${GPU_LIB_CUDPP_SOURCES} ${GPU_OBJS}) target_link_libraries(gpu ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY}) target_include_directories(gpu PRIVATE ${LAMMPS_LIB_BINARY_DIR}/gpu ${CUDA_INCLUDE_DIRS}) - target_compile_definitions(gpu PRIVATE -D_${GPU_PREC} -DMPI_GERYON -DUCL_NO_EXIT) + target_compile_definitions(gpu PRIVATE -D_${GPU_PREC_SETTING} -DMPI_GERYON -DUCL_NO_EXIT) if(CUDPP_OPT) target_include_directories(gpu PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini) target_compile_definitions(gpu PRIVATE -DUSE_CUDPP) @@ -736,15 +1102,18 @@ if(PKG_GPU) target_include_directories(nvc_get_devices PRIVATE ${CUDA_INCLUDE_DIRS}) - elseif(GPU_API STREQUAL "OpenCL") + elseif(GPU_API STREQUAL "OPENCL") find_package(OpenCL REQUIRED) - set(OCL_TUNE "GENERIC" CACHE STRING "OpenCL Device Tuning") - set_property(CACHE OCL_TUNE PROPERTY STRINGS INTEL FERMI KEPLER CYPRESS GENERIC) + set(OCL_TUNE "generic" CACHE STRING "OpenCL Device Tuning") + set(OCL_TUNE_VALUES intel fermi kepler cypress generic) + set_property(CACHE OCL_TUNE PROPERTY STRINGS ${OCL_TUNE_VALUES}) + validate_option(OCL_TUNE OCL_TUNE_VALUES) + string(TOUPPER ${OCL_TUNE} OCL_TUNE) include(OpenCLUtils) set(OCL_COMMON_HEADERS ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_preprocessor.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_aux_fun1.h) - file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/*.cu) + file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu) list(REMOVE_ITEM GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne.cu ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne_lj.cu) foreach(GPU_KERNEL ${GPU_LIB_CU}) @@ -761,7 +1130,7 @@ if(PKG_GPU) add_library(gpu STATIC ${GPU_LIB_SOURCES}) target_link_libraries(gpu ${OpenCL_LIBRARIES}) target_include_directories(gpu PRIVATE ${CMAKE_CURRENT_BINARY_DIR}/gpu ${OpenCL_INCLUDE_DIRS}) - target_compile_definitions(gpu PRIVATE -D_${GPU_PREC} -D${OCL_TUNE}_OCL -DMPI_GERYON -DUCL_NO_EXIT) + target_compile_definitions(gpu PRIVATE -D_${GPU_PREC_SETTING} -D${OCL_TUNE}_OCL -DMPI_GERYON -DUCL_NO_EXIT) target_compile_definitions(gpu PRIVATE -DUSE_OPENCL) list(APPEND LAMMPS_LINK_LIBS gpu) @@ -797,37 +1166,143 @@ GenerateStyleHeaders(${LAMMPS_STYLE_HEADERS_DIR}) include_directories(${LAMMPS_SOURCE_DIR}) include_directories(${LAMMPS_STYLE_HEADERS_DIR}) +###################################### +# Generate lmpinstalledpkgs.h +###################################### +set(temp "#ifndef LMP_INSTALLED_PKGS_H\n#define LMP_INSTALLED_PKGS_H\n") +set(temp "${temp}const char * LAMMPS_NS::LAMMPS::installed_packages[] = {\n") +set(temp_PKG_LIST ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES} ${OTHER_PACKAGES}) +list(SORT temp_PKG_LIST) +foreach(PKG ${temp_PKG_LIST}) + if(PKG_${PKG}) + set(temp "${temp} \"${PKG}\",\n") + endif() +endforeach() +set(temp "${temp} NULL\n};\n#endif\n\n") +message(STATUS "Generating lmpinstalledpkgs.h...") +file(WRITE "${LAMMPS_STYLE_HEADERS_DIR}/lmpinstalledpkgs.h.tmp" "${temp}" ) +execute_process(COMMAND ${CMAKE_COMMAND} -E copy_if_different "${LAMMPS_STYLE_HEADERS_DIR}/lmpinstalledpkgs.h.tmp" "${LAMMPS_STYLE_HEADERS_DIR}/lmpinstalledpkgs.h") + ########################################### # Actually add executable and lib to build ############################################ -add_library(lammps ${LIB_SOURCES}) get_property(LANGUAGES GLOBAL PROPERTY ENABLED_LANGUAGES) list (FIND LANGUAGES "Fortran" _index) if (${_index} GREATER -1) list(APPEND LAMMPS_LINK_LIBS ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES}) endif() list(REMOVE_DUPLICATES LAMMPS_LINK_LIBS) -target_link_libraries(lammps ${LAMMPS_LINK_LIBS}) -if(LAMMPS_DEPS) - add_dependencies(lammps ${LAMMPS_DEPS}) -endif() -set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LAMMPS_MACHINE}) -if(BUILD_SHARED_LIBS) +if(BUILD_LIB) + add_library(lammps ${LIB_SOURCES}) + target_link_libraries(lammps ${LAMMPS_LINK_LIBS}) + if(LAMMPS_DEPS) + add_dependencies(lammps ${LAMMPS_DEPS}) + endif() + set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LAMMPS_LIB_SUFFIX}) set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION}) install(TARGETS lammps LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}) install(FILES ${LAMMPS_SOURCE_DIR}/library.h DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps) - configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_MACHINE}.pc @ONLY) - install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_MACHINE}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig) + configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_LIB_SUFFIX}.pc @ONLY) + install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_LIB_SUFFIX}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig) + configure_file(FindLAMMPS.cmake.in ${CMAKE_CURRENT_BINARY_DIR}/FindLAMMPS${LAMMPS_LIB_SUFFIX}.cmake @ONLY) + install(FILES ${CMAKE_CURRENT_BINARY_DIR}/FindLAMMPS${LAMMPS_LIB_SUFFIX}.cmake DESTINATION ${CMAKE_INSTALL_DATADIR}/cmake/Module) +else() + list(APPEND LMP_SOURCES ${LIB_SOURCES}) endif() -add_executable(lmp ${LMP_SOURCES}) -target_link_libraries(lmp lammps) -set_target_properties(lmp PROPERTIES OUTPUT_NAME lmp${LAMMPS_MACHINE}) -install(TARGETS lmp DESTINATION ${CMAKE_INSTALL_BINDIR}) -if(ENABLE_TESTING) - add_test(ShowHelp lmp${LAMMPS_MACHINE} -help) +if(BUILD_EXE) + add_executable(lmp ${LMP_SOURCES}) + if(BUILD_LIB) + target_link_libraries(lmp lammps) + else() + target_link_libraries(lmp ${LAMMPS_LINK_LIBS}) + if(LAMMPS_DEPS) + add_dependencies(lmp ${LAMMPS_DEPS}) + endif() + endif() + + set_target_properties(lmp PROPERTIES OUTPUT_NAME ${LAMMPS_BINARY}) + install(TARGETS lmp DESTINATION ${CMAKE_INSTALL_BINDIR}) + install(FILES ${LAMMPS_DOC_DIR}/lammps.1 DESTINATION ${CMAKE_INSTALL_MANDIR}/man1 RENAME ${LAMMPS_BINARY}.1) + if(ENABLE_TESTING) + add_test(ShowHelp ${LAMMPS_BINARY} -help) + endif() endif() +############################################################################### +# Build documentation +############################################################################### +option(BUILD_DOC "Build LAMMPS documentation" OFF) +if(BUILD_DOC) + include(ProcessorCount) + ProcessorCount(NPROCS) + find_package(PythonInterp 3 REQUIRED) + + set(VIRTUALENV ${PYTHON_EXECUTABLE} -m virtualenv) + + file(GLOB DOC_SOURCES ${LAMMPS_DOC_DIR}/src/[^.]*.txt) + file(GLOB PDF_EXTRA_SOURCES ${LAMMPS_DOC_DIR}/src/lammps_commands*.txt ${LAMMPS_DOC_DIR}/src/lammps_support.txt ${LAMMPS_DOC_DIR}/src/lammps_tutorials.txt) + list(REMOVE_ITEM DOC_SOURCES ${PDF_EXTRA_SOURCES}) + + add_custom_command( + OUTPUT docenv + COMMAND ${VIRTUALENV} docenv + ) + + set(DOCENV_BINARY_DIR ${CMAKE_BINARY_DIR}/docenv/bin) + + add_custom_command( + OUTPUT requirements.txt + DEPENDS docenv + COMMAND ${CMAKE_COMMAND} -E copy ${LAMMPS_DOC_DIR}/utils/requirements.txt requirements.txt + COMMAND ${DOCENV_BINARY_DIR}/pip install -r requirements.txt --upgrade + COMMAND ${DOCENV_BINARY_DIR}/pip install --upgrade ${LAMMPS_DOC_DIR}/utils/converters + ) + + set(RST_FILES "") + set(RST_DIR ${CMAKE_BINARY_DIR}/rst) + file(MAKE_DIRECTORY ${RST_DIR}) + foreach(TXT_FILE ${DOC_SOURCES}) + get_filename_component(FILENAME ${TXT_FILE} NAME_WE) + set(RST_FILE ${RST_DIR}/${FILENAME}.rst) + list(APPEND RST_FILES ${RST_FILE}) + add_custom_command( + OUTPUT ${RST_FILE} + DEPENDS requirements.txt docenv ${TXT_FILE} + COMMAND ${DOCENV_BINARY_DIR}/txt2rst -o ${RST_DIR} ${TXT_FILE} + ) + endforeach() + + add_custom_command( + OUTPUT html + DEPENDS ${RST_FILES} + COMMAND ${CMAKE_COMMAND} -E copy_directory ${LAMMPS_DOC_DIR}/src ${RST_DIR} + COMMAND ${DOCENV_BINARY_DIR}/sphinx-build -j ${NPROCS} -b html -c ${LAMMPS_DOC_DIR}/utils/sphinx-config -d ${CMAKE_BINARY_DIR}/doctrees ${RST_DIR} html + ) + + add_custom_target( + doc ALL + DEPENDS html + SOURCES ${LAMMPS_DOC_DIR}/utils/requirements.txt ${DOC_SOURCES} + ) + + install(DIRECTORY ${CMAKE_BINARY_DIR}/html DESTINATION ${CMAKE_INSTALL_DOCDIR}) +endif() + +############################################################################### +# Install potential files in data directory +############################################################################### +set(LAMMPS_POTENTIALS_DIR ${CMAKE_INSTALL_FULL_DATADIR}/lammps/potentials) +install(DIRECTORY ${LAMMPS_SOURCE_DIR}/../potentials/ DESTINATION ${LAMMPS_POTENTIALS_DIR}) + +configure_file(etc/profile.d/lammps.sh.in ${CMAKE_BINARY_DIR}/etc/profile.d/lammps.sh @ONLY) +configure_file(etc/profile.d/lammps.csh.in ${CMAKE_BINARY_DIR}/etc/profile.d/lammps.csh @ONLY) +install( + FILES ${CMAKE_BINARY_DIR}/etc/profile.d/lammps.sh + ${CMAKE_BINARY_DIR}/etc/profile.d/lammps.csh + DESTINATION ${CMAKE_INSTALL_SYSCONFDIR}/profile.d +) + ############################################################################### # Testing # @@ -860,7 +1335,7 @@ endif() ############################################################################### # Print package summary ############################################################################### -foreach(PKG ${DEFAULT_PACKAGES} ${OTHER_PACKAGES} ${ACCEL_PACKAGES}) +foreach(PKG ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES} ${OTHER_PACKAGES}) if(PKG_${PKG}) message(STATUS "Building package: ${PKG}") endif() @@ -869,7 +1344,7 @@ endforeach() string(TOUPPER "${CMAKE_BUILD_TYPE}" BTYPE) get_directory_property(CPPFLAGS DIRECTORY ${CMAKE_SOURCE_DIR} COMPILE_DEFINITIONS) include(FeatureSummary) -feature_summary(INCLUDE_QUIET_PACKAGES WHAT ALL) +feature_summary(DESCRIPTION "The following packages have been found:" WHAT PACKAGES_FOUND) message(STATUS "<<< Build configuration >>> Build type ${CMAKE_BUILD_TYPE} Install path ${CMAKE_INSTALL_PREFIX} @@ -907,13 +1382,17 @@ message(STATUS "Link libraries: ${LAMMPS_LINK_LIBS}") if(BUILD_MPI) message(STATUS "Using mpi with headers in ${MPI_CXX_INCLUDE_PATH} and ${MPI_CXX_LIBRARIES}") endif() -if(ENABLED_GPU) +if(PKG_GPU) message(STATUS "GPU Api: ${GPU_API}") if(GPU_API STREQUAL "CUDA") message(STATUS "GPU Arch: ${GPU_ARCH}") - elseif(GPU_API STREQUAL "OpenCL") + elseif(GPU_API STREQUAL "OPENCL") message(STATUS "OCL Tune: ${OCL_TUNE}") endif() + message(STATUS "GPU Precision: ${GPU_PREC}") +endif() +if(PKG_KOKKOS) + message(STATUS "Kokkos Arch: ${KOKKOS_ARCH}") endif() if(PKG_KSPACE) message(STATUS "Using ${FFT} as FFT") diff --git a/cmake/FindLAMMPS.cmake.in b/cmake/FindLAMMPS.cmake.in new file mode 100644 index 0000000000..586df83c2d --- /dev/null +++ b/cmake/FindLAMMPS.cmake.in @@ -0,0 +1,48 @@ +# - Find liblammps +# Find the native liblammps headers and libraries. +# +# The following variables will set: +# LAMMPS_INCLUDE_DIRS - where to find lammps/library.h, etc. +# LAMMPS_LIBRARIES - List of libraries when using lammps. +# LAMMPS_API_DEFINES - lammps library api defines +# LAMMPS_VERSION - lammps library version +# LAMMPS_FOUND - True if liblammps found. +# +# In addition a LAMMPS::LAMMPS imported target is getting created. +# +# LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator +# http://lammps.sandia.gov, Sandia National Laboratories +# Steve Plimpton, sjplimp@sandia.gov +# +# Copyright (2003) Sandia Corporation. Under the terms of Contract +# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains +# certain rights in this software. This software is distributed under +# the GNU General Public License. +# +# See the README file in the top-level LAMMPS directory. +# + +find_package(PkgConfig) + +pkg_check_modules(PC_LAMMPS liblammps@LAMMPS_LIB_SUFFIX@) +find_path(LAMMPS_INCLUDE_DIR lammps/library.h HINTS ${PC_LAMMPS_INCLUDE_DIRS} @CMAKE_INSTALL_FULL_INCLUDEDIR@) + +set(LAMMPS_VERSION @LAMMPS_VERSION@) +set(LAMMPS_API_DEFINES @LAMMPS_API_DEFINES@) + +find_library(LAMMPS_LIBRARY NAMES lammps@LAMMPS_LIB_SUFFIX@ HINTS ${PC_LAMMPS_LIBRARY_DIRS} @CMAKE_INSTALL_FULL_LIBDIR@) + +set(LAMMPS_INCLUDE_DIRS "${LAMMPS_INCLUDE_DIR}") +set(LAMMPS_LIBRARIES "${LAMMPS_LIBRARY}") + +include(FindPackageHandleStandardArgs) +# handle the QUIETLY and REQUIRED arguments and set LAMMPS_FOUND to TRUE +# if all listed variables are TRUE +find_package_handle_standard_args(LAMMPS REQUIRED_VARS LAMMPS_LIBRARY LAMMPS_INCLUDE_DIR VERSION_VAR LAMMPS_VERSION) + +mark_as_advanced(LAMMPS_INCLUDE_DIR LAMMPS_LIBRARY) + +if(LAMMPS_FOUND AND NOT TARGET LAMMPS::LAMMPS) + add_library(LAMMPS::LAMMPS UNKNOWN IMPORTED) + set_target_properties(LAMMPS::LAMMPS PROPERTIES IMPORTED_LOCATION "${LAMMPS_LIBRARY}" INTERFACE_INCLUDE_DIRECTORIES "${LAMMPS_INCLUDE_DIR}" INTERFACE_COMPILE_DEFINITIONS "${LAMMPS_API_DEFINES}") +endif() diff --git a/cmake/Modules/FindQUIP.cmake b/cmake/Modules/FindQUIP.cmake index 4ee1baf4f8..b6d87d11fa 100644 --- a/cmake/Modules/FindQUIP.cmake +++ b/cmake/Modules/FindQUIP.cmake @@ -1,8 +1,8 @@ # - Find quip # Find the native QUIP libraries. # -# QUIP_LIBRARIES - List of libraries when using fftw3. -# QUIP_FOUND - True if fftw3 found. +# QUIP_LIBRARIES - List of libraries of the QUIP package +# QUIP_FOUND - True if QUIP library was found. # find_library(QUIP_LIBRARY NAMES quip) diff --git a/cmake/Modules/FindTBB.cmake b/cmake/Modules/FindTBB.cmake new file mode 100644 index 0000000000..8cc050817e --- /dev/null +++ b/cmake/Modules/FindTBB.cmake @@ -0,0 +1,46 @@ +# - Find parts of TBB +# Find the native TBB headers and libraries. +# +# TBB_INCLUDE_DIRS - where to find tbb.h, etc. +# TBB_LIBRARIES - List of libraries when using tbb. +# TBB_FOUND - True if tbb found. +# + +######################################################## +# TBB + +# TODO use more generic FindTBB + +find_path(TBB_INCLUDE_DIR NAMES tbb/tbb.h PATHS $ENV{TBBROOT}/include) +find_library(TBB_LIBRARY NAMES tbb PATHS $ENV{TBBROOT}/lib/intel64/gcc4.7 + $ENV{TBBROOT}/lib/intel64/gcc4.4 + $ENV{TBBROOT}/lib/intel64/gcc4.1) +set(TBB_LIBRARIES ${TBB_LIBRARY}) +set(TBB_INCLUDE_DIRS ${TBB_INCLUDE_DIR}) + +include(FindPackageHandleStandardArgs) +# handle the QUIETLY and REQUIRED arguments and set TBB_FOUND to TRUE +# if all listed variables are TRUE + +find_package_handle_standard_args(TBB DEFAULT_MSG TBB_LIBRARY TBB_INCLUDE_DIR) + +mark_as_advanced(TBB_INCLUDE_DIR TBB_LIBRARY ) + +######################################################## +# TBB Malloc + +find_path(TBB_MALLOC_INCLUDE_DIR NAMES tbb/tbb.h PATHS $ENV{TBBROOT}/include) +find_library(TBB_MALLOC_LIBRARY NAMES tbbmalloc PATHS $ENV{TBBROOT}/lib/intel64/gcc4.7 + $ENV{TBBROOT}/lib/intel64/gcc4.4 + $ENV{TBBROOT}/lib/intel64/gcc4.1) + +set(TBB_MALLOC_LIBRARIES ${TBB_MALLOC_LIBRARY}) +set(TBB_MALLOC_INCLUDE_DIRS ${TBB_MALLOC_INCLUDE_DIR}) + +include(FindPackageHandleStandardArgs) +# handle the QUIETLY and REQUIRED arguments and set TBB_MALLOC_FOUND to TRUE +# if all listed variables are TRUE + +find_package_handle_standard_args(TBB_MALLOC DEFAULT_MSG TBB_MALLOC_LIBRARY TBB_MALLOC_INCLUDE_DIR) + +mark_as_advanced(TBB_MALLOC_INCLUDE_DIR TBB_MALLOC_LIBRARY ) diff --git a/cmake/Modules/FindZMQ.cmake b/cmake/Modules/FindZMQ.cmake new file mode 100644 index 0000000000..608ccda777 --- /dev/null +++ b/cmake/Modules/FindZMQ.cmake @@ -0,0 +1,8 @@ +find_path(ZMQ_INCLUDE_DIR zmq.h) +find_library(ZMQ_LIBRARY NAMES zmq) + +set(ZMQ_LIBRARIES ${ZMQ_LIBRARY}) +set(ZMQ_INCLUDE_DIRS ${ZMQ_INCLUDE_DIR}) + +include(FindPackageHandleStandardArgs) +find_package_handle_standard_args(ZMQ DEFAULT_MSG ZMQ_LIBRARY ZMQ_INCLUDE_DIR) diff --git a/cmake/Modules/StyleHeaderUtils.cmake b/cmake/Modules/StyleHeaderUtils.cmake index c6f580f463..a89d098dd0 100644 --- a/cmake/Modules/StyleHeaderUtils.cmake +++ b/cmake/Modules/StyleHeaderUtils.cmake @@ -45,15 +45,16 @@ function(FindStyleHeadersExt path style_class extension headers sources) endfunction(FindStyleHeadersExt) function(CreateStyleHeader path filename) - math(EXPR N "${ARGC}-2") - set(temp "") - if(N GREATER 0) - math(EXPR ARG_END "${ARGC}-1") - - foreach(IDX RANGE 2 ${ARG_END}) - list(GET ARGV ${IDX} FNAME) + if(ARGC GREATER 2) + list(REMOVE_AT ARGV 0 1) + set(header_list) + foreach(FNAME ${ARGV}) get_filename_component(FNAME ${FNAME} NAME) + list(APPEND header_list ${FNAME}) + endforeach() + list(SORT header_list) + foreach(FNAME ${header_list}) set(temp "${temp}#include \"${FNAME}\"\n") endforeach() endif() @@ -84,19 +85,23 @@ function(RegisterNPairStyle path) AddStyleHeader(${path} NPAIR) endfunction(RegisterNPairStyle) +function(RegisterFixStyle path) + AddStyleHeader(${path} FIX) +endfunction(RegisterFixStyle) + function(RegisterStyles search_path) FindStyleHeaders(${search_path} ANGLE_CLASS angle_ ANGLE ) # angle ) # force FindStyleHeaders(${search_path} ATOM_CLASS atom_vec_ ATOM_VEC ) # atom ) # atom atom_vec_hybrid FindStyleHeaders(${search_path} BODY_CLASS body_ BODY ) # body ) # atom_vec_body FindStyleHeaders(${search_path} BOND_CLASS bond_ BOND ) # bond ) # force - FindStyleHeaders(${search_path} COMMAND_CLASS "" COMMAND ) # command ) # input + FindStyleHeaders(${search_path} COMMAND_CLASS "[^.]" COMMAND ) # command ) # input FindStyleHeaders(${search_path} COMPUTE_CLASS compute_ COMPUTE ) # compute ) # modify FindStyleHeaders(${search_path} DIHEDRAL_CLASS dihedral_ DIHEDRAL ) # dihedral ) # force FindStyleHeaders(${search_path} DUMP_CLASS dump_ DUMP ) # dump ) # output write_dump FindStyleHeaders(${search_path} FIX_CLASS fix_ FIX ) # fix ) # modify FindStyleHeaders(${search_path} IMPROPER_CLASS improper_ IMPROPER ) # improper ) # force - FindStyleHeaders(${search_path} INTEGRATE_CLASS "" INTEGRATE ) # integrate ) # update - FindStyleHeaders(${search_path} KSPACE_CLASS "" KSPACE ) # kspace ) # force + FindStyleHeaders(${search_path} INTEGRATE_CLASS "[^.]" INTEGRATE ) # integrate ) # update + FindStyleHeaders(${search_path} KSPACE_CLASS "[^.]" KSPACE ) # kspace ) # force FindStyleHeaders(${search_path} MINIMIZE_CLASS min_ MINIMIZE ) # minimize ) # update FindStyleHeaders(${search_path} NBIN_CLASS nbin_ NBIN ) # nbin ) # neighbor FindStyleHeaders(${search_path} NPAIR_CLASS npair_ NPAIR ) # npair ) # neighbor @@ -107,35 +112,6 @@ function(RegisterStyles search_path) FindStyleHeaders(${search_path} REGION_CLASS region_ REGION ) # region ) # domain endfunction(RegisterStyles) -function(RemovePackageHeader headers pkg_header) - get_property(hlist GLOBAL PROPERTY ${headers}) - list(REMOVE_ITEM hlist ${pkg_header}) - set_property(GLOBAL PROPERTY ${headers} "${hlist}") -endfunction(RemovePackageHeader) - -function(DetectAndRemovePackageHeader fname) - RemovePackageHeader(ANGLE ${fname}) - RemovePackageHeader(ATOM_VEC ${fname}) - RemovePackageHeader(BODY ${fname}) - RemovePackageHeader(BOND ${fname}) - RemovePackageHeader(COMMAND ${fname}) - RemovePackageHeader(COMPUTE ${fname}) - RemovePackageHeader(DIHEDRAL ${fname}) - RemovePackageHeader(DUMP ${fname}) - RemovePackageHeader(FIX ${fname}) - RemovePackageHeader(IMPROPER ${fname}) - RemovePackageHeader(INTEGRATE ${fname}) - RemovePackageHeader(KSPACE ${fname}) - RemovePackageHeader(MINIMIZE ${fname}) - RemovePackageHeader(NBIN ${fname}) - RemovePackageHeader(NPAIR ${fname}) - RemovePackageHeader(NSTENCIL ${fname}) - RemovePackageHeader(NTOPO ${fname}) - RemovePackageHeader(PAIR ${fname}) - RemovePackageHeader(READER ${fname}) - RemovePackageHeader(REGION ${fname}) -endfunction(DetectAndRemovePackageHeader) - function(RegisterStylesExt search_path extension sources) FindStyleHeadersExt(${search_path} ANGLE_CLASS ${extension} ANGLE ${sources}) FindStyleHeadersExt(${search_path} ATOM_CLASS ${extension} ATOM_VEC ${sources}) @@ -181,3 +157,21 @@ function(GenerateStyleHeaders output_path) GenerateStyleHeader(${output_path} READER reader ) # read_dump GenerateStyleHeader(${output_path} REGION region ) # domain endfunction(GenerateStyleHeaders) + +function(DetectBuildSystemConflict lammps_src_dir) + if(ARGC GREATER 1) + list(REMOVE_AT ARGV 0) + foreach(SRC_FILE ${ARGV}) + get_filename_component(FILENAME ${SRC_FILE} NAME) + if(EXISTS ${lammps_src_dir}/${FILENAME}) + message(FATAL_ERROR "\n########################################################################\n" + "Found package(s) installed by the make-based build system\n" + "\n" + "Please run\n" + "make -C ${lammps_src_dir} no-all purge\n" + "to uninstall\n" + "########################################################################") + endif() + endforeach() + endif() +endfunction(DetectBuildSystemConflict) diff --git a/cmake/README.md b/cmake/README.md index 8a582d82d9..21e728c1f0 100644 --- a/cmake/README.md +++ b/cmake/README.md @@ -22,6 +22,7 @@ tasks, act as a reference and provide examples of typical use cases. * [Building LAMMPS using cmake](#building-lammps-using-cmake-1) * [Prerequisites](#prerequisites) * [Build directory vs. Source Directory](#build-directory-vs-source-directory) + * [Defining and using presets](#defining-and-using-presets) * [Reference](#reference) * [Common CMAKE Configuration Options](#common-cmake-configuration-options) * [LAMMPS Configuration Options](#lammps-configuration-options) @@ -61,7 +62,7 @@ should get you started. git clone https://github.com/lammps/lammps.git mkdir lammps/build cd lammps/build -cmake ../cmake [-DOPTION_A=VALUE_A -DOPTION_B=VALUE_B ...] +cmake [-D OPTION_A=VALUE_A -D OPTION_B=VALUE_B ...] ../cmake make ``` @@ -150,6 +151,31 @@ build directory. ``` make ``` +# Defining and using presets + +The CMake build exposes a lot of different options. In the old build system +some of the package selections were possible by using special make target like +`make yes-std` or `make no-lib`. Achieving the same result with cmake requires +specifying all options manually. This can quickly become a very long command +line that is hard to handle. While these could be stored in a simple script +file, there is another way of defining "presets" to compile LAMMPS in a certain +way. + +A preset is a regular CMake script file that can use constructs such as +variables, lists and for-loops to manipulate configuration options and create +an [*initial cache*](https://cmake.org/cmake/help/v3.12/manual/cmake.1.html). +Options must be set with the `CACHE` and `FORCE` flag to ensure they are +considered even during a second cmake run. + +Such a file can then be passed to cmake via the `-C` flag. Several examples of +presets can be found in the `cmake/presets` folder. + +```bash +# build LAMMPS with all "standard" packages which don't use libraries and enable GPU package +mkdir build +cd build +cmake -C ../cmake/presets/std_nolib.cmake -D PKG_GPU=on ../cmake +``` # Reference @@ -239,6 +265,26 @@ make + + BUILD_LIB + control whether to build LAMMPS as a library + +
+
off (default)
+
on
+
+ + + + BUILD_EXE + control whether to build LAMMPS executable + +
+
on (default)
+
off
+
+ + BUILD_SHARED_LIBS control whether to build LAMMPS as a shared-library @@ -249,6 +295,16 @@ make + + BUILD_DOC + control whether to build LAMMPS documentation + +
+
off (default)
+
on
+
+ + LAMMPS_LONGLONG_TO_LONG Workaround if your system or MPI version does not recognize long long data types @@ -279,8 +335,8 @@ make `mpicxx` in your path and use this MPI implementation.
-
off (default)
-
on
+
on (default, if found)
+
off
@@ -289,8 +345,8 @@ make control whether to build LAMMPS with OpenMP support.
-
off (default)
-
on
+
on (default, if found)
+
off
@@ -374,16 +430,6 @@ make - - ENABLE_ALL - Enable all default packages - -
-
off (default)
-
on
-
- - PKG_ASPHERE Computes, time-integration fixes, and pair styles for aspherical particle models including ellipsoids, 2d lines, and 3d triangles. @@ -1245,7 +1291,7 @@ providing the identical features and USER interface.

-
KISSFFT
+
KISS
FFTW3
FFTW2
MKL
@@ -1253,13 +1299,13 @@ providing the identical features and USER interface.

- PACK_ARRAY + FFT_PACK Optimization for FFT
-
PACK_ARRAY
-
PACK_POINTER
-
PACK_MEMCPY
+
array (default)
+
pointer
+
memcpy
@@ -1351,6 +1397,29 @@ TODO ### PYTHON Package +### USER-INTEL Package + + + + + + + + + + + + + + + + +
OptionDescriptionValues
INTEL_ARCHTarget architecture for USER-INTEL package +
+
cpu (default)
+
knl
+
+
### GPU Package The GPU package builds a support library which can either use OpenCL or CUDA as @@ -1370,8 +1439,8 @@ target API. API used by GPU package
-
OpenCL (default)
-
CUDA
+
opencl (default)
+
cuda
@@ -1380,9 +1449,9 @@ target API. Precision size used by GPU package kernels
-
SINGLE_DOUBLE
-
SINGLE_SINGLE
-
DOUBLE_DOUBLE
+
mixed (default)
+
single
+
double
@@ -1391,12 +1460,12 @@ target API. Tuning target for OpenCL driver code
-
GENERIC (default)
-
INTEL (Intel CPU)
-
PHI (Intel Xeon Phi)
-
FERMI (NVIDIA)
-
KEPLER (NVIDIA)
-
CYPRESS (AMD)
+
generic (default)
+
intel (Intel CPU)
+
phi (Intel Xeon Phi)
+
fermi (NVIDIA)
+
kepler (NVIDIA)
+
cypress (AMD)
@@ -1405,11 +1474,11 @@ target API. CUDA SM architecture targeted by GPU package
-
sm20 (Fermi)
-
sm30 (Kepler)
-
sm50 (Maxwell)
-
sm60 (Pascal)
-
sm70 (Volta)
+
sm_20 (Fermi)
+
sm_30 (Kepler)
+
sm_50 (Maxwell)
+
sm_60 (Pascal)
+
sm_70 (Volta)
@@ -1491,6 +1560,16 @@ Requires a Eigen3 installation + + WITH_JPEG + Enables/Disable JPEG support in LAMMPS + +
+
yes (default, if found)
+
no
+
+ + JPEG_INCLUDE_DIR @@ -1518,6 +1597,16 @@ Requires a Eigen3 installation + + WITH_PNG + Enables/Disable PNG support in LAMMPS + +
+
yes (default, if found)
+
no
+
+ + PNG_INCLUDE_DIR @@ -1546,6 +1635,16 @@ requires `gzip` to be in your `PATH` + + WITH_GZIP + Enables/Disable GZIP support in LAMMPS + +
+
yes (default, if found)
+
no
+
+ + GZIP_EXECUTABLE @@ -1568,6 +1667,16 @@ requires `ffmpeg` to be in your `PATH` + + WITH_FFMPEG + Enables/Disable FFMPEG support in LAMMPS + +
+
yes (default, if found)
+
no
+
+ + FFMPEG_EXECUTABLE @@ -1580,8 +1689,13 @@ requires `ffmpeg` to be in your `PATH` ## Compilers -By default, `cmake` will use your environment C/C++/Fortran compilers for a build. It uses the `CC`, `CXX` and `FC` environment variables to detect which compilers should be used. However, these values -will be cached after the first run of `cmake`. Subsequent runs of `cmake` will ignore changes in these environment variables. To ensure the correct values are used you avoid the cache by setting the `CMAKE_C_COMPILER`, `CMAKE_CXX_COMPILER`, `CMAKE_Fortran_COMPILER` options directly. +By default, `cmake` will use your environment C/C++/Fortran compilers for a +build. It uses the `CC`, `CXX` and `FC` environment variables to detect which +compilers should be used. However, these values will be cached after the first +run of `cmake`. Subsequent runs of `cmake` will ignore changes in these +environment variables. To ensure the correct values are used you avoid the +cache by setting the `CMAKE_C_COMPILER`, `CMAKE_CXX_COMPILER`, +`CMAKE_Fortran_COMPILER` options directly. @@ -1617,20 +1731,20 @@ will be cached after the first run of `cmake`. Subsequent runs of `cmake` will i ### Building with GNU Compilers ```bash -cmake ../cmake -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DCMAKE_Fortran_COMPILER=gfortran +cmake -D CMAKE_C_COMPILER=gcc -D CMAKE_CXX_COMPILER=g++ -D CMAKE_Fortran_COMPILER=gfortran ../cmake ``` ### Building with Intel Compilers ```bash -cmake ../cmake -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc -DCMAKE_Fortran_COMPILER=ifort +cmake -D CMAKE_C_COMPILER=icc -D CMAKE_CXX_COMPILER=icpc -D CMAKE_Fortran_COMPILER=ifort ../cmake ``` ### Building with LLVM/Clang Compilers ```bash -cmake ../cmake -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_Fortran_COMPILER=flang +cmake -D CMAKE_C_COMPILER=clang -D CMAKE_CXX_COMPILER=clang++ -D CMAKE_Fortran_COMPILER=flang ../cmake ``` diff --git a/cmake/etc/profile.d/lammps.csh.in b/cmake/etc/profile.d/lammps.csh.in new file mode 100644 index 0000000000..def49bf75c --- /dev/null +++ b/cmake/etc/profile.d/lammps.csh.in @@ -0,0 +1,2 @@ +# set environment for LAMMPS executables to find potential files +if ( "$?LAMMPS_POTENTIALS" == 0 ) setenv LAMMPS_POTENTIALS @LAMMPS_POTENTIALS_DIR@ diff --git a/cmake/etc/profile.d/lammps.sh.in b/cmake/etc/profile.d/lammps.sh.in new file mode 100644 index 0000000000..acd75fa0cf --- /dev/null +++ b/cmake/etc/profile.d/lammps.sh.in @@ -0,0 +1,2 @@ +# set environment for LAMMPS executables to find potential files +export LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS-@LAMMPS_POTENTIALS_DIR@} diff --git a/cmake/pkgconfig/liblammps.pc.in b/cmake/pkgconfig/liblammps.pc.in index c5e1701782..7850972f3b 100644 --- a/cmake/pkgconfig/liblammps.pc.in +++ b/cmake/pkgconfig/liblammps.pc.in @@ -4,15 +4,15 @@ # after you added @CMAKE_INSTALL_FULL_LIBDIR@/pkg-config to PKG_CONFIG_PATH, # e.g. export PKG_CONFIG_PATH=@CMAKE_INSTALL_FULL_LIBDIR@/pkgconfig -prefix=@CMAKE_INSTALL_FULL_PREFIX@ +prefix=@CMAKE_INSTALL_PREFIX@ libdir=@CMAKE_INSTALL_FULL_LIBDIR@ includedir=@CMAKE_INSTALL_FULL_INCLUDEDIR@ Name: liblammps@LAMMPS_MACHINE@ Description: Large-scale Atomic/Molecular Massively Parallel Simulator Library URL: http://lammps.sandia.gov -Version: +Version: @LAMMPS_VERSION@ Requires: -Libs: -L${libdir} -llammps@LAMMPS_MACHINE@ +Libs: -L${libdir} -llammps@LAMMPS_LIB_SUFFIX@ Libs.private: -lm Cflags: -I${includedir} @LAMMPS_API_DEFINES@ diff --git a/cmake/presets/all_off.cmake b/cmake/presets/all_off.cmake new file mode 100644 index 0000000000..f7e90ddbb4 --- /dev/null +++ b/cmake/presets/all_off.cmake @@ -0,0 +1,22 @@ +set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU + GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MEAM MISC + MOLECULE MPIIO MSCG OPT PERI POEMS + PYTHON QEQ REAX REPLICA RIGID SHOCK SNAP SRD VORONOI) + +set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS + USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD + USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO + USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE + USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB + USER-QUIP USER-REAXC USER-SMD USER-SMTBQ USER-SPH USER-TALLY + USER-UEF USER-VTK) + +set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI + USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE + USER-NETCDF USER-QMMM USER-QUIP USER-SMD USER-VTK) + +set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES}) + +foreach(PKG ${ALL_PACKAGES}) + set(PKG_${PKG} OFF CACHE BOOL "" FORCE) +endforeach() diff --git a/cmake/presets/all_on.cmake b/cmake/presets/all_on.cmake new file mode 100644 index 0000000000..2c6f67904e --- /dev/null +++ b/cmake/presets/all_on.cmake @@ -0,0 +1,22 @@ +set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU + GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MEAM MISC + MOLECULE MPIIO MSCG OPT PERI POEMS + PYTHON QEQ REAX REPLICA RIGID SHOCK SNAP SRD VORONOI) + +set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS + USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD + USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO + USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE + USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB + USER-QUIP USER-REAXC USER-SMD USER-SMTBQ USER-SPH USER-TALLY + USER-UEF USER-VTK) + +set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI + USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE + USER-NETCDF USER-QMMM USER-QUIP USER-SMD USER-VTK) + +set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES}) + +foreach(PKG ${ALL_PACKAGES}) + set(PKG_${PKG} ON CACHE BOOL "" FORCE) +endforeach() diff --git a/cmake/presets/manual_selection.cmake b/cmake/presets/manual_selection.cmake new file mode 100644 index 0000000000..6c03d983f6 --- /dev/null +++ b/cmake/presets/manual_selection.cmake @@ -0,0 +1,69 @@ +set(PKG_ASPHERE OFF CACHE BOOL "" FORCE) +set(PKG_BODY OFF CACHE BOOL "" FORCE) +set(PKG_CLASS2 OFF CACHE BOOL "" FORCE) +set(PKG_COLLOID OFF CACHE BOOL "" FORCE) +set(PKG_COMPRESS OFF CACHE BOOL "" FORCE) +set(PKG_CORESHELL OFF CACHE BOOL "" FORCE) +set(PKG_DIPOLE OFF CACHE BOOL "" FORCE) +set(PKG_GPU OFF CACHE BOOL "" FORCE) +set(PKG_GRANULAR OFF CACHE BOOL "" FORCE) +set(PKG_KIM OFF CACHE BOOL "" FORCE) +set(PKG_KOKKOS OFF CACHE BOOL "" FORCE) +set(PKG_KSPACE OFF CACHE BOOL "" FORCE) +set(PKG_LATTE OFF CACHE BOOL "" FORCE) +set(PKG_LIB OFF CACHE BOOL "" FORCE) +set(PKG_MANYBODY OFF CACHE BOOL "" FORCE) +set(PKG_MC OFF CACHE BOOL "" FORCE) +set(PKG_MEAM OFF CACHE BOOL "" FORCE) +set(PKG_MISC OFF CACHE BOOL "" FORCE) +set(PKG_MOLECULE OFF CACHE BOOL "" FORCE) +set(PKG_MPIIO OFF CACHE BOOL "" FORCE) +set(PKG_MSCG OFF CACHE BOOL "" FORCE) +set(PKG_OPT OFF CACHE BOOL "" FORCE) +set(PKG_PERI OFF CACHE BOOL "" FORCE) +set(PKG_POEMS OFF CACHE BOOL "" FORCE) +set(PKG_PYTHOFF OFF CACHE BOOL "" FORCE) +set(PKG_QEQ OFF CACHE BOOL "" FORCE) +set(PKG_REAX OFF CACHE BOOL "" FORCE) +set(PKG_REPLICA OFF CACHE BOOL "" FORCE) +set(PKG_RIGID OFF CACHE BOOL "" FORCE) +set(PKG_SHOCK OFF CACHE BOOL "" FORCE) +set(PKG_SNAP OFF CACHE BOOL "" FORCE) +set(PKG_SRD OFF CACHE BOOL "" FORCE) +set(PKG_VOROFFOI OFF CACHE BOOL "" FORCE) + +set(PKG_USER OFF CACHE BOOL "" FORCE) +set(PKG_USER-ATC OFF CACHE BOOL "" FORCE) +set(PKG_USER-AWPMD OFF CACHE BOOL "" FORCE) +set(PKG_USER-BOCS OFF CACHE BOOL "" FORCE) +set(PKG_USER-CGDNA OFF CACHE BOOL "" FORCE) +set(PKG_USER-CGSDK OFF CACHE BOOL "" FORCE) +set(PKG_USER-COLVARS OFF CACHE BOOL "" FORCE) +set(PKG_USER-DIFFRACTIOFF OFF CACHE BOOL "" FORCE) +set(PKG_USER-DPD OFF CACHE BOOL "" FORCE) +set(PKG_USER-DRUDE OFF CACHE BOOL "" FORCE) +set(PKG_USER-EFF OFF CACHE BOOL "" FORCE) +set(PKG_USER-FEP OFF CACHE BOOL "" FORCE) +set(PKG_USER-H5MD OFF CACHE BOOL "" FORCE) +set(PKG_USER-INTEL OFF CACHE BOOL "" FORCE) +set(PKG_USER-LB OFF CACHE BOOL "" FORCE) +set(PKG_USER-MANIFOLD OFF CACHE BOOL "" FORCE) +set(PKG_USER-MEAMC OFF CACHE BOOL "" FORCE) +set(PKG_USER-MESO OFF CACHE BOOL "" FORCE) +set(PKG_USER-MGPT OFF CACHE BOOL "" FORCE) +set(PKG_USER-MISC OFF CACHE BOOL "" FORCE) +set(PKG_USER-MOFFF OFF CACHE BOOL "" FORCE) +set(PKG_USER-MOLFILE OFF CACHE BOOL "" FORCE) +set(PKG_USER-NETCDF OFF CACHE BOOL "" FORCE) +set(PKG_USER-OMP OFF CACHE BOOL "" FORCE) +set(PKG_USER-PHOFFOFF OFF CACHE BOOL "" FORCE) +set(PKG_USER-QMMM OFF CACHE BOOL "" FORCE) +set(PKG_USER-QTB OFF CACHE BOOL "" FORCE) +set(PKG_USER-QUIP OFF CACHE BOOL "" FORCE) +set(PKG_USER-REAXC OFF CACHE BOOL "" FORCE) +set(PKG_USER-SMD OFF CACHE BOOL "" FORCE) +set(PKG_USER-SMTBQ OFF CACHE BOOL "" FORCE) +set(PKG_USER-SPH OFF CACHE BOOL "" FORCE) +set(PKG_USER-TALLY OFF CACHE BOOL "" FORCE) +set(PKG_USER-UEF OFF CACHE BOOL "" FORCE) +set(PKG_USER-VTK OFF CACHE BOOL "" FORCE) diff --git a/cmake/presets/nolib.cmake b/cmake/presets/nolib.cmake new file mode 100644 index 0000000000..cd603aa804 --- /dev/null +++ b/cmake/presets/nolib.cmake @@ -0,0 +1,22 @@ +set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU + GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MEAM MISC + MOLECULE MPIIO MSCG OPT PERI POEMS + PYTHON QEQ REAX REPLICA RIGID SHOCK SNAP SRD VORONOI) + +set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS + USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD + USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO + USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE + USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB + USER-QUIP USER-REAXC USER-SMD USER-SMTBQ USER-SPH USER-TALLY + USER-UEF USER-VTK) + +set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI + USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE + USER-NETCDF USER-QMMM USER-QUIP USER-SMD USER-VTK) + +set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES}) + +foreach(PKG ${PACKAGES_WITH_LIB}) + set(PKG_${PKG} OFF CACHE BOOL "" FORCE) +endforeach() diff --git a/cmake/presets/std.cmake b/cmake/presets/std.cmake new file mode 100644 index 0000000000..36da897957 --- /dev/null +++ b/cmake/presets/std.cmake @@ -0,0 +1,22 @@ +set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU + GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MEAM MISC + MOLECULE MPIIO MSCG OPT PERI POEMS + PYTHON QEQ REAX REPLICA RIGID SHOCK SNAP SRD VORONOI) + +set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS + USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD + USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO + USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE + USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB + USER-QUIP USER-REAXC USER-SMD USER-SMTBQ USER-SPH USER-TALLY + USER-UEF USER-VTK) + +set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI + USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE + USER-NETCDF USER-QMMM USER-QUIP USER-SMD USER-VTK) + +set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES}) + +foreach(PKG ${STANDARD_PACKAGES}) + set(PKG_${PKG} ON CACHE BOOL "" FORCE) +endforeach() diff --git a/cmake/presets/std_nolib.cmake b/cmake/presets/std_nolib.cmake new file mode 100644 index 0000000000..9bffefcbe0 --- /dev/null +++ b/cmake/presets/std_nolib.cmake @@ -0,0 +1,26 @@ +set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU + GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MEAM MISC + MOLECULE MPIIO MSCG OPT PERI POEMS + PYTHON QEQ REAX REPLICA RIGID SHOCK SNAP SRD VORONOI) + +set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS + USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD + USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO + USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE + USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB + USER-QUIP USER-REAXC USER-SMD USER-SMTBQ USER-SPH USER-TALLY + USER-UEF USER-VTK) + +set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI + USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE + USER-NETCDF USER-QMMM USER-QUIP USER-SMD USER-VTK) + +set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES}) + +foreach(PKG ${STANDARD_PACKAGES}) + set(PKG_${PKG} ON CACHE BOOL "" FORCE) +endforeach() + +foreach(PKG ${PACKAGES_WITH_LIB}) + set(PKG_${PKG} OFF CACHE BOOL "" FORCE) +endforeach() diff --git a/cmake/presets/user.cmake b/cmake/presets/user.cmake new file mode 100644 index 0000000000..cb81b67558 --- /dev/null +++ b/cmake/presets/user.cmake @@ -0,0 +1,22 @@ +set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU + GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MEAM MISC + MOLECULE MPIIO MSCG OPT PERI POEMS + PYTHON QEQ REAX REPLICA RIGID SHOCK SNAP SRD VORONOI) + +set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS + USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD + USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO + USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE + USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB + USER-QUIP USER-REAXC USER-SMD USER-SMTBQ USER-SPH USER-TALLY + USER-UEF USER-VTK) + +set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI + USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE + USER-NETCDF USER-QMMM USER-QUIP USER-SMD USER-VTK) + +set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES}) + +foreach(PKG ${USER_PACKAGES}) + set(PKG_${PKG} ON CACHE BOOL "" FORCE) +endforeach() diff --git a/doc/Makefile b/doc/Makefile index c8cc8bc1bd..9069fa1d60 100644 --- a/doc/Makefile +++ b/doc/Makefile @@ -31,7 +31,7 @@ SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocess SOURCES=$(filter-out $(wildcard src/lammps_commands*.txt) src/lammps_support.txt src/lammps_tutorials.txt,$(wildcard src/*.txt)) OBJECTS=$(SOURCES:src/%.txt=$(RSTDIR)/%.rst) -.PHONY: help clean-all clean epub html pdf old venv spelling anchor_check +.PHONY: help clean-all clean epub mobi html pdf old venv spelling anchor_check # ------------------------------------------ @@ -42,6 +42,8 @@ help: @echo " old create old-style HTML doc pages in old dir" @echo " fetch fetch HTML and PDF files from LAMMPS web site" @echo " epub create ePUB format manual for e-book readers" + @echo " mobi convert ePUB to MOBI format manual for e-book readers (e.g. Kindle)" + @echo " (requires ebook-convert tool from calibre)" @echo " clean remove all intermediate RST files" @echo " clean-all reset the entire build environment" @echo " txt2html build txt2html tool" @@ -49,11 +51,11 @@ help: # ------------------------------------------ -clean-all: +clean-all: clean rm -rf $(BUILDDIR)/* utils/txt2html/txt2html.exe clean: - rm -rf $(RSTDIR) html + rm -rf $(RSTDIR) html old epub rm -rf spelling clean-spelling: @@ -106,6 +108,11 @@ epub: $(OBJECTS) @rm -rf epub @echo "Build finished. The ePUB manual file is created." +mobi: epub + @rm -f LAMMPS.mobi + @ebook-convert LAMMPS.epub LAMMPS.mobi + @echo "Conversion finished. The MOBI manual file is created." + pdf: utils/txt2html/txt2html.exe @(\ set -e; \ @@ -157,7 +164,7 @@ $(RSTDIR)/%.rst : src/%.txt $(TXT2RST) @(\ mkdir -p $(RSTDIR) ; \ . $(VENV)/bin/activate ;\ - txt2rst $< > $@ ;\ + txt2rst -v $< > $@ ;\ deactivate ;\ ) diff --git a/doc/lammps.1 b/doc/lammps.1 new file mode 100644 index 0000000000..d49650bfaa --- /dev/null +++ b/doc/lammps.1 @@ -0,0 +1,45 @@ +.TH LAMMPS "2018-08-22" +.SH NAME +.B LAMMPS +\- Molecular Dynamics Simulator. + +.SH SYNOPSIS +.B lmp +-in in.file + +or + +mpirun \-np 2 +.B lmp +-in in.file + +.SH DESCRIPTION +.B LAMMPS +LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale +Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials for soft +materials (biomolecules, polymers) and solid-state materials (metals, +semiconductors) and coarse-grained or mesoscopic systems. It can be used to +model atoms or, more generically, as a parallel particle simulator at the +atomic, meso, or continuum scale. + +See http://lammps.sandia.gov/ for documentation. + +.SH OPTIONS +See https://lammps.sandia.gov/doc/Run_options.html for details on +command-line options. + +.SH COPYRIGHT +© 2003--2018 Sandia Corporation + +This package is free software; you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation; either version 2 of the License, or +(at your option) any later version. + +This package is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. + +On Debian systems, the complete text of the GNU General +Public License can be found in `/usr/share/common-licenses/GPL-2'. diff --git a/doc/src/Build.txt b/doc/src/Build.txt new file mode 100644 index 0000000000..df30af36f5 --- /dev/null +++ b/doc/src/Build.txt @@ -0,0 +1,49 @@ +"Previous Section"_Install.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Run_head.html :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Build LAMMPS :h2 + +LAMMPS can be built as an executable or library from source code via +either traditional makefiles (which may require manual editing) +for use with GNU make or gmake, or a build environment generated by CMake +(Unix Makefiles, Xcode, Visual Studio, KDevelop or more). As an +alternative you can download a package with pre-built executables +as described on the "Install"_Install.html doc page. + + + + + +"Build LAMMPS with CMake"_Build_cmake.html +"Build LAMMPS with make"_Build_make.html +"Link LAMMPS as a library to another code"_Build_link.html +"Basic build options"_Build_basics.html +"Optional build settings"_Build_settings.html +"Include packages in build"_Build_package.html +"Packages with extra build options"_Build_extras.html +"Notes for building LAMMPS on Windows"_Build_windows.html :all(b) + +If you have problems building LAMMPS, it is often due to software +issues on your local machine. If you can, find a local expert to +help. If you're still stuck, send an email to the "LAMMPS mail +list"_http://lammps.sandia.gov/mail.html. diff --git a/doc/src/Build_basics.txt b/doc/src/Build_basics.txt new file mode 100644 index 0000000000..4b3a347bf1 --- /dev/null +++ b/doc/src/Build_basics.txt @@ -0,0 +1,319 @@ +"Higher level section"_Build.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Basic build options :h3 + +The following topics are covered on this page, for building both with +CMake and make: + +"Serial vs parallel build"_#serial +"Choice of compiler and compile/link options"_#compile +"Build LAMMPS as an executable or a library"_#exe +"Build the LAMMPS documentation"_#doc +"Install LAMMPS after a build"_#install :ul + +:line + +Serial vs parallel build :h4,link(serial) + +LAMMPS can be built to run in parallel using the ubiquitous "MPI +(message-passing +interface)"_https://en.wikipedia.org/wiki/Message_Passing_Interface +library. Or it can built to run on a single processor (serial) +without MPI. It can also be built with support for OpenMP threading +(see more discussion below). + +[CMake variables]: + +-D BUILD_MPI=value # yes or no, default is yes if CMake finds MPI, else no +-D BUILD_OMP=value # yes or no (default) +-D LAMMPS_MACHINE=name # name = mpi, serial, mybox, titan, laptop, etc + # no default value :pre + +The executable created by CMake (after running make) is lmp_name. If +the LAMMPS_MACHINE variable is not specified, the executable is just +lmp. Using BUILD_MPI=no will produce a serial executable. + +[Traditional make]: + +cd lammps/src +make mpi # parallel build, produces lmp_mpi using Makefile.mpi +make serial # serial build, produces lmp_serial using Makefile/serial +make mybox :pre # uses Makefile.mybox to produce lmp_mybox :pre + +Serial build (see src/MAKE/Makefile.serial): + +MPI_INC = -I../STUBS +MPI_PATH = -L../STUBS +MPI_LIB = -lmpi_stubs :pre + +For a parallel build, if MPI is installed on your system in the usual +place (e.g. under /usr/local), you do not need to specify the 3 +variables MPI_INC, MPI_PATH, MPI_LIB. The MPI wrapper on the compiler +(e.g. mpicxx, mpiCC) knows where to find the needed include and +library files. Failing this, these 3 variables can be used to specify +where the mpi.h file (MPI_INC), and the MPI library files (MPI_PATH) +are found, and the name of the library files (MPI_LIB). + +For a serial build, you need to specify the 3 variables, as shown +above. + +For a serial LAMMPS build, use the dummy MPI library provided in +src/STUBS. You also need to build the STUBS library for your platform +before making LAMMPS itself. A "make serial" build does this for. +Otherwise, type "make mpi-stubs" from the src directory, or "make" +from the src/STUBS dir. If the build fails, you will need to edit the +STUBS/Makefile for your platform. + +The file STUBS/mpi.c provides a CPU timer function called MPI_Wtime() +that calls gettimeofday() . If your system doesn't support +gettimeofday() , you'll need to insert code to call another timer. +Note that the ANSI-standard function clock() rolls over after an hour +or so, and is therefore insufficient for timing long LAMMPS +simulations. + +[CMake and make info]: + +If you are installing MPI yourself, we recommend MPICH2 from Argonne +National Laboratory or OpenMPI. MPICH can be downloaded from the +"Argonne MPI site"_http://www.mcs.anl.gov/research/projects/mpich2/. +OpenMPI can be downloaded from the "OpenMPI +site"_http://www.open-mpi.org. Other MPI packages should also work. +If you are running on a large parallel machine, your system admins or +the vendor should have already installed a version of MPI, which is +likely to be faster than a self-installed MPICH or OpenMPI, so find +out how to build and link with it. + +The majority of OpenMP (threading) support in LAMMPS is provided by +the USER-OMP package; see the "Speed omp"_Speed_omp.html doc page for +details. The USER-INTEL package also provides OpenMP support (it is +compatible with USER-OMP) and adds vectorization support when compiled +with the Intel compilers on top of that. Also, the KOKKOS package can +be compiled for using OpenMP threading. + +However, there are a few commands in LAMMPS that have native OpenMP +support. These are commands in the MPIIO, SNAP, USER-DIFFRACTION, and +USER-DPD packages. In addition some packages support OpenMP threading +indirectly through the libraries they interface to: e.g. LATTE and +USER-COLVARS. See the "Packages details"_Packages_details.html doc +page for more info on these packages and the doc pages for their +respective commands for OpenMP threading info. + +For CMake, if you use BUILD_OMP=yes, you can use these packages and +turn on their native OpenMP support and turn on their native OpenMP +support at run time, by setting the OMP_NUM_THREADS environment +variable before you launch LAMMPS. + +For building via conventional make, the CCFLAGS and LINKFLAGS +variables in Makefile.machine need to include the compiler flag that +enables OpenMP. For GNU compilers it is -fopenmp. For (recent) Intel +compilers it is -qopenmp. If you are using a different compiler, +please refer to its documentation. + +:line + +Choice of compiler and compile/link options :h4,link(compile) + +The choice of compiler and compiler flags can be important for +performance. Vendor compilers can produce faster code than +open-source compilers like GNU. On boxes with Intel CPUs, we suggest +trying the "Intel C++ compiler"_intel. + +:link(intel,https://software.intel.com/en-us/intel-compilers) + +On parallel clusters or supercomputers which use "modules" for their +compile/link environments, you can often access different compilers by +simply loading the appropriate module before building LAMMPS. + +[CMake variables]: + +-D CMAKE_CXX_COMPILER=name # name of C++ compiler +-D CMAKE_C_COMPILER=name # name of C compiler +-D CMAKE_Fortran_COMPILER=name # name of Fortran compiler :pre + +-D CMAKE_CXX_FlAGS=string # flags to use with C++ compiler +-D CMAKE_C_FlAGS=string # flags to use with C compiler +-D CMAKE_Fortran_FlAGS=string # flags to use with Fortran compiler :pre + +By default CMake will use a compiler it finds and it will add +optimization flags appropriate to that compiler and any "accelerator +packages"_Speed_packages.html you have included in the build. + +You can tell CMake to look for a specific compiler with these variable +settings. Likewise you can specify the FLAGS variables if you want to +experiment with alternate optimization flags. You should specify all +3 compilers, so that the small number of LAMMPS source files written +in C or Fortran are built with a compiler consistent with the one used +for all the C++ files: + +Building with GNU Compilers: +cmake ../cmake -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DCMAKE_Fortran_COMPILER=gfortran +Building with Intel Compilers: +cmake ../cmake -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc -DCMAKE_Fortran_COMPILER=ifort +Building with LLVM/Clang Compilers: +cmake ../cmake -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_Fortran_COMPILER=flang :pre + +NOTE: When the cmake command completes, it prints info to the screen +as to which compilers it is using, and what flags will be used in the +compilation. Note that if the top-level compiler is mpicxx, it is +simply a wrapper on a real compiler. The underlying compiler info is +what will be listed in the CMake output. You should check to insure +you are using the compiler and optimization flags are the ones you +want. + +[Makefile.machine settings]: + +Parallel build (see src/MAKE/Makefile.mpi): + +CC = mpicxx +CCFLAGS = -g -O3 +LINK = mpicxx +LINKFLAGS = -g -O :pre + +Serial build (see src/MAKE/Makefile.serial): + +CC = g++ +CCFLAGS = -g -O3 +LINK = g++ +LINKFLAGS = -g -O :pre + +The "compiler/linker settings" section of a Makefile.machine lists +compiler and linker settings for your C++ compiler, including +optimization flags. You should always use mpicxx or mpiCC for +a parallel build, since these compiler wrappers will include +a variety of settings appropriate for your MPI installation. + +NOTE: If you build LAMMPS with any "accelerator +packages"_Speed_packages.html included, they have specific +optimization flags that are either required or recommended for optimal +performance. You need to include these in the CCFLAGS and LINKFLAGS +settings above. For details, see the individual package doc pages +listed on the "Speed packages"_Speed_packages.html doc page. Or +examine these files in the src/MAKE/OPTIONS directory. They +correspond to each of the 5 accelerator packages and their hardware +variants: + +Makefile.opt # OPT package +Makefile.omp # USER-OMP package +Makefile.intel_cpu # USER-INTEL package for CPUs +Makefile.intel_coprocessor # USER-INTEL package for KNLs +Makefile.gpu # GPU package +Makefile.kokkos_cuda_mpi # KOKKOS package for GPUs +Makefile.kokkos_omp # KOKKOS package for CPUs (OpenMP) +Makefile.kokkos_phi # KOKKOS package for KNLs (OpenMP) :pre + +:line + +Build LAMMPS as an executable or a library :h4,link(exe) + +LAMMPS can be built as either an executable or as a static or shared +library. The LAMMPS library can be called from another application or +a scripting language. See the "Howto couple"_Howto_couple.html doc +page for more info on coupling LAMMPS to other codes. See the +"Python"_Python_head.html doc page for more info on wrapping and +running LAMMPS from Python via its library interface. + +[CMake variables]: + +-D BUILD_EXE=value # yes (default) or no +-D BUILD_LIB=value # yes or no (default) +-D BUILD_SHARED_LIBS=value # yes or no (default) :pre + +Setting BUILD_EXE=no will not produce an executable. Setting +BUILD_LIB=yes will produce a static library named liblammps.a. +Setting both BUILD_LIB=yes and BUILD_SHARED_LIBS=yes will produce a +shared library named liblammps.so. + +[Traditional make]: + +cd lammps/src +make machine # build LAMMPS executable lmp_machine +make mode=lib machine # build LAMMPS static lib liblammps_machine.a +make mode=shlib machine # build LAMMPS shared lib liblammps_machine.so :pre + +The two library builds also create generic soft links, named +liblammps.a and liblammps.so, which point to the liblammps_machine +files. + +[CMake and make info]: + +Note that for a shared library to be usable by a calling program, all +the auxiliary libraries it depends on must also exist as shared +libraries. This will be the case for libraries included with LAMMPS, +such as the dummy MPI library in src/STUBS or any package libraries in +the lib/packages directory, since they are always built as shared +libraries using the -fPIC switch. However, if a library like MPI or +FFTW does not exist as a shared library, the shared library build will +generate an error. This means you will need to install a shared +library version of the auxiliary library. The build instructions for +the library should tell you how to do this. + +As an example, here is how to build and install the "MPICH +library"_mpich, a popular open-source version of MPI, distributed by +Argonne National Lab, as a shared library in the default +/usr/local/lib location: + +:link(mpich,http://www-unix.mcs.anl.gov/mpi) + +./configure --enable-shared +make +make install :pre + +You may need to use "sudo make install" in place of the last line if +you do not have write privileges for /usr/local/lib. The end result +should be the file /usr/local/lib/libmpich.so. + +:line + +Build the LAMMPS documentation :h4,link(doc) + +[CMake variable]: + +-D BUILD_DOC=value # yes or no (default) :pre + +This will create the HTML doc pages within the CMake build directory. +The reason to do this is if you want to "install" LAMMPS on a system +after the CMake build via "make install", and include the doc pages in +the install. + +[Traditional make]: + +cd lammps/doc +make html # html doc pages +make pdf # single Manual.pdf file :pre + +This will create a lammps/doc/html dir with the HTML doc pages so that +you can browse them locally on your system. Type "make" from the +lammps/doc dir to see other options. + +NOTE: You can also download a tarball of the documention for the +current LAMMPS version (HTML and PDF files), from the website +"download page"_http://lammps.sandia.gov/download.html. + +:line + +Install LAMMPS after a build :h4,link(install) + +After building LAMMPS, you may wish to copy the LAMMPS executable of +library, along with other LAMMPS files (library header, doc files) to +a globally visible place on your system, for others to access. Note +that you may need super-user privileges (e.g. sudo) if the directory +you want to copy files to is protected. + +[CMake variable]: + +cmake -D CMAKE_INSTALL_PREFIX=path \[options ...\] ../cmake +make # perform make after CMake command +make install # perform the installation into prefix :pre + +[Traditional make]: + +There is no "install" option in the src/Makefile for LAMMPS. If you +wish to do this you will need to first build LAMMPS, then manually +copy the desired LAMMPS files to the appropriate system directories. diff --git a/doc/src/Build_cmake.txt b/doc/src/Build_cmake.txt new file mode 100644 index 0000000000..f8b52056fc --- /dev/null +++ b/doc/src/Build_cmake.txt @@ -0,0 +1,196 @@ +"Higher level section"_Build.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Build LAMMPS with CMake :h3 + +This page is a short summary of how to use CMake to build LAMMPS. +Details on CMake variables that enable specific LAMMPS build options +are given on the pages linked to from the "Build"_Build.html doc page. + +Richard Berger (Temple U) has also written a "more comprehensive +guide"_https://github.com/lammps/lammps/blob/master/cmake/README.md +for how to use CMake to build LAMMPS. If you are new to CMake it is a +good place to start. + +:line + +Building LAMMPS with CMake is a two-step process. First you use CMake +to create a build environment in a new directory. On Linux systems, +this will be based on makefiles for use with make. Then you use the +make command to build LAMMPS, which uses the created +Makefile(s). Example: + +cd lammps # change to the LAMMPS distribution directory +mkdir build; cd build # create a new directory (folder) for build +cmake ../cmake \[options ...\] # configuration with (command-line) cmake +make # compilation :pre + +The cmake command will detect available features, enable selected +packages and options, and will generate the build environment. The make +command will then compile and link LAMMPS, producing (by default) an +executable called "lmp" and a library called "liblammps.a" in the +"build" folder. + +If your machine has multiple CPU cores (most do these days), using a +command like "make -jN" (with N being the number of available local +CPU cores) can be much faster. If you plan to do development on +LAMMPS or need to re-compile LAMMPS repeatedly, installation of the +ccache (= Compiler Cache) software may speed up compilation even more. + +After compilation, you can optionally copy the LAMMPS executable and +library into your system folders (by default under /usr/local) with: + +make install # optional, copy LAMMPS executable & library elsewhere :pre + +:line + +There are 3 variants of CMake: a command-line version (cmake), a text mode +UI version (ccmake), and a graphical GUI version (cmake-GUI). You can use +any of them interchangeably to configure and create the LAMMPS build +environment. On Linux all the versions produce a Makefile as their +output. See more details on each below. + +You can specify a variety of options with any of the 3 versions, which +affect how the build is performed and what is included in the LAMMPS +executable. Links to pages explaining all the options are listed on +the "Build"_Build.html doc page. + +You must perform the CMake build system generation and compilation in +a new directory you create. It can be anywhere on your local machine. +In these Build pages we assume that you are building in a directory +called "lammps/build". You can perform separate builds independently +with different options, so long as you perform each of them in a +separate directory you create. All the auxiliary files created by one +build process (executable, object files, log files, etc) are stored in +this directory or sub-directories within it that CMake creates. + +NOTE: To perform a CMake build, no packages can be installed or a +build been previously attempted in the LAMMPS src directory by using +"make" commands to "perform a conventional LAMMPS +build"_Build_make.html. CMake detects if this is the case and +generates an error, telling you to type "make no-all purge" in the src +directory to un-install all packages. The purge removes all the *.h +files auto-generated by make. + +You must have CMake version 2.8 or later on your system to build +LAMMPS. A handful of LAMMPS packages (KOKKOS, LATTE, MSCG) require a +later version. CMake will print a message telling you if a later +version is required. Installation instructions for CMake are below. + +After the initial build, if you edit LAMMPS source files, or add your +own new files to the source directory, you can just re-type make from +your build directory and it will re-compile only the files that have +changed. If you want to change CMake options you can run cmake (or +ccmake or cmake-gui) again from the same build directory and alter +various options; see details below. Or you can remove the entire build +folder, recreate the directory and start over. + +:line + +[Command-line version of CMake]: + +cmake \[options ...\] /path/to/lammps/cmake # build from any dir +cmake \[options ...\] ../cmake # build from lammps/build :pre + +The cmake command takes one required argument, which is the LAMMPS +cmake directory which contains the CMakeLists.txt file. + +The argument can be preceeded or followed by various CMake +command-line options. Several useful ones are: + +-D CMAKE_INSTALL_PREFIX=path # where to install LAMMPS executable/lib if desired +-D CMAKE_BUILD_TYPE=type # type = Release or Debug +-G output # style of output CMake generates +-DVARIABLE=value # setting for a LAMMPS feature to enable +-D VARIABLE=value # ditto, but cannot come after CMakeLists.txt dir :pre + +All the LAMMPS-specific -D variables that a LAMMPS build supports are +described on the pages linked to from the "Build"_Build.html doc page. +All of these variable names are upper-case and their values are +lower-case, e.g. -D LAMMPS_SIZES=smallbig. For boolean values, any of +these forms can be used: yes/no, on/off, 1/0. + +On Unix/Linux machines, CMake generates a Makefile by default to +perform the LAMMPS build. Alternate forms of build info can be +generated via the -G switch, e.g. Visual Studio on a Windows machine, +Xcode on MacOS, or KDevelop on Linux. Type "cmake --help" to see the +"Generator" styles of output your system supports. + +NOTE: When CMake runs, it prints configuration info to the screen. +You should review this to verify all the features you requested were +enabled, including packages. You can also see what compilers and +compile options will be used for the build. Any errors in CMake +variable syntax will also be flagged, e.g. mis-typed variable names or +variable values. + +CMake creates a CMakeCache.txt file when it runs. This stores all the +settings, so that when running CMake again you can use the current +folder '.' instead of the path to the LAMMPS cmake folder as the +required argument to the CMake command. Either way the existing +settings will be inherited unless the CMakeCache.txt file is removed. + +If you later want to change a setting you can rerun cmake in the build +directory with different setting. Please note that some automatically +detected variables will not change their value when you rerun cmake. +In these cases it is usually better to first remove all the +files/directories in the build directory, or start with a fresh build +directory. + +:line + +[Curses version (terminal-style menu) of CMake]: + +ccmake ../cmake :pre + +You initiate the configuration and build environment generation steps +separately. For the first you have to type [c], for the second you +have to type [g]. You may need to type [c] multiple times, and may be +required to edit some of the entries of CMake configuration variables +in between. Please see the "ccmake +manual"_https://cmake.org/cmake/help/latest/manual/ccmake.1.html for +more information. + +:line + +[GUI version of CMake]: + +cmake-gui ../cmake :pre + +You initiate the configuration and build environment generation steps +separately. For the first you have to click on the [Configure] button, +for the second you have to click on the [Generate] button. You may +need to click on [Configure] multiple times, and may be required to +edit some of the entries of CMake configuration variables in between. +Please see the "cmake-gui +manual"_https://cmake.org/cmake/help/latest/manual/cmake-gui.1.html +for more information. + +:line + +[Installing CMake] + +Check if your machine already has CMake installed: + +which cmake # do you have it? +which cmake3 # version 3 may have this name +cmake --version # what specific version you have :pre + +On clusters or supercomputers which use environment modules to manage +software packages, do this: + +module list # is a cmake module already loaded? +module avail # is a cmake module available? +module load cmake3 # load cmake module with appropriate name :pre + +Most Linux distributions offer pre-compiled cmake packages through +their package management system. If you do not have CMake or a new +enough version, you can download the latest version at +"https://cmake.org/download/"_https://cmake.org/download/. +Instructions on how to install it on various platforms can be found +"on this page"_https://cmake.org/install/. diff --git a/doc/src/Build_extras.txt b/doc/src/Build_extras.txt new file mode 100644 index 0000000000..fb96699743 --- /dev/null +++ b/doc/src/Build_extras.txt @@ -0,0 +1,1026 @@ +"Higher level section"_Build.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Packages with extra build options :h3 + +When building with some packages, additional steps may be required, +in addition to: + +-D PKG_NAME=yes # CMake +make yes-name # make :pre + +as described on the "Build_package"_Build_package.html doc page. + +For a CMake build there may be additional optional or required +variables to set. For a build with make, a provided library under the +lammps/lib directory may need to be built first. Or an external +library may need to exist on your system or be downloaded and built. +You may need to tell LAMMPS where it is found on your system. + +This is the list of packages that may require additional steps. + +"COMPRESS"_#compress, +"GPU"_#gpu, +"KIM"_#kim, +"KOKKOS"_#kokkos, +"LATTE"_#latte, +"MEAM"_#meam, +"MESSAGE"_#message, +"MSCG"_#mscg, +"OPT"_#opt, +"POEMS"_#poems, +"PYTHON"_#python, +"REAX"_#reax, +"VORONOI"_#voronoi, +"USER-ATC"_#user-atc, +"USER-AWPMD"_#user-awpmd, +"USER-COLVARS"_#user-colvars, +"USER-H5MD"_#user-h5md, +"USER-INTEL"_#user-intel, +"USER-MOLFILE"_#user-molfile, +"USER-NETCDF"_#user-netcdf, +"USER-OMP"_#user-omp, +"USER-QMMM"_#user-qmmm, +"USER-QUIP"_#user-quip, +"USER-SCAFACOS"_#user-scafacos, +"USER-SMD"_#user-smd, +"USER-VTK"_#user-vtk :tb(c=6,ea=c,a=l) + +:line + +COMPRESS package :h4,link(compress) + +To build with this package you must have the zlib compression library +available on your system. + +[CMake build]: + +If CMake cannot find the library, you can set these variables: + +-D ZLIB_INCLUDE_DIR=path # path to zlib.h header file +-D ZLIB_LIBRARIES=path # path to libz.a (.so) file :pre + +[Traditional make]: + +If make cannot find the library, you can edit the +lib/compress/Makefile.lammps file to specify the paths and library +name. + +:line + +GPU package :h4,link(gpu) + +To build with this package, you must choose options for precision and +which GPU hardware to build for. + +[CMake build]: + +-D GPU_API=value # value = opencl (default) or cuda +-D GPU_PREC=value # precision setting + # value = double or mixed (default) or single +-D OCL_TUNE=value # hardware choice for GPU_API=opencl + # generic (default) or intel (Intel CPU) or fermi, kepler, cypress (NVIDIA) +-D GPU_ARCH=value # hardware choice for GPU_API=cuda + # value = sm_XX, see below + # default is Cuda-compiler dependent, but typically sm_20 +-D CUDPP_OPT=value # optimization setting for GPU_API=cudea + # enables CUDA Performance Primitives Optimizations + # yes (default) or no :pre + +GPU_ARCH settings for different GPU hardware is as follows: + +sm_20 for Fermi (C2050/C2070, deprecated as of CUDA 8.0) or GeForce GTX 580 or similar +sm_30 for Kepler (K10) +sm_35 for Kepler (K40) or GeForce GTX Titan or similar +sm_37 for Kepler (dual K80) +sm_50 for Maxwell +sm_60 for Pascal (P100) +sm_70 for Volta :ul + +[Traditional make]: + +Before building LAMMPS, you must build the GPU library in lib/gpu. +You can do this manually if you prefer; follow the instructions in +lib/gpu/README. Note that the GPU library uses MPI calls, so you must +use the same MPI library (or the STUBS library) settings as the main +LAMMPS code. This also applies to the -DLAMMPS_BIGBIG, +-DLAMMPS_SMALLBIG, or -DLAMMPS_SMALLSMALL settings in whichever +Makefile you use. + +You can also build the library in one step from the lammps/src dir, +using a command like these, which simply invoke the lib/gpu/Install.py +script with the specified args: + +make lib-gpu # print help message +make lib-gpu args="-b" # build GPU library with default Makefile.linux +make lib-gpu args="-m xk7 -p single -o xk7.single" # create new Makefile.xk7.single, altered for single-precision +make lib-gpu args="-m mpi -a sm_60 -p mixed -b" # build GPU library with mixed precision and P100 using other settings in Makefile.mpi :pre + +Note that this procedure starts with a Makefile.machine in lib/gpu, as +specified by the "-m" switch. For your convenience, machine makefiles +for "mpi" and "serial" are provided, which have the same settings as +the corresponding machine makefiles in the main LAMMPS source +folder. In addition you can alter 4 important settings in the +Makefile.machine you start from via the corresponding -h, -a, -p, -e +switches (as in the examples above), and also save a copy of the new +Makefile if desired: + +CUDA_HOME = where NVIDIA CUDA software is installed on your system +CUDA_ARCH = sm_XX, what GPU hardware you have, same as CMake GPU_ARCH above +CUDA_PRECISION = precision (double, mixed, single) +EXTRAMAKE = which Makefile.lammps.* file to copy to Makefile.lammps :ul + +If the library build is successful, 3 files should be created: +lib/gpu/libgpu.a, lib/gpu/nvc_get_devices, and +lib/gpu/Makefile.lammps. The latter has settings that enable LAMMPS +to link with CUDA libraries. If the settings in Makefile.lammps for +your machine are not correct, the LAMMPS build will fail, and +lib/gpu/Makefile.lammps may need to be edited. + +NOTE: If you re-build the GPU library in lib/gpu, you should always +un-install the GPU package in lammps/src, then re-install it and +re-build LAMMPS. This is because the compilation of files in the GPU +package uses the library settings from the lib/gpu/Makefile.machine +used to build the GPU library. + +:line + +KIM package :h4,link(kim) + +To build with this package, the KIM library must be downloaded and +built on your system. It must include the KIM models that you want to +use with LAMMPS. + +Note that in LAMMPS lingo, a KIM model driver is a pair style +(e.g. EAM or Tersoff). A KIM model is a pair style for a particular +element or alloy and set of parameters, e.g. EAM for Cu with a +specific EAM potential file. Also note that installing the KIM API +library with all its models, may take around 30 min to build. Of +course you only need to do that once. + +See the list of KIM model drivers here: +https://openkim.org/kim-items/model-drivers/alphabetical + +See the list of all KIM models here: +https://openkim.org/kim-items/models/by-model-drivers + +See the list of example KIM models included by default here: +https://openkim.org/kim-api on the "What is in the KIM API source +package?" page. + +[CMake build]: + +-D DOWNLOAD_KIM=value # download OpenKIM API v1 for build, value = no (default) or yes +-D KIM_LIBRARY=path # KIM library file (only needed if a custom location) +-D KIM_INCLUDE_DIR=path # KIM include directory (only needed if a custom location) :pre + +If DOWNLOAD_KIM is set, the KIM library will be downloaded and built +inside the CMake build directory. If the KIM library is already on +your system (in a location CMake cannot find it), KIM_LIBRARY is the +filename (plus path) of the KIM library file, not the directory the +library file is in. KIM_INCLUDE_DIR is the directory the KIM include +file is in. + +[Traditional make]: + +You can download and build the KIM library manually if you prefer; +follow the instructions in lib/kim/README. You can also do it in one +step from the lammps/src dir, using a command like these, which simply +invoke the lib/kim/Install.py script with the specified args. + +make lib-kim # print help message +make lib-kim args="-b " # (re-)install KIM API lib with only example models +make lib-kim args="-b -a Glue_Ercolessi_Adams_Al__MO_324507536345_001" # ditto plus one model +make lib-kim args="-b -a everything" # install KIM API lib with all models +make lib-kim args="-n -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # add one model or model driver +make lib-kim args="-p /usr/local/kim-api" # use an existing KIM API installation at the provided location +make lib-kim args="-p /usr/local/kim-api -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # ditto but add one model or driver :pre + +:line + +KOKKOS package :h4,link(kokkos) + +To build with this package, you must choose which hardware you want to +build for, either CPUs (multi-threading via OpenMP) or KNLs (OpenMP) +or GPUs (NVIDIA Cuda). + +For a CMake or make build, these are the possible choices for the +KOKKOS_ARCH settings described below. Note that for CMake, these are +really Kokkos variables, not LAMMPS variables. Hence you must use +case-sensitive values, e.g. BDW, not bdw. + +ARMv80 = ARMv8.0 Compatible CPU +ARMv81 = ARMv8.1 Compatible CPU +ARMv8-ThunderX = ARMv8 Cavium ThunderX CPU +BGQ = IBM Blue Gene/Q CPUs +Power8 = IBM POWER8 CPUs +Power9 = IBM POWER9 CPUs +SNB = Intel Sandy/Ivy Bridge CPUs +HSW = Intel Haswell CPUs +BDW = Intel Broadwell Xeon E-class CPUs +SKX = Intel Sky Lake Xeon E-class HPC CPUs (AVX512) +KNC = Intel Knights Corner Xeon Phi +KNL = Intel Knights Landing Xeon Phi +Kepler30 = NVIDIA Kepler generation CC 3.0 +Kepler32 = NVIDIA Kepler generation CC 3.2 +Kepler35 = NVIDIA Kepler generation CC 3.5 +Kepler37 = NVIDIA Kepler generation CC 3.7 +Maxwell50 = NVIDIA Maxwell generation CC 5.0 +Maxwell52 = NVIDIA Maxwell generation CC 5.2 +Maxwell53 = NVIDIA Maxwell generation CC 5.3 +Pascal60 = NVIDIA Pascal generation CC 6.0 +Pascal61 = NVIDIA Pascal generation CC 6.1 :ul + +[CMake build]: + +For multicore CPUs using OpenMP, set these 2 variables. + +-D KOKKOS_ARCH=archCPU # archCPU = CPU from list above +-D KOKKOS_ENABLE_OPENMP=yes :pre + +For Intel KNLs using OpenMP, set these 2 variables: + +-D KOKKOS_ARCH=KNL +-D KOKKOS_ENABLE_OPENMP=yes :pre + +For NVIDIA GPUs using CUDA, set these 4 variables: + +-D KOKKOS_ARCH="archCPU;archGPU" # archCPU = CPU from list above that is hosting the GPU + # archGPU = GPU from list above +-D KOKKOS_ENABLE_CUDA=yes +-D KOKKOS_ENABLE_OPENMP=yes +-D CMAKE_CXX_COMPILER=wrapper # wrapper = full path to Cuda nvcc wrapper :pre + +The wrapper value is the Cuda nvcc compiler wrapper provided in the +Kokkos library: lib/kokkos/bin/nvcc_wrapper. The setting should +include the full path name to the wrapper, e.g. + +-D CMAKE_CXX_COMPILER=/home/username/lammps/lib/kokkos/bin/nvcc_wrapper :pre + +[Traditional make]: + +Choose which hardware to support in Makefile.machine via +KOKKOS_DEVICES and KOKKOS_ARCH settings. See the +src/MAKE/OPTIONS/Makefile.kokkos* files for examples. + +For multicore CPUs using OpenMP: + +KOKKOS_DEVICES = OpenMP +KOKKOS_ARCH = archCPU # archCPU = CPU from list above :pre + +For Intel KNLs using OpenMP: + +KOKKOS_DEVICES = OpenMP +KOKKOS_ARCH = KNL :pre + +For NVIDIA GPUs using CUDA: + +KOKKOS_DEVICES = Cuda +KOKKOS_ARCH = archCPU,archGPU # archCPU = CPU from list above that is hosting the GPU + # archGPU = GPU from list above :pre + +For GPUs, you also need these 2 lines in your Makefile.machine before +the CC line is defined, in this case for use with OpenMPI mpicxx. The +2 lines define a nvcc wrapper compiler, which will use nvcc for +compiling CUDA files and use a C++ compiler for non-Kokkos, non-CUDA +files. + +KOKKOS_ABSOLUTE_PATH = $(shell cd $(KOKKOS_PATH); pwd) +export OMPI_CXX = $(KOKKOS_ABSOLUTE_PATH)/config/nvcc_wrapper +CC = mpicxx :pre + +:line + +LATTE package :h4,link(latte) + +To build with this package, you must download and build the LATTE +library. + +[CMake build]: + +-D DOWNLOAD_LATTE=value # download LATTE for build, value = no (default) or yes +-D LATTE_LIBRARY=path # LATTE library file (only needed if a custom location) :pre + +If DOWNLOAD_LATTE is set, the LATTE library will be downloaded and +built inside the CMake build directory. If the LATTE library is +already on your system (in a location CMake cannot find it), +LATTE_LIBRARY is the filename (plus path) of the LATTE library file, +not the directory the library file is in. + +[Traditional make]: + +You can download and build the LATTE library manually if you prefer; +follow the instructions in lib/latte/README. You can also do it in +one step from the lammps/src dir, using a command like these, which +simply invokes the lib/latte/Install.py script with the specified +args: + +make lib-latte # print help message +make lib-latte args="-b" # download and build in lib/latte/LATTE-master +make lib-latte args="-p $HOME/latte" # use existing LATTE installation in $HOME/latte +make lib-latte args="-b -m gfortran" # download and build in lib/latte and + # copy Makefile.lammps.gfortran to Makefile.lammps +:pre + +Note that 3 symbolic (soft) links, "includelink" and "liblink" and +"filelink.o", are created in lib/latte to point into the LATTE home +dir. When LAMMPS itself is built it will use these links. You should +also check that the Makefile.lammps file you create is appropriate for +the compiler you use on your system to build LATTE. + +:line + +MEAM package :h4,link(meam) + +NOTE: the use of the MEAM package is discouraged, as it has been +superseded by the USER-MEAMC package, which is a direct translation of +the Fortran code in the MEAM library to C++. The code in USER-MEAMC +should be functionally equivalent to the MEAM package, fully supports +use of "pair_style hybrid"_pair_hybrid.html (the MEAM package does +not), and has optimizations that make it significantly faster than the +MEAM package. + +[CMake build]: + +No additional settings are needed besides "-D PKG_MEAM=yes". + +[Traditional make]: + +Before building LAMMPS, you must build the MEAM library in lib/meam. +You can build the MEAM library manually if you prefer; follow the +instructions in lib/meam/README. You can also do it in one step from +the lammps/src dir, using a command like these, which simply invoke +the lib/meam/Install.py script with the specified args: + +make lib-meam # print help message +make lib-meam args="-m mpi" # build with default Fortran compiler compatible with your MPI library +make lib-meam args="-m serial" # build with compiler compatible with "make serial" (GNU Fortran) +make lib-meam args="-m ifort" # build with Intel Fortran compiler using Makefile.ifort :pre + +NOTE: You should test building the MEAM library with both the Intel +and GNU compilers to see if a simulation runs faster with one versus +the other on your system. + +The build should produce two files: lib/meam/libmeam.a and +lib/meam/Makefile.lammps. The latter is copied from an existing +Makefile.lammps.* and has settings needed to link C++ (LAMMPS) with +Fortran (MEAM library). Typically the two compilers used for LAMMPS +and the MEAM library need to be consistent (e.g. both Intel or both +GNU compilers). If necessary, you can edit/create a new +lib/meam/Makefile.machine file for your system, which should define an +EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine +file. + +:line + +MESSAGE package :h4,link(message) + +This package can optionally include support for messaging via sockets, +using the open-source "ZeroMQ library"_http://zeromq.org, which must +be installed on your system. + +[CMake build]: + +-D MESSAGE_ZMQ=value # build with ZeroMQ support, value = no (default) or yes + +[Traditional make]: + +Before building LAMMPS, you must build the CSlib library in +lib/message. You can build the CSlib library manually if you prefer; +follow the instructions in lib/message/README. You can also do it in +one step from the lammps/src dir, using a command like these, which +simply invoke the lib/message/Install.py script with the specified args: + +make lib-message # print help message +make lib-message args="-m -z" # build with MPI and socket (ZMQ) support +make lib-message args="-s" # build as serial lib with no ZMQ support + +The build should produce two files: lib/message/cslib/src/libmessage.a +and lib/message/Makefile.lammps. The latter is copied from an +existing Makefile.lammps.* and has settings to link with the ZeroMQ +library if requested in the build. + +:line + +MSCG package :h4,link(mscg) + +To build with this package, you must download and build the MS-CG +library. Building the MS-CG library and using it from LAMMPS requires +a C++11 compatible compiler and that the GSL (GNU Scientific Library) +headers and libraries are installed on your machine. See the +lib/mscg/README and MSCG/Install files for more details. + +[CMake build]: + +-D DOWNLOAD_MSCG=value # download MSCG for build, value = no (default) or yes +-D MSCG_LIBRARY=path # MSCG library file (only needed if a custom location) +-D MSCG_INCLUDE_DIR=path # MSCG include directory (only needed if a custom location) :pre + +If DOWNLOAD_MSCG is set, the MSCG library will be downloaded and built +inside the CMake build directory. If the MSCG library is already on +your system (in a location CMake cannot find it), MSCG_LIBRARY is the +filename (plus path) of the MSCG library file, not the directory the +library file is in. MSCG_INCLUDE_DIR is the directory the MSCG +include file is in. + +[Traditional make]: + +You can download and build the MS-CG library manually if you prefer; +follow the instructions in lib/mscg/README. You can also do it in one +step from the lammps/src dir, using a command like these, which simply +invoke the lib/mscg/Install.py script with the specified args: + +make lib-mscg # print help message +make lib-mscg args="-b -m serial" # download and build in lib/mscg/MSCG-release-master + # with the settings compatible with "make serial" +make lib-mscg args="-b -m mpi" # download and build in lib/mscg/MSCG-release-master + # with the settings compatible with "make mpi" +make lib-mscg args="-p /usr/local/mscg-release" # use the existing MS-CG installation in /usr/local/mscg-release :pre + +Note that 2 symbolic (soft) links, "includelink" and "liblink", will +be created in lib/mscg to point to the MS-CG src/installation dir. +When LAMMPS is built in src it will use these links. You should not +need to edit the lib/mscg/Makefile.lammps file. + +:line + +OPT package :h4,link(opt) + +[CMake build]: + +No additional settings are needed besides "-D PKG_OPT=yes". + +[Traditional make]: + +The compile flag "-restrict" must be used to build LAMMPS with the OPT +package when using Intel compilers. It should be added to the CCFLAGS +line of your Makefile.machine. See src/MAKE/OPTIONS/Makefile.opt for +an example. + +:line + +POEMS package :h4,link(poems) + +[CMake build]: + +No additional settings are needed besides "-D PKG_OPT=yes". + +[Traditional make]: + +Before building LAMMPS, you must build the POEMS library in lib/poems. +You can do this manually if you prefer; follow the instructions in +lib/poems/README. You can also do it in one step from the lammps/src +dir, using a command like these, which simply invoke the +lib/poems/Install.py script with the specified args: + +make lib-poems # print help message +make lib-poems args="-m serial" # build with GNU g++ compiler (settings as with "make serial") +make lib-poems args="-m mpi" # build with default MPI C++ compiler (settings as with "make mpi") +make lib-poems args="-m icc" # build with Intel icc compiler :pre + +The build should produce two files: lib/poems/libpoems.a and +lib/poems/Makefile.lammps. The latter is copied from an existing +Makefile.lammps.* and has settings needed to build LAMMPS with the +POEMS library (though typically the settings are just blank). If +necessary, you can edit/create a new lib/poems/Makefile.machine file +for your system, which should define an EXTRAMAKE variable to specify +a corresponding Makefile.lammps.machine file. + +:line + +PYTHON package :h4,link(python) + +Building with the PYTHON package requires you have a Python shared +library available on your system, which needs to be a Python 2 +version, 2.6 or later. Python 3 is not yet supported. See +lib/python/README for more details. + +[CMake build]: + +-D PYTHON_EXECUTABLE=path # path to Python executable to use :pre + +Without this setting, CMake will guess the default Python on your +system. To use a different Python version, you can either create a +virtualenv, activate it and then run cmake. Or you can set the +PYTHON_EXECUTABLE variable to specify which Python interpreter should +be used. Note note that you will also need to have the development +headers installed for this version, e.g. python2-devel. + +[Traditional make]: + +The build uses the lib/python/Makefile.lammps file in the compile/link +process to find Python. You should only need to create a new +Makefile.lammps.* file (and copy it to Makefile.lammps) if the LAMMPS +build fails. + +:line + +REAX package :h4,link(reax) + +NOTE: the use of the REAX package and its "pair_style +reax"_pair_reax.html command is discouraged, as it is no longer +maintained. Please use the USER-REAXC package and its "pair_style +reax/c"_pair_reaxc.html command instead, and possibly its KOKKOS +enabled variant (pair_style reax/c/kk), which has a more robust memory +management. See the "pair_style reax/c"_pair_reaxc.html doc page for +details. + +[CMake build]: + +No additional settings are needed besides "-D PKG_REAX=yes". + +[Traditional make]: + +Before building LAMMPS, you must build the REAX library in lib/reax. +You can do this manually if you prefer; follow the instructions in +lib/reax/README. You can also do it in one step from the lammps/src +dir, using a command like these, which simply invoke the +lib/reax/Install.py script with the specified args: + +make lib-reax # print help message +make lib-reax args="-m serial" # build with GNU Fortran compiler (settings as with "make serial") +make lib-reax args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi") +make lib-reax args="-m ifort" # build with Intel ifort compiler :pre + +The build should produce two files: lib/reax/libreax.a and +lib/reax/Makefile.lammps. The latter is copied from an existing +Makefile.lammps.* and has settings needed to link C++ (LAMMPS) with +Fortran (REAX library). Typically the two compilers used for LAMMPS +and the REAX library need to be consistent (e.g. both Intel or both +GNU compilers). If necessary, you can edit/create a new +lib/reax/Makefile.machine file for your system, which should define an +EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine +file. + +:line + +VORONOI package :h4,link(voronoi) + +To build with this package, you must download and build the "Voro++ +library"_voro_home. + +:link(voro_home,http://math.lbl.gov/voro++) + +[CMake build]: + +-D DOWNLOAD_VORO=value # download Voro++ for build, value = no (default) or yes +-D VORO_LIBRARY=path # Voro++ library file (only needed if at custom location) +-D VORO_INCLUDE_DIR=path # Voro++ include directory (only needed if at custom location) :pre + +If DOWNLOAD_VORO is set, the Voro++ library will be downloaded and +built inside the CMake build directory. If the Voro++ library is +already on your system (in a location CMake cannot find it), +VORO_LIBRARY is the filename (plus path) of the Voro++ library file, +not the directory the library file is in. VORO_INCLUDE_DIR is the +directory the Voro++ include file is in. + +[Traditional make]: + +You can download and build the Voro++ library manually if you prefer; +follow the instructions in lib/voronoi/README. You can also do it in +one step from the lammps/src dir, using a command like these, which +simply invoke the lib/voronoi/Install.py script with the specified +args: + +make lib-voronoi # print help message +make lib-voronoi args="-b" # download and build the default version in lib/voronoi/voro++- +make lib-voronoi args="-p $HOME/voro++" # use existing Voro++ installation in $HOME/voro++ +make lib-voronoi args="-b -v voro++0.4.6" # download and build the 0.4.6 version in lib/voronoi/voro++-0.4.6 :pre + +Note that 2 symbolic (soft) links, "includelink" and "liblink", are +created in lib/voronoi to point to the Voro++ src dir. When LAMMPS +builds in src it will use these links. You should not need to edit +the lib/voronoi/Makefile.lammps file. + +:line + +USER-ATC package :h4,link(user-atc) + +The USER-ATC package requires the MANYBODY package also be installed. + +[CMake build]: + +No additional settings are needed besides "-D PKG_REAX=yes" and "-D +PKG_MANYBODY=yes". + +[Traditional make]: + +Before building LAMMPS, you must build the ATC library in lib/atc. +You can do this manually if you prefer; follow the instructions in +lib/atc/README. You can also do it in one step from the lammps/src +dir, using a command like these, which simply invoke the +lib/atc/Install.py script with the specified args: + +make lib-atc # print help message +make lib-atc args="-m serial" # build with GNU g++ compiler and MPI STUBS (settings as with "make serial") +make lib-atc args="-m mpi" # build with default MPI compiler (settings as with "make mpi") +make lib-atc args="-m icc" # build with Intel icc compiler :pre + +The build should produce two files: lib/atc/libatc.a and +lib/atc/Makefile.lammps. The latter is copied from an existing +Makefile.lammps.* and has settings needed to build LAMMPS with the ATC +library. If necessary, you can edit/create a new +lib/atc/Makefile.machine file for your system, which should define an +EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine +file. + +Note that the Makefile.lammps file has settings for the BLAS and +LAPACK linear algebra libraries. As explained in lib/atc/README these +can either exist on your system, or you can use the files provided in +lib/linalg. In the latter case you also need to build the library in +lib/linalg with a command like these: + +make lib-linalg # print help message +make lib-linalg args="-m serial" # build with GNU Fortran compiler (settings as with "make serial") +make lib-linalg args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi") +make lib-linalg args="-m gfortran" # build with GNU Fortran compiler :pre + +:line + +USER-AWPMD package :h4,link(user-awpmd) + +[CMake build]: + +No additional settings are needed besides "-D PKG_USER-AQPMD=yes". + +[Traditional make]: + +Before building LAMMPS, you must build the AWPMD library in lib/awpmd. +You can do this manually if you prefer; follow the instructions in +lib/awpmd/README. You can also do it in one step from the lammps/src +dir, using a command like these, which simply invoke the +lib/awpmd/Install.py script with the specified args: + +make lib-awpmd # print help message +make lib-awpmd args="-m serial" # build with GNU g++ compiler and MPI STUBS (settings as with "make serial") +make lib-awpmd args="-m mpi" # build with default MPI compiler (settings as with "make mpi") +make lib-awpmd args="-m icc" # build with Intel icc compiler :pre + +The build should produce two files: lib/awpmd/libawpmd.a and +lib/awpmd/Makefile.lammps. The latter is copied from an existing +Makefile.lammps.* and has settings needed to build LAMMPS with the +AWPMD library. If necessary, you can edit/create a new +lib/awpmd/Makefile.machine file for your system, which should define +an EXTRAMAKE variable to specify a corresponding +Makefile.lammps.machine file. + +Note that the Makefile.lammps file has settings for the BLAS and +LAPACK linear algebra libraries. As explained in lib/awpmd/README +these can either exist on your system, or you can use the files +provided in lib/linalg. In the latter case you also need to build the +library in lib/linalg with a command like these: + +make lib-linalg # print help message +make lib-linalg args="-m serial" # build with GNU Fortran compiler (settings as with "make serial") +make lib-linalg args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi") +make lib-linalg args="-m gfortran" # build with GNU Fortran compiler :pre + +:line + +USER-COLVARS package :h4,link(user-colvars) + +[CMake build]: + +No additional settings are needed besides "-D PKG_USER-COLVARS=yes". + +[Traditional make]: + +Before building LAMMPS, you must build the COLVARS library in +lib/colvars. You can do this manually if you prefer; follow the +instructions in lib/colvars/README. You can also do it in one step +from the lammps/src dir, using a command like these, which simply +invoke the lib/colvars/Install.py script with the specified args: + +make lib-colvars # print help message +make lib-colvars args="-m serial" # build with GNU g++ compiler (settings as with "make serial") +make lib-colvars args="-m mpi" # build with default MPI compiler (settings as with "make mpi") +make lib-colvars args="-m g++-debug" # build with GNU g++ compiler and colvars debugging enabled :pre + +The build should produce two files: lib/colvars/libcolvars.a and +lib/colvars/Makefile.lammps. The latter is copied from an existing +Makefile.lammps.* and has settings needed to build LAMMPS with the +COLVARS library (though typically the settings are just blank). If +necessary, you can edit/create a new lib/colvars/Makefile.machine file +for your system, which should define an EXTRAMAKE variable to specify +a corresponding Makefile.lammps.machine file. + +:line + +USER-H5MD package :h4,link(user-h5md) + +To build with this package you must have the HDF5 software package +installed on your system, which should include the h5cc compiler and +the HDF5 library. + +[CMake build]: + +No additional settings are needed besides "-D PKG_USER-H5MD=yes". + +This should auto-detect the H5MD library on your system. Several +advanced CMake H5MD options exist if you need to specify where it is +installed. Use the ccmake (terminal window) or cmake-gui (graphical) +tools to see these options and set them interactively from their user +interfaces. + +[Traditional make]: + +Before building LAMMPS, you must build the CH5MD library in lib/h5md. +You can do this manually if you prefer; follow the instructions in +lib/h5md/README. You can also do it in one step from the lammps/src +dir, using a command like these, which simply invoke the +lib/h5md/Install.py script with the specified args: + +make lib-h5md # print help message +make lib-hm5d args="-m h5cc" # build with h5cc compiler :pre + +The build should produce two files: lib/h5md/libch5md.a and +lib/h5md/Makefile.lammps. The latter is copied from an existing +Makefile.lammps.* and has settings needed to build LAMMPS with the +system HDF5 library. If necessary, you can edit/create a new +lib/h5md/Makefile.machine file for your system, which should define an +EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine +file. + +:line + +USER-INTEL package :h4,link(user-intel) + +To build with this package, you must choose which hardware you want to +build for, either Intel CPUs or Intel KNLs. You should also typically +"install the USER-OMP package"_#user-omp, as it can be used in tandem +with the USER-INTEL package to good effect, as explained on the "Speed +intel"_Speed_intel.html doc page. + +[CMake build]: + +-D INTEL_ARCH=value # value = cpu (default) or knl +-D BUILD_OMP=yes # also required to build with the USER-INTEl package :pre + +Requires an Intel compiler as well as the Intel TBB and MKL libraries. + +[Traditional make]: + +Choose which hardware to compile for in Makefile.machine via the +following settings. See src/MAKE/OPTIONS/Makefile.intel_cpu* and +Makefile.knl files for examples. + +For CPUs: + +OPTFLAGS = -xHost -O2 -fp-model fast=2 -no-prec-div -qoverride-limits -qopt-zmm-usage=high +CCFLAGS = -g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload -fno-alias -ansi-alias -restrict $(OPTFLAGS) +LINKFLAGS = -g -qopenmp $(OPTFLAGS) +LIB = -ltbbmalloc :pre + +For KNLs: + +OPTFLAGS = -xMIC-AVX512 -O2 -fp-model fast=2 -no-prec-div -qoverride-limits +CCFLAGS = -g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload -fno-alias -ansi-alias -restrict $(OPTFLAGS) +LINKFLAGS = -g -qopenmp $(OPTFLAGS) +LIB = -ltbbmalloc :pre + +:line + +USER-MOLFILE package :h4,link(user-molfile) + +[CMake build]: + +No additional settings are needed besides "-D PKG_USER-MOLFILE=yes". + +[Traditional make]: + +The lib/molfile/Makefile.lammps file has a setting for a dynamic +loading library libdl.a that is typically present on all systems. It +is required for LAMMPS to link with this package. If the setting is +not valid for your system, you will need to edit the Makefile.lammps +file. See lib/molfile/README and lib/molfile/Makefile.lammps for +details. + +:line + +USER-NETCDF package :h4,link(user-netcdf) + +To build with this package you must have the NetCDF library installed +on your system. + +[CMake build]: + +No additional settings are needed besides "-D PKG_USER-NETCDF=yes". + +This should auto-detect the NETCDF library if it is installed on your +system at standard locations. Several advanced CMake NETCDF options +exist if you need to specify where it was installed. Use the ccmake +(terminal window) or cmake-gui (graphical) tools to see these options +and set them interactively from their user interfaces. + +[Traditional make]: + +The lib/netcdf/Makefile.lammps file has settings for NetCDF include +and library files which LAMMPS needs to build with this package. If +the settings are not valid for your system, you will need to edit the +Makefile.lammps file. See lib/netcdf/README for details. + +:line + +USER-OMP package :h4,link(user-omp) + +[CMake build]: + +No additional settings are required besides "-D PKG_USER-OMP=yes". If +CMake detects OpenMP support, the USER-OMP code will be compiled with +multi-threading support enabled, otherwise as optimized serial code. + +[Traditional make]: + +To enable multi-threading support in the USER-OMP package (and other +styles supporting OpenMP) the following compile and link flags must +be added to your Makefile.machine file. +See src/MAKE/OPTIONS/Makefile.omp for an example. + +CCFLAGS: -fopenmp # for GNU Compilers +CCFLAGS: -qopenmp -restrict # for Intel compilers on Linux +LINKFLAGS: -fopenmp # for GNU Compilers +LINKFLAGS: -qopenmp # for Intel compilers on Linux :pre + +For other platforms and compilers, please consult the documentation +about OpenMP support for your compiler. + +:line + +USER-QMMM package :h4,link(user-qmmm) + +NOTE: The LAMMPS executable these steps produce is not yet functional +for a QM/MM simulation. You must also build Quantum ESPRESSO and +create a new executable (pwqmmm.x) which links LAMMPS and Quantum +ESPRESSO together. These are steps 3 and 4 described in the +lib/qmmm/README file. Unfortunately, the Quantum ESPRESSO developers +have been breaking the interface that the QM/MM code in LAMMPS is using, +so that currently (Summer 2018) using this feature requires either +correcting the library interface feature in recent Quantum ESPRESSO +releases, or using an outdated version of QE. The last version of +Quantum ESPRESSO known to work with this QM/MM interface was version +5.4.1 from 2016. + +[CMake build]: + +The CMake build system currently does not support building the full +QM/MM-capable hybrid executable of LAMMPS and QE called pwqmmm.x. +You must use the traditional make build for this package. + +[Traditional make]: + +Before building LAMMPS, you must build the QMMM library in lib/qmmm. +You can do this manually if you prefer; follow the first two steps +explained in lib/qmmm/README. You can also do it in one step from the +lammps/src dir, using a command like these, which simply invoke the +lib/qmmm/Install.py script with the specified args: + +make lib-qmmm # print help message +make lib-qmmm args="-m serial" # build with GNU Fortran compiler (settings as in "make serial") +make lib-qmmm args="-m mpi" # build with default MPI compiler (settings as in "make mpi") +make lib-qmmm args="-m gfortran" # build with GNU Fortran compiler :pre + +The build should produce two files: lib/qmmm/libqmmm.a and +lib/qmmm/Makefile.lammps. The latter is copied from an existing +Makefile.lammps.* and has settings needed to build LAMMPS with the +QMMM library (though typically the settings are just blank). If +necessary, you can edit/create a new lib/qmmm/Makefile.machine file +for your system, which should define an EXTRAMAKE variable to specify +a corresponding Makefile.lammps.machine file. + +You can then install QMMM package and build LAMMPS in the usual +manner. After completing the LAMMPS build and compiling Quantum +ESPRESSO with external library support, go back to the lib/qmmm folder +and follow the instructions on the README file to build the combined +LAMMPS/QE QM/MM executable (pwqmmm.x) in the lib/qmmm folder. + +:line + +USER-QUIP package :h4,link(user-quip) + +To build with this package, you must download and build the QUIP +library. It can be obtained from GitHub. For support of GAP +potentials, additional files with specific licensing conditions need +to be downloaded and configured. See step 1 and step 1.1 in the +lib/quip/README file for details on how to do this. + +[CMake build]: + +-D QUIP_LIBRARIES=path # path to libquip.a (only needed if a custom location) :pre + +CMake will not download and build the QUIP library. But once you have +done that, a CMake build of LAMMPS with "-D PKG_USER-QUIP=yes" should +work. Set QUIP_LIBRARIES if CMake cannot find the QUIP library. + +[Traditional make]: + +The download/build procedure for the QUIP library, described in +lib/quip/README file requires setting two environment variables, +QUIP_ROOT and QUIP_ARCH. These are accessed by the +lib/quip/Makefile.lammps file which is used when you compile and link +LAMMPS with this package. You should only need to edit +Makefile.lammps if the LAMMPS build can not use its settings to +successfully build on your system. + +:line + +USER-SCAFACOS package :h4,link(user-scafacos) + +To build with this package, you must download and build the "ScaFaCoS +Coulomb solver library"_scafacos_home + +:link(scafacos_home,http://www.scafacos.de) + +[CMake build]: + +-D DOWNLOAD_SCAFACOS=value # download ScaFaCoS for build, value = no (default) or yes +-D SCAFACOS_LIBRARY=path # ScaFaCos library file (only needed if at custom location) +-D SCAFACOS_INCLUDE_DIR=path # ScaFaCoS include directory (only needed if at custom location) :pre + +If DOWNLOAD_SCAFACOS is set, the ScaFaCoS library will be downloaded +and built inside the CMake build directory. If the ScaFaCoS library +is already on your system (in a location CMake cannot find it), +SCAFACOS_LIBRARY is the filename (plus path) of the ScaFaCoS library +file, not the directory the library file is in. SCAFACOS_INCLUDE_DIR +is the directory the ScaFaCoS include file is in. + +[Traditional make]: + +You can download and build the ScaFaCoS library manually if you +prefer; follow the instructions in lib/scafacos/README. You can also +do it in one step from the lammps/src dir, using a command like these, +which simply invoke the lib/scafacos/Install.py script with the +specified args: + +make lib-scafacos # print help message +make lib-scafacos args="-b" # download and build in lib/scafacos/scafacos- +make lib-scafacos args="-p $HOME/scafacos # use existing ScaFaCoS installation in $HOME/scafacos + +Note that 2 symbolic (soft) links, "includelink" and "liblink", are +created in lib/scafacos to point to the ScaFaCoS src dir. When LAMMPS +builds in src it will use these links. You should not need to edit +the lib/scafacos/Makefile.lammps file. + +:line + +USER-SMD package :h4,link(user-smd) + +To build with this package, you must download the Eigen3 library. +Eigen3 is a template library, so you do not need to build it. + +[CMake build]: + +-D DOWNLOAD_EIGEN3 # download Eigen3, value = no (default) or yes +-D EIGEN3_INCLUDE_DIR=path # path to Eigen library (only needed if a custom location) :pre + +If DOWNLOAD_EIGEN3 is set, the Eigen3 library will be downloaded and +inside the CMake build directory. If the Eigen3 library is already on +your system (in a location CMake cannot find it), EIGEN3_INCLUDE_DIR +is the directory the Eigen3++ include file is in. + +[Traditional make]: + +You can download the Eigen3 library manually if you prefer; follow the +instructions in lib/smd/README. You can also do it in one step from +the lammps/src dir, using a command like these, which simply invoke +the lib/smd/Install.py script with the specified args: + +make lib-smd # print help message +make lib-smd args="-b" # download to lib/smd/eigen3 +make lib-smd args="-p /usr/include/eigen3" # use existing Eigen installation in /usr/include/eigen3 :pre + +Note that a symbolic (soft) link named "includelink" is created in +lib/smd to point to the Eigen dir. When LAMMPS builds it will use +this link. You should not need to edit the lib/smd/Makefile.lammps +file. + +:line + +USER-VTK package :h4,link(user-vtk) + +To build with this package you must have the VTK library installed on +your system. + +[CMake build]: + +No additional settings are needed besides "-D PKG_USER-VTK=yes". + +This should auto-detect the VTK library if it is installed on your +system at standard locations. Several advanced VTK options exist if +you need to specify where it was installed. Use the ccmake (terminal +window) or cmake-gui (graphical) tools to see these options and set +them interactively from their user interfaces. + +[Traditional make]: + +The lib/vtk/Makefile.lammps file has settings for accessing VTK files +and its library, which LAMMPS needs to build with this package. If +the settings are not valid for your system, check if one of the other +lib/vtk/Makefile.lammps.* files is compatible and copy it to +Makefile.lammps. If none of the provided files work, you will need to +edit the Makefile.lammps file. See lib/vtk/README for details. diff --git a/doc/src/Build_link.txt b/doc/src/Build_link.txt new file mode 100644 index 0000000000..1a1b387f3f --- /dev/null +++ b/doc/src/Build_link.txt @@ -0,0 +1,85 @@ +"Higher level section"_Build.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Link LAMMPS as a library to another code :h3 + +LAMMPS can be used as a library by another application, including +Python scripts. The files src/library.cpp and library.h define the +C-style API for using LAMMPS as a library. See the "Howto +library"_Howto_library.html doc page for a description of the +interface and how to extend it for your needs. + +The "Build basics"_Build_basics.html doc page explains how to build +LAMMPS as either a shared or static library. This results in one of +these 2 files: + +liblammps.so # shared library +liblammps.a # static library + +:line + +[Link with LAMMPS as a static library]: + +The calling application can link to LAMMPS as a static library with a +link command like this: + +g++ caller.o -L/home/sjplimp/lammps/src -llammps -o caller + +The -L argument is the path to where the liblammps.a file is. The +-llammps argument is shorthand for the file liblammps.a. + +:line + +[Link with LAMMPS as a shared library]: + +If you wish to link to liblammps.so, the operating system finds shared +libraries to load at run-time using the environment variable +LD_LIBRARY_PATH. To enable this you can do one of two things: + +(1) Copy the liblammps.so file to a location the system can find it, +such as /usr/local/lib. I.e. a directory already listed in your +LD_LIBRARY_PATH variable. You can type + +printenv LD_LIBRARY_PATH :pre + +to see what directories are in that list. + +(2) Add the LAMMPS src directory (or the directory you perform CMake +build in) to your LD_LIBRARY_PATH, so that the current version of the +shared library is always available to programs that use it. + +For the csh or tcsh shells, you would add something like this to your +~/.cshrc file: + +setenv LD_LIBRARY_PATH $\{LD_LIBRARY_PATH\}:/home/sjplimp/lammps/src :pre + +:line + +[Calling the LAMMPS library]: + +Either flavor of library (static or shared) allows one or more LAMMPS +objects to be instantiated from the calling program. + +When used from a C++ program, all of LAMMPS is wrapped in a LAMMPS_NS +namespace; you can safely use any of its classes and methods from +within the calling code, as needed. + +When used from a C or Fortran program, the library has a simple +C-style interface, provided in src/library.cpp and src/library.h. + +See the "Python library"_Python_library.html doc page for a +description of the Python interface to LAMMPS, which wraps the C-style +interface. + +See the sample codes in examples/COUPLE/simple for examples of C++ and +C and Fortran codes that invoke LAMMPS thru its library interface. +Other examples in the COUPLE directory use coupling ideas discussed on +the "Howto couple"_Howto_couple.html doc page. + + diff --git a/doc/src/Build_make.txt b/doc/src/Build_make.txt new file mode 100644 index 0000000000..ad18695e46 --- /dev/null +++ b/doc/src/Build_make.txt @@ -0,0 +1,85 @@ +"Higher level section"_Build.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Build LAMMPS with make :h3 + +Building LAMMPS with traditional makefiles requires that you have a +Makefile."machine" file appropriate for your system in the src/MAKE, +src/MAKE/MACHINES, src/MAKE/OPTIONS, or src/MAKE/MINE directory (see +below). It can include various options for customizing your LAMMPS +build with a number of global compilation options and features. + +To include LAMMPS packages (i.e. optional commands and styles) you +must install them first, as discussed on the "Build +package"_Build_package.html doc page. If the packages require +provided or external libraries, you must build those libraries before +building LAMMPS. Building "LAMMPS with CMake"_Build_cmake.html can +automate all of this for many types of machines, especially +workstations, desktops and laptops, so we suggest you try it first. + +These commands perform a default LAMMPS build, producing the LAMMPS +executable lmp_serial or lmp_mpi in lammps/src: + +cd lammps/src +make serial # build a serial LAMMPS executable +make mpi # build a parallel LAMMPS executable with MPI +make # see a variety of make options :pre + +This initial compilation can take a long time, since LAMMPS is a large +project with many features. If your machine has multiple CPU cores +(most do these days), using a command like "make -jN mpi" (with N = +the number of available CPU cores) can be much faster. If you plan to +do development on LAMMPS or need to re-compile LAMMPS repeatedly, the +installation of the ccache (= Compiler Cache) software may speed up +compilation even more. + +After the initial build, whenever you edit LAMMPS source files, or add +or remove new files to the source directory (e.g. by installing or +uninstalling packages), you must re-compile and relink the LAMMPS +executable with the same "make" command. This makefiles dependencies +should insure that only the subset of files that need to be are +re-compiled. + +NOTE: When you build LAMMPS for the first time, a long list of *.d +files will be printed out rapidly. This is not an error; it is the +Makefile doing its normal creation of dependencies. + +:line + +The lammps/src/MAKE tree contains all the Makefile.machine files +included in the LAMMPS distribution. Typing "make machine" uses +Makefile.machine. Thus the "make serial" or "make mpi" lines above +use Makefile.serial and Makefile.mpi. Others are in these dirs: + +OPTIONS # Makefiles which enable specific options +MACHINES # Makefiles for specific machines +MINE # customized Makefiles you create (you may need to create this folder) :pre + +Typing "make" lists all the available Makefile.machine files. A file +with the same name can appear in multiple folders (not a good idea). +The order the dirs are searched is as follows: src/MAKE/MINE, +src/MAKE, src/MAKE/OPTIONS, src/MAKE/MACHINES. This gives preference +to a customized file you put in src/MAKE/MINE. + +Makefiles you may wish to try include these (some require a package +first be installed). Many of these include specific compiler flags +for optimized performance. Please note, however, that some of these +customized machine Makefile are contributed by users. Since both +compilers, OS configurations, and LAMMPS itself keep changing, their +settings may become outdated: + +make mac # build serial LAMMPS on a Mac +make mac_mpi # build parallel LAMMPS on a Mac +make intel_cpu # build with the USER-INTEL package optimized for CPUs +make knl # build with the USER-INTEL package optimized for KNLs +make opt # build with the OPT package optimized for CPUs +make omp # build with the USER-OMP package optimized for OpenMP +make kokkos_omp # build with the KOKKOS package for OpenMP +make kokkos_cuda_mpi # build with the KOKKOS package for GPUs +make kokkos_phi # build with the KOKKOS package for KNLs :pre diff --git a/doc/src/Build_package.txt b/doc/src/Build_package.txt new file mode 100644 index 0000000000..f1aa4bb671 --- /dev/null +++ b/doc/src/Build_package.txt @@ -0,0 +1,225 @@ +"Higher level section"_Build.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Include packages in build :h3 + +In LAMMPS, a package is a group of files that enable a specific set of +features. For example, force fields for molecular systems or +rigid-body constraints are in packages. In the src directory, each +package is a sub-directory with the package name in capital letters. + +An overview of packages is given on the "Packages"_Packages.html doc +page. Brief overviews of each package are on the "Packages +details"_Packages_details.html doc page. + +When building LAMMPS, you can choose to include or exclude each +package. In general there is no need to include a package if you +never plan to use its features. + +If you get a run-time error that a LAMMPS command or style is +"Unknown", it is often because the command is contained in a package, +and your build did not include that package. Running LAMMPS with the +"-h command-line switch"_Run_options.html will print all the included +packages and commands for that executable. + +For the majority of packages, if you follow the single step below to +include it, you can then build LAMMPS exactly the same as you would +without any packages installed. A few packages may require additional +steps, as explained on the "Build extras"_Build_extras.html doc page. + +These links take you to the extra instructions for those select +packages: + +"COMPRESS"_Build_extras.html#compress, +"GPU"_Build_extras.html#gpu, +"KIM"_Build_extras.html#kim, +"KOKKOS"_Build_extras.html#kokkos, +"LATTE"_Build_extras.html#latte, +"MEAM"_Build_extras.html#meam, +"MESSAGE"_Build_extras.html#message, +"MSCG"_Build_extras.html#mscg, +"OPT"_Build_extras.html#opt, +"POEMS"_Build_extras.html#poems, +"PYTHON"_Build_extras.html#python, +"REAX"_Build_extras.html#reax, +"VORONOI"_Build_extras.html#voronoi, +"USER-ATC"_Build_extras.html#user-atc, +"USER-AWPMD"_Build_extras.html#user-awpmd, +"USER-COLVARS"_Build_extras.html#user-colvars, +"USER-H5MD"_Build_extras.html#user-h5md, +"USER-INTEL"_Build_extras.html#user-intel, +"USER-MOLFILE"_Build_extras.html#user-molfile, +"USER-NETCDF"_Build_extras.html#user-netcdf, +"USER-OMP"_Build_extras.html#user-omp, +"USER-QMMM"_Build_extras.html#user-qmmm, +"USER-QUIP"_Build_extras.html#user-quip, +"USER-SCAFACOS"_Build_extras.html#user-scafacos, +"USER-SMD"_Build_extras.html#user-smd, +"USER-VTK"_Build_extras.html#user-vtk :tb(c=6,ea=c,a=l) + +The mechanism for including packages is simple but different for CMake +versus make. + +[CMake variables]: + +-D PKG_NAME=value # yes or no (default) :pre + +Examples: + +-D PKG_MANYBODY=yes +-D PKG_USER-INTEL=yes :pre + +All standard and user packages are included the same way. Note that +USER packages have a hyphen between USER and the rest of the package +name, not an underscore. + +See the shortcut section below for how to install many packages at +once with CMake. + +NOTE: If you toggle back and forth between building with CMake vs +make, no packages in the src directory can be installed when you +invoke cmake. CMake will give an error if that is not the case, +indicating how you can un-install all packages in the src dir. + +[Traditional make]: + +cd lammps/src +make ps # check which packages are currently installed +make yes-name # install a package with name +make no-name # un-install a package with name +make mpi # build LAMMPS with whatever packages are now installed :pre + +Examples: + +make no-rigid +make yes-user-intel :pre + +All standard and user packages are included the same way. + +See the shortcut section below for how to install many packages at +once with make. + +NOTE: You must always re-build LAMMPS (via make) after installing or +un-installing a package, for the action to take effect. + +NOTE: You cannot install or un-install packages and build LAMMPS in a +single make command with multiple targets, e.g. make yes-colloid mpi. +This is because the make procedure creates a list of source files that +will be out-of-date for the build if the package configuration changes +within the same command. You can include or exclude multiple packages +in a single make command, e.g. make yes-colloid no-manybody. + +[CMake and make info]: + +Any package can be included or excluded in a LAMMPS build, independent +of all other packages. However, some packages include files derived +from files in other packages. LAMMPS checks for this and does the +right thing. Individual files are only included if their dependencies +are already included. Likewise, if a package is excluded, other files +dependent on that package are also excluded. + +When you download a LAMMPS tarball or download LAMMPS source files +from the Git or SVN repositories, no packages are pre-installed in the +src directory. + +NOTE: Prior to Aug 2018, if you downloaded a tarball, 3 packages +(KSPACE, MANYBODY, MOLECULE) were pre-installed in the src directory. +That is no longer the case, so that CMake will build as-is without the +need to un-install those packages. + +:line + +[CMake shortcuts for installing many packages]: + +Instead of specifying all the CMake options via the command-line, +CMake allows initializing the variable cache using script files. These +are regular CMake files which can manipulate and set variables, and +can also contain control flow constructs. + +LAMMPS includes several of these files to define configuration +"presets", similar to the options that exist for the Make based +system. Using these files you can enable/disable portions of the +available packages in LAMMPS. If you need a custom preset you can take +one of them as a starting point and customize it to your needs. + +cmake -C ../cmake/presets/all_on.cmake \[OPTIONS\] ../cmake | enable all packages +cmake -C ../cmake/presets/all_off.cmake \[OPTIONS\] ../cmake | disable all packages +cmake -C ../cmake/presets/std.cmake \[OPTIONS\] ../cmake | enable standard packages +cmake -C ../cmake/presets/user.cmake \[OPTIONS\] ../cmake | enable user packages +cmake -C ../cmake/presets/std_nolib.cmake \[OPTIONS\] ../cmake | enable standard packages that do not require extra libraries +cmake -C ../cmake/presets/nolib.cmake \[OPTIONS\] ../cmake | disable all packages that do not require extra libraries +cmake -C ../cmake/presets/manual_selection.cmake \[OPTIONS\] ../cmake | example of how to create a manual selection of packages :tb(s=|,a=l) + +NOTE: Running cmake this way manipulates the variable cache in your +current build directory. You can combine presets and options with +multiple cmake runs. + +[Example:] + +# build LAMMPS with all "standard" packages which don't +# use libraries and enable GPU package +mkdir build +cd build +cmake -C ../cmake/presets/std_nolib.cmake -D PKG_GPU=on ../cmake :pre + +:line + +[Make shortcuts for installing many packages]: + +The following commands are useful for managing package source files +and their installation when building LAMMPS via traditional make. +Just type "make" in lammps/src to see a one-line summary. + +These commands install/un-install sets of packages: + +make yes-all | install all packages +make no-all | un-install all packages +make yes-standard or make yes-std | install standard packages +make no-standard or make no-std| un-install standard packages +make yes-user | install user packages +make no-user | un-install user packages +make yes-lib | install packages that require extra libraries +make no-lib | un-install packages that require extra libraries +make yes-ext | install packages that require external libraries +make no-ext | un-install packages that require external libraries :tb(s=|,a=l) + +which install/un-install various sets of packages. Typing "make +package" will list all the these commands. + +NOTE: Installing or un-installing a package works by simply copying +files back and forth between the main src directory and +sub-directories with the package name (e.g. src/KSPACE, src/USER-ATC), +so that the files are included or excluded when LAMMPS is built. + +The following make commands help manage files that exist in both the +src directory and in package sub-directories. You do not normally +need to use these commands unless you are editing LAMMPS files or are +"installing a patch"_Install_patch.html downloaded from the LAMMPS web +site. + +Type "make package-status" or "make ps" to show which packages are +currently installed. For those that are installed, it will list any +files that are different in the src directory and package +sub-directory. + +Type "make package-installed" or "make pi" to show which packages are +currently installed, without listing the status of packages that are +not installed. + +Type "make package-update" or "make pu" to overwrite src files with +files from the package sub-directories if the package is installed. +It should be used after a "patch has been applied"_Install_patch.html, +since patches only update the files in the package sub-directory, but +not the src files. + +Type "make package-overwrite" to overwrite files in the package +sub-directories with src files. + +Type "make package-diff" to list all differences between pairs of +files in both the src dir and a package dir. diff --git a/doc/src/Build_settings.txt b/doc/src/Build_settings.txt new file mode 100644 index 0000000000..500130ecee --- /dev/null +++ b/doc/src/Build_settings.txt @@ -0,0 +1,341 @@ +"Higher level section"_Build.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Optional build settings :h3 + +LAMMPS can be built with several optional settings. Each sub-section +explain how to do this for building both with CMake and make. + +"FFT library"_#fft for use with the "kspace_style pppm"_kspace_style.html command +"Size of LAMMPS data types"_#size +"Read or write compressed files"_#gzip +"Output of JPG and PNG files"_#graphics via the "dump image"_dump_image.html command +"Output of movie files"_#graphics via the "dump_movie"_dump_image.html command +"Memory allocation alignment"_#align +"Workaround for long long integers"_#longlong +"Error handling exceptions"_#exceptions when using LAMMPS as a library :all(b) + +:line + +FFT library :h4,link(fft) + +When the KSPACE package is included in a LAMMPS build, the +"kspace_style pppm"_kspace_style.html command performs 3d FFTs which +require use of an FFT library to compute 1d FFTs. The KISS FFT +library is included with LAMMPS but other libraries can be faster. +LAMMPS can use them if they are available on your system. + +[CMake variables]: + +-D FFT=value # FFTW3 or MKL or KISS, default is FFTW3 if found, else KISS +-D FFT_SINGLE=value # yes or no (default), no = double precision +-D FFT_PACK=value # array (default) or pointer or memcpy :pre + +NOTE: The values for the FFT variable must be in upper-case. This is +an exception to the rule that all CMake variables can be specified +with lower-case values. + +Usually these settings are all that is needed. If CMake cannot find +the FFT library, you can set these variables: + +-D FFTW3_INCLUDE_DIRS=path # path to FFTW3 include files +-D FFTW3_LIBRARIES=path # path to FFTW3 libraries +-D MKL_INCLUDE_DIRS=path # ditto for Intel MKL library +-D MKL_LIBRARIES=path :pre + +[Makefile.machine settings]: + +FFT_INC = -DFFT_FFTW3 # -DFFT_FFTW3, -DFFT_FFTW (same as -DFFT_FFTW3), -DFFT_MKL, or -DFFT_KISS + # default is KISS if not specified +FFT_INC = -DFFT_SINGLE # do not specify for double precision +FFT_INC = -DFFT_PACK_ARRAY # or -DFFT_PACK_POINTER or -DFFT_PACK_MEMCPY :pre + # default is FFT_PACK_ARRAY if not specified + +FFT_INC = -I/usr/local/include +FFT_PATH = -L/usr/local/lib +FFT_LIB = -lfftw3 # FFTW3 double precision +FFT_LIB = -lfftw3 -lfftw3f # FFTW3 single precision +FFT_LIB = -lmkl_intel_lp64 -lmkl_sequential -lmkl_core # MKL with Intel compiler +FFT_LIB = -lmkl_gf_lp64 -lmkl_sequential -lmkl_core # MKL with GNU compier :pre + +As with CMake, you do not need to set paths in FFT_INC or FFT_PATH, if +make can find the FFT header and library files. You must specify +FFT_LIB with the appropriate FFT libraries to include in the link. + +[CMake and make info]: + +The "KISS FFT library"_http://kissfft.sf.net is included in the LAMMPS +distribution. It is portable across all platforms. Depending on the +size of the FFTs and the number of processors used, the other +libraries listed here can be faster. + +However, note that long-range Coulombics are only a portion of the +per-timestep CPU cost, FFTs are only a portion of long-range +Coulombics, and 1d FFTs are only a portion of the FFT cost (parallel +communication can be costly). A breakdown of these timings is printed +to the screen at the end of a run using the "kspace_style +pppm"_kspace_style.html command. The "Run output"_Run_output.html +doc page gives more details. + +FFTW is a fast, portable FFT library that should also work on any +platform and can be faster than the KISS FFT library. You can +download it from "www.fftw.org"_http://www.fftw.org. LAMMPS requires +version 3.X; the legacy version 2.1.X is no longer supported. + +Building FFTW for your box should be as simple as ./configure; make; +make install. The install command typically requires root privileges +(e.g. invoke it via sudo), unless you specify a local directory with +the "--prefix" option of configure. Type "./configure --help" to see +various options. + +The Intel MKL math library is part of the Intel compiler suite. It +can be used with the Intel or GNU compiler (see FFT_LIB setting above). + +Performing 3d FFTs in parallel can be time consuming due to data +access and required communication. This cost can be reduced by +performing single-precision FFTs instead of double precision. Single +precision means the real and imaginary parts of a complex datum are +4-byte floats. Double precision means they are 8-byte doubles. Note +that Fourier transform and related PPPM operations are somewhat less +sensitive to floating point truncation errors and thus the resulting +error is less than the difference in precision. Using the -DFFT_SINGLE +setting trades off a little accuracy for reduced memory use and +parallel communication costs for transposing 3d FFT data. + +When using -DFFT_SINGLE with FFTW3 you may need to build the FFTW +library a second time with support for single-precision. + +For FFTW3, do the following, which should produce the additional +library libfftw3f.a + +make clean +./configure --enable-single; make; make install :pre + +Performing 3d FFTs requires communication to transpose the 3d FFT +grid. The data packing/unpacking for this can be done in one of 3 +modes (ARRAY, POINTER, MEMCPY) as set by the FFT_PACK syntax above. +Depending on the machine, the size of the FFT grid, the number of +processors used, one option may be slightly faster. The default is +ARRAY mode. + +:line + +Size of LAMMPS data types :h4,link(size) + +LAMMPS has a few integer data types which can be defined as 4-byte or +8-byte integers. The default setting of "smallbig" is almost always +adequate. + +[CMake variable]: + +-D LAMMPS_SIZES=value # smallbig (default) or bigbig or smallsmall :pre + +[Makefile.machine setting]: + +LMP_INC = -DLAMMPS_SMALLBIG # or -DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL :pre + # default is LAMMMPS_SMALLBIG if not specified +[CMake and make info]: + +The default "smallbig" setting allows for simulations with: + +total atom count = 2^63 atoms (about 9e18) +total timesteps = 2^63 (about 9e18) +atom IDs = 2^31 (about 2 billion) +image flags = roll over at 512 :ul + +The "bigbig" setting increases the latter two limits. It allows for: + +total atom count = 2^63 atoms (about 9e18) +total timesteps = 2^63 (about 9e18) +atom IDs = 2^63 (about 9e18) +image flags = roll over at about 1 million (2^20) :ul + +The "smallsmall" setting is only needed if your machine does not +support 8-byte integers. It allows for: + +total atom count = 2^31 atoms (about 2 billion) +total timesteps = 2^31 (about 2 billion) +atom IDs = 2^31 (about 2 billion) +image flags = roll over at 512 (2^9) :ul + +Atom IDs are not required for atomic systems which do not store bond +topology information, though IDs are enabled by default. The +"atom_modify id no"_atom_modify.html command will turn them off. Atom +IDs are required for molecular systems with bond topology (bonds, +angles, dihedrals, etc). Thus if you model a molecular system with +more than 2 billion atoms, you need the "bigbig" setting. + +Image flags store 3 values per atom which count the number of times an +atom has moved through the periodic box in each dimension. See the +"dump"_dump.html doc page for a discussion. If an atom moves through +the periodic box more than this limit, the value will "roll over", +e.g. from 511 to -512, which can cause diagnostics like the +mean-squared displacement, as calculated by the "compute +msd"_compute_msd.html command, to be faulty. + +Note that the USER-ATC package is not currently compatible with the +"bigbig" setting. + +Also note that the GPU package requires its lib/gpu library to be +compiled with the same size setting, or the link will fail. A CMake +build does this automatically. When building with make, the setting +in whichever lib/gpu/Makefile is used must be the same as above. + +:line + +Output of JPG, PNG, and movie files :h4,link(graphics) + +The "dump image"_dump_image.html command has options to output JPEG or +PNG image files. Likewise the "dump movie"_dump_image.html command +outputs movie files in MPEG format. Using these options requires the +following settings: + +[CMake variables]: + +-D WITH_JPEG=value # yes or no + # default = yes if CMake finds JPEG files, else no +-D WITH_PNG=value # yes or no + # default = yes if CMake finds PNG and ZLIB files, else no +-D WITH_FFMPEG=value # yes or no + # default = yes if CMake can find ffmpeg, else no :pre + +Usually these settings are all that is needed. If CMake cannot find +the graphics header, library, executable files, you can set these +variables: + +-D JPEG_INCLUDE_DIR=path # path to jpeglib.h header file +-D JPEG_LIBRARIES=path # path to libjpeg.a (.so) file +-D PNG_INCLUDE_DIR=path # path to png.h header file +-D PNG_LIBRARIES=path # path to libpng.a (.so) file +-D ZLIB_INCLUDE_DIR=path # path to zlib.h header file +-D ZLIB_LIBRARIES=path # path to libz.a (.so) file +-D FFMPEG_EXECUTABLE=path # path to ffmpeg executable :pre + +[Makefile.machine settings]: + +LMP_INC = -DLAMMPS_JPEG +LMP_INC = -DLAMMPS_PNG +LMP_INC = -DLAMMPS_FFMPEG :pre + +JPG_INC = -I/usr/local/include # path to jpeglib.h, png.h, zlib.h header files if make cannot find them +JPG_PATH = -L/usr/lib # paths to libjpeg.a, libpng.a, libz.a (.so) files if make cannot find them +JPG_LIB = -ljpeg -lpng -lz # library names :pre + +As with CMake, you do not need to set JPG_INC or JPG_PATH, if make can +find the graphics header and library files. You must specify JPG_LIB +with a list of graphics libraries to include in the link. You must +insure ffmpeg is in a directory where LAMMPS can find it at runtime, +i.e. a dir in your PATH environment variable. + +[CMake and make info]: + +Using ffmpeg to output movie files requires that your machine +supports the "popen" function in the standard runtime library. + +NOTE: On some clusters with high-speed networks, using the fork() +library calls (required by popen()) can interfere with the fast +communication library and lead to simulations using ffmpeg to hang or +crash. + +:line + +Read or write compressed files :h4,link(gzip) + +If this option is enabled, large files can be read or written with +gzip compression by several LAMMPS commands, including +"read_data"_read_data.html, "rerun"_rerun.html, and "dump"_dump.html. + +[CMake variables]: + +-D WITH_GZIP=value # yes or no + # default is yes if CMake can find gzip, else no +-D GZIP_EXECUTABLE=path # path to gzip executable if CMake cannot find it :pre + +[Makefile.machine setting]: + +LMP_INC = -DLAMMPS_GZIP :pre + +[CMake and make info]: + +This option requires that your machine supports the "popen()" function +in the standard runtime library and that a gzip executable can be +found by LAMMPS during a run. + +NOTE: On some clusters with high-speed networks, using the fork() +library calls (required by popen()) can interfere with the fast +communication library and lead to simulations using compressed output +or input to hang or crash. For selected operations, compressed file +I/O is also available using a compression library instead, which is +what the "COMPRESS package"_Packages_details.html#PKG-COMPRESS enables. + +:line + +Memory allocation alignment :h4,link(align) + +This setting enables the use of the posix_memalign() call instead of +malloc() when LAMMPS allocates large chunks or memory. This can make +vector instructions on CPUs more efficient, if dynamically allocated +memory is aligned on larger-than-default byte boundaries. +On most current systems, the malloc() implementation returns +pointers that are aligned to 16-byte boundaries. Using SSE vector +instructions efficiently, however, requires memory blocks being +aligned on 64-byte boundaries. + +[CMake variable]: + +-D LAMMPS_MEMALIGN=value # 0, 8, 16, 32, 64 (default) :pre + +Use a LAMMPS_MEMALIGN value of 0 to disable using posix_memalign() +and revert to using the malloc() C-library function instead. When +compiling LAMMPS for Windows systems, malloc() will always be used +and this setting ignored. + +[Makefile.machine setting]: + +LMP_INC = -DLAMMPS_MEMALIGN=value # 8, 16, 32, 64 :pre + +Do not set -DLAMMPS_MEMALIGN, if you want to have memory allocated +with the malloc() function call instead. -DLAMMPS_MEMALIGN [cannot] +be used on Windows, as it does use different function calls for +allocating aligned memory, that are not compatible with how LAMMPS +manages its dynamical memory. + +:line + +Workaround for long long integers :h4,link(longlong) + +If your system or MPI version does not recognize "long long" data +types, the following setting will be needed. It converts "long long" +to a "long" data type, which should be the desired 8-byte integer on +those systems: + +[CMake variable]: + +-D LAMMPS_LONGLONG_TO_LONG=value # yes or no (default) :pre + +[Makefile.machine setting]: + +LMP_INC = -DLAMMPS_LONGLONG_TO_LONG :pre + +:line + +Exception handling when using LAMMPS as a library :h4,link(exceptions) + +This setting is useful when external codes drive LAMMPS as a library. +With this option enabled LAMMPS errors do not kill the caller. +Instead, the call stack is unwound and control returns to the caller, +e.g. to Python. + +[CMake variable]: + +-D LAMMPS_EXCEPTIONS=value # yes or no (default) :pre + +[Makefile.machine setting]: + +LMP_INC = -DLAMMPS_EXCEPTIONS :pre diff --git a/doc/src/Build_windows.txt b/doc/src/Build_windows.txt new file mode 100644 index 0000000000..0caad589fb --- /dev/null +++ b/doc/src/Build_windows.txt @@ -0,0 +1,97 @@ +"Higher level section"_Build.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Notes for building LAMMPS on Windows :h3 + +"General remarks"_#generic +"Running Linux on Windows"_#linux +"Using GNU GCC ported to Windows"_#gnu +"Using a cross-compiler"_#cross :ul + +:line + +General remarks :h4,link(generic) + +LAMMPS is developed and tested primarily on Linux machines. The vast +majority of HPC clusters and supercomputers today runs on Linux as well. +Thus portability to other platforms is desired, but not always achieved. +The LAMMPS developers strongly rely on LAMMPS users giving feedback and +providing assistance in resolving portability issues. This particularly +true for compiling LAMMPS on Windows, since this platform has significant +differences with some low-level functionality. + + +Running Linux on Windows :h4,link(linux) + +So before trying to build LAMMPS on Windows, please consider if using +the pre-compiled Windows binary packages are sufficient for your needs +(as an aside, those packages themselves are build on a Linux machine +using cross-compilers). If it is necessary for your to compile LAMMPS +on a Windows machine (e.g. because it is your main desktop), please also +consider using a virtual machine software and run a Linux virtual machine, +or - if have a recently updated Windows 10 installation - consider using +the Windows subsystem for Linux, which allows to run a bash shell from +Ubuntu and from there on, you can pretty much use that shell like you +are running on an Ubuntu Linux machine (e.g. installing software via +apt-get). For more details on that, please see "this tutorial"_Howto_bash.html + + +Using GNU GCC ported to Windows :h4,link(gnu) + +One option for compiling LAMMPS on Windows natively, that has been known +to work in the past is to install a bash shell, unix shell utilities, +perl, GNU make, and a GNU compiler ported to Windows. The Cygwin package +provides a unix/linux interface to low-level Windows functions, so LAMMPS +can be compiled on Windows. The necessary (minor) modifications to LAMMPS +are included, but may not always up-to-date for recently added functionality +and the corresponding new code. A machine makefile for using cygwin for +the old build system is provided. The CMake build system is untested +for this; you will have to request that makefiles are generated and +manually set the compiler. + +When compiling for Windows [not] set the -DLAMMPS_MEMALIGN define +in the LMP_INC makefile variable and add -lwsock32 -lpsapi to the linker +flags in LIB makefile variable. Try adding -static-libgcc or -static or +both to the linker flags when your resulting LAMMPS Windows executable +complains about missing .dll files. The CMake configuration should set +this up automatically, but is untested. + +In case of problems, you are recommended to contact somebody with +experience in using cygwin. If you do come across portability problems +requiring changes to the LAMMPS source code, or figure out corrections +yourself, please report them on the lammps-users mailing list, or file +them as an issue or pull request on the LAMMPS github project. + + +Using a cross-compiler :h4,link(cross) + +If you need to provide custom LAMMPS binaries for Windows, but do not +need to do the compilation on Windows, please consider using a Linux +to Windows cross-compiler. This is how currently the Windows binary +packages are created by the LAMMPS developers. Because of that, this is +probably the currently best tested and supported way to build LAMMPS +executables for Windows. There are makefiles provided for the +traditional build system, but CMake has also been successfully tested +using the mingw32-cmake and mingw64-cmake wrappers that are bundled +with the cross-compiler environment on Fedora machines. + +Please keep in mind, though, that this only applies to compiling LAMMPS. +Whether the resulting binaries do work correctly is no tested by the +LAMMPS developers. We instead rely on the feedback of the users +of these pre-compiled LAMMPS packages for Windows. We will try to resolve +issues to the best of our abilities if we become aware of them. However +this is subject to time constraints and focus on HPC platforms. + + +Native Visual C++ support :h4,link(native) + +Support for the Visual C++ compilers is currently not available. The +CMake build system is capable of creating suitable a Visual Studio +style build environment, but the LAMMPS code itself is not fully ported +to support Visual C++. Volunteers to take on this task are welcome. diff --git a/doc/src/Commands.txt b/doc/src/Commands.txt new file mode 100644 index 0000000000..a1a94c6d29 --- /dev/null +++ b/doc/src/Commands.txt @@ -0,0 +1,53 @@ +"Previous Section"_Run_head.html - "LAMMPS WWW Site"_lws - +"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next +Section"_Packages.html :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html#comm) + +:line + +Commands :h2 + +These pages describe how a LAMMPS input script is formatted and the +commands in it are used to define a LAMMPS simulation. + + + + + +"LAMMPS input scripts"_Commands_input.html +"Parsing rules for input scripts"_Commands_parse.html +"Input script structure"_Commands_structure.html +"Commands by category"_Commands_category.html :all(b) + +"All commands"_Commands_all.html +"Fix commands"_Commands_fix.html +"Compute commands"_Commands_compute.html +"Pair commands"_Commands_pair.html +"Bond, angle, dihedral, improper commands"_Commands_bond.html +"KSpace solvers"_Commands_kspace.html :all(b) + + + diff --git a/doc/src/Commands_all.txt b/doc/src/Commands_all.txt new file mode 100644 index 0000000000..6f54681342 --- /dev/null +++ b/doc/src/Commands_all.txt @@ -0,0 +1,130 @@ +"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +"All commands"_Commands_all.html, +"Fix styles"_Commands_fix.html, +"Compute styles"_Commands_compute.html, +"Pair styles"_Commands_pair.html, +"Bond styles"_Commands_bond.html, +"Angle styles"_Commands_bond.html#angle, +"Dihedral styles"_Commands_bond.html#dihedral, +"Improper styles"_Commands_bond.html#improper, +"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c) + +All commands :h3 + +An alphabetic list of all LAMMPS commands. + +"angle_coeff"_angle_coeff.html, +"angle_style"_angle_style.html, +"atom_modify"_atom_modify.html, +"atom_style"_atom_style.html, +"balance"_balance.html, +"bond_coeff"_bond_coeff.html, +"bond_style"_bond_style.html, +"bond_write"_bond_write.html, +"boundary"_boundary.html, +"box"_box.html, +"change_box"_change_box.html, +"clear"_clear.html, +"comm_modify"_comm_modify.html, +"comm_style"_comm_style.html, +"compute"_compute.html, +"compute_modify"_compute_modify.html, +"create_atoms"_create_atoms.html, +"create_bonds"_create_bonds.html, +"create_box"_create_box.html, +"delete_atoms"_delete_atoms.html, +"delete_bonds"_delete_bonds.html, +"dielectric"_dielectric.html, +"dihedral_coeff"_dihedral_coeff.html, +"dihedral_style"_dihedral_style.html, +"dimension"_dimension.html, +"displace_atoms"_displace_atoms.html, +"dump"_dump.html, +"dump image"_dump_image.html, +"dump_modify"_dump_modify.html, +"dump movie"_dump_image.html, +"dump netcdf"_dump_netcdf.html, +"dump netcdf/mpiio"_dump_netcdf.html, +"dump vtk"_dump_vtk.html, +"echo"_echo.html, +"fix"_fix.html, +"fix_modify"_fix_modify.html, +"group"_group.html, +"group2ndx"_group2ndx.html, +"if"_if.html, +"info"_info.html, +"improper_coeff"_improper_coeff.html, +"improper_style"_improper_style.html, +"include"_include.html, +"jump"_jump.html, +"kspace_modify"_kspace_modify.html, +"kspace_style"_kspace_style.html, +"label"_label.html, +"lattice"_lattice.html, +"log"_log.html, +"mass"_mass.html, +"message"_message.html, +"minimize"_minimize.html, +"min_modify"_min_modify.html, +"min_style"_min_style.html, +"molecule"_molecule.html, +"ndx2group"_group2ndx.html, +"neb"_neb.html, +"neigh_modify"_neigh_modify.html, +"neighbor"_neighbor.html, +"newton"_newton.html, +"next"_next.html, +"package"_package.html, +"pair_coeff"_pair_coeff.html, +"pair_modify"_pair_modify.html, +"pair_style"_pair_style.html, +"pair_write"_pair_write.html, +"partition"_partition.html, +"prd"_prd.html, +"print"_print.html, +"processors"_processors.html, +"python"_python.html, +"quit"_quit.html, +"read_data"_read_data.html, +"read_dump"_read_dump.html, +"read_restart"_read_restart.html, +"region"_region.html, +"replicate"_replicate.html, +"rerun"_rerun.html, +"reset_ids"_reset_ids.html, +"reset_timestep"_reset_timestep.html, +"restart"_restart.html, +"run"_run.html, +"run_style"_run_style.html, +"server"_server.html, +"set"_set.html, +"shell"_shell.html, +"special_bonds"_special_bonds.html, +"suffix"_suffix.html, +"tad"_tad.html, +"temper"_temper.html, +"temper/grem"_temper_grem.html, +"temper/npt"_temper_npt.html, +"thermo"_thermo.html, +"thermo_modify"_thermo_modify.html, +"thermo_style"_thermo_style.html, +"timer"_timer.html, +"timestep"_timestep.html, +"uncompute"_uncompute.html, +"undump"_undump.html, +"unfix"_unfix.html, +"units"_units.html, +"variable"_variable.html, +"velocity"_velocity.html, +"write_coeff"_write_coeff.html, +"write_data"_write_data.html, +"write_dump"_write_dump.html, +"write_restart"_write_restart.html :tb(c=6,ea=c) diff --git a/doc/src/Commands_bond.txt b/doc/src/Commands_bond.txt new file mode 100644 index 0000000000..0cf433d53a --- /dev/null +++ b/doc/src/Commands_bond.txt @@ -0,0 +1,124 @@ +"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +"All commands"_Commands_all.html, +"Fix styles"_Commands_fix.html, +"Compute styles"_Commands_compute.html, +"Pair styles"_Commands_pair.html, +"Bond styles"_Commands_bond.html#bond, +"Angle styles"_Commands_bond.html#angle, +"Dihedral styles"_Commands_bond.html#dihedral, +"Improper styles"_Commands_bond.html#improper, +"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c) + +Bond, angle, dihedral, and improper commands :h3 + +:line + +Bond_style potentials :h3,link(bond) + +All LAMMPS "bond_style"_bond_style.html commands. Some styles have +accelerated versions. This is indicated by additional letters in +parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = +OPT. + +"none"_bond_none.html, +"zero"_bond_zero.html, +"hybrid"_bond_hybrid.html :tb(c=3,ea=c) + +"class2 (ko)"_bond_class2.html, +"fene (iko)"_bond_fene.html, +"fene/expand (o)"_bond_fene_expand.html, +"gromos (o)"_bond_gromos.html, +"harmonic (ko)"_bond_harmonic.html, +"harmonic/shift (o)"_bond_harmonic_shift.html, +"harmonic/shift/cut (o)"_bond_harmonic_shift_cut.html, +"morse (o)"_bond_morse.html, +"nonlinear (o)"_bond_nonlinear.html, +"oxdna/fene"_bond_oxdna.html, +"oxdna2/fene"_bond_oxdna.html, +"quartic (o)"_bond_quartic.html, +"table (o)"_bond_table.html :tb(c=4,ea=c) + +:line + +Angle_style potentials :h3,link(angle) + +All LAMMPS "angle_style"_angle_style.html commands. Some styles have +accelerated versions. This is indicated by additional letters in +parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = +OPT. + +"none"_angle_none.html, +"zero"_angle_zero.html, +"hybrid"_angle_hybrid.html :tb(c=3,ea=c) + +"charmm (ko)"_angle_charmm.html, +"class2 (ko)"_angle_class2.html, +"cosine (o)"_angle_cosine.html, +"cosine/delta (o)"_angle_cosine_delta.html, +"cosine/periodic (o)"_angle_cosine_periodic.html, +"cosine/shift (o)"_angle_cosine_shift.html, +"cosine/shift/exp (o)"_angle_cosine_shift_exp.html, +"cosine/squared (o)"_angle_cosine_squared.html, +"dipole (o)"_angle_dipole.html, +"fourier (o)"_angle_fourier.html, +"fourier/simple (o)"_angle_fourier_simple.html, +"harmonic (iko)"_angle_harmonic.html, +"quartic (o)"_angle_quartic.html, +"sdk"_angle_sdk.html, +"table (o)"_angle_table.html :tb(c=4,ea=c) + +:line + +Dihedral_style potentials :h3,link(dihedral) + +All LAMMPS "dihedral_style"_dihedral_style.html commands. Some styles +have accelerated versions. This is indicated by additional letters in +parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = +OPT. + +"none"_dihedral_none.html, +"zero"_dihedral_zero.html, +"hybrid"_dihedral_hybrid.html :tb(c=3,ea=c) + +"charmm (iko)"_dihedral_charmm.html, +"charmmfsw"_dihedral_charmm.html, +"class2 (ko)"_dihedral_class2.html, +"cosine/shift/exp (o)"_dihedral_cosine_shift_exp.html, +"fourier (io)"_dihedral_fourier.html, +"harmonic (io)"_dihedral_harmonic.html, +"helix (o)"_dihedral_helix.html, +"multi/harmonic (o)"_dihedral_multi_harmonic.html, +"nharmonic (o)"_dihedral_nharmonic.html, +"opls (iko)"_dihedral_opls.html, +"quadratic (o)"_dihedral_quadratic.html, +"spherical (o)"_dihedral_spherical.html, +"table (o)"_dihedral_table.html, +"table/cut"_dihedral_table_cut.html :tb(c=4,ea=c) + +:line + +Improper_style potentials :h3,link(improper) + +All LAMMPS "improper_style"_improper_style.html commands. Some styles +have accelerated versions. This is indicated by additional letters in +parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = +OPT. + +"none"_improper_none.html, +"zero"_improper_zero.html, +"hybrid"_improper_hybrid.html :tb(c=3,ea=c) + +"class2 (ko)"_improper_class2.html, +"cossq (o)"_improper_cossq.html, +"cvff (io)"_improper_cvff.html, +"distance"_improper_distance.html, +"fourier (o)"_improper_fourier.html, +"harmonic (iko)"_improper_harmonic.html, +"ring (o)"_improper_ring.html, +"umbrella (o)"_improper_umbrella.html :tb(c=4,ea=c) diff --git a/doc/src/Commands_category.txt b/doc/src/Commands_category.txt new file mode 100644 index 0000000000..5d047c6727 --- /dev/null +++ b/doc/src/Commands_category.txt @@ -0,0 +1,141 @@ +"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Commands by category :h3 + +This page lists most of the LAMMPS commands, grouped by category. The +"Commands all"_Commands_all.html doc page lists all commands +alphabetically. It also includes long lists of style options for +entries that appear in the following categories as a single command +(fix, compute, pair, etc). + +Initialization: + +"newton"_newton.html, +"package"_package.html, +"processors"_processors.html, +"suffix"_suffix.html, +"units"_units.html :ul + +Setup simulation box: + +"boundary"_boundary.html, +"box"_box.html, +"change_box"_change_box.html, +"create_box"_create_box.html, +"dimension"_dimension.html, +"lattice"_lattice.html, +"region"_region.html :ul + +Setup atoms: + +"atom_modify"_atom_modify.html, +"atom_style"_atom_style.html, +"balance"_balance.html, +"create_atoms"_create_atoms.html, +"create_bonds"_create_bonds.html, +"delete_atoms"_delete_atoms.html, +"delete_bonds"_delete_bonds.html, +"displace_atoms"_displace_atoms.html, +"group"_group.html, +"mass"_mass.html, +"molecule"_molecule.html, +"read_data"_read_data.html, +"read_dump"_read_dump.html, +"read_restart"_read_restart.html, +"replicate"_replicate.html, +"set"_set.html, +"velocity"_velocity.html :ul + +Force fields: + +"angle_coeff"_angle_coeff.html, +"angle_style"_angle_style.html, +"bond_coeff"_bond_coeff.html, +"bond_style"_bond_style.html, +"bond_write"_bond_write.html, +"dielectric"_dielectric.html, +"dihedral_coeff"_dihedral_coeff.html, +"dihedral_style"_dihedral_style.html, +"improper_coeff"_improper_coeff.html, +"improper_style"_improper_style.html, +"kspace_modify"_kspace_modify.html, +"kspace_style"_kspace_style.html, +"pair_coeff"_pair_coeff.html, +"pair_modify"_pair_modify.html, +"pair_style"_pair_style.html, +"pair_write"_pair_write.html, +"special_bonds"_special_bonds.html :ul + +Settings: + +"comm_modify"_comm_modify.html, +"comm_style"_comm_style.html, +"info"_info.html, +"min_modify"_min_modify.html, +"min_style"_min_style.html, +"neigh_modify"_neigh_modify.html, +"neighbor"_neighbor.html, +"partition"_partition.html, +"reset_timestep"_reset_timestep.html, +"run_style"_run_style.html, +"timer"_timer.html, +"timestep"_timestep.html :ul + +Operations within timestepping (fixes) and diagnostics (computes): + +"compute"_compute.html, +"compute_modify"_compute_modify.html, +"fix"_fix.html, +"fix_modify"_fix_modify.html, +"uncompute"_uncompute.html, +"unfix"_unfix.html :ul + +Output: + +"dump image"_dump_image.html, +"dump movie"_dump_image.html, +"dump"_dump.html, +"dump_modify"_dump_modify.html, +"restart"_restart.html, +"thermo"_thermo.html, +"thermo_modify"_thermo_modify.html, +"thermo_style"_thermo_style.html, +"undump"_undump.html, +"write_coeff"_write_coeff.html, +"write_data"_write_data.html, +"write_dump"_write_dump.html, +"write_restart"_write_restart.html :ul + +Actions: + +"minimize"_minimize.html, +"neb"_neb.html, +"prd"_prd.html, +"rerun"_rerun.html, +"run"_run.html, +"tad"_tad.html, +"temper"_temper.html :ul + +Input script control: + +"clear"_clear.html, +"echo"_echo.html, +"if"_if.html, +"include"_include.html, +"jump"_jump.html, +"label"_label.html, +"log"_log.html, +"next"_next.html, +"print"_print.html, +"python"_python.html, +"quit"_quit.html, +"shell"_shell.html, +"variable"_variable.html :ul + diff --git a/doc/src/Commands_compute.txt b/doc/src/Commands_compute.txt new file mode 100644 index 0000000000..6185634187 --- /dev/null +++ b/doc/src/Commands_compute.txt @@ -0,0 +1,155 @@ +"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +"All commands"_Commands_all.html, +"Fix styles"_Commands_fix.html, +"Compute styles"_Commands_compute.html, +"Pair styles"_Commands_pair.html, +"Bond styles"_Commands_bond.html, +"Angle styles"_Commands_bond.html#angle, +"Dihedral styles"_Commands_bond.html#dihedral, +"Improper styles"_Commands_bond.html#improper, +"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c) + +Compute commands :h3 + +An alphabetic list of all LAMMPS "compute"_compute.html commands. +Some styles have accelerated versions. This is indicated by +additional letters in parenthesis: g = GPU, i = USER-INTEL, k = +KOKKOS, o = USER-OMP, t = OPT. + +"ackland/atom"_compute_ackland_atom.html, +"aggregate/atom"_compute_cluster_atom.html, +"angle"_compute_angle.html, +"angle/local"_compute_angle_local.html, +"angmom/chunk"_compute_angmom_chunk.html, +"basal/atom"_compute_basal_atom.html, +"body/local"_compute_body_local.html, +"bond"_compute_bond.html, +"bond/local"_compute_bond_local.html, +"centro/atom"_compute_centro_atom.html, +"chunk/atom"_compute_chunk_atom.html, +"chunk/spread/atom"_compute_chunk_spread_atom.html, +"cluster/atom"_compute_cluster_atom.html, +"cna/atom"_compute_cna_atom.html, +"cnp/atom"_compute_cnp_atom.html, +"com"_compute_com.html, +"com/chunk"_compute_com_chunk.html, +"contact/atom"_compute_contact_atom.html, +"coord/atom"_compute_coord_atom.html, +"damage/atom"_compute_damage_atom.html, +"dihedral"_compute_dihedral.html, +"dihedral/local"_compute_dihedral_local.html, +"dilatation/atom"_compute_dilatation_atom.html, +"dipole/chunk"_compute_dipole_chunk.html, +"displace/atom"_compute_displace_atom.html, +"dpd"_compute_dpd.html, +"dpd/atom"_compute_dpd_atom.html, +"edpd/temp/atom"_compute_edpd_temp_atom.html, +"entropy/atom"_compute_entropy_atom.html, +"erotate/asphere"_compute_erotate_asphere.html, +"erotate/rigid"_compute_erotate_rigid.html, +"erotate/sphere"_compute_erotate_sphere.html, +"erotate/sphere/atom"_compute_erotate_sphere_atom.html, +"event/displace"_compute_event_displace.html, +"fep"_compute_fep.html, +"force/tally"_compute_tally.html, +"fragment/atom"_compute_cluster_atom.html, +"global/atom"_compute_global_atom.html, +"group/group"_compute_group_group.html, +"gyration"_compute_gyration.html, +"gyration/chunk"_compute_gyration_chunk.html, +"heat/flux"_compute_heat_flux.html, +"heat/flux/tally"_compute_tally.html, +"hexorder/atom"_compute_hexorder_atom.html, +"improper"_compute_improper.html, +"improper/local"_compute_improper_local.html, +"inertia/chunk"_compute_inertia_chunk.html, +"ke"_compute_ke.html, +"ke/atom"_compute_ke_atom.html, +"ke/atom/eff"_compute_ke_atom_eff.html, +"ke/eff"_compute_ke_eff.html, +"ke/rigid"_compute_ke_rigid.html, +"meso/e/atom"_compute_meso_e_atom.html, +"meso/rho/atom"_compute_meso_rho_atom.html, +"meso/t/atom"_compute_meso_t_atom.html, +"msd"_compute_msd.html, +"msd/chunk"_compute_msd_chunk.html, +"msd/nongauss"_compute_msd_nongauss.html, +"omega/chunk"_compute_omega_chunk.html, +"orientorder/atom"_compute_orientorder_atom.html, +"pair"_compute_pair.html, +"pair/local"_compute_pair_local.html, +"pe"_compute_pe.html, +"pe/atom"_compute_pe_atom.html, +"pe/mol/tally"_compute_tally.html, +"pe/tally"_compute_tally.html, +"plasticity/atom"_compute_plasticity_atom.html, +"pressure"_compute_pressure.html, +"pressure/uef"_compute_pressure_uef.html, +"property/atom"_compute_property_atom.html, +"property/chunk"_compute_property_chunk.html, +"property/local"_compute_property_local.html, +"rdf"_compute_rdf.html, +"reduce"_compute_reduce.html, +"reduce/chunk"_compute_reduce_chunk.html, +"reduce/region"_compute_reduce.html, +"rigid/local"_compute_rigid_local.html, +"saed"_compute_saed.html, +"slice"_compute_slice.html, +"smd/contact/radius"_compute_smd_contact_radius.html, +"smd/damage"_compute_smd_damage.html, +"smd/hourglass/error"_compute_smd_hourglass_error.html, +"smd/internal/energy"_compute_smd_internal_energy.html, +"smd/plastic/strain"_compute_smd_plastic_strain.html, +"smd/plastic/strain/rate"_compute_smd_plastic_strain_rate.html, +"smd/rho"_compute_smd_rho.html, +"smd/tlsph/defgrad"_compute_smd_tlsph_defgrad.html, +"smd/tlsph/dt"_compute_smd_tlsph_dt.html, +"smd/tlsph/num/neighs"_compute_smd_tlsph_num_neighs.html, +"smd/tlsph/shape"_compute_smd_tlsph_shape.html, +"smd/tlsph/strain"_compute_smd_tlsph_strain.html, +"smd/tlsph/strain/rate"_compute_smd_tlsph_strain_rate.html, +"smd/tlsph/stress"_compute_smd_tlsph_stress.html, +"smd/triangle/mesh/vertices"_compute_smd_triangle_mesh_vertices.html, +"smd/ulsph/num/neighs"_compute_smd_ulsph_num_neighs.html, +"smd/ulsph/strain"_compute_smd_ulsph_strain.html, +"smd/ulsph/strain/rate"_compute_smd_ulsph_strain_rate.html, +"smd/ulsph/stress"_compute_smd_ulsph_stress.html, +"smd/vol"_compute_smd_vol.html, +"sna/atom"_compute_sna_atom.html, +"snad/atom"_compute_sna_atom.html, +"snav/atom"_compute_sna_atom.html, +"spin"_compute_spin.html, +"stress/atom"_compute_stress_atom.html, +"stress/tally"_compute_tally.html, +"tdpd/cc/atom"_compute_tdpd_cc_atom.html, +"temp (k)"_compute_temp.html, +"temp/asphere"_compute_temp_asphere.html, +"temp/body"_compute_temp_body.html, +"temp/chunk"_compute_temp_chunk.html, +"temp/com"_compute_temp_com.html, +"temp/deform"_compute_temp_deform.html, +"temp/deform/eff"_compute_temp_deform_eff.html, +"temp/drude"_compute_temp_drude.html, +"temp/eff"_compute_temp_eff.html, +"temp/partial"_compute_temp_partial.html, +"temp/profile"_compute_temp_profile.html, +"temp/ramp"_compute_temp_ramp.html, +"temp/region"_compute_temp_region.html, +"temp/region/eff"_compute_temp_region_eff.html, +"temp/rotate"_compute_temp_rotate.html, +"temp/sphere"_compute_temp_sphere.html, +"temp/uef"_compute_temp_uef.html, +"ti"_compute_ti.html, +"torque/chunk"_compute_torque_chunk.html, +"vacf"_compute_vacf.html, +"vcm/chunk"_compute_vcm_chunk.html, +"voronoi/atom"_compute_voronoi_atom.html, +"xrd"_compute_xrd.html :tb(c=6,ea=c) diff --git a/doc/src/Commands_fix.txt b/doc/src/Commands_fix.txt new file mode 100644 index 0000000000..e002c11770 --- /dev/null +++ b/doc/src/Commands_fix.txt @@ -0,0 +1,229 @@ +"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +"All commands"_Commands_all.html, +"Fix styles"_Commands_fix.html, +"Compute styles"_Commands_compute.html, +"Pair styles"_Commands_pair.html, +"Bond styles"_Commands_bond.html, +"Angle styles"_Commands_bond.html#angle, +"Dihedral styles"_Commands_bond.html#dihedral, +"Improper styles"_Commands_bond.html#improper, +"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c) + +Fix commands :h3 + +An alphabetic list of all LAMMPS "fix"_fix.html commands. Some styles +have accelerated versions. This is indicated by additional letters in +parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = +OPT. + +"adapt"_fix_adapt.html, +"adapt/fep"_fix_adapt_fep.html, +"addforce"_fix_addforce.html, +"addtorque"_fix_addtorque.html, +"append/atoms"_fix_append_atoms.html, +"atc"_fix_atc.html, +"atom/swap"_fix_atom_swap.html, +"ave/atom"_fix_ave_atom.html, +"ave/chunk"_fix_ave_chunk.html, +"ave/correlate"_fix_ave_correlate.html, +"ave/correlate/long"_fix_ave_correlate_long.html, +"ave/histo"_fix_ave_histo.html, +"ave/histo/weight"_fix_ave_histo.html, +"ave/time"_fix_ave_time.html, +"aveforce"_fix_aveforce.html, +"balance"_fix_balance.html, +"bond/break"_fix_bond_break.html, +"bond/create"_fix_bond_create.html, +"bond/react"_fix_bond_react.html, +"bond/swap"_fix_bond_swap.html, +"box/relax"_fix_box_relax.html, +"cmap"_fix_cmap.html, +"colvars"_fix_colvars.html, +"controller"_fix_controller.html, +"deform (k)"_fix_deform.html, +"deposit"_fix_deposit.html, +"dpd/energy (k)"_fix_dpd_energy.html, +"drag"_fix_drag.html, +"drude"_fix_drude.html, +"drude/transform/direct"_fix_drude_transform.html, +"drude/transform/reverse"_fix_drude_transform.html, +"dt/reset"_fix_dt_reset.html, +"edpd/source"_fix_dpd_source.html, +"efield"_fix_efield.html, +"ehex"_fix_ehex.html, +"enforce2d (k)"_fix_enforce2d.html, +"eos/cv"_fix_eos_cv.html, +"eos/table"_fix_eos_table.html, +"eos/table/rx (k)"_fix_eos_table_rx.html, +"evaporate"_fix_evaporate.html, +"external"_fix_external.html, +"filter/corotate"_fix_filter_corotate.html, +"flow/gauss"_fix_flow_gauss.html, +"freeze"_fix_freeze.html, +"gcmc"_fix_gcmc.html, +"gld"_fix_gld.html, +"gle"_fix_gle.html, +"gravity (o)"_fix_gravity.html, +"grem"_fix_grem.html, +"halt"_fix_halt.html, +"heat"_fix_heat.html, +"imd"_fix_imd.html, +"indent"_fix_indent.html, +"ipi"_fix_ipi.html, +"langevin (k)"_fix_langevin.html, +"langevin/drude"_fix_langevin_drude.html, +"langevin/eff"_fix_langevin_eff.html, +"langevin/spin"_fix_langevin_spin.html, +"latte"_fix_latte.html, +"lb/fluid"_fix_lb_fluid.html, +"lb/momentum"_fix_lb_momentum.html, +"lb/pc"_fix_lb_pc.html, +"lb/rigid/pc/sphere"_fix_lb_rigid_pc_sphere.html, +"lb/viscous"_fix_lb_viscous.html, +"lineforce"_fix_lineforce.html, +"manifoldforce"_fix_manifoldforce.html, +"meso"_fix_meso.html, +"meso/stationary"_fix_meso_stationary.html, +"momentum (k)"_fix_momentum.html, +"move"_fix_move.html, +"mscg"_fix_mscg.html, +"msst"_fix_msst.html, +"mvv/dpd"_fix_mvv_dpd.html, +"mvv/edpd"_fix_mvv_dpd.html, +"mvv/tdpd"_fix_mvv_dpd.html, +"neb"_fix_neb.html, +"nph (ko)"_fix_nh.html, +"nph/asphere (o)"_fix_nph_asphere.html, +"nph/body"_fix_nph_body.html, +"nph/eff"_fix_nh_eff.html, +"nph/sphere (o)"_fix_nph_sphere.html, +"nphug (o)"_fix_nphug.html, +"npt (kio)"_fix_nh.html, +"npt/asphere (o)"_fix_npt_asphere.html, +"npt/body"_fix_npt_body.html, +"npt/eff"_fix_nh_eff.html, +"npt/sphere (o)"_fix_npt_sphere.html, +"npt/uef"_fix_nh_uef.html, +"nve (kio)"_fix_nve.html, +"nve/asphere (i)"_fix_nve_asphere.html, +"nve/asphere/noforce"_fix_nve_asphere_noforce.html, +"nve/body"_fix_nve_body.html, +"nve/dot"_fix_nve_dot.html, +"nve/dotc/langevin"_fix_nve_dotc_langevin.html, +"nve/eff"_fix_nve_eff.html, +"nve/limit"_fix_nve_limit.html, +"nve/line"_fix_nve_line.html, +"nve/manifold/rattle"_fix_nve_manifold_rattle.html, +"nve/noforce"_fix_nve_noforce.html, +"nve/sphere (o)"_fix_nve_sphere.html, +"nve/spin"_fix_nve_spin.html, +"nve/tri"_fix_nve_tri.html, +"nvk"_fix_nvk.html, +"nvt (iko)"_fix_nh.html, +"nvt/asphere (o)"_fix_nvt_asphere.html, +"nvt/body"_fix_nvt_body.html, +"nvt/eff"_fix_nh_eff.html, +"nvt/manifold/rattle"_fix_nvt_manifold_rattle.html, +"nvt/sllod (io)"_fix_nvt_sllod.html, +"nvt/sllod/eff"_fix_nvt_sllod_eff.html, +"nvt/sphere (o)"_fix_nvt_sphere.html, +"nvt/uef"_fix_nh_uef.html, +"oneway"_fix_oneway.html, +"orient/bcc"_fix_orient.html, +"orient/fcc"_fix_orient.html, +"phonon"_fix_phonon.html, +"pimd"_fix_pimd.html, +"planeforce"_fix_planeforce.html, +"poems"_fix_poems.html, +"pour"_fix_pour.html, +"precession/spin"_fix_precession_spin.html, +"press/berendsen"_fix_press_berendsen.html, +"print"_fix_print.html, +"property/atom (k)"_fix_property_atom.html, +"python/invoke"_fix_python_invoke.html, +"python/move"_fix_python_move.html, +"qbmsst"_fix_qbmsst.html, +"qeq/comb (o)"_fix_qeq_comb.html, +"qeq/dynamic"_fix_qeq.html, +"qeq/fire"_fix_qeq.html, +"qeq/point"_fix_qeq.html, +"qeq/reax (ko)"_fix_qeq_reax.html, +"qeq/shielded"_fix_qeq.html, +"qeq/slater"_fix_qeq.html, +"qmmm"_fix_qmmm.html, +"qtb"_fix_qtb.html, +"rattle"_fix_shake.html, +"reax/bonds"_fix_reax_bonds.html, +"reax/c/bonds (k)"_fix_reax_bonds.html, +"reax/c/species (k)"_fix_reaxc_species.html, +"recenter"_fix_recenter.html, +"restrain"_fix_restrain.html, +"rhok"_fix_rhok.html, +"rigid (o)"_fix_rigid.html, +"rigid/nph (o)"_fix_rigid.html, +"rigid/npt (o)"_fix_rigid.html, +"rigid/nve (o)"_fix_rigid.html, +"rigid/nvt (o)"_fix_rigid.html, +"rigid/small (o)"_fix_rigid.html, +"rigid/small/nph"_fix_rigid.html, +"rigid/small/npt"_fix_rigid.html, +"rigid/small/nve"_fix_rigid.html, +"rigid/small/nvt"_fix_rigid.html, +"rx (k)"_fix_rx.html, +"saed/vtk"_fix_saed_vtk.html, +"setforce (k)"_fix_setforce.html, +"shake"_fix_shake.html, +"shardlow (k)"_fix_shardlow.html, +"smd"_fix_smd.html, +"smd/adjust/dt"_fix_smd_adjust_dt.html, +"smd/integrate/tlsph"_fix_smd_integrate_tlsph.html, +"smd/integrate/ulsph"_fix_smd_integrate_ulsph.html, +"smd/move/triangulated/surface"_fix_smd_move_triangulated_surface.html, +"smd/setvel"_fix_smd_setvel.html, +"smd/wall/surface"_fix_smd_wall_surface.html, +"spring"_fix_spring.html, +"spring/chunk"_fix_spring_chunk.html, +"spring/rg"_fix_spring_rg.html, +"spring/self"_fix_spring_self.html, +"srd"_fix_srd.html, +"store/force"_fix_store_force.html, +"store/state"_fix_store_state.html, +"tdpd/source"_fix_dpd_source.html, +"temp/berendsen"_fix_temp_berendsen.html, +"temp/csld"_fix_temp_csvr.html, +"temp/csvr"_fix_temp_csvr.html, +"temp/rescale"_fix_temp_rescale.html, +"temp/rescale/eff"_fix_temp_rescale_eff.html, +"tfmc"_fix_tfmc.html, +"thermal/conductivity"_fix_thermal_conductivity.html, +"ti/spring"_fix_ti_spring.html, +"tmd"_fix_tmd.html, +"ttm"_fix_ttm.html, +"ttm/mod"_fix_ttm.html, +"tune/kspace"_fix_tune_kspace.html, +"vector"_fix_vector.html, +"viscosity"_fix_viscosity.html, +"viscous"_fix_viscous.html, +"wall/body/polygon"_fix_wall_body_polygon.html, +"wall/body/polyhedron"_fix_wall_body_polyhedron.html, +"wall/colloid"_fix_wall.html, +"wall/ees"_fix_wall_ees.html, +"wall/gran"_fix_wall_gran.html, +"wall/gran/region"_fix_wall_gran_region.html, +"wall/harmonic"_fix_wall.html, +"wall/lj1043"_fix_wall.html, +"wall/lj126"_fix_wall.html, +"wall/lj93 (k)"_fix_wall.html, +"wall/piston"_fix_wall_piston.html, +"wall/reflect (k)"_fix_wall_reflect.html, +"wall/region"_fix_wall_region.html, +"wall/region/ees"_fix_wall_ees.html, +"wall/srd"_fix_wall_srd.html :tb(c=8,ea=c) diff --git a/doc/src/Commands_input.txt b/doc/src/Commands_input.txt new file mode 100644 index 0000000000..8b3dda741b --- /dev/null +++ b/doc/src/Commands_input.txt @@ -0,0 +1,60 @@ +"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +LAMMPS input scripts :h3 + +LAMMPS executes by reading commands from a input script (text file), +one line at a time. When the input script ends, LAMMPS exits. Each +command causes LAMMPS to take some action. It may set an internal +variable, read in a file, or run a simulation. Most commands have +default settings, which means you only need to use the command if you +wish to change the default. + +In many cases, the ordering of commands in an input script is not +important. However the following rules apply: + +(1) LAMMPS does not read your entire input script and then perform a +simulation with all the settings. Rather, the input script is read +one line at a time and each command takes effect when it is read. +Thus this sequence of commands: + +timestep 0.5 +run 100 +run 100 :pre + +does something different than this sequence: + +run 100 +timestep 0.5 +run 100 :pre + +In the first case, the specified timestep (0.5 fs) is used for two +simulations of 100 timesteps each. In the 2nd case, the default +timestep (1.0 fs) is used for the 1st 100 step simulation and a 0.5 fs +timestep is used for the 2nd one. + +(2) Some commands are only valid when they follow other commands. For +example you cannot set the temperature of a group of atoms until atoms +have been defined and a group command is used to define which atoms +belong to the group. + +(3) Sometimes command B will use values that can be set by command A. +This means command A must precede command B in the input script if it +is to have the desired effect. For example, the +"read_data"_read_data.html command initializes the system by setting +up the simulation box and assigning atoms to processors. If default +values are not desired, the "processors"_processors.html and +"boundary"_boundary.html commands need to be used before read_data to +tell LAMMPS how to map processors to the simulation box. + +Many input script errors are detected by LAMMPS and an ERROR or +WARNING message is printed. The "Errors"_Errors.html doc page gives +more information on what errors mean. The documentation for each +command lists restrictions on how the command can be used. + diff --git a/doc/src/Commands_kspace.txt b/doc/src/Commands_kspace.txt new file mode 100644 index 0000000000..d56b7fa767 --- /dev/null +++ b/doc/src/Commands_kspace.txt @@ -0,0 +1,37 @@ +"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands.html) + +:line + +"All commands"_Commands_all.html, +"Fix styles"_Commands_fix.html, +"Compute styles"_Commands_compute.html, +"Pair styles"_Commands_pair.html, +"Bond styles"_Commands_bond.html, +"Angle styles"_Commands_bond.html#angle, +"Dihedral styles"_Commands_bond.html#dihedral, +"Improper styles"_Commands_bond.html#improper, +"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c) + +KSpace solvers :h3 + +All LAMMPS "kspace_style"_kspace_style.html solvers. Some styles have +accelerated versions. This is indicated by additional letters in +parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = +OPT. + +"ewald (o)"_kspace_style.html, +"ewald/disp"_kspace_style.html, +"msm (o)"_kspace_style.html, +"msm/cg (o)"_kspace_style.html, +"pppm (gok)"_kspace_style.html, +"pppm/cg (o)"_kspace_style.html, +"pppm/disp (i)"_kspace_style.html, +"pppm/disp/tip4p"_kspace_style.html, +"pppm/stagger"_kspace_style.html, +"pppm/tip4p (o)"_kspace_style.html, +"scafacos"_kspace_style.html :tb(c=4,ea=c) diff --git a/doc/src/Commands_pair.txt b/doc/src/Commands_pair.txt new file mode 100644 index 0000000000..33890df1fe --- /dev/null +++ b/doc/src/Commands_pair.txt @@ -0,0 +1,232 @@ +"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +"All commands"_Commands_all.html, +"Fix styles"_Commands_fix.html, +"Compute styles"_Commands_compute.html, +"Pair styles"_Commands_pair.html, +"Bond styles"_Commands_bond.html, +"Angle styles"_Commands_bond.html#angle, +"Dihedral styles"_Commands_bond.html#dihedral, +"Improper styles"_Commands_bond.html#improper, +"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c) + +Pair_style potentials :h3 + +All LAMMPS "pair_style"_pair_style.html commands. Some styles have +accelerated versions. This is indicated by additional letters in +parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = +OPT. + +"none"_pair_none.html, +"zero"_pair_zero.html, +"hybrid"_pair_hybrid.html, +"hybrid/overlay (k)"_pair_hybrid.html :tb(c=4,ea=c) + +"adp (o)"_pair_adp.html, +"agni (o)"_pair_agni.html, +"airebo (oi)"_pair_airebo.html, +"airebo/morse (oi)"_pair_airebo.html, +"atm"_pair_atm.html, +"awpmd/cut"_pair_awpmd.html, +"beck (go)"_pair_beck.html, +"body/nparticle"_pair_body_nparticle.html, +"body/rounded/polygon"_pair_body_rounded_polygon.html, +"body/rounded/polyhedron"_pair_body_rounded_polyhedron.html, +"bop"_pair_bop.html, +"born (go)"_pair_born.html, +"born/coul/dsf"_pair_born.html, +"born/coul/dsf/cs"_pair_born.html, +"born/coul/long (go)"_pair_born.html, +"born/coul/long/cs"_pair_born.html, +"born/coul/msm (o)"_pair_born.html, +"born/coul/wolf (go)"_pair_born.html, +"born/coul/wolf/cs"_pair_born.html, +"brownian (o)"_pair_brownian.html, +"brownian/poly (o)"_pair_brownian.html, +"buck (giko)"_pair_buck.html, +"buck/coul/cut (giko)"_pair_buck.html, +"buck/coul/long (giko)"_pair_buck.html, +"buck/coul/long/cs"_pair_buck.html, +"buck/coul/msm (o)"_pair_buck.html, +"buck/long/coul/long (o)"_pair_buck_long.html, +"buck/mdf"_pair_mdf.html, +"colloid (go)"_pair_colloid.html, +"comb (o)"_pair_comb.html, +"comb3"_pair_comb.html, +"coul/cut (gko)"_pair_coul.html, +"coul/cut/soft (o)"_pair_lj_soft.html, +"coul/debye (gko)"_pair_coul.html, +"coul/diel (o)"_pair_coul_diel.html, +"coul/dsf (gko)"_pair_coul.html, +"coul/long (gko)"_pair_coul.html, +"coul/long/cs"_pair_coul.html, +"coul/long/soft (o)"_pair_lj_soft.html, +"coul/msm"_pair_coul.html, +"coul/shield"_pair_coul_shield.html, +"coul/streitz"_pair_coul.html, +"coul/wolf (ko)"_pair_coul.html, +"coul/wolf/cs"_pair_coul.html, +"dpd (gio)"_pair_dpd.html, +"dpd/fdt"_pair_dpd_fdt.html, +"dpd/fdt/energy (k)"_pair_dpd_fdt.html, +"dpd/tstat (go)"_pair_dpd.html, +"dsmc"_pair_dsmc.html, +"eam (gikot)"_pair_eam.html, +"eam/alloy (gikot)"_pair_eam.html, +"eam/cd (o)"_pair_eam.html, +"eam/fs (gikot)"_pair_eam.html, +"edip (o)"_pair_edip.html, +"edip/multi"_pair_edip.html, +"edpd"_pair_meso.html, +"eff/cut"_pair_eff.html, +"eim (o)"_pair_eim.html, +"exp6/rx (k)"_pair_exp6_rx.html, +"extep"_pair_extep.html, +"gauss (go)"_pair_gauss.html, +"gauss/cut"_pair_gauss.html, +"gayberne (gio)"_pair_gayberne.html, +"gran/hertz/history (o)"_pair_gran.html, +"gran/hooke (o)"_pair_gran.html, +"gran/hooke/history (o)"_pair_gran.html, +"gw"_pair_gw.html, +"gw/zbl"_pair_gw.html, +"hbond/dreiding/lj (o)"_pair_hbond_dreiding.html, +"hbond/dreiding/morse (o)"_pair_hbond_dreiding.html, +"ilp/graphene/hbn"_pair_ilp_graphene_hbn.html, +"kim"_pair_kim.html, +"kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html, +"kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html, +"lcbop"_pair_lcbop.html, +"lennard/mdf"_pair_mdf.html, +"line/lj"_pair_line_lj.html, +"list"_pair_list.html, +"lj/charmm/coul/charmm (iko)"_pair_charmm.html, +"lj/charmm/coul/charmm/implicit (ko)"_pair_charmm.html, +"lj/charmm/coul/long (giko)"_pair_charmm.html, +"lj/charmm/coul/long/soft (o)"_pair_charmm.html, +"lj/charmm/coul/msm"_pair_charmm.html, +"lj/charmmfsw/coul/charmmfsh"_pair_charmm.html, +"lj/charmmfsw/coul/long"_pair_charmm.html, +"lj/class2 (gko)"_pair_class2.html, +"lj/class2/coul/cut (ko)"_pair_class2.html, +"lj/class2/coul/long (gko)"_pair_class2.html, +"lj/cubic (go)"_pair_lj_cubic.html, +"lj/cut (gikot)"_pair_lj.html, +"lj/cut/coul/cut (gko)"_pair_lj.html, +"lj/cut/coul/cut/soft (o)"_pair_lj_soft.html, +"lj/cut/coul/debye (gko)"_pair_lj.html, +"lj/cut/coul/dsf (gko)"_pair_lj.html, +"lj/cut/coul/long (gikot)"_pair_lj.html, +"lj/cut/coul/long/cs"_pair_lj.html, +"lj/cut/coul/long/soft (o)"_pair_lj_soft.html, +"lj/cut/coul/msm (go)"_pair_lj.html, +"lj/cut/coul/wolf (o)"_pair_lj.html, +"lj/cut/dipole/cut (go)"_pair_dipole.html, +"lj/cut/dipole/long"_pair_dipole.html, +"lj/cut/dipole/sf (go)"_pair_dipole.html, +"lj/cut/soft (o)"_pair_lj_soft.html, +"lj/cut/thole/long (o)"_pair_thole.html, +"lj/cut/tip4p/cut (o)"_pair_lj.html, +"lj/cut/tip4p/long (ot)"_pair_lj.html, +"lj/cut/tip4p/long/soft (o)"_pair_lj_soft.html, +"lj/expand (gko)"_pair_lj_expand.html, +"lj/gromacs (gko)"_pair_gromacs.html, +"lj/gromacs/coul/gromacs (ko)"_pair_gromacs.html, +"lj/long/coul/long (io)"_pair_lj_long.html, +"lj/long/dipole/long"_pair_dipole.html, +"lj/long/tip4p/long"_pair_lj_long.html, +"lj/mdf"_pair_mdf.html, +"lj/sdk (gko)"_pair_sdk.html, +"lj/sdk/coul/long (go)"_pair_sdk.html, +"lj/sdk/coul/msm (o)"_pair_sdk.html, +"lj/smooth (o)"_pair_lj_smooth.html, +"lj/smooth/linear (o)"_pair_lj_smooth_linear.html, +"lj96/cut (go)"_pair_lj96.html, +"lubricate (o)"_pair_lubricate.html, +"lubricate/poly (o)"_pair_lubricate.html, +"lubricateU"_pair_lubricateU.html, +"lubricateU/poly"_pair_lubricateU.html, +"mdpd"_pair_meso.html, +"mdpd/rhosum"_pair_meso.html, +"meam"_pair_meam.html, +"meam/c"_pair_meam.html, +"meam/spline (o)"_pair_meam_spline.html, +"meam/sw/spline"_pair_meam_sw_spline.html, +"mgpt"_pair_mgpt.html, +"mie/cut (o)"_pair_mie.html, +"momb"_pair_momb.html, +"morse (gkot)"_pair_morse.html, +"morse/smooth/linear"_pair_morse.html, +"morse/soft"_pair_morse.html, +"multi/lucy"_pair_multi_lucy.html, +"multi/lucy/rx (k)"_pair_multi_lucy_rx.html, +"nb3b/harmonic (o)"_pair_nb3b_harmonic.html, +"nm/cut (o)"_pair_nm.html, +"nm/cut/coul/cut (o)"_pair_nm.html, +"nm/cut/coul/long (o)"_pair_nm.html, +"oxdna/coaxstk"_pair_oxdna.html, +"oxdna/excv"_pair_oxdna.html, +"oxdna/hbond"_pair_oxdna.html, +"oxdna/stk"_pair_oxdna.html, +"oxdna/xstk"_pair_oxdna.html, +"oxdna2/coaxstk"_pair_oxdna2.html, +"oxdna2/dh"_pair_oxdna2.html, +"oxdna2/excv"_pair_oxdna2.html, +"oxdna2/stk"_pair_oxdna2.html, +"peri/eps"_pair_peri.html, +"peri/lps (o)"_pair_peri.html, +"peri/pmb (o)"_pair_peri.html, +"peri/ves"_pair_peri.html, +"polymorphic"_pair_polymorphic.html, +"python"_pair_python.html, +"quip"_pair_quip.html, +"reax"_pair_reax.html, +"reax/c (ko)"_pair_reaxc.html, +"rebo (oi)"_pair_airebo.html, +"resquared (go)"_pair_resquared.html, +"smd/hertz"_pair_smd_hertz.html, +"smd/tlsph"_pair_smd_tlsph.html, +"smd/triangulated/surface"_pair_smd_triangulated_surface.html, +"smd/ulsph"_pair_smd_ulsph.html, +"smtbq"_pair_smtbq.html, +"snap (k)"_pair_snap.html, +"snap (k)"_pair_snap.html, +"soft (go)"_pair_soft.html, +"sph/heatconduction"_pair_sph_heatconduction.html, +"sph/idealgas"_pair_sph_idealgas.html, +"sph/lj"_pair_sph_lj.html, +"sph/rhosum"_pair_sph_rhosum.html, +"sph/taitwater"_pair_sph_taitwater.html, +"sph/taitwater/morris"_pair_sph_taitwater_morris.html, +"spin/dmi"_pair_spin_dmi.html, +"spin/exchange"_pair_spin_exchange.html, +"spin/magelec"_pair_spin_magelec.html, +"spin/neel"_pair_spin_neel.html, +"srp"_pair_srp.html, +"sw (giko)"_pair_sw.html, +"table (gko)"_pair_table.html, +"table/rx (k)"_pair_table_rx.html, +"tdpd"_pair_meso.html, +"tersoff (giko)"_pair_tersoff.html, +"tersoff/mod (gko)"_pair_tersoff_mod.html, +"tersoff/mod/c (o)"_pair_tersoff_mod.html, +"tersoff/table (o)"_pair_tersoff.html, +"tersoff/zbl (gko)"_pair_tersoff_zbl.html, +"thole"_pair_thole.html, +"tip4p/cut (o)"_pair_coul.html, +"tip4p/long (o)"_pair_coul.html, +"tip4p/long/soft (o)"_pair_lj_soft.html, +"tri/lj"_pair_tri_lj.html, +"ufm (got)"_pair_ufm.html, +"vashishta (ko)"_pair_vashishta.html, +"vashishta/table (o)"_pair_vashishta.html, +"yukawa (gok)"_pair_yukawa.html, +"yukawa/colloid (go)"_pair_yukawa_colloid.html, +"zbl (gok)"_pair_zbl.html :tb(c=4,ea=c) diff --git a/doc/src/Commands_parse.txt b/doc/src/Commands_parse.txt new file mode 100644 index 0000000000..1d7c754fa7 --- /dev/null +++ b/doc/src/Commands_parse.txt @@ -0,0 +1,136 @@ +"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Parsing rules for input scripts :h3 + +Each non-blank line in the input script is treated as a command. +LAMMPS commands are case sensitive. Command names are lower-case, as +are specified command arguments. Upper case letters may be used in +file names or user-chosen ID strings. + +Here are 6 rules for how each line in the input script is parsed by +LAMMPS: + +(1) If the last printable character on the line is a "&" character, +the command is assumed to continue on the next line. The next line is +concatenated to the previous line by removing the "&" character and +line break. This allows long commands to be continued across two or +more lines. See the discussion of triple quotes in (6) for how to +continue a command across multiple line without using "&" characters. + +(2) All characters from the first "#" character onward are treated as +comment and discarded. See an exception in (6). Note that a +comment after a trailing "&" character will prevent the command from +continuing on the next line. Also note that for multi-line commands a +single leading "#" will comment out the entire command. + +(3) The line is searched repeatedly for $ characters, which indicate +variables that are replaced with a text string. See an exception in +(6). + +If the $ is followed by curly brackets, then the variable name is the +text inside the curly brackets. If no curly brackets follow the $, +then the variable name is the single character immediately following +the $. Thus $\{myTemp\} and $x refer to variable names "myTemp" and +"x". + +How the variable is converted to a text string depends on what style +of variable it is; see the "variable"_variable.html doc page for details. +It can be a variable that stores multiple text strings, and return one +of them. The returned text string can be multiple "words" (space +separated) which will then be interpreted as multiple arguments in the +input command. The variable can also store a numeric formula which +will be evaluated and its numeric result returned as a string. + +As a special case, if the $ is followed by parenthesis, then the text +inside the parenthesis is treated as an "immediate" variable and +evaluated as an "equal-style variable"_variable.html. This is a way +to use numeric formulas in an input script without having to assign +them to variable names. For example, these 3 input script lines: + +variable X equal (xlo+xhi)/2+sqrt(v_area) +region 1 block $X 2 INF INF EDGE EDGE +variable X delete :pre + +can be replaced by + +region 1 block $((xlo+xhi)/2+sqrt(v_area)) 2 INF INF EDGE EDGE :pre + +so that you do not have to define (or discard) a temporary variable X. + +Additionally, the "immediate" variable expression may be followed by a +colon, followed by a C-style format string, e.g. ":%f" or ":%.10g". +The format string must be appropriate for a double-precision +floating-point value. The format string is used to output the result +of the variable expression evaluation. If a format string is not +specified a high-precision "%.20g" is used as the default. + +This can be useful for formatting print output to a desired precision: + +print "Final energy per atom: $(pe/atoms:%10.3f) eV/atom" :pre + +Note that neither the curly-bracket or immediate form of variables can +contain nested $ characters for other variables to substitute for. +Thus you cannot do this: + +variable a equal 2 +variable b2 equal 4 +print "B2 = $\{b$a\}" :pre + +Nor can you specify this $($x-1.0) for an immediate variable, but +you could use $(v_x-1.0), since the latter is valid syntax for an +"equal-style variable"_variable.html. + +See the "variable"_variable.html command for more details of how +strings are assigned to variables and evaluated, and how they can be +used in input script commands. + +(4) The line is broken into "words" separated by whitespace (tabs, +spaces). Note that words can thus contain letters, digits, +underscores, or punctuation characters. + +(5) The first word is the command name. All successive words in the +line are arguments. + +(6) If you want text with spaces to be treated as a single argument, +it can be enclosed in either single or double or triple quotes. A +long single argument enclosed in single or double quotes can span +multiple lines if the "&" character is used, as described above. When +the lines are concatenated together (and the "&" characters and line +breaks removed), the text will become a single line. If you want +multiple lines of an argument to retain their line breaks, the text +can be enclosed in triple quotes, in which case "&" characters are not +needed. For example: + +print "Volume = $v" +print 'Volume = $v' +if "$\{steps\} > 1000" then quit +variable a string "red green blue & + purple orange cyan" +print """ +System volume = $v +System temperature = $t +""" :pre + +In each case, the single, double, or triple quotes are removed when +the single argument they enclose is stored internally. + +See the "dump modify format"_dump_modify.html, "print"_print.html, +"if"_if.html, and "python"_python.html commands for examples. + +A "#" or "$" character that is between quotes will not be treated as a +comment indicator in (2) or substituted for as a variable in (3). + +NOTE: If the argument is itself a command that requires a quoted +argument (e.g. using a "print"_print.html command as part of an +"if"_if.html or "run every"_run.html command), then single, double, or +triple quotes can be nested in the usual manner. See the doc pages +for those commands for examples. Only one of level of nesting is +allowed, but that should be sufficient for most use cases. + diff --git a/doc/src/Commands_structure.txt b/doc/src/Commands_structure.txt new file mode 100644 index 0000000000..b5d2c7b07b --- /dev/null +++ b/doc/src/Commands_structure.txt @@ -0,0 +1,95 @@ +"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Input script structure :h3 + +This page describes the structure of a typical LAMMPS input script. +The examples directory in the LAMMPS distribution contains many sample +input scripts; it is discussed on the "Examples"_Examples.html doc +page. + +A LAMMPS input script typically has 4 parts: + +Initialization +Atom definition +Settings +Run a simulation :ol + +The last 2 parts can be repeated as many times as desired. I.e. run a +simulation, change some settings, run some more, etc. Each of the 4 +parts is now described in more detail. Remember that almost all +commands need only be used if a non-default value is desired. + +(1) Initialization + +Set parameters that need to be defined before atoms are created or +read-in from a file. + +The relevant commands are "units"_units.html, +"dimension"_dimension.html, "newton"_newton.html, +"processors"_processors.html, "boundary"_boundary.html, +"atom_style"_atom_style.html, "atom_modify"_atom_modify.html. + +If force-field parameters appear in the files that will be read, these +commands tell LAMMPS what kinds of force fields are being used: +"pair_style"_pair_style.html, "bond_style"_bond_style.html, +"angle_style"_angle_style.html, "dihedral_style"_dihedral_style.html, +"improper_style"_improper_style.html. + +(2) Atom definition + +There are 3 ways to define atoms in LAMMPS. Read them in from a data +or restart file via the "read_data"_read_data.html or +"read_restart"_read_restart.html commands. These files can contain +molecular topology information. Or create atoms on a lattice (with no +molecular topology), using these commands: "lattice"_lattice.html, +"region"_region.html, "create_box"_create_box.html, +"create_atoms"_create_atoms.html. The entire set of atoms can be +duplicated to make a larger simulation using the +"replicate"_replicate.html command. + +(3) Settings + +Once atoms and molecular topology are defined, a variety of settings +can be specified: force field coefficients, simulation parameters, +output options, etc. + +Force field coefficients are set by these commands (they can also be +set in the read-in files): "pair_coeff"_pair_coeff.html, +"bond_coeff"_bond_coeff.html, "angle_coeff"_angle_coeff.html, +"dihedral_coeff"_dihedral_coeff.html, +"improper_coeff"_improper_coeff.html, +"kspace_style"_kspace_style.html, "dielectric"_dielectric.html, +"special_bonds"_special_bonds.html. + +Various simulation parameters are set by these commands: +"neighbor"_neighbor.html, "neigh_modify"_neigh_modify.html, +"group"_group.html, "timestep"_timestep.html, +"reset_timestep"_reset_timestep.html, "run_style"_run_style.html, +"min_style"_min_style.html, "min_modify"_min_modify.html. + +Fixes impose a variety of boundary conditions, time integration, and +diagnostic options. The "fix"_fix.html command comes in many flavors. + +Various computations can be specified for execution during a +simulation using the "compute"_compute.html, +"compute_modify"_compute_modify.html, and "variable"_variable.html +commands. + +Output options are set by the "thermo"_thermo.html, "dump"_dump.html, +and "restart"_restart.html commands. + +(4) Run a simulation + +A molecular dynamics simulation is run using the "run"_run.html +command. Energy minimization (molecular statics) is performed using +the "minimize"_minimize.html command. A parallel tempering +(replica-exchange) simulation can be run using the +"temper"_temper.html command. + diff --git a/doc/src/Developer/developer.tex b/doc/src/Developer/developer.tex index 9d9a93a53d..8852f44168 100644 --- a/doc/src/Developer/developer.tex +++ b/doc/src/Developer/developer.tex @@ -476,7 +476,7 @@ is the name of the class. This code allows LAMMPS to find your fix when it parses input script. In addition, your fix header must be included in the file "style\_fix.h". In case if you use LAMMPS make, this file is generated automatically - all files starting with prefix -fix\_ are included, so call your header the same way. Otherwise, donÕt +fix\_ are included, so call your header the same way. Otherwise, don't forget to add your include into "style\_fix.h". Let's write a simple fix which will print average velocity at the end diff --git a/doc/src/Eqs/fix_integration_spin_stdecomposition.jpg b/doc/src/Eqs/fix_integration_spin_stdecomposition.jpg new file mode 100644 index 0000000000..9cd8214b4c Binary files /dev/null and b/doc/src/Eqs/fix_integration_spin_stdecomposition.jpg differ diff --git a/doc/src/Eqs/fix_integration_spin_stdecomposition.tex b/doc/src/Eqs/fix_integration_spin_stdecomposition.tex new file mode 100644 index 0000000000..8c7baf296d --- /dev/null +++ b/doc/src/Eqs/fix_integration_spin_stdecomposition.tex @@ -0,0 +1,40 @@ +\documentclass[preview]{standalone} +\usepackage{varwidth} +\usepackage[utf8x]{inputenc} +\usepackage{amsmath,amssymb,amsthm,bm,tikz} +\usetikzlibrary{automata,arrows,shapes,snakes} +\begin{document} +\begin{varwidth}{50in} +\begin{tikzpicture} + +%Global +\node (v1) at (0,6.0) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] { $\bm{v} \leftarrow \bm{v}+L_v.\Delta t/2$ }; +\node (s1) at (0,4.5) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] { $\bm{s} \leftarrow \bm{s}+L_s.\Delta t/2$ }; +\node (r) at (0,3.0) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] { $\bm{r} \leftarrow \bm{r}+L_r.\Delta t$ }; +\node (s2) at (0,1.5) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] { $\bm{s} \leftarrow \bm{s}+L_s.\Delta t/2$ }; +\node (v2) at (0,0.0) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] { $\bm{v} \leftarrow \bm{v}+L_v.\Delta t/2$ }; + +\draw[line width=2pt, ->] (v1) -- (s1); +\draw[line width=2pt, ->] (s1) -- (r); +\draw[line width=2pt, ->] (r) -- (s2); +\draw[line width=2pt, ->] (s2) -- (v2); + +%Spin +\node (s01) at (6,6.0) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] {$\bm{s}_0 \leftarrow \bm{s}_0+L_{s_0}.\Delta t/4$ }; +\node (sN1) at (6,4.5) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] {$\bm{s}_{\rm N-1}\leftarrow\bm{s}_{\rm N-1}+L_{s_{\rm N-1}}.\Delta t/4$}; +\node (sN) at (6,3.0) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] {$\bm{s}_{\rm N} \leftarrow \bm{s}_{\rm N}+L_{s_{\rm N}}.\Delta t/2$ }; +\node (sN2) at (6,1.5) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] {$\bm{s}_{\rm N-1}\leftarrow\bm{s}_{\rm N-1}+L_{s_{\rm N-1}}.\Delta t/4$}; +\node (s02) at (6,0.0) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] {$\bm{s}_0 \leftarrow \bm{s}_0+L_{s_0}.\Delta t/4$ }; + +\draw[line width=2pt,dashed, ->] (s01) -- (sN1); +\draw[line width=2pt, ->] (sN1) -- (sN); +\draw[line width=2pt, ->] (sN) -- (sN2); +\draw[line width=2pt,dashed, ->] (sN2) -- (s02); + +%from Global to Spin +\draw[line width=2pt, dashed, ->] (s1) -- (s01.west); +\draw[line width=2pt, dashed, ->] (s1) -- (s02.west); + +\end{tikzpicture} +\end{varwidth} +\end{document} diff --git a/doc/src/Eqs/fix_langevin_spin_sLLG.jpg b/doc/src/Eqs/fix_langevin_spin_sLLG.jpg new file mode 100644 index 0000000000..f83aadd9eb Binary files /dev/null and b/doc/src/Eqs/fix_langevin_spin_sLLG.jpg differ diff --git a/doc/src/Eqs/fix_langevin_spin_sLLG.tex b/doc/src/Eqs/fix_langevin_spin_sLLG.tex new file mode 100644 index 0000000000..346dde9cec --- /dev/null +++ b/doc/src/Eqs/fix_langevin_spin_sLLG.tex @@ -0,0 +1,14 @@ +\documentclass[preview]{standalone} +\usepackage{varwidth} +\usepackage[utf8x]{inputenc} +\usepackage{amsmath, amssymb, graphics, setspace} + +\begin{document} +\begin{varwidth}{50in} + \begin{equation} + \frac{d \vec{s}_{i}}{dt} = \frac{1}{\left(1+\lambda^2 \right)} \left( \left( + \vec{\omega}_{i} +\vec{\eta} \right) \times \vec{s}_{i} + \lambda\, \vec{s}_{i} + \times\left( \vec{\omega}_{i} \times\vec{s}_{i} \right) \right), \nonumber + \end{equation} +\end{varwidth} +\end{document} diff --git a/doc/src/Eqs/force_spin_aniso.jpg b/doc/src/Eqs/force_spin_aniso.jpg new file mode 100644 index 0000000000..8bc9d7421c Binary files /dev/null and b/doc/src/Eqs/force_spin_aniso.jpg differ diff --git a/doc/src/Eqs/force_spin_aniso.tex b/doc/src/Eqs/force_spin_aniso.tex new file mode 100644 index 0000000000..d6abfd580d --- /dev/null +++ b/doc/src/Eqs/force_spin_aniso.tex @@ -0,0 +1,11 @@ +\documentclass[preview]{standalone} +\usepackage{varwidth} +\usepackage[utf8x]{inputenc} +\usepackage{amsmath,amssymb,amsthm,bm} +\begin{document} +\begin{varwidth}{50in} + \begin{equation} + \bm{H}_{aniso} = -\sum_{{ i}=1}^{N} K_{an}(\bm{r}_{i})\, \left( \vec{s}_{i} \cdot \vec{n}_{i} \right)^2, \nonumber + \end{equation} +\end{varwidth} +\end{document} diff --git a/doc/src/Eqs/force_spin_zeeman.jpg b/doc/src/Eqs/force_spin_zeeman.jpg new file mode 100644 index 0000000000..14fb5500cf Binary files /dev/null and b/doc/src/Eqs/force_spin_zeeman.jpg differ diff --git a/doc/src/Eqs/force_spin_zeeman.tex b/doc/src/Eqs/force_spin_zeeman.tex new file mode 100644 index 0000000000..d623ef85ae --- /dev/null +++ b/doc/src/Eqs/force_spin_zeeman.tex @@ -0,0 +1,11 @@ +\documentclass[preview]{standalone} +\usepackage{varwidth} +\usepackage[utf8x]{inputenc} +\usepackage{amsmath,amssymb,amsthm,bm} +\begin{document} +\begin{varwidth}{50in} + \begin{equation} + \bm{H}_{zeeman} = -\mu_{B}\mu_0\sum_{i=0}^{N}g_{i} \vec{s}_{i} \cdot \vec{H}_{ext} \nonumber + \end{equation} +\end{varwidth} +\end{document} diff --git a/doc/src/Eqs/pair_atm.jpg b/doc/src/Eqs/pair_atm.jpg new file mode 100644 index 0000000000..d2e6d704e9 Binary files /dev/null and b/doc/src/Eqs/pair_atm.jpg differ diff --git a/doc/src/Eqs/pair_atm.tex b/doc/src/Eqs/pair_atm.tex new file mode 100644 index 0000000000..fce1db99b8 --- /dev/null +++ b/doc/src/Eqs/pair_atm.tex @@ -0,0 +1,9 @@ +\documentclass[12pt]{article} + +\begin{document} + +\begin{equation} +E=\nu\frac{1+3\cos\gamma_1\cos\gamma_2\cos\gamma_3}{r_{12}^3r_{23}^3r_{31}^3} +\end{equation} + +\end{document} diff --git a/doc/src/Eqs/pair_body_rounded.jpg b/doc/src/Eqs/pair_body_rounded.jpg new file mode 100644 index 0000000000..e7136ddd20 Binary files /dev/null and b/doc/src/Eqs/pair_body_rounded.jpg differ diff --git a/doc/src/Eqs/pair_body_rounded.tex b/doc/src/Eqs/pair_body_rounded.tex new file mode 100644 index 0000000000..54e095340f --- /dev/null +++ b/doc/src/Eqs/pair_body_rounded.tex @@ -0,0 +1,13 @@ +\documentstyle[12pt]{article} + +\begin{document} + +\begin{eqnarray*} + F_n &=& k_n \delta_n - c_n v_n, \qquad \delta_n \le 0 \\ + &=& -k_{na} \delta_n - c_n v_n, \qquad 0 < \delta_n \le r_c \\ + &=& 0 \qquad \qquad \qquad \qquad \delta_n > r_c \\ + F_t &=& \mu k_n \delta_n - c_t v_t, \qquad \delta_n \le 0 \\ + &=& 0 \qquad \qquad \qquad \qquad \delta_n > 0 +\end{eqnarray*} + +\end{document} diff --git a/doc/src/Eqs/pair_entropy.jpg b/doc/src/Eqs/pair_entropy.jpg new file mode 100644 index 0000000000..44161e6aa0 Binary files /dev/null and b/doc/src/Eqs/pair_entropy.jpg differ diff --git a/doc/src/Eqs/pair_entropy.tex b/doc/src/Eqs/pair_entropy.tex new file mode 100644 index 0000000000..304c9d6138 --- /dev/null +++ b/doc/src/Eqs/pair_entropy.tex @@ -0,0 +1,10 @@ +\documentclass[12pt]{article} + +\begin{document} +\thispagestyle{empty} + +$$ + s_S^i=-2\pi\rho k_B \int\limits_0^{r_m} \left [ g(r) \ln g(r) - g(r) + 1 \right ] r^2 dr , +$$ + +\end{document} diff --git a/doc/src/Eqs/pair_entropy2.jpg b/doc/src/Eqs/pair_entropy2.jpg new file mode 100644 index 0000000000..db3dcb0ca7 Binary files /dev/null and b/doc/src/Eqs/pair_entropy2.jpg differ diff --git a/doc/src/Eqs/pair_entropy2.tex b/doc/src/Eqs/pair_entropy2.tex new file mode 100644 index 0000000000..c91004840f --- /dev/null +++ b/doc/src/Eqs/pair_entropy2.tex @@ -0,0 +1,10 @@ +\documentclass[12pt]{article} + +\begin{document} +\thispagestyle{empty} + +$$ + g_m^i(r) = \frac{1}{4 \pi \rho r^2} \sum\limits_{j} \frac{1}{\sqrt{2 \pi \sigma^2}} e^{-(r-r_{ij})^2/(2\sigma^2)} , +$$ + +\end{document} diff --git a/doc/src/Eqs/pair_entropy3.jpg b/doc/src/Eqs/pair_entropy3.jpg new file mode 100644 index 0000000000..0d5e0025b7 Binary files /dev/null and b/doc/src/Eqs/pair_entropy3.jpg differ diff --git a/doc/src/Eqs/pair_entropy3.tex b/doc/src/Eqs/pair_entropy3.tex new file mode 100644 index 0000000000..b0b3c76358 --- /dev/null +++ b/doc/src/Eqs/pair_entropy3.tex @@ -0,0 +1,10 @@ +\documentclass[12pt]{article} + +\begin{document} +\thispagestyle{empty} + +$$ + \bar{s}_S^i = \frac{\sum_j s_S^j + s_S^i}{N + 1} , +$$ + +\end{document} diff --git a/doc/src/Eqs/pair_spin_dmi_forces.jpg b/doc/src/Eqs/pair_spin_dmi_forces.jpg new file mode 100644 index 0000000000..fba6a91cbf Binary files /dev/null and b/doc/src/Eqs/pair_spin_dmi_forces.jpg differ diff --git a/doc/src/Eqs/pair_spin_dmi_forces.tex b/doc/src/Eqs/pair_spin_dmi_forces.tex new file mode 100644 index 0000000000..1c0c246db4 --- /dev/null +++ b/doc/src/Eqs/pair_spin_dmi_forces.tex @@ -0,0 +1,14 @@ +\documentclass[preview]{standalone} +\usepackage{varwidth} +\usepackage[utf8x]{inputenc} +\usepackage{amsmath,amssymb,amsthm,bm} +\begin{document} +\begin{varwidth}{50in} + \begin{equation} + \vec{\omega}_i = -\frac{1}{\hbar} \sum_{j}^{Neighb} \vec{s}_{j}\times \left(\vec{e}_{ij}\times \vec{D} \right) + ~~{\rm and}~~ + \vec{F}_i = -\sum_{j}^{Neighb} \frac{1}{r_{ij}} \vec{D} \times \left( \vec{s}_{i}\times \vec{s}_{j} \right) + , \nonumber + \end{equation} +\end{varwidth} +\end{document} diff --git a/doc/src/Eqs/pair_spin_dmi_interaction.jpg b/doc/src/Eqs/pair_spin_dmi_interaction.jpg new file mode 100644 index 0000000000..3eb24c67e3 Binary files /dev/null and b/doc/src/Eqs/pair_spin_dmi_interaction.jpg differ diff --git a/doc/src/Eqs/pair_spin_dmi_interaction.tex b/doc/src/Eqs/pair_spin_dmi_interaction.tex new file mode 100644 index 0000000000..79f63a333a --- /dev/null +++ b/doc/src/Eqs/pair_spin_dmi_interaction.tex @@ -0,0 +1,16 @@ +\documentclass[preview]{standalone} +\usepackage{varwidth} +\usepackage[utf8x]{inputenc} +\usepackage{amsmath,amssymb,amsthm,bm} +\begin{document} +\begin{varwidth}{50in} + \begin{equation} + \bm{H}_{dm} = \sum_{{ i,j}=1,i\neq j}^{N} + \left( \vec{e}_{ij} \times \vec{D} \right) + \cdot\left(\vec{s}_{i}\times \vec{s}_{j}\right), + \nonumber + \end{equation} +\end{varwidth} +\end{document} + \vec{D}\left(r_{ij}\right) + {\rm ~and~} \vec{D}\left(r_{ij}\right) = \vec{e}_{ij} \times \vec{D} diff --git a/doc/src/Eqs/pair_spin_exchange_forces.jpg b/doc/src/Eqs/pair_spin_exchange_forces.jpg new file mode 100644 index 0000000000..b312a9ccda Binary files /dev/null and b/doc/src/Eqs/pair_spin_exchange_forces.jpg differ diff --git a/doc/src/Eqs/pair_spin_exchange_forces.tex b/doc/src/Eqs/pair_spin_exchange_forces.tex new file mode 100644 index 0000000000..ac5ef682f3 --- /dev/null +++ b/doc/src/Eqs/pair_spin_exchange_forces.tex @@ -0,0 +1,16 @@ +\documentclass[preview]{standalone} +\usepackage{varwidth} +\usepackage[utf8x]{inputenc} +\usepackage{amsmath,amssymb,amsthm,bm} +\begin{document} +\begin{varwidth}{50in} + \begin{equation} + \vec{\omega}_{i} = \frac{1}{\hbar} \sum_{j}^{Neighb} {J} + \left(r_{ij} \right)\,\vec{s}_{j} + ~~{\rm and}~~ + \vec{F}_{i} = \sum_{j}^{Neighb} \frac{\partial {J} \left(r_{ij} \right)}{ + \partial r_{ij}} \left( \vec{s}_{i}\cdot \vec{s}_{j} \right) \vec{e}_{ij} + \nonumber + \end{equation} +\end{varwidth} +\end{document} diff --git a/doc/src/Eqs/pair_spin_exchange_function.jpg b/doc/src/Eqs/pair_spin_exchange_function.jpg new file mode 100644 index 0000000000..d9a7ed3ce0 Binary files /dev/null and b/doc/src/Eqs/pair_spin_exchange_function.jpg differ diff --git a/doc/src/Eqs/pair_spin_exchange_function.tex b/doc/src/Eqs/pair_spin_exchange_function.tex new file mode 100644 index 0000000000..054c6992f0 --- /dev/null +++ b/doc/src/Eqs/pair_spin_exchange_function.tex @@ -0,0 +1,13 @@ +\documentclass[preview]{standalone} +\usepackage{varwidth} +\usepackage[utf8x]{inputenc} +\usepackage{amsmath, amssymb, graphics, setspace} + +\begin{document} +\begin{varwidth}{50in} + \begin{equation} + {J}\left( r_{ij} \right) = 4 a \left( \frac{r_{ij}}{d} \right)^2 \left( 1 - b \left( \frac{r_{ij}}{d} \right)^2 \right) e^{-\left( \frac{r_{ij}}{d} + \right)^2 }\Theta (R_c - r_{ij}) \nonumber + \end{equation} +\end{varwidth} +\end{document} diff --git a/doc/src/Eqs/pair_spin_exchange_interaction.jpg b/doc/src/Eqs/pair_spin_exchange_interaction.jpg new file mode 100644 index 0000000000..c70d8a6554 Binary files /dev/null and b/doc/src/Eqs/pair_spin_exchange_interaction.jpg differ diff --git a/doc/src/Eqs/pair_spin_exchange_interaction.tex b/doc/src/Eqs/pair_spin_exchange_interaction.tex new file mode 100644 index 0000000000..f20b3e5740 --- /dev/null +++ b/doc/src/Eqs/pair_spin_exchange_interaction.tex @@ -0,0 +1,11 @@ +\documentclass[preview]{standalone} +\usepackage{varwidth} +\usepackage[utf8x]{inputenc} +\usepackage{amsmath,amssymb,amsthm,bm} +\begin{document} +\begin{varwidth}{50in} + \begin{equation} + \bm{H}_{ex} ~=~ -\sum_{i,j,i\neq j}^{N} {J} \left(r_{ij} \right)\, \vec{s}_{i}\cdot \vec{s}_{j} \nonumber + \end{equation} +\end{varwidth} +\end{document} diff --git a/doc/src/Eqs/pair_spin_me_forces.jpg b/doc/src/Eqs/pair_spin_me_forces.jpg new file mode 100644 index 0000000000..d9ae440fb5 Binary files /dev/null and b/doc/src/Eqs/pair_spin_me_forces.jpg differ diff --git a/doc/src/Eqs/pair_spin_me_forces.tex b/doc/src/Eqs/pair_spin_me_forces.tex new file mode 100644 index 0000000000..f9462fc3d5 --- /dev/null +++ b/doc/src/Eqs/pair_spin_me_forces.tex @@ -0,0 +1,13 @@ +\documentclass[preview]{standalone} +\usepackage{varwidth} +\usepackage[utf8x]{inputenc} +\usepackage{amsmath,amssymb,amsthm,bm} +\begin{document} +\begin{varwidth}{50in} + \begin{equation} + \vec{F}^{i} = -\sum_{j}^{Neighbor} \left( \vec{s}_{i}\times \vec{s}_{j} \right) + \times \vec{E} ~~{\rm and}~~ \vec{\omega}^{i} = -\frac{1}{\hbar} + \sum_{j}^{Neighbor} \vec{s}_j \times \left(\vec{E}\times r_{ij} \right),\nonumber + \end{equation} +\end{varwidth} +\end{document} diff --git a/doc/src/Eqs/pair_spin_me_interaction.jpg b/doc/src/Eqs/pair_spin_me_interaction.jpg new file mode 100644 index 0000000000..8ecddc9592 Binary files /dev/null and b/doc/src/Eqs/pair_spin_me_interaction.jpg differ diff --git a/doc/src/Eqs/pair_spin_me_interaction.tex b/doc/src/Eqs/pair_spin_me_interaction.tex new file mode 100644 index 0000000000..64501e9c2f --- /dev/null +++ b/doc/src/Eqs/pair_spin_me_interaction.tex @@ -0,0 +1,12 @@ +\documentclass[preview]{standalone} +\usepackage{varwidth} +\usepackage[utf8x]{inputenc} +\usepackage{amsmath,amssymb,amsthm,bm} +\begin{document} +\begin{varwidth}{50in} + \begin{equation} + \vec{\omega}_i = -\frac{1}{\hbar} \sum_{j}^{Neighb} \vec{s}_{j}\times\vec{D}(r_{ij}) ~~{\rm and}~~ + \vec{F}_i = -\sum_{j}^{Neighb} \frac{\partial D(r_{ij})}{\partial r_{ij}} \left(\vec{s}_{i}\times \vec{s}_{j} \right) \cdot \vec{r}_{ij}, \nonumber + \end{equation} +\end{varwidth} +\end{document} diff --git a/doc/src/Eqs/pair_spin_neel_functions.jpg b/doc/src/Eqs/pair_spin_neel_functions.jpg new file mode 100644 index 0000000000..57023634bf Binary files /dev/null and b/doc/src/Eqs/pair_spin_neel_functions.jpg differ diff --git a/doc/src/Eqs/pair_spin_neel_functions.tex b/doc/src/Eqs/pair_spin_neel_functions.tex new file mode 100644 index 0000000000..ead5a2b87a --- /dev/null +++ b/doc/src/Eqs/pair_spin_neel_functions.tex @@ -0,0 +1,13 @@ +\documentclass[preview]{standalone} +\usepackage{varwidth} +\usepackage[utf8x]{inputenc} +\usepackage{amsmath,amssymb,amsthm,bm} +\begin{document} +\begin{varwidth}{50in} + \begin{eqnarray} + g_1(r_{ij}) &=& g(r_{ij}) + \frac{12}{35} q(r_{ij}) \nonumber \\ + q_1(r_{ij}) &=& \frac{9}{5} q(r_{ij}) \nonumber \\ + q_2(r_{ij}) &=& - \frac{2}{5} q(r_{ij}) \nonumber + \end{eqnarray} +\end{varwidth} +\end{document} diff --git a/doc/src/Eqs/pair_spin_neel_interaction.jpg b/doc/src/Eqs/pair_spin_neel_interaction.jpg new file mode 100644 index 0000000000..c30600d840 Binary files /dev/null and b/doc/src/Eqs/pair_spin_neel_interaction.jpg differ diff --git a/doc/src/Eqs/pair_spin_neel_interaction.tex b/doc/src/Eqs/pair_spin_neel_interaction.tex new file mode 100644 index 0000000000..8b4ac33e73 --- /dev/null +++ b/doc/src/Eqs/pair_spin_neel_interaction.tex @@ -0,0 +1,16 @@ +\documentclass[preview]{standalone} +\usepackage{varwidth} +\usepackage[utf8x]{inputenc} +\usepackage{amsmath,amssymb,amsthm,bm} +\begin{document} +\begin{varwidth}{50in} + \begin{equation} + \mathcal{H}_{N\acute{e}el}=-\sum_{{ i,j=1,i\neq j}}^N g_1(r_{ij})\left(({\bm e}_{ij}\cdot {\bm s}_{i})({\bm e}_{ij} + \cdot {\bm s}_{j})-\frac{{\bm s}_{i}\cdot{\bm s}_{j}}{3} \right) + +q_1(r_{ij})\left( ({\bm e}_{ij}\cdot {\bm s}_{i})^2 -\frac{{\bm s}_{i}\cdot{\bm s}_{j}}{3}\right) + \left( ({\bm e}_{ij}\cdot {\bm s}_{i})^2 -\frac{{\bm s}_{i}\cdot{\bm s}_{j}}{3} \right) + + q_2(r_{ij}) \Big( ({\bm e}_{ij}\cdot {\bm s}_{i}) ({\bm e}_{ij}\cdot {\bm s}_{j})^3 + ({\bm e}_{ij}\cdot + {\bm s}_{j}) ({\bm e}_{ij}\cdot {\bm s}_{i})^3\Big) \nonumber + \end{equation} +\end{varwidth} +\end{document} diff --git a/doc/src/Errors.txt b/doc/src/Errors.txt new file mode 100644 index 0000000000..10f84874a3 --- /dev/null +++ b/doc/src/Errors.txt @@ -0,0 +1,38 @@ +"Previous Section"_Python_head.html - "LAMMPS WWW Site"_lws - +"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next +Section"_Manual.html :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Errors :h2 + +These doc pages describe the errors you can encounter when using +LAMMPS. The common problems include conceptual issues. The messages +and warnings doc pages give complete lists of all the messages the +code may generate (except those generated by USER packages), with +additional details for many of them. + + + + + +"Common problems"_Errors_common.html +"Reporting bugs"_Errors_bugs.html +"Error messages"_Errors_messages.html +"Warning messages"_Errors_warnings.html :all(b) + + diff --git a/doc/src/Errors_bugs.txt b/doc/src/Errors_bugs.txt new file mode 100644 index 0000000000..4a8e62e775 --- /dev/null +++ b/doc/src/Errors_bugs.txt @@ -0,0 +1,35 @@ +"Higher level section"_Errors.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Reporting bugs :h3 + +If you are confident that you have found a bug in LAMMPS, follow these +steps. + +Check the "New features and bug +fixes"_http://lammps.sandia.gov/bug.html section of the "LAMMPS WWW +site"_lws to see if the bug has already been reported or fixed or the +"Unfixed bug"_http://lammps.sandia.gov/unbug.html to see if a fix is +pending. + +Check the "mailing list"_http://lammps.sandia.gov/mail.html to see if +it has been discussed before. + +If not, send an email to the mailing list describing the problem with +any ideas you have as to what is causing it or where in the code the +problem might be. The developers will ask for more info if needed, +such as an input script or data files. + +The most useful thing you can do to help us fix the bug is to isolate +the problem. Run it on the smallest number of atoms and fewest number +of processors and with the simplest input script that reproduces the +bug and try to identify what command or combination of commands is +causing the problem. + +NOTE: this page needs to have GitHub issues info added diff --git a/doc/src/Errors_common.txt b/doc/src/Errors_common.txt new file mode 100644 index 0000000000..651040ebc9 --- /dev/null +++ b/doc/src/Errors_common.txt @@ -0,0 +1,123 @@ +"Higher level section"_Errors.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Common problems :h3 + +If two LAMMPS runs do not produce the exact same answer on different +machines or different numbers of processors, this is typically not a +bug. In theory you should get identical answers on any number of +processors and on any machine. In practice, numerical round-off can +cause slight differences and eventual divergence of molecular dynamics +phase space trajectories within a few 100s or few 1000s of timesteps. +However, the statistical properties of the two runs (e.g. average +energy or temperature) should still be the same. + +If the "velocity"_velocity.html command is used to set initial atom +velocities, a particular atom can be assigned a different velocity +when the problem is run on a different number of processors or on +different machines. If this happens, the phase space trajectories of +the two simulations will rapidly diverge. See the discussion of the +{loop} option in the "velocity"_velocity.html command for details and +options that avoid this issue. + +Similarly, the "create_atoms"_create_atoms.html command generates a +lattice of atoms. For the same physical system, the ordering and +numbering of atoms by atom ID may be different depending on the number +of processors. + +Some commands use random number generators which may be setup to +produce different random number streams on each processor and hence +will produce different effects when run on different numbers of +processors. A commonly-used example is the "fix +langevin"_fix_langevin.html command for thermostatting. + +A LAMMPS simulation typically has two stages, setup and run. Most +LAMMPS errors are detected at setup time; others like a bond +stretching too far may not occur until the middle of a run. + +LAMMPS tries to flag errors and print informative error messages so +you can fix the problem. For most errors it will also print the last +input script command that it was processing. Of course, LAMMPS cannot +figure out your physics or numerical mistakes, like choosing too big a +timestep, specifying erroneous force field coefficients, or putting 2 +atoms on top of each other! If you run into errors that LAMMPS +doesn't catch that you think it should flag, please send an email to +the "developers"_http://lammps.sandia.gov/authors.html. + +If you get an error message about an invalid command in your input +script, you can determine what command is causing the problem by +looking in the log.lammps file or using the "echo command"_echo.html +to see it on the screen. If you get an error like "Invalid ... +style", with ... being fix, compute, pair, etc, it means that you +mistyped the style name or that the command is part of an optional +package which was not compiled into your executable. The list of +available styles in your executable can be listed by using "the -h +command-line swith"_Run_options.html. The installation and +compilation of optional packages is explained on the "Build +packages"_Build_package.html doc page. + +For a given command, LAMMPS expects certain arguments in a specified +order. If you mess this up, LAMMPS will often flag the error, but it +may also simply read a bogus argument and assign a value that is +valid, but not what you wanted. E.g. trying to read the string "abc" +as an integer value of 0. Careful reading of the associated doc page +for the command should allow you to fix these problems. In most cases, +where LAMMPS expects to read a number, either integer or floating point, +it performs a stringent test on whether the provided input actually +is an integer or floating-point number, respectively, and reject the +input with an error message (for instance, when an integer is required, +but a floating-point number 1.0 is provided): + +ERROR: Expected integer parameter in input script or data file :pre + +Some commands allow for using variable references in place of numeric +constants so that the value can be evaluated and may change over the +course of a run. This is typically done with the syntax {v_name} for a +parameter, where name is the name of the variable. On the other hand, +immediate variable expansion with the syntax ${name} is performed while +reading the input and before parsing commands, + +NOTE: Using a variable reference (i.e. {v_name}) is only allowed if +the documentation of the corresponding command explicitly says it is. + +Generally, LAMMPS will print a message to the screen and logfile and +exit gracefully when it encounters a fatal error. Sometimes it will +print a WARNING to the screen and logfile and continue on; you can +decide if the WARNING is important or not. A WARNING message that is +generated in the middle of a run is only printed to the screen, not to +the logfile, to avoid cluttering up thermodynamic output. If LAMMPS +crashes or hangs without spitting out an error message first then it +could be a bug (see "this section"_Errors_bugs.html) or one of the following +cases: + +LAMMPS runs in the available memory a processor allows to be +allocated. Most reasonable MD runs are compute limited, not memory +limited, so this shouldn't be a bottleneck on most platforms. Almost +all large memory allocations in the code are done via C-style malloc's +which will generate an error message if you run out of memory. +Smaller chunks of memory are allocated via C++ "new" statements. If +you are unlucky you could run out of memory just when one of these +small requests is made, in which case the code will crash or hang (in +parallel), since LAMMPS doesn't trap on those errors. + +Illegal arithmetic can cause LAMMPS to run slow or crash. This is +typically due to invalid physics and numerics that your simulation is +computing. If you see wild thermodynamic values or NaN values in your +LAMMPS output, something is wrong with your simulation. If you +suspect this is happening, it is a good idea to print out +thermodynamic info frequently (e.g. every timestep) via the +"thermo"_thermo.html so you can monitor what is happening. +Visualizing the atom movement is also a good idea to insure your model +is behaving as you expect. + +In parallel, one way LAMMPS can hang is due to how different MPI +implementations handle buffering of messages. If the code hangs +without an error message, it may be that you need to specify an MPI +setting or two (usually via an environment variable) to enable +buffering or boost the sizes of messages that can be buffered. diff --git a/doc/src/Section_errors.txt b/doc/src/Errors_messages.txt similarity index 87% rename from doc/src/Section_errors.txt rename to doc/src/Errors_messages.txt index 95482b06dc..a74182967c 100644 --- a/doc/src/Section_errors.txt +++ b/doc/src/Errors_messages.txt @@ -1,192 +1,33 @@ -"Previous Section"_Section_python.html - "LAMMPS WWW Site"_lws - -"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next -Section"_Section_history.html :c +"Higher level section"_Errors.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line -12. Errors :h2 +Error messages :h3 -This section describes the errors you can encounter when using LAMMPS, -either conceptually, or as printed out by the program. +This is an alphabetic list of the ERROR messages LAMMPS prints out and +the reason why. If the explanation here is not sufficient, the +documentation for the offending command may help. Error messages also +list the source file and line number where the error was generated. +For example, a message like this: -12.1 "Common problems"_#err_1 -12.2 "Reporting bugs"_#err_2 -12.3 "Error & warning messages"_#err_3 :all(b) - -:line -:line - -12.1 Common problems :link(err_1),h4 - -If two LAMMPS runs do not produce the exact same answer on different -machines or different numbers of processors, this is typically not a -bug. In theory you should get identical answers on any number of -processors and on any machine. In practice, numerical round-off can -cause slight differences and eventual divergence of molecular dynamics -phase space trajectories within a few 100s or few 1000s of timesteps. -However, the statistical properties of the two runs (e.g. average -energy or temperature) should still be the same. - -If the "velocity"_velocity.html command is used to set initial atom -velocities, a particular atom can be assigned a different velocity -when the problem is run on a different number of processors or on -different machines. If this happens, the phase space trajectories of -the two simulations will rapidly diverge. See the discussion of the -{loop} option in the "velocity"_velocity.html command for details and -options that avoid this issue. - -Similarly, the "create_atoms"_create_atoms.html command generates a -lattice of atoms. For the same physical system, the ordering and -numbering of atoms by atom ID may be different depending on the number -of processors. - -Some commands use random number generators which may be setup to -produce different random number streams on each processor and hence -will produce different effects when run on different numbers of -processors. A commonly-used example is the "fix -langevin"_fix_langevin.html command for thermostatting. - -A LAMMPS simulation typically has two stages, setup and run. Most -LAMMPS errors are detected at setup time; others like a bond -stretching too far may not occur until the middle of a run. - -LAMMPS tries to flag errors and print informative error messages so -you can fix the problem. For most errors it will also print the last -input script command that it was processing. Of course, LAMMPS cannot -figure out your physics or numerical mistakes, like choosing too big a -timestep, specifying erroneous force field coefficients, or putting 2 -atoms on top of each other! If you run into errors that LAMMPS -doesn't catch that you think it should flag, please send an email to -the "developers"_http://lammps.sandia.gov/authors.html. - -If you get an error message about an invalid command in your input -script, you can determine what command is causing the problem by -looking in the log.lammps file or using the "echo command"_echo.html -to see it on the screen. If you get an error like "Invalid ... -style", with ... being fix, compute, pair, etc, it means that you -mistyped the style name or that the command is part of an optional -package which was not compiled into your executable. The list of -available styles in your executable can be listed by using "the -h -command-line argument"_Section_start.html#start_6. The installation -and compilation of optional packages is explained in the "installation -instructions"_Section_start.html#start_3. - -For a given command, LAMMPS expects certain arguments in a specified -order. If you mess this up, LAMMPS will often flag the error, but it -may also simply read a bogus argument and assign a value that is -valid, but not what you wanted. E.g. trying to read the string "abc" -as an integer value of 0. Careful reading of the associated doc page -for the command should allow you to fix these problems. In most cases, -where LAMMPS expects to read a number, either integer or floating point, -it performs a stringent test on whether the provided input actually -is an integer or floating-point number, respectively, and reject the -input with an error message (for instance, when an integer is required, -but a floating-point number 1.0 is provided): - -ERROR: Expected integer parameter in input script or data file :pre - -Some commands allow for using variable references in place of numeric -constants so that the value can be evaluated and may change over the -course of a run. This is typically done with the syntax {v_name} for a -parameter, where name is the name of the variable. On the other hand, -immediate variable expansion with the syntax ${name} is performed while -reading the input and before parsing commands, - -NOTE: Using a variable reference (i.e. {v_name}) is only allowed if -the documentation of the corresponding command explicitly says it is. - -Generally, LAMMPS will print a message to the screen and logfile and -exit gracefully when it encounters a fatal error. Sometimes it will -print a WARNING to the screen and logfile and continue on; you can -decide if the WARNING is important or not. A WARNING message that is -generated in the middle of a run is only printed to the screen, not to -the logfile, to avoid cluttering up thermodynamic output. If LAMMPS -crashes or hangs without spitting out an error message first then it -could be a bug (see "this section"_#err_2) or one of the following -cases: - -LAMMPS runs in the available memory a processor allows to be -allocated. Most reasonable MD runs are compute limited, not memory -limited, so this shouldn't be a bottleneck on most platforms. Almost -all large memory allocations in the code are done via C-style malloc's -which will generate an error message if you run out of memory. -Smaller chunks of memory are allocated via C++ "new" statements. If -you are unlucky you could run out of memory just when one of these -small requests is made, in which case the code will crash or hang (in -parallel), since LAMMPS doesn't trap on those errors. - -Illegal arithmetic can cause LAMMPS to run slow or crash. This is -typically due to invalid physics and numerics that your simulation is -computing. If you see wild thermodynamic values or NaN values in your -LAMMPS output, something is wrong with your simulation. If you -suspect this is happening, it is a good idea to print out -thermodynamic info frequently (e.g. every timestep) via the -"thermo"_thermo.html so you can monitor what is happening. -Visualizing the atom movement is also a good idea to insure your model -is behaving as you expect. - -In parallel, one way LAMMPS can hang is due to how different MPI -implementations handle buffering of messages. If the code hangs -without an error message, it may be that you need to specify an MPI -setting or two (usually via an environment variable) to enable -buffering or boost the sizes of messages that can be buffered. - -:line - -12.2 Reporting bugs :link(err_2),h4 - -If you are confident that you have found a bug in LAMMPS, follow these -steps. - -Check the "New features and bug -fixes"_http://lammps.sandia.gov/bug.html section of the "LAMMPS WWW -site"_lws to see if the bug has already been reported or fixed or the -"Unfixed bug"_http://lammps.sandia.gov/unbug.html to see if a fix is -pending. - -Check the "mailing list"_http://lammps.sandia.gov/mail.html -to see if it has been discussed before. - -If not, send an email to the mailing list describing the problem with -any ideas you have as to what is causing it or where in the code the -problem might be. The developers will ask for more info if needed, -such as an input script or data files. - -The most useful thing you can do to help us fix the bug is to isolate -the problem. Run it on the smallest number of atoms and fewest number -of processors and with the simplest input script that reproduces the -bug and try to identify what command or combination of commands is -causing the problem. - -As a last resort, you can send an email directly to the -"developers"_http://lammps.sandia.gov/authors.html. - -:line - -12.3 Error & warning messages :h3,link(err_3) - -These are two alphabetic lists of the "ERROR"_#error and -"WARNING"_#warn messages LAMMPS prints out and the reason why. If the -explanation here is not sufficient, the documentation for the -offending command may help. -Error and warning messages also list the source file and line number -where the error was generated. For example, this message - -ERROR: Illegal velocity command (velocity.cpp:78) +ERROR: Illegal velocity command (velocity.cpp:78) :pre means that line #78 in the file src/velocity.cpp generated the error. Looking in the source code may help you figure out what went wrong. Note that error messages from "user-contributed -packages"_Section_start.html#start_3 are not listed here. If such an -error occurs and is not self-explanatory, you'll need to look in the -source code or contact the author of the package. +packages"_Packages_user.html are not listed here. If such an error +occurs and is not self-explanatory, you'll need to look in the source +code or contact the author of the package. -Errors: :h3,link(error) +Doc page with "WARNING messages"_Errors_warnings.html + +:line :dlb @@ -803,13 +644,6 @@ lo value must be less than the hi value for all 3 dimensions. :dd The box command cannot be used after a read_data, read_restart, or create_box command. :dd -{BUG: restartinfo=1 but no restart support in pair style} :dt - -The pair style has a bug, where it does not support reading -and writing information to a restart file, but does not set -the member variable restartinfo to 0 as required in that case. :dd - - {CPU neighbor lists must be used for ellipsoid/sphere mix.} :dt When using Gay-Berne or RE-squared pair styles with both ellipsoidal and @@ -909,7 +743,7 @@ Self-explanatory. :dd Self-explanatory. :dd -{Cannot (yet) use single precision with MSM (remove -DFFT_SINGLE from Makefile and recompile)} :dt +{Cannot (yet) use single precision with MSM (remove -DFFT_SINGLE from Makefile and re-compile)} :dt Single precision cannot be used with MSM. :dd @@ -5244,7 +5078,7 @@ Self-explanatory. :dd Occurs when number of neighbor atoms for an atom increased too much during a run. Increase SAFE_ZONE and MIN_CAP in fix_qeq.h and -recompile. :dd +re-compile. :dd {Fix qeq/point requires atom attribute q} :dt @@ -5258,7 +5092,7 @@ Self-explanatory. :dd Occurs when number of neighbor atoms for an atom increased too much during a run. Increase SAFE_ZONE and MIN_CAP in fix_qeq.h and -recompile. :dd +re-compile. :dd {Fix qeq/shielded requires atom attribute q} :dt @@ -5276,7 +5110,7 @@ Self-explanatory. :dd Occurs when number of neighbor atoms for an atom increased too much during a run. Increase SAFE_ZONE and MIN_CAP in fix_qeq.h and -recompile. :dd +re-compile. :dd {Fix qeq/slater requires atom attribute q} :dt @@ -5707,7 +5541,7 @@ See the package gpu command. :dd {GPUs are requested but Kokkos has not been compiled for CUDA} :dt -Recompile Kokkos with CUDA support to use GPUs. :dd +Re-compile Kokkos with CUDA support to use GPUs. :dd {Ghost velocity forward comm not yet implemented with Kokkos} :dt @@ -8077,8 +7911,8 @@ Atom IDs must be positive integers. :dd {One or more atom IDs is too big} :dt The limit on atom IDs is set by the SMALLBIG, BIGBIG, SMALLSMALL -setting in your Makefile. See Section_start 2.2 of the manual for -more details. :dd +setting in your LAMMPS build. See the "Build +settings"_Build_settings.html doc page for more info. :dd {One or more atom IDs is zero} :dt @@ -11003,904 +10837,3 @@ Self-explanatory. :dd Self-explanatory. :dd :dle - -Warnings: :h3,link(warn) - -:dlb - -{Adjusting Coulombic cutoff for MSM, new cutoff = %g} :dt - -The adjust/cutoff command is turned on and the Coulombic cutoff has been -adjusted to match the user-specified accuracy. :dd - -{Angle atoms missing at step %ld} :dt - -One or more of 3 atoms needed to compute a particular angle are -missing on this processor. Typically this is because the pairwise -cutoff is set too short or the angle has blown apart and an atom is -too far away. :dd - -{Angle style in data file differs from currently defined angle style} :dt - -Self-explanatory. :dd - -{Atom style in data file differs from currently defined atom style} :dt - -Self-explanatory. :dd - -{Bond atom missing in box size check} :dt - -The 2nd atoms needed to compute a particular bond is missing on this -processor. Typically this is because the pairwise cutoff is set too -short or the bond has blown apart and an atom is too far away. :dd - -{Bond atom missing in image check} :dt - -The 2nd atom in a particular bond is missing on this processor. -Typically this is because the pairwise cutoff is set too short or the -bond has blown apart and an atom is too far away. :dd - -{Bond atoms missing at step %ld} :dt - -The 2nd atom needed to compute a particular bond is missing on this -processor. Typically this is because the pairwise cutoff is set too -short or the bond has blown apart and an atom is too far away. :dd - -{Bond style in data file differs from currently defined bond style} :dt - -Self-explanatory. :dd - -{Bond/angle/dihedral extent > half of periodic box length} :dt - -This is a restriction because LAMMPS can be confused about which image -of an atom in the bonded interaction is the correct one to use. -"Extent" in this context means the maximum end-to-end length of the -bond/angle/dihedral. LAMMPS computes this by taking the maximum bond -length, multiplying by the number of bonds in the interaction (e.g. 3 -for a dihedral) and adding a small amount of stretch. :dd - -{Both groups in compute group/group have a net charge; the Kspace boundary correction to energy will be non-zero} :dt - -Self-explanatory. :dd - -{Calling write_dump before a full system init.} :dt - -The write_dump command is used before the system has been fully -initialized as part of a 'run' or 'minimize' command. Not all dump -styles and features are fully supported at this point and thus the -command may fail or produce incomplete or incorrect output. Insert -a "run 0" command, if a full system init is required. :dd - -{Cannot count rigid body degrees-of-freedom before bodies are fully initialized} :dt - -This means the temperature associated with the rigid bodies may be -incorrect on this timestep. :dd - -{Cannot count rigid body degrees-of-freedom before bodies are initialized} :dt - -This means the temperature associated with the rigid bodies may be -incorrect on this timestep. :dd - -{Cannot include log terms without 1/r terms; setting flagHI to 1} :dt - -Self-explanatory. :dd - -{Cannot include log terms without 1/r terms; setting flagHI to 1.} :dt - -Self-explanatory. :dd - -{Charges are set, but coulombic solver is not used} :dt - -Self-explanatory. :dd - -{Charges did not converge at step %ld: %lg} :dt - -Self-explanatory. :dd - -{Communication cutoff is too small for SNAP micro load balancing, increased to %lf} :dt - -Self-explanatory. :dd - -{Compute cna/atom cutoff may be too large to find ghost atom neighbors} :dt - -The neighbor cutoff used may not encompass enough ghost atoms -to perform this operation correctly. :dd - -{Computing temperature of portions of rigid bodies} :dt - -The group defined by the temperature compute does not encompass all -the atoms in one or more rigid bodies, so the change in -degrees-of-freedom for the atoms in those partial rigid bodies will -not be accounted for. :dd - -{Create_bonds max distance > minimum neighbor cutoff} :dt - -This means atom pairs for some atom types may not be in the neighbor -list and thus no bond can be created between them. :dd - -{Delete_atoms cutoff > minimum neighbor cutoff} :dt - -This means atom pairs for some atom types may not be in the neighbor -list and thus an atom in that pair cannot be deleted. :dd - -{Dihedral atoms missing at step %ld} :dt - -One or more of 4 atoms needed to compute a particular dihedral are -missing on this processor. Typically this is because the pairwise -cutoff is set too short or the dihedral has blown apart and an atom is -too far away. :dd - -{Dihedral problem} :dt - -Conformation of the 4 listed dihedral atoms is extreme; you may want -to check your simulation geometry. :dd - -{Dihedral problem: %d %ld %d %d %d %d} :dt - -Conformation of the 4 listed dihedral atoms is extreme; you may want -to check your simulation geometry. :dd - -{Dihedral style in data file differs from currently defined dihedral style} :dt - -Self-explanatory. :dd - -{Dump dcd/xtc timestamp may be wrong with fix dt/reset} :dt - -If the fix changes the timestep, the dump dcd file will not -reflect the change. :dd - -{Energy due to X extra global DOFs will be included in minimizer energies} :dt - -When using fixes like box/relax, the potential energy used by the minimizer -is augmented by an additional energy provided by the fix. Thus the printed -converged energy may be different from the total potential energy. :dd - -{Energy tally does not account for 'zero yes'} :dt - -The energy removed by using the 'zero yes' flag is not accounted -for in the energy tally and thus energy conservation cannot be -monitored in this case. :dd - -{Estimated error in splitting of dispersion coeffs is %g} :dt - -Error is greater than 0.0001 percent. :dd - -{Ewald/disp Newton solver failed, using old method to estimate g_ewald} :dt - -Self-explanatory. Choosing a different cutoff value may help. :dd - -{FENE bond too long} :dt - -A FENE bond has stretched dangerously far. It's interaction strength -will be truncated to attempt to prevent the bond from blowing up. :dd - -{FENE bond too long: %ld %d %d %g} :dt - -A FENE bond has stretched dangerously far. It's interaction strength -will be truncated to attempt to prevent the bond from blowing up. :dd - -{FENE bond too long: %ld %g} :dt - -A FENE bond has stretched dangerously far. It's interaction strength -will be truncated to attempt to prevent the bond from blowing up. :dd - -{Fix SRD walls overlap but fix srd overlap not set} :dt - -You likely want to set this in your input script. :dd - -{Fix bond/swap will ignore defined angles} :dt - -See the doc page for fix bond/swap for more info on this -restriction. :dd - -{Fix deposit near setting < possible overlap separation %g} :dt - -This test is performed for finite size particles with a diameter, not -for point particles. The near setting is smaller than the particle -diameter which can lead to overlaps. :dd - -{Fix evaporate may delete atom with non-zero molecule ID} :dt - -This is probably an error, since you should not delete only one atom -of a molecule. :dd - -{Fix gcmc using full_energy option} :dt - -Fix gcmc has automatically turned on the full_energy option since it -is required for systems like the one specified by the user. User input -included one or more of the following: kspace, triclinic, a hybrid -pair style, an eam pair style, or no "single" function for the pair -style. :dd - -{Fix property/atom mol or charge w/out ghost communication} :dt - -A model typically needs these properties defined for ghost atoms. :dd - -{Fix qeq CG convergence failed (%g) after %d iterations at %ld step} :dt - -Self-explanatory. :dd - -{Fix qeq has non-zero lower Taper radius cutoff} :dt - -Absolute value must be <= 0.01. :dd - -{Fix qeq has very low Taper radius cutoff} :dt - -Value should typically be >= 5.0. :dd - -{Fix qeq/dynamic tolerance may be too small for damped dynamics} :dt - -Self-explanatory. :dd - -{Fix qeq/fire tolerance may be too small for damped fires} :dt - -Self-explanatory. :dd - -{Fix rattle should come after all other integration fixes} :dt - -This fix is designed to work after all other integration fixes change -atom positions. Thus it should be the last integration fix specified. -If not, it will not satisfy the desired constraints as well as it -otherwise would. :dd - -{Fix recenter should come after all other integration fixes} :dt - -Other fixes may change the position of the center-of-mass, so -fix recenter should come last. :dd - -{Fix srd SRD moves may trigger frequent reneighboring} :dt - -This is because the SRD particles may move long distances. :dd - -{Fix srd grid size > 1/4 of big particle diameter} :dt - -This may cause accuracy problems. :dd - -{Fix srd particle moved outside valid domain} :dt - -This may indicate a problem with your simulation parameters. :dd - -{Fix srd particles may move > big particle diameter} :dt - -This may cause accuracy problems. :dd - -{Fix srd viscosity < 0.0 due to low SRD density} :dt - -This may cause accuracy problems. :dd - -{Fix thermal/conductivity comes before fix ave/spatial} :dt - -The order of these 2 fixes in your input script is such that fix -thermal/conductivity comes first. If you are using fix ave/spatial to -measure the temperature profile induced by fix viscosity, then this -may cause a glitch in the profile since you are averaging immediately -after swaps have occurred. Flipping the order of the 2 fixes -typically helps. :dd - -{Fix viscosity comes before fix ave/spatial} :dt - -The order of these 2 fixes in your input script is such that -fix viscosity comes first. If you are using fix ave/spatial -to measure the velocity profile induced by fix viscosity, then -this may cause a glitch in the profile since you are averaging -immediately after swaps have occurred. Flipping the order -of the 2 fixes typically helps. :dd - -{Fixes cannot send data in Kokkos communication, switching to classic communication} :dt - -This is current restriction with Kokkos. :dd - -{For better accuracy use 'pair_modify table 0'} :dt - -The user-specified force accuracy cannot be achieved unless the table -feature is disabled by using 'pair_modify table 0'. :dd - -{Geometric mixing assumed for 1/r^6 coefficients} :dt - -Self-explanatory. :dd - -{Group for fix_modify temp != fix group} :dt - -The fix_modify command is specifying a temperature computation that -computes a temperature on a different group of atoms than the fix -itself operates on. This is probably not what you want to do. :dd - -{H matrix size has been exceeded: m_fill=%d H.m=%d\n} :dt - -This is the size of the matrix. :dd - -{Ignoring unknown or incorrect info command flag} :dt - -Self-explanatory. An unknown argument was given to the info command. -Compare your input with the documentation. :dd - -{Improper atoms missing at step %ld} :dt - -One or more of 4 atoms needed to compute a particular improper are -missing on this processor. Typically this is because the pairwise -cutoff is set too short or the improper has blown apart and an atom is -too far away. :dd - -{Improper problem: %d %ld %d %d %d %d} :dt - -Conformation of the 4 listed improper atoms is extreme; you may want -to check your simulation geometry. :dd - -{Improper style in data file differs from currently defined improper style} :dt - -Self-explanatory. :dd - -{Inconsistent image flags} :dt - -The image flags for a pair on bonded atoms appear to be inconsistent. -Inconsistent means that when the coordinates of the two atoms are -unwrapped using the image flags, the two atoms are far apart. -Specifically they are further apart than half a periodic box length. -Or they are more than a box length apart in a non-periodic dimension. -This is usually due to the initial data file not having correct image -flags for the 2 atoms in a bond that straddles a periodic boundary. -They should be different by 1 in that case. This is a warning because -inconsistent image flags will not cause problems for dynamics or most -LAMMPS simulations. However they can cause problems when such atoms -are used with the fix rigid or replicate commands. Note that if you -have an infinite periodic crystal with bonds then it is impossible to -have fully consistent image flags, since some bonds will cross -periodic boundaries and connect two atoms with the same image -flag. :dd - -{KIM Model does not provide 'energy'; Potential energy will be zero} :dt - -Self-explanatory. :dd - -{KIM Model does not provide 'forces'; Forces will be zero} :dt - -Self-explanatory. :dd - -{KIM Model does not provide 'particleEnergy'; energy per atom will be zero} :dt - -Self-explanatory. :dd - -{KIM Model does not provide 'particleVirial'; virial per atom will be zero} :dt - -Self-explanatory. :dd - -{Kspace_modify slab param < 2.0 may cause unphysical behavior} :dt - -The kspace_modify slab parameter should be larger to insure periodic -grids padded with empty space do not overlap. :dd - -{Less insertions than requested} :dt - -The fix pour command was unsuccessful at finding open space -for as many particles as it tried to insert. :dd - -{Library error in lammps_gather_atoms} :dt - -This library function cannot be used if atom IDs are not defined -or are not consecutively numbered. :dd - -{Library error in lammps_scatter_atoms} :dt - -This library function cannot be used if atom IDs are not defined or -are not consecutively numbered, or if no atom map is defined. See the -atom_modify command for details about atom maps. :dd - -{Lost atoms via change_box: original %ld current %ld} :dt - -The command options you have used caused atoms to be lost. :dd - -{Lost atoms via displace_atoms: original %ld current %ld} :dt - -The command options you have used caused atoms to be lost. :dd - -{Lost atoms: original %ld current %ld} :dt - -Lost atoms are checked for each time thermo output is done. See the -thermo_modify lost command for options. Lost atoms usually indicate -bad dynamics, e.g. atoms have been blown far out of the simulation -box, or moved further than one processor's sub-domain away before -reneighboring. :dd - -{MSM mesh too small, increasing to 2 points in each direction} :dt - -Self-explanatory. :dd - -{Mismatch between velocity and compute groups} :dt - -The temperature computation used by the velocity command will not be -on the same group of atoms that velocities are being set for. :dd - -{Mixing forced for lj coefficients} :dt - -Self-explanatory. :dd - -{Molecule attributes do not match system attributes} :dt - -An attribute is specified (e.g. diameter, charge) that is -not defined for the specified atom style. :dd - -{Molecule has bond topology but no special bond settings} :dt - -This means the bonded atoms will not be excluded in pair-wise -interactions. :dd - -{Molecule template for create_atoms has multiple molecules} :dt - -The create_atoms command will only create molecules of a single type, -i.e. the first molecule in the template. :dd - -{Molecule template for fix gcmc has multiple molecules} :dt - -The fix gcmc command will only create molecules of a single type, -i.e. the first molecule in the template. :dd - -{Molecule template for fix shake has multiple molecules} :dt - -The fix shake command will only recognize molecules of a single -type, i.e. the first molecule in the template. :dd - -{More than one compute centro/atom} :dt - -It is not efficient to use compute centro/atom more than once. :dd - -{More than one compute cluster/atom} :dt - -It is not efficient to use compute cluster/atom more than once. :dd - -{More than one compute cna/atom defined} :dt - -It is not efficient to use compute cna/atom more than once. :dd - -{More than one compute contact/atom} :dt - -It is not efficient to use compute contact/atom more than once. :dd - -{More than one compute coord/atom} :dt - -It is not efficient to use compute coord/atom more than once. :dd - -{More than one compute damage/atom} :dt - -It is not efficient to use compute ke/atom more than once. :dd - -{More than one compute dilatation/atom} :dt - -Self-explanatory. :dd - -{More than one compute erotate/sphere/atom} :dt - -It is not efficient to use compute erorate/sphere/atom more than once. :dd - -{More than one compute hexorder/atom} :dt - -It is not efficient to use compute hexorder/atom more than once. :dd - -{More than one compute ke/atom} :dt - -It is not efficient to use compute ke/atom more than once. :dd - -{More than one compute orientorder/atom} :dt - -It is not efficient to use compute orientorder/atom more than once. :dd - -{More than one compute plasticity/atom} :dt - -Self-explanatory. :dd - -{More than one compute sna/atom} :dt - -Self-explanatory. :dd - -{More than one compute snad/atom} :dt - -Self-explanatory. :dd - -{More than one compute snav/atom} :dt - -Self-explanatory. :dd - -{More than one fix poems} :dt - -It is not efficient to use fix poems more than once. :dd - -{More than one fix rigid} :dt - -It is not efficient to use fix rigid more than once. :dd - -{Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies} :dt - -This is because excluding specific pair interactions also excludes -them from long-range interactions which may not be the desired effect. -The special_bonds command handles this consistently by insuring -excluded (or weighted) 1-2, 1-3, 1-4 interactions are treated -consistently by both the short-range pair style and the long-range -solver. This is not done for exclusions of charged atom pairs via the -neigh_modify exclude command. :dd - -{New thermo_style command, previous thermo_modify settings will be lost} :dt - -If a thermo_style command is used after a thermo_modify command, the -settings changed by the thermo_modify command will be reset to their -default values. This is because the thermo_modify command acts on -the currently defined thermo style, and a thermo_style command creates -a new style. :dd - -{No Kspace calculation with verlet/split} :dt - -The 2nd partition performs a kspace calculation so the kspace_style -command must be used. :dd - -{No automatic unit conversion to XTC file format conventions possible for units lj} :dt - -This means no scaling will be performed. :dd - -{No fixes defined, atoms won't move} :dt - -If you are not using a fix like nve, nvt, npt then atom velocities and -coordinates will not be updated during timestepping. :dd - -{No joints between rigid bodies, use fix rigid instead} :dt - -The bodies defined by fix poems are not connected by joints. POEMS -will integrate the body motion, but it would be more efficient to use -fix rigid. :dd - -{Not using real units with pair reax} :dt - -This is most likely an error, unless you have created your own ReaxFF -parameter file in a different set of units. :dd - -{Number of MSM mesh points changed to be a multiple of 2} :dt - -MSM requires that the number of grid points in each direction be a multiple -of two and the number of grid points in one or more directions have been -adjusted to meet this requirement. :dd - -{OMP_NUM_THREADS environment is not set.} :dt - -This environment variable must be set appropriately to use the -USER-OMP package. :dd - -{One or more atoms are time integrated more than once} :dt - -This is probably an error since you typically do not want to -advance the positions or velocities of an atom more than once -per timestep. :dd - -{One or more chunks do not contain all atoms in molecule} :dt - -This may not be what you intended. :dd - -{One or more dynamic groups may not be updated at correct point in timestep} :dt - -If there are other fixes that act immediately after the initial stage -of time integration within a timestep (i.e. after atoms move), then -the command that sets up the dynamic group should appear after those -fixes. This will insure that dynamic group assignments are made -after all atoms have moved. :dd - -{One or more respa levels compute no forces} :dt - -This is computationally inefficient. :dd - -{Pair COMB charge %.10f with force %.10f hit max barrier} :dt - -Something is possibly wrong with your model. :dd - -{Pair COMB charge %.10f with force %.10f hit min barrier} :dt - -Something is possibly wrong with your model. :dd - -{Pair brownian needs newton pair on for momentum conservation} :dt - -Self-explanatory. :dd - -{Pair dpd needs newton pair on for momentum conservation} :dt - -Self-explanatory. :dd - -{Pair dsmc: num_of_collisions > number_of_A} :dt - -Collision model in DSMC is breaking down. :dd - -{Pair dsmc: num_of_collisions > number_of_B} :dt - -Collision model in DSMC is breaking down. :dd - -{Pair style in data file differs from currently defined pair style} :dt - -Self-explanatory. :dd - -{Particle deposition was unsuccessful} :dt - -The fix deposit command was not able to insert as many atoms as -needed. The requested volume fraction may be too high, or other atoms -may be in the insertion region. :dd - -{Proc sub-domain size < neighbor skin, could lead to lost atoms} :dt - -The decomposition of the physical domain (likely due to load -balancing) has led to a processor's sub-domain being smaller than the -neighbor skin in one or more dimensions. Since reneighboring is -triggered by atoms moving the skin distance, this may lead to lost -atoms, if an atom moves all the way across a neighboring processor's -sub-domain before reneighboring is triggered. :dd - -{Reducing PPPM order b/c stencil extends beyond nearest neighbor processor} :dt - -This may lead to a larger grid than desired. See the kspace_modify overlap -command to prevent changing of the PPPM order. :dd - -{Reducing PPPMDisp Coulomb order b/c stencil extends beyond neighbor processor} :dt - -This may lead to a larger grid than desired. See the kspace_modify overlap -command to prevent changing of the PPPM order. :dd - -{Reducing PPPMDisp dispersion order b/c stencil extends beyond neighbor processor} :dt - -This may lead to a larger grid than desired. See the kspace_modify overlap -command to prevent changing of the PPPM order. :dd - -{Replacing a fix, but new group != old group} :dt - -The ID and style of a fix match for a fix you are changing with a fix -command, but the new group you are specifying does not match the old -group. :dd - -{Replicating in a non-periodic dimension} :dt - -The parameters for a replicate command will cause a non-periodic -dimension to be replicated; this may cause unwanted behavior. :dd - -{Resetting reneighboring criteria during PRD} :dt - -A PRD simulation requires that neigh_modify settings be delay = 0, -every = 1, check = yes. Since these settings were not in place, -LAMMPS changed them and will restore them to their original values -after the PRD simulation. :dd - -{Resetting reneighboring criteria during TAD} :dt - -A TAD simulation requires that neigh_modify settings be delay = 0, -every = 1, check = yes. Since these settings were not in place, -LAMMPS changed them and will restore them to their original values -after the PRD simulation. :dd - -{Resetting reneighboring criteria during minimization} :dt - -Minimization requires that neigh_modify settings be delay = 0, every = -1, check = yes. Since these settings were not in place, LAMMPS -changed them and will restore them to their original values after the -minimization. :dd - -{Restart file used different # of processors} :dt - -The restart file was written out by a LAMMPS simulation running on a -different number of processors. Due to round-off, the trajectories of -your restarted simulation may diverge a little more quickly than if -you ran on the same # of processors. :dd - -{Restart file used different 3d processor grid} :dt - -The restart file was written out by a LAMMPS simulation running on a -different 3d grid of processors. Due to round-off, the trajectories -of your restarted simulation may diverge a little more quickly than if -you ran on the same # of processors. :dd - -{Restart file used different boundary settings, using restart file values} :dt - -Your input script cannot change these restart file settings. :dd - -{Restart file used different newton bond setting, using restart file value} :dt - -The restart file value will override the setting in the input script. :dd - -{Restart file used different newton pair setting, using input script value} :dt - -The input script value will override the setting in the restart file. :dd - -{Restrain problem: %d %ld %d %d %d %d} :dt - -Conformation of the 4 listed dihedral atoms is extreme; you may want -to check your simulation geometry. :dd - -{Running PRD with only one replica} :dt - -This is allowed, but you will get no parallel speed-up. :dd - -{SRD bin shifting turned on due to small lamda} :dt - -This is done to try to preserve accuracy. :dd - -{SRD bin size for fix srd differs from user request} :dt - -Fix SRD had to adjust the bin size to fit the simulation box. See the -cubic keyword if you want this message to be an error vs warning. :dd - -{SRD bins for fix srd are not cubic enough} :dt - -The bin shape is not within tolerance of cubic. See the cubic -keyword if you want this message to be an error vs warning. :dd - -{SRD particle %d started inside big particle %d on step %ld bounce %d} :dt - -See the inside keyword if you want this message to be an error vs -warning. :dd - -{SRD particle %d started inside wall %d on step %ld bounce %d} :dt - -See the inside keyword if you want this message to be an error vs -warning. :dd - -{Shake determinant < 0.0} :dt - -The determinant of the quadratic equation being solved for a single -cluster specified by the fix shake command is numerically suspect. LAMMPS -will set it to 0.0 and continue. :dd - -{Shell command '%s' failed with error '%s'} :dt - -Self-explanatory. :dd - -{Shell command returned with non-zero status} :dt - -This may indicate the shell command did not operate as expected. :dd - -{Should not allow rigid bodies to bounce off relecting walls} :dt - -LAMMPS allows this, but their dynamics are not computed correctly. :dd - -{Should not use fix nve/limit with fix shake or fix rattle} :dt - -This will lead to invalid constraint forces in the SHAKE/RATTLE -computation. :dd - -{Simulations might be very slow because of large number of structure factors} :dt - -Self-explanatory. :dd - -{Slab correction not needed for MSM} :dt - -Slab correction is intended to be used with Ewald or PPPM and is not needed by MSM. :dd - -{System is not charge neutral, net charge = %g} :dt - -The total charge on all atoms on the system is not 0.0. -For some KSpace solvers this is only a warning. :dd - -{Table inner cutoff >= outer cutoff} :dt - -You specified an inner cutoff for a Coulombic table that is longer -than the global cutoff. Probably not what you wanted. :dd - -{Temperature for MSST is not for group all} :dt - -User-assigned temperature to MSST fix does not compute temperature for -all atoms. Since MSST computes a global pressure, the kinetic energy -contribution from the temperature is assumed to also be for all atoms. -Thus the pressure used by MSST could be inaccurate. :dd - -{Temperature for NPT is not for group all} :dt - -User-assigned temperature to NPT fix does not compute temperature for -all atoms. Since NPT computes a global pressure, the kinetic energy -contribution from the temperature is assumed to also be for all atoms. -Thus the pressure used by NPT could be inaccurate. :dd - -{Temperature for fix modify is not for group all} :dt - -The temperature compute is being used with a pressure calculation -which does operate on group all, so this may be inconsistent. :dd - -{Temperature for thermo pressure is not for group all} :dt - -User-assigned temperature to thermo via the thermo_modify command does -not compute temperature for all atoms. Since thermo computes a global -pressure, the kinetic energy contribution from the temperature is -assumed to also be for all atoms. Thus the pressure printed by thermo -could be inaccurate. :dd - -{The fix ave/spatial command has been replaced by the more flexible fix ave/chunk and compute chunk/atom commands -- fix ave/spatial will be removed in the summer of 2015} :dt - -Self-explanatory. :dd - -{The minimizer does not re-orient dipoles when using fix efield} :dt - -This means that only the atom coordinates will be minimized, -not the orientation of the dipoles. :dd - -{Too many common neighbors in CNA %d times} :dt - -More than the maximum # of neighbors was found multiple times. This -was unexpected. :dd - -{Too many inner timesteps in fix ttm} :dt - -Self-explanatory. :dd - -{Too many neighbors in CNA for %d atoms} :dt - -More than the maximum # of neighbors was found multiple times. This -was unexpected. :dd - -{Triclinic box skew is large} :dt - -The displacement in a skewed direction is normally required to be less -than half the box length in that dimension. E.g. the xy tilt must be -between -half and +half of the x box length. You have relaxed the -constraint using the box tilt command, but the warning means that a -LAMMPS simulation may be inefficient as a result. :dd - -{Use special bonds = 0,1,1 with bond style fene} :dt - -Most FENE models need this setting for the special_bonds command. :dd - -{Use special bonds = 0,1,1 with bond style fene/expand} :dt - -Most FENE models need this setting for the special_bonds command. :dd - -{Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions} :dt - -This is likely not what you want to do. The exclusion settings will -eliminate neighbors in the neighbor list, which the manybody potential -needs to calculated its terms correctly. :dd - -{Using compute temp/deform with inconsistent fix deform remap option} :dt - -Fix nvt/sllod assumes deforming atoms have a velocity profile provided -by "remap v" or "remap none" as a fix deform option. :dd - -{Using compute temp/deform with no fix deform defined} :dt - -This is probably an error, since it makes little sense to use -compute temp/deform in this case. :dd - -{Using fix srd with box deformation but no SRD thermostat} :dt - -The deformation will heat the SRD particles so this can -be dangerous. :dd - -{Using kspace solver on system with no charge} :dt - -Self-explanatory. :dd - -{Using largest cut-off for lj/long/dipole/long long long} :dt - -Self-explanatory. :dd - -{Using largest cutoff for buck/long/coul/long} :dt - -Self-explanatory. :dd - -{Using largest cutoff for lj/long/coul/long} :dt - -Self-explanatory. :dd - -{Using largest cutoff for pair_style lj/long/tip4p/long} :dt - -Self-explanatory. :dd - -{Using package gpu without any pair style defined} :dt - -Self-explanatory. :dd - -{Using pair potential shift with pair_modify compute no} :dt - -The shift effects will thus not be computed. :dd - -{Using pair tail corrections with nonperiodic system} :dt - -This is probably a bogus thing to do, since tail corrections are -computed by integrating the density of a periodic system out to -infinity. :dd - -{Using pair tail corrections with pair_modify compute no} :dt - -The tail corrections will thus not be computed. :dd - -{pair style reax is now deprecated and will soon be retired. Users should switch to pair_style reax/c} :dt - -Self-explanatory. :dd - -:dle - diff --git a/doc/src/Errors_warnings.txt b/doc/src/Errors_warnings.txt new file mode 100644 index 0000000000..98b66f2aa5 --- /dev/null +++ b/doc/src/Errors_warnings.txt @@ -0,0 +1,934 @@ +"Higher level section"_Errors.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Warning messages :h3 + +This is an alphabetic list of the WARNING messages LAMMPS prints out +and the reason why. If the explanation here is not sufficient, the +documentation for the offending command may help. Warning messages +also list the source file and line number where the warning was +generated. For example, a message like this: + +WARNING: Bond atom missing in box size check (domain.cpp:187) :pre + +means that line #187 in the file src/domain.cpp generated the error. +Looking in the source code may help you figure out what went wrong. + +Note that warning messages from "user-contributed +packages"_Packages_user.html are not listed here. If such a warning +occurs and is not self-explanatory, you'll need to look in the source +code or contact the author of the package. + +Doc page with "ERROR messages"_Errors_messages.html + +:line + +:dlb + +{Adjusting Coulombic cutoff for MSM, new cutoff = %g} :dt + +The adjust/cutoff command is turned on and the Coulombic cutoff has been +adjusted to match the user-specified accuracy. :dd + +{Angle atoms missing at step %ld} :dt + +One or more of 3 atoms needed to compute a particular angle are +missing on this processor. Typically this is because the pairwise +cutoff is set too short or the angle has blown apart and an atom is +too far away. :dd + +{Angle style in data file differs from currently defined angle style} :dt + +Self-explanatory. :dd + +{Atom style in data file differs from currently defined atom style} :dt + +Self-explanatory. :dd + +{Bond atom missing in box size check} :dt + +The 2nd atoms needed to compute a particular bond is missing on this +processor. Typically this is because the pairwise cutoff is set too +short or the bond has blown apart and an atom is too far away. :dd + +{Bond atom missing in image check} :dt + +The 2nd atom in a particular bond is missing on this processor. +Typically this is because the pairwise cutoff is set too short or the +bond has blown apart and an atom is too far away. :dd + +{Bond atoms missing at step %ld} :dt + +The 2nd atom needed to compute a particular bond is missing on this +processor. Typically this is because the pairwise cutoff is set too +short or the bond has blown apart and an atom is too far away. :dd + +{Bond style in data file differs from currently defined bond style} :dt + +Self-explanatory. :dd + +{Bond/angle/dihedral extent > half of periodic box length} :dt + +This is a restriction because LAMMPS can be confused about which image +of an atom in the bonded interaction is the correct one to use. +"Extent" in this context means the maximum end-to-end length of the +bond/angle/dihedral. LAMMPS computes this by taking the maximum bond +length, multiplying by the number of bonds in the interaction (e.g. 3 +for a dihedral) and adding a small amount of stretch. :dd + +{Both groups in compute group/group have a net charge; the Kspace boundary correction to energy will be non-zero} :dt + +Self-explanatory. :dd + +{Calling write_dump before a full system init.} :dt + +The write_dump command is used before the system has been fully +initialized as part of a 'run' or 'minimize' command. Not all dump +styles and features are fully supported at this point and thus the +command may fail or produce incomplete or incorrect output. Insert +a "run 0" command, if a full system init is required. :dd + +{Cannot count rigid body degrees-of-freedom before bodies are fully initialized} :dt + +This means the temperature associated with the rigid bodies may be +incorrect on this timestep. :dd + +{Cannot count rigid body degrees-of-freedom before bodies are initialized} :dt + +This means the temperature associated with the rigid bodies may be +incorrect on this timestep. :dd + +{Cannot include log terms without 1/r terms; setting flagHI to 1} :dt + +Self-explanatory. :dd + +{Cannot include log terms without 1/r terms; setting flagHI to 1.} :dt + +Self-explanatory. :dd + +{Charges are set, but coulombic solver is not used} :dt + +Self-explanatory. :dd + +{Charges did not converge at step %ld: %lg} :dt + +Self-explanatory. :dd + +{Communication cutoff is too small for SNAP micro load balancing, increased to %lf} :dt + +Self-explanatory. :dd + +{Compute cna/atom cutoff may be too large to find ghost atom neighbors} :dt + +The neighbor cutoff used may not encompass enough ghost atoms +to perform this operation correctly. :dd + +{Computing temperature of portions of rigid bodies} :dt + +The group defined by the temperature compute does not encompass all +the atoms in one or more rigid bodies, so the change in +degrees-of-freedom for the atoms in those partial rigid bodies will +not be accounted for. :dd + +{Create_bonds max distance > minimum neighbor cutoff} :dt + +This means atom pairs for some atom types may not be in the neighbor +list and thus no bond can be created between them. :dd + +{Delete_atoms cutoff > minimum neighbor cutoff} :dt + +This means atom pairs for some atom types may not be in the neighbor +list and thus an atom in that pair cannot be deleted. :dd + +{Dihedral atoms missing at step %ld} :dt + +One or more of 4 atoms needed to compute a particular dihedral are +missing on this processor. Typically this is because the pairwise +cutoff is set too short or the dihedral has blown apart and an atom is +too far away. :dd + +{Dihedral problem} :dt + +Conformation of the 4 listed dihedral atoms is extreme; you may want +to check your simulation geometry. :dd + +{Dihedral problem: %d %ld %d %d %d %d} :dt + +Conformation of the 4 listed dihedral atoms is extreme; you may want +to check your simulation geometry. :dd + +{Dihedral style in data file differs from currently defined dihedral style} :dt + +Self-explanatory. :dd + +{Dump dcd/xtc timestamp may be wrong with fix dt/reset} :dt + +If the fix changes the timestep, the dump dcd file will not +reflect the change. :dd + +{Energy due to X extra global DOFs will be included in minimizer energies} :dt + +When using fixes like box/relax, the potential energy used by the minimizer +is augmented by an additional energy provided by the fix. Thus the printed +converged energy may be different from the total potential energy. :dd + +{Energy tally does not account for 'zero yes'} :dt + +The energy removed by using the 'zero yes' flag is not accounted +for in the energy tally and thus energy conservation cannot be +monitored in this case. :dd + +{Estimated error in splitting of dispersion coeffs is %g} :dt + +Error is greater than 0.0001 percent. :dd + +{Ewald/disp Newton solver failed, using old method to estimate g_ewald} :dt + +Self-explanatory. Choosing a different cutoff value may help. :dd + +{FENE bond too long} :dt + +A FENE bond has stretched dangerously far. It's interaction strength +will be truncated to attempt to prevent the bond from blowing up. :dd + +{FENE bond too long: %ld %d %d %g} :dt + +A FENE bond has stretched dangerously far. It's interaction strength +will be truncated to attempt to prevent the bond from blowing up. :dd + +{FENE bond too long: %ld %g} :dt + +A FENE bond has stretched dangerously far. It's interaction strength +will be truncated to attempt to prevent the bond from blowing up. :dd + +{Fix SRD walls overlap but fix srd overlap not set} :dt + +You likely want to set this in your input script. :dd + +{Fix bond/swap will ignore defined angles} :dt + +See the doc page for fix bond/swap for more info on this +restriction. :dd + +{Fix deposit near setting < possible overlap separation %g} :dt + +This test is performed for finite size particles with a diameter, not +for point particles. The near setting is smaller than the particle +diameter which can lead to overlaps. :dd + +{Fix evaporate may delete atom with non-zero molecule ID} :dt + +This is probably an error, since you should not delete only one atom +of a molecule. :dd + +{Fix gcmc using full_energy option} :dt + +Fix gcmc has automatically turned on the full_energy option since it +is required for systems like the one specified by the user. User input +included one or more of the following: kspace, triclinic, a hybrid +pair style, an eam pair style, or no "single" function for the pair +style. :dd + +{Fix property/atom mol or charge w/out ghost communication} :dt + +A model typically needs these properties defined for ghost atoms. :dd + +{Fix qeq CG convergence failed (%g) after %d iterations at %ld step} :dt + +Self-explanatory. :dd + +{Fix qeq has non-zero lower Taper radius cutoff} :dt + +Absolute value must be <= 0.01. :dd + +{Fix qeq has very low Taper radius cutoff} :dt + +Value should typically be >= 5.0. :dd + +{Fix qeq/dynamic tolerance may be too small for damped dynamics} :dt + +Self-explanatory. :dd + +{Fix qeq/fire tolerance may be too small for damped fires} :dt + +Self-explanatory. :dd + +{Fix rattle should come after all other integration fixes} :dt + +This fix is designed to work after all other integration fixes change +atom positions. Thus it should be the last integration fix specified. +If not, it will not satisfy the desired constraints as well as it +otherwise would. :dd + +{Fix recenter should come after all other integration fixes} :dt + +Other fixes may change the position of the center-of-mass, so +fix recenter should come last. :dd + +{Fix srd SRD moves may trigger frequent reneighboring} :dt + +This is because the SRD particles may move long distances. :dd + +{Fix srd grid size > 1/4 of big particle diameter} :dt + +This may cause accuracy problems. :dd + +{Fix srd particle moved outside valid domain} :dt + +This may indicate a problem with your simulation parameters. :dd + +{Fix srd particles may move > big particle diameter} :dt + +This may cause accuracy problems. :dd + +{Fix srd viscosity < 0.0 due to low SRD density} :dt + +This may cause accuracy problems. :dd + +{Fix thermal/conductivity comes before fix ave/spatial} :dt + +The order of these 2 fixes in your input script is such that fix +thermal/conductivity comes first. If you are using fix ave/spatial to +measure the temperature profile induced by fix viscosity, then this +may cause a glitch in the profile since you are averaging immediately +after swaps have occurred. Flipping the order of the 2 fixes +typically helps. :dd + +{Fix viscosity comes before fix ave/spatial} :dt + +The order of these 2 fixes in your input script is such that +fix viscosity comes first. If you are using fix ave/spatial +to measure the velocity profile induced by fix viscosity, then +this may cause a glitch in the profile since you are averaging +immediately after swaps have occurred. Flipping the order +of the 2 fixes typically helps. :dd + +{Fixes cannot send data in Kokkos communication, switching to classic communication} :dt + +This is current restriction with Kokkos. :dd + +{For better accuracy use 'pair_modify table 0'} :dt + +The user-specified force accuracy cannot be achieved unless the table +feature is disabled by using 'pair_modify table 0'. :dd + +{Geometric mixing assumed for 1/r^6 coefficients} :dt + +Self-explanatory. :dd + +{Group for fix_modify temp != fix group} :dt + +The fix_modify command is specifying a temperature computation that +computes a temperature on a different group of atoms than the fix +itself operates on. This is probably not what you want to do. :dd + +{H matrix size has been exceeded: m_fill=%d H.m=%d\n} :dt + +This is the size of the matrix. :dd + +{Ignoring unknown or incorrect info command flag} :dt + +Self-explanatory. An unknown argument was given to the info command. +Compare your input with the documentation. :dd + +{Improper atoms missing at step %ld} :dt + +One or more of 4 atoms needed to compute a particular improper are +missing on this processor. Typically this is because the pairwise +cutoff is set too short or the improper has blown apart and an atom is +too far away. :dd + +{Improper problem: %d %ld %d %d %d %d} :dt + +Conformation of the 4 listed improper atoms is extreme; you may want +to check your simulation geometry. :dd + +{Improper style in data file differs from currently defined improper style} :dt + +Self-explanatory. :dd + +{Inconsistent image flags} :dt + +The image flags for a pair on bonded atoms appear to be inconsistent. +Inconsistent means that when the coordinates of the two atoms are +unwrapped using the image flags, the two atoms are far apart. +Specifically they are further apart than half a periodic box length. +Or they are more than a box length apart in a non-periodic dimension. +This is usually due to the initial data file not having correct image +flags for the 2 atoms in a bond that straddles a periodic boundary. +They should be different by 1 in that case. This is a warning because +inconsistent image flags will not cause problems for dynamics or most +LAMMPS simulations. However they can cause problems when such atoms +are used with the fix rigid or replicate commands. Note that if you +have an infinite periodic crystal with bonds then it is impossible to +have fully consistent image flags, since some bonds will cross +periodic boundaries and connect two atoms with the same image +flag. :dd + +{KIM Model does not provide 'energy'; Potential energy will be zero} :dt + +Self-explanatory. :dd + +{KIM Model does not provide 'forces'; Forces will be zero} :dt + +Self-explanatory. :dd + +{KIM Model does not provide 'particleEnergy'; energy per atom will be zero} :dt + +Self-explanatory. :dd + +{KIM Model does not provide 'particleVirial'; virial per atom will be zero} :dt + +Self-explanatory. :dd + +{Kspace_modify slab param < 2.0 may cause unphysical behavior} :dt + +The kspace_modify slab parameter should be larger to insure periodic +grids padded with empty space do not overlap. :dd + +{Less insertions than requested} :dt + +The fix pour command was unsuccessful at finding open space +for as many particles as it tried to insert. :dd + +{Library error in lammps_gather_atoms} :dt + +This library function cannot be used if atom IDs are not defined +or are not consecutively numbered. :dd + +{Library error in lammps_scatter_atoms} :dt + +This library function cannot be used if atom IDs are not defined or +are not consecutively numbered, or if no atom map is defined. See the +atom_modify command for details about atom maps. :dd + +{Lost atoms via change_box: original %ld current %ld} :dt + +The command options you have used caused atoms to be lost. :dd + +{Lost atoms via displace_atoms: original %ld current %ld} :dt + +The command options you have used caused atoms to be lost. :dd + +{Lost atoms: original %ld current %ld} :dt + +Lost atoms are checked for each time thermo output is done. See the +thermo_modify lost command for options. Lost atoms usually indicate +bad dynamics, e.g. atoms have been blown far out of the simulation +box, or moved further than one processor's sub-domain away before +reneighboring. :dd + +{MSM mesh too small, increasing to 2 points in each direction} :dt + +Self-explanatory. :dd + +{Mismatch between velocity and compute groups} :dt + +The temperature computation used by the velocity command will not be +on the same group of atoms that velocities are being set for. :dd + +{Mixing forced for lj coefficients} :dt + +Self-explanatory. :dd + +{Molecule attributes do not match system attributes} :dt + +An attribute is specified (e.g. diameter, charge) that is +not defined for the specified atom style. :dd + +{Molecule has bond topology but no special bond settings} :dt + +This means the bonded atoms will not be excluded in pair-wise +interactions. :dd + +{Molecule template for create_atoms has multiple molecules} :dt + +The create_atoms command will only create molecules of a single type, +i.e. the first molecule in the template. :dd + +{Molecule template for fix gcmc has multiple molecules} :dt + +The fix gcmc command will only create molecules of a single type, +i.e. the first molecule in the template. :dd + +{Molecule template for fix shake has multiple molecules} :dt + +The fix shake command will only recognize molecules of a single +type, i.e. the first molecule in the template. :dd + +{More than one compute centro/atom} :dt + +It is not efficient to use compute centro/atom more than once. :dd + +{More than one compute cluster/atom} :dt + +It is not efficient to use compute cluster/atom more than once. :dd + +{More than one compute cna/atom defined} :dt + +It is not efficient to use compute cna/atom more than once. :dd + +{More than one compute contact/atom} :dt + +It is not efficient to use compute contact/atom more than once. :dd + +{More than one compute coord/atom} :dt + +It is not efficient to use compute coord/atom more than once. :dd + +{More than one compute damage/atom} :dt + +It is not efficient to use compute ke/atom more than once. :dd + +{More than one compute dilatation/atom} :dt + +Self-explanatory. :dd + +{More than one compute erotate/sphere/atom} :dt + +It is not efficient to use compute erorate/sphere/atom more than once. :dd + +{More than one compute hexorder/atom} :dt + +It is not efficient to use compute hexorder/atom more than once. :dd + +{More than one compute ke/atom} :dt + +It is not efficient to use compute ke/atom more than once. :dd + +{More than one compute orientorder/atom} :dt + +It is not efficient to use compute orientorder/atom more than once. :dd + +{More than one compute plasticity/atom} :dt + +Self-explanatory. :dd + +{More than one compute sna/atom} :dt + +Self-explanatory. :dd + +{More than one compute snad/atom} :dt + +Self-explanatory. :dd + +{More than one compute snav/atom} :dt + +Self-explanatory. :dd + +{More than one fix poems} :dt + +It is not efficient to use fix poems more than once. :dd + +{More than one fix rigid} :dt + +It is not efficient to use fix rigid more than once. :dd + +{Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies} :dt + +This is because excluding specific pair interactions also excludes +them from long-range interactions which may not be the desired effect. +The special_bonds command handles this consistently by insuring +excluded (or weighted) 1-2, 1-3, 1-4 interactions are treated +consistently by both the short-range pair style and the long-range +solver. This is not done for exclusions of charged atom pairs via the +neigh_modify exclude command. :dd + +{New thermo_style command, previous thermo_modify settings will be lost} :dt + +If a thermo_style command is used after a thermo_modify command, the +settings changed by the thermo_modify command will be reset to their +default values. This is because the thermo_modify command acts on +the currently defined thermo style, and a thermo_style command creates +a new style. :dd + +{No Kspace calculation with verlet/split} :dt + +The 2nd partition performs a kspace calculation so the kspace_style +command must be used. :dd + +{No automatic unit conversion to XTC file format conventions possible for units lj} :dt + +This means no scaling will be performed. :dd + +{No fixes defined, atoms won't move} :dt + +If you are not using a fix like nve, nvt, npt then atom velocities and +coordinates will not be updated during timestepping. :dd + +{No joints between rigid bodies, use fix rigid instead} :dt + +The bodies defined by fix poems are not connected by joints. POEMS +will integrate the body motion, but it would be more efficient to use +fix rigid. :dd + +{Not using real units with pair reax} :dt + +This is most likely an error, unless you have created your own ReaxFF +parameter file in a different set of units. :dd + +{Number of MSM mesh points changed to be a multiple of 2} :dt + +MSM requires that the number of grid points in each direction be a multiple +of two and the number of grid points in one or more directions have been +adjusted to meet this requirement. :dd + +{OMP_NUM_THREADS environment is not set.} :dt + +This environment variable must be set appropriately to use the +USER-OMP package. :dd + +{One or more atoms are time integrated more than once} :dt + +This is probably an error since you typically do not want to +advance the positions or velocities of an atom more than once +per timestep. :dd + +{One or more chunks do not contain all atoms in molecule} :dt + +This may not be what you intended. :dd + +{One or more dynamic groups may not be updated at correct point in timestep} :dt + +If there are other fixes that act immediately after the initial stage +of time integration within a timestep (i.e. after atoms move), then +the command that sets up the dynamic group should appear after those +fixes. This will insure that dynamic group assignments are made +after all atoms have moved. :dd + +{One or more respa levels compute no forces} :dt + +This is computationally inefficient. :dd + +{Pair COMB charge %.10f with force %.10f hit max barrier} :dt + +Something is possibly wrong with your model. :dd + +{Pair COMB charge %.10f with force %.10f hit min barrier} :dt + +Something is possibly wrong with your model. :dd + +{Pair brownian needs newton pair on for momentum conservation} :dt + +Self-explanatory. :dd + +{Pair dpd needs newton pair on for momentum conservation} :dt + +Self-explanatory. :dd + +{Pair dsmc: num_of_collisions > number_of_A} :dt + +Collision model in DSMC is breaking down. :dd + +{Pair dsmc: num_of_collisions > number_of_B} :dt + +Collision model in DSMC is breaking down. :dd + +{Pair style in data file differs from currently defined pair style} :dt + +Self-explanatory. :dd + +{Pair style restartinfo set but has no restart support} :dt + +This pair style has a bug, where it does not support reading and +writing information to a restart file, but does not set the member +variable "restartinfo" to 0 as required in that case. :dd + +{Particle deposition was unsuccessful} :dt + +The fix deposit command was not able to insert as many atoms as +needed. The requested volume fraction may be too high, or other atoms +may be in the insertion region. :dd + +{Proc sub-domain size < neighbor skin, could lead to lost atoms} :dt + +The decomposition of the physical domain (likely due to load +balancing) has led to a processor's sub-domain being smaller than the +neighbor skin in one or more dimensions. Since reneighboring is +triggered by atoms moving the skin distance, this may lead to lost +atoms, if an atom moves all the way across a neighboring processor's +sub-domain before reneighboring is triggered. :dd + +{Reducing PPPM order b/c stencil extends beyond nearest neighbor processor} :dt + +This may lead to a larger grid than desired. See the kspace_modify overlap +command to prevent changing of the PPPM order. :dd + +{Reducing PPPMDisp Coulomb order b/c stencil extends beyond neighbor processor} :dt + +This may lead to a larger grid than desired. See the kspace_modify overlap +command to prevent changing of the PPPM order. :dd + +{Reducing PPPMDisp dispersion order b/c stencil extends beyond neighbor processor} :dt + +This may lead to a larger grid than desired. See the kspace_modify overlap +command to prevent changing of the PPPM order. :dd + +{Replacing a fix, but new group != old group} :dt + +The ID and style of a fix match for a fix you are changing with a fix +command, but the new group you are specifying does not match the old +group. :dd + +{Replicating in a non-periodic dimension} :dt + +The parameters for a replicate command will cause a non-periodic +dimension to be replicated; this may cause unwanted behavior. :dd + +{Resetting reneighboring criteria during PRD} :dt + +A PRD simulation requires that neigh_modify settings be delay = 0, +every = 1, check = yes. Since these settings were not in place, +LAMMPS changed them and will restore them to their original values +after the PRD simulation. :dd + +{Resetting reneighboring criteria during TAD} :dt + +A TAD simulation requires that neigh_modify settings be delay = 0, +every = 1, check = yes. Since these settings were not in place, +LAMMPS changed them and will restore them to their original values +after the PRD simulation. :dd + +{Resetting reneighboring criteria during minimization} :dt + +Minimization requires that neigh_modify settings be delay = 0, every = +1, check = yes. Since these settings were not in place, LAMMPS +changed them and will restore them to their original values after the +minimization. :dd + +{Restart file used different # of processors} :dt + +The restart file was written out by a LAMMPS simulation running on a +different number of processors. Due to round-off, the trajectories of +your restarted simulation may diverge a little more quickly than if +you ran on the same # of processors. :dd + +{Restart file used different 3d processor grid} :dt + +The restart file was written out by a LAMMPS simulation running on a +different 3d grid of processors. Due to round-off, the trajectories +of your restarted simulation may diverge a little more quickly than if +you ran on the same # of processors. :dd + +{Restart file used different boundary settings, using restart file values} :dt + +Your input script cannot change these restart file settings. :dd + +{Restart file used different newton bond setting, using restart file value} :dt + +The restart file value will override the setting in the input script. :dd + +{Restart file used different newton pair setting, using input script value} :dt + +The input script value will override the setting in the restart file. :dd + +{Restrain problem: %d %ld %d %d %d %d} :dt + +Conformation of the 4 listed dihedral atoms is extreme; you may want +to check your simulation geometry. :dd + +{Running PRD with only one replica} :dt + +This is allowed, but you will get no parallel speed-up. :dd + +{SRD bin shifting turned on due to small lamda} :dt + +This is done to try to preserve accuracy. :dd + +{SRD bin size for fix srd differs from user request} :dt + +Fix SRD had to adjust the bin size to fit the simulation box. See the +cubic keyword if you want this message to be an error vs warning. :dd + +{SRD bins for fix srd are not cubic enough} :dt + +The bin shape is not within tolerance of cubic. See the cubic +keyword if you want this message to be an error vs warning. :dd + +{SRD particle %d started inside big particle %d on step %ld bounce %d} :dt + +See the inside keyword if you want this message to be an error vs +warning. :dd + +{SRD particle %d started inside wall %d on step %ld bounce %d} :dt + +See the inside keyword if you want this message to be an error vs +warning. :dd + +{Shake determinant < 0.0} :dt + +The determinant of the quadratic equation being solved for a single +cluster specified by the fix shake command is numerically suspect. LAMMPS +will set it to 0.0 and continue. :dd + +{Shell command '%s' failed with error '%s'} :dt + +Self-explanatory. :dd + +{Shell command returned with non-zero status} :dt + +This may indicate the shell command did not operate as expected. :dd + +{Should not allow rigid bodies to bounce off relecting walls} :dt + +LAMMPS allows this, but their dynamics are not computed correctly. :dd + +{Should not use fix nve/limit with fix shake or fix rattle} :dt + +This will lead to invalid constraint forces in the SHAKE/RATTLE +computation. :dd + +{Simulations might be very slow because of large number of structure factors} :dt + +Self-explanatory. :dd + +{Slab correction not needed for MSM} :dt + +Slab correction is intended to be used with Ewald or PPPM and is not needed by MSM. :dd + +{System is not charge neutral, net charge = %g} :dt + +The total charge on all atoms on the system is not 0.0. +For some KSpace solvers this is only a warning. :dd + +{Table inner cutoff >= outer cutoff} :dt + +You specified an inner cutoff for a Coulombic table that is longer +than the global cutoff. Probably not what you wanted. :dd + +{Temperature for MSST is not for group all} :dt + +User-assigned temperature to MSST fix does not compute temperature for +all atoms. Since MSST computes a global pressure, the kinetic energy +contribution from the temperature is assumed to also be for all atoms. +Thus the pressure used by MSST could be inaccurate. :dd + +{Temperature for NPT is not for group all} :dt + +User-assigned temperature to NPT fix does not compute temperature for +all atoms. Since NPT computes a global pressure, the kinetic energy +contribution from the temperature is assumed to also be for all atoms. +Thus the pressure used by NPT could be inaccurate. :dd + +{Temperature for fix modify is not for group all} :dt + +The temperature compute is being used with a pressure calculation +which does operate on group all, so this may be inconsistent. :dd + +{Temperature for thermo pressure is not for group all} :dt + +User-assigned temperature to thermo via the thermo_modify command does +not compute temperature for all atoms. Since thermo computes a global +pressure, the kinetic energy contribution from the temperature is +assumed to also be for all atoms. Thus the pressure printed by thermo +could be inaccurate. :dd + +{The fix ave/spatial command has been replaced by the more flexible fix ave/chunk and compute chunk/atom commands -- fix ave/spatial will be removed in the summer of 2015} :dt + +Self-explanatory. :dd + +{The minimizer does not re-orient dipoles when using fix efield} :dt + +This means that only the atom coordinates will be minimized, +not the orientation of the dipoles. :dd + +{Too many common neighbors in CNA %d times} :dt + +More than the maximum # of neighbors was found multiple times. This +was unexpected. :dd + +{Too many inner timesteps in fix ttm} :dt + +Self-explanatory. :dd + +{Too many neighbors in CNA for %d atoms} :dt + +More than the maximum # of neighbors was found multiple times. This +was unexpected. :dd + +{Triclinic box skew is large} :dt + +The displacement in a skewed direction is normally required to be less +than half the box length in that dimension. E.g. the xy tilt must be +between -half and +half of the x box length. You have relaxed the +constraint using the box tilt command, but the warning means that a +LAMMPS simulation may be inefficient as a result. :dd + +{Use special bonds = 0,1,1 with bond style fene} :dt + +Most FENE models need this setting for the special_bonds command. :dd + +{Use special bonds = 0,1,1 with bond style fene/expand} :dt + +Most FENE models need this setting for the special_bonds command. :dd + +{Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions} :dt + +This is likely not what you want to do. The exclusion settings will +eliminate neighbors in the neighbor list, which the manybody potential +needs to calculated its terms correctly. :dd + +{Using compute temp/deform with inconsistent fix deform remap option} :dt + +Fix nvt/sllod assumes deforming atoms have a velocity profile provided +by "remap v" or "remap none" as a fix deform option. :dd + +{Using compute temp/deform with no fix deform defined} :dt + +This is probably an error, since it makes little sense to use +compute temp/deform in this case. :dd + +{Using fix srd with box deformation but no SRD thermostat} :dt + +The deformation will heat the SRD particles so this can +be dangerous. :dd + +{Using kspace solver on system with no charge} :dt + +Self-explanatory. :dd + +{Using largest cut-off for lj/long/dipole/long long long} :dt + +Self-explanatory. :dd + +{Using largest cutoff for buck/long/coul/long} :dt + +Self-explanatory. :dd + +{Using largest cutoff for lj/long/coul/long} :dt + +Self-explanatory. :dd + +{Using largest cutoff for pair_style lj/long/tip4p/long} :dt + +Self-explanatory. :dd + +{Using package gpu without any pair style defined} :dt + +Self-explanatory. :dd + +{Using pair potential shift with pair_modify compute no} :dt + +The shift effects will thus not be computed. :dd + +{Using pair tail corrections with nonperiodic system} :dt + +This is probably a bogus thing to do, since tail corrections are +computed by integrating the density of a periodic system out to +infinity. :dd + +{Using pair tail corrections with pair_modify compute no} :dt + +The tail corrections will thus not be computed. :dd + +{pair style reax is now deprecated and will soon be retired. Users should switch to pair_style reax/c} :dt + +Self-explanatory. :dd + +:dle diff --git a/doc/src/Section_example.txt b/doc/src/Examples.txt similarity index 91% rename from doc/src/Section_example.txt rename to doc/src/Examples.txt index a2a9940f48..4b6db8a047 100644 --- a/doc/src/Section_example.txt +++ b/doc/src/Examples.txt @@ -1,12 +1,14 @@ -"Previous Section"_Section_howto.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Section_perf.html :c +"Previous Section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc - "Next +Section"_Tools.html :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line -7. Example problems :h2 +Example scripts :h3 The LAMMPS distribution includes an examples sub-directory with many sample problems. Many are 2d models that run quickly are are @@ -46,7 +48,7 @@ Lists of both kinds of directories are given below. :line -Lowercase directories :h3 +Lowercase directories :h4 accelerate: run with various acceleration options (OpenMP, GPU, Phi) airebo: polyethylene with AIREBO potential @@ -110,10 +112,10 @@ web site. If you uncomment the "dump image"_dump_image.html line(s) in the input script a series of JPG images will be produced by the run (assuming -you built LAMMPS with JPG support; see "Section -2.2"_Section_start.html#start_2 for details). These can be viewed -individually or turned into a movie or animated by tools like -ImageMagick or QuickTime or various Windows-based tools. See the +you built LAMMPS with JPG support; see the +"Build_settings"_Build_settings.html doc page for details). These can +be viewed individually or turned into a movie or animated by tools +like ImageMagick or QuickTime or various Windows-based tools. See the "dump image"_dump_image.html doc page for more details. E.g. this Imagemagick command would create a GIF file suitable for viewing in a browser. @@ -122,7 +124,7 @@ browser. :line -Uppercase directories :h3 +Uppercase directories :h4 ASPHERE: various aspherical particle models, using ellipsoids, rigid bodies, line/triangle particles, etc COUPLE: examples of how to use LAMMPS as a library @@ -141,5 +143,5 @@ The USER directory has a large number of sub-directories which correspond by name to a USER package. They contain scripts that illustrate how to use the command(s) provided in that package. Many of the sub-directories have their own README files which give further -instructions. See the "Section 4"_Section_packages.html doc +instructions. See the "Packages_details"_Packages_details.html doc page for more info on specific USER packages. diff --git a/doc/src/Howto.txt b/doc/src/Howto.txt new file mode 100644 index 0000000000..730b492699 --- /dev/null +++ b/doc/src/Howto.txt @@ -0,0 +1,191 @@ +"Previous Section"_Performance.html - "LAMMPS WWW Site"_lws - +"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next +Section"_Examples.html :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands.html#comm) + +:line + +Howto discussions :h2 + +These doc pages describe how to perform various tasks with LAMMPS, +both for users and developers. The +"glossary"_http://lammps.sandia.gov website page also lists MD +terminology with links to corresponding LAMMPS manual pages. The +example input scripts included in the examples dir of the LAMMPS +distribution and highlighted on the "Examples"_Examples.html doc page +also show how to setup and run various kinds of simulations. + +Tutorials howto :h3 + + + + + +"Using GitHub with LAMMPS"_Howto_github.html +"PyLAMMPS interface to LAMMPS"_Howto_pylammps.html +"Using LAMMPS with bash on Windows"_Howto_bash.html :all(b) + + + +General howto :h3 + + + + + +"Restart a simulation"_Howto_restart.html +"Visualize LAMMPS snapshots"_Howto_viz.html +"Run multiple simulations from one input script"_Howto_multiple.html +"Multi-replica simulations"_Howto_replica.html +"Library interface to LAMMPS"_Howto_library.html +"Couple LAMMPS to other codes"_Howto_couple.html +"Using LAMMPS in client/server mode"_Howto_client_server.html :all(b) + + + +Settings howto :h3 + + + + + +"2d simulations"_Howto_2d.html +"Triclinic (non-orthogonal) simulation boxes"_Howto_triclinic.html +"Thermostats"_Howto_thermostat.html +"Barostats"_Howto_barostat.html +"Walls"_Howto_walls.html +"NEMD simulations"_Howto_nemd.html +"Long-range dispersion settings"_Howto_dispersion.html :all(b) + + + + +Analysis howto :h3 + + + + + +"Output from LAMMPS (thermo, dumps, computes, fixes, variables)"_Howto_output.html +"Use chunks to calculate system properties"_Howto_chunk.html :all(b) +"Calculate temperature"_Howto_temperature.html +"Calculate elastic constants"_Howto_elastic.html +"Calculate thermal conductivity"_Howto_kappa.html +"Calculate viscosity"_Howto_viscosity.html +"Calculate a diffusion coefficient"_Howto_diffusion.html :all(b) + + + +Force fields howto :h3 + + + + + +"CHARMM, AMBER, and DREIDING force fields"_Howto_bioFF.html +"TIP3P water model"_Howto_tip3p.html +"TIP4P water model"_Howto_tip4p.html +"SPC water model"_Howto_spc.html :all(b) + + + +Packages howto :h3 + + + + + + +"Finite-size spherical and aspherical particles"_Howto_spherical.html +"Granular models"_Howto_granular.html +"Body style particles"_Howto_body.html +"Polarizable models"_Howto_polarizable.html +"Adiabatic core/shell model"_Howto_coreshell.html +"Drude induced dipoles"_Howto_drude.html +"Drude induced dipoles (extended)"_Howto_drude2.html +"Manifolds (surfaces)"_Howto_manifold.html +"Magnetic spins"_Howto_spins.html :all(b) + + diff --git a/doc/src/Howto_2d.txt b/doc/src/Howto_2d.txt new file mode 100644 index 0000000000..e1758c05d5 --- /dev/null +++ b/doc/src/Howto_2d.txt @@ -0,0 +1,48 @@ +"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +2d simulations :h3 + +Use the "dimension"_dimension.html command to specify a 2d simulation. + +Make the simulation box periodic in z via the "boundary"_boundary.html +command. This is the default. + +If using the "create box"_create_box.html command to define a +simulation box, set the z dimensions narrow, but finite, so that the +create_atoms command will tile the 3d simulation box with a single z +plane of atoms - e.g. + +"create box"_create_box.html 1 -10 10 -10 10 -0.25 0.25 :pre + +If using the "read data"_read_data.html command to read in a file of +atom coordinates, set the "zlo zhi" values to be finite but narrow, +similar to the create_box command settings just described. For each +atom in the file, assign a z coordinate so it falls inside the +z-boundaries of the box - e.g. 0.0. + +Use the "fix enforce2d"_fix_enforce2d.html command as the last +defined fix to insure that the z-components of velocities and forces +are zeroed out every timestep. The reason to make it the last fix is +so that any forces induced by other fixes will be zeroed out. + +Many of the example input scripts included in the LAMMPS distribution +are for 2d models. + +NOTE: Some models in LAMMPS treat particles as finite-size spheres, as +opposed to point particles. See the "atom_style +sphere"_atom_style.html and "fix nve/sphere"_fix_nve_sphere.html +commands for details. By default, for 2d simulations, such particles +will still be modeled as 3d spheres, not 2d discs (circles), meaning +their moment of inertia will be that of a sphere. If you wish to +model them as 2d discs, see the "set density/disc"_set.html command +and the {disc} option for the "fix nve/sphere"_fix_nve_sphere.html, +"fix nvt/sphere"_fix_nvt_sphere.html, "fix +nph/sphere"_fix_nph_sphere.html, "fix npt/sphere"_fix_npt_sphere.html +commands. diff --git a/doc/src/Howto_barostat.txt b/doc/src/Howto_barostat.txt new file mode 100644 index 0000000000..3323334600 --- /dev/null +++ b/doc/src/Howto_barostat.txt @@ -0,0 +1,75 @@ +"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Barostats :h3 + +Barostatting means controlling the pressure in an MD simulation. +"Thermostatting"_Howto_thermostat.html means controlling the +temperature of the particles. Since the pressure includes a kinetic +component due to particle velocities, both these operations require +calculation of the temperature. Typically a target temperature (T) +and/or pressure (P) is specified by the user, and the thermostat or +barostat attempts to equilibrate the system to the requested T and/or +P. + +Barostatting in LAMMPS is performed by "fixes"_fix.html. Two +barosttating methods are currently available: Nose-Hoover (npt and +nph) and Berendsen: + +"fix npt"_fix_nh.html +"fix npt/sphere"_fix_npt_sphere.html +"fix npt/asphere"_fix_npt_asphere.html +"fix nph"_fix_nh.html +"fix press/berendsen"_fix_press_berendsen.html :ul + +The "fix npt"_fix_nh.html commands include a Nose-Hoover thermostat +and barostat. "Fix nph"_fix_nh.html is just a Nose/Hoover barostat; +it does no thermostatting. Both "fix nph"_fix_nh.html and "fix +press/berendsen"_fix_press_berendsen.html can be used in conjunction +with any of the thermostatting fixes. + +As with the "thermostats"_Howto_thermostat.html, "fix npt"_fix_nh.html +and "fix nph"_fix_nh.html only use translational motion of the +particles in computing T and P and performing thermo/barostatting. +"Fix npt/sphere"_fix_npt_sphere.html and "fix +npt/asphere"_fix_npt_asphere.html thermo/barostat using not only +translation velocities but also rotational velocities for spherical +and aspherical particles. + +All of the barostatting fixes use the "compute +pressure"_compute_pressure.html compute to calculate a current +pressure. By default, this compute is created with a simple "compute +temp"_compute_temp.html (see the last argument of the "compute +pressure"_compute_pressure.html command), which is used to calculated +the kinetic component of the pressure. The barostatting fixes can +also use temperature computes that remove bias for the purpose of +computing the kinetic component which contributes to the current +pressure. See the doc pages for the individual fixes and for the +"fix_modify"_fix_modify.html command for instructions on how to assign +a temperature or pressure compute to a barostatting fix. + +NOTE: As with the thermostats, the Nose/Hoover methods ("fix +npt"_fix_nh.html and "fix nph"_fix_nh.html) perform time integration. +"Fix press/berendsen"_fix_press_berendsen.html does NOT, so it should +be used with one of the constant NVE fixes or with one of the NVT +fixes. + +Thermodynamic output, which can be setup via the +"thermo_style"_thermo_style.html command, often includes pressure +values. As explained on the doc page for the +"thermo_style"_thermo_style.html command, the default pressure is +setup by the thermo command itself. It is NOT the pressure associated +with any barostatting fix you have defined or with any compute you +have defined that calculates a pressure. The doc pages for the +barostatting fixes explain the ID of the pressure compute they create. +Thus if you want to view these pressures, you need to specify them +explicitly via the "thermo_style custom"_thermo_style.html command. +Or you can use the "thermo_modify"_thermo_modify.html command to +re-define what pressure compute is used for default thermodynamic +output. diff --git a/doc/src/tutorial_bash_on_windows.txt b/doc/src/Howto_bash.txt old mode 100644 new mode 100755 similarity index 99% rename from doc/src/tutorial_bash_on_windows.txt rename to doc/src/Howto_bash.txt index 66712bdffa..f1438418e7 --- a/doc/src/tutorial_bash_on_windows.txt +++ b/doc/src/Howto_bash.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -10,6 +10,7 @@ Using LAMMPS with Bash on Windows :h3 [written by Richard Berger] :line + Starting with Windows 10 you can install Linux tools directly in Windows. This allows you to compile LAMMPS following the same procedure as on a real Ubuntu Linux installation. Software can be easily installed using the package manager diff --git a/doc/src/Howto_bioFF.txt b/doc/src/Howto_bioFF.txt new file mode 100644 index 0000000000..deb5b31441 --- /dev/null +++ b/doc/src/Howto_bioFF.txt @@ -0,0 +1,105 @@ +"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +CHARMM, AMBER, and DREIDING force fields :h3 + +A force field has 2 parts: the formulas that define it and the +coefficients used for a particular system. Here we only discuss +formulas implemented in LAMMPS that correspond to formulas commonly +used in the CHARMM, AMBER, and DREIDING force fields. Setting +coefficients is done in the input data file via the +"read_data"_read_data.html command or in the input script with +commands like "pair_coeff"_pair_coeff.html or +"bond_coeff"_bond_coeff.html. See the "Tools"_Tools.html doc page for +additional tools that can use CHARMM or AMBER to assign force field +coefficients and convert their output into LAMMPS input. + +See "(MacKerell)"_#howto-MacKerell for a description of the CHARMM force +field. See "(Cornell)"_#howto-Cornell for a description of the AMBER force +field. + +:link(charmm,http://www.scripps.edu/brooks) +:link(amber,http://amber.scripps.edu) + +These style choices compute force field formulas that are consistent +with common options in CHARMM or AMBER. See each command's +documentation for the formula it computes. + +"bond_style"_bond_harmonic.html harmonic +"angle_style"_angle_charmm.html charmm +"dihedral_style"_dihedral_charmm.html charmmfsh +"dihedral_style"_dihedral_charmm.html charmm +"pair_style"_pair_charmm.html lj/charmmfsw/coul/charmmfsh +"pair_style"_pair_charmm.html lj/charmmfsw/coul/long +"pair_style"_pair_charmm.html lj/charmm/coul/charmm +"pair_style"_pair_charmm.html lj/charmm/coul/charmm/implicit +"pair_style"_pair_charmm.html lj/charmm/coul/long :ul + +"special_bonds"_special_bonds.html charmm +"special_bonds"_special_bonds.html amber :ul + +NOTE: For CHARMM, newer {charmmfsw} or {charmmfsh} styles were +released in March 2017. We recommend they be used instead of the +older {charmm} styles. See discussion of the differences on the "pair +charmm"_pair_charmm.html and "dihedral charmm"_dihedral_charmm.html +doc pages. + +DREIDING is a generic force field developed by the "Goddard +group"_http://www.wag.caltech.edu at Caltech and is useful for +predicting structures and dynamics of organic, biological and +main-group inorganic molecules. The philosophy in DREIDING is to use +general force constants and geometry parameters based on simple +hybridization considerations, rather than individual force constants +and geometric parameters that depend on the particular combinations of +atoms involved in the bond, angle, or torsion terms. DREIDING has an +"explicit hydrogen bond term"_pair_hbond_dreiding.html to describe +interactions involving a hydrogen atom on very electronegative atoms +(N, O, F). + +See "(Mayo)"_#howto-Mayo for a description of the DREIDING force field + +These style choices compute force field formulas that are consistent +with the DREIDING force field. See each command's +documentation for the formula it computes. + +"bond_style"_bond_harmonic.html harmonic +"bond_style"_bond_morse.html morse :ul + +"angle_style"_angle_harmonic.html harmonic +"angle_style"_angle_cosine.html cosine +"angle_style"_angle_cosine_periodic.html cosine/periodic :ul + +"dihedral_style"_dihedral_charmm.html charmm +"improper_style"_improper_umbrella.html umbrella :ul + +"pair_style"_pair_buck.html buck +"pair_style"_pair_buck.html buck/coul/cut +"pair_style"_pair_buck.html buck/coul/long +"pair_style"_pair_lj.html lj/cut +"pair_style"_pair_lj.html lj/cut/coul/cut +"pair_style"_pair_lj.html lj/cut/coul/long :ul + +"pair_style"_pair_hbond_dreiding.html hbond/dreiding/lj +"pair_style"_pair_hbond_dreiding.html hbond/dreiding/morse :ul + +"special_bonds"_special_bonds.html dreiding :ul + +:line + +:link(howto-MacKerell) +[(MacKerell)] MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field, +Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998). + +:link(howto-Cornell) +[(Cornell)] Cornell, Cieplak, Bayly, Gould, Merz, Ferguson, +Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995). + +:link(howto-Mayo) +[(Mayo)] Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909 +(1990). diff --git a/doc/src/body.txt b/doc/src/Howto_body.txt similarity index 52% rename from doc/src/body.txt rename to doc/src/Howto_body.txt index 8d49efdae4..3e7db9bc8e 100644 --- a/doc/src/body.txt +++ b/doc/src/Howto_body.txt @@ -1,24 +1,24 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c +"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line -Body particles :h2 +Body particles :h3 [Overview:] -This doc page is not about a LAMMPS input script command, but about -body particles, which are generalized finite-size particles. +In LAMMPS, body particles are generalized finite-size particles. Individual body particles can represent complex entities, such as surface meshes of discrete points, collections of sub-particles, deformable objects, etc. Note that other kinds of finite-size spherical and aspherical particles are also supported by LAMMPS, such as spheres, ellipsoids, line segments, and triangles, but they are -simpler entities that body particles. See "Section -6.14"_Section_howto.html#howto_14 for a general overview of all +simpler entities that body particles. See the "Howto +spherical"_Howto_spherical.html doc page for a general overview of all these particle types. Body particles are used via the "atom_style body"_atom_style.html @@ -27,19 +27,17 @@ styles supported by LAMMPS are as follows. The name in the first column is used as the {bstyle} argument for the "atom_style body"_atom_style.html command. -{nparticle} | rigid body with N sub-particles | -{rounded/polygon} | 2d convex polygon with N vertices :tb(c=2,s=|) +{nparticle} : rigid body with N sub-particles +{rounded/polygon} : 2d polygons with N vertices +{rounded/polyhedron} : 3d polyhedra with N vertices, E edges and F faces :tb(s=:) The body style determines what attributes are stored for each body and thus how they can be used to compute pairwise body/body or bond/non-body (point particle) interactions. More details of each style are described below. -NOTE: The rounded/polygon style listed in the table above and -described below has not yet been relesed in LAMMPS. It will be soon. - -We hope to add more styles in the future. See "Section -10.12"_Section_modify.html#mod_12 for details on how to add a new body +More styles may be added in the future. See the "Modify +body"_Modify_body.html doc page for details on how to add a new body style to the code. :line @@ -61,7 +59,7 @@ the simple particles. By contrast, when body particles are used, LAMMPS treats an entire body as a single particle for purposes of computing pairwise interactions, building neighbor lists, migrating particles between -processors, outputting particles to a dump file, etc. This means that +processors, output of particles to a dump file, etc. This means that interactions between pairs of bodies or between a body and non-body (point) particle need to be encoded in an appropriate pair style. If such a pair style were to mimic the "fix rigid"_fix_rigid.html model, @@ -72,17 +70,20 @@ single body/body interaction was computed. Thus it only makes sense to use body particles and develop such a pair style, when particle/particle interactions are more complex than what the "fix rigid"_fix_rigid.html command can already calculate. For -example, if particles have one or more of the following attributes: +example, consider particles with one or more of the following +attributes: represented by a surface mesh represented by a collection of geometric entities (e.g. planes + spheres) deformable internal stress that induces fragmentation :ul -then the interaction between pairs of particles is likely to be more -complex than the summation of simple sub-particle interactions. An -example is contact or frictional forces between particles with planar -surfaces that inter-penetrate. +For these models, the interaction between pairs of particles is likely +to be more complex than the summation of simple pairwise interactions. +An example is contact or frictional forces between particles with +planar surfaces that inter-penetrate. Likewise, the body particle may +store internal state, such as a stress tensor used to compute a +fracture criterion. These are additional LAMMPS commands that can be used with body particles of different styles @@ -130,7 +131,9 @@ x1 y1 z1 ... xN yN zN :pre -N is the number of sub-particles in the body particle. M = 6 + 3*N. +where M = 6 + 3*N, and N is the number of sub-particles in the body +particle. + The integer line has a single value N. The floating point line(s) list 6 moments of inertia followed by the coordinates of the N sub-particles (x1 to zN) as 3N values. These values can be listed on @@ -148,8 +151,8 @@ center-of-mass position of the particle is specified by the x,y,z values in the {Atoms} section of the data file, as is the total mass of the body particle. -The "pair_style body"_pair_body.html command can be used with this -body style to compute body/body and body/non-body interactions. +The "pair_style body/nparticle"_pair_body_nparticle.html command can be used +with this body style to compute body/body and body/non-body interactions. For output purposes via the "compute body/local"_compute_body_local.html and "dump local"_dump.html @@ -175,15 +178,18 @@ The {bflag2} argument is ignored. [Specifics of body style rounded/polygon:] -NOTE: Aug 2016 - This body style has not yet been added to LAMMPS. -The info below is a placeholder. +The {rounded/polygon} body style represents body particles as a 2d +polygon with a variable number of N vertices. This style can only be +used for 2d models; see the "boundary"_boundary.html command. See the +"pair_style body/rounded/polygon" doc page for a diagram of two +squares with rounded circles at the vertices. Special cases for N = 1 +(circle) and N = 2 (rod with rounded ends) can also be specified. -The {rounded/polygon} body style represents body particles as a convex -polygon with a variable number N > 2 of vertices, which can only be -used for 2d models. One example use of this body style is for 2d -discrete element models, as described in "Fraige"_#Fraige. Similar to -body style {nparticle}, the atom_style body command for this body -style takes two additional arguments: +One use of this body style is for 2d discrete element models, as +described in "Fraige"_#body-Fraige. + +Similar to body style {nparticle}, the atom_style body command for +this body style takes two additional arguments: atom_style body rounded/polygon Nmin Nmax Nmin = minimum # of vertices in any body in the system @@ -203,17 +209,20 @@ x1 y1 z1 ... xN yN zN i j j k k ... -radius :pre +diameter :pre -N is the number of vertices in the body particle. M = 6 + 3*N + 2*N + -1. The integer line has a single value N. The floating point line(s) +where M = 6 + 3*N + 2*N + 1, and N is the number of vertices in the +body particle. + +The integer line has a single value N. The floating point line(s) list 6 moments of inertia followed by the coordinates of the N -vertices (x1 to zN) as 3N values, followed by 2N vertex indices -corresponding to the end points of the N edges, followed by a single -radius value = the smallest circle encompassing the polygon. That -last value is used to facilitate the body/body contact detection. -These floating-point values can be listed on as many lines as you -wish; see the "read_data"_read_data.html command for more details. +vertices (x1 to zN) as 3N values (with z = 0.0 for each), followed by +2N vertex indices corresponding to the end points of the N edges, +followed by a single diameter value = the rounded diameter of the +circle that surrounds each vertex. The diameter value can be different +for each body particle. These floating-point values can be listed on +as many lines as you wish; see the "read_data"_read_data.html command +for more details. The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the values consistent with the current orientation of the rigid body @@ -225,8 +234,11 @@ from the center-of-mass of the body particle. The center-of-mass position of the particle is specified by the x,y,z values in the {Atoms} section of the data file. -For example, the following information would specify a square -particles whose edge length is sqrt(2): +For example, the following information would specify a square particle +whose edge length is sqrt(2) and rounded diameter is 1.0. The +orientation of the square is aligned with the xy coordinate axes which +is consistent with the 6 moments of inertia: ixx iyy izz ixy ixz iyz = +1 1 4 0 0 0. Note that only Izz matters in 2D simulations. 3 1 27 4 @@ -235,12 +247,178 @@ particles whose edge length is sqrt(2): -0.7071 0.7071 0 0.7071 0.7071 0 0.7071 -0.7071 0 -0 1 1 2 2 3 3 0 +0 1 +1 2 +2 3 +3 0 1.0 :pre +A rod in 2D, whose length is 4.0, mass 1.0, rounded at two ends +by circles of diameter 0.5, is specified as follows: + +1 1 13 +2 +1 1 1.33333 0 0 0 +-2 0 0 +2 0 0 +0.5 :pre + +A disk, whose diameter is 3.0, mass 1.0, is specified as follows: + +1 1 10 +1 +1 1 4.5 0 0 0 +0 0 0 +3.0 :pre + The "pair_style body/rounded/polygon"_pair_body_rounded_polygon.html command can be used with this body style to compute body/body -interactions. +interactions. The "fix wall/body/polygon"_fix_wall_body_polygon.html +command can be used with this body style to compute the interaction of +body particles with a wall. + +:line + +[Specifics of body style rounded/polyhedron:] + +The {rounded/polyhedron} body style represents body particles as a 3d +polyhedron with a variable number of N vertices, E edges and F faces. +This style can only be used for 3d models; see the +"boundary"_boundary.html command. See the "pair_style +body/rounded/polygon" doc page for a diagram of a two 2d squares with +rounded circles at the vertices. A 3d cube with rounded spheres at +the 8 vertices and 12 rounded edges would be similar. Special cases +for N = 1 (sphere) and N = 2 (rod with rounded ends) can also be +specified. + +This body style is for 3d discrete element models, as described in +"Wang"_#body-Wang. + +Similar to body style {rounded/polygon}, the atom_style body command +for this body style takes two additional arguments: + +atom_style body rounded/polyhedron Nmin Nmax +Nmin = minimum # of vertices in any body in the system +Nmax = maximum # of vertices in any body in the system :pre + +The Nmin and Nmax arguments are used to bound the size of data +structures used internally by each particle. + +When the "read_data"_read_data.html command reads a data file for this +body style, the following information must be provided for each entry +in the {Bodies} section of the data file: + +atom-ID 3 M +N E F +ixx iyy izz ixy ixz iyz +x1 y1 z1 +... +xN yN zN +0 1 +1 2 +2 3 +... +0 1 2 -1 +0 2 3 -1 +... +1 2 3 4 +diameter :pre + +where M = 6 + 3*N + 2*E + 4*F + 1, and N is the number of vertices in +the body particle, E = number of edges, F = number of faces. + +The integer line has three values: number of vertices (N), number of +edges (E) and number of faces (F). The floating point line(s) list 6 +moments of inertia followed by the coordinates of the N vertices (x1 +to zN) as 3N values, followed by 2N vertex indices corresponding to +the end points of the E edges, then 4*F vertex indices defining F +faces. The last value is the diameter value = the rounded diameter of +the sphere that surrounds each vertex. The diameter value can be +different for each body particle. These floating-point values can be +listed on as many lines as you wish; see the +"read_data"_read_data.html command for more details. Because the +maximum number of vertices per face is hard-coded to be 4 +(i.e. quadrilaterals), faces with more than 4 vertices need to be +split into triangles or quadrilaterals. For triangular faces, the +last vertex index should be set to -1. + +The ordering of the 4 vertices within a face should follow +the right-hand rule so that the normal vector of the face points +outwards from the center of mass. + +The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the +values consistent with the current orientation of the rigid body +around its center of mass. The values are with respect to the +simulation box XYZ axes, not with respect to the principal axes of the +rigid body itself. LAMMPS performs the latter calculation internally. +The coordinates of each vertex are specified as its x,y,z displacement +from the center-of-mass of the body particle. The center-of-mass +position of the particle is specified by the x,y,z values in the +{Atoms} section of the data file. + +For example, the following information would specify a cubic particle +whose edge length is 2.0 and rounded diameter is 0.5. +The orientation of the cube is aligned with the xyz coordinate axes +which is consistent with the 6 moments of inertia: ixx iyy izz ixy ixz +iyz = 0.667 0.667 0.667 0 0 0. + +1 3 79 +8 12 6 +0.667 0.667 0.667 0 0 0 +1 1 1 +1 -1 1 +-1 -1 1 +-1 1 1 +1 1 -1 +1 -1 -1 +-1 -1 -1 +-1 1 -1 +0 1 +1 2 +2 3 +3 0 +4 5 +5 6 +6 7 +7 4 +0 4 +1 5 +2 6 +3 7 +0 1 2 3 +4 5 6 7 +0 1 5 4 +1 2 6 5 +2 3 7 6 +3 0 4 7 +0.5 :pre + +A rod in 3D, whose length is 4.0, mass 1.0 and rounded at two ends +by circles of diameter 0.5, is specified as follows: + +1 1 13 +2 +0 1.33333 1.33333 0 0 0 +-2 0 0 +2 0 0 +0.5 :pre + +A sphere whose diameter is 3.0 and mass 1.0, is specified as follows: + +1 1 10 +1 +0.9 0.9 0.9 0 0 0 +0 0 0 +3.0 :pre + +The "pair_style +body/rounded/polhedron"_pair_body_rounded_polyhedron.html command can +be used with this body style to compute body/body interactions. The +"fix wall/body/polyhedron"_fix_wall_body_polygon.html command can be +used with this body style to compute the interaction of body particles +with a wall. + +:line For output purposes via the "compute body/local"_compute_body_local.html and "dump local"_dump.html @@ -257,10 +435,10 @@ the body particle itself. These values are calculated using the current COM and orientation of the body particle. For images created by the "dump image"_dump_image.html command, if the -{body} keyword is set, then each body particle is drawn as a convex -polygon consisting of N line segments. Note that the line segments -are drawn between the N vertices, which does not correspond exactly to -the physical extent of the body (because the "pair_style +{body} keyword is set, then each body particle is drawn as a polygon +consisting of N line segments. Note that the line segments are drawn +between the N vertices, which does not correspond exactly to the +physical extent of the body (because the "pair_style rounded/polygon"_pair_body_rounded_polygon.html defines finite-size spheres at those point and the line segments between the spheres are tangent to the spheres). The drawn diameter of each line segment is @@ -269,6 +447,10 @@ determined by the {bflag1} parameter for the {body} keyword. The :line -:link(Fraige) +:link(body-Fraige) [(Fraige)] F. Y. Fraige, P. A. Langston, A. J. Matchett, J. Dodds, Particuology, 6, 455 (2008). + +:link(body-Wang) +[(Wang)] J. Wang, H. S. Yu, P. A. Langston, F. Y. Fraige, Granular +Matter, 13, 1 (2011). diff --git a/doc/src/Howto_chunk.txt b/doc/src/Howto_chunk.txt new file mode 100644 index 0000000000..82a4450d17 --- /dev/null +++ b/doc/src/Howto_chunk.txt @@ -0,0 +1,195 @@ +"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Use chunks to calculate system properties :h3 + +In LAMMS, "chunks" are collections of atoms, as defined by the +"compute chunk/atom"_compute_chunk_atom.html command, which assigns +each atom to a chunk ID (or to no chunk at all). The number of chunks +and the assignment of chunk IDs to atoms can be static or change over +time. Examples of "chunks" are molecules or spatial bins or atoms +with similar values (e.g. coordination number or potential energy). + +The per-atom chunk IDs can be used as input to two other kinds of +commands, to calculate various properties of a system: + +"fix ave/chunk"_fix_ave_chunk.html +any of the "compute */chunk"_compute.html commands :ul + +Here, each of the 4 kinds of chunk-related commands is briefly +overviewed. Then some examples are given of how to compute different +properties with chunk commands. + +Compute chunk/atom command: :h4 + +This compute can assign atoms to chunks of various styles. Only atoms +in the specified group and optional specified region are assigned to a +chunk. Here are some possible chunk definitions: + +atoms in same molecule | chunk ID = molecule ID | +atoms of same atom type | chunk ID = atom type | +all atoms with same atom property (charge, radius, etc) | chunk ID = output of compute property/atom | +atoms in same cluster | chunk ID = output of "compute cluster/atom"_compute_cluster_atom.html command | +atoms in same spatial bin | chunk ID = bin ID | +atoms in same rigid body | chunk ID = molecule ID used to define rigid bodies | +atoms with similar potential energy | chunk ID = output of "compute pe/atom"_compute_pe_atom.html | +atoms with same local defect structure | chunk ID = output of "compute centro/atom"_compute_centro_atom.html or "compute coord/atom"_compute_coord_atom.html command :tb(s=|,c=2) + +Note that chunk IDs are integer values, so for atom properties or +computes that produce a floating point value, they will be truncated +to an integer. You could also use the compute in a variable that +scales the floating point value to spread it across multiple integers. + +Spatial bins can be of various kinds, e.g. 1d bins = slabs, 2d bins = +pencils, 3d bins = boxes, spherical bins, cylindrical bins. + +This compute also calculates the number of chunks {Nchunk}, which is +used by other commands to tally per-chunk data. {Nchunk} can be a +static value or change over time (e.g. the number of clusters). The +chunk ID for an individual atom can also be static (e.g. a molecule +ID), or dynamic (e.g. what spatial bin an atom is in as it moves). + +Note that this compute allows the per-atom output of other +"computes"_compute.html, "fixes"_fix.html, and +"variables"_variable.html to be used to define chunk IDs for each +atom. This means you can write your own compute or fix to output a +per-atom quantity to use as chunk ID. See the "Modify"_Modify.html +doc pages for info on how to do this. You can also define a "per-atom +variable"_variable.html in the input script that uses a formula to +generate a chunk ID for each atom. + +Fix ave/chunk command: :h4 + +This fix takes the ID of a "compute +chunk/atom"_compute_chunk_atom.html command as input. For each chunk, +it then sums one or more specified per-atom values over the atoms in +each chunk. The per-atom values can be any atom property, such as +velocity, force, charge, potential energy, kinetic energy, stress, +etc. Additional keywords are defined for per-chunk properties like +density and temperature. More generally any per-atom value generated +by other "computes"_compute.html, "fixes"_fix.html, and "per-atom +variables"_variable.html, can be summed over atoms in each chunk. + +Similar to other averaging fixes, this fix allows the summed per-chunk +values to be time-averaged in various ways, and output to a file. The +fix produces a global array as output with one row of values per +chunk. + +Compute */chunk commands: :h4 + +The following computes operate on chunks of atoms to produce per-chunk +values. Any compute whose style name ends in "/chunk" is in this +category: + +"compute com/chunk"_compute_com_chunk.html +"compute gyration/chunk"_compute_gyration_chunk.html +"compute inertia/chunk"_compute_inertia_chunk.html +"compute msd/chunk"_compute_msd_chunk.html +"compute property/chunk"_compute_property_chunk.html +"compute temp/chunk"_compute_temp_chunk.html +"compute torque/chunk"_compute_vcm_chunk.html +"compute vcm/chunk"_compute_vcm_chunk.html :ul + +They each take the ID of a "compute +chunk/atom"_compute_chunk_atom.html command as input. As their names +indicate, they calculate the center-of-mass, radius of gyration, +moments of inertia, mean-squared displacement, temperature, torque, +and velocity of center-of-mass for each chunk of atoms. The "compute +property/chunk"_compute_property_chunk.html command can tally the +count of atoms in each chunk and extract other per-chunk properties. + +The reason these various calculations are not part of the "fix +ave/chunk command"_fix_ave_chunk.html, is that each requires a more +complicated operation than simply summing and averaging over per-atom +values in each chunk. For example, many of them require calculation +of a center of mass, which requires summing mass*position over the +atoms and then dividing by summed mass. + +All of these computes produce a global vector or global array as +output, wih one or more values per chunk. The output can be used in +various ways: + +As input to the "fix ave/time"_fix_ave_time.html command, which can +write the values to a file and optionally time average them. :ulb,l + +As input to the "fix ave/histo"_fix_ave_histo.html command to +histogram values across chunks. E.g. a histogram of cluster sizes or +molecule diffusion rates. :l + +As input to special functions of "equal-style +variables"_variable.html, like sum() and max() and ave(). E.g. to +find the largest cluster or fastest diffusing molecule or average +radius-of-gyration of a set of molecules (chunks). :l,ule + +Other chunk commands: :h4 + +"compute chunk/spread/atom"_compute_chunk_spread_atom.html +"compute reduce/chunk"_compute_reduce_chunk.html :ul + +The "compute chunk/spread/atom"_compute_chunk_spread_atom.html command +spreads per-chunk values to each atom in the chunk, producing per-atom +values as its output. This can be useful for outputting per-chunk +values to a per-atom "dump file"_dump.html. Or for using an atom's +associated chunk value in an "atom-style variable"_variable.html. + +The "compute reduce/chunk"_compute_reduce_chunk.html command reduces a +peratom value across the atoms in each chunk to produce a value per +chunk. When used with the "compute +chunk/spread/atom"_compute_chunk_spread_atom.html command it can +create peratom values that induce a new set of chunks with a second +"compute chunk/atom"_compute_chunk_atom.html command. + +Example calculations with chunks :h4 + +Here are examples using chunk commands to calculate various +properties: + +(1) Average velocity in each of 1000 2d spatial bins: + +compute cc1 all chunk/atom bin/2d x 0.0 0.1 y lower 0.01 units reduced +fix 1 all ave/chunk 100 10 1000 cc1 vx vy file tmp.out :pre + +(2) Temperature in each spatial bin, after subtracting a flow +velocity: + +compute cc1 all chunk/atom bin/2d x 0.0 0.1 y lower 0.1 units reduced +compute vbias all temp/profile 1 0 0 y 10 +fix 1 all ave/chunk 100 10 1000 cc1 temp bias vbias file tmp.out :pre + +(3) Center of mass of each molecule: + +compute cc1 all chunk/atom molecule +compute myChunk all com/chunk cc1 +fix 1 all ave/time 100 1 100 c_myChunk\[*\] file tmp.out mode vector :pre + +(4) Total force on each molecule and ave/max across all molecules: + +compute cc1 all chunk/atom molecule +fix 1 all ave/chunk 1000 1 1000 cc1 fx fy fz file tmp.out +variable xave equal ave(f_1\[2\]) +variable xmax equal max(f_1\[2\]) +thermo 1000 +thermo_style custom step temp v_xave v_xmax :pre + +(5) Histogram of cluster sizes: + +compute cluster all cluster/atom 1.0 +compute cc1 all chunk/atom c_cluster compress yes +compute size all property/chunk cc1 count +fix 1 all ave/histo 100 1 100 0 20 20 c_size mode vector ave running beyond ignore file tmp.histo :pre + +(6) An example of using a per-chunk value to apply per-atom forces to +compress individual polymer chains (molecules) in a mixture, is +explained on the "compute +chunk/spread/atom"_compute_chunk_spread_atom.html command doc page. + +(7) An example of using one set of per-chunk values for molecule +chunks, to create a 2nd set of micelle-scale chunks (clustered +molecules, due to hydrophobicity), is explained on the "compute +chunk/reduce"_compute_reduce_chunk.html command doc page. diff --git a/doc/src/Howto_client_server.txt b/doc/src/Howto_client_server.txt new file mode 100644 index 0000000000..aa6b8eab76 --- /dev/null +++ b/doc/src/Howto_client_server.txt @@ -0,0 +1,131 @@ +"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Using LAMMPS in client/server mode :h3 + +Client/server coupling of two codes is where one code is the "client" +and sends request messages to a "server" code. The server responds to +each request with a reply message. This enables the two codes to work +in tandem to perform a simulation. LAMMPS can act as either a client +or server code. + +Some advantages of client/server coupling are that the two codes run +as stand-alone executables; they are not linked together. Thus +neither code needs to have a library interface. This often makes it +easier to run the two codes on different numbers of processors. If a +message protocol (format and content) is defined for a particular kind +of simulation, then in principle any code that implements the +client-side protocol can be used in tandem with any code that +implements the server-side protocol, without the two codes needing to +know anything more specific about each other. + +A simple example of client/server coupling is where LAMMPS is the +client code performing MD timestepping. Each timestep it sends a +message to a server quantum code containing current coords of all the +atoms. The quantum code computes energy and forces based on the +coords. It returns them as a message to LAMMPS, which completes the +timestep. + +Alternate methods for code coupling with LAMMPS are described on +the "Howto couple"_Howto_couple.html doc page. + +LAMMPS support for client/server coupling is in its "MESSAGE +package"_Packages_details.html#PKG-MESSAGE which implements several +commands that enable LAMMPS to act as a client or server, as discussed +below. The MESSAGE package also wraps a client/server library called +CSlib which enables two codes to exchange messages in different ways, +either via files, sockets, or MPI. The CSlib is provided with LAMMPS +in the lib/message dir. The CSlib has its own +"website"_http://cslib.sandia.gov with documentation and test +programs. + +NOTE: For client/server coupling to work between LAMMPS and another +code, the other code also has to use the CSlib. This can sometimes be +done without any modifications to the other code by simply wrapping it +with a Python script that exchanges CSlib messages with LAMMPS and +prepares input for or processes output from the other code. The other +code also has to implement a matching protocol for the format and +content of messages that LAMMPS exchanges with it. + +These are the commands currently in the MESSAGE package for two +protocols, MD and MC (Monte Carlo). New protocols can easily be +defined and added to this directory, where LAMMPS acts as either the +client or server. + +"message"_message.html +"fix client md"_fix_client_md.html = LAMMPS is a client for running MD +"server md"_server_md.html = LAMMPS is a server for computing MD forces +"server mc"_server_mc.html = LAMMPS is a server for computing a Monte Carlo energy :ul + +The server doc files give details of the message protocols +for data that is exchanged bewteen the client and server. + +These example directories illustrate how to use LAMMPS as either a +client or server code: + +examples/message +examples/COUPLE/README +examples/COUPLE/lammps_mc +examples/COUPLE/lammps_vasp :ul + +The examples/message dir couples a client instance of LAMMPS to a +server instance of LAMMPS. + +The lammps_mc dir shows how to couple LAMMPS as a server to a simple +Monte Carlo client code as the driver. + +The lammps_vasp dir shows how to couple LAMMPS as a client code +running MD timestepping to VASP acting as a server providing quantum +DFT forces, thru a Python wrapper script on VASP. + +Here is how to launch a client and server code together for any of the +4 modes of message exchange that the "message"_message.html command +and the CSlib support. Here LAMMPS is used as both the client and +server code. Another code could be subsitituted for either. + +The examples below show launching both codes from the same window (or +batch script), using the "&" character to launch the first code in the +background. For all modes except {mpi/one}, you could also launch the +codes in separate windows on your desktop machine. It does not +matter whether you launch the client or server first. + +In these examples either code can be run on one or more processors. +If running in a non-MPI mode (file or zmq) you can launch a code on a +single processor without using mpirun. + +IMPORTANT: If you run in mpi/two mode, you must launch both codes via +mpirun, even if one or both of them runs on a single processor. This +is so that MPI can figure out how to connect both MPI processes +together to exchange MPI messages between them. + +For message exchange in {file}, {zmq}, or {mpi/two} modes: + +% mpirun -np 1 lmp_mpi -log log.client < in.client & +% mpirun -np 2 lmp_mpi -log log.server < in.server :pre + +% mpirun -np 4 lmp_mpi -log log.client < in.client & +% mpirun -np 1 lmp_mpi -log log.server < in.server :pre + +% mpirun -np 2 lmp_mpi -log log.client < in.client & +% mpirun -np 4 lmp_mpi -log log.server < in.server :pre + +For message exchange in {mpi/one} mode: + +Launch both codes in a single mpirun command: + +mpirun -np 2 lmp_mpi -mpicolor 0 -in in.message.client -log log.client : -np 4 lmp_mpi -mpicolor 1 -in in.message.server -log log.server :pre + +The two -np values determine how many procs the client and the server +run on. + +A LAMMPS executable run in this manner must use the -mpicolor color +command-line option as their its option, where color is an integer +label that will be used to distinguish one executable from another in +the multiple executables that the mpirun command launches. In this +example the client was colored with a 0, and the server with a 1. diff --git a/doc/src/Howto_coreshell.txt b/doc/src/Howto_coreshell.txt new file mode 100644 index 0000000000..7503fa1ebe --- /dev/null +++ b/doc/src/Howto_coreshell.txt @@ -0,0 +1,253 @@ +"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Adiabatic core/shell model :h3 + +The adiabatic core-shell model by "Mitchell and +Fincham"_#MitchellFincham is a simple method for adding polarizability +to a system. In order to mimic the electron shell of an ion, a +satellite particle is attached to it. This way the ions are split into +a core and a shell where the latter is meant to react to the +electrostatic environment inducing polarizability. See the "Howto +polarizable"_Howto_polarizable.html doc page for a discussion of all +the polarizable models available in LAMMPS. + +Technically, shells are attached to the cores by a spring force f = +k*r where k is a parametrized spring constant and r is the distance +between the core and the shell. The charges of the core and the shell +add up to the ion charge, thus q(ion) = q(core) + q(shell). This +setup introduces the ion polarizability (alpha) given by +alpha = q(shell)^2 / k. In a +similar fashion the mass of the ion is distributed on the core and the +shell with the core having the larger mass. + +To run this model in LAMMPS, "atom_style"_atom_style.html {full} can +be used since atom charge and bonds are needed. Each kind of +core/shell pair requires two atom types and a bond type. The core and +shell of a core/shell pair should be bonded to each other with a +harmonic bond that provides the spring force. For example, a data file +for NaCl, as found in examples/coreshell, has this format: + +432 atoms # core and shell atoms +216 bonds # number of core/shell springs :pre + +4 atom types # 2 cores and 2 shells for Na and Cl +2 bond types :pre + +0.0 24.09597 xlo xhi +0.0 24.09597 ylo yhi +0.0 24.09597 zlo zhi :pre + +Masses # core/shell mass ratio = 0.1 :pre + +1 20.690784 # Na core +2 31.90500 # Cl core +3 2.298976 # Na shell +4 3.54500 # Cl shell :pre + +Atoms :pre + +1 1 2 1.5005 0.00000000 0.00000000 0.00000000 # core of core/shell pair 1 +2 1 4 -2.5005 0.00000000 0.00000000 0.00000000 # shell of core/shell pair 1 +3 2 1 1.5056 4.01599500 4.01599500 4.01599500 # core of core/shell pair 2 +4 2 3 -0.5056 4.01599500 4.01599500 4.01599500 # shell of core/shell pair 2 +(...) :pre + +Bonds # Bond topology for spring forces :pre + +1 2 1 2 # spring for core/shell pair 1 +2 2 3 4 # spring for core/shell pair 2 +(...) :pre + +Non-Coulombic (e.g. Lennard-Jones) pairwise interactions are only +defined between the shells. Coulombic interactions are defined +between all cores and shells. If desired, additional bonds can be +specified between cores. + +The "special_bonds"_special_bonds.html command should be used to +turn-off the Coulombic interaction within core/shell pairs, since that +interaction is set by the bond spring. This is done using the +"special_bonds"_special_bonds.html command with a 1-2 weight = 0.0, +which is the default value. It needs to be considered whether one has +to adjust the "special_bonds"_special_bonds.html weighting according +to the molecular topology since the interactions of the shells are +bypassed over an extra bond. + +Note that this core/shell implementation does not require all ions to +be polarized. One can mix core/shell pairs and ions without a +satellite particle if desired. + +Since the core/shell model permits distances of r = 0.0 between the +core and shell, a pair style with a "cs" suffix needs to be used to +implement a valid long-range Coulombic correction. Several such pair +styles are provided in the CORESHELL package. See "this doc +page"_pair_cs.html for details. All of the core/shell enabled pair +styles require the use of a long-range Coulombic solver, as specified +by the "kspace_style"_kspace_style.html command. Either the PPPM or +Ewald solvers can be used. + +For the NaCL example problem, these pair style and bond style settings +are used: + +pair_style born/coul/long/cs 20.0 20.0 +pair_coeff * * 0.0 1.000 0.00 0.00 0.00 +pair_coeff 3 3 487.0 0.23768 0.00 1.05 0.50 #Na-Na +pair_coeff 3 4 145134.0 0.23768 0.00 6.99 8.70 #Na-Cl +pair_coeff 4 4 405774.0 0.23768 0.00 72.40 145.40 #Cl-Cl :pre + +bond_style harmonic +bond_coeff 1 63.014 0.0 +bond_coeff 2 25.724 0.0 :pre + +When running dynamics with the adiabatic core/shell model, the +following issues should be considered. The relative motion of +the core and shell particles corresponds to the polarization, +hereby an instantaneous relaxation of the shells is approximated +and a fast core/shell spring frequency ensures a nearly constant +internal kinetic energy during the simulation. +Thermostats can alter this polarization behaviour, by scaling the +internal kinetic energy, meaning the shell will not react freely to +its electrostatic environment. +Therefore it is typically desirable to decouple the relative motion of +the core/shell pair, which is an imaginary degree of freedom, from the +real physical system. To do that, the "compute +temp/cs"_compute_temp_cs.html command can be used, in conjunction with +any of the thermostat fixes, such as "fix nvt"_fix_nh.html or "fix +langevin"_fix_langevin.html. This compute uses the center-of-mass velocity +of the core/shell pairs to calculate a temperature, and insures that +velocity is what is rescaled for thermostatting purposes. This +compute also works for a system with both core/shell pairs and +non-polarized ions (ions without an attached satellite particle). The +"compute temp/cs"_compute_temp_cs.html command requires input of two +groups, one for the core atoms, another for the shell atoms. +Non-polarized ions which might also be included in the treated system +should not be included into either of these groups, they are taken +into account by the {group-ID} (2nd argument) of the compute. The +groups can be defined using the "group {type}"_group.html command. +Note that to perform thermostatting using this definition of +temperature, the "fix modify temp"_fix_modify.html command should be +used to assign the compute to the thermostat fix. Likewise the +"thermo_modify temp"_thermo_modify.html command can be used to make +this temperature be output for the overall system. + +For the NaCl example, this can be done as follows: + +group cores type 1 2 +group shells type 3 4 +compute CSequ all temp/cs cores shells +fix thermoberendsen all temp/berendsen 1427 1427 0.4 # thermostat for the true physical system +fix thermostatequ all nve # integrator as needed for the berendsen thermostat +fix_modify thermoberendsen temp CSequ +thermo_modify temp CSequ # output of center-of-mass derived temperature :pre + +The pressure for the core/shell system is computed via the regular +LAMMPS convention by "treating the cores and shells as individual +particles"_#MitchellFincham2. For the thermo output of the pressure +as well as for the application of a barostat, it is necessary to +use an additional "pressure"_compute_pressure.html compute based on +the default "temperature"_compute_temp.html and specifying it as a +second argument in "fix modify"_fix_modify.html and +"thermo_modify"_thermo_modify.html resulting in: + +(...) +compute CSequ all temp/cs cores shells +compute thermo_press_lmp all pressure thermo_temp # pressure for individual particles +thermo_modify temp CSequ press thermo_press_lmp # modify thermo to regular pressure +fix press_bar all npt temp 300 300 0.04 iso 0 0 0.4 +fix_modify press_bar temp CSequ press thermo_press_lmp # pressure modification for correct kinetic scalar :pre + +If "compute temp/cs"_compute_temp_cs.html is used, the decoupled +relative motion of the core and the shell should in theory be +stable. However numerical fluctuation can introduce a small +momentum to the system, which is noticable over long trajectories. +Therefore it is recommendable to use the "fix +momentum"_fix_momentum.html command in combination with "compute +temp/cs"_compute_temp_cs.html when equilibrating the system to +prevent any drift. + +When initializing the velocities of a system with core/shell pairs, it +is also desirable to not introduce energy into the relative motion of +the core/shell particles, but only assign a center-of-mass velocity to +the pairs. This can be done by using the {bias} keyword of the +"velocity create"_velocity.html command and assigning the "compute +temp/cs"_compute_temp_cs.html command to the {temp} keyword of the +"velocity"_velocity.html command, e.g. + +velocity all create 1427 134 bias yes temp CSequ +velocity all scale 1427 temp CSequ :pre + +To maintain the correct polarizability of the core/shell pairs, the +kinetic energy of the internal motion shall remain nearly constant. +Therefore the choice of spring force and mass ratio need to ensure +much faster relative motion of the 2 atoms within the core/shell pair +than their center-of-mass velocity. This allows the shells to +effectively react instantaneously to the electrostatic environment and +limits energy transfer to or from the core/shell oscillators. +This fast movement also dictates the timestep that can be used. + +The primary literature of the adiabatic core/shell model suggests that +the fast relative motion of the core/shell pairs only allows negligible +energy transfer to the environment. +The mentioned energy transfer will typically lead to a small drift +in total energy over time. This internal energy can be monitored +using the "compute chunk/atom"_compute_chunk_atom.html and "compute +temp/chunk"_compute_temp_chunk.html commands. The internal kinetic +energies of each core/shell pair can then be summed using the sum() +special function of the "variable"_variable.html command. Or they can +be time/averaged and output using the "fix ave/time"_fix_ave_time.html +command. To use these commands, each core/shell pair must be defined +as a "chunk". If each core/shell pair is defined as its own molecule, +the molecule ID can be used to define the chunks. If cores are bonded +to each other to form larger molecules, the chunks can be identified +by the "fix property/atom"_fix_property_atom.html via assigning a +core/shell ID to each atom using a special field in the data file read +by the "read_data"_read_data.html command. This field can then be +accessed by the "compute property/atom"_compute_property_atom.html +command, to use as input to the "compute +chunk/atom"_compute_chunk_atom.html command to define the core/shell +pairs as chunks. + +For example if core/shell pairs are the only molecules: + +read_data NaCl_CS_x0.1_prop.data +compute prop all property/atom molecule +compute cs_chunk all chunk/atom c_prop +compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0 # note the chosen degrees of freedom for the core/shell pairs +fix ave_chunk all ave/time 10 1 10 c_cstherm file chunk.dump mode vector :pre + +For example if core/shell pairs and other molecules are present: + +fix csinfo all property/atom i_CSID # property/atom command +read_data NaCl_CS_x0.1_prop.data fix csinfo NULL CS-Info # atom property added in the data-file +compute prop all property/atom i_CSID +(...) :pre + +The additional section in the date file would be formatted like this: + +CS-Info # header of additional section :pre + +1 1 # column 1 = atom ID, column 2 = core/shell ID +2 1 +3 2 +4 2 +5 3 +6 3 +7 4 +8 4 +(...) :pre + +:line + +:link(MitchellFincham) +[(Mitchell and Fincham)] Mitchell, Fincham, J Phys Condensed Matter, +5, 1031-1038 (1993). + +:link(MitchellFincham2) +[(Fincham)] Fincham, Mackrodt and Mitchell, J Phys Condensed Matter, +6, 393-404 (1994). diff --git a/doc/src/Howto_couple.txt b/doc/src/Howto_couple.txt new file mode 100644 index 0000000000..0214db1ece --- /dev/null +++ b/doc/src/Howto_couple.txt @@ -0,0 +1,116 @@ +"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Coupling LAMMPS to other codes :h3 + +LAMMPS is designed to allow it to be coupled to other codes. For +example, a quantum mechanics code might compute forces on a subset of +atoms and pass those forces to LAMMPS. Or a continuum finite element +(FE) simulation might use atom positions as boundary conditions on FE +nodal points, compute a FE solution, and return interpolated forces on +MD atoms. + +LAMMPS can be coupled to other codes in at least 4 ways. Each has +advantages and disadvantages, which you'll have to think about in the +context of your application. + +:line + +(1) Define a new "fix"_fix.html command that calls the other code. In +this scenario, LAMMPS is the driver code. During its timestepping, +the fix is invoked, and can make library calls to the other code, +which has been linked to LAMMPS as a library. This is the way the +"POEMS"_poems package that performs constrained rigid-body motion on +groups of atoms is hooked to LAMMPS. See the "fix +poems"_fix_poems.html command for more details. See the +"Modify"_Modify.html doc pages for info on how to add a new fix to +LAMMPS. + +:link(poems,http://www.rpi.edu/~anderk5/lab) + +:line + +(2) Define a new LAMMPS command that calls the other code. This is +conceptually similar to method (1), but in this case LAMMPS and the +other code are on a more equal footing. Note that now the other code +is not called during the timestepping of a LAMMPS run, but between +runs. The LAMMPS input script can be used to alternate LAMMPS runs +with calls to the other code, invoked via the new command. The +"run"_run.html command facilitates this with its {every} option, which +makes it easy to run a few steps, invoke the command, run a few steps, +invoke the command, etc. + +In this scenario, the other code can be called as a library, as in +(1), or it could be a stand-alone code, invoked by a system() call +made by the command (assuming your parallel machine allows one or more +processors to start up another program). In the latter case the +stand-alone code could communicate with LAMMPS thru files that the +command writes and reads. + +See the "Modify command"_Modify_command.html doc page for info on how +to add a new command to LAMMPS. + +:line + +(3) Use LAMMPS as a library called by another code. In this case the +other code is the driver and calls LAMMPS as needed. Or a wrapper +code could link and call both LAMMPS and another code as libraries. +Again, the "run"_run.html command has options that allow it to be +invoked with minimal overhead (no setup or clean-up) if you wish to do +multiple short runs, driven by another program. + +Examples of driver codes that call LAMMPS as a library are included in +the examples/COUPLE directory of the LAMMPS distribution; see +examples/COUPLE/README for more details: + +simple: simple driver programs in C++ and C which invoke LAMMPS as a +library :ulb,l + +lammps_quest: coupling of LAMMPS and "Quest"_quest, to run classical +MD with quantum forces calculated by a density functional code :l + +lammps_spparks: coupling of LAMMPS and "SPPARKS"_spparks, to couple +a kinetic Monte Carlo model for grain growth using MD to calculate +strain induced across grain boundaries :l +:ule + +:link(quest,http://dft.sandia.gov/Quest) +:link(spparks,http://www.sandia.gov/~sjplimp/spparks.html) + +The "Build basics"_Build_basics.html doc page describes how to build +LAMMPS as a library. Once this is done, you can interface with LAMMPS +either via C++, C, Fortran, or Python (or any other language that +supports a vanilla C-like interface). For example, from C++ you could +create one (or more) "instances" of LAMMPS, pass it an input script to +process, or execute individual commands, all by invoking the correct +class methods in LAMMPS. From C or Fortran you can make function +calls to do the same things. See the "Python"_Python_head.html doc +pages for a description of the Python wrapper provided with LAMMPS +that operates through the LAMMPS library interface. + +The files src/library.cpp and library.h contain the C-style interface +to LAMMPS. See the "Howto library"_Howto_library.html doc page for a +description of the interface and how to extend it for your needs. + +Note that the lammps_open() function that creates an instance of +LAMMPS takes an MPI communicator as an argument. This means that +instance of LAMMPS will run on the set of processors in the +communicator. Thus the calling code can run LAMMPS on all or a subset +of processors. For example, a wrapper script might decide to +alternate between LAMMPS and another code, allowing them both to run +on all the processors. Or it might allocate half the processors to +LAMMPS and half to the other code and run both codes simultaneously +before syncing them up periodically. Or it might instantiate multiple +instances of LAMMPS to perform different calculations. + +:line + +(4) Couple LAMMPS with another code in a client/server mode. This is +described on the "Howto client/server"_Howto_client_server.html doc +page. diff --git a/doc/src/Howto_diffusion.txt b/doc/src/Howto_diffusion.txt new file mode 100644 index 0000000000..6c920c9bc3 --- /dev/null +++ b/doc/src/Howto_diffusion.txt @@ -0,0 +1,31 @@ +"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Calculate diffusion coefficients :h3 + +The diffusion coefficient D of a material can be measured in at least +2 ways using various options in LAMMPS. See the examples/DIFFUSE +directory for scripts that implement the 2 methods discussed here for +a simple Lennard-Jones fluid model. + +The first method is to measure the mean-squared displacement (MSD) of +the system, via the "compute msd"_compute_msd.html command. The slope +of the MSD versus time is proportional to the diffusion coefficient. +The instantaneous MSD values can be accumulated in a vector via the +"fix vector"_fix_vector.html command, and a line fit to the vector to +compute its slope via the "variable slope"_variable.html function, and +thus extract D. + +The second method is to measure the velocity auto-correlation function +(VACF) of the system, via the "compute vacf"_compute_vacf.html +command. The time-integral of the VACF is proportional to the +diffusion coefficient. The instantaneous VACF values can be +accumulated in a vector via the "fix vector"_fix_vector.html command, +and time integrated via the "variable trap"_variable.html function, +and thus extract D. diff --git a/doc/src/Howto_dispersion.txt b/doc/src/Howto_dispersion.txt new file mode 100644 index 0000000000..8a5953d84d --- /dev/null +++ b/doc/src/Howto_dispersion.txt @@ -0,0 +1,108 @@ +"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Long-range dispersion settings :h3 + +The PPPM method computes interactions by splitting the pair potential +into two parts, one of which is computed in a normal pairwise fashion, +the so-called real-space part, and one of which is computed using the +Fourier transform, the so called reciprocal-space or kspace part. For +both parts, the potential is not computed exactly but is approximated. +Thus, there is an error in both parts of the computation, the +real-space and the kspace error. The just mentioned facts are true +both for the PPPM for Coulomb as well as dispersion interactions. The +deciding difference - and also the reason why the parameters for +pppm/disp have to be selected with more care - is the impact of the +errors on the results: The kspace error of the PPPM for Coulomb and +dispersion interaction and the real-space error of the PPPM for +Coulomb interaction have the character of noise. In contrast, the +real-space error of the PPPM for dispersion has a clear physical +interpretation: the underprediction of cohesion. As a consequence, the +real-space error has a much stronger effect than the kspace error on +simulation results for pppm/disp. Parameters must thus be chosen in a +way that this error is much smaller than the kspace error. + +When using pppm/disp and not making any specifications on the PPPM +parameters via the kspace modify command, parameters will be tuned +such that the real-space error and the kspace error are equal. This +will result in simulations that are either inaccurate or slow, both of +which is not desirable. For selecting parameters for the pppm/disp +that provide fast and accurate simulations, there are two approaches, +which both have their up- and downsides. + +The first approach is to set desired real-space an kspace accuracies +via the {kspace_modify force/disp/real} and {kspace_modify +force/disp/kspace} commands. Note that the accuracies have to be +specified in force units and are thus dependent on the chosen unit +settings. For real units, 0.0001 and 0.002 seem to provide reasonable +accurate and efficient computations for the real-space and kspace +accuracies. 0.002 and 0.05 work well for most systems using lj +units. PPPM parameters will be generated based on the desired +accuracies. The upside of this approach is that it usually provides a +good set of parameters and will work for both the {kspace_modify diff +ad} and {kspace_modify diff ik} options. The downside of the method +is that setting the PPPM parameters will take some time during the +initialization of the simulation. + +The second approach is to set the parameters for the pppm/disp +explicitly using the {kspace_modify mesh/disp}, {kspace_modify +order/disp}, and {kspace_modify gewald/disp} commands. This approach +requires a more experienced user who understands well the impact of +the choice of parameters on the simulation accuracy and +performance. This approach provides a fast initialization of the +simulation. However, it is sensitive to errors: A combination of +parameters that will perform well for one system might result in +far-from-optimal conditions for other simulations. For example, +parameters that provide accurate and fast computations for +all-atomistic force fields can provide insufficient accuracy or +united-atomistic force fields (which is related to that the latter +typically have larger dispersion coefficients). + +To avoid inaccurate or inefficient simulations, the pppm/disp stops +simulations with an error message if no action is taken to control the +PPPM parameters. If the automatic parameter generation is desired and +real-space and kspace accuracies are desired to be equal, this error +message can be suppressed using the {kspace_modify disp/auto yes} +command. + +A reasonable approach that combines the upsides of both methods is to +make the first run using the {kspace_modify force/disp/real} and +{kspace_modify force/disp/kspace} commands, write down the PPPM +parameters from the outut, and specify these parameters using the +second approach in subsequent runs (which have the same composition, +force field, and approximately the same volume). + +Concerning the performance of the pppm/disp there are two more things +to consider. The first is that when using the pppm/disp, the cutoff +parameter does no longer affect the accuracy of the simulation +(subject to that gewald/disp is adjusted when changing the cutoff). +The performance can thus be increased by examining different values +for the cutoff parameter. A lower bound for the cutoff is only set by +the truncation error of the repulsive term of pair potentials. + +The second is that the mixing rule of the pair style has an impact on +the computation time when using the pppm/disp. Fastest computations +are achieved when using the geometric mixing rule. Using the +arithmetic mixing rule substantially increases the computational cost. +The computational overhead can be reduced using the {kspace_modify +mix/disp geom} and {kspace_modify splittol} commands. The first +command simply enforces geometric mixing of the dispersion +coefficients in kspace computations. This introduces some error in +the computations but will also significantly speed-up the +simulations. The second keyword sets the accuracy with which the +dispersion coefficients are approximated using a matrix factorization +approach. This may result in better accuracy then using the first +command, but will usually also not provide an equally good increase of +efficiency. + +Finally, pppm/disp can also be used when no mixing rules apply. +This can be achieved using the {kspace_modify mix/disp none} command. +Note that the code does not check automatically whether any mixing +rule is fulfilled. If mixing rules do not apply, the user will have +to specify this command explicitly. diff --git a/doc/src/Howto_drude.txt b/doc/src/Howto_drude.txt new file mode 100644 index 0000000000..ebdf5f8658 --- /dev/null +++ b/doc/src/Howto_drude.txt @@ -0,0 +1,77 @@ +"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Drude induced dipoles :h3 + +The thermalized Drude model represents induced dipoles by a pair of +charges (the core atom and the Drude particle) connected by a harmonic +spring. See the "Howto polarizable"_Howto_polarizable.html doc page +for a discussion of all the polarizable models available in LAMMPS. + +The Drude model has a number of features aimed at its use in +molecular systems ("Lamoureux and Roux"_#howto-Lamoureux): + +Thermostating of the additional degrees of freedom associated with the +induced dipoles at very low temperature, in terms of the reduced +coordinates of the Drude particles with respect to their cores. This +makes the trajectory close to that of relaxed induced dipoles. :ulb,l + +Consistent definition of 1-2 to 1-4 neighbors. A core-Drude particle +pair represents a single (polarizable) atom, so the special screening +factors in a covalent structure should be the same for the core and +the Drude particle. Drude particles have to inherit the 1-2, 1-3, 1-4 +special neighbor relations from their respective cores. :l + +Stabilization of the interactions between induced dipoles. Drude +dipoles on covalently bonded atoms interact too strongly due to the +short distances, so an atom may capture the Drude particle of a +neighbor, or the induced dipoles within the same molecule may align +too much. To avoid this, damping at short range can be done by Thole +functions (for which there are physical grounds). This Thole damping +is applied to the point charges composing the induced dipole (the +charge of the Drude particle and the opposite charge on the core, not +to the total charge of the core atom). :l,ule + +A detailed tutorial covering the usage of Drude induced dipoles in +LAMMPS is on the "Howto drude2e"_Howto_drude2.html doc page. + +As with the core-shell model, the cores and Drude particles should +appear in the data file as standard atoms. The same holds for the +springs between them, which are described by standard harmonic bonds. +The nature of the atoms (core, Drude particle or non-polarizable) is +specified via the "fix drude"_fix_drude.html command. The special +list of neighbors is automatically refactored to account for the +equivalence of core and Drude particles as regards special 1-2 to 1-4 +screening. It may be necessary to use the {extra/special/per/atom} +keyword of the "read_data"_read_data.html command. If using "fix +shake"_fix_shake.html, make sure no Drude particle is in this fix +group. + +There are two ways to thermostat the Drude particles at a low +temperature: use either "fix langevin/drude"_fix_langevin_drude.html +for a Langevin thermostat, or "fix +drude/transform/*"_fix_drude_transform.html for a Nose-Hoover +thermostat. The former requires use of the command "comm_modify vel +yes"_comm_modify.html. The latter requires two separate integration +fixes like {nvt} or {npt}. The correct temperatures of the reduced +degrees of freedom can be calculated using the "compute +temp/drude"_compute_temp_drude.html. This requires also to use the +command {comm_modify vel yes}. + +Short-range damping of the induced dipole interactions can be achieved +using Thole functions through the "pair style +thole"_pair_thole.html in "pair_style hybrid/overlay"_pair_hybrid.html +with a Coulomb pair style. It may be useful to use {coul/long/cs} or +similar from the CORESHELL package if the core and Drude particle come +too close, which can cause numerical issues. + +:line + +:link(howto-Lamoureux) +[(Lamoureux and Roux)] G. Lamoureux, B. Roux, J. Chem. Phys 119, 3025 (2003) diff --git a/doc/src/tutorial_drude.txt b/doc/src/Howto_drude2.txt similarity index 99% rename from doc/src/tutorial_drude.txt rename to doc/src/Howto_drude2.txt index f6e7eed40b..a342d4a87d 100644 --- a/doc/src/tutorial_drude.txt +++ b/doc/src/Howto_drude2.txt @@ -9,7 +9,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Howto_elastic.txt b/doc/src/Howto_elastic.txt new file mode 100644 index 0000000000..68b30970ca --- /dev/null +++ b/doc/src/Howto_elastic.txt @@ -0,0 +1,47 @@ +"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Calculate elastic constants :h3 + +Elastic constants characterize the stiffness of a material. The formal +definition is provided by the linear relation that holds between the +stress and strain tensors in the limit of infinitesimal deformation. +In tensor notation, this is expressed as s_ij = C_ijkl * e_kl, where +the repeated indices imply summation. s_ij are the elements of the +symmetric stress tensor. e_kl are the elements of the symmetric strain +tensor. C_ijkl are the elements of the fourth rank tensor of elastic +constants. In three dimensions, this tensor has 3^4=81 elements. Using +Voigt notation, the tensor can be written as a 6x6 matrix, where C_ij +is now the derivative of s_i w.r.t. e_j. Because s_i is itself a +derivative w.r.t. e_i, it follows that C_ij is also symmetric, with at +most 7*6/2 = 21 distinct elements. + +At zero temperature, it is easy to estimate these derivatives by +deforming the simulation box in one of the six directions using the +"change_box"_change_box.html command and measuring the change in the +stress tensor. A general-purpose script that does this is given in the +examples/elastic directory described on the "Examples"_Examples.html +doc page. + +Calculating elastic constants at finite temperature is more +challenging, because it is necessary to run a simulation that perfoms +time averages of differential properties. One way to do this is to +measure the change in average stress tensor in an NVT simulations when +the cell volume undergoes a finite deformation. In order to balance +the systematic and statistical errors in this method, the magnitude of +the deformation must be chosen judiciously, and care must be taken to +fully equilibrate the deformed cell before sampling the stress +tensor. Another approach is to sample the triclinic cell fluctuations +that occur in an NPT simulation. This method can also be slow to +converge and requires careful post-processing "(Shinoda)"_#Shinoda1 + +:line + +:link(Shinoda1) +[(Shinoda)] Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004). diff --git a/doc/src/tutorial_github.txt b/doc/src/Howto_github.txt similarity index 98% rename from doc/src/tutorial_github.txt rename to doc/src/Howto_github.txt index 3e10b821ae..720b3317f0 100644 --- a/doc/src/tutorial_github.txt +++ b/doc/src/Howto_github.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -26,7 +26,7 @@ work required by the LAMMPS developers. Consequently, creating a pull request will increase your chances to have your contribution included and will reduce the time until the integration is complete. For more information on the requirements to have your code included into LAMMPS -please see "Section 10.15"_Section_modify.html#mod_15 +please see the "Modify contribute"_Modify_contribute.html doc page. :line @@ -124,7 +124,7 @@ unrelated feature, you should switch branches! After everything is done, add the files to the branch and commit them: - $ git add doc/src/tutorial_github.txt + $ git add doc/src/Howto_github.txt $ git add doc/src/JPG/tutorial*.png :pre IMPORTANT NOTE: Do not use {git commit -a} (or {git add -A}). The -a @@ -318,7 +318,7 @@ Because the changes are OK with us, we are going to merge by clicking on Now, since in the meantime our local text for the tutorial also changed, we need to pull Axel's change back into our branch, and merge them: - $ git add tutorial_github.txt + $ git add Howto_github.txt $ git add JPG/tutorial_reverse_pull_request*.png $ git commit -m "Updated text and images on reverse pull requests" $ git pull :pre @@ -331,7 +331,7 @@ With Axel's changes merged in and some final text updates, our feature branch is now perfect as far as we are concerned, so we are going to commit and push again: - $ git add tutorial_github.txt + $ git add Howto_github.txt $ git add JPG/tutorial_reverse_pull_request6.png $ git commit -m "Merged Axel's suggestions and updated text" $ git push git@github.com:Pakketeretet2/lammps :pre diff --git a/doc/src/Howto_granular.txt b/doc/src/Howto_granular.txt new file mode 100644 index 0000000000..758b1cebee --- /dev/null +++ b/doc/src/Howto_granular.txt @@ -0,0 +1,57 @@ +"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Granular models :h3 + +Granular system are composed of spherical particles with a diameter, +as opposed to point particles. This means they have an angular +velocity and torque can be imparted to them to cause them to rotate. + +To run a simulation of a granular model, you will want to use +the following commands: + +"atom_style sphere"_atom_style.html +"fix nve/sphere"_fix_nve_sphere.html +"fix gravity"_fix_gravity.html :ul + +This compute + +"compute erotate/sphere"_compute_erotate_sphere.html :ul + +calculates rotational kinetic energy which can be "output with +thermodynamic info"_Howto_output.html. + +Use one of these 3 pair potentials, which compute forces and torques +between interacting pairs of particles: + +"pair_style"_pair_style.html gran/history +"pair_style"_pair_style.html gran/no_history +"pair_style"_pair_style.html gran/hertzian :ul + +These commands implement fix options specific to granular systems: + +"fix freeze"_fix_freeze.html +"fix pour"_fix_pour.html +"fix viscous"_fix_viscous.html +"fix wall/gran"_fix_wall_gran.html :ul + +The fix style {freeze} zeroes both the force and torque of frozen +atoms, and should be used for granular system instead of the fix style +{setforce}. + +For computational efficiency, you can eliminate needless pairwise +computations between frozen atoms by using this command: + +"neigh_modify"_neigh_modify.html exclude :ul + +NOTE: By default, for 2d systems, granular particles are still modeled +as 3d spheres, not 2d discs (circles), meaning their moment of inertia +will be the same as in 3d. If you wish to model granular particles in +2d as 2d discs, see the note on this topic on the "Howto 2d"_Howto_2d.html +doc page, where 2d simulations are discussed. diff --git a/doc/src/Howto_kappa.txt b/doc/src/Howto_kappa.txt new file mode 100644 index 0000000000..b2a57ef49b --- /dev/null +++ b/doc/src/Howto_kappa.txt @@ -0,0 +1,90 @@ +"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Calculate thermal conductivity :h3 + +The thermal conductivity kappa of a material can be measured in at +least 4 ways using various options in LAMMPS. See the examples/KAPPA +directory for scripts that implement the 4 methods discussed here for +a simple Lennard-Jones fluid model. Also, see the "Howto +viscosity"_Howto_viscosity.html doc page for an analogous discussion +for viscosity. + +The thermal conductivity tensor kappa is a measure of the propensity +of a material to transmit heat energy in a diffusive manner as given +by Fourier's law + +J = -kappa grad(T) + +where J is the heat flux in units of energy per area per time and +grad(T) is the spatial gradient of temperature. The thermal +conductivity thus has units of energy per distance per time per degree +K and is often approximated as an isotropic quantity, i.e. as a +scalar. + +The first method is to setup two thermostatted regions at opposite +ends of a simulation box, or one in the middle and one at the end of a +periodic box. By holding the two regions at different temperatures +with a "thermostatting fix"_Howto_thermostat.html, the energy added to +the hot region should equal the energy subtracted from the cold region +and be proportional to the heat flux moving between the regions. See +the papers by "Ikeshoji and Hafskjold"_#howto-Ikeshoji and +"Wirnsberger et al"_#howto-Wirnsberger for details of this idea. Note +that thermostatting fixes such as "fix nvt"_fix_nh.html, "fix +langevin"_fix_langevin.html, and "fix +temp/rescale"_fix_temp_rescale.html store the cumulative energy they +add/subtract. + +Alternatively, as a second method, the "fix heat"_fix_heat.html or +"fix ehex"_fix_ehex.html commands can be used in place of thermostats +on each of two regions to add/subtract specified amounts of energy to +both regions. In both cases, the resulting temperatures of the two +regions can be monitored with the "compute temp/region" command and +the temperature profile of the intermediate region can be monitored +with the "fix ave/chunk"_fix_ave_chunk.html and "compute +ke/atom"_compute_ke_atom.html commands. + +The third method is to perform a reverse non-equilibrium MD simulation +using the "fix thermal/conductivity"_fix_thermal_conductivity.html +command which implements the rNEMD algorithm of Muller-Plathe. +Kinetic energy is swapped between atoms in two different layers of the +simulation box. This induces a temperature gradient between the two +layers which can be monitored with the "fix +ave/chunk"_fix_ave_chunk.html and "compute +ke/atom"_compute_ke_atom.html commands. The fix tallies the +cumulative energy transfer that it performs. See the "fix +thermal/conductivity"_fix_thermal_conductivity.html command for +details. + +The fourth method is based on the Green-Kubo (GK) formula which +relates the ensemble average of the auto-correlation of the heat flux +to kappa. The heat flux can be calculated from the fluctuations of +per-atom potential and kinetic energies and per-atom stress tensor in +a steady-state equilibrated simulation. This is in contrast to the +two preceding non-equilibrium methods, where energy flows continuously +between hot and cold regions of the simulation box. + +The "compute heat/flux"_compute_heat_flux.html command can calculate +the needed heat flux and describes how to implement the Green_Kubo +formalism using additional LAMMPS commands, such as the "fix +ave/correlate"_fix_ave_correlate.html command to calculate the needed +auto-correlation. See the doc page for the "compute +heat/flux"_compute_heat_flux.html command for an example input script +that calculates the thermal conductivity of solid Ar via the GK +formalism. + +:line + +:link(howto-Ikeshoji) +[(Ikeshoji)] Ikeshoji and Hafskjold, Molecular Physics, 81, 251-261 +(1994). + +:link(howto-Wirnsberger) +[(Wirnsberger)] Wirnsberger, Frenkel, and Dellago, J Chem Phys, 143, 124104 +(2015). diff --git a/doc/src/Howto_library.txt b/doc/src/Howto_library.txt new file mode 100644 index 0000000000..9a9656784c --- /dev/null +++ b/doc/src/Howto_library.txt @@ -0,0 +1,207 @@ +"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Library interface to LAMMPS :h3 + +As described on the "Build basics"_Build_basics.html doc page, LAMMPS +can be built as a library, so that it can be called by another code, +used in a "coupled manner"_Howto_couple.html with other codes, or +driven through a "Python interface"_Python_head.html. + +All of these methodologies use a C-style interface to LAMMPS that is +provided in the files src/library.cpp and src/library.h. The +functions therein have a C-style argument list, but contain C++ code +you could write yourself in a C++ application that was invoking LAMMPS +directly. The C++ code in the functions illustrates how to invoke +internal LAMMPS operations. Note that LAMMPS classes are defined +within a LAMMPS namespace (LAMMPS_NS) if you use them from another C++ +application. + +The examples/COUPLE and python/examples directories have example C++ +and C and Python codes which show how a driver code can link to LAMMPS +as a library, run LAMMPS on a subset of processors, grab data from +LAMMPS, change it, and put it back into LAMMPS. + +The file src/library.cpp contains the following functions for creating +and destroying an instance of LAMMPS and sending it commands to +execute. See the documentation in the src/library.cpp file for +details. + +NOTE: You can write code for additional functions as needed to define +how your code talks to LAMMPS and add them to src/library.cpp and +src/library.h, as well as to the "Python interface"_Python_head.html. +The added functions can access or change any internal LAMMPS data you +wish. + +void lammps_open(int, char **, MPI_Comm, void **) +void lammps_open_no_mpi(int, char **, void **) +void lammps_close(void *) +int lammps_version(void *) +void lammps_file(void *, char *) +char *lammps_command(void *, char *) +void lammps_commands_list(void *, int, char **) +void lammps_commands_string(void *, char *) +void lammps_free(void *) :pre + +The lammps_open() function is used to initialize LAMMPS, passing in a +list of strings as if they were "command-line +arguments"_Run_options.html when LAMMPS is run in stand-alone mode +from the command line, and a MPI communicator for LAMMPS to run under. +It returns a ptr to the LAMMPS object that is created, and which is +used in subsequent library calls. The lammps_open() function can be +called multiple times, to create multiple instances of LAMMPS. + +LAMMPS will run on the set of processors in the communicator. This +means the calling code can run LAMMPS on all or a subset of +processors. For example, a wrapper script might decide to alternate +between LAMMPS and another code, allowing them both to run on all the +processors. Or it might allocate half the processors to LAMMPS and +half to the other code and run both codes simultaneously before +syncing them up periodically. Or it might instantiate multiple +instances of LAMMPS to perform different calculations. + +The lammps_open_no_mpi() function is similar except that no MPI +communicator is passed from the caller. Instead, MPI_COMM_WORLD is +used to instantiate LAMMPS, and MPI is initialized if necessary. + +The lammps_close() function is used to shut down an instance of LAMMPS +and free all its memory. + +The lammps_version() function can be used to determined the specific +version of the underlying LAMMPS code. This is particularly useful +when loading LAMMPS as a shared library via dlopen(). The code using +the library interface can than use this information to adapt to +changes to the LAMMPS command syntax between versions. The returned +LAMMPS version code is an integer (e.g. 2 Sep 2015 results in +20150902) that grows with every new LAMMPS version. + +The lammps_file(), lammps_command(), lammps_commands_list(), and +lammps_commands_string() functions are used to pass one or more +commands to LAMMPS to execute, the same as if they were coming from an +input script. + +Via these functions, the calling code can read or generate a series of +LAMMPS commands one or multiple at a time and pass it thru the library +interface to setup a problem and then run it in stages. The caller +can interleave the command function calls with operations it performs, +calls to extract information from or set information within LAMMPS, or +calls to another code's library. + +The lammps_file() function passes the filename of an input script. +The lammps_command() function passes a single command as a string. +The lammps_commands_list() function passes multiple commands in a +char** list. In both lammps_command() and lammps_commands_list(), +individual commands may or may not have a trailing newline. The +lammps_commands_string() function passes multiple commands +concatenated into one long string, separated by newline characters. +In both lammps_commands_list() and lammps_commands_string(), a single +command can be spread across multiple lines, if the last printable +character of all but the last line is "&", the same as if the lines +appeared in an input script. + +The lammps_free() function is a clean-up function to free memory that +the library allocated previously via other function calls. See +comments in src/library.cpp file for which other functions need this +clean-up. + +The file src/library.cpp also contains these functions for extracting +information from LAMMPS and setting value within LAMMPS. Again, see +the documentation in the src/library.cpp file for details, including +which quantities can be queried by name: + +int lammps_extract_setting(void *, char *) +void *lammps_extract_global(void *, char *) +void lammps_extract_box(void *, double *, double *, + double *, double *, double *, int *, int *) +void *lammps_extract_atom(void *, char *) +void *lammps_extract_compute(void *, char *, int, int) +void *lammps_extract_fix(void *, char *, int, int, int, int) +void *lammps_extract_variable(void *, char *, char *) :pre + +The extract_setting() function returns info on the size +of data types (e.g. 32-bit or 64-bit atom IDs) used +by the LAMMPS executable (a compile-time choice). + +The other extract functions return a pointer to various global or +per-atom quantities stored in LAMMPS or to values calculated by a +compute, fix, or variable. The pointer returned by the +extract_global() function can be used as a permanent reference to a +value which may change. For the extract_atom() method, see the +extract() method in the src/atom.cpp file for a list of valid per-atom +properties. New names could easily be added if the property you want +is not listed. For the other extract functions, the underlying +storage may be reallocated as LAMMPS runs, so you need to re-call the +function to assure a current pointer or returned value(s). + +double lammps_get_thermo(void *, char *) +int lammps_get_natoms(void *) :pre + +int lammps_set_variable(void *, char *, char *) +void lammps_reset_box(void *, double *, double *, double, double, double) :pre + +The lammps_get_thermo() function returns the current value of a thermo +keyword as a double precision value. + +The lammps_get_natoms() function returns the total number of atoms in +the system and can be used by the caller to allocate memory for the +lammps_gather_atoms() and lammps_scatter_atoms() functions. + +The lammps_set_variable() function can set an existing string-style +variable to a new string value, so that subsequent LAMMPS commands can +access the variable. + +The lammps_reset_box() function resets the size and shape of the +simulation box, e.g. as part of restoring a previously extracted and +saved state of a simulation. + +void lammps_gather_atoms(void *, char *, int, int, void *) +void lammps_gather_atoms_concat(void *, char *, int, int, void *) +void lammps_gather_atoms_subset(void *, char *, int, int, int, int *, void *) +void lammps_scatter_atoms(void *, char *, int, int, void *) +void lammps_scatter_atoms_subset(void *, char *, int, int, int, int *, void *) :pre + +void lammps_create_atoms(void *, int, tagint *, int *, double *, double *, + imageint *, int) :pre + +The gather functions collect peratom info of the requested type (atom +coords, atom types, forces, etc) from all processors, and returns the +same vector of values to each calling processor. The scatter +functions do the inverse. They distribute a vector of peratom values, +passed by all calling processors, to individual atoms, which may be +owned by different processors. + +The lammps_gather_atoms() function does this for all N atoms in the +system, ordered by atom ID, from 1 to N. The +lammps_gather_atoms_concat() function does it for all N atoms, but +simply concatenates the subset of atoms owned by each processor. The +resulting vector is not ordered by atom ID. Atom IDs can be requested +by the same function if the caller needs to know the ordering. The +lammps_gather_subset() function allows the caller to request values +for only a subset of atoms (identified by ID). +For all 3 gather function, per-atom image flags can be retrieved in 2 ways. +If the count is specified as 1, they are returned +in a packed format with all three image flags stored in a single integer. +If the count is specified as 3, the values are unpacked into xyz flags +by the library before returning them. + +The lammps_scatter_atoms() function takes a list of values for all N +atoms in the system, ordered by atom ID, from 1 to N, and assigns +those values to each atom in the system. The +lammps_scatter_atoms_subset() function takes a subset of IDs as an +argument and only scatters those values to the owning atoms. + +The lammps_create_atoms() function takes a list of N atoms as input +with atom types and coords (required), an optionally atom IDs and +velocities and image flags. It uses the coords of each atom to assign +it as a new atom to the processor that owns it. This function is +useful to add atoms to a simulation or (in tandem with +lammps_reset_box()) to restore a previously extracted and saved state +of a simulation. Additional properties for the new atoms can then be +assigned via the lammps_scatter_atoms() or lammps_extract_atom() +functions. diff --git a/doc/src/manifolds.txt b/doc/src/Howto_manifold.txt similarity index 97% rename from doc/src/manifolds.txt rename to doc/src/Howto_manifold.txt index 1013d8fab6..09a936f7d3 100644 --- a/doc/src/manifolds.txt +++ b/doc/src/Howto_manifold.txt @@ -2,11 +2,11 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line -Manifolds (surfaces) :h2 +Manifolds (surfaces) :h3 [Overview:] diff --git a/doc/src/Howto_multiple.txt b/doc/src/Howto_multiple.txt new file mode 100644 index 0000000000..9ad872fedc --- /dev/null +++ b/doc/src/Howto_multiple.txt @@ -0,0 +1,94 @@ +"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Run multiple simulations from one input script :h3 + +This can be done in several ways. See the documentation for +individual commands for more details on how these examples work. + +If "multiple simulations" means continue a previous simulation for +more timesteps, then you simply use the "run"_run.html command +multiple times. For example, this script + +units lj +atom_style atomic +read_data data.lj +run 10000 +run 10000 +run 10000 +run 10000 +run 10000 :pre + +would run 5 successive simulations of the same system for a total of +50,000 timesteps. + +If you wish to run totally different simulations, one after the other, +the "clear"_clear.html command can be used in between them to +re-initialize LAMMPS. For example, this script + +units lj +atom_style atomic +read_data data.lj +run 10000 +clear +units lj +atom_style atomic +read_data data.lj.new +run 10000 :pre + +would run 2 independent simulations, one after the other. + +For large numbers of independent simulations, you can use +"variables"_variable.html and the "next"_next.html and +"jump"_jump.html commands to loop over the same input script +multiple times with different settings. For example, this +script, named in.polymer + +variable d index run1 run2 run3 run4 run5 run6 run7 run8 +shell cd $d +read_data data.polymer +run 10000 +shell cd .. +clear +next d +jump in.polymer :pre + +would run 8 simulations in different directories, using a data.polymer +file in each directory. The same concept could be used to run the +same system at 8 different temperatures, using a temperature variable +and storing the output in different log and dump files, for example + +variable a loop 8 +variable t index 0.8 0.85 0.9 0.95 1.0 1.05 1.1 1.15 +log log.$a +read data.polymer +velocity all create $t 352839 +fix 1 all nvt $t $t 100.0 +dump 1 all atom 1000 dump.$a +run 100000 +clear +next t +next a +jump in.polymer :pre + +All of the above examples work whether you are running on 1 or +multiple processors, but assumed you are running LAMMPS on a single +partition of processors. LAMMPS can be run on multiple partitions via +the "-partition command-line switch"_Run_options.html. + +In the last 2 examples, if LAMMPS were run on 3 partitions, the same +scripts could be used if the "index" and "loop" variables were +replaced with {universe}-style variables, as described in the +"variable"_variable.html command. Also, the "next t" and "next a" +commands would need to be replaced with a single "next a t" command. +With these modifications, the 8 simulations of each script would run +on the 3 partitions one after the other until all were finished. +Initially, 3 simulations would be started simultaneously, one on each +partition. When one finished, that partition would then start +the 4th simulation, and so forth, until all 8 were completed. diff --git a/doc/src/Howto_nemd.txt b/doc/src/Howto_nemd.txt new file mode 100644 index 0000000000..f787801c36 --- /dev/null +++ b/doc/src/Howto_nemd.txt @@ -0,0 +1,48 @@ +"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +NEMD simulations :h3 + +Non-equilibrium molecular dynamics or NEMD simulations are typically +used to measure a fluid's rheological properties such as viscosity. +In LAMMPS, such simulations can be performed by first setting up a +non-orthogonal simulation box (see the preceding Howto section). + +A shear strain can be applied to the simulation box at a desired +strain rate by using the "fix deform"_fix_deform.html command. The +"fix nvt/sllod"_fix_nvt_sllod.html command can be used to thermostat +the sheared fluid and integrate the SLLOD equations of motion for the +system. Fix nvt/sllod uses "compute +temp/deform"_compute_temp_deform.html to compute a thermal temperature +by subtracting out the streaming velocity of the shearing atoms. The +velocity profile or other properties of the fluid can be monitored via +the "fix ave/chunk"_fix_ave_chunk.html command. + +As discussed in the previous section on non-orthogonal simulation +boxes, the amount of tilt or skew that can be applied is limited by +LAMMPS for computational efficiency to be 1/2 of the parallel box +length. However, "fix deform"_fix_deform.html can continuously strain +a box by an arbitrary amount. As discussed in the "fix +deform"_fix_deform.html command, when the tilt value reaches a limit, +the box is flipped to the opposite limit which is an equivalent tiling +of periodic space. The strain rate can then continue to change as +before. In a long NEMD simulation these box re-shaping events may +occur many times. + +In a NEMD simulation, the "remap" option of "fix +deform"_fix_deform.html should be set to "remap v", since that is what +"fix nvt/sllod"_fix_nvt_sllod.html assumes to generate a velocity +profile consistent with the applied shear strain rate. + +An alternative method for calculating viscosities is provided via the +"fix viscosity"_fix_viscosity.html command. + +NEMD simulations can also be used to measure transport properties of a fluid +through a pore or channel. Simulations of steady-state flow can be performed +using the "fix flow/gauss"_fix_flow_gauss.html command. diff --git a/doc/src/Howto_output.txt b/doc/src/Howto_output.txt new file mode 100644 index 0000000000..a204a3cc96 --- /dev/null +++ b/doc/src/Howto_output.txt @@ -0,0 +1,307 @@ +"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Output from LAMMPS (thermo, dumps, computes, fixes, variables) :h3 + +There are four basic kinds of LAMMPS output: + +"Thermodynamic output"_thermo_style.html, which is a list +of quantities printed every few timesteps to the screen and logfile. :ulb,l + +"Dump files"_dump.html, which contain snapshots of atoms and various +per-atom values and are written at a specified frequency. :l + +Certain fixes can output user-specified quantities to files: "fix +ave/time"_fix_ave_time.html for time averaging, "fix +ave/chunk"_fix_ave_chunk.html for spatial or other averaging, and "fix +print"_fix_print.html for single-line output of +"variables"_variable.html. Fix print can also output to the +screen. :l + +"Restart files"_restart.html. :l +:ule + +A simulation prints one set of thermodynamic output and (optionally) +restart files. It can generate any number of dump files and fix +output files, depending on what "dump"_dump.html and "fix"_fix.html +commands you specify. + +As discussed below, LAMMPS gives you a variety of ways to determine +what quantities are computed and printed when the thermodynamics, +dump, or fix commands listed above perform output. Throughout this +discussion, note that users can also "add their own computes and fixes +to LAMMPS"_Modify.html which can then generate values that can then be +output with these commands. + +The following sub-sections discuss different LAMMPS command related +to output and the kind of data they operate on and produce: + +"Global/per-atom/local data"_#global +"Scalar/vector/array data"_#scalar +"Thermodynamic output"_#thermo +"Dump file output"_#dump +"Fixes that write output files"_#fixoutput +"Computes that process output quantities"_#computeoutput +"Fixes that process output quantities"_#fixprocoutput +"Computes that generate values to output"_#compute +"Fixes that generate values to output"_#fix +"Variables that generate values to output"_#variable +"Summary table of output options and data flow between commands"_#table :ul + +Global/per-atom/local data :h4,link(global) + +Various output-related commands work with three different styles of +data: global, per-atom, or local. A global datum is one or more +system-wide values, e.g. the temperature of the system. A per-atom +datum is one or more values per atom, e.g. the kinetic energy of each +atom. Local datums are calculated by each processor based on the +atoms it owns, but there may be zero or more per atom, e.g. a list of +bond distances. + +Scalar/vector/array data :h4,link(scalar) + +Global, per-atom, and local datums can each come in three kinds: a +single scalar value, a vector of values, or a 2d array of values. The +doc page for a "compute" or "fix" or "variable" that generates data +will specify both the style and kind of data it produces, e.g. a +per-atom vector. + +When a quantity is accessed, as in many of the output commands +discussed below, it can be referenced via the following bracket +notation, where ID in this case is the ID of a compute. The leading +"c_" would be replaced by "f_" for a fix, or "v_" for a variable: + +c_ID | entire scalar, vector, or array +c_ID\[I\] | one element of vector, one column of array +c_ID\[I\]\[J\] | one element of array :tb(s=|) + +In other words, using one bracket reduces the dimension of the data +once (vector -> scalar, array -> vector). Using two brackets reduces +the dimension twice (array -> scalar). Thus a command that uses +scalar values as input can typically also process elements of a vector +or array. + +Thermodynamic output :h4,link(thermo) + +The frequency and format of thermodynamic output is set by the +"thermo"_thermo.html, "thermo_style"_thermo_style.html, and +"thermo_modify"_thermo_modify.html commands. The +"thermo_style"_thermo_style.html command also specifies what values +are calculated and written out. Pre-defined keywords can be specified +(e.g. press, etotal, etc). Three additional kinds of keywords can +also be specified (c_ID, f_ID, v_name), where a "compute"_compute.html +or "fix"_fix.html or "variable"_variable.html provides the value to be +output. In each case, the compute, fix, or variable must generate +global values for input to the "thermo_style custom"_dump.html +command. + +Note that thermodynamic output values can be "extensive" or +"intensive". The former scale with the number of atoms in the system +(e.g. total energy), the latter do not (e.g. temperature). The +setting for "thermo_modify norm"_thermo_modify.html determines whether +extensive quantities are normalized or not. Computes and fixes +produce either extensive or intensive values; see their individual doc +pages for details. "Equal-style variables"_variable.html produce only +intensive values; you can include a division by "natoms" in the +formula if desired, to make an extensive calculation produce an +intensive result. + +Dump file output :h4,link(dump) + +Dump file output is specified by the "dump"_dump.html and +"dump_modify"_dump_modify.html commands. There are several +pre-defined formats (dump atom, dump xtc, etc). + +There is also a "dump custom"_dump.html format where the user +specifies what values are output with each atom. Pre-defined atom +attributes can be specified (id, x, fx, etc). Three additional kinds +of keywords can also be specified (c_ID, f_ID, v_name), where a +"compute"_compute.html or "fix"_fix.html or "variable"_variable.html +provides the values to be output. In each case, the compute, fix, or +variable must generate per-atom values for input to the "dump +custom"_dump.html command. + +There is also a "dump local"_dump.html format where the user specifies +what local values to output. A pre-defined index keyword can be +specified to enumerate the local values. Two additional kinds of +keywords can also be specified (c_ID, f_ID), where a +"compute"_compute.html or "fix"_fix.html or "variable"_variable.html +provides the values to be output. In each case, the compute or fix +must generate local values for input to the "dump local"_dump.html +command. + +Fixes that write output files :h4,link(fixoutput) + +Several fixes take various quantities as input and can write output +files: "fix ave/time"_fix_ave_time.html, "fix +ave/chunk"_fix_ave_chunk.html, "fix ave/histo"_fix_ave_histo.html, +"fix ave/correlate"_fix_ave_correlate.html, and "fix +print"_fix_print.html. + +The "fix ave/time"_fix_ave_time.html command enables direct output to +a file and/or time-averaging of global scalars or vectors. The user +specifies one or more quantities as input. These can be global +"compute"_compute.html values, global "fix"_fix.html values, or +"variables"_variable.html of any style except the atom style which +produces per-atom values. Since a variable can refer to keywords used +by the "thermo_style custom"_thermo_style.html command (like temp or +press) and individual per-atom values, a wide variety of quantities +can be time averaged and/or output in this way. If the inputs are one +or more scalar values, then the fix generate a global scalar or vector +of output. If the inputs are one or more vector values, then the fix +generates a global vector or array of output. The time-averaged +output of this fix can also be used as input to other output commands. + +The "fix ave/chunk"_fix_ave_chunk.html command enables direct output +to a file of chunk-averaged per-atom quantities like those output in +dump files. Chunks can represent spatial bins or other collections of +atoms, e.g. individual molecules. The per-atom quantities can be atom +density (mass or number) or atom attributes such as position, +velocity, force. They can also be per-atom quantities calculated by a +"compute"_compute.html, by a "fix"_fix.html, or by an atom-style +"variable"_variable.html. The chunk-averaged output of this fix can +also be used as input to other output commands. + +The "fix ave/histo"_fix_ave_histo.html command enables direct output +to a file of histogrammed quantities, which can be global or per-atom +or local quantities. The histogram output of this fix can also be +used as input to other output commands. + +The "fix ave/correlate"_fix_ave_correlate.html command enables direct +output to a file of time-correlated quantities, which can be global +values. The correlation matrix output of this fix can also be used as +input to other output commands. + +The "fix print"_fix_print.html command can generate a line of output +written to the screen and log file or to a separate file, periodically +during a running simulation. The line can contain one or more +"variable"_variable.html values for any style variable except the +vector or atom styles). As explained above, variables themselves can +contain references to global values generated by "thermodynamic +keywords"_thermo_style.html, "computes"_compute.html, +"fixes"_fix.html, or other "variables"_variable.html, or to per-atom +values for a specific atom. Thus the "fix print"_fix_print.html +command is a means to output a wide variety of quantities separate +from normal thermodynamic or dump file output. + +Computes that process output quantities :h4,link(computeoutput) + +The "compute reduce"_compute_reduce.html and "compute +reduce/region"_compute_reduce.html commands take one or more per-atom +or local vector quantities as inputs and "reduce" them (sum, min, max, +ave) to scalar quantities. These are produced as output values which +can be used as input to other output commands. + +The "compute slice"_compute_slice.html command take one or more global +vector or array quantities as inputs and extracts a subset of their +values to create a new vector or array. These are produced as output +values which can be used as input to other output commands. + +The "compute property/atom"_compute_property_atom.html command takes a +list of one or more pre-defined atom attributes (id, x, fx, etc) and +stores the values in a per-atom vector or array. These are produced +as output values which can be used as input to other output commands. +The list of atom attributes is the same as for the "dump +custom"_dump.html command. + +The "compute property/local"_compute_property_local.html command takes +a list of one or more pre-defined local attributes (bond info, angle +info, etc) and stores the values in a local vector or array. These +are produced as output values which can be used as input to other +output commands. + +Fixes that process output quantities :h4,link(fixprocoutput) + +The "fix vector"_fix_vector.html command can create global vectors as +output from global scalars as input, accumulating them one element at +a time. + +The "fix ave/atom"_fix_ave_atom.html command performs time-averaging +of per-atom vectors. The per-atom quantities can be atom attributes +such as position, velocity, force. They can also be per-atom +quantities calculated by a "compute"_compute.html, by a +"fix"_fix.html, or by an atom-style "variable"_variable.html. The +time-averaged per-atom output of this fix can be used as input to +other output commands. + +The "fix store/state"_fix_store_state.html command can archive one or +more per-atom attributes at a particular time, so that the old values +can be used in a future calculation or output. The list of atom +attributes is the same as for the "dump custom"_dump.html command, +including per-atom quantities calculated by a "compute"_compute.html, +by a "fix"_fix.html, or by an atom-style "variable"_variable.html. +The output of this fix can be used as input to other output commands. + +Computes that generate values to output :h4,link(compute) + +Every "compute"_compute.html in LAMMPS produces either global or +per-atom or local values. The values can be scalars or vectors or +arrays of data. These values can be output using the other commands +described in this section. The doc page for each compute command +describes what it produces. Computes that produce per-atom or local +values have the word "atom" or "local" in their style name. Computes +without the word "atom" or "local" produce global values. + +Fixes that generate values to output :h4,link(fix) + +Some "fixes"_fix.html in LAMMPS produces either global or per-atom or +local values which can be accessed by other commands. The values can +be scalars or vectors or arrays of data. These values can be output +using the other commands described in this section. The doc page for +each fix command tells whether it produces any output quantities and +describes them. + +Variables that generate values to output :h4,link(variable) + +"Variables"_variable.html defined in an input script can store one or +more strings. But equal-style, vector-style, and atom-style or +atomfile-style variables generate a global scalar value, global vector +or values, or a per-atom vector, respectively, when accessed. The +formulas used to define these variables can contain references to the +thermodynamic keywords and to global and per-atom data generated by +computes, fixes, and other variables. The values generated by +variables can be used as input to and thus output by the other +commands described in this section. + +Summary table of output options and data flow between commands :h4,link(table) + +This table summarizes the various commands that can be used for +generating output from LAMMPS. Each command produces output data of +some kind and/or writes data to a file. Most of the commands can take +data from other commands as input. Thus you can link many of these +commands together in pipeline form, where data produced by one command +is used as input to another command and eventually written to the +screen or to a file. Note that to hook two commands together the +output and input data types must match, e.g. global/per-atom/local +data and scalar/vector/array data. + +Also note that, as described above, when a command takes a scalar as +input, that could be an element of a vector or array. Likewise a +vector input could be a column of an array. + +Command: Input: Output: +"thermo_style custom"_thermo_style.html: global scalars: screen, log file: +"dump custom"_dump.html: per-atom vectors: dump file: +"dump local"_dump.html: local vectors: dump file: +"fix print"_fix_print.html: global scalar from variable: screen, file: +"print"_print.html: global scalar from variable: screen: +"computes"_compute.html: N/A: global/per-atom/local scalar/vector/array: +"fixes"_fix.html: N/A: global/per-atom/local scalar/vector/array: +"variables"_variable.html: global scalars and vectors, per-atom vectors: global scalar and vector, per-atom vector: +"compute reduce"_compute_reduce.html: per-atom/local vectors: global scalar/vector: +"compute slice"_compute_slice.html: global vectors/arrays: global vector/array: +"compute property/atom"_compute_property_atom.html: per-atom vectors: per-atom vector/array: +"compute property/local"_compute_property_local.html: local vectors: local vector/array: +"fix vector"_fix_vector.html: global scalars: global vector: +"fix ave/atom"_fix_ave_atom.html: per-atom vectors: per-atom vector/array: +"fix ave/time"_fix_ave_time.html: global scalars/vectors: global scalar/vector/array, file: +"fix ave/chunk"_fix_ave_chunk.html: per-atom vectors: global array, file: +"fix ave/histo"_fix_ave_histo.html: global/per-atom/local scalars and vectors: global array, file: +"fix ave/correlate"_fix_ave_correlate.html: global scalars: global array, file: +"fix store/state"_fix_store_state.html: per-atom vectors: per-atom vector/array :tb(c=3,s=:) diff --git a/doc/src/Howto_polarizable.txt b/doc/src/Howto_polarizable.txt new file mode 100644 index 0000000000..b2653b117e --- /dev/null +++ b/doc/src/Howto_polarizable.txt @@ -0,0 +1,81 @@ +"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Polarizable models :h3 + +In polarizable force fields the charge distributions in molecules and +materials respond to their electrostatic environments. Polarizable +systems can be simulated in LAMMPS using three methods: + +the fluctuating charge method, implemented in the "QEQ"_fix_qeq.html +package, :ulb,l +the adiabatic core-shell method, implemented in the +"CORESHELL"_Howto_coreshell.html package, :l +the thermalized Drude dipole method, implemented in the +"USER-DRUDE"_Howto_drude.html package. :l,ule + +The fluctuating charge method calculates instantaneous charges on +interacting atoms based on the electronegativity equalization +principle. It is implemented in the "fix qeq"_fix_qeq.html which is +available in several variants. It is a relatively efficient technique +since no additional particles are introduced. This method allows for +charge transfer between molecules or atom groups. However, because the +charges are located at the interaction sites, off-plane components of +polarization cannot be represented in planar molecules or atom groups. + +The two other methods share the same basic idea: polarizable atoms are +split into one core atom and one satellite particle (called shell or +Drude particle) attached to it by a harmonic spring. Both atoms bear +a charge and they represent collectively an induced electric dipole. +These techniques are computationally more expensive than the QEq +method because of additional particles and bonds. These two +charge-on-spring methods differ in certain features, with the +core-shell model being normally used for ionic/crystalline materials, +whereas the so-called Drude model is normally used for molecular +systems and fluid states. + +The core-shell model is applicable to crystalline materials where the +high symmetry around each site leads to stable trajectories of the +core-shell pairs. However, bonded atoms in molecules can be so close +that a core would interact too strongly or even capture the Drude +particle of a neighbor. The Drude dipole model is relatively more +complex in order to remediate this and other issues. Specifically, the +Drude model includes specific thermostating of the core-Drude pairs +and short-range damping of the induced dipoles. + +The three polarization methods can be implemented through a +self-consistent calculation of charges or induced dipoles at each +timestep. In the fluctuating charge scheme this is done by the matrix +inversion method in "fix qeq/point"_fix_qeq.html, but for core-shell +or Drude-dipoles the relaxed-dipoles technique would require an slow +iterative procedure. These self-consistent solutions yield accurate +trajectories since the additional degrees of freedom representing +polarization are massless. An alternative is to attribute a mass to +the additional degrees of freedom and perform time integration using +an extended Lagrangian technique. For the fluctuating charge scheme +this is done by "fix qeq/dynamic"_fix_qeq.html, and for the +charge-on-spring models by the methods outlined in the next two +sections. The assignment of masses to the additional degrees of +freedom can lead to unphysical trajectories if care is not exerted in +choosing the parameters of the polarizable models and the simulation +conditions. + +In the core-shell model the vibration of the shells is kept faster +than the ionic vibrations to mimic the fast response of the +polarizable electrons. But in molecular systems thermalizing the +core-Drude pairs at temperatures comparable to the rest of the +simulation leads to several problems (kinetic energy transfer, too +short a timestep, etc.) In order to avoid these problems the relative +motion of the Drude particles with respect to their cores is kept +"cold" so the vibration of the core-Drude pairs is very slow, +approaching the self-consistent regime. In both models the +temperature is regulated using the velocities of the center of mass of +core+shell (or Drude) pairs, but in the Drude model the actual +relative core-Drude particle motion is thermostated separately as +well. diff --git a/doc/src/tutorial_pylammps.txt b/doc/src/Howto_pylammps.txt similarity index 95% rename from doc/src/tutorial_pylammps.txt rename to doc/src/Howto_pylammps.txt index 11cddb3cbf..a12bf13f2e 100644 --- a/doc/src/tutorial_pylammps.txt +++ b/doc/src/Howto_pylammps.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -15,13 +15,19 @@ END_RST --> Overview :h4 -PyLammps is a Python wrapper class which can be created on its own or use an -existing lammps Python object. It creates a simpler, Python-like interface to -common LAMMPS functionality. Unlike the original flat C-types interface, it -exposes a discoverable API. It no longer requires knowledge of the underlying -C++ code implementation. Finally, the IPyLammps wrapper builds on top of -PyLammps and adds some additional features for IPython integration into IPython -notebooks, e.g. for embedded visualization output from dump/image. +PyLammps is a Python wrapper class which can be created on its own or +use an existing lammps Python object. It creates a simpler, +Python-like interface to common LAMMPS functionality, in contrast to +the lammps.py wrapper on the C-style LAMMPS library interface which is +written using Python ctypes. The lammps.py wrapper is discussed on +the "Python library"_Python_library.html doc page. + +Unlike the flat ctypes interface, PyLammps exposes a discoverable API. +It no longer requires knowledge of the underlying C++ code +implementation. Finally, the IPyLammps wrapper builds on top of +PyLammps and adds some additional features for IPython integration +into IPython notebooks, e.g. for embedded visualization output from +dump/image. Comparison of lammps and PyLammps interfaces :h5 @@ -40,7 +46,6 @@ communication with LAMMPS is hidden from API user shorter, more concise Python better IPython integration, designed for quick prototyping :ul - Quick Start :h4 System-wide Installation :h5 @@ -68,7 +73,7 @@ that package into your current Python installation. cd $LAMMPS_DIR/python python install.py :pre -NOTE: Recompiling the shared library requires reinstalling the Python package +NOTE: Recompiling the shared library requires re-installing the Python package Installation inside of a virtualenv :h5 diff --git a/doc/src/Howto_replica.txt b/doc/src/Howto_replica.txt new file mode 100644 index 0000000000..2135e52e0e --- /dev/null +++ b/doc/src/Howto_replica.txt @@ -0,0 +1,60 @@ +"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Multi-replica simulations :h3 + +Several commands in LAMMPS run mutli-replica simulations, meaning +that multiple instances (replicas) of your simulation are run +simultaneously, with small amounts of data exchanged between replicas +periodically. + +These are the relevant commands: + +"neb"_neb.html for nudged elastic band calculations +"prd"_prd.html for parallel replica dynamics +"tad"_tad.html for temperature accelerated dynamics +"temper"_temper.html for parallel tempering +"fix pimd"_fix_pimd.html for path-integral molecular dynamics (PIMD) :ul + +NEB is a method for finding transition states and barrier energies. +PRD and TAD are methods for performing accelerated dynamics to find +and perform infrequent events. Parallel tempering or replica exchange +runs different replicas at a series of temperature to facilitate +rare-event sampling. + +These commands can only be used if LAMMPS was built with the REPLICA +package. See the "Build package"_Build_package.html doc page for more +info. + +PIMD runs different replicas whose individual particles are coupled +together by springs to model a system or ring-polymers. + +This commands can only be used if LAMMPS was built with the USER-MISC +package. See the "Build package"_Build_package.html doc page for more +info. + +In all these cases, you must run with one or more processors per +replica. The processors assigned to each replica are determined at +run-time by using the "-partition command-line +switch"_Run_options.html to launch LAMMPS on multiple partitions, +which in this context are the same as replicas. E.g. these commands: + +mpirun -np 16 lmp_linux -partition 8x2 -in in.temper +mpirun -np 8 lmp_linux -partition 8x1 -in in.neb :pre + +would each run 8 replicas, on either 16 or 8 processors. Note the use +of the "-in command-line switch"_Run_options.html to specify the input +script which is required when running in multi-replica mode. + +Also note that with MPI installed on a machine (e.g. your desktop), +you can run on more (virtual) processors than you have physical +processors. Thus the above commands could be run on a +single-processor (or few-processor) desktop so that you can run +a multi-replica simulation on more replicas than you have +physical processors. diff --git a/doc/src/Howto_restart.txt b/doc/src/Howto_restart.txt new file mode 100644 index 0000000000..bc67daa78e --- /dev/null +++ b/doc/src/Howto_restart.txt @@ -0,0 +1,97 @@ +"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Restart a simulation :h3 + +There are 3 ways to continue a long LAMMPS simulation. Multiple +"run"_run.html commands can be used in the same input script. Each +run will continue from where the previous run left off. Or binary +restart files can be saved to disk using the "restart"_restart.html +command. At a later time, these binary files can be read via a +"read_restart"_read_restart.html command in a new script. Or they can +be converted to text data files using the "-r command-line +switch"_Run_options.html and read by a "read_data"_read_data.html +command in a new script. + +Here we give examples of 2 scripts that read either a binary restart +file or a converted data file and then issue a new run command to +continue where the previous run left off. They illustrate what +settings must be made in the new script. Details are discussed in the +documentation for the "read_restart"_read_restart.html and +"read_data"_read_data.html commands. + +Look at the {in.chain} input script provided in the {bench} directory +of the LAMMPS distribution to see the original script that these 2 +scripts are based on. If that script had the line + +restart 50 tmp.restart :pre + +added to it, it would produce 2 binary restart files (tmp.restart.50 +and tmp.restart.100) as it ran. + +This script could be used to read the 1st restart file and re-run the +last 50 timesteps: + +read_restart tmp.restart.50 :pre + +neighbor 0.4 bin +neigh_modify every 1 delay 1 :pre + +fix 1 all nve +fix 2 all langevin 1.0 1.0 10.0 904297 :pre + +timestep 0.012 :pre + +run 50 :pre + +Note that the following commands do not need to be repeated because +their settings are included in the restart file: {units, atom_style, +special_bonds, pair_style, bond_style}. However these commands do +need to be used, since their settings are not in the restart file: +{neighbor, fix, timestep}. + +If you actually use this script to perform a restarted run, you will +notice that the thermodynamic data match at step 50 (if you also put a +"thermo 50" command in the original script), but do not match at step +100. This is because the "fix langevin"_fix_langevin.html command +uses random numbers in a way that does not allow for perfect restarts. + +As an alternate approach, the restart file could be converted to a data +file as follows: + +lmp_g++ -r tmp.restart.50 tmp.restart.data :pre + +Then, this script could be used to re-run the last 50 steps: + +units lj +atom_style bond +pair_style lj/cut 1.12 +pair_modify shift yes +bond_style fene +special_bonds 0.0 1.0 1.0 :pre + +read_data tmp.restart.data :pre + +neighbor 0.4 bin +neigh_modify every 1 delay 1 :pre + +fix 1 all nve +fix 2 all langevin 1.0 1.0 10.0 904297 :pre + +timestep 0.012 :pre + +reset_timestep 50 +run 50 :pre + +Note that nearly all the settings specified in the original {in.chain} +script must be repeated, except the {pair_coeff} and {bond_coeff} +commands since the new data file lists the force field coefficients. +Also, the "reset_timestep"_reset_timestep.html command is used to tell +LAMMPS the current timestep. This value is stored in restart files, +but not in data files. diff --git a/doc/src/Howto_spc.txt b/doc/src/Howto_spc.txt new file mode 100644 index 0000000000..2cbf16547b --- /dev/null +++ b/doc/src/Howto_spc.txt @@ -0,0 +1,54 @@ +"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +SPC water model :h3 + +The SPC water model specifies a 3-site rigid water molecule with +charges and Lennard-Jones parameters assigned to each of the 3 atoms. +In LAMMPS the "fix shake"_fix_shake.html command can be used to hold +the two O-H bonds and the H-O-H angle rigid. A bond style of +{harmonic} and an angle style of {harmonic} or {charmm} should also be +used. + +These are the additional parameters (in real units) to set for O and H +atoms and the water molecule to run a rigid SPC model. + +O mass = 15.9994 +H mass = 1.008 +O charge = -0.820 +H charge = 0.410 +LJ epsilon of OO = 0.1553 +LJ sigma of OO = 3.166 +LJ epsilon, sigma of OH, HH = 0.0 +r0 of OH bond = 1.0 +theta of HOH angle = 109.47 :all(b),p + +Note that as originally proposed, the SPC model was run with a 9 +Angstrom cutoff for both LJ and Coulommbic terms. It can also be used +with long-range Coulombics (Ewald or PPPM in LAMMPS), without changing +any of the parameters above, though it becomes a different model in +that mode of usage. + +The SPC/E (extended) water model is the same, except +the partial charge assignments change: + +O charge = -0.8476 +H charge = 0.4238 :all(b),p + +See the "(Berendsen)"_#howto-Berendsen reference for more details on both +the SPC and SPC/E models. + +Wikipedia also has a nice article on "water +models"_http://en.wikipedia.org/wiki/Water_model. + +:line + +:link(howto-Berendsen) +[(Berendsen)] Berendsen, Grigera, Straatsma, J Phys Chem, 91, +6269-6271 (1987). diff --git a/doc/src/Howto_spherical.txt b/doc/src/Howto_spherical.txt new file mode 100644 index 0000000000..4dfe4e2f6c --- /dev/null +++ b/doc/src/Howto_spherical.txt @@ -0,0 +1,243 @@ +"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Finite-size spherical and aspherical particles :h3 + +Typical MD models treat atoms or particles as point masses. Sometimes +it is desirable to have a model with finite-size particles such as +spheroids or ellipsoids or generalized aspherical bodies. The +difference is that such particles have a moment of inertia, rotational +energy, and angular momentum. Rotation is induced by torque coming +from interactions with other particles. + +LAMMPS has several options for running simulations with these kinds of +particles. The following aspects are discussed in turn: + +atom styles +pair potentials +time integration +computes, thermodynamics, and dump output +rigid bodies composed of finite-size particles :ul + +Example input scripts for these kinds of models are in the body, +colloid, dipole, ellipse, line, peri, pour, and tri directories of the +"examples directory"_Examples.html in the LAMMPS distribution. + +Atom styles :h4 + +There are several "atom styles"_atom_style.html that allow for +definition of finite-size particles: sphere, dipole, ellipsoid, line, +tri, peri, and body. + +The sphere style defines particles that are spheriods and each +particle can have a unique diameter and mass (or density). These +particles store an angular velocity (omega) and can be acted upon by +torque. The "set" command can be used to modify the diameter and mass +of individual particles, after then are created. + +The dipole style does not actually define finite-size particles, but +is often used in conjunction with spherical particles, via a command +like + +atom_style hybrid sphere dipole :pre + +This is because when dipoles interact with each other, they induce +torques, and a particle must be finite-size (i.e. have a moment of +inertia) in order to respond and rotate. See the "atom_style +dipole"_atom_style.html command for details. The "set" command can be +used to modify the orientation and length of the dipole moment of +individual particles, after then are created. + +The ellipsoid style defines particles that are ellipsoids and thus can +be aspherical. Each particle has a shape, specified by 3 diameters, +and mass (or density). These particles store an angular momentum and +their orientation (quaternion), and can be acted upon by torque. They +do not store an angular velocity (omega), which can be in a different +direction than angular momentum, rather they compute it as needed. +The "set" command can be used to modify the diameter, orientation, and +mass of individual particles, after then are created. It also has a +brief explanation of what quaternions are. + +The line style defines line segment particles with two end points and +a mass (or density). They can be used in 2d simulations, and they can +be joined together to form rigid bodies which represent arbitrary +polygons. + +The tri style defines triangular particles with three corner points +and a mass (or density). They can be used in 3d simulations, and they +can be joined together to form rigid bodies which represent arbitrary +particles with a triangulated surface. + +The peri style is used with "Peridynamic models"_pair_peri.html and +defines particles as having a volume, that is used internally in the +"pair_style peri"_pair_peri.html potentials. + +The body style allows for definition of particles which can represent +complex entities, such as surface meshes of discrete points, +collections of sub-particles, deformable objects, etc. The body style +is discussed in more detail on the "Howto body"_Howto_body.html doc +page. + +Note that if one of these atom styles is used (or multiple styles via +the "atom_style hybrid"_atom_style.html command), not all particles in +the system are required to be finite-size or aspherical. + +For example, in the ellipsoid style, if the 3 shape parameters are set +to the same value, the particle will be a sphere rather than an +ellipsoid. If the 3 shape parameters are all set to 0.0 or if the +diameter is set to 0.0, it will be a point particle. In the line or +tri style, if the lineflag or triflag is specified as 0, then it +will be a point particle. + +Some of the pair styles used to compute pairwise interactions between +finite-size particles also compute the correct interaction with point +particles as well, e.g. the interaction between a point particle and a +finite-size particle or between two point particles. If necessary, +"pair_style hybrid"_pair_hybrid.html can be used to insure the correct +interactions are computed for the appropriate style of interactions. +Likewise, using groups to partition particles (ellipsoids versus +spheres versus point particles) will allow you to use the appropriate +time integrators and temperature computations for each class of +particles. See the doc pages for various commands for details. + +Also note that for "2d simulations"_dimension.html, atom styles sphere +and ellipsoid still use 3d particles, rather than as circular disks or +ellipses. This means they have the same moment of inertia as the 3d +object. When temperature is computed, the correct degrees of freedom +are used for rotation in a 2d versus 3d system. + +Pair potentials :h4 + +When a system with finite-size particles is defined, the particles +will only rotate and experience torque if the force field computes +such interactions. These are the various "pair +styles"_pair_style.html that generate torque: + +"pair_style gran/history"_pair_gran.html +"pair_style gran/hertzian"_pair_gran.html +"pair_style gran/no_history"_pair_gran.html +"pair_style dipole/cut"_pair_dipole.html +"pair_style gayberne"_pair_gayberne.html +"pair_style resquared"_pair_resquared.html +"pair_style brownian"_pair_brownian.html +"pair_style lubricate"_pair_lubricate.html +"pair_style line/lj"_pair_line_lj.html +"pair_style tri/lj"_pair_tri_lj.html +"pair_style body/nparticle"_pair_body_nparticle.html :ul + +The granular pair styles are used with spherical particles. The +dipole pair style is used with the dipole atom style, which could be +applied to spherical or ellipsoidal particles. The GayBerne and +REsquared potentials require ellipsoidal particles, though they will +also work if the 3 shape parameters are the same (a sphere). The +Brownian and lubrication potentials are used with spherical particles. +The line, tri, and body potentials are used with line segment, +triangular, and body particles respectively. + +Time integration :h4 + +There are several fixes that perform time integration on finite-size +spherical particles, meaning the integrators update the rotational +orientation and angular velocity or angular momentum of the particles: + +"fix nve/sphere"_fix_nve_sphere.html +"fix nvt/sphere"_fix_nvt_sphere.html +"fix npt/sphere"_fix_npt_sphere.html :ul + +Likewise, there are 3 fixes that perform time integration on +ellipsoidal particles: + +"fix nve/asphere"_fix_nve_asphere.html +"fix nvt/asphere"_fix_nvt_asphere.html +"fix npt/asphere"_fix_npt_asphere.html :ul + +The advantage of these fixes is that those which thermostat the +particles include the rotational degrees of freedom in the temperature +calculation and thermostatting. The "fix langevin"_fix_langevin.html +command can also be used with its {omgea} or {angmom} options to +thermostat the rotational degrees of freedom for spherical or +ellipsoidal particles. Other thermostatting fixes only operate on the +translational kinetic energy of finite-size particles. + +These fixes perform constant NVE time integration on line segment, +triangular, and body particles: + +"fix nve/line"_fix_nve_line.html +"fix nve/tri"_fix_nve_tri.html +"fix nve/body"_fix_nve_body.html :ul + +Note that for mixtures of point and finite-size particles, these +integration fixes can only be used with "groups"_group.html which +contain finite-size particles. + +Computes, thermodynamics, and dump output :h4 + +There are several computes that calculate the temperature or +rotational energy of spherical or ellipsoidal particles: + +"compute temp/sphere"_compute_temp_sphere.html +"compute temp/asphere"_compute_temp_asphere.html +"compute erotate/sphere"_compute_erotate_sphere.html +"compute erotate/asphere"_compute_erotate_asphere.html :ul + +These include rotational degrees of freedom in their computation. If +you wish the thermodynamic output of temperature or pressure to use +one of these computes (e.g. for a system entirely composed of +finite-size particles), then the compute can be defined and the +"thermo_modify"_thermo_modify.html command used. Note that by default +thermodynamic quantities will be calculated with a temperature that +only includes translational degrees of freedom. See the +"thermo_style"_thermo_style.html command for details. + +These commands can be used to output various attributes of finite-size +particles: + +"dump custom"_dump.html +"compute property/atom"_compute_property_atom.html +"dump local"_dump.html +"compute body/local"_compute_body_local.html :ul + +Attributes include the dipole moment, the angular velocity, the +angular momentum, the quaternion, the torque, the end-point and +corner-point coordinates (for line and tri particles), and +sub-particle attributes of body particles. + +Rigid bodies composed of finite-size particles :h4 + +The "fix rigid"_fix_rigid.html command treats a collection of +particles as a rigid body, computes its inertia tensor, sums the total +force and torque on the rigid body each timestep due to forces on its +constituent particles, and integrates the motion of the rigid body. + +If any of the constituent particles of a rigid body are finite-size +particles (spheres or ellipsoids or line segments or triangles), then +their contribution to the inertia tensor of the body is different than +if they were point particles. This means the rotational dynamics of +the rigid body will be different. Thus a model of a dimer is +different if the dimer consists of two point masses versus two +spheroids, even if the two particles have the same mass. Finite-size +particles that experience torque due to their interaction with other +particles will also impart that torque to a rigid body they are part +of. + +See the "fix rigid" command for example of complex rigid-body models +it is possible to define in LAMMPS. + +Note that the "fix shake"_fix_shake.html command can also be used to +treat 2, 3, or 4 particles as a rigid body, but it always assumes the +particles are point masses. + +Also note that body particles cannot be modeled with the "fix +rigid"_fix_rigid.html command. Body particles are treated by LAMMPS +as single particles, though they can store internal state, such as a +list of sub-particles. Individual body partices are typically treated +as rigid bodies, and their motion integrated with a command like "fix +nve/body"_fix_nve_body.html. Interactions between pairs of body +particles are computed via a command like "pair_style +body/nparticle"_pair_body_nparticle.html. diff --git a/doc/src/Howto_spins.txt b/doc/src/Howto_spins.txt new file mode 100644 index 0000000000..b549f99be2 --- /dev/null +++ b/doc/src/Howto_spins.txt @@ -0,0 +1,59 @@ +"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Magnetic spins :h3 + +The magnetic spin simulations are enabled by the SPIN package, whose +implementation is detailed in "Tranchida"_#Tranchida7. + +The model represents the simulation of atomic magnetic spins coupled +to lattice vibrations. The dynamics of those magnetic spins can be used +to simulate a broad range a phenomena related to magneto-elasticity, or +or to study the influence of defects on the magnetic properties of +materials. + +The magnetic spins are interacting with each others and with the +lattice via pair interactions. Typically, the magnetic exchange +interaction can be defined using the +"pair/spin/exchange"_pair_spin_exchange.html command. This exchange +applies a magnetic torque to a given spin, considering the orientation +of its neighboring spins and their relative distances. +It also applies a force on the atoms as a function of the spin +orientations and their associated inter-atomic distances. + +The command "fix precession/spin"_fix_precession_spin.html allows to +apply a constant magnetic torque on all the spins in the system. This +torque can be an external magnetic field (Zeeman interaction), or an +uniaxial magnetic anisotropy. + +A Langevin thermostat can be applied to those magnetic spins using +"fix langevin/spin"_fix_langevin_spin.html. Typically, this thermostat +can be coupled to another Langevin thermostat applied to the atoms +using "fix langevin"_fix_langevin.html in order to simulate +thermostated spin-lattice system. + +The magnetic Gilbert damping can also be applied using "fix +langevin/spin"_fix_langevin_spin.html. It allows to either dissipate +the thermal energy of the Langevin thermostat, or to perform a +relaxation of the magnetic configuration toward an equilibrium state. + +All the computed magnetic properties can be output by two main +commands. The first one is "compute spin"_compute_spin.html, that +enables to evaluate magnetic averaged quantities, such as the total +magnetization of the system along x, y, or z, the spin temperature, or +the magnetic energy. The second command is "compute +property/atom"_compute_property_atom.html. It enables to output all the +per atom magnetic quantities. Typically, the orientation of a given +magnetic spin, or the magnetic force acting on this spin. + +:line + +:link(Tranchida7) +[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson, +arXiv preprint arXiv:1801.10233, (2018). diff --git a/doc/src/Howto_temperature.txt b/doc/src/Howto_temperature.txt new file mode 100644 index 0000000000..896cc96a40 --- /dev/null +++ b/doc/src/Howto_temperature.txt @@ -0,0 +1,43 @@ +"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Calculate temperature :h3 + +Temperature is computed as kinetic energy divided by some number of +degrees of freedom (and the Boltzmann constant). Since kinetic energy +is a function of particle velocity, there is often a need to +distinguish between a particle's advection velocity (due to some +aggregate motion of particles) and its thermal velocity. The sum of +the two is the particle's total velocity, but the latter is often what +is wanted to compute a temperature. + +LAMMPS has several options for computing temperatures, any of which +can be used in "thermostatting"_Howto_thermostat.html and +"barostatting"_Howto_barostat.html. These "compute +commands"_compute.html calculate temperature: + +"compute temp"_compute_temp.html +"compute temp/sphere"_compute_temp_sphere.html +"compute temp/asphere"_compute_temp_asphere.html +"compute temp/com"_compute_temp_com.html +"compute temp/deform"_compute_temp_deform.html +"compute temp/partial"_compute_temp_partial.html +"compute temp/profile"_compute_temp_profile.html +"compute temp/ramp"_compute_temp_ramp.html +"compute temp/region"_compute_temp_region.html :ul + +All but the first 3 calculate velocity biases directly (e.g. advection +velocities) that are removed when computing the thermal temperature. +"Compute temp/sphere"_compute_temp_sphere.html and "compute +temp/asphere"_compute_temp_asphere.html compute kinetic energy for +finite-size particles that includes rotational degrees of freedom. +They both allow for velocity biases indirectly, via an optional extra +argument which is another temperature compute that subtracts a +velocity bias. This allows the translational velocity of spherical or +aspherical particles to be adjusted in prescribed ways. diff --git a/doc/src/Howto_thermostat.txt b/doc/src/Howto_thermostat.txt new file mode 100644 index 0000000000..0e2feb1869 --- /dev/null +++ b/doc/src/Howto_thermostat.txt @@ -0,0 +1,89 @@ +"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Thermostats :h3 + +Thermostatting means controlling the temperature of particles in an MD +simulation. "Barostatting"_Howto_barostat.html means controlling the +pressure. Since the pressure includes a kinetic component due to +particle velocities, both these operations require calculation of the +temperature. Typically a target temperature (T) and/or pressure (P) +is specified by the user, and the thermostat or barostat attempts to +equilibrate the system to the requested T and/or P. + +Thermostatting in LAMMPS is performed by "fixes"_fix.html, or in one +case by a pair style. Several thermostatting fixes are available: +Nose-Hoover (nvt), Berendsen, CSVR, Langevin, and direct rescaling +(temp/rescale). Dissipative particle dynamics (DPD) thermostatting +can be invoked via the {dpd/tstat} pair style: + +"fix nvt"_fix_nh.html +"fix nvt/sphere"_fix_nvt_sphere.html +"fix nvt/asphere"_fix_nvt_asphere.html +"fix nvt/sllod"_fix_nvt_sllod.html +"fix temp/berendsen"_fix_temp_berendsen.html +"fix temp/csvr"_fix_temp_csvr.html +"fix langevin"_fix_langevin.html +"fix temp/rescale"_fix_temp_rescale.html +"pair_style dpd/tstat"_pair_dpd.html :ul + +"Fix nvt"_fix_nh.html only thermostats the translational velocity of +particles. "Fix nvt/sllod"_fix_nvt_sllod.html also does this, except +that it subtracts out a velocity bias due to a deforming box and +integrates the SLLOD equations of motion. See the "Howto +nemd"_Howto_nemd.html doc page for further details. "Fix +nvt/sphere"_fix_nvt_sphere.html and "fix +nvt/asphere"_fix_nvt_asphere.html thermostat not only translation +velocities but also rotational velocities for spherical and aspherical +particles. + +DPD thermostatting alters pairwise interactions in a manner analogous +to the per-particle thermostatting of "fix +langevin"_fix_langevin.html. + +Any of the thermostatting fixes can use "temperature +computes"_Howto_thermostat.html that remove bias which has two +effects. First, the current calculated temperature, which is compared +to the requested target temperature, is calculated with the velocity +bias removed. Second, the thermostat adjusts only the thermal +temperature component of the particle's velocities, which are the +velocities with the bias removed. The removed bias is then added back +to the adjusted velocities. See the doc pages for the individual +fixes and for the "fix_modify"_fix_modify.html command for +instructions on how to assign a temperature compute to a +thermostatting fix. For example, you can apply a thermostat to only +the x and z components of velocity by using it in conjunction with +"compute temp/partial"_compute_temp_partial.html. Of you could +thermostat only the thermal temperature of a streaming flow of +particles without affecting the streaming velocity, by using "compute +temp/profile"_compute_temp_profile.html. + +NOTE: Only the nvt fixes perform time integration, meaning they update +the velocities and positions of particles due to forces and velocities +respectively. The other thermostat fixes only adjust velocities; they +do NOT perform time integration updates. Thus they should be used in +conjunction with a constant NVE integration fix such as these: + +"fix nve"_fix_nve.html +"fix nve/sphere"_fix_nve_sphere.html +"fix nve/asphere"_fix_nve_asphere.html :ul + +Thermodynamic output, which can be setup via the +"thermo_style"_thermo_style.html command, often includes temperature +values. As explained on the doc page for the +"thermo_style"_thermo_style.html command, the default temperature is +setup by the thermo command itself. It is NOT the temperature +associated with any thermostatting fix you have defined or with any +compute you have defined that calculates a temperature. The doc pages +for the thermostatting fixes explain the ID of the temperature compute +they create. Thus if you want to view these temperatures, you need to +specify them explicitly via the "thermo_style +custom"_thermo_style.html command. Or you can use the +"thermo_modify"_thermo_modify.html command to re-define what +temperature compute is used for default thermodynamic output. diff --git a/doc/src/Howto_tip3p.txt b/doc/src/Howto_tip3p.txt new file mode 100644 index 0000000000..942b42aea1 --- /dev/null +++ b/doc/src/Howto_tip3p.txt @@ -0,0 +1,69 @@ +"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +TIP3P water model :h3 + +The TIP3P water model as implemented in CHARMM +"(MacKerell)"_#howto-MacKerell specifies a 3-site rigid water molecule with +charges and Lennard-Jones parameters assigned to each of the 3 atoms. +In LAMMPS the "fix shake"_fix_shake.html command can be used to hold +the two O-H bonds and the H-O-H angle rigid. A bond style of +{harmonic} and an angle style of {harmonic} or {charmm} should also be +used. + +These are the additional parameters (in real units) to set for O and H +atoms and the water molecule to run a rigid TIP3P-CHARMM model with a +cutoff. The K values can be used if a flexible TIP3P model (without +fix shake) is desired. If the LJ epsilon and sigma for HH and OH are +set to 0.0, it corresponds to the original 1983 TIP3P model +"(Jorgensen)"_#Jorgensen1. + +O mass = 15.9994 +H mass = 1.008 +O charge = -0.834 +H charge = 0.417 +LJ epsilon of OO = 0.1521 +LJ sigma of OO = 3.1507 +LJ epsilon of HH = 0.0460 +LJ sigma of HH = 0.4000 +LJ epsilon of OH = 0.0836 +LJ sigma of OH = 1.7753 +K of OH bond = 450 +r0 of OH bond = 0.9572 +K of HOH angle = 55 +theta of HOH angle = 104.52 :all(b),p + +These are the parameters to use for TIP3P with a long-range Coulombic +solver (e.g. Ewald or PPPM in LAMMPS), see "(Price)"_#Price1 for +details: + +O mass = 15.9994 +H mass = 1.008 +O charge = -0.830 +H charge = 0.415 +LJ epsilon of OO = 0.102 +LJ sigma of OO = 3.188 +LJ epsilon, sigma of OH, HH = 0.0 +K of OH bond = 450 +r0 of OH bond = 0.9572 +K of HOH angle = 55 +theta of HOH angle = 104.52 :all(b),p + +Wikipedia also has a nice article on "water +models"_http://en.wikipedia.org/wiki/Water_model. + +:line + +:link(Jorgensen1) +[(Jorgensen)] Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem +Phys, 79, 926 (1983). + +:link(Price1) +[(Price)] Price and Brooks, J Chem Phys, 121, 10096 (2004). + diff --git a/doc/src/Howto_tip4p.txt b/doc/src/Howto_tip4p.txt new file mode 100644 index 0000000000..9f7f141314 --- /dev/null +++ b/doc/src/Howto_tip4p.txt @@ -0,0 +1,112 @@ +"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +TIP4P water model :h3 + +The four-point TIP4P rigid water model extends the traditional +three-point TIP3P model by adding an additional site, usually +massless, where the charge associated with the oxygen atom is placed. +This site M is located at a fixed distance away from the oxygen along +the bisector of the HOH bond angle. A bond style of {harmonic} and an +angle style of {harmonic} or {charmm} should also be used. + +A TIP4P model is run with LAMMPS using either this command +for a cutoff model: + +"pair_style lj/cut/tip4p/cut"_pair_lj.html + +or these two commands for a long-range model: + +"pair_style lj/cut/tip4p/long"_pair_lj.html +"kspace_style pppm/tip4p"_kspace_style.html :ul + +For both models, the bond lengths and bond angles should be held fixed +using the "fix shake"_fix_shake.html command. + +These are the additional parameters (in real units) to set for O and H +atoms and the water molecule to run a rigid TIP4P model with a cutoff +"(Jorgensen)"_#Jorgensen5. Note that the OM distance is specified in +the "pair_style"_pair_style.html command, not as part of the pair +coefficients. + +O mass = 15.9994 +H mass = 1.008 +O charge = -1.040 +H charge = 0.520 +r0 of OH bond = 0.9572 +theta of HOH angle = 104.52 +OM distance = 0.15 +LJ epsilon of O-O = 0.1550 +LJ sigma of O-O = 3.1536 +LJ epsilon, sigma of OH, HH = 0.0 +Coulombic cutoff = 8.5 :all(b),p + +For the TIP4/Ice model (J Chem Phys, 122, 234511 (2005); +http://dx.doi.org/10.1063/1.1931662) these values can be used: + +O mass = 15.9994 +H mass = 1.008 +O charge = -1.1794 +H charge = 0.5897 +r0 of OH bond = 0.9572 +theta of HOH angle = 104.52 +OM distance = 0.1577 +LJ epsilon of O-O = 0.21084 +LJ sigma of O-O = 3.1668 +LJ epsilon, sigma of OH, HH = 0.0 +Coulombic cutoff = 8.5 :all(b),p + +For the TIP4P/2005 model (J Chem Phys, 123, 234505 (2005); +http://dx.doi.org/10.1063/1.2121687), these values can be used: + +O mass = 15.9994 +H mass = 1.008 +O charge = -1.1128 +H charge = 0.5564 +r0 of OH bond = 0.9572 +theta of HOH angle = 104.52 +OM distance = 0.1546 +LJ epsilon of O-O = 0.1852 +LJ sigma of O-O = 3.1589 +LJ epsilon, sigma of OH, HH = 0.0 +Coulombic cutoff = 8.5 :all(b),p + +These are the parameters to use for TIP4P with a long-range Coulombic +solver (e.g. Ewald or PPPM in LAMMPS): + +O mass = 15.9994 +H mass = 1.008 +O charge = -1.0484 +H charge = 0.5242 +r0 of OH bond = 0.9572 +theta of HOH angle = 104.52 +OM distance = 0.1250 +LJ epsilon of O-O = 0.16275 +LJ sigma of O-O = 3.16435 +LJ epsilon, sigma of OH, HH = 0.0 :all(b),p + +Note that the when using the TIP4P pair style, the neighbor list +cutoff for Coulomb interactions is effectively extended by a distance +2 * (OM distance), to account for the offset distance of the +fictitious charges on O atoms in water molecules. Thus it is +typically best in an efficiency sense to use a LJ cutoff >= Coulomb +cutoff + 2*(OM distance), to shrink the size of the neighbor list. +This leads to slightly larger cost for the long-range calculation, so +you can test the trade-off for your model. The OM distance and the LJ +and Coulombic cutoffs are set in the "pair_style +lj/cut/tip4p/long"_pair_lj.html command. + +Wikipedia also has a nice article on "water +models"_http://en.wikipedia.org/wiki/Water_model. + +:line + +:link(Jorgensen5) +[(Jorgensen)] Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem +Phys, 79, 926 (1983). diff --git a/doc/src/Howto_triclinic.txt b/doc/src/Howto_triclinic.txt new file mode 100644 index 0000000000..4b299e5ae1 --- /dev/null +++ b/doc/src/Howto_triclinic.txt @@ -0,0 +1,213 @@ +"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +Triclinic (non-orthogonal) simulation boxes :h3 + +By default, LAMMPS uses an orthogonal simulation box to encompass the +particles. The "boundary"_boundary.html command sets the boundary +conditions of the box (periodic, non-periodic, etc). The orthogonal +box has its "origin" at (xlo,ylo,zlo) and is defined by 3 edge vectors +starting from the origin given by [a] = (xhi-xlo,0,0); [b] = +(0,yhi-ylo,0); [c] = (0,0,zhi-zlo). The 6 parameters +(xlo,xhi,ylo,yhi,zlo,zhi) are defined at the time the simulation box +is created, e.g. by the "create_box"_create_box.html or +"read_data"_read_data.html or "read_restart"_read_restart.html +commands. Additionally, LAMMPS defines box size parameters lx,ly,lz +where lx = xhi-xlo, and similarly in the y and z dimensions. The 6 +parameters, as well as lx,ly,lz, can be output via the "thermo_style +custom"_thermo_style.html command. + +LAMMPS also allows simulations to be performed in triclinic +(non-orthogonal) simulation boxes shaped as a parallelepiped with +triclinic symmetry. The parallelepiped has its "origin" at +(xlo,ylo,zlo) and is defined by 3 edge vectors starting from the +origin given by [a] = (xhi-xlo,0,0); [b] = (xy,yhi-ylo,0); [c] = +(xz,yz,zhi-zlo). {xy,xz,yz} can be 0.0 or positive or negative values +and are called "tilt factors" because they are the amount of +displacement applied to faces of an originally orthogonal box to +transform it into the parallelepiped. In LAMMPS the triclinic +simulation box edge vectors [a], [b], and [c] cannot be arbitrary +vectors. As indicated, [a] must lie on the positive x axis. [b] must +lie in the xy plane, with strictly positive y component. [c] may have +any orientation with strictly positive z component. The requirement +that [a], [b], and [c] have strictly positive x, y, and z components, +respectively, ensures that [a], [b], and [c] form a complete +right-handed basis. These restrictions impose no loss of generality, +since it is possible to rotate/invert any set of 3 crystal basis +vectors so that they conform to the restrictions. + +For example, assume that the 3 vectors [A],[B],[C] are the edge +vectors of a general parallelepiped, where there is no restriction on +[A],[B],[C] other than they form a complete right-handed basis i.e. +[A] x [B] . [C] > 0. The equivalent LAMMPS [a],[b],[c] are a linear +rotation of [A], [B], and [C] and can be computed as follows: + +:c,image(Eqs/transform.jpg) + +where A = | [A] | indicates the scalar length of [A]. The hat symbol (^) +indicates the corresponding unit vector. {beta} and {gamma} are angles +between the vectors described below. Note that by construction, +[a], [b], and [c] have strictly positive x, y, and z components, respectively. +If it should happen that +[A], [B], and [C] form a left-handed basis, then the above equations +are not valid for [c]. In this case, it is necessary +to first apply an inversion. This can be achieved +by interchanging two basis vectors or by changing the sign of one of them. + +For consistency, the same rotation/inversion applied to the basis vectors +must also be applied to atom positions, velocities, +and any other vector quantities. +This can be conveniently achieved by first converting to +fractional coordinates in the +old basis and then converting to distance coordinates in the new basis. +The transformation is given by the following equation: + +:c,image(Eqs/rotate.jpg) + +where {V} is the volume of the box, [X] is the original vector quantity and +[x] is the vector in the LAMMPS basis. + +There is no requirement that a triclinic box be periodic in any +dimension, though it typically should be in at least the 2nd dimension +of the tilt (y in xy) if you want to enforce a shift in periodic +boundary conditions across that boundary. Some commands that work +with triclinic boxes, e.g. the "fix deform"_fix_deform.html and "fix +npt"_fix_nh.html commands, require periodicity or non-shrink-wrap +boundary conditions in specific dimensions. See the command doc pages +for details. + +The 9 parameters (xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz) are defined at the +time the simulation box is created. This happens in one of 3 ways. +If the "create_box"_create_box.html command is used with a region of +style {prism}, then a triclinic box is setup. See the +"region"_region.html command for details. If the +"read_data"_read_data.html command is used to define the simulation +box, and the header of the data file contains a line with the "xy xz +yz" keyword, then a triclinic box is setup. See the +"read_data"_read_data.html command for details. Finally, if the +"read_restart"_read_restart.html command reads a restart file which +was written from a simulation using a triclinic box, then a triclinic +box will be setup for the restarted simulation. + +Note that you can define a triclinic box with all 3 tilt factors = +0.0, so that it is initially orthogonal. This is necessary if the box +will become non-orthogonal, e.g. due to the "fix npt"_fix_nh.html or +"fix deform"_fix_deform.html commands. Alternatively, you can use the +"change_box"_change_box.html command to convert a simulation box from +orthogonal to triclinic and vice versa. + +As with orthogonal boxes, LAMMPS defines triclinic box size parameters +lx,ly,lz where lx = xhi-xlo, and similarly in the y and z dimensions. +The 9 parameters, as well as lx,ly,lz, can be output via the +"thermo_style custom"_thermo_style.html command. + +To avoid extremely tilted boxes (which would be computationally +inefficient), LAMMPS normally requires that no tilt factor can skew +the box more than half the distance of the parallel box length, which +is the 1st dimension in the tilt factor (x for xz). This is required +both when the simulation box is created, e.g. via the +"create_box"_create_box.html or "read_data"_read_data.html commands, +as well as when the box shape changes dynamically during a simulation, +e.g. via the "fix deform"_fix_deform.html or "fix npt"_fix_nh.html +commands. + +For example, if xlo = 2 and xhi = 12, then the x box length is 10 and +the xy tilt factor must be between -5 and 5. Similarly, both xz and +yz must be between -(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is +not a limitation, since if the maximum tilt factor is 5 (as in this +example), then configurations with tilt = ..., -15, -5, 5, 15, 25, +... are geometrically all equivalent. If the box tilt exceeds this +limit during a dynamics run (e.g. via the "fix deform"_fix_deform.html +command), then the box is "flipped" to an equivalent shape with a tilt +factor within the bounds, so the run can continue. See the "fix +deform"_fix_deform.html doc page for further details. + +One exception to this rule is if the 1st dimension in the tilt +factor (x for xy) is non-periodic. In that case, the limits on the +tilt factor are not enforced, since flipping the box in that dimension +does not change the atom positions due to non-periodicity. In this +mode, if you tilt the system to extreme angles, the simulation will +simply become inefficient, due to the highly skewed simulation box. + +The limitation on not creating a simulation box with a tilt factor +skewing the box more than half the distance of the parallel box length +can be overridden via the "box"_box.html command. Setting the {tilt} +keyword to {large} allows any tilt factors to be specified. + +Box flips that may occur using the "fix deform"_fix_deform.html or +"fix npt"_fix_nh.html commands can be turned off using the {flip no} +option with either of the commands. + +Note that if a simulation box has a large tilt factor, LAMMPS will run +less efficiently, due to the large volume of communication needed to +acquire ghost atoms around a processor's irregular-shaped sub-domain. +For extreme values of tilt, LAMMPS may also lose atoms and generate an +error. + +Triclinic crystal structures are often defined using three lattice +constants {a}, {b}, and {c}, and three angles {alpha}, {beta} and +{gamma}. Note that in this nomenclature, the a, b, and c lattice +constants are the scalar lengths of the edge vectors [a], [b], and [c] +defined above. The relationship between these 6 quantities +(a,b,c,alpha,beta,gamma) and the LAMMPS box sizes (lx,ly,lz) = +(xhi-xlo,yhi-ylo,zhi-zlo) and tilt factors (xy,xz,yz) is as follows: + +:c,image(Eqs/box.jpg) + +The inverse relationship can be written as follows: + +:c,image(Eqs/box_inverse.jpg) + +The values of {a}, {b}, {c} , {alpha}, {beta} , and {gamma} can be printed +out or accessed by computes using the +"thermo_style custom"_thermo_style.html keywords +{cella}, {cellb}, {cellc}, {cellalpha}, {cellbeta}, {cellgamma}, +respectively. + +As discussed on the "dump"_dump.html command doc page, when the BOX +BOUNDS for a snapshot is written to a dump file for a triclinic box, +an orthogonal bounding box which encloses the triclinic simulation box +is output, along with the 3 tilt factors (xy, xz, yz) of the triclinic +box, formatted as follows: + +ITEM: BOX BOUNDS xy xz yz +xlo_bound xhi_bound xy +ylo_bound yhi_bound xz +zlo_bound zhi_bound yz :pre + +This bounding box is convenient for many visualization programs and is +calculated from the 9 triclinic box parameters +(xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz) as follows: + +xlo_bound = xlo + MIN(0.0,xy,xz,xy+xz) +xhi_bound = xhi + MAX(0.0,xy,xz,xy+xz) +ylo_bound = ylo + MIN(0.0,yz) +yhi_bound = yhi + MAX(0.0,yz) +zlo_bound = zlo +zhi_bound = zhi :pre + +These formulas can be inverted if you need to convert the bounding box +back into the triclinic box parameters, e.g. xlo = xlo_bound - +MIN(0.0,xy,xz,xy+xz). + +One use of triclinic simulation boxes is to model solid-state crystals +with triclinic symmetry. The "lattice"_lattice.html command can be +used with non-orthogonal basis vectors to define a lattice that will +tile a triclinic simulation box via the +"create_atoms"_create_atoms.html command. + +A second use is to run Parinello-Rahman dynamics via the "fix +npt"_fix_nh.html command, which will adjust the xy, xz, yz tilt +factors to compensate for off-diagonal components of the pressure +tensor. The analog for an "energy minimization"_minimize.html is +the "fix box/relax"_fix_box_relax.html command. + +A third use is to shear a bulk solid to study the response of the +material. The "fix deform"_fix_deform.html command can be used for +this purpose. It allows dynamic control of the xy, xz, yz tilt +factors as a simulation runs. This is discussed in the next section +on non-equilibrium MD (NEMD) simulations. diff --git a/doc/src/Howto_viscosity.txt b/doc/src/Howto_viscosity.txt new file mode 100644 index 0000000000..8bcab6dd24 --- /dev/null +++ b/doc/src/Howto_viscosity.txt @@ -0,0 +1,133 @@ +"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Calculate viscosity :h3 + +The shear viscosity eta of a fluid can be measured in at least 5 ways +using various options in LAMMPS. See the examples/VISCOSITY directory +for scripts that implement the 5 methods discussed here for a simple +Lennard-Jones fluid model. Also, see the "Howto +kappa"_Howto_kappa.html doc page for an analogous discussion for +thermal conductivity. + +Eta is a measure of the propensity of a fluid to transmit momentum in +a direction perpendicular to the direction of velocity or momentum +flow. Alternatively it is the resistance the fluid has to being +sheared. It is given by + +J = -eta grad(Vstream) + +where J is the momentum flux in units of momentum per area per time. +and grad(Vstream) is the spatial gradient of the velocity of the fluid +moving in another direction, normal to the area through which the +momentum flows. Viscosity thus has units of pressure-time. + +The first method is to perform a non-equilibrium MD (NEMD) simulation +by shearing the simulation box via the "fix deform"_fix_deform.html +command, and using the "fix nvt/sllod"_fix_nvt_sllod.html command to +thermostat the fluid via the SLLOD equations of motion. +Alternatively, as a second method, one or more moving walls can be +used to shear the fluid in between them, again with some kind of +thermostat that modifies only the thermal (non-shearing) components of +velocity to prevent the fluid from heating up. + +In both cases, the velocity profile setup in the fluid by this +procedure can be monitored by the "fix ave/chunk"_fix_ave_chunk.html +command, which determines grad(Vstream) in the equation above. +E.g. the derivative in the y-direction of the Vx component of fluid +motion or grad(Vstream) = dVx/dy. The Pxy off-diagonal component of +the pressure or stress tensor, as calculated by the "compute +pressure"_compute_pressure.html command, can also be monitored, which +is the J term in the equation above. See the "Howto +nemd"_Howto_nemd.html doc page for details on NEMD simulations. + +The third method is to perform a reverse non-equilibrium MD simulation +using the "fix viscosity"_fix_viscosity.html command which implements +the rNEMD algorithm of Muller-Plathe. Momentum in one dimension is +swapped between atoms in two different layers of the simulation box in +a different dimension. This induces a velocity gradient which can be +monitored with the "fix ave/chunk"_fix_ave_chunk.html command. +The fix tallies the cumulative momentum transfer that it performs. +See the "fix viscosity"_fix_viscosity.html command for details. + +The fourth method is based on the Green-Kubo (GK) formula which +relates the ensemble average of the auto-correlation of the +stress/pressure tensor to eta. This can be done in a fully +equilibrated simulation which is in contrast to the two preceding +non-equilibrium methods, where momentum flows continuously through the +simulation box. + +Here is an example input script that calculates the viscosity of +liquid Ar via the GK formalism: + +# Sample LAMMPS input script for viscosity of liquid Ar :pre + +units real +variable T equal 86.4956 +variable V equal vol +variable dt equal 4.0 +variable p equal 400 # correlation length +variable s equal 5 # sample interval +variable d equal $p*$s # dump interval :pre + +# convert from LAMMPS real units to SI :pre + +variable kB equal 1.3806504e-23 # \[J/K/] Boltzmann +variable atm2Pa equal 101325.0 +variable A2m equal 1.0e-10 +variable fs2s equal 1.0e-15 +variable convert equal $\{atm2Pa\}*$\{atm2Pa\}*$\{fs2s\}*$\{A2m\}*$\{A2m\}*$\{A2m\} :pre + +# setup problem :pre + +dimension 3 +boundary p p p +lattice fcc 5.376 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 +region box block 0 4 0 4 0 4 +create_box 1 box +create_atoms 1 box +mass 1 39.948 +pair_style lj/cut 13.0 +pair_coeff * * 0.2381 3.405 +timestep $\{dt\} +thermo $d :pre + +# equilibration and thermalization :pre + +velocity all create $T 102486 mom yes rot yes dist gaussian +fix NVT all nvt temp $T $T 10 drag 0.2 +run 8000 :pre + +# viscosity calculation, switch to NVE if desired :pre + +#unfix NVT +#fix NVE all nve :pre + +reset_timestep 0 +variable pxy equal pxy +variable pxz equal pxz +variable pyz equal pyz +fix SS all ave/correlate $s $p $d & + v_pxy v_pxz v_pyz type auto file S0St.dat ave running +variable scale equal $\{convert\}/($\{kB\}*$T)*$V*$s*$\{dt\} +variable v11 equal trap(f_SS\[3\])*$\{scale\} +variable v22 equal trap(f_SS\[4\])*$\{scale\} +variable v33 equal trap(f_SS\[5\])*$\{scale\} +thermo_style custom step temp press v_pxy v_pxz v_pyz v_v11 v_v22 v_v33 +run 100000 +variable v equal (v_v11+v_v22+v_v33)/3.0 +variable ndens equal count(all)/vol +print "average viscosity: $v \[Pa.s\] @ $T K, $\{ndens\} /A^3" :pre + +The fifth method is related to the above Green-Kubo method, +but uses the Einstein formulation, analogous to the Einstein +mean-square-displacement formulation for self-diffusivity. The +time-integrated momentum fluxes play the role of Cartesian +coordinates, whose mean-square displacement increases linearly +with time at sufficiently long times. diff --git a/doc/src/Howto_viz.txt b/doc/src/Howto_viz.txt new file mode 100644 index 0000000000..00c329c50b --- /dev/null +++ b/doc/src/Howto_viz.txt @@ -0,0 +1,40 @@ +"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Visualize LAMMPS snapshots :h3 + +LAMMPS itself does not do visualization, but snapshots from LAMMPS +simulations can be visualized (and analyzed) in a variety of ways. + +Mention dump image and dump movie. + +LAMMPS snapshots are created by the "dump"_dump.html command which can +create files in several formats. The native LAMMPS dump format is a +text file (see "dump atom" or "dump custom") which can be visualized +by several popular visualization tools. The "dump +image"_dump_image.html and "dump movie"_dump_image.html styles can +output internally rendered images and convert a sequence of them to a +movie during the MD run. Several programs included with LAMMPS as +auxiliary tools can convert between LAMMPS format files and other +formats. See the "Tools"_Tools.html doc page for details. + +A Python-based toolkit distributed by our group can read native LAMMPS +dump files, including custom dump files with additional columns of +user-specified atom information, and convert them to various formats +or pipe them into visualization software directly. See the "Pizza.py +WWW site"_pizza for details. Specifically, Pizza.py can convert +LAMMPS dump files into PDB, XYZ, "Ensight"_ensight, and VTK formats. +Pizza.py can pipe LAMMPS dump files directly into the Raster3d and +RasMol visualization programs. Pizza.py has tools that do interactive +3d OpenGL visualization and one that creates SVG images of dump file +snapshots. + +:link(pizza,http://www.sandia.gov/~sjplimp/pizza.html) +:link(ensight,http://www.ensight.com) +:link(atomeye,http://mt.seas.upenn.edu/Archive/Graphics/A) diff --git a/doc/src/Howto_walls.txt b/doc/src/Howto_walls.txt new file mode 100644 index 0000000000..7522118582 --- /dev/null +++ b/doc/src/Howto_walls.txt @@ -0,0 +1,80 @@ +"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Walls :h3 + +Walls in an MD simulation are typically used to bound particle motion, +i.e. to serve as a boundary condition. + +Walls in LAMMPS can be of rough (made of particles) or idealized +surfaces. Ideal walls can be smooth, generating forces only in the +normal direction, or frictional, generating forces also in the +tangential direction. + +Rough walls, built of particles, can be created in various ways. The +particles themselves can be generated like any other particle, via the +"lattice"_lattice.html and "create_atoms"_create_atoms.html commands, +or read in via the "read_data"_read_data.html command. + +Their motion can be constrained by many different commands, so that +they do not move at all, move together as a group at constant velocity +or in response to a net force acting on them, move in a prescribed +fashion (e.g. rotate around a point), etc. Note that if a time +integration fix like "fix nve"_fix_nve.html or "fix nvt"_fix_nh.html +is not used with the group that contains wall particles, their +positions and velocities will not be updated. + +"fix aveforce"_fix_aveforce.html - set force on particles to average value, so they move together +"fix setforce"_fix_setforce.html - set force on particles to a value, e.g. 0.0 +"fix freeze"_fix_freeze.html - freeze particles for use as granular walls +"fix nve/noforce"_fix_nve_noforce.html - advect particles by their velocity, but without force +"fix move"_fix_move.html - prescribe motion of particles by a linear velocity, oscillation, rotation, variable :ul + +The "fix move"_fix_move.html command offers the most generality, since +the motion of individual particles can be specified with +"variable"_variable.html formula which depends on time and/or the +particle position. + +For rough walls, it may be useful to turn off pairwise interactions +between wall particles via the "neigh_modify +exclude"_neigh_modify.html command. + +Rough walls can also be created by specifying frozen particles that do +not move and do not interact with mobile particles, and then tethering +other particles to the fixed particles, via a "bond"_bond_style.html. +The bonded particles do interact with other mobile particles. + +Idealized walls can be specified via several fix commands. "Fix +wall/gran"_fix_wall_gran.html creates frictional walls for use with +granular particles; all the other commands create smooth walls. + +"fix wall/reflect"_fix_wall_reflect.html - reflective flat walls +"fix wall/lj93"_fix_wall.html - flat walls, with Lennard-Jones 9/3 potential +"fix wall/lj126"_fix_wall.html - flat walls, with Lennard-Jones 12/6 potential +"fix wall/colloid"_fix_wall.html - flat walls, with "pair_style colloid"_pair_colloid.html potential +"fix wall/harmonic"_fix_wall.html - flat walls, with repulsive harmonic spring potential +"fix wall/region"_fix_wall_region.html - use region surface as wall +"fix wall/gran"_fix_wall_gran.html - flat or curved walls with "pair_style granular"_pair_gran.html potential :ul + +The {lj93}, {lj126}, {colloid}, and {harmonic} styles all allow the +flat walls to move with a constant velocity, or oscillate in time. +The "fix wall/region"_fix_wall_region.html command offers the most +generality, since the region surface is treated as a wall, and the +geometry of the region can be a simple primitive volume (e.g. a +sphere, or cube, or plane), or a complex volume made from the union +and intersection of primitive volumes. "Regions"_region.html can also +specify a volume "interior" or "exterior" to the specified primitive +shape or {union} or {intersection}. "Regions"_region.html can also be +"dynamic" meaning they move with constant velocity, oscillate, or +rotate. + +The only frictional idealized walls currently in LAMMPS are flat or +curved surfaces specified by the "fix wall/gran"_fix_wall_gran.html +command. At some point we plan to allow regoin surfaces to be used as +frictional walls, as well as triangulated surfaces. diff --git a/doc/src/Install.txt b/doc/src/Install.txt new file mode 100644 index 0000000000..0a2e870a5d --- /dev/null +++ b/doc/src/Install.txt @@ -0,0 +1,65 @@ +"Previous Section"_Intro.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Build.html +:c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Install LAMMPS :h2 + +You can download LAMMPS as an executable or as source code. + +With source code, you also have to "build LAMMPS"_Build.html. But you +have more flexibility as to what features to include or exclude in the +build. If you plan to "modify or extend LAMMPS"_Modify.html, then you +need the source code. + + + + + +"Download an executable for Linux"_Install_linux.html +"Download an executable for Mac"_Install_mac.html +"Download an executable for Windows"_Install_windows.html :all(b) + +"Download source as a tarball"_Install_tarball.html +"Donwload source via Git"_Install_git.html +"Donwload source via SVN"_Install_svn.html +"Install patch files"_Install_patch.html :all(b) + + + +These are the files and sub-directories in the LAMMPS distribution: + +README: text file +LICENSE: GNU General Public License (GPL) +bench: benchmark problems +cmake: CMake build files +doc: documentation +examples: simple test problems +lib: additional provided or external libraries +potentials: interatomic potential files +python: Python wrapper on LAMMPS +src: source files +tools: pre- and post-processing tools :tb(s=:,a=l) + +You will have all of these if you download source. You will only have +some of them if you download executables, as explained on the pages +listed above. diff --git a/doc/src/Install_git.txt b/doc/src/Install_git.txt new file mode 100644 index 0000000000..538fa8aff8 --- /dev/null +++ b/doc/src/Install_git.txt @@ -0,0 +1,120 @@ +"Higher level section"_Install.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Download source via Git :h3 + +All LAMMPS development is coordinated through the "LAMMPS GitHub +site". If you clone the LAMMPS repository onto your local machine, it +has several advantages: + +You can stay current with changes to LAMMPS with a single git +command. :ulb,l + +You can create your own development branches to add code to LAMMPS. :l + +You can submit your new features back to GitHub for inclusion in +LAMMPS. :l,ule + +You must have "Git"_git installed on your system to communicate with +the public Git server for LAMMPS. + +IMPORTANT NOTE: As of Oct 2016, the official home of public LAMMPS +development is on GitHub. The previously advertised LAMMPS git +repositories on git.lammps.org and bitbucket.org are now deprecated, +may not be up-to-date, and may go away at any time. + +:link(git,http://git-scm.com) + +You can follow LAMMPS development on 3 different Git branches: + +[stable] : this branch is updated with every stable release +[unstable] : this branch is updated with every patch release +[master] : this branch continuously follows ongoing development :ul + +To access the Git repositories on your box, use the clone command to +create a local copy of the LAMMPS repository with a command like: + +git clone -b unstable https://github.com/lammps/lammps.git mylammps :pre + +where "mylammps" is the name of the directory you wish to create on +your machine and "unstable" is one of the 3 branches listed above. +(Note that you actually download all 3 branches; you can switch +between them at any time using "git checkout ".) + +Once the command completes, your directory will contain the same files +as if you unpacked a current LAMMPS tarball, with two exceptions: + +1) No LAMMPS packages are initially installed in the src dir (a few +packages are installed by default in the tarball src dir). You can +install whichever packages you wish before building LAMMPS; type "make +package" from the src dir to see the options, and the +"Packages"_Packages.html doc page for a discussion of packages. + +2) The HTML documentation files are not included. They can be fetched +from the LAMMPS website by typing "make fetch" in the doc directory. +Or they can be generated from the content provided in doc/src by +typing "make html" from the the doc directory. + +After initial cloning, as bug fixes and new features are added to +LAMMPS, as listed on "this page"_Errors_bugs.html, you can stay +up-to-date by typing the following Git commands from within the +"mylammps" directory: + +git checkout unstable # not needed if you always stay in this branch +git checkout stable # use one of the 3 checkout commands +git checkout master +git pull :pre + +Doing a "pull" will not change any files you have added to the LAMMPS +directory structure. It will also not change any existing LAMMPS +files you have edited, unless those files have changed in the +repository. In that case, Git will attempt to merge the new +repository file with your version of the file and tell you if there +are any conflicts. See the Git documentation for details. + +If you want to access a particular previous release version of LAMMPS, +you can instead "checkout" any version with a published tag. See the +output of "git tag -l" for the list of tags. The Git command to do +this is as follows. + +git checkout tagID :pre + +Stable versions and what tagID to use for a particular stable version +are discussed on "this page"_Errors_bugs.html. Note that this command +will print some warnings, because in order to get back to the latest +revision and to be able to update with "git pull" again, you first +will need to first type "git checkout unstable" (or check out any +other desired branch). + +Once you have updated your local files with a "git pull" (or "git +checkout"), you still need to re-build LAMMPS if any source files have +changed. To do this, you should cd to the src directory and type: + +make purge # remove any deprecated src files +make package-update # sync package files with src files +make foo # re-build for your machine (mpi, serial, etc) :pre + +just as described on the "Install patch"_Install_patch.html doc page, +after a patch has been installed. + +IMPORTANT NOTE: If you wish to edit/change a src file that is from a +package, you should edit the version of the file inside the package +sub-directory with src, then re-install the package. The version in +the src dir is merely a copy and will be wiped out if you type "make +package-update". + +IMPORTANT NOTE: The GitHub servers support both the "git://" and +"https://" access protocols for anonymous read-only access. If you +have a correspondingly configured GitHub account, you may also use SSH +with "git@github.com:/lammps/lammps.git". + +The LAMMPS GitHub project is managed by Christoph Junghans (LANL, +junghans at lanl.gov), Axel Kohlmeyer (Temple U, akohlmey at +gmail.com) and Richard Berger (Temple U, richard.berger at +temple.edu). diff --git a/doc/src/Install_linux.txt b/doc/src/Install_linux.txt new file mode 100644 index 0000000000..cc15ac0ae0 --- /dev/null +++ b/doc/src/Install_linux.txt @@ -0,0 +1,119 @@ +"Higher level section"_Install.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Download an executable for Linux :h3 + +Binaries are available for many different versions of Linux: + +"Pre-built binary RPMs for Fedora/RedHat/CentOS/openSUSE"_#rpm +"Pre-built Ubuntu Linux executables"_#ubuntu +"Pre-built Gentoo Linux executable"_#gentoo :all(b) + +:line + +Pre-built binary RPMs for Fedora/RedHat/CentOS/openSUSE :h4,link(rpm) + +Pre-built LAMMPS executables for various Linux distributions +can be downloaded as binary RPM files from this site: + +"http://rpm.lammps.org"_http://rpm.lammps.org + +There are multiple package variants supporting serial, parallel and +Python wrapper versions. The LAMMPS binaries contain all optional +packages included in the source distribution except: GPU, KIM, REAX, +and USER-INTEL. + +Installation instructions for the various versions are here: + +"http://rpm.lammps.org/install.html"_http://rpm.lammps.org/install.html + +The instructions show how to enable the repository in the respective +system's package management system. Installing and updating are then +straightforward and automatic. + +Thanks to Axel Kohlmeyer (Temple U, akohlmey at gmail.com) for setting +up this RPM capability. + +:line + +Pre-built Ubuntu Linux executables :h4,link(ubuntu) + +A pre-built LAMMPS executable suitable for running on the latest +Ubuntu Linux versions, can be downloaded as a Debian package. This +allows you to install LAMMPS with a single command, and stay +up-to-date with the current version of LAMMPS by simply updating your +operating system. + +To install the appropriate personal-package archive (PPA), do the +following once: + +sudo add-apt-repository ppa:gladky-anton/lammps +sudo apt-get update :pre + +To install LAMMPS do the following once: + +sudo apt-get install lammps-daily :pre + +This downloads an executable named "lammps-daily" to your box, which +can then be used in the usual way to run input scripts: + +lammps-daily < in.lj :pre + +To update LAMMPS to the most current version, do the following: + +sudo apt-get update :pre + +which will also update other packages on your system. + +To get a copy of the current documentation and examples: + +sudo apt-get install lammps-daily-doc :pre + +which will download the doc files in +/usr/share/doc/lammps-daily-doc/doc and example problems in +/usr/share/doc/lammps-doc/examples. + +Note that you may still wish to download the tarball to get potential +files and auxiliary tools. + +To un-install LAMMPS, do the following: + +sudo apt-get remove lammps-daily :pre + +Note that the lammps-daily executable is built with the following +sequence of make commands, as if you had done the same with the +unpacked tarball files in the src directory: + +make yes-all; make no-lib; make openmpi + +Thus it builds with FFTW3 and OpenMPI. + +Thanks to Anton Gladky (gladky.anton at gmail.com) for setting up this +Ubuntu package capability. + +:line + +Pre-built Gentoo Linux executable :h4,link(gentoo) + +LAMMPS is part of Gentoo's main package tree and can be installed by +typing: + +% emerge --ask lammps :pre + +Note that in Gentoo the LAMMPS source is downloaded and the package is +built on the your machine. + +Certain LAMMPS packages can be enable via USE flags, type + +% equery uses lammps :pre + +for details. + +Thanks to Nicolas Bock and Christoph Junghans (LANL) for setting up +this Gentoo capability. diff --git a/doc/src/Install_mac.txt b/doc/src/Install_mac.txt new file mode 100644 index 0000000000..3fcc55b8ab --- /dev/null +++ b/doc/src/Install_mac.txt @@ -0,0 +1,55 @@ +"Higher level section"_Install.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Download an executable for Mac :h3 + +LAMMPS can be downloaded, built, and configured for OS X on a Mac with +"Homebrew"_homebrew. Only four of the LAMMPS packages are unavailable +at this time because of additional needs not yet met: KIM, GPU, +USER-INTEL, USER-ATC. + +After installing Homebrew, you can install LAMMPS on your system with +the following commands: + +% brew tap homebrew/science +% brew install lammps # serial version +% brew install lammps --with-mpi # mpi support :pre + +This will install the executable "lammps", a python module named +"lammps", and additional resources with all the standard packages. To +get the location of the additional resources type this: + +% brew info lammps :pre + +This command also tells you additional installation options available. +The user-packages are available as options, just install them like +this example for the USER-OMP package: + +% brew install lammps --enable-user-omp :pre + +It is usually best to install LAMMPS with the most up to date source +files, which can be done with the "--HEAD" option: + +% brew install lammps --HEAD :pre + +To re-install the LAMMPS HEAD, run this command occasionally (make sure +to use the desired options). + +% brew install --force lammps --HEAD $\{options\} :pre + +Once LAMMPS is installed, you can test the installation with the +Lennard-Jones benchmark file: + +% brew test lammps -v :pre + +If you have problems with the installation you can post issues to +"this link"_https://github.com/Homebrew/homebrew-science/issues. + +Thanks to Derek Thomas (derekt at cello.t.u-tokyo.ac.jp) for setting +up the Homebrew capability. diff --git a/doc/src/Install_patch.txt b/doc/src/Install_patch.txt new file mode 100644 index 0000000000..ff9b14c12c --- /dev/null +++ b/doc/src/Install_patch.txt @@ -0,0 +1,68 @@ +"Higher level section"_Install.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Applying patches :h3 + +It is easy to stay current with the most recent LAMMPS patch releases +if you use Git or SVN to track LAMMPS development. Instructions for +how to stay current are on the "Install git"_Install_git.html and +"Install svn"_Install_svn.html doc pages. + +If you prefer to download a tarball, as described on the "Install +git"_Install_tarball.html doc page, you can stay current by +downloading "patch files" when new patch releases are made. A link to +a patch file is posted on the "bug and feature +page"_http://lammps.sandia.gov/bug.html of the LAMMPS website, along +with a list of changed files and details about what is in the new patch +release. This page explains how to apply the patch file to your local +LAMMPS directory. + +NOTE: You should not apply patch files to a local Git or SVN repo of +LAMMPS, only to an unpacked tarball. Use Git and SVN commands to +update repo versions of LAMMPS. + +Here are the steps to apply a patch file. Note that if your version +of LAMMPS is several patch releases behind, you need to apply all the +intervening patch files in succession to bring your version of LAMMPS +up to date. + +Download the patch file. You may have to shift-click in your browser +to download the file instead of display it. Patch files have names +like patch.12Dec16. :ulb,l + +Put the patch file in your top-level LAMMPS directory, where the +LICENSE and README files are. :l + +Apply the patch by typing the following command from your top-level +LAMMPS directory, where the redirected file is the name of the patch +file. :l + +patch -bp1 < patch.12Dec16 :pre + +A list of updated files print out to the screen. The -b switch +creates backup files of your originals (e.g. src/force.cpp.orig), so +you can manually undo the patch if something goes wrong. :l + +Type the following from the src directory, to enforce consistency +between the src and package directories. This is OK to do even if you +don't use one or more packages. If you are applying several patches +successively, you only need to type this once at the end. The purge +command removes deprecated src files if any were removed by the patch +from package sub-directories. :l + +make purge +make package-update :pre + +Re-build LAMMPS via the "make" command. :l,ule + +IMPORTANT NOTE: If you wish to edit/change a src file that is from a +package, you should edit the version of the file inside the package +sub-dir of src, then re-install the package. The version in the src +dir is merely a copy and will be wiped out if you type "make +package-update". diff --git a/doc/src/Install_svn.txt b/doc/src/Install_svn.txt new file mode 100644 index 0000000000..7a0211ab65 --- /dev/null +++ b/doc/src/Install_svn.txt @@ -0,0 +1,95 @@ +"Higher level section"_Install.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Download source via SVN :h3 + +IMPORTANT NOTE: As of Oct 2016, SVN support is now implemented via a +git-to-subversion interface service on GitHub and no longer through a +mirror of the internal SVN repository at Sandia. + +You must have the "Subversion (SVN) client software"_svn installed on +your system to communicate with the Git server in this mode. + +:link(svn,http://subversion.apache.org) + +You can follow LAMMPS development on 3 different SVN branches: + +[stable] : this branch is updated with every stable release +[unstable] : this branch is updated with every patch release +[master] : this branch continuously follows ongoing development :ul + +The corresponding command lines to do an initial checkout are as +follows. (Note that unlike Git, you must perform a separate checkout +into a unique directory for each of the 3 branches.) + +svn checkout https://github.com/lammps/lammps.git/branches/unstable mylammps +svn checkout https://github.com/lammps/lammps.git/branches/stable mylammps +svn checkout https://github.com/lammps/lammps.git/trunk mylammps :pre + +where "mylammps" is the name of the directory you wish to create on +your machine. + +Once the command completes, your directory will contain the same files +as if you unpacked a current LAMMPS tarball, with two exceptions: + +1) No LAMMPS packages are initially installed in the src dir (a few +packages are installed by default in the tarball src dir). You can +install whichever packages you wish before building LAMMPS; type "make +package" from the src dir to see the options, and the +"Packages"_Packages.html doc page for a discussion of packages. + +2) The HTML documentation files are not included. They can be fetched +from the LAMMPS website by typing "make fetch" in the doc directory. +Or they can be generated from the content provided in doc/src by +typing "make html" from the the doc directory. + +After initial checkout, as bug fixes and new features are added to +LAMMPS, as listed on "this page"_Errors_bugs.html, you can stay +up-to-date by typing the following SVN commands from within the +"mylammps" directory: + +svn update :pre + +You can also check if there are any updates by typing: + +svn -qu status :pre + +Doing an "update" will not change any files you have added to the +LAMMPS directory structure. It will also not change any existing +LAMMPS files you have edited, unless those files have changed in the +repository. In that case, SVN will attempt to merge the new +repository file with your version of the file and tell you if there +are any conflicts. See the SVN documentation for details. + +Please refer to the "subversion client support help pages on +GitHub"_https://help.github.com/articles/support-for-subversion-clients +if you want to use advanced features like accessing particular +previous release versions via tags. + +Once you have updated your local files with an "svn update" (or "svn +co"), you still need to re-build LAMMPS if any source files have +changed. To do this, you should cd to the src directory and type: + +make purge # remove any deprecated src files +make package-update # sync package files with src files +make foo # re-build for your machine (mpi, serial, etc) :pre + +just as described on the "Install patch"_Install_patch.html doc page, +after a patch has been installed. + +IMPORTANT NOTE: If you wish to edit/change a src file that is from a +package, you should edit the version of the file inside the package +sub-directory with src, then re-install the package. The version in +the src dir is merely a copy and will be wiped out if you type "make +package-update". + +The LAMMPS GitHub project is managed by Christoph Junghans (LANL, +junghans at lanl.gov), Axel Kohlmeyer (Temple U, akohlmey at +gmail.com) and Richard Berger (Temple U, richard.berger at +temple.edu). diff --git a/doc/src/Install_tarball.txt b/doc/src/Install_tarball.txt new file mode 100644 index 0000000000..7ba5d15ac4 --- /dev/null +++ b/doc/src/Install_tarball.txt @@ -0,0 +1,68 @@ +"Higher level section"_Install.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Download source and documentation as a tarball :h3 + +You can download a current LAMMPS tarball from the "download page"_download +of the "LAMMPS website"_lws. + +:link(download,http://lammps.sandia.gov/download.html) +:link(bug,http://lammps.sandia.gov/bug.html) +:link(older,http://lammps.sandia.gov/tars) + +You have two choices of tarballs, either the most recent stable +release or the most current patch release. Stable releases occur a +few times per year, and undergo more testing before release. Patch +releases occur a couple times per month. The new contents in all +releases are listed on the "bug and feature page"_bug of the website. + +Both tarballs include LAMMPS documentation (HTML and PDF files) +corresponding to that version. The download page also has an option +to download the current-version LAMMPS documentation by itself. + +Older versions of LAMMPS can also be downloaded from "this +page"_older. + +Once you have a tarball, unzip and untar it with the following +command: + +tar -xzvf lammps*.tar.gz :pre + +This will create a LAMMPS directory with the version date +in its name, e.g. lammps-23Jun18. + +:line + +You can also download a zip file via the "Clone or download" button on +the "LAMMPS GitHub site"_git. The file name will be lammps-master.zip +which can be unzipped with the following command, to create +a lammps-master dir: + +unzip lammps*.zip :pre + +This version is the most up-to-date LAMMPS development version. It +will have the date of the most recent patch release (see the file +src/version.h). But it will also include any new bug-fixes or +features added since the last patch release. They will be included in +the next patch release tarball. + +:link(git,https://github.com/lammps/lammps) + +:line + +If you download a current LAMMPS tarball, one way to stay current as +new patch tarballs are released, is to download a patch file which you +can apply to your local directory to update it for each new patch +release. (Or of course you could just download the newest tarball +periodically.) + +The patch files are posted on the "bug and feature page"_bug of the +website, along with a list of changed files and details about what is +in the new patch release. Instructions for applying a patch file are +on the "Install patch"_Install_patch.html doc page. diff --git a/doc/src/Install_windows.txt b/doc/src/Install_windows.txt new file mode 100644 index 0000000000..df87754c5f --- /dev/null +++ b/doc/src/Install_windows.txt @@ -0,0 +1,52 @@ +"Higher level section"_Install.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Download an executable for Windows :h3 + +Pre-compiled Windows installers which install LAMMPS executables on a +Windows system can be downloaded from this site: + +"http://rpm.lammps.org/windows.html"_http://rpm.lammps.org/windows.html + +Note that each installer package has a date in its name, which +corresponds to the LAMMPS version of the same date. Installers for +current and older versions of LAMMPS are available. 32-bit and 64-bit +installers are available, and each installer contains both a serial +and parallel executable. The installer site also explains how to +install the Windows MPI package (MPICH2 from Argonne National Labs), +needed to run in parallel. + +The LAMMPS binaries contain all optional packages included in the +source distribution except: KIM, REAX, KOKKOS, USER-INTEL, +and USER-QMMM. The serial version also does not include the MPIIO and +USER-LB packages. GPU support is provided for OpenCL. + +The installer site also has instructions on how to run LAMMPS under +Windows, once it is installed, in both serial and parallel. + +When you download the installer package, you run it on your Windows +machine. It will then prompt you with a dialog, where you can choose +the installation directory, unpack and copy several executables, +potential files, documentation pdfs, selected example files, etc. It +will then update a few system settings (e.g. PATH, LAMMPS_POTENTIALS) +and add an entry into the Start Menu (with references to the +documentation, LAMMPS homepage and more). From that menu, there is +also a link to an uninstaller that removes the files and undoes the +environment manipulations. + +Note that to update to a newer version of LAMMPS, you should typically +uninstall the version you currently have, download a new installer, +and go thru the install procedure described above. I.e. the same +procedure for installing/updating most Windows programs. You can +install multiple versions of LAMMPS (in different directories), but +only the executable for the last-installed package will be found +automatically, so this should only be done for debugging purposes. + +Thanks to Axel Kohlmeyer (Temple U, akohlmey at gmail.com) for setting +up this Windows capability. diff --git a/doc/src/Intro.txt b/doc/src/Intro.txt new file mode 100644 index 0000000000..c8725e0085 --- /dev/null +++ b/doc/src/Intro.txt @@ -0,0 +1,39 @@ +"Previous Section"_Manual.html - "LAMMPS WWW Site"_lws - +"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next +Section"_Install.html :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands.html#comm) + +:line + +Introduction :h2 + +These pages provide a brief introduction to LAMMPS. + + + + + +"Overview of LAMMPS"_Intro_overview.html +"LAMMPS features"_Intro_features.html +"LAMMPS non-features"_Intro_nonfeatures.html +"LAMMPS open-source license"_Intro_license.html +"LAMMPS authors"_Intro_authors.html +"Additional website links"_Intro_website.html :all(b) + + diff --git a/doc/src/Intro_authors.txt b/doc/src/Intro_authors.txt new file mode 100644 index 0000000000..b909265a3e --- /dev/null +++ b/doc/src/Intro_authors.txt @@ -0,0 +1,66 @@ +"Higher level section"_Intro.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Authors of LAMMPS :h3 + +The primary LAMMPS developers are at Sandia National Labs and Temple +University: + +"Steve Plimpton"_sjp, sjplimp at sandia.gov +Aidan Thompson, athomps at sandia.gov +Stan Moore, stamoor at sandia.gov +Axel Kohlmeyer, akohlmey at gmail.com +Richard Berger, richard.berger at temple.edu :ul + +:link(sjp,http://www.cs.sandia.gov/~sjplimp) + +Past developers include Paul Crozier and Mark Stevens, both at Sandia, +and Ray Shan, now at Materials Design. + +:line + +The "Authors page"_http://lammps.sandia.gov/authors.html of the +"LAMMPS website"_lws has a comprehensive list of all the individuals +who have contributed code for a new feature or command or tool to +LAMMPS. + +:line + +The following folks deserve special recognition. Many of the packages +they have written are unique for an MD code and LAMMPS would not be as +general-purpose as it is without their expertise and efforts. + +Metin Aktulga (MSU), USER-REAXC package for C version of ReaxFF +Mike Brown (Intel), GPU and USER-INTEL packages +Colin Denniston (U Western Ontario), USER-LB package +Georg Ganzenmuller (EMI), USER-SMD and USER-SPH packages +Andres Jaramillo-Botero (Caltech), USER-EFF package for electron force field +Reese Jones (Sandia) and colleagues, USER-ATC package for atom/continuum coupling +Christoph Kloss (DCS Computing), LIGGGHTS code for granular materials, built on top of LAMMPS +Rudra Mukherjee (JPL), POEMS package for articulated rigid body motion +Trung Ngyuen (Northwestern U), GPU and RIGID and BODY packages +Mike Parks (Sandia), PERI package for Peridynamics +Roy Pollock (LLNL), Ewald and PPPM solvers +Christian Trott (Sandia), USER-CUDA and KOKKOS packages +Ilya Valuev (JIHT), USER-AWPMD package for wave-packet MD +Greg Wagner (Northwestern U), MEAM package for MEAM potential :ul + +:line + +As discussed on the "History +page"_http://lammps.sandia.gov/history.html of the website, LAMMPS +originated as a cooperative project between DOE labs and industrial +partners. Folks involved in the design and testing of the original +version of LAMMPS were the following: + +John Carpenter (Mayo Clinic, formerly at Cray Research) +Terry Stouch (Lexicon Pharmaceuticals, formerly at Bristol Myers Squibb) +Steve Lustig (Dupont) +Jim Belak and Roy Pollock (LLNL) :ul + diff --git a/doc/src/Intro_features.txt b/doc/src/Intro_features.txt new file mode 100644 index 0000000000..07c549c156 --- /dev/null +++ b/doc/src/Intro_features.txt @@ -0,0 +1,202 @@ +"Higher level section"_Intro.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +LAMMPS features :h3 + +LAMMPS is a classical molecular dynamics (MD) code with these general +classes of functionality: + +"General features"_#general +"Particle and model types"_#particle +"Interatomic potentials (force fields)"_#ff +"Atom creation"_#create +"Ensembles, constraints, and boundary conditions"_#ensemble +"Integrators"_#integrate +"Diagnostics"_#diag +"Output"_#output +"Multi-replica models"_#replica1 +"Pre- and post-processing"_#prepost +"Specialized features (beyond MD itself)"_#special :ul + +:line + +General features :h4,link(general) + + runs on a single processor or in parallel + distributed-memory message-passing parallelism (MPI) + spatial-decomposition of simulation domain for parallelism + open-source distribution + highly portable C++ + optional libraries used: MPI and single-processor FFT + GPU (CUDA and OpenCL), Intel Xeon Phi, and OpenMP support for many code features + easy to extend with new features and functionality + runs from an input script + syntax for defining and using variables and formulas + syntax for looping over runs and breaking out of loops + run one or multiple simulations simultaneously (in parallel) from one script + build as library, invoke LAMMPS thru library interface or provided Python wrapper + couple with other codes: LAMMPS calls other code, other code calls LAMMPS, umbrella code calls both :ul + +Particle and model types :h4,link(particle) +("atom style"_atom_style.html command) + + atoms + coarse-grained particles (e.g. bead-spring polymers) + united-atom polymers or organic molecules + all-atom polymers, organic molecules, proteins, DNA + metals + granular materials + coarse-grained mesoscale models + finite-size spherical and ellipsoidal particles + finite-size line segment (2d) and triangle (3d) particles + point dipole particles + rigid collections of particles + hybrid combinations of these :ul + +Interatomic potentials (force fields) :h4,link(ff) +("pair style"_pair_style.html, "bond style"_bond_style.html, +"angle style"_angle_style.html, "dihedral style"_dihedral_style.html, +"improper style"_improper_style.html, "kspace style"_kspace_style.html +commands) + + pairwise potentials: Lennard-Jones, Buckingham, Morse, Born-Mayer-Huggins, \ + Yukawa, soft, class 2 (COMPASS), hydrogen bond, tabulated + charged pairwise potentials: Coulombic, point-dipole + manybody potentials: EAM, Finnis/Sinclair EAM, modified EAM (MEAM), \ + embedded ion method (EIM), EDIP, ADP, Stillinger-Weber, Tersoff, \ + REBO, AIREBO, ReaxFF, COMB, SNAP, Streitz-Mintmire, 3-body polymorphic + long-range interactions for charge, point-dipoles, and LJ dispersion: \ + Ewald, Wolf, PPPM (similar to particle-mesh Ewald) + polarization models: "QEq"_fix_qeq.html, \ + "core/shell model"_Howto_coreshell.html, \ + "Drude dipole model"_Howto_drude.html + charge equilibration (QEq via dynamic, point, shielded, Slater methods) + coarse-grained potentials: DPD, GayBerne, REsquared, colloidal, DLVO + mesoscopic potentials: granular, Peridynamics, SPH + electron force field (eFF, AWPMD) + bond potentials: harmonic, FENE, Morse, nonlinear, class 2, \ + quartic (breakable) + angle potentials: harmonic, CHARMM, cosine, cosine/squared, cosine/periodic, \ + class 2 (COMPASS) + dihedral potentials: harmonic, CHARMM, multi-harmonic, helix, \ + class 2 (COMPASS), OPLS + improper potentials: harmonic, cvff, umbrella, class 2 (COMPASS) + polymer potentials: all-atom, united-atom, bead-spring, breakable + water potentials: TIP3P, TIP4P, SPC + implicit solvent potentials: hydrodynamic lubrication, Debye + force-field compatibility with common CHARMM, AMBER, DREIDING, \ + OPLS, GROMACS, COMPASS options + access to "KIM archive"_http://openkim.org of potentials via \ + "pair kim"_pair_kim.html + hybrid potentials: multiple pair, bond, angle, dihedral, improper \ + potentials can be used in one simulation + overlaid potentials: superposition of multiple pair potentials :ul + +Atom creation :h4,link(create) +("read_data"_read_data.html, "lattice"_lattice.html, +"create_atoms"_create_atoms.html, "delete_atoms"_delete_atoms.html, +"displace_atoms"_displace_atoms.html, "replicate"_replicate.html commands) + + read in atom coords from files + create atoms on one or more lattices (e.g. grain boundaries) + delete geometric or logical groups of atoms (e.g. voids) + replicate existing atoms multiple times + displace atoms :ul + +Ensembles, constraints, and boundary conditions :h4,link(ensemble) +("fix"_fix.html command) + + 2d or 3d systems + orthogonal or non-orthogonal (triclinic symmetry) simulation domains + constant NVE, NVT, NPT, NPH, Parinello/Rahman integrators + thermostatting options for groups and geometric regions of atoms + pressure control via Nose/Hoover or Berendsen barostatting in 1 to 3 dimensions + simulation box deformation (tensile and shear) + harmonic (umbrella) constraint forces + rigid body constraints + SHAKE bond and angle constraints + Monte Carlo bond breaking, formation, swapping + atom/molecule insertion and deletion + walls of various kinds + non-equilibrium molecular dynamics (NEMD) + variety of additional boundary conditions and constraints :ul + +Integrators :h4,link(integrate) +("run"_run.html, "run_style"_run_style.html, "minimize"_minimize.html commands) + + velocity-Verlet integrator + Brownian dynamics + rigid body integration + energy minimization via conjugate gradient or steepest descent relaxation + rRESPA hierarchical timestepping + rerun command for post-processing of dump files :ul + +Diagnostics :h4,link(diag) + + see various flavors of the "fix"_fix.html and "compute"_compute.html commands :ul + +Output :h4,link(output) +("dump"_dump.html, "restart"_restart.html commands) + + log file of thermodynamic info + text dump files of atom coords, velocities, other per-atom quantities + binary restart files + parallel I/O of dump and restart files + per-atom quantities (energy, stress, centro-symmetry parameter, CNA, etc) + user-defined system-wide (log file) or per-atom (dump file) calculations + spatial and time averaging of per-atom quantities + time averaging of system-wide quantities + atom snapshots in native, XYZ, XTC, DCD, CFG formats :ul + +Multi-replica models :h4,link(replica1) + +"nudged elastic band"_neb.html +"parallel replica dynamics"_prd.html +"temperature accelerated dynamics"_tad.html +"parallel tempering"_temper.html :ul + +Pre- and post-processing :h4,link(prepost) + +A handful of pre- and post-processing tools are packaged with LAMMPS, +some of which can convert input and output files to/from formats used +by other codes; see the "Toos"_Tools.html doc page. :ulb,l + +Our group has also written and released a separate toolkit called +"Pizza.py"_pizza which provides tools for doing setup, analysis, +plotting, and visualization for LAMMPS simulations. Pizza.py is +written in "Python"_python and is available for download from "the +Pizza.py WWW site"_pizza. :l,ule + +:link(pizza,http://www.sandia.gov/~sjplimp/pizza.html) +:link(python,http://www.python.org) + +Specialized features :h4,link(special) + +LAMMPS can be built with optional packages which implement a variety +of additional capabilities. See the "Packages"_Packages.html doc +page for details. + +These are LAMMPS capabilities which you may not think of as typical +classical MD options: + +"static"_balance.html and "dynamic load-balancing"_fix_balance.html +"generalized aspherical particles"_Howto_body.html +"stochastic rotation dynamics (SRD)"_fix_srd.html +"real-time visualization and interactive MD"_fix_imd.html +calculate "virtual diffraction patterns"_compute_xrd.html +"atom-to-continuum coupling"_fix_atc.html with finite elements +coupled rigid body integration via the "POEMS"_fix_poems.html library +"QM/MM coupling"_fix_qmmm.html +Monte Carlo via "GCMC"_fix_gcmc.html and "tfMC"_fix_tfmc.html and "atom swapping"_fix_atom_swap.html +"path-integral molecular dynamics (PIMD)"_fix_ipi.html and "this as well"_fix_pimd.html +"Direct Simulation Monte Carlo"_pair_dsmc.html for low-density fluids +"Peridynamics mesoscale modeling"_pair_peri.html +"Lattice Boltzmann fluid"_fix_lb_fluid.html +"targeted"_fix_tmd.html and "steered"_fix_smd.html molecular dynamics +"two-temperature electron model"_fix_ttm.html :ul diff --git a/doc/src/Intro_nonfeatures.txt b/doc/src/Intro_nonfeatures.txt new file mode 100644 index 0000000000..2acf6db71f --- /dev/null +++ b/doc/src/Intro_nonfeatures.txt @@ -0,0 +1,83 @@ +"Higher level section"_Intro.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +LAMMPS non-features :h3 + +LAMMPS is designed to be a fast, parallel engine for molecular +dynamics (MD) simulations. It provides only a modest amount of +functionality for setting up simulations and analyzing their output. + +Specifically, LAMMPS does not: + +run thru a GUI +build molecular systems +assign force-field coefficients automagically +perform sophisticated analyses of your MD simulation +visualize your MD simulation interactively +plot your output data :ul + +Here are suggestions on how to perform these tasks: + +GUI: LAMMPS can be built as a library and a Python wrapper that wraps +the library interface is provided. Thus, GUI interfaces can be +written in Python (or C or C++ if desired) that run LAMMPS and +visualize or plot its output. Examples of this are provided in the +python directory and described on the "Python"_Python_head.html doc +page. :ulb,l + +Builder: Several pre-processing tools are packaged with LAMMPS. Some +of them convert input files in formats produced by other MD codes such +as CHARMM, AMBER, or Insight into LAMMPS input formats. Some of them +are simple programs that will build simple molecular systems, such as +linear bead-spring polymer chains. The moltemplate program is a true +molecular builder that will generate complex molecular models. See +the "Tools"_Tools.html doc page for details on tools packaged with +LAMMPS. The "Pre/post processing +page"_http:/lammps.sandia.gov/prepost.html of the LAMMPS website +describes a variety of 3rd party tools for this task. :l + +Force-field assignment: The conversion tools described in the previous +bullet for CHARMM, AMBER, and Insight will also assign force field +coefficients in the LAMMPS format, assuming you provide CHARMM, AMBER, +or Accelerys force field files. :l + +Simulation analyses: If you want to perform analyses on-the-fly as +your simulation runs, see the "compute"_compute.html and +"fix"_fix.html doc pages, which list commands that can be used in a +LAMMPS input script. Also see the "Modify"_Modify.html doc page for +info on how to add your own analysis code or algorithms to LAMMPS. +For post-processing, LAMMPS output such as "dump file +snapshots"_dump.html can be converted into formats used by other MD or +post-processing codes. Some post-processing tools packaged with +LAMMPS will do these conversions. Scripts provided in the +tools/python directory can extract and massage data in dump files to +make it easier to import into other programs. See the +"Tools"_Tools.html doc page for details on these various options. :l + +Visualization: LAMMPS can produce JPG or PNG snapshot images +on-the-fly via its "dump image"_dump_image.html command. For +high-quality, interactive visualization there are many excellent and +free tools available. See the "Other Codes +page"_http://lammps.sandia.gov/viz.html page of the LAMMPS website for +visualization packages that can use LAMMPS output data. :l + +Plotting: See the next bullet about Pizza.py as well as the +"Python"_Python_head.html doc page for examples of plotting LAMMPS +output. Scripts provided with the {python} tool in the tools +directory will extract and massage data in log and dump files to make +it easier to analyze and plot. See the "Tools"_Tools.html doc page +for more discussion of the various tools. :l + +Pizza.py: Our group has also written a separate toolkit called +"Pizza.py"_http://pizza.sandia.gov which can do certain kinds of +setup, analysis, plotting, and visualization (via OpenGL) for LAMMPS +simulations. It thus provides some functionality for several of the +above bullets. Pizza.py is written in "Python"_http://www.python.org +and is available for download from "this +page"_http://www.cs.sandia.gov/~sjplimp/download.html. :l,ule diff --git a/doc/src/Intro_opensource.txt b/doc/src/Intro_opensource.txt new file mode 100644 index 0000000000..e0d57f7ce1 --- /dev/null +++ b/doc/src/Intro_opensource.txt @@ -0,0 +1,44 @@ +"Higher level section"_Intro.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +LAMMPS open-source license :h3 + +LAMMPS is a freely-available open-source code, distributed under the +terms of the "GNU Public License"_gnu, which means you can use or +modify the code however you wish. + +LAMMPS comes with no warranty of any kind. As each source file states +in its header, it is a copyrighted code that is distributed free-of- +charge, under the terms of the "GNU Public License"_gnu (GPL). This +is often referred to as open-source distribution - see +"www.gnu.org"_gnuorg or "www.opensource.org"_opensource. The legal +text of the GPL is in the LICENSE file included in the LAMMPS +distribution. + +:link(gnu,http://www.gnu.org/copyleft/gpl.html) +:link(gnuorg,http://www.gnu.org) +:link(opensource,http://www.opensource.org) + +Here is a summary of what the GPL means for LAMMPS users: + +(1) Anyone is free to use, modify, or extend LAMMPS in any way they +choose, including for commercial purposes. + +(2) If you distribute a modified version of LAMMPS, it must remain +open-source, meaning you distribute it under the terms of the GPL. +You should clearly annotate such a code as a derivative version of +LAMMPS. + +(3) If you release any code that includes LAMMPS source code, then it +must also be open-sourced, meaning you distribute it under the terms +of the GPL. + +(4) If you give LAMMPS files to someone else, the GPL LICENSE file and +source file headers (including the copyright and GPL notices) should +remain part of the code. diff --git a/doc/src/Intro_overview.txt b/doc/src/Intro_overview.txt new file mode 100644 index 0000000000..cd822c778f --- /dev/null +++ b/doc/src/Intro_overview.txt @@ -0,0 +1,58 @@ +"Higher level section"_Intro.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Overview of LAMMPS :h3 + +LAMMPS is a classical molecular dynamics (MD) code that models +ensembles of particles in a liquid, solid, or gaseous state. It can +model atomic, polymeric, biological, solid-state (metals, ceramics, +oxides), granular, coarse-grained, or macroscopic systems using a +variety of interatomic potentials (force fields) and boundary +conditions. It can model 2d or 3d systems with only a few particles +up to millions or billions. + +LAMMPS can be built and run on a laptop or desktop machine, but is +designed for parallel computers. It will run on any parallel machine +that supports the "MPI"_mpi message-passing library. This includes +shared-memory boxes and distributed-memory clusters and +supercomputers. + +:link(mpi,http://www-unix.mcs.anl.gov/mpi) + +LAMMPS is written in C++. Earlier versions were written in F77 and +F90. See the "History page"_http://lammps.sandia.gov/history.html of +the website for details. All versions can be downloaded from the +"LAMMPS website"_lws. + +LAMMPS is designed to be easy to modify or extend with new +capabilities, such as new force fields, atom types, boundary +conditions, or diagnostics. See the "Modify"_Modify.html doc page for +more details. + +In the most general sense, LAMMPS integrates Newton's equations of +motion for a collection of interacting particles. A single particle +can be an atom or molecule or electron, a coarse-grained cluster of +atoms, or a mesoscopic or macroscopic clump of material. The +interaction models that LAMMPS includes are mostly short-range in +nature; some long-range models are included as well. + +LAMMPS uses neighbor lists to keep track of nearby particles. The +lists are optimized for systems with particles that are repulsive at +short distances, so that the local density of particles never becomes +too large. This is in contrast to methods used for modeling plasma +or gravitational bodies (e.g. galaxy formation). + +On parallel machines, LAMMPS uses spatial-decomposition techniques to +partition the simulation domain into small sub-domains of equal +computational cost, one of which is assigned to each processor. +Processors communicate and store "ghost" atom information for atoms +that border their sub-domain. + + + diff --git a/doc/src/Intro_website.txt b/doc/src/Intro_website.txt new file mode 100644 index 0000000000..a8af94157c --- /dev/null +++ b/doc/src/Intro_website.txt @@ -0,0 +1,42 @@ +"Higher level section"_Intro.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Additional website links :h3 + +The "LAMMPS website"_lws has a variety of additional info about +LAMMPS, beyond what is in this manual. Some of the other pages in +this Intr are included in this list. + +"Brief intro and recently added significant features"_lws +"List of features"_http://lammps.sandia.gov/features.html +"List of non-features"_http://lammps.sandia.gov/non_features.html +"Recent bug fixes and new features"_http://lammps.sandia.gov/bug.html :ul + +"Download info"_http://lammps.sandia.gov/download.html +"GitHub site"_https://github.com/lammps/lammps +"SourceForge site"_https://sourceforge.net/projects/lammps +"LAMMPS open-source license"_http://lammps.sandia.gov/open_source.html :ul + +"Glossary of MD terms relevant to LAMMPS"_http://lammps.sandia.gov/glossary.html +"LAMMPS highlights with images"_http://lammps.sandia.gov/pictures.html +"LAMMPS highlights with movies"_http://lammps.sandia.gov/movies.html +"Mail list"_http://lammps.sandia.gov/mail.html +"Workshops"_http://lammps.sandia.gov/workshops.html +"Tutorials"_http://lammps.sandia.gov/tutorials.html +"Developer guide"_http://lammps.sandia.gov/Developer.pdf :ul + +"Pre- and post-processing tools for LAMMPS"_http://lammps.sandia.gov/prepost.html +"Other software usable with LAMMPS"_http://lammps.sandia.gov/offsite.html +"Viz tools usable with LAMMPS"_http://lammps.sandia.gov/viz.html :ul + +"Benchmark performance"_http://lammps.sandia.gov/bench.html +"Publications that have cited LAMMPS"_http://lammps.sandia.gov/papers.html +"Authors of LAMMPS"_http://lammps.sandia.gov/authors.html +"History of LAMMPS development"_http://lammps.sandia.gov/history.html +"Funding for LAMMPS"_http://lammps.sandia.gov/funding.html :ul diff --git a/doc/src/JPG/pair_atm_dia.jpg b/doc/src/JPG/pair_atm_dia.jpg new file mode 100644 index 0000000000..fd8edc5e67 Binary files /dev/null and b/doc/src/JPG/pair_atm_dia.jpg differ diff --git a/doc/src/JPG/pair_body_rounded.jpg b/doc/src/JPG/pair_body_rounded.jpg new file mode 100644 index 0000000000..cd745c44e2 Binary files /dev/null and b/doc/src/JPG/pair_body_rounded.jpg differ diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt index e302b061e3..5af157d8ea 100644 --- a/doc/src/Manual.txt +++ b/doc/src/Manual.txt @@ -1,134 +1,97 @@ LAMMPS Users Manual - + +

+ "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html#comm) :line LAMMPS Documentation :c,h1 -22 Jun 2018 version :c,h2 +5 Sep 2018 version :c,h2 -Version info: :h3 - -The LAMMPS "version" is the date when it was released, such as 1 May -2010. LAMMPS is updated continuously. Whenever we fix a bug or add a -feature, we release it immediately, and post a notice on "this page of -the WWW site"_bug. Every 2-4 months one of the incremental releases -is subjected to more thorough testing and labeled as a {stable} version. - -Each dated copy of LAMMPS contains all the -features and bug-fixes up to and including that version date. The -version date is printed to the screen and logfile every time you run -LAMMPS. It is also in the file src/version.h and in the LAMMPS -directory name created when you unpack a tarball, and at the top of -the first page of the manual (this page). - -If you browse the HTML doc pages on the LAMMPS WWW site, they always -describe the most current [development] version of LAMMPS. :ulb,l - -If you browse the HTML doc pages included in your tarball, they -describe the version you have. :l - -The "PDF file"_Manual.pdf on the WWW site or in the tarball is updated -about once per month. This is because it is large, and we don't want -it to be part of every patch. :l - -There is also a "Developer.pdf"_Developer.pdf file in the doc -directory, which describes the internal structure and algorithms of -LAMMPS. :l -:ule +"What is a LAMMPS version?"_Manual_version.html LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel Simulator. -LAMMPS is a classical molecular dynamics simulation code designed to -run efficiently on parallel computers. It was developed at Sandia -National Laboratories, a US Department of Energy facility, with -funding from the DOE. It is an open-source code, distributed freely -under the terms of the GNU Public License (GPL). +LAMMPS is a classical molecular dynamics simulation code with a focus +on materials modeling. It was designed to run efficiently on parallel +computers. It was developed originally at Sandia National +Laboratories, a US Department of Energy facility. The majority of +funding for LAMMPS has come from the US Department of Energy (DOE). +LAMMPS is an open-source code, distributed freely under the terms of +the GNU Public License (GPL). -The current core group of LAMMPS developers is at Sandia National -Labs and Temple University: - -"Steve Plimpton"_sjp, sjplimp at sandia.gov :ulb,l -Aidan Thompson, athomps at sandia.gov :l -Stan Moore, stamoor at sandia.gov :l -"Axel Kohlmeyer"_ako, akohlmey at gmail.com :l -:ule - -Past core developers include Paul Crozier, Ray Shan and Mark Stevens, -all at Sandia. The [LAMMPS home page] at -"http://lammps.sandia.gov"_http://lammps.sandia.gov has more information -about the code and its uses. Interaction with external LAMMPS developers, -bug reports and feature requests are mainly coordinated through the -"LAMMPS project on GitHub."_https://github.com/lammps/lammps -The lammps.org domain, currently hosting "public continuous integration -testing"_https://ci.lammps.org/job/lammps/ and "precompiled Linux -RPM and Windows installer packages"_http://packages.lammps.org is located -at Temple University and managed by Richard Berger, -richard.berger at temple.edu. - -:link(bug,http://lammps.sandia.gov/bug.html) -:link(sjp,http://www.sandia.gov/~sjplimp) -:link(ako,http://goo.gl/1wk0) +The "LAMMPS website"_lws has a variety of information about the code. +It includes links to an on-line version of this manual, a "mail +list"_http://lammps.sandia.gov/mail.html where users can post +questions, and a "GitHub site"https://github.com/lammps/lammps where +all LAMMPS development is coordinated. :line -The LAMMPS documentation is organized into the following sections. If -you find errors or omissions in this manual or have suggestions for -useful information to add, please send an email to the developers so -we can improve the LAMMPS documentation. - -Once you are familiar with LAMMPS, you may want to bookmark "this -page"_Section_commands.html#comm at Section_commands.html#comm since -it gives quick access to documentation for all LAMMPS commands. - "PDF file"_Manual.pdf of the entire manual, generated by "htmldoc"_http://freecode.com/projects/htmldoc +The content for this manual is part of the LAMMPS distribution. You +can build a local copy of the Manual as HTML pages or a PDF file, by +following the steps on the "Manual build"_Manual_build.html doc page. + +There is also a "Developer.pdf"_Developer.pdf document which gives +a brief description of the basic code structure of LAMMPS. + +:line + +This manual is organized into the following sections. + +Once you are familiar with LAMMPS, you may want to bookmark "this +page"_Commands.html since it gives quick access to a doc page for +every LAMMPS command. + -"Introduction"_Section_intro.html :olb,l - 1.1 "What is LAMMPS"_intro_1 :ulb,b - 1.2 "LAMMPS features"_intro_2 :b - 1.3 "LAMMPS non-features"_intro_3 :b - 1.4 "Open source distribution"_intro_4 :b - 1.5 "Acknowledgments and citations"_intro_5 :ule,b -"Getting started"_Section_start.html :l - 2.1 "What's in the LAMMPS distribution"_start_1 :ulb,b - 2.2 "Making LAMMPS"_start_2 :b - 2.3 "Making LAMMPS with optional packages"_start_3 :b - 2.4 "Building LAMMPS as a library"_start_4 :b - 2.5 "Running LAMMPS"_start_5 :b - 2.6 "Command-line options"_start_6 :b - 2.7 "Screen output"_start_7 :b - 2.8 "Tips for users of previous versions"_start_8 :ule,b -"Commands"_Section_commands.html :l - 3.1 "LAMMPS input script"_cmd_1 :ulb,b - 3.2 "Parsing rules"_cmd_2 :b - 3.3 "Input script structure"_cmd_3 :b - 3.4 "Commands listed by category"_cmd_4 :b - 3.5 "Commands listed alphabetically"_cmd_5 :ule,b -"Packages"_Section_packages.html :l - 4.1 "Standard packages"_pkg_1 :ulb,b - 4.2 "User packages"_pkg_2 :ule,b -"Accelerating LAMMPS performance"_Section_accelerate.html :l - 5.1 "Measuring performance"_acc_1 :ulb,b - 5.2 "Algorithms and code options to boost performace"_acc_2 :b - 5.3 "Accelerator packages with optimized styles"_acc_3 :b - 5.3.1 "GPU package"_accelerate_gpu.html :b - 5.3.2 "USER-INTEL package"_accelerate_intel.html :b - 5.3.3 "KOKKOS package"_accelerate_kokkos.html :b - 5.3.4 "USER-OMP package"_accelerate_omp.html :b - 5.3.5 "OPT package"_accelerate_opt.html :b - 5.4 "Comparison of various accelerator packages"_acc_4 :ule,b -"How-to discussions"_Section_howto.html :l - 6.1 "Restarting a simulation"_howto_1 :ulb,b - 6.2 "2d simulations"_howto_2 :b - 6.3 "CHARMM and AMBER force fields"_howto_3 :b - 6.4 "Running multiple simulations from one input script"_howto_4 :b - 6.5 "Multi-replica simulations"_howto_5 :b - 6.6 "Granular models"_howto_6 :b - 6.7 "TIP3P water model"_howto_7 :b - 6.8 "TIP4P water model"_howto_8 :b - 6.9 "SPC water model"_howto_9 :b - 6.10 "Coupling LAMMPS to other codes"_howto_10 :b - 6.11 "Visualizing LAMMPS snapshots"_howto_11 :b - 6.12 "Triclinic (non-orthogonal) simulation boxes"_howto_12 :b - 6.13 "NEMD simulations"_howto_13 :b - 6.14 "Finite-size spherical and aspherical particles"_howto_14 :b - 6.15 "Output from LAMMPS (thermo, dumps, computes, fixes, variables)"_howto_15 :b - 6.16 "Thermostatting, barostatting, and compute temperature"_howto_16 :b - 6.17 "Walls"_howto_17 :b - 6.18 "Elastic constants"_howto_18 :b - 6.19 "Library interface to LAMMPS"_howto_19 :b - 6.20 "Calculating thermal conductivity"_howto_20 :b - 6.21 "Calculating viscosity"_howto_21 :b - 6.22 "Calculating a diffusion coefficient"_howto_22 :b - 6.23 "Using chunks to calculate system properties"_howto_23 :b - 6.24 "Setting parameters for pppm/disp"_howto_24 :b - 6.25 "Polarizable models"_howto_25 :b - 6.26 "Adiabatic core/shell model"_howto_26 :b - 6.27 "Drude induced dipoles"_howto_27 :ule,b -"Example problems"_Section_example.html :l -"Performance & scalability"_Section_perf.html :l -"Additional tools"_Section_tools.html :l -"Modifying & extending LAMMPS"_Section_modify.html :l - 10.1 "Atom styles"_mod_1 :ulb,b - 10.2 "Bond, angle, dihedral, improper potentials"_mod_2 :b - 10.3 "Compute styles"_mod_3 :b - 10.4 "Dump styles"_mod_4 :b - 10.5 "Dump custom output options"_mod_5 :b - 10.6 "Fix styles"_mod_6 :b - 10.7 "Input script commands"_mod_7 :b - 10.8 "Kspace computations"_mod_8 :b - 10.9 "Minimization styles"_mod_9 :b - 10.10 "Pairwise potentials"_mod_10 :b - 10.11 "Region styles"_mod_11 :b - 10.12 "Body styles"_mod_12 :b - 10.13 "Thermodynamic output options"_mod_13 :b - 10.14 "Variable options"_mod_14 :b - 10.15 "Submitting new features for inclusion in LAMMPS"_mod_15 :ule,b -"Python interface"_Section_python.html :l - 11.1 "Overview of running LAMMPS from Python"_py_1 :ulb,b - 11.2 "Overview of using Python from a LAMMPS script"_py_2 :b - 11.3 "Building LAMMPS as a shared library"_py_3 :b - 11.4 "Installing the Python wrapper into Python"_py_4 :b - 11.5 "Extending Python with MPI to run in parallel"_py_5 :b - 11.6 "Testing the Python-LAMMPS interface"_py_6 :b - 11.7 "Using LAMMPS from Python"_py_7 :b - 11.8 "Example Python scripts that use LAMMPS"_py_8 :ule,b -"Errors"_Section_errors.html :l - 12.1 "Common problems"_err_1 :ulb,b - 12.2 "Reporting bugs"_err_2 :b - 12.3 "Error & warning messages"_err_3 :ule,b -"Future and history"_Section_history.html :l - 13.1 "Coming attractions"_hist_1 :ulb,b - 13.2 "Past versions"_hist_2 :ule,b +"Introduction"_Intro.html :olb,l +"Install LAMMPS"_Install.html :l +"Build LAMMPS"_Build.html :l +"Run LAMMPS"_Run_head.html :l +"Commands"_Commands.html :l +"Optional packages"_Packages.html :l +"Accelerate performance"_Speed.html :l +"How-to discussions"_Howto.html :l +"Example scripts"_Examples.html :l +"Auxiliary tools"_Tools.html :l +"Modify & extend LAMMPS"_Modify.html :l +"Use Python with LAMMPS"_Python_head.html :l +"Errors"_Errors.html :l +"Building the LAMMPS manual"_Manual_build.html :l :ole -:link(intro_1,Section_intro.html#intro_1) -:link(intro_2,Section_intro.html#intro_2) -:link(intro_3,Section_intro.html#intro_3) -:link(intro_4,Section_intro.html#intro_4) -:link(intro_5,Section_intro.html#intro_5) - -:link(start_1,Section_start.html#start_1) -:link(start_2,Section_start.html#start_2) -:link(start_3,Section_start.html#start_3) -:link(start_4,Section_start.html#start_4) -:link(start_5,Section_start.html#start_5) -:link(start_6,Section_start.html#start_6) -:link(start_7,Section_start.html#start_7) -:link(start_8,Section_start.html#start_8) - -:link(cmd_1,Section_commands.html#cmd_1) -:link(cmd_2,Section_commands.html#cmd_2) -:link(cmd_3,Section_commands.html#cmd_3) -:link(cmd_4,Section_commands.html#cmd_4) -:link(cmd_5,Section_commands.html#cmd_5) - -:link(pkg_1,Section_packages.html#pkg_1) -:link(pkg_2,Section_packages.html#pkg_2) - -:link(acc_1,Section_accelerate.html#acc_1) -:link(acc_2,Section_accelerate.html#acc_2) -:link(acc_3,Section_accelerate.html#acc_3) -:link(acc_4,Section_accelerate.html#acc_4) - -:link(howto_1,Section_howto.html#howto_1) -:link(howto_2,Section_howto.html#howto_2) -:link(howto_3,Section_howto.html#howto_3) -:link(howto_4,Section_howto.html#howto_4) -:link(howto_5,Section_howto.html#howto_5) -:link(howto_6,Section_howto.html#howto_6) -:link(howto_7,Section_howto.html#howto_7) -:link(howto_8,Section_howto.html#howto_8) -:link(howto_9,Section_howto.html#howto_9) -:link(howto_10,Section_howto.html#howto_10) -:link(howto_11,Section_howto.html#howto_11) -:link(howto_12,Section_howto.html#howto_12) -:link(howto_13,Section_howto.html#howto_13) -:link(howto_14,Section_howto.html#howto_14) -:link(howto_15,Section_howto.html#howto_15) -:link(howto_16,Section_howto.html#howto_16) -:link(howto_17,Section_howto.html#howto_17) -:link(howto_18,Section_howto.html#howto_18) -:link(howto_19,Section_howto.html#howto_19) -:link(howto_20,Section_howto.html#howto_20) -:link(howto_21,Section_howto.html#howto_21) -:link(howto_22,Section_howto.html#howto_22) -:link(howto_23,Section_howto.html#howto_23) -:link(howto_24,Section_howto.html#howto_24) -:link(howto_25,Section_howto.html#howto_25) -:link(howto_26,Section_howto.html#howto_26) -:link(howto_27,Section_howto.html#howto_27) - -:link(mod_1,Section_modify.html#mod_1) -:link(mod_2,Section_modify.html#mod_2) -:link(mod_3,Section_modify.html#mod_3) -:link(mod_4,Section_modify.html#mod_4) -:link(mod_5,Section_modify.html#mod_5) -:link(mod_6,Section_modify.html#mod_6) -:link(mod_7,Section_modify.html#mod_7) -:link(mod_8,Section_modify.html#mod_8) -:link(mod_9,Section_modify.html#mod_9) -:link(mod_10,Section_modify.html#mod_10) -:link(mod_11,Section_modify.html#mod_11) -:link(mod_12,Section_modify.html#mod_12) -:link(mod_13,Section_modify.html#mod_13) -:link(mod_14,Section_modify.html#mod_14) -:link(mod_15,Section_modify.html#mod_15) - -:link(py_1,Section_python.html#py_1) -:link(py_2,Section_python.html#py_2) -:link(py_3,Section_python.html#py_3) -:link(py_4,Section_python.html#py_4) -:link(py_5,Section_python.html#py_5) -:link(py_6,Section_python.html#py_6) - -:link(err_1,Section_errors.html#err_1) -:link(err_2,Section_errors.html#err_2) -:link(err_3,Section_errors.html#err_3) - -:link(hist_1,Section_history.html#hist_1) -:link(hist_2,Section_history.html#hist_2) diff --git a/doc/src/Manual_build.txt b/doc/src/Manual_build.txt new file mode 100644 index 0000000000..ac12dd7b2e --- /dev/null +++ b/doc/src/Manual_build.txt @@ -0,0 +1,124 @@ +"Previous Section"_Errors.html - "LAMMPS WWW Site"_lws - +"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next +Section"_Manual.html :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Building the LAMMPS manual :h2 + +Depending on how you obtained LAMMPS, the doc directory has 2 or 3 +sub-directories and optionally 2 PDF files and 2 e-book format files: + +src # content files for LAMMPS documentation +html # HTML version of the LAMMPS manual (see html/Manual.html) +tools # tools and settings for building the documentation +Manual.pdf # large PDF version of entire manual +Developer.pdf # small PDF with info about how LAMMPS is structured +LAMMPS.epub # Manual in ePUB e-book format +LAMMPS.mobi # Manual in MOBI e-book format :pre + +If you downloaded LAMMPS as a tarball from the web site, all these +directories and files should be included. + +If you downloaded LAMMPS from the public SVN or Git repositories, then +the HTML and PDF files are not included. Instead you need to create +them, in one of three ways: + +(a) You can "fetch" the current HTML and PDF files from the LAMMPS web +site. Just type "make fetch". This should create a html_www dir and +Manual_www.pdf/Developer_www.pdf files. Note that if new LAMMPS +features have been added more recently than the date of your version, +the fetched documentation will include those changes (but your source +code will not, unless you update your local repository). + +(b) You can build the HTML and PDF files yourself, by typing "make +html" followed by "make pdf". Note that the PDF make requires the +HTML files already exist. This requires various tools including +Sphinx, which the build process will attempt to download and install +on your system, if not already available. See more details below. + +(c) You can generate an older, simpler, less-fancy style of HTML +documentation by typing "make old". This will create an "old" +directory. This can be useful if (b) does not work on your box for +some reason, or you want to quickly view the HTML version of a doc +page you have created or edited yourself within the src directory. +E.g. if you are planning to submit a new feature to LAMMPS. + +:line + +The generation of all documentation is managed by the Makefile in +the doc dir. + +Documentation Build Options: :pre + +make html # generate HTML in html dir using Sphinx +make pdf # generate 2 PDF files (Manual.pdf,Developer.pdf) + # in doc dir via htmldoc and pdflatex +make old # generate old-style HTML pages in old dir via txt2html +make fetch # fetch HTML doc pages and 2 PDF files from web site + # as a tarball and unpack into html dir and 2 PDFs +make epub # generate LAMMPS.epub in ePUB format using Sphinx +make mobi # generate LAMMPS.mobi in MOBI format using ebook-convert +make clean # remove intermediate RST files created by HTML build +make clean-all # remove entire build folder and any cached data :pre + +:line + +Installing prerequisites for HTML build :h3 + +To run the HTML documentation build toolchain, Python 3 and virtualenv +have to be installed. Here are instructions for common setups: + +Ubuntu :h4 + +sudo apt-get install python-virtualenv :pre + +Fedora (up to version 21) and Red Hat Enterprise Linux or CentOS (up to version 7.x) :h4 + +sudo yum install python3-virtualenv :pre + +Fedora (since version 22) :h4 + +sudo dnf install python3-virtualenv :pre + +MacOS X :h4 + +Python 3 :h5 + +Download the latest Python 3 MacOS X package from +"https://www.python.org"_https://www.python.org +and install it. This will install both Python 3 +and pip3. + +virtualenv :h5 + +Once Python 3 is installed, open a Terminal and type + +pip3 install virtualenv :pre + +This will install virtualenv from the Python Package Index. + +:line + +Installing prerequisites for PDF build + +[TBA] + +:line + +Installing prerequisites for epub build :h3 + +ePUB :h4 + +Same as for HTML. This uses the same tools and configuration +files as the HTML tree. + +For converting the generated ePUB file to a MOBI format file +(for e-book readers like Kindle, that cannot read ePUB), you +also need to have the 'ebook-convert' tool from the "calibre" +software installed. "http://calibre-ebook.com/"_http://calibre-ebook.com/ +You first create the ePUB file and then convert it with 'make mobi' diff --git a/doc/src/Manual_version.txt b/doc/src/Manual_version.txt new file mode 100644 index 0000000000..436e531246 --- /dev/null +++ b/doc/src/Manual_version.txt @@ -0,0 +1,33 @@ +"Higher level section"_Manual.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +What does a LAMMPS version mean :h3 + +The LAMMPS "version" is the date when it was released, such as 1 May +2014. LAMMPS is updated continuously. Whenever we fix a bug or add a +feature, we release it in the next {patch} release, which are +typically made every couple of weeks. Info on patch releases are on +"this website page"_http://lammps.sandia.gov/bug.html. Every few +months, the latest patch release is subjected to more thorough testing +and labeled as a {stable} version. + +Each version of LAMMPS contains all the features and bug-fixes up to +and including its version date. + +The version date is printed to the screen and logfile every time you +run LAMMPS. It is also in the file src/version.h and in the LAMMPS +directory name created when you unpack a tarball. And it is on the +first page of the "manual"_Manual.html. + +If you browse the HTML doc pages on the LAMMPS WWW site, they always +describe the most current patch release of LAMMPS. :ulb,l + +If you browse the HTML doc pages included in your tarball, they +describe the version you have, which may be older. :l,ule + diff --git a/doc/src/Modify.txt b/doc/src/Modify.txt new file mode 100644 index 0000000000..38fbf17dd9 --- /dev/null +++ b/doc/src/Modify.txt @@ -0,0 +1,70 @@ +"Previous Section"_Tools.html - "LAMMPS WWW Site"_lws - +"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next +Section"_Python_head.html :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Modify & extend LAMMPS :h2 + +LAMMPS is designed in a modular fashion so as to be easy to modify and +extend with new functionality. In fact, about 95% of its source code +is add-on files. These doc pages give basic instructions on how to do +this. + +If you add a new feature to LAMMPS and think it will be of interest to +general users, we encourage you to submit it for inclusion in LAMMPS +as a pull request on our "GitHub +site"_https://github.com/lammps/lammps, after reading the "Modify +contribute"_Modify_contribute.html doc page. + + + + + +"Overview"_Modify_overview.html +"Submitting new features for inclusion in LAMMPS"_Modify_contribute.html :all(b) + +"Atom styles"_Modify_atom.html +"Pair styles"_Modify_pair.html +"Bond, angle, dihedral, improper styles"_Modify_bond.html +"Compute styles"_Modify_compute.html +"Fix styles"_Modify_fix.html +"Input script command styles"_Modify_command.html +"Dump styles"_Modify_dump.html +"Kspace styles"_Modify_kspace.html +"Minimization styles"_Modify_min.html +"Region styles"_Modify_region.html +"Body styles"_Modify_body.html +"Thermodynamic output options"_Modify_thermo.html +"Variable options"_Modify_variable.html :all(b) + + diff --git a/doc/src/Modify_atom.txt b/doc/src/Modify_atom.txt new file mode 100644 index 0000000000..60c7dccb29 --- /dev/null +++ b/doc/src/Modify_atom.txt @@ -0,0 +1,90 @@ +"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Atom styles :h3 + +Classes that define an "atom style"_atom_style.html are derived from +the AtomVec class and managed by the Atom class. The atom style +determines what attributes are associated with an atom. A new atom +style can be created if one of the existing atom styles does not +define all the attributes you need to store and communicate with +atoms. + +Atom_vec_atomic.cpp is a simple example of an atom style. + +Here is a brief description of methods you define in your new derived +class. See atom_vec.h for details. + +init: one time setup (optional) +grow: re-allocate atom arrays to longer lengths (required) +grow_reset: make array pointers in Atom and AtomVec classes consistent (required) +copy: copy info for one atom to another atom's array locations (required) +pack_comm: store an atom's info in a buffer communicated every timestep (required) +pack_comm_vel: add velocity info to communication buffer (required) +pack_comm_hybrid: store extra info unique to this atom style (optional) +unpack_comm: retrieve an atom's info from the buffer (required) +unpack_comm_vel: also retrieve velocity info (required) +unpack_comm_hybrid: retrieve extra info unique to this atom style (optional) +pack_reverse: store an atom's info in a buffer communicating partial forces (required) +pack_reverse_hybrid: store extra info unique to this atom style (optional) +unpack_reverse: retrieve an atom's info from the buffer (required) +unpack_reverse_hybrid: retrieve extra info unique to this atom style (optional) +pack_border: store an atom's info in a buffer communicated on neighbor re-builds (required) +pack_border_vel: add velocity info to buffer (required) +pack_border_hybrid: store extra info unique to this atom style (optional) +unpack_border: retrieve an atom's info from the buffer (required) +unpack_border_vel: also retrieve velocity info (required) +unpack_border_hybrid: retrieve extra info unique to this atom style (optional) +pack_exchange: store all an atom's info to migrate to another processor (required) +unpack_exchange: retrieve an atom's info from the buffer (required) +size_restart: number of restart quantities associated with proc's atoms (required) +pack_restart: pack atom quantities into a buffer (required) +unpack_restart: unpack atom quantities from a buffer (required) +create_atom: create an individual atom of this style (required) +data_atom: parse an atom line from the data file (required) +data_atom_hybrid: parse additional atom info unique to this atom style (optional) +data_vel: parse one line of velocity information from data file (optional) +data_vel_hybrid: parse additional velocity data unique to this atom style (optional) +memory_usage: tally memory allocated by atom arrays (required) :tb(s=:) + +The constructor of the derived class sets values for several variables +that you must set when defining a new atom style, which are documented +in atom_vec.h. New atom arrays are defined in atom.cpp. Search for +the word "customize" and you will find locations you will need to +modify. + +NOTE: It is possible to add some attributes, such as a molecule ID, to +atom styles that do not have them via the "fix +property/atom"_fix_property_atom.html command. This command also +allows new custom attributes consisting of extra integer or +floating-point values to be added to atoms. See the "fix +property/atom"_fix_property_atom.html doc page for examples of cases +where this is useful and details on how to initialize, access, and +output the custom values. + +New "pair styles"_pair_style.html, "fixes"_fix.html, or +"computes"_compute.html can be added to LAMMPS, as discussed below. +The code for these classes can use the per-atom properties defined by +fix property/atom. The Atom class has a find_custom() method that is +useful in this context: + +int index = atom->find_custom(char *name, int &flag); :pre + +The "name" of a custom attribute, as specified in the "fix +property/atom"_fix_property_atom.html command, is checked to verify +that it exists and its index is returned. The method also sets flag = +0/1 depending on whether it is an integer or floating-point attribute. +The vector of values associated with the attribute can then be +accessed using the returned index as + +int *ivector = atom->ivector\[index\]; +double *dvector = atom->dvector\[index\]; :pre + +Ivector or dvector are vectors of length Nlocal = # of owned atoms, +which store the attributes of individual atoms. diff --git a/doc/src/Modify_body.txt b/doc/src/Modify_body.txt new file mode 100644 index 0000000000..0114ae10c8 --- /dev/null +++ b/doc/src/Modify_body.txt @@ -0,0 +1,34 @@ +"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Body styles :h3 + +Classes that define body particles are derived from the Body class. +Body particles can represent complex entities, such as surface meshes +of discrete points, collections of sub-particles, deformable objects, +etc. + +See the "Howto body"_Howto_body.html doc page for an overview of using +body particles and the various body styles LAMMPS supports. New +styles can be created to add new kinds of body particles to LAMMPS. + +Body_nparticle.cpp is an example of a body particle that is treated as +a rigid body containing N sub-particles. + +Here is a brief description of methods you define in your new derived +class. See body.h for details. + +data_body: process a line from the Bodies section of a data file +noutrow: number of sub-particles output is generated for +noutcol: number of values per-sub-particle output is generated for +output: output values for the Mth sub-particle +pack_comm_body: body attributes to communicate every timestep +unpack_comm_body: unpacking of those attributes +pack_border_body: body attributes to communicate when reneighboring is done +unpack_border_body: unpacking of those attributes :tb(s=:) diff --git a/doc/src/Modify_bond.txt b/doc/src/Modify_bond.txt new file mode 100644 index 0000000000..7ceea3f910 --- /dev/null +++ b/doc/src/Modify_bond.txt @@ -0,0 +1,33 @@ +"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Bond, angle, dihedral, improper styles :h3 + +Classes that compute molecular interactions are derived from the Bond, +Angle, Dihedral, and Improper classes. New styles can be created to +add new potentials to LAMMPS. + +Bond_harmonic.cpp is the simplest example of a bond style. Ditto for +the harmonic forms of the angle, dihedral, and improper style +commands. + +Here is a brief description of common methods you define in your +new derived class. See bond.h, angle.h, dihedral.h, and improper.h +for details and specific additional methods. + +init: check if all coefficients are set, calls {init_style} (optional) +init_style: check if style specific conditions are met (optional) +compute: compute the molecular interactions (required) +settings: apply global settings for all types (optional) +coeff: set coefficients for one type (required) +equilibrium_distance: length of bond, used by SHAKE (required, bond only) +equilibrium_angle: opening of angle, used by SHAKE (required, angle only) +write & read_restart: writes/reads coeffs to restart files (required) +single: force and energy of a single bond or angle (required, bond or angle only) +memory_usage: tally memory allocated by the style (optional) :tb(s=:) diff --git a/doc/src/Modify_command.txt b/doc/src/Modify_command.txt new file mode 100644 index 0000000000..4576f6c806 --- /dev/null +++ b/doc/src/Modify_command.txt @@ -0,0 +1,27 @@ +"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Input script command style :h3 + +New commands can be added to LAMMPS input scripts by adding new +classes that have a "command" method. For example, the create_atoms, +read_data, velocity, and run commands are all implemented in this +fashion. When such a command is encountered in the LAMMPS input +script, LAMMPS simply creates a class with the corresponding name, +invokes the "command" method of the class, and passes it the arguments +from the input script. The command method can perform whatever +operations it wishes on LAMMPS data structures. + +The single method your new class must define is as follows: + +command: operations performed by the new command :tb(s=:) + +Of course, the new class can define other methods and variables as +needed. + diff --git a/doc/src/Modify_compute.txt b/doc/src/Modify_compute.txt new file mode 100644 index 0000000000..2f6481dbd5 --- /dev/null +++ b/doc/src/Modify_compute.txt @@ -0,0 +1,49 @@ +"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Compute styles :h3 + +Classes that compute scalar and vector quantities like temperature +and the pressure tensor, as well as classes that compute per-atom +quantities like kinetic energy and the centro-symmetry parameter +are derived from the Compute class. New styles can be created +to add new calculations to LAMMPS. + +Compute_temp.cpp is a simple example of computing a scalar +temperature. Compute_ke_atom.cpp is a simple example of computing +per-atom kinetic energy. + +Here is a brief description of methods you define in your new derived +class. See compute.h for details. + +init: perform one time setup (required) +init_list: neighbor list setup, if needed (optional) +compute_scalar: compute a scalar quantity (optional) +compute_vector: compute a vector of quantities (optional) +compute_peratom: compute one or more quantities per atom (optional) +compute_local: compute one or more quantities per processor (optional) +pack_comm: pack a buffer with items to communicate (optional) +unpack_comm: unpack the buffer (optional) +pack_reverse: pack a buffer with items to reverse communicate (optional) +unpack_reverse: unpack the buffer (optional) +remove_bias: remove velocity bias from one atom (optional) +remove_bias_all: remove velocity bias from all atoms in group (optional) +restore_bias: restore velocity bias for one atom after remove_bias (optional) +restore_bias_all: same as before, but for all atoms in group (optional) +pair_tally_callback: callback function for {tally}-style computes (optional). +memory_usage: tally memory usage (optional) :tb(s=:) + +Tally-style computes are a special case, as their computation is done +in two stages: the callback function is registered with the pair style +and then called from the Pair::ev_tally() function, which is called for +each pair after force and energy has been computed for this pair. Then +the tallied values are retrieved with the standard compute_scalar or +compute_vector or compute_peratom methods. The USER-TALLY package +provides {examples}_compute_tally.html for utilizing this mechanism. + diff --git a/doc/src/Modify_contribute.txt b/doc/src/Modify_contribute.txt new file mode 100644 index 0000000000..8cbea8bb31 --- /dev/null +++ b/doc/src/Modify_contribute.txt @@ -0,0 +1,212 @@ +"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Submitting new features for inclusion in LAMMPS :h3 + +We encourage users to submit new features or modifications for LAMMPS +to "the core developers"_http://lammps.sandia.gov/authors.html so they +can be added to the LAMMPS distribution. The preferred way to manage +and coordinate this is as of Fall 2016 via the LAMMPS project on +"GitHub"_https://github.com/lammps/lammps. An alternative is to +contact the LAMMPS developers or the indicated developer of a package +or feature directly and send in your contribution via e-mail. + +For any larger modifications or programming project, you are +encouraged to contact the LAMMPS developers ahead of time, in order to +discuss implementation strategies and coding guidelines, that will +make it easier to integrate your contribution and result in less work +for everybody involved. You are also encouraged to search through the +list of "open issues on +GitHub"_https://github.com/lammps/lammps/issues and submit a new issue +for a planned feature, so you would not duplicate the work of others +(and possibly get scooped by them) or have your work duplicated by +others. + +How quickly your contribution will be integrated depends largely on +how much effort it will cause to integrate and test it, how much it +requires changes to the core codebase, and of how much interest it is +to the larger LAMMPS community. Please see below for a checklist of +typical requirements. Once you have prepared everything, see the +"Howto github"_Howto_github.html doc page for instructions on how to +submit your changes or new files through a GitHub pull request. If you +prefer to submit patches or full files, you should first make certain, +that your code works correctly with the latest patch-level version of +LAMMPS and contains all bugfixes from it. Then create a gzipped tar +file of all changed or added files or a corresponding patch file using +'diff -u' or 'diff -c' and compress it with gzip. Please only use gzip +compression, as this works well on all platforms. + +If the new features/files are broadly useful we may add them as core +files to LAMMPS or as part of a "standard +package"_Packages_standard.html. Else we will add them as a +user-contributed file or "user package"_Packages_user.html. Examples +of user packages are in src sub-directories that start with USER. The +USER-MISC package is simply a collection of (mostly) unrelated single +files, which is the simplest way to have your contribution quickly +added to the LAMMPS distribution. All the standard and user packages +are listed and described on the "Packages +details"_Packages_details.html doc page. + +Note that by providing us files to release, you are agreeing to make +them open-source, i.e. we can release them under the terms of the GPL, +used as a license for the rest of LAMMPS. See the "Open +source"_http://lammps.sandia.gov/open_source.html page on the LAMMPS +website for details. + +With user packages and files, all we are really providing (aside from +the fame and fortune that accompanies having your name in the source +code and on the "Authors page"_http://lammps.sandia.gov/authors.html +of the "LAMMPS WWW site"_lws), is a means for you to distribute your +work to the LAMMPS user community, and a mechanism for others to +easily try out your new feature. This may help you find bugs or make +contact with new collaborators. Note that you're also implicitly +agreeing to support your code which means answer questions, fix bugs, +and maintain it if LAMMPS changes in some way that breaks it (an +unusual event). + +NOTE: If you prefer to actively develop and support your add-on +feature yourself, then you may wish to make it available for download +from your own website, as a user package that LAMMPS users can add to +their copy of LAMMPS. See the "Offsite LAMMPS packages and +tools"_http://lammps.sandia.gov/offsite.html page of the LAMMPS web +site for examples of groups that do this. We are happy to advertise +your package and web site from that page. Simply email the +"developers"_http://lammps.sandia.gov/authors.html with info about +your package and we will post it there. + +The previous sections of this doc page describe how to add new "style" +files of various kinds to LAMMPS. Packages are simply collections of +one or more new class files which are invoked as a new style within a +LAMMPS input script. If designed correctly, these additions typically +do not require changes to the main core of LAMMPS; they are simply +add-on files. If you think your new feature requires non-trivial +changes in core LAMMPS files, you'll need to "communicate with the +developers"_http://lammps.sandia.gov/authors.html, since we may or may +not want to make those changes. An example of a trivial change is +making a parent-class method "virtual" when you derive a new child +class from it. + +Here is a checklist of steps you need to follow to submit a single file +or user package for our consideration. Following these steps will save +both you and us time. See existing files in packages in the src dir for +examples. If you are uncertain, please ask. + +All source files you provide must compile with the most current +version of LAMMPS with multiple configurations. In particular you +need to test compiling LAMMPS from scratch with -DLAMMPS_BIGBIG +set in addition to the default -DLAMMPS_SMALLBIG setting. Your code +will need to work correctly in serial and in parallel using MPI. :ulb,l + +For consistency with the rest of LAMMPS and especially, if you want +your contribution(s) to be added to main LAMMPS code or one of its +standard packages, it needs to be written in a style compatible with +other LAMMPS source files. This means: 2-character indentation per +level, [no tabs], no lines over 80 characters. I/O is done via +the C-style stdio library, class header files should not import any +system headers outside , STL containers should be avoided +in headers, and forward declarations used where possible or needed. +All added code should be placed into the LAMMPS_NS namespace or a +sub-namespace; global or static variables should be avoided, as they +conflict with the modular nature of LAMMPS and the C++ class structure. +Header files must [not] import namespaces with {using}. +This all is so the developers can more easily understand, integrate, +and maintain your contribution and reduce conflicts with other parts +of LAMMPS. This basically means that the code accesses data +structures, performs its operations, and is formatted similar to other +LAMMPS source files, including the use of the error class for error +and warning messages. :l + +If you want your contribution to be added as a user-contributed +feature, and it's a single file (actually a *.cpp and *.h file) it can +rapidly be added to the USER-MISC directory. Send us the one-line +entry to add to the USER-MISC/README file in that dir, along with the +2 source files. You can do this multiple times if you wish to +contribute several individual features. :l + +If you want your contribution to be added as a user-contribution and +it is several related features, it is probably best to make it a user +package directory with a name like USER-FOO. In addition to your new +files, the directory should contain a README text file. The README +should contain your name and contact information and a brief +description of what your new package does. If your files depend on +other LAMMPS style files also being installed (e.g. because your file +is a derived class from the other LAMMPS class), then an Install.sh +file is also needed to check for those dependencies. See other README +and Install.sh files in other USER directories as examples. Send us a +tarball of this USER-FOO directory. :l + +Your new source files need to have the LAMMPS copyright, GPL notice, +and your name and email address at the top, like other +user-contributed LAMMPS source files. They need to create a class +that is inside the LAMMPS namespace. If the file is for one of the + +USER packages, including USER-MISC, then we are not as picky about the +coding style (see above). I.e. the files do not need to be in the +same stylistic format and syntax as other LAMMPS files, though that +would be nice for developers as well as users who try to read your +code. :l + +You [must] also create a [documentation] file for each new command or +style you are adding to LAMMPS. For simplicity and convenience, the +documentation of groups of closely related commands or styles may be +combined into a single file. This will be one file for a single-file +feature. For a package, it might be several files. These are simple +text files with a specific markup language, that are then auto-converted +to HTML and PDF. The tools for this conversion are included in the +source distribution, and the translation can be as simple as doing +"make html pdf" in the doc folder. +Thus the documentation source files must be in the same format and +style as other *.txt files in the lammps/doc/src directory for similar +commands and styles; use one or more of them as a starting point. +A description of the markup can also be found in +lammps/doc/utils/txt2html/README.html +As appropriate, the text files can include links to equations +(see doc/Eqs/*.tex for examples, we auto-create the associated JPG +files), or figures (see doc/JPG for examples), or even additional PDF +files with further details (see doc/PDF for examples). The doc page +should also include literature citations as appropriate; see the +bottom of doc/fix_nh.txt for examples and the earlier part of the same +file for how to format the cite itself. The "Restrictions" section of +the doc page should indicate that your command is only available if +LAMMPS is built with the appropriate USER-MISC or USER-FOO package. +See other user package doc files for examples of how to do this. The +prerequisite for building the HTML format files are Python 3.x and +virtualenv, the requirement for generating the PDF format manual +is the "htmldoc"_http://www.htmldoc.org/ software. Please run at least +"make html" and carefully inspect and proofread the resulting HTML format +doc page before submitting your code. :l + +For a new package (or even a single command) you should include one or +more example scripts demonstrating its use. These should run in no +more than a couple minutes, even on a single processor, and not require +large data files as input. See directories under examples/USER for +examples of input scripts other users provided for their packages. +These example inputs are also required for validating memory accesses +and testing for memory leaks with valgrind :l + +If there is a paper of yours describing your feature (either the +algorithm/science behind the feature itself, or its initial usage, or +its implementation in LAMMPS), you can add the citation to the *.cpp +source file. See src/USER-EFF/atom_vec_electron.cpp for an example. +A LaTeX citation is stored in a variable at the top of the file and a +single line of code that references the variable is added to the +constructor of the class. Whenever a user invokes your feature from +their input script, this will cause LAMMPS to output the citation to a +log.cite file and prompt the user to examine the file. Note that you +should only use this for a paper you or your group authored. +E.g. adding a cite in the code for a paper by Nose and Hoover if you +write a fix that implements their integrator is not the intended +usage. That kind of citation should just be in the doc page you +provide. :l +:ule + +Finally, as a general rule-of-thumb, the more clear and +self-explanatory you make your documentation and README files, and the +easier you make it for people to get started, e.g. by providing example +scripts, the more likely it is that users will try out your new feature. diff --git a/doc/src/Modify_dump.txt b/doc/src/Modify_dump.txt new file mode 100644 index 0000000000..cfe96f5d3d --- /dev/null +++ b/doc/src/Modify_dump.txt @@ -0,0 +1,35 @@ +"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Dump styles :h3 + +Classes that dump per-atom info to files are derived from the Dump +class. To dump new quantities or in a new format, a new derived dump +class can be added, but it is typically simpler to modify the +DumpCustom class contained in the dump_custom.cpp file. + +Dump_atom.cpp is a simple example of a derived dump class. + +Here is a brief description of methods you define in your new derived +class. See dump.h for details. + +write_header: write the header section of a snapshot of atoms +count: count the number of lines a processor will output +pack: pack a proc's output data into a buffer +write_data: write a proc's data to a file :tb(s=:) + +See the "dump"_dump.html command and its {custom} style for a list of +keywords for atom information that can already be dumped by +DumpCustom. It includes options to dump per-atom info from Compute +classes, so adding a new derived Compute class is one way to calculate +new quantities to dump. + +Note that new keywords for atom properties are not typically +added to the "dump custom"_dump.html command. Instead they are added +to the "compute property/atom"_compute_property_atom.html command. diff --git a/doc/src/Modify_fix.txt b/doc/src/Modify_fix.txt new file mode 100644 index 0000000000..b095ebc4b5 --- /dev/null +++ b/doc/src/Modify_fix.txt @@ -0,0 +1,107 @@ +"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Fix styles :h3 + +In LAMMPS, a "fix" is any operation that is computed during +timestepping that alters some property of the system. Essentially +everything that happens during a simulation besides force computation, +neighbor list construction, and output, is a "fix". This includes +time integration (update of coordinates and velocities), force +constraints or boundary conditions (SHAKE or walls), and diagnostics +(compute a diffusion coefficient). New styles can be created to add +new options to LAMMPS. + +Fix_setforce.cpp is a simple example of setting forces on atoms to +prescribed values. There are dozens of fix options already in LAMMPS; +choose one as a template that is similar to what you want to +implement. + +Here is a brief description of methods you can define in your new +derived class. See fix.h for details. + +setmask: determines when the fix is called during the timestep (required) +init: initialization before a run (optional) +setup_pre_exchange: called before atom exchange in setup (optional) +setup_pre_force: called before force computation in setup (optional) +setup: called immediately before the 1st timestep and after forces are computed (optional) +min_setup_pre_force: like setup_pre_force, but for minimizations instead of MD runs (optional) +min_setup: like setup, but for minimizations instead of MD runs (optional) +initial_integrate: called at very beginning of each timestep (optional) +pre_exchange: called before atom exchange on re-neighboring steps (optional) +pre_neighbor: called before neighbor list build (optional) +pre_force: called before pair & molecular forces are computed (optional) +post_force: called after pair & molecular forces are computed and communicated (optional) +final_integrate: called at end of each timestep (optional) +end_of_step: called at very end of timestep (optional) +write_restart: dumps fix info to restart file (optional) +restart: uses info from restart file to re-initialize the fix (optional) +grow_arrays: allocate memory for atom-based arrays used by fix (optional) +copy_arrays: copy atom info when an atom migrates to a new processor (optional) +pack_exchange: store atom's data in a buffer (optional) +unpack_exchange: retrieve atom's data from a buffer (optional) +pack_restart: store atom's data for writing to restart file (optional) +unpack_restart: retrieve atom's data from a restart file buffer (optional) +size_restart: size of atom's data (optional) +maxsize_restart: max size of atom's data (optional) +setup_pre_force_respa: same as setup_pre_force, but for rRESPA (optional) +initial_integrate_respa: same as initial_integrate, but for rRESPA (optional) +post_integrate_respa: called after the first half integration step is done in rRESPA (optional) +pre_force_respa: same as pre_force, but for rRESPA (optional) +post_force_respa: same as post_force, but for rRESPA (optional) +final_integrate_respa: same as final_integrate, but for rRESPA (optional) +min_pre_force: called after pair & molecular forces are computed in minimizer (optional) +min_post_force: called after pair & molecular forces are computed and communicated in minimizer (optional) +min_store: store extra data for linesearch based minimization on a LIFO stack (optional) +min_pushstore: push the minimization LIFO stack one element down (optional) +min_popstore: pop the minimization LIFO stack one element up (optional) +min_clearstore: clear minimization LIFO stack (optional) +min_step: reset or move forward on line search minimization (optional) +min_dof: report number of degrees of freedom {added} by this fix in minimization (optional) +max_alpha: report maximum allowed step size during linesearch minimization (optional) +pack_comm: pack a buffer to communicate a per-atom quantity (optional) +unpack_comm: unpack a buffer to communicate a per-atom quantity (optional) +pack_reverse_comm: pack a buffer to reverse communicate a per-atom quantity (optional) +unpack_reverse_comm: unpack a buffer to reverse communicate a per-atom quantity (optional) +dof: report number of degrees of freedom {removed} by this fix during MD (optional) +compute_scalar: return a global scalar property that the fix computes (optional) +compute_vector: return a component of a vector property that the fix computes (optional) +compute_array: return a component of an array property that the fix computes (optional) +deform: called when the box size is changed (optional) +reset_target: called when a change of the target temperature is requested during a run (optional) +reset_dt: is called when a change of the time step is requested during a run (optional) +modify_param: called when a fix_modify request is executed (optional) +memory_usage: report memory used by fix (optional) +thermo: compute quantities for thermodynamic output (optional) :tb(s=:) + +Typically, only a small fraction of these methods are defined for a +particular fix. Setmask is mandatory, as it determines when the fix +will be invoked during the timestep. Fixes that perform time +integration ({nve}, {nvt}, {npt}) implement initial_integrate() and +final_integrate() to perform velocity Verlet updates. Fixes that +constrain forces implement post_force(). + +Fixes that perform diagnostics typically implement end_of_step(). For +an end_of_step fix, one of your fix arguments must be the variable +"nevery" which is used to determine when to call the fix and you must +set this variable in the constructor of your fix. By convention, this +is the first argument the fix defines (after the ID, group-ID, style). + +If the fix needs to store information for each atom that persists from +timestep to timestep, it can manage that memory and migrate the info +with the atoms as they move from processors to processor by +implementing the grow_arrays, copy_arrays, pack_exchange, and +unpack_exchange methods. Similarly, the pack_restart and +unpack_restart methods can be implemented to store information about +the fix in restart files. If you wish an integrator or force +constraint fix to work with rRESPA (see the "run_style"_run_style.html +command), the initial_integrate, post_force_integrate, and +final_integrate_respa methods can be implemented. The thermo method +enables a fix to contribute values to thermodynamic output, as printed +quantities and/or to be summed to the potential energy of the system. diff --git a/doc/src/Modify_kspace.txt b/doc/src/Modify_kspace.txt new file mode 100644 index 0000000000..d5f018411d --- /dev/null +++ b/doc/src/Modify_kspace.txt @@ -0,0 +1,25 @@ +"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Kspace styles :h3 + +Classes that compute long-range Coulombic interactions via K-space +representations (Ewald, PPPM) are derived from the KSpace class. New +styles can be created to add new K-space options to LAMMPS. + +Ewald.cpp is an example of computing K-space interactions. + +Here is a brief description of methods you define in your new derived +class. See kspace.h for details. + +init: initialize the calculation before a run +setup: computation before the 1st timestep of a run +compute: every-timestep computation +memory_usage: tally of memory usage :tb(s=:) + diff --git a/doc/src/Modify_min.txt b/doc/src/Modify_min.txt new file mode 100644 index 0000000000..8252a576f3 --- /dev/null +++ b/doc/src/Modify_min.txt @@ -0,0 +1,23 @@ +"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Minimization styles :h3 + +Classes that perform energy minimization derived from the Min class. +New styles can be created to add new minimization algorithms to +LAMMPS. + +Min_cg.cpp is an example of conjugate gradient minimization. + +Here is a brief description of methods you define in your new derived +class. See min.h for details. + +init: initialize the minimization before a run +run: perform the minimization +memory_usage: tally of memory usage :tb(s=:) diff --git a/doc/src/Modify_overview.txt b/doc/src/Modify_overview.txt new file mode 100644 index 0000000000..4ab1eddf21 --- /dev/null +++ b/doc/src/Modify_overview.txt @@ -0,0 +1,101 @@ +"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Overview :h3 + +The best way to add a new feature to LAMMPS is to find a similar +feature and look at the corresponding source and header files to figure +out what it does. You will need some knowledge of C++ to be able to +understand the hi-level structure of LAMMPS and its class +organization, but functions (class methods) that do actual +computations are written in vanilla C-style code and operate on simple +C-style data structures (vectors and arrays). + +Most of the new features described on the "Modify"_Modify.html doc +page require you to write a new C++ derived class (except for +exceptions described below, where you can make small edits to existing +files). Creating a new class requires 2 files, a source code file +(*.cpp) and a header file (*.h). The derived class must provide +certain methods to work as a new option. Depending on how different +your new feature is compared to existing features, you can either +derive from the base class itself, or from a derived class that +already exists. Enabling LAMMPS to invoke the new class is as simple +as putting the two source files in the src dir and re-building LAMMPS. + +The advantage of C++ and its object-orientation is that all the code +and variables needed to define the new feature are in the 2 files you +write, and thus shouldn't make the rest of LAMMPS more complex or +cause side-effect bugs. + +Here is a concrete example. Suppose you write 2 files pair_foo.cpp +and pair_foo.h that define a new class PairFoo that computes pairwise +potentials described in the classic 1997 "paper"_#Foo by Foo, et al. +If you wish to invoke those potentials in a LAMMPS input script with a +command like + +pair_style foo 0.1 3.5 :pre + +then your pair_foo.h file should be structured as follows: + +#ifdef PAIR_CLASS +PairStyle(foo,PairFoo) +#else +... +(class definition for PairFoo) +... +#endif :pre + +where "foo" is the style keyword in the pair_style command, and +PairFoo is the class name defined in your pair_foo.cpp and pair_foo.h +files. + +When you re-build LAMMPS, your new pairwise potential becomes part of +the executable and can be invoked with a pair_style command like the +example above. Arguments like 0.1 and 3.5 can be defined and +processed by your new class. + +As illustrated by this pairwise example, many kinds of options are +referred to in the LAMMPS documentation as the "style" of a particular +command. + +The "Modify page"_Modify.html lists all the common styles in LAMMPS, +and discusses the header file for the base class that these styles are +derived from. Public variables in that file are ones used and set by +the derived classes which are also used by the base class. Sometimes +they are also used by the rest of LAMMPS. Virtual functions in the +base class header file which are set = 0 are ones you must define in +your new derived class to give it the functionality LAMMPS expects. +Virtual functions that are not set to 0 are functions you can +optionally define. + +Additionally, new output options can be added directly to the +thermo.cpp, dump_custom.cpp, and variable.cpp files. These are also +listed on the "Modify page"_Modify.html. + +Here are additional guidelines for modifying LAMMPS and adding new +functionality: + +Think about whether what you want to do would be better as a pre- or +post-processing step. Many computations are more easily and more +quickly done that way. :ulb,l + +Don't do anything within the timestepping of a run that isn't +parallel. E.g. don't accumulate a bunch of data on a single processor +and analyze it. You run the risk of seriously degrading the parallel +efficiency. :l + +If your new feature reads arguments or writes output, make sure you +follow the unit conventions discussed by the "units"_units.html +command. :l +:ule + +:line + +:link(Foo) +[(Foo)] Foo, Morefoo, and Maxfoo, J of Classic Potentials, 75, 345 (1997). diff --git a/doc/src/Modify_pair.txt b/doc/src/Modify_pair.txt new file mode 100644 index 0000000000..0ebf2daa30 --- /dev/null +++ b/doc/src/Modify_pair.txt @@ -0,0 +1,33 @@ +"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Pair styles :h3 + +Classes that compute pairwise interactions are derived from the Pair +class. In LAMMPS, pairwise calculation include manybody potentials +such as EAM or Tersoff where particles interact without a static bond +topology. New styles can be created to add new pair potentials to +LAMMPS. + +Pair_lj_cut.cpp is a simple example of a Pair class, though it +includes some optional methods to enable its use with rRESPA. + +Here is a brief description of the class methods in pair.h: + +compute: workhorse routine that computes pairwise interactions +settings: reads the input script line with arguments you define +coeff: set coefficients for one i,j type pair +init_one: perform initialization for one i,j type pair +init_style: initialization specific to this pair style +write & read_restart: write/read i,j pair coeffs to restart files +write & read_restart_settings: write/read global settings to restart files +single: force and energy of a single pairwise interaction between 2 atoms +compute_inner/middle/outer: versions of compute used by rRESPA :tb(s=:) + +The inner/middle/outer routines are optional. diff --git a/doc/src/Modify_region.txt b/doc/src/Modify_region.txt new file mode 100644 index 0000000000..cdf192323a --- /dev/null +++ b/doc/src/Modify_region.txt @@ -0,0 +1,25 @@ +"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Region styles :h3 + +Classes that define geometric regions are derived from the Region +class. Regions are used elsewhere in LAMMPS to group atoms, delete +atoms to create a void, insert atoms in a specified region, etc. New +styles can be created to add new region shapes to LAMMPS. + +Region_sphere.cpp is an example of a spherical region. + +Here is a brief description of methods you define in your new derived +class. See region.h for details. + +inside: determine whether a point is in the region +surface_interior: determine if a point is within a cutoff distance inside of surc +surface_exterior: determine if a point is within a cutoff distance outside of surf +shape_update : change region shape if set by time-dependent variable :tb(s=:) diff --git a/doc/src/Modify_thermo.txt b/doc/src/Modify_thermo.txt new file mode 100644 index 0000000000..1772bae87a --- /dev/null +++ b/doc/src/Modify_thermo.txt @@ -0,0 +1,35 @@ +"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Thermodynamic output options :h3 + +There is one class that computes and prints thermodynamic information +to the screen and log file; see the file thermo.cpp. + +There are two styles defined in thermo.cpp: "one" and "multi". There +is also a flexible "custom" style which allows the user to explicitly +list keywords for quantities to print when thermodynamic info is +output. See the "thermo_style"_thermo_style.html command for a list +of defined quantities. + +The thermo styles (one, multi, etc) are simply lists of keywords. +Adding a new style thus only requires defining a new list of keywords. +Search for the word "customize" with references to "thermo style" in +thermo.cpp to see the two locations where code will need to be added. + +New keywords can also be added to thermo.cpp to compute new quantities +for output. Search for the word "customize" with references to +"keyword" in thermo.cpp to see the several locations where code will +need to be added. + +Note that the "thermo_style custom"_thermo.html command already allows +for thermo output of quantities calculated by "fixes"_fix.html, +"computes"_compute.html, and "variables"_variable.html. Thus, it may +be simpler to compute what you wish via one of those constructs, than +by adding a new keyword to the thermo command. diff --git a/doc/src/Modify_variable.txt b/doc/src/Modify_variable.txt new file mode 100644 index 0000000000..b163272f3e --- /dev/null +++ b/doc/src/Modify_variable.txt @@ -0,0 +1,46 @@ +"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Variable options :h3 + +There is one class that computes and stores "variable"_variable.html +information in LAMMPS; see the file variable.cpp. The value +associated with a variable can be periodically printed to the screen +via the "print"_print.html, "fix print"_fix_print.html, or +"thermo_style custom"_thermo_style.html commands. Variables of style +"equal" can compute complex equations that involve the following types +of arguments: + +thermo keywords = ke, vol, atoms, ... +other variables = v_a, v_myvar, ... +math functions = div(x,y), mult(x,y), add(x,y), ... +group functions = mass(group), xcm(group,x), ... +atom values = x\[123\], y\[3\], vx\[34\], ... +compute values = c_mytemp\[0\], c_thermo_press\[3\], ... :pre + +Adding keywords for the "thermo_style custom"_thermo_style.html +command (which can then be accessed by variables) is discussed on the +"Modify thermo"_Modify_thermo.html doc page. + +Adding a new math function of one or two arguments can be done by +editing one section of the Variable::evaluate() method. Search for +the word "customize" to find the appropriate location. + +Adding a new group function can be done by editing one section of the +Variable::evaluate() method. Search for the word "customize" to find +the appropriate location. You may need to add a new method to the +Group class as well (see the group.cpp file). + +Accessing a new atom-based vector can be done by editing one section +of the Variable::evaluate() method. Search for the word "customize" +to find the appropriate location. + +Adding new "compute styles"_compute.html (whose calculated values can +then be accessed by variables) is discussed on the "Modify +compute"_Modify_compute.html doc page. diff --git a/doc/src/Packages.txt b/doc/src/Packages.txt new file mode 100644 index 0000000000..231c8528e9 --- /dev/null +++ b/doc/src/Packages.txt @@ -0,0 +1,40 @@ +"Previous Section"_Commands.html - "LAMMPS WWW Site"_lws - +"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next +Section"_Speed.html :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Optional packages :h2 + +This section gives an overview of the optional packages that extend +LAMMPS functionality. Packages are groups of files that enable a +specific set of features. For example, force fields for molecular +systems or rigid-body constraints are in packages. You can see the +list of all packages and "make" commands to manage them by typing +"make package" from within the src directory of the LAMMPS +distribution. The "Build package"_Build_package.html doc page gives +general info on how to install and un-install packages as part of the +LAMMPS build process. + + + + + +"Standard packages"_Packages_standard.html +"User packages"_Packages_user.html +"Details on each package"_Packages_details.html :ul + + diff --git a/doc/src/Packages_details.txt b/doc/src/Packages_details.txt new file mode 100644 index 0000000000..494f393a16 --- /dev/null +++ b/doc/src/Packages_details.txt @@ -0,0 +1,2059 @@ +"Higher level section"_Packages.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Package details :h3 + +Here is a brief description of all the standard and user packages in +LAMMPS. It lists authors (if applicable) and summarizes the package +contents. It has specific instructions on how to install the package, +including, if necessary, info on how to download or build any extra +library it requires. It also gives links to documentation, example +scripts, and pictures/movies (if available) that illustrate use of the +package. + +The majority of packages can be included in a LAMMPS build with a +single setting (-D PGK_NAME for CMake) or command ("make yes-name" for +make). See the "Build package"_Build_package.html doc page for more +info. A few packages may require additional steps; this is indicated +in the descriptions below. The "Build extras"_Build_extras.html doc +page gives those details. + +NOTE: To see the complete list of commands a package adds to LAMMPS, +you can examine the files in its src directory, e.g. "ls +src/GRANULAR". Files with names that start with fix, compute, atom, +pair, bond, angle, etc correspond to commands with the same style name +as contained in the file name. + +"ASPHERE"_#PKG-ASPHERE, +"BODY"_#PKG-BODY, +"CLASS2"_#PKG-CLASS2, +"COLLOID"_#PKG-COLLOID, +"COMPRESS"_#PKG-COMPRESS, +"CORESHELL"_#PKG-CORESHELL, +"DIPOLE"_#PKG-DIPOLE, +"GPU"_#PKG-GPU, +"GRANULAR"_#PKG-GRANULAR, +"KIM"_#PKG-KIM, +"KOKKOS"_#PKG-KOKKOS, +"KSPACE"_#PKG-KSPACE, +"LATTE"_#PKG-LATTE, +"MANYBODY"_#PKG-MANYBODY, +"MC"_#PKG-MC, +"MEAM"_#PKG-MEAM, +"MESSAGE"_#PKG-MESSAGE, +"MISC"_#PKG-MISC, +"MOLECULE"_#PKG-MOLECULE, +"MPIIO"_#PKG-MPIIO, +"MSCG"_#PKG-MSCG, +"OPT"_#PKG-OPT, +"PERI"_#PKG-PERI, +"POEMS"_#PKG-POEMS, +"PYTHON"_#PKG-PYTHON, +"QEQ"_#PKG-QEQ, +"REAX"_#PKG-REAX, +"REPLICA"_#PKG-REPLICA2, +"RIGID"_#PKG-RIGID, +"SHOCK"_#PKG-SHOCK, +"SNAP"_#PKG-SNAP, +"SPIN"_#PKG-SPIN, +"SRD"_#PKG-SRD, +"VORONOI"_#PKG-VORONOI :tb(c=6,ea=c) + +"USER-ATC"_#PKG-USER-ATC, +"USER-AWPMD"_#PKG-USER-AWPMD, +"USER-BOCS"_#PKG-USER-BOCS, +"USER-CGDNA"_#PKG-USER-CGDNA, +"USER-CGSDK"_#PKG-USER-CGSDK, +"USER-COLVARS"_#PKG-USER-COLVARS, +"USER-DIFFRACTION"_#PKG-USER-DIFFRACTION, +"USER-DPD"_#PKG-USER-DPD, +"USER-DRUDE"_#PKG-USER-DRUDE, +"USER-EFF"_#PKG-USER-EFF, +"USER-FEP"_#PKG-USER-FEP, +"USER-H5MD"_#PKG-USER-H5MD, +"USER-INTEL"_#PKG-USER-INTEL, +"USER-LB"_#PKG-USER-LB, +"USER-MANIFOLD"_#PKG-USER-MANIFOLD, +"USER-MEAMC"_#PKG-USER-MEAMC, +"USER-MESO"_#PKG-USER-MESO, +"USER-MGPT"_#PKG-USER-MGPT, +"USER-MISC"_#PKG-USER-MISC, +"USER-MOFFF"_#PKG-USER-MOFFF, +"USER-MOLFILE"_#PKG-USER-MOLFILE, +"USER-NETCDF"_#PKG-USER-NETCDF, +"USER-OMP"_#PKG-USER-OMP, +"USER-PHONON"_#PKG-USER-PHONON, +"USER-QMMM"_#PKG-USER-QMMM, +"USER-QTB"_#PKG-USER-QTB, +"USER-QUIP"_#PKG-USER-QUIP, +"USER-REAXC"_#PKG-USER-REAXC, +"USER-SCAFACOS"_#PKG-USER-SCAFACOS, +"USER-SMD"_#PKG-USER-SMD, +"USER-SMTBQ"_#PKG-USER-SMTBQ, +"USER-SPH"_#PKG-USER-SPH, +"USER-TALLY"_#PKG-USER-TALLY, +"USER-UEF"_#PKG-USER-UEF, +"USER-VTK"_#PKG-USER-VTK :tb(c=6,ea=c) + +:line + +ASPHERE package :link(PKG-ASPHERE),h4 + +[Contents:] + +Computes, time-integration fixes, and pair styles for aspherical +particle models including ellipsoids, 2d lines, and 3d triangles. + +[Supporting info:] + +src/ASPHERE: filenames -> commands +"Howto spherical"_Howto_spherical.html +"pair_style gayberne"_pair_gayberne.html +"pair_style resquared"_pair_resquared.html +"doc/PDF/pair_gayberne_extra.pdf"_PDF/pair_gayberne_extra.pdf +"doc/PDF/pair_resquared_extra.pdf"_PDF/pair_resquared_extra.pdf +examples/ASPHERE +examples/ellipse +http://lammps.sandia.gov/movies.html#line +http://lammps.sandia.gov/movies.html#tri :ul + +:line + +BODY package :link(PKG-BODY),h4 + +[Contents:] + +Body-style particles with internal structure. Computes, +time-integration fixes, pair styles, as well as the body styles +themselves. See the "Howto body"_Howto_body.html doc page for an +overview. + +[Supporting info:] + +src/BODY filenames -> commands +"Howto_body"_Howto_body.html +"atom_style body"_atom_style.html +"fix nve/body"_fix_nve_body.html +"pair_style body/nparticle"_pair_body_nparticle.html +examples/body :ul + +:line + +CLASS2 package :link(PKG-CLASS2),h4 + +[Contents:] + +Bond, angle, dihedral, improper, and pair styles for the COMPASS +CLASS2 molecular force field. + +[Supporting info:] + +src/CLASS2: filenames -> commands +"bond_style class2"_bond_class2.html +"angle_style class2"_angle_class2.html +"dihedral_style class2"_dihedral_class2.html +"improper_style class2"_improper_class2.html +"pair_style lj/class2"_pair_class2.html :ul + +:line + +COLLOID package :link(PKG-COLLOID),h4 + +[Contents:] + +Coarse-grained finite-size colloidal particles. Pair styles and fix +wall styles for colloidal interactions. Includes the Fast Lubrication +Dynamics (FLD) method for hydrodynamic interactions, which is a +simplified approximation to Stokesian dynamics. + +[Authors:] This package includes Fast Lubrication Dynamics pair styles +which were created by Amit Kumar and Michael Bybee from Jonathan +Higdon's group at UIUC. + +[Supporting info:] + +src/COLLOID: filenames -> commands +"fix wall/colloid"_fix_wall.html +"pair_style colloid"_pair_colloid.html +"pair_style yukawa/colloid"_pair_yukawa_colloid.html +"pair_style brownian"_pair_brownian.html +"pair_style lubricate"_pair_lubricate.html +"pair_style lubricateU"_pair_lubricateU.html +examples/colloid +examples/srd :ul + +:line + +COMPRESS package :link(PKG-COMPRESS),h4 + +[Contents:] + +Compressed output of dump files via the zlib compression library, +using dump styles with a "gz" in their style name. + +To use this package you must have the zlib compression library +available on your system. + +[Author:] Axel Kohlmeyer (Temple U). + +[Install:] + +This package has "specific installation +instructions"_Build_extras.html#gpu on the "Build +extras"_Build_extras.html doc page. + +[Supporting info:] + +src/COMPRESS: filenames -> commands +src/COMPRESS/README +lib/compress/README +"dump atom/gz"_dump.html +"dump cfg/gz"_dump.html +"dump custom/gz"_dump.html +"dump xyz/gz"_dump.html :ul + +:line + +CORESHELL package :link(PKG-CORESHELL),h4 + +[Contents:] + +Compute and pair styles that implement the adiabatic core/shell model +for polarizability. The pair styles augment Born, Buckingham, and +Lennard-Jones styles with core/shell capabilities. The "compute +temp/cs"_compute_temp_cs.html command calculates the temperature of a +system with core/shell particles. See the "Howto +coreshell"_Howto_coreshell.html doc page for an overview of how to use +this package. + +[Author:] Hendrik Heenen (Technical U of Munich). + +[Supporting info:] + +src/CORESHELL: filenames -> commands +"Howto coreshell"_Howto_coreshell.html +"Howto polarizable"_Howto_polarizable.html +"compute temp/cs"_compute_temp_cs.html +"pair_style born/coul/long/cs"_pair_cs.html +"pair_style buck/coul/long/cs"_pair_cs.html +"pair_style lj/cut/coul/long/cs"_pair_lj.html +examples/coreshell :ul + +:line + +DIPOLE package :link(PKG-DIPOLE),h4 + +[Contents:] + +An atom style and several pair styles for point dipole models with +short-range or long-range interactions. + +[Supporting info:] + +src/DIPOLE: filenames -> commands +"atom_style dipole"_atom_style.html +"pair_style lj/cut/dipole/cut"_pair_dipole.html +"pair_style lj/cut/dipole/long"_pair_dipole.html +"pair_style lj/long/dipole/long"_pair_dipole.html +examples/dipole :ul + +:line + +GPU package :link(PKG-GPU),h4 + +[Contents:] + +Dozens of pair styles and a version of the PPPM long-range Coulombic +solver optimized for GPUs. All such styles have a "gpu" as a suffix +in their style name. The GPU code can be compiled with either CUDA or +OpenCL, however the OpenCL variants are no longer actively maintained +and only the CUDA versions are regularly tested. The "Speed +gpu"_Speed_gpu.html doc page gives details of what hardware and GPU +software is required on your system, and details on how to build and +use this package. Its styles can be invoked at run time via the "-sf +gpu" or "-suffix gpu" "command-line switches"_Run_options.html. See +also the "KOKKOS"_#PKG-KOKKOS package, which has GPU-enabled styles. + +[Authors:] Mike Brown (Intel) while at Sandia and ORNL and Trung Nguyen +(Northwestern U) while at ORNL. + +[Install:] + +This package has "specific installation +instructions"_Build_extras.html#gpu on the "Build +extras"_Build_extras.html doc page. + +[Supporting info:] + +src/GPU: filenames -> commands +src/GPU/README +lib/gpu/README +"Speed packages"_Speed_packages.html +"Speed gpu"_Speed_gpu.html +"Section 2.6 -sf gpu"_Run_options.html +"Section 2.6 -pk gpu"_Run_options.html +"package gpu"_package.html +"Commands all"_lc pages (pair,kspace) for styles followed by (g) +"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul + +:line + +GRANULAR package :link(PKG-GRANULAR),h4 + +[Contents:] + +Pair styles and fixes for finite-size granular particles, which +interact with each other and boundaries via frictional and dissipative +potentials. + +[Supporting info:] + +src/GRANULAR: filenames -> commands +"Howto granular"_Howto_granular.html +"fix pour"_fix_pour.html +"fix wall/gran"_fix_wall_gran.html +"pair_style gran/hooke"_pair_gran.html +"pair_style gran/hertz/history"_pair_gran.html +examples/granregion +examples/pour +bench/in.chute +http://lammps.sandia.gov/pictures.html#jamming +http://lammps.sandia.gov/movies.html#hopper +http://lammps.sandia.gov/movies.html#dem +http://lammps.sandia.gov/movies.html#brazil +http://lammps.sandia.gov/movies.html#granregion :ul + +:line + +KIM package :link(PKG-KIM),h4 + +[Contents:] + +A "pair_style kim"_pair_kim.html command which is a wrapper on the +Knowledge Base for Interatomic Models (KIM) repository of interatomic +potentials, enabling any of them to be used in LAMMPS simulations. + +To use this package you must have the KIM library available on your +system. + +Information about the KIM project can be found at its website: +https://openkim.org. The KIM project is led by Ellad Tadmor and Ryan +Elliott (U Minnesota) and James Sethna (Cornell U). + +[Authors:] Ryan Elliott (U Minnesota) is the main developer for the KIM +API which the "pair_style kim"_pair_kim.html command uses. He +developed the pair style in collaboration with Valeriu Smirichinski (U +Minnesota). + +[Install:] + +This package has "specific installation +instructions"_Build_extras.html#gpu on the "Build +extras"_Build_extras.html doc page. + +[Supporting info:] + +src/KIM: filenames -> commands +src/KIM/README +lib/kim/README +"pair_style kim"_pair_kim.html +examples/kim :ul + +:line + +KOKKOS package :link(PKG-KOKKOS),h4 + +[Contents:] + +Dozens of atom, pair, bond, angle, dihedral, improper, fix, compute +styles adapted to compile using the Kokkos library which can convert +them to OpenMP or CUDA code so that they run efficiently on multicore +CPUs, KNLs, or GPUs. All the styles have a "kk" as a suffix in their +style name. The "Speed kokkos"_Speed_kokkos.html doc page gives +details of what hardware and software is required on your system, and +how to build and use this package. Its styles can be invoked at run +time via the "-sf kk" or "-suffix kk" "command-line +switches"_Run_options.html. Also see the "GPU"_#PKG-GPU, "OPT"_#PKG-OPT, +"USER-INTEL"_#PKG-USER-INTEL, and "USER-OMP"_#PKG-USER-OMP packages, which +have styles optimized for CPUs, KNLs, and GPUs. + +You must have a C++11 compatible compiler to use this package. +KOKKOS makes extensive use of advanced C++ features, which can +expose compiler bugs, especially when compiling for maximum +performance at high optimization levels. Please see the file +lib/kokkos/README for a list of compilers and their respective +platforms, that are known to work. + +[Authors:] The KOKKOS package was created primarily by Christian Trott +and Stan Moore (Sandia), with contributions from other folks as well. +It uses the open-source "Kokkos library"_https://github.com/kokkos +which was developed by Carter Edwards, Christian Trott, and others at +Sandia, and which is included in the LAMMPS distribution in +lib/kokkos. + +[Install:] + +This package has "specific installation +instructions"_Build_extras.html#gpu on the "Build +extras"_Build_extras.html doc page. + +[Supporting info:] + +src/KOKKOS: filenames -> commands +src/KOKKOS/README +lib/kokkos/README +"Speed packages"_Speed_packages.html +"Speed kokkos"_Speed_kokkos.html +"Section 2.6 -k on ..."_Run_options.html +"Section 2.6 -sf kk"_Run_options.html +"Section 2.6 -pk kokkos"_Run_options.html +"package kokkos"_package.html +"Commands all"_lc pages (fix,compute,pair,etc) for styles followed by (k) +"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul + +:line + +KSPACE package :link(PKG-KSPACE),h4 + +[Contents:] + +A variety of long-range Coulombic solvers, as well as pair styles +which compute the corresponding short-range pairwise Coulombic +interactions. These include Ewald, particle-particle particle-mesh +(PPPM), and multilevel summation method (MSM) solvers. + +[Install:] + +Building with this package requires a 1d FFT library be present on +your system for use by the PPPM solvers. This can be the KISS FFT +library provided with LAMMPS, 3rd party libraries like FFTW, or a +vendor-supplied FFT library. See the "Build +settings"_Build_settings.html doc page for details on how to select +different FFT options for your LAMPMS build. + +[Supporting info:] + +src/KSPACE: filenames -> commands +"kspace_style"_kspace_style.html +"doc/PDF/kspace.pdf"_PDF/kspace.pdf +"Howto tip3p"_Howto_tip3p.html +"Howto tip4p"_Howto_tip4p.html +"Howto spc"_Howto_spc.html +"pair_style coul"_pair_coul.html +"Commands pair"_Commands_pair.html page for styles with "long" or "msm" in name +examples/peptide +bench/in.rhodo :ul + +:line + +LATTE package :link(PKG-LATTE),h4 + +[Contents:] + +A fix command which wraps the LATTE DFTB code, so that molecular +dynamics can be run with LAMMPS using density-functional tight-binding +quantum forces calculated by LATTE. + +More information on LATTE can be found at this web site: +"https://github.com/lanl/LATTE"_latte_home. A brief technical +description is given with the "fix latte"_fix_latte.html command. + +:link(latte_home,https://github.com/lanl/LATTE) + +[Authors:] Christian Negre (LANL) and Steve Plimpton (Sandia). LATTE +itself is developed at Los Alamos National Laboratory by Marc +Cawkwell, Anders Niklasson, and Christian Negre. + +[Install:] + +This package has "specific installation +instructions"_Build_extras.html#gpu on the "Build +extras"_Build_extras.html doc page. + +[Supporting info:] + +src/LATTE: filenames -> commands +src/LATTE/README +lib/latte/README +"fix latte"_fix_latte.html +examples/latte +"LAMMPS-LATTE tutorial"_https://github.com/lanl/LATTE/wiki/Using-LATTE-through-LAMMPS :ul + +:line + +MANYBODY package :link(PKG-MANYBODY),h4 + +[Contents:] + +A variety of manybody and bond-order potentials. These include +(AI)REBO, BOP, EAM, EIM, Stillinger-Weber, and Tersoff potentials. + +[Supporting info:] + +src/MANYBODY: filenames -> commands +"Commands pair"_Commands_pair.html page +examples/comb +examples/eim +examples/nb3d +examples/shear +examples/streitz +examples/vashishta +bench/in.eam :ul + +:line + +MC package :link(PKG-MC),h4 + +[Contents:] + +Several fixes and a pair style that have Monte Carlo (MC) or MC-like +attributes. These include fixes for creating, breaking, and swapping +bonds, for performing atomic swaps, and performing grand-canonical MC +(GCMC) in conjuction with dynamics. + +[Supporting info:] + +src/MC: filenames -> commands +"fix atom/swap"_fix_atom_swap.html +"fix bond/break"_fix_bond_break.html +"fix bond/create"_fix_bond_create.html +"fix bond/swap"_fix_bond_swap.html +"fix gcmc"_fix_gcmc.html +"pair_style dsmc"_pair_dsmc.html +http://lammps.sandia.gov/movies.html#gcmc :ul + +:line + +MEAM package :link(PKG-MEAM),h4 + +[Contents:] + +A pair style for the modified embedded atom (MEAM) potential. + +Please note that the use of the MEAM package is discouraged as +it has been superseded by the "USER-MEAMC"_#PKG-USER-MEAMC package, +which is a direct translation of the MEAM package to C++. +USER-MEAMC contains additional optimizations making it run faster +than MEAM on most machines, while providing the identical features +and user interface. + +[Author:] Greg Wagner (Northwestern U) while at Sandia. + +[Install:] + +This package has "specific installation +instructions"_Build_extras.html#gpu on the "Build +extras"_Build_extras.html doc page. + +[Supporting info:] + +src/MEAM: filenames -> commands +src/meam/README +lib/meam/README +"pair_style meam"_pair_meam.html +examples/meam :ul + +:line + +MESSAGE package :link(PKG-MESSAGE),h4 + +[Contents:] + +Commands to use LAMMPS as either a client or server and couple it to +another application. + +[Install:] + +This package has "specific installation +instructions"_Build_extras.html#message on the "Build +extras"_Build_extras.html doc page. + +[Supporting info:] + +src/MESSAGE: filenames -> commands +lib/message/README +"message"_message.html +"fix client/md"_fix_client_md.html +"server md"_server_md.html +"server mc"_server_mc.html +examples/message :ul + +:line + +MISC package :link(PKG-MISC),h4 + +[Contents:] + +A variety of compute, fix, pair, dump styles with specialized +capabilities that don't align with other packages. Do a directory +listing, "ls src/MISC", to see the list of commands. + +NOTE: the MISC package contains styles that require using the +-restrict flag, when compiling with Intel compilers. + +[Supporting info:] + +src/MISC: filenames -> commands +"compute ti"_compute_ti.html +"fix evaporate"_fix_evaporate.html +"fix orient/fcc"_fix_orient.html +"fix ttm"_fix_ttm.html +"fix thermal/conductivity"_fix_thermal_conductivity.html +"fix viscosity"_fix_viscosity.html +examples/KAPPA +examples/VISCOSITY +http://lammps.sandia.gov/pictures.html#ttm +http://lammps.sandia.gov/movies.html#evaporation :ul + +:line + +MOLECULE package :link(PKG-MOLECULE),h4 + +[Contents:] + +A large number of atom, pair, bond, angle, dihedral, improper styles +that are used to model molecular systems with fixed covalent bonds. +The pair styles include the Dreiding (hydrogen-bonding) and CHARMM +force fields, and a TIP4P water model. + +[Supporting info:] + +src/MOLECULE: filenames -> commands +"atom_style"_atom_style.html +"bond_style"_bond_style.html +"angle_style"_angle_style.html +"dihedral_style"_dihedral_style.html +"improper_style"_improper_style.html +"pair_style hbond/dreiding/lj"_pair_hbond_dreiding.html +"pair_style lj/charmm/coul/charmm"_pair_charmm.html +"Howto bioFF"_Howto_bioFF.html +examples/cmap +examples/dreiding +examples/micelle, +examples/peptide +bench/in.chain +bench/in.rhodo :ul + +:line + +MPIIO package :link(PKG-MPIIO),h4 + +[Contents:] + +Support for parallel output/input of dump and restart files via the +MPIIO library. It adds "dump styles"_dump.html with a "mpiio" in +their style name. Restart files with an ".mpiio" suffix are also +written and read in parallel. + +[Supporting info:] + +src/MPIIO: filenames -> commands +"dump"_dump.html +"restart"_restart.html +"write_restart"_write_restart.html +"read_restart"_read_restart.html :ul + +:line + +MSCG package :link(PKG-mscg),h4 + +[Contents:] + +A "fix mscg"_fix_mscg.html command which can parameterize a +Multi-Scale Coarse-Graining (MSCG) model using the open-source "MS-CG +library"_mscg_home. + +:link(mscg_home,https://github.com/uchicago-voth/MSCG-release) + +To use this package you must have the MS-CG library available on your +system. + +[Authors:] The fix was written by Lauren Abbott (Sandia). The MS-CG +library was developed by Jacob Wagner in Greg Voth's group at the +University of Chicago. + +[Install:] + +This package has "specific installation +instructions"_Build_extras.html#gpu on the "Build +extras"_Build_extras.html doc page. + +[Supporting info:] + +src/MSCG: filenames -> commands +src/MSCG/README +lib/mscg/README +examples/mscg :ul + +:line + +OPT package :link(PKG-OPT),h4 + +[Contents:] + +A handful of pair styles which are optimized for improved CPU +performance on single or multiple cores. These include EAM, LJ, +CHARMM, and Morse potentials. The styles have an "opt" suffix in +their style name. The "Speed opt"_Speed_opt.html doc page gives +details of how to build and use this package. Its styles can be +invoked at run time via the "-sf opt" or "-suffix opt" "command-line +switches"_Run_options.html. See also the "KOKKOS"_#PKG-KOKKOS, +"USER-INTEL"_#PKG-USER-INTEL, and "USER-OMP"_#PKG-USER-OMP packages, which +have styles optimized for CPU performance. + +[Authors:] James Fischer (High Performance Technologies), David Richie, +and Vincent Natoli (Stone Ridge Technolgy). + +[Install:] + +This package has "specific installation +instructions"_Build_extras.html#gpu on the "Build +extras"_Build_extras.html doc page. + +[Supporting info:] + +src/OPT: filenames -> commands +"Speed packages"_Speed_packages.html +"Speed opt"_Speed_opt.html +"Section 2.6 -sf opt"_Run_options.html +"Commands pair"_Commands_pair.html for styles followed by (t) +"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul + +:line + +PERI package :link(PKG-PERI),h4 + +[Contents:] + +An atom style, several pair styles which implement different +Peridynamics materials models, and several computes which calculate +diagnostics. Peridynamics is a a particle-based meshless continuum +model. + +[Authors:] The original package was created by Mike Parks (Sandia). +Additional Peridynamics models were added by Rezwanur Rahman and John +Foster (UTSA). + +[Supporting info:] + +src/PERI: filenames -> commands +"doc/PDF/PDLammps_overview.pdf"_PDF/PDLammps_overview.pdf +"doc/PDF/PDLammps_EPS.pdf"_PDF/PDLammps_EPS.pdf +"doc/PDF/PDLammps_VES.pdf"_PDF/PDLammps_VES.pdf +"atom_style peri"_atom_style.html +"pair_style peri/*"_pair_peri.html +"compute damage/atom"_compute_damage_atom.html +"compute plasticity/atom"_compute_plasticity_atom.html +examples/peri +http://lammps.sandia.gov/movies.html#peri :ul + +:line + +POEMS package :link(PKG-POEMS),h4 + +[Contents:] + +A fix that wraps the Parallelizable Open source Efficient Multibody +Software (POEMS) library, which is able to simulate the dynamics of +articulated body systems. These are systems with multiple rigid +bodies (collections of particles) whose motion is coupled by +connections at hinge points. + +[Author:] Rudra Mukherjee (JPL) while at RPI. + +[Install:] + +This package has "specific installation +instructions"_Build_extras.html#gpu on the "Build +extras"_Build_extras.html doc page. + +[Supporting info:] + +src/POEMS: filenames -> commands +src/POEMS/README +lib/poems/README +"fix poems"_fix_poems.html +examples/rigid :ul + +:line + +PYTHON package :link(PKG-PYTHON),h4 + +[Contents:] + +A "python"_python.html command which allow you to execute Python code +from a LAMMPS input script. The code can be in a separate file or +embedded in the input script itself. See the "Python +call"_Python_call.html doc page for an overview of using Python from +LAMMPS in this manner and all the "Python"_Python_head.html doc pages +for other ways to use LAMMPS and Python together. + +NOTE: Building with the PYTHON package assumes you have a Python +shared library available on your system, which needs to be a Python 2 +version, 2.6 or later. Python 3 is not yet supported. See the +lib/python/README for more details. + +[Install:] + +This package has "specific installation +instructions"_Build_extras.html#gpu on the "Build +extras"_Build_extras.html doc page. + +[Supporting info:] + +src/PYTHON: filenames -> commands +"Python call"_Python_head.html +lib/python/README +examples/python :ul + +:line + +QEQ package :link(PKG-QEQ),h4 + +[Contents:] + +Several fixes for performing charge equilibration (QEq) via different +algorithms. These can be used with pair styles that perform QEq as +part of their formulation. + +[Supporting info:] + +src/QEQ: filenames -> commands +"fix qeq/*"_fix_qeq.html +examples/qeq +examples/streitz :ul + +:line + +REAX package :link(PKG-REAX),h4 + +[Contents:] + +NOTE: the use of the REAX package is discouraged, as it is no longer +maintained. Please use the "USER-REAXC"_#PKG-USER-REAXC package instead, +and possibly the KOKKOS enabled variant of that, which has a more robust +memory management. + +A pair style which wraps a Fortran library which implements the ReaxFF +potential, which is a universal reactive force field. Also included is +a "fix reax/bonds"_fix_reax_bonds.html command for monitoring molecules +as bonds are created and destroyed. + +[Author:] Aidan Thompson (Sandia). + +[Install:] + +This package has "specific installation +instructions"_Build_extras.html#gpu on the "Build +extras"_Build_extras.html doc page. + +[Supporting info:] + +src/REAX: filenames -> commands +lib/reax/README +"pair_style reax"_pair_reax.html +"fix reax/bonds"_fix_reax_bonds.html +examples/reax :ul + +:line + +REPLICA package :link(PKG-REPLICA2),h4 + +[Contents:] + +A collection of multi-replica methods which can be used when running +multiple LAMMPS simulations (replicas). See the "Howto +replica"_Howto_replica.html doc page for an overview of how to run +multi-replica simulations in LAMMPS. Methods in the package include +nudged elastic band (NEB), parallel replica dynamics (PRD), +temperature accelerated dynamics (TAD), parallel tempering, and a +verlet/split algorithm for performing long-range Coulombics on one set +of processors, and the remainder of the force field calculation on +another set. + +[Supporting info:] + +src/REPLICA: filenames -> commands +"Howto replica"_Howto_replica.html +"neb"_neb.html +"prd"_prd.html +"tad"_tad.html +"temper"_temper.html, +"run_style verlet/split"_run_style.html +examples/neb +examples/prd +examples/tad :ul + +:line + +RIGID package :link(PKG-RIGID),h4 + +[Contents:] + +Fixes which enforce rigid constraints on collections of atoms or +particles. This includes SHAKE and RATTLE, as well as various +rigid-body integrators for a few large bodies or many small bodies. +Also several computes which calculate properties of rigid bodies. + +[Supporting info:] + +src/RIGID: filenames -> commands +"compute erotate/rigid"_compute_erotate_rigid.html +fix shake"_fix_shake.html +"fix rattle"_fix_shake.html +"fix rigid/*"_fix_rigid.html +examples/ASPHERE +examples/rigid +bench/in.rhodo +http://lammps.sandia.gov/movies.html#box +http://lammps.sandia.gov/movies.html#star :ul + +:line + +SHOCK package :link(PKG-SHOCK),h4 + +[Contents:] + +Fixes for running impact simulations where a shock-wave passes through +a material. + +[Supporting info:] + +src/SHOCK: filenames -> commands +"fix append/atoms"_fix_append_atoms.html +"fix msst"_fix_msst.html +"fix nphug"_fix_nphug.html +"fix wall/piston"_fix_wall_piston.html +examples/hugoniostat +examples/msst :ul + +:line + +SNAP package :link(PKG-SNAP),h4 + +[Contents:] + +A pair style for the spectral neighbor analysis potential (SNAP). +SNAP is methodology for deriving a highly accurate classical potential +fit to a large archive of quantum mechanical (DFT) data. Also several +computes which analyze attributes of the potential. + +[Author:] Aidan Thompson (Sandia). + +[Supporting info:] + +src/SNAP: filenames -> commands +"pair_style snap"_pair_snap.html +"compute sna/atom"_compute_sna_atom.html +"compute snad/atom"_compute_sna_atom.html +"compute snav/atom"_compute_sna_atom.html +examples/snap :ul + +:line + +SPIN package :link(PKG-SPIN),h4 + +[Contents:] + +Model atomic magnetic spins classically, coupled to atoms moving in +the usual manner via MD. Various pair, fix, and compute styles. + +[Author:] Julian Tranchida (Sandia). + +[Supporting info:] + +src/SPIN: filenames -> commands +"Howto spins"_Howto_spins.html +"pair_style spin/dmi"_pair_spin_dmi.html +"pair_style spin/exchange"_pair_spin_exchange.html +"pair_style spin/magelec"_pair_spin_magelec.html +"pair_style spin/neel"_pair_spin_neel.html +"fix nve/spin"_fix_nve_spin.html +"fix precession/spin"_fix_precession_spin.html +"compute spin"_compute_spin.html +examples/SPIN :ul + +:line + +SRD package :link(PKG-SRD),h4 + +[Contents:] + +A pair of fixes which implement the Stochastic Rotation Dynamics (SRD) +method for coarse-graining of a solvent, typically around large +colloidal particles. + +[Supporting info:] + +src/SRD: filenames -> commands +"fix srd"_fix_srd.html +"fix wall/srd"_fix_wall_srd.html +examples/srd +examples/ASPHERE +http://lammps.sandia.gov/movies.html#tri +http://lammps.sandia.gov/movies.html#line +http://lammps.sandia.gov/movies.html#poly :ul + +:line + +VORONOI package :link(PKG-VORONOI),h4 + +[Contents:] + +A compute command which calculates the Voronoi tesselation of a +collection of atoms by wrapping the "Voro++ library"_voro_home. This +can be used to calculate the local volume or each atoms or its near +neighbors. + +:link(voro_home,http://math.lbl.gov/voro++) + +To use this package you must have the Voro++ library available on your +system. + +[Author:] Daniel Schwen (INL) while at LANL. The open-source Voro++ +library was written by Chris Rycroft (Harvard U) while at UC Berkeley +and LBNL. + +[Install:] + +This package has "specific installation +instructions"_Build_extras.html#gpu on the "Build +extras"_Build_extras.html doc page. + +[Supporting info:] + +src/VORONOI: filenames -> commands +src/VORONOI/README +lib/voronoi/README +"compute voronoi/atom"_compute_voronoi_atom.html +examples/voronoi :ul + +:line + +USER-ATC package :link(PKG-USER-ATC),h4 + +[Contents:] + +ATC stands for atoms-to-continuum. This package implements a "fix +atc"_fix_atc.html command to either couple molecular dynamics with +continuum finite element equations or perform on-the-fly conversion of +atomic information to continuum fields. + +[Authors:] Reese Jones, Jeremy Templeton, Jon Zimmerman (Sandia). + +[Install:] + +This package has "specific installation +instructions"_Build_extras.html#gpu on the "Build +extras"_Build_extras.html doc page. + +[Supporting info:] + +src/USER-ATC: filenames -> commands +src/USER-ATC/README +"fix atc"_fix_atc.html +examples/USER/atc +http://lammps.sandia.gov/pictures.html#atc :ul + +:line + +USER-AWPMD package :link(PKG-USER-AWPMD),h4 + +[Contents:] + +AWPMD stands for Antisymmetrized Wave Packet Molecular Dynamics. This +package implements an atom, pair, and fix style which allows electrons +to be treated as explicit particles in a classical molecular dynamics +model. + +[Author:] Ilya Valuev (JIHT, Russia). + +[Install:] + +This package has "specific installation +instructions"_Build_extras.html#gpu on the "Build +extras"_Build_extras.html doc page. + +[Supporting info:] + +src/USER-AWPMD: filenames -> commands +src/USER-AWPMD/README +"pair_style awpmd/cut"_pair_awpmd.html +examples/USER/awpmd :ul + +:line + +USER-BOCS package :link(PKG-USER-BOCS),h4 + +[Contents:] + +This package provides "fix bocs"_fix_bocs.html, a modified version +of "fix npt"_fix_nh.html which includes the pressure correction to +the barostat as outlined in: + +N. J. H. Dunn and W. G. Noid, "Bottom-up coarse-grained models that +accurately describe the structure, pressure, and compressibility of +molecular liquids," J. Chem. Phys. 143, 243148 (2015). + +[Authors:] Nicholas J. H. Dunn and Michael R. DeLyser (The +Pennsylvania State University) + +[Supporting info:] + +The USER-BOCS user package for LAMMPS is part of the BOCS software package: +"https://github.com/noid-group/BOCS"_https://github.com/noid-group/BOCS + +See the following reference for information about the entire package: + +Dunn, NJH; Lebold, KM; DeLyser, MR; Rudzinski, JF; Noid, WG. +"BOCS: Bottom-Up Open-Source Coarse-Graining Software." +J. Phys. Chem. B. 122, 13, 3363-3377 (2018). + +Example inputs are in the examples/USER/bocs folder. + +:line + +USER-CGDNA package :link(PKG-USER-CGDNA),h4 + +[Contents:] + +Several pair styles, a bond style, and integration fixes for +coarse-grained models of single- and double-stranded DNA based on the +oxDNA model of Doye, Louis and Ouldridge at the University of Oxford. +This includes Langevin-type rigid-body integrators with improved +stability. + +[Author:] Oliver Henrich (University of Strathclyde, Glasgow). + +[Supporting info:] + +src/USER-CGDNA: filenames -> commands +/src/USER-CGDNA/README +"pair_style oxdna/*"_pair_oxdna.html +"pair_style oxdna2/*"_pair_oxdna2.html +"bond_style oxdna/*"_bond_oxdna.html +"bond_style oxdna2/*"_bond_oxdna.html +"fix nve/dotc/langevin"_fix_nve_dotc_langevin.html :ul + +:line + +USER-CGSDK package :link(PKG-USER-CGSDK),h4 + +[Contents:] + +Several pair styles and an angle style which implement the +coarse-grained SDK model of Shinoda, DeVane, and Klein which enables +simulation of ionic liquids, electrolytes, lipids and charged amino +acids. + +[Author:] Axel Kohlmeyer (Temple U). + +[Supporting info:] + +src/USER-CGSDK: filenames -> commands +src/USER-CGSDK/README +"pair_style lj/sdk/*"_pair_sdk.html +"angle_style sdk"_angle_sdk.html +examples/USER/cgsdk +http://lammps.sandia.gov/pictures.html#cg :ul + +:line + +USER-COLVARS package :link(PKG-USER-COLVARS),h4 + +[Contents:] + +COLVARS stands for collective variables, which can be used to +implement various enhanced sampling methods, including Adaptive +Biasing Force, Metadynamics, Steered MD, Umbrella Sampling and +Restraints. A "fix colvars"_fix_colvars.html command is implemented +which wraps a COLVARS library, which implements these methods. +simulations. + +[Authors:] The COLVARS library is written and maintained by +Giacomo Fiorin (ICMS, Temple University, Philadelphia, PA, USA) +and Jerome Henin (LISM, CNRS, Marseille, France), originally for +the NAMD MD code, but with portability in mind. Axel Kohlmeyer +(Temple U) provided the interface to LAMMPS. + +[Install:] + +This package has "specific installation +instructions"_Build_extras.html#gpu on the "Build +extras"_Build_extras.html doc page. + +[Supporting info:] + +src/USER-COLVARS: filenames -> commands +"doc/PDF/colvars-refman-lammps.pdf"_PDF/colvars-refman-lammps.pdf +src/USER-COLVARS/README +lib/colvars/README +"fix colvars"_fix_colvars.html +examples/USER/colvars :ul + +:line + +USER-DIFFRACTION package :link(PKG-USER-DIFFRACTION),h4 + +[Contents:] + +Two computes and a fix for calculating x-ray and electron diffraction +intensities based on kinematic diffraction theory. + +[Author:] Shawn Coleman while at the U Arkansas. + +[Supporting info:] + +src/USER-DIFFRACTION: filenames -> commands +"compute saed"_compute_saed.html +"compute xrd"_compute_xrd.html +"fix saed/vtk"_fix_saed_vtk.html +examples/USER/diffraction :ul + +:line + +USER-DPD package :link(PKG-USER-DPD),h4 + +[Contents:] + +DPD stands for dissipative particle dynamics. This package implements +coarse-grained DPD-based models for energetic, reactive molecular +crystalline materials. It includes many pair styles specific to these +systems, including for reactive DPD, where each particle has internal +state for multiple species and a coupled set of chemical reaction ODEs +are integrated each timestep. Highly accurate time integrators for +isothermal, isoenergetic, isobaric and isenthalpic conditions are +included. These enable long timesteps via the Shardlow splitting +algorithm. + +[Authors:] Jim Larentzos (ARL), Tim Mattox (Engility Corp), and and John +Brennan (ARL). + +[Supporting info:] + +src/USER-DPD: filenames -> commands +/src/USER-DPD/README +"compute dpd"_compute_dpd.html +"compute dpd/atom"_compute_dpd_atom.html +"fix eos/cv"_fix_eos_table.html +"fix eos/table"_fix_eos_table.html +"fix eos/table/rx"_fix_eos_table_rx.html +"fix shardlow"_fix_shardlow.html +"fix rx"_fix_rx.html +"pair_style table/rx"_pair_table_rx.html +"pair_style dpd/fdt"_pair_dpd_fdt.html +"pair_style dpd/fdt/energy"_pair_dpd_fdt.html +"pair_style exp6/rx"_pair_exp6_rx.html +"pair_style multi/lucy"_pair_multi_lucy.html +"pair_style multi/lucy/rx"_pair_multi_lucy_rx.html +examples/USER/dpd :ul + +:line + +USER-DRUDE package :link(PKG-USER-DRUDE),h4 + +[Contents:] + +Fixes, pair styles, and a compute to simulate thermalized Drude +oscillators as a model of polarization. See the "Howto +drude"_Howto_drude.html and "Howto drude2"_Howto_drude2.html doc pages +for an overview of how to use the package. There are auxiliary tools +for using this package in tools/drude. + +[Authors:] Alain Dequidt (U Blaise Pascal Clermont-Ferrand), Julien +Devemy (CNRS), and Agilio Padua (U Blaise Pascal). + +[Supporting info:] + +src/USER-DRUDE: filenames -> commands +"Howto drude"_Howto_drude.html +"Howto drude2"_Howto_drude2.html +"Howto polarizable"_Howto_polarizable.html +src/USER-DRUDE/README +"fix drude"_fix_drude.html +"fix drude/transform/*"_fix_drude_transform.html +"compute temp/drude"_compute_temp_drude.html +"pair_style thole"_pair_thole.html +"pair_style lj/cut/thole/long"_pair_thole.html +examples/USER/drude +tools/drude :ul + +:line + +USER-EFF package :link(PKG-USER-EFF),h4 + +[Contents:] + +EFF stands for electron force field which allows a classical MD code +to model electrons as particles of variable radius. This package +contains atom, pair, fix and compute styles which implement the eFF as +described in A. Jaramillo-Botero, J. Su, Q. An, and W.A. Goddard III, +JCC, 2010. The eFF potential was first introduced by Su and Goddard, +in 2007. There are auxiliary tools for using this package in +tools/eff; see its README file. + +[Author:] Andres Jaramillo-Botero (CalTech). + +[Supporting info:] + +src/USER-EFF: filenames -> commands +src/USER-EFF/README +"atom_style electron"_atom_style.html +"fix nve/eff"_fix_nve_eff.html +"fix nvt/eff"_fix_nh_eff.html +"fix npt/eff"_fix_nh_eff.html +"fix langevin/eff"_fix_langevin_eff.html +"compute temp/eff"_compute_temp_eff.html +"pair_style eff/cut"_pair_eff.html +"pair_style eff/inline"_pair_eff.html +examples/USER/eff +tools/eff/README +tools/eff +http://lammps.sandia.gov/movies.html#eff :ul + +:line + +USER-FEP package :link(PKG-USER-FEP),h4 + +[Contents:] + +FEP stands for free energy perturbation. This package provides +methods for performing FEP simulations by using a "fix +adapt/fep"_fix_adapt_fep.html command with soft-core pair potentials, +which have a "soft" in their style name. There are auxiliary tools +for using this package in tools/fep; see its README file. + +[Author:] Agilio Padua (Universite Blaise Pascal Clermont-Ferrand) + +[Supporting info:] + +src/USER-FEP: filenames -> commands +src/USER-FEP/README +"fix adapt/fep"_fix_adapt_fep.html +"compute fep"_compute_fep.html +"pair_style */soft"_pair_lj_soft.html +examples/USER/fep +tools/fep/README +tools/fep :ul + +:line + +USER-H5MD package :link(PKG-USER-H5MD),h4 + +[Contents:] + +H5MD stands for HDF5 for MD. "HDF5"_HDF5 is a portable, binary, +self-describing file format, used by many scientific simulations. +H5MD is a format for molecular simulations, built on top of HDF5. +This package implements a "dump h5md"_dump_h5md.html command to output +LAMMPS snapshots in this format. + +:link(HDF5,http://www.hdfgroup.org/HDF5) + +To use this package you must have the HDF5 library available on your +system. + +[Author:] Pierre de Buyl (KU Leuven) created both the package and the +H5MD format. + +[Install:] + +This package has "specific installation +instructions"_Build_extras.html#gpu on the "Build +extras"_Build_extras.html doc page. + +[Supporting info:] + +src/USER-H5MD: filenames -> commands +src/USER-H5MD/README +lib/h5md/README +"dump h5md"_dump_h5md.html :ul + +:line + +USER-INTEL package :link(PKG-USER-INTEL),h4 + +[Contents:] + +Dozens of pair, fix, bond, angle, dihedral, improper, and kspace +styles which are optimized for Intel CPUs and KNLs (Knights Landing). +All of them have an "intel" in their style name. The "Speed +intel"_Speed_intel.html doc page gives details of what hardware and +compilers are required on your system, and how to build and use this +package. Its styles can be invoked at run time via the "-sf intel" or +"-suffix intel" "command-line switches"_Run_options.html. Also see +the "KOKKOS"_#PKG-KOKKOS, "OPT"_#PKG-OPT, and "USER-OMP"_#PKG-USER-OMP packages, +which have styles optimized for CPUs and KNLs. + +You need to have an Intel compiler, version 14 or higher to take full +advantage of this package. While compilation with GNU compilers is +supported, performance will be sub-optimal. + +NOTE: the USER-INTEL package contains styles that require using the +-restrict flag, when compiling with Intel compilers. + +[Author:] Mike Brown (Intel). + +[Install:] + +This package has "specific installation +instructions"_Build_extras.html#gpu on the "Build +extras"_Build_extras.html doc page. + +[Supporting info:] + +src/USER-INTEL: filenames -> commands +src/USER-INTEL/README +"Speed packages"_Speed_packages.html +"Speed intel"_Speed_intel.html +"Section 2.6 -sf intel"_Run_options.html +"Section 2.6 -pk intel"_Run_options.html +"package intel"_package.html +"Commands all"_lc pages (fix,compute,pair,etc) for styles followed by (i) +src/USER-INTEL/TEST +"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul + +:line + +USER-LB package :link(PKG-USER-LB),h4 + +[Contents:] + +Fixes which implement a background Lattice-Boltzmann (LB) fluid, which +can be used to model MD particles influenced by hydrodynamic forces. + +[Authors:] Frances Mackay and Colin Denniston (University of Western +Ontario). + +[Supporting info:] + +src/USER-LB: filenames -> commands +src/USER-LB/README +"fix lb/fluid"_fix_lb_fluid.html +"fix lb/momentum"_fix_lb_momentum.html +"fix lb/viscous"_fix_lb_viscous.html +examples/USER/lb :ul + +:line + +USER-MGPT package :link(PKG-USER-MGPT),h4 + +[Contents:] + +A pair style which provides a fast implementation of the quantum-based +MGPT multi-ion potentials. The MGPT or model GPT method derives from +first-principles DFT-based generalized pseudopotential theory (GPT) +through a series of systematic approximations valid for mid-period +transition metals with nearly half-filled d bands. The MGPT method +was originally developed by John Moriarty at LLNL. The pair style in +this package calculates forces and energies using an optimized +matrix-MGPT algorithm due to Tomas Oppelstrup at LLNL. + +[Authors:] Tomas Oppelstrup and John Moriarty (LLNL). + +[Supporting info:] + +src/USER-MGPT: filenames -> commands +src/USER-MGPT/README +"pair_style mgpt"_pair_mgpt.html +examples/USER/mgpt :ul + +:line + +USER-MISC package :link(PKG-USER-MISC),h4 + +[Contents:] + +A potpourri of (mostly) unrelated features contributed to LAMMPS by +users. Each feature is a single fix, compute, pair, bond, angle, +dihedral, improper, or command style. + +[Authors:] The author for each style in the package is listed in the +src/USER-MISC/README file. + +[Supporting info:] + +src/USER-MISC: filenames -> commands +src/USER-MISC/README +one doc page per individual command listed in src/USER-MISC/README +examples/USER/misc :ul + +:line + +USER-MANIFOLD package :link(PKG-USER-MANIFOLD),h4 + +[Contents:] + +Several fixes and a "manifold" class which enable simulations of +particles constrained to a manifold (a 2D surface within the 3D +simulation box). This is done by applying the RATTLE constraint +algorithm to formulate single-particle constraint functions +g(xi,yi,zi) = 0 and their derivative (i.e. the normal of the manifold) +n = grad(g). + +[Author:] Stefan Paquay (until 2017: Eindhoven University of +Technology (TU/e), The Netherlands; since 2017: Brandeis University, +Waltham, MA, USA) + +[Supporting info:] + +src/USER-MANIFOLD: filenames -> commands +src/USER-MANIFOLD/README +"Howto manifold"_Howto_manifold.html +"fix manifoldforce"_fix_manifoldforce.html +"fix nve/manifold/rattle"_fix_nve_manifold_rattle.html +"fix nvt/manifold/rattle"_fix_nvt_manifold_rattle.html +examples/USER/manifold +http://lammps.sandia.gov/movies.html#manifold :ul + +:line + +USER-MEAMC package :link(PKG-USER-MEAMC),h4 + +[Contents:] + +A pair style for the modified embedded atom (MEAM) potential +translated from the Fortran version in the "MEAM"_MEAM package +to plain C++. In contrast to the MEAM package, no library +needs to be compiled and the pair style can be instantiated +multiple times. + +[Author:] Sebastian Huetter, (Otto-von-Guericke University Magdeburg) +based on the Fortran version of Greg Wagner (Northwestern U) while at +Sandia. + +[Supporting info:] + +src/USER-MEAMC: filenames -> commands +src/USER-MEAMC/README +"pair_style meam/c"_pair_meam.html +examples/meam :ul + +:line + +USER-MESO package :link(PKG-USER-MESO),h4 + +[Contents:] + +Several extensions of the the dissipative particle dynamics (DPD) +method. Specifically, energy-conserving DPD (eDPD) that can model +non-isothermal processes, many-body DPD (mDPD) for simulating +vapor-liquid coexistence, and transport DPD (tDPD) for modeling +advection-diffusion-reaction systems. The equations of motion of these +DPD extensions are integrated through a modified velocity-Verlet (MVV) +algorithm. + +[Author:] Zhen Li (Division of Applied Mathematics, Brown University) + +[Supporting info:] + +src/USER-MESO: filenames -> commands +src/USER-MESO/README +"atom_style edpd"_atom_style.html +"pair_style edpd"_pair_meso.html +"pair_style mdpd"_pair_meso.html +"pair_style tdpd"_pair_meso.html +"fix mvv/dpd"_fix_mvv_dpd.html +examples/USER/meso +http://lammps.sandia.gov/movies.html#mesodpd :ul + +:line + +USER-MOFFF package :link(PKG-USER-MOFFF),h4 + +[Contents:] + +Pair, angle and improper styles needed to employ the MOF-FF +force field by Schmid and coworkers with LAMMPS. +MOF-FF is a first principles derived force field with the primary aim +to simulate MOFs and related porous framework materials, using spherical +Gaussian charges. It is described in S. Bureekaew et al., Phys. Stat. Sol. B +2013, 250, 1128-1141. +For the usage of MOF-FF see the example in the example directory as +well as the "MOF+"_MOFplus website. + +:link(MOFplus,https://www.mofplus.org/content/show/MOF-FF) + +[Author:] Hendrik Heenen (Technical U of Munich), +Rochus Schmid (Ruhr-University Bochum). + +[Supporting info:] + +src/USER-MOFFF: filenames -> commands +src/USER-MOFFF/README +"pair_style buck6d/coul/gauss"_pair_buck6d_coul_gauss.html +"angle_style class2"_angle_class2.html +"angle_style cosine/buck6d"_angle_cosine_buck6d.html +"improper_style inversion/harmonic"_improper_inversion_harmonic.html +examples/USER/mofff :ul + +:line + +USER-MOLFILE package :link(PKG-USER-MOLFILE),h4 + +[Contents:] + +A "dump molfile"_dump_molfile.html command which uses molfile plugins +that are bundled with the "VMD"_vmd_home +molecular visualization and analysis program, to enable LAMMPS to dump +snapshots in formats compatible with various molecular simulation +tools. + +To use this package you must have the desired VMD plugins available on +your system. + +Note that this package only provides the interface code, not the +plugins themselves, which will be accessed when requesting a specific +plugin via the "dump molfile"_dump_molfile.html command. Plugins can +be obtained from a VMD installation which has to match the platform +that you are using to compile LAMMPS for. By adding plugins to VMD, +support for new file formats can be added to LAMMPS (or VMD or other +programs that use them) without having to re-compile the application +itself. More information about the VMD molfile plugins can be found +at +"http://www.ks.uiuc.edu/Research/vmd/plugins/molfile"_http://www.ks.uiuc.edu/Research/vmd/plugins/molfile. + +[Author:] Axel Kohlmeyer (Temple U). + +[Install:] + +This package has "specific installation +instructions"_Build_extras.html#gpu on the "Build +extras"_Build_extras.html doc page. + +[Supporting info:] + +src/USER-MOLFILE: filenames -> commands +src/USER-MOLFILE/README +lib/molfile/README +"dump molfile"_dump_molfile.html :ul + +:line + +USER-NETCDF package :link(PKG-USER-NETCDF),h4 + +[Contents:] + +Dump styles for writing NetCDF formatted dump files. NetCDF is a +portable, binary, self-describing file format developed on top of +HDF5. The file contents follow the AMBER NetCDF trajectory conventions +(http://ambermd.org/netcdf/nctraj.xhtml), but include extensions. + +To use this package you must have the NetCDF library available on your +system. + +Note that NetCDF files can be directly visualized with the following +tools: + +"Ovito"_ovito (Ovito supports the AMBER convention and the extensions mentioned above) +"VMD"_vmd_home +"AtomEye"_atomeye (the libAtoms version of AtomEye contains a NetCDF reader not present in the standard distribution) :ul + +:link(ovito,http://www.ovito.org) +:link(vmd_home,https://www.ks.uiuc.edu/Research/vmd/) +:link(atomeye,http://www.libatoms.org) + +[Author:] Lars Pastewka (Karlsruhe Institute of Technology). + +[Install:] + +This package has "specific installation +instructions"_Build_extras.html#gpu on the "Build +extras"_Build_extras.html doc page. + +[Supporting info:] + +src/USER-NETCDF: filenames -> commands +src/USER-NETCDF/README +lib/netcdf/README +"dump netcdf"_dump_netcdf.html :ul + +:line + +USER-OMP package :link(PKG-USER-OMP),h4 + +[Contents:] + +Hundreds of pair, fix, compute, bond, angle, dihedral, improper, and +kspace styles which are altered to enable threading on many-core CPUs +via OpenMP directives. All of them have an "omp" in their style name. +The "Speed omp"_Speed_omp.html doc page gives details of what hardware +and compilers are required on your system, and how to build and use +this package. Its styles can be invoked at run time via the "-sf omp" +or "-suffix omp" "command-line switches"_Run_options.html. Also see +the "KOKKOS"_#PKG-KOKKOS, "OPT"_#PKG-OPT, and "USER-INTEL"_#PKG-USER-INTEL +packages, which have styles optimized for CPUs. + +[Author:] Axel Kohlmeyer (Temple U). + +NOTE: To enable multi-threading support the compile flag "-fopenmp" +and the link flag "-fopenmp" (for GNU compilers, you have to look up +the equivalent flags for other compilers) must be used to build LAMMPS. +When using Intel compilers, also the "-restrict" flag is required. +The USER-OMP package can be compiled without enabling OpenMP; then +all code will be compiled as serial and the only improvement over the +regular styles are some data access optimization. These flags should +be added to the CCFLAGS and LINKFLAGS lines of your Makefile.machine. +See src/MAKE/OPTIONS/Makefile.omp for an example. + +Once you have an appropriate Makefile.machine, you can +install/un-install the package and build LAMMPS in the usual manner: + +[Install:] + +This package has "specific installation +instructions"_Build_extras.html#gpu on the "Build +extras"_Build_extras.html doc page. + +[Supporting info:] + +src/USER-OMP: filenames -> commands +src/USER-OMP/README +"Speed packages"_Speed_packages.html +"Speed omp"_Speed_omp.html +"Section 2.6 -sf omp"_Run_options.html +"Section 2.6 -pk omp"_Run_options.html +"package omp"_package.html +"Commands all"_lc pages (fix,compute,pair,etc) for styles followed by (o) +"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul + +:line + +USER-PHONON package :link(PKG-USER-PHONON),h4 + +[Contents:] + +A "fix phonon"_fix_phonon.html command that calculates dynamical +matrices, which can then be used to compute phonon dispersion +relations, directly from molecular dynamics simulations. + +[Author:] Ling-Ti Kong (Shanghai Jiao Tong University). + +[Supporting info:] + +src/USER-PHONON: filenames -> commands +src/USER-PHONON/README +"fix phonon"_fix_phonon.html +examples/USER/phonon :ul + +:line + +USER-QMMM package :link(PKG-USER-QMMM),h4 + +[Contents:] + +A "fix qmmm"_fix_qmmm.html command which allows LAMMPS to be used in a +QM/MM simulation, currently only in combination with the "Quantum +ESPRESSO"_espresso package. + +:link(espresso,http://www.quantum-espresso.org) + +To use this package you must have Quantum ESPRESSO available on your +system. + +The current implementation only supports an ONIOM style mechanical +coupling to the Quantum ESPRESSO plane wave DFT package. +Electrostatic coupling is in preparation and the interface has been +written in a manner that coupling to other QM codes should be possible +without changes to LAMMPS itself. + +[Author:] Axel Kohlmeyer (Temple U). + +[Install:] + +This package has "specific installation +instructions"_Build_extras.html#gpu on the "Build +extras"_Build_extras.html doc page. + +[Supporting info:] + +src/USER-QMMM: filenames -> commands +src/USER-QMMM/README +lib/qmmm/README +"fix phonon"_fix_phonon.html +lib/qmmm/example-ec/README +lib/qmmm/example-mc/README :ul + +:line + +USER-QTB package :link(PKG-USER-QTB),h4 + +[Contents:] + +Two fixes which provide a self-consistent quantum treatment of +vibrational modes in a classical molecular dynamics simulation. By +coupling the MD simulation to a colored thermostat, it introduces zero +point energy into the system, altering the energy power spectrum and +the heat capacity to account for their quantum nature. This is useful +when modeling systems at temperatures lower than their classical +limits or when temperatures ramp across the classical limits in a +simulation. + +[Author:] Yuan Shen (Stanford U). + +[Supporting info:] + +src/USER-QTB: filenames -> commands +src/USER-QTB/README +"fix qtb"_fix_qtb.html +"fix qbmsst"_fix_qbmsst.html +examples/USER/qtb :ul + +:line + +USER-QUIP package :link(PKG-USER-QUIP),h4 + +[Contents:] + +A "pair_style quip"_pair_quip.html command which wraps the "QUIP +libAtoms library"_quip, which includes a variety of interatomic +potentials, including Gaussian Approximation Potential (GAP) models +developed by the Cambridge University group. + +:link(quip,https://github.com/libAtoms/QUIP) + +To use this package you must have the QUIP libAtoms library available +on your system. + +[Author:] Albert Bartok (Cambridge University) + +[Install:] + +This package has "specific installation +instructions"_Build_extras.html#gpu on the "Build +extras"_Build_extras.html doc page. + +[Supporting info:] + +src/USER-QUIP: filenames -> commands +src/USER-QUIP/README +"pair_style quip"_pair_quip.html +examples/USER/quip :ul + +:line + +USER-REAXC package :link(PKG-USER-REAXC),h4 + +[Contents:] + +A pair style which implements the ReaxFF potential in C/C++ (in +contrast to the "REAX package"_#PKG-REAX and its Fortran library). ReaxFF +is universal reactive force field. See the src/USER-REAXC/README file +for more info on differences between the two packages. Also two fixes +for monitoring molecules as bonds are created and destroyed. + +[Author:] Hasan Metin Aktulga (MSU) while at Purdue University. + +[Supporting info:] + +src/USER-REAXC: filenames -> commands +src/USER-REAXC/README +"pair_style reax/c"_pair_reaxc.html +"fix reax/c/bonds"_fix_reax_bonds.html +"fix reax/c/species"_fix_reaxc_species.html +examples/reax :ul + +:line + +USER-SCAFACOS package :link(PKG-USER-SCAFACOS),h4 + +[Contents:] + +A KSpace style which wraps the "ScaFaCoS Coulomb solver +library"_http://www.scafacos.de to compute long-range Coulombic +interactions. + +To use this package you must have the ScaFaCoS library available on +your system. + +[Author:] Rene Halver (JSC) wrote the scafacos LAMMPS command. + +ScaFaCoS itself was developed by a consortium of German research +facilities with a BMBF (German Ministry of Science and Education) +funded project in 2009-2012. Participants of the consortium were the +Universities of Bonn, Chemnitz, Stuttgart, and Wuppertal as well as +the Forschungszentrum Juelich. + +[Install:] + +This package has "specific installation +instructions"_Build_extras.html#user-scafacos on the "Build +extras"_Build_extras.html doc page. + +[Supporting info:] + +src/USER-SCAFACOS: filenames -> commands +src/USER-SCAFACOS/README +"kspace_style scafacos"_kspace_style.html +"kspace_modify"_kspace_modify.html +examples/USER/scafacos :ul + +:line + +USER-SMD package :link(PKG-USER-SMD),h4 + +[Contents:] + +An atom style, fixes, computes, and several pair styles which +implements smoothed Mach dynamics (SMD) for solids, which is a model +related to smoothed particle hydrodynamics (SPH) for liquids (see the +"USER-SPH package"_#PKG-USER-SPH). + +This package solves solids mechanics problems via a state of the art +stabilized meshless method with hourglass control. It can specify +hydrostatic interactions independently from material strength models, +i.e. pressure and deviatoric stresses are separated. It provides many +material models (Johnson-Cook, plasticity with hardening, +Mie-Grueneisen, Polynomial EOS) and allows new material models to be +added. It implements rigid boundary conditions (walls) which can be +specified as surface geometries from *.STL files. + +[Author:] Georg Ganzenmuller (Fraunhofer-Institute for High-Speed +Dynamics, Ernst Mach Institute, Germany). + +[Install:] + +This package has "specific installation +instructions"_Build_extras.html#gpu on the "Build +extras"_Build_extras.html doc page. + +[Supporting info:] + +src/USER-SMD: filenames -> commands +src/USER-SMD/README +doc/PDF/SMD_LAMMPS_userguide.pdf +examples/USER/smd +http://lammps.sandia.gov/movies.html#smd :ul + +:line + +USER-SMTBQ package :link(PKG-USER-SMTBQ),h4 + +[Contents:] + +A pair style which implements a Second Moment Tight Binding model with +QEq charge equilibration (SMTBQ) potential for the description of +ionocovalent bonds in oxides. + +[Authors:] Nicolas Salles, Emile Maras, Olivier Politano, and Robert +Tetot (LAAS-CNRS, France). + +[Supporting info:] + +src/USER-SMTBQ: filenames -> commands +src/USER-SMTBQ/README +"pair_style smtbq"_pair_smtbq.html +examples/USER/smtbq :ul + +:line + +USER-SPH package :link(PKG-USER-SPH),h4 + +[Contents:] + +An atom style, fixes, computes, and several pair styles which +implements smoothed particle hydrodynamics (SPH) for liquids. See the +related "USER-SMD package"_#PKG-USER-SMD package for smooth Mach dynamics +(SMD) for solids. + +This package contains ideal gas, Lennard-Jones equation of states, +Tait, and full support for complete (i.e. internal-energy dependent) +equations of state. It allows for plain or Monaghans XSPH integration +of the equations of motion. It has options for density continuity or +density summation to propagate the density field. It has +"set"_set.html command options to set the internal energy and density +of particles from the input script and allows the same quantities to +be output with thermodynamic output or to dump files via the "compute +property/atom"_compute_property_atom.html command. + +[Author:] Georg Ganzenmuller (Fraunhofer-Institute for High-Speed +Dynamics, Ernst Mach Institute, Germany). + +[Supporting info:] + +src/USER-SPH: filenames -> commands +src/USER-SPH/README +doc/PDF/SPH_LAMMPS_userguide.pdf +examples/USER/sph +http://lammps.sandia.gov/movies.html#sph :ul + +:line + +USER-TALLY package :link(PKG-USER-TALLY),h4 + +[Contents:] + +Several compute styles that can be called when pairwise interactions +are calculated to tally information (forces, heat flux, energy, +stress, etc) about individual interactions. + +[Author:] Axel Kohlmeyer (Temple U). + +[Supporting info:] + +src/USER-TALLY: filenames -> commands +src/USER-TALLY/README +"compute */tally"_compute_tally.html +examples/USER/tally :ul + +:line + +USER-UEF package :link(PKG-USER-UEF),h4 + +[Contents:] + +A fix style for the integration of the equations of motion under +extensional flow with proper boundary conditions, as well as several +supporting compute styles and an output option. + +[Author:] David Nicholson (MIT). + +[Supporting info:] + +src/USER-UEF: filenames -> commands +src/USER-UEF/README +"fix nvt/uef"_fix_nh_uef.html +"fix npt/uef"_fix_nh_uef.html +"compute pressure/uef"_compute_pressure_uef.html +"compute temp/uef"_compute_temp_uef.html +"dump cfg/uef"_dump_cfg_uef.html +examples/uef :ul + +:line + +USER-VTK package :link(PKG-USER-VTK),h4 + +[Contents:] + +A "dump vtk"_dump_vtk.html command which outputs snapshot info in the +"VTK format"_vtk, enabling visualization by "Paraview"_paraview or +other visualization packages. + +:link(vtk,http://www.vtk.org) +:link(paraview,http://www.paraview.org) + +To use this package you must have VTK library available on your +system. + +[Authors:] Richard Berger (JKU) and Daniel Queteschiner (DCS Computing). + +[Install:] + +This package has "specific installation +instructions"_Build_extras.html#gpu on the "Build +extras"_Build_extras.html doc page. + +[Supporting info:] + +src/USER-VTK: filenames -> commands +src/USER-VTK/README +lib/vtk/README +"dump vtk"_dump_vtk.html :ul + + diff --git a/doc/src/Packages_standard.txt b/doc/src/Packages_standard.txt new file mode 100644 index 0000000000..583ecf39fe --- /dev/null +++ b/doc/src/Packages_standard.txt @@ -0,0 +1,67 @@ +"Higher level section"_Packages.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Standard packages :h3 + +This is the list of standard packages in LAMMPS. The link for each +package name gives more details. + +Standard packages are supported by the LAMMPS developers and are +written in a syntax and style consistent with the rest of LAMMPS. +This means the developers will answer questions about them, debug and +fix them if necessary, and keep them compatible with future changes to +LAMMPS. + +The "Example" column is a sub-directory in the examples directory of +the distribution which has an input script that uses the package. +E.g. "peptide" refers to the examples/peptide directory; USER/atc +refers to the examples/USER/atc directory. The "Library" column +indicates whether an extra library is needed to build and use the +package: + +no = no library +sys = system library: you likely have it on your machine +int = internal library: provided with LAMMPS, but you may need to build it +ext = external library: you will need to download and install it on your machine :ul + +Package, Description, Doc page, Example, Library +"ASPHERE"_Packages_details.html#PKG-ASPHERE, aspherical particle models, "Howto spherical"_Howto_spherical.html, ellipse, no +"BODY"_Packages_details.html#PKG-BODY, body-style particles, "Howto body"_Howto_body.html, body, no +"CLASS2"_Packages_details.html#PKG-CLASS2, class 2 force fields, "pair_style lj/class2"_pair_class2.html, n/a, no +"COLLOID"_Packages_details.html#PKG-COLLOID, colloidal particles, "atom_style colloid"_atom_style.html, colloid, no +"COMPRESS"_Packages_details.html#PKG-COMPRESS, I/O compression, "dump */gz"_dump.html, n/a, sys +"CORESHELL"_Packages_details.html#PKG-CORESHELL, adiabatic core/shell model, "Howto coreshell"_Howto_coreshell.html, coreshell, no +"DIPOLE"_Packages_details.html#PKG-DIPOLE, point dipole particles, "pair_style dipole/cut"_pair_dipole.html, dipole, no +"GPU"_Packages_details.html#PKG-GPU, GPU-enabled styles, "Section gpu"_Speed_gpu.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, int +"GRANULAR"_Packages_details.html#PKG-GRANULAR, granular systems, "Howto granular"_Howto_granular.html, pour, no +"KIM"_Packages_details.html#PKG-KIM, OpenKIM wrapper, "pair_style kim"_pair_kim.html, kim, ext +"KOKKOS"_Packages_details.html#PKG-KOKKOS, Kokkos-enabled styles, "Speed kokkos"_Speed_kokkos.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, no +"KSPACE"_Packages_details.html#PKG-KSPACE, long-range Coulombic solvers, "kspace_style"_kspace_style.html, peptide, no +"LATTE"_Packages_details.html#PKG-LATTE, quantum DFTB forces via LATTE, "fix latte"_fix_latte.html, latte, ext +"MANYBODY"_Packages_details.html#PKG-MANYBODY, many-body potentials, "pair_style tersoff"_pair_tersoff.html, shear, no +"MC"_Packages_details.html#PKG-MC, Monte Carlo options, "fix gcmc"_fix_gcmc.html, n/a, no +"MEAM"_Packages_details.html#PKG-MEAM, modified EAM potential, "pair_style meam"_pair_meam.html, meam, int +"MESSAGE"_Packages_details.html#PKG-MESSAGE, client/server messaging, "message"_message.html, message, int +"MISC"_Packages_details.html#PKG-MISC, miscellaneous single-file commands, n/a, no, no +"MOLECULE"_Packages_details.html#PKG-MOLECULE, molecular system force fields, "Howto bioFF"_Howto_bioFF.html, peptide, no +"MPIIO"_Packages_details.html#PKG-MPIIO, MPI parallel I/O dump and restart, "dump"_dump.html, n/a, no +"MSCG"_Packages_details.html#PKG-MSCG, multi-scale coarse-graining wrapper, "fix mscg"_fix_mscg.html, mscg, ext +"OPT"_Packages_details.html#PKG-OPT, optimized pair styles, "Speed opt"_Speed_opt.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, no +"PERI"_Packages_details.html#PKG-PERI, Peridynamics models, "pair_style peri"_pair_peri.html, peri, no +"POEMS"_Packages_details.html#PKG-POEMS, coupled rigid body motion, "fix poems"_fix_poems.html, rigid, int +"PYTHON"_Packages_details.html#PKG-PYTHON, embed Python code in an input script, "python"_python.html, python, sys +"QEQ"_Packages_details.html#PKG-QEQ, QEq charge equilibration, "fix qeq"_fix_qeq.html, qeq, no +"REAX"_Packages_details.html#PKG-REAX, ReaxFF potential (Fortran), "pair_style reax"_pair_reax.html, reax, int +"REPLICA"_Packages_details.html#PKG-REPLICA2, multi-replica methods, "Howto replica"_Howto_replica.html, tad, no +"RIGID"_Packages_details.html#PKG-RIGID, rigid bodies and constraints, "fix rigid"_fix_rigid.html, rigid, no +"SHOCK"_Packages_details.html#PKG-SHOCK, shock loading methods, "fix msst"_fix_msst.html, n/a, no +"SNAP"_Packages_details.html#PKG-SNAP, quantum-fitted potential, "pair_style snap"_pair_snap.html, snap, no +"SPIN"_Packages_details.html#PKG-SPIN, magnetic atomic spin dynamics, "Howto spins"_Howto_spins.html, SPIN, no +"SRD"_Packages_details.html#PKG-SRD, stochastic rotation dynamics, "fix srd"_fix_srd.html, srd, no +"VORONOI"_Packages_details.html#PKG-VORONOI, Voronoi tesselation, "compute voronoi/atom"_compute_voronoi_atom.html, n/a, ext :tb(ea=c,ca1=l) diff --git a/doc/src/Packages_user.txt b/doc/src/Packages_user.txt new file mode 100644 index 0000000000..70ac6022b6 --- /dev/null +++ b/doc/src/Packages_user.txt @@ -0,0 +1,75 @@ +"Higher level section"_Packages.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +User packages :h3 + +This is a list of user packages in LAMMPS. The link for each package +name gives more details. + +User packages have been contributed by users, and begin with the +"user" prefix. If a contribution is a single command (single file), +it is typically in the user-misc package. User packages don't +necessarily meet the requirements of the "standard +packages"_Packages_standard.html. This means the developers will try +to keep things working and usually can answer technical questions +about compiling the package. If you have problems using a specific +feature provided in a user package, you may need to contact the +contributor directly to get help. Information on how to submit +additions you make to LAMMPS as single files or as a standard or user +package is explained on the "Modify contribute"_Modify_contribute.html +doc page. + +The "Example" column is a sub-directory in the examples directory of +the distribution which has an input script that uses the package. +E.g. "peptide" refers to the examples/peptide directory; USER/atc +refers to the examples/USER/atc directory. The "Library" column +indicates whether an extra library is needed to build and use the +package: + +no = no library +sys = system library: you likely have it on your machine +int = internal library: provided with LAMMPS, but you may need to build it +ext = external library: you will need to download and install it on your machine :ul + +Package, Description, Doc page, Example, Library +"USER-ATC"_Packages_details.html#PKG-USER-ATC, atom-to-continuum coupling, "fix atc"_fix_atc.html, USER/atc, int +"USER-AWPMD"_Packages_details.html#PKG-USER-AWPMD, wave-packet MD, "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, int +"USER-BOCS"_Packages_details.html#PKG-USER-BOCS, BOCS bottom up coarse graining, "fix bocs"_fix_bocs.html, USER/bocs, no +"USER-CGDNA"_Packages_details.html#PKG-USER-CGDNA, coarse-grained DNA force fields, src/USER-CGDNA/README, USER/cgdna, no +"USER-CGSDK"_Packages_details.html#PKG-USER-CGSDK, SDK coarse-graining model, "pair_style lj/sdk"_pair_sdk.html, USER/cgsdk, no +"USER-COLVARS"_Packages_details.html#PKG-USER-COLVARS, collective variables library, "fix colvars"_fix_colvars.html, USER/colvars, int +"USER-DIFFRACTION"_Packages_details.html#PKG-USER-DIFFRACTION, virtual x-ray and electron diffraction,"compute xrd"_compute_xrd.html, USER/diffraction, no +"USER-DPD"_Packages_details.html#PKG-USER-DPD, reactive dissipative particle dynamics, src/USER-DPD/README, USER/dpd, no +"USER-DRUDE"_Packages_details.html#PKG-USER-DRUDE, Drude oscillators, "Howto drude"_Howto_drude.html, USER/drude, no +"USER-EFF"_Packages_details.html#PKG-USER-EFF, electron force field,"pair_style eff/cut"_pair_eff.html, USER/eff, no +"USER-FEP"_Packages_details.html#PKG-USER-FEP, free energy perturbation,"compute fep"_compute_fep.html, USER/fep, no +"USER-H5MD"_Packages_details.html#PKG-USER-H5MD, dump output via HDF5,"dump h5md"_dump_h5md.html, n/a, ext +"USER-INTEL"_Packages_details.html#PKG-USER-INTEL, optimized Intel CPU and KNL styles,"Speed intel"_Speed_intel.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, no +"USER-LB"_Packages_details.html#PKG-USER-LB, Lattice Boltzmann fluid,"fix lb/fluid"_fix_lb_fluid.html, USER/lb, no +"USER-MANIFOLD"_Packages_details.html#PKG-USER-MANIFOLD, motion on 2d surfaces,"fix manifoldforce"_fix_manifoldforce.html, USER/manifold, no +"USER-MEAMC"_Packages_details.html#PKG-USER-MEAMC, modified EAM potential (C++), "pair_style meam/c"_pair_meam.html, meam, no +"USER-MESO"_Packages_details.html#PKG-USER-MESO, mesoscale DPD models, "pair_style edpd"_pair_meso.html, USER/meso, no +"USER-MGPT"_Packages_details.html#PKG-USER-MGPT, fast MGPT multi-ion potentials, "pair_style mgpt"_pair_mgpt.html, USER/mgpt, no +"USER-MISC"_Packages_details.html#PKG-USER-MISC, single-file contributions, USER-MISC/README, USER/misc, no +"USER-MOFFF"_Packages_details.html#PKG-USER-MOFFF, styles for "MOF-FF"_MOFplus force field, "pair_style buck6d/coul/gauss"_pair_buck6d_coul_gauss.html, USER/mofff, no +"USER-MOLFILE"_Packages_details.html#PKG-USER-MOLFILE, "VMD"_https://www.ks.uiuc.edu/Research/vmd/ molfile plug-ins,"dump molfile"_dump_molfile.html, n/a, ext +"USER-NETCDF"_Packages_details.html#PKG-USER-NETCDF, dump output via NetCDF,"dump netcdf"_dump_netcdf.html, n/a, ext +"USER-OMP"_Packages_details.html#PKG-USER-OMP, OpenMP-enabled styles,"Speed omp"_Speed_omp.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, no +"USER-PHONON"_Packages_details.html#PKG-USER-PHONON, phonon dynamical matrix,"fix phonon"_fix_phonon.html, USER/phonon, no +"USER-QMMM"_Packages_details.html#PKG-USER-QMMM, QM/MM coupling,"fix qmmm"_fix_qmmm.html, USER/qmmm, ext +"USER-QTB"_Packages_details.html#PKG-USER-QTB, quantum nuclear effects,"fix qtb"_fix_qtb.html "fix qbmsst"_fix_qbmsst.html, qtb, no +"USER-QUIP"_Packages_details.html#PKG-USER-QUIP, QUIP/libatoms interface,"pair_style quip"_pair_quip.html, USER/quip, ext +"USER-REAXC"_Packages_details.html#PKG-USER-REAXC, ReaxFF potential (C/C++) ,"pair_style reaxc"_pair_reaxc.html, reax, no +"USER-SCAFACOS"_Packages_details.html#PKG-USER-SCAFACOS, wrapper on ScaFaCoS solver,"kspace_style scafacos"_kspace_style.html, USER/scafacos, ext +"USER-SMD"_Packages_details.html#PKG-USER-SMD, smoothed Mach dynamics,"SMD User Guide"_PDF/SMD_LAMMPS_userguide.pdf, USER/smd, ext +"USER-SMTBQ"_Packages_details.html#PKG-USER-SMTBQ, second moment tight binding QEq potential,"pair_style smtbq"_pair_smtbq.html, USER/smtbq, no +"USER-SPH"_Packages_details.html#PKG-USER-SPH, smoothed particle hydrodynamics,"SPH User Guide"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, no +"USER-TALLY"_Packages_details.html#PKG-USER-TALLY, pairwise tally computes,"compute XXX/tally"_compute_tally.html, USER/tally, no +"USER-UEF"_Packages_details.html#PKG-USER-UEF, extensional flow,"fix nvt/uef"_fix_nh_uef.html, USER/uef, no +"USER-VTK"_Packages_details.html#PKG-USER-VTK, dump output via VTK, "compute vtk"_dump_vtk.html, n/a, ext :tb(ea=c,ca1=l) diff --git a/doc/src/Python_call.txt b/doc/src/Python_call.txt new file mode 100644 index 0000000000..3c382de1ba --- /dev/null +++ b/doc/src/Python_call.txt @@ -0,0 +1,85 @@ +"Higher level section"_Python_head.html - "LAMMPS WWW Site"_lws - +"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Call Python from a LAMMPS input script :h3 + +LAMMPS has several commands which can be used to invoke Python +code directly from an input script: + +"python"_python.html +"variable python"_variable.html +"fix python/invoke"_fix_python_invoke.html +"pair_style python"_pair_python.html :ul + +The "python"_python.html command which can be used to define and +execute a Python function that you write the code for. The Python +function can also be assigned to a LAMMPS python-style variable via +the "variable"_variable.html command. Each time the variable is +evaluated, either in the LAMMPS input script itself, or by another +LAMMPS command that uses the variable, this will trigger the Python +function to be invoked. + +The Python code for the function can be included directly in the input +script or in an auxiliary file. The function can have arguments which +are mapped to LAMMPS variables (also defined in the input script) and +it can return a value to a LAMMPS variable. This is thus a mechanism +for your input script to pass information to a piece of Python code, +ask Python to execute the code, and return information to your input +script. + +Note that a Python function can be arbitrarily complex. It can import +other Python modules, instantiate Python classes, call other Python +functions, etc. The Python code that you provide can contain more +code than the single function. It can contain other functions or +Python classes, as well as global variables or other mechanisms for +storing state between calls from LAMMPS to the function. + +The Python function you provide can consist of "pure" Python code that +only performs operations provided by standard Python. However, the +Python function can also "call back" to LAMMPS through its +Python-wrapped library interface, in the manner described in the +"Python run"_Python_run.html doc page. This means it can issue LAMMPS +input script commands or query and set internal LAMMPS state. As an +example, this can be useful in an input script to create a more +complex loop with branching logic, than can be created using the +simple looping and branching logic enabled by the "next"_next.html and +"if"_if.html commands. + +See the "python"_python.html doc page and the "variable"_variable.html +doc page for its python-style variables for more info, including +examples of Python code you can write for both pure Python operations +and callbacks to LAMMPS. + +The "fix python/invoke"_fix_python_invoke.html command can execute +Python code at selected timesteps during a simulation run. + +The "pair_style python"_pair_python.html command allows you to define +pairwise potentials as python code which encodes a single pairwise +interaction. This is useful for rapid development and debugging of a +new potential. + +To use any of these commands, you only need to build LAMMPS with the +PYTHON package installed: + +make yes-python +make machine :pre + +Note that this will link LAMMPS with the Python library on your +system, which typically requires several auxiliary system libraries to +also be linked. The list of these libraries and the paths to find +them are specified in the lib/python/Makefile.lammps file. You need +to insure that file contains the correct information for your version +of Python and your machine to successfully build LAMMPS. See the +lib/python/README file for more info. + +If you want to write Python code with callbacks to LAMMPS, then you +must also follow the steps overviewed in the "Python +run"_Python_run.html doc page. I.e. you must build LAMMPS as a shared +library and insure that Python can find the python/lammps.py file and +the shared library. diff --git a/doc/src/Python_examples.txt b/doc/src/Python_examples.txt new file mode 100644 index 0000000000..f4b2197464 --- /dev/null +++ b/doc/src/Python_examples.txt @@ -0,0 +1,81 @@ +"Higher level section"_Python_head.html - "LAMMPS WWW Site"_lws - +"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Example Python scripts that use LAMMPS :h3 + +These are the Python scripts included as demos in the python/examples +directory of the LAMMPS distribution, to illustrate the kinds of +things that are possible when Python wraps LAMMPS. If you create your +own scripts, send them to us and we can include them in the LAMMPS +distribution. + +trivial.py, read/run a LAMMPS input script thru Python, +demo.py, invoke various LAMMPS library interface routines, +simple.py, run in parallel, similar to examples/COUPLE/simple/simple.cpp, +split.py, same as simple.py but running in parallel on a subset of procs, +gui.py, GUI go/stop/temperature-slider to control LAMMPS, +plot.py, real-time temperature plot with GnuPlot via Pizza.py, +viz_tool.py, real-time viz via some viz package, +vizplotgui_tool.py, combination of viz_tool.py and plot.py and gui.py :tb(c=2) + +:line + +For the viz_tool.py and vizplotgui_tool.py commands, replace "tool" +with "gl" or "atomeye" or "pymol" or "vmd", depending on what +visualization package you have installed. + +Note that for GL, you need to be able to run the Pizza.py GL tool, +which is included in the pizza sub-directory. See the "Pizza.py doc +pages"_pizza for more info: + +:link(pizza,http://www.sandia.gov/~sjplimp/pizza.html) + +Note that for AtomEye, you need version 3, and there is a line in the +scripts that specifies the path and name of the executable. See the +AtomEye WWW pages "here"_atomeye or "here"_atomeye3 for more details: + +http://mt.seas.upenn.edu/Archive/Graphics/A +http://mt.seas.upenn.edu/Archive/Graphics/A3/A3.html :pre + +:link(atomeye,http://mt.seas.upenn.edu/Archive/Graphics/A) +:link(atomeye3,http://mt.seas.upenn.edu/Archive/Graphics/A3/A3.html) + +The latter link is to AtomEye 3 which has the scriping +capability needed by these Python scripts. + +Note that for PyMol, you need to have built and installed the +open-source version of PyMol in your Python, so that you can import it +from a Python script. See the PyMol WWW pages "here"_pymolhome or +"here"_pymolopen for more details: + +http://www.pymol.org +http://sourceforge.net/scm/?type=svn&group_id=4546 :pre + +:link(pymolhome,http://www.pymol.org) +:link(pymolopen,http://sourceforge.net/scm/?type=svn&group_id=4546) + +The latter link is to the open-source version. + +Note that for VMD, you need a fairly current version (1.8.7 works for +me) and there are some lines in the pizza/vmd.py script for 4 PIZZA +variables that have to match the VMD installation on your system. + +:line + +See the python/README file for instructions on how to run them and the +source code for individual scripts for comments about what they do. + +Here are screenshots of the vizplotgui_tool.py script in action for +different visualization package options. Click to see larger images: + +:image(JPG/screenshot_gl_small.jpg,JPG/screenshot_gl.jpg) +:image(JPG/screenshot_atomeye_small.jpg,JPG/screenshot_atomeye.jpg) +:image(JPG/screenshot_pymol_small.jpg,JPG/screenshot_pymol.jpg) +:image(JPG/screenshot_vmd_small.jpg,JPG/screenshot_vmd.jpg) + diff --git a/doc/src/Python_head.txt b/doc/src/Python_head.txt new file mode 100644 index 0000000000..54f995c565 --- /dev/null +++ b/doc/src/Python_head.txt @@ -0,0 +1,72 @@ +"Previous Section"_Modify.html - "LAMMPS WWW Site"_lws - +"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next +Section"_Errors.html :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Use Python with LAMMPS :h2 + +These doc pages describe various ways that LAMMPS and Python can be +used together. + + + + + +"Overview of Python and LAMMPS"_Python_overview.html +"Run LAMMPS from Python"_Python_run.html +"Build LAMMPS as a shared library"_Python_shlib.html +"Install LAMMPS in Python"_Python_install.html +"Extend Python to run in parallel"_Python_mpi.html +"Test the Python/LAMMPS interface"_Python_test.html +"Python library interface"_Python_library.html +"PyLammps interface"_Python_pylammps.html +"Example Python scripts that use LAMMPS"_Python_examples.html +"Call Python from a LAMMPS input script"_Python_call.html :all(b) + + + +If you're not familiar with "Python"_http://www.python.org, it's a +powerful scripting and programming language which can do most +everything that lower-level languages like C or C++ can do in fewer +lines of code. The only drawback is slower execution speed. Python +is also easy to use as a "glue" language to drive a program through +its library interface, or to hook multiple pieces of software +together, such as a simulation code plus a visualization tool, or to +run a coupled multiscale or multiphysics model. + +See the "Howto_couple"_Howto_couple.html doc page for more ideas about +coupling LAMMPS to other codes. See the "Howto +library"_Howto_library.html doc page for a description of the LAMMPS +library interface provided in src/library.h and src/library.h. That +interface is exposed to Python either when calling LAMMPS from Python +or when calling Python from a LAMMPS input script and then calling +back to LAMMPS from Python code. The library interface is designed to +be easy to add functionality to. Thus the Python interface to LAMMPS +is also easy to extend as well. + +If you create interesting Python scripts that run LAMMPS or +interesting Python functions that can be called from a LAMMPS input +script, that you think would be generally useful, please post them as +a pull request to our "GitHub site"_https://github.com/lammps/lammps, +and they can be added to the LAMMPS distribution or webpage. diff --git a/doc/src/Python_install.txt b/doc/src/Python_install.txt new file mode 100644 index 0000000000..97f6bf3c3a --- /dev/null +++ b/doc/src/Python_install.txt @@ -0,0 +1,74 @@ +"Higher level section"_Python_head.html - "LAMMPS WWW Site"_lws - +"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Installing LAMMPS in Python :h3 + +For Python to invoke LAMMPS, there are 2 files it needs to know about: + +python/lammps.py +src/liblammps.so :ul + +Lammps.py is the Python wrapper on the LAMMPS library interface. +Liblammps.so is the shared LAMMPS library that Python loads, as +described above. + +You can insure Python can find these files in one of two ways: + +set two environment variables +run the python/install.py script :ul + +If you set the paths to these files as environment variables, you only +have to do it once. For the csh or tcsh shells, add something like +this to your ~/.cshrc file, one line for each of the two files: + +setenv PYTHONPATH $\{PYTHONPATH\}:/home/sjplimp/lammps/python +setenv LD_LIBRARY_PATH $\{LD_LIBRARY_PATH\}:/home/sjplimp/lammps/src :pre + +If you use the python/install.py script, you need to invoke it every +time you rebuild LAMMPS (as a shared library) or make changes to the +python/lammps.py file. + +You can invoke install.py from the python directory as + +% python install.py \[libdir\] \[pydir\] :pre + +The optional libdir is where to copy the LAMMPS shared library to; the +default is /usr/local/lib. The optional pydir is where to copy the +lammps.py file to; the default is the site-packages directory of the +version of Python that is running the install script. + +Note that libdir must be a location that is in your default +LD_LIBRARY_PATH, like /usr/local/lib or /usr/lib. And pydir must be a +location that Python looks in by default for imported modules, like +its site-packages dir. If you want to copy these files to +non-standard locations, such as within your own user space, you will +need to set your PYTHONPATH and LD_LIBRARY_PATH environment variables +accordingly, as above. + +If the install.py script does not allow you to copy files into system +directories, prefix the python command with "sudo". If you do this, +make sure that the Python that root runs is the same as the Python you +run. E.g. you may need to do something like + +% sudo /usr/local/bin/python install.py \[libdir\] \[pydir\] :pre + +You can also invoke install.py from the make command in the src +directory as + +% make install-python :pre + +In this mode you cannot append optional arguments. Again, you may +need to prefix this with "sudo". In this mode you cannot control +which Python is invoked by root. + +Note that if you want Python to be able to load different versions of +the LAMMPS shared library (see "this section"_Python_shlib.html), you will +need to manually copy files like liblammps_g++.so into the appropriate +system directory. This is not needed if you set the LD_LIBRARY_PATH +environment variable as described above. diff --git a/doc/src/Python_library.txt b/doc/src/Python_library.txt new file mode 100644 index 0000000000..e76af83962 --- /dev/null +++ b/doc/src/Python_library.txt @@ -0,0 +1,256 @@ +"Higher level section"_Python_head.html - "LAMMPS WWW Site"_lws - +"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Python library interface :h3 + +As described previously, the Python interface to LAMMPS consists of a +Python "lammps" module, the source code for which is in +python/lammps.py, which creates a "lammps" object, with a set of +methods that can be invoked on that object. The sample Python code +below assumes you have first imported the "lammps" module in your +Python script, as follows: + +from lammps import lammps :pre + +These are the methods defined by the lammps module. If you look at +the files src/library.cpp and src/library.h you will see they +correspond one-to-one with calls you can make to the LAMMPS library +from a C++ or C or Fortran program, and which are described on the +"Howto library"_Howto_library.html doc page. + +The python/examples directory has Python scripts which show how Python +can run LAMMPS, grab data, change it, and put it back into LAMMPS. + +lmp = lammps() # create a LAMMPS object using the default liblammps.so library + # 4 optional args are allowed: name, cmdargs, ptr, comm +lmp = lammps(ptr=lmpptr) # use lmpptr as previously created LAMMPS object +lmp = lammps(comm=split) # create a LAMMPS object with a custom communicator, requires mpi4py 2.0.0 or later +lmp = lammps(name="g++") # create a LAMMPS object using the liblammps_g++.so library +lmp = lammps(name="g++",cmdargs=list) # add LAMMPS command-line args, e.g. list = \["-echo","screen"\] :pre + +lmp.close() # destroy a LAMMPS object :pre + +version = lmp.version() # return the numerical version id, e.g. LAMMPS 2 Sep 2015 -> 20150902 :pre + +lmp.file(file) # run an entire input script, file = "in.lj" +lmp.command(cmd) # invoke a single LAMMPS command, cmd = "run 100" +lmp.commands_list(cmdlist) # invoke commands in cmdlist = ["run 10", "run 20"] +lmp.commands_string(multicmd) # invoke commands in multicmd = "run 10\nrun 20" :pre + +size = lmp.extract_setting(name) # return data type info :pre + +xlo = lmp.extract_global(name,type) # extract a global quantity + # name = "boxxlo", "nlocal", etc + # type = 0 = int + # 1 = double :pre + +boxlo,boxhi,xy,yz,xz,periodicity,box_change = lmp.extract_box() # extract box info :pre + +coords = lmp.extract_atom(name,type) # extract a per-atom quantity + # name = "x", "type", etc + # type = 0 = vector of ints + # 1 = array of ints + # 2 = vector of doubles + # 3 = array of doubles :pre + +eng = lmp.extract_compute(id,style,type) # extract value(s) from a compute +v3 = lmp.extract_fix(id,style,type,i,j) # extract value(s) from a fix + # id = ID of compute or fix + # style = 0 = global data + # 1 = per-atom data + # 2 = local data + # type = 0 = scalar + # 1 = vector + # 2 = array + # i,j = indices of value in global vector or array :pre + +var = lmp.extract_variable(name,group,flag) # extract value(s) from a variable + # name = name of variable + # group = group ID (ignored for equal-style variables) + # flag = 0 = equal-style variable + # 1 = atom-style variable :pre + +value = lmp.get_thermo(name) # return current value of a thermo keyword +natoms = lmp.get_natoms() # total # of atoms as int :pre + +flag = lmp.set_variable(name,value) # set existing named string-style variable to value, flag = 0 if successful +lmp.reset_box(boxlo,boxhi,xy,yz,xz) # reset the simulation box size :pre + +data = lmp.gather_atoms(name,type,count) # return per-atom property of all atoms gathered into data, ordered by atom ID + # name = "x", "charge", "type", etc +data = lmp.gather_atoms_concat(name,type,count) # ditto, but concatenated atom values from each proc (unordered) +data = lmp.gather_atoms_subset(name,type,count,ndata,ids) # ditto, but for subset of Ndata atoms with IDs :pre + +lmp.scatter_atoms(name,type,count,data) # scatter per-atom property to all atoms from data, ordered by atom ID + # name = "x", "charge", "type", etc + # count = # of per-atom values, 1 or 3, etc :pre +lmp.scatter_atoms_subset(name,type,count,ndata,ids,data) # ditto, but for subset of Ndata atoms with IDs :pre + +lmp.create_atoms(n,ids,types,x,v,image,shrinkexceed) # create N atoms with IDs, types, x, v, and image flags :pre + +:line + +The lines + +from lammps import lammps +lmp = lammps() :pre + +create an instance of LAMMPS, wrapped in a Python class by the lammps +Python module, and return an instance of the Python class as lmp. It +is used to make all subsequent calls to the LAMMPS library. + +Additional arguments to lammps() can be used to tell Python the name +of the shared library to load or to pass arguments to the LAMMPS +instance, the same as if LAMMPS were launched from a command-line +prompt. + +If the ptr argument is set like this: + +lmp = lammps(ptr=lmpptr) :pre + +then lmpptr must be an argument passed to Python via the LAMMPS +"python"_python.html command, when it is used to define a Python +function that is invoked by the LAMMPS input script. This mode of +calling Python from LAMMPS is described in the "Python +call"_Python_call.html doc page. The variable lmpptr refers to the +instance of LAMMPS that called the embedded Python interpreter. Using +it as an argument to lammps() allows the returned Python class +instance "lmp" to make calls to that instance of LAMMPS. See the +"python"_python.html command doc page for examples using this syntax. + +Note that you can create multiple LAMMPS objects in your Python +script, and coordinate and run multiple simulations, e.g. + +from lammps import lammps +lmp1 = lammps() +lmp2 = lammps() +lmp1.file("in.file1") +lmp2.file("in.file2") :pre + +The file(), command(), commands_list(), commands_string() methods +allow an input script, a single command, or multiple commands to be +invoked. + +The extract_setting(), extract_global(), extract_box(), +extract_atom(), extract_compute(), extract_fix(), and +extract_variable() methods return values or pointers to data +structures internal to LAMMPS. + +For extract_global() see the src/library.cpp file for the list of +valid names. New names could easily be added. A double or integer is +returned. You need to specify the appropriate data type via the type +argument. + +For extract_atom(), a pointer to internal LAMMPS atom-based data is +returned, which you can use via normal Python subscripting. See the +extract() method in the src/atom.cpp file for a list of valid names. +Again, new names could easily be added if the property you want is not +listed. A pointer to a vector of doubles or integers, or a pointer to +an array of doubles (double **) or integers (int **) is returned. You +need to specify the appropriate data type via the type argument. + +For extract_compute() and extract_fix(), the global, per-atom, or +local data calculated by the compute or fix can be accessed. What is +returned depends on whether the compute or fix calculates a scalar or +vector or array. For a scalar, a single double value is returned. If +the compute or fix calculates a vector or array, a pointer to the +internal LAMMPS data is returned, which you can use via normal Python +subscripting. The one exception is that for a fix that calculates a +global vector or array, a single double value from the vector or array +is returned, indexed by I (vector) or I and J (array). I,J are +zero-based indices. The I,J arguments can be left out if not needed. +See the "Howto output"_Howto_output.html doc page for a discussion of +global, per-atom, and local data, and of scalar, vector, and array +data types. See the doc pages for individual "computes"_compute.html +and "fixes"_fix.html for a description of what they calculate and +store. + +For extract_variable(), an "equal-style or atom-style +variable"_variable.html is evaluated and its result returned. + +For equal-style variables a single double value is returned and the +group argument is ignored. For atom-style variables, a vector of +doubles is returned, one value per atom, which you can use via normal +Python subscripting. The values will be zero for atoms not in the +specified group. + +The get_thermo() method returns returns the current value of a thermo +keyword as a float. + +The get_natoms() method returns the total number of atoms in the +simulation, as an int. + +The set_variable() method sets an existing string-style variable to a +new string value, so that subsequent LAMMPS commands can access the +variable. + +The reset_box() method resets the size and shape of the simulation +box, e.g. as part of restoring a previously extracted and saved state +of a simulation. + +The gather methods collect peratom info of the requested type (atom +coords, atom types, forces, etc) from all processors, and returns the +same vector of values to each calling processor. The scatter +functions do the inverse. They distribute a vector of peratom values, +passed by all calling processors, to individual atoms, which may be +owned by different processors. + +Note that the data returned by the gather methods, +e.g. gather_atoms("x"), is different from the data structure returned +by extract_atom("x") in four ways. (1) Gather_atoms() returns a +vector which you index as x\[i\]; extract_atom() returns an array +which you index as x\[i\]\[j\]. (2) Gather_atoms() orders the atoms +by atom ID while extract_atom() does not. (3) Gather_atoms() returns +a list of all atoms in the simulation; extract_atoms() returns just +the atoms local to each processor. (4) Finally, the gather_atoms() +data structure is a copy of the atom coords stored internally in +LAMMPS, whereas extract_atom() returns an array that effectively +points directly to the internal data. This means you can change +values inside LAMMPS from Python by assigning a new values to the +extract_atom() array. To do this with the gather_atoms() vector, you +need to change values in the vector, then invoke the scatter_atoms() +method. + +For the scatter methods, the array of coordinates passed to must be a +ctypes vector of ints or doubles, allocated and initialized something +like this: + +from ctypes import * +natoms = lmp.get_natoms() +n3 = 3*natoms +x = (n3*c_double)() +x\[0\] = x coord of atom with ID 1 +x\[1\] = y coord of atom with ID 1 +x\[2\] = z coord of atom with ID 1 +x\[3\] = x coord of atom with ID 2 +... +x\[n3-1\] = z coord of atom with ID natoms +lmp.scatter_atoms("x",1,3,x) :pre + +Alternatively, you can just change values in the vector returned by +the gather methods, since they are also ctypes vectors. + +:line + +As noted above, these Python class methods correspond one-to-one with +the functions in the LAMMPS library interface in src/library.cpp and +library.h. This means you can extend the Python wrapper via the +following steps: + +Add a new interface function to src/library.cpp and +src/library.h. :ulb,l + +Rebuild LAMMPS as a shared library. :l + +Add a wrapper method to python/lammps.py for this interface +function. :l + +You should now be able to invoke the new interface function from a +Python script. :l +:ule diff --git a/doc/src/Python_mpi.txt b/doc/src/Python_mpi.txt new file mode 100644 index 0000000000..96c42e0d0f --- /dev/null +++ b/doc/src/Python_mpi.txt @@ -0,0 +1,67 @@ +"Higher level section"_Python_head.html - "LAMMPS WWW Site"_lws - +"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Extending Python to run in parallel :h3 + +If you wish to run LAMMPS in parallel from Python, you need to extend +your Python with an interface to MPI. This also allows you to +make MPI calls directly from Python in your script, if you desire. + +We recommend use of mpi4py: + +"PyPar"_https://github.com/daleroberts/pypar :ul + +As of version 2.0.0 it allows passing a custom MPI communicator to +the LAMMPS constructor, which means one can easily run one or more +LAMMPS instances on subsets of the total MPI ranks. + +To install mpi4py (version mpi4py-2.0.0 as of Oct 2015), unpack it +and from its main directory, type + +python setup.py build +sudo python setup.py install :pre + +Again, the "sudo" is only needed if required to copy mpi4py files into +your Python distribution's site-packages directory. To install with +user privilege into the user local directory type + +python setup.py install --user :pre + +If you have successfully installed mpi4py, you should be able to run +Python and type + +from mpi4py import MPI :pre + +without error. You should also be able to run python in parallel +on a simple test script + +% mpirun -np 4 python test.py :pre + +where test.py contains the lines + +from mpi4py import MPI +comm = MPI.COMM_WORLD +print "Proc %d out of %d procs" % (comm.Get_rank(),comm.Get_size()) :pre + +and see one line of output for each processor you run on. + +NOTE: To use mpi4py and LAMMPS in parallel from Python, you must +insure both are using the same version of MPI. If you only have one +MPI installed on your system, this is not an issue, but it can be if +you have multiple MPIs. Your LAMMPS build is explicit about which MPI +it is using, since you specify the details in your lo-level +src/MAKE/Makefile.foo file. Mpi4py uses the "mpicc" command to find +information about the MPI it uses to build against. And it tries to +load "libmpi.so" from the LD_LIBRARY_PATH. This may or may not find +the MPI library that LAMMPS is using. If you have problems running +both mpi4py and LAMMPS together, this is an issue you may need to +address, e.g. by moving other MPI installations so that mpi4py finds +the right one. + + diff --git a/doc/src/Python_overview.txt b/doc/src/Python_overview.txt new file mode 100644 index 0000000000..a5d6a469ff --- /dev/null +++ b/doc/src/Python_overview.txt @@ -0,0 +1,35 @@ +"Previous Section"_Examples.html - "LAMMPS WWW Site"_lws - +"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next +Section"_Tools.html :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands.html#comm) + +:line + +Overview of Python and LAMMPS :h3 + +LAMMPS can work together with Python in three ways. First, Python can +wrap LAMMPS through the its "library interface"_Howto_library.html, so +that a Python script can create one or more instances of LAMMPS and +launch one or more simulations. In Python lingo, this is "extending" +Python with LAMMPS. + +Second, a lower-level Python interface can be used indirectly through +provided PyLammps and IPyLammps wrapper classes, written in Python. +These wrappers try to simplify the usage of LAMMPS in Python by +providing an object-based interface to common LAMMPS functionality. +They also reduces the amount of code necessary to parameterize LAMMPS +scripts through Python and make variables and computes directly +accessible. + +Third, LAMMPS can use the Python interpreter, so that a LAMMPS +input script can invoke Python code directly, and pass information +back-and-forth between the input script and Python functions you +write. This Python code can also callback to LAMMPS to query or change +its attributes. In Python lingo, this is "embedding" Python in +LAMMPS. When used in this mode, Python can perform operations that +the simple LAMMPS input script syntax cannot. + + diff --git a/doc/src/Python_pylammps.txt b/doc/src/Python_pylammps.txt new file mode 100644 index 0000000000..303ac21a27 --- /dev/null +++ b/doc/src/Python_pylammps.txt @@ -0,0 +1,14 @@ +"Higher level section"_Python_head.html - "LAMMPS WWW Site"_lws - +"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +PyLammps interface :h3 + +PyLammps is a Python wrapper class which can be created on its own or +use an existing lammps Python object. It has its own "Howto +pylammps"_Howto_pylammps.html doc page. diff --git a/doc/src/Python_run.txt b/doc/src/Python_run.txt new file mode 100644 index 0000000000..963248efce --- /dev/null +++ b/doc/src/Python_run.txt @@ -0,0 +1,40 @@ +"Higher level section"_Python_head.html - "LAMMPS WWW Site"_lws - +"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Run LAMMPS from Python :h3 + +The LAMMPS distribution includes a python directory with all you need +to run LAMMPS from Python. The python/lammps.py file wraps the LAMMPS +library interface, with one wrapper function per LAMMPS library +function. This file makes it is possible to do the following either +from a Python script, or interactively from a Python prompt: create +one or more instances of LAMMPS, invoke LAMMPS commands or give it an +input script, run LAMMPS incrementally, extract LAMMPS results, an +modify internal LAMMPS variables. From a Python script you can do +this in serial or parallel. Running Python interactively in parallel +does not generally work, unless you have a version of Python that +extends Python to enable multiple instances of Python to read what you +type. + +To do all of this, you must first build LAMMPS as a shared library, +then insure that your Python can find the python/lammps.py file and +the shared library. + +Two advantages of using Python to run LAMMPS are how concise the +language is, and that it can be run interactively, enabling rapid +development and debugging. If you use it to mostly invoke costly +operations within LAMMPS, such as running a simulation for a +reasonable number of timesteps, then the overhead cost of invoking +LAMMPS thru Python will be negligible. + +The Python wrapper for LAMMPS uses the "ctypes" package in Python, +which auto-generates the interface code needed between Python and a +set of C-style library functions. Ctypes is part of standard Python +for versions 2.5 and later. You can check which version of Python you +have by simply typing "python" at a shell prompt. diff --git a/doc/src/Python_shlib.txt b/doc/src/Python_shlib.txt new file mode 100644 index 0000000000..91c90d9a8f --- /dev/null +++ b/doc/src/Python_shlib.txt @@ -0,0 +1,73 @@ +"Higher level section"_Python_head.html - "LAMMPS WWW Site"_lws - +"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Build LAMMPS as a shared library :h3 + +Build LAMMPS as a shared library using make :h4 + +Instructions on how to build LAMMPS as a shared library are given on +the "Build_basics"_Build_basics.html doc page. A shared library is +one that is dynamically loadable, which is what Python requires to +wrap LAMMPS. On Linux this is a library file that ends in ".so", not +".a". + +From the src directory, type + +make foo mode=shlib :pre + +where foo is the machine target name, such as mpi or serial. +This should create the file liblammps_foo.so in the src directory, as +well as a soft link liblammps.so, which is what the Python wrapper will +load by default. Note that if you are building multiple machine +versions of the shared library, the soft link is always set to the +most recently built version. + +NOTE: If you are building LAMMPS with an MPI or FFT library or other +auxiliary libraries (used by various packages), then all of these +extra libraries must also be shared libraries. If the LAMMPS +shared-library build fails with an error complaining about this, see +the "Build_basics"_Build_basics.html doc page. + +Build LAMMPS as a shared library using CMake :h4 + +When using CMake the following two options are necessary to generate the LAMMPS +shared library: + +-D BUILD_LIB=on # enable building LAMMPS as a library +-D BUILD_SHARED_LIBS=on # enable building of LAMMPS shared library (both options are needed!) :pre + +What this does is create a liblammps.so which contains the majority of LAMMPS +code. The generated lmp binary also dynamically links to this library. This +means that either this liblammps.so file has to be in the same directory, a system +library path (e.g. /usr/lib64/) or in the LD_LIBRARY_PATH. + +If you want to use the shared library with Python the recommended way is to create a virtualenv and use it as +CMAKE_INSTALL_PREFIX. + +# create virtualenv +virtualenv --python=$(which python3) myenv3 +source myenv3/bin/activate :pre + +# build library +mkdir build +cd build +cmake -D PKG_PYTHON=on -D BUILD_LIB=on -D BUILD_SHARED_LIBS=on -D CMAKE_INSTALL_PREFIX=$VIRTUAL_ENV ../cmake +make -j 4 :pre + +# install into prefix +make install :pre + +This will also install the Python module into your virtualenv. Since virtualenv +doesn't change your LD_LIBRARY_PATH, you still need to add its lib64 folder to +it, which contains the installed liblammps.so. + +export LD_LIBRARY_PATH=$VIRTUAL_ENV/lib64:$LD_LIBRARY_PATH :pre + +Starting Python outside (!) of your build directory, but with the virtualenv +enabled and with the LD_LIBRARY_PATH set gives you access to LAMMPS via Python. diff --git a/doc/src/Python_test.txt b/doc/src/Python_test.txt new file mode 100644 index 0000000000..2bfec91bd6 --- /dev/null +++ b/doc/src/Python_test.txt @@ -0,0 +1,131 @@ +"Higher level section"_Python_head.html - "LAMMPS WWW Site"_lws - +"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Test the Python/LAMMPS interface :h3 + +To test if LAMMPS is callable from Python, launch Python interactively +and type: + +>>> from lammps import lammps +>>> lmp = lammps() :pre + +If you get no errors, you're ready to use LAMMPS from Python. If the +2nd command fails, the most common error to see is + +OSError: Could not load LAMMPS dynamic library :pre + +which means Python was unable to load the LAMMPS shared library. This +typically occurs if the system can't find the LAMMPS shared library or +one of the auxiliary shared libraries it depends on, or if something +about the library is incompatible with your Python. The error message +should give you an indication of what went wrong. + +You can also test the load directly in Python as follows, without +first importing from the lammps.py file: + +>>> from ctypes import CDLL +>>> CDLL("liblammps.so") :pre + +If an error occurs, carefully go thru the steps on the +"Build_basics"_Build_basics.html doc page about building a shared +library and the "Python_install"_Python_install.html doc page about +insuring Python can find the necessary two files it needs. + +[Test LAMMPS and Python in serial:] :h4 + +To run a LAMMPS test in serial, type these lines into Python +interactively from the bench directory: + +>>> from lammps import lammps +>>> lmp = lammps() +>>> lmp.file("in.lj") :pre + +Or put the same lines in the file test.py and run it as + +% python test.py :pre + +Either way, you should see the results of running the in.lj benchmark +on a single processor appear on the screen, the same as if you had +typed something like: + +lmp_g++ -in in.lj :pre + +[Test LAMMPS and Python in parallel:] :h4 + +To run LAMMPS in parallel, assuming you have installed the +"PyPar"_https://github.com/daleroberts/pypar package as discussed +above, create a test.py file containing these lines: + +import pypar +from lammps import lammps +lmp = lammps() +lmp.file("in.lj") +print "Proc %d out of %d procs has" % (pypar.rank(),pypar.size()),lmp +pypar.finalize() :pre + +To run LAMMPS in parallel, assuming you have installed the +"mpi4py"_https://bitbucket.org/mpi4py/mpi4py package as discussed +above, create a test.py file containing these lines: + +from mpi4py import MPI +from lammps import lammps +lmp = lammps() +lmp.file("in.lj") +me = MPI.COMM_WORLD.Get_rank() +nprocs = MPI.COMM_WORLD.Get_size() +print "Proc %d out of %d procs has" % (me,nprocs),lmp +MPI.Finalize() :pre + +You can either script in parallel as: + +% mpirun -np 4 python test.py :pre + +and you should see the same output as if you had typed + +% mpirun -np 4 lmp_g++ -in in.lj :pre + +Note that if you leave out the 3 lines from test.py that specify PyPar +commands you will instantiate and run LAMMPS independently on each of +the P processors specified in the mpirun command. In this case you +should get 4 sets of output, each showing that a LAMMPS run was made +on a single processor, instead of one set of output showing that +LAMMPS ran on 4 processors. If the 1-processor outputs occur, it +means that PyPar is not working correctly. + +Also note that once you import the PyPar module, PyPar initializes MPI +for you, and you can use MPI calls directly in your Python script, as +described in the PyPar documentation. The last line of your Python +script should be pypar.finalize(), to insure MPI is shut down +correctly. + +[Running Python scripts:] :h4 + +Note that any Python script (not just for LAMMPS) can be invoked in +one of several ways: + +% python foo.script +% python -i foo.script +% foo.script :pre + +The last command requires that the first line of the script be +something like this: + +#!/usr/local/bin/python +#!/usr/local/bin/python -i :pre + +where the path points to where you have Python installed, and that you +have made the script file executable: + +% chmod +x foo.script :pre + +Without the "-i" flag, Python will exit when the script finishes. +With the "-i" flag, you will be left in the Python interpreter when +the script finishes, so you can type subsequent commands. As +mentioned above, you can only run Python interactively when running +Python on a single processor, not in parallel. diff --git a/doc/src/Run_basics.txt b/doc/src/Run_basics.txt new file mode 100644 index 0000000000..1b7387b46b --- /dev/null +++ b/doc/src/Run_basics.txt @@ -0,0 +1,89 @@ +"Higher level section"_Run_head.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Basics of running LAMMPS :h3 + +LAMMPS is run from the command line, reading commands from a +file via the -in command line flag, or from standard input. +Using the "-in in.file" variant is recommended: + +lmp_serial < in.file +lmp_serial -in in.file +/path/to/lammps/src/lmp_serial < in.file +mpirun -np 4 lmp_mpi -in in.file +mpirun -np 8 /path/to//lammps/src/lmp_mpi -in in.file +mpirun -np 6 /usr/local/bin/lmp -in in.file :pre + +You normally run the LAMMPS command in the directory where your +input script is located. That is also where output files are +produced by default, unless you provide specific other paths in +your input script or on the command line. As in some of the +examples above, the LAMMPS executable itself can be placed elsewhere. + +NOTE: The redirection operator "<" will not always work when running +in parallel with mpirun; for those systems the -in form is required. + +As LAMMPS runs it prints info to the screen and a logfile named +log.lammps. More info about output is given on the "Run +output"_Run_output.html doc page. + +If LAMMPS encounters errors in the input script or while running a +simulation it will print an ERROR message and stop or a WARNING +message and continue. See the "Errors"_Errors.html doc page for a +discussion of the various kinds of errors LAMMPS can or can't detect, +a list of all ERROR and WARNING messages, and what to do about them. + +:line + +LAMMPS can run the same problem on any number of processors, including +a single processor. In theory you should get identical answers on any +number of processors and on any machine. In practice, numerical +round-off can cause slight differences and eventual divergence of +molecular dynamics phase space trajectories. See the "Errors +common"_Errors_common.html doc page for discussion of this. + +LAMMPS can run as large a problem as will fit in the physical memory +of one or more processors. If you run out of memory, you must run on +more processors or define a smaller problem. + +If you run LAMMPS in parallel via mpirun, you should be aware of the +"processors"_processors.html command which controls how MPI tasks are +mapped to the simulation box, as well as mpirun options that control +how MPI tasks are assigned to physical cores of the node(s) of the +machine you are running on. These settings can improve performance, +though the defaults are often adequate. + +For example, it is often important to bind MPI tasks (processes) to +physical cores (processor affinity), so that the operating system does +not migrate them during a simulation. If this is not the default +behavior on your machine, the mpirun option "--bind-to core" (OpenMPI) +or "-bind-to core" (MPICH) can be used. + +If the LAMMPS command(s) you are using support multi-threading, you +can set the number of threads per MPI task via the environment +variable OMP_NUM_THREADS, before you launch LAMMPS: + +export OMP_NUM_THREADS=2 # bash +setenv OMP_NUM_THREADS 2 # csh or tcsh :pre + +This can also be done via the "package"_package.html command or via +the "-pk command-line switch"_Run_options.html which invokes the +package command. See the "package"_package.html command or +"Speed"_Speed.html doc pages for more details about which accelerator +packages and which commands support multi-threading. + +:line + +You can experiment with running LAMMPS using any of the input scripts +provided in the examples or bench directory. Input scripts are named +in.* and sample outputs are named log.*.P where P is the number of +processors it was run on. + +Some of the examples or benchmarks require LAMMPS to be built with +optional packages. diff --git a/doc/src/Run_head.txt b/doc/src/Run_head.txt new file mode 100644 index 0000000000..5e2c0fe235 --- /dev/null +++ b/doc/src/Run_head.txt @@ -0,0 +1,38 @@ +"Previous Section"_Build.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc - "Next +Section"_Commands.html :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Run LAMMPS :h2 + +These pages explain how to run LAMMPS once you have "installed an +executable"_Install.html or "downloaded the source code"_Install.html +and "built an executable"_Build.html. The "Commands"_Commands.html +doc page describes how input scripts are structured and the commands +they can contain. + + + + + +"Basics of running LAMMPS"_Run_basics.html +"Command-line options"_Run_options.html +"Screen and logfile output"_Run_output.html +"Running LAMMPS on Windows"_Run_windows.html :all(b) + + diff --git a/doc/src/Run_options.txt b/doc/src/Run_options.txt new file mode 100644 index 0000000000..1fc00bc2e3 --- /dev/null +++ b/doc/src/Run_options.txt @@ -0,0 +1,494 @@ +"Higher level section"_Run_head.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Command-line options :h3 + +At run time, LAMMPS recognizes several optional command-line switches +which may be used in any order. Either the full word or a one-or-two +letter abbreviation can be used: + +"-e or -echo"_#echo +"-h or -help"_#help +"-i or -in"_#file +"-k or -kokkos"_#run-kokkos +"-l or -log"_#log +"-m or -mpicolor"_#mpicolor +"-nc or -nocite"_#nocite +"-pk or -package"_#package +"-p or -partition"_#partition +"-pl or -plog"_#plog +"-ps or -pscreen"_#pscreen +"-r or -restart"_#restart +"-ro or -reorder"_#reorder +"-sc or -screen"_#screen +"-sf or -suffix"_#suffix +"-v or -var"_#var :ul + +For example, the lmp_mpi executable might be launched as follows: + +mpirun -np 16 lmp_mpi -v f tmp.out -l my.log -sc none -i in.alloy +mpirun -np 16 lmp_mpi -var f tmp.out -log my.log -screen none -in in.alloy :pre + +:line + +[-echo style] :link(echo) + +Set the style of command echoing. The style can be {none} or {screen} +or {log} or {both}. Depending on the style, each command read from +the input script will be echoed to the screen and/or logfile. This +can be useful to figure out which line of your script is causing an +input error. The default value is {log}. The echo style can also be +set by using the "echo"_echo.html command in the input script itself. + +:line + +[-help] :link(help) + +Print a brief help summary and a list of options compiled into this +executable for each LAMMPS style (atom_style, fix, compute, +pair_style, bond_style, etc). This can tell you if the command you +want to use was included via the appropriate package at compile time. +LAMMPS will print the info and immediately exit if this switch is +used. + +:line + +[-in file] :link(file) + +Specify a file to use as an input script. This is an optional switch +when running LAMMPS in one-partition mode. If it is not specified, +LAMMPS reads its script from standard input, typically from a script +via I/O redirection; e.g. lmp_linux < in.run. I/O redirection should +also work in parallel, but if it does not (in the unlikely case that +an MPI implementation does not support it), then use the -in flag. +Note that this is a required switch when running LAMMPS in +multi-partition mode, since multiple processors cannot all read from +stdin. + +:line + +[-kokkos on/off keyword/value ...] :link(run-kokkos) + +Explicitly enable or disable KOKKOS support, as provided by the KOKKOS +package. Even if LAMMPS is built with this package, as described +in "Speed kokkos"_Speed_kokkos.html, this switch must be set to enable +running with the KOKKOS-enabled styles the package provides. If the +switch is not set (the default), LAMMPS will operate as if the KOKKOS +package were not installed; i.e. you can run standard LAMMPS or with +the GPU or USER-OMP packages, for testing or benchmarking purposes. + +Additional optional keyword/value pairs can be specified which +determine how Kokkos will use the underlying hardware on your +platform. These settings apply to each MPI task you launch via the +"mpirun" or "mpiexec" command. You may choose to run one or more MPI +tasks per physical node. Note that if you are running on a desktop +machine, you typically have one physical node. On a cluster or +supercomputer there may be dozens or 1000s of physical nodes. + +Either the full word or an abbreviation can be used for the keywords. +Note that the keywords do not use a leading minus sign. I.e. the +keyword is "t", not "-t". Also note that each of the keywords has a +default setting. Examples of when to use these options and what +settings to use on different platforms is given on the "Speed +kokkos"_Speed_kokkos.html doc page. + +d or device +g or gpus +t or threads +n or numa :ul + +device Nd :pre + +This option is only relevant if you built LAMMPS with CUDA=yes, you +have more than one GPU per node, and if you are running with only one +MPI task per node. The Nd setting is the ID of the GPU on the node to +run on. By default Nd = 0. If you have multiple GPUs per node, they +have consecutive IDs numbered as 0,1,2,etc. This setting allows you +to launch multiple independent jobs on the node, each with a single +MPI task per node, and assign each job to run on a different GPU. + +gpus Ng Ns :pre + +This option is only relevant if you built LAMMPS with CUDA=yes, you +have more than one GPU per node, and you are running with multiple MPI +tasks per node (up to one per GPU). The Ng setting is how many GPUs +you will use. The Ns setting is optional. If set, it is the ID of a +GPU to skip when assigning MPI tasks to GPUs. This may be useful if +your desktop system reserves one GPU to drive the screen and the rest +are intended for computational work like running LAMMPS. By default +Ng = 1 and Ns is not set. + +Depending on which flavor of MPI you are running, LAMMPS will look for +one of these 3 environment variables + +SLURM_LOCALID (various MPI variants compiled with SLURM support) +MV2_COMM_WORLD_LOCAL_RANK (Mvapich) +OMPI_COMM_WORLD_LOCAL_RANK (OpenMPI) :pre + +which are initialized by the "srun", "mpirun" or "mpiexec" commands. +The environment variable setting for each MPI rank is used to assign a +unique GPU ID to the MPI task. + +threads Nt :pre + +This option assigns Nt number of threads to each MPI task for +performing work when Kokkos is executing in OpenMP or pthreads mode. +The default is Nt = 1, which essentially runs in MPI-only mode. If +there are Np MPI tasks per physical node, you generally want Np*Nt = +the number of physical cores per node, to use your available hardware +optimally. This also sets the number of threads used by the host when +LAMMPS is compiled with CUDA=yes. + +numa Nm :pre + +This option is only relevant when using pthreads with hwloc support. +In this case Nm defines the number of NUMA regions (typically sockets) +on a node which will be utilized by a single MPI rank. By default Nm += 1. If this option is used the total number of worker-threads per +MPI rank is threads*numa. Currently it is always almost better to +assign at least one MPI rank per NUMA region, and leave numa set to +its default value of 1. This is because letting a single process span +multiple NUMA regions induces a significant amount of cross NUMA data +traffic which is slow. + +:line + +[-log file] :link(log) + +Specify a log file for LAMMPS to write status information to. In +one-partition mode, if the switch is not used, LAMMPS writes to the +file log.lammps. If this switch is used, LAMMPS writes to the +specified file. In multi-partition mode, if the switch is not used, a +log.lammps file is created with hi-level status information. Each +partition also writes to a log.lammps.N file where N is the partition +ID. If the switch is specified in multi-partition mode, the hi-level +logfile is named "file" and each partition also logs information to a +file.N. For both one-partition and multi-partition mode, if the +specified file is "none", then no log files are created. Using a +"log"_log.html command in the input script will override this setting. +Option -plog will override the name of the partition log files file.N. + +:line + +[-mpicolor] color :link(mpicolor) + +If used, this must be the first command-line argument after the LAMMPS +executable name. It is only used when LAMMPS is launched by an mpirun +command which also launches another executable(s) at the same time. +(The other executable could be LAMMPS as well.) The color is an +integer value which should be different for each executable (another +application may set this value in a different way). LAMMPS and the +other executable(s) perform an MPI_Comm_split() with their own colors +to shrink the MPI_COMM_WORLD communication to be the subset of +processors they are actually running on. + +Currently, this is only used in LAMMPS to perform client/server +messaging with another application. LAMMPS can act as either a client +or server (or both). More details are given on the "Howto +client/server"_Howto_client_server.html doc page. + +Specifically, this refers to the "mpi/one" mode of messaging provided +by the "message"_message.html command and the CSlib library LAMMPS +links with from the lib/message directory. See the +"message"_message.html command for more details. + +:line + +[-nocite] :link(nocite) + +Disable writing the log.cite file which is normally written to list +references for specific cite-able features used during a LAMMPS run. +See the "citation page"_http://lammps.sandia.gov/cite.html for more +details. + +:line + +[-package style args ....] :link(package) + +Invoke the "package"_package.html command with style and args. The +syntax is the same as if the command appeared at the top of the input +script. For example "-package gpu 2" or "-pk gpu 2" is the same as +"package gpu 2"_package.html in the input script. The possible styles +and args are documented on the "package"_package.html doc page. This +switch can be used multiple times, e.g. to set options for the +USER-INTEL and USER-OMP packages which can be used together. + +Along with the "-suffix" command-line switch, this is a convenient +mechanism for invoking accelerator packages and their options without +having to edit an input script. + +:line + +[-partition 8x2 4 5 ...] :link(partition) + +Invoke LAMMPS in multi-partition mode. When LAMMPS is run on P +processors and this switch is not used, LAMMPS runs in one partition, +i.e. all P processors run a single simulation. If this switch is +used, the P processors are split into separate partitions and each +partition runs its own simulation. The arguments to the switch +specify the number of processors in each partition. Arguments of the +form MxN mean M partitions, each with N processors. Arguments of the +form N mean a single partition with N processors. The sum of +processors in all partitions must equal P. Thus the command +"-partition 8x2 4 5" has 10 partitions and runs on a total of 25 +processors. + +Running with multiple partitions can be useful for running +"multi-replica simulations"_Howto_replica.html, where each replica +runs on on one or a few processors. Note that with MPI installed on a +machine (e.g. your desktop), you can run on more (virtual) processors +than you have physical processors. + +To run multiple independent simulations from one input script, using +multiple partitions, see the "Howto multiple"_Howto_multiple.html doc +page. World- and universe-style "variables"_variable.html are useful +in this context. + +:line + +[-plog file] :link(plog) + +Specify the base name for the partition log files, so partition N +writes log information to file.N. If file is none, then no partition +log files are created. This overrides the filename specified in the +-log command-line option. This option is useful when working with +large numbers of partitions, allowing the partition log files to be +suppressed (-plog none) or placed in a sub-directory (-plog +replica_files/log.lammps) If this option is not used the log file for +partition N is log.lammps.N or whatever is specified by the -log +command-line option. + +:line + +[-pscreen file] :link(pscreen) + +Specify the base name for the partition screen file, so partition N +writes screen information to file.N. If file is none, then no +partition screen files are created. This overrides the filename +specified in the -screen command-line option. This option is useful +when working with large numbers of partitions, allowing the partition +screen files to be suppressed (-pscreen none) or placed in a +sub-directory (-pscreen replica_files/screen). If this option is not +used the screen file for partition N is screen.N or whatever is +specified by the -screen command-line option. + +:line + +[-restart restartfile {remap} datafile keyword value ...] :link(restart) + +Convert the restart file into a data file and immediately exit. This +is the same operation as if the following 2-line input script were +run: + +read_restart restartfile {remap} +write_data datafile keyword value ... :pre + +Note that the specified restartfile and datafile can have wild-card +characters ("*",%") as described by the +"read_restart"_read_restart.html and "write_data"_write_data.html +commands. But a filename such as file.* will need to be enclosed in +quotes to avoid shell expansion of the "*" character. + +Note that following restartfile, the optional flag {remap} can be +used. This has the same effect as adding it to the +"read_restart"_read_restart.html command, as explained on its doc +page. This is only useful if the reading of the restart file triggers +an error that atoms have been lost. In that case, use of the remap +flag should allow the data file to still be produced. + +Also note that following datafile, the same optional keyword/value +pairs can be listed as used by the "write_data"_write_data.html +command. + +:line + +[-reorder] :link(reorder) + +This option has 2 forms: + +-reorder nth N +-reorder custom filename :pre + +Reorder the processors in the MPI communicator used to instantiate +LAMMPS, in one of several ways. The original MPI communicator ranks +all P processors from 0 to P-1. The mapping of these ranks to +physical processors is done by MPI before LAMMPS begins. It may be +useful in some cases to alter the rank order. E.g. to insure that +cores within each node are ranked in a desired order. Or when using +the "run_style verlet/split"_run_style.html command with 2 partitions +to insure that a specific Kspace processor (in the 2nd partition) is +matched up with a specific set of processors in the 1st partition. +See the "Speed tips"_Speed_tips.html doc page for more details. + +If the keyword {nth} is used with a setting {N}, then it means every +Nth processor will be moved to the end of the ranking. This is useful +when using the "run_style verlet/split"_run_style.html command with 2 +partitions via the -partition command-line switch. The first set of +processors will be in the first partition, the 2nd set in the 2nd +partition. The -reorder command-line switch can alter this so that +the 1st N procs in the 1st partition and one proc in the 2nd partition +will be ordered consecutively, e.g. as the cores on one physical node. +This can boost performance. For example, if you use "-reorder nth 4" +and "-partition 9 3" and you are running on 12 processors, the +processors will be reordered from + +0 1 2 3 4 5 6 7 8 9 10 11 :pre + +to + +0 1 2 4 5 6 8 9 10 3 7 11 :pre + +so that the processors in each partition will be + +0 1 2 4 5 6 8 9 10 +3 7 11 :pre + +See the "processors" command for how to insure processors from each +partition could then be grouped optimally for quad-core nodes. + +If the keyword is {custom}, then a file that specifies a permutation +of the processor ranks is also specified. The format of the reorder +file is as follows. Any number of initial blank or comment lines +(starting with a "#" character) can be present. These should be +followed by P lines of the form: + +I J :pre + +where P is the number of processors LAMMPS was launched with. Note +that if running in multi-partition mode (see the -partition switch +above) P is the total number of processors in all partitions. The I +and J values describe a permutation of the P processors. Every I and +J should be values from 0 to P-1 inclusive. In the set of P I values, +every proc ID should appear exactly once. Ditto for the set of P J +values. A single I,J pairing means that the physical processor with +rank I in the original MPI communicator will have rank J in the +reordered communicator. + +Note that rank ordering can also be specified by many MPI +implementations, either by environment variables that specify how to +order physical processors, or by config files that specify what +physical processors to assign to each MPI rank. The -reorder switch +simply gives you a portable way to do this without relying on MPI +itself. See the "processors out"_processors.html command for how +to output info on the final assignment of physical processors to +the LAMMPS simulation domain. + +:line + +[-screen file] :link(screen) + +Specify a file for LAMMPS to write its screen information to. In +one-partition mode, if the switch is not used, LAMMPS writes to the +screen. If this switch is used, LAMMPS writes to the specified file +instead and you will see no screen output. In multi-partition mode, +if the switch is not used, hi-level status information is written to +the screen. Each partition also writes to a screen.N file where N is +the partition ID. If the switch is specified in multi-partition mode, +the hi-level screen dump is named "file" and each partition also +writes screen information to a file.N. For both one-partition and +multi-partition mode, if the specified file is "none", then no screen +output is performed. Option -pscreen will override the name of the +partition screen files file.N. + +:line + +[-suffix style args] :link(suffix) + +Use variants of various styles if they exist. The specified style can +be {cuda}, {gpu}, {intel}, {kk}, {omp}, {opt}, or {hybrid}. These +refer to optional packages that LAMMPS can be built with, as described +in "Accelerate performance"_Speed.html. The "gpu" style corresponds to the +GPU package, the "intel" style to the USER-INTEL package, the "kk" +style to the KOKKOS package, the "opt" style to the OPT package, and +the "omp" style to the USER-OMP package. The hybrid style is the only +style that accepts arguments. It allows for two packages to be +specified. The first package specified is the default and will be used +if it is available. If no style is available for the first package, +the style for the second package will be used if available. For +example, "-suffix hybrid intel omp" will use styles from the +USER-INTEL package if they are installed and available, but styles for +the USER-OMP package otherwise. + +Along with the "-package" command-line switch, this is a convenient +mechanism for invoking accelerator packages and their options without +having to edit an input script. + +As an example, all of the packages provide a "pair_style +lj/cut"_pair_lj.html variant, with style names lj/cut/gpu, +lj/cut/intel, lj/cut/kk, lj/cut/omp, and lj/cut/opt. A variant style +can be specified explicitly in your input script, e.g. pair_style +lj/cut/gpu. If the -suffix switch is used the specified suffix +(gpu,intel,kk,omp,opt) is automatically appended whenever your input +script command creates a new "atom"_atom_style.html, +"pair"_pair_style.html, "fix"_fix.html, "compute"_compute.html, or +"run"_run_style.html style. If the variant version does not exist, +the standard version is created. + +For the GPU package, using this command-line switch also invokes the +default GPU settings, as if the command "package gpu 1" were used at +the top of your input script. These settings can be changed by using +the "-package gpu" command-line switch or the "package +gpu"_package.html command in your script. + +For the USER-INTEL package, using this command-line switch also +invokes the default USER-INTEL settings, as if the command "package +intel 1" were used at the top of your input script. These settings +can be changed by using the "-package intel" command-line switch or +the "package intel"_package.html command in your script. If the +USER-OMP package is also installed, the hybrid style with "intel omp" +arguments can be used to make the omp suffix a second choice, if a +requested style is not available in the USER-INTEL package. It will +also invoke the default USER-OMP settings, as if the command "package +omp 0" were used at the top of your input script. These settings can +be changed by using the "-package omp" command-line switch or the +"package omp"_package.html command in your script. + +For the KOKKOS package, using this command-line switch also invokes +the default KOKKOS settings, as if the command "package kokkos" were +used at the top of your input script. These settings can be changed +by using the "-package kokkos" command-line switch or the "package +kokkos"_package.html command in your script. + +For the OMP package, using this command-line switch also invokes the +default OMP settings, as if the command "package omp 0" were used at +the top of your input script. These settings can be changed by using +the "-package omp" command-line switch or the "package +omp"_package.html command in your script. + +The "suffix"_suffix.html command can also be used within an input +script to set a suffix, or to turn off or back on any suffix setting +made via the command line. + +:line + +[-var name value1 value2 ...] :link(var) + +Specify a variable that will be defined for substitution purposes when +the input script is read. This switch can be used multiple times to +define multiple variables. "Name" is the variable name which can be a +single character (referenced as $x in the input script) or a full +string (referenced as $\{abc\}). An "index-style +variable"_variable.html will be created and populated with the +subsequent values, e.g. a set of filenames. Using this command-line +option is equivalent to putting the line "variable name index value1 +value2 ..." at the beginning of the input script. Defining an index +variable as a command-line argument overrides any setting for the same +index variable in the input script, since index variables cannot be +re-defined. + +See the "variable"_variable.html command for more info on defining +index and other kinds of variables and the "Commands +parse"_Commands_parse.html page for more info on using variables in +input scripts. + +NOTE: Currently, the command-line parser looks for arguments that +start with "-" to indicate new switches. Thus you cannot specify +multiple variable values if any of them start with a "-", e.g. a +negative numeric value. It is OK if the first value1 starts with a +"-", since it is automatically skipped. diff --git a/doc/src/Run_output.txt b/doc/src/Run_output.txt new file mode 100644 index 0000000000..7d5a9e6ae6 --- /dev/null +++ b/doc/src/Run_output.txt @@ -0,0 +1,176 @@ +"Higher level section"_Run_head.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Screen and logfile output :h3 + +As LAMMPS reads an input script, it prints information to both the +screen and a log file about significant actions it takes to setup a +simulation. When the simulation is ready to begin, LAMMPS performs +various initializations, and prints info about the run it is about to +perform, including the amount of memory (in MBytes per processor) that +the simulation requires. It also prints details of the initial +thermodynamic state of the system. During the run itself, +thermodynamic information is printed periodically, every few +timesteps. When the run concludes, LAMMPS prints the final +thermodynamic state and a total run time for the simulation. It also +appends statistics about the CPU time and storage requirements for the +simulation. An example set of statistics is shown here: + +Loop time of 2.81192 on 4 procs for 300 steps with 2004 atoms :pre + +Performance: 18.436 ns/day 1.302 hours/ns 106.689 timesteps/s +97.0% CPU use with 4 MPI tasks x no OpenMP threads :pre + +MPI task timings breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.9808 | 2.0134 | 2.0318 | 1.4 | 71.60 +Bond | 0.0021894 | 0.0060319 | 0.010058 | 4.7 | 0.21 +Kspace | 0.3207 | 0.3366 | 0.36616 | 3.1 | 11.97 +Neigh | 0.28411 | 0.28464 | 0.28516 | 0.1 | 10.12 +Comm | 0.075732 | 0.077018 | 0.07883 | 0.4 | 2.74 +Output | 0.00030518 | 0.00042665 | 0.00078821 | 1.0 | 0.02 +Modify | 0.086606 | 0.086631 | 0.086668 | 0.0 | 3.08 +Other | | 0.007178 | | | 0.26 :pre + +Nlocal: 501 ave 508 max 490 min +Histogram: 1 0 0 0 0 0 1 1 0 1 +Nghost: 6586.25 ave 6628 max 6548 min +Histogram: 1 0 1 0 0 0 1 0 0 1 +Neighs: 177007 ave 180562 max 170212 min +Histogram: 1 0 0 0 0 0 0 1 1 1 :pre + +Total # of neighbors = 708028 +Ave neighs/atom = 353.307 +Ave special neighs/atom = 2.34032 +Neighbor list builds = 26 +Dangerous builds = 0 :pre + +:line + +The first section provides a global loop timing summary. The {loop +time} is the total wall-clock time for the simulation to run. The +{Performance} line is provided for convenience to help predict how +long it will take to run a desired physical simulation. The {CPU use} +line provides the CPU utilization per MPI task; it should be close to +100% times the number of OpenMP threads (or 1 of not using OpenMP). +Lower numbers correspond to delays due to file I/O or insufficient +thread utilization. + +:line + +The {MPI task} section gives the breakdown of the CPU run time (in +seconds) into major categories: + +{Pair} = non-bonded force computations +{Bond} = bonded interactions: bonds, angles, dihedrals, impropers +{Kspace} = long-range interactions: Ewald, PPPM, MSM +{Neigh} = neighbor list construction +{Comm} = inter-processor communication of atoms and their properties +{Output} = output of thermodynamic info and dump files +{Modify} = fixes and computes invoked by fixes +{Other} = all the remaining time :ul + +For each category, there is a breakdown of the least, average and most +amount of wall time any processor spent on this category of +computation. The "%varavg" is the percentage by which the max or min +varies from the average. This is an indication of load imbalance. A +percentage close to 0 is perfect load balance. A large percentage is +imbalance. The final "%total" column is the percentage of the total +loop time is spent in this category. + +When using the "timer full"_timer.html setting, an additional column +is added that also prints the CPU utilization in percent. In addition, +when using {timer full} and the "package omp"_package.html command are +active, a similar timing summary of time spent in threaded regions to +monitor thread utilization and load balance is provided. A new {Thread +timings} section is also added, which lists the time spent in reducing +the per-thread data elements to the storage for non-threaded +computation. These thread timings are measured for the first MPI rank +only and and thus, because the breakdown for MPI tasks can change from +MPI rank to MPI rank, this breakdown can be very different for +individual ranks. Here is an example output for this section: + +Thread timings breakdown (MPI rank 0): +Total threaded time 0.6846 / 90.6% +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.5127 | 0.5147 | 0.5167 | 0.3 | 75.18 +Bond | 0.0043139 | 0.0046779 | 0.0050418 | 0.5 | 0.68 +Kspace | 0.070572 | 0.074541 | 0.07851 | 1.5 | 10.89 +Neigh | 0.084778 | 0.086969 | 0.089161 | 0.7 | 12.70 +Reduce | 0.0036485 | 0.003737 | 0.0038254 | 0.1 | 0.55 :pre + +:line + +The third section above lists the number of owned atoms (Nlocal), +ghost atoms (Nghost), and pair-wise neighbors stored per processor. +The max and min values give the spread of these values across +processors with a 10-bin histogram showing the distribution. The total +number of histogram counts is equal to the number of processors. + +:line + +The last section gives aggregate statistics (across all processors) +for pair-wise neighbors and special neighbors that LAMMPS keeps track +of (see the "special_bonds"_special_bonds.html command). The number +of times neighbor lists were rebuilt is tallied, as is the number of +potentially {dangerous} rebuilds. If atom movement triggered neighbor +list rebuilding (see the "neigh_modify"_neigh_modify.html command), +then dangerous reneighborings are those that were triggered on the +first timestep atom movement was checked for. If this count is +non-zero you may wish to reduce the delay factor to insure no force +interactions are missed by atoms moving beyond the neighbor skin +distance before a rebuild takes place. + +:line + +If an energy minimization was performed via the +"minimize"_minimize.html command, additional information is printed, +e.g. + +Minimization stats: + Stopping criterion = linesearch alpha is zero + Energy initial, next-to-last, final = + -6372.3765206 -8328.46998942 -8328.46998942 + Force two-norm initial, final = 1059.36 5.36874 + Force max component initial, final = 58.6026 1.46872 + Final line search alpha, max atom move = 2.7842e-10 4.0892e-10 + Iterations, force evaluations = 701 1516 :pre + +The first line prints the criterion that determined minimization was +converged. The next line lists the initial and final energy, as well +as the energy on the next-to-last iteration. The next 2 lines give a +measure of the gradient of the energy (force on all atoms). The +2-norm is the "length" of this 3N-component force vector; the largest +component (x, y, or z) of force (infinity-norm) is also given. Then +information is provided about the line search and statistics on how +many iterations and force-evaluations the minimizer required. +Multiple force evaluations are typically done at each iteration to +perform a 1d line minimization in the search direction. See the +"minimize"_minimize.html doc page for more details. + +:line + +If a "kspace_style"_kspace_style.html long-range Coulombics solver +that performs FFTs was used during the run (PPPM, Ewald), then +additional information is printed, e.g. + +FFT time (% of Kspce) = 0.200313 (8.34477) +FFT Gflps 3d 1d-only = 2.31074 9.19989 :pre + +The first line is the time spent doing 3d FFTs (several per timestep) +and the fraction it represents of the total KSpace time (listed +above). Each 3d FFT requires computation (3 sets of 1d FFTs) and +communication (transposes). The total flops performed is 5Nlog_2(N), +where N is the number of points in the 3d grid. The FFTs are timed +with and without the communication and a Gflop rate is computed. The +3d rate is with communication; the 1d rate is without (just the 1d +FFTs). Thus you can estimate what fraction of your FFT time was spent +in communication, roughly 75% in the example above. diff --git a/doc/src/Run_windows.txt b/doc/src/Run_windows.txt new file mode 100644 index 0000000000..85c9a6550d --- /dev/null +++ b/doc/src/Run_windows.txt @@ -0,0 +1,73 @@ +"Higher level section"_Run_head.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Running LAMMPS on Windows :h3 + +To run a serial (non-MPI) executable, follow these steps: + +Get a command prompt by going to Start->Run... , +then typing "cmd". :ulb,l + +Move to the directory where you have your input script, +(e.g. by typing: cd "Documents"). :l + +At the command prompt, type "lmp_serial -in in.file", where +in.file is the name of your LAMMPS input script. :l,ule + +Note that the serial executable includes support for multi-threading +parallelization from the styles in the USER-OMP packages. To run with +4 threads, you can type this: + +lmp_serial -in in.lj -pk omp 4 -sf omp :pre + +:line + +For the MPI executable, which allows you to run LAMMPS under Windows +in parallel, follow these steps. + +Download and install a compatible MPI library binary package: + +for 32-bit Windows: "mpich2-1.4.1p1-win-ia32.msi"_http://download.lammps.org/thirdparty/mpich2-1.4.1p1-win-ia32.msi +for 64-bit Windows: "mpich2-1.4.1p1-win-x86-64.msi"_http://download.lammps.org/thirdparty/mpich2-1.4.1p1-win-x86-64.msi :ul + +The LAMMPS Windows installer packages will automatically adjust your +path for the default location of this MPI package. After the +installation of the MPICH2 software, it needs to be integrated into +the system. For this you need to start a Command Prompt in +{Administrator Mode} (right click on the icon and select it). Change +into the MPICH2 installation directory, then into the subdirectory +[bin] and execute [smpd.exe -install]. Exit the command window. + +Get a new, regular command prompt by going to Start->Run... , +then typing "cmd". :ulb,l + +Move to the directory where you have your input file +(e.g. by typing: cd "Documents"). :l,ule + +Then type something like this: + +mpiexec -localonly 4 lmp_mpi -in in.file +mpiexec -np 4 lmp_mpi -in in.file :pre + +where in.file is the name of your LAMMPS input script. For the latter +case, you may be prompted to enter your password. + +In this mode, output may not immediately show up on the screen, so if +your input script takes a long time to execute, you may need to be +patient before the output shows up. + +The parallel executable can also run on a single processor by typing +something like this: + +lmp_mpi -in in.lj :pre + +Note that the parallel executable also includes OpenMP +multi-threading, which can be combined with MPI using something like: + +mpiexec -localonly 2 lmp_mpi -in in.lj -pk omp 2 -sf omp :pre diff --git a/doc/src/Section_accelerate.txt b/doc/src/Section_accelerate.txt deleted file mode 100644 index d5cbf77a84..0000000000 --- a/doc/src/Section_accelerate.txt +++ /dev/null @@ -1,391 +0,0 @@ -"Previous Section"_Section_packages.html - "LAMMPS WWW Site"_lws - -"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next -Section"_Section_howto.html :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Section_commands.html#comm) - -:line - -5. Accelerating LAMMPS performance :h2 - -This section describes various methods for improving LAMMPS -performance for different classes of problems running on different -kinds of machines. - -There are two thrusts to the discussion that follows. The -first is using code options that implement alternate algorithms -that can speed-up a simulation. The second is to use one -of the several accelerator packages provided with LAMMPS that -contain code optimized for certain kinds of hardware, including -multi-core CPUs, GPUs, and Intel Xeon Phi coprocessors. - -5.1 "Measuring performance"_#acc_1 :ulb,l -5.2 "Algorithms and code options to boost performace"_#acc_2 :l -5.3 "Accelerator packages with optimized styles"_#acc_3 :l - 5.3.1 "GPU package"_accelerate_gpu.html :l - 5.3.2 "USER-INTEL package"_accelerate_intel.html :l - 5.3.3 "KOKKOS package"_accelerate_kokkos.html :l - 5.3.4 "USER-OMP package"_accelerate_omp.html :l - 5.3.5 "OPT package"_accelerate_opt.html :l -5.4 "Comparison of various accelerator packages"_#acc_4 :l -:ule - -The "Benchmark page"_http://lammps.sandia.gov/bench.html of the LAMMPS -web site gives performance results for the various accelerator -packages discussed in Section 5.2, for several of the standard LAMMPS -benchmark problems, as a function of problem size and number of -compute nodes, on different hardware platforms. - -:line -:line - -5.1 Measuring performance :h3,link(acc_1) - -Before trying to make your simulation run faster, you should -understand how it currently performs and where the bottlenecks are. - -The best way to do this is run the your system (actual number of -atoms) for a modest number of timesteps (say 100 steps) on several -different processor counts, including a single processor if possible. -Do this for an equilibrium version of your system, so that the -100-step timings are representative of a much longer run. There is -typically no need to run for 1000s of timesteps to get accurate -timings; you can simply extrapolate from short runs. - -For the set of runs, look at the timing data printed to the screen and -log file at the end of each LAMMPS run. "This -section"_Section_start.html#start_7 of the manual has an overview. - -Running on one (or a few processors) should give a good estimate of -the serial performance and what portions of the timestep are taking -the most time. Running the same problem on a few different processor -counts should give an estimate of parallel scalability. I.e. if the -simulation runs 16x faster on 16 processors, its 100% parallel -efficient; if it runs 8x faster on 16 processors, it's 50% efficient. - -The most important data to look at in the timing info is the timing -breakdown and relative percentages. For example, trying different -options for speeding up the long-range solvers will have little impact -if they only consume 10% of the run time. If the pairwise time is -dominating, you may want to look at GPU or OMP versions of the pair -style, as discussed below. Comparing how the percentages change as -you increase the processor count gives you a sense of how different -operations within the timestep are scaling. Note that if you are -running with a Kspace solver, there is additional output on the -breakdown of the Kspace time. For PPPM, this includes the fraction -spent on FFTs, which can be communication intensive. - -Another important detail in the timing info are the histograms of -atoms counts and neighbor counts. If these vary widely across -processors, you have a load-imbalance issue. This often results in -inaccurate relative timing data, because processors have to wait when -communication occurs for other processors to catch up. Thus the -reported times for "Communication" or "Other" may be higher than they -really are, due to load-imbalance. If this is an issue, you can -uncomment the MPI_Barrier() lines in src/timer.cpp, and recompile -LAMMPS, to obtain synchronized timings. - -:line - -5.2 General strategies :h3,link(acc_2) - -NOTE: this section 5.2 is still a work in progress - -Here is a list of general ideas for improving simulation performance. -Most of them are only applicable to certain models and certain -bottlenecks in the current performance, so let the timing data you -generate be your guide. It is hard, if not impossible, to predict how -much difference these options will make, since it is a function of -problem size, number of processors used, and your machine. There is -no substitute for identifying performance bottlenecks, and trying out -various options. - -rRESPA -2-FFT PPPM -Staggered PPPM -single vs double PPPM -partial charge PPPM -verlet/split run style -processor command for proc layout and numa layout -load-balancing: balance and fix balance :ul - -2-FFT PPPM, also called {analytic differentiation} or {ad} PPPM, uses -2 FFTs instead of the 4 FFTs used by the default {ik differentiation} -PPPM. However, 2-FFT PPPM also requires a slightly larger mesh size to -achieve the same accuracy as 4-FFT PPPM. For problems where the FFT -cost is the performance bottleneck (typically large problems running -on many processors), 2-FFT PPPM may be faster than 4-FFT PPPM. - -Staggered PPPM performs calculations using two different meshes, one -shifted slightly with respect to the other. This can reduce force -aliasing errors and increase the accuracy of the method, but also -doubles the amount of work required. For high relative accuracy, using -staggered PPPM allows one to half the mesh size in each dimension as -compared to regular PPPM, which can give around a 4x speedup in the -kspace time. However, for low relative accuracy, using staggered PPPM -gives little benefit and can be up to 2x slower in the kspace -time. For example, the rhodopsin benchmark was run on a single -processor, and results for kspace time vs. relative accuracy for the -different methods are shown in the figure below. For this system, -staggered PPPM (using ik differentiation) becomes useful when using a -relative accuracy of slightly greater than 1e-5 and above. - -:c,image(JPG/rhodo_staggered.jpg) - -NOTE: Using staggered PPPM may not give the same increase in accuracy -of energy and pressure as it does in forces, so some caution must be -used if energy and/or pressure are quantities of interest, such as -when using a barostat. - -:line - -5.3 Packages with optimized styles :h3,link(acc_3) - -Accelerated versions of various "pair_style"_pair_style.html, -"fixes"_fix.html, "computes"_compute.html, and other commands have -been added to LAMMPS, which will typically run faster than the -standard non-accelerated versions. Some require appropriate hardware -to be present on your system, e.g. GPUs or Intel Xeon Phi -coprocessors. - -All of these commands are in packages provided with LAMMPS. An -overview of packages is give in "Section -packages"_Section_packages.html. - -These are the accelerator packages -currently in LAMMPS, either as standard or user packages: - -"GPU Package"_accelerate_gpu.html : for NVIDIA GPUs as well as OpenCL support -"USER-INTEL Package"_accelerate_intel.html : for Intel CPUs and Intel Xeon Phi -"KOKKOS Package"_accelerate_kokkos.html : for Nvidia GPUs, Intel Xeon Phi, and OpenMP threading -"USER-OMP Package"_accelerate_omp.html : for OpenMP threading and generic CPU optimizations -"OPT Package"_accelerate_opt.html : generic CPU optimizations :tb(s=:) - - - -Inverting this list, LAMMPS currently has acceleration support for -three kinds of hardware, via the listed packages: - -Many-core CPUs : "USER-INTEL"_accelerate_intel.html, "KOKKOS"_accelerate_kokkos.html, "USER-OMP"_accelerate_omp.html, "OPT"_accelerate_opt.html packages -NVIDIA GPUs : "GPU"_accelerate_gpu.html, "KOKKOS"_accelerate_kokkos.html packages -Intel Phi : "USER-INTEL"_accelerate_intel.html, "KOKKOS"_accelerate_kokkos.html packages :tb(s=:) - -Which package is fastest for your hardware may depend on the size -problem you are running and what commands (accelerated and -non-accelerated) are invoked by your input script. While these doc -pages include performance guidelines, there is no substitute for -trying out the different packages appropriate to your hardware. - -Any accelerated style has the same name as the corresponding standard -style, except that a suffix is appended. Otherwise, the syntax for -the command that uses the style is identical, their functionality is -the same, and the numerical results it produces should also be the -same, except for precision and round-off effects. - -For example, all of these styles are accelerated variants of the -Lennard-Jones "pair_style lj/cut"_pair_lj.html: - -"pair_style lj/cut/gpu"_pair_lj.html -"pair_style lj/cut/intel"_pair_lj.html -"pair_style lj/cut/kk"_pair_lj.html -"pair_style lj/cut/omp"_pair_lj.html -"pair_style lj/cut/opt"_pair_lj.html :ul - -To see what accelerate styles are currently available, see -"Section 3.5"_Section_commands.html#cmd_5 of the manual. The -doc pages for individual commands (e.g. "pair lj/cut"_pair_lj.html or -"fix nve"_fix_nve.html) also list any accelerated variants available -for that style. - -To use an accelerator package in LAMMPS, and one or more of the styles -it provides, follow these general steps. Details vary from package to -package and are explained in the individual accelerator doc pages, -listed above: - -build the accelerator library | - only for GPU package | -install the accelerator package | - make yes-opt, make yes-user-intel, etc | -add compile/link flags to Makefile.machine in src/MAKE | - only for USER-INTEL, KOKKOS, USER-OMP, OPT packages | -re-build LAMMPS | - make machine | -prepare and test a regular LAMMPS simulation | - lmp_machine -in in.script; mpirun -np 32 lmp_machine -in in.script | -enable specific accelerator support via '-k on' "command-line switch"_Section_start.html#start_6, | - only needed for KOKKOS package | -set any needed options for the package via "-pk" "command-line switch"_Section_start.html#start_6 or "package"_package.html command, | - only if defaults need to be changed | -use accelerated styles in your input via "-sf" "command-line switch"_Section_start.html#start_6 or "suffix"_suffix.html command | lmp_machine -in in.script -sf gpu -:tb(c=2,s=|) - -Note that the first 4 steps can be done as a single command with -suitable make command invocations. This is discussed in "Section -4"_Section_packages.html of the manual, and its use is -illustrated in the individual accelerator sections. Typically these -steps only need to be done once, to create an executable that uses one -or more accelerator packages. - -The last 4 steps can all be done from the command-line when LAMMPS is -launched, without changing your input script, as illustrated in the -individual accelerator sections. Or you can add -"package"_package.html and "suffix"_suffix.html commands to your input -script. - -NOTE: With a few exceptions, you can build a single LAMMPS executable -with all its accelerator packages installed. Note however that the -USER-INTEL and KOKKOS packages require you to choose one of their -hardware options when building for a specific platform. I.e. CPU or -Phi option for the USER-INTEL package. Or the OpenMP, Cuda, or Phi -option for the KOKKOS package. - -These are the exceptions. You cannot build a single executable with: - -both the USER-INTEL Phi and KOKKOS Phi options -the USER-INTEL Phi or Kokkos Phi option, and the GPU package :ul - -See the examples/accelerate/README and make.list files for sample -Make.py commands that build LAMMPS with any or all of the accelerator -packages. As an example, here is a command that builds with all the -GPU related packages installed (GPU, KOKKOS with Cuda), including -settings to build the needed auxiliary GPU libraries for Kepler GPUs: - -Make.py -j 16 -p omp gpu kokkos -cc nvcc wrap=mpi \ - -gpu mode=double arch=35 -kokkos cuda arch=35 lib-all file mpi :pre - -The examples/accelerate directory also has input scripts that can be -used with all of the accelerator packages. See its README file for -details. - -Likewise, the bench directory has FERMI and KEPLER and PHI -sub-directories with Make.py commands and input scripts for using all -the accelerator packages on various machines. See the README files in -those dirs. - -As mentioned above, the "Benchmark -page"_http://lammps.sandia.gov/bench.html of the LAMMPS web site gives -performance results for the various accelerator packages for several -of the standard LAMMPS benchmark problems, as a function of problem -size and number of compute nodes, on different hardware platforms. - -Here is a brief summary of what the various packages provide. Details -are in the individual accelerator sections. - -Styles with a "gpu" suffix are part of the GPU package, and can be run -on NVIDIA GPUs. The speed-up on a GPU depends on a variety of -factors, discussed in the accelerator sections. :ulb,l - -Styles with an "intel" suffix are part of the USER-INTEL -package. These styles support vectorized single and mixed precision -calculations, in addition to full double precision. In extreme cases, -this can provide speedups over 3.5x on CPUs. The package also -supports acceleration in "offload" mode to Intel(R) Xeon Phi(TM) -coprocessors. This can result in additional speedup over 2x depending -on the hardware configuration. :l - -Styles with a "kk" suffix are part of the KOKKOS package, and can be -run using OpenMP on multicore CPUs, on an NVIDIA GPU, or on an Intel -Xeon Phi in "native" mode. The speed-up depends on a variety of -factors, as discussed on the KOKKOS accelerator page. :l - -Styles with an "omp" suffix are part of the USER-OMP package and allow -a pair-style to be run in multi-threaded mode using OpenMP. This can -be useful on nodes with high-core counts when using less MPI processes -than cores is advantageous, e.g. when running with PPPM so that FFTs -are run on fewer MPI processors or when the many MPI tasks would -overload the available bandwidth for communication. :l - -Styles with an "opt" suffix are part of the OPT package and typically -speed-up the pairwise calculations of your simulation by 5-25% on a -CPU. :l -:ule - -The individual accelerator package doc pages explain: - -what hardware and software the accelerated package requires -how to build LAMMPS with the accelerated package -how to run with the accelerated package either via command-line switches or modifying the input script -speed-ups to expect -guidelines for best performance -restrictions :ul - -:line - -5.4 Comparison of various accelerator packages :h3,link(acc_4) - -NOTE: this section still needs to be re-worked with additional KOKKOS -and USER-INTEL information. - -The next section compares and contrasts the various accelerator -options, since there are multiple ways to perform OpenMP threading, -run on GPUs, and run on Intel Xeon Phi coprocessors. - -All 3 of these packages accelerate a LAMMPS calculation using NVIDIA -hardware, but they do it in different ways. - -As a consequence, for a particular simulation on specific hardware, -one package may be faster than the other. We give guidelines below, -but the best way to determine which package is faster for your input -script is to try both of them on your machine. See the benchmarking -section below for examples where this has been done. - -[Guidelines for using each package optimally:] - -The GPU package allows you to assign multiple CPUs (cores) to a single -GPU (a common configuration for "hybrid" nodes that contain multicore -CPU(s) and GPU(s)) and works effectively in this mode. :ulb,l - -The GPU package moves per-atom data (coordinates, forces) -back-and-forth between the CPU and GPU every timestep. The -KOKKOS/CUDA package only does this on timesteps when a CPU calculation -is required (e.g. to invoke a fix or compute that is non-GPU-ized). -Hence, if you can formulate your input script to only use GPU-ized -fixes and computes, and avoid doing I/O too often (thermo output, dump -file snapshots, restart files), then the data transfer cost of the -KOKKOS/CUDA package can be very low, causing it to run faster than the -GPU package. :l - -The GPU package is often faster than the KOKKOS/CUDA package, if the -number of atoms per GPU is smaller. The crossover point, in terms of -atoms/GPU at which the KOKKOS/CUDA package becomes faster depends -strongly on the pair style. For example, for a simple Lennard Jones -system the crossover (in single precision) is often about 50K-100K -atoms per GPU. When performing double precision calculations the -crossover point can be significantly smaller. :l - -Both packages compute bonded interactions (bonds, angles, etc) on the -CPU. If the GPU package is running with several MPI processes -assigned to one GPU, the cost of computing the bonded interactions is -spread across more CPUs and hence the GPU package can run faster. :l - -When using the GPU package with multiple CPUs assigned to one GPU, its -performance depends to some extent on high bandwidth between the CPUs -and the GPU. Hence its performance is affected if full 16 PCIe lanes -are not available for each GPU. In HPC environments this can be the -case if S2050/70 servers are used, where two devices generally share -one PCIe 2.0 16x slot. Also many multi-GPU mainboards do not provide -full 16 lanes to each of the PCIe 2.0 16x slots. :l -:ule - -[Differences between the two packages:] - -The GPU package accelerates only pair force, neighbor list, and PPPM -calculations. :ulb,l - -The GPU package requires neighbor lists to be built on the CPU when using -exclusion lists, hybrid pair styles, or a triclinic simulation box. :l -:ule diff --git a/doc/src/Section_commands.txt b/doc/src/Section_commands.txt deleted file mode 100644 index 891abc2428..0000000000 --- a/doc/src/Section_commands.txt +++ /dev/null @@ -1,1279 +0,0 @@ -"Previous Section"_Section_start.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Section_packages.html :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Section_commands.html#comm) - -:line - -3. Commands :h2 - -This section describes how a LAMMPS input script is formatted and the -input script commands used to define a LAMMPS simulation. - -3.1 "LAMMPS input script"_#cmd_1 -3.2 "Parsing rules"_#cmd_2 -3.3 "Input script structure"_#cmd_3 -3.4 "Commands listed by category"_#cmd_4 -3.5 "Commands listed alphabetically"_#cmd_5 :all(b) - -:line -:line - -3.1 LAMMPS input script :link(cmd_1),h4 - -LAMMPS executes by reading commands from a input script (text file), -one line at a time. When the input script ends, LAMMPS exits. Each -command causes LAMMPS to take some action. It may set an internal -variable, read in a file, or run a simulation. Most commands have -default settings, which means you only need to use the command if you -wish to change the default. - -In many cases, the ordering of commands in an input script is not -important. However the following rules apply: - -(1) LAMMPS does not read your entire input script and then perform a -simulation with all the settings. Rather, the input script is read -one line at a time and each command takes effect when it is read. -Thus this sequence of commands: - -timestep 0.5 -run 100 -run 100 :pre - -does something different than this sequence: - -run 100 -timestep 0.5 -run 100 :pre - -In the first case, the specified timestep (0.5 fmsec) is used for two -simulations of 100 timesteps each. In the 2nd case, the default -timestep (1.0 fmsec) is used for the 1st 100 step simulation and a 0.5 -fmsec timestep is used for the 2nd one. - -(2) Some commands are only valid when they follow other commands. For -example you cannot set the temperature of a group of atoms until atoms -have been defined and a group command is used to define which atoms -belong to the group. - -(3) Sometimes command B will use values that can be set by command A. -This means command A must precede command B in the input script if it -is to have the desired effect. For example, the -"read_data"_read_data.html command initializes the system by setting -up the simulation box and assigning atoms to processors. If default -values are not desired, the "processors"_processors.html and -"boundary"_boundary.html commands need to be used before read_data to -tell LAMMPS how to map processors to the simulation box. - -Many input script errors are detected by LAMMPS and an ERROR or -WARNING message is printed. "This section"_Section_errors.html gives -more information on what errors mean. The documentation for each -command lists restrictions on how the command can be used. - -:line - -3.2 Parsing rules :link(cmd_2),h4 - -Each non-blank line in the input script is treated as a command. -LAMMPS commands are case sensitive. Command names are lower-case, as -are specified command arguments. Upper case letters may be used in -file names or user-chosen ID strings. - -Here is how each line in the input script is parsed by LAMMPS: - -(1) If the last printable character on the line is a "&" character, -the command is assumed to continue on the next line. The next line is -concatenated to the previous line by removing the "&" character and -line break. This allows long commands to be continued across two or -more lines. See the discussion of triple quotes in (6) for how to -continue a command across multiple line without using "&" characters. - -(2) All characters from the first "#" character onward are treated as -comment and discarded. See an exception in (6). Note that a -comment after a trailing "&" character will prevent the command from -continuing on the next line. Also note that for multi-line commands a -single leading "#" will comment out the entire command. - -(3) The line is searched repeatedly for $ characters, which indicate -variables that are replaced with a text string. See an exception in -(6). - -If the $ is followed by curly brackets, then the variable name is the -text inside the curly brackets. If no curly brackets follow the $, -then the variable name is the single character immediately following -the $. Thus $\{myTemp\} and $x refer to variable names "myTemp" and -"x". - -How the variable is converted to a text string depends on what style -of variable it is; see the "variable"_variable.html doc page for details. -It can be a variable that stores multiple text strings, and return one -of them. The returned text string can be multiple "words" (space -separated) which will then be interpreted as multiple arguments in the -input command. The variable can also store a numeric formula which -will be evaluated and its numeric result returned as a string. - -As a special case, if the $ is followed by parenthesis, then the text -inside the parenthesis is treated as an "immediate" variable and -evaluated as an "equal-style variable"_variable.html. This is a way -to use numeric formulas in an input script without having to assign -them to variable names. For example, these 3 input script lines: - -variable X equal (xlo+xhi)/2+sqrt(v_area) -region 1 block $X 2 INF INF EDGE EDGE -variable X delete :pre - -can be replaced by - -region 1 block $((xlo+xhi)/2+sqrt(v_area)) 2 INF INF EDGE EDGE :pre - -so that you do not have to define (or discard) a temporary variable X. - -Additionally, the "immediate" variable expression may be followed by a -colon, followed by a C-style format string, e.g. ":%f" or ":%.10g". -The format string must be appropriate for a double-precision -floating-point value. The format string is used to output the result -of the variable expression evaluation. If a format string is not -specified a high-precision "%.20g" is used as the default. - -This can be useful for formatting print output to a desired precion: - -print "Final energy per atom: $(pe/atoms:%10.3f) eV/atom" :pre - -Note that neither the curly-bracket or immediate form of variables can -contain nested $ characters for other variables to substitute for. -Thus you cannot do this: - -variable a equal 2 -variable b2 equal 4 -print "B2 = $\{b$a\}" :pre - -Nor can you specify this $($x-1.0) for an immediate variable, but -you could use $(v_x-1.0), since the latter is valid syntax for an -"equal-style variable"_variable.html. - -See the "variable"_variable.html command for more details of how -strings are assigned to variables and evaluated, and how they can be -used in input script commands. - -(4) The line is broken into "words" separated by whitespace (tabs, -spaces). Note that words can thus contain letters, digits, -underscores, or punctuation characters. - -(5) The first word is the command name. All successive words in the -line are arguments. - -(6) If you want text with spaces to be treated as a single argument, -it can be enclosed in either single or double or triple quotes. A -long single argument enclosed in single or double quotes can span -multiple lines if the "&" character is used, as described above. When -the lines are concatenated together (and the "&" characters and line -breaks removed), the text will become a single line. If you want -multiple lines of an argument to retain their line breaks, the text -can be enclosed in triple quotes, in which case "&" characters are not -needed. For example: - -print "Volume = $v" -print 'Volume = $v' -if "$\{steps\} > 1000" then quit -variable a string "red green blue & - purple orange cyan" -print """ -System volume = $v -System temperature = $t -""" :pre - -In each case, the single, double, or triple quotes are removed when -the single argument they enclose is stored internally. - -See the "dump modify format"_dump_modify.html, "print"_print.html, -"if"_if.html, and "python"_python.html commands for examples. - -A "#" or "$" character that is between quotes will not be treated as a -comment indicator in (2) or substituted for as a variable in (3). - -NOTE: If the argument is itself a command that requires a quoted -argument (e.g. using a "print"_print.html command as part of an -"if"_if.html or "run every"_run.html command), then single, double, or -triple quotes can be nested in the usual manner. See the doc pages -for those commands for examples. Only one of level of nesting is -allowed, but that should be sufficient for most use cases. - -:line - -3.3 Input script structure :h3,link(cmd_3) - -This section describes the structure of a typical LAMMPS input script. -The "examples" directory in the LAMMPS distribution contains many -sample input scripts; the corresponding problems are discussed in -"Section 7"_Section_example.html, and animated on the "LAMMPS -WWW Site"_lws. - -A LAMMPS input script typically has 4 parts: - -Initialization -Atom definition -Settings -Run a simulation :ol - -The last 2 parts can be repeated as many times as desired. I.e. run a -simulation, change some settings, run some more, etc. Each of the 4 -parts is now described in more detail. Remember that almost all the -commands need only be used if a non-default value is desired. - -(1) Initialization - -Set parameters that need to be defined before atoms are created or -read-in from a file. - -The relevant commands are "units"_units.html, -"dimension"_dimension.html, "newton"_newton.html, -"processors"_processors.html, "boundary"_boundary.html, -"atom_style"_atom_style.html, "atom_modify"_atom_modify.html. - -If force-field parameters appear in the files that will be read, these -commands tell LAMMPS what kinds of force fields are being used: -"pair_style"_pair_style.html, "bond_style"_bond_style.html, -"angle_style"_angle_style.html, "dihedral_style"_dihedral_style.html, -"improper_style"_improper_style.html. - -(2) Atom definition - -There are 3 ways to define atoms in LAMMPS. Read them in from a data -or restart file via the "read_data"_read_data.html or -"read_restart"_read_restart.html commands. These files can contain -molecular topology information. Or create atoms on a lattice (with no -molecular topology), using these commands: "lattice"_lattice.html, -"region"_region.html, "create_box"_create_box.html, -"create_atoms"_create_atoms.html. The entire set of atoms can be -duplicated to make a larger simulation using the -"replicate"_replicate.html command. - -(3) Settings - -Once atoms and molecular topology are defined, a variety of settings -can be specified: force field coefficients, simulation parameters, -output options, etc. - -Force field coefficients are set by these commands (they can also be -set in the read-in files): "pair_coeff"_pair_coeff.html, -"bond_coeff"_bond_coeff.html, "angle_coeff"_angle_coeff.html, -"dihedral_coeff"_dihedral_coeff.html, -"improper_coeff"_improper_coeff.html, -"kspace_style"_kspace_style.html, "dielectric"_dielectric.html, -"special_bonds"_special_bonds.html. - -Various simulation parameters are set by these commands: -"neighbor"_neighbor.html, "neigh_modify"_neigh_modify.html, -"group"_group.html, "timestep"_timestep.html, -"reset_timestep"_reset_timestep.html, "run_style"_run_style.html, -"min_style"_min_style.html, "min_modify"_min_modify.html. - -Fixes impose a variety of boundary conditions, time integration, and -diagnostic options. The "fix"_fix.html command comes in many flavors. - -Various computations can be specified for execution during a -simulation using the "compute"_compute.html, -"compute_modify"_compute_modify.html, and "variable"_variable.html -commands. - -Output options are set by the "thermo"_thermo.html, "dump"_dump.html, -and "restart"_restart.html commands. - -(4) Run a simulation - -A molecular dynamics simulation is run using the "run"_run.html -command. Energy minimization (molecular statics) is performed using -the "minimize"_minimize.html command. A parallel tempering -(replica-exchange) simulation can be run using the -"temper"_temper.html command. - -:line - -3.4 Commands listed by category :link(cmd_4),h4 - -This section lists core LAMMPS commands, grouped by category. -The "next section"_#cmd_5 lists all commands alphabetically. The -next section also includes (long) lists of style options for entries -that appear in the following categories as a single command (fix, -compute, pair, etc). Commands that are added by user packages are not -included in the categories here, but they are in the next section. - -Initialization: - -"newton"_newton.html, -"package"_package.html, -"processors"_processors.html, -"suffix"_suffix.html, -"units"_units.html - -Setup simulation box: - -"boundary"_boundary.html, -"box"_box.html, -"change_box"_change_box.html, -"create_box"_create_box.html, -"dimension"_dimension.html, -"lattice"_lattice.html, -"region"_region.html - -Setup atoms: - -"atom_modify"_atom_modify.html, -"atom_style"_atom_style.html, -"balance"_balance.html, -"create_atoms"_create_atoms.html, -"create_bonds"_create_bonds.html, -"delete_atoms"_delete_atoms.html, -"delete_bonds"_delete_bonds.html, -"displace_atoms"_displace_atoms.html, -"group"_group.html, -"mass"_mass.html, -"molecule"_molecule.html, -"read_data"_read_data.html, -"read_dump"_read_dump.html, -"read_restart"_read_restart.html, -"replicate"_replicate.html, -"set"_set.html, -"velocity"_velocity.html - -Force fields: - -"angle_coeff"_angle_coeff.html, -"angle_style"_angle_style.html, -"bond_coeff"_bond_coeff.html, -"bond_style"_bond_style.html, -"bond_write"_bond_write.html, -"dielectric"_dielectric.html, -"dihedral_coeff"_dihedral_coeff.html, -"dihedral_style"_dihedral_style.html, -"improper_coeff"_improper_coeff.html, -"improper_style"_improper_style.html, -"kspace_modify"_kspace_modify.html, -"kspace_style"_kspace_style.html, -"pair_coeff"_pair_coeff.html, -"pair_modify"_pair_modify.html, -"pair_style"_pair_style.html, -"pair_write"_pair_write.html, -"special_bonds"_special_bonds.html - -Settings: - -"comm_modify"_comm_modify.html, -"comm_style"_comm_style.html, -"info"_info.html, -"min_modify"_min_modify.html, -"min_style"_min_style.html, -"neigh_modify"_neigh_modify.html, -"neighbor"_neighbor.html, -"partition"_partition.html, -"reset_timestep"_reset_timestep.html, -"run_style"_run_style.html, -"timer"_timer.html, -"timestep"_timestep.html - -Operations within timestepping (fixes) and diagnostics (computes): - -"compute"_compute.html, -"compute_modify"_compute_modify.html, -"fix"_fix.html, -"fix_modify"_fix_modify.html, -"uncompute"_uncompute.html, -"unfix"_unfix.html - -Output: - -"dump image"_dump_image.html, -"dump movie"_dump_image.html, -"dump"_dump.html, -"dump_modify"_dump_modify.html, -"restart"_restart.html, -"thermo"_thermo.html, -"thermo_modify"_thermo_modify.html, -"thermo_style"_thermo_style.html, -"undump"_undump.html, -"write_coeff"_write_coeff.html, -"write_data"_write_data.html, -"write_dump"_write_dump.html, -"write_restart"_write_restart.html - -Actions: - -"minimize"_minimize.html, -"neb"_neb.html, -"prd"_prd.html, -"rerun"_rerun.html, -"run"_run.html, -"tad"_tad.html, -"temper"_temper.html - -Input script control: - -"clear"_clear.html, -"echo"_echo.html, -"if"_if.html, -"include"_include.html, -"jump"_jump.html, -"label"_label.html, -"log"_log.html, -"next"_next.html, -"print"_print.html, -"python"_python.html, -"quit"_quit.html, -"shell"_shell.html, -"variable"_variable.html - -:line - -3.5 Individual commands :h3,link(cmd_5),link(comm) - -This section lists all LAMMPS commands alphabetically, with a separate -listing below of styles within certain commands. The "previous -section"_#cmd_4 lists the same commands, grouped by category. Note -that some style options for some commands are part of specific LAMMPS -packages, which means they cannot be used unless the package was -included when LAMMPS was built. Not all packages are included in a -default LAMMPS build. These dependencies are listed as Restrictions -in the command's documentation. - -"angle_coeff"_angle_coeff.html, -"angle_style"_angle_style.html, -"atom_modify"_atom_modify.html, -"atom_style"_atom_style.html, -"balance"_balance.html, -"bond_coeff"_bond_coeff.html, -"bond_style"_bond_style.html, -"bond_write"_bond_write.html, -"boundary"_boundary.html, -"box"_box.html, -"change_box"_change_box.html, -"clear"_clear.html, -"comm_modify"_comm_modify.html, -"comm_style"_comm_style.html, -"compute"_compute.html, -"compute_modify"_compute_modify.html, -"create_atoms"_create_atoms.html, -"create_bonds"_create_bonds.html, -"create_box"_create_box.html, -"delete_atoms"_delete_atoms.html, -"delete_bonds"_delete_bonds.html, -"dielectric"_dielectric.html, -"dihedral_coeff"_dihedral_coeff.html, -"dihedral_style"_dihedral_style.html, -"dimension"_dimension.html, -"displace_atoms"_displace_atoms.html, -"dump"_dump.html, -"dump image"_dump_image.html, -"dump_modify"_dump_modify.html, -"dump movie"_dump_image.html, -"echo"_echo.html, -"fix"_fix.html, -"fix_modify"_fix_modify.html, -"group"_group.html, -"if"_if.html, -"info"_info.html, -"improper_coeff"_improper_coeff.html, -"improper_style"_improper_style.html, -"include"_include.html, -"jump"_jump.html, -"kspace_modify"_kspace_modify.html, -"kspace_style"_kspace_style.html, -"label"_label.html, -"lattice"_lattice.html, -"log"_log.html, -"mass"_mass.html, -"minimize"_minimize.html, -"min_modify"_min_modify.html, -"min_style"_min_style.html, -"molecule"_molecule.html, -"neb"_neb.html, -"neigh_modify"_neigh_modify.html, -"neighbor"_neighbor.html, -"newton"_newton.html, -"next"_next.html, -"package"_package.html, -"pair_coeff"_pair_coeff.html, -"pair_modify"_pair_modify.html, -"pair_style"_pair_style.html, -"pair_write"_pair_write.html, -"partition"_partition.html, -"prd"_prd.html, -"print"_print.html, -"processors"_processors.html, -"python"_python.html, -"quit"_quit.html, -"read_data"_read_data.html, -"read_dump"_read_dump.html, -"read_restart"_read_restart.html, -"region"_region.html, -"replicate"_replicate.html, -"rerun"_rerun.html, -"reset_ids"_reset_ids.html, -"reset_timestep"_reset_timestep.html, -"restart"_restart.html, -"run"_run.html, -"run_style"_run_style.html, -"set"_set.html, -"shell"_shell.html, -"special_bonds"_special_bonds.html, -"suffix"_suffix.html, -"tad"_tad.html, -"temper"_temper.html, -"thermo"_thermo.html, -"thermo_modify"_thermo_modify.html, -"thermo_style"_thermo_style.html, -"timer"_timer.html, -"timestep"_timestep.html, -"uncompute"_uncompute.html, -"undump"_undump.html, -"unfix"_unfix.html, -"units"_units.html, -"variable"_variable.html, -"velocity"_velocity.html, -"write_coeff"_write_coeff.html, -"write_data"_write_data.html, -"write_dump"_write_dump.html, -"write_restart"_write_restart.html :tb(c=6,ea=c) - -These are additional commands in USER packages, which can be used if -"LAMMPS is built with the appropriate -package"_Section_start.html#start_3. - -"dump netcdf"_dump_netcdf.html, -"dump netcdf/mpiio"_dump_netcdf.html, -"dump vtk"_dump_vtk.html, -"group2ndx"_group2ndx.html, -"ndx2group"_group2ndx.html, -"temper/grem"_temper_grem.html, -"temper/npt"_temper_npt.html :tb(c=3,ea=c) - -:line - -Fix styles :h3 - -See the "fix"_fix.html command for one-line descriptions of each style -or click on the style itself for a full description. Some of the -styles have accelerated versions, which can be used if LAMMPS is built -with the "appropriate accelerated package"_Section_accelerate.html. -This is indicated by additional letters in parenthesis: g = GPU, i = -USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT. - -"adapt"_fix_adapt.html, -"addforce"_fix_addforce.html, -"append/atoms"_fix_append_atoms.html, -"atom/swap"_fix_atom_swap.html, -"aveforce"_fix_aveforce.html, -"ave/atom"_fix_ave_atom.html, -"ave/chunk"_fix_ave_chunk.html, -"ave/correlate"_fix_ave_correlate.html, -"ave/histo"_fix_ave_histo.html, -"ave/histo/weight"_fix_ave_histo.html, -"ave/time"_fix_ave_time.html, -"balance"_fix_balance.html, -"bond/break"_fix_bond_break.html, -"bond/create"_fix_bond_create.html, -"bond/swap"_fix_bond_swap.html, -"box/relax"_fix_box_relax.html, -"cmap"_fix_cmap.html, -"controller"_fix_controller.html, -"deform (k)"_fix_deform.html, -"deposit"_fix_deposit.html, -"drag"_fix_drag.html, -"dt/reset"_fix_dt_reset.html, -"efield"_fix_efield.html, -"ehex"_fix_ehex.html, -"enforce2d"_fix_enforce2d.html, -"evaporate"_fix_evaporate.html, -"external"_fix_external.html, -"freeze"_fix_freeze.html, -"gcmc"_fix_gcmc.html, -"gld"_fix_gld.html, -"gravity (o)"_fix_gravity.html, -"halt"_fix_halt.html, -"heat"_fix_heat.html, -"indent"_fix_indent.html, -"latte"_fix_latte.html, -"langevin (k)"_fix_langevin.html, -"lineforce"_fix_lineforce.html, -"momentum (k)"_fix_momentum.html, -"move"_fix_move.html, -"mscg"_fix_mscg.html, -"msst"_fix_msst.html, -"neb"_fix_neb.html, -"nph (ko)"_fix_nh.html, -"nphug (o)"_fix_nphug.html, -"nph/asphere (o)"_fix_nph_asphere.html, -"nph/body"_fix_nph_body.html, -"nph/sphere (o)"_fix_nph_sphere.html, -"npt (kio)"_fix_nh.html, -"npt/asphere (o)"_fix_npt_asphere.html, -"npt/body"_fix_npt_body.html, -"npt/sphere (o)"_fix_npt_sphere.html, -"nve (kio)"_fix_nve.html, -"nve/asphere (i)"_fix_nve_asphere.html, -"nve/asphere/noforce"_fix_nve_asphere_noforce.html, -"nve/body"_fix_nve_body.html, -"nve/limit"_fix_nve_limit.html, -"nve/line"_fix_nve_line.html, -"nve/noforce"_fix_nve_noforce.html, -"nve/sphere (o)"_fix_nve_sphere.html, -"nve/tri"_fix_nve_tri.html, -"nvt (iko)"_fix_nh.html, -"nvt/asphere (o)"_fix_nvt_asphere.html, -"nvt/body"_fix_nvt_body.html, -"nvt/sllod (io)"_fix_nvt_sllod.html, -"nvt/sphere (o)"_fix_nvt_sphere.html, -"oneway"_fix_oneway.html, -"orient/bcc"_fix_orient.html, -"orient/fcc"_fix_orient.html, -"planeforce"_fix_planeforce.html, -"poems"_fix_poems.html, -"pour"_fix_pour.html, -"press/berendsen"_fix_press_berendsen.html, -"print"_fix_print.html, -"property/atom (k)"_fix_property_atom.html, -"python/invoke"_fix_python_invoke.html, -"python/move"_fix_python_move.html, -"qeq/comb (o)"_fix_qeq_comb.html, -"qeq/dynamic"_fix_qeq.html, -"qeq/fire"_fix_qeq.html, -"qeq/point"_fix_qeq.html, -"qeq/shielded"_fix_qeq.html, -"qeq/slater"_fix_qeq.html, -"rattle"_fix_shake.html, -"reax/bonds"_fix_reax_bonds.html, -"recenter"_fix_recenter.html, -"restrain"_fix_restrain.html, -"rigid (o)"_fix_rigid.html, -"rigid/nph (o)"_fix_rigid.html, -"rigid/npt (o)"_fix_rigid.html, -"rigid/nve (o)"_fix_rigid.html, -"rigid/nvt (o)"_fix_rigid.html, -"rigid/small (o)"_fix_rigid.html, -"rigid/small/nph"_fix_rigid.html, -"rigid/small/npt"_fix_rigid.html, -"rigid/small/nve"_fix_rigid.html, -"rigid/small/nvt"_fix_rigid.html, -"setforce (k)"_fix_setforce.html, -"shake"_fix_shake.html, -"spring"_fix_spring.html, -"spring/chunk"_fix_spring_chunk.html, -"spring/rg"_fix_spring_rg.html, -"spring/self"_fix_spring_self.html, -"srd"_fix_srd.html, -"store/force"_fix_store_force.html, -"store/state"_fix_store_state.html, -"temp/berendsen"_fix_temp_berendsen.html, -"temp/csld"_fix_temp_csvr.html, -"temp/csvr"_fix_temp_csvr.html, -"temp/rescale"_fix_temp_rescale.html, -"tfmc"_fix_tfmc.html, -"thermal/conductivity"_fix_thermal_conductivity.html, -"tmd"_fix_tmd.html, -"ttm"_fix_ttm.html, -"tune/kspace"_fix_tune_kspace.html, -"vector"_fix_vector.html, -"viscosity"_fix_viscosity.html, -"viscous"_fix_viscous.html, -"wall/colloid"_fix_wall.html, -"wall/gran"_fix_wall_gran.html, -"wall/gran/region"_fix_wall_gran_region.html, -"wall/harmonic"_fix_wall.html, -"wall/lj1043"_fix_wall.html, -"wall/lj126"_fix_wall.html, -"wall/lj93 (k)"_fix_wall.html, -"wall/piston"_fix_wall_piston.html, -"wall/reflect (k)"_fix_wall_reflect.html, -"wall/region"_fix_wall_region.html, -"wall/srd"_fix_wall_srd.html :tb(c=8,ea=c) - -These are additional fix styles in USER packages, which can be used if -"LAMMPS is built with the appropriate -package"_Section_start.html#start_3. - -"adapt/fep"_fix_adapt_fep.html, -"addtorque"_fix_addtorque.html, -"atc"_fix_atc.html, -"ave/correlate/long"_fix_ave_correlate_long.html, -"bond/react"_fix_bond_react.html, -"colvars"_fix_colvars.html, -"dpd/energy (k)"_fix_dpd_energy.html, -"drude"_fix_drude.html, -"drude/transform/direct"_fix_drude_transform.html, -"drude/transform/reverse"_fix_drude_transform.html, -"edpd/source"_fix_dpd_source.html, -"eos/cv"_fix_eos_cv.html, -"eos/table"_fix_eos_table.html, -"eos/table/rx (k)"_fix_eos_table_rx.html, -"filter/corotate"_fix_filter_corotate.html, -"flow/gauss"_fix_flow_gauss.html, -"gle"_fix_gle.html, -"grem"_fix_grem.html, -"imd"_fix_imd.html, -"ipi"_fix_ipi.html, -"langevin/drude"_fix_langevin_drude.html, -"langevin/eff"_fix_langevin_eff.html, -"lb/fluid"_fix_lb_fluid.html, -"lb/momentum"_fix_lb_momentum.html, -"lb/pc"_fix_lb_pc.html, -"lb/rigid/pc/sphere"_fix_lb_rigid_pc_sphere.html, -"lb/viscous"_fix_lb_viscous.html, -"meso"_fix_meso.html, -"manifoldforce"_fix_manifoldforce.html, -"meso/stationary"_fix_meso_stationary.html, -"mvv/dpd"_fix_mvv_dpd.html, -"mvv/edpd"_fix_mvv_dpd.html, -"mvv/tdpd"_fix_mvv_dpd.html, -"nph/eff"_fix_nh_eff.html, -"npt/eff"_fix_nh_eff.html, -"npt/uef"_fix_nh_uef.html, -"nve/dot"_fix_nve_dot.html, -"nve/dotc/langevin"_fix_nve_dotc_langevin.html, -"nve/eff"_fix_nve_eff.html, -"nve/manifold/rattle"_fix_nve_manifold_rattle.html, -"nvk"_fix_nvk.html, -"nvt/eff"_fix_nh_eff.html, -"nvt/manifold/rattle"_fix_nvt_manifold_rattle.html, -"nvt/sllod/eff"_fix_nvt_sllod_eff.html, -"nvt/uef"_fix_nh_uef.html, -"phonon"_fix_phonon.html, -"pimd"_fix_pimd.html, -"qbmsst"_fix_qbmsst.html, -"qeq/reax (ko)"_fix_qeq_reax.html, -"qmmm"_fix_qmmm.html, -"qtb"_fix_qtb.html, -"reax/c/bonds (k)"_fix_reax_bonds.html, -"reax/c/species (k)"_fix_reaxc_species.html, -"rhok"_fix_rhok.html, -"rx (k)"_fix_rx.html, -"saed/vtk"_fix_saed_vtk.html, -"shardlow (k)"_fix_shardlow.html, -"smd"_fix_smd.html, -"smd/adjust/dt"_fix_smd_adjust_dt.html, -"smd/integrate/tlsph"_fix_smd_integrate_tlsph.html, -"smd/integrate/ulsph"_fix_smd_integrate_ulsph.html, -"smd/move/triangulated/surface"_fix_smd_move_triangulated_surface.html, -"smd/setvel"_fix_smd_setvel.html, -"smd/wall/surface"_fix_smd_wall_surface.html, -"tdpd/source"_fix_dpd_source.html, -"temp/rescale/eff"_fix_temp_rescale_eff.html, -"ti/spring"_fix_ti_spring.html, -"ttm/mod"_fix_ttm.html, -"wall/ees"_fix_wall_ees.html, -"wall/region/ees"_fix_wall_ees.html :tb(c=6,ea=c) - -:line - -Compute styles :h3 - -See the "compute"_compute.html command for one-line descriptions of -each style or click on the style itself for a full description. Some -of the styles have accelerated versions, which can be used if LAMMPS -is built with the "appropriate accelerated -package"_Section_accelerate.html. This is indicated by additional -letters in parenthesis: g = GPU, i = USER-INTEL, k = -KOKKOS, o = USER-OMP, t = OPT. - -"aggregate/atom"_compute_cluster_atom.html, -"angle"_compute_angle.html, -"angle/local"_compute_angle_local.html, -"angmom/chunk"_compute_angmom_chunk.html, -"body/local"_compute_body_local.html, -"bond"_compute_bond.html, -"bond/local"_compute_bond_local.html, -"centro/atom"_compute_centro_atom.html, -"chunk/atom"_compute_chunk_atom.html, -"cluster/atom"_compute_cluster_atom.html, -"cna/atom"_compute_cna_atom.html, -"com"_compute_com.html, -"com/chunk"_compute_com_chunk.html, -"contact/atom"_compute_contact_atom.html, -"coord/atom"_compute_coord_atom.html, -"damage/atom"_compute_damage_atom.html, -"dihedral"_compute_dihedral.html, -"dihedral/local"_compute_dihedral_local.html, -"dilatation/atom"_compute_dilatation_atom.html, -"dipole/chunk"_compute_dipole_chunk.html, -"displace/atom"_compute_displace_atom.html, -"erotate/asphere"_compute_erotate_asphere.html, -"erotate/rigid"_compute_erotate_rigid.html, -"erotate/sphere"_compute_erotate_sphere.html, -"erotate/sphere/atom"_compute_erotate_sphere_atom.html, -"event/displace"_compute_event_displace.html, -"fragment/atom"_compute_cluster_atom.html, -"global/atom"_compute_global_atom.html, -"group/group"_compute_group_group.html, -"gyration"_compute_gyration.html, -"gyration/chunk"_compute_gyration_chunk.html, -"heat/flux"_compute_heat_flux.html, -"hexorder/atom"_compute_hexorder_atom.html, -"improper"_compute_improper.html, -"improper/local"_compute_improper_local.html, -"inertia/chunk"_compute_inertia_chunk.html, -"ke"_compute_ke.html, -"ke/atom"_compute_ke_atom.html, -"ke/rigid"_compute_ke_rigid.html, -"msd"_compute_msd.html, -"msd/chunk"_compute_msd_chunk.html, -"msd/nongauss"_compute_msd_nongauss.html, -"omega/chunk"_compute_omega_chunk.html, -"orientorder/atom"_compute_orientorder_atom.html, -"pair"_compute_pair.html, -"pair/local"_compute_pair_local.html, -"pe"_compute_pe.html, -"pe/atom"_compute_pe_atom.html, -"plasticity/atom"_compute_plasticity_atom.html, -"pressure"_compute_pressure.html, -"property/atom"_compute_property_atom.html, -"property/local"_compute_property_local.html, -"property/chunk"_compute_property_chunk.html, -"rdf"_compute_rdf.html, -"reduce"_compute_reduce.html, -"reduce/region"_compute_reduce.html, -"rigid/local"_compute_rigid_local.html, -"slice"_compute_slice.html, -"sna/atom"_compute_sna_atom.html, -"snad/atom"_compute_sna_atom.html, -"snav/atom"_compute_sna_atom.html, -"stress/atom"_compute_stress_atom.html, -"temp (k)"_compute_temp.html, -"temp/asphere"_compute_temp_asphere.html, -"temp/body"_compute_temp_body.html, -"temp/chunk"_compute_temp_chunk.html, -"temp/com"_compute_temp_com.html, -"temp/deform"_compute_temp_deform.html, -"temp/partial"_compute_temp_partial.html, -"temp/profile"_compute_temp_profile.html, -"temp/ramp"_compute_temp_ramp.html, -"temp/region"_compute_temp_region.html, -"temp/sphere"_compute_temp_sphere.html, -"ti"_compute_ti.html, -"torque/chunk"_compute_torque_chunk.html, -"vacf"_compute_vacf.html, -"vcm/chunk"_compute_vcm_chunk.html, -"voronoi/atom"_compute_voronoi_atom.html :tb(c=6,ea=c) - -These are additional compute styles in USER packages, which can be -used if "LAMMPS is built with the appropriate -package"_Section_start.html#start_3. - -"ackland/atom"_compute_ackland_atom.html, -"basal/atom"_compute_basal_atom.html, -"cnp/atom"_compute_cnp_atom.html, -"dpd"_compute_dpd.html, -"dpd/atom"_compute_dpd_atom.html, -"edpd/temp/atom"_compute_edpd_temp_atom.html, -"fep"_compute_fep.html, -"force/tally"_compute_tally.html, -"heat/flux/tally"_compute_tally.html, -"ke/eff"_compute_ke_eff.html, -"ke/atom/eff"_compute_ke_atom_eff.html, -"meso/e/atom"_compute_meso_e_atom.html, -"meso/rho/atom"_compute_meso_rho_atom.html, -"meso/t/atom"_compute_meso_t_atom.html, -"pe/tally"_compute_tally.html, -"pe/mol/tally"_compute_tally.html, -"pressure/uef"_compute_pressure_uef.html, -"saed"_compute_saed.html, -"smd/contact/radius"_compute_smd_contact_radius.html, -"smd/damage"_compute_smd_damage.html, -"smd/hourglass/error"_compute_smd_hourglass_error.html, -"smd/internal/energy"_compute_smd_internal_energy.html, -"smd/plastic/strain"_compute_smd_plastic_strain.html, -"smd/plastic/strain/rate"_compute_smd_plastic_strain_rate.html, -"smd/rho"_compute_smd_rho.html, -"smd/tlsph/defgrad"_compute_smd_tlsph_defgrad.html, -"smd/tlsph/dt"_compute_smd_tlsph_dt.html, -"smd/tlsph/num/neighs"_compute_smd_tlsph_num_neighs.html, -"smd/tlsph/shape"_compute_smd_tlsph_shape.html, -"smd/tlsph/strain"_compute_smd_tlsph_strain.html, -"smd/tlsph/strain/rate"_compute_smd_tlsph_strain_rate.html, -"smd/tlsph/stress"_compute_smd_tlsph_stress.html, -"smd/triangle/mesh/vertices"_compute_smd_triangle_mesh_vertices.html, -"smd/ulsph/num/neighs"_compute_smd_ulsph_num_neighs.html, -"smd/ulsph/strain"_compute_smd_ulsph_strain.html, -"smd/ulsph/strain/rate"_compute_smd_ulsph_strain_rate.html, -"smd/ulsph/stress"_compute_smd_ulsph_stress.html, -"smd/vol"_compute_smd_vol.html, -"stress/tally"_compute_tally.html, -"tdpd/cc/atom"_compute_tdpd_cc_atom.html, -"temp/drude"_compute_temp_drude.html, -"temp/eff"_compute_temp_eff.html, -"temp/deform/eff"_compute_temp_deform_eff.html, -"temp/region/eff"_compute_temp_region_eff.html, -"temp/rotate"_compute_temp_rotate.html, -"temp/uef"_compute_temp_uef.html, -"xrd"_compute_xrd.html :tb(c=6,ea=c) - -:line - -Pair_style potentials :h3 - -See the "pair_style"_pair_style.html command for an overview of pair -potentials. Click on the style itself for a full description. Many -of the styles have accelerated versions, which can be used if LAMMPS -is built with the "appropriate accelerated -package"_Section_accelerate.html. This is indicated by additional -letters in parenthesis: g = GPU, i = USER-INTEL, k = -KOKKOS, o = USER-OMP, t = OPT. - -"none"_pair_none.html, -"zero"_pair_zero.html, -"hybrid"_pair_hybrid.html, -"hybrid/overlay (k)"_pair_hybrid.html, -"adp (o)"_pair_adp.html, -"airebo (oi)"_pair_airebo.html, -"airebo/morse (oi)"_pair_airebo.html, -"beck (go)"_pair_beck.html, -"body"_pair_body.html, -"bop"_pair_bop.html, -"born (go)"_pair_born.html, -"born/coul/dsf"_pair_born.html, -"born/coul/dsf/cs"_pair_born.html, -"born/coul/long (go)"_pair_born.html, -"born/coul/long/cs"_pair_born.html, -"born/coul/msm (o)"_pair_born.html, -"born/coul/wolf (go)"_pair_born.html, -"born/coul/wolf/cs"_pair_born.html, -"brownian (o)"_pair_brownian.html, -"brownian/poly (o)"_pair_brownian.html, -"buck (giko)"_pair_buck.html, -"buck/coul/cut (giko)"_pair_buck.html, -"buck/coul/long (giko)"_pair_buck.html, -"buck/coul/long/cs"_pair_buck.html, -"buck/coul/msm (o)"_pair_buck.html, -"buck/long/coul/long (o)"_pair_buck_long.html, -"colloid (go)"_pair_colloid.html, -"comb (o)"_pair_comb.html, -"comb3"_pair_comb.html, -"coul/cut (gko)"_pair_coul.html, -"coul/debye (gko)"_pair_coul.html, -"coul/dsf (gko)"_pair_coul.html, -"coul/long (gko)"_pair_coul.html, -"coul/long/cs"_pair_coul.html, -"coul/msm"_pair_coul.html, -"coul/streitz"_pair_coul.html, -"coul/wolf (ko)"_pair_coul.html, -"coul/wolf/cs"_pair_coul.html, -"dpd (gio)"_pair_dpd.html, -"dpd/tstat (go)"_pair_dpd.html, -"dsmc"_pair_dsmc.html, -"eam (gikot)"_pair_eam.html, -"eam/alloy (gikot)"_pair_eam.html, -"eam/fs (gikot)"_pair_eam.html, -"eim (o)"_pair_eim.html, -"gauss (go)"_pair_gauss.html, -"gayberne (gio)"_pair_gayberne.html, -"gran/hertz/history (o)"_pair_gran.html, -"gran/hooke (o)"_pair_gran.html, -"gran/hooke/history (o)"_pair_gran.html, -"gw"_pair_gw.html, -"gw/zbl"_pair_gw.html, -"hbond/dreiding/lj (o)"_pair_hbond_dreiding.html, -"hbond/dreiding/morse (o)"_pair_hbond_dreiding.html, -"kim"_pair_kim.html, -"lcbop"_pair_lcbop.html, -"line/lj"_pair_line_lj.html, -"lj/charmm/coul/charmm (iko)"_pair_charmm.html, -"lj/charmm/coul/charmm/implicit (ko)"_pair_charmm.html, -"lj/charmm/coul/long (giko)"_pair_charmm.html, -"lj/charmm/coul/msm"_pair_charmm.html, -"lj/charmmfsw/coul/charmmfsh"_pair_charmm.html, -"lj/charmmfsw/coul/long"_pair_charmm.html, -"lj/class2 (gko)"_pair_class2.html, -"lj/class2/coul/cut (ko)"_pair_class2.html, -"lj/class2/coul/long (gko)"_pair_class2.html, -"lj/cubic (go)"_pair_lj_cubic.html, -"lj/cut (gikot)"_pair_lj.html, -"lj/cut/coul/cut (gko)"_pair_lj.html, -"lj/cut/coul/debye (gko)"_pair_lj.html, -"lj/cut/coul/dsf (gko)"_pair_lj.html, -"lj/cut/coul/long (gikot)"_pair_lj.html, -"lj/cut/coul/long/cs"_pair_lj.html, -"lj/cut/coul/msm (go)"_pair_lj.html, -"lj/cut/coul/wolf (o)"_pair_lj.html, -"lj/cut/dipole/cut (go)"_pair_dipole.html, -"lj/cut/dipole/long"_pair_dipole.html, -"lj/cut/tip4p/cut (o)"_pair_lj.html, -"lj/cut/tip4p/long (ot)"_pair_lj.html, -"lj/expand (gko)"_pair_lj_expand.html, -"lj/gromacs (gko)"_pair_gromacs.html, -"lj/gromacs/coul/gromacs (ko)"_pair_gromacs.html, -"lj/long/coul/long (io)"_pair_lj_long.html, -"lj/long/dipole/long"_pair_dipole.html, -"lj/long/tip4p/long"_pair_lj_long.html, -"lj/smooth (o)"_pair_lj_smooth.html, -"lj/smooth/linear (o)"_pair_lj_smooth_linear.html, -"lj96/cut (go)"_pair_lj96.html, -"lubricate (o)"_pair_lubricate.html, -"lubricate/poly (o)"_pair_lubricate.html, -"lubricateU"_pair_lubricateU.html, -"lubricateU/poly"_pair_lubricateU.html, -"meam"_pair_meam.html, -"mie/cut (o)"_pair_mie.html, -"morse (gkot)"_pair_morse.html, -"nb3b/harmonic (o)"_pair_nb3b_harmonic.html, -"nm/cut (o)"_pair_nm.html, -"nm/cut/coul/cut (o)"_pair_nm.html, -"nm/cut/coul/long (o)"_pair_nm.html, -"peri/eps"_pair_peri.html, -"peri/lps (o)"_pair_peri.html, -"peri/pmb (o)"_pair_peri.html, -"peri/ves"_pair_peri.html, -"polymorphic"_pair_polymorphic.html, -"python"_pair_python.html, -"reax"_pair_reax.html, -"rebo (oi)"_pair_airebo.html, -"resquared (go)"_pair_resquared.html, -"snap (k)"_pair_snap.html, -"soft (go)"_pair_soft.html, -"sw (giko)"_pair_sw.html, -"table (gko)"_pair_table.html, -"tersoff (giko)"_pair_tersoff.html, -"tersoff/mod (gko)"_pair_tersoff_mod.html, -"tersoff/mod/c (o)"_pair_tersoff_mod.html, -"tersoff/zbl (gko)"_pair_tersoff_zbl.html, -"tip4p/cut (o)"_pair_coul.html, -"tip4p/long (o)"_pair_coul.html, -"tri/lj"_pair_tri_lj.html, -"ufm (got)"_pair_ufm.html, -"vashishta (ko)"_pair_vashishta.html, -"vashishta/table (o)"_pair_vashishta.html, -"yukawa (gok)"_pair_yukawa.html, -"yukawa/colloid (go)"_pair_yukawa_colloid.html, -"zbl (gok)"_pair_zbl.html :tb(c=4,ea=c) - -These are additional pair styles in USER packages, which can be used -if "LAMMPS is built with the appropriate -package"_Section_start.html#start_3. - -"agni (o)"_pair_agni.html, -"awpmd/cut"_pair_awpmd.html, -"buck/mdf"_pair_mdf.html, -"coul/cut/soft (o)"_pair_lj_soft.html, -"coul/diel (o)"_pair_coul_diel.html, -"coul/long/soft (o)"_pair_lj_soft.html, -"coul/shield"_pair_coul_shield.html, -"dpd/fdt"_pair_dpd_fdt.html, -"dpd/fdt/energy (k)"_pair_dpd_fdt.html, -"eam/cd (o)"_pair_eam.html, -"edip (o)"_pair_edip.html, -"edip/multi"_pair_edip.html, -"edpd"_pair_meso.html, -"eff/cut"_pair_eff.html, -"exp6/rx (k)"_pair_exp6_rx.html, -"extep"_pair_extep.html, -"gauss/cut"_pair_gauss.html, -"ilp/graphene/hbn"_pair_ilp_graphene_hbn.html, -"kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html, -"kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html, -"lennard/mdf"_pair_mdf.html, -"list"_pair_list.html, -"lj/charmm/coul/long/soft (o)"_pair_charmm.html, -"lj/cut/coul/cut/soft (o)"_pair_lj_soft.html, -"lj/cut/coul/long/soft (o)"_pair_lj_soft.html, -"lj/cut/dipole/sf (go)"_pair_dipole.html, -"lj/cut/soft (o)"_pair_lj_soft.html, -"lj/cut/thole/long (o)"_pair_thole.html, -"lj/cut/tip4p/long/soft (o)"_pair_lj_soft.html, -"lj/mdf"_pair_mdf.html, -"lj/sdk (gko)"_pair_sdk.html, -"lj/sdk/coul/long (go)"_pair_sdk.html, -"lj/sdk/coul/msm (o)"_pair_sdk.html, -"mdpd"_pair_meso.html, -"mdpd/rhosum"_pair_meso.html, -"meam/c"_pair_meam.html, -"meam/spline (o)"_pair_meam_spline.html, -"meam/sw/spline"_pair_meam_sw_spline.html, -"mgpt"_pair_mgpt.html, -"momb"_pair_momb.html, -"morse/smooth/linear"_pair_morse.html, -"morse/soft"_pair_morse.html, -"multi/lucy"_pair_multi_lucy.html, -"multi/lucy/rx (k)"_pair_multi_lucy_rx.html, -"oxdna/coaxstk"_pair_oxdna.html, -"oxdna/excv"_pair_oxdna.html, -"oxdna/hbond"_pair_oxdna.html, -"oxdna/stk"_pair_oxdna.html, -"oxdna/xstk"_pair_oxdna.html, -"oxdna2/coaxstk"_pair_oxdna2.html, -"oxdna2/dh"_pair_oxdna2.html, -"oxdna2/excv"_pair_oxdna2.html, -"oxdna2/stk"_pair_oxdna2.html, -"quip"_pair_quip.html, -"reax/c (ko)"_pair_reaxc.html, -"smd/hertz"_pair_smd_hertz.html, -"smd/tlsph"_pair_smd_tlsph.html, -"smd/triangulated/surface"_pair_smd_triangulated_surface.html, -"smd/ulsph"_pair_smd_ulsph.html, -"smtbq"_pair_smtbq.html, -"snap (k)"_pair_snap.html, -"sph/heatconduction"_pair_sph_heatconduction.html, -"sph/idealgas"_pair_sph_idealgas.html, -"sph/lj"_pair_sph_lj.html, -"sph/rhosum"_pair_sph_rhosum.html, -"sph/taitwater"_pair_sph_taitwater.html, -"sph/taitwater/morris"_pair_sph_taitwater_morris.html, -"srp"_pair_srp.html, -"table/rx (k)"_pair_table_rx.html, -"tdpd"_pair_meso.html, -"tersoff/table (o)"_pair_tersoff.html, -"thole"_pair_thole.html, -"tip4p/long/soft (o)"_pair_lj_soft.html :tb(c=4,ea=c) - -:line - -Bond_style potentials :h3 - -See the "bond_style"_bond_style.html command for an overview of bond -potentials. Click on the style itself for a full description. Some -of the styles have accelerated versions, which can be used if LAMMPS -is built with the "appropriate accelerated -package"_Section_accelerate.html. This is indicated by additional -letters in parenthesis: g = GPU, i = USER-INTEL, k = -KOKKOS, o = USER-OMP, t = OPT. - -"none"_bond_none.html, -"zero"_bond_zero.html, -"hybrid"_bond_hybrid.html, -"class2 (ko)"_bond_class2.html, -"fene (iko)"_bond_fene.html, -"fene/expand (o)"_bond_fene_expand.html, -"gromos (o)"_bond_gromos.html, -"harmonic (ko)"_bond_harmonic.html, -"morse (o)"_bond_morse.html, -"nonlinear (o)"_bond_nonlinear.html, -"quartic (o)"_bond_quartic.html, -"table (o)"_bond_table.html :tb(c=4,ea=c) - -These are additional bond styles in USER packages, which can be used -if "LAMMPS is built with the appropriate -package"_Section_start.html#start_3. - -"harmonic/shift (o)"_bond_harmonic_shift.html, -"harmonic/shift/cut (o)"_bond_harmonic_shift_cut.html, -"oxdna/fene"_bond_oxdna.html, -"oxdna2/fene"_bond_oxdna.html :tb(c=4,ea=c) - -:line - -Angle_style potentials :h3 - -See the "angle_style"_angle_style.html command for an overview of -angle potentials. Click on the style itself for a full description. -Some of the styles have accelerated versions, which can be used if -LAMMPS is built with the "appropriate accelerated -package"_Section_accelerate.html. This is indicated by additional -letters in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = -USER-OMP, t = OPT. - -"none"_angle_none.html, -"zero"_angle_zero.html, -"hybrid"_angle_hybrid.html, -"charmm (ko)"_angle_charmm.html, -"class2 (ko)"_angle_class2.html, -"cosine (o)"_angle_cosine.html, -"cosine/delta (o)"_angle_cosine_delta.html, -"cosine/periodic (o)"_angle_cosine_periodic.html, -"cosine/squared (o)"_angle_cosine_squared.html, -"harmonic (iko)"_angle_harmonic.html, -"table (o)"_angle_table.html :tb(c=4,ea=c) - -These are additional angle styles in USER packages, which can be used -if "LAMMPS is built with the appropriate -package"_Section_start.html#start_3. - -"cosine/shift (o)"_angle_cosine_shift.html, -"cosine/shift/exp (o)"_angle_cosine_shift_exp.html, -"dipole (o)"_angle_dipole.html, -"fourier (o)"_angle_fourier.html, -"fourier/simple (o)"_angle_fourier_simple.html, -"quartic (o)"_angle_quartic.html, -"sdk"_angle_sdk.html :tb(c=4,ea=c) - -:line - -Dihedral_style potentials :h3 - -See the "dihedral_style"_dihedral_style.html command for an overview -of dihedral potentials. Click on the style itself for a full -description. Some of the styles have accelerated versions, which can -be used if LAMMPS is built with the "appropriate accelerated -package"_Section_accelerate.html. This is indicated by additional -letters in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = -USER-OMP, t = OPT. - -"none"_dihedral_none.html, -"zero"_dihedral_zero.html, -"hybrid"_dihedral_hybrid.html, -"charmm (iko)"_dihedral_charmm.html, -"charmmfsw"_dihedral_charmm.html, -"class2 (ko)"_dihedral_class2.html, -"harmonic (io)"_dihedral_harmonic.html, -"helix (o)"_dihedral_helix.html, -"multi/harmonic (o)"_dihedral_multi_harmonic.html, -"opls (iko)"_dihedral_opls.html :tb(c=4,ea=c) - -These are additional dihedral styles in USER packages, which can be -used if "LAMMPS is built with the appropriate -package"_Section_start.html#start_3. - -"cosine/shift/exp (o)"_dihedral_cosine_shift_exp.html, -"fourier (io)"_dihedral_fourier.html, -"nharmonic (o)"_dihedral_nharmonic.html, -"quadratic (o)"_dihedral_quadratic.html, -"spherical (o)"_dihedral_spherical.html, -"table (o)"_dihedral_table.html, -"table/cut"_dihedral_table_cut.html :tb(c=4,ea=c) - -:line - -Improper_style potentials :h3 - -See the "improper_style"_improper_style.html command for an overview -of improper potentials. Click on the style itself for a full -description. Some of the styles have accelerated versions, which can -be used if LAMMPS is built with the "appropriate accelerated -package"_Section_accelerate.html. This is indicated by additional -letters in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = -USER-OMP, t = OPT. - -"none"_improper_none.html, -"zero"_improper_zero.html, -"hybrid"_improper_hybrid.html, -"class2 (ko)"_improper_class2.html, -"cvff (io)"_improper_cvff.html, -"harmonic (iko)"_improper_harmonic.html, -"umbrella (o)"_improper_umbrella.html :tb(c=4,ea=c) - -These are additional improper styles in USER packages, which can be -used if "LAMMPS is built with the appropriate -package"_Section_start.html#start_3. - -"cossq (o)"_improper_cossq.html, -"distance"_improper_distance.html, -"fourier (o)"_improper_fourier.html, -"ring (o)"_improper_ring.html :tb(c=4,ea=c) - -:line - -Kspace solvers :h3 - -See the "kspace_style"_kspace_style.html command for an overview of -Kspace solvers. Click on the style itself for a full description. -Some of the styles have accelerated versions, which can be used if -LAMMPS is built with the "appropriate accelerated -package"_Section_accelerate.html. This is indicated by additional -letters in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = -USER-OMP, t = OPT. - -"ewald (o)"_kspace_style.html, -"ewald/disp"_kspace_style.html, -"msm (o)"_kspace_style.html, -"msm/cg (o)"_kspace_style.html, -"pppm (gok)"_kspace_style.html, -"pppm/cg (o)"_kspace_style.html, -"pppm/disp (i)"_kspace_style.html, -"pppm/disp/tip4p"_kspace_style.html, -"pppm/stagger"_kspace_style.html, -"pppm/tip4p (o)"_kspace_style.html :tb(c=4,ea=c) diff --git a/doc/src/Section_history.txt b/doc/src/Section_history.txt deleted file mode 100644 index 7b90410628..0000000000 --- a/doc/src/Section_history.txt +++ /dev/null @@ -1,135 +0,0 @@ -"Previous Section"_Section_errors.html - "LAMMPS WWW Site"_lws - -"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next -Section"_Manual.html :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Section_commands.html#comm) - -:line - -13. Future and history :h2 - -This section lists features we plan to add to LAMMPS, features of -previous versions of LAMMPS, and features of other parallel molecular -dynamics codes our group has distributed. - -13.1 "Coming attractions"_#hist_1 -13.2 "Past versions"_#hist_2 :all(b) - -:line -:line - -13.1 Coming attractions :h3,link(hist_1) - -As of summer 2016 we are using the "LAMMPS project issue tracker -on GitHub"_https://github.com/lammps/lammps/issues for keeping -track of suggested, planned or pending new features. This includes -discussions of how to best implement them, or why they would be -useful. Especially if a planned or proposed feature is non-trivial -to add, e.g. because it requires changes to some of the core -classes of LAMMPS, people planning to contribute a new feature to -LAMMS are encouraged to submit an issue about their planned -implementation this way in order to receive feedback from the -LAMMPS core developers. They will provide suggestions about -the validity of the proposed approach and possible improvements, -pitfalls or alternatives. - -Please see some of the closed issues for examples of how to -suggest code enhancements, submit proposed changes, or report -possible bugs and how they are resolved. - -As an alternative to using GitHub, you may e-mail the -"core developers"_http://lammps.sandia.gov/authors.html or send -an e-mail to the "LAMMPS Mail list"_http://lammps.sandia.gov/mail.html -if you want to have your suggestion added to the list. - -:line - -13.2 Past versions :h3,link(hist_2) - -LAMMPS development began in the mid 1990s under a cooperative research -& development agreement (CRADA) between two DOE labs (Sandia and LLNL) -and 3 companies (Cray, Bristol Myers Squibb, and Dupont). The goal was -to develop a large-scale parallel classical MD code; the coding effort -was led by Steve Plimpton at Sandia. - -After the CRADA ended, a final F77 version, LAMMPS 99, was -released. As development of LAMMPS continued at Sandia, its memory -management was converted to F90; a final F90 version was released as -LAMMPS 2001. - -The current LAMMPS is a rewrite in C++ and was first publicly released -as an open source code in 2004. It includes many new features beyond -those in LAMMPS 99 or 2001. It also includes features from older -parallel MD codes written at Sandia, namely ParaDyn, Warp, and -GranFlow (see below). - -In late 2006 we began merging new capabilities into LAMMPS that were -developed by Aidan Thompson at Sandia for his MD code GRASP, which has -a parallel framework similar to LAMMPS. Most notably, these have -included many-body potentials - Stillinger-Weber, Tersoff, ReaxFF - -and the associated charge-equilibration routines needed for ReaxFF. - -The "History link"_http://lammps.sandia.gov/history.html on the -LAMMPS WWW page gives a timeline of features added to the -C++ open-source version of LAMMPS over the last several years. - -These older codes are available for download from the "LAMMPS WWW -site"_lws, except for Warp & GranFlow which were primarily used -internally. A brief listing of their features is given here. - -LAMMPS 2001 - - F90 + MPI - dynamic memory - spatial-decomposition parallelism - NVE, NVT, NPT, NPH, rRESPA integrators - LJ and Coulombic pairwise force fields - all-atom, united-atom, bead-spring polymer force fields - CHARMM-compatible force fields - class 2 force fields - 3d/2d Ewald & PPPM - various force and temperature constraints - SHAKE - Hessian-free truncated-Newton minimizer - user-defined diagnostics :ul - -LAMMPS 99 - - F77 + MPI - static memory allocation - spatial-decomposition parallelism - most of the LAMMPS 2001 features with a few exceptions - no 2d Ewald & PPPM - molecular force fields are missing a few CHARMM terms - no SHAKE :ul - -Warp - - F90 + MPI - spatial-decomposition parallelism - embedded atom method (EAM) metal potentials + LJ - lattice and grain-boundary atom creation - NVE, NVT integrators - boundary conditions for applying shear stresses - temperature controls for actively sheared systems - per-atom energy and centro-symmetry computation and output :ul - -ParaDyn - - F77 + MPI - atom- and force-decomposition parallelism - embedded atom method (EAM) metal potentials - lattice atom creation - NVE, NVT, NPT integrators - all serial DYNAMO features for controls and constraints :ul - -GranFlow - - F90 + MPI - spatial-decomposition parallelism - frictional granular potentials - NVE integrator - boundary conditions for granular flow and packing and walls - particle insertion :ul diff --git a/doc/src/Section_howto.txt b/doc/src/Section_howto.txt deleted file mode 100644 index e852e0abd4..0000000000 --- a/doc/src/Section_howto.txt +++ /dev/null @@ -1,2959 +0,0 @@ -"Previous Section"_Section_accelerate.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Section_example.html :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Section_commands.html#comm) - -:line - -6. How-to discussions :h2 - -This section describes how to perform common tasks using LAMMPS. - -6.1 "Restarting a simulation"_#howto_1 -6.2 "2d simulations"_#howto_2 -6.3 "CHARMM, AMBER, and DREIDING force fields"_#howto_3 -6.4 "Running multiple simulations from one input script"_#howto_4 -6.5 "Multi-replica simulations"_#howto_5 -6.6 "Granular models"_#howto_6 -6.7 "TIP3P water model"_#howto_7 -6.8 "TIP4P water model"_#howto_8 -6.9 "SPC water model"_#howto_9 -6.10 "Coupling LAMMPS to other codes"_#howto_10 -6.11 "Visualizing LAMMPS snapshots"_#howto_11 -6.12 "Triclinic (non-orthogonal) simulation boxes"_#howto_12 -6.13 "NEMD simulations"_#howto_13 -6.14 "Finite-size spherical and aspherical particles"_#howto_14 -6.15 "Output from LAMMPS (thermo, dumps, computes, fixes, variables)"_#howto_15 -6.16 "Thermostatting, barostatting and computing temperature"_#howto_16 -6.17 "Walls"_#howto_17 -6.18 "Elastic constants"_#howto_18 -6.19 "Library interface to LAMMPS"_#howto_19 -6.20 "Calculating thermal conductivity"_#howto_20 -6.21 "Calculating viscosity"_#howto_21 -6.22 "Calculating a diffusion coefficient"_#howto_22 -6.23 "Using chunks to calculate system properties"_#howto_23 -6.24 "Setting parameters for the kspace_style pppm/disp command"_#howto_24 -6.25 "Polarizable models"_#howto_25 -6.26 "Adiabatic core/shell model"_#howto_26 -6.27 "Drude induced dipoles"_#howto_27 :all(b) - -The example input scripts included in the LAMMPS distribution and -highlighted in "Section 7"_Section_example.html also show how to -setup and run various kinds of simulations. - -:line -:line - -6.1 Restarting a simulation :link(howto_1),h4 - -There are 3 ways to continue a long LAMMPS simulation. Multiple -"run"_run.html commands can be used in the same input script. Each -run will continue from where the previous run left off. Or binary -restart files can be saved to disk using the "restart"_restart.html -command. At a later time, these binary files can be read via a -"read_restart"_read_restart.html command in a new script. Or they can -be converted to text data files using the "-r command-line -switch"_Section_start.html#start_6 and read by a -"read_data"_read_data.html command in a new script. - -Here we give examples of 2 scripts that read either a binary restart -file or a converted data file and then issue a new run command to -continue where the previous run left off. They illustrate what -settings must be made in the new script. Details are discussed in the -documentation for the "read_restart"_read_restart.html and -"read_data"_read_data.html commands. - -Look at the {in.chain} input script provided in the {bench} directory -of the LAMMPS distribution to see the original script that these 2 -scripts are based on. If that script had the line - -restart 50 tmp.restart :pre - -added to it, it would produce 2 binary restart files (tmp.restart.50 -and tmp.restart.100) as it ran. - -This script could be used to read the 1st restart file and re-run the -last 50 timesteps: - -read_restart tmp.restart.50 :pre - -neighbor 0.4 bin -neigh_modify every 1 delay 1 :pre - -fix 1 all nve -fix 2 all langevin 1.0 1.0 10.0 904297 :pre - -timestep 0.012 :pre - -run 50 :pre - -Note that the following commands do not need to be repeated because -their settings are included in the restart file: {units, atom_style, -special_bonds, pair_style, bond_style}. However these commands do -need to be used, since their settings are not in the restart file: -{neighbor, fix, timestep}. - -If you actually use this script to perform a restarted run, you will -notice that the thermodynamic data match at step 50 (if you also put a -"thermo 50" command in the original script), but do not match at step -100. This is because the "fix langevin"_fix_langevin.html command -uses random numbers in a way that does not allow for perfect restarts. - -As an alternate approach, the restart file could be converted to a data -file as follows: - -lmp_g++ -r tmp.restart.50 tmp.restart.data :pre - -Then, this script could be used to re-run the last 50 steps: - -units lj -atom_style bond -pair_style lj/cut 1.12 -pair_modify shift yes -bond_style fene -special_bonds 0.0 1.0 1.0 :pre - -read_data tmp.restart.data :pre - -neighbor 0.4 bin -neigh_modify every 1 delay 1 :pre - -fix 1 all nve -fix 2 all langevin 1.0 1.0 10.0 904297 :pre - -timestep 0.012 :pre - -reset_timestep 50 -run 50 :pre - -Note that nearly all the settings specified in the original {in.chain} -script must be repeated, except the {pair_coeff} and {bond_coeff} -commands since the new data file lists the force field coefficients. -Also, the "reset_timestep"_reset_timestep.html command is used to tell -LAMMPS the current timestep. This value is stored in restart files, -but not in data files. - -:line - -6.2 2d simulations :link(howto_2),h4 - -Use the "dimension"_dimension.html command to specify a 2d simulation. - -Make the simulation box periodic in z via the "boundary"_boundary.html -command. This is the default. - -If using the "create box"_create_box.html command to define a -simulation box, set the z dimensions narrow, but finite, so that the -create_atoms command will tile the 3d simulation box with a single z -plane of atoms - e.g. - -"create box"_create_box.html 1 -10 10 -10 10 -0.25 0.25 :pre - -If using the "read data"_read_data.html command to read in a file of -atom coordinates, set the "zlo zhi" values to be finite but narrow, -similar to the create_box command settings just described. For each -atom in the file, assign a z coordinate so it falls inside the -z-boundaries of the box - e.g. 0.0. - -Use the "fix enforce2d"_fix_enforce2d.html command as the last -defined fix to insure that the z-components of velocities and forces -are zeroed out every timestep. The reason to make it the last fix is -so that any forces induced by other fixes will be zeroed out. - -Many of the example input scripts included in the LAMMPS distribution -are for 2d models. - -NOTE: Some models in LAMMPS treat particles as finite-size spheres, as -opposed to point particles. See the "atom_style -sphere"_atom_style.html and "fix nve/sphere"_fix_nve_sphere.html -commands for details. By default, for 2d simulations, such particles -will still be modeled as 3d spheres, not 2d discs (circles), meaning -their moment of inertia will be that of a sphere. If you wish to -model them as 2d discs, see the "set density/disc"_set.html command -and the {disc} option for the "fix nve/sphere"_fix_nve_sphere.html, -"fix nvt/sphere"_fix_nvt_sphere.html, "fix -nph/sphere"_fix_nph_sphere.html, "fix npt/sphere"_fix_npt_sphere.html -commands. - -:line - -6.3 CHARMM, AMBER, and DREIDING force fields :link(howto_3),h4 - -A force field has 2 parts: the formulas that define it and the -coefficients used for a particular system. Here we only discuss -formulas implemented in LAMMPS that correspond to formulas commonly -used in the CHARMM, AMBER, and DREIDING force fields. Setting -coefficients is done in the input data file via the -"read_data"_read_data.html command or in the input script with -commands like "pair_coeff"_pair_coeff.html or -"bond_coeff"_bond_coeff.html. See "Section 9"_Section_tools.html -for additional tools that can use CHARMM or AMBER to assign force -field coefficients and convert their output into LAMMPS input. - -See "(MacKerell)"_#howto-MacKerell for a description of the CHARMM force -field. See "(Cornell)"_#howto-Cornell for a description of the AMBER force -field. - -:link(charmm,http://www.scripps.edu/brooks) -:link(amber,http://amber.scripps.edu) - -These style choices compute force field formulas that are consistent -with common options in CHARMM or AMBER. See each command's -documentation for the formula it computes. - -"bond_style"_bond_harmonic.html harmonic -"angle_style"_angle_charmm.html charmm -"dihedral_style"_dihedral_charmm.html charmmfsh -"dihedral_style"_dihedral_charmm.html charmm -"pair_style"_pair_charmm.html lj/charmmfsw/coul/charmmfsh -"pair_style"_pair_charmm.html lj/charmmfsw/coul/long -"pair_style"_pair_charmm.html lj/charmm/coul/charmm -"pair_style"_pair_charmm.html lj/charmm/coul/charmm/implicit -"pair_style"_pair_charmm.html lj/charmm/coul/long :ul - -"special_bonds"_special_bonds.html charmm -"special_bonds"_special_bonds.html amber :ul - -NOTE: For CHARMM, newer {charmmfsw} or {charmmfsh} styles were -released in March 2017. We recommend they be used instead of the -older {charmm} styles. See discussion of the differences on the "pair -charmm"_pair_charmm.html and "dihedral charmm"_dihedral_charmm.html -doc pages. - -DREIDING is a generic force field developed by the "Goddard -group"_http://www.wag.caltech.edu at Caltech and is useful for -predicting structures and dynamics of organic, biological and -main-group inorganic molecules. The philosophy in DREIDING is to use -general force constants and geometry parameters based on simple -hybridization considerations, rather than individual force constants -and geometric parameters that depend on the particular combinations of -atoms involved in the bond, angle, or torsion terms. DREIDING has an -"explicit hydrogen bond term"_pair_hbond_dreiding.html to describe -interactions involving a hydrogen atom on very electronegative atoms -(N, O, F). - -See "(Mayo)"_#howto-Mayo for a description of the DREIDING force field - -These style choices compute force field formulas that are consistent -with the DREIDING force field. See each command's -documentation for the formula it computes. - -"bond_style"_bond_harmonic.html harmonic -"bond_style"_bond_morse.html morse :ul - -"angle_style"_angle_harmonic.html harmonic -"angle_style"_angle_cosine.html cosine -"angle_style"_angle_cosine_periodic.html cosine/periodic :ul - -"dihedral_style"_dihedral_charmm.html charmm -"improper_style"_improper_umbrella.html umbrella :ul - -"pair_style"_pair_buck.html buck -"pair_style"_pair_buck.html buck/coul/cut -"pair_style"_pair_buck.html buck/coul/long -"pair_style"_pair_lj.html lj/cut -"pair_style"_pair_lj.html lj/cut/coul/cut -"pair_style"_pair_lj.html lj/cut/coul/long :ul - -"pair_style"_pair_hbond_dreiding.html hbond/dreiding/lj -"pair_style"_pair_hbond_dreiding.html hbond/dreiding/morse :ul - -"special_bonds"_special_bonds.html dreiding :ul - -:line - -6.4 Running multiple simulations from one input script :link(howto_4),h4 - -This can be done in several ways. See the documentation for -individual commands for more details on how these examples work. - -If "multiple simulations" means continue a previous simulation for -more timesteps, then you simply use the "run"_run.html command -multiple times. For example, this script - -units lj -atom_style atomic -read_data data.lj -run 10000 -run 10000 -run 10000 -run 10000 -run 10000 :pre - -would run 5 successive simulations of the same system for a total of -50,000 timesteps. - -If you wish to run totally different simulations, one after the other, -the "clear"_clear.html command can be used in between them to -re-initialize LAMMPS. For example, this script - -units lj -atom_style atomic -read_data data.lj -run 10000 -clear -units lj -atom_style atomic -read_data data.lj.new -run 10000 :pre - -would run 2 independent simulations, one after the other. - -For large numbers of independent simulations, you can use -"variables"_variable.html and the "next"_next.html and -"jump"_jump.html commands to loop over the same input script -multiple times with different settings. For example, this -script, named in.polymer - -variable d index run1 run2 run3 run4 run5 run6 run7 run8 -shell cd $d -read_data data.polymer -run 10000 -shell cd .. -clear -next d -jump in.polymer :pre - -would run 8 simulations in different directories, using a data.polymer -file in each directory. The same concept could be used to run the -same system at 8 different temperatures, using a temperature variable -and storing the output in different log and dump files, for example - -variable a loop 8 -variable t index 0.8 0.85 0.9 0.95 1.0 1.05 1.1 1.15 -log log.$a -read data.polymer -velocity all create $t 352839 -fix 1 all nvt $t $t 100.0 -dump 1 all atom 1000 dump.$a -run 100000 -clear -next t -next a -jump in.polymer :pre - -All of the above examples work whether you are running on 1 or -multiple processors, but assumed you are running LAMMPS on a single -partition of processors. LAMMPS can be run on multiple partitions via -the "-partition" command-line switch as described in "this -section"_Section_start.html#start_6 of the manual. - -In the last 2 examples, if LAMMPS were run on 3 partitions, the same -scripts could be used if the "index" and "loop" variables were -replaced with {universe}-style variables, as described in the -"variable"_variable.html command. Also, the "next t" and "next a" -commands would need to be replaced with a single "next a t" command. -With these modifications, the 8 simulations of each script would run -on the 3 partitions one after the other until all were finished. -Initially, 3 simulations would be started simultaneously, one on each -partition. When one finished, that partition would then start -the 4th simulation, and so forth, until all 8 were completed. - -:line - -6.5 Multi-replica simulations :link(howto_5),h4 - -Several commands in LAMMPS run mutli-replica simulations, meaning -that multiple instances (replicas) of your simulation are run -simultaneously, with small amounts of data exchanged between replicas -periodically. - -These are the relevant commands: - -"neb"_neb.html for nudged elastic band calculations -"prd"_prd.html for parallel replica dynamics -"tad"_tad.html for temperature accelerated dynamics -"temper"_temper.html for parallel tempering -"fix pimd"_fix_pimd.html for path-integral molecular dynamics (PIMD) :ul - -NEB is a method for finding transition states and barrier energies. -PRD and TAD are methods for performing accelerated dynamics to find -and perform infrequent events. Parallel tempering or replica exchange -runs different replicas at a series of temperature to facilitate -rare-event sampling. - -These commands can only be used if LAMMPS was built with the REPLICA -package. See the "Making LAMMPS"_Section_start.html#start_3 section -for more info on packages. - -PIMD runs different replicas whose individual particles are coupled -together by springs to model a system or ring-polymers. - -This commands can only be used if LAMMPS was built with the USER-MISC -package. See the "Making LAMMPS"_Section_start.html#start_3 section -for more info on packages. - -In all these cases, you must run with one or more processors per -replica. The processors assigned to each replica are determined at -run-time by using the "-partition command-line -switch"_Section_start.html#start_6 to launch LAMMPS on multiple -partitions, which in this context are the same as replicas. E.g. -these commands: - -mpirun -np 16 lmp_linux -partition 8x2 -in in.temper -mpirun -np 8 lmp_linux -partition 8x1 -in in.neb :pre - -would each run 8 replicas, on either 16 or 8 processors. Note the use -of the "-in command-line switch"_Section_start.html#start_6 to specify -the input script which is required when running in multi-replica mode. - -Also note that with MPI installed on a machine (e.g. your desktop), -you can run on more (virtual) processors than you have physical -processors. Thus the above commands could be run on a -single-processor (or few-processor) desktop so that you can run -a multi-replica simulation on more replicas than you have -physical processors. - -:line - -6.6 Granular models :link(howto_6),h4 - -Granular system are composed of spherical particles with a diameter, -as opposed to point particles. This means they have an angular -velocity and torque can be imparted to them to cause them to rotate. - -To run a simulation of a granular model, you will want to use -the following commands: - -"atom_style sphere"_atom_style.html -"fix nve/sphere"_fix_nve_sphere.html -"fix gravity"_fix_gravity.html :ul - -This compute - -"compute erotate/sphere"_compute_erotate_sphere.html :ul - -calculates rotational kinetic energy which can be "output with -thermodynamic info"_Section_howto.html#howto_15. - -Use one of these 3 pair potentials, which compute forces and torques -between interacting pairs of particles: - -"pair_style"_pair_style.html gran/history -"pair_style"_pair_style.html gran/no_history -"pair_style"_pair_style.html gran/hertzian :ul - -These commands implement fix options specific to granular systems: - -"fix freeze"_fix_freeze.html -"fix pour"_fix_pour.html -"fix viscous"_fix_viscous.html -"fix wall/gran"_fix_wall_gran.html :ul - -The fix style {freeze} zeroes both the force and torque of frozen -atoms, and should be used for granular system instead of the fix style -{setforce}. - -For computational efficiency, you can eliminate needless pairwise -computations between frozen atoms by using this command: - -"neigh_modify"_neigh_modify.html exclude :ul - -NOTE: By default, for 2d systems, granular particles are still modeled -as 3d spheres, not 2d discs (circles), meaning their moment of inertia -will be the same as in 3d. If you wish to model granular particles in -2d as 2d discs, see the note on this topic in "Section -6.2"_Section_howto.html#howto_2, where 2d simulations are discussed. - -:line - -6.7 TIP3P water model :link(howto_7),h4 - -The TIP3P water model as implemented in CHARMM -"(MacKerell)"_#howto-MacKerell specifies a 3-site rigid water molecule with -charges and Lennard-Jones parameters assigned to each of the 3 atoms. -In LAMMPS the "fix shake"_fix_shake.html command can be used to hold -the two O-H bonds and the H-O-H angle rigid. A bond style of -{harmonic} and an angle style of {harmonic} or {charmm} should also be -used. - -These are the additional parameters (in real units) to set for O and H -atoms and the water molecule to run a rigid TIP3P-CHARMM model with a -cutoff. The K values can be used if a flexible TIP3P model (without -fix shake) is desired. If the LJ epsilon and sigma for HH and OH are -set to 0.0, it corresponds to the original 1983 TIP3P model -"(Jorgensen)"_#Jorgensen1. - -O mass = 15.9994 -H mass = 1.008 -O charge = -0.834 -H charge = 0.417 -LJ epsilon of OO = 0.1521 -LJ sigma of OO = 3.1507 -LJ epsilon of HH = 0.0460 -LJ sigma of HH = 0.4000 -LJ epsilon of OH = 0.0836 -LJ sigma of OH = 1.7753 -K of OH bond = 450 -r0 of OH bond = 0.9572 -K of HOH angle = 55 -theta of HOH angle = 104.52 :all(b),p - -These are the parameters to use for TIP3P with a long-range Coulombic -solver (e.g. Ewald or PPPM in LAMMPS), see "(Price)"_#Price1 for -details: - -O mass = 15.9994 -H mass = 1.008 -O charge = -0.830 -H charge = 0.415 -LJ epsilon of OO = 0.102 -LJ sigma of OO = 3.188 -LJ epsilon, sigma of OH, HH = 0.0 -K of OH bond = 450 -r0 of OH bond = 0.9572 -K of HOH angle = 55 -theta of HOH angle = 104.52 :all(b),p - -Wikipedia also has a nice article on "water -models"_http://en.wikipedia.org/wiki/Water_model. - -:line - -6.8 TIP4P water model :link(howto_8),h4 - -The four-point TIP4P rigid water model extends the traditional -three-point TIP3P model by adding an additional site, usually -massless, where the charge associated with the oxygen atom is placed. -This site M is located at a fixed distance away from the oxygen along -the bisector of the HOH bond angle. A bond style of {harmonic} and an -angle style of {harmonic} or {charmm} should also be used. - -A TIP4P model is run with LAMMPS using either this command -for a cutoff model: - -"pair_style lj/cut/tip4p/cut"_pair_lj.html - -or these two commands for a long-range model: - -"pair_style lj/cut/tip4p/long"_pair_lj.html -"kspace_style pppm/tip4p"_kspace_style.html :ul - -For both models, the bond lengths and bond angles should be held fixed -using the "fix shake"_fix_shake.html command. - -These are the additional parameters (in real units) to set for O and H -atoms and the water molecule to run a rigid TIP4P model with a cutoff -"(Jorgensen)"_#Jorgensen1. Note that the OM distance is specified in -the "pair_style"_pair_style.html command, not as part of the pair -coefficients. - -O mass = 15.9994 -H mass = 1.008 -O charge = -1.040 -H charge = 0.520 -r0 of OH bond = 0.9572 -theta of HOH angle = 104.52 -OM distance = 0.15 -LJ epsilon of O-O = 0.1550 -LJ sigma of O-O = 3.1536 -LJ epsilon, sigma of OH, HH = 0.0 -Coulombic cutoff = 8.5 :all(b),p - -For the TIP4/Ice model (J Chem Phys, 122, 234511 (2005); -http://dx.doi.org/10.1063/1.1931662) these values can be used: - -O mass = 15.9994 -H mass = 1.008 -O charge = -1.1794 -H charge = 0.5897 -r0 of OH bond = 0.9572 -theta of HOH angle = 104.52 -OM distance = 0.1577 -LJ epsilon of O-O = 0.21084 -LJ sigma of O-O = 3.1668 -LJ epsilon, sigma of OH, HH = 0.0 -Coulombic cutoff = 8.5 :all(b),p - -For the TIP4P/2005 model (J Chem Phys, 123, 234505 (2005); -http://dx.doi.org/10.1063/1.2121687), these values can be used: - -O mass = 15.9994 -H mass = 1.008 -O charge = -1.1128 -H charge = 0.5564 -r0 of OH bond = 0.9572 -theta of HOH angle = 104.52 -OM distance = 0.1546 -LJ epsilon of O-O = 0.1852 -LJ sigma of O-O = 3.1589 -LJ epsilon, sigma of OH, HH = 0.0 -Coulombic cutoff = 8.5 :all(b),p - -These are the parameters to use for TIP4P with a long-range Coulombic -solver (e.g. Ewald or PPPM in LAMMPS): - -O mass = 15.9994 -H mass = 1.008 -O charge = -1.0484 -H charge = 0.5242 -r0 of OH bond = 0.9572 -theta of HOH angle = 104.52 -OM distance = 0.1250 -LJ epsilon of O-O = 0.16275 -LJ sigma of O-O = 3.16435 -LJ epsilon, sigma of OH, HH = 0.0 :all(b),p - -Note that the when using the TIP4P pair style, the neighbor list -cutoff for Coulomb interactions is effectively extended by a distance -2 * (OM distance), to account for the offset distance of the -fictitious charges on O atoms in water molecules. Thus it is -typically best in an efficiency sense to use a LJ cutoff >= Coulomb -cutoff + 2*(OM distance), to shrink the size of the neighbor list. -This leads to slightly larger cost for the long-range calculation, so -you can test the trade-off for your model. The OM distance and the LJ -and Coulombic cutoffs are set in the "pair_style -lj/cut/tip4p/long"_pair_lj.html command. - -Wikipedia also has a nice article on "water -models"_http://en.wikipedia.org/wiki/Water_model. - -:line - -6.9 SPC water model :link(howto_9),h4 - -The SPC water model specifies a 3-site rigid water molecule with -charges and Lennard-Jones parameters assigned to each of the 3 atoms. -In LAMMPS the "fix shake"_fix_shake.html command can be used to hold -the two O-H bonds and the H-O-H angle rigid. A bond style of -{harmonic} and an angle style of {harmonic} or {charmm} should also be -used. - -These are the additional parameters (in real units) to set for O and H -atoms and the water molecule to run a rigid SPC model. - -O mass = 15.9994 -H mass = 1.008 -O charge = -0.820 -H charge = 0.410 -LJ epsilon of OO = 0.1553 -LJ sigma of OO = 3.166 -LJ epsilon, sigma of OH, HH = 0.0 -r0 of OH bond = 1.0 -theta of HOH angle = 109.47 :all(b),p - -Note that as originally proposed, the SPC model was run with a 9 -Angstrom cutoff for both LJ and Coulommbic terms. It can also be used -with long-range Coulombics (Ewald or PPPM in LAMMPS), without changing -any of the parameters above, though it becomes a different model in -that mode of usage. - -The SPC/E (extended) water model is the same, except -the partial charge assignments change: - -O charge = -0.8476 -H charge = 0.4238 :all(b),p - -See the "(Berendsen)"_#howto-Berendsen reference for more details on both -the SPC and SPC/E models. - -Wikipedia also has a nice article on "water -models"_http://en.wikipedia.org/wiki/Water_model. - -:line - -6.10 Coupling LAMMPS to other codes :link(howto_10),h4 - -LAMMPS is designed to allow it to be coupled to other codes. For -example, a quantum mechanics code might compute forces on a subset of -atoms and pass those forces to LAMMPS. Or a continuum finite element -(FE) simulation might use atom positions as boundary conditions on FE -nodal points, compute a FE solution, and return interpolated forces on -MD atoms. - -LAMMPS can be coupled to other codes in at least 3 ways. Each has -advantages and disadvantages, which you'll have to think about in the -context of your application. - -(1) Define a new "fix"_fix.html command that calls the other code. In -this scenario, LAMMPS is the driver code. During its timestepping, -the fix is invoked, and can make library calls to the other code, -which has been linked to LAMMPS as a library. This is the way the -"POEMS"_poems package that performs constrained rigid-body motion on -groups of atoms is hooked to LAMMPS. See the -"fix poems"_fix_poems.html command for more details. See "this -section"_Section_modify.html of the documentation for info on how to add -a new fix to LAMMPS. - -:link(poems,http://www.rpi.edu/~anderk5/lab) - -(2) Define a new LAMMPS command that calls the other code. This is -conceptually similar to method (1), but in this case LAMMPS and the -other code are on a more equal footing. Note that now the other code -is not called during the timestepping of a LAMMPS run, but between -runs. The LAMMPS input script can be used to alternate LAMMPS runs -with calls to the other code, invoked via the new command. The -"run"_run.html command facilitates this with its {every} option, which -makes it easy to run a few steps, invoke the command, run a few steps, -invoke the command, etc. - -In this scenario, the other code can be called as a library, as in -(1), or it could be a stand-alone code, invoked by a system() call -made by the command (assuming your parallel machine allows one or more -processors to start up another program). In the latter case the -stand-alone code could communicate with LAMMPS thru files that the -command writes and reads. - -See "Section 10"_Section_modify.html of the documentation for how -to add a new command to LAMMPS. - -(3) Use LAMMPS as a library called by another code. In this case the -other code is the driver and calls LAMMPS as needed. Or a wrapper -code could link and call both LAMMPS and another code as libraries. -Again, the "run"_run.html command has options that allow it to be -invoked with minimal overhead (no setup or clean-up) if you wish to do -multiple short runs, driven by another program. - -Examples of driver codes that call LAMMPS as a library are included in -the examples/COUPLE directory of the LAMMPS distribution; see -examples/COUPLE/README for more details: - -simple: simple driver programs in C++ and C which invoke LAMMPS as a -library :ulb,l - -lammps_quest: coupling of LAMMPS and "Quest"_quest, to run classical -MD with quantum forces calculated by a density functional code :l - -lammps_spparks: coupling of LAMMPS and "SPPARKS"_spparks, to couple -a kinetic Monte Carlo model for grain growth using MD to calculate -strain induced across grain boundaries :l -:ule - -:link(quest,http://dft.sandia.gov/Quest) -:link(spparks,http://www.sandia.gov/~sjplimp/spparks.html) - -"This section"_Section_start.html#start_5 of the documentation -describes how to build LAMMPS as a library. Once this is done, you -can interface with LAMMPS either via C++, C, Fortran, or Python (or -any other language that supports a vanilla C-like interface). For -example, from C++ you could create one (or more) "instances" of -LAMMPS, pass it an input script to process, or execute individual -commands, all by invoking the correct class methods in LAMMPS. From C -or Fortran you can make function calls to do the same things. See -"Section 11"_Section_python.html of the manual for a description -of the Python wrapper provided with LAMMPS that operates through the -LAMMPS library interface. - -The files src/library.cpp and library.h contain the C-style interface -to LAMMPS. See "Section 6.19"_Section_howto.html#howto_19 of the -manual for a description of the interface and how to extend it for -your needs. - -Note that the lammps_open() function that creates an instance of -LAMMPS takes an MPI communicator as an argument. This means that -instance of LAMMPS will run on the set of processors in the -communicator. Thus the calling code can run LAMMPS on all or a subset -of processors. For example, a wrapper script might decide to -alternate between LAMMPS and another code, allowing them both to run -on all the processors. Or it might allocate half the processors to -LAMMPS and half to the other code and run both codes simultaneously -before syncing them up periodically. Or it might instantiate multiple -instances of LAMMPS to perform different calculations. - -:line - -6.11 Visualizing LAMMPS snapshots :link(howto_11),h4 - -LAMMPS itself does not do visualization, but snapshots from LAMMPS -simulations can be visualized (and analyzed) in a variety of ways. - -LAMMPS snapshots are created by the "dump"_dump.html command which can -create files in several formats. The native LAMMPS dump format is a -text file (see "dump atom" or "dump custom") which can be visualized -by several popular visualization tools. The "dump image"_dump_image.html -and "dump movie"_dump_image.html styles can output internally rendered -images and convert a sequence of them to a movie during the MD run. -Several programs included with LAMMPS as auxiliary tools can convert -between LAMMPS format files and other formats. -See the "Section 9"_Section_tools.html doc page for details. - -A Python-based toolkit distributed by our group can read native LAMMPS -dump files, including custom dump files with additional columns of -user-specified atom information, and convert them to various formats -or pipe them into visualization software directly. See the "Pizza.py -WWW site"_pizza for details. Specifically, Pizza.py can convert -LAMMPS dump files into PDB, XYZ, "Ensight"_ensight, and VTK formats. -Pizza.py can pipe LAMMPS dump files directly into the Raster3d and -RasMol visualization programs. Pizza.py has tools that do interactive -3d OpenGL visualization and one that creates SVG images of dump file -snapshots. - -:link(pizza,http://www.sandia.gov/~sjplimp/pizza.html) -:link(ensight,http://www.ensight.com) -:link(atomeye,http://mt.seas.upenn.edu/Archive/Graphics/A) - -:line - -6.12 Triclinic (non-orthogonal) simulation boxes :link(howto_12),h4 - -By default, LAMMPS uses an orthogonal simulation box to encompass the -particles. The "boundary"_boundary.html command sets the boundary -conditions of the box (periodic, non-periodic, etc). The orthogonal -box has its "origin" at (xlo,ylo,zlo) and is defined by 3 edge vectors -starting from the origin given by [a] = (xhi-xlo,0,0); [b] = -(0,yhi-ylo,0); [c] = (0,0,zhi-zlo). The 6 parameters -(xlo,xhi,ylo,yhi,zlo,zhi) are defined at the time the simulation box -is created, e.g. by the "create_box"_create_box.html or -"read_data"_read_data.html or "read_restart"_read_restart.html -commands. Additionally, LAMMPS defines box size parameters lx,ly,lz -where lx = xhi-xlo, and similarly in the y and z dimensions. The 6 -parameters, as well as lx,ly,lz, can be output via the "thermo_style -custom"_thermo_style.html command. - -LAMMPS also allows simulations to be performed in triclinic -(non-orthogonal) simulation boxes shaped as a parallelepiped with -triclinic symmetry. The parallelepiped has its "origin" at -(xlo,ylo,zlo) and is defined by 3 edge vectors starting from the -origin given by [a] = (xhi-xlo,0,0); [b] = (xy,yhi-ylo,0); [c] = -(xz,yz,zhi-zlo). {xy,xz,yz} can be 0.0 or positive or negative values -and are called "tilt factors" because they are the amount of -displacement applied to faces of an originally orthogonal box to -transform it into the parallelepiped. In LAMMPS the triclinic -simulation box edge vectors [a], [b], and [c] cannot be arbitrary -vectors. As indicated, [a] must lie on the positive x axis. [b] must -lie in the xy plane, with strictly positive y component. [c] may have -any orientation with strictly positive z component. The requirement -that [a], [b], and [c] have strictly positive x, y, and z components, -respectively, ensures that [a], [b], and [c] form a complete -right-handed basis. These restrictions impose no loss of generality, -since it is possible to rotate/invert any set of 3 crystal basis -vectors so that they conform to the restrictions. - -For example, assume that the 3 vectors [A],[B],[C] are the edge -vectors of a general parallelepiped, where there is no restriction on -[A],[B],[C] other than they form a complete right-handed basis i.e. -[A] x [B] . [C] > 0. The equivalent LAMMPS [a],[b],[c] are a linear -rotation of [A], [B], and [C] and can be computed as follows: - -:c,image(Eqs/transform.jpg) - -where A = | [A] | indicates the scalar length of [A]. The hat symbol (^) -indicates the corresponding unit vector. {beta} and {gamma} are angles -between the vectors described below. Note that by construction, -[a], [b], and [c] have strictly positive x, y, and z components, respectively. -If it should happen that -[A], [B], and [C] form a left-handed basis, then the above equations -are not valid for [c]. In this case, it is necessary -to first apply an inversion. This can be achieved -by interchanging two basis vectors or by changing the sign of one of them. - -For consistency, the same rotation/inversion applied to the basis vectors -must also be applied to atom positions, velocities, -and any other vector quantities. -This can be conveniently achieved by first converting to -fractional coordinates in the -old basis and then converting to distance coordinates in the new basis. -The transformation is given by the following equation: - -:c,image(Eqs/rotate.jpg) - -where {V} is the volume of the box, [X] is the original vector quantity and -[x] is the vector in the LAMMPS basis. - -There is no requirement that a triclinic box be periodic in any -dimension, though it typically should be in at least the 2nd dimension -of the tilt (y in xy) if you want to enforce a shift in periodic -boundary conditions across that boundary. Some commands that work -with triclinic boxes, e.g. the "fix deform"_fix_deform.html and "fix -npt"_fix_nh.html commands, require periodicity or non-shrink-wrap -boundary conditions in specific dimensions. See the command doc pages -for details. - -The 9 parameters (xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz) are defined at the -time the simulation box is created. This happens in one of 3 ways. -If the "create_box"_create_box.html command is used with a region of -style {prism}, then a triclinic box is setup. See the -"region"_region.html command for details. If the -"read_data"_read_data.html command is used to define the simulation -box, and the header of the data file contains a line with the "xy xz -yz" keyword, then a triclinic box is setup. See the -"read_data"_read_data.html command for details. Finally, if the -"read_restart"_read_restart.html command reads a restart file which -was written from a simulation using a triclinic box, then a triclinic -box will be setup for the restarted simulation. - -Note that you can define a triclinic box with all 3 tilt factors = -0.0, so that it is initially orthogonal. This is necessary if the box -will become non-orthogonal, e.g. due to the "fix npt"_fix_nh.html or -"fix deform"_fix_deform.html commands. Alternatively, you can use the -"change_box"_change_box.html command to convert a simulation box from -orthogonal to triclinic and vice versa. - -As with orthogonal boxes, LAMMPS defines triclinic box size parameters -lx,ly,lz where lx = xhi-xlo, and similarly in the y and z dimensions. -The 9 parameters, as well as lx,ly,lz, can be output via the -"thermo_style custom"_thermo_style.html command. - -To avoid extremely tilted boxes (which would be computationally -inefficient), LAMMPS normally requires that no tilt factor can skew -the box more than half the distance of the parallel box length, which -is the 1st dimension in the tilt factor (x for xz). This is required -both when the simulation box is created, e.g. via the -"create_box"_create_box.html or "read_data"_read_data.html commands, -as well as when the box shape changes dynamically during a simulation, -e.g. via the "fix deform"_fix_deform.html or "fix npt"_fix_nh.html -commands. - -For example, if xlo = 2 and xhi = 12, then the x box length is 10 and -the xy tilt factor must be between -5 and 5. Similarly, both xz and -yz must be between -(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is -not a limitation, since if the maximum tilt factor is 5 (as in this -example), then configurations with tilt = ..., -15, -5, 5, 15, 25, -... are geometrically all equivalent. If the box tilt exceeds this -limit during a dynamics run (e.g. via the "fix deform"_fix_deform.html -command), then the box is "flipped" to an equivalent shape with a tilt -factor within the bounds, so the run can continue. See the "fix -deform"_fix_deform.html doc page for further details. - -One exception to this rule is if the 1st dimension in the tilt -factor (x for xy) is non-periodic. In that case, the limits on the -tilt factor are not enforced, since flipping the box in that dimension -does not change the atom positions due to non-periodicity. In this -mode, if you tilt the system to extreme angles, the simulation will -simply become inefficient, due to the highly skewed simulation box. - -The limitation on not creating a simulation box with a tilt factor -skewing the box more than half the distance of the parallel box length -can be overridden via the "box"_box.html command. Setting the {tilt} -keyword to {large} allows any tilt factors to be specified. - -Box flips that may occur using the "fix deform"_fix_deform.html or -"fix npt"_fix_nh.html commands can be turned off using the {flip no} -option with either of the commands. - -Note that if a simulation box has a large tilt factor, LAMMPS will run -less efficiently, due to the large volume of communication needed to -acquire ghost atoms around a processor's irregular-shaped sub-domain. -For extreme values of tilt, LAMMPS may also lose atoms and generate an -error. - -Triclinic crystal structures are often defined using three lattice -constants {a}, {b}, and {c}, and three angles {alpha}, {beta} and -{gamma}. Note that in this nomenclature, the a, b, and c lattice -constants are the scalar lengths of the edge vectors [a], [b], and [c] -defined above. The relationship between these 6 quantities -(a,b,c,alpha,beta,gamma) and the LAMMPS box sizes (lx,ly,lz) = -(xhi-xlo,yhi-ylo,zhi-zlo) and tilt factors (xy,xz,yz) is as follows: - -:c,image(Eqs/box.jpg) - -The inverse relationship can be written as follows: - -:c,image(Eqs/box_inverse.jpg) - -The values of {a}, {b}, {c} , {alpha}, {beta} , and {gamma} can be printed -out or accessed by computes using the -"thermo_style custom"_thermo_style.html keywords -{cella}, {cellb}, {cellc}, {cellalpha}, {cellbeta}, {cellgamma}, -respectively. - -As discussed on the "dump"_dump.html command doc page, when the BOX -BOUNDS for a snapshot is written to a dump file for a triclinic box, -an orthogonal bounding box which encloses the triclinic simulation box -is output, along with the 3 tilt factors (xy, xz, yz) of the triclinic -box, formatted as follows: - -ITEM: BOX BOUNDS xy xz yz -xlo_bound xhi_bound xy -ylo_bound yhi_bound xz -zlo_bound zhi_bound yz :pre - -This bounding box is convenient for many visualization programs and is -calculated from the 9 triclinic box parameters -(xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz) as follows: - -xlo_bound = xlo + MIN(0.0,xy,xz,xy+xz) -xhi_bound = xhi + MAX(0.0,xy,xz,xy+xz) -ylo_bound = ylo + MIN(0.0,yz) -yhi_bound = yhi + MAX(0.0,yz) -zlo_bound = zlo -zhi_bound = zhi :pre - -These formulas can be inverted if you need to convert the bounding box -back into the triclinic box parameters, e.g. xlo = xlo_bound - -MIN(0.0,xy,xz,xy+xz). - -One use of triclinic simulation boxes is to model solid-state crystals -with triclinic symmetry. The "lattice"_lattice.html command can be -used with non-orthogonal basis vectors to define a lattice that will -tile a triclinic simulation box via the -"create_atoms"_create_atoms.html command. - -A second use is to run Parinello-Rahman dynamics via the "fix -npt"_fix_nh.html command, which will adjust the xy, xz, yz tilt -factors to compensate for off-diagonal components of the pressure -tensor. The analog for an "energy minimization"_minimize.html is -the "fix box/relax"_fix_box_relax.html command. - -A third use is to shear a bulk solid to study the response of the -material. The "fix deform"_fix_deform.html command can be used for -this purpose. It allows dynamic control of the xy, xz, yz tilt -factors as a simulation runs. This is discussed in the next section -on non-equilibrium MD (NEMD) simulations. - -:line - -6.13 NEMD simulations :link(howto_13),h4 - -Non-equilibrium molecular dynamics or NEMD simulations are typically -used to measure a fluid's rheological properties such as viscosity. -In LAMMPS, such simulations can be performed by first setting up a -non-orthogonal simulation box (see the preceding Howto section). - -A shear strain can be applied to the simulation box at a desired -strain rate by using the "fix deform"_fix_deform.html command. The -"fix nvt/sllod"_fix_nvt_sllod.html command can be used to thermostat -the sheared fluid and integrate the SLLOD equations of motion for the -system. Fix nvt/sllod uses "compute -temp/deform"_compute_temp_deform.html to compute a thermal temperature -by subtracting out the streaming velocity of the shearing atoms. The -velocity profile or other properties of the fluid can be monitored via -the "fix ave/chunk"_fix_ave_chunk.html command. - -As discussed in the previous section on non-orthogonal simulation -boxes, the amount of tilt or skew that can be applied is limited by -LAMMPS for computational efficiency to be 1/2 of the parallel box -length. However, "fix deform"_fix_deform.html can continuously strain -a box by an arbitrary amount. As discussed in the "fix -deform"_fix_deform.html command, when the tilt value reaches a limit, -the box is flipped to the opposite limit which is an equivalent tiling -of periodic space. The strain rate can then continue to change as -before. In a long NEMD simulation these box re-shaping events may -occur many times. - -In a NEMD simulation, the "remap" option of "fix -deform"_fix_deform.html should be set to "remap v", since that is what -"fix nvt/sllod"_fix_nvt_sllod.html assumes to generate a velocity -profile consistent with the applied shear strain rate. - -An alternative method for calculating viscosities is provided via the -"fix viscosity"_fix_viscosity.html command. - -NEMD simulations can also be used to measure transport properties of a fluid -through a pore or channel. Simulations of steady-state flow can be performed -using the "fix flow/gauss"_fix_flow_gauss.html command. - -:line - -6.14 Finite-size spherical and aspherical particles :link(howto_14),h4 - -Typical MD models treat atoms or particles as point masses. Sometimes -it is desirable to have a model with finite-size particles such as -spheroids or ellipsoids or generalized aspherical bodies. The -difference is that such particles have a moment of inertia, rotational -energy, and angular momentum. Rotation is induced by torque coming -from interactions with other particles. - -LAMMPS has several options for running simulations with these kinds of -particles. The following aspects are discussed in turn: - -atom styles -pair potentials -time integration -computes, thermodynamics, and dump output -rigid bodies composed of finite-size particles :ul - -Example input scripts for these kinds of models are in the body, -colloid, dipole, ellipse, line, peri, pour, and tri directories of the -"examples directory"_Section_example.html in the LAMMPS distribution. - -Atom styles :h4 - -There are several "atom styles"_atom_style.html that allow for -definition of finite-size particles: sphere, dipole, ellipsoid, line, -tri, peri, and body. - -The sphere style defines particles that are spheriods and each -particle can have a unique diameter and mass (or density). These -particles store an angular velocity (omega) and can be acted upon by -torque. The "set" command can be used to modify the diameter and mass -of individual particles, after then are created. - -The dipole style does not actually define finite-size particles, but -is often used in conjunction with spherical particles, via a command -like - -atom_style hybrid sphere dipole :pre - -This is because when dipoles interact with each other, they induce -torques, and a particle must be finite-size (i.e. have a moment of -inertia) in order to respond and rotate. See the "atom_style -dipole"_atom_style.html command for details. The "set" command can be -used to modify the orientation and length of the dipole moment of -individual particles, after then are created. - -The ellipsoid style defines particles that are ellipsoids and thus can -be aspherical. Each particle has a shape, specified by 3 diameters, -and mass (or density). These particles store an angular momentum and -their orientation (quaternion), and can be acted upon by torque. They -do not store an angular velocity (omega), which can be in a different -direction than angular momentum, rather they compute it as needed. -The "set" command can be used to modify the diameter, orientation, and -mass of individual particles, after then are created. It also has a -brief explanation of what quaternions are. - -The line style defines line segment particles with two end points and -a mass (or density). They can be used in 2d simulations, and they can -be joined together to form rigid bodies which represent arbitrary -polygons. - -The tri style defines triangular particles with three corner points -and a mass (or density). They can be used in 3d simulations, and they -can be joined together to form rigid bodies which represent arbitrary -particles with a triangulated surface. - -The peri style is used with "Peridynamic models"_pair_peri.html and -defines particles as having a volume, that is used internally in the -"pair_style peri"_pair_peri.html potentials. - -The body style allows for definition of particles which can represent -complex entities, such as surface meshes of discrete points, -collections of sub-particles, deformable objects, etc. The body style -is discussed in more detail on the "body"_body.html doc page. - -Note that if one of these atom styles is used (or multiple styles via -the "atom_style hybrid"_atom_style.html command), not all particles in -the system are required to be finite-size or aspherical. - -For example, in the ellipsoid style, if the 3 shape parameters are set -to the same value, the particle will be a sphere rather than an -ellipsoid. If the 3 shape parameters are all set to 0.0 or if the -diameter is set to 0.0, it will be a point particle. In the line or -tri style, if the lineflag or triflag is specified as 0, then it -will be a point particle. - -Some of the pair styles used to compute pairwise interactions between -finite-size particles also compute the correct interaction with point -particles as well, e.g. the interaction between a point particle and a -finite-size particle or between two point particles. If necessary, -"pair_style hybrid"_pair_hybrid.html can be used to insure the correct -interactions are computed for the appropriate style of interactions. -Likewise, using groups to partition particles (ellipsoids versus -spheres versus point particles) will allow you to use the appropriate -time integrators and temperature computations for each class of -particles. See the doc pages for various commands for details. - -Also note that for "2d simulations"_dimension.html, atom styles sphere -and ellipsoid still use 3d particles, rather than as circular disks or -ellipses. This means they have the same moment of inertia as the 3d -object. When temperature is computed, the correct degrees of freedom -are used for rotation in a 2d versus 3d system. - -Pair potentials :h4 - -When a system with finite-size particles is defined, the particles -will only rotate and experience torque if the force field computes -such interactions. These are the various "pair -styles"_pair_style.html that generate torque: - -"pair_style gran/history"_pair_gran.html -"pair_style gran/hertzian"_pair_gran.html -"pair_style gran/no_history"_pair_gran.html -"pair_style dipole/cut"_pair_dipole.html -"pair_style gayberne"_pair_gayberne.html -"pair_style resquared"_pair_resquared.html -"pair_style brownian"_pair_brownian.html -"pair_style lubricate"_pair_lubricate.html -"pair_style line/lj"_pair_line_lj.html -"pair_style tri/lj"_pair_tri_lj.html -"pair_style body"_pair_body.html :ul - -The granular pair styles are used with spherical particles. The -dipole pair style is used with the dipole atom style, which could be -applied to spherical or ellipsoidal particles. The GayBerne and -REsquared potentials require ellipsoidal particles, though they will -also work if the 3 shape parameters are the same (a sphere). The -Brownian and lubrication potentials are used with spherical particles. -The line, tri, and body potentials are used with line segment, -triangular, and body particles respectively. - -Time integration :h4 - -There are several fixes that perform time integration on finite-size -spherical particles, meaning the integrators update the rotational -orientation and angular velocity or angular momentum of the particles: - -"fix nve/sphere"_fix_nve_sphere.html -"fix nvt/sphere"_fix_nvt_sphere.html -"fix npt/sphere"_fix_npt_sphere.html :ul - -Likewise, there are 3 fixes that perform time integration on -ellipsoidal particles: - -"fix nve/asphere"_fix_nve_asphere.html -"fix nvt/asphere"_fix_nvt_asphere.html -"fix npt/asphere"_fix_npt_asphere.html :ul - -The advantage of these fixes is that those which thermostat the -particles include the rotational degrees of freedom in the temperature -calculation and thermostatting. The "fix langevin"_fix_langevin -command can also be used with its {omgea} or {angmom} options to -thermostat the rotational degrees of freedom for spherical or -ellipsoidal particles. Other thermostatting fixes only operate on the -translational kinetic energy of finite-size particles. - -These fixes perform constant NVE time integration on line segment, -triangular, and body particles: - -"fix nve/line"_fix_nve_line.html -"fix nve/tri"_fix_nve_tri.html -"fix nve/body"_fix_nve_body.html :ul - -Note that for mixtures of point and finite-size particles, these -integration fixes can only be used with "groups"_group.html which -contain finite-size particles. - -Computes, thermodynamics, and dump output :h4 - -There are several computes that calculate the temperature or -rotational energy of spherical or ellipsoidal particles: - -"compute temp/sphere"_compute_temp_sphere.html -"compute temp/asphere"_compute_temp_asphere.html -"compute erotate/sphere"_compute_erotate_sphere.html -"compute erotate/asphere"_compute_erotate_asphere.html :ul - -These include rotational degrees of freedom in their computation. If -you wish the thermodynamic output of temperature or pressure to use -one of these computes (e.g. for a system entirely composed of -finite-size particles), then the compute can be defined and the -"thermo_modify"_thermo_modify.html command used. Note that by default -thermodynamic quantities will be calculated with a temperature that -only includes translational degrees of freedom. See the -"thermo_style"_thermo_style.html command for details. - -These commands can be used to output various attributes of finite-size -particles: - -"dump custom"_dump.html -"compute property/atom"_compute_property_atom.html -"dump local"_dump.html -"compute body/local"_compute_body_local.html :ul - -Attributes include the dipole moment, the angular velocity, the -angular momentum, the quaternion, the torque, the end-point and -corner-point coordinates (for line and tri particles), and -sub-particle attributes of body particles. - -Rigid bodies composed of finite-size particles :h4 - -The "fix rigid"_fix_rigid.html command treats a collection of -particles as a rigid body, computes its inertia tensor, sums the total -force and torque on the rigid body each timestep due to forces on its -constituent particles, and integrates the motion of the rigid body. - -If any of the constituent particles of a rigid body are finite-size -particles (spheres or ellipsoids or line segments or triangles), then -their contribution to the inertia tensor of the body is different than -if they were point particles. This means the rotational dynamics of -the rigid body will be different. Thus a model of a dimer is -different if the dimer consists of two point masses versus two -spheroids, even if the two particles have the same mass. Finite-size -particles that experience torque due to their interaction with other -particles will also impart that torque to a rigid body they are part -of. - -See the "fix rigid" command for example of complex rigid-body models -it is possible to define in LAMMPS. - -Note that the "fix shake"_fix_shake.html command can also be used to -treat 2, 3, or 4 particles as a rigid body, but it always assumes the -particles are point masses. - -Also note that body particles cannot be modeled with the "fix -rigid"_fix_rigid.html command. Body particles are treated by LAMMPS -as single particles, though they can store internal state, such as a -list of sub-particles. Individual body partices are typically treated -as rigid bodies, and their motion integrated with a command like "fix -nve/body"_fix_nve_body.html. Interactions between pairs of body -particles are computed via a command like "pair_style -body"_pair_body.html. - -:line - -6.15 Output from LAMMPS (thermo, dumps, computes, fixes, variables) :link(howto_15),h4 - -There are four basic kinds of LAMMPS output: - -"Thermodynamic output"_thermo_style.html, which is a list -of quantities printed every few timesteps to the screen and logfile. :ulb,l - -"Dump files"_dump.html, which contain snapshots of atoms and various -per-atom values and are written at a specified frequency. :l - -Certain fixes can output user-specified quantities to files: "fix -ave/time"_fix_ave_time.html for time averaging, "fix -ave/chunk"_fix_ave_chunk.html for spatial or other averaging, and "fix -print"_fix_print.html for single-line output of -"variables"_variable.html. Fix print can also output to the -screen. :l - -"Restart files"_restart.html. :l -:ule - -A simulation prints one set of thermodynamic output and (optionally) -restart files. It can generate any number of dump files and fix -output files, depending on what "dump"_dump.html and "fix"_fix.html -commands you specify. - -As discussed below, LAMMPS gives you a variety of ways to determine -what quantities are computed and printed when the thermodynamics, -dump, or fix commands listed above perform output. Throughout this -discussion, note that users can also "add their own computes and fixes -to LAMMPS"_Section_modify.html which can then generate values that can -then be output with these commands. - -The following sub-sections discuss different LAMMPS command related -to output and the kind of data they operate on and produce: - -"Global/per-atom/local data"_#global -"Scalar/vector/array data"_#scalar -"Thermodynamic output"_#thermo -"Dump file output"_#dump -"Fixes that write output files"_#fixoutput -"Computes that process output quantities"_#computeoutput -"Fixes that process output quantities"_#fixprocoutput -"Computes that generate values to output"_#compute -"Fixes that generate values to output"_#fix -"Variables that generate values to output"_#variable -"Summary table of output options and data flow between commands"_#table :ul - -Global/per-atom/local data :h4,link(global) - -Various output-related commands work with three different styles of -data: global, per-atom, or local. A global datum is one or more -system-wide values, e.g. the temperature of the system. A per-atom -datum is one or more values per atom, e.g. the kinetic energy of each -atom. Local datums are calculated by each processor based on the -atoms it owns, but there may be zero or more per atom, e.g. a list of -bond distances. - -Scalar/vector/array data :h4,link(scalar) - -Global, per-atom, and local datums can each come in three kinds: a -single scalar value, a vector of values, or a 2d array of values. The -doc page for a "compute" or "fix" or "variable" that generates data -will specify both the style and kind of data it produces, e.g. a -per-atom vector. - -When a quantity is accessed, as in many of the output commands -discussed below, it can be referenced via the following bracket -notation, where ID in this case is the ID of a compute. The leading -"c_" would be replaced by "f_" for a fix, or "v_" for a variable: - -c_ID | entire scalar, vector, or array -c_ID\[I\] | one element of vector, one column of array -c_ID\[I\]\[J\] | one element of array :tb(s=|) - -In other words, using one bracket reduces the dimension of the data -once (vector -> scalar, array -> vector). Using two brackets reduces -the dimension twice (array -> scalar). Thus a command that uses -scalar values as input can typically also process elements of a vector -or array. - -Thermodynamic output :h4,link(thermo) - -The frequency and format of thermodynamic output is set by the -"thermo"_thermo.html, "thermo_style"_thermo_style.html, and -"thermo_modify"_thermo_modify.html commands. The -"thermo_style"_thermo_style.html command also specifies what values -are calculated and written out. Pre-defined keywords can be specified -(e.g. press, etotal, etc). Three additional kinds of keywords can -also be specified (c_ID, f_ID, v_name), where a "compute"_compute.html -or "fix"_fix.html or "variable"_variable.html provides the value to be -output. In each case, the compute, fix, or variable must generate -global values for input to the "thermo_style custom"_dump.html -command. - -Note that thermodynamic output values can be "extensive" or -"intensive". The former scale with the number of atoms in the system -(e.g. total energy), the latter do not (e.g. temperature). The -setting for "thermo_modify norm"_thermo_modify.html determines whether -extensive quantities are normalized or not. Computes and fixes -produce either extensive or intensive values; see their individual doc -pages for details. "Equal-style variables"_variable.html produce only -intensive values; you can include a division by "natoms" in the -formula if desired, to make an extensive calculation produce an -intensive result. - -Dump file output :h4,link(dump) - -Dump file output is specified by the "dump"_dump.html and -"dump_modify"_dump_modify.html commands. There are several -pre-defined formats (dump atom, dump xtc, etc). - -There is also a "dump custom"_dump.html format where the user -specifies what values are output with each atom. Pre-defined atom -attributes can be specified (id, x, fx, etc). Three additional kinds -of keywords can also be specified (c_ID, f_ID, v_name), where a -"compute"_compute.html or "fix"_fix.html or "variable"_variable.html -provides the values to be output. In each case, the compute, fix, or -variable must generate per-atom values for input to the "dump -custom"_dump.html command. - -There is also a "dump local"_dump.html format where the user specifies -what local values to output. A pre-defined index keyword can be -specified to enumerate the local values. Two additional kinds of -keywords can also be specified (c_ID, f_ID), where a -"compute"_compute.html or "fix"_fix.html or "variable"_variable.html -provides the values to be output. In each case, the compute or fix -must generate local values for input to the "dump local"_dump.html -command. - -Fixes that write output files :h4,link(fixoutput) - -Several fixes take various quantities as input and can write output -files: "fix ave/time"_fix_ave_time.html, "fix -ave/chunk"_fix_ave_chunk.html, "fix ave/histo"_fix_ave_histo.html, -"fix ave/correlate"_fix_ave_correlate.html, and "fix -print"_fix_print.html. - -The "fix ave/time"_fix_ave_time.html command enables direct output to -a file and/or time-averaging of global scalars or vectors. The user -specifies one or more quantities as input. These can be global -"compute"_compute.html values, global "fix"_fix.html values, or -"variables"_variable.html of any style except the atom style which -produces per-atom values. Since a variable can refer to keywords used -by the "thermo_style custom"_thermo_style.html command (like temp or -press) and individual per-atom values, a wide variety of quantities -can be time averaged and/or output in this way. If the inputs are one -or more scalar values, then the fix generate a global scalar or vector -of output. If the inputs are one or more vector values, then the fix -generates a global vector or array of output. The time-averaged -output of this fix can also be used as input to other output commands. - -The "fix ave/chunk"_fix_ave_chunk.html command enables direct output -to a file of chunk-averaged per-atom quantities like those output in -dump files. Chunks can represent spatial bins or other collections of -atoms, e.g. individual molecules. The per-atom quantities can be atom -density (mass or number) or atom attributes such as position, -velocity, force. They can also be per-atom quantities calculated by a -"compute"_compute.html, by a "fix"_fix.html, or by an atom-style -"variable"_variable.html. The chunk-averaged output of this fix can -also be used as input to other output commands. - -The "fix ave/histo"_fix_ave_histo.html command enables direct output -to a file of histogrammed quantities, which can be global or per-atom -or local quantities. The histogram output of this fix can also be -used as input to other output commands. - -The "fix ave/correlate"_fix_ave_correlate.html command enables direct -output to a file of time-correlated quantities, which can be global -values. The correlation matrix output of this fix can also be used as -input to other output commands. - -The "fix print"_fix_print.html command can generate a line of output -written to the screen and log file or to a separate file, periodically -during a running simulation. The line can contain one or more -"variable"_variable.html values for any style variable except the -vector or atom styles). As explained above, variables themselves can -contain references to global values generated by "thermodynamic -keywords"_thermo_style.html, "computes"_compute.html, -"fixes"_fix.html, or other "variables"_variable.html, or to per-atom -values for a specific atom. Thus the "fix print"_fix_print.html -command is a means to output a wide variety of quantities separate -from normal thermodynamic or dump file output. - -Computes that process output quantities :h4,link(computeoutput) - -The "compute reduce"_compute_reduce.html and "compute -reduce/region"_compute_reduce.html commands take one or more per-atom -or local vector quantities as inputs and "reduce" them (sum, min, max, -ave) to scalar quantities. These are produced as output values which -can be used as input to other output commands. - -The "compute slice"_compute_slice.html command take one or more global -vector or array quantities as inputs and extracts a subset of their -values to create a new vector or array. These are produced as output -values which can be used as input to other output commands. - -The "compute property/atom"_compute_property_atom.html command takes a -list of one or more pre-defined atom attributes (id, x, fx, etc) and -stores the values in a per-atom vector or array. These are produced -as output values which can be used as input to other output commands. -The list of atom attributes is the same as for the "dump -custom"_dump.html command. - -The "compute property/local"_compute_property_local.html command takes -a list of one or more pre-defined local attributes (bond info, angle -info, etc) and stores the values in a local vector or array. These -are produced as output values which can be used as input to other -output commands. - -Fixes that process output quantities :h4,link(fixprocoutput) - -The "fix vector"_fix_vector.html command can create global vectors as -output from global scalars as input, accumulating them one element at -a time. - -The "fix ave/atom"_fix_ave_atom.html command performs time-averaging -of per-atom vectors. The per-atom quantities can be atom attributes -such as position, velocity, force. They can also be per-atom -quantities calculated by a "compute"_compute.html, by a -"fix"_fix.html, or by an atom-style "variable"_variable.html. The -time-averaged per-atom output of this fix can be used as input to -other output commands. - -The "fix store/state"_fix_store_state.html command can archive one or -more per-atom attributes at a particular time, so that the old values -can be used in a future calculation or output. The list of atom -attributes is the same as for the "dump custom"_dump.html command, -including per-atom quantities calculated by a "compute"_compute.html, -by a "fix"_fix.html, or by an atom-style "variable"_variable.html. -The output of this fix can be used as input to other output commands. - -Computes that generate values to output :h4,link(compute) - -Every "compute"_compute.html in LAMMPS produces either global or -per-atom or local values. The values can be scalars or vectors or -arrays of data. These values can be output using the other commands -described in this section. The doc page for each compute command -describes what it produces. Computes that produce per-atom or local -values have the word "atom" or "local" in their style name. Computes -without the word "atom" or "local" produce global values. - -Fixes that generate values to output :h4,link(fix) - -Some "fixes"_fix.html in LAMMPS produces either global or per-atom or -local values which can be accessed by other commands. The values can -be scalars or vectors or arrays of data. These values can be output -using the other commands described in this section. The doc page for -each fix command tells whether it produces any output quantities and -describes them. - -Variables that generate values to output :h4,link(variable) - -"Variables"_variable.html defined in an input script can store one or -more strings. But equal-style, vector-style, and atom-style or -atomfile-style variables generate a global scalar value, global vector -or values, or a per-atom vector, respectively, when accessed. The -formulas used to define these variables can contain references to the -thermodynamic keywords and to global and per-atom data generated by -computes, fixes, and other variables. The values generated by -variables can be used as input to and thus output by the other -commands described in this section. - -Summary table of output options and data flow between commands :h4,link(table) - -This table summarizes the various commands that can be used for -generating output from LAMMPS. Each command produces output data of -some kind and/or writes data to a file. Most of the commands can take -data from other commands as input. Thus you can link many of these -commands together in pipeline form, where data produced by one command -is used as input to another command and eventually written to the -screen or to a file. Note that to hook two commands together the -output and input data types must match, e.g. global/per-atom/local -data and scalar/vector/array data. - -Also note that, as described above, when a command takes a scalar as -input, that could be an element of a vector or array. Likewise a -vector input could be a column of an array. - -Command: Input: Output: -"thermo_style custom"_thermo_style.html: global scalars: screen, log file: -"dump custom"_dump.html: per-atom vectors: dump file: -"dump local"_dump.html: local vectors: dump file: -"fix print"_fix_print.html: global scalar from variable: screen, file: -"print"_print.html: global scalar from variable: screen: -"computes"_compute.html: N/A: global/per-atom/local scalar/vector/array: -"fixes"_fix.html: N/A: global/per-atom/local scalar/vector/array: -"variables"_variable.html: global scalars and vectors, per-atom vectors: global scalar and vector, per-atom vector: -"compute reduce"_compute_reduce.html: per-atom/local vectors: global scalar/vector: -"compute slice"_compute_slice.html: global vectors/arrays: global vector/array: -"compute property/atom"_compute_property_atom.html: per-atom vectors: per-atom vector/array: -"compute property/local"_compute_property_local.html: local vectors: local vector/array: -"fix vector"_fix_vector.html: global scalars: global vector: -"fix ave/atom"_fix_ave_atom.html: per-atom vectors: per-atom vector/array: -"fix ave/time"_fix_ave_time.html: global scalars/vectors: global scalar/vector/array, file: -"fix ave/chunk"_fix_ave_chunk.html: per-atom vectors: global array, file: -"fix ave/histo"_fix_ave_histo.html: global/per-atom/local scalars and vectors: global array, file: -"fix ave/correlate"_fix_ave_correlate.html: global scalars: global array, file: -"fix store/state"_fix_store_state.html: per-atom vectors: per-atom vector/array :tb(c=3,s=:) - -:line - -6.16 Thermostatting, barostatting, and computing temperature :link(howto_16),h4 - -Thermostatting means controlling the temperature of particles in an MD -simulation. Barostatting means controlling the pressure. Since the -pressure includes a kinetic component due to particle velocities, both -these operations require calculation of the temperature. Typically a -target temperature (T) and/or pressure (P) is specified by the user, -and the thermostat or barostat attempts to equilibrate the system to -the requested T and/or P. - -Temperature is computed as kinetic energy divided by some number of -degrees of freedom (and the Boltzmann constant). Since kinetic energy -is a function of particle velocity, there is often a need to -distinguish between a particle's advection velocity (due to some -aggregate motion of particles) and its thermal velocity. The sum of -the two is the particle's total velocity, but the latter is often what -is wanted to compute a temperature. - -LAMMPS has several options for computing temperatures, any of which -can be used in thermostatting and barostatting. These "compute -commands"_compute.html calculate temperature, and the "compute -pressure"_compute_pressure.html command calculates pressure. - -"compute temp"_compute_temp.html -"compute temp/sphere"_compute_temp_sphere.html -"compute temp/asphere"_compute_temp_asphere.html -"compute temp/com"_compute_temp_com.html -"compute temp/deform"_compute_temp_deform.html -"compute temp/partial"_compute_temp_partial.html -"compute temp/profile"_compute_temp_profile.html -"compute temp/ramp"_compute_temp_ramp.html -"compute temp/region"_compute_temp_region.html :ul - -All but the first 3 calculate velocity biases directly (e.g. advection -velocities) that are removed when computing the thermal temperature. -"Compute temp/sphere"_compute_temp_sphere.html and "compute -temp/asphere"_compute_temp_asphere.html compute kinetic energy for -finite-size particles that includes rotational degrees of freedom. -They both allow for velocity biases indirectly, via an optional extra -argument, another temperature compute that subtracts a velocity bias. -This allows the translational velocity of spherical or aspherical -particles to be adjusted in prescribed ways. - -Thermostatting in LAMMPS is performed by "fixes"_fix.html, or in one -case by a pair style. Several thermostatting fixes are available: -Nose-Hoover (nvt), Berendsen, CSVR, Langevin, and direct rescaling -(temp/rescale). Dissipative particle dynamics (DPD) thermostatting -can be invoked via the {dpd/tstat} pair style: - -"fix nvt"_fix_nh.html -"fix nvt/sphere"_fix_nvt_sphere.html -"fix nvt/asphere"_fix_nvt_asphere.html -"fix nvt/sllod"_fix_nvt_sllod.html -"fix temp/berendsen"_fix_temp_berendsen.html -"fix temp/csvr"_fix_temp_csvr.html -"fix langevin"_fix_langevin.html -"fix temp/rescale"_fix_temp_rescale.html -"pair_style dpd/tstat"_pair_dpd.html :ul - -"Fix nvt"_fix_nh.html only thermostats the translational velocity of -particles. "Fix nvt/sllod"_fix_nvt_sllod.html also does this, except -that it subtracts out a velocity bias due to a deforming box and -integrates the SLLOD equations of motion. See the "NEMD -simulations"_#howto_13 section of this page for further details. "Fix -nvt/sphere"_fix_nvt_sphere.html and "fix -nvt/asphere"_fix_nvt_asphere.html thermostat not only translation -velocities but also rotational velocities for spherical and aspherical -particles. - -DPD thermostatting alters pairwise interactions in a manner analogous -to the per-particle thermostatting of "fix -langevin"_fix_langevin.html. - -Any of the thermostatting fixes can use temperature computes that -remove bias which has two effects. First, the current calculated -temperature, which is compared to the requested target temperature, is -calculated with the velocity bias removed. Second, the thermostat -adjusts only the thermal temperature component of the particle's -velocities, which are the velocities with the bias removed. The -removed bias is then added back to the adjusted velocities. See the -doc pages for the individual fixes and for the -"fix_modify"_fix_modify.html command for instructions on how to assign -a temperature compute to a thermostatting fix. For example, you can -apply a thermostat to only the x and z components of velocity by using -it in conjunction with "compute -temp/partial"_compute_temp_partial.html. Of you could thermostat only -the thermal temperature of a streaming flow of particles without -affecting the streaming velocity, by using "compute -temp/profile"_compute_temp_profile.html. - -NOTE: Only the nvt fixes perform time integration, meaning they update -the velocities and positions of particles due to forces and velocities -respectively. The other thermostat fixes only adjust velocities; they -do NOT perform time integration updates. Thus they should be used in -conjunction with a constant NVE integration fix such as these: - -"fix nve"_fix_nve.html -"fix nve/sphere"_fix_nve_sphere.html -"fix nve/asphere"_fix_nve_asphere.html :ul - -Barostatting in LAMMPS is also performed by "fixes"_fix.html. Two -barosttating methods are currently available: Nose-Hoover (npt and -nph) and Berendsen: - -"fix npt"_fix_nh.html -"fix npt/sphere"_fix_npt_sphere.html -"fix npt/asphere"_fix_npt_asphere.html -"fix nph"_fix_nh.html -"fix press/berendsen"_fix_press_berendsen.html :ul - -The "fix npt"_fix_nh.html commands include a Nose-Hoover thermostat -and barostat. "Fix nph"_fix_nh.html is just a Nose/Hoover barostat; -it does no thermostatting. Both "fix nph"_fix_nh.html and "fix -press/berendsen"_fix_press_berendsen.html can be used in conjunction -with any of the thermostatting fixes. - -As with the thermostats, "fix npt"_fix_nh.html and "fix -nph"_fix_nh.html only use translational motion of the particles in -computing T and P and performing thermo/barostatting. "Fix -npt/sphere"_fix_npt_sphere.html and "fix -npt/asphere"_fix_npt_asphere.html thermo/barostat using not only -translation velocities but also rotational velocities for spherical -and aspherical particles. - -All of the barostatting fixes use the "compute -pressure"_compute_pressure.html compute to calculate a current -pressure. By default, this compute is created with a simple "compute -temp"_compute_temp.html (see the last argument of the "compute -pressure"_compute_pressure.html command), which is used to calculated -the kinetic component of the pressure. The barostatting fixes can -also use temperature computes that remove bias for the purpose of -computing the kinetic component which contributes to the current -pressure. See the doc pages for the individual fixes and for the -"fix_modify"_fix_modify.html command for instructions on how to assign -a temperature or pressure compute to a barostatting fix. - -NOTE: As with the thermostats, the Nose/Hoover methods ("fix -npt"_fix_nh.html and "fix nph"_fix_nh.html) perform time integration. -"Fix press/berendsen"_fix_press_berendsen.html does NOT, so it should -be used with one of the constant NVE fixes or with one of the NVT -fixes. - -Finally, thermodynamic output, which can be setup via the -"thermo_style"_thermo_style.html command, often includes temperature -and pressure values. As explained on the doc page for the -"thermo_style"_thermo_style.html command, the default T and P are -setup by the thermo command itself. They are NOT the ones associated -with any thermostatting or barostatting fix you have defined or with -any compute that calculates a temperature or pressure. Thus if you -want to view these values of T and P, you need to specify them -explicitly via a "thermo_style custom"_thermo_style.html command. Or -you can use the "thermo_modify"_thermo_modify.html command to -re-define what temperature or pressure compute is used for default -thermodynamic output. - -:line - -6.17 Walls :link(howto_17),h4 - -Walls in an MD simulation are typically used to bound particle motion, -i.e. to serve as a boundary condition. - -Walls in LAMMPS can be of rough (made of particles) or idealized -surfaces. Ideal walls can be smooth, generating forces only in the -normal direction, or frictional, generating forces also in the -tangential direction. - -Rough walls, built of particles, can be created in various ways. The -particles themselves can be generated like any other particle, via the -"lattice"_lattice.html and "create_atoms"_create_atoms.html commands, -or read in via the "read_data"_read_data.html command. - -Their motion can be constrained by many different commands, so that -they do not move at all, move together as a group at constant velocity -or in response to a net force acting on them, move in a prescribed -fashion (e.g. rotate around a point), etc. Note that if a time -integration fix like "fix nve"_fix_nve.html or "fix nvt"_fix_nh.html -is not used with the group that contains wall particles, their -positions and velocities will not be updated. - -"fix aveforce"_fix_aveforce.html - set force on particles to average value, so they move together -"fix setforce"_fix_setforce.html - set force on particles to a value, e.g. 0.0 -"fix freeze"_fix_freeze.html - freeze particles for use as granular walls -"fix nve/noforce"_fix_nve_noforce.html - advect particles by their velocity, but without force -"fix move"_fix_move.html - prescribe motion of particles by a linear velocity, oscillation, rotation, variable :ul - -The "fix move"_fix_move.html command offers the most generality, since -the motion of individual particles can be specified with -"variable"_variable.html formula which depends on time and/or the -particle position. - -For rough walls, it may be useful to turn off pairwise interactions -between wall particles via the "neigh_modify -exclude"_neigh_modify.html command. - -Rough walls can also be created by specifying frozen particles that do -not move and do not interact with mobile particles, and then tethering -other particles to the fixed particles, via a "bond"_bond_style.html. -The bonded particles do interact with other mobile particles. - -Idealized walls can be specified via several fix commands. "Fix -wall/gran"_fix_wall_gran.html creates frictional walls for use with -granular particles; all the other commands create smooth walls. - -"fix wall/reflect"_fix_wall_reflect.html - reflective flat walls -"fix wall/lj93"_fix_wall.html - flat walls, with Lennard-Jones 9/3 potential -"fix wall/lj126"_fix_wall.html - flat walls, with Lennard-Jones 12/6 potential -"fix wall/colloid"_fix_wall.html - flat walls, with "pair_style colloid"_pair_colloid.html potential -"fix wall/harmonic"_fix_wall.html - flat walls, with repulsive harmonic spring potential -"fix wall/region"_fix_wall_region.html - use region surface as wall -"fix wall/gran"_fix_wall_gran.html - flat or curved walls with "pair_style granular"_pair_gran.html potential :ul - -The {lj93}, {lj126}, {colloid}, and {harmonic} styles all allow the -flat walls to move with a constant velocity, or oscillate in time. -The "fix wall/region"_fix_wall_region.html command offers the most -generality, since the region surface is treated as a wall, and the -geometry of the region can be a simple primitive volume (e.g. a -sphere, or cube, or plane), or a complex volume made from the union -and intersection of primitive volumes. "Regions"_region.html can also -specify a volume "interior" or "exterior" to the specified primitive -shape or {union} or {intersection}. "Regions"_region.html can also be -"dynamic" meaning they move with constant velocity, oscillate, or -rotate. - -The only frictional idealized walls currently in LAMMPS are flat or -curved surfaces specified by the "fix wall/gran"_fix_wall_gran.html -command. At some point we plan to allow regoin surfaces to be used as -frictional walls, as well as triangulated surfaces. - -:line - -6.18 Elastic constants :link(howto_18),h4 - -Elastic constants characterize the stiffness of a material. The formal -definition is provided by the linear relation that holds between the -stress and strain tensors in the limit of infinitesimal deformation. -In tensor notation, this is expressed as s_ij = C_ijkl * e_kl, where -the repeated indices imply summation. s_ij are the elements of the -symmetric stress tensor. e_kl are the elements of the symmetric strain -tensor. C_ijkl are the elements of the fourth rank tensor of elastic -constants. In three dimensions, this tensor has 3^4=81 elements. Using -Voigt notation, the tensor can be written as a 6x6 matrix, where C_ij -is now the derivative of s_i w.r.t. e_j. Because s_i is itself a -derivative w.r.t. e_i, it follows that C_ij is also symmetric, with at -most 7*6/2 = 21 distinct elements. - -At zero temperature, it is easy to estimate these derivatives by -deforming the simulation box in one of the six directions using the -"change_box"_change_box.html command and measuring the change in the -stress tensor. A general-purpose script that does this is given in the -examples/elastic directory described in "this -section"_Section_example.html. - -Calculating elastic constants at finite temperature is more -challenging, because it is necessary to run a simulation that perfoms -time averages of differential properties. One way to do this is to -measure the change in average stress tensor in an NVT simulations when -the cell volume undergoes a finite deformation. In order to balance -the systematic and statistical errors in this method, the magnitude of -the deformation must be chosen judiciously, and care must be taken to -fully equilibrate the deformed cell before sampling the stress -tensor. Another approach is to sample the triclinic cell fluctuations -that occur in an NPT simulation. This method can also be slow to -converge and requires careful post-processing "(Shinoda)"_#Shinoda1 - -:line - -6.19 Library interface to LAMMPS :link(howto_19),h4 - -As described in "Section 2.5"_Section_start.html#start_5, LAMMPS -can be built as a library, so that it can be called by another code, -used in a "coupled manner"_Section_howto.html#howto_10 with other -codes, or driven through a "Python interface"_Section_python.html. - -All of these methodologies use a C-style interface to LAMMPS that is -provided in the files src/library.cpp and src/library.h. The -functions therein have a C-style argument list, but contain C++ code -you could write yourself in a C++ application that was invoking LAMMPS -directly. The C++ code in the functions illustrates how to invoke -internal LAMMPS operations. Note that LAMMPS classes are defined -within a LAMMPS namespace (LAMMPS_NS) if you use them from another C++ -application. - -The examples/COUPLE and python/examples directories have example C++ -and C and Python codes which show how a driver code can link to LAMMPS -as a library, run LAMMPS on a subset of processors, grab data from -LAMMPS, change it, and put it back into LAMMPS. - -The file src/library.cpp contains the following functions for creating -and destroying an instance of LAMMPS and sending it commands to -execute. See the documentation in the src/library.cpp file for -details. - -NOTE: You can write code for additional functions as needed to define -how your code talks to LAMMPS and add them to src/library.cpp and -src/library.h, as well as to the "Python -interface"_Section_python.html. The added functions can access or -change any internal LAMMPS data you wish. - -void lammps_open(int, char **, MPI_Comm, void **) -void lammps_open_no_mpi(int, char **, void **) -void lammps_close(void *) -int lammps_version(void *) -void lammps_file(void *, char *) -char *lammps_command(void *, char *) -void lammps_commands_list(void *, int, char **) -void lammps_commands_string(void *, char *) -void lammps_free(void *) :pre - -The lammps_open() function is used to initialize LAMMPS, passing in a -list of strings as if they were "command-line -arguments"_Section_start.html#start_6 when LAMMPS is run in -stand-alone mode from the command line, and a MPI communicator for -LAMMPS to run under. It returns a ptr to the LAMMPS object that is -created, and which is used in subsequent library calls. The -lammps_open() function can be called multiple times, to create -multiple instances of LAMMPS. - -LAMMPS will run on the set of processors in the communicator. This -means the calling code can run LAMMPS on all or a subset of -processors. For example, a wrapper script might decide to alternate -between LAMMPS and another code, allowing them both to run on all the -processors. Or it might allocate half the processors to LAMMPS and -half to the other code and run both codes simultaneously before -syncing them up periodically. Or it might instantiate multiple -instances of LAMMPS to perform different calculations. - -The lammps_open_no_mpi() function is similar except that no MPI -communicator is passed from the caller. Instead, MPI_COMM_WORLD is -used to instantiate LAMMPS, and MPI is initialized if necessary. - -The lammps_close() function is used to shut down an instance of LAMMPS -and free all its memory. - -The lammps_version() function can be used to determined the specific -version of the underlying LAMMPS code. This is particularly useful -when loading LAMMPS as a shared library via dlopen(). The code using -the library interface can than use this information to adapt to -changes to the LAMMPS command syntax between versions. The returned -LAMMPS version code is an integer (e.g. 2 Sep 2015 results in -20150902) that grows with every new LAMMPS version. - -The lammps_file(), lammps_command(), lammps_commands_list(), and -lammps_commands_string() functions are used to pass one or more -commands to LAMMPS to execute, the same as if they were coming from an -input script. - -Via these functions, the calling code can read or generate a series of -LAMMPS commands one or multiple at a time and pass it thru the library -interface to setup a problem and then run it in stages. The caller -can interleave the command function calls with operations it performs, -calls to extract information from or set information within LAMMPS, or -calls to another code's library. - -The lammps_file() function passes the filename of an input script. -The lammps_command() function passes a single command as a string. -The lammps_commands_list() function passes multiple commands in a -char** list. In both lammps_command() and lammps_commands_list(), -individual commands may or may not have a trailing newline. The -lammps_commands_string() function passes multiple commands -concatenated into one long string, separated by newline characters. -In both lammps_commands_list() and lammps_commands_string(), a single -command can be spread across multiple lines, if the last printable -character of all but the last line is "&", the same as if the lines -appeared in an input script. - -The lammps_free() function is a clean-up function to free memory that -the library allocated previously via other function calls. See -comments in src/library.cpp file for which other functions need this -clean-up. - -The file src/library.cpp also contains these functions for extracting -information from LAMMPS and setting value within LAMMPS. Again, see -the documentation in the src/library.cpp file for details, including -which quantities can be queried by name: - -int lammps_extract_setting(void *, char *) -void *lammps_extract_global(void *, char *) -void lammps_extract_box(void *, double *, double *, - double *, double *, double *, int *, int *) -void *lammps_extract_atom(void *, char *) -void *lammps_extract_compute(void *, char *, int, int) -void *lammps_extract_fix(void *, char *, int, int, int, int) -void *lammps_extract_variable(void *, char *, char *) :pre - -The extract_setting() function returns info on the size -of data types (e.g. 32-bit or 64-bit atom IDs) used -by the LAMMPS executable (a compile-time choice). - -The other extract functions return a pointer to various global or -per-atom quantities stored in LAMMPS or to values calculated by a -compute, fix, or variable. The pointer returned by the -extract_global() function can be used as a permanent reference to a -value which may change. For the extract_atom() method, see the -extract() method in the src/atom.cpp file for a list of valid per-atom -properties. New names could easily be added if the property you want -is not listed. For the other extract functions, the underlying -storage may be reallocated as LAMMPS runs, so you need to re-call the -function to assure a current pointer or returned value(s). - -double lammps_get_thermo(void *, char *) -int lammps_get_natoms(void *) :pre - -int lammps_set_variable(void *, char *, char *) -void lammps_reset_box(void *, double *, double *, double, double, double) :pre - -The lammps_get_thermo() function returns the current value of a thermo -keyword as a double precision value. - -The lammps_get_natoms() function returns the total number of atoms in -the system and can be used by the caller to allocate memory for the -lammps_gather_atoms() and lammps_scatter_atoms() functions. - -The lammps_set_variable() function can set an existing string-style -variable to a new string value, so that subsequent LAMMPS commands can -access the variable. - -The lammps_reset_box() function resets the size and shape of the -simulation box, e.g. as part of restoring a previously extracted and -saved state of a simulation. - -void lammps_gather_atoms(void *, char *, int, int, void *) -void lammps_gather_atoms_concat(void *, char *, int, int, void *) -void lammps_gather_atoms_subset(void *, char *, int, int, int, int *, void *) -void lammps_scatter_atoms(void *, char *, int, int, void *) -void lammps_scatter_atoms_subset(void *, char *, int, int, int, int *, void *) :pre - -void lammps_create_atoms(void *, int, tagint *, int *, double *, double *, - imageint *, int) :pre - -The gather functions collect peratom info of the requested type (atom -coords, atom types, forces, etc) from all processors, and returns the -same vector of values to each callling processor. The scatter -functions do the inverse. They distribute a vector of peratom values, -passed by all calling processors, to invididual atoms, which may be -owned by different processos. - -The lammps_gather_atoms() function does this for all N atoms in the -system, ordered by atom ID, from 1 to N. The -lammps_gather_atoms_concat() function does it for all N atoms, but -simply concatenates the subset of atoms owned by each processor. The -resulting vector is not ordered by atom ID. Atom IDs can be requetsed -by the same function if the caller needs to know the ordering. The -lammps_gather_subset() function allows the caller to request values -for only a subset of atoms (identified by ID). -For all 3 gather function, per-atom image flags can be retrieved in 2 ways. -If the count is specified as 1, they are returned -in a packed format with all three image flags stored in a single integer. -If the count is specified as 3, the values are unpacked into xyz flags -by the library before returning them. - -The lammps_scatter_atoms() function takes a list of values for all N -atoms in the system, ordered by atom ID, from 1 to N, and assigns -those values to each atom in the system. The -lammps_scatter_atoms_subset() function takes a subset of IDs as an -argument and only scatters those values to the owning atoms. - -The lammps_create_atoms() function takes a list of N atoms as input -with atom types and coords (required), an optionally atom IDs and -velocities and image flags. It uses the coords of each atom to assign -it as a new atom to the processor that owns it. This function is -useful to add atoms to a simulation or (in tandem with -lammps_reset_box()) to restore a previously extracted and saved state -of a simulation. Additional properties for the new atoms can then be -assigned via the lammps_scatter_atoms() or lammps_extract_atom() -functions. - -:line - -6.20 Calculating thermal conductivity :link(howto_20),h4 - -The thermal conductivity kappa of a material can be measured in at -least 4 ways using various options in LAMMPS. See the examples/KAPPA -directory for scripts that implement the 4 methods discussed here for -a simple Lennard-Jones fluid model. Also, see "this -section"_Section_howto.html#howto_21 of the manual for an analogous -discussion for viscosity. - -The thermal conductivity tensor kappa is a measure of the propensity -of a material to transmit heat energy in a diffusive manner as given -by Fourier's law - -J = -kappa grad(T) - -where J is the heat flux in units of energy per area per time and -grad(T) is the spatial gradient of temperature. The thermal -conductivity thus has units of energy per distance per time per degree -K and is often approximated as an isotropic quantity, i.e. as a -scalar. - -The first method is to setup two thermostatted regions at opposite -ends of a simulation box, or one in the middle and one at the end of a -periodic box. By holding the two regions at different temperatures -with a "thermostatting fix"_Section_howto.html#howto_13, the energy -added to the hot region should equal the energy subtracted from the -cold region and be proportional to the heat flux moving between the -regions. See the papers by "Ikeshoji and Hafskjold"_#howto-Ikeshoji -and "Wirnsberger et al"_#howto-Wirnsberger for details of this idea. -Note that thermostatting fixes such as "fix nvt"_fix_nh.html, "fix -langevin"_fix_langevin.html, and "fix -temp/rescale"_fix_temp_rescale.html store the cumulative energy they -add/subtract. - -Alternatively, as a second method, the "fix heat"_fix_heat.html or -"fix ehex"_fix_ehex.html commands can be used in place of thermostats -on each of two regions to add/subtract specified amounts of energy to -both regions. In both cases, the resulting temperatures of the two -regions can be monitored with the "compute temp/region" command and -the temperature profile of the intermediate region can be monitored -with the "fix ave/chunk"_fix_ave_chunk.html and "compute -ke/atom"_compute_ke_atom.html commands. - -The third method is to perform a reverse non-equilibrium MD simulation -using the "fix thermal/conductivity"_fix_thermal_conductivity.html -command which implements the rNEMD algorithm of Muller-Plathe. -Kinetic energy is swapped between atoms in two different layers of the -simulation box. This induces a temperature gradient between the two -layers which can be monitored with the "fix -ave/chunk"_fix_ave_chunk.html and "compute -ke/atom"_compute_ke_atom.html commands. The fix tallies the -cumulative energy transfer that it performs. See the "fix -thermal/conductivity"_fix_thermal_conductivity.html command for -details. - -The fourth method is based on the Green-Kubo (GK) formula which -relates the ensemble average of the auto-correlation of the heat flux -to kappa. The heat flux can be calculated from the fluctuations of -per-atom potential and kinetic energies and per-atom stress tensor in -a steady-state equilibrated simulation. This is in contrast to the -two preceding non-equilibrium methods, where energy flows continuously -between hot and cold regions of the simulation box. - -The "compute heat/flux"_compute_heat_flux.html command can calculate -the needed heat flux and describes how to implement the Green_Kubo -formalism using additional LAMMPS commands, such as the "fix -ave/correlate"_fix_ave_correlate.html command to calculate the needed -auto-correlation. See the doc page for the "compute -heat/flux"_compute_heat_flux.html command for an example input script -that calculates the thermal conductivity of solid Ar via the GK -formalism. - -:line - -6.21 Calculating viscosity :link(howto_21),h4 - -The shear viscosity eta of a fluid can be measured in at least 5 ways -using various options in LAMMPS. See the examples/VISCOSITY directory -for scripts that implement the 5 methods discussed here for a simple -Lennard-Jones fluid model. Also, see "this -section"_Section_howto.html#howto_20 of the manual for an analogous -discussion for thermal conductivity. - -Eta is a measure of the propensity of a fluid to transmit momentum in -a direction perpendicular to the direction of velocity or momentum -flow. Alternatively it is the resistance the fluid has to being -sheared. It is given by - -J = -eta grad(Vstream) - -where J is the momentum flux in units of momentum per area per time. -and grad(Vstream) is the spatial gradient of the velocity of the fluid -moving in another direction, normal to the area through which the -momentum flows. Viscosity thus has units of pressure-time. - -The first method is to perform a non-equilibrium MD (NEMD) simulation -by shearing the simulation box via the "fix deform"_fix_deform.html -command, and using the "fix nvt/sllod"_fix_nvt_sllod.html command to -thermostat the fluid via the SLLOD equations of motion. -Alternatively, as a second method, one or more moving walls can be -used to shear the fluid in between them, again with some kind of -thermostat that modifies only the thermal (non-shearing) components of -velocity to prevent the fluid from heating up. - -In both cases, the velocity profile setup in the fluid by this -procedure can be monitored by the "fix -ave/chunk"_fix_ave_chunk.html command, which determines -grad(Vstream) in the equation above. E.g. the derivative in the -y-direction of the Vx component of fluid motion or grad(Vstream) = -dVx/dy. The Pxy off-diagonal component of the pressure or stress -tensor, as calculated by the "compute pressure"_compute_pressure.html -command, can also be monitored, which is the J term in the equation -above. See "this section"_Section_howto.html#howto_13 of the manual -for details on NEMD simulations. - -The third method is to perform a reverse non-equilibrium MD simulation -using the "fix viscosity"_fix_viscosity.html command which implements -the rNEMD algorithm of Muller-Plathe. Momentum in one dimension is -swapped between atoms in two different layers of the simulation box in -a different dimension. This induces a velocity gradient which can be -monitored with the "fix ave/chunk"_fix_ave_chunk.html command. -The fix tallies the cumulative momentum transfer that it performs. -See the "fix viscosity"_fix_viscosity.html command for details. - -The fourth method is based on the Green-Kubo (GK) formula which -relates the ensemble average of the auto-correlation of the -stress/pressure tensor to eta. This can be done in a fully -equilibrated simulation which is in contrast to the two preceding -non-equilibrium methods, where momentum flows continuously through the -simulation box. - -Here is an example input script that calculates the viscosity of -liquid Ar via the GK formalism: - -# Sample LAMMPS input script for viscosity of liquid Ar :pre - -units real -variable T equal 86.4956 -variable V equal vol -variable dt equal 4.0 -variable p equal 400 # correlation length -variable s equal 5 # sample interval -variable d equal $p*$s # dump interval :pre - -# convert from LAMMPS real units to SI :pre - -variable kB equal 1.3806504e-23 # \[J/K/] Boltzmann -variable atm2Pa equal 101325.0 -variable A2m equal 1.0e-10 -variable fs2s equal 1.0e-15 -variable convert equal $\{atm2Pa\}*$\{atm2Pa\}*$\{fs2s\}*$\{A2m\}*$\{A2m\}*$\{A2m\} :pre - -# setup problem :pre - -dimension 3 -boundary p p p -lattice fcc 5.376 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 -region box block 0 4 0 4 0 4 -create_box 1 box -create_atoms 1 box -mass 1 39.948 -pair_style lj/cut 13.0 -pair_coeff * * 0.2381 3.405 -timestep $\{dt\} -thermo $d :pre - -# equilibration and thermalization :pre - -velocity all create $T 102486 mom yes rot yes dist gaussian -fix NVT all nvt temp $T $T 10 drag 0.2 -run 8000 :pre - -# viscosity calculation, switch to NVE if desired :pre - -#unfix NVT -#fix NVE all nve :pre - -reset_timestep 0 -variable pxy equal pxy -variable pxz equal pxz -variable pyz equal pyz -fix SS all ave/correlate $s $p $d & - v_pxy v_pxz v_pyz type auto file S0St.dat ave running -variable scale equal $\{convert\}/($\{kB\}*$T)*$V*$s*$\{dt\} -variable v11 equal trap(f_SS\[3\])*$\{scale\} -variable v22 equal trap(f_SS\[4\])*$\{scale\} -variable v33 equal trap(f_SS\[5\])*$\{scale\} -thermo_style custom step temp press v_pxy v_pxz v_pyz v_v11 v_v22 v_v33 -run 100000 -variable v equal (v_v11+v_v22+v_v33)/3.0 -variable ndens equal count(all)/vol -print "average viscosity: $v \[Pa.s\] @ $T K, $\{ndens\} /A^3" :pre - -The fifth method is related to the above Green-Kubo method, -but uses the Einstein formulation, analogous to the Einstein -mean-square-displacement formulation for self-diffusivity. The -time-integrated momentum fluxes play the role of Cartesian -coordinates, whose mean-square displacement increases linearly -with time at sufficiently long times. - -:line - -6.22 Calculating a diffusion coefficient :link(howto_22),h4 - -The diffusion coefficient D of a material can be measured in at least -2 ways using various options in LAMMPS. See the examples/DIFFUSE -directory for scripts that implement the 2 methods discussed here for -a simple Lennard-Jones fluid model. - -The first method is to measure the mean-squared displacement (MSD) of -the system, via the "compute msd"_compute_msd.html command. The slope -of the MSD versus time is proportional to the diffusion coefficient. -The instantaneous MSD values can be accumulated in a vector via the -"fix vector"_fix_vector.html command, and a line fit to the vector to -compute its slope via the "variable slope"_variable.html function, and -thus extract D. - -The second method is to measure the velocity auto-correlation function -(VACF) of the system, via the "compute vacf"_compute_vacf.html -command. The time-integral of the VACF is proportional to the -diffusion coefficient. The instantaneous VACF values can be -accumulated in a vector via the "fix vector"_fix_vector.html command, -and time integrated via the "variable trap"_variable.html function, -and thus extract D. - -:line - -6.23 Using chunks to calculate system properties :link(howto_23),h4 - -In LAMMS, "chunks" are collections of atoms, as defined by the -"compute chunk/atom"_compute_chunk_atom.html command, which assigns -each atom to a chunk ID (or to no chunk at all). The number of chunks -and the assignment of chunk IDs to atoms can be static or change over -time. Examples of "chunks" are molecules or spatial bins or atoms -with similar values (e.g. coordination number or potential energy). - -The per-atom chunk IDs can be used as input to two other kinds of -commands, to calculate various properties of a system: - -"fix ave/chunk"_fix_ave_chunk.html -any of the "compute */chunk"_compute.html commands :ul - -Here, each of the 3 kinds of chunk-related commands is briefly -overviewed. Then some examples are given of how to compute different -properties with chunk commands. - -Compute chunk/atom command: :h4 - -This compute can assign atoms to chunks of various styles. Only atoms -in the specified group and optional specified region are assigned to a -chunk. Here are some possible chunk definitions: - -atoms in same molecule | chunk ID = molecule ID | -atoms of same atom type | chunk ID = atom type | -all atoms with same atom property (charge, radius, etc) | chunk ID = output of compute property/atom | -atoms in same cluster | chunk ID = output of "compute cluster/atom"_compute_cluster_atom.html command | -atoms in same spatial bin | chunk ID = bin ID | -atoms in same rigid body | chunk ID = molecule ID used to define rigid bodies | -atoms with similar potential energy | chunk ID = output of "compute pe/atom"_compute_pe_atom.html | -atoms with same local defect structure | chunk ID = output of "compute centro/atom"_compute_centro_atom.html or "compute coord/atom"_compute_coord_atom.html command :tb(s=|,c=2) - -Note that chunk IDs are integer values, so for atom properties or -computes that produce a floating point value, they will be truncated -to an integer. You could also use the compute in a variable that -scales the floating point value to spread it across multiple integers. - -Spatial bins can be of various kinds, e.g. 1d bins = slabs, 2d bins = -pencils, 3d bins = boxes, spherical bins, cylindrical bins. - -This compute also calculates the number of chunks {Nchunk}, which is -used by other commands to tally per-chunk data. {Nchunk} can be a -static value or change over time (e.g. the number of clusters). The -chunk ID for an individual atom can also be static (e.g. a molecule -ID), or dynamic (e.g. what spatial bin an atom is in as it moves). - -Note that this compute allows the per-atom output of other -"computes"_compute.html, "fixes"_fix.html, and -"variables"_variable.html to be used to define chunk IDs for each -atom. This means you can write your own compute or fix to output a -per-atom quantity to use as chunk ID. See -"Section 10"_Section_modify.html of the documentation for how to -do this. You can also define a "per-atom variable"_variable.html in -the input script that uses a formula to generate a chunk ID for each -atom. - -Fix ave/chunk command: :h4 - -This fix takes the ID of a "compute -chunk/atom"_compute_chunk_atom.html command as input. For each chunk, -it then sums one or more specified per-atom values over the atoms in -each chunk. The per-atom values can be any atom property, such as -velocity, force, charge, potential energy, kinetic energy, stress, -etc. Additional keywords are defined for per-chunk properties like -density and temperature. More generally any per-atom value generated -by other "computes"_compute.html, "fixes"_fix.html, and "per-atom -variables"_variable.html, can be summed over atoms in each chunk. - -Similar to other averaging fixes, this fix allows the summed per-chunk -values to be time-averaged in various ways, and output to a file. The -fix produces a global array as output with one row of values per -chunk. - -Compute */chunk commands: :h4 - -Currently the following computes operate on chunks of atoms to produce -per-chunk values. - -"compute com/chunk"_compute_com_chunk.html -"compute gyration/chunk"_compute_gyration_chunk.html -"compute inertia/chunk"_compute_inertia_chunk.html -"compute msd/chunk"_compute_msd_chunk.html -"compute property/chunk"_compute_property_chunk.html -"compute temp/chunk"_compute_temp_chunk.html -"compute torque/chunk"_compute_vcm_chunk.html -"compute vcm/chunk"_compute_vcm_chunk.html :ul - -They each take the ID of a "compute -chunk/atom"_compute_chunk_atom.html command as input. As their names -indicate, they calculate the center-of-mass, radius of gyration, -moments of inertia, mean-squared displacement, temperature, torque, -and velocity of center-of-mass for each chunk of atoms. The "compute -property/chunk"_compute_property_chunk.html command can tally the -count of atoms in each chunk and extract other per-chunk properties. - -The reason these various calculations are not part of the "fix -ave/chunk command"_fix_ave_chunk.html, is that each requires a more -complicated operation than simply summing and averaging over per-atom -values in each chunk. For example, many of them require calculation -of a center of mass, which requires summing mass*position over the -atoms and then dividing by summed mass. - -All of these computes produce a global vector or global array as -output, wih one or more values per chunk. They can be used -in various ways: - -As input to the "fix ave/time"_fix_ave_time.html command, which can -write the values to a file and optionally time average them. :ulb,l - -As input to the "fix ave/histo"_fix_ave_histo.html command to -histogram values across chunks. E.g. a histogram of cluster sizes or -molecule diffusion rates. :l - -As input to special functions of "equal-style -variables"_variable.html, like sum() and max(). E.g. to find the -largest cluster or fastest diffusing molecule. :l -:ule - -Example calculations with chunks :h4 - -Here are examples using chunk commands to calculate various -properties: - -(1) Average velocity in each of 1000 2d spatial bins: - -compute cc1 all chunk/atom bin/2d x 0.0 0.1 y lower 0.01 units reduced -fix 1 all ave/chunk 100 10 1000 cc1 vx vy file tmp.out :pre - -(2) Temperature in each spatial bin, after subtracting a flow -velocity: - -compute cc1 all chunk/atom bin/2d x 0.0 0.1 y lower 0.1 units reduced -compute vbias all temp/profile 1 0 0 y 10 -fix 1 all ave/chunk 100 10 1000 cc1 temp bias vbias file tmp.out :pre - -(3) Center of mass of each molecule: - -compute cc1 all chunk/atom molecule -compute myChunk all com/chunk cc1 -fix 1 all ave/time 100 1 100 c_myChunk\[*\] file tmp.out mode vector :pre - -(4) Total force on each molecule and ave/max across all molecules: - -compute cc1 all chunk/atom molecule -fix 1 all ave/chunk 1000 1 1000 cc1 fx fy fz file tmp.out -variable xave equal ave(f_1\[2\]) -variable xmax equal max(f_1\[2\]) -thermo 1000 -thermo_style custom step temp v_xave v_xmax :pre - -(5) Histogram of cluster sizes: - -compute cluster all cluster/atom 1.0 -compute cc1 all chunk/atom c_cluster compress yes -compute size all property/chunk cc1 count -fix 1 all ave/histo 100 1 100 0 20 20 c_size mode vector ave running beyond ignore file tmp.histo :pre - -:line - -6.24 Setting parameters for the "kspace_style pppm/disp"_kspace_style.html command :link(howto_24),h4 - -The PPPM method computes interactions by splitting the pair potential -into two parts, one of which is computed in a normal pairwise fashion, -the so-called real-space part, and one of which is computed using the -Fourier transform, the so called reciprocal-space or kspace part. For -both parts, the potential is not computed exactly but is approximated. -Thus, there is an error in both parts of the computation, the -real-space and the kspace error. The just mentioned facts are true -both for the PPPM for Coulomb as well as dispersion interactions. The -deciding difference - and also the reason why the parameters for -pppm/disp have to be selected with more care - is the impact of the -errors on the results: The kspace error of the PPPM for Coulomb and -dispersion interaction and the real-space error of the PPPM for -Coulomb interaction have the character of noise. In contrast, the -real-space error of the PPPM for dispersion has a clear physical -interpretation: the underprediction of cohesion. As a consequence, the -real-space error has a much stronger effect than the kspace error on -simulation results for pppm/disp. Parameters must thus be chosen in a -way that this error is much smaller than the kspace error. - -When using pppm/disp and not making any specifications on the PPPM -parameters via the kspace modify command, parameters will be tuned -such that the real-space error and the kspace error are equal. This -will result in simulations that are either inaccurate or slow, both of -which is not desirable. For selecting parameters for the pppm/disp -that provide fast and accurate simulations, there are two approaches, -which both have their up- and downsides. - -The first approach is to set desired real-space an kspace accuracies -via the {kspace_modify force/disp/real} and {kspace_modify -force/disp/kspace} commands. Note that the accuracies have to be -specified in force units and are thus dependent on the chosen unit -settings. For real units, 0.0001 and 0.002 seem to provide reasonable -accurate and efficient computations for the real-space and kspace -accuracies. 0.002 and 0.05 work well for most systems using lj -units. PPPM parameters will be generated based on the desired -accuracies. The upside of this approach is that it usually provides a -good set of parameters and will work for both the {kspace_modify diff -ad} and {kspace_modify diff ik} options. The downside of the method -is that setting the PPPM parameters will take some time during the -initialization of the simulation. - -The second approach is to set the parameters for the pppm/disp -explicitly using the {kspace_modify mesh/disp}, {kspace_modify -order/disp}, and {kspace_modify gewald/disp} commands. This approach -requires a more experienced user who understands well the impact of -the choice of parameters on the simulation accuracy and -performance. This approach provides a fast initialization of the -simulation. However, it is sensitive to errors: A combination of -parameters that will perform well for one system might result in -far-from-optimal conditions for other simulations. For example, -parameters that provide accurate and fast computations for -all-atomistic force fields can provide insufficient accuracy or -united-atomistic force fields (which is related to that the latter -typically have larger dispersion coefficients). - -To avoid inaccurate or inefficient simulations, the pppm/disp stops -simulations with an error message if no action is taken to control the -PPPM parameters. If the automatic parameter generation is desired and -real-space and kspace accuracies are desired to be equal, this error -message can be suppressed using the {kspace_modify disp/auto yes} -command. - -A reasonable approach that combines the upsides of both methods is to -make the first run using the {kspace_modify force/disp/real} and -{kspace_modify force/disp/kspace} commands, write down the PPPM -parameters from the outut, and specify these parameters using the -second approach in subsequent runs (which have the same composition, -force field, and approximately the same volume). - -Concerning the performance of the pppm/disp there are two more things -to consider. The first is that when using the pppm/disp, the cutoff -parameter does no longer affect the accuracy of the simulation -(subject to that gewald/disp is adjusted when changing the cutoff). -The performance can thus be increased by examining different values -for the cutoff parameter. A lower bound for the cutoff is only set by -the truncation error of the repulsive term of pair potentials. - -The second is that the mixing rule of the pair style has an impact on -the computation time when using the pppm/disp. Fastest computations -are achieved when using the geometric mixing rule. Using the -arithmetic mixing rule substantially increases the computational cost. -The computational overhead can be reduced using the {kspace_modify -mix/disp geom} and {kspace_modify splittol} commands. The first -command simply enforces geometric mixing of the dispersion -coefficients in kspace computations. This introduces some error in -the computations but will also significantly speed-up the -simulations. The second keyword sets the accuracy with which the -dispersion coefficients are approximated using a matrix factorization -approach. This may result in better accuracy then using the first -command, but will usually also not provide an equally good increase of -efficiency. - -Finally, pppm/disp can also be used when no mixing rules apply. -This can be achieved using the {kspace_modify mix/disp none} command. -Note that the code does not check automatically whether any mixing -rule is fulfilled. If mixing rules do not apply, the user will have -to specify this command explicitly. - -:line - -6.25 Polarizable models :link(howto_25),h4 - -In polarizable force fields the charge distributions in molecules and -materials respond to their electrostatic environments. Polarizable -systems can be simulated in LAMMPS using three methods: - -the fluctuating charge method, implemented in the "QEQ"_fix_qeq.html -package, :ulb,l -the adiabatic core-shell method, implemented in the -"CORESHELL"_#howto_26 package, :l -the thermalized Drude dipole method, implemented in the -"USER-DRUDE"_#howto_27 package. :l -:ule - -The fluctuating charge method calculates instantaneous charges on -interacting atoms based on the electronegativity equalization -principle. It is implemented in the "fix qeq"_fix_qeq.html which is -available in several variants. It is a relatively efficient technique -since no additional particles are introduced. This method allows for -charge transfer between molecules or atom groups. However, because the -charges are located at the interaction sites, off-plane components of -polarization cannot be represented in planar molecules or atom groups. - -The two other methods share the same basic idea: polarizable atoms are -split into one core atom and one satellite particle (called shell or -Drude particle) attached to it by a harmonic spring. Both atoms bear -a charge and they represent collectively an induced electric dipole. -These techniques are computationally more expensive than the QEq -method because of additional particles and bonds. These two -charge-on-spring methods differ in certain features, with the -core-shell model being normally used for ionic/crystalline materials, -whereas the so-called Drude model is normally used for molecular -systems and fluid states. - -The core-shell model is applicable to crystalline materials where the -high symmetry around each site leads to stable trajectories of the -core-shell pairs. However, bonded atoms in molecules can be so close -that a core would interact too strongly or even capture the Drude -particle of a neighbor. The Drude dipole model is relatively more -complex in order to remediate this and other issues. Specifically, the -Drude model includes specific thermostating of the core-Drude pairs -and short-range damping of the induced dipoles. - -The three polarization methods can be implemented through a -self-consistent calculation of charges or induced dipoles at each -timestep. In the fluctuating charge scheme this is done by the matrix -inversion method in "fix qeq/point"_fix_qeq.html, but for core-shell -or Drude-dipoles the relaxed-dipoles technique would require an slow -iterative procedure. These self-consistent solutions yield accurate -trajectories since the additional degrees of freedom representing -polarization are massless. An alternative is to attribute a mass to -the additional degrees of freedom and perform time integration using -an extended Lagrangian technique. For the fluctuating charge scheme -this is done by "fix qeq/dynamic"_fix_qeq.html, and for the -charge-on-spring models by the methods outlined in the next two -sections. The assignment of masses to the additional degrees of -freedom can lead to unphysical trajectories if care is not exerted in -choosing the parameters of the polarizable models and the simulation -conditions. - -In the core-shell model the vibration of the shells is kept faster -than the ionic vibrations to mimic the fast response of the -polarizable electrons. But in molecular systems thermalizing the -core-Drude pairs at temperatures comparable to the rest of the -simulation leads to several problems (kinetic energy transfer, too -short a timestep, etc.) In order to avoid these problems the relative -motion of the Drude particles with respect to their cores is kept -"cold" so the vibration of the core-Drude pairs is very slow, -approaching the self-consistent regime. In both models the -temperature is regulated using the velocities of the center of mass of -core+shell (or Drude) pairs, but in the Drude model the actual -relative core-Drude particle motion is thermostated separately as -well. - -:line - -6.26 Adiabatic core/shell model :link(howto_26),h4 - -The adiabatic core-shell model by "Mitchell and -Fincham"_#MitchellFincham is a simple method for adding -polarizability to a system. In order to mimic the electron shell of -an ion, a satellite particle is attached to it. This way the ions are -split into a core and a shell where the latter is meant to react to -the electrostatic environment inducing polarizability. - -Technically, shells are attached to the cores by a spring force f = -k*r where k is a parametrized spring constant and r is the distance -between the core and the shell. The charges of the core and the shell -add up to the ion charge, thus q(ion) = q(core) + q(shell). This -setup introduces the ion polarizability (alpha) given by -alpha = q(shell)^2 / k. In a -similar fashion the mass of the ion is distributed on the core and the -shell with the core having the larger mass. - -To run this model in LAMMPS, "atom_style"_atom_style.html {full} can -be used since atom charge and bonds are needed. Each kind of -core/shell pair requires two atom types and a bond type. The core and -shell of a core/shell pair should be bonded to each other with a -harmonic bond that provides the spring force. For example, a data file -for NaCl, as found in examples/coreshell, has this format: - -432 atoms # core and shell atoms -216 bonds # number of core/shell springs :pre - -4 atom types # 2 cores and 2 shells for Na and Cl -2 bond types :pre - -0.0 24.09597 xlo xhi -0.0 24.09597 ylo yhi -0.0 24.09597 zlo zhi :pre - -Masses # core/shell mass ratio = 0.1 :pre - -1 20.690784 # Na core -2 31.90500 # Cl core -3 2.298976 # Na shell -4 3.54500 # Cl shell :pre - -Atoms :pre - -1 1 2 1.5005 0.00000000 0.00000000 0.00000000 # core of core/shell pair 1 -2 1 4 -2.5005 0.00000000 0.00000000 0.00000000 # shell of core/shell pair 1 -3 2 1 1.5056 4.01599500 4.01599500 4.01599500 # core of core/shell pair 2 -4 2 3 -0.5056 4.01599500 4.01599500 4.01599500 # shell of core/shell pair 2 -(...) :pre - -Bonds # Bond topology for spring forces :pre - -1 2 1 2 # spring for core/shell pair 1 -2 2 3 4 # spring for core/shell pair 2 -(...) :pre - -Non-Coulombic (e.g. Lennard-Jones) pairwise interactions are only -defined between the shells. Coulombic interactions are defined -between all cores and shells. If desired, additional bonds can be -specified between cores. - -The "special_bonds"_special_bonds.html command should be used to -turn-off the Coulombic interaction within core/shell pairs, since that -interaction is set by the bond spring. This is done using the -"special_bonds"_special_bonds.html command with a 1-2 weight = 0.0, -which is the default value. It needs to be considered whether one has -to adjust the "special_bonds"_special_bonds.html weighting according -to the molecular topology since the interactions of the shells are -bypassed over an extra bond. - -Note that this core/shell implementation does not require all ions to -be polarized. One can mix core/shell pairs and ions without a -satellite particle if desired. - -Since the core/shell model permits distances of r = 0.0 between the -core and shell, a pair style with a "cs" suffix needs to be used to -implement a valid long-range Coulombic correction. Several such pair -styles are provided in the CORESHELL package. See "this doc -page"_pair_cs.html for details. All of the core/shell enabled pair -styles require the use of a long-range Coulombic solver, as specified -by the "kspace_style"_kspace_style.html command. Either the PPPM or -Ewald solvers can be used. - -For the NaCL example problem, these pair style and bond style settings -are used: - -pair_style born/coul/long/cs 20.0 20.0 -pair_coeff * * 0.0 1.000 0.00 0.00 0.00 -pair_coeff 3 3 487.0 0.23768 0.00 1.05 0.50 #Na-Na -pair_coeff 3 4 145134.0 0.23768 0.00 6.99 8.70 #Na-Cl -pair_coeff 4 4 405774.0 0.23768 0.00 72.40 145.40 #Cl-Cl :pre - -bond_style harmonic -bond_coeff 1 63.014 0.0 -bond_coeff 2 25.724 0.0 :pre - -When running dynamics with the adiabatic core/shell model, the -following issues should be considered. The relative motion of -the core and shell particles corresponds to the polarization, -hereby an instantaneous relaxation of the shells is approximated -and a fast core/shell spring frequency ensures a nearly constant -internal kinetic energy during the simulation. -Thermostats can alter this polarization behaviour, by scaling the -internal kinetic energy, meaning the shell will not react freely to -its electrostatic environment. -Therefore it is typically desirable to decouple the relative motion of -the core/shell pair, which is an imaginary degree of freedom, from the -real physical system. To do that, the "compute -temp/cs"_compute_temp_cs.html command can be used, in conjunction with -any of the thermostat fixes, such as "fix nvt"_fix_nh.html or "fix -langevin"_fix_langevin. This compute uses the center-of-mass velocity -of the core/shell pairs to calculate a temperature, and insures that -velocity is what is rescaled for thermostatting purposes. This -compute also works for a system with both core/shell pairs and -non-polarized ions (ions without an attached satellite particle). The -"compute temp/cs"_compute_temp_cs.html command requires input of two -groups, one for the core atoms, another for the shell atoms. -Non-polarized ions which might also be included in the treated system -should not be included into either of these groups, they are taken -into account by the {group-ID} (2nd argument) of the compute. The -groups can be defined using the "group {type}"_group.html command. -Note that to perform thermostatting using this definition of -temperature, the "fix modify temp"_fix_modify.html command should be -used to assign the compute to the thermostat fix. Likewise the -"thermo_modify temp"_thermo_modify.html command can be used to make -this temperature be output for the overall system. - -For the NaCl example, this can be done as follows: - -group cores type 1 2 -group shells type 3 4 -compute CSequ all temp/cs cores shells -fix thermoberendsen all temp/berendsen 1427 1427 0.4 # thermostat for the true physical system -fix thermostatequ all nve # integrator as needed for the berendsen thermostat -fix_modify thermoberendsen temp CSequ -thermo_modify temp CSequ # output of center-of-mass derived temperature :pre - -The pressure for the core/shell system is computed via the regular -LAMMPS convention by "treating the cores and shells as individual -particles"_#MitchellFincham2. For the thermo output of the pressure -as well as for the application of a barostat, it is necessary to -use an additional "pressure"_compute_pressure compute based on the -default "temperature"_compute_temp and specifying it as a second -argument in "fix modify"_fix_modify.html and -"thermo_modify"_thermo_modify.html resulting in: - -(...) -compute CSequ all temp/cs cores shells -compute thermo_press_lmp all pressure thermo_temp # pressure for individual particles -thermo_modify temp CSequ press thermo_press_lmp # modify thermo to regular pressure -fix press_bar all npt temp 300 300 0.04 iso 0 0 0.4 -fix_modify press_bar temp CSequ press thermo_press_lmp # pressure modification for correct kinetic scalar :pre - -If "compute temp/cs"_compute_temp_cs.html is used, the decoupled -relative motion of the core and the shell should in theory be -stable. However numerical fluctuation can introduce a small -momentum to the system, which is noticable over long trajectories. -Therefore it is recommendable to use the "fix -momentum"_fix_momentum.html command in combination with "compute -temp/cs"_compute_temp_cs.html when equilibrating the system to -prevent any drift. - -When initializing the velocities of a system with core/shell pairs, it -is also desirable to not introduce energy into the relative motion of -the core/shell particles, but only assign a center-of-mass velocity to -the pairs. This can be done by using the {bias} keyword of the -"velocity create"_velocity.html command and assigning the "compute -temp/cs"_compute_temp_cs.html command to the {temp} keyword of the -"velocity"_velocity.html command, e.g. - -velocity all create 1427 134 bias yes temp CSequ -velocity all scale 1427 temp CSequ :pre - -To maintain the correct polarizability of the core/shell pairs, the -kinetic energy of the internal motion shall remain nearly constant. -Therefore the choice of spring force and mass ratio need to ensure -much faster relative motion of the 2 atoms within the core/shell pair -than their center-of-mass velocity. This allows the shells to -effectively react instantaneously to the electrostatic environment and -limits energy transfer to or from the core/shell oscillators. -This fast movement also dictates the timestep that can be used. - -The primary literature of the adiabatic core/shell model suggests that -the fast relative motion of the core/shell pairs only allows negligible -energy transfer to the environment. -The mentioned energy transfer will typically lead to a small drift -in total energy over time. This internal energy can be monitored -using the "compute chunk/atom"_compute_chunk_atom.html and "compute -temp/chunk"_compute_temp_chunk.html commands. The internal kinetic -energies of each core/shell pair can then be summed using the sum() -special function of the "variable"_variable.html command. Or they can -be time/averaged and output using the "fix ave/time"_fix_ave_time.html -command. To use these commands, each core/shell pair must be defined -as a "chunk". If each core/shell pair is defined as its own molecule, -the molecule ID can be used to define the chunks. If cores are bonded -to each other to form larger molecules, the chunks can be identified -by the "fix property/atom"_fix_property_atom.html via assigning a -core/shell ID to each atom using a special field in the data file read -by the "read_data"_read_data.html command. This field can then be -accessed by the "compute property/atom"_compute_property_atom.html -command, to use as input to the "compute -chunk/atom"_compute_chunk_atom.html command to define the core/shell -pairs as chunks. - -For example if core/shell pairs are the only molecules: - -read_data NaCl_CS_x0.1_prop.data -compute prop all property/atom molecule -compute cs_chunk all chunk/atom c_prop -compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0 # note the chosen degrees of freedom for the core/shell pairs -fix ave_chunk all ave/time 10 1 10 c_cstherm file chunk.dump mode vector :pre - -For example if core/shell pairs and other molecules are present: - -fix csinfo all property/atom i_CSID # property/atom command -read_data NaCl_CS_x0.1_prop.data fix csinfo NULL CS-Info # atom property added in the data-file -compute prop all property/atom i_CSID -(...) :pre - -The additional section in the date file would be formatted like this: - -CS-Info # header of additional section :pre - -1 1 # column 1 = atom ID, column 2 = core/shell ID -2 1 -3 2 -4 2 -5 3 -6 3 -7 4 -8 4 -(...) :pre - -:line - -6.27 Drude induced dipoles :link(howto_27),h4 - -The thermalized Drude model, similarly to the "core-shell"_#howto_26 -model, represents induced dipoles by a pair of charges (the core atom -and the Drude particle) connected by a harmonic spring. The Drude -model has a number of features aimed at its use in molecular systems -("Lamoureux and Roux"_#howto-Lamoureux): - -Thermostating of the additional degrees of freedom associated with the -induced dipoles at very low temperature, in terms of the reduced -coordinates of the Drude particles with respect to their cores. This -makes the trajectory close to that of relaxed induced dipoles. :ulb,l - -Consistent definition of 1-2 to 1-4 neighbors. A core-Drude particle -pair represents a single (polarizable) atom, so the special screening -factors in a covalent structure should be the same for the core and -the Drude particle. Drude particles have to inherit the 1-2, 1-3, 1-4 -special neighbor relations from their respective cores. :l - -Stabilization of the interactions between induced dipoles. Drude -dipoles on covalently bonded atoms interact too strongly due to the -short distances, so an atom may capture the Drude particle of a -neighbor, or the induced dipoles within the same molecule may align -too much. To avoid this, damping at short range can be done by Thole -functions (for which there are physical grounds). This Thole damping -is applied to the point charges composing the induced dipole (the -charge of the Drude particle and the opposite charge on the core, not -to the total charge of the core atom). :l -:ule - -A detailed tutorial covering the usage of Drude induced dipoles in -LAMMPS is "available here"_tutorial_drude.html. - -As with the core-shell model, the cores and Drude particles should -appear in the data file as standard atoms. The same holds for the -springs between them, which are described by standard harmonic bonds. -The nature of the atoms (core, Drude particle or non-polarizable) is -specified via the "fix drude"_fix_drude.html command. The special -list of neighbors is automatically refactored to account for the -equivalence of core and Drude particles as regards special 1-2 to 1-4 -screening. It may be necessary to use the {extra/special/per/atom} -keyword of the "read_data"_read_data.html command. If using "fix -shake"_fix_shake.html, make sure no Drude particle is in this fix -group. - -There are two ways to thermostat the Drude particles at a low -temperature: use either "fix langevin/drude"_fix_langevin_drude.html -for a Langevin thermostat, or "fix -drude/transform/*"_fix_drude_transform.html for a Nose-Hoover -thermostat. The former requires use of the command "comm_modify vel -yes"_comm_modify.html. The latter requires two separate integration -fixes like {nvt} or {npt}. The correct temperatures of the reduced -degrees of freedom can be calculated using the "compute -temp/drude"_compute_temp_drude.html. This requires also to use the -command {comm_modify vel yes}. - -Short-range damping of the induced dipole interactions can be achieved -using Thole functions through the "pair style -thole"_pair_thole.html in "pair_style hybrid/overlay"_pair_hybrid.html -with a Coulomb pair style. It may be useful to use {coul/long/cs} or -similar from the CORESHELL package if the core and Drude particle come -too close, which can cause numerical issues. - -:line -:line - -:link(howto-Berendsen) -[(Berendsen)] Berendsen, Grigera, Straatsma, J Phys Chem, 91, -6269-6271 (1987). - -:link(howto-Cornell) -[(Cornell)] Cornell, Cieplak, Bayly, Gould, Merz, Ferguson, -Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995). - -:link(Horn) -[(Horn)] Horn, Swope, Pitera, Madura, Dick, Hura, and Head-Gordon, -J Chem Phys, 120, 9665 (2004). - -:link(howto-Ikeshoji) -[(Ikeshoji)] Ikeshoji and Hafskjold, Molecular Physics, 81, 251-261 -(1994). - -:link(howto-Wirnsberger) -[(Wirnsberger)] Wirnsberger, Frenkel, and Dellago, J Chem Phys, 143, 124104 -(2015). - -:link(howto-MacKerell) -[(MacKerell)] MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field, -Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998). - -:link(howto-Mayo) -[(Mayo)] Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909 -(1990). - -:link(Jorgensen1) -[(Jorgensen)] Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem -Phys, 79, 926 (1983). - -:link(Price1) -[(Price)] Price and Brooks, J Chem Phys, 121, 10096 (2004). - -:link(Shinoda1) -[(Shinoda)] Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004). - -:link(MitchellFincham) -[(Mitchell and Fincham)] Mitchell, Fincham, J Phys Condensed Matter, -5, 1031-1038 (1993). - -:link(MitchellFincham2) -[(Fincham)] Fincham, Mackrodt and Mitchell, J Phys Condensed Matter, -6, 393-404 (1994). - -:link(howto-Lamoureux) -[(Lamoureux and Roux)] G. Lamoureux, B. Roux, J. Chem. Phys 119, 3025 (2003) diff --git a/doc/src/Section_intro.txt b/doc/src/Section_intro.txt deleted file mode 100644 index 67293b2ee3..0000000000 --- a/doc/src/Section_intro.txt +++ /dev/null @@ -1,549 +0,0 @@ -"Previous Section"_Manual.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Section_start.html :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Section_commands.html#comm) - -:line - -1. Introduction :h2 - -This section provides an overview of what LAMMPS can and can't do, -describes what it means for LAMMPS to be an open-source code, and -acknowledges the funding and people who have contributed to LAMMPS -over the years. - -1.1 "What is LAMMPS"_#intro_1 -1.2 "LAMMPS features"_#intro_2 -1.3 "LAMMPS non-features"_#intro_3 -1.4 "Open source distribution"_#intro_4 -1.5 "Acknowledgments and citations"_#intro_5 :all(b) - -:line -:line - -1.1 What is LAMMPS :link(intro_1),h4 - -LAMMPS is a classical molecular dynamics code that models an ensemble -of particles in a liquid, solid, or gaseous state. It can model -atomic, polymeric, biological, metallic, granular, and coarse-grained -systems using a variety of force fields and boundary conditions. - -For examples of LAMMPS simulations, see the Publications page of the -"LAMMPS WWW Site"_lws. - -LAMMPS runs efficiently on single-processor desktop or laptop -machines, but is designed for parallel computers. It will run on any -parallel machine that compiles C++ and supports the "MPI"_mpi -message-passing library. This includes distributed- or shared-memory -parallel machines and Beowulf-style clusters. - -:link(mpi,http://www-unix.mcs.anl.gov/mpi) - -LAMMPS can model systems with only a few particles up to millions or -billions. See "Section 8"_Section_perf.html for information on -LAMMPS performance and scalability, or the Benchmarks section of the -"LAMMPS WWW Site"_lws. - -LAMMPS is a freely-available open-source code, distributed under the -terms of the "GNU Public License"_gnu, which means you can use or -modify the code however you wish. See "this section"_#intro_4 for a -brief discussion of the open-source philosophy. - -:link(gnu,http://www.gnu.org/copyleft/gpl.html) - -LAMMPS is designed to be easy to modify or extend with new -capabilities, such as new force fields, atom types, boundary -conditions, or diagnostics. See "Section 10"_Section_modify.html -for more details. - -The current version of LAMMPS is written in C++. Earlier versions -were written in F77 and F90. See -"Section 13"_Section_history.html for more information on -different versions. All versions can be downloaded from the "LAMMPS -WWW Site"_lws. - -LAMMPS was originally developed under a US Department of Energy CRADA -(Cooperative Research and Development Agreement) between two DOE labs -and 3 companies. It is distributed by "Sandia National Labs"_snl. -See "this section"_#intro_5 for more information on LAMMPS funding and -individuals who have contributed to LAMMPS. - -:link(snl,http://www.sandia.gov) - -In the most general sense, LAMMPS integrates Newton's equations of -motion for collections of atoms, molecules, or macroscopic particles -that interact via short- or long-range forces with a variety of -initial and/or boundary conditions. For computational efficiency -LAMMPS uses neighbor lists to keep track of nearby particles. The -lists are optimized for systems with particles that are repulsive at -short distances, so that the local density of particles never becomes -too large. On parallel machines, LAMMPS uses spatial-decomposition -techniques to partition the simulation domain into small 3d -sub-domains, one of which is assigned to each processor. Processors -communicate and store "ghost" atom information for atoms that border -their sub-domain. LAMMPS is most efficient (in a parallel sense) for -systems whose particles fill a 3d rectangular box with roughly uniform -density. Papers with technical details of the algorithms used in -LAMMPS are listed in "this section"_#intro_5. - -:line - -1.2 LAMMPS features :link(intro_2),h4 - -This section highlights LAMMPS features, with pointers to specific -commands which give more details. If LAMMPS doesn't have your -favorite interatomic potential, boundary condition, or atom type, see -"Section 10"_Section_modify.html, which describes how you can add -it to LAMMPS. - -General features :h4 - - runs on a single processor or in parallel - distributed-memory message-passing parallelism (MPI) - spatial-decomposition of simulation domain for parallelism - open-source distribution - highly portable C++ - optional libraries used: MPI and single-processor FFT - GPU (CUDA and OpenCL), Intel(R) Xeon Phi(TM) coprocessors, and OpenMP support for many code features - easy to extend with new features and functionality - runs from an input script - syntax for defining and using variables and formulas - syntax for looping over runs and breaking out of loops - run one or multiple simulations simultaneously (in parallel) from one script - build as library, invoke LAMMPS thru library interface or provided Python wrapper - couple with other codes: LAMMPS calls other code, other code calls LAMMPS, umbrella code calls both :ul - -Particle and model types :h4 -("atom style"_atom_style.html command) - - atoms - coarse-grained particles (e.g. bead-spring polymers) - united-atom polymers or organic molecules - all-atom polymers, organic molecules, proteins, DNA - metals - granular materials - coarse-grained mesoscale models - finite-size spherical and ellipsoidal particles - finite-size line segment (2d) and triangle (3d) particles - point dipole particles - rigid collections of particles - hybrid combinations of these :ul - -Force fields :h4 -("pair style"_pair_style.html, "bond style"_bond_style.html, -"angle style"_angle_style.html, "dihedral style"_dihedral_style.html, -"improper style"_improper_style.html, "kspace style"_kspace_style.html -commands) - - pairwise potentials: Lennard-Jones, Buckingham, Morse, Born-Mayer-Huggins, \ - Yukawa, soft, class 2 (COMPASS), hydrogen bond, tabulated - charged pairwise potentials: Coulombic, point-dipole - manybody potentials: EAM, Finnis/Sinclair EAM, modified EAM (MEAM), \ - embedded ion method (EIM), EDIP, ADP, Stillinger-Weber, Tersoff, \ - REBO, AIREBO, ReaxFF, COMB, SNAP, Streitz-Mintmire, 3-body polymorphic - long-range interactions for charge, point-dipoles, and LJ dispersion: \ - Ewald, Wolf, PPPM (similar to particle-mesh Ewald) - polarization models: "QEq"_fix_qeq.html, \ - "core/shell model"_Section_howto.html#howto_26, \ - "Drude dipole model"_Section_howto.html#howto_27 - charge equilibration (QEq via dynamic, point, shielded, Slater methods) - coarse-grained potentials: DPD, GayBerne, REsquared, colloidal, DLVO - mesoscopic potentials: granular, Peridynamics, SPH - electron force field (eFF, AWPMD) - bond potentials: harmonic, FENE, Morse, nonlinear, class 2, \ - quartic (breakable) - angle potentials: harmonic, CHARMM, cosine, cosine/squared, cosine/periodic, \ - class 2 (COMPASS) - dihedral potentials: harmonic, CHARMM, multi-harmonic, helix, \ - class 2 (COMPASS), OPLS - improper potentials: harmonic, cvff, umbrella, class 2 (COMPASS) - polymer potentials: all-atom, united-atom, bead-spring, breakable - water potentials: TIP3P, TIP4P, SPC - implicit solvent potentials: hydrodynamic lubrication, Debye - force-field compatibility with common CHARMM, AMBER, DREIDING, \ - OPLS, GROMACS, COMPASS options - access to "KIM archive"_http://openkim.org of potentials via \ - "pair kim"_pair_kim.html - hybrid potentials: multiple pair, bond, angle, dihedral, improper \ - potentials can be used in one simulation - overlaid potentials: superposition of multiple pair potentials :ul - -Atom creation :h4 -("read_data"_read_data.html, "lattice"_lattice.html, -"create_atoms"_create_atoms.html, "delete_atoms"_delete_atoms.html, -"displace_atoms"_displace_atoms.html, "replicate"_replicate.html commands) - - read in atom coords from files - create atoms on one or more lattices (e.g. grain boundaries) - delete geometric or logical groups of atoms (e.g. voids) - replicate existing atoms multiple times - displace atoms :ul - -Ensembles, constraints, and boundary conditions :h4 -("fix"_fix.html command) - - 2d or 3d systems - orthogonal or non-orthogonal (triclinic symmetry) simulation domains - constant NVE, NVT, NPT, NPH, Parinello/Rahman integrators - thermostatting options for groups and geometric regions of atoms - pressure control via Nose/Hoover or Berendsen barostatting in 1 to 3 dimensions - simulation box deformation (tensile and shear) - harmonic (umbrella) constraint forces - rigid body constraints - SHAKE bond and angle constraints - Monte Carlo bond breaking, formation, swapping - atom/molecule insertion and deletion - walls of various kinds - non-equilibrium molecular dynamics (NEMD) - variety of additional boundary conditions and constraints :ul - -Integrators :h4 -("run"_run.html, "run_style"_run_style.html, "minimize"_minimize.html commands) - - velocity-Verlet integrator - Brownian dynamics - rigid body integration - energy minimization via conjugate gradient or steepest descent relaxation - rRESPA hierarchical timestepping - rerun command for post-processing of dump files :ul - -Diagnostics :h4 - - see the various flavors of the "fix"_fix.html and "compute"_compute.html commands :ul - -Output :h4 -("dump"_dump.html, "restart"_restart.html commands) - - log file of thermodynamic info - text dump files of atom coords, velocities, other per-atom quantities - binary restart files - parallel I/O of dump and restart files - per-atom quantities (energy, stress, centro-symmetry parameter, CNA, etc) - user-defined system-wide (log file) or per-atom (dump file) calculations - spatial and time averaging of per-atom quantities - time averaging of system-wide quantities - atom snapshots in native, XYZ, XTC, DCD, CFG formats :ul - -Multi-replica models :h4 - -"nudged elastic band"_neb.html -"parallel replica dynamics"_prd.html -"temperature accelerated dynamics"_tad.html -"parallel tempering"_temper.html - -Pre- and post-processing :h4 - -Various pre- and post-processing serial tools are packaged -with LAMMPS; see these "doc pages"_Section_tools.html. :ulb,l - -Our group has also written and released a separate toolkit called -"Pizza.py"_pizza which provides tools for doing setup, analysis, -plotting, and visualization for LAMMPS simulations. Pizza.py is -written in "Python"_python and is available for download from "the -Pizza.py WWW site"_pizza. :l -:ule - -:link(pizza,http://www.sandia.gov/~sjplimp/pizza.html) -:link(python,http://www.python.org) - -Specialized features :h4 - -LAMMPS can be built with optional packages which implement a variety -of additional capabilities. An overview of all the packages is "given -here"_Section_packages.html. - -These are some LAMMPS capabilities which you may not think of as -typical classical molecular dynamics options: - -"static"_balance.html and "dynamic load-balancing"_fix_balance.html -"generalized aspherical particles"_body.html -"stochastic rotation dynamics (SRD)"_fix_srd.html -"real-time visualization and interactive MD"_fix_imd.html -calculate "virtual diffraction patterns"_compute_xrd.html -"atom-to-continuum coupling"_fix_atc.html with finite elements -coupled rigid body integration via the "POEMS"_fix_poems.html library -"QM/MM coupling"_fix_qmmm.html -"path-integral molecular dynamics (PIMD)"_fix_ipi.html and "this as well"_fix_pimd.html -Monte Carlo via "GCMC"_fix_gcmc.html and "tfMC"_fix_tfmc.html "atom swapping"_fix_atom_swap.html and "bond swapping"_fix_bond_swap.html -"Direct Simulation Monte Carlo"_pair_dsmc.html for low-density fluids -"Peridynamics mesoscale modeling"_pair_peri.html -"Lattice Boltzmann fluid"_fix_lb_fluid.html -"targeted"_fix_tmd.html and "steered"_fix_smd.html molecular dynamics -"two-temperature electron model"_fix_ttm.html :ul - -:line - -1.3 LAMMPS non-features :link(intro_3),h4 - -LAMMPS is designed to efficiently compute Newton's equations of motion -for a system of interacting particles. Many of the tools needed to -pre- and post-process the data for such simulations are not included -in the LAMMPS kernel for several reasons: - -the desire to keep LAMMPS simple -they are not parallel operations -other codes already do them -limited development resources :ul - -Specifically, LAMMPS itself does not: - -run thru a GUI -build molecular systems -assign force-field coefficients automagically -perform sophisticated analyses of your MD simulation -visualize your MD simulation -plot your output data :ul - -A few tools for pre- and post-processing tasks are provided as part of -the LAMMPS package; they are described in "this -section"_Section_tools.html. However, many people use other codes or -write their own tools for these tasks. - -As noted above, our group has also written and released a separate -toolkit called "Pizza.py"_pizza which addresses some of the listed -bullets. It provides tools for doing setup, analysis, plotting, and -visualization for LAMMPS simulations. Pizza.py is written in -"Python"_python and is available for download from "the Pizza.py WWW -site"_pizza. - -LAMMPS requires as input a list of initial atom coordinates and types, -molecular topology information, and force-field coefficients assigned -to all atoms and bonds. LAMMPS will not build molecular systems and -assign force-field parameters for you. - -For atomic systems LAMMPS provides a "create_atoms"_create_atoms.html -command which places atoms on solid-state lattices (fcc, bcc, -user-defined, etc). Assigning small numbers of force field -coefficients can be done via the "pair coeff"_pair_coeff.html, "bond -coeff"_bond_coeff.html, "angle coeff"_angle_coeff.html, etc commands. -For molecular systems or more complicated simulation geometries, users -typically use another code as a builder and convert its output to -LAMMPS input format, or write their own code to generate atom -coordinate and molecular topology for LAMMPS to read in. - -For complicated molecular systems (e.g. a protein), a multitude of -topology information and hundreds of force-field coefficients must -typically be specified. We suggest you use a program like -"CHARMM"_charmm or "AMBER"_amber or other molecular builders to setup -such problems and dump its information to a file. You can then -reformat the file as LAMMPS input. Some of the tools in "this -section"_Section_tools.html can assist in this process. - -Similarly, LAMMPS creates output files in a simple format. Most users -post-process these files with their own analysis tools or re-format -them for input into other programs, including visualization packages. -If you are convinced you need to compute something on-the-fly as -LAMMPS runs, see "Section 10"_Section_modify.html for a discussion -of how you can use the "dump"_dump.html and "compute"_compute.html and -"fix"_fix.html commands to print out data of your choosing. Keep in -mind that complicated computations can slow down the molecular -dynamics timestepping, particularly if the computations are not -parallel, so it is often better to leave such analysis to -post-processing codes. - -For high-quality visualization we recommend the -following packages: - -"VMD"_http://www.ks.uiuc.edu/Research/vmd -"AtomEye"_http://mt.seas.upenn.edu/Archive/Graphics/A -"OVITO"_http://www.ovito.org/ -"ParaView"_http://www.paraview.org/ -"PyMol"_http://www.pymol.org -"Raster3d"_http://www.bmsc.washington.edu/raster3d/raster3d.html -"RasMol"_http://www.openrasmol.org :ul - -Other features that LAMMPS does not yet (and may never) support are -discussed in "Section 13"_Section_history.html. - -Finally, these are freely-available molecular dynamics codes, most of -them parallel, which may be well-suited to the problems you want to -model. They can also be used in conjunction with LAMMPS to perform -complementary modeling tasks. - -"CHARMM"_charmm -"AMBER"_amber -"NAMD"_namd -"NWCHEM"_nwchem -"DL_POLY"_dlpoly -"Tinker"_tinker :ul - -:link(charmm,http://www.charmm.org) -:link(amber,http://ambermd.org) -:link(namd,http://www.ks.uiuc.edu/Research/namd/) -:link(nwchem,http://www.emsl.pnl.gov/docs/nwchem/nwchem.html) -:link(dlpoly,http://www.ccp5.ac.uk/DL_POLY_CLASSIC) -:link(tinker,http://dasher.wustl.edu/tinker) - -CHARMM, AMBER, NAMD, NWCHEM, and Tinker are designed primarily for -modeling biological molecules. CHARMM and AMBER use -atom-decomposition (replicated-data) strategies for parallelism; NAMD -and NWCHEM use spatial-decomposition approaches, similar to LAMMPS. -Tinker is a serial code. DL_POLY includes potentials for a variety of -biological and non-biological materials; both a replicated-data and -spatial-decomposition version exist. - -:line - -1.4 Open source distribution :link(intro_4),h4 - -LAMMPS comes with no warranty of any kind. As each source file states -in its header, it is a copyrighted code that is distributed free-of- -charge, under the terms of the "GNU Public License"_gnu (GPL). This -is often referred to as open-source distribution - see -"www.gnu.org"_gnuorg or "www.opensource.org"_opensource for more -details. The legal text of the GPL is in the LICENSE file that is -included in the LAMMPS distribution. - -:link(gnuorg,http://www.gnu.org) -:link(opensource,http://www.opensource.org) - -Here is a summary of what the GPL means for LAMMPS users: - -(1) Anyone is free to use, modify, or extend LAMMPS in any way they -choose, including for commercial purposes. - -(2) If you distribute a modified version of LAMMPS, it must remain -open-source, meaning you distribute it under the terms of the GPL. -You should clearly annotate such a code as a derivative version of -LAMMPS. - -(3) If you release any code that includes LAMMPS source code, then it -must also be open-sourced, meaning you distribute it under the terms -of the GPL. - -(4) If you give LAMMPS files to someone else, the GPL LICENSE file and -source file headers (including the copyright and GPL notices) should -remain part of the code. - -In the spirit of an open-source code, these are various ways you can -contribute to making LAMMPS better. You can send email to the -"developers"_http://lammps.sandia.gov/authors.html on any of these -items. - -Point prospective users to the "LAMMPS WWW Site"_lws. Mention it in -talks or link to it from your WWW site. :ulb,l - -If you find an error or omission in this manual or on the "LAMMPS WWW -Site"_lws, or have a suggestion for something to clarify or include, -send an email to the -"developers"_http://lammps.sandia.gov/authors.html. :l - -If you find a bug, "Section 12.2"_Section_errors.html#err_2 -describes how to report it. :l - -If you publish a paper using LAMMPS results, send the citation (and -any cool pictures or movies if you like) to add to the Publications, -Pictures, and Movies pages of the "LAMMPS WWW Site"_lws, with links -and attributions back to you. :l - -Create a new Makefile.machine that can be added to the src/MAKE -directory. :l - -The tools sub-directory of the LAMMPS distribution has various -stand-alone codes for pre- and post-processing of LAMMPS data. More -details are given in "Section 9"_Section_tools.html. If you write -a new tool that users will find useful, it can be added to the LAMMPS -distribution. :l - -LAMMPS is designed to be easy to extend with new code for features -like potentials, boundary conditions, diagnostic computations, etc. -"This section"_Section_modify.html gives details. If you add a -feature of general interest, it can be added to the LAMMPS -distribution. :l - -The Benchmark page of the "LAMMPS WWW Site"_lws lists LAMMPS -performance on various platforms. The files needed to run the -benchmarks are part of the LAMMPS distribution. If your machine is -sufficiently different from those listed, your timing data can be -added to the page. :l - -You can send feedback for the User Comments page of the "LAMMPS WWW -Site"_lws. It might be added to the page. No promises. :l - -Cash. Small denominations, unmarked bills preferred. Paper sack OK. -Leave on desk. VISA also accepted. Chocolate chip cookies -encouraged. :l -:ule - -:line - -1.5 Acknowledgments and citations :h3,link(intro_5) - -LAMMPS development has been funded by the "US Department of -Energy"_doe (DOE), through its CRADA, LDRD, ASCI, and Genomes-to-Life -programs and its "OASCR"_oascr and "OBER"_ober offices. - -Specifically, work on the latest version was funded in part by the US -Department of Energy's Genomics:GTL program -("www.doegenomestolife.org"_gtl) under the "project"_ourgtl, "Carbon -Sequestration in Synechococcus Sp.: From Molecular Machines to -Hierarchical Modeling". - -:link(doe,http://www.doe.gov) -:link(gtl,http://www.doegenomestolife.org) -:link(ourgtl,http://www.genomes2life.org) -:link(oascr,http://www.sc.doe.gov/ascr/home.html) -:link(ober,http://www.er.doe.gov/production/ober/ober_top.html) - -The following paper describe the basic parallel algorithms used in -LAMMPS. If you use LAMMPS results in your published work, please cite -this paper and include a pointer to the "LAMMPS WWW Site"_lws -(http://lammps.sandia.gov): - -S. Plimpton, [Fast Parallel Algorithms for Short-Range Molecular -Dynamics], J Comp Phys, 117, 1-19 (1995). - -Other papers describing specific algorithms used in LAMMPS are listed -under the "Citing LAMMPS link"_http://lammps.sandia.gov/cite.html of -the LAMMPS WWW page. - -The "Publications link"_http://lammps.sandia.gov/papers.html on the -LAMMPS WWW page lists papers that have cited LAMMPS. If your paper is -not listed there for some reason, feel free to send us the info. If -the simulations in your paper produced cool pictures or animations, -we'll be pleased to add them to the -"Pictures"_http://lammps.sandia.gov/pictures.html or -"Movies"_http://lammps.sandia.gov/movies.html pages of the LAMMPS WWW -site. - -The primary LAMMPS developers are at Sandia National Labs and Temple University: - -Steve Plimpton, sjplimp at sandia.gov -Aidan Thompson, athomps at sandia.gov -Stan Moore, stamoor at sandia.gov -Axel Kohlmeyer, akohlmey at gmail.com :ul - -Past primary developers include Paul Crozier and Mark Stevens, -both at Sandia, and Ray Shan, now at Materials Design. - -The following folks are responsible for significant contributions to -the code, or other aspects of the LAMMPS development effort. Many of -the packages they have written are somewhat unique to LAMMPS and the -code would not be as general-purpose as it is without their expertise -and efforts. - -Axel Kohlmeyer (Temple U), akohlmey at gmail.com, SVN and Git repositories, indefatigable mail list responder, USER-CGSDK, USER-OMP, USER-COLVARS, USER-MOLFILE, USER-QMMM, USER-TALLY, and COMPRESS packages -Roy Pollock (LLNL), Ewald and PPPM solvers -Mike Brown (ORNL), brownw at ornl.gov, GPU and USER-INTEL package -Greg Wagner (Sandia), gjwagne at sandia.gov, MEAM package for MEAM potential (superseded by USER-MEAMC) -Mike Parks (Sandia), mlparks at sandia.gov, PERI package for Peridynamics -Rudra Mukherjee (JPL), Rudranarayan.M.Mukherjee at jpl.nasa.gov, POEMS package for articulated rigid body motion -Reese Jones (Sandia) and collaborators, rjones at sandia.gov, USER-ATC package for atom/continuum coupling -Ilya Valuev (JIHT), valuev at physik.hu-berlin.de, USER-AWPMD package for wave-packet MD -Christian Trott (U Tech Ilmenau), christian.trott at tu-ilmenau.de, USER-CUDA (obsoleted by KOKKOS) and KOKKOS packages -Andres Jaramillo-Botero (Caltech), ajaramil at wag.caltech.edu, USER-EFF package for electron force field -Christoph Kloss (JKU), Christoph.Kloss at jku.at, LIGGGHTS fork for granular models and granular/fluid coupling -Metin Aktulga (LBL), hmaktulga at lbl.gov, USER-REAXC package for C version of ReaxFF -Georg Gunzenmuller (EMI), georg.ganzenmueller at emi.fhg.de, USER-SMD and USER-SPH packages -Colin Denniston (U Western Ontario), cdennist at uwo.ca, USER-LB package :ul - -As discussed in "Section 13"_Section_history.html, LAMMPS -originated as a cooperative project between DOE labs and industrial -partners. Folks involved in the design and testing of the original -version of LAMMPS were the following: - -John Carpenter (Mayo Clinic, formerly at Cray Research) -Terry Stouch (Lexicon Pharmaceuticals, formerly at Bristol Myers Squibb) -Steve Lustig (Dupont) -Jim Belak (LLNL) :ul diff --git a/doc/src/Section_modify.txt b/doc/src/Section_modify.txt deleted file mode 100644 index f1d55758c8..0000000000 --- a/doc/src/Section_modify.txt +++ /dev/null @@ -1,827 +0,0 @@ - "Previous Section"_Section_tools.html - "LAMMPS WWW Site"_lws - -"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next -Section"_Section_python.html :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Section_commands.html#comm) - -:line - -10. Modifying & extending LAMMPS :h2 - -This section describes how to customize LAMMPS by modifying -and extending its source code. - -10.1 "Atom styles"_#mod_1 -10.2 "Bond, angle, dihedral, improper potentials"_#mod_2 -10.3 "Compute styles"_#mod_3 -10.4 "Dump styles"_#mod_4 -10.5 "Dump custom output options"_#mod_5 -10.6 "Fix styles"_#mod_6 which include integrators, \ - temperature and pressure control, force constraints, \ - boundary conditions, diagnostic output, etc -10.7 "Input script commands"_#mod_7 -10.8 "Kspace computations"_#mod_8 -10.9 "Minimization styles"_#mod_9 -10.10 "Pairwise potentials"_#mod_10 -10.11 "Region styles"_#mod_11 -10.12 "Body styles"_#mod_12 -10.13 "Thermodynamic output options"_#mod_13 -10.14 "Variable options"_#mod_14 -10.15 "Submitting new features for inclusion in LAMMPS"_#mod_15 :all(b) - -LAMMPS is designed in a modular fashion so as to be easy to modify and -extend with new functionality. In fact, about 75% of its source code -is files added in this fashion. - -In this section, changes and additions users can make are listed along -with minimal instructions. If you add a new feature to LAMMPS and -think it will be of interest to general users, we encourage you to -submit it to the developers for inclusion in the released version of -LAMMPS. Information about how to do this is provided -"below"_#mod_14. - -The best way to add a new feature is to find a similar feature in -LAMMPS and look at the corresponding source and header files to figure -out what it does. You will need some knowledge of C++ to be able to -understand the hi-level structure of LAMMPS and its class -organization, but functions (class methods) that do actual -computations are written in vanilla C-style code and operate on simple -C-style data structures (vectors and arrays). - -Most of the new features described in this section require you to -write a new C++ derived class (except for exceptions described below, -where you can make small edits to existing files). Creating a new -class requires 2 files, a source code file (*.cpp) and a header file -(*.h). The derived class must provide certain methods to work as a -new option. Depending on how different your new feature is compared -to existing features, you can either derive from the base class -itself, or from a derived class that already exists. Enabling LAMMPS -to invoke the new class is as simple as putting the two source -files in the src dir and re-building LAMMPS. - -The advantage of C++ and its object-orientation is that all the code -and variables needed to define the new feature are in the 2 files you -write, and thus shouldn't make the rest of LAMMPS more complex or -cause side-effect bugs. - -Here is a concrete example. Suppose you write 2 files pair_foo.cpp -and pair_foo.h that define a new class PairFoo that computes pairwise -potentials described in the classic 1997 "paper"_#Foo by Foo, et al. -If you wish to invoke those potentials in a LAMMPS input script with a -command like - -pair_style foo 0.1 3.5 :pre - -then your pair_foo.h file should be structured as follows: - -#ifdef PAIR_CLASS -PairStyle(foo,PairFoo) -#else -... -(class definition for PairFoo) -... -#endif :pre - -where "foo" is the style keyword in the pair_style command, and -PairFoo is the class name defined in your pair_foo.cpp and pair_foo.h -files. - -When you re-build LAMMPS, your new pairwise potential becomes part of -the executable and can be invoked with a pair_style command like the -example above. Arguments like 0.1 and 3.5 can be defined and -processed by your new class. - -As illustrated by this pairwise example, many kinds of options are -referred to in the LAMMPS documentation as the "style" of a particular -command. - -The instructions below give the header file for the base class that -these styles are derived from. Public variables in that file are ones -used and set by the derived classes which are also used by the base -class. Sometimes they are also used by the rest of LAMMPS. Virtual -functions in the base class header file which are set = 0 are ones you -must define in your new derived class to give it the functionality -LAMMPS expects. Virtual functions that are not set to 0 are functions -you can optionally define. - -Additionally, new output options can be added directly to the -thermo.cpp, dump_custom.cpp, and variable.cpp files as explained -below. - -Here are additional guidelines for modifying LAMMPS and adding new -functionality: - -Think about whether what you want to do would be better as a pre- or -post-processing step. Many computations are more easily and more -quickly done that way. :ulb,l - -Don't do anything within the timestepping of a run that isn't -parallel. E.g. don't accumulate a bunch of data on a single processor -and analyze it. You run the risk of seriously degrading the parallel -efficiency. :l - -If your new feature reads arguments or writes output, make sure you -follow the unit conventions discussed by the "units"_units.html -command. :l - -If you add something you think is truly useful and doesn't impact -LAMMPS performance when it isn't used, send an email to the -"developers"_http://lammps.sandia.gov/authors.html. We might be -interested in adding it to the LAMMPS distribution. See further -details on this at the bottom of this page. :l -:ule - -:line -:line - -10.1 Atom styles :link(mod_1),h4 - -Classes that define an "atom style"_atom_style.html are derived from -the AtomVec class and managed by the Atom class. The atom style -determines what attributes are associated with an atom. A new atom -style can be created if one of the existing atom styles does not -define all the attributes you need to store and communicate with -atoms. - -Atom_vec_atomic.cpp is a simple example of an atom style. - -Here is a brief description of methods you define in your new derived -class. See atom_vec.h for details. - -init: one time setup (optional) -grow: re-allocate atom arrays to longer lengths (required) -grow_reset: make array pointers in Atom and AtomVec classes consistent (required) -copy: copy info for one atom to another atom's array locations (required) -pack_comm: store an atom's info in a buffer communicated every timestep (required) -pack_comm_vel: add velocity info to communication buffer (required) -pack_comm_hybrid: store extra info unique to this atom style (optional) -unpack_comm: retrieve an atom's info from the buffer (required) -unpack_comm_vel: also retrieve velocity info (required) -unpack_comm_hybrid: retrieve extra info unique to this atom style (optional) -pack_reverse: store an atom's info in a buffer communicating partial forces (required) -pack_reverse_hybrid: store extra info unique to this atom style (optional) -unpack_reverse: retrieve an atom's info from the buffer (required) -unpack_reverse_hybrid: retrieve extra info unique to this atom style (optional) -pack_border: store an atom's info in a buffer communicated on neighbor re-builds (required) -pack_border_vel: add velocity info to buffer (required) -pack_border_hybrid: store extra info unique to this atom style (optional) -unpack_border: retrieve an atom's info from the buffer (required) -unpack_border_vel: also retrieve velocity info (required) -unpack_border_hybrid: retrieve extra info unique to this atom style (optional) -pack_exchange: store all an atom's info to migrate to another processor (required) -unpack_exchange: retrieve an atom's info from the buffer (required) -size_restart: number of restart quantities associated with proc's atoms (required) -pack_restart: pack atom quantities into a buffer (required) -unpack_restart: unpack atom quantities from a buffer (required) -create_atom: create an individual atom of this style (required) -data_atom: parse an atom line from the data file (required) -data_atom_hybrid: parse additional atom info unique to this atom style (optional) -data_vel: parse one line of velocity information from data file (optional) -data_vel_hybrid: parse additional velocity data unique to this atom style (optional) -memory_usage: tally memory allocated by atom arrays (required) :tb(s=:) - -The constructor of the derived class sets values for several variables -that you must set when defining a new atom style, which are documented -in atom_vec.h. New atom arrays are defined in atom.cpp. Search for -the word "customize" and you will find locations you will need to -modify. - -NOTE: It is possible to add some attributes, such as a molecule ID, to -atom styles that do not have them via the "fix -property/atom"_fix_property_atom.html command. This command also -allows new custom attributes consisting of extra integer or -floating-point values to be added to atoms. See the "fix -property/atom"_fix_property_atom.html doc page for examples of cases -where this is useful and details on how to initialize, access, and -output the custom values. - -New "pair styles"_pair_style.html, "fixes"_fix.html, or -"computes"_compute.html can be added to LAMMPS, as discussed below. -The code for these classes can use the per-atom properties defined by -fix property/atom. The Atom class has a find_custom() method that is -useful in this context: - -int index = atom->find_custom(char *name, int &flag); :pre - -The "name" of a custom attribute, as specified in the "fix -property/atom"_fix_property_atom.html command, is checked to verify -that it exists and its index is returned. The method also sets flag = -0/1 depending on whether it is an integer or floating-point attribute. -The vector of values associated with the attribute can then be -accessed using the returned index as - -int *ivector = atom->ivector\[index\]; -double *dvector = atom->dvector\[index\]; :pre - -Ivector or dvector are vectors of length Nlocal = # of owned atoms, -which store the attributes of individual atoms. - -:line - -10.2 Bond, angle, dihedral, improper potentials :link(mod_2),h4 - -Classes that compute molecular interactions are derived from the Bond, -Angle, Dihedral, and Improper classes. New styles can be created to -add new potentials to LAMMPS. - -Bond_harmonic.cpp is the simplest example of a bond style. Ditto for -the harmonic forms of the angle, dihedral, and improper style -commands. - -Here is a brief description of common methods you define in your -new derived class. See bond.h, angle.h, dihedral.h, and improper.h -for details and specific additional methods. - -init: check if all coefficients are set, calls {init_style} (optional) -init_style: check if style specific conditions are met (optional) -compute: compute the molecular interactions (required) -settings: apply global settings for all types (optional) -coeff: set coefficients for one type (required) -equilibrium_distance: length of bond, used by SHAKE (required, bond only) -equilibrium_angle: opening of angle, used by SHAKE (required, angle only) -write & read_restart: writes/reads coeffs to restart files (required) -single: force and energy of a single bond or angle (required, bond or angle only) -memory_usage: tally memory allocated by the style (optional) :tb(s=:) - -:line - -10.3 Compute styles :link(mod_3),h4 - -Classes that compute scalar and vector quantities like temperature -and the pressure tensor, as well as classes that compute per-atom -quantities like kinetic energy and the centro-symmetry parameter -are derived from the Compute class. New styles can be created -to add new calculations to LAMMPS. - -Compute_temp.cpp is a simple example of computing a scalar -temperature. Compute_ke_atom.cpp is a simple example of computing -per-atom kinetic energy. - -Here is a brief description of methods you define in your new derived -class. See compute.h for details. - -init: perform one time setup (required) -init_list: neighbor list setup, if needed (optional) -compute_scalar: compute a scalar quantity (optional) -compute_vector: compute a vector of quantities (optional) -compute_peratom: compute one or more quantities per atom (optional) -compute_local: compute one or more quantities per processor (optional) -pack_comm: pack a buffer with items to communicate (optional) -unpack_comm: unpack the buffer (optional) -pack_reverse: pack a buffer with items to reverse communicate (optional) -unpack_reverse: unpack the buffer (optional) -remove_bias: remove velocity bias from one atom (optional) -remove_bias_all: remove velocity bias from all atoms in group (optional) -restore_bias: restore velocity bias for one atom after remove_bias (optional) -restore_bias_all: same as before, but for all atoms in group (optional) -pair_tally_callback: callback function for {tally}-style computes (optional). -memory_usage: tally memory usage (optional) :tb(s=:) - -Tally-style computes are a special case, as their computation is done -in two stages: the callback function is registered with the pair style -and then called from the Pair::ev_tally() function, which is called for -each pair after force and energy has been computed for this pair. Then -the tallied values are retrieved with the standard compute_scalar or -compute_vector or compute_peratom methods. The USER-TALLY package -provides {examples}_compute_tally.html for utilizing this mechanism. - -:line - -10.4 Dump styles :link(mod_4),h4 -10.5 Dump custom output options :link(mod_5),h4 - -Classes that dump per-atom info to files are derived from the Dump -class. To dump new quantities or in a new format, a new derived dump -class can be added, but it is typically simpler to modify the -DumpCustom class contained in the dump_custom.cpp file. - -Dump_atom.cpp is a simple example of a derived dump class. - -Here is a brief description of methods you define in your new derived -class. See dump.h for details. - -write_header: write the header section of a snapshot of atoms -count: count the number of lines a processor will output -pack: pack a proc's output data into a buffer -write_data: write a proc's data to a file :tb(s=:) - -See the "dump"_dump.html command and its {custom} style for a list of -keywords for atom information that can already be dumped by -DumpCustom. It includes options to dump per-atom info from Compute -classes, so adding a new derived Compute class is one way to calculate -new quantities to dump. - -Alternatively, you can add new keywords to the dump custom command. -Search for the word "customize" in dump_custom.cpp to see the -half-dozen or so locations where code will need to be added. - -:line - -10.6 Fix styles :link(mod_6),h4 - -In LAMMPS, a "fix" is any operation that is computed during -timestepping that alters some property of the system. Essentially -everything that happens during a simulation besides force computation, -neighbor list construction, and output, is a "fix". This includes -time integration (update of coordinates and velocities), force -constraints or boundary conditions (SHAKE or walls), and diagnostics -(compute a diffusion coefficient). New styles can be created to add -new options to LAMMPS. - -Fix_setforce.cpp is a simple example of setting forces on atoms to -prescribed values. There are dozens of fix options already in LAMMPS; -choose one as a template that is similar to what you want to -implement. - -Here is a brief description of methods you can define in your new -derived class. See fix.h for details. - -setmask: determines when the fix is called during the timestep (required) -init: initialization before a run (optional) -setup_pre_exchange: called before atom exchange in setup (optional) -setup_pre_force: called before force computation in setup (optional) -setup: called immediately before the 1st timestep and after forces are computed (optional) -min_setup_pre_force: like setup_pre_force, but for minimizations instead of MD runs (optional) -min_setup: like setup, but for minimizations instead of MD runs (optional) -initial_integrate: called at very beginning of each timestep (optional) -pre_exchange: called before atom exchange on re-neighboring steps (optional) -pre_neighbor: called before neighbor list build (optional) -pre_force: called before pair & molecular forces are computed (optional) -post_force: called after pair & molecular forces are computed and communicated (optional) -final_integrate: called at end of each timestep (optional) -end_of_step: called at very end of timestep (optional) -write_restart: dumps fix info to restart file (optional) -restart: uses info from restart file to re-initialize the fix (optional) -grow_arrays: allocate memory for atom-based arrays used by fix (optional) -copy_arrays: copy atom info when an atom migrates to a new processor (optional) -pack_exchange: store atom's data in a buffer (optional) -unpack_exchange: retrieve atom's data from a buffer (optional) -pack_restart: store atom's data for writing to restart file (optional) -unpack_restart: retrieve atom's data from a restart file buffer (optional) -size_restart: size of atom's data (optional) -maxsize_restart: max size of atom's data (optional) -setup_pre_force_respa: same as setup_pre_force, but for rRESPA (optional) -initial_integrate_respa: same as initial_integrate, but for rRESPA (optional) -post_integrate_respa: called after the first half integration step is done in rRESPA (optional) -pre_force_respa: same as pre_force, but for rRESPA (optional) -post_force_respa: same as post_force, but for rRESPA (optional) -final_integrate_respa: same as final_integrate, but for rRESPA (optional) -min_pre_force: called after pair & molecular forces are computed in minimizer (optional) -min_post_force: called after pair & molecular forces are computed and communicated in minimizer (optional) -min_store: store extra data for linesearch based minimization on a LIFO stack (optional) -min_pushstore: push the minimization LIFO stack one element down (optional) -min_popstore: pop the minimization LIFO stack one element up (optional) -min_clearstore: clear minimization LIFO stack (optional) -min_step: reset or move forward on line search minimization (optional) -min_dof: report number of degrees of freedom {added} by this fix in minimization (optional) -max_alpha: report maximum allowed step size during linesearch minimization (optional) -pack_comm: pack a buffer to communicate a per-atom quantity (optional) -unpack_comm: unpack a buffer to communicate a per-atom quantity (optional) -pack_reverse_comm: pack a buffer to reverse communicate a per-atom quantity (optional) -unpack_reverse_comm: unpack a buffer to reverse communicate a per-atom quantity (optional) -dof: report number of degrees of freedom {removed} by this fix during MD (optional) -compute_scalar: return a global scalar property that the fix computes (optional) -compute_vector: return a component of a vector property that the fix computes (optional) -compute_array: return a component of an array property that the fix computes (optional) -deform: called when the box size is changed (optional) -reset_target: called when a change of the target temperature is requested during a run (optional) -reset_dt: is called when a change of the time step is requested during a run (optional) -modify_param: called when a fix_modify request is executed (optional) -memory_usage: report memory used by fix (optional) -thermo: compute quantities for thermodynamic output (optional) :tb(s=:) - -Typically, only a small fraction of these methods are defined for a -particular fix. Setmask is mandatory, as it determines when the fix -will be invoked during the timestep. Fixes that perform time -integration ({nve}, {nvt}, {npt}) implement initial_integrate() and -final_integrate() to perform velocity Verlet updates. Fixes that -constrain forces implement post_force(). - -Fixes that perform diagnostics typically implement end_of_step(). For -an end_of_step fix, one of your fix arguments must be the variable -"nevery" which is used to determine when to call the fix and you must -set this variable in the constructor of your fix. By convention, this -is the first argument the fix defines (after the ID, group-ID, style). - -If the fix needs to store information for each atom that persists from -timestep to timestep, it can manage that memory and migrate the info -with the atoms as they move from processors to processor by -implementing the grow_arrays, copy_arrays, pack_exchange, and -unpack_exchange methods. Similarly, the pack_restart and -unpack_restart methods can be implemented to store information about -the fix in restart files. If you wish an integrator or force -constraint fix to work with rRESPA (see the "run_style"_run_style.html -command), the initial_integrate, post_force_integrate, and -final_integrate_respa methods can be implemented. The thermo method -enables a fix to contribute values to thermodynamic output, as printed -quantities and/or to be summed to the potential energy of the system. - -:line - -10.7 Input script commands :link(mod_7),h4 - -New commands can be added to LAMMPS input scripts by adding new -classes that have a "command" method. For example, the create_atoms, -read_data, velocity, and run commands are all implemented in this -fashion. When such a command is encountered in the LAMMPS input -script, LAMMPS simply creates a class with the corresponding name, -invokes the "command" method of the class, and passes it the arguments -from the input script. The command method can perform whatever -operations it wishes on LAMMPS data structures. - -The single method your new class must define is as follows: - -command: operations performed by the new command :tb(s=:) - -Of course, the new class can define other methods and variables as -needed. - -:line - -10.8 Kspace computations :link(mod_8),h4 - -Classes that compute long-range Coulombic interactions via K-space -representations (Ewald, PPPM) are derived from the KSpace class. New -styles can be created to add new K-space options to LAMMPS. - -Ewald.cpp is an example of computing K-space interactions. - -Here is a brief description of methods you define in your new derived -class. See kspace.h for details. - -init: initialize the calculation before a run -setup: computation before the 1st timestep of a run -compute: every-timestep computation -memory_usage: tally of memory usage :tb(s=:) - -:line - -10.9 Minimization styles :link(mod_9),h4 - -Classes that perform energy minimization derived from the Min class. -New styles can be created to add new minimization algorithms to -LAMMPS. - -Min_cg.cpp is an example of conjugate gradient minimization. - -Here is a brief description of methods you define in your new derived -class. See min.h for details. - -init: initialize the minimization before a run -run: perform the minimization -memory_usage: tally of memory usage :tb(s=:) - -:line - -10.10 Pairwise potentials :link(mod_10),h4 - -Classes that compute pairwise interactions are derived from the Pair -class. In LAMMPS, pairwise calculation include manybody potentials -such as EAM or Tersoff where particles interact without a static bond -topology. New styles can be created to add new pair potentials to -LAMMPS. - -Pair_lj_cut.cpp is a simple example of a Pair class, though it -includes some optional methods to enable its use with rRESPA. - -Here is a brief description of the class methods in pair.h: - -compute: workhorse routine that computes pairwise interactions -settings: reads the input script line with arguments you define -coeff: set coefficients for one i,j type pair -init_one: perform initialization for one i,j type pair -init_style: initialization specific to this pair style -write & read_restart: write/read i,j pair coeffs to restart files -write & read_restart_settings: write/read global settings to restart files -single: force and energy of a single pairwise interaction between 2 atoms -compute_inner/middle/outer: versions of compute used by rRESPA :tb(s=:) - -The inner/middle/outer routines are optional. - -:line - -10.11 Region styles :link(mod_11),h4 - -Classes that define geometric regions are derived from the Region -class. Regions are used elsewhere in LAMMPS to group atoms, delete -atoms to create a void, insert atoms in a specified region, etc. New -styles can be created to add new region shapes to LAMMPS. - -Region_sphere.cpp is an example of a spherical region. - -Here is a brief description of methods you define in your new derived -class. See region.h for details. - -inside: determine whether a point is in the region -surface_interior: determine if a point is within a cutoff distance inside of surc -surface_exterior: determine if a point is within a cutoff distance outside of surf -shape_update : change region shape if set by time-dependent variable :tb(s=:) - -:line - -10.12 Body styles :link(mod_12),h4 - -Classes that define body particles are derived from the Body class. -Body particles can represent complex entities, such as surface meshes -of discrete points, collections of sub-particles, deformable objects, -etc. - -See "Section 6.14"_Section_howto.html#howto_14 of the manual for -an overview of using body particles and the "body"_body.html doc page -for details on the various body styles LAMMPS supports. New styles -can be created to add new kinds of body particles to LAMMPS. - -Body_nparticle.cpp is an example of a body particle that is treated as -a rigid body containing N sub-particles. - -Here is a brief description of methods you define in your new derived -class. See body.h for details. - -data_body: process a line from the Bodies section of a data file -noutrow: number of sub-particles output is generated for -noutcol: number of values per-sub-particle output is generated for -output: output values for the Mth sub-particle -pack_comm_body: body attributes to communicate every timestep -unpack_comm_body: unpacking of those attributes -pack_border_body: body attributes to communicate when reneighboring is done -unpack_border_body: unpacking of those attributes :tb(s=:) - -:line - -10.13 Thermodynamic output options :link(mod_13),h4 - -There is one class that computes and prints thermodynamic information -to the screen and log file; see the file thermo.cpp. - -There are two styles defined in thermo.cpp: "one" and "multi". There -is also a flexible "custom" style which allows the user to explicitly -list keywords for quantities to print when thermodynamic info is -output. See the "thermo_style"_thermo_style.html command for a list -of defined quantities. - -The thermo styles (one, multi, etc) are simply lists of keywords. -Adding a new style thus only requires defining a new list of keywords. -Search for the word "customize" with references to "thermo style" in -thermo.cpp to see the two locations where code will need to be added. - -New keywords can also be added to thermo.cpp to compute new quantities -for output. Search for the word "customize" with references to -"keyword" in thermo.cpp to see the several locations where code will -need to be added. - -Note that the "thermo_style custom"_thermo.html command already allows -for thermo output of quantities calculated by "fixes"_fix.html, -"computes"_compute.html, and "variables"_variable.html. Thus, it may -be simpler to compute what you wish via one of those constructs, than -by adding a new keyword to the thermo command. - -:line - -10.14 Variable options :link(mod_14),h4 - -There is one class that computes and stores "variable"_variable.html -information in LAMMPS; see the file variable.cpp. The value -associated with a variable can be periodically printed to the screen -via the "print"_print.html, "fix print"_fix_print.html, or -"thermo_style custom"_thermo_style.html commands. Variables of style -"equal" can compute complex equations that involve the following types -of arguments: - -thermo keywords = ke, vol, atoms, ... -other variables = v_a, v_myvar, ... -math functions = div(x,y), mult(x,y), add(x,y), ... -group functions = mass(group), xcm(group,x), ... -atom values = x\[123\], y\[3\], vx\[34\], ... -compute values = c_mytemp\[0\], c_thermo_press\[3\], ... :pre - -Adding keywords for the "thermo_style custom"_thermo_style.html command -(which can then be accessed by variables) was discussed -"here"_Section_modify.html#mod_13 on this page. - -Adding a new math function of one or two arguments can be done by -editing one section of the Variable::evaluate() method. Search for -the word "customize" to find the appropriate location. - -Adding a new group function can be done by editing one section of the -Variable::evaluate() method. Search for the word "customize" to find -the appropriate location. You may need to add a new method to the -Group class as well (see the group.cpp file). - -Accessing a new atom-based vector can be done by editing one section -of the Variable::evaluate() method. Search for the word "customize" -to find the appropriate location. - -Adding new "compute styles"_compute.html (whose calculated values can -then be accessed by variables) was discussed -"here"_Section_modify.html#mod_3 on this page. - -:line -:line - -10.15 Submitting new features for inclusion in LAMMPS :link(mod_15),h4 - -We encourage users to submit new features or modifications for -LAMMPS to "the core developers"_http://lammps.sandia.gov/authors.html -so they can be added to the LAMMPS distribution. The preferred way to -manage and coordinate this is as of Fall 2016 via the LAMMPS project on -"GitHub"_https://github.com/lammps/lammps. An alternative is to contact -the LAMMPS developers or the indicated developer of a package or feature -directly and send in your contribution via e-mail. - -For any larger modifications or programming project, you are encouraged -to contact the LAMMPS developers ahead of time, in order to discuss -implementation strategies and coding guidelines, that will make it -easier to integrate your contribution and result in less work for -everybody involved. You are also encouraged to search through the list -of "open issues on GitHub"_https://github.com/lammps/lammps/issues and -submit a new issue for a planned feature, so you would not duplicate -the work of others (and possibly get scooped by them) or have your work -duplicated by others. - -How quickly your contribution will be integrated -depends largely on how much effort it will cause to integrate and test -it, how much it requires changes to the core codebase, and of how much -interest it is to the larger LAMMPS community. Please see below for a -checklist of typical requirements. Once you have prepared everything, -see "this tutorial"_tutorial_github.html for instructions on how to -submit your changes or new files through a GitHub pull request. If you -prefer to submit patches or full files, you should first make certain, -that your code works correctly with the latest patch-level version of -LAMMPS and contains all bugfixes from it. Then create a gzipped tar -file of all changed or added files or a corresponding patch file using -'diff -u' or 'diff -c' and compress it with gzip. Please only use -gzip compression, as this works well on all platforms. - -If the new features/files are broadly useful we may add them as core -files to LAMMPS or as part of a "standard -package"_Section_start.html#start_3. Else we will add them as a -user-contributed file or package. Examples of user packages are in -src sub-directories that start with USER. The USER-MISC package is -simply a collection of (mostly) unrelated single files, which is the -simplest way to have your contribution quickly added to the LAMMPS -distribution. You can see a list of the both standard and user -packages by typing "make package" in the LAMMPS src directory. - -Note that by providing us files to release, you are agreeing to make -them open-source, i.e. we can release them under the terms of the GPL, -used as a license for the rest of LAMMPS. See "Section -1.4"_Section_intro.html#intro_4 for details. - -With user packages and files, all we are really providing (aside from -the fame and fortune that accompanies having your name in the source -code and on the "Authors page"_http://lammps.sandia.gov/authors.html -of the "LAMMPS WWW site"_lws), is a means for you to distribute your -work to the LAMMPS user community, and a mechanism for others to -easily try out your new feature. This may help you find bugs or make -contact with new collaborators. Note that you're also implicitly -agreeing to support your code which means answer questions, fix bugs, -and maintain it if LAMMPS changes in some way that breaks it (an -unusual event). - -NOTE: If you prefer to actively develop and support your add-on -feature yourself, then you may wish to make it available for download -from your own website, as a user package that LAMMPS users can add to -their copy of LAMMPS. See the "Offsite LAMMPS packages and -tools"_http://lammps.sandia.gov/offsite.html page of the LAMMPS web -site for examples of groups that do this. We are happy to advertise -your package and web site from that page. Simply email the -"developers"_http://lammps.sandia.gov/authors.html with info about -your package and we will post it there. - -The previous sections of this doc page describe how to add new "style" -files of various kinds to LAMMPS. Packages are simply collections of -one or more new class files which are invoked as a new style within a -LAMMPS input script. If designed correctly, these additions typically -do not require changes to the main core of LAMMPS; they are simply -add-on files. If you think your new feature requires non-trivial -changes in core LAMMPS files, you'll need to "communicate with the -developers"_http://lammps.sandia.gov/authors.html, since we may or may -not want to make those changes. An example of a trivial change is -making a parent-class method "virtual" when you derive a new child -class from it. - -Here is a checklist of steps you need to follow to submit a single file -or user package for our consideration. Following these steps will save -both you and us time. See existing files in packages in the src dir for -examples. If you are uncertain, please ask. - -All source files you provide must compile with the most current -version of LAMMPS with multiple configurations. In particular you -need to test compiling LAMMPS from scratch with -DLAMMPS_BIGBIG -set in addition to the default -DLAMMPS_SMALLBIG setting. Your code -will need to work correctly in serial and in parallel using MPI. :ulb,l - -For consistency with the rest of LAMMPS and especially, if you want -your contribution(s) to be added to main LAMMPS code or one of its -standard packages, it needs to be written in a style compatible with -other LAMMPS source files. This means: 2-character indentation per -level, [no tabs], no lines over 80 characters. I/O is done via -the C-style stdio library, class header files should not import any -system headers outside , STL containers should be avoided -in headers, and forward declarations used where possible or needed. -All added code should be placed into the LAMMPS_NS namespace or a -sub-namespace; global or static variables should be avoided, as they -conflict with the modular nature of LAMMPS and the C++ class structure. -Header files must [not] import namespaces with {using}. -This all is so the developers can more easily understand, integrate, -and maintain your contribution and reduce conflicts with other parts -of LAMMPS. This basically means that the code accesses data -structures, performs its operations, and is formatted similar to other -LAMMPS source files, including the use of the error class for error -and warning messages. :l - -If you want your contribution to be added as a user-contributed -feature, and it's a single file (actually a *.cpp and *.h file) it can -rapidly be added to the USER-MISC directory. Send us the one-line -entry to add to the USER-MISC/README file in that dir, along with the -2 source files. You can do this multiple times if you wish to -contribute several individual features. :l - -If you want your contribution to be added as a user-contribution and -it is several related features, it is probably best to make it a user -package directory with a name like USER-FOO. In addition to your new -files, the directory should contain a README text file. The README -should contain your name and contact information and a brief -description of what your new package does. If your files depend on -other LAMMPS style files also being installed (e.g. because your file -is a derived class from the other LAMMPS class), then an Install.sh -file is also needed to check for those dependencies. See other README -and Install.sh files in other USER directories as examples. Send us a -tarball of this USER-FOO directory. :l - -Your new source files need to have the LAMMPS copyright, GPL notice, -and your name and email address at the top, like other -user-contributed LAMMPS source files. They need to create a class -that is inside the LAMMPS namespace. If the file is for one of the -USER packages, including USER-MISC, then we are not as picky about the -coding style (see above). I.e. the files do not need to be in the -same stylistic format and syntax as other LAMMPS files, though that -would be nice for developers as well as users who try to read your -code. :l - -You [must] also create a [documentation] file for each new command or -style you are adding to LAMMPS. For simplicity and convenience, the -documentation of groups of closely related commands or styles may be -combined into a single file. This will be one file for a single-file -feature. For a package, it might be several files. These are simple -text files with a specific markup language, that are then auto-converted -to HTML and PDF. The tools for this conversion are included in the -source distribution, and the translation can be as simple as doing -"make html pdf" in the doc folder. -Thus the documentation source files must be in the same format and -style as other *.txt files in the lammps/doc/src directory for similar -commands and styles; use one or more of them as a starting point. -A description of the markup can also be found in -lammps/doc/utils/txt2html/README.html -As appropriate, the text files can include links to equations -(see doc/Eqs/*.tex for examples, we auto-create the associated JPG -files), or figures (see doc/JPG for examples), or even additional PDF -files with further details (see doc/PDF for examples). The doc page -should also include literature citations as appropriate; see the -bottom of doc/fix_nh.txt for examples and the earlier part of the same -file for how to format the cite itself. The "Restrictions" section of -the doc page should indicate that your command is only available if -LAMMPS is built with the appropriate USER-MISC or USER-FOO package. -See other user package doc files for examples of how to do this. The -prerequisite for building the HTML format files are Python 3.x and -virtualenv, the requirement for generating the PDF format manual -is the "htmldoc"_http://www.htmldoc.org/ software. Please run at least -"make html" and carefully inspect and proofread the resulting HTML format -doc page before submitting your code. :l - -For a new package (or even a single command) you should include one or -more example scripts demonstrating its use. These should run in no -more than a couple minutes, even on a single processor, and not require -large data files as input. See directories under examples/USER for -examples of input scripts other users provided for their packages. -These example inputs are also required for validating memory accesses -and testing for memory leaks with valgrind :l - -If there is a paper of yours describing your feature (either the -algorithm/science behind the feature itself, or its initial usage, or -its implementation in LAMMPS), you can add the citation to the *.cpp -source file. See src/USER-EFF/atom_vec_electron.cpp for an example. -A LaTeX citation is stored in a variable at the top of the file and a -single line of code that references the variable is added to the -constructor of the class. Whenever a user invokes your feature from -their input script, this will cause LAMMPS to output the citation to a -log.cite file and prompt the user to examine the file. Note that you -should only use this for a paper you or your group authored. -E.g. adding a cite in the code for a paper by Nose and Hoover if you -write a fix that implements their integrator is not the intended -usage. That kind of citation should just be in the doc page you -provide. :l -:ule - -Finally, as a general rule-of-thumb, the more clear and -self-explanatory you make your documentation and README files, and the -easier you make it for people to get started, e.g. by providing example -scripts, the more likely it is that users will try out your new feature. - -:line -:line - -:link(Foo) -[(Foo)] Foo, Morefoo, and Maxfoo, J of Classic Potentials, 75, 345 (1997). diff --git a/doc/src/Section_packages.txt b/doc/src/Section_packages.txt deleted file mode 100644 index e9387fe35f..0000000000 --- a/doc/src/Section_packages.txt +++ /dev/null @@ -1,2922 +0,0 @@ -"Previous Section"_Section_commands.html - "LAMMPS WWW Site"_lws - -"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next -Section"_Section_accelerate.html :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Section_commands.html#comm) - -:line - -4. Packages :h2 - -This section gives an overview of the optional packages that extend -LAMMPS functionality with instructions on how to build LAMMPS with -each of them. Packages are groups of files that enable a specific set -of features. For example, force fields for molecular systems or -granular systems are in packages. You can see the list of all -packages and "make" commands to manage them by typing "make package" -from within the src directory of the LAMMPS distribution. "Section -2.3"_Section_start.html#start_3 gives general info on how to install -and un-install packages as part of the LAMMPS build process. - -There are two kinds of packages in LAMMPS, standard and user packages: - -"Table of standard packages"_#table_standard -"Table of user packages"_#table_user :ul - -Either of these kinds of packages may work as is, may require some -additional code compiled located in the lib folder, or may require -an external library to be downloaded, compiled, installed, and LAMMPS -configured to know about its location and additional compiler flags. -You can often do the build of the internal or external libraries -in one step by typing "make lib-name args='...'" from the src dir, -with appropriate arguments included in args='...'. If you just type -"make lib-name" you should see a help message about supported flags -and some examples. For more details about this, please study the -tables below and the sections about the individual packages. - -Standard packages are supported by the LAMMPS developers and are -written in a syntax and style consistent with the rest of LAMMPS. -This means the developers will answer questions about them, debug and -fix them if necessary, and keep them compatible with future changes to -LAMMPS. - -User packages have been contributed by users, and begin with the -"user" prefix. If they are a single command (single file), they are -typically in the user-misc package. User packages don't necessarily -meet the requirements of the standard packages. This means the -developers will try to keep things working and usually can answer -technical questions about compiling the package. If you have problems -using a feature provided in a user package, you may need to contact -the contributor directly to get help. Information on how to submit -additions you make to LAMMPS as single files or as a standard or user -package are given in "this section"_Section_modify.html#mod_15 of the -manual. - -Following the next two tables is a sub-section for each package. It -lists authors (if applicable) and summarizes the package contents. It -has specific instructions on how to install the package, including (if -necessary) downloading or building any extra library it requires. It -also gives links to documentation, example scripts, and -pictures/movies (if available) that illustrate use of the package. - -NOTE: To see the complete list of commands a package adds to LAMMPS, -just look at the files in its src directory, e.g. "ls src/GRANULAR". -Files with names that start with fix, compute, atom, pair, bond, -angle, etc correspond to commands with the same style names. - -In these two tables, the "Example" column is a sub-directory in the -examples directory of the distribution which has an input script that -uses the package. E.g. "peptide" refers to the examples/peptide -directory; USER/atc refers to the examples/USER/atc directory. The -"Library" column indicates whether an extra library is needed to build -and use the package: - -dash = no library -sys = system library: you likely have it on your machine -int = internal library: provided with LAMMPS, but you may need to build it -ext = external library: you will need to download and install it on your machine :ul - -:line -:line - -[Standard packages] :link(table_standard),p - -Package, Description, Doc page, Example, Library -"ASPHERE"_#ASPHERE, aspherical particle models, "Section 6.6.14"_Section_howto.html#howto_14, ellipse, - -"BODY"_#BODY, body-style particles, "body"_body.html, body, - -"CLASS2"_#CLASS2, class 2 force fields, "pair_style lj/class2"_pair_class2.html, -, - -"COLLOID"_#COLLOID, colloidal particles, "atom_style colloid"_atom_style.html, colloid, - -"COMPRESS"_#COMPRESS, I/O compression, "dump */gz"_dump.html, -, sys -"CORESHELL"_#CORESHELL, adiabatic core/shell model, "Section 6.6.25"_Section_howto.html#howto_25, coreshell, - -"DIPOLE"_#DIPOLE, point dipole particles, "pair_style dipole/cut"_pair_dipole.html, dipole, - -"GPU"_#GPU, GPU-enabled styles, "Section 5.3.1"_accelerate_gpu.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, int -"GRANULAR"_#GRANULAR, granular systems, "Section 6.6.6"_Section_howto.html#howto_6, pour, - -"KIM"_#KIM, OpenKIM wrapper, "pair_style kim"_pair_kim.html, kim, ext -"KOKKOS"_#KOKKOS, Kokkos-enabled styles, "Section 5.3.3"_accelerate_kokkos.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, - -"KSPACE"_#KSPACE, long-range Coulombic solvers, "kspace_style"_kspace_style.html, peptide, - -"LATTE"_#LATTE, quantum DFTB forces via LATTE, "fix latte"_fix_latte.html, latte, ext -"MANYBODY"_#MANYBODY, many-body potentials, "pair_style tersoff"_pair_tersoff.html, shear, - -"MC"_#MC, Monte Carlo options, "fix gcmc"_fix_gcmc.html, -, - -"MEAM"_#MEAM, modified EAM potential, "pair_style meam"_pair_meam.html, meam, int -"MISC"_#MISC, miscellanous single-file commands, -, -, - -"MOLECULE"_#MOLECULE, molecular system force fields, "Section 6.6.3"_Section_howto.html#howto_3, peptide, - -"MPIIO"_#MPIIO, MPI parallel I/O dump and restart, "dump"_dump.html, -, - -"MSCG"_#MSCG, multi-scale coarse-graining wrapper, "fix mscg"_fix_mscg.html, mscg, ext -"OPT"_#OPT, optimized pair styles, "Section 5.3.5"_accelerate_opt.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, - -"PERI"_#PERI, Peridynamics models, "pair_style peri"_pair_peri.html, peri, - -"POEMS"_#POEMS, coupled rigid body motion, "fix poems"_fix_poems.html, rigid, int -"PYTHON"_#PYTHON, embed Python code in an input script, "python"_python.html, python, sys -"QEQ"_#QEQ, QEq charge equilibration, "fix qeq"_fix_qeq.html, qeq, - -"REAX"_#REAX, ReaxFF potential (Fortran), "pair_style reax"_pair_reax.html, reax, int -"REPLICA"_#REPLICA, multi-replica methods, "Section 6.6.5"_Section_howto.html#howto_5, tad, - -"RIGID"_#RIGID, rigid bodies and constraints, "fix rigid"_fix_rigid.html, rigid, - -"SHOCK"_#SHOCK, shock loading methods, "fix msst"_fix_msst.html, -, - -"SNAP"_#SNAP, quantum-fitted potential, "pair_style snap"_pair_snap.html, snap, - -"SRD"_#SRD, stochastic rotation dynamics, "fix srd"_fix_srd.html, srd, - -"VORONOI"_#VORONOI, Voronoi tesselation, "compute voronoi/atom"_compute_voronoi_atom.html, -, ext :tb(ea=c,ca1=l) - -[USER packages] :link(table_user),p - -Package, Description, Doc page, Example, Library -"USER-ATC"_#USER-ATC, atom-to-continuum coupling, "fix atc"_fix_atc.html, USER/atc, int -"USER-AWPMD"_#USER-AWPMD, wave-packet MD, "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, int -"USER-BOCS"_#USER-BOCS, BOCS bottom up coarse graining, "fix bocs"_fix_bocs.html, USER/bocs, - -"USER-CGDNA"_#USER-CGDNA, coarse-grained DNA force fields, src/USER-CGDNA/README, USER/cgdna, - -"USER-CGSDK"_#USER-CGSDK, SDK coarse-graining model, "pair_style lj/sdk"_pair_sdk.html, USER/cgsdk, - -"USER-COLVARS"_#USER-COLVARS, collective variables library, "fix colvars"_fix_colvars.html, USER/colvars, int -"USER-DIFFRACTION"_#USER-DIFFRACTION, virtual x-ray and electron diffraction,"compute xrd"_compute_xrd.html, USER/diffraction, - -"USER-DPD"_#USER-DPD, reactive dissipative particle dynamics, src/USER-DPD/README, USER/dpd, - -"USER-DRUDE"_#USER-DRUDE, Drude oscillators, "tutorial"_tutorial_drude.html, USER/drude, - -"USER-EFF"_#USER-EFF, electron force field,"pair_style eff/cut"_pair_eff.html, USER/eff, - -"USER-FEP"_#USER-FEP, free energy perturbation,"compute fep"_compute_fep.html, USER/fep, - -"USER-H5MD"_#USER-H5MD, dump output via HDF5,"dump h5md"_dump_h5md.html, -, ext -"USER-INTEL"_#USER-INTEL, optimized Intel CPU and KNL styles,"Section 5.3.2"_accelerate_intel.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, - -"USER-LB"_#USER-LB, Lattice Boltzmann fluid,"fix lb/fluid"_fix_lb_fluid.html, USER/lb, - -"USER-MANIFOLD"_#USER-MANIFOLD, motion on 2d surfaces,"fix manifoldforce"_fix_manifoldforce.html, USER/manifold, - -"USER-MEAMC"_#USER-MEAMC, modified EAM potential (C++), "pair_style meam/c"_pair_meam.html, meam, - -"USER-MESO"_#USER-MESO, mesoscale DPD models, "pair_style edpd"_pair_meso.html, USER/meso, - -"USER-MGPT"_#USER-MGPT, fast MGPT multi-ion potentials, "pair_style mgpt"_pair_mgpt.html, USER/mgpt, - -"USER-MISC"_#USER-MISC, single-file contributions, USER-MISC/README, USER/misc, - -"USER-MOFFF"_#USER-MOFFF, styles for "MOF-FF"_MOFplus force field, "pair_style buck6d/coul/gauss"_pair_buck6d_coul_gauss.html, USER/mofff, - -"USER-MOLFILE"_#USER-MOLFILE, "VMD"_vmd_home molfile plug-ins,"dump molfile"_dump_molfile.html, -, ext -"USER-NETCDF"_#USER-NETCDF, dump output via NetCDF,"dump netcdf"_dump_netcdf.html, -, ext -"USER-OMP"_#USER-OMP, OpenMP-enabled styles,"Section 5.3.4"_accelerate_omp.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, - -"USER-PHONON"_#USER-PHONON, phonon dynamical matrix,"fix phonon"_fix_phonon.html, USER/phonon, - -"USER-QMMM"_#USER-QMMM, QM/MM coupling,"fix qmmm"_fix_qmmm.html, USER/qmmm, ext -"USER-QTB"_#USER-QTB, quantum nuclear effects,"fix qtb"_fix_qtb.html "fix qbmsst"_fix_qbmsst.html, qtb, - -"USER-QUIP"_#USER-QUIP, QUIP/libatoms interface,"pair_style quip"_pair_quip.html, USER/quip, ext -"USER-REAXC"_#USER-REAXC, ReaxFF potential (C/C++) ,"pair_style reaxc"_pair_reaxc.html, reax, - -"USER-SMD"_#USER-SMD, smoothed Mach dynamics,"SMD User Guide"_PDF/SMD_LAMMPS_userguide.pdf, USER/smd, ext -"USER-SMTBQ"_#USER-SMTBQ, second moment tight binding QEq potential,"pair_style smtbq"_pair_smtbq.html, USER/smtbq, - -"USER-SPH"_#USER-SPH, smoothed particle hydrodynamics,"SPH User Guide"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, - -"USER-TALLY"_#USER-TALLY, pairwise tally computes,"compute XXX/tally"_compute_tally.html, USER/tally, - -"USER-UEF"_#USER-UEF, extensional flow,"fix nvt/uef"_fix_nh_uef.html, USER/uef, - -"USER-VTK"_#USER-VTK, dump output via VTK, "compute vtk"_dump_vtk.html, -, ext :tb(ea=c,ca1=l) - -:line -:line - -ASPHERE package :link(ASPHERE),h4 - -[Contents:] - -Computes, time-integration fixes, and pair styles for aspherical -particle models including ellipsoids, 2d lines, and 3d triangles. - -[Install or un-install:] - -make yes-asphere -make machine :pre - -make no-asphere -make machine :pre - -[Supporting info:] - -src/ASPHERE: filenames -> commands -"Section 6.14"_Section_howto.html#howto_14 -"pair_style gayberne"_pair_gayberne.html -"pair_style resquared"_pair_resquared.html -"doc/PDF/pair_gayberne_extra.pdf"_PDF/pair_gayberne_extra.pdf -"doc/PDF/pair_resquared_extra.pdf"_PDF/pair_resquared_extra.pdf -examples/ASPHERE -examples/ellipse -http://lammps.sandia.gov/movies.html#line -http://lammps.sandia.gov/movies.html#tri :ul - -:line - -BODY package :link(BODY),h4 - -[Contents:] - -Body-style particles with internal structure. Computes, -time-integration fixes, pair styles, as well as the body styles -themselves. See the "body"_body.html doc page for an overview. - -[Install or un-install:] - -make yes-body -make machine :pre - -make no-body -make machine :pre - -[Supporting info:] - -src/BODY filenames -> commands -"body"_body.html -"atom_style body"_atom_style.html -"fix nve/body"_fix_nve_body.html -"pair_style body"_pair_body.html -examples/body :ul - -:line - -CLASS2 package :link(CLASS2),h4 - -[Contents:] - -Bond, angle, dihedral, improper, and pair styles for the COMPASS -CLASS2 molecular force field. - -[Install or un-install:] - -make yes-class2 -make machine :pre - -make no-class2 -make machine :pre - -[Supporting info:] - -src/CLASS2: filenames -> commands -"bond_style class2"_bond_class2.html -"angle_style class2"_angle_class2.html -"dihedral_style class2"_dihedral_class2.html -"improper_style class2"_improper_class2.html -"pair_style lj/class2"_pair_class2.html :ul - -:line - -COLLOID package :link(COLLOID),h4 - -[Contents:] - -Coarse-grained finite-size colloidal particles. Pair styles and fix -wall styles for colloidal interactions. Includes the Fast Lubrication -Dynamics (FLD) method for hydrodynamic interactions, which is a -simplified approximation to Stokesian dynamics. - -[Authors:] This package includes Fast Lubrication Dynamics pair styles -which were created by Amit Kumar and Michael Bybee from Jonathan -Higdon's group at UIUC. - -[Install or un-install:] - -make yes-colloid -make machine :pre - -make no-colloid -make machine :pre - -[Supporting info:] - -src/COLLOID: filenames -> commands -"fix wall/colloid"_fix_wall.html -"pair_style colloid"_pair_colloid.html -"pair_style yukawa/colloid"_pair_yukawa_colloid.html -"pair_style brownian"_pair_brownian.html -"pair_style lubricate"_pair_lubricate.html -"pair_style lubricateU"_pair_lubricateU.html -examples/colloid -examples/srd :ul - -:line - -COMPRESS package :link(COMPRESS),h4 - -[Contents:] - -Compressed output of dump files via the zlib compression library, -using dump styles with a "gz" in their style name. - -To use this package you must have the zlib compression library -available on your system. - -[Author:] Axel Kohlmeyer (Temple U). - -[Install or un-install:] - -Note that building with this package assumes you have the zlib -compression library available on your system. The LAMMPS build uses -the settings in the lib/compress/Makefile.lammps file in the -compile/link process. You should only need to edit this file if the -LAMMPS build fails on your system. - -make yes-compress -make machine :pre - -make no-compress -make machine :pre - -[Supporting info:] - -src/COMPRESS: filenames -> commands -src/COMPRESS/README -lib/compress/README -"dump atom/gz"_dump.html -"dump cfg/gz"_dump.html -"dump custom/gz"_dump.html -"dump xyz/gz"_dump.html :ul - -:line - -CORESHELL package :link(CORESHELL),h4 - -[Contents:] - -Compute and pair styles that implement the adiabatic core/shell model -for polarizability. The pair styles augment Born, Buckingham, and -Lennard-Jones styles with core/shell capabilities. The "compute -temp/cs"_compute_temp_cs.html command calculates the temperature of a -system with core/shell particles. See "Section -6.26"_Section_howto.html#howto_26 for an overview of how to use this -package. - -[Author:] Hendrik Heenen (Technical U of Munich). - -[Install or un-install:] - -make yes-coreshell -make machine :pre - -make no-coreshell -make machine :pre - -[Supporting info:] - -src/CORESHELL: filenames -> commands -"Section 6.26"_Section_howto.html#howto_26 -"Section 6.25"_Section_howto.html#howto_25 -"compute temp/cs"_compute_temp_cs.html -"pair_style born/coul/long/cs"_pair_cs.html -"pair_style buck/coul/long/cs"_pair_cs.html -"pair_style lj/cut/coul/long/cs"_pair_lj.html -examples/coreshell :ul - -:line - -DIPOLE package :link(DIPOLE),h4 - -[Contents:] - -An atom style and several pair styles for point dipole models with -short-range or long-range interactions. - -[Install or un-install:] - -make yes-dipole -make machine :pre - -make no-dipole -make machine :pre - -[Supporting info:] - -src/DIPOLE: filenames -> commands -"atom_style dipole"_atom_style.html -"pair_style lj/cut/dipole/cut"_pair_dipole.html -"pair_style lj/cut/dipole/long"_pair_dipole.html -"pair_style lj/long/dipole/long"_pair_dipole.html -examples/dipole :ul - -:line - -GPU package :link(GPU),h4 - -[Contents:] - -Dozens of pair styles and a version of the PPPM long-range Coulombic -solver optimized for GPUs. All such styles have a "gpu" as a -suffix in their style name. The GPU code can be compiled with either -CUDA or OpenCL, however the OpenCL variants are no longer actively -maintained and only the CUDA versions are regularly tested. -"Section 5.3.1"_accelerate_gpu.html gives details of what -hardware and GPU software is required on your system, -and details on how to build and use this package. Its styles can be -invoked at run time via the "-sf gpu" or "-suffix gpu" "command-line -switches"_Section_start.html#start_6. See also the "KOKKOS"_#KOKKOS -package, which has GPU-enabled styles. - -[Authors:] Mike Brown (Intel) while at Sandia and ORNL and Trung Nguyen -(Northwestern U) while at ORNL. - -[Install or un-install:] - -Before building LAMMPS with this package, you must first build the GPU -library in lib/gpu from a set of provided C and CUDA files. You can -do this manually if you prefer; follow the instructions in -lib/gpu/README. Please note, that the GPU library uses MPI calls, so -you have to make certain to use the same MPI library (or the STUBS -library) settings as the main LAMMPS code. That same applies to the --DLAMMPS_BIGBIG, -DLAMMPS_SMALLBIG, or -DLAMMPS_SMALLSMALL define. - -You can also do it in one step from the lammps/src -dir, using a command like these, which simply invoke the -lib/gpu/Install.py script with the specified args: - -make lib-gpu # print help message -make lib-gpu args="-b" # build GPU library with default Makefile.linux -make lib-gpu args="-m xk7 -p single -o xk7.single" # create new Makefile.xk7.single, altered for single-precision -make lib-gpu args="-m mpi -p mixed -b" # build GPU library with mixed precision using settings in Makefile.mpi :pre - -Note that this procedure through the '-m machine' flag starts with one of -the existing Makefile.machine files in lib/gpu. For your convenience, -machine makefiles for "mpi" and "serial" are provided, which have the -same settings as the corresponding machine makefiles in the main LAMMPS -source folder. In addition you can alter 4 important settings in that -Makefile, via the -h, -a, -p, -e switches, and also save a copy of the -new Makefile, if desired: - -CUDA_HOME = where NVIDIA CUDA software is installed on your system -CUDA_ARCH = what GPU hardware you have (see help message for details) -CUDA_PRECISION = precision (double, mixed, single) -EXTRAMAKE = which Makefile.lammps.* file to copy to Makefile.lammps :ul - -If the library build is successful, at least 3 files should be created: -lib/gpu/libgpu.a, lib/gpu/nvc_get_devices, and lib/gpu/Makefile.lammps. -The latter has settings that enable LAMMPS to link with CUDA libraries. -If the settings in Makefile.lammps for your machine are not correct, -the LAMMPS build will fail, and lib/gpu/Makefile.lammps may need to -be edited. - -You can then install/un-install the package and build LAMMPS in the -usual manner: - -make yes-gpu -make machine :pre - -make no-gpu -make machine :pre - -NOTE: If you re-build the GPU library in lib/gpu, you should always -un-install the GPU package, then re-install it and re-build LAMMPS. -This is because the compilation of files in the GPU package use the -library settings from the lib/gpu/Makefile.machine used to build the -GPU library. - -[Supporting info:] - -src/GPU: filenames -> commands -src/GPU/README -lib/gpu/README -"Section 5.3"_Section_accelerate.html#acc_3 -"Section 5.3.1"_accelerate_gpu.html -"Section 2.6 -sf gpu"_Section_start.html#start_6 -"Section 2.6 -pk gpu"_Section_start.html#start_6 -"package gpu"_package.html -Pair Styles section of "Section 3.5"_Section_commands.html#cmd_5 for pair styles followed by (g) -"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul - -:line - -GRANULAR package :link(GRANULAR),h4 - -[Contents:] - -Pair styles and fixes for finite-size granular particles, which -interact with each other and boundaries via frictional and dissipative -potentials. - -[Install or un-install:] - -make yes-granular -make machine :pre - -make no-granular -make machine :pre - -[Supporting info:] - -src/GRANULAR: filenames -> commands -"Section 6.6"_Section_howto.html#howto_6, -"fix pour"_fix_pour.html -"fix wall/gran"_fix_wall_gran.html -"pair_style gran/hooke"_pair_gran.html -"pair_style gran/hertz/history"_pair_gran.html -examples/granregion -examples/pour -bench/in.chute -http://lammps.sandia.gov/pictures.html#jamming -http://lammps.sandia.gov/movies.html#hopper -http://lammps.sandia.gov/movies.html#dem -http://lammps.sandia.gov/movies.html#brazil -http://lammps.sandia.gov/movies.html#granregion :ul - -:line - -KIM package :link(KIM),h4 - -[Contents:] - -A "pair_style kim"_pair_kim.html command which is a wrapper on the -Knowledge Base for Interatomic Models (KIM) repository of interatomic -potentials, enabling any of them to be used in LAMMPS simulations. - -To use this package you must have the KIM library available on your -system. - -Information about the KIM project can be found at its website: -https://openkim.org. The KIM project is led by Ellad Tadmor and Ryan -Elliott (U Minnesota) and James Sethna (Cornell U). - -[Authors:] Ryan Elliott (U Minnesota) is the main developer for the KIM -API which the "pair_style kim"_pair_kim.html command uses. He -developed the pair style in collaboration with Valeriu Smirichinski (U -Minnesota). - -[Install or un-install:] - -Before building LAMMPS with this package, you must first download and -build the KIM library and include the KIM models that you want to -use. You can do this manually if you prefer; follow the instructions -in lib/kim/README. You can also do it in one step from the lammps/src -dir, using a command like these, which simply invoke the -lib/kim/Install.py script with the specified args. - -make lib-kim # print help message -make lib-kim args="-b " # (re-)install KIM API lib with only example models -make lib-kim args="-b -a Glue_Ercolessi_Adams_Al__MO_324507536345_001" # ditto plus one model -make lib-kim args="-b -a everything" # install KIM API lib with all models -make lib-kim args="-n -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # add one model or model driver -make lib-kim args="-p /usr/local/kim-api" # use an existing KIM API installation at the provided location -make lib-kim args="-p /usr/local/kim-api -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # ditto but add one model or driver :pre - -Note that in LAMMPS lingo, a KIM model driver is a pair style -(e.g. EAM or Tersoff). A KIM model is a pair style for a particular -element or alloy and set of parameters, e.g. EAM for Cu with a -specific EAM potential file. Also note that installing the KIM API -library with all its models, may take around 30 min to build. Of -course you only need to do that once. - -See the list of KIM model drivers here: -https://openkim.org/kim-items/model-drivers/alphabetical - -See the list of all KIM models here: -https://openkim.org/kim-items/models/by-model-drivers - -See the list of example KIM models included by default here: -https://openkim.org/kim-api in the "What is in the KIM API source -package?" section - -You can then install/un-install the package and build LAMMPS in the -usual manner: - -make yes-kim -make machine :pre - -make no-kim -make machine :pre - -[Supporting info:] - -src/KIM: filenames -> commands -src/KIM/README -lib/kim/README -"pair_style kim"_pair_kim.html -examples/kim :ul - -:line - -KOKKOS package :link(KOKKOS),h4 - -[Contents:] - -Dozens of atom, pair, bond, angle, dihedral, improper, fix, compute -styles adapted to compile using the Kokkos library which can convert -them to OpenMP or CUDA code so that they run efficiently on multicore -CPUs, KNLs, or GPUs. All the styles have a "kk" as a suffix in their -style name. "Section 5.3.3"_accelerate_kokkos.html gives details of -what hardware and software is required on your system, and how to -build and use this package. Its styles can be invoked at run time via -the "-sf kk" or "-suffix kk" "command-line -switches"_Section_start.html#start_6. Also see the "GPU"_#GPU, -"OPT"_#OPT, "USER-INTEL"_#USER-INTEL, and "USER-OMP"_#USER-OMP -packages, which have styles optimized for CPUs, KNLs, and GPUs. - -You must have a C++11 compatible compiler to use this package. - -[Authors:] The KOKKOS package was created primarily by Christian Trott -and Stan Moore (Sandia), with contributions from other folks as well. -It uses the open-source "Kokkos library"_https://github.com/kokkos -which was developed by Carter Edwards, Christian Trott, and others at -Sandia, and which is included in the LAMMPS distribution in -lib/kokkos. - -[Install or un-install:] - -For the KOKKOS package, you have 3 choices when building. You can -build with either CPU or KNL or GPU support. Each choice requires -additional settings in your Makefile.machine for the KOKKOS_DEVICES -and KOKKOS_ARCH settings. See the src/MAKE/OPTIONS/Makefile.kokkos* -files for examples. - -For multicore CPUs using OpenMP: - -KOKKOS_DEVICES = OpenMP -KOKKOS_ARCH = HSW # HSW = Haswell, SNB = SandyBridge, BDW = Broadwell, etc :pre - -For Intel KNLs using OpenMP: - -KOKKOS_DEVICES = OpenMP -KOKKOS_ARCH = KNL :pre - -For NVIDIA GPUs using CUDA: - -KOKKOS_DEVICES = Cuda -KOKKOS_ARCH = Pascal60,Power8 # P100 hosted by an IBM Power8, etc -KOKKOS_ARCH = Kepler37,Power8 # K80 hosted by an IBM Power8, etc :pre - -For GPUs, you also need these 2 lines in your Makefile.machine before -the CC line is defined, in this case for use with OpenMPI mpicxx. The -2 lines define a nvcc wrapper compiler, which will use nvcc for -compiling CUDA files or use a C++ compiler for non-Kokkos, non-CUDA -files. - -KOKKOS_ABSOLUTE_PATH = $(shell cd $(KOKKOS_PATH); pwd) -export OMPI_CXX = $(KOKKOS_ABSOLUTE_PATH)/config/nvcc_wrapper -CC = mpicxx :pre - -Once you have an appropriate Makefile.machine, you can -install/un-install the package and build LAMMPS in the usual manner. -Note that you cannot build one executable to run on multiple hardware -targets (CPU or KNL or GPU). You need to build LAMMPS once for each -hardware target, to produce a separate executable. Also note that we -do not recommend building with other acceleration packages installed -(GPU, OPT, USER-INTEL, USER-OMP) when also building with KOKKOS. - -make yes-kokkos -make machine :pre - -make no-kokkos -make machine :pre - -[Supporting info:] - -src/KOKKOS: filenames -> commands -src/KOKKOS/README -lib/kokkos/README -"Section 5.3"_Section_accelerate.html#acc_3 -"Section 5.3.3"_accelerate_kokkos.html -"Section 2.6 -k on ..."_Section_start.html#start_6 -"Section 2.6 -sf kk"_Section_start.html#start_6 -"Section 2.6 -pk kokkos"_Section_start.html#start_6 -"package kokkos"_package.html -Styles sections of "Section 3.5"_Section_commands.html#cmd_5 for styles followed by (k) -"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul - -:line - -KSPACE package :link(KSPACE),h4 - -[Contents:] - -A variety of long-range Coulombic solvers, as well as pair styles -which compute the corresponding short-range pairwise Coulombic -interactions. These include Ewald, particle-particle particle-mesh -(PPPM), and multilevel summation method (MSM) solvers. - -[Install or un-install:] - -Building with this package requires a 1d FFT library be present on -your system for use by the PPPM solvers. This can be the KISS FFT -library provided with LAMMPS, 3rd party libraries like FFTW, or a -vendor-supplied FFT library. See step 6 of "Section -2.2.2"_Section_start.html#start_2_2 of the manual for details on how -to select different FFT options in your machine Makefile. - -make yes-kspace -make machine :pre - -make no-kspace -make machine :pre - -[Supporting info:] - -src/KSPACE: filenames -> commands -"kspace_style"_kspace_style.html -"doc/PDF/kspace.pdf"_PDF/kspace.pdf -"Section 6.7"_Section_howto.html#howto_7 -"Section 6.8"_Section_howto.html#howto_8 -"Section 6.9"_Section_howto.html#howto_9 -"pair_style coul"_pair_coul.html -Pair Styles section of "Section 3.5"_Section_commands.html#cmd_5 with "long" or "msm" in pair style name -examples/peptide -bench/in.rhodo :ul - -:line - -LATTE package :link(LATTE),h4 - -[Contents:] - -A fix command which wraps the LATTE DFTB code, so that molecular -dynamics can be run with LAMMPS using density-functional tight-binding -quantum forces calculated by LATTE. - -More information on LATTE can be found at this web site: -"https://github.com/lanl/LATTE"_latte_home. A brief technical -description is given with the "fix latte"_fix_latte.html command. - -:link(latte_home,https://github.com/lanl/LATTE) - -[Authors:] Christian Negre (LANL) and Steve Plimpton (Sandia). LATTE -itself is developed at Los Alamos National Laboratory by Marc -Cawkwell, Anders Niklasson, and Christian Negre. - -[Install or un-install:] - -Before building LAMMPS with this package, you must first download and -build the LATTE library. You can do this manually if you prefer; -follow the instructions in lib/latte/README. You can also do it in -one step from the lammps/src dir, using a command like these, which -simply invokes the lib/latte/Install.py script with the specified -args: - -make lib-latte # print help message -make lib-latte args="-b" # download and build in lib/latte/LATTE-master -make lib-latte args="-p $HOME/latte" # use existing LATTE installation in $HOME/latte -make lib-latte args="-b -m gfortran" # download and build in lib/latte and - # copy Makefile.lammps.gfortran to Makefile.lammps -:pre - -Note that 3 symbolic (soft) links, "includelink" and "liblink" and -"filelink.o", are created in lib/latte to point into the LATTE home dir. -When LAMMPS builds in src it will use these links. You should -also check that the Makefile.lammps file you create is appropriate -for the compiler you use on your system to build LATTE. - -You can then install/un-install the package and build LAMMPS in the -usual manner: - -make yes-latte -make machine :pre - -make no-latte -make machine :pre - -[Supporting info:] - -src/LATTE: filenames -> commands -src/LATTE/README -lib/latte/README -"fix latte"_fix_latte.html -examples/latte -"LAMMPS-LATTE tutorial"_https://github.com/lanl/LATTE/wiki/Using-LATTE-through-LAMMPS :ul - -:line - -MANYBODY package :link(MANYBODY),h4 - -[Contents:] - -A variety of manybody and bond-order potentials. These include -(AI)REBO, BOP, EAM, EIM, Stillinger-Weber, and Tersoff potentials. - -[Install or un-install:] - -make yes-manybody -make machine :pre - -make no-manybody -make machine :pre - -[Supporting info:] - -src/MANYBODY: filenames -> commands -Pair Styles section of "Section 3.5"_Section_commands.html#cmd_5 -examples/comb -examples/eim -examples/nb3d -examples/shear -examples/streitz -examples/vashishta -bench/in.eam :ul - -:line - -MC package :link(MC),h4 - -[Contents:] - -Several fixes and a pair style that have Monte Carlo (MC) or MC-like -attributes. These include fixes for creating, breaking, and swapping -bonds, for performing atomic swaps, and performing grand-canonical MC -(GCMC) in conjuction with dynamics. - -[Install or un-install:] - -make yes-mc -make machine :pre - -make no-mc -make machine :pre - -[Supporting info:] - -src/MC: filenames -> commands -"fix atom/swap"_fix_atom_swap.html -"fix bond/break"_fix_bond_break.html -"fix bond/create"_fix_bond_create.html -"fix bond/swap"_fix_bond_swap.html -"fix gcmc"_fix_gcmc.html -"pair_style dsmc"_pair_dsmc.html -http://lammps.sandia.gov/movies.html#gcmc :ul - -:line - -MEAM package :link(MEAM),h4 - -[Contents:] - -A pair style for the modified embedded atom (MEAM) potential. - -Please note that the MEAM package has been superseded by the -"USER-MEAMC"_#USER-MEAMC package, which is a direct translation -of the MEAM package to C++. USER-MEAMC contains additional -optimizations making it run faster than MEAM on most machines, -while providing the identical features and USER interface. - -[Author:] Greg Wagner (Northwestern U) while at Sandia. - -[Install or un-install:] - -Before building LAMMPS with this package, you must first build the -MEAM library in lib/meam. You can do this manually if you prefer; -follow the instructions in lib/meam/README. You can also do it in one -step from the lammps/src dir, using a command like these, which simply -invoke the lib/meam/Install.py script with the specified args: - -make lib-meam # print help message -make lib-meam args="-m mpi" # build with default Fortran compiler compatible with your MPI library -make lib-meam args="-m serial" # build with compiler compatible with "make serial" (GNU Fortran) -make lib-meam args="-m ifort" # build with Intel Fortran compiler using Makefile.ifort :pre - -The build should produce two files: lib/meam/libmeam.a and -lib/meam/Makefile.lammps. The latter is copied from an existing -Makefile.lammps.* and has settings needed to link C++ (LAMMPS) with -Fortran (MEAM library). Typically the two compilers used for LAMMPS -and the MEAM library need to be consistent (e.g. both Intel or both -GNU compilers). If necessary, you can edit/create a new -lib/meam/Makefile.machine file for your system, which should define an -EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine -file. - -You can then install/un-install the package and build LAMMPS in the -usual manner: - -make yes-meam -make machine :pre - -make no-meam -make machine :pre - -NOTE: You should test building the MEAM library with both the Intel -and GNU compilers to see if a simulation runs faster with one versus -the other on your system. - -[Supporting info:] - -src/MEAM: filenames -> commands -src/meam/README -lib/meam/README -"pair_style meam"_pair_meam.html -examples/meam :ul - -:line - -MISC package :link(MISC),h4 - -[Contents:] - -A variety of compute, fix, pair, dump styles with specialized -capabilities that don't align with other packages. Do a directory -listing, "ls src/MISC", to see the list of commands. - -NOTE: the MISC package contains styles that require using the --restrict flag, when compiling with Intel compilers. - -[Install or un-install:] - -make yes-misc -make machine :pre - -make no-misc -make machine :pre - -[Supporting info:] - -src/MISC: filenames -> commands -"compute ti"_compute_ti.html -"fix evaporate"_fix_evaporate.html -"fix orient/fcc"_fix_orient.html -"fix ttm"_fix_ttm.html -"fix thermal/conductivity"_fix_thermal_conductivity.html -"fix viscosity"_fix_viscosity.html -examples/KAPPA -examples/VISCOSITY -http://lammps.sandia.gov/pictures.html#ttm -http://lammps.sandia.gov/movies.html#evaporation :ul - -:line - -MOLECULE package :link(MOLECULE),h4 - -[Contents:] - -A large number of atom, pair, bond, angle, dihedral, improper styles -that are used to model molecular systems with fixed covalent bonds. -The pair styles include the Dreiding (hydrogen-bonding) and CHARMM -force fields, and a TIP4P water model. - -[Install or un-install:] - -make yes-molecule -make machine :pre - -make no-molecule -make machine :pre - -[Supporting info:] - -src/MOLECULE: filenames -> commands -"atom_style"_atom_style.html -"bond_style"_bond_style.html -"angle_style"_angle_style.html -"dihedral_style"_dihedral_style.html -"improper_style"_improper_style.html -"pair_style hbond/dreiding/lj"_pair_hbond_dreiding.html -"pair_style lj/charmm/coul/charmm"_pair_charmm.html -"Section 6.3"_Section_howto.html#howto_3 -examples/cmap -examples/dreiding -examples/micelle, -examples/peptide -bench/in.chain -bench/in.rhodo :ul - -:line - -MPIIO package :link(MPIIO),h4 - -[Contents:] - -Support for parallel output/input of dump and restart files via the -MPIIO library. It adds "dump styles"_dump.html with a "mpiio" in -their style name. Restart files with an ".mpiio" suffix are also -written and read in parallel. - -[Install or un-install:] - -Note that MPIIO is part of the standard message-passing interface -(MPI) library, so you should not need any additional compiler or link -settings, beyond what LAMMPS normally uses for MPI on your system. - -make yes-mpiio -make machine :pre - -make no-mpiio -make machine :pre - -[Supporting info:] - -src/MPIIO: filenames -> commands -"dump"_dump.html -"restart"_restart.html -"write_restart"_write_restart.html -"read_restart"_read_restart.html :ul - -:line - -MSCG package :link(mscg),h4 - -[Contents:] - -A "fix mscg"_fix_mscg.html command which can parameterize a -Multi-Scale Coarse-Graining (MSCG) model using the open-source "MS-CG -library"_mscg_home. - -:link(mscg_home,https://github.com/uchicago-voth/MSCG-release) - -To use this package you must have the MS-CG library available on your -system. - -[Authors:] The fix was written by Lauren Abbott (Sandia). The MS-CG -library was developed by Jacob Wagner in Greg Voth's group at the -University of Chicago. - -[Install or un-install:] - -Before building LAMMPS with this package, you must first download and -build the MS-CG library. Building the MS-CG library and using it from -LAMMPS requires a C++11 compatible compiler and that the GSL -(GNU Scientific Library) headers and libraries are installed on your -machine. See the lib/mscg/README and MSCG/Install files for more details. - -Assuming these libraries are in place, you can do the download and -build of MS-CG manually if you prefer; follow the instructions in -lib/mscg/README. You can also do it in one step from the lammps/src -dir, using a command like these, which simply invoke the -lib/mscg/Install.py script with the specified args: - -make lib-mscg # print help message -make lib-mscg args="-b -m serial" # download and build in lib/mscg/MSCG-release-master - # with the settings compatible with "make serial" -make lib-mscg args="-b -m mpi" # download and build in lib/mscg/MSCG-release-master - # with the settings compatible with "make mpi" -make lib-mscg args="-p /usr/local/mscg-release" # use the existing MS-CG installation in /usr/local/mscg-release :pre - -Note that 2 symbolic (soft) links, "includelink" and "liblink", will be created in lib/mscg -to point to the MS-CG src/installation dir. When LAMMPS is built in src it will use these links. -You should not need to edit the lib/mscg/Makefile.lammps file. - -You can then install/un-install the package and build LAMMPS in the -usual manner: - -make yes-mscg -make machine :pre - -make no-mscg -make machine :pre - -[Supporting info:] - -src/MSCG: filenames -> commands -src/MSCG/README -lib/mscg/README -examples/mscg :ul - -:line - -OPT package :link(OPT),h4 - -[Contents:] - -A handful of pair styles which are optimized for improved CPU -performance on single or multiple cores. These include EAM, LJ, -CHARMM, and Morse potentials. The styles have an "opt" suffix in -their style name. "Section 5.3.5"_accelerate_opt.html gives details -of how to build and use this package. Its styles can be invoked at -run time via the "-sf opt" or "-suffix opt" "command-line -switches"_Section_start.html#start_6. See also the "KOKKOS"_#KOKKOS, -"USER-INTEL"_#USER-INTEL, and "USER-OMP"_#USER-OMP packages, which -have styles optimized for CPU performance. - -[Authors:] James Fischer (High Performance Technologies), David Richie, -and Vincent Natoli (Stone Ridge Technolgy). - -[Install or un-install:] - -make yes-opt -make machine :pre - -make no-opt -make machine :pre - -NOTE: The compile flag "-restrict" must be used to build LAMMPS with -the OPT package when using Intel compilers. It should be added to -the CCFLAGS line of your Makefile.machine. See Makefile.opt in -src/MAKE/OPTIONS for an example. - -CCFLAGS: add -restrict for Intel compilers :ul - -[Supporting info:] - -src/OPT: filenames -> commands -"Section 5.3"_Section_accelerate.html#acc_3 -"Section 5.3.5"_accelerate_opt.html -"Section 2.6 -sf opt"_Section_start.html#start_6 -Pair Styles section of "Section 3.5"_Section_commands.html#cmd_5 for pair styles followed by (t) -"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul - -:line - -PERI package :link(PERI),h4 - -[Contents:] - -An atom style, several pair styles which implement different -Peridynamics materials models, and several computes which calculate -diagnostics. Peridynamics is a a particle-based meshless continuum -model. - -[Authors:] The original package was created by Mike Parks (Sandia). -Additional Peridynamics models were added by Rezwanur Rahman and John -Foster (UTSA). - -[Install or un-install:] - -make yes-peri -make machine :pre - -make no-peri -make machine :pre - -[Supporting info:] - -src/PERI: filenames -> commands -"doc/PDF/PDLammps_overview.pdf"_PDF/PDLammps_overview.pdf -"doc/PDF/PDLammps_EPS.pdf"_PDF/PDLammps_EPS.pdf -"doc/PDF/PDLammps_VES.pdf"_PDF/PDLammps_VES.pdf -"atom_style peri"_atom_style.html -"pair_style peri/*"_pair_peri.html -"compute damage/atom"_compute_damage_atom.html -"compute plasticity/atom"_compute_plasticity_atom.html -examples/peri -http://lammps.sandia.gov/movies.html#peri :ul - -:line - -POEMS package :link(POEMS),h4 - -[Contents:] - -A fix that wraps the Parallelizable Open source Efficient Multibody -Software (POEMS) library, which is able to simulate the dynamics of -articulated body systems. These are systems with multiple rigid -bodies (collections of particles) whose motion is coupled by -connections at hinge points. - -[Author:] Rudra Mukherjee (JPL) while at RPI. - -[Install or un-install:] - -Before building LAMMPS with this package, you must first build the -POEMS library in lib/poems. You can do this manually if you prefer; -follow the instructions in lib/poems/README. You can also do it in -one step from the lammps/src dir, using a command like these, which -simply invoke the lib/poems/Install.py script with the specified args: - -make lib-poems # print help message -make lib-poems args="-m serial" # build with GNU g++ compiler (settings as with "make serial") -make lib-poems args="-m mpi" # build with default MPI C++ compiler (settings as with "make mpi") -make lib-poems args="-m icc" # build with Intel icc compiler :pre - -The build should produce two files: lib/poems/libpoems.a and -lib/poems/Makefile.lammps. The latter is copied from an existing -Makefile.lammps.* and has settings needed to build LAMMPS with the -POEMS library (though typically the settings are just blank). If -necessary, you can edit/create a new lib/poems/Makefile.machine file -for your system, which should define an EXTRAMAKE variable to specify -a corresponding Makefile.lammps.machine file. - -You can then install/un-install the package and build LAMMPS in the -usual manner: - -make yes-poems -make machine :pre - -make no-meam -make machine :pre - -[Supporting info:] - -src/POEMS: filenames -> commands -src/POEMS/README -lib/poems/README -"fix poems"_fix_poems.html -examples/rigid :ul - -:line - -PYTHON package :link(PYTHON),h4 - -[Contents:] - -A "python"_python.html command which allow you to execute Python code -from a LAMMPS input script. The code can be in a separate file or -embedded in the input script itself. See "Section -11.2"_Section_python.html#py_2 for an overview of using Python from -LAMMPS in this manner and the entire section for other ways to use -LAMMPS and Python together. - -[Install or un-install:] - -make yes-python -make machine :pre - -make no-python -make machine :pre - -NOTE: Building with the PYTHON package assumes you have a Python -shared library available on your system, which needs to be a Python 2 -version, 2.6 or later. Python 3 is not yet supported. See the -lib/python/README for more details. Note that the build uses the -lib/python/Makefile.lammps file in the compile/link process. You -should only need to create a new Makefile.lammps.* file (and copy it -to Makefile.lammps) if the LAMMPS build fails. - -[Supporting info:] - -src/PYTHON: filenames -> commands -"Section 11"_Section_python.html -lib/python/README -examples/python :ul - -:line - -QEQ package :link(QEQ),h4 - -[Contents:] - -Several fixes for performing charge equilibration (QEq) via different -algorithms. These can be used with pair styles that perform QEq as -part of their formulation. - -[Install or un-install:] - -make yes-qeq -make machine :pre - -make no-qeq -make machine :pre - -[Supporting info:] - -src/QEQ: filenames -> commands -"fix qeq/*"_fix_qeq.html -examples/qeq -examples/streitz :ul - -:line - -REAX package :link(REAX),h4 - -[Contents:] - -A pair style which wraps a Fortran library which implements the ReaxFF -potential, which is a universal reactive force field. See the -"USER-REAXC package"_#USER-REAXC for an alternate implementation in -C/C++. Also a "fix reax/bonds"_fix_reax_bonds.html command for -monitoring molecules as bonds are created and destroyed. - -[Author:] Aidan Thompson (Sandia). - -[Install or un-install:] - -Before building LAMMPS with this package, you must first build the -REAX library in lib/reax. You can do this manually if you prefer; -follow the instructions in lib/reax/README. You can also do it in one -step from the lammps/src dir, using a command like these, which simply -invoke the lib/reax/Install.py script with the specified args: - -make lib-reax # print help message -make lib-reax args="-m serial" # build with GNU Fortran compiler (settings as with "make serial") -make lib-reax args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi") -make lib-reax args="-m ifort" # build with Intel ifort compiler :pre - -The build should produce two files: lib/reax/libreax.a and -lib/reax/Makefile.lammps. The latter is copied from an existing -Makefile.lammps.* and has settings needed to link C++ (LAMMPS) with -Fortran (REAX library). Typically the two compilers used for LAMMPS -and the REAX library need to be consistent (e.g. both Intel or both -GNU compilers). If necessary, you can edit/create a new -lib/reax/Makefile.machine file for your system, which should define an -EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine -file. - -You can then install/un-install the package and build LAMMPS in the -usual manner: - -make yes-reax -make machine :pre - -make no-reax -make machine :pre - -[Supporting info:] - -src/REAX: filenames -> commands -lib/reax/README -"pair_style reax"_pair_reax.html -"fix reax/bonds"_fix_reax_bonds.html -examples/reax :ul - -:line - -REPLICA package :link(REPLICA),h4 - -[Contents:] - -A collection of multi-replica methods which can be used when running -multiple LAMMPS simulations (replicas). See "Section -6.5"_Section_howto.html#howto_5 for an overview of how to run -multi-replica simulations in LAMMPS. Methods in the package include -nudged elastic band (NEB), parallel replica dynamics (PRD), -temperature accelerated dynamics (TAD), parallel tempering, and a -verlet/split algorithm for performing long-range Coulombics on one set -of processors, and the remainder of the force field calcalation on -another set. - -[Install or un-install:] - -make yes-replica -make machine :pre - -make no-replica -make machine :pre - -[Supporting info:] - -src/REPLICA: filenames -> commands -"Section 6.5"_Section_howto.html#howto_5 -"neb"_neb.html -"prd"_prd.html -"tad"_tad.html -"temper"_temper.html, -"run_style verlet/split"_run_style.html -examples/neb -examples/prd -examples/tad :ul - -:line - -RIGID package :link(RIGID),h4 - -[Contents:] - -Fixes which enforce rigid constraints on collections of atoms or -particles. This includes SHAKE and RATTLE, as well as varous -rigid-body integrators for a few large bodies or many small bodies. -Also several computes which calculate properties of rigid bodies. - -To install/build: - -make yes-rigid -make machine :pre - -To un-install/re-build: - -make no-rigid -make machine :pre - -[Supporting info:] - -src/RIGID: filenames -> commands -"compute erotate/rigid"_compute_erotate_rigid.html -fix shake"_fix_shake.html -"fix rattle"_fix_shake.html -"fix rigid/*"_fix_rigid.html -examples/ASPHERE -examples/rigid -bench/in.rhodo -http://lammps.sandia.gov/movies.html#box -http://lammps.sandia.gov/movies.html#star :ul - -:line - -SHOCK package :link(SHOCK),h4 - -[Contents:] - -Fixes for running impact simulations where a shock-wave passes through -a material. - -[Install or un-install:] - -make yes-shock -make machine :pre - -make no-shock -make machine :pre - -[Supporting info:] - -src/SHOCK: filenames -> commands -"fix append/atoms"_fix_append_atoms.html -"fix msst"_fix_msst.html -"fix nphug"_fix_nphug.html -"fix wall/piston"_fix_wall_piston.html -examples/hugoniostat -examples/msst :ul - -:line - -SNAP package :link(SNAP),h4 - -[Contents:] - -A pair style for the spectral neighbor analysis potential (SNAP). -SNAP is methodology for deriving a highly accurate classical potential -fit to a large archive of quantum mechanical (DFT) data. Also several -computes which analyze attributes of the potential. - -[Author:] Aidan Thompson (Sandia). - -[Install or un-install:] - -make yes-snap -make machine :pre - -make no-snap -make machine :pre - -[Supporting info:] - -src/SNAP: filenames -> commands -"pair_style snap"_pair_snap.html -"compute sna/atom"_compute_sna_atom.html -"compute snad/atom"_compute_sna_atom.html -"compute snav/atom"_compute_sna_atom.html -examples/snap :ul - -:line - -SRD package :link(SRD),h4 - -[Contents:] - -A pair of fixes which implement the Stochastic Rotation Dynamics (SRD) -method for coarse-graining of a solvent, typically around large -colloidal particles. - -To install/build: - -make yes-srd -make machine :pre - -To un-install/re-build: - -make no-srd -make machine :pre - -[Supporting info:] - -src/SRD: filenames -> commands -"fix srd"_fix_srd.html -"fix wall/srd"_fix_wall_srd.html -examples/srd -examples/ASPHERE -http://lammps.sandia.gov/movies.html#tri -http://lammps.sandia.gov/movies.html#line -http://lammps.sandia.gov/movies.html#poly :ul - -:line - -VORONOI package :link(VORONOI),h4 - -[Contents:] - -A compute command which calculates the Voronoi tesselation of a -collection of atoms by wrapping the "Voro++ library"_voro_home. This -can be used to calculate the local volume or each atoms or its near -neighbors. - -:link(voro_home,http://math.lbl.gov/voro++) - -To use this package you must have the Voro++ library available on your -system. - -[Author:] Daniel Schwen (INL) while at LANL. The open-source Voro++ -library was written by Chris Rycroft (Harvard U) while at UC Berkeley -and LBNL. - -[Install or un-install:] - -Before building LAMMPS with this package, you must first download and -build the Voro++ library. You can do this manually if you prefer; -follow the instructions in lib/voronoi/README. You can also do it in -one step from the lammps/src dir, using a command like these, which -simply invoke the lib/voronoi/Install.py script with the specified -args: - -make lib-voronoi # print help message -make lib-voronoi args="-b" # download and build the default version in lib/voronoi/voro++- -make lib-voronoi args="-p $HOME/voro++" # use existing Voro++ installation in $HOME/voro++ -make lib-voronoi args="-b -v voro++0.4.6" # download and build the 0.4.6 version in lib/voronoi/voro++-0.4.6 :pre - -Note that 2 symbolic (soft) links, "includelink" and "liblink", are -created in lib/voronoi to point to the Voro++ src dir. When LAMMPS -builds in src it will use these links. You should not need to edit -the lib/voronoi/Makefile.lammps file. - -You can then install/un-install the package and build LAMMPS in the -usual manner: - -make yes-voronoi -make machine :pre - -make no-voronoi -make machine :pre - -[Supporting info:] - -src/VORONOI: filenames -> commands -src/VORONOI/README -lib/voronoi/README -"compute voronoi/atom"_compute_voronoi_atom.html -examples/voronoi :ul - -:line -:line - -USER-ATC package :link(USER-ATC),h4 - -[Contents:] - -ATC stands for atoms-to-continuum. This package implements a "fix -atc"_fix_atc.html command to either couple molecular dynamics with -continuum finite element equations or perform on-the-fly conversion of -atomic information to continuum fields. - -[Authors:] Reese Jones, Jeremy Templeton, Jon Zimmerman (Sandia). - -[Install or un-install:] - -Before building LAMMPS with this package, you must first build the ATC -library in lib/atc. You can do this manually if you prefer; follow -the instructions in lib/atc/README. You can also do it in one step -from the lammps/src dir, using a command like these, which simply -invoke the lib/atc/Install.py script with the specified args: - -make lib-atc # print help message -make lib-atc args="-m serial" # build with GNU g++ compiler and MPI STUBS (settings as with "make serial") -make lib-atc args="-m mpi" # build with default MPI compiler (settings as with "make mpi") -make lib-atc args="-m icc" # build with Intel icc compiler :pre - -The build should produce two files: lib/atc/libatc.a and -lib/atc/Makefile.lammps. The latter is copied from an existing -Makefile.lammps.* and has settings needed to build LAMMPS with the ATC -library. If necessary, you can edit/create a new -lib/atc/Makefile.machine file for your system, which should define an -EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine -file. - -Note that the Makefile.lammps file has settings for the BLAS and -LAPACK linear algebra libraries. As explained in lib/atc/README these -can either exist on your system, or you can use the files provided in -lib/linalg. In the latter case you also need to build the library -in lib/linalg with a command like these: - -make lib-linalg # print help message -make lib-linalg args="-m serial" # build with GNU Fortran compiler (settings as with "make serial") -make lib-linalg args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi") -make lib-linalg args="-m gfortran" # build with GNU Fortran compiler :pre - -You can then install/un-install the package and build LAMMPS in the -usual manner: - -make yes-user-atc -make machine :pre - -make no-user-atc -make machine :pre - -[Supporting info:] - -src/USER-ATC: filenames -> commands -src/USER-ATC/README -"fix atc"_fix_atc.html -examples/USER/atc -http://lammps.sandia.gov/pictures.html#atc :ul - -:line - -USER-AWPMD package :link(USER-AWPMD),h4 - -[Contents:] - -AWPMD stands for Antisymmetrized Wave Packet Molecular Dynamics. This -package implements an atom, pair, and fix style which allows electrons -to be treated as explicit particles in a classical molecular dynamics -model. - -[Author:] Ilya Valuev (JIHT, Russia). - -[Install or un-install:] - -Before building LAMMPS with this package, you must first build the -AWPMD library in lib/awpmd. You can do this manually if you prefer; -follow the instructions in lib/awpmd/README. You can also do it in -one step from the lammps/src dir, using a command like these, which -simply invoke the lib/awpmd/Install.py script with the specified args: - -make lib-awpmd # print help message -make lib-awpmd args="-m serial" # build with GNU g++ compiler and MPI STUBS (settings as with "make serial") -make lib-awpmd args="-m mpi" # build with default MPI compiler (settings as with "make mpi") -make lib-awpmd args="-m icc" # build with Intel icc compiler :pre - -The build should produce two files: lib/awpmd/libawpmd.a and -lib/awpmd/Makefile.lammps. The latter is copied from an existing -Makefile.lammps.* and has settings needed to build LAMMPS with the -AWPMD library. If necessary, you can edit/create a new -lib/awpmd/Makefile.machine file for your system, which should define -an EXTRAMAKE variable to specify a corresponding -Makefile.lammps.machine file. - -Note that the Makefile.lammps file has settings for the BLAS and -LAPACK linear algebra libraries. As explained in lib/awpmd/README -these can either exist on your system, or you can use the files -provided in lib/linalg. In the latter case you also need to build the -library in lib/linalg with a command like these: - -make lib-linalg # print help message -make lib-linalg args="-m serial" # build with GNU Fortran compiler (settings as with "make serial") -make lib-linalg args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi") -make lib-linalg args="-m gfortran" # build with GNU Fortran compiler :pre - -You can then install/un-install the package and build LAMMPS in the -usual manner: - -make yes-user-awpmd -make machine :pre - -make no-user-awpmd -make machine :pre - -[Supporting info:] - -src/USER-AWPMD: filenames -> commands -src/USER-AWPMD/README -"pair_style awpmd/cut"_pair_awpmd.html -examples/USER/awpmd :ul - -:line - -USER-BOCS package :link(USER-BOCS),h4 - -[Contents:] - -This package provides "fix bocs"_fix_bocs.html, a modified version -of "fix npt"_fix_nh.html which includes the pressure correction to -the barostat as outlined in: - -N. J. H. Dunn and W. G. Noid, "Bottom-up coarse-grained models that -accurately describe the structure, pressure, and compressibility of -molecular liquids," J. Chem. Phys. 143, 243148 (2015). - -[Authors:] Nicholas J. H. Dunn and Michael R. DeLyser (The Pennsylvania State University) - -[Install or un-install:] - -make yes-user-bocs -make machine :pre - -make no-user-bocs -make machine :pre - -[Supporting info:] - -The USER-BOCS user package for LAMMPS is part of the BOCS software package: -"https://github.com/noid-group/BOCS"_https://github.com/noid-group/BOCS - -See the following reference for information about the entire package: - -Dunn, NJH; Lebold, KM; DeLyser, MR; Rudzinski, JF; Noid, WG. -"BOCS: Bottom-Up Open-Source Coarse-Graining Software." -J. Phys. Chem. B. 122, 13, 3363-3377 (2018). - -Example inputs are in the examples/USER/bocs folder. - -:line - -USER-CGDNA package :link(USER-CGDNA),h4 - -[Contents:] - -Several pair styles, a bond style, and integration fixes for -coarse-grained models of single- and double-stranded DNA based on the -oxDNA model of Doye, Louis and Ouldridge at the University of Oxford. -This includes Langevin-type rigid-body integrators with improved -stability. - -[Author:] Oliver Henrich (University of Strathclyde, Glasgow). - -[Install or un-install:] - -make yes-user-cgdna -make machine :pre - -make no-user-cgdna -make machine :pre - -[Supporting info:] - -src/USER-CGDNA: filenames -> commands -/src/USER-CGDNA/README -"pair_style oxdna/*"_pair_oxdna.html -"pair_style oxdna2/*"_pair_oxdna2.html -"bond_style oxdna/*"_bond_oxdna.html -"bond_style oxdna2/*"_bond_oxdna.html -"fix nve/dotc/langevin"_fix_nve_dotc_langevin.html :ul - -:line - -USER-CGSDK package :link(USER-CGSDK),h4 - -[Contents:] - -Several pair styles and an angle style which implement the -coarse-grained SDK model of Shinoda, DeVane, and Klein which enables -simulation of ionic liquids, electrolytes, lipids and charged amino -acids. - -[Author:] Axel Kohlmeyer (Temple U). - -[Install or un-install:] - -make yes-user-cgsdk -make machine :pre - -make no-user-cgsdk -make machine :pre - -[Supporting info:] - -src/USER-CGSDK: filenames -> commands -src/USER-CGSDK/README -"pair_style lj/sdk/*"_pair_sdk.html -"angle_style sdk"_angle_sdk.html -examples/USER/cgsdk -http://lammps.sandia.gov/pictures.html#cg :ul - -:line - -USER-COLVARS package :link(USER-COLVARS),h4 - -[Contents:] - -COLVARS stands for collective variables, which can be used to -implement various enhanced sampling methods, including Adaptive -Biasing Force, Metadynamics, Steered MD, Umbrella Sampling and -Restraints. A "fix colvars"_fix_colvars.html command is implemented -which wraps a COLVARS library, which implements these methods. -simulations. - -[Authors:] The COLVARS library is written and maintained by -Giacomo Fiorin (ICMS, Temple University, Philadelphia, PA, USA) -and Jerome Henin (LISM, CNRS, Marseille, France), originally for -the NAMD MD code, but with portability in mind. Axel Kohlmeyer -(Temple U) provided the interface to LAMMPS. - -[Install or un-install:] - -Before building LAMMPS with this package, you must first build the -COLVARS library in lib/colvars. You can do this manually if you -prefer; follow the instructions in lib/colvars/README. You can also -do it in one step from the lammps/src dir, using a command like these, -which simply invoke the lib/colvars/Install.py script with the -specified args: - -make lib-colvars # print help message -make lib-colvars args="-m serial" # build with GNU g++ compiler (settings as with "make serial") -make lib-colvars args="-m mpi" # build with default MPI compiler (settings as with "make mpi") -make lib-colvars args="-m g++-debug" # build with GNU g++ compiler and colvars debugging enabled :pre - -The build should produce two files: lib/colvars/libcolvars.a and -lib/colvars/Makefile.lammps. The latter is copied from an existing -Makefile.lammps.* and has settings needed to build LAMMPS with the -COLVARS library (though typically the settings are just blank). If -necessary, you can edit/create a new lib/colvars/Makefile.machine file -for your system, which should define an EXTRAMAKE variable to specify -a corresponding Makefile.lammps.machine file. - -You can then install/un-install the package and build LAMMPS in the -usual manner: - -make yes-user-colvars -make machine :pre - -make no-user-colvars -make machine :pre - -[Supporting info:] - -src/USER-COLVARS: filenames -> commands -"doc/PDF/colvars-refman-lammps.pdf"_PDF/colvars-refman-lammps.pdf -src/USER-COLVARS/README -lib/colvars/README -"fix colvars"_fix_colvars.html -examples/USER/colvars :ul - -:line - -USER-DIFFRACTION package :link(USER-DIFFRACTION),h4 - -[Contents:] - -Two computes and a fix for calculating x-ray and electron diffraction -intensities based on kinematic diffraction theory. - -[Author:] Shawn Coleman while at the U Arkansas. - -[Install or un-install:] - -make yes-user-diffraction -make machine :pre - -make no-user-diffraction -make machine :pre - -[Supporting info:] - -src/USER-DIFFRACTION: filenames -> commands -"compute saed"_compute_saed.html -"compute xrd"_compute_xrd.html -"fix saed/vtk"_fix_saed_vtk.html -examples/USER/diffraction :ul - -:line - -USER-DPD package :link(USER-DPD),h4 - -[Contents:] - -DPD stands for dissipative particle dynamics. This package implements -coarse-grained DPD-based models for energetic, reactive molecular -crystalline materials. It includes many pair styles specific to these -systems, including for reactive DPD, where each particle has internal -state for multiple species and a coupled set of chemical reaction ODEs -are integrated each timestep. Highly accurate time integrators for -isothermal, isoenergetic, isobaric and isenthalpic conditions are -included. These enable long timesteps via the Shardlow splitting -algorithm. - -[Authors:] Jim Larentzos (ARL), Tim Mattox (Engility Corp), and and John -Brennan (ARL). - -[Install or un-install:] - -make yes-user-dpd -make machine :pre - -make no-user-dpd -make machine :pre - -[Supporting info:] - -src/USER-DPD: filenames -> commands -/src/USER-DPD/README -"compute dpd"_compute_dpd.html -"compute dpd/atom"_compute_dpd_atom.html -"fix eos/cv"_fix_eos_table.html -"fix eos/table"_fix_eos_table.html -"fix eos/table/rx"_fix_eos_table_rx.html -"fix shardlow"_fix_shardlow.html -"fix rx"_fix_rx.html -"pair_style table/rx"_pair_table_rx.html -"pair_style dpd/fdt"_pair_dpd_fdt.html -"pair_style dpd/fdt/energy"_pair_dpd_fdt.html -"pair_style exp6/rx"_pair_exp6_rx.html -"pair_style multi/lucy"_pair_multi_lucy.html -"pair_style multi/lucy/rx"_pair_multi_lucy_rx.html -examples/USER/dpd :ul - -:line - -USER-DRUDE package :link(USER-DRUDE),h4 - -[Contents:] - -Fixes, pair styles, and a compute to simulate thermalized Drude -oscillators as a model of polarization. See "Section -6.27"_Section_howto.html#howto_27 for an overview of how to use the -package. There are auxiliary tools for using this package in -tools/drude. - -[Authors:] Alain Dequidt (U Blaise Pascal Clermont-Ferrand), Julien -Devemy (CNRS), and Agilio Padua (U Blaise Pascal). - -[Install or un-install:] - -make yes-user-drude -make machine :pre - -make no-user-drude -make machine :pre - -[Supporting info:] - -src/USER-DRUDE: filenames -> commands -"Section 6.27"_Section_howto.html#howto_27 -"Section 6.25"_Section_howto.html#howto_25 -src/USER-DRUDE/README -"fix drude"_fix_drude.html -"fix drude/transform/*"_fix_drude_transform.html -"compute temp/drude"_compute_temp_drude.html -"pair_style thole"_pair_thole.html -"pair_style lj/cut/thole/long"_pair_thole.html -examples/USER/drude -tools/drude :ul - -:line - -USER-EFF package :link(USER-EFF),h4 - -[Contents:] - -EFF stands for electron force field which allows a classical MD code -to model electrons as particles of variable radius. This package -contains atom, pair, fix and compute styles which implement the eFF as -described in A. Jaramillo-Botero, J. Su, Q. An, and W.A. Goddard III, -JCC, 2010. The eFF potential was first introduced by Su and Goddard, -in 2007. There are auxiliary tools for using this package in -tools/eff; see its README file. - -[Author:] Andres Jaramillo-Botero (CalTech). - -[Install or un-install:] - -make yes-user-eff -make machine :pre - -make no-user-eff -make machine :pre - -[Supporting info:] - -src/USER-EFF: filenames -> commands -src/USER-EFF/README -"atom_style electron"_atom_style.html -"fix nve/eff"_fix_nve_eff.html -"fix nvt/eff"_fix_nh_eff.html -"fix npt/eff"_fix_nh_eff.html -"fix langevin/eff"_fix_langevin_eff.html -"compute temp/eff"_compute_temp_eff.html -"pair_style eff/cut"_pair_eff.html -"pair_style eff/inline"_pair_eff.html -examples/USER/eff -tools/eff/README -tools/eff -http://lammps.sandia.gov/movies.html#eff :ul - -:line - -USER-FEP package :link(USER-FEP),h4 - -[Contents:] - -FEP stands for free energy perturbation. This package provides -methods for performing FEP simulations by using a "fix -adapt/fep"_fix_adapt_fep.html command with soft-core pair potentials, -which have a "soft" in their style name. There are auxiliary tools -for using this package in tools/fep; see its README file. - -[Author:] Agilio Padua (Universite Blaise Pascal Clermont-Ferrand) - -[Install or un-install:] - -make yes-user-fep -make machine :pre - -make no-user-fep -make machine :pre - -[Supporting info:] - -src/USER-FEP: filenames -> commands -src/USER-FEP/README -"fix adapt/fep"_fix_adapt_fep.html -"compute fep"_compute_fep.html -"pair_style */soft"_pair_lj_soft.html -examples/USER/fep -tools/fep/README -tools/fep :ul - -:line - -USER-H5MD package :link(USER-H5MD),h4 - -[Contents:] - -H5MD stands for HDF5 for MD. "HDF5"_HDF5 is a portable, binary, -self-describing file format, used by many scientific simulations. -H5MD is a format for molecular simulations, built on top of HDF5. -This package implements a "dump h5md"_dump_h5md.html command to output -LAMMPS snapshots in this format. - -:link(HDF5,http://www.hdfgroup.org/HDF5) - -To use this package you must have the HDF5 library available on your -system. - -[Author:] Pierre de Buyl (KU Leuven) created both the package and the -H5MD format. - -[Install or un-install:] - -Note that to follow these steps to compile and link to the CH5MD -library, you need the standard HDF5 software package installed on your -system, which should include the h5cc compiler and the HDF5 library. - -Before building LAMMPS with this package, you must first build the -CH5MD library in lib/h5md. You can do this manually if you prefer; -follow the instructions in lib/h5md/README. You can also do it in one -step from the lammps/src dir, using a command like these, which simply -invoke the lib/h5md/Install.py script with the specified args: - -make lib-h5md # print help message -make lib-hm5d args="-m h5cc" # build with h5cc compiler :pre - -The build should produce two files: lib/h5md/libch5md.a and -lib/h5md/Makefile.lammps. The latter is copied from an existing -Makefile.lammps.* and has settings needed to build LAMMPS with the -system HDF5 library. If necessary, you can edit/create a new -lib/h5md/Makefile.machine file for your system, which should define an -EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine -file. - -You can then install/un-install the package and build LAMMPS in the -usual manner: - -make yes-user-h5md -make machine :pre - -make no-user-h5md -make machine :pre - -[Supporting info:] - -src/USER-H5MD: filenames -> commands -src/USER-H5MD/README -lib/h5md/README -"dump h5md"_dump_h5md.html :ul - -:line - -USER-INTEL package :link(USER-INTEL),h4 - -[Contents:] - -Dozens of pair, fix, bond, angle, dihedral, improper, and kspace -styles which are optimized for Intel CPUs and KNLs (Knights Landing). -All of them have an "intel" in their style name. "Section -5.3.2"_accelerate_intel.html gives details of what hardware and -compilers are required on your system, and how to build and use this -package. Its styles can be invoked at run time via the "-sf intel" or -"-suffix intel" "command-line switches"_Section_start.html#start_6. -Also see the "KOKKOS"_#KOKKOS, "OPT"_#OPT, and "USER-OMP"_#USER-OMP -packages, which have styles optimized for CPUs and KNLs. - -You need to have an Intel compiler, version 14 or higher to take full -advantage of this package. While compilation with GNU compilers is -supported, performance will be suboptimal. - -NOTE: the USER-INTEL package contains styles that require using the --restrict flag, when compiling with Intel compilers. - - -[Author:] Mike Brown (Intel). - -[Install or un-install:] - -For the USER-INTEL package, you have 2 choices when building. You can -build with either CPU or KNL support. Each choice requires additional -settings in your Makefile.machine for CCFLAGS and LINKFLAGS and -optimized malloc libraries. See the -src/MAKE/OPTIONS/Makefile.intel_cpu and src/MAKE/OPTIONS/Makefile.knl -files for examples. - -For CPUs: - -OPTFLAGS = -xHost -O2 -fp-model fast=2 -no-prec-div -qoverride-limits -CCFLAGS = -g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload \ --fno-alias -ansi-alias -restrict $(OPTFLAGS) -LINKFLAGS = -g -qopenmp $(OPTFLAGS) -LIB = -ltbbmalloc -ltbbmalloc_proxy :pre - -For KNLs: - -OPTFLAGS = -xMIC-AVX512 -O2 -fp-model fast=2 -no-prec-div -qoverride-limits -CCFLAGS = -g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload \ --fno-alias -ansi-alias -restrict $(OPTFLAGS) -LINKFLAGS = -g -qopenmp $(OPTFLAGS) -LIB = -ltbbmalloc :pre - -Once you have an appropriate Makefile.machine, you can -install/un-install the package and build LAMMPS in the usual manner. -Note that you cannot build one executable to run on multiple hardware -targets (Intel CPUs or KNL). You need to build LAMMPS once for each -hardware target, to produce a separate executable. - -You should also typically install the USER-OMP package, as it can be -used in tandem with the USER-INTEL package to good effect, as -explained in "Section 5.3.2"_accelerate_intel.html. - -make yes-user-intel yes-user-omp -make machine :pre - -make no-user-intel no-user-omp -make machine :pre - -[Supporting info:] - -src/USER-INTEL: filenames -> commands -src/USER-INTEL/README -"Section 5.3"_Section_accelerate.html#acc_3 -"Section 5.3.2"_accelerate_gpu.html -"Section 2.6 -sf intel"_Section_start.html#start_6 -"Section 2.6 -pk intel"_Section_start.html#start_6 -"package intel"_package.html -Styles sections of "Section 3.5"_Section_commands.html#cmd_5 for styles followed by (i) -src/USER-INTEL/TEST -"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul - -:line - -USER-LB package :link(USER-LB),h4 - -[Contents:] - -Fixes which implement a background Lattice-Boltzmann (LB) fluid, which -can be used to model MD particles influenced by hydrodynamic forces. - -[Authors:] Frances Mackay and Colin Denniston (University of Western -Ontario). - -[Install or un-install:] - -make yes-user-lb -make machine :pre - -make no-user-lb -make machine :pre - -[Supporting info:] - -src/USER-LB: filenames -> commands -src/USER-LB/README -"fix lb/fluid"_fix_lb_fluid.html -"fix lb/momentum"_fix_lb_momentum.html -"fix lb/viscous"_fix_lb_viscous.html -examples/USER/lb :ul - -:line - -USER-MGPT package :link(USER-MGPT),h4 - -[Contents:] - -A pair style which provides a fast implementation of the quantum-based -MGPT multi-ion potentials. The MGPT or model GPT method derives from -first-principles DFT-based generalized pseudopotential theory (GPT) -through a series of systematic approximations valid for mid-period -transition metals with nearly half-filled d bands. The MGPT method -was originally developed by John Moriarty at LLNL. The pair style in -this package calculates forces and energies using an optimized -matrix-MGPT algorithm due to Tomas Oppelstrup at LLNL. - -[Authors:] Tomas Oppelstrup and John Moriarty (LLNL). - -[Install or un-install:] - -make yes-user-mgpt -make machine :pre - -make no-user-mgpt -make machine :pre - -[Supporting info:] - -src/USER-MGPT: filenames -> commands -src/USER-MGPT/README -"pair_style mgpt"_pair_mgpt.html -examples/USER/mgpt :ul - -:line - -USER-MISC package :link(USER-MISC),h4 - -[Contents:] - -A potpourri of (mostly) unrelated features contributed to LAMMPS by -users. Each feature is a single fix, compute, pair, bond, angle, -dihedral, improper, or command style. - -[Authors:] The author for each style in the package is listed in the -src/USER-MISC/README file. - -[Install or un-install:] - -make yes-user-misc -make machine :pre - -make no-user-misc -make machine :pre - -[Supporting info:] - -src/USER-MISC: filenames -> commands -src/USER-MISC/README -one doc page per individual command listed in src/USER-MISC/README -examples/USER/misc :ul - -:line - -USER-MANIFOLD package :link(USER-MANIFOLD),h4 - -[Contents:] - -Several fixes and a "manifold" class which enable simulations of -particles constrained to a manifold (a 2D surface within the 3D -simulation box). This is done by applying the RATTLE constraint -algorithm to formulate single-particle constraint functions -g(xi,yi,zi) = 0 and their derivative (i.e. the normal of the manifold) -n = grad(g). - -[Author:] Stefan Paquay (until 2017: Eindhoven University of Technology (TU/e), The -Netherlands; since 2017: Brandeis University, Waltham, MA, USA) - -[Install or un-install:] - -make yes-user-manifold -make machine :pre - -make no-user-manifold -make machine :pre - -[Supporting info:] - -src/USER-MANIFOLD: filenames -> commands -src/USER-MANIFOLD/README -"doc/manifolds"_manifolds.html -"fix manifoldforce"_fix_manifoldforce.html -"fix nve/manifold/rattle"_fix_nve_manifold_rattle.html -"fix nvt/manifold/rattle"_fix_nvt_manifold_rattle.html -examples/USER/manifold -http://lammps.sandia.gov/movies.html#manifold :ul - -:line - -USER-MEAMC package :link(USER-MEAMC),h4 - -[Contents:] - -A pair style for the modified embedded atom (MEAM) potential -translated from the Fortran version in the "MEAM"_MEAM package -to plain C++. In contrast to the MEAM package, no library -needs to be compiled and the pair style can be instantiated -multiple times. - -[Author:] Sebastian Huetter, (Otto-von-Guericke University Magdeburg) -based on the Fortran version of Greg Wagner (Northwestern U) while at -Sandia. - -[Install or un-install:] - -make yes-user-meamc -make machine :pre - -make no-user-meamc -make machine :pre - -[Supporting info:] - -src/USER-MEAMC: filenames -> commands -src/USER-MEAMC/README -"pair_style meam/c"_pair_meam.html -examples/meam :ul - -:line - -USER-MESO package :link(USER-MESO),h4 - -[Contents:] - -Several extensions of the the dissipative particle dynamics (DPD) -method. Specifically, energy-conserving DPD (eDPD) that can model -non-isothermal processes, many-body DPD (mDPD) for simulating -vapor-liquid coexistence, and transport DPD (tDPD) for modeling -advection-diffusion-reaction systems. The equations of motion of these -DPD extensions are integrated through a modified velocity-Verlet (MVV) -algorithm. - -[Author:] Zhen Li (Division of Applied Mathematics, Brown University) - -[Install or un-install:] - -make yes-user-meso -make machine :pre - -make no-user-meso -make machine :pre - -[Supporting info:] - -src/USER-MESO: filenames -> commands -src/USER-MESO/README -"atom_style edpd"_atom_style.html -"pair_style edpd"_pair_meso.html -"pair_style mdpd"_pair_meso.html -"pair_style tdpd"_pair_meso.html -"fix mvv/dpd"_fix_mvv_dpd.html -examples/USER/meso -http://lammps.sandia.gov/movies.html#mesodpd :ul - -:line - -USER-MOFFF package :link(USER-MOFFF),h4 - -[Contents:] - -Pair, angle and improper styles needed to employ the MOF-FF -force field by Schmid and coworkers with LAMMPS. -MOF-FF is a first principles derived force field with the primary aim -to simulate MOFs and related porous framework materials, using spherical -Gaussian charges. It is described in S. Bureekaew et al., Phys. Stat. Sol. B -2013, 250, 1128-1141. -For the usage of MOF-FF see the example in the example directory as -well as the "MOF+"_MOFplus website. - -:link(MOFplus,https://www.mofplus.org/content/show/MOF-FF) - -[Author:] Hendrik Heenen (Technical U of Munich), -Rochus Schmid (Ruhr-University Bochum). - -[Install or un-install:] - -make yes-user-mofff -make machine :pre - -make no-user-mofff -make machine :pre - -[Supporting info:] - -src/USER-MOFFF: filenames -> commands -src/USER-MOFFF/README -"pair_style buck6d/coul/gauss"_pair_buck6d_coul_gauss.html -"angle_style class2"_angle_class2.html -"angle_style cosine/buck6d"_angle_cosine_buck6d.html -"improper_style inversion/harmonic"_improper_inversion_harmonic.html -examples/USER/mofff :ul - -:line - -USER-MOLFILE package :link(USER-MOLFILE),h4 - -[Contents:] - -A "dump molfile"_dump_molfile.html command which uses molfile plugins -that are bundled with the "VMD"_vmd_home -molecular visualization and analysis program, to enable LAMMPS to dump -snapshots in formats compatible with various molecular simulation -tools. - -:link(vmd_home,http://www.ks.uiuc.edu/Research/vmd) - -To use this package you must have the desired VMD plugins available on -your system. - -Note that this package only provides the interface code, not the -plugins themselves, which will be accessed when requesting a specific -plugin via the "dump molfile"_dump_molfile.html command. Plugins can -be obtained from a VMD installation which has to match the platform -that you are using to compile LAMMPS for. By adding plugins to VMD, -support for new file formats can be added to LAMMPS (or VMD or other -programs that use them) without having to recompile the application -itself. More information about the VMD molfile plugins can be found -at -"http://www.ks.uiuc.edu/Research/vmd/plugins/molfile"_http://www.ks.uiuc.edu/Research/vmd/plugins/molfile. - -[Author:] Axel Kohlmeyer (Temple U). - -[Install or un-install:] - -Note that the lib/molfile/Makefile.lammps file has a setting for a -dynamic loading library libdl.a that should is typically present on -all systems, which is required for LAMMPS to link with this package. -If the setting is not valid for your system, you will need to edit the -Makefile.lammps file. See lib/molfile/README and -lib/molfile/Makefile.lammps for details. - -make yes-user-molfile -make machine :pre - -make no-user-molfile -make machine :pre - -[Supporting info:] - -src/USER-MOLFILE: filenames -> commands -src/USER-MOLFILE/README -lib/molfile/README -"dump molfile"_dump_molfile.html :ul - -:line - -USER-NETCDF package :link(USER-NETCDF),h4 - -[Contents:] - -Dump styles for writing NetCDF formatted dump files. NetCDF is a -portable, binary, self-describing file format developed on top of -HDF5. The file contents follow the AMBER NetCDF trajectory conventions -(http://ambermd.org/netcdf/nctraj.xhtml), but include extensions. - -To use this package you must have the NetCDF library available on your -system. - -Note that NetCDF files can be directly visualized with the following -tools: - -"Ovito"_ovito (Ovito supports the AMBER convention and the extensions mentioned above) -"VMD"_vmd_home -"AtomEye"_atomeye (the libAtoms version of AtomEye contains a NetCDF reader not present in the standard distribution) :ul - -:link(ovito,http://www.ovito.org) -:link(atomeye,http://www.libatoms.org) - -[Author:] Lars Pastewka (Karlsruhe Institute of Technology). - -[Install or un-install:] - -Note that to follow these steps, you need the standard NetCDF software -package installed on your system. The lib/netcdf/Makefile.lammps file -has settings for NetCDF include and library files that LAMMPS needs to -compile and linkk with this package. If the settings are not valid -for your system, you will need to edit the Makefile.lammps file. See -lib/netcdf/README for details. - -make yes-user-netcdf -make machine :pre - -make no-user-netcdf -make machine :pre - -[Supporting info:] - -src/USER-NETCDF: filenames -> commands -src/USER-NETCDF/README -lib/netcdf/README -"dump netcdf"_dump_netcdf.html :ul - -:line - -USER-OMP package :link(USER-OMP),h4 - -[Contents:] - -Hundreds of pair, fix, compute, bond, angle, dihedral, improper, and -kspace styles which are altered to enable threading on many-core CPUs -via OpenMP directives. All of them have an "omp" in their style name. -"Section 5.3.4"_accelerate_omp.html gives details of what hardware and -compilers are required on your system, and how to build and use this -package. Its styles can be invoked at run time via the "-sf omp" or -"-suffix omp" "command-line switches"_Section_start.html#start_6. -Also see the "KOKKOS"_#KOKKOS, "OPT"_#OPT, and -"USER-INTEL"_#USER-INTEL packages, which have styles optimized for -CPUs. - -[Author:] Axel Kohlmeyer (Temple U). - -NOTE: To enable multi-threading support the compile flag "-fopenmp" -and the link flag "-fopenmp" (for GNU compilers, you have to look up -the equivalent flags for other compilers) must be used to build LAMMPS. -When using Intel compilers, also the "-restrict" flag is required. -The USER-OMP package can be compiled without enabling OpenMP; then -all code will be compiled as serial and the only improvement over the -regular styles are some data access optimization. These flags should -be added to the CCFLAGS and LINKFLAGS lines of your Makefile.machine. -See src/MAKE/OPTIONS/Makefile.omp for an example. - -Once you have an appropriate Makefile.machine, you can -install/un-install the package and build LAMMPS in the usual manner: - -[Install or un-install:] - -make yes-user-omp -make machine :pre - -make no-user-omp -make machine :pre - -CCFLAGS: add -fopenmp (and -restrict when using Intel compilers) -LINKFLAGS: add -fopenmp :ul - -[Supporting info:] - -src/USER-OMP: filenames -> commands -src/USER-OMP/README -"Section 5.3"_Section_accelerate.html#acc_3 -"Section 5.3.4"_accelerate_omp.html -"Section 2.6 -sf omp"_Section_start.html#start_6 -"Section 2.6 -pk omp"_Section_start.html#start_6 -"package omp"_package.html -Styles sections of "Section 3.5"_Section_commands.html#cmd_5 for styles followed by (o) -"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul - -:line - -USER-PHONON package :link(USER-PHONON),h4 - -[Contents:] - -A "fix phonon"_fix_phonon.html command that calculates dynamical -matrices, which can then be used to compute phonon dispersion -relations, directly from molecular dynamics simulations. - -[Author:] Ling-Ti Kong (Shanghai Jiao Tong University). - -[Install or un-install:] - -make yes-user-phonon -make machine :pre - -make no-user-phonon -make machine :pre - -[Supporting info:] - -src/USER-PHONON: filenames -> commands -src/USER-PHONON/README -"fix phonon"_fix_phonon.html -examples/USER/phonon :ul - -:line - -USER-QMMM package :link(USER-QMMM),h4 - -[Contents:] - -A "fix qmmm"_fix_qmmm.html command which allows LAMMPS to be used in a -QM/MM simulation, currently only in combination with the "Quantum -ESPRESSO"_espresso package. - -:link(espresso,http://www.quantum-espresso.org) - -To use this package you must have Quantum ESPRESSO available on your -system. - -The current implementation only supports an ONIOM style mechanical -coupling to the Quantum ESPRESSO plane wave DFT package. -Electrostatic coupling is in preparation and the interface has been -written in a manner that coupling to other QM codes should be possible -without changes to LAMMPS itself. - -[Author:] Axel Kohlmeyer (Temple U). - -[Install or un-install:] - -Before building LAMMPS with this package, you must first build the -QMMM library in lib/qmmm. You can do this manually if you prefer; -follow the first two steps explained in lib/qmmm/README. You can -also do it in one step from the lammps/src dir, using a command like -these, which simply invoke the lib/qmmm/Install.py script with the -specified args: - -make lib-qmmm # print help message -make lib-qmmm args="-m serial" # build with GNU Fortran compiler (settings as in "make serial") -make lib-qmmm args="-m mpi" # build with default MPI compiler (settings as in "make mpi") -make lib-qmmm args="-m gfortran" # build with GNU Fortran compiler :pre - -The build should produce two files: lib/qmmm/libqmmm.a and -lib/qmmm/Makefile.lammps. The latter is copied from an existing -Makefile.lammps.* and has settings needed to build LAMMPS with the -QMMM library (though typically the settings are just blank). If -necessary, you can edit/create a new lib/qmmm/Makefile.machine file -for your system, which should define an EXTRAMAKE variable to specify -a corresponding Makefile.lammps.machine file. - -You can then install/un-install the package and build LAMMPS in the -usual manner: - -make yes-user-qmmm -make machine :pre - -make no-user-qmmm -make machine :pre - -NOTE: The LAMMPS executable these steps produce is not yet functional -for a QM/MM simulation. You must also build Quantum ESPRESSO and -create a new executable which links LAMMPS and Quantum ESPRESSO -together. These are steps 3 and 4 described in the lib/qmmm/README -file. - -[Supporting info:] - -src/USER-QMMM: filenames -> commands -src/USER-QMMM/README -lib/qmmm/README -"fix phonon"_fix_phonon.html -lib/qmmm/example-ec/README -lib/qmmm/example-mc/README :ul - -:line - -USER-QTB package :link(USER-QTB),h4 - -[Contents:] - -Two fixes which provide a self-consistent quantum treatment of -vibrational modes in a classical molecular dynamics simulation. By -coupling the MD simulation to a colored thermostat, it introduces zero -point energy into the system, altering the energy power spectrum and -the heat capacity to account for their quantum nature. This is useful -when modeling systems at temperatures lower than their classical -limits or when temperatures ramp across the classical limits in a -simulation. - -[Author:] Yuan Shen (Stanford U). - -[Install or un-install:] - -make yes-user-qtb -make machine :pre - -make no-user-qtb -make machine :pre - -[Supporting info:] - -src/USER-QTB: filenames -> commands -src/USER-QTB/README -"fix qtb"_fix_qtb.html -"fix qbmsst"_fix_qbmsst.html -examples/USER/qtb :ul - -:line - -USER-QUIP package :link(USER-QUIP),h4 - -[Contents:] - -A "pair_style quip"_pair_quip.html command which wraps the "QUIP -libAtoms library"_quip, which includes a variety of interatomic -potentials, including Gaussian Approximation Potential (GAP) models -developed by the Cambridge University group. - -:link(quip,https://github.com/libAtoms/QUIP) - -To use this package you must have the QUIP libAtoms library available -on your system. - -[Author:] Albert Bartok (Cambridge University) - -[Install or un-install:] - -Note that to follow these steps to compile and link to the QUIP -library, you must first download and build QUIP on your systems. It -can be obtained from GitHub. See step 1 and step 1.1 in the -lib/quip/README file for details on how to do this. Note that it -requires setting two environment variables, QUIP_ROOT and QUIP_ARCH, -which will be accessed by the lib/quip/Makefile.lammps file which is -used when you compile and link LAMMPS with this package. You should -only need to edit this file if the LAMMPS build can not use its -settings to successfully build on your system. - -You can then install/un-install the package and build LAMMPS in the -usual manner: - -make yes-user-quip -make machine :pre - -make no-user-quip -make machine :pre - -[Supporting info:] - -src/USER-QUIP: filenames -> commands -src/USER-QUIP/README -"pair_style quip"_pair_quip.html -examples/USER/quip :ul - -:line - -USER-REAXC package :link(USER-REAXC),h4 - -[Contents:] - -A pair style which implements the ReaxFF potential in C/C++ (in -contrast to the "REAX package"_#REAX and its Fortran library). ReaxFF -is universal reactive force field. See the src/USER-REAXC/README file -for more info on differences between the two packages. Also two fixes -for monitoring molecules as bonds are created and destroyed. - -[Author:] Hasan Metin Aktulga (MSU) while at Purdue University. - -[Install or un-install:] - -make yes-user-reaxc -make machine :pre - -make no-user-reaxc -make machine :pre - -[Supporting info:] - -src/USER-REAXC: filenames -> commands -src/USER-REAXC/README -"pair_style reax/c"_pair_reaxc.html -"fix reax/c/bonds"_fix_reax_bonds.html -"fix reax/c/species"_fix_reaxc_species.html -examples/reax :ul - -:line - -USER-SMD package :link(USER-SMD),h4 - -[Contents:] - -An atom style, fixes, computes, and several pair styles which -implements smoothed Mach dynamics (SMD) for solids, which is a model -related to smoothed particle hydrodynamics (SPH) for liquids (see the -"USER-SPH package"_#USER-SPH). - -This package solves solids mechanics problems via a state of the art -stabilized meshless method with hourglass control. It can specify -hydrostatic interactions independently from material strength models, -i.e. pressure and deviatoric stresses are separated. It provides many -material models (Johnson-Cook, plasticity with hardening, -Mie-Grueneisen, Polynomial EOS) and allows new material models to be -added. It implements rigid boundary conditions (walls) which can be -specified as surface geometries from *.STL files. - -[Author:] Georg Ganzenmuller (Fraunhofer-Institute for High-Speed -Dynamics, Ernst Mach Institute, Germany). - -[Install or un-install:] - -Before building LAMMPS with this package, you must first download the -Eigen library. Eigen is a template library, so you do not need to -build it, just download it. You can do this manually if you prefer; -follow the instructions in lib/smd/README. You can also do it in one -step from the lammps/src dir, using a command like these, which simply -invoke the lib/smd/Install.py script with the specified args: - -make lib-smd # print help message -make lib-smd args="-b" # download and build in default lib/smd/eigen-eigen-... -make lib-smd args="-p /usr/include/eigen3" # use existing Eigen installation in /usr/include/eigen3 :pre - -Note that a symbolic (soft) link named "includelink" is created in -lib/smd to point to the Eigen dir. When LAMMPS builds it will use -this link. You should not need to edit the lib/smd/Makefile.lammps file. - -You can then install/un-install the package and build LAMMPS in the -usual manner: - -make yes-user-smd -make machine :pre - -make no-user-smd -make machine :pre - -[Supporting info:] - -src/USER-SMD: filenames -> commands -src/USER-SMD/README -doc/PDF/SMD_LAMMPS_userguide.pdf -examples/USER/smd -http://lammps.sandia.gov/movies.html#smd :ul - -:line - -USER-SMTBQ package :link(USER-SMTBQ),h4 - -[Contents:] - -A pair style which implements a Second Moment Tight Binding model with -QEq charge equilibration (SMTBQ) potential for the description of -ionocovalent bonds in oxides. - -[Authors:] Nicolas Salles, Emile Maras, Olivier Politano, and Robert -Tetot (LAAS-CNRS, France). - -[Install or un-install:] - -make yes-user-smtbq -make machine :pre - -make no-user-smtbq -make machine :pre - -[Supporting info:] - -src/USER-SMTBQ: filenames -> commands -src/USER-SMTBQ/README -"pair_style smtbq"_pair_smtbq.html -examples/USER/smtbq :ul - -:line - -USER-SPH package :link(USER-SPH),h4 - -[Contents:] - -An atom style, fixes, computes, and several pair styles which -implements smoothed particle hydrodynamics (SPH) for liquids. See the -related "USER-SMD package"_#USER-SMD package for smooth Mach dynamics -(SMD) for solids. - -This package contains ideal gas, Lennard-Jones equation of states, -Tait, and full support for complete (i.e. internal-energy dependent) -equations of state. It allows for plain or Monaghans XSPH integration -of the equations of motion. It has options for density continuity or -density summation to propagate the density field. It has -"set"_set.html command options to set the internal energy and density -of particles from the input script and allows the same quantities to -be output with thermodynamic output or to dump files via the "compute -property/atom"_compute_property_atom.html command. - -[Author:] Georg Ganzenmuller (Fraunhofer-Institute for High-Speed -Dynamics, Ernst Mach Institute, Germany). - -[Install or un-install:] - -make yes-user-sph -make machine :pre - -make no-user-sph -make machine :pre - -[Supporting info:] - -src/USER-SPH: filenames -> commands -src/USER-SPH/README -doc/PDF/SPH_LAMMPS_userguide.pdf -examples/USER/sph -http://lammps.sandia.gov/movies.html#sph :ul - -:line - -USER-TALLY package :link(USER-TALLY),h4 - -[Contents:] - -Several compute styles that can be called when pairwise interactions -are calculated to tally information (forces, heat flux, energy, -stress, etc) about individual interactions. - -[Author:] Axel Kohlmeyer (Temple U). - -[Install or un-install:] - -make yes-user-tally -make machine :pre - -make no-user-tally -make machine :pre - -[Supporting info:] - -src/USER-TALLY: filenames -> commands -src/USER-TALLY/README -"compute */tally"_compute_tally.html -examples/USER/tally :ul - -:line - -USER-UEF package :link(USER-UEF),h4 - -[Contents:] - -A fix style for the integration of the equations of motion under -extensional flow with proper boundary conditions, as well as several -supporting compute styles and an output option. - -[Author:] David Nicholson (MIT). - -[Install or un-install:] - -make yes-user-uef -make machine :pre - -make no-user-uef -make machine :pre - -[Supporting info:] - -src/USER-UEF: filenames -> commands -src/USER-UEF/README -"fix nvt/uef"_fix_nh_uef.html -"fix npt/uef"_fix_nh_uef.html -"compute pressure/uef"_compute_pressure_uef.html -"compute temp/uef"_compute_temp_uef.html -"dump cfg/uef"_dump_cfg_uef.html -examples/uef :ul - -:line - -USER-VTK package :link(USER-VTK),h4 - -[Contents:] - -A "dump vtk"_dump_vtk.html command which outputs snapshot info in the -"VTK format"_vtk, enabling visualization by "Paraview"_paraview or -other visualization packages. - -:link(vtk,http://www.vtk.org) -:link(paraview,http://www.paraview.org) - -To use this package you must have VTK library available on your -system. - -[Authors:] Richard Berger (JKU) and Daniel Queteschiner (DCS Computing). - -[Install or un-install:] - -The lib/vtk/Makefile.lammps file has settings for accessing VTK files -and its library, which are required for LAMMPS to build and link with -this package. If the settings are not valid for your system, check if -one of the other lib/vtk/Makefile.lammps.* files is compatible and -copy it to Makefile.lammps. If none of the provided files work, you -will need to edit the Makefile.lammps file. - -You can then install/un-install the package and build LAMMPS in the -usual manner: - -make yes-user-vtk -make machine :pre - -make no-user-vtk -make machine :pre - -[Supporting info:] - -src/USER-VTK: filenames -> commands -src/USER-VTK/README -lib/vtk/README -"dump vtk"_dump_vtk.html :ul diff --git a/doc/src/Section_python.txt b/doc/src/Section_python.txt deleted file mode 100644 index 5427cd67f2..0000000000 --- a/doc/src/Section_python.txt +++ /dev/null @@ -1,867 +0,0 @@ -"Previous Section"_Section_modify.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Section_errors.html :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Section_commands.html#comm) - -:line - -11. Python interface to LAMMPS :h2 - -LAMMPS can work together with Python in three ways. First, Python can -wrap LAMMPS through the "LAMMPS library -interface"_Section_howto.html#howto_19, so that a Python script can -create one or more instances of LAMMPS and launch one or more -simulations. In Python lingo, this is "extending" Python with LAMMPS. - -Second, the low-level Python interface can be used indirectly through the -PyLammps and IPyLammps wrapper classes in Python. These wrappers try to -simplify the usage of LAMMPS in Python by providing an object-based interface -to common LAMMPS functionality. It also reduces the amount of code necessary to -parameterize LAMMPS scripts through Python and makes variables and computes -directly accessible. See "PyLammps interface"_#py_9 for more details. - -Third, LAMMPS can use the Python interpreter, so that a LAMMPS input -script can invoke Python code, and pass information back-and-forth -between the input script and Python functions you write. The Python -code can also callback to LAMMPS to query or change its attributes. -In Python lingo, this is "embedding" Python in LAMMPS. - -This section describes how to use these three approaches. - -11.1 "Overview of running LAMMPS from Python"_#py_1 -11.2 "Overview of using Python from a LAMMPS script"_#py_2 -11.3 "Building LAMMPS as a shared library"_#py_3 -11.4 "Installing the Python wrapper into Python"_#py_4 -11.5 "Extending Python with MPI to run in parallel"_#py_5 -11.6 "Testing the Python-LAMMPS interface"_#py_6 -11.7 "Using LAMMPS from Python"_#py_7 -11.8 "Example Python scripts that use LAMMPS"_#py_8 -11.9 "PyLammps interface"_#py_9 :ul - -If you are not familiar with it, "Python"_http://www.python.org is a -powerful scripting and programming language which can essentially do -anything that faster, lower-level languages like C or C++ can do, but -typically with much fewer lines of code. When used in embedded mode, -Python can perform operations that the simplistic LAMMPS input script -syntax cannot. Python can be also be used as a "glue" language to -drive a program through its library interface, or to hook multiple -pieces of software together, such as a simulation package plus a -visualization package, or to run a coupled multiscale or multiphysics -model. - -See "Section 6.10"_Section_howto.html#howto_10 of the manual and -the couple directory of the distribution for more ideas about coupling -LAMMPS to other codes. See "Section -6.19"_Section_howto.html#howto_19 for a description of the LAMMPS -library interface provided in src/library.cpp and src/library.h, and -how to extend it for your needs. As described below, that interface -is what is exposed to Python either when calling LAMMPS from Python or -when calling Python from a LAMMPS input script and then calling back -to LAMMPS from Python code. The library interface is designed to be -easy to add functions to. Thus the Python interface to LAMMPS is also -easy to extend as well. - -If you create interesting Python scripts that run LAMMPS or -interesting Python functions that can be called from a LAMMPS input -script, that you think would be useful to other users, please "email -them to the developers"_http://lammps.sandia.gov/authors.html. We can -include them in the LAMMPS distribution. - -:line -:line - -11.1 Overview of running LAMMPS from Python :link(py_1),h4 - -The LAMMPS distribution includes a python directory with all you need -to run LAMMPS from Python. The python/lammps.py file wraps the LAMMPS -library interface, with one wrapper function per LAMMPS library -function. This file makes it is possible to do the following either -from a Python script, or interactively from a Python prompt: create -one or more instances of LAMMPS, invoke LAMMPS commands or give it an -input script, run LAMMPS incrementally, extract LAMMPS results, an -modify internal LAMMPS variables. From a Python script you can do -this in serial or parallel. Running Python interactively in parallel -does not generally work, unless you have a version of Python that -extends standard Python to enable multiple instances of Python to read -what you type. - -To do all of this, you must first build LAMMPS as a shared library, -then insure that your Python can find the python/lammps.py file and -the shared library. These steps are explained in subsequent sections -11.3 and 11.4. Sections 11.5 and 11.6 discuss using MPI from a -parallel Python program and how to test that you are ready to use -LAMMPS from Python. Section 11.7 lists all the functions in the -current LAMMPS library interface and how to call them from Python. - -Section 11.8 gives some examples of coupling LAMMPS to other tools via -Python. For example, LAMMPS can easily be coupled to a GUI or other -visualization tools that display graphs or animations in real time as -LAMMPS runs. Examples of such scripts are included in the python -directory. - -Two advantages of using Python to run LAMMPS are how concise the -language is, and that it can be run interactively, enabling rapid -development and debugging of programs. If you use it to mostly invoke -costly operations within LAMMPS, such as running a simulation for a -reasonable number of timesteps, then the overhead cost of invoking -LAMMPS thru Python will be negligible. - -The Python wrapper for LAMMPS uses the amazing and magical (to me) -"ctypes" package in Python, which auto-generates the interface code -needed between Python and a set of C interface routines for a library. -Ctypes is part of standard Python for versions 2.5 and later. You can -check which version of Python you have installed, by simply typing -"python" at a shell prompt. - -:line - -11.2 Overview of using Python from a LAMMPS script :link(py_2),h4 - -LAMMPS has several commands which can be used to invoke Python -code directly from an input script: - -"python"_python.html -"variable python"_variable.html -"fix python/invoke"_fix_python_invoke.html -"pair_style python"_pair_python.html :ul - -The "python"_python.html command which can be used to define and -execute a Python function that you write the code for. The Python -function can also be assigned to a LAMMPS python-style variable via -the "variable"_variable.html command. Each time the variable is -evaluated, either in the LAMMPS input script itself, or by another -LAMMPS command that uses the variable, this will trigger the Python -function to be invoked. - -The Python code for the function can be included directly in the input -script or in an auxiliary file. The function can have arguments which -are mapped to LAMMPS variables (also defined in the input script) and -it can return a value to a LAMMPS variable. This is thus a mechanism -for your input script to pass information to a piece of Python code, -ask Python to execute the code, and return information to your input -script. - -Note that a Python function can be arbitrarily complex. It can import -other Python modules, instantiate Python classes, call other Python -functions, etc. The Python code that you provide can contain more -code than the single function. It can contain other functions or -Python classes, as well as global variables or other mechanisms for -storing state between calls from LAMMPS to the function. - -The Python function you provide can consist of "pure" Python code that -only performs operations provided by standard Python. However, the -Python function can also "call back" to LAMMPS through its -Python-wrapped library interface, in the manner described in the -previous section 11.1. This means it can issue LAMMPS input script -commands or query and set internal LAMMPS state. As an example, this -can be useful in an input script to create a more complex loop with -branching logic, than can be created using the simple looping and -branching logic enabled by the "next"_next.html and "if"_if.html -commands. - -See the "python"_python.html doc page and the "variable"_variable.html -doc page for its python-style variables for more info, including -examples of Python code you can write for both pure Python operations -and callbacks to LAMMPS. - -The "fix python/invoke"_fix_python_invoke.html command can execute -Python code at selected timesteps during a simulation run. - -The "pair_style python"_pair_python command allows you to define -pairwise potentials as python code which encodes a single pairwise -interaction. This is useful for rapid-developement and debugging of a -new potential. - -To use any of these commands, you only need to build LAMMPS with the -PYTHON package installed: - -make yes-python -make machine :pre - -Note that this will link LAMMPS with the Python library on your -system, which typically requires several auxiliary system libraries to -also be linked. The list of these libraries and the paths to find -them are specified in the lib/python/Makefile.lammps file. You need -to insure that file contains the correct information for your version -of Python and your machine to successfully build LAMMPS. See the -lib/python/README file for more info. - -If you want to write Python code with callbacks to LAMMPS, then you -must also follow the steps overviewed in the preceding section (11.1) -for running LAMMPS from Python. I.e. you must build LAMMPS as a -shared library and insure that Python can find the python/lammps.py -file and the shared library. - -:line - -11.3 Building LAMMPS as a shared library :link(py_3),h4 - -Instructions on how to build LAMMPS as a shared library are given in -"Section 2.4"_Section_start.html#start_4. A shared library is one -that is dynamically loadable, which is what Python requires to wrap -LAMMPS. On Linux this is a library file that ends in ".so", not ".a". - -From the src directory, type - -make foo mode=shlib :pre - -where foo is the machine target name, such as linux or g++ or serial. -This should create the file liblammps_foo.so in the src directory, as -well as a soft link liblammps.so, which is what the Python wrapper will -load by default. Note that if you are building multiple machine -versions of the shared library, the soft link is always set to the -most recently built version. - -NOTE: If you are building LAMMPS with an MPI or FFT library or other -auxiliary libraries (used by various packages), then all of these -extra libraries must also be shared libraries. If the LAMMPS -shared-library build fails with an error complaining about this, see -"Section 2.4"_Section_start.html#start_4 for more details. - -:line - -11.4 Installing the Python wrapper into Python :link(py_4),h4 - -For Python to invoke LAMMPS, there are 2 files it needs to know about: - -python/lammps.py -src/liblammps.so :ul - -Lammps.py is the Python wrapper on the LAMMPS library interface. -Liblammps.so is the shared LAMMPS library that Python loads, as -described above. - -You can insure Python can find these files in one of two ways: - -set two environment variables -run the python/install.py script :ul - -If you set the paths to these files as environment variables, you only -have to do it once. For the csh or tcsh shells, add something like -this to your ~/.cshrc file, one line for each of the two files: - -setenv PYTHONPATH $\{PYTHONPATH\}:/home/sjplimp/lammps/python -setenv LD_LIBRARY_PATH $\{LD_LIBRARY_PATH\}:/home/sjplimp/lammps/src :pre - -If you use the python/install.py script, you need to invoke it every -time you rebuild LAMMPS (as a shared library) or make changes to the -python/lammps.py file. - -You can invoke install.py from the python directory as - -% python install.py \[libdir\] \[pydir\] :pre - -The optional libdir is where to copy the LAMMPS shared library to; the -default is /usr/local/lib. The optional pydir is where to copy the -lammps.py file to; the default is the site-packages directory of the -version of Python that is running the install script. - -Note that libdir must be a location that is in your default -LD_LIBRARY_PATH, like /usr/local/lib or /usr/lib. And pydir must be a -location that Python looks in by default for imported modules, like -its site-packages dir. If you want to copy these files to -non-standard locations, such as within your own user space, you will -need to set your PYTHONPATH and LD_LIBRARY_PATH environment variables -accordingly, as above. - -If the install.py script does not allow you to copy files into system -directories, prefix the python command with "sudo". If you do this, -make sure that the Python that root runs is the same as the Python you -run. E.g. you may need to do something like - -% sudo /usr/local/bin/python install.py \[libdir\] \[pydir\] :pre - -You can also invoke install.py from the make command in the src -directory as - -% make install-python :pre - -In this mode you cannot append optional arguments. Again, you may -need to prefix this with "sudo". In this mode you cannot control -which Python is invoked by root. - -Note that if you want Python to be able to load different versions of -the LAMMPS shared library (see "this section"_#py_5 below), you will -need to manually copy files like liblammps_g++.so into the appropriate -system directory. This is not needed if you set the LD_LIBRARY_PATH -environment variable as described above. - -:line - -11.5 Extending Python with MPI to run in parallel :link(py_5),h4 - -If you wish to run LAMMPS in parallel from Python, you need to extend -your Python with an interface to MPI. This also allows you to -make MPI calls directly from Python in your script, if you desire. - -There are several Python packages available that purport to wrap MPI -as a library and allow MPI functions to be called from Python. However, -development on most of them seems to be halted except on: - -"mpi4py"_https://bitbucket.org/mpi4py/mpi4py -"PyPar"_https://github.com/daleroberts/pypar :ul - -Both packages, PyPar and mpi4py have been successfully tested with -LAMMPS. PyPar is simpler and easy to set up and use, but supports -only a subset of MPI. Mpi4py is more MPI-feature complete, but also a -bit more complex to use. As of version 2.0.0, mpi4py is the only -python MPI wrapper that allows passing a custom MPI communicator to -the LAMMPS constructor, which means one can easily run one or more -LAMMPS instances on subsets of the total MPI ranks. - -:line - -PyPar requires the ubiquitous "Numpy package"_http://numpy.scipy.org -be installed in your Python. After launching Python, type - -import numpy :pre - -to see if it is installed. If not, here is how to install it (version -1.3.0b1 as of April 2009). Unpack the numpy tarball and from its -top-level directory, type - -python setup.py build -sudo python setup.py install :pre - -The "sudo" is only needed if required to copy Numpy files into your -Python distribution's site-packages directory. - -To install PyPar (version pypar-2.1.4_94 as of Aug 2012), unpack it -and from its "source" directory, type - -python setup.py build -sudo python setup.py install :pre - -Again, the "sudo" is only needed if required to copy PyPar files into -your Python distribution's site-packages directory. - -If you have successfully installed PyPar, you should be able to run -Python and type - -import pypar :pre - -without error. You should also be able to run python in parallel -on a simple test script - -% mpirun -np 4 python test.py :pre - -where test.py contains the lines - -import pypar -print "Proc %d out of %d procs" % (pypar.rank(),pypar.size()) :pre - -and see one line of output for each processor you run on. - -NOTE: To use PyPar and LAMMPS in parallel from Python, you must insure -both are using the same version of MPI. If you only have one MPI -installed on your system, this is not an issue, but it can be if you -have multiple MPIs. Your LAMMPS build is explicit about which MPI it -is using, since you specify the details in your lo-level -src/MAKE/Makefile.foo file. PyPar uses the "mpicc" command to find -information about the MPI it uses to build against. And it tries to -load "libmpi.so" from the LD_LIBRARY_PATH. This may or may not find -the MPI library that LAMMPS is using. If you have problems running -both PyPar and LAMMPS together, this is an issue you may need to -address, e.g. by moving other MPI installations so that PyPar finds -the right one. - -:line - -To install mpi4py (version mpi4py-2.0.0 as of Oct 2015), unpack it -and from its main directory, type - -python setup.py build -sudo python setup.py install :pre - -Again, the "sudo" is only needed if required to copy mpi4py files into -your Python distribution's site-packages directory. To install with -user privilege into the user local directory type - -python setup.py install --user :pre - -If you have successfully installed mpi4py, you should be able to run -Python and type - -from mpi4py import MPI :pre - -without error. You should also be able to run python in parallel -on a simple test script - -% mpirun -np 4 python test.py :pre - -where test.py contains the lines - -from mpi4py import MPI -comm = MPI.COMM_WORLD -print "Proc %d out of %d procs" % (comm.Get_rank(),comm.Get_size()) :pre - -and see one line of output for each processor you run on. - -NOTE: To use mpi4py and LAMMPS in parallel from Python, you must -insure both are using the same version of MPI. If you only have one -MPI installed on your system, this is not an issue, but it can be if -you have multiple MPIs. Your LAMMPS build is explicit about which MPI -it is using, since you specify the details in your lo-level -src/MAKE/Makefile.foo file. Mpi4py uses the "mpicc" command to find -information about the MPI it uses to build against. And it tries to -load "libmpi.so" from the LD_LIBRARY_PATH. This may or may not find -the MPI library that LAMMPS is using. If you have problems running -both mpi4py and LAMMPS together, this is an issue you may need to -address, e.g. by moving other MPI installations so that mpi4py finds -the right one. - -:line - -11.6 Testing the Python-LAMMPS interface :link(py_6),h4 - -To test if LAMMPS is callable from Python, launch Python interactively -and type: - ->>> from lammps import lammps ->>> lmp = lammps() :pre - -If you get no errors, you're ready to use LAMMPS from Python. If the -2nd command fails, the most common error to see is - -OSError: Could not load LAMMPS dynamic library :pre - -which means Python was unable to load the LAMMPS shared library. This -typically occurs if the system can't find the LAMMPS shared library or -one of the auxiliary shared libraries it depends on, or if something -about the library is incompatible with your Python. The error message -should give you an indication of what went wrong. - -You can also test the load directly in Python as follows, without -first importing from the lammps.py file: - ->>> from ctypes import CDLL ->>> CDLL("liblammps.so") :pre - -If an error occurs, carefully go thru the steps in "Section -2.4"_Section_start.html#start_4 and above about building a shared -library and about insuring Python can find the necessary two files -it needs. - -[Test LAMMPS and Python in serial:] :h4 - -To run a LAMMPS test in serial, type these lines into Python -interactively from the bench directory: - ->>> from lammps import lammps ->>> lmp = lammps() ->>> lmp.file("in.lj") :pre - -Or put the same lines in the file test.py and run it as - -% python test.py :pre - -Either way, you should see the results of running the in.lj benchmark -on a single processor appear on the screen, the same as if you had -typed something like: - -lmp_g++ -in in.lj :pre - -[Test LAMMPS and Python in parallel:] :h4 - -To run LAMMPS in parallel, assuming you have installed the -"PyPar"_https://github.com/daleroberts/pypar package as discussed -above, create a test.py file containing these lines: - -import pypar -from lammps import lammps -lmp = lammps() -lmp.file("in.lj") -print "Proc %d out of %d procs has" % (pypar.rank(),pypar.size()),lmp -pypar.finalize() :pre - -To run LAMMPS in parallel, assuming you have installed the -"mpi4py"_https://bitbucket.org/mpi4py/mpi4py package as discussed -above, create a test.py file containing these lines: - -from mpi4py import MPI -from lammps import lammps -lmp = lammps() -lmp.file("in.lj") -me = MPI.COMM_WORLD.Get_rank() -nprocs = MPI.COMM_WORLD.Get_size() -print "Proc %d out of %d procs has" % (me,nprocs),lmp -MPI.Finalize() :pre - -You can either script in parallel as: - -% mpirun -np 4 python test.py :pre - -and you should see the same output as if you had typed - -% mpirun -np 4 lmp_g++ -in in.lj :pre - -Note that if you leave out the 3 lines from test.py that specify PyPar -commands you will instantiate and run LAMMPS independently on each of -the P processors specified in the mpirun command. In this case you -should get 4 sets of output, each showing that a LAMMPS run was made -on a single processor, instead of one set of output showing that -LAMMPS ran on 4 processors. If the 1-processor outputs occur, it -means that PyPar is not working correctly. - -Also note that once you import the PyPar module, PyPar initializes MPI -for you, and you can use MPI calls directly in your Python script, as -described in the PyPar documentation. The last line of your Python -script should be pypar.finalize(), to insure MPI is shut down -correctly. - -[Running Python scripts:] :h4 - -Note that any Python script (not just for LAMMPS) can be invoked in -one of several ways: - -% python foo.script -% python -i foo.script -% foo.script :pre - -The last command requires that the first line of the script be -something like this: - -#!/usr/local/bin/python -#!/usr/local/bin/python -i :pre - -where the path points to where you have Python installed, and that you -have made the script file executable: - -% chmod +x foo.script :pre - -Without the "-i" flag, Python will exit when the script finishes. -With the "-i" flag, you will be left in the Python interpreter when -the script finishes, so you can type subsequent commands. As -mentioned above, you can only run Python interactively when running -Python on a single processor, not in parallel. - -:line -:line - -11.7 Using LAMMPS from Python :link(py_7),h4 - -As described above, the Python interface to LAMMPS consists of a -Python "lammps" module, the source code for which is in -python/lammps.py, which creates a "lammps" object, with a set of -methods that can be invoked on that object. The sample Python code -below assumes you have first imported the "lammps" module in your -Python script, as follows: - -from lammps import lammps :pre - -These are the methods defined by the lammps module. If you look at -the files src/library.cpp and src/library.h you will see they -correspond one-to-one with calls you can make to the LAMMPS library -from a C++ or C or Fortran program, and which are described in -"Section 6.19"_Section_howto.html#howto_19 of the manual. - -The python/examples directory has Python scripts which show how Python -can run LAMMPS, grab data, change it, and put it back into LAMMPS. - -lmp = lammps() # create a LAMMPS object using the default liblammps.so library - # 4 optional args are allowed: name, cmdargs, ptr, comm -lmp = lammps(ptr=lmpptr) # use lmpptr as previously created LAMMPS object -lmp = lammps(comm=split) # create a LAMMPS object with a custom communicator, requires mpi4py 2.0.0 or later -lmp = lammps(name="g++") # create a LAMMPS object using the liblammps_g++.so library -lmp = lammps(name="g++",cmdargs=list) # add LAMMPS command-line args, e.g. list = \["-echo","screen"\] :pre - -lmp.close() # destroy a LAMMPS object :pre - -version = lmp.version() # return the numerical version id, e.g. LAMMPS 2 Sep 2015 -> 20150902 :pre - -lmp.file(file) # run an entire input script, file = "in.lj" -lmp.command(cmd) # invoke a single LAMMPS command, cmd = "run 100" -lmp.commands_list(cmdlist) # invoke commands in cmdlist = ["run 10", "run 20"] -lmp.commands_string(multicmd) # invoke commands in multicmd = "run 10\nrun 20" :pre - -size = lmp.extract_setting(name) # return data type info :pre - -xlo = lmp.extract_global(name,type) # extract a global quantity - # name = "boxxlo", "nlocal", etc - # type = 0 = int - # 1 = double :pre - -boxlo,boxhi,xy,yz,xz,periodicity,box_change = lmp.extract_box() # extract box info :pre - -coords = lmp.extract_atom(name,type) # extract a per-atom quantity - # name = "x", "type", etc - # type = 0 = vector of ints - # 1 = array of ints - # 2 = vector of doubles - # 3 = array of doubles :pre - -eng = lmp.extract_compute(id,style,type) # extract value(s) from a compute -v3 = lmp.extract_fix(id,style,type,i,j) # extract value(s) from a fix - # id = ID of compute or fix - # style = 0 = global data - # 1 = per-atom data - # 2 = local data - # type = 0 = scalar - # 1 = vector - # 2 = array - # i,j = indices of value in global vector or array :pre - -var = lmp.extract_variable(name,group,flag) # extract value(s) from a variable - # name = name of variable - # group = group ID (ignored for equal-style variables) - # flag = 0 = equal-style variable - # 1 = atom-style variable :pre - -value = lmp.get_thermo(name) # return current value of a thermo keyword -natoms = lmp.get_natoms() # total # of atoms as int :pre - -flag = lmp.set_variable(name,value) # set existing named string-style variable to value, flag = 0 if successful -lmp.reset_box(boxlo,boxhi,xy,yz,xz) # reset the simulation box size :pre - -data = lmp.gather_atoms(name,type,count) # return per-atom property of all atoms gathered into data, ordered by atom ID - # name = "x", "charge", "type", etc -data = lmp.gather_atoms_concat(name,type,count) # ditto, but concatenated atom values from each proc (unordered) -data = lmp.gather_atoms_subset(name,type,count,ndata,ids) # ditto, but for subset of Ndata atoms with IDs :pre - -lmp.scatter_atoms(name,type,count,data) # scatter per-atom property to all atoms from data, ordered by atom ID - # name = "x", "charge", "type", etc - # count = # of per-atom values, 1 or 3, etc :pre -lmp.scatter_atoms_subset(name,type,count,ndata,ids,data) # ditto, but for subset of Ndata atoms with IDs :pre - -lmp.create_atoms(n,ids,types,x,v,image,shrinkexceed) # create N atoms with IDs, types, x, v, and image flags :pre - -:line - -The lines - -from lammps import lammps -lmp = lammps() :pre - -create an instance of LAMMPS, wrapped in a Python class by the lammps -Python module, and return an instance of the Python class as lmp. It -is used to make all subsequent calls to the LAMMPS library. - -Additional arguments to lammps() can be used to tell Python the name -of the shared library to load or to pass arguments to the LAMMPS -instance, the same as if LAMMPS were launched from a command-line -prompt. - -If the ptr argument is set like this: - -lmp = lammps(ptr=lmpptr) :pre - -then lmpptr must be an argument passed to Python via the LAMMPS -"python"_python.html command, when it is used to define a Python -function that is invoked by the LAMMPS input script. This mode of -using Python with LAMMPS is described above in 11.2. The variable -lmpptr refers to the instance of LAMMPS that called the embedded -Python interpreter. Using it as an argument to lammps() allows the -returned Python class instance "lmp" to make calls to that instance of -LAMMPS. See the "python"_python.html command doc page for examples -using this syntax. - -Note that you can create multiple LAMMPS objects in your Python -script, and coordinate and run multiple simulations, e.g. - -from lammps import lammps -lmp1 = lammps() -lmp2 = lammps() -lmp1.file("in.file1") -lmp2.file("in.file2") :pre - -The file(), command(), commands_list(), commands_string() methods -allow an input script, a single command, or multiple commands to be -invoked. - -The extract_setting(), extract_global(), extract_box(), -extract_atom(), extract_compute(), extract_fix(), and -extract_variable() methods return values or pointers to data -structures internal to LAMMPS. - -For extract_global() see the src/library.cpp file for the list of -valid names. New names could easily be added. A double or integer is -returned. You need to specify the appropriate data type via the type -argument. - -For extract_atom(), a pointer to internal LAMMPS atom-based data is -returned, which you can use via normal Python subscripting. See the -extract() method in the src/atom.cpp file for a list of valid names. -Again, new names could easily be added if the property you want is not -listed. A pointer to a vector of doubles or integers, or a pointer to -an array of doubles (double **) or integers (int **) is returned. You -need to specify the appropriate data type via the type argument. - -For extract_compute() and extract_fix(), the global, per-atom, or -local data calculated by the compute or fix can be accessed. What is -returned depends on whether the compute or fix calculates a scalar or -vector or array. For a scalar, a single double value is returned. If -the compute or fix calculates a vector or array, a pointer to the -internal LAMMPS data is returned, which you can use via normal Python -subscripting. The one exception is that for a fix that calculates a -global vector or array, a single double value from the vector or array -is returned, indexed by I (vector) or I and J (array). I,J are -zero-based indices. The I,J arguments can be left out if not needed. -See "Section 6.15"_Section_howto.html#howto_15 of the manual for a -discussion of global, per-atom, and local data, and of scalar, vector, -and array data types. See the doc pages for individual -"computes"_compute.html and "fixes"_fix.html for a description of what -they calculate and store. - -For extract_variable(), an "equal-style or atom-style -variable"_variable.html is evaluated and its result returned. - -For equal-style variables a single double value is returned and the -group argument is ignored. For atom-style variables, a vector of -doubles is returned, one value per atom, which you can use via normal -Python subscripting. The values will be zero for atoms not in the -specified group. - -The get_thermo() method returns returns the current value of a thermo -keyword as a float. - -The get_natoms() method returns the total number of atoms in the -simulation, as an int. - -The set_variable() methosd sets an existing string-style variable to a -new string value, so that subsequent LAMMPS commands can access the -variable. - -The reset_box() emthods resets the size and shape of the simulation -box, e.g. as part of restoring a previously extracted and saved state -of a simulation. - -The gather methods collect peratom info of the requested type (atom -coords, atom types, forces, etc) from all processors, and returns the -same vector of values to each callling processor. The scatter -functions do the inverse. They distribute a vector of peratom values, -passed by all calling processors, to invididual atoms, which may be -owned by different processos. - -Note that the data returned by the gather methods, -e.g. gather_atoms("x"), is different from the data structure returned -by extract_atom("x") in four ways. (1) Gather_atoms() returns a -vector which you index as x\[i\]; extract_atom() returns an array -which you index as x\[i\]\[j\]. (2) Gather_atoms() orders the atoms -by atom ID while extract_atom() does not. (3) Gather_atoms() returns -a list of all atoms in the simulation; extract_atoms() returns just -the atoms local to each processor. (4) Finally, the gather_atoms() -data structure is a copy of the atom coords stored internally in -LAMMPS, whereas extract_atom() returns an array that effectively -points directly to the internal data. This means you can change -values inside LAMMPS from Python by assigning a new values to the -extract_atom() array. To do this with the gather_atoms() vector, you -need to change values in the vector, then invoke the scatter_atoms() -method. - -For the scatter methods, the array of coordinates passed to must be a -ctypes vector of ints or doubles, allocated and initialized something -like this: - -from ctypes import * -natoms = lmp.get_natoms() -n3 = 3*natoms -x = (n3*c_double)() -x\[0\] = x coord of atom with ID 1 -x\[1\] = y coord of atom with ID 1 -x\[2\] = z coord of atom with ID 1 -x\[3\] = x coord of atom with ID 2 -... -x\[n3-1\] = z coord of atom with ID natoms -lmp.scatter_atoms("x",1,3,x) :pre - -Alternatively, you can just change values in the vector returned by -the gather methods, since they are also ctypes vectors. - -:line - -As noted above, these Python class methods correspond one-to-one with -the functions in the LAMMPS library interface in src/library.cpp and -library.h. This means you can extend the Python wrapper via the -following steps: - -Add a new interface function to src/library.cpp and -src/library.h. :ulb,l - -Rebuild LAMMPS as a shared library. :l - -Add a wrapper method to python/lammps.py for this interface -function. :l - -You should now be able to invoke the new interface function from a -Python script. Isn't ctypes amazing? :l -:ule - -:line -:line - -11.8 Example Python scripts that use LAMMPS :link(py_8),h4 - -These are the Python scripts included as demos in the python/examples -directory of the LAMMPS distribution, to illustrate the kinds of -things that are possible when Python wraps LAMMPS. If you create your -own scripts, send them to us and we can include them in the LAMMPS -distribution. - -trivial.py, read/run a LAMMPS input script thru Python, -demo.py, invoke various LAMMPS library interface routines, -simple.py, run in parallel, similar to examples/COUPLE/simple/simple.cpp, -split.py, same as simple.py but running in parallel on a subset of procs, -gui.py, GUI go/stop/temperature-slider to control LAMMPS, -plot.py, real-time temperature plot with GnuPlot via Pizza.py, -viz_tool.py, real-time viz via some viz package, -vizplotgui_tool.py, combination of viz_tool.py and plot.py and gui.py :tb(c=2) - -:line - -For the viz_tool.py and vizplotgui_tool.py commands, replace "tool" -with "gl" or "atomeye" or "pymol" or "vmd", depending on what -visualization package you have installed. - -Note that for GL, you need to be able to run the Pizza.py GL tool, -which is included in the pizza sub-directory. See the "Pizza.py doc -pages"_pizza for more info: - -:link(pizza,http://www.sandia.gov/~sjplimp/pizza.html) - -Note that for AtomEye, you need version 3, and there is a line in the -scripts that specifies the path and name of the executable. See the -AtomEye WWW pages "here"_atomeye or "here"_atomeye3 for more details: - -http://mt.seas.upenn.edu/Archive/Graphics/A -http://mt.seas.upenn.edu/Archive/Graphics/A3/A3.html :pre - -:link(atomeye,http://mt.seas.upenn.edu/Archive/Graphics/A) -:link(atomeye3,http://mt.seas.upenn.edu/Archive/Graphics/A3/A3.html) - -The latter link is to AtomEye 3 which has the scriping -capability needed by these Python scripts. - -Note that for PyMol, you need to have built and installed the -open-source version of PyMol in your Python, so that you can import it -from a Python script. See the PyMol WWW pages "here"_pymolhome or -"here"_pymolopen for more details: - -http://www.pymol.org -http://sourceforge.net/scm/?type=svn&group_id=4546 :pre - -:link(pymolhome,http://www.pymol.org) -:link(pymolopen,http://sourceforge.net/scm/?type=svn&group_id=4546) - -The latter link is to the open-source version. - -Note that for VMD, you need a fairly current version (1.8.7 works for -me) and there are some lines in the pizza/vmd.py script for 4 PIZZA -variables that have to match the VMD installation on your system. - -:line - -See the python/README file for instructions on how to run them and the -source code for individual scripts for comments about what they do. - -Here are screenshots of the vizplotgui_tool.py script in action for -different visualization package options. Click to see larger images: - -:image(JPG/screenshot_gl_small.jpg,JPG/screenshot_gl.jpg) -:image(JPG/screenshot_atomeye_small.jpg,JPG/screenshot_atomeye.jpg) -:image(JPG/screenshot_pymol_small.jpg,JPG/screenshot_pymol.jpg) -:image(JPG/screenshot_vmd_small.jpg,JPG/screenshot_vmd.jpg) - -11.9 PyLammps interface :link(py_9),h4 - -Please see the "PyLammps Tutorial"_tutorial_pylammps.html. diff --git a/doc/src/Section_start.txt b/doc/src/Section_start.txt deleted file mode 100644 index 7d456171dc..0000000000 --- a/doc/src/Section_start.txt +++ /dev/null @@ -1,1817 +0,0 @@ -"Previous Section"_Section_intro.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Section_commands.html :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Section_commands.html#comm) - -:line - -2. Getting Started :h2 - -This section describes how to build and run LAMMPS, for both new and -experienced users. - -2.1 "What's in the LAMMPS distribution"_#start_1 -2.2 "Making LAMMPS"_#start_2 -2.3 "Making LAMMPS with optional packages"_#start_3 -2.4 "Building LAMMPS as a library"_#start_4 -2.5 "Running LAMMPS"_#start_5 -2.6 "Command-line options"_#start_6 -2.7 "Screen output"_#start_7 -2.8 "Tips for users of previous versions"_#start_8 :all(b) - -:line - -2.1 What's in the LAMMPS distribution :h3,link(start_1) - -When you download a LAMMPS tarball you will need to unzip and untar -the downloaded file with the following commands, after placing the -tarball in an appropriate directory. - -tar -xzvf lammps*.tar.gz :pre - -This will create a LAMMPS directory containing two files and several -sub-directories: - -README: text file -LICENSE: the GNU General Public License (GPL) -bench: benchmark problems -doc: documentation -examples: simple test problems -potentials: embedded atom method (EAM) potential files -src: source files -tools: pre- and post-processing tools :tb(s=:) - -Note that the "download page"_download also has links to download -pre-build Windows installers, as well as pre-built packages for -several widely used Linux distributions. It also has instructions -for how to download/install LAMMPS for Macs (via Homebrew), and to -download and update LAMMPS from SVN and Git repositories, which gives -you access to the up-to-date sources that are used by the LAMMPS -core developers. - -:link(download,http://lammps.sandia.gov/download.html) - -The Windows and Linux packages for serial or parallel include -only selected packages and bug-fixes/upgrades listed on "this -page"_http://lammps.sandia.gov/bug.html up to a certain date, as -stated on the download page. If you want an executable with -non-included packages or that is more current, then you'll need to -build LAMMPS yourself, as discussed in the next section. - -Skip to the "Running LAMMPS"_#start_6 sections for info on how to -launch a LAMMPS Windows executable on a Windows box. - -:line - -2.2 Making LAMMPS :h3,link(start_2) - -This section has the following sub-sections: - -2.2.1 "Read this first"_#start_2_1 -2.2.1 "Steps to build a LAMMPS executable"_#start_2_2 -2.2.3 "Common errors that can occur when making LAMMPS"_#start_2_3 -2.2.4 "Additional build tips"_#start_2_4 -2.2.5 "Building for a Mac"_#start_2_5 -2.2.6 "Building for Windows"_#start_2_6 :all(b) - -:line - -Read this first :h4,link(start_2_1) - -If you want to avoid building LAMMPS yourself, read the preceding -section about options available for downloading and installing -executables. Details are discussed on the "download"_download page. - -Building LAMMPS can be simple or not-so-simple. If all you need are -the default packages installed in LAMMPS, and MPI is already installed -on your machine, or you just want to run LAMMPS in serial, then you -can typically use the Makefile.mpi or Makefile.serial files in -src/MAKE by typing one of these lines (from the src dir): - -make mpi -make serial :pre - -Note that on a facility supercomputer, there are often "modules" -loaded in your environment that provide the compilers and MPI you -should use. In this case, the "mpicxx" compile/link command in -Makefile.mpi should simply work by accessing those modules. - -It may be the case that one of the other Makefile.machine files in the -src/MAKE sub-directories is a better match to your system (type "make" -to see a list), you can use it as-is by typing (for example): - -make stampede :pre - -If any of these builds (with an existing Makefile.machine) works on -your system, then you're done! - -If you need to install an optional package with a LAMMPS command you -want to use, and the package does not depend on an extra library, you -can simply type - -make name :pre - -before invoking (or re-invoking) the above steps. "Name" is the -lower-case name of the package, e.g. replica or user-misc. - -If you want to do one of the following: - -use a LAMMPS command that requires an extra library (e.g. "dump image"_dump_image.html) -build with a package that requires an extra library -build with an accelerator package that requires special compiler/linker settings -run on a machine that has its own compilers, settings, or libraries :ul - -then building LAMMPS is more complicated. You may need to find where -extra libraries exist on your machine or install them if they don't. -You may need to build extra libraries that are included in the LAMMPS -distribution, before building LAMMPS itself. You may need to edit a -Makefile.machine file to make it compatible with your system. - -Please read the following sections carefully. If you are not -comfortable with makefiles, or building codes on a Unix platform, or -running an MPI job on your machine, please find a local expert to help -you. Many compilation, linking, and run problems users experience are -often not LAMMPS issues - they are peculiar to the user's system, -compilers, libraries, etc. Such questions are better answered by a -local expert. - -If you have a build problem that you are convinced is a LAMMPS issue -(e.g. the compiler complains about a line of LAMMPS source code), then -please post the issue to the "LAMMPS mail -list"_http://lammps.sandia.gov/mail.html. - -If you succeed in building LAMMPS on a new kind of machine, for which -there isn't a similar machine Makefile included in the -src/MAKE/MACHINES directory, then send it to the developers and we can -include it in the LAMMPS distribution. - -:line - -Steps to build a LAMMPS executable :h4,link(start_2_2) - -Step 0 :h5 - -The src directory contains the C++ source and header files for LAMMPS. -It also contains a top-level Makefile and a MAKE sub-directory with -low-level Makefile.* files for many systems and machines. See the -src/MAKE/README file for a quick overview of what files are available -and what sub-directories they are in. - -The src/MAKE dir has a few files that should work as-is on many -platforms. The src/MAKE/OPTIONS dir has more that invoke additional -compiler, MPI, and other setting options commonly used by LAMMPS, to -illustrate their syntax. The src/MAKE/MACHINES dir has many more that -have been tweaked or optimized for specific machines. These files are -all good starting points if you find you need to change them for your -machine. Put any file you edit into the src/MAKE/MINE directory and -it will be never be touched by any LAMMPS updates. - ->From within the src directory, type "make" or "gmake". You should see -a list of available choices from src/MAKE and all of its -sub-directories. If one of those has the options you want or is the -machine you want, you can type a command like: - -make mpi :pre -or - -make serial :pre -or - -gmake mac :pre - -Note that the corresponding Makefile.machine can exist in src/MAKE or -any of its sub-directories. If a file with the same name appears in -multiple places (not a good idea), the order they are used is as -follows: src/MAKE/MINE, src/MAKE, src/MAKE/OPTIONS, src/MAKE/MACHINES. -This gives preference to a file you have created/edited and put in -src/MAKE/MINE. - -Note that on a multi-processor or multi-core platform you can launch a -parallel make, by using the "-j" switch with the make command, which -will build LAMMPS more quickly. - -If you get no errors and an executable like [lmp_mpi] or [lmp_serial] -or [lmp_mac] is produced, then you're done; it's your lucky day. - -Note that by default only a few of LAMMPS optional packages are -installed. To build LAMMPS with optional packages, see "this -section"_#start_3 below. - -Step 1 :h5 - -If Step 0 did not work, you will need to create a low-level Makefile -for your machine, like Makefile.foo. You should make a copy of an -existing Makefile.* in src/MAKE or one of its sub-directories as a -starting point. The only portions of the file you need to edit are -the first line, the "compiler/linker settings" section, and the -"LAMMPS-specific settings" section. When it works, put the edited -file in src/MAKE/MINE and it will not be altered by any future LAMMPS -updates. - -Step 2 :h5 - -Change the first line of Makefile.foo to list the word "foo" after the -"#", and whatever other options it will set. This is the line you -will see if you just type "make". - -Step 3 :h5 - -The "compiler/linker settings" section lists compiler and linker -settings for your C++ compiler, including optimization flags. You can -use g++, the open-source GNU compiler, which is available on all Unix -systems. You can also use mpicxx which will typically be available if -MPI is installed on your system, though you should check which actual -compiler it wraps. Vendor compilers often produce faster code. On -boxes with Intel CPUs, we suggest using the Intel icc compiler, which -can be downloaded from "Intel's compiler site"_intel. - -:link(intel,http://www.intel.com/software/products/noncom) - -If building a C++ code on your machine requires additional libraries, -then you should list them as part of the LIB variable. You should -not need to do this if you use mpicxx. - -The DEPFLAGS setting is what triggers the C++ compiler to create a -dependency list for a source file. This speeds re-compilation when -source (*.cpp) or header (*.h) files are edited. Some compilers do -not support dependency file creation, or may use a different switch -than -D. GNU g++ and Intel icc works with -D. If your compiler can't -create dependency files, then you'll need to create a Makefile.foo -patterned after Makefile.storm, which uses different rules that do not -involve dependency files. Note that when you build LAMMPS for the -first time on a new platform, a long list of *.d files will be printed -out rapidly. This is not an error; it is the Makefile doing its -normal creation of dependencies. - -Step 4 :h5 - -The "system-specific settings" section has several parts. Note that -if you change any -D setting in this section, you should do a full -re-compile, after typing "make clean" (which will describe different -clean options). - -The LMP_INC variable is used to include options that turn on ifdefs -within the LAMMPS code. The options that are currently recognized are: - --DLAMMPS_GZIP --DLAMMPS_JPEG --DLAMMPS_PNG --DLAMMPS_FFMPEG --DLAMMPS_MEMALIGN --DLAMMPS_SMALLBIG --DLAMMPS_BIGBIG --DLAMMPS_SMALLSMALL --DLAMMPS_LONGLONG_TO_LONG --DLAMMPS_EXCEPTIONS --DPACK_ARRAY --DPACK_POINTER --DPACK_MEMCPY :ul - -The read_data and dump commands will read/write gzipped files if you -compile with -DLAMMPS_GZIP. It requires that your machine supports -the "popen()" function in the standard runtime library and that a gzip -executable can be found by LAMMPS during a run. - -NOTE: on some clusters with high-speed networks, using the fork() -library calls (required by popen()) can interfere with the fast -communication library and lead to simulations using compressed output -or input to hang or crash. For selected operations, compressed file -I/O is also available using a compression library instead, which are -provided in the COMPRESS package. From more details about compiling -LAMMPS with packages, please see below. - -If you use -DLAMMPS_JPEG, the "dump image"_dump_image.html command -will be able to write out JPEG image files. For JPEG files, you must -also link LAMMPS with a JPEG library, as described below. If you use --DLAMMPS_PNG, the "dump image"_dump.html command will be able to write -out PNG image files. For PNG files, you must also link LAMMPS with a -PNG library, as described below. If neither of those two defines are -used, LAMMPS will only be able to write out uncompressed PPM image -files. - -If you use -DLAMMPS_FFMPEG, the "dump movie"_dump_image.html command -will be available to support on-the-fly generation of rendered movies -the need to store intermediate image files. It requires that your -machines supports the "popen" function in the standard runtime library -and that an FFmpeg executable can be found by LAMMPS during the run. - -NOTE: Similar to the note above, this option can conflict with -high-speed networks, because it uses popen(). - -Using -DLAMMPS_MEMALIGN= enables the use of the -posix_memalign() call instead of malloc() when large chunks or memory -are allocated by LAMMPS. This can help to make more efficient use of -vector instructions of modern CPUS, since dynamically allocated memory -has to be aligned on larger than default byte boundaries (e.g. 16 -bytes instead of 8 bytes on x86 type platforms) for optimal -performance. - -Use at most one of the -DLAMMPS_SMALLBIG, -DLAMMPS_BIGBIG, --DLAMMPS_SMALLSMALL settings. The default is -DLAMMPS_SMALLBIG. These -settings refer to use of 4-byte (small) vs 8-byte (big) integers -within LAMMPS, as specified in src/lmptype.h. The only reason to use -the BIGBIG setting is to enable simulation of huge molecular systems -(which store bond topology info) with more than 2 billion atoms, or to -track the image flags of moving atoms that wrap around a periodic box -more than 512 times. Normally, the only reason to use SMALLSMALL is -if your machine does not support 64-bit integers, though you can use -SMALLSMALL setting if you are running in serial or on a desktop -machine or small cluster where you will never run large systems or for -long time (more than 2 billion atoms, more than 2 billion timesteps). -See the "Additional build tips"_#start_2_4 section below for more -details on these settings. - -Note that the USER-ATC package is not currently compatible with --DLAMMPS_BIGBIG. Also the GPU package requires the lib/gpu library to -be compiled with the same setting, or the link will fail. - -The -DLAMMPS_LONGLONG_TO_LONG setting may be needed if your system or -MPI version does not recognize "long long" data types. In this case a -"long" data type is likely already 64-bits, in which case this setting -will convert to that data type. - -The -DLAMMPS_EXCEPTIONS setting can be used to activate alternative -versions of error handling inside of LAMMPS. This is useful when -external codes drive LAMMPS as a library. Using this option, LAMMPS -errors do not kill the caller. Instead, the call stack is unwound and -control returns to the caller. The library interface provides the -lammps_has_error() and lammps_get_last_error_message() functions to -detect and find out more about a LAMMPS error. - -Using one of the -DPACK_ARRAY, -DPACK_POINTER, and -DPACK_MEMCPY -options can make for faster parallel FFTs (in the PPPM solver) on some -platforms. The -DPACK_ARRAY setting is the default. See the -"kspace_style"_kspace_style.html command for info about PPPM. See -Step 6 below for info about building LAMMPS with an FFT library. - -Step 5 :h5 - -The 3 MPI variables are used to specify an MPI library to build LAMMPS -with. Note that you do not need to set these if you use the MPI -compiler mpicxx for your CC and LINK setting in the section above. -The MPI wrapper knows where to find the needed files. - -If you want LAMMPS to run in parallel, you must have an MPI library -installed on your platform. If MPI is installed on your system in the -usual place (under /usr/local), you also may not need to specify these -3 variables, assuming /usr/local is in your path. On some large -parallel machines which use "modules" for their compile/link -environments, you may simply need to include the correct module in -your build environment, before building LAMMPS. Or the parallel -machine may have a vendor-provided MPI which the compiler has no -trouble finding. - -Failing this, these 3 variables can be used to specify where the mpi.h -file (MPI_INC) and the MPI library file (MPI_PATH) are found and the -name of the library file (MPI_LIB). - -If you are installing MPI yourself, we recommend Argonne's MPICH2 -or OpenMPI. MPICH can be downloaded from the "Argonne MPI -site"_http://www.mcs.anl.gov/research/projects/mpich2/. OpenMPI can -be downloaded from the "OpenMPI site"_http://www.open-mpi.org. -Other MPI packages should also work. If you are running on a big -parallel platform, your system people or the vendor should have -already installed a version of MPI, which is likely to be faster -than a self-installed MPICH or OpenMPI, so find out how to build -and link with it. If you use MPICH or OpenMPI, you will have to -configure and build it for your platform. The MPI configure script -should have compiler options to enable you to use the same compiler -you are using for the LAMMPS build, which can avoid problems that can -arise when linking LAMMPS to the MPI library. - -If you just want to run LAMMPS on a single processor, you can use the -dummy MPI library provided in src/STUBS, since you don't need a true -MPI library installed on your system. See src/MAKE/Makefile.serial -for how to specify the 3 MPI variables in this case. You will also -need to build the STUBS library for your platform before making LAMMPS -itself. Note that if you are building with src/MAKE/Makefile.serial, -e.g. by typing "make serial", then the STUBS library is built for you. - -To build the STUBS library from the src directory, type "make -mpi-stubs", or from the src/STUBS dir, type "make". This should -create a libmpi_stubs.a file suitable for linking to LAMMPS. If the -build fails, you will need to edit the STUBS/Makefile for your -platform. - -The file STUBS/mpi.c provides a CPU timer function called MPI_Wtime() -that calls gettimeofday() . If your system doesn't support -gettimeofday() , you'll need to insert code to call another timer. -Note that the ANSI-standard function clock() rolls over after an hour -or so, and is therefore insufficient for timing long LAMMPS -simulations. - -Step 6 :h5 - -The 3 FFT variables allow you to specify an FFT library which LAMMPS -uses (for performing 1d FFTs) when running the particle-particle -particle-mesh (PPPM) option for long-range Coulombics via the -"kspace_style"_kspace_style.html command. - -LAMMPS supports common open-source or vendor-supplied FFT libraries -for this purpose. If you leave these 3 variables blank, LAMMPS will -use the open-source "KISS FFT library"_http://kissfft.sf.net, which is -included in the LAMMPS distribution. This library is portable to all -platforms and for typical LAMMPS simulations is almost as fast as FFTW -or vendor optimized libraries. If you are not including the KSPACE -package in your build, you can also leave the 3 variables blank. - -Otherwise, select which kinds of FFTs to use as part of the FFT_INC -setting by a switch of the form -DFFT_XXX. Recommended values for XXX -are: MKL or FFTW3. FFTW2 and NONE are supported as legacy options. -Selecting -DFFT_FFTW will use the FFTW3 library and -DFFT_NONE will -use the KISS library described above. - -You may also need to set the FFT_INC, FFT_PATH, and FFT_LIB variables, -so the compiler and linker can find the needed FFT header and library -files. Note that on some large parallel machines which use "modules" -for their compile/link environments, you may simply need to include -the correct module in your build environment. Or the parallel machine -may have a vendor-provided FFT library which the compiler has no -trouble finding. See the src/MAKE/OPTIONS/Makefile.fftw file for an -example of how to specify these variables to use the FFTW3 library. - -FFTW is fast, portable library that should also work on any platform -and typically be faster than KISS FFT. You can download it from -"www.fftw.org"_http://www.fftw.org. Both the legacy version 2.1.X and -the newer 3.X versions are supported as -DFFT_FFTW2 or -DFFT_FFTW3. -Building FFTW for your box should be as simple as ./configure; make; -make install. The install command typically requires root privileges -(e.g. invoke it via sudo), unless you specify a local directory with -the "--prefix" option of configure. Type "./configure --help" to see -various options. - -If you wish to have FFTW support for single-precision FFTs (see below -about -DFFT_SINGLE) in addition to the default double-precision FFTs, -you will need to build FFTW a second time for single-precision. For -FFTW3, do this via: - -make clean -./configure --enable-single; make; make install :pre - -which should produce the additional library libfftw3f.a. - -For FFTW2, do this: - -make clean -./configure --enable-float --enable-type-prefix; make; make install :pre - -which should produce the additional library libsfftw.a and additional -include file sfttw.a. Note that on some platforms FFTW2 has been -pre-installed for both single- and double-precision, and may already -have these files as well as libdfftw.a and dfftw.h for double -precision. - -The FFT_INC variable also allows for a -DFFT_SINGLE setting that will -use single-precision FFTs with PPPM, which can speed-up long-range -calculations, particularly in parallel or on GPUs. Fourier transform -and related PPPM operations are somewhat insensitive to floating point -truncation errors and thus do not always need to be performed in -double precision. Using the -DFFT_SINGLE setting trades off a little -accuracy for reduced memory use and parallel communication costs for -transposing 3d FFT data. Note that single precision FFTs have only -been tested with the FFTW3, FFTW2, MKL, and KISS FFT options. - -When using -DFFT_SINGLE with FFTW3 or FFTW2, you need to build FFTW -with support for single-precision, as explained above. For FFTW3 you -also need to include -lfftw3f with the FFT_LIB setting, in addition to --lfftw3. For FFTW2, you also need to specify -DFFT_SIZE with the -FFT_INC setting and -lsfftw with the FFT_LIB setting (in place of --lfftw). Similarly, if FFTW2 has been pre-installed with an explicit -double-precision library (libdfftw.a and not the default libfftw.a), -then you can specify -DFFT_SIZE (and not -DFFT_SINGLE), and specify --ldfftw to use double-precision FFTs. - -Step 7 :h5 - -The 3 JPG variables allow you to specify a JPEG and/or PNG library -which LAMMPS uses when writing out JPEG or PNG files via the "dump -image"_dump_image.html command. These can be left blank if you do not -use the -DLAMMPS_JPEG or -DLAMMPS_PNG switches discussed above in Step -4, since in that case JPEG/PNG output will be disabled. - -A standard JPEG library usually goes by the name libjpeg.a or -libjpeg.so and has an associated header file jpeglib.h. Whichever -JPEG library you have on your platform, you'll need to set the -appropriate JPG_INC, JPG_PATH, and JPG_LIB variables, so that the -compiler and linker can find it. - -A standard PNG library usually goes by the name libpng.a or libpng.so -and has an associated header file png.h. Whichever PNG library you -have on your platform, you'll need to set the appropriate JPG_INC, -JPG_PATH, and JPG_LIB variables, so that the compiler and linker can -find it. - -As before, if these header and library files are in the usual place on -your machine, you may not need to set these variables. - -Step 8 :h5 - -Note that by default only a few of LAMMPS optional packages are -installed. To build LAMMPS with optional packages, see "this -section"_#start_3 below, before proceeding to Step 9. - -Step 9 :h5 - -That's it. Once you have a correct Makefile.foo, and you have -pre-built any other needed libraries (e.g. MPI, FFT, etc) all you need -to do from the src directory is type something like this: - -make foo -make -j N foo -gmake foo -gmake -j N foo :pre - -The -j or -j N switches perform a parallel build which can be much -faster, depending on how many cores your compilation machine has. N -is the number of cores the build runs on. - -You should get the executable lmp_foo when the build is complete. - -:line - -Errors that can occur when making LAMMPS :h4 :link(start_2_3) - -If an error occurs when building LAMMPS, the compiler or linker will -state very explicitly what the problem is. The error message should -give you a hint as to which of the steps above has failed, and what -you need to do in order to fix it. Building a code with a Makefile is -a very logical process. The compiler and linker need to find the -appropriate files and those files need to be compatible with LAMMPS -settings and source files. When a make fails, there is usually a very -simple reason, which you or a local expert will need to fix. - -Here are two non-obvious errors that can occur: - -(1) If the make command breaks immediately with errors that indicate -it can't find files with a "*" in their names, this can be because -your machine's native make doesn't support wildcard expansion in a -makefile. Try gmake instead of make. If that doesn't work, try using -a -f switch with your make command to use a pre-generated -Makefile.list which explicitly lists all the needed files, e.g. - -make makelist -make -f Makefile.list linux -gmake -f Makefile.list mac :pre - -The first "make" command will create a current Makefile.list with all -the file names in your src dir. The 2nd "make" command (make or -gmake) will use it to build LAMMPS. Note that you should -include/exclude any desired optional packages before using the "make -makelist" command. - -(2) If you get an error that says something like 'identifier "atoll" -is undefined', then your machine does not support "long long" -integers. Try using the -DLAMMPS_LONGLONG_TO_LONG setting described -above in Step 4. - -:line - -Additional build tips :h4,link(start_2_4) - -Building LAMMPS for multiple platforms. :h5 - -You can make LAMMPS for multiple platforms from the same src -directory. Each target creates its own object sub-directory called -Obj_target where it stores the system-specific *.o files. - -Cleaning up. :h5 - -Typing "make clean-all" or "make clean-machine" will delete *.o object -files created when LAMMPS is built, for either all builds or for a -particular machine. - -Changing the LAMMPS size limits via -DLAMMPS_SMALLBIG or -DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL :h5 - -As explained above, any of these 3 settings can be specified on the -LMP_INC line in your low-level src/MAKE/Makefile.foo. - -The default is -DLAMMPS_SMALLBIG which allows for systems with up to -2^63 atoms and 2^63 timesteps (about 9e18). The atom limit is for -atomic systems which do not store bond topology info and thus do not -require atom IDs. If you use atom IDs for atomic systems (which is -the default) or if you use a molecular model, which stores bond -topology info and thus requires atom IDs, the limit is 2^31 atoms -(about 2 billion). This is because the IDs are stored in 32-bit -integers. - -Likewise, with this setting, the 3 image flags for each atom (see the -"dump"_dump.html doc page for a discussion) are stored in a 32-bit -integer, which means the atoms can only wrap around a periodic box (in -each dimension) at most 512 times. If atoms move through the periodic -box more than this many times, the image flags will "roll over", -e.g. from 511 to -512, which can cause diagnostics like the -mean-squared displacement, as calculated by the "compute -msd"_compute_msd.html command, to be faulty. - -To allow for larger atomic systems with atom IDs or larger molecular -systems or larger image flags, compile with -DLAMMPS_BIGBIG. This -stores atom IDs and image flags in 64-bit integers. This enables -atomic or molecular systems with atom IDS of up to 2^63 atoms (about -9e18). And image flags will not "roll over" until they reach 2^20 = -1048576. - -If your system does not support 8-byte integers, you will need to -compile with the -DLAMMPS_SMALLSMALL setting. This will restrict the -total number of atoms (for atomic or molecular systems) and timesteps -to 2^31 (about 2 billion). Image flags will roll over at 2^9 = 512. - -Note that in src/lmptype.h there are definitions of all these data -types as well as the MPI data types associated with them. The MPI -types need to be consistent with the associated C data types, or else -LAMMPS will generate a run-time error. As far as we know, the -settings defined in src/lmptype.h are portable and work on every -current system. - -In all cases, the size of problem that can be run on a per-processor -basis is limited by 4-byte integer storage to 2^31 atoms per processor -(about 2 billion). This should not normally be a limitation since such -a problem would have a huge per-processor memory footprint due to -neighbor lists and would run very slowly in terms of CPU secs/timestep. - -:line - -Building for a Mac :h4,link(start_2_5) - -OS X is a derivative of BSD Unix, so it should just work. See the -src/MAKE/MACHINES/Makefile.mac and Makefile.mac_mpi files. - -:line - -Building for Windows :h4,link(start_2_6) - -If you want to build a Windows version of LAMMPS, you can build it -yourself, but it may require some effort. LAMMPS expects a Unix-like -build environment for the default build procedure. This can be done -using either Cygwin or MinGW; the latter also exists as a ready-to-use -Linux-to-Windows cross-compiler in several Linux distributions. In -these cases, you can do the installation after installing several -unix-style commands like make, grep, sed and bash with some shell -utilities. - -For Cygwin and the MinGW cross-compilers, suitable makefiles are -provided in src/MAKE/MACHINES. When using other compilers, like -Visual C++ or Intel compilers for Windows, you may have to implement -your own build system. Due to differences between the Windows OS -and Windows system libraries to Unix-like environments like Linux -or MacOS, when compiling for Windows a few adjustments may be needed: - -Do [not] set the -DLAMMPS_MEMALIGN define (see LMP_INC makefile variable) -Add -lwsock32 -lpsapi to the linker flags (see LIB makefile variable) -Try adding -static-libgcc or -static or both to the linker flags when your LAMMPS executable complains about missing .dll files :ul - -Since none of the current LAMMPS core developers has significant -experience building executables on Windows, we are happy to distribute -contributed instructions and modifications to improve the situation, -but we cannot provide support for those. - -With the so-called "Anniversary Update" to Windows 10, there is a -Ubuntu Linux subsystem available for Windows, that can be installed -and then used to compile/install LAMMPS as if you are running on a -Ubuntu Linux system instead of Windows. - -As an alternative, you can download pre-compiled installer packages from -"packages.lammps.org/windows.html"_http://packages.lammps.org/windows.html. -These executables are built with most optional packages included and the -download includes documentation, potential files, some tools and many -examples, but no source code. - -:line - -2.3 Making LAMMPS with optional packages :h3,link(start_3) - -This section has the following sub-sections: - -2.3.1 "Package basics"_#start_3_1 -2.3.2 "Including/excluding packages"_#start_3_2 -2.3.3 "Packages that require extra libraries"_#start_3_3 :all(b) - -:line - -Package basics: :h4,link(start_3_1) - -The source code for LAMMPS is structured as a set of core files which -are always included, plus optional packages. Packages are groups of -files that enable a specific set of features. For example, force -fields for molecular systems or granular systems are in packages. - -"Section 4"_Section_packages.html in the manual has details about all -the packages, which come in two flavors: [standard] and [user] -packages. It also has specific instructions for building LAMMPS with -any package which requires an extra library. General instructions are -below. - -You can see the list of all packages by typing "make package" from -within the src directory of the LAMMPS distribution. It will also -list various make commands that can be used to manage packages. - -If you use a command in a LAMMPS input script that is part of a -package, you must have built LAMMPS with that package, else you will -get an error that the style is invalid or the command is unknown. -Every command's doc page specifies if it is part of a package. You can -type - -lmp_machine -h :pre - -to run your executable with the optional "-h command-line -switch"_#start_6 for "help", which will list the styles and commands -known to your executable, and immediately exit. - -:line - -Including/excluding packages :h4,link(start_3_2) - -To use (or not use) a package you must install it (or un-install it) -before building LAMMPS. From the src directory, this is as simple as: - -make yes-colloid -make mpi :pre - -or - -make no-user-omp -make mpi :pre - -NOTE: You should NOT install/un-install packages and build LAMMPS in a -single make command using multiple targets, e.g. make yes-colloid mpi. -This is because the make procedure creates a list of source files that -will be out-of-date for the build if the package configuration changes -within the same command. - -Any package can be installed or not in a LAMMPS build, independent of -all other packages. However, some packages include files derived from -files in other packages. LAMMPS checks for this and does the right -thing. I.e. individual files are only included if their dependencies -are already included. Likewise, if a package is excluded, other files -dependent on that package are also excluded. - -NOTE: The one exception is that we do not recommend building with both -the KOKKOS package installed and any of the other acceleration -packages (GPU, OPT, USER-INTEL, USER-OMP) also installed. This is -because of how Kokkos sometimes builds using a wrapper compiler which -can make it difficult to invoke all the compile/link flags correctly -for both Kokkos and non-Kokkos files. - -If you will never run simulations that use the features in a -particular packages, there is no reason to include it in your build. -For some packages, this will keep you from having to build extra -libraries, and will also produce a smaller executable which may run a -bit faster. - -When you download a LAMMPS tarball, three packages are pre-installed -in the src directory -- KSPACE, MANYBODY, MOLECULE -- because they are -so commonly used. When you download LAMMPS source files from the SVN -or Git repositories, no packages are pre-installed. - -Packages are installed or un-installed by typing - -make yes-name -make no-name :pre - -where "name" is the name of the package in lower-case, e.g. name = -kspace for the KSPACE package or name = user-atc for the USER-ATC -package. You can also type any of these commands: - -make yes-all | install all packages -make no-all | un-install all packages -make yes-standard or make yes-std | install standard packages -make no-standard or make no-std| un-install standard packages -make yes-user | install user packages -make no-user | un-install user packages -make yes-lib | install packages that require extra libraries -make no-lib | un-install packages that require extra libraries -make yes-ext | install packages that require external libraries -make no-ext | un-install packages that require external libraries :tb(s=|) - -which install/un-install various sets of packages. Typing "make -package" will list all the these commands. - -NOTE: Installing or un-installing a package works by simply moving -files back and forth between the main src directory and -sub-directories with the package name (e.g. src/KSPACE, src/USER-ATC), -so that the files are included or excluded when LAMMPS is built. -After you have installed or un-installed a package, you must re-build -LAMMPS for the action to take effect. - -The following make commands help manage files that exist in both the -src directory and in package sub-directories. You do not normally -need to use these commands unless you are editing LAMMPS files or have -downloaded a patch from the LAMMPS web site. - -Typing "make package-status" or "make ps" will show which packages are -currently installed. For those that are installed, it will list any -files that are different in the src directory and package -sub-directory. - -Typing "make package-installed" or "make pi" will list which packages are -currently installed, without listing the status of packages that are not -installed. - -Typing "make package-update" or "make pu" will overwrite src files -with files from the package sub-directories if the package is -installed. It should be used after a patch has been applied, since -patches only update the files in the package sub-directory, but not -the src files. - -Typing "make package-overwrite" will overwrite files in the package -sub-directories with src files. - -Typing "make package-diff" lists all differences between these files. - -Again, just type "make package" to see all of the package-related make -options. - -:line - -Packages that require extra libraries :h4,link(start_3_3) - -A few of the standard and user packages require extra libraries. See -"Section 4"_Section_packages.html for two tables of packages which -indicate which ones require libraries. For each such package, the -Section 4 doc page gives details on how to build the extra library, -including how to download it if necessary. The basic ideas are -summarized here. - -[System libraries:] - -Packages in the tables "Section 4"_Section_packages.html with a "sys" -in the last column link to system libraries that typically already -exist on your machine. E.g. the python package links to a system -Python library. If your machine does not have the required library, -you will have to download and install it on your machine, in either -the system or user space. - -[Internal libraries:] - -Packages in the tables "Section 4"_Section_packages.html with an "int" -in the last column link to internal libraries whose source code is -included with LAMMPS, in the lib/name directory where name is the -package name. You must first build the library in that directory -before building LAMMPS with that package installed. E.g. the gpu -package links to a library you build in the lib/gpu dir. You can -often do the build in one step by typing "make lib-name args=..." -from the src dir, with appropriate arguments. You can leave off the -args to see a help message. See "Section 4"_Section_packages.html for -details for each package. - -[External libraries:] - -Packages in the tables "Section 4"_Section_packages.html with an "ext" -in the last column link to external libraries whose source code is not -included with LAMMPS. You must first download and install the library -before building LAMMPS with that package installed. E.g. the voronoi -package links to the freely available "Voro++ library"_voro_home2. You -can often do the download/build in one step by typing "make lib-name -args=..." from the src dir, with appropriate arguments. You can leave -off the args to see a help message. See "Section -4"_Section_packages.html for details for each package. - -:link(voro_home2,http://math.lbl.gov/voro++) - -[Possible errors:] - -There are various common errors which can occur when building extra -libraries or when building LAMMPS with packages that require the extra -libraries. - -If you cannot build the extra library itself successfully, you may -need to edit or create an appropriate Makefile for your machine, e.g. -with appropriate compiler or system settings. Provided makefiles are -typically in the lib/name directory. E.g. see the Makefile.* files in -lib/gpu. - -The LAMMPS build often uses settings in a lib/name/Makefile.lammps -file which either exists in the LAMMPS distribution or is created or -copied from a lib/name/Makefile.lammps.* file when the library is -built. If those settings are not correct for your machine you will -need to edit or create an appropriate Makefile.lammps file. - -Package-specific details for these steps are given in "Section -4"_Section_packages.html an in README files in the lib/name -directories. - -[Compiler options needed for accelerator packages:] - -Several packages contain code that is optimized for specific hardware, -e.g. CPU, KNL, or GPU. These are the OPT, GPU, KOKKOS, USER-INTEL, -and USER-OMP packages. Compiling and linking the source files in -these accelerator packages for optimal performance requires specific -settings in the Makefile.machine file you use. - -A summary of the Makefile.machine settings needed for each of these -packages is given in "Section 4"_Section_packages.html. More info is -given on the doc pages that describe each package in detail: - -5.3.1 "USER-INTEL package"_accelerate_intel.html -5.3.2 "GPU package"_accelerate_intel.html -5.3.3 "KOKKOS package"_accelerate_kokkos.html -5.3.4 "USER-OMP package"_accelerate_omp.html -5.3.5 "OPT package"_accelerate_opt.html :all(b) - -You can also use or examine the following machine Makefiles in -src/MAKE/OPTIONS, which include the settings. Note that the -USER-INTEL and KOKKOS packages can use settings that build LAMMPS for -different hardware. The USER-INTEL package can be compiled for Intel -CPUs and KNLs; the KOKKOS package builds for CPUs (OpenMP), GPUs -(CUDA), and Intel KNLs. - -Makefile.intel_cpu -Makefile.intel_phi -Makefile.kokkos_omp -Makefile.kokkos_cuda_mpi -Makefile.kokkos_phi -Makefile.omp -Makefile.opt :ul - -:line - -2.4 Building LAMMPS as a library :h3,link(start_4) - -LAMMPS can be built as either a static or shared library, which can -then be called from another application or a scripting language. See -"this section"_Section_howto.html#howto_10 for more info on coupling -LAMMPS to other codes. See "this section"_Section_python.html for -more info on wrapping and running LAMMPS from Python. - -Static library :h4 - -To build LAMMPS as a static library (*.a file on Linux), type - -make foo mode=lib :pre - -where foo is the machine name. This kind of library is typically used -to statically link a driver application to LAMMPS, so that you can -insure all dependencies are satisfied at compile time. This will use -the ARCHIVE and ARFLAGS settings in src/MAKE/Makefile.foo. The build -will create the file liblammps_foo.a which another application can -link to. It will also create a soft link liblammps.a, which will -point to the most recently built static library. - -Shared library :h4 - -To build LAMMPS as a shared library (*.so file on Linux), which can be -dynamically loaded, e.g. from Python, type - -make foo mode=shlib :pre - -where foo is the machine name. This kind of library is required when -wrapping LAMMPS with Python; see "Section 11"_Section_python.html -for details. This will use the SHFLAGS and SHLIBFLAGS settings in -src/MAKE/Makefile.foo and perform the build in the directory -Obj_shared_foo. This is so that each file can be compiled with the --fPIC flag which is required for inclusion in a shared library. The -build will create the file liblammps_foo.so which another application -can link to dynamically. It will also create a soft link liblammps.so, -which will point to the most recently built shared library. This is -the file the Python wrapper loads by default. - -Note that for a shared library to be usable by a calling program, all -the auxiliary libraries it depends on must also exist as shared -libraries. This will be the case for libraries included with LAMMPS, -such as the dummy MPI library in src/STUBS or any package libraries in -lib/packages, since they are always built as shared libraries using -the -fPIC switch. However, if a library like MPI or FFTW does not -exist as a shared library, the shared library build will generate an -error. This means you will need to install a shared library version -of the auxiliary library. The build instructions for the library -should tell you how to do this. - -Here is an example of such errors when the system FFTW or provided -lib/colvars library have not been built as shared libraries: - -/usr/bin/ld: /usr/local/lib/libfftw3.a(mapflags.o): relocation -R_X86_64_32 against '.rodata' can not be used when making a shared -object; recompile with -fPIC -/usr/local/lib/libfftw3.a: could not read symbols: Bad value :pre - -/usr/bin/ld: ../../lib/colvars/libcolvars.a(colvarmodule.o): -relocation R_X86_64_32 against '__pthread_key_create' can not be used -when making a shared object; recompile with -fPIC -../../lib/colvars/libcolvars.a: error adding symbols: Bad value :pre - -As an example, here is how to build and install the "MPICH -library"_mpich, a popular open-source version of MPI, distributed by -Argonne National Labs, as a shared library in the default -/usr/local/lib location: - -:link(mpich,http://www-unix.mcs.anl.gov/mpi) - -./configure --enable-shared -make -make install :pre - -You may need to use "sudo make install" in place of the last line if -you do not have write privileges for /usr/local/lib. The end result -should be the file /usr/local/lib/libmpich.so. - -[Additional requirement for using a shared library:] :h4 - -The operating system finds shared libraries to load at run-time using -the environment variable LD_LIBRARY_PATH. So you may wish to copy the -file src/liblammps.so or src/liblammps_g++.so (for example) to a place -the system can find it by default, such as /usr/local/lib, or you may -wish to add the LAMMPS src directory to LD_LIBRARY_PATH, so that the -current version of the shared library is always available to programs -that use it. - -For the csh or tcsh shells, you would add something like this to your -~/.cshrc file: - -setenv LD_LIBRARY_PATH $\{LD_LIBRARY_PATH\}:/home/sjplimp/lammps/src :pre - -Calling the LAMMPS library :h4 - -Either flavor of library (static or shared) allows one or more LAMMPS -objects to be instantiated from the calling program. - -When used from a C++ program, all of LAMMPS is wrapped in a LAMMPS_NS -namespace; you can safely use any of its classes and methods from -within the calling code, as needed. - -When used from a C or Fortran program or a scripting language like -Python, the library has a simple function-style interface, provided in -src/library.cpp and src/library.h. - -See the sample codes in examples/COUPLE/simple for examples of C++ and -C and Fortran codes that invoke LAMMPS thru its library interface. -There are other examples as well in the COUPLE directory which are -discussed in "Section 6.10"_Section_howto.html#howto_10 of the -manual. See "Section 11"_Section_python.html of the manual for a -description of the Python wrapper provided with LAMMPS that operates -through the LAMMPS library interface. - -The files src/library.cpp and library.h define the C-style API for -using LAMMPS as a library. See "Section -6.19"_Section_howto.html#howto_19 of the manual for a description of the -interface and how to extend it for your needs. - -:line - -2.5 Running LAMMPS :h3,link(start_5) - -By default, LAMMPS runs by reading commands from standard input. Thus -if you run the LAMMPS executable by itself, e.g. - -lmp_linux :pre - -it will simply wait, expecting commands from the keyboard. Typically -you should put commands in an input script and use I/O redirection, -e.g. - -lmp_linux < in.file :pre - -For parallel environments this should also work. If it does not, use -the '-in' command-line switch, e.g. - -lmp_linux -in in.file :pre - -"This section"_Section_commands.html describes how input scripts are -structured and what commands they contain. - -You can test LAMMPS on any of the sample inputs provided in the -examples or bench directory. Input scripts are named in.* and sample -outputs are named log.*.name.P where name is a machine and P is the -number of processors it was run on. - -Here is how you might run a standard Lennard-Jones benchmark on a -Linux box, using mpirun to launch a parallel job: - -cd src -make linux -cp lmp_linux ../bench -cd ../bench -mpirun -np 4 lmp_linux -in in.lj :pre - -See "this page"_bench for timings for this and the other benchmarks on -various platforms. Note that some of the example scripts require -LAMMPS to be built with one or more of its optional packages. - -:link(bench,http://lammps.sandia.gov/bench.html) - -:line - -On a Windows box, you can skip making LAMMPS and simply download an -installer package from "here"_http://packages.lammps.org/windows.html - -For running the non-MPI executable, follow these steps: - -Get a command prompt by going to Start->Run... , -then typing "cmd". :ulb,l - -Move to the directory where you have your input, e.g. a copy of -the [in.lj] input from the bench folder. (e.g. by typing: cd "Documents"). :l - -At the command prompt, type "lmp_serial -in in.lj", replacing [in.lj] -with the name of your LAMMPS input script. :l - -The serial executable includes support for multi-threading -parallelization from the styles in the USER-OMP packages. - -To run with, e.g. 4 threads, type "lmp_serial -in in.lj -pk omp 4 -sf omp" -:ule - -For the MPI version, which allows you to run LAMMPS under Windows with -the more general message passing parallel library (LAMMPS has been -designed from ground up to use MPI efficiently), follow these steps: - -Download and install a compatible MPI library binary package: -for 32-bit Windows -"mpich2-1.4.1p1-win-ia32.msi"_download.lammps.org/thirdparty/mpich2-1.4.1p1-win-ia32.msi -and for 64-bit Windows -"mpich2-1.4.1p1-win-x86-64.msi"_download.lammps.org/thirdparty/mpich2-1.4.1p1-win-x86-64.msi -:ulb,l - -The LAMMPS Windows installer packages will automatically adjust your -path for the default location of this MPI package. After the installation -of the MPICH2 software, it needs to be integrated into the system. -For this you need to start a Command Prompt in {Administrator Mode} -(right click on the icon and select it). Change into the MPICH2 -installation directory, then into the subdirectory [bin] and execute -[smpd.exe -install]. Exit the command window. - -Get a new, regular command prompt by going to Start->Run... , -then typing "cmd". :l - -Move to the directory where you have your input file -(e.g. by typing: cd "Documents"). :l - -Then type something like this: - -mpiexec -localonly 4 lmp_mpi -in in.lj :pre -or - -mpiexec -np 4 lmp_mpi -in in.lj :pre - -replacing [in.lj] with the name of your LAMMPS input script. For the latter -case, you may be prompted to enter your password. :l - -In this mode, output may not immediately show up on the screen, so if -your input script takes a long time to execute, you may need to be -patient before the output shows up. :l - -The parallel executable can also run on a single processor by typing -something like: - -lmp_mpi -in in.lj :pre - -And the parallel executable also includes OpenMP multi-threading, which -can be combined with MPI using something like: - -mpiexec -localonly 2 lmp_mpi -in in.lj -pk omp 2 -sf omp :pre - -:ule - -:line - -The screen output from LAMMPS is described in a section below. As it -runs, LAMMPS also writes a log.lammps file with the same information. - -Note that this sequence of commands copies the LAMMPS executable -(lmp_linux) to the directory with the input files. This may not be -necessary, but some versions of MPI reset the working directory to -where the executable is, rather than leave it as the directory where -you launch mpirun from (if you launch lmp_linux on its own and not -under mpirun). If that happens, LAMMPS will look for additional input -files and write its output files to the executable directory, rather -than your working directory, which is probably not what you want. - -If LAMMPS encounters errors in the input script or while running a -simulation it will print an ERROR message and stop or a WARNING -message and continue. See "Section 12"_Section_errors.html for a -discussion of the various kinds of errors LAMMPS can or can't detect, -a list of all ERROR and WARNING messages, and what to do about them. - -LAMMPS can run a problem on any number of processors, including a -single processor. In theory you should get identical answers on any -number of processors and on any machine. In practice, numerical -round-off can cause slight differences and eventual divergence of -molecular dynamics phase space trajectories. - -LAMMPS can run as large a problem as will fit in the physical memory -of one or more processors. If you run out of memory, you must run on -more processors or setup a smaller problem. - -:line - -2.6 Command-line options :h3,link(start_6) - -At run time, LAMMPS recognizes several optional command-line switches -which may be used in any order. Either the full word or a one-or-two -letter abbreviation can be used: - --e or -echo --h or -help --i or -in --k or -kokkos --l or -log --nc or -nocite --pk or -package --p or -partition --pl or -plog --ps or -pscreen --r or -restart --ro or -reorder --sc or -screen --sf or -suffix --v or -var :ul - -For example, lmp_ibm might be launched as follows: - -mpirun -np 16 lmp_ibm -v f tmp.out -l my.log -sc none -in in.alloy -mpirun -np 16 lmp_ibm -var f tmp.out -log my.log -screen none -in in.alloy :pre - -Here are the details on the options: - --echo style :pre - -Set the style of command echoing. The style can be {none} or {screen} -or {log} or {both}. Depending on the style, each command read from -the input script will be echoed to the screen and/or logfile. This -can be useful to figure out which line of your script is causing an -input error. The default value is {log}. The echo style can also be -set by using the "echo"_echo.html command in the input script itself. - --help :pre - -Print a brief help summary and a list of options compiled into this -executable for each LAMMPS style (atom_style, fix, compute, -pair_style, bond_style, etc). This can tell you if the command you -want to use was included via the appropriate package at compile time. -LAMMPS will print the info and immediately exit if this switch is -used. - --in file :pre - -Specify a file to use as an input script. This is an optional switch -when running LAMMPS in one-partition mode. If it is not specified, -LAMMPS reads its script from standard input, typically from a script -via I/O redirection; e.g. lmp_linux < in.run. I/O redirection should -also work in parallel, but if it does not (in the unlikely case that -an MPI implementation does not support it), then use the -in flag. -Note that this is a required switch when running LAMMPS in -multi-partition mode, since multiple processors cannot all read from -stdin. - --kokkos on/off keyword/value ... :pre - -Explicitly enable or disable KOKKOS support, as provided by the KOKKOS -package. Even if LAMMPS is built with this package, as described -above in "Section 2.3"_#start_3, this switch must be set to enable -running with the KOKKOS-enabled styles the package provides. If the -switch is not set (the default), LAMMPS will operate as if the KOKKOS -package were not installed; i.e. you can run standard LAMMPS or with -the GPU or USER-OMP packages, for testing or benchmarking purposes. - -Additional optional keyword/value pairs can be specified which -determine how Kokkos will use the underlying hardware on your -platform. These settings apply to each MPI task you launch via the -"mpirun" or "mpiexec" command. You may choose to run one or more MPI -tasks per physical node. Note that if you are running on a desktop -machine, you typically have one physical node. On a cluster or -supercomputer there may be dozens or 1000s of physical nodes. - -Either the full word or an abbreviation can be used for the keywords. -Note that the keywords do not use a leading minus sign. I.e. the -keyword is "t", not "-t". Also note that each of the keywords has a -default setting. Example of when to use these options and what -settings to use on different platforms is given in "Section -5.3"_Section_accelerate.html#acc_3. - -d or device -g or gpus -t or threads -n or numa :ul - -device Nd :pre - -This option is only relevant if you built LAMMPS with CUDA=yes, you -have more than one GPU per node, and if you are running with only one -MPI task per node. The Nd setting is the ID of the GPU on the node to -run on. By default Nd = 0. If you have multiple GPUs per node, they -have consecutive IDs numbered as 0,1,2,etc. This setting allows you -to launch multiple independent jobs on the node, each with a single -MPI task per node, and assign each job to run on a different GPU. - -gpus Ng Ns :pre - -This option is only relevant if you built LAMMPS with CUDA=yes, you -have more than one GPU per node, and you are running with multiple MPI -tasks per node (up to one per GPU). The Ng setting is how many GPUs -you will use. The Ns setting is optional. If set, it is the ID of a -GPU to skip when assigning MPI tasks to GPUs. This may be useful if -your desktop system reserves one GPU to drive the screen and the rest -are intended for computational work like running LAMMPS. By default -Ng = 1 and Ns is not set. - -Depending on which flavor of MPI you are running, LAMMPS will look for -one of these 3 environment variables - -SLURM_LOCALID (various MPI variants compiled with SLURM support) -MV2_COMM_WORLD_LOCAL_RANK (Mvapich) -OMPI_COMM_WORLD_LOCAL_RANK (OpenMPI) :pre - -which are initialized by the "srun", "mpirun" or "mpiexec" commands. -The environment variable setting for each MPI rank is used to assign a -unique GPU ID to the MPI task. - -threads Nt :pre - -This option assigns Nt number of threads to each MPI task for -performing work when Kokkos is executing in OpenMP or pthreads mode. -The default is Nt = 1, which essentially runs in MPI-only mode. If -there are Np MPI tasks per physical node, you generally want Np*Nt = -the number of physical cores per node, to use your available hardware -optimally. This also sets the number of threads used by the host when -LAMMPS is compiled with CUDA=yes. - -numa Nm :pre - -This option is only relevant when using pthreads with hwloc support. -In this case Nm defines the number of NUMA regions (typically sockets) -on a node which will be utilized by a single MPI rank. By default Nm -= 1. If this option is used the total number of worker-threads per -MPI rank is threads*numa. Currently it is always almost better to -assign at least one MPI rank per NUMA region, and leave numa set to -its default value of 1. This is because letting a single process span -multiple NUMA regions induces a significant amount of cross NUMA data -traffic which is slow. - --log file :pre - -Specify a log file for LAMMPS to write status information to. In -one-partition mode, if the switch is not used, LAMMPS writes to the -file log.lammps. If this switch is used, LAMMPS writes to the -specified file. In multi-partition mode, if the switch is not used, a -log.lammps file is created with hi-level status information. Each -partition also writes to a log.lammps.N file where N is the partition -ID. If the switch is specified in multi-partition mode, the hi-level -logfile is named "file" and each partition also logs information to a -file.N. For both one-partition and multi-partition mode, if the -specified file is "none", then no log files are created. Using a -"log"_log.html command in the input script will override this setting. -Option -plog will override the name of the partition log files file.N. - --nocite :pre - -Disable writing the log.cite file which is normally written to list -references for specific cite-able features used during a LAMMPS run. -See the "citation page"_http://lammps.sandia.gov/cite.html for more -details. - --package style args .... :pre - -Invoke the "package"_package.html command with style and args. The -syntax is the same as if the command appeared at the top of the input -script. For example "-package gpu 2" or "-pk gpu 2" is the same as -"package gpu 2"_package.html in the input script. The possible styles -and args are documented on the "package"_package.html doc page. This -switch can be used multiple times, e.g. to set options for the -USER-INTEL and USER-OMP packages which can be used together. - -Along with the "-suffix" command-line switch, this is a convenient -mechanism for invoking accelerator packages and their options without -having to edit an input script. - --partition 8x2 4 5 ... :pre - -Invoke LAMMPS in multi-partition mode. When LAMMPS is run on P -processors and this switch is not used, LAMMPS runs in one partition, -i.e. all P processors run a single simulation. If this switch is -used, the P processors are split into separate partitions and each -partition runs its own simulation. The arguments to the switch -specify the number of processors in each partition. Arguments of the -form MxN mean M partitions, each with N processors. Arguments of the -form N mean a single partition with N processors. The sum of -processors in all partitions must equal P. Thus the command -"-partition 8x2 4 5" has 10 partitions and runs on a total of 25 -processors. - -Running with multiple partitions can e useful for running -"multi-replica simulations"_Section_howto.html#howto_5, where each -replica runs on on one or a few processors. Note that with MPI -installed on a machine (e.g. your desktop), you can run on more -(virtual) processors than you have physical processors. - -To run multiple independent simulations from one input script, using -multiple partitions, see "Section 6.4"_Section_howto.html#howto_4 -of the manual. World- and universe-style "variables"_variable.html -are useful in this context. - --plog file :pre - -Specify the base name for the partition log files, so partition N -writes log information to file.N. If file is none, then no partition -log files are created. This overrides the filename specified in the --log command-line option. This option is useful when working with -large numbers of partitions, allowing the partition log files to be -suppressed (-plog none) or placed in a sub-directory (-plog -replica_files/log.lammps) If this option is not used the log file for -partition N is log.lammps.N or whatever is specified by the -log -command-line option. - --pscreen file :pre - -Specify the base name for the partition screen file, so partition N -writes screen information to file.N. If file is none, then no -partition screen files are created. This overrides the filename -specified in the -screen command-line option. This option is useful -when working with large numbers of partitions, allowing the partition -screen files to be suppressed (-pscreen none) or placed in a -sub-directory (-pscreen replica_files/screen). If this option is not -used the screen file for partition N is screen.N or whatever is -specified by the -screen command-line option. - --restart restartfile {remap} datafile keyword value ... :pre - -Convert the restart file into a data file and immediately exit. This -is the same operation as if the following 2-line input script were -run: - -read_restart restartfile {remap} -write_data datafile keyword value ... :pre - -Note that the specified restartfile and datafile can have wild-card -characters ("*",%") as described by the -"read_restart"_read_restart.html and "write_data"_write_data.html -commands. But a filename such as file.* will need to be enclosed in -quotes to avoid shell expansion of the "*" character. - -Note that following restartfile, the optional flag {remap} can be -used. This has the same effect as adding it to the -"read_restart"_read_restart.html command, as explained on its doc -page. This is only useful if the reading of the restart file triggers -an error that atoms have been lost. In that case, use of the remap -flag should allow the data file to still be produced. - -Also note that following datafile, the same optional keyword/value -pairs can be listed as used by the "write_data"_write_data.html -command. - --reorder nth N --reorder custom filename :pre - -Reorder the processors in the MPI communicator used to instantiate -LAMMPS, in one of several ways. The original MPI communicator ranks -all P processors from 0 to P-1. The mapping of these ranks to -physical processors is done by MPI before LAMMPS begins. It may be -useful in some cases to alter the rank order. E.g. to insure that -cores within each node are ranked in a desired order. Or when using -the "run_style verlet/split"_run_style.html command with 2 partitions -to insure that a specific Kspace processor (in the 2nd partition) is -matched up with a specific set of processors in the 1st partition. -See the "Section 5"_Section_accelerate.html doc pages for -more details. - -If the keyword {nth} is used with a setting {N}, then it means every -Nth processor will be moved to the end of the ranking. This is useful -when using the "run_style verlet/split"_run_style.html command with 2 -partitions via the -partition command-line switch. The first set of -processors will be in the first partition, the 2nd set in the 2nd -partition. The -reorder command-line switch can alter this so that -the 1st N procs in the 1st partition and one proc in the 2nd partition -will be ordered consecutively, e.g. as the cores on one physical node. -This can boost performance. For example, if you use "-reorder nth 4" -and "-partition 9 3" and you are running on 12 processors, the -processors will be reordered from - -0 1 2 3 4 5 6 7 8 9 10 11 :pre - -to - -0 1 2 4 5 6 8 9 10 3 7 11 :pre - -so that the processors in each partition will be - -0 1 2 4 5 6 8 9 10 -3 7 11 :pre - -See the "processors" command for how to insure processors from each -partition could then be grouped optimally for quad-core nodes. - -If the keyword is {custom}, then a file that specifies a permutation -of the processor ranks is also specified. The format of the reorder -file is as follows. Any number of initial blank or comment lines -(starting with a "#" character) can be present. These should be -followed by P lines of the form: - -I J :pre - -where P is the number of processors LAMMPS was launched with. Note -that if running in multi-partition mode (see the -partition switch -above) P is the total number of processors in all partitions. The I -and J values describe a permutation of the P processors. Every I and -J should be values from 0 to P-1 inclusive. In the set of P I values, -every proc ID should appear exactly once. Ditto for the set of P J -values. A single I,J pairing means that the physical processor with -rank I in the original MPI communicator will have rank J in the -reordered communicator. - -Note that rank ordering can also be specified by many MPI -implementations, either by environment variables that specify how to -order physical processors, or by config files that specify what -physical processors to assign to each MPI rank. The -reorder switch -simply gives you a portable way to do this without relying on MPI -itself. See the "processors out"_processors.html command for how -to output info on the final assignment of physical processors to -the LAMMPS simulation domain. - --screen file :pre - -Specify a file for LAMMPS to write its screen information to. In -one-partition mode, if the switch is not used, LAMMPS writes to the -screen. If this switch is used, LAMMPS writes to the specified file -instead and you will see no screen output. In multi-partition mode, -if the switch is not used, hi-level status information is written to -the screen. Each partition also writes to a screen.N file where N is -the partition ID. If the switch is specified in multi-partition mode, -the hi-level screen dump is named "file" and each partition also -writes screen information to a file.N. For both one-partition and -multi-partition mode, if the specified file is "none", then no screen -output is performed. Option -pscreen will override the name of the -partition screen files file.N. - --suffix style args :pre - -Use variants of various styles if they exist. The specified style can -be {cuda}, {gpu}, {intel}, {kk}, {omp}, {opt}, or {hybrid}. These -refer to optional packages that LAMMPS can be built with, as described -above in "Section 2.3"_#start_3. The "gpu" style corresponds to the -GPU package, the "intel" style to the USER-INTEL package, the "kk" -style to the KOKKOS package, the "opt" style to the OPT package, and -the "omp" style to the USER-OMP package. The hybrid style is the only -style that accepts arguments. It allows for two packages to be -specified. The first package specified is the default and will be used -if it is available. If no style is available for the first package, -the style for the second package will be used if available. For -example, "-suffix hybrid intel omp" will use styles from the -USER-INTEL package if they are installed and available, but styles for -the USER-OMP package otherwise. - -Along with the "-package" command-line switch, this is a convenient -mechanism for invoking accelerator packages and their options without -having to edit an input script. - -As an example, all of the packages provide a "pair_style -lj/cut"_pair_lj.html variant, with style names lj/cut/gpu, -lj/cut/intel, lj/cut/kk, lj/cut/omp, and lj/cut/opt. A variant style -can be specified explicitly in your input script, e.g. pair_style -lj/cut/gpu. If the -suffix switch is used the specified suffix -(gpu,intel,kk,omp,opt) is automatically appended whenever your input -script command creates a new "atom"_atom_style.html, -"pair"_pair_style.html, "fix"_fix.html, "compute"_compute.html, or -"run"_run_style.html style. If the variant version does not exist, -the standard version is created. - -For the GPU package, using this command-line switch also invokes the -default GPU settings, as if the command "package gpu 1" were used at -the top of your input script. These settings can be changed by using -the "-package gpu" command-line switch or the "package -gpu"_package.html command in your script. - -For the USER-INTEL package, using this command-line switch also -invokes the default USER-INTEL settings, as if the command "package -intel 1" were used at the top of your input script. These settings -can be changed by using the "-package intel" command-line switch or -the "package intel"_package.html command in your script. If the -USER-OMP package is also installed, the hybrid style with "intel omp" -arguments can be used to make the omp suffix a second choice, if a -requested style is not available in the USER-INTEL package. It will -also invoke the default USER-OMP settings, as if the command "package -omp 0" were used at the top of your input script. These settings can -be changed by using the "-package omp" command-line switch or the -"package omp"_package.html command in your script. - -For the KOKKOS package, using this command-line switch also invokes -the default KOKKOS settings, as if the command "package kokkos" were -used at the top of your input script. These settings can be changed -by using the "-package kokkos" command-line switch or the "package -kokkos"_package.html command in your script. - -For the OMP package, using this command-line switch also invokes the -default OMP settings, as if the command "package omp 0" were used at -the top of your input script. These settings can be changed by using -the "-package omp" command-line switch or the "package -omp"_package.html command in your script. - -The "suffix"_suffix.html command can also be used within an input -script to set a suffix, or to turn off or back on any suffix setting -made via the command line. - --var name value1 value2 ... :pre - -Specify a variable that will be defined for substitution purposes when -the input script is read. This switch can be used multiple times to -define multiple variables. "Name" is the variable name which can be a -single character (referenced as $x in the input script) or a full -string (referenced as $\{abc\}). An "index-style -variable"_variable.html will be created and populated with the -subsequent values, e.g. a set of filenames. Using this command-line -option is equivalent to putting the line "variable name index value1 -value2 ..." at the beginning of the input script. Defining an index -variable as a command-line argument overrides any setting for the same -index variable in the input script, since index variables cannot be -re-defined. See the "variable"_variable.html command for more info on -defining index and other kinds of variables and "this -section"_Section_commands.html#cmd_2 for more info on using variables -in input scripts. - -NOTE: Currently, the command-line parser looks for arguments that -start with "-" to indicate new switches. Thus you cannot specify -multiple variable values if any of they start with a "-", e.g. a -negative numeric value. It is OK if the first value1 starts with a -"-", since it is automatically skipped. - -:line - -2.7 LAMMPS screen output :h3,link(start_7) - -As LAMMPS reads an input script, it prints information to both the -screen and a log file about significant actions it takes to setup a -simulation. When the simulation is ready to begin, LAMMPS performs -various initializations and prints the amount of memory (in MBytes per -processor) that the simulation requires. It also prints details of -the initial thermodynamic state of the system. During the run itself, -thermodynamic information is printed periodically, every few -timesteps. When the run concludes, LAMMPS prints the final -thermodynamic state and a total run time for the simulation. It then -appends statistics about the CPU time and storage requirements for the -simulation. An example set of statistics is shown here: - -Loop time of 2.81192 on 4 procs for 300 steps with 2004 atoms :pre - -Performance: 18.436 ns/day 1.302 hours/ns 106.689 timesteps/s -97.0% CPU use with 4 MPI tasks x no OpenMP threads :pre - -MPI task timings breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 1.9808 | 2.0134 | 2.0318 | 1.4 | 71.60 -Bond | 0.0021894 | 0.0060319 | 0.010058 | 4.7 | 0.21 -Kspace | 0.3207 | 0.3366 | 0.36616 | 3.1 | 11.97 -Neigh | 0.28411 | 0.28464 | 0.28516 | 0.1 | 10.12 -Comm | 0.075732 | 0.077018 | 0.07883 | 0.4 | 2.74 -Output | 0.00030518 | 0.00042665 | 0.00078821 | 1.0 | 0.02 -Modify | 0.086606 | 0.086631 | 0.086668 | 0.0 | 3.08 -Other | | 0.007178 | | | 0.26 :pre - -Nlocal: 501 ave 508 max 490 min -Histogram: 1 0 0 0 0 0 1 1 0 1 -Nghost: 6586.25 ave 6628 max 6548 min -Histogram: 1 0 1 0 0 0 1 0 0 1 -Neighs: 177007 ave 180562 max 170212 min -Histogram: 1 0 0 0 0 0 0 1 1 1 :pre - -Total # of neighbors = 708028 -Ave neighs/atom = 353.307 -Ave special neighs/atom = 2.34032 -Neighbor list builds = 26 -Dangerous builds = 0 :pre - -The first section provides a global loop timing summary. The {loop time} -is the total wall time for the section. The {Performance} line is -provided for convenience to help predicting the number of loop -continuations required and for comparing performance with other, -similar MD codes. The {CPU use} line provides the CPU utilization per -MPI task; it should be close to 100% times the number of OpenMP -threads (or 1 of no OpenMP). Lower numbers correspond to delays due -to file I/O or insufficient thread utilization. - -The MPI task section gives the breakdown of the CPU run time (in -seconds) into major categories: - -{Pair} stands for all non-bonded force computation -{Bond} stands for bonded interactions: bonds, angles, dihedrals, impropers -{Kspace} stands for reciprocal space interactions: Ewald, PPPM, MSM -{Neigh} stands for neighbor list construction -{Comm} stands for communicating atoms and their properties -{Output} stands for writing dumps and thermo output -{Modify} stands for fixes and computes called by them -{Other} is the remaining time :ul - -For each category, there is a breakdown of the least, average and most -amount of wall time a processor spent on this section. Also you have the -variation from the average time. Together these numbers allow to gauge -the amount of load imbalance in this segment of the calculation. Ideally -the difference between minimum, maximum and average is small and thus -the variation from the average close to zero. The final column shows -the percentage of the total loop time is spent in this section. - -When using the "timer full"_timer.html setting, an additional column -is present that also prints the CPU utilization in percent. In -addition, when using {timer full} and the "package omp"_package.html -command are active, a similar timing summary of time spent in threaded -regions to monitor thread utilization and load balance is provided. A -new entry is the {Reduce} section, which lists the time spent in -reducing the per-thread data elements to the storage for non-threaded -computation. These thread timings are taking from the first MPI rank -only and and thus, as the breakdown for MPI tasks can change from MPI -rank to MPI rank, this breakdown can be very different for individual -ranks. Here is an example output for this section: - -Thread timings breakdown (MPI rank 0): -Total threaded time 0.6846 / 90.6% -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.5127 | 0.5147 | 0.5167 | 0.3 | 75.18 -Bond | 0.0043139 | 0.0046779 | 0.0050418 | 0.5 | 0.68 -Kspace | 0.070572 | 0.074541 | 0.07851 | 1.5 | 10.89 -Neigh | 0.084778 | 0.086969 | 0.089161 | 0.7 | 12.70 -Reduce | 0.0036485 | 0.003737 | 0.0038254 | 0.1 | 0.55 :pre - -The third section lists the number of owned atoms (Nlocal), ghost atoms -(Nghost), and pair-wise neighbors stored per processor. The max and min -values give the spread of these values across processors with a 10-bin -histogram showing the distribution. The total number of histogram counts -is equal to the number of processors. - -The last section gives aggregate statistics for pair-wise neighbors -and special neighbors that LAMMPS keeps track of (see the -"special_bonds"_special_bonds.html command). The number of times -neighbor lists were rebuilt during the run is given as well as the -number of potentially "dangerous" rebuilds. If atom movement -triggered neighbor list rebuilding (see the -"neigh_modify"_neigh_modify.html command), then dangerous -reneighborings are those that were triggered on the first timestep -atom movement was checked for. If this count is non-zero you may wish -to reduce the delay factor to insure no force interactions are missed -by atoms moving beyond the neighbor skin distance before a rebuild -takes place. - -If an energy minimization was performed via the -"minimize"_minimize.html command, additional information is printed, -e.g. - -Minimization stats: - Stopping criterion = linesearch alpha is zero - Energy initial, next-to-last, final = - -6372.3765206 -8328.46998942 -8328.46998942 - Force two-norm initial, final = 1059.36 5.36874 - Force max component initial, final = 58.6026 1.46872 - Final line search alpha, max atom move = 2.7842e-10 4.0892e-10 - Iterations, force evaluations = 701 1516 :pre - -The first line prints the criterion that determined the minimization -to be completed. The third line lists the initial and final energy, -as well as the energy on the next-to-last iteration. The next 2 lines -give a measure of the gradient of the energy (force on all atoms). -The 2-norm is the "length" of this force vector; the inf-norm is the -largest component. Then some information about the line search and -statistics on how many iterations and force-evaluations the minimizer -required. Multiple force evaluations are typically done at each -iteration to perform a 1d line minimization in the search direction. - -If a "kspace_style"_kspace_style.html long-range Coulombics solve was -performed during the run (PPPM, Ewald), then additional information is -printed, e.g. - -FFT time (% of Kspce) = 0.200313 (8.34477) -FFT Gflps 3d 1d-only = 2.31074 9.19989 :pre - -The first line gives the time spent doing 3d FFTs (4 per timestep) and -the fraction it represents of the total KSpace time (listed above). -Each 3d FFT requires computation (3 sets of 1d FFTs) and communication -(transposes). The total flops performed is 5Nlog_2(N), where N is the -number of points in the 3d grid. The FFTs are timed with and without -the communication and a Gflop rate is computed. The 3d rate is with -communication; the 1d rate is without (just the 1d FFTs). Thus you -can estimate what fraction of your FFT time was spent in -communication, roughly 75% in the example above. - -:line - -2.8 Tips for users of previous LAMMPS versions :h3,link(start_8) - -The current C++ began with a complete rewrite of LAMMPS 2001, which -was written in F90. Features of earlier versions of LAMMPS are listed -in "Section 13"_Section_history.html. The F90 and F77 versions -(2001 and 99) are also freely distributed as open-source codes; check -the "LAMMPS WWW Site"_lws for distribution information if you prefer -those versions. The 99 and 2001 versions are no longer under active -development; they do not have all the features of C++ LAMMPS. - -If you are a previous user of LAMMPS 2001, these are the most -significant changes you will notice in C++ LAMMPS: - -(1) The names and arguments of many input script commands have -changed. All commands are now a single word (e.g. read_data instead -of read data). - -(2) All the functionality of LAMMPS 2001 is included in C++ LAMMPS, -but you may need to specify the relevant commands in different ways. - -(3) The format of the data file can be streamlined for some problems. -See the "read_data"_read_data.html command for details. The data file -section "Nonbond Coeff" has been renamed to "Pair Coeff" in C++ LAMMPS. - -(4) Binary restart files written by LAMMPS 2001 cannot be read by C++ -LAMMPS with a "read_restart"_read_restart.html command. This is -because they were output by F90 which writes in a different binary -format than C or C++ writes or reads. Use the {restart2data} tool -provided with LAMMPS 2001 to convert the 2001 restart file to a text -data file. Then edit the data file as necessary before using the C++ -LAMMPS "read_data"_read_data.html command to read it in. - -(5) There are numerous small numerical changes in C++ LAMMPS that mean -you will not get identical answers when comparing to a 2001 run. -However, your initial thermodynamic energy and MD trajectory should be -close if you have setup the problem for both codes the same. diff --git a/doc/src/Speed.txt b/doc/src/Speed.txt new file mode 100644 index 0000000000..dd2052bac1 --- /dev/null +++ b/doc/src/Speed.txt @@ -0,0 +1,57 @@ +"Previous Section"_Package.html - "LAMMPS WWW Site"_lws - +"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next +Section"_Howto.html :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Accelerate performance :h2 + +This section describes various methods for improving LAMMPS +performance for different classes of problems running on different +kinds of machines. + +There are two thrusts to the discussion that follows. The first is +using code options that implement alternate algorithms that can +speed-up a simulation. The second is to use one of the several +accelerator packages provided with LAMMPS that contain code optimized +for certain kinds of hardware, including multi-core CPUs, GPUs, and +Intel Xeon Phi coprocessors. + +The "Benchmark page"_http://lammps.sandia.gov/bench.html of the LAMMPS +web site gives performance results for the various accelerator +packages discussed on the "Speed packages"_Speed_packages.html doc +page, for several of the standard LAMMPS benchmark problems, as a +function of problem size and number of compute nodes, on different +hardware platforms. + + + + + +"Benchmarks"_Speed_bench.html +"Measuring performance"_Speed_measure.html +"General tips"_Speed_tips.html +"Accelerator packages"_Speed_packages.html +"GPU package"_Speed_gpu.html +"USER-INTEL package"_Speed_intel.html +"KOKKOS package"_Speed_kokkos.html +"USER-OMP package"_Speed_omp.html +"OPT package"_Speed_opt.html +"Comparison of accelerator packages"_Speed_compare.html :all(b) + + diff --git a/doc/src/Section_perf.txt b/doc/src/Speed_bench.txt similarity index 82% rename from doc/src/Section_perf.txt rename to doc/src/Speed_bench.txt index 9998cb0d9a..a3d0bf4f46 100644 --- a/doc/src/Section_perf.txt +++ b/doc/src/Speed_bench.txt @@ -1,17 +1,18 @@ -"Previous Section"_Section_example.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Section_tools.html :c +"Higher level section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line -8. Performance & scalability :h2 +Benchmarks :h3 -Current LAMMPS performance is discussed on the Benchmarks page of the -"LAMMPS WWW Site"_lws where CPU timings and parallel efficiencies are -listed. The page has several sections, which are briefly described -below: +Current LAMMPS performance is discussed on the "Benchmarks +page"_http://lammps.sandia.gov/bench.html of the "LAMMPS website"_lws +where timings and parallel efficiency are listed. The page has +several sections, which are briefly described below: CPU performance on 5 standard problems, strong and weak scaling GPU and Xeon Phi performance on same and related problems @@ -51,8 +52,8 @@ of these 5 problems on 1 or 4 cores of Linux desktop. The bench/FERMI and bench/KEPLER dirs have input files and scripts and instructions for running the same (or similar) problems using OpenMP or GPU or Xeon Phi acceleration options. See the README files in those dirs and the -"Section 5.3"_Section_accelerate.html#acc_3 doc pages for -instructions on how to build LAMMPS and run on that kind of hardware. +"Speed packages"_Speed_packages.html doc pages for instructions on how +to build LAMMPS and run on that kind of hardware. The bench/POTENTIALS directory has input files which correspond to the table of results on the @@ -76,8 +77,8 @@ style, force field, cutoff, etc) can then be estimated. Performance on a parallel machine can also be predicted from one-core or one-node timings if the parallel efficiency can be estimated. The communication bandwidth and latency of a particular parallel machine -affects the efficiency. On most machines LAMMPS will give parallel -efficiencies on these benchmarks above 50% so long as the number of +affects the efficiency. On most machines LAMMPS will give a parallel +efficiency on these benchmarks above 50% so long as the number of atoms/core is a few 100 or greater, and closer to 100% for large numbers of atoms/core. This is for all-MPI mode with one MPI task per core. For nodes with accelerator options or hardware (OpenMP, GPU, diff --git a/doc/src/Speed_compare.txt b/doc/src/Speed_compare.txt new file mode 100644 index 0000000000..c93407515e --- /dev/null +++ b/doc/src/Speed_compare.txt @@ -0,0 +1,116 @@ +"Higher level section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Comparison of various accelerator packages :h3 + +The next section compares and contrasts the various accelerator +options, since there are multiple ways to perform OpenMP threading, +run on GPUs, optimize for vector units on CPUs and run on Intel +Xeon Phi (co-)processors. + +All of these packages can accelerate a LAMMPS calculation taking +advantage of hardware features, but they do it in different ways +and acceleration is not always guaranteed. + +As a consequence, for a particular simulation on specific hardware, +one package may be faster than the other. We give some guidelines +below, but the best way to determine which package is faster for your +input script is to try multiple of them on your machine and experiment +with available performance tuning settings. See the benchmarking +section below for examples where this has been done. + +[Guidelines for using each package optimally:] + +Both, the GPU and the KOKKOS package allows you to assign multiple +MPI ranks (= CPU cores) to the same GPU. For the GPU package, this +can lead to a speedup through better utilization of the GPU (by +overlapping computation and data transfer) and more efficient +computation of the non-GPU accelerated parts of LAMMPS through MPI +parallelization, as all system data is maintained and updated on +the host. For KOKKOS, there is less to no benefit from this, due +to its different memory management model, which tries to retain +data on the GPU. + :ulb,l + +The GPU package moves per-atom data (coordinates, forces, and +(optionally) neighbor list data, if not computed on the GPU) between +the CPU and GPU at every timestep. The KOKKOS/CUDA package only does +this on timesteps when a CPU calculation is required (e.g. to invoke +a fix or compute that is non-GPU-ized). Hence, if you can formulate +your input script to only use GPU-ized fixes and computes, and avoid +doing I/O too often (thermo output, dump file snapshots, restart files), +then the data transfer cost of the KOKKOS/CUDA package can be very low, +causing it to run faster than the GPU package. :l + +The GPU package is often faster than the KOKKOS/CUDA package, when the +number of atoms per GPU is on the smaller side. The crossover point, +in terms of atoms/GPU at which the KOKKOS/CUDA package becomes faster +depends strongly on the pair style. For example, for a simple Lennard Jones +system the crossover (in single precision) is often about 50K-100K +atoms per GPU. When performing double precision calculations the +crossover point can be significantly smaller. :l + +Both KOKKOS and GPU package compute bonded interactions (bonds, angles, +etc) on the CPU. If the GPU package is running with several MPI processes +assigned to one GPU, the cost of computing the bonded interactions is +spread across more CPUs and hence the GPU package can run faster in these +cases. :l + +When using LAMMPS with multiple MPI ranks assigned to the same GPU, its +performance depends to some extent on the available bandwidth between +the CPUs and the GPU. This can differ significantly based on the +available bus technology, capability of the host CPU and mainboard, +the wiring of the buses and whether switches are used to increase the +number of available bus slots, or if GPUs are housed in an external +enclosure. This can become quite complex. :l + +To achieve significant acceleration through GPUs, both KOKKOS and GPU +package require capable GPUs with fast on-device memory and efficient +data transfer rates. This requests capable upper mid-level to high-end +(desktop) GPUs. Using lower performance GPUs (e.g. on laptops) may +result in a slowdown instead. :l + +For the GPU package, specifically when running in parallel with MPI, +if it often more efficient to exclude the PPPM kspace style from GPU +acceleration and instead run it - concurrently with a GPU accelerated +pair style - on the CPU. This can often be easily achieved with placing +a {suffix off} command before and a {suffix on} command after the +{kspace_style pppm} command. :l + +The KOKKOS/OpenMP and USER-OMP package have different thread management +strategies, which should result in USER-OMP being more efficient for a +small number of threads with increasing overhead as the number of threads +per MPI rank grows. The KOKKOS/OpenMP kernels have less overhead in that +case, but have lower performance with few threads. :l + +The USER-INTEL package contains many options and settings for achieving +additional performance on Intel hardware (CPU and accelerator cards), but +to unlock this potential, an Intel compiler is required. The package code +will compile with GNU gcc, but it will not be as efficient. :l +:ule + +[Differences between the GPU and KOKKOS packages:] + +The GPU package accelerates only pair force, neighbor list, and (parts +of) PPPM calculations. The KOKKOS package attempts to run most of the +calculation on the GPU, but can transparently support non-accelerated +code (with a performance penalty due to having data transfers between +host and GPU). :ulb,l + +The GPU package requires neighbor lists to be built on the CPU when using +exclusion lists, hybrid pair styles, or a triclinic simulation box. :l + +The GPU package can be compiled for CUDA or OpenCL and thus supports +both, Nvidia and AMD GPUs well. On Nvidia hardware, using CUDA is typically +resulting in equal or better performance over OpenCL. :l + +OpenCL in the GPU package does theoretically also support Intel CPUs or +Intel Xeon Phi, but the native support for those in KOKKOS (or USER-INTEL) +is superior. :l +:ule diff --git a/doc/src/accelerate_gpu.txt b/doc/src/Speed_gpu.txt similarity index 58% rename from doc/src/accelerate_gpu.txt rename to doc/src/Speed_gpu.txt index 816a31c788..bddefc5031 100644 --- a/doc/src/accelerate_gpu.txt +++ b/doc/src/Speed_gpu.txt @@ -1,27 +1,25 @@ -"Previous Section"_Section_packages.html - "LAMMPS WWW Site"_lws - -"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c +"Higher level section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line -"Return to Section accelerate overview"_Section_accelerate.html +GPU package :h3 -5.3.1 GPU package :h5 - -The GPU package was developed by Mike Brown at ORNL and his -collaborators, particularly Trung Nguyen (ORNL). It provides GPU -versions of many pair styles, including the 3-body Stillinger-Weber -pair style, and for "kspace_style pppm"_kspace_style.html for -long-range Coulombics. It has the following general features: +The GPU package was developed by Mike Brown while at SNL and ORNL +and his collaborators, particularly Trung Nguyen (now at Northwestern). +It provides GPU versions of many pair styles and for parts of the +"kspace_style pppm"_kspace_style.html for long-range Coulombics. +It has the following general features: It is designed to exploit common GPU hardware configurations where one or more GPUs are coupled to many cores of one or more multi-core CPUs, e.g. within a node of a parallel machine. :ulb,l -Atom-based data (e.g. coordinates, forces) moves back-and-forth +Atom-based data (e.g. coordinates, forces) are moved back-and-forth between the CPU(s) and GPU every timestep. :l Neighbor lists can be built on the CPU or on the GPU :l @@ -30,8 +28,8 @@ The charge assignment and force interpolation portions of PPPM can be run on the GPU. The FFT portion, which requires MPI communication between processors, runs on the CPU. :l -Asynchronous force computations can be performed simultaneously on the -CPU(s) and GPU. :l +Force computations of different style (pair vs. bond/angle/dihedral/improper) +can be performed concurrently on the GPU and CPU(s), respectively. :l It allows for GPU computations to be performed in single or double precision, or in mixed-mode precision, where pairwise forces are @@ -41,94 +39,37 @@ force vectors. :l LAMMPS-specific code is in the GPU package. It makes calls to a generic GPU library in the lib/gpu directory. This library provides NVIDIA support as well as more general OpenCL support, so that the -same functionality can eventually be supported on a variety of GPU -hardware. :l +same functionality is supported on a variety of hardware. :l :ule -Here is a quick overview of how to enable and use the GPU package: - -build the library in lib/gpu for your GPU hardware with the desired precision settings -install the GPU package and build LAMMPS as usual -use the mpirun command to set the number of MPI tasks/node which determines the number of MPI tasks/GPU -specify the # of GPUs per node -use GPU styles in your input script :ul - -The latter two steps can be done using the "-pk gpu" and "-sf gpu" -"command-line switches"_Section_start.html#start_6 respectively. Or -the effect of the "-pk" or "-sf" switches can be duplicated by adding -the "package gpu"_package.html or "suffix gpu"_suffix.html commands -respectively to your input script. - [Required hardware/software:] -To use this package, you currently need to have an NVIDIA GPU and -install the NVIDIA CUDA software on your system: +To compile and use this package in CUDA mode, you currently need +to have an NVIDIA GPU and install the corresponding NVIDIA CUDA +toolkit software on your system (this is primarily tested on Linux +and completely unsupported on Windows): -Check if you have an NVIDIA GPU: cat /proc/driver/nvidia/gpus/0/information -Go to http://www.nvidia.com/object/cuda_get.html -Install a driver and toolkit appropriate for your system (SDK is not necessary) -Run lammps/lib/gpu/nvc_get_devices (after building the GPU library, see below) to list supported devices and properties :ul +Check if you have an NVIDIA GPU: cat /proc/driver/nvidia/gpus/*/information :ulb,l +Go to http://www.nvidia.com/object/cuda_get.html :l +Install a driver and toolkit appropriate for your system (SDK is not necessary) :l +Run lammps/lib/gpu/nvc_get_devices (after building the GPU library, see below) to +list supported devices and properties :ule,l + +To compile and use this package in OpenCL mode, you currently need +to have the OpenCL headers and the (vendor neutral) OpenCL library installed. +In OpenCL mode, the acceleration depends on having an "OpenCL Installable Client +Driver (ICD)"_https://www.khronos.org/news/permalink/opencl-installable-client-driver-icd-loader +installed. There can be multiple of them for the same or different hardware +(GPUs, CPUs, Accelerators) installed at the same time. OpenCL refers to those +as 'platforms'. The GPU library will select the [first] suitable platform, +but this can be overridden using the device option of the "package"_package.html +command. run lammps/lib/gpu/ocl_get_devices to get a list of available +platforms and devices with a suitable ICD available. [Building LAMMPS with the GPU package:] -This requires two steps (a,b): build the GPU library, then build -LAMMPS with the GPU package. - -You can do both these steps in one line as described in -"Section 4"_Section_packages.html of the manual. - -Or you can follow these two (a,b) steps: - -(a) Build the GPU library - -The GPU library is in lammps/lib/gpu. Select a Makefile.machine (in -lib/gpu) appropriate for your system. You should pay special -attention to 3 settings in this makefile. - -CUDA_HOME = needs to be where NVIDIA CUDA software is installed on your system -CUDA_ARCH = needs to be appropriate to your GPUs -CUDA_PREC = precision (double, mixed, single) you desire :ul - -See lib/gpu/Makefile.linux.double for examples of the ARCH settings -for different GPU choices, e.g. Fermi vs Kepler. It also lists the -possible precision settings: - -CUDA_PREC = -D_SINGLE_SINGLE # single precision for all calculations -CUDA_PREC = -D_DOUBLE_DOUBLE # double precision for all calculations -CUDA_PREC = -D_SINGLE_DOUBLE # accumulation of forces, etc, in double :pre - -The last setting is the mixed mode referred to above. Note that your -GPU must support double precision to use either the 2nd or 3rd of -these settings. - -To build the library, type: - -make -f Makefile.machine :pre - -If successful, it will produce the files libgpu.a and Makefile.lammps. - -The latter file has 3 settings that need to be appropriate for the -paths and settings for the CUDA system software on your machine. -Makefile.lammps is a copy of the file specified by the EXTRAMAKE -setting in Makefile.machine. You can change EXTRAMAKE or create your -own Makefile.lammps.machine if needed. - -Note that to change the precision of the GPU library, you need to -re-build the entire library. Do a "clean" first, e.g. "make -f -Makefile.linux clean", followed by the make command above. - -(b) Build LAMMPS with the GPU package - -cd lammps/src -make yes-gpu -make machine :pre - -No additional compile/link flags are needed in Makefile.machine. - -Note that if you change the GPU library precision (discussed above) -and rebuild the GPU library, then you also need to re-install the GPU -package and re-build LAMMPS, so that all affected files are -re-compiled and linked to the new GPU library. +See the "Build extras"_Build_extras.html#gpu doc page for +instructions. [Run with the GPU package from the command line:] @@ -146,10 +87,10 @@ automatically if you create more MPI tasks/node than there are GPUs/mode. E.g. with 8 MPI tasks/node and 2 GPUs, each GPU will be shared by 4 MPI tasks. -Use the "-sf gpu" "command-line switch"_Section_start.html#start_6, -which will automatically append "gpu" to styles that support it. Use -the "-pk gpu Ng" "command-line switch"_Section_start.html#start_6 to -set Ng = # of GPUs/node to use. +Use the "-sf gpu" "command-line switch"_Run_options.html, which will +automatically append "gpu" to styles that support it. Use the "-pk +gpu Ng" "command-line switch"_Run_options.html to set Ng = # of +GPUs/node to use. lmp_machine -sf gpu -pk gpu 1 -in in.script # 1 MPI task uses 1 GPU mpirun -np 12 lmp_machine -sf gpu -pk gpu 2 -in in.script # 12 MPI tasks share 2 GPUs on a single 16-core (or whatever) node @@ -183,14 +124,17 @@ pair_style lj/cut/gpu 2.5 :pre You must also use the "package gpu"_package.html command to enable the GPU package, unless the "-sf gpu" or "-pk gpu" "command-line -switches"_Section_start.html#start_6 were used. It specifies the -number of GPUs/node to use, as well as other options. +switches"_Run_options.html were used. It specifies the number of +GPUs/node to use, as well as other options. [Speed-ups to expect:] The performance of a GPU versus a multi-core CPU is a function of your hardware, which pair style is used, the number of atoms/GPU, and the -precision used on the GPU (double, single, mixed). +precision used on the GPU (double, single, mixed). Using the GPU package +in OpenCL mode on CPUs (which uses vectorization and multithreading) is +usually resulting in inferior performance compared to using LAMMPS' native +threading and vectorization support in the USER-OMP and USER-INTEL packages. See the "Benchmark page"_http://lammps.sandia.gov/bench.html of the LAMMPS web site for performance of the GPU package on various @@ -216,7 +160,7 @@ The "package gpu"_package.html command has several options for tuning performance. Neighbor lists can be built on the GPU or CPU. Force calculations can be dynamically balanced across the CPU cores and GPUs. GPU-specific settings can be made which can be optimized -for different hardware. See the "packakge"_package.html command +for different hardware. See the "package"_package.html command doc page for details. :l As described by the "package gpu"_package.html command, GPU diff --git a/doc/src/accelerate_intel.txt b/doc/src/Speed_intel.txt similarity index 87% rename from doc/src/accelerate_intel.txt rename to doc/src/Speed_intel.txt index 71f5185b15..bf078fb576 100644 --- a/doc/src/accelerate_intel.txt +++ b/doc/src/Speed_intel.txt @@ -1,15 +1,13 @@ -"Previous Section"_Section_packages.html - "LAMMPS WWW Site"_lws - -"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c +"Higher level section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line -"Return to Section accelerate overview"_Section_accelerate.html - -5.3.2 USER-INTEL package :h5 +USER-INTEL package :h3 The USER-INTEL package is maintained by Mike Brown at Intel Corporation. It provides two methods for accelerating simulations, @@ -70,7 +68,7 @@ In most molecular dynamics software, parallelization parameters to changing the order of operations with finite-precision calculations. The USER-INTEL package is deterministic. This means that the results should be reproducible from run to run with the -{same} parallel configurations and when using determinstic +{same} parallel configurations and when using deterministic libraries or library settings (MPI, OpenMP, FFT). However, there are differences in the USER-INTEL package that can change the order of operations compared to LAMMPS without acceleration: @@ -188,8 +186,8 @@ can start running so that the CPU pipeline is still being used efficiently. Although benefits can be seen by launching a MPI task for every hardware thread, for multinode simulations, we recommend that OpenMP threads are used for SMT instead, either with the -USER-INTEL package, "USER-OMP package"_accelerate_omp.html, or -"KOKKOS package"_accelerate_kokkos.html. In the example above, up +USER-INTEL package, "USER-OMP package"_Speed_omp.html, or +"KOKKOS package"_Speed_kokkos.html. In the example above, up to 36X speedups can be observed by using all 36 physical cores with LAMMPS. By using all 72 hardware threads, an additional 10-30% performance gain can be achieved. @@ -205,16 +203,12 @@ cat /proc/cpuinfo :pre [Building LAMMPS with the USER-INTEL package:] -NOTE: See the src/USER-INTEL/README file for additional flags that -might be needed for best performance on Intel server processors -code-named "Skylake". +See the "Build extras"_Build_extras.html#user-intel doc page for +instructions. Some additional details are covered here. -The USER-INTEL package must be installed into the source directory: - -make yes-user-intel :pre - -Several example Makefiles for building with the Intel compiler are -included with LAMMPS in the src/MAKE/OPTIONS/ directory: +For building with make, several example Makefiles for building with +the Intel compiler are included with LAMMPS in the src/MAKE/OPTIONS/ +directory: Makefile.intel_cpu_intelmpi # Intel Compiler, Intel MPI, No Offload Makefile.knl # Intel Compiler, Intel MPI, No Offload @@ -223,20 +217,16 @@ Makefile.intel_cpu_openpmi # Intel Compiler, OpenMPI, No Offload Makefile.intel_coprocessor # Intel Compiler, Intel MPI, Offload :pre Makefile.knl is identical to Makefile.intel_cpu_intelmpi except that -it explicitly specifies that vectorization should be for Intel -Xeon Phi x200 processors making it easier to cross-compile. For -users with recent installations of Intel Parallel Studio, the -process can be as simple as: +it explicitly specifies that vectorization should be for Intel Xeon +Phi x200 processors making it easier to cross-compile. For users with +recent installations of Intel Parallel Studio, the process can be as +simple as: make yes-user-intel source /opt/intel/parallel_studio_xe_2016.3.067/psxevars.sh # or psxevars.csh for C-shell make intel_cpu_intelmpi :pre -Alternatively this can be done as a single command with -suitable make command invocations. This is discussed in "Section -4"_Section_packages.html of the manual. - Note that if you build with support for a Phi coprocessor, the same binary can be used on nodes with or without coprocessors installed. However, if you do not have coprocessors on your system, building @@ -255,6 +245,10 @@ required for CCFLAGS and "-qoffload" is required for LINKFLAGS. Other recommended CCFLAG options for best performance are "-O2 -fno-alias -ansi-alias -qoverride-limits fp-model fast=2 -no-prec-div". +NOTE: See the src/USER-INTEL/README file for additional flags that +might be needed for best performance on Intel server processors +code-named "Skylake". + NOTE: The vectorization and math capabilities can differ depending on the CPU. For Intel compilers, the "-x" flag specifies the type of processor for which to optimize. "-xHost" specifies that the compiler @@ -308,31 +302,31 @@ Hyper-Threading technology disabled. [Run with the USER-INTEL package from the command line:] To enable USER-INTEL optimizations for all available styles used in -the input script, the "-sf intel" -"command-line switch"_Section_start.html#start_6 can be used without -any requirement for editing the input script. This switch will -automatically append "intel" to styles that support it. It also -invokes a default command: "package intel 1"_package.html. This -package command is used to set options for the USER-INTEL package. -The default package command will specify that USER-INTEL calculations -are performed in mixed precision, that the number of OpenMP threads -is specified by the OMP_NUM_THREADS environment variable, and that -if coprocessors are present and the binary was built with offload -support, that 1 coprocessor per node will be used with automatic -balancing of work between the CPU and the coprocessor. +the input script, the "-sf intel" "command-line +switch"_Run_options.html can be used without any requirement for +editing the input script. This switch will automatically append +"intel" to styles that support it. It also invokes a default command: +"package intel 1"_package.html. This package command is used to set +options for the USER-INTEL package. The default package command will +specify that USER-INTEL calculations are performed in mixed precision, +that the number of OpenMP threads is specified by the OMP_NUM_THREADS +environment variable, and that if coprocessors are present and the +binary was built with offload support, that 1 coprocessor per node +will be used with automatic balancing of work between the CPU and the +coprocessor. You can specify different options for the USER-INTEL package by using -the "-pk intel Nphi" "command-line switch"_Section_start.html#start_6 -with keyword/value pairs as specified in the documentation. Here, -Nphi = # of Xeon Phi coprocessors/node (ignored without offload +the "-pk intel Nphi" "command-line switch"_Run_options.html with +keyword/value pairs as specified in the documentation. Here, Nphi = # +of Xeon Phi coprocessors/node (ignored without offload support). Common options to the USER-INTEL package include {omp} to override any OMP_NUM_THREADS setting and specify the number of OpenMP -threads, {mode} to set the floating-point precision mode, and -{lrt} to enable Long-Range Thread mode as described below. See the -"package intel"_package.html command for details, including the -default values used for all its options if not specified, and how to -set the number of OpenMP threads via the OMP_NUM_THREADS environment -variable if desired. +threads, {mode} to set the floating-point precision mode, and {lrt} to +enable Long-Range Thread mode as described below. See the "package +intel"_package.html command for details, including the default values +used for all its options if not specified, and how to set the number +of OpenMP threads via the OMP_NUM_THREADS environment variable if +desired. Examples (see documentation for your MPI/Machine for differences in launching MPI applications): @@ -391,23 +385,22 @@ performance and/or scalability for simple 2-body potentials such as lj/cut or when using LRT mode on processors supporting AVX-512. Not all styles are supported in the USER-INTEL package. You can mix -the USER-INTEL package with styles from the "OPT"_accelerate_opt.html -package or the "USER-OMP package"_accelerate_omp.html. Of course, -this requires that these packages were installed at build time. This -can performed automatically by using "-sf hybrid intel opt" or -"-sf hybrid intel omp" command-line options. Alternatively, the "opt" -and "omp" suffixes can be appended manually in the input script. For -the latter, the "package omp"_package.html command must be in the -input script or the "-pk omp Nt" "command-line -switch"_Section_start.html#start_6 must be used where Nt is the -number of OpenMP threads. The number of OpenMP threads should not be -set differently for the different packages. Note that the "suffix -hybrid intel omp"_suffix.html command can also be used within the -input script to automatically append the "omp" suffix to styles when -USER-INTEL styles are not available. +the USER-INTEL package with styles from the "OPT"_Speed_opt.html +package or the "USER-OMP package"_Speed_omp.html. Of course, this +requires that these packages were installed at build time. This can +performed automatically by using "-sf hybrid intel opt" or "-sf hybrid +intel omp" command-line options. Alternatively, the "opt" and "omp" +suffixes can be appended manually in the input script. For the latter, +the "package omp"_package.html command must be in the input script or +the "-pk omp Nt" "command-line switch"_Run_options.html must be used +where Nt is the number of OpenMP threads. The number of OpenMP threads +should not be set differently for the different packages. Note that +the "suffix hybrid intel omp"_suffix.html command can also be used +within the input script to automatically append the "omp" suffix to +styles when USER-INTEL styles are not available. NOTE: For simulations on higher node counts, add "processors * * * -grid numa"_processors.html" to the beginning of the input script for +grid numa"_processors.html to the beginning of the input script for better scalability. When running on many nodes, performance might be better when using @@ -498,8 +491,8 @@ sorting"_atom_modify.html is changed to 1 so that the per-atom data is effectively sorted at every rebuild of the neighbor lists. All the available coprocessor threads on each Phi will be divided among MPI tasks, unless the {tptask} option of the "-pk intel" "command-line -switch"_Section_start.html#start_6 is used to limit the coprocessor -threads per MPI task. +switch"_Run_options.html is used to limit the coprocessor threads per +MPI task. [Restrictions:] diff --git a/doc/src/Speed_kokkos.txt b/doc/src/Speed_kokkos.txt new file mode 100644 index 0000000000..f74c9c9ed7 --- /dev/null +++ b/doc/src/Speed_kokkos.txt @@ -0,0 +1,402 @@ +"Higher level section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +KOKKOS package :h3 + +Kokkos is a templated C++ library that provides abstractions to allow +a single implementation of an application kernel (e.g. a pair style) +to run efficiently on different kinds of hardware, such as GPUs, Intel +Xeon Phis, or many-core CPUs. Kokkos maps the C++ kernel onto +different backend languages such as CUDA, OpenMP, or Pthreads. The +Kokkos library also provides data abstractions to adjust (at compile +time) the memory layout of data structures like 2d and 3d arrays to +optimize performance on different hardware. For more information on +Kokkos, see "Github"_https://github.com/kokkos/kokkos. Kokkos is part +of "Trilinos"_http://trilinos.sandia.gov/packages/kokkos. The Kokkos +library was written primarily by Carter Edwards, Christian Trott, and +Dan Sunderland (all Sandia). + +The LAMMPS KOKKOS package contains versions of pair, fix, and atom +styles that use data structures and macros provided by the Kokkos +library, which is included with LAMMPS in /lib/kokkos. The KOKKOS +package was developed primarily by Christian Trott (Sandia) and Stan +Moore (Sandia) with contributions of various styles by others, +including Sikandar Mashayak (UIUC), Ray Shan (Sandia), and Dan Ibanez +(Sandia). For more information on developing using Kokkos abstractions +see the Kokkos programmers' guide at /lib/kokkos/doc/Kokkos_PG.pdf. + +Kokkos currently provides support for 3 modes of execution (per MPI +task). These are Serial (MPI-only for CPUs and Intel Phi), OpenMP +(threading for many-core CPUs and Intel Phi), and CUDA (for NVIDIA +GPUs). You choose the mode at build time to produce an executable +compatible with specific hardware. + +NOTE: Kokkos support within LAMMPS must be built with a C++11 compatible +compiler. This means GCC version 4.7.2 or later, Intel 14.0.4 or later, or +Clang 3.5.2 or later is required. + +NOTE: To build with Kokkos support for NVIDIA GPUs, NVIDIA CUDA +software version 7.5 or later must be installed on your system. See +the discussion for the "GPU package"_Speed_gpu.html for details of how +to check and do this. + +NOTE: Kokkos with CUDA currently implicitly assumes, that the MPI +library is CUDA-aware and has support for GPU-direct. This is not +always the case, especially when using pre-compiled MPI libraries +provided by a Linux distribution. This is not a problem when using +only a single GPU and a single MPI rank on a desktop. When running +with multiple MPI ranks, you may see segmentation faults without +GPU-direct support. These can be avoided by adding the flags "-pk +kokkos gpu/direct off"_Run_options.html to the LAMMPS command line or +by using the command "package kokkos gpu/direct off"_package.html in +the input file. + +[Building LAMMPS with the KOKKOS package:] + +See the "Build extras"_Build_extras.html#kokkos doc page for instructions. + +[Running LAMMPS with the KOKKOS package:] + +All Kokkos operations occur within the context of an individual MPI +task running on a single node of the machine. The total number of MPI +tasks used by LAMMPS (one or multiple per compute node) is set in the +usual manner via the mpirun or mpiexec commands, and is independent of +Kokkos. E.g. the mpirun command in OpenMPI does this via its -np and +-npernode switches. Ditto for MPICH via -np and -ppn. + +[Running on a multi-core CPU:] + +Here is a quick overview of how to use the KOKKOS package +for CPU acceleration, assuming one or more 16-core nodes. + +mpirun -np 16 lmp_kokkos_mpi_only -k on -sf kk -in in.lj # 1 node, 16 MPI tasks/node, no multi-threading +mpirun -np 2 -ppn 1 lmp_kokkos_omp -k on t 16 -sf kk -in in.lj # 2 nodes, 1 MPI task/node, 16 threads/task +mpirun -np 2 lmp_kokkos_omp -k on t 8 -sf kk -in in.lj # 1 node, 2 MPI tasks/node, 8 threads/task +mpirun -np 32 -ppn 4 lmp_kokkos_omp -k on t 4 -sf kk -in in.lj # 8 nodes, 4 MPI tasks/node, 4 threads/task :pre + +To run using the KOKKOS package, use the "-k on", "-sf kk" and "-pk +kokkos" "command-line switches"_Run_options.html in your mpirun +command. You must use the "-k on" "command-line +switch"_Run_options.html to enable the KOKKOS package. It takes +additional arguments for hardware settings appropriate to your system. +For OpenMP use: + +-k on t Nt :pre + +The "t Nt" option specifies how many OpenMP threads per MPI task to +use with a node. The default is Nt = 1, which is MPI-only mode. Note +that the product of MPI tasks * OpenMP threads/task should not exceed +the physical number of cores (on a node), otherwise performance will +suffer. If Hyper-Threading (HT) is enabled, then the product of MPI +tasks * OpenMP threads/task should not exceed the physical number of +cores * hardware threads. The "-k on" switch also issues a +"package kokkos" command (with no additional arguments) which sets +various KOKKOS options to default values, as discussed on the +"package"_package.html command doc page. + +The "-sf kk" "command-line switch"_Run_options.html will automatically +append the "/kk" suffix to styles that support it. In this manner no +modification to the input script is needed. Alternatively, one can run +with the KOKKOS package by editing the input script as described +below. + +NOTE: When using a single OpenMP thread, the Kokkos Serial backend (i.e. +Makefile.kokkos_mpi_only) will give better performance than the OpenMP +backend (i.e. Makefile.kokkos_omp) because some of the overhead to make +the code thread-safe is removed. + +NOTE: The default for the "package kokkos"_package.html command is to +use "full" neighbor lists and set the Newton flag to "off" for both +pairwise and bonded interactions. However, when running on CPUs, it +will typically be faster to use "half" neighbor lists and set the +Newton flag to "on", just as is the case for non-accelerated pair +styles. It can also be faster to use non-threaded communication. Use +the "-pk kokkos" "command-line switch"_Run_options.html to change the +default "package kokkos"_package.html options. See its doc page for +details and default settings. Experimenting with its options can +provide a speed-up for specific calculations. For example: + +mpirun -np 16 lmp_kokkos_mpi_only -k on -sf kk -pk kokkos newton on neigh half comm no -in in.lj # Newton on, Half neighbor list, non-threaded comm :pre + +If the "newton"_newton.html command is used in the input +script, it can also override the Newton flag defaults. + +For half neighbor lists and OpenMP, the KOKKOS package uses data +duplication (i.e. thread-private arrays) by default to avoid +thread-level write conflicts in the force arrays (and other data +structures as necessary). Data duplication is typically fastest for +small numbers of threads (i.e. 8 or less) but does increase memory +footprint and is not scalable to large numbers of threads. An +alternative to data duplication is to use thread-level atomics, which +don't require duplication. The use of atomics can be forced by compiling +with the "-DLMP_KOKKOS_USE_ATOMICS" compile switch. Most but not all +Kokkos-enabled pair_styles support data duplication. Alternatively, full +neighbor lists avoid the need for duplication or atomics but require +more compute operations per atom. When using the Kokkos Serial backend +or the OpenMP backend with a single thread, no duplication or atomics are +used. For CUDA and half neighbor lists, the KOKKOS package always uses +atomics. + +[Core and Thread Affinity:] + +When using multi-threading, it is important for performance to bind +both MPI tasks to physical cores, and threads to physical cores, so +they do not migrate during a simulation. + +If you are not certain MPI tasks are being bound (check the defaults +for your MPI installation), binding can be forced with these flags: + +OpenMPI 1.8: mpirun -np 2 --bind-to socket --map-by socket ./lmp_openmpi ... +Mvapich2 2.0: mpiexec -np 2 --bind-to socket --map-by socket ./lmp_mvapich ... :pre + +For binding threads with KOKKOS OpenMP, use thread affinity +environment variables to force binding. With OpenMP 3.1 (gcc 4.7 or +later, intel 12 or later) setting the environment variable +OMP_PROC_BIND=true should be sufficient. In general, for best +performance with OpenMP 4.0 or better set OMP_PROC_BIND=spread and +OMP_PLACES=threads. For binding threads with the KOKKOS pthreads +option, compile LAMMPS the KOKKOS HWLOC=yes option as described below. + +[Running on Knight's Landing (KNL) Intel Xeon Phi:] + +Here is a quick overview of how to use the KOKKOS package for the +Intel Knight's Landing (KNL) Xeon Phi: + +KNL Intel Phi chips have 68 physical cores. Typically 1 to 4 cores are +reserved for the OS, and only 64 or 66 cores are used. Each core has 4 +Hyper-Threads,so there are effectively N = 256 (4*64) or N = 264 (4*66) +cores to run on. The product of MPI tasks * OpenMP threads/task should +not exceed this limit, otherwise performance will suffer. Note that +with the KOKKOS package you do not need to specify how many KNLs there +are per node; each KNL is simply treated as running some number of MPI +tasks. + +Examples of mpirun commands that follow these rules are shown below. + +Intel KNL node with 68 cores (272 threads/node via 4x hardware threading): +mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -in in.lj # 1 node, 64 MPI tasks/node, 4 threads/task +mpirun -np 66 lmp_kokkos_phi -k on t 4 -sf kk -in in.lj # 1 node, 66 MPI tasks/node, 4 threads/task +mpirun -np 32 lmp_kokkos_phi -k on t 8 -sf kk -in in.lj # 1 node, 32 MPI tasks/node, 8 threads/task +mpirun -np 512 -ppn 64 lmp_kokkos_phi -k on t 4 -sf kk -in in.lj # 8 nodes, 64 MPI tasks/node, 4 threads/task :pre + +The -np setting of the mpirun command sets the number of MPI +tasks/node. The "-k on t Nt" command-line switch sets the number of +threads/task as Nt. The product of these two values should be N, i.e. +256 or 264. + +NOTE: The default for the "package kokkos"_package.html command is to +use "full" neighbor lists and set the Newton flag to "off" for both +pairwise and bonded interactions. When running on KNL, this will +typically be best for pair-wise potentials. For manybody potentials, +using "half" neighbor lists and setting the Newton flag to "on" may be +faster. It can also be faster to use non-threaded communication. Use +the "-pk kokkos" "command-line switch"_Run_options.html to change the +default "package kokkos"_package.html options. See its doc page for +details and default settings. Experimenting with its options can +provide a speed-up for specific calculations. For example: + +mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -pk kokkos comm no -in in.lj # Newton off, full neighbor list, non-threaded comm +mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -pk kokkos newton on neigh half comm no -in in.reax # Newton on, half neighbor list, non-threaded comm :pre + +NOTE: MPI tasks and threads should be bound to cores as described +above for CPUs. + +NOTE: To build with Kokkos support for Intel Xeon Phi coprocessors +such as Knight's Corner (KNC), your system must be configured to use +them in "native" mode, not "offload" mode like the USER-INTEL package +supports. + +[Running on GPUs:] + +Use the "-k" "command-line switch"_Run_options.html to +specify the number of GPUs per node. Typically the -np setting of the +mpirun command should set the number of MPI tasks/node to be equal to +the number of physical GPUs on the node. You can assign multiple MPI +tasks to the same GPU with the KOKKOS package, but this is usually +only faster if significant portions of the input script have not +been ported to use Kokkos. Using CUDA MPS is recommended in this +scenario. Using a CUDA-aware MPI library with support for GPU-direct +is highly recommended. GPU-direct use can be avoided by using +"-pk kokkos gpu/direct no"_package.html. +As above for multi-core CPUs (and no GPU), if N is the number of +physical cores/node, then the number of MPI tasks/node should not +exceed N. + +-k on g Ng :pre + +Here are examples of how to use the KOKKOS package for GPUs, assuming +one or more nodes, each with two GPUs: + +mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -in in.lj # 1 node, 2 MPI tasks/node, 2 GPUs/node +mpirun -np 32 -ppn 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -in in.lj # 16 nodes, 2 MPI tasks/node, 2 GPUs/node (32 GPUs total) :pre + +NOTE: The default for the "package kokkos"_package.html command is to +use "full" neighbor lists and set the Newton flag to "off" for both +pairwise and bonded interactions, along with threaded communication. +When running on Maxwell or Kepler GPUs, this will typically be +best. For Pascal GPUs, using "half" neighbor lists and setting the +Newton flag to "on" may be faster. For many pair styles, setting the +neighbor binsize equal to the ghost atom cutoff will give speedup. +Use the "-pk kokkos" "command-line switch"_Run_options.html to change +the default "package kokkos"_package.html options. See its doc page +for details and default settings. Experimenting with its options can +provide a speed-up for specific calculations. For example: + +mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -pk kokkos binsize 2.8 -in in.lj # Set binsize = neighbor ghost cutoff +mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -pk kokkos newton on neigh half binsize 2.8 -in in.lj # Newton on, half neighbor list, set binsize = neighbor ghost cutoff :pre + +NOTE: For good performance of the KOKKOS package on GPUs, you must +have Kepler generation GPUs (or later). The Kokkos library exploits +texture cache options not supported by Telsa generation GPUs (or +older). + +NOTE: When using a GPU, you will achieve the best performance if your +input script does not use fix or compute styles which are not yet +Kokkos-enabled. This allows data to stay on the GPU for multiple +timesteps, without being copied back to the host CPU. Invoking a +non-Kokkos fix or compute, or performing I/O for +"thermo"_thermo_style.html or "dump"_dump.html output will cause data +to be copied back to the CPU incurring a performance penalty. + +NOTE: To get an accurate timing breakdown between time spend in pair, +kspace, etc., you must set the environment variable CUDA_LAUNCH_BLOCKING=1. +However, this will reduce performance and is not recommended for production runs. + +[Run with the KOKKOS package by editing an input script:] + +Alternatively the effect of the "-sf" or "-pk" switches can be +duplicated by adding the "package kokkos"_package.html or "suffix +kk"_suffix.html commands to your input script. + +The discussion above for building LAMMPS with the KOKKOS package, the +mpirun/mpiexec command, and setting appropriate thread are the same. + +You must still use the "-k on" "command-line switch"_Run_options.html +to enable the KOKKOS package, and specify its additional arguments for +hardware options appropriate to your system, as documented above. + +You can use the "suffix kk"_suffix.html command, or you can explicitly add a +"kk" suffix to individual styles in your input script, e.g. + +pair_style lj/cut/kk 2.5 :pre + +You only need to use the "package kokkos"_package.html command if you +wish to change any of its option defaults, as set by the "-k on" +"command-line switch"_Run_options.html. + +[Using OpenMP threading and CUDA together (experimental):] + +With the KOKKOS package, both OpenMP multi-threading and GPUs can be +used together in a few special cases. In the Makefile, the +KOKKOS_DEVICES variable must include both "Cuda" and "OpenMP", as is +the case for /src/MAKE/OPTIONS/Makefile.kokkos_cuda_mpi + +KOKKOS_DEVICES=Cuda,OpenMP :pre + +The suffix "/kk" is equivalent to "/kk/device", and for Kokkos CUDA, +using the "-sf kk" in the command line gives the default CUDA version +everywhere. However, if the "/kk/host" suffix is added to a specific +style in the input script, the Kokkos OpenMP (CPU) version of that +specific style will be used instead. Set the number of OpenMP threads +as "t Nt" and the number of GPUs as "g Ng" + +-k on t Nt g Ng :pre + +For example, the command to run with 1 GPU and 8 OpenMP threads is then: + +mpiexec -np 1 lmp_kokkos_cuda_openmpi -in in.lj -k on g 1 t 8 -sf kk :pre + +Conversely, if the "-sf kk/host" is used in the command line and then +the "/kk" or "/kk/device" suffix is added to a specific style in your +input script, then only that specific style will run on the GPU while +everything else will run on the CPU in OpenMP mode. Note that the +execution of the CPU and GPU styles will NOT overlap, except for a +special case: + +A kspace style and/or molecular topology (bonds, angles, etc.) running +on the host CPU can overlap with a pair style running on the +GPU. First compile with "--default-stream per-thread" added to CCFLAGS +in the Kokkos CUDA Makefile. Then explicitly use the "/kk/host" +suffix for kspace and bonds, angles, etc. in the input file and the +"kk" suffix (equal to "kk/device") on the command line. Also make +sure the environment variable CUDA_LAUNCH_BLOCKING is not set to "1" +so CPU/GPU overlap can occur. + +[Speed-ups to expect:] + +The performance of KOKKOS running in different modes is a function of +your hardware, which KOKKOS-enable styles are used, and the problem +size. + +Generally speaking, the following rules of thumb apply: + +When running on CPUs only, with a single thread per MPI task, +performance of a KOKKOS style is somewhere between the standard +(un-accelerated) styles (MPI-only mode), and those provided by the +USER-OMP package. However the difference between all 3 is small (less +than 20%). :ulb,l + +When running on CPUs only, with multiple threads per MPI task, +performance of a KOKKOS style is a bit slower than the USER-OMP +package. :l + +When running large number of atoms per GPU, KOKKOS is typically faster +than the GPU package. :l + +When running on Intel hardware, KOKKOS is not as fast as +the USER-INTEL package, which is optimized for that hardware. :l +:ule + +See the "Benchmark page"_http://lammps.sandia.gov/bench.html of the +LAMMPS web site for performance of the KOKKOS package on different +hardware. + +[Advanced Kokkos options:] + +There are other allowed options when building with the KOKKOS package. +As explained on the "Build extras"_Build_extras.html#kokkos doc page, +they can be set either as variables on the make command line or in +Makefile.machine, or they can be specified as CMake variables. Each +takes a value shown below. The default value is listed, which is set +in the lib/kokkos/Makefile.kokkos file. + +KOKKOS_DEBUG, values = {yes}, {no}, default = {no} +KOKKOS_USE_TPLS, values = {hwloc}, {librt}, {experimental_memkind}, default = {none} +KOKKOS_CXX_STANDARD, values = {c++11}, {c++1z}, default = {c++11} +KOKKOS_OPTIONS, values = {aggressive_vectorization}, {disable_profiling}, default = {none} +KOKKOS_CUDA_OPTIONS, values = {force_uvm}, {use_ldg}, {rdc}, {enable_lambda}, default = {enable_lambda} :ul + +KOKKOS_USE_TPLS=hwloc binds threads to hardware cores, so they do not +migrate during a simulation. KOKKOS_USE_TPLS=hwloc should always be +used if running with KOKKOS_DEVICES=Pthreads for pthreads. It is not +necessary for KOKKOS_DEVICES=OpenMP for OpenMP, because OpenMP +provides alternative methods via environment variables for binding +threads to hardware cores. More info on binding threads to cores is +given on the "Speed omp"_Speed_omp.html doc page. + +KOKKOS_USE_TPLS=librt enables use of a more accurate timer mechanism +on most Unix platforms. This library is not available on all +platforms. + +KOKKOS_DEBUG is only useful when developing a Kokkos-enabled style +within LAMMPS. KOKKOS_DEBUG=yes enables printing of run-time +debugging information that can be useful. It also enables runtime +bounds checking on Kokkos data structures. + +KOKKOS_CXX_STANDARD and KOKKOS_OPTIONS are typically not changed when +building LAMMPS. + +KOKKOS_CUDA_OPTIONS are additional options for CUDA. The LAMMPS KOKKOS +package must be compiled with the {enable_lambda} option when using +GPUs. + +[Restrictions:] + +Currently, there are no precision options with the KOKKOS package. All +compilation and computation is performed in double precision. diff --git a/doc/src/Speed_measure.txt b/doc/src/Speed_measure.txt new file mode 100644 index 0000000000..dd12685dc5 --- /dev/null +++ b/doc/src/Speed_measure.txt @@ -0,0 +1,55 @@ +"Higher level section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Measuring performance :h3 + +Before trying to make your simulation run faster, you should +understand how it currently performs and where the bottlenecks are. + +The best way to do this is run the your system (actual number of +atoms) for a modest number of timesteps (say 100 steps) on several +different processor counts, including a single processor if possible. +Do this for an equilibrium version of your system, so that the +100-step timings are representative of a much longer run. There is +typically no need to run for 1000s of timesteps to get accurate +timings; you can simply extrapolate from short runs. + +For the set of runs, look at the timing data printed to the screen and +log file at the end of each LAMMPS run. The +"Run_output"_Run_output.html doc page gives an overview. + +Running on one (or a few processors) should give a good estimate of +the serial performance and what portions of the timestep are taking +the most time. Running the same problem on a few different processor +counts should give an estimate of parallel scalability. I.e. if the +simulation runs 16x faster on 16 processors, its 100% parallel +efficient; if it runs 8x faster on 16 processors, it's 50% efficient. + +The most important data to look at in the timing info is the timing +breakdown and relative percentages. For example, trying different +options for speeding up the long-range solvers will have little impact +if they only consume 10% of the run time. If the pairwise time is +dominating, you may want to look at GPU or OMP versions of the pair +style, as discussed below. Comparing how the percentages change as +you increase the processor count gives you a sense of how different +operations within the timestep are scaling. Note that if you are +running with a Kspace solver, there is additional output on the +breakdown of the Kspace time. For PPPM, this includes the fraction +spent on FFTs, which can be communication intensive. + +Another important detail in the timing info are the histograms of +atoms counts and neighbor counts. If these vary widely across +processors, you have a load-imbalance issue. This often results in +inaccurate relative timing data, because processors have to wait when +communication occurs for other processors to catch up. Thus the +reported times for "Communication" or "Other" may be higher than they +really are, due to load-imbalance. If this is an issue, you can +uncomment the MPI_Barrier() lines in src/timer.cpp, and re-compile +LAMMPS, to obtain synchronized timings. + diff --git a/doc/src/accelerate_omp.txt b/doc/src/Speed_omp.txt similarity index 71% rename from doc/src/accelerate_omp.txt rename to doc/src/Speed_omp.txt index fa7bef1a52..238909d1b4 100644 --- a/doc/src/accelerate_omp.txt +++ b/doc/src/Speed_omp.txt @@ -1,52 +1,41 @@ -"Previous Section"_Section_packages.html - "LAMMPS WWW Site"_lws - -"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c +"Higher level section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line -"Return to Section 5 overview"_Section_accelerate.html - -5.3.4 USER-OMP package :h5 +USER-OMP package :h3 The USER-OMP package was developed by Axel Kohlmeyer at Temple -University. It provides multi-threaded versions of most pair styles, -nearly all bonded styles (bond, angle, dihedral, improper), several -Kspace styles, and a few fix styles. The package currently uses the -OpenMP interface for multi-threading. - -Here is a quick overview of how to use the USER-OMP package, assuming -one or more 16-core nodes. More details follow. - -use -fopenmp with CCFLAGS and LINKFLAGS in Makefile.machine -make yes-user-omp -make mpi # build with USER-OMP package, if settings added to Makefile.mpi -make omp # or Makefile.omp already has settings :pre - -lmp_mpi -sf omp -pk omp 16 < in.script # 1 MPI task, 16 threads -mpirun -np 4 lmp_mpi -sf omp -pk omp 4 -in in.script # 4 MPI tasks, 4 threads/task -mpirun -np 32 -ppn 4 lmp_mpi -sf omp -pk omp 4 -in in.script # 8 nodes, 4 MPI tasks/node, 4 threads/task :pre +University. It provides optimized and multi-threaded versions +of many pair styles, nearly all bonded styles (bond, angle, dihedral, +improper), several Kspace styles, and a few fix styles. It uses +the OpenMP interface for multi-threading, but can also be compiled +without OpenMP support, providing optimized serial styles in that case. [Required hardware/software:] -Your compiler must support the OpenMP interface. You should have one -or more multi-core CPUs so that multiple threads can be launched by -each MPI task running on a CPU. +To enable multi-threading, your compiler must support the OpenMP interface. +You should have one or more multi-core CPUs, as multiple threads can only be +launched by each MPI task on the local node (using shared memory). [Building LAMMPS with the USER-OMP package:] -The lines above illustrate how to include/build with the USER-OMP -package in two steps, using the "make" command. Or how to do it with -one command as described in "Section 4"_Section_packages.html of the manual. - -Note that the CCFLAGS and LINKFLAGS settings in Makefile.machine must -include "-fopenmp". Likewise, if you use an Intel compiler, the -CCFLAGS setting must include "-restrict". +See the "Build extras"_Build_extras.html#user-omp doc page for +instructions. [Run with the USER-OMP package from the command line:] +These examples assume one or more 16-core nodes. + +env OMP_NUM_THREADS=16 lmp_omp -sf omp -in in.script # 1 MPI task, 16 threads according to OMP_NUM_THREADS +lmp_mpi -sf omp -in in.script # 1 MPI task, no threads, optimized kernels +mpirun -np 4 lmp_omp -sf omp -pk omp 4 -in in.script # 4 MPI tasks, 4 threads/task +mpirun -np 32 -ppn 4 lmp_omp -sf omp -pk omp 4 -in in.script # 8 nodes, 4 MPI tasks/node, 4 threads/task :pre + The mpirun or mpiexec command sets the total number of MPI tasks used by LAMMPS (one or multiple per compute node) and the number of MPI tasks used per node. E.g. the mpirun command in MPICH does this via @@ -58,19 +47,18 @@ threads/task should not exceed the physical number of cores (on a node), otherwise performance will suffer. As in the lines above, use the "-sf omp" "command-line -switch"_Section_start.html#start_6, which will automatically append -"omp" to styles that support it. The "-sf omp" switch also issues a -default "package omp 0"_package.html command, which will set the -number of threads per MPI task via the OMP_NUM_THREADS environment -variable. +switch"_Run_options.html, which will automatically append "omp" to +styles that support it. The "-sf omp" switch also issues a default +"package omp 0"_package.html command, which will set the number of +threads per MPI task via the OMP_NUM_THREADS environment variable. You can also use the "-pk omp Nt" "command-line -switch"_Section_start.html#start_6, to explicitly set Nt = # of OpenMP -threads per MPI task to use, as well as additional options. Its -syntax is the same as the "package omp"_package.html command whose doc -page gives details, including the default values used if it is not -specified. It also gives more details on how to set the number of -threads via the OMP_NUM_THREADS environment variable. +switch"_Run_options.html, to explicitly set Nt = # of OpenMP threads +per MPI task to use, as well as additional options. Its syntax is the +same as the "package omp"_package.html command whose doc page gives +details, including the default values used if it is not specified. It +also gives more details on how to set the number of threads via the +OMP_NUM_THREADS environment variable. [Or run with the USER-OMP package by editing an input script:] @@ -100,7 +88,7 @@ task, versus running standard LAMMPS with its standard un-accelerated styles (in serial or all-MPI parallelization with 1 task/core). This is because many of the USER-OMP styles contain similar optimizations to those used in the OPT package, described in "Section -5.3.5"_accelerate_opt.html. +5.3.5"_Speed_opt.html. With multiple threads/task, the optimal choice of number of MPI tasks/node and OpenMP threads/task can vary a lot and should always be diff --git a/doc/src/accelerate_opt.txt b/doc/src/Speed_opt.txt similarity index 55% rename from doc/src/accelerate_opt.txt rename to doc/src/Speed_opt.txt index 845264b522..7dd83a84bf 100644 --- a/doc/src/accelerate_opt.txt +++ b/doc/src/Speed_opt.txt @@ -1,15 +1,13 @@ -"Previous Section"_Section_packages.html - "LAMMPS WWW Site"_lws - -"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c +"Higher level section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line -"Return to Section accelerate overview"_Section_accelerate.html - -5.3.5 OPT package :h5 +OPT package :h3 The OPT package was developed by James Fischer (High Performance Technologies), David Richie, and Vincent Natoli (Stone Ridge @@ -17,33 +15,21 @@ Technologies). It contains a handful of pair styles whose compute() methods were rewritten in C++ templated form to reduce the overhead due to if tests and other conditional code. -Here is a quick overview of how to use the OPT package. More details -follow. - -make yes-opt -make mpi # build with the OPT package :pre - -lmp_mpi -sf opt -in in.script # run in serial -mpirun -np 4 lmp_mpi -sf opt -in in.script # run in parallel :pre - [Required hardware/software:] None. [Building LAMMPS with the OPT package:] -The lines above illustrate how to build LAMMPS with the OPT package in -two steps, using the "make" command. Or how to do it with one command -as described in "Section 4"_Section_packages.html of the manual. - -Note that if you use an Intel compiler to build with the OPT package, -the CCFLAGS setting in your Makefile.machine must include "-restrict". +See the "Build extras"_Build_extras.html#opt doc page for instructions. [Run with the OPT package from the command line:] -As in the lines above, use the "-sf opt" "command-line -switch"_Section_start.html#start_6, which will automatically append -"opt" to styles that support it. +lmp_mpi -sf opt -in in.script # run in serial +mpirun -np 4 lmp_mpi -sf opt -in in.script # run in parallel :pre + +Use the "-sf opt" "command-line switch"_Run_options.html, which will +automatically append "opt" to styles that support it. [Or run with the OPT package by editing an input script:] diff --git a/doc/src/Speed_packages.txt b/doc/src/Speed_packages.txt new file mode 100644 index 0000000000..4c87091e7e --- /dev/null +++ b/doc/src/Speed_packages.txt @@ -0,0 +1,192 @@ +"Higher level section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Accelerator packages :h3 + +Accelerated versions of various "pair_style"_pair_style.html, +"fixes"_fix.html, "computes"_compute.html, and other commands have +been added to LAMMPS, which will typically run faster than the +standard non-accelerated versions. Some require appropriate hardware +to be present on your system, e.g. GPUs or Intel Xeon Phi +coprocessors. + +All of these commands are in packages provided with LAMMPS. An +overview of packages is give on the "Packages"_Packages.html doc +pages. + +These are the accelerator packages currently in LAMMPS, either as +standard or user packages: + +"GPU Package"_Speed_gpu.html : for NVIDIA GPUs as well as OpenCL support +"USER-INTEL Package"_Speed_intel.html : for Intel CPUs and Intel Xeon Phi +"KOKKOS Package"_Speed_kokkos.html : for Nvidia GPUs, Intel Xeon Phi, and OpenMP threading +"USER-OMP Package"_Speed_omp.html : for OpenMP threading and generic CPU optimizations +"OPT Package"_Speed_opt.html : generic CPU optimizations :tb(s=:) + + + +Inverting this list, LAMMPS currently has acceleration support for +three kinds of hardware, via the listed packages: + +Many-core CPUs : "USER-INTEL"_Speed_intel.html, "KOKKOS"_Speed_kokkos.html, "USER-OMP"_Speed_omp.html, "OPT"_Speed_opt.html packages +NVIDIA GPUs : "GPU"_Speed_gpu.html, "KOKKOS"_Speed_kokkos.html packages +Intel Phi : "USER-INTEL"_Speed_intel.html, "KOKKOS"_Speed_kokkos.html packages :tb(s=:) + +Which package is fastest for your hardware may depend on the size +problem you are running and what commands (accelerated and +non-accelerated) are invoked by your input script. While these doc +pages include performance guidelines, there is no substitute for +trying out the different packages appropriate to your hardware. + +Any accelerated style has the same name as the corresponding standard +style, except that a suffix is appended. Otherwise, the syntax for +the command that uses the style is identical, their functionality is +the same, and the numerical results it produces should also be the +same, except for precision and round-off effects. + +For example, all of these styles are accelerated variants of the +Lennard-Jones "pair_style lj/cut"_pair_lj.html: + +"pair_style lj/cut/gpu"_pair_lj.html +"pair_style lj/cut/intel"_pair_lj.html +"pair_style lj/cut/kk"_pair_lj.html +"pair_style lj/cut/omp"_pair_lj.html +"pair_style lj/cut/opt"_pair_lj.html :ul + +To see what accelerate styles are currently available for a particular +style, find the style name in the "Commands_all"_lc +style pages (fix,compute,pair,etc) and see what suffixes are listed +(g,i,k,o,t) with it. The doc pages for individual commands +(e.g. "pair lj/cut"_pair_lj.html or "fix nve"_fix_nve.html) also list +any accelerated variants available for that style. + +To use an accelerator package in LAMMPS, and one or more of the styles +it provides, follow these general steps. Details vary from package to +package and are explained in the individual accelerator doc pages, +listed above: + +build the accelerator library | + only for GPU package | +install the accelerator package | + make yes-opt, make yes-user-intel, etc | +add compile/link flags to Makefile.machine in src/MAKE | + only for USER-INTEL, KOKKOS, USER-OMP, OPT packages | +re-build LAMMPS | + make machine | +prepare and test a regular LAMMPS simulation | + lmp_machine -in in.script; mpirun -np 32 lmp_machine -in in.script | +enable specific accelerator support via '-k on' "command-line switch"_Run_options.html, | + only needed for KOKKOS package | +set any needed options for the package via "-pk" "command-line switch"_Run_options.html or "package"_package.html command, | + only if defaults need to be changed | +use accelerated styles in your input via "-sf" "command-line switch"_Run_options.html or "suffix"_suffix.html command | lmp_machine -in in.script -sf gpu +:tb(c=2,s=|) + +Note that the first 4 steps can be done as a single command with +suitable make command invocations. This is discussed on the +"Packages"_Packages.html doc pages, and its use is illustrated in the +individual accelerator sections. Typically these steps only need to +be done once, to create an executable that uses one or more +accelerator packages. + +The last 4 steps can all be done from the command-line when LAMMPS is +launched, without changing your input script, as illustrated in the +individual accelerator sections. Or you can add +"package"_package.html and "suffix"_suffix.html commands to your input +script. + +NOTE: With a few exceptions, you can build a single LAMMPS executable +with all its accelerator packages installed. Note however that the +USER-INTEL and KOKKOS packages require you to choose one of their +hardware options when building for a specific platform. I.e. CPU or +Phi option for the USER-INTEL package. Or the OpenMP, Cuda, or Phi +option for the KOKKOS package. + +These are the exceptions. You cannot build a single executable with: + +both the USER-INTEL Phi and KOKKOS Phi options +the USER-INTEL Phi or Kokkos Phi option, and the GPU package :ul + +See the examples/accelerate/README and make.list files for sample +Make.py commands that build LAMMPS with any or all of the accelerator +packages. As an example, here is a command that builds with all the +GPU related packages installed (GPU, KOKKOS with Cuda), including +settings to build the needed auxiliary GPU libraries for Kepler GPUs: + +Make.py -j 16 -p omp gpu kokkos -cc nvcc wrap=mpi \ + -gpu mode=double arch=35 -kokkos cuda arch=35 lib-all file mpi :pre + +The examples/accelerate directory also has input scripts that can be +used with all of the accelerator packages. See its README file for +details. + +Likewise, the bench directory has FERMI and KEPLER and PHI +sub-directories with Make.py commands and input scripts for using all +the accelerator packages on various machines. See the README files in +those dirs. + +As mentioned above, the "Benchmark +page"_http://lammps.sandia.gov/bench.html of the LAMMPS web site gives +performance results for the various accelerator packages for several +of the standard LAMMPS benchmark problems, as a function of problem +size and number of compute nodes, on different hardware platforms. + +Here is a brief summary of what the various packages provide. Details +are in the individual accelerator sections. + +Styles with a "gpu" suffix are part of the GPU package, and can be run +on NVIDIA GPUs. The speed-up on a GPU depends on a variety of +factors, discussed in the accelerator sections. :ulb,l + +Styles with an "intel" suffix are part of the USER-INTEL +package. These styles support vectorized single and mixed precision +calculations, in addition to full double precision. In extreme cases, +this can provide speedups over 3.5x on CPUs. The package also +supports acceleration in "offload" mode to Intel(R) Xeon Phi(TM) +coprocessors. This can result in additional speedup over 2x depending +on the hardware configuration. :l + +Styles with a "kk" suffix are part of the KOKKOS package, and can be +run using OpenMP on multicore CPUs, on an NVIDIA GPU, or on an Intel +Xeon Phi in "native" mode. The speed-up depends on a variety of +factors, as discussed on the KOKKOS accelerator page. :l + +Styles with an "omp" suffix are part of the USER-OMP package and allow +a pair-style to be run in multi-threaded mode using OpenMP. This can +be useful on nodes with high-core counts when using less MPI processes +than cores is advantageous, e.g. when running with PPPM so that FFTs +are run on fewer MPI processors or when the many MPI tasks would +overload the available bandwidth for communication. :l + +Styles with an "opt" suffix are part of the OPT package and typically +speed-up the pairwise calculations of your simulation by 5-25% on a +CPU. :l +:ule + +The individual accelerator package doc pages explain: + +what hardware and software the accelerated package requires +how to build LAMMPS with the accelerated package +how to run with the accelerated package either via command-line switches or modifying the input script +speed-ups to expect +guidelines for best performance +restrictions :ul + diff --git a/doc/src/Speed_tips.txt b/doc/src/Speed_tips.txt new file mode 100644 index 0000000000..858b1d493f --- /dev/null +++ b/doc/src/Speed_tips.txt @@ -0,0 +1,59 @@ +"Higher level section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +General tips :h3 + +NOTE: this page is still a work in progress + +Here is a list of general ideas for improving simulation performance. +Most of them are only applicable to certain models and certain +bottlenecks in the current performance, so let the timing data you +generate be your guide. It is hard, if not impossible, to predict how +much difference these options will make, since it is a function of +problem size, number of processors used, and your machine. There is +no substitute for identifying performance bottlenecks, and trying out +various options. + +rRESPA +Two-FFT PPPM +Staggered PPPM +single vs double PPPM +partial charge PPPM +verlet/split run style +processor command for proc layout and numa layout +load-balancing: balance and fix balance :ul + +Two-FFT PPPM, also called {analytic differentiation} or {ad} PPPM, +uses 2 FFTs instead of the 4 FFTs used by the default {ik +differentiation} PPPM. However, 2-FFT PPPM also requires a slightly +larger mesh size to achieve the same accuracy as 4-FFT PPPM. For +problems where the FFT cost is the performance bottleneck (typically +large problems running on many processors), 2-FFT PPPM may be faster +than 4-FFT PPPM. + +Staggered PPPM performs calculations using two different meshes, one +shifted slightly with respect to the other. This can reduce force +aliasing errors and increase the accuracy of the method, but also +doubles the amount of work required. For high relative accuracy, using +staggered PPPM allows one to half the mesh size in each dimension as +compared to regular PPPM, which can give around a 4x speedup in the +kspace time. However, for low relative accuracy, using staggered PPPM +gives little benefit and can be up to 2x slower in the kspace +time. For example, the rhodopsin benchmark was run on a single +processor, and results for kspace time vs. relative accuracy for the +different methods are shown in the figure below. For this system, +staggered PPPM (using ik differentiation) becomes useful when using a +relative accuracy of slightly greater than 1e-5 and above. + +:c,image(JPG/rhodo_staggered.jpg) + +NOTE: Using staggered PPPM may not give the same increase in accuracy +of energy and pressure as it does in forces, so some caution must be +used if energy and/or pressure are quantities of interest, such as +when using a barostat. diff --git a/doc/src/Section_tools.txt b/doc/src/Tools.txt similarity index 83% rename from doc/src/Section_tools.txt rename to doc/src/Tools.txt index 7cc07cbec5..a9ad5032ce 100644 --- a/doc/src/Section_tools.txt +++ b/doc/src/Tools.txt @@ -1,40 +1,41 @@ -"Previous Section"_Section_perf.html - "LAMMPS WWW Site"_lws - "LAMMPS +"Previous Section"_Examples.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next -Section"_Section_modify.html :c +Section"_Modify.html :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line -9. Additional tools :h2 +Auxiliary tools :h2 LAMMPS is designed to be a computational kernel for performing molecular dynamics computations. Additional pre- and post-processing -steps are often necessary to setup and analyze a simulation. A -list of such tools can be found on the LAMMPS home page -at "http://lammps.sandia.gov/prepost.html"_http://lammps.sandia.gov/prepost.html +steps are often necessary to setup and analyze a simulation. A list +of such tools can be found on the "LAMMPS webpage"_lws at these links: -A few additional tools are provided with the LAMMPS distribution -and are described in this section. +"Pre/Post processing"_http://lammps.sandia.gov/prepost.html +"Offsite LAMMPS packages & tools"_http://lammps.sandia.gov/offsite.html +"Pizza.py toolkit"_pizza :ul -Our group has also written and released a separate toolkit called -"Pizza.py"_pizza which provides tools for doing setup, analysis, -plotting, and visualization for LAMMPS simulations. Pizza.py is -written in "Python"_python and is available for download from "the -Pizza.py WWW site"_pizza. +The last link for "Pizza.py"_pizza is a Python-based tool developed at +Sandia which provides tools for doing setup, analysis, plotting, and +visualization for LAMMPS simulations. -:link(pizza,http://www.sandia.gov/~sjplimp/pizza.html) +:link(pizza,http://pizza.sandia.gov) :link(python,http://www.python.org) +Additional tools included in the LAMMPS distribution are described on +this page. + Note that many users write their own setup or analysis tools or use other existing codes and convert their output to a LAMMPS input format or vice versa. The tools listed here are included in the LAMMPS distribution as examples of auxiliary tools. Some of them are not -actively supported by Sandia, as they were contributed by LAMMPS -users. If you have problems using them, we can direct you to the -authors. +actively supported by the LAMMPS developers, as they were contributed +by LAMMPS users. If you have problems using them, we can direct you +to the authors. The source code for each of these codes is in the tools sub-directory of the LAMMPS distribution. There is a Makefile (which you may need @@ -42,40 +43,55 @@ to edit for your platform) which will build several of the tools which reside in that directory. Most of them are larger packages in their own sub-directories with their own Makefiles and/or README files. -"amber2lmp"_#amber -"binary2txt"_#binary -"ch2lmp"_#charmm -"chain"_#chain -"colvars"_#colvars -"createatoms"_#createatoms -"doxygen"_#doxygen -"drude"_#drude -"eam database"_#eamdb -"eam generate"_#eamgn -"eff"_#eff -"emacs"_#emacs -"fep"_#fep -"i-pi"_#ipi -"ipp"_#ipp -"kate"_#kate -"lmp2arc"_#arc -"lmp2cfg"_#cfg -"matlab"_#matlab -"micelle2d"_#micelle -"moltemplate"_#moltemplate -"msi2lmp"_#msi -"phonon"_#phonon -"polybond"_#polybond -"pymol_asphere"_#pymol -"python"_#pythontools -"reax"_#reax_tool -"smd"_#smd -"vim"_#vim -"xmgrace"_#xmgrace +:line + +Pre-processing tools :h3 + +"amber2lmp"_#amber, +"ch2lmp"_#charmm, +"chain"_#chain, +"createatoms"_#createatoms, +"drude"_#drude, +"eam database"_#eamdb, +"eam generate"_#eamgn, +"eff"_#eff, +"ipp"_#ipp, +"micelle2d"_#micelle, +"moltemplate"_#moltemplate, +"msi2lmp"_#msi, +"polybond"_#polybond :tb(c=6,ea=c,a=l) + +Post-processing tools :h3 + +"amber2lmp"_#amber, +"binary2txt"_#binary, +"ch2lmp"_#charmm, +"colvars"_#colvars, +"eff"_#eff, +"fep"_#fep, +"lmp2arc"_#arc, +"lmp2cfg"_#cfg, +"matlab"_#matlab, +"phonon"_#phonon, +"pymol_asphere"_#pymol, +"python"_#pythontools, +"reax"_#reax_tool, +"smd"_#smd, +"xmgrace"_#xmgrace :tb(c=6,ea=c,a=l) + +Miscellaneous tools :h3 + +"doxygen"_#doxygen, +"emacs"_#emacs, +"i-pi"_#ipi, +"kate"_#kate, +"vim"_#vim :tb(c=5,ea=c,a=l) :line -amber2lmp tool :h3,link(amber) +Tool descriptions :h3 + +amber2lmp tool :h4,link(amber) The amber2lmp sub-directory contains two Python scripts for converting files back-and-forth between the AMBER MD code and LAMMPS. See the @@ -90,7 +106,7 @@ necessary modifications yourself. :line -binary2txt tool :h3,link(binary) +binary2txt tool :h4,link(binary) The file binary2txt.cpp converts one or more binary LAMMPS dump file into ASCII text files. The syntax for running the tool is @@ -103,7 +119,7 @@ since binary files are not compatible across all platforms. :line -ch2lmp tool :h3,link(charmm) +ch2lmp tool :h4,link(charmm) The ch2lmp sub-directory contains tools for converting files back-and-forth between the CHARMM MD code and LAMMPS. @@ -128,7 +144,7 @@ Chris Lorenz (chris.lorenz at kcl.ac.uk), King's College London. :line -chain tool :h3,link(chain) +chain tool :h4,link(chain) The file chain.f creates a LAMMPS data file containing bead-spring polymer chains and/or monomer solvent atoms. It uses a text file @@ -140,12 +156,12 @@ The syntax for running the tool is chain < def.chain > data.file :pre See the def.chain or def.chain.ab files in the tools directory for -examples of definition files. This tool was used to create the -system for the "chain benchmark"_Section_perf.html. +examples of definition files. This tool was used to create the system +for the "chain benchmark"_Speed_bench.html. :line -colvars tools :h3,link(colvars) +colvars tools :h4,link(colvars) The colvars directory contains a collection of tools for postprocessing data produced by the colvars collective variable library. @@ -167,7 +183,7 @@ gmail.com) at ICTP, Italy. :line -createatoms tool :h3,link(createatoms) +createatoms tool :h4,link(createatoms) The tools/createatoms directory contains a Fortran program called createAtoms.f which can generate a variety of interesting crystal @@ -180,7 +196,7 @@ The tool is authored by Xiaowang Zhou (Sandia), xzhou at sandia.gov. :line -doxygen tool :h3,link(doxygen) +doxygen tool :h4,link(doxygen) The tools/doxygen directory contains a shell script called doxygen.sh which can generate a call graph and API lists using @@ -192,7 +208,7 @@ The tool is authored by Nandor Tamaskovics, numericalfreedom at googlemail.com. :line -drude tool :h3,link(drude) +drude tool :h4,link(drude) The tools/drude directory contains a Python script called polarizer.py which can add Drude oscillators to a LAMMPS @@ -205,7 +221,7 @@ at univ-bpclermont.fr, alain.dequidt at univ-bpclermont.fr :line -eam database tool :h3,link(eamdb) +eam database tool :h4,link(eamdb) The tools/eam_database directory contains a Fortran program that will generate EAM alloy setfl potential files for any combination of 16 @@ -221,7 +237,7 @@ X. W. Zhou, R. A. Johnson, and H. N. G. Wadley, Phys. Rev. B, 69, :line -eam generate tool :h3,link(eamgn) +eam generate tool :h4,link(eamgn) The tools/eam_generate directory contains several one-file C programs that convert an analytic formula into a tabulated "embedded atom @@ -234,7 +250,7 @@ The source files and potentials were provided by Gerolf Ziegenhain :line -eff tool :h3,link(eff) +eff tool :h4,link(eff) The tools/eff directory contains various scripts for generating structures and post-processing output for simulations using the @@ -245,18 +261,18 @@ These tools were provided by Andres Jaramillo-Botero at CalTech :line -emacs tool :h3,link(emacs) +emacs tool :h4,link(emacs) -The tools/emacs directory contains a Lips add-on file for Emacs that -enables a lammps-mode for editing of input scripts when using Emacs, -with various highlighting options setup. +The tools/emacs directory contains an Emacs Lisp add-on file for GNU Emacs +that enables a lammps-mode for editing input scripts when using GNU Emacs, +with various highlighting options set up. These tools were provided by Aidan Thompson at Sandia (athomps at sandia.gov). :line -fep tool :h3,link(fep) +fep tool :h4,link(fep) The tools/fep directory contains Python scripts useful for post-processing results from performing free-energy perturbation @@ -269,7 +285,7 @@ See README file in the tools/fep directory. :line -i-pi tool :h3,link(ipi) +i-pi tool :h4,link(ipi) The tools/i-pi directory contains a version of the i-PI package, with all the LAMMPS-unrelated files removed. It is provided so that it can @@ -286,7 +302,7 @@ calculations with LAMMPS. :line -ipp tool :h3,link(ipp) +ipp tool :h4,link(ipp) The tools/ipp directory contains a Perl script ipp which can be used to facilitate the creation of a complicated file (say, a lammps input @@ -300,7 +316,7 @@ tools/createatoms tool's input file. :line -kate tool :h3,link(kate) +kate tool :h4,link(kate) The file in the tools/kate directory is an add-on to the Kate editor in the KDE suite that allow syntax highlighting of LAMMPS input @@ -311,7 +327,7 @@ The file was provided by Alessandro Luigi Sellerio :line -lmp2arc tool :h3,link(arc) +lmp2arc tool :h4,link(arc) The lmp2arc sub-directory contains a tool for converting LAMMPS output files to the format for Accelrys' Insight MD code (formerly @@ -327,7 +343,7 @@ Greathouse at Sandia (jagreat at sandia.gov). :line -lmp2cfg tool :h3,link(cfg) +lmp2cfg tool :h4,link(cfg) The lmp2cfg sub-directory contains a tool for converting LAMMPS output files into a series of *.cfg files which can be read into the @@ -338,7 +354,7 @@ This tool was written by Ara Kooser at Sandia (askoose at sandia.gov). :line -matlab tool :h3,link(matlab) +matlab tool :h4,link(matlab) The matlab sub-directory contains several "MATLAB"_matlabhome scripts for post-processing LAMMPS output. The scripts include readers for log @@ -356,7 +372,7 @@ These scripts were written by Arun Subramaniyan at Purdue Univ :line -micelle2d tool :h3,link(micelle) +micelle2d tool :h4,link(micelle) The file micelle2d.f creates a LAMMPS data file containing short lipid chains in a monomer solution. It uses a text file containing lipid @@ -369,11 +385,11 @@ micelle2d < def.micelle2d > data.file :pre See the def.micelle2d file in the tools directory for an example of a definition file. This tool was used to create the system for the -"micelle example"_Section_example.html. +"micelle example"_Examples.html. :line -moltemplate tool :h3,link(moltemplate) +moltemplate tool :h4,link(moltemplate) The moltemplate sub-directory contains a Python-based tool for building molecular systems based on a text-file description, and @@ -387,7 +403,7 @@ supports it. It has its own WWW page at :line -msi2lmp tool :h3,link(msi) +msi2lmp tool :h4,link(msi) The msi2lmp sub-directory contains a tool for creating LAMMPS template input and data files from BIOVIA's Materias Studio files (formerly Accelrys' @@ -404,7 +420,7 @@ See the README file in the tools/msi2lmp folder for more information. :line -phonon tool :h3,link(phonon) +phonon tool :h4,link(phonon) The phonon sub-directory contains a post-processing tool useful for analyzing the output of the "fix phonon"_fix_phonon.html command in @@ -419,7 +435,7 @@ University. :line -polybond tool :h3,link(polybond) +polybond tool :h4,link(polybond) The polybond sub-directory contains a Python-based tool useful for performing "programmable polymer bonding". The Python file @@ -433,7 +449,7 @@ This tool was written by Zachary Kraus at Georgia Tech. :line -pymol_asphere tool :h3,link(pymol) +pymol_asphere tool :h4,link(pymol) The pymol_asphere sub-directory contains a tool for converting a LAMMPS dump file that contains orientation info for ellipsoidal @@ -451,7 +467,7 @@ This tool was written by Mike Brown at Sandia. :line -python tool :h3,link(pythontools) +python tool :h4,link(pythontools) The python sub-directory contains several Python scripts that perform common LAMMPS post-processing tasks, such as: @@ -467,7 +483,7 @@ README for more info on Pizza.py and how to use these scripts. :line -reax tool :h3,link(reax_tool) +reax tool :h4,link(reax_tool) The reax sub-directory contains stand-alond codes that can post-process the output of the "fix reax/bonds"_fix_reax_bonds.html @@ -478,7 +494,7 @@ These tools were written by Aidan Thompson at Sandia. :line -smd tool :h3,link(smd) +smd tool :h4,link(smd) The smd sub-directory contains a C++ file dump2vtk_tris.cpp and Makefile which can be compiled and used to convert triangle output @@ -494,7 +510,7 @@ Ernst Mach Institute in Germany (georg.ganzenmueller at emi.fhg.de). :line -vim tool :h3,link(vim) +vim tool :h4,link(vim) The files in the tools/vim directory are add-ons to the VIM editor that allow easier editing of LAMMPS input scripts. See the README.txt @@ -505,7 +521,7 @@ ziegenhain.com) :line -xmgrace tool :h3,link(xmgrace) +xmgrace tool :h4,link(xmgrace) The files in the tools/xmgrace directory can be used to plot the thermodynamic data in LAMMPS log files via the xmgrace plotting @@ -517,4 +533,3 @@ simulation. See the README file for details. These files were provided by Vikas Varshney (vv0210 at gmail.com) - diff --git a/doc/src/USER/atc/man_add_molecule.html b/doc/src/USER/atc/man_add_molecule.html index 8d9625e1bd..4e7810aa61 100644 --- a/doc/src/USER/atc/man_add_molecule.html +++ b/doc/src/USER/atc/man_add_molecule.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_add_species.html b/doc/src/USER/atc/man_add_species.html index 9beded1b16..a990ab626f 100644 --- a/doc/src/USER/atc/man_add_species.html +++ b/doc/src/USER/atc/man_add_species.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_atom_element_map.html b/doc/src/USER/atc/man_atom_element_map.html index 6725170928..a5707d280e 100644 --- a/doc/src/USER/atc/man_atom_element_map.html +++ b/doc/src/USER/atc/man_atom_element_map.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_atom_weight.html b/doc/src/USER/atc/man_atom_weight.html index 28bc90fa01..350ab13b92 100644 --- a/doc/src/USER/atc/man_atom_weight.html +++ b/doc/src/USER/atc/man_atom_weight.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_atomic_charge.html b/doc/src/USER/atc/man_atomic_charge.html index ef787f53ac..17e854a37f 100644 --- a/doc/src/USER/atc/man_atomic_charge.html +++ b/doc/src/USER/atc/man_atomic_charge.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_boundary.html b/doc/src/USER/atc/man_boundary.html index 61596d3b31..8dcf328dd3 100644 --- a/doc/src/USER/atc/man_boundary.html +++ b/doc/src/USER/atc/man_boundary.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_boundary_dynamics.html b/doc/src/USER/atc/man_boundary_dynamics.html index 40b82f3f61..335ff2d209 100644 --- a/doc/src/USER/atc/man_boundary_dynamics.html +++ b/doc/src/USER/atc/man_boundary_dynamics.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_boundary_faceset.html b/doc/src/USER/atc/man_boundary_faceset.html index 7eb950f78e..6c2fb84940 100644 --- a/doc/src/USER/atc/man_boundary_faceset.html +++ b/doc/src/USER/atc/man_boundary_faceset.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_boundary_integral.html b/doc/src/USER/atc/man_boundary_integral.html index 0663dba176..c4b0d4865e 100644 --- a/doc/src/USER/atc/man_boundary_integral.html +++ b/doc/src/USER/atc/man_boundary_integral.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_consistent_fe_initialization.html b/doc/src/USER/atc/man_consistent_fe_initialization.html index a731b09116..baa306a1c8 100644 --- a/doc/src/USER/atc/man_consistent_fe_initialization.html +++ b/doc/src/USER/atc/man_consistent_fe_initialization.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_contour_integral.html b/doc/src/USER/atc/man_contour_integral.html index 690f0fcc98..16f6d9abad 100644 --- a/doc/src/USER/atc/man_contour_integral.html +++ b/doc/src/USER/atc/man_contour_integral.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_control.html b/doc/src/USER/atc/man_control.html index 900952ba0b..e94a9a52ef 100644 --- a/doc/src/USER/atc/man_control.html +++ b/doc/src/USER/atc/man_control.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_control_momentum.html b/doc/src/USER/atc/man_control_momentum.html index 8f4f486595..e3074eae8f 100644 --- a/doc/src/USER/atc/man_control_momentum.html +++ b/doc/src/USER/atc/man_control_momentum.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_control_thermal.html b/doc/src/USER/atc/man_control_thermal.html index eab186f715..8d32f1c4f9 100644 --- a/doc/src/USER/atc/man_control_thermal.html +++ b/doc/src/USER/atc/man_control_thermal.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_control_thermal_correction_max_iterations.html b/doc/src/USER/atc/man_control_thermal_correction_max_iterations.html index a337a495e0..d28ec334f5 100644 --- a/doc/src/USER/atc/man_control_thermal_correction_max_iterations.html +++ b/doc/src/USER/atc/man_control_thermal_correction_max_iterations.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_decomposition.html b/doc/src/USER/atc/man_decomposition.html index d54a201034..98eedafa6c 100644 --- a/doc/src/USER/atc/man_decomposition.html +++ b/doc/src/USER/atc/man_decomposition.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_electron_integration.html b/doc/src/USER/atc/man_electron_integration.html index ab454c16d2..7cf40f6813 100644 --- a/doc/src/USER/atc/man_electron_integration.html +++ b/doc/src/USER/atc/man_electron_integration.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_equilibrium_start.html b/doc/src/USER/atc/man_equilibrium_start.html index d01253c4b3..8c81ce5925 100644 --- a/doc/src/USER/atc/man_equilibrium_start.html +++ b/doc/src/USER/atc/man_equilibrium_start.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_extrinsic_exchange.html b/doc/src/USER/atc/man_extrinsic_exchange.html index 4f1f5962d9..f4d1b01e88 100644 --- a/doc/src/USER/atc/man_extrinsic_exchange.html +++ b/doc/src/USER/atc/man_extrinsic_exchange.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_fe_md_boundary.html b/doc/src/USER/atc/man_fe_md_boundary.html index e517dd4855..e39ddd3cec 100644 --- a/doc/src/USER/atc/man_fe_md_boundary.html +++ b/doc/src/USER/atc/man_fe_md_boundary.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_fem_mesh.html b/doc/src/USER/atc/man_fem_mesh.html index b8ba584816..485b8c95a0 100644 --- a/doc/src/USER/atc/man_fem_mesh.html +++ b/doc/src/USER/atc/man_fem_mesh.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_filter_scale.html b/doc/src/USER/atc/man_filter_scale.html index 7a871f5c81..e2190dea21 100644 --- a/doc/src/USER/atc/man_filter_scale.html +++ b/doc/src/USER/atc/man_filter_scale.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_filter_type.html b/doc/src/USER/atc/man_filter_type.html index 2711d128e9..0928139d7d 100644 --- a/doc/src/USER/atc/man_filter_type.html +++ b/doc/src/USER/atc/man_filter_type.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_fix_atc.html b/doc/src/USER/atc/man_fix_atc.html index 7cc6cfea5b..f6f7b43a38 100644 --- a/doc/src/USER/atc/man_fix_atc.html +++ b/doc/src/USER/atc/man_fix_atc.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_fix_flux.html b/doc/src/USER/atc/man_fix_flux.html index 42815def6b..31bd5619a3 100644 --- a/doc/src/USER/atc/man_fix_flux.html +++ b/doc/src/USER/atc/man_fix_flux.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_fix_nodes.html b/doc/src/USER/atc/man_fix_nodes.html index 03cf86eb92..2245e32607 100644 --- a/doc/src/USER/atc/man_fix_nodes.html +++ b/doc/src/USER/atc/man_fix_nodes.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_hardy_computes.html b/doc/src/USER/atc/man_hardy_computes.html index b45b7dfb01..ec2dc3ccb9 100644 --- a/doc/src/USER/atc/man_hardy_computes.html +++ b/doc/src/USER/atc/man_hardy_computes.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_hardy_fields.html b/doc/src/USER/atc/man_hardy_fields.html index 17903aabd0..483e5be6bd 100644 --- a/doc/src/USER/atc/man_hardy_fields.html +++ b/doc/src/USER/atc/man_hardy_fields.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_hardy_gradients.html b/doc/src/USER/atc/man_hardy_gradients.html index 00935f0ae2..1874ad152e 100644 --- a/doc/src/USER/atc/man_hardy_gradients.html +++ b/doc/src/USER/atc/man_hardy_gradients.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_hardy_kernel.html b/doc/src/USER/atc/man_hardy_kernel.html index f97037784c..620b9b1d36 100644 --- a/doc/src/USER/atc/man_hardy_kernel.html +++ b/doc/src/USER/atc/man_hardy_kernel.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
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diff --git a/doc/src/USER/atc/man_hardy_rates.html b/doc/src/USER/atc/man_hardy_rates.html index e51cbc9873..337a92517e 100644 --- a/doc/src/USER/atc/man_hardy_rates.html +++ b/doc/src/USER/atc/man_hardy_rates.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_initial.html b/doc/src/USER/atc/man_initial.html index 41ae06eb8c..c8348c45ed 100644 --- a/doc/src/USER/atc/man_initial.html +++ b/doc/src/USER/atc/man_initial.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_internal_atom_integrate.html b/doc/src/USER/atc/man_internal_atom_integrate.html index dfa19474e5..f76607cc91 100644 --- a/doc/src/USER/atc/man_internal_atom_integrate.html +++ b/doc/src/USER/atc/man_internal_atom_integrate.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_internal_element_set.html b/doc/src/USER/atc/man_internal_element_set.html index 849e8f0671..a5d893f2a3 100644 --- a/doc/src/USER/atc/man_internal_element_set.html +++ b/doc/src/USER/atc/man_internal_element_set.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_internal_quadrature.html b/doc/src/USER/atc/man_internal_quadrature.html index 7f10e17076..6af543cbae 100644 --- a/doc/src/USER/atc/man_internal_quadrature.html +++ b/doc/src/USER/atc/man_internal_quadrature.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_kernel_function.html b/doc/src/USER/atc/man_kernel_function.html index 92db590198..cb02c05c23 100644 --- a/doc/src/USER/atc/man_kernel_function.html +++ b/doc/src/USER/atc/man_kernel_function.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_localized_lambda.html b/doc/src/USER/atc/man_localized_lambda.html index fd845d0a71..88442d63a1 100644 --- a/doc/src/USER/atc/man_localized_lambda.html +++ b/doc/src/USER/atc/man_localized_lambda.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
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diff --git a/doc/src/USER/atc/man_mask_direction.html b/doc/src/USER/atc/man_mask_direction.html index 31c18b4f1f..ea5a6e357b 100644 --- a/doc/src/USER/atc/man_mask_direction.html +++ b/doc/src/USER/atc/man_mask_direction.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_mass_matrix.html b/doc/src/USER/atc/man_mass_matrix.html index 140b745f09..fd744e5bbf 100644 --- a/doc/src/USER/atc/man_mass_matrix.html +++ b/doc/src/USER/atc/man_mass_matrix.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_material.html b/doc/src/USER/atc/man_material.html index c31ab4938d..1646abc671 100644 --- a/doc/src/USER/atc/man_material.html +++ b/doc/src/USER/atc/man_material.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_mesh_add_to_nodeset.html b/doc/src/USER/atc/man_mesh_add_to_nodeset.html index 25a5c2cdae..c4976f699d 100644 --- a/doc/src/USER/atc/man_mesh_add_to_nodeset.html +++ b/doc/src/USER/atc/man_mesh_add_to_nodeset.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_mesh_create.html b/doc/src/USER/atc/man_mesh_create.html index a7ee112614..98989bd015 100644 --- a/doc/src/USER/atc/man_mesh_create.html +++ b/doc/src/USER/atc/man_mesh_create.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_mesh_create_elementset.html b/doc/src/USER/atc/man_mesh_create_elementset.html index 2ac383a974..735d462b73 100644 --- a/doc/src/USER/atc/man_mesh_create_elementset.html +++ b/doc/src/USER/atc/man_mesh_create_elementset.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
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diff --git a/doc/src/USER/atc/man_mesh_create_nodeset.html b/doc/src/USER/atc/man_mesh_create_nodeset.html index 39bfffd119..0e3624cf8a 100644 --- a/doc/src/USER/atc/man_mesh_create_nodeset.html +++ b/doc/src/USER/atc/man_mesh_create_nodeset.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_mesh_delete_elements.html b/doc/src/USER/atc/man_mesh_delete_elements.html index 60a2fe59a1..e39cc54d41 100644 --- a/doc/src/USER/atc/man_mesh_delete_elements.html +++ b/doc/src/USER/atc/man_mesh_delete_elements.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_mesh_nodeset_to_elementset.html b/doc/src/USER/atc/man_mesh_nodeset_to_elementset.html index d05429ebab..66b55a48fb 100644 --- a/doc/src/USER/atc/man_mesh_nodeset_to_elementset.html +++ b/doc/src/USER/atc/man_mesh_nodeset_to_elementset.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_mesh_output.html b/doc/src/USER/atc/man_mesh_output.html index f768a29c41..1d2983afff 100644 --- a/doc/src/USER/atc/man_mesh_output.html +++ b/doc/src/USER/atc/man_mesh_output.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
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diff --git a/doc/src/USER/atc/man_mesh_read.html b/doc/src/USER/atc/man_mesh_read.html index e0571ccf88..315180e1db 100644 --- a/doc/src/USER/atc/man_mesh_read.html +++ b/doc/src/USER/atc/man_mesh_read.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_mesh_write.html b/doc/src/USER/atc/man_mesh_write.html index 756cf49922..f709c02a84 100644 --- a/doc/src/USER/atc/man_mesh_write.html +++ b/doc/src/USER/atc/man_mesh_write.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_momentum_time_integration.html b/doc/src/USER/atc/man_momentum_time_integration.html index 60fbfcd888..ee0505847c 100644 --- a/doc/src/USER/atc/man_momentum_time_integration.html +++ b/doc/src/USER/atc/man_momentum_time_integration.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_output.html b/doc/src/USER/atc/man_output.html index aec1d5d55a..d0a08fa0da 100644 --- a/doc/src/USER/atc/man_output.html +++ b/doc/src/USER/atc/man_output.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_output_elementset.html b/doc/src/USER/atc/man_output_elementset.html index 54079027c5..18afe0aa97 100644 --- a/doc/src/USER/atc/man_output_elementset.html +++ b/doc/src/USER/atc/man_output_elementset.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_output_nodeset.html b/doc/src/USER/atc/man_output_nodeset.html index 2fc6e02681..7906c5fc52 100644 --- a/doc/src/USER/atc/man_output_nodeset.html +++ b/doc/src/USER/atc/man_output_nodeset.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_pair_interactions.html b/doc/src/USER/atc/man_pair_interactions.html index 2cb2cb6113..3ec2eecc60 100644 --- a/doc/src/USER/atc/man_pair_interactions.html +++ b/doc/src/USER/atc/man_pair_interactions.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_poisson_solver.html b/doc/src/USER/atc/man_poisson_solver.html index b6fabbb27c..3e22a51f3e 100644 --- a/doc/src/USER/atc/man_poisson_solver.html +++ b/doc/src/USER/atc/man_poisson_solver.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_read_restart.html b/doc/src/USER/atc/man_read_restart.html index 5fc21282f6..d13151a12e 100644 --- a/doc/src/USER/atc/man_read_restart.html +++ b/doc/src/USER/atc/man_read_restart.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_remove_molecule.html b/doc/src/USER/atc/man_remove_molecule.html index e6ad418de6..54e4e3419f 100644 --- a/doc/src/USER/atc/man_remove_molecule.html +++ b/doc/src/USER/atc/man_remove_molecule.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_remove_source.html b/doc/src/USER/atc/man_remove_source.html index acea7a5607..c15e0ca46d 100644 --- a/doc/src/USER/atc/man_remove_source.html +++ b/doc/src/USER/atc/man_remove_source.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_remove_species.html b/doc/src/USER/atc/man_remove_species.html index 561364518f..ee063ce57f 100644 --- a/doc/src/USER/atc/man_remove_species.html +++ b/doc/src/USER/atc/man_remove_species.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_reset_atomic_reference_positions.html b/doc/src/USER/atc/man_reset_atomic_reference_positions.html index 88e6748001..3c43861054 100644 --- a/doc/src/USER/atc/man_reset_atomic_reference_positions.html +++ b/doc/src/USER/atc/man_reset_atomic_reference_positions.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_reset_time.html b/doc/src/USER/atc/man_reset_time.html index a6429bf6d6..9607848e1a 100644 --- a/doc/src/USER/atc/man_reset_time.html +++ b/doc/src/USER/atc/man_reset_time.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_sample_frequency.html b/doc/src/USER/atc/man_sample_frequency.html index 4e48c4bb29..9a9a8e3a02 100644 --- a/doc/src/USER/atc/man_sample_frequency.html +++ b/doc/src/USER/atc/man_sample_frequency.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_set.html b/doc/src/USER/atc/man_set.html index cf775c9b36..55ad8d952b 100644 --- a/doc/src/USER/atc/man_set.html +++ b/doc/src/USER/atc/man_set.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_source.html b/doc/src/USER/atc/man_source.html index c7239f2c41..78fb1652eb 100644 --- a/doc/src/USER/atc/man_source.html +++ b/doc/src/USER/atc/man_source.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_source_integration.html b/doc/src/USER/atc/man_source_integration.html index 3f43340af8..3b261b7810 100644 --- a/doc/src/USER/atc/man_source_integration.html +++ b/doc/src/USER/atc/man_source_integration.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_temperature_definition.html b/doc/src/USER/atc/man_temperature_definition.html index a07ba29cab..c317c06c00 100644 --- a/doc/src/USER/atc/man_temperature_definition.html +++ b/doc/src/USER/atc/man_temperature_definition.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_thermal_time_integration.html b/doc/src/USER/atc/man_thermal_time_integration.html index fe293138be..830591921e 100644 --- a/doc/src/USER/atc/man_thermal_time_integration.html +++ b/doc/src/USER/atc/man_thermal_time_integration.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_time_filter.html b/doc/src/USER/atc/man_time_filter.html index 732eaa3a36..5000fb079d 100644 --- a/doc/src/USER/atc/man_time_filter.html +++ b/doc/src/USER/atc/man_time_filter.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_track_displacement.html b/doc/src/USER/atc/man_track_displacement.html index f5410816d7..2c7cf26150 100644 --- a/doc/src/USER/atc/man_track_displacement.html +++ b/doc/src/USER/atc/man_track_displacement.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_unfix_flux.html b/doc/src/USER/atc/man_unfix_flux.html index 95e1f4be5a..551896431a 100644 --- a/doc/src/USER/atc/man_unfix_flux.html +++ b/doc/src/USER/atc/man_unfix_flux.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_unfix_nodes.html b/doc/src/USER/atc/man_unfix_nodes.html index 78495c928a..4dfd9b3cfc 100644 --- a/doc/src/USER/atc/man_unfix_nodes.html +++ b/doc/src/USER/atc/man_unfix_nodes.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_write_atom_weights.html b/doc/src/USER/atc/man_write_atom_weights.html index 8a0e5b62a8..1722d74f67 100644 --- a/doc/src/USER/atc/man_write_atom_weights.html +++ b/doc/src/USER/atc/man_write_atom_weights.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/USER/atc/man_write_restart.html b/doc/src/USER/atc/man_write_restart.html index 6dca57673b..74c6e2d289 100644 --- a/doc/src/USER/atc/man_write_restart.html +++ b/doc/src/USER/atc/man_write_restart.html @@ -11,7 +11,7 @@ LAMMPS Website     LAMMPS Manual     USER-AtC Manual     - Commands + Commands
diff --git a/doc/src/accelerate_kokkos.txt b/doc/src/accelerate_kokkos.txt deleted file mode 100644 index 0c9178d6e4..0000000000 --- a/doc/src/accelerate_kokkos.txt +++ /dev/null @@ -1,458 +0,0 @@ -"Previous Section"_Section_packages.html - "LAMMPS WWW Site"_lws - -"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Section_commands.html#comm) - -:line - -"Return to Section accelerate overview"_Section_accelerate.html - -5.3.3 KOKKOS package :h5 - -Kokkos is a templated C++ library that provides abstractions to allow -a single implementation of an application kernel (e.g. a pair style) to run efficiently on -different kinds of hardware, such as GPUs, Intel Xeon Phis, or many-core -CPUs. Kokkos maps the C++ kernel onto different backend languages such as CUDA, OpenMP, or Pthreads. -The Kokkos library also provides data abstractions to adjust (at -compile time) the memory layout of data structures like 2d and -3d arrays to optimize performance on different hardware. For more information on Kokkos, see -"Github"_https://github.com/kokkos/kokkos. Kokkos is part of -"Trilinos"_http://trilinos.sandia.gov/packages/kokkos. The Kokkos library was written primarily by Carter Edwards, -Christian Trott, and Dan Sunderland (all Sandia). - -The LAMMPS KOKKOS package contains versions of pair, fix, and atom styles -that use data structures and macros provided by the Kokkos library, -which is included with LAMMPS in /lib/kokkos. The KOKKOS package was developed primarily by Christian Trott (Sandia) -and Stan Moore (Sandia) with contributions of various styles by others, including Sikandar -Mashayak (UIUC), Ray Shan (Sandia), and Dan Ibanez (Sandia). For more information on developing using Kokkos abstractions -see the Kokkos programmers' guide at /lib/kokkos/doc/Kokkos_PG.pdf. - -Kokkos currently provides support for 3 modes of execution (per MPI -task). These are Serial (MPI-only for CPUs and Intel Phi), OpenMP (threading -for many-core CPUs and Intel Phi), and CUDA (for NVIDIA GPUs). You choose the mode at build time to -produce an executable compatible with specific hardware. - -[Building LAMMPS with the KOKKOS package:] - -NOTE: Kokkos support within LAMMPS must be built with a C++11 compatible -compiler. This means GCC version 4.7.2 or later, Intel 14.0.4 or later, or -Clang 3.5.2 or later is required. - -The recommended method of building the KOKKOS package is to start with the provided Kokkos -Makefiles in /src/MAKE/OPTIONS/. You may need to modify the KOKKOS_ARCH variable in the Makefile -to match your specific hardware. For example: - -for Sandy Bridge CPUs, set KOKKOS_ARCH=SNB -for Broadwell CPUs, set KOKKOS_ARCH=BWD -for K80 GPUs, set KOKKOS_ARCH=Kepler37 -for P100 GPUs and Power8 CPUs, set KOKKOS_ARCH=Pascal60,Power8 :ul - -See the [Advanced Kokkos Options] section below for a listing of all KOKKOS_ARCH options. - -[Compile for CPU-only (MPI only, no threading):] - -use a C++11 compatible compiler and set KOKKOS_ARCH variable in -/src/MAKE/OPTIONS/Makefile.kokkos_mpi_only as described above. Then do the -following: - -cd lammps/src -make yes-kokkos -make kokkos_mpi_only :pre - -[Compile for CPU-only (MPI plus OpenMP threading):] - -NOTE: To build with Kokkos support for OpenMP threading, your compiler must support the -OpenMP interface. You should have one or more multi-core CPUs so that -multiple threads can be launched by each MPI task running on a CPU. - -use a C++11 compatible compiler and set KOKKOS_ARCH variable in -/src/MAKE/OPTIONS/Makefile.kokkos_omp as described above. Then do the -following: - -cd lammps/src -make yes-kokkos -make kokkos_omp :pre - -[Compile for Intel KNL Xeon Phi (Intel Compiler, OpenMPI):] - -use a C++11 compatible compiler and do the following: - -cd lammps/src -make yes-kokkos -make kokkos_phi :pre - -[Compile for CPUs and GPUs (with OpenMPI or MPICH):] - -NOTE: To build with Kokkos support for NVIDIA GPUs, NVIDIA CUDA software -version 7.5 or later must be installed on your system. See the -discussion for the "GPU"_accelerate_gpu.html package for details of -how to check and do this. - -use a C++11 compatible compiler and set KOKKOS_ARCH variable in -/src/MAKE/OPTIONS/Makefile.kokkos_cuda_mpi for both GPU and CPU as described -above. Then do the following: - -cd lammps/src -make yes-kokkos -make kokkos_cuda_mpi :pre - -[Alternative Methods of Compiling:] - -Alternatively, the KOKKOS package can be built by specifying Kokkos variables -on the make command line. For example: - -make mpi KOKKOS_DEVICES=OpenMP KOKKOS_ARCH=SNB # set the KOKKOS_DEVICES and KOKKOS_ARCH variable explicitly -make kokkos_cuda_mpi KOKKOS_ARCH=Pascal60,Power8 # set the KOKKOS_ARCH variable explicitly :pre - -Setting the KOKKOS_DEVICES and KOKKOS_ARCH variables on the -make command line requires a GNU-compatible make command. Try -"gmake" if your system's standard make complains. - -NOTE: If you build using make line variables and re-build LAMMPS twice -with different KOKKOS options and the *same* target, then you *must* perform a "make clean-all" -or "make clean-machine" before each build. This is to force all the -KOKKOS-dependent files to be re-compiled with the new options. - -[Running LAMMPS with the KOKKOS package:] - -All Kokkos operations occur within the -context of an individual MPI task running on a single node of the -machine. The total number of MPI tasks used by LAMMPS (one or -multiple per compute node) is set in the usual manner via the mpirun -or mpiexec commands, and is independent of Kokkos. E.g. the mpirun -command in OpenMPI does this via its --np and -npernode switches. Ditto for MPICH via -np and -ppn. - -[Running on a multi-core CPU:] - -Here is a quick overview of how to use the KOKKOS package -for CPU acceleration, assuming one or more 16-core nodes. - -mpirun -np 16 lmp_kokkos_mpi_only -k on -sf kk -in in.lj # 1 node, 16 MPI tasks/node, no multi-threading -mpirun -np 2 -ppn 1 lmp_kokkos_omp -k on t 16 -sf kk -in in.lj # 2 nodes, 1 MPI task/node, 16 threads/task -mpirun -np 2 lmp_kokkos_omp -k on t 8 -sf kk -in in.lj # 1 node, 2 MPI tasks/node, 8 threads/task -mpirun -np 32 -ppn 4 lmp_kokkos_omp -k on t 4 -sf kk -in in.lj # 8 nodes, 4 MPI tasks/node, 4 threads/task :pre - -To run using the KOKKOS package, use the "-k on", "-sf kk" and "-pk kokkos" "command-line switches"_Section_start.html#start_7 in your mpirun command. -You must use the "-k on" "command-line -switch"_Section_start.html#start_7 to enable the KOKKOS package. It -takes additional arguments for hardware settings appropriate to your -system. Those arguments are "documented -here"_Section_start.html#start_7. For OpenMP use: - --k on t Nt :pre - -The "t Nt" option specifies how many OpenMP threads per MPI -task to use with a node. The default is Nt = 1, which is MPI-only mode. -Note that the product of MPI tasks * OpenMP -threads/task should not exceed the physical number of cores (on a -node), otherwise performance will suffer. If hyperthreading is enabled, then -the product of MPI tasks * OpenMP threads/task should not exceed the -physical number of cores * hardware threads. -The "-k on" switch also issues a "package kokkos" command (with no -additional arguments) which sets various KOKKOS options to default -values, as discussed on the "package"_package.html command doc page. - -The "-sf kk" "command-line switch"_Section_start.html#start_7 -will automatically append the "/kk" suffix to styles that support it. -In this manner no modification to the input script is needed. Alternatively, -one can run with the KOKKOS package by editing the input script as described below. - -NOTE: The default for the "package kokkos"_package.html command is -to use "full" neighbor lists and set the Newton flag to "off" for both -pairwise and bonded interactions. However, when running on CPUs, it -will typically be faster to use "half" neighbor lists and set the -Newton flag to "on", just as is the case for non-accelerated pair -styles. It can also be faster to use non-threaded communication. -Use the "-pk kokkos" "command-line switch"_Section_start.html#start_7 to -change the default "package kokkos"_package.html -options. See its doc page for details and default settings. Experimenting with -its options can provide a speed-up for specific calculations. For example: - -mpirun -np 16 lmp_kokkos_mpi_only -k on -sf kk -pk kokkos newton on neigh half comm no -in in.lj # Newton on, Half neighbor list, non-threaded comm :pre - -If the "newton"_newton.html command is used in the input -script, it can also override the Newton flag defaults. - -[Core and Thread Affinity:] - -When using multi-threading, it is important for -performance to bind both MPI tasks to physical cores, and threads to -physical cores, so they do not migrate during a simulation. - -If you are not certain MPI tasks are being bound (check the defaults -for your MPI installation), binding can be forced with these flags: - -OpenMPI 1.8: mpirun -np 2 --bind-to socket --map-by socket ./lmp_openmpi ... -Mvapich2 2.0: mpiexec -np 2 --bind-to socket --map-by socket ./lmp_mvapich ... :pre - -For binding threads with KOKKOS OpenMP, use thread affinity -environment variables to force binding. With OpenMP 3.1 (gcc 4.7 or -later, intel 12 or later) setting the environment variable -OMP_PROC_BIND=true should be sufficient. In general, for best performance -with OpenMP 4.0 or better set OMP_PROC_BIND=spread and OMP_PLACES=threads. -For binding threads with the -KOKKOS pthreads option, compile LAMMPS the KOKKOS HWLOC=yes option -as described below. - -[Running on Knight's Landing (KNL) Intel Xeon Phi:] - -Here is a quick overview of how to use the KOKKOS package -for the Intel Knight's Landing (KNL) Xeon Phi: - -KNL Intel Phi chips have 68 physical cores. Typically 1 to 4 cores -are reserved for the OS, and only 64 or 66 cores are used. Each core -has 4 hyperthreads,so there are effectively N = 256 (4*64) or -N = 264 (4*66) cores to run on. The product of MPI tasks * OpenMP threads/task should not exceed this limit, -otherwise performance will suffer. Note that with the KOKKOS package you do not need to -specify how many KNLs there are per node; each -KNL is simply treated as running some number of MPI tasks. - -Examples of mpirun commands that follow these rules are shown below. - -Intel KNL node with 68 cores (272 threads/node via 4x hardware threading): -mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -in in.lj # 1 node, 64 MPI tasks/node, 4 threads/task -mpirun -np 66 lmp_kokkos_phi -k on t 4 -sf kk -in in.lj # 1 node, 66 MPI tasks/node, 4 threads/task -mpirun -np 32 lmp_kokkos_phi -k on t 8 -sf kk -in in.lj # 1 node, 32 MPI tasks/node, 8 threads/task -mpirun -np 512 -ppn 64 lmp_kokkos_phi -k on t 4 -sf kk -in in.lj # 8 nodes, 64 MPI tasks/node, 4 threads/task :pre - -The -np setting of the mpirun command sets the number of MPI -tasks/node. The "-k on t Nt" command-line switch sets the number of -threads/task as Nt. The product of these two values should be N, i.e. -256 or 264. - -NOTE: The default for the "package kokkos"_package.html command is -to use "full" neighbor lists and set the Newton flag to "off" for both -pairwise and bonded interactions. When running on KNL, this -will typically be best for pair-wise potentials. For manybody potentials, -using "half" neighbor lists and setting the -Newton flag to "on" may be faster. It can also be faster to use non-threaded communication. -Use the "-pk kokkos" "command-line switch"_Section_start.html#start_7 to -change the default "package kokkos"_package.html -options. See its doc page for details and default settings. Experimenting with -its options can provide a speed-up for specific calculations. For example: - -mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -pk kokkos comm no -in in.lj # Newton off, full neighbor list, non-threaded comm -mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -pk kokkos newton on neigh half comm no -in in.reax # Newton on, half neighbor list, non-threaded comm :pre - -NOTE: MPI tasks and threads should be bound to cores as described above for CPUs. - -NOTE: To build with Kokkos support for Intel Xeon Phi coprocessors such as Knight's Corner (KNC), your -system must be configured to use them in "native" mode, not "offload" -mode like the USER-INTEL package supports. - -[Running on GPUs:] - -Use the "-k" "command-line switch"_Section_commands.html#start_7 to -specify the number of GPUs per node. Typically the -np setting -of the mpirun command should set the number of MPI -tasks/node to be equal to the # of physical GPUs on the node. -You can assign multiple MPI tasks to the same GPU with the -KOKKOS package, but this is usually only faster if significant portions -of the input script have not been ported to use Kokkos. Using CUDA MPS -is recommended in this scenario. As above for multi-core CPUs (and no GPU), if N is the number -of physical cores/node, then the number of MPI tasks/node should not exceed N. - --k on g Ng :pre - -Here are examples of how to use the KOKKOS package for GPUs, -assuming one or more nodes, each with two GPUs: - -mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -in in.lj # 1 node, 2 MPI tasks/node, 2 GPUs/node -mpirun -np 32 -ppn 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -in in.lj # 16 nodes, 2 MPI tasks/node, 2 GPUs/node (32 GPUs total) :pre - -NOTE: The default for the "package kokkos"_package.html command is -to use "full" neighbor lists and set the Newton flag to "off" for both -pairwise and bonded interactions, along with threaded communication. -When running on Maxwell or Kepler GPUs, this will typically be best. For Pascal GPUs, -using "half" neighbor lists and setting the -Newton flag to "on" may be faster. For many pair styles, setting the neighbor binsize -equal to the ghost atom cutoff will give speedup. -Use the "-pk kokkos" "command-line switch"_Section_start.html#start_7 to -change the default "package kokkos"_package.html -options. See its doc page for details and default settings. Experimenting with -its options can provide a speed-up for specific calculations. For example: - -mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -pk kokkos binsize 2.8 -in in.lj # Set binsize = neighbor ghost cutoff -mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -pk kokkos newton on neigh half binsize 2.8 -in in.lj # Newton on, half neighborlist, set binsize = neighbor ghost cutoff :pre - -NOTE: For good performance of the KOKKOS package on GPUs, you must -have Kepler generation GPUs (or later). The Kokkos library exploits -texture cache options not supported by Telsa generation GPUs (or -older). - -NOTE: When using a GPU, you will achieve the best performance if your -input script does not use fix or compute styles which are not yet -Kokkos-enabled. This allows data to stay on the GPU for multiple -timesteps, without being copied back to the host CPU. Invoking a -non-Kokkos fix or compute, or performing I/O for -"thermo"_thermo_style.html or "dump"_dump.html output will cause data -to be copied back to the CPU incurring a performance penalty. - -NOTE: To get an accurate timing breakdown between time spend in pair, -kspace, etc., you must set the environment variable CUDA_LAUNCH_BLOCKING=1. -However, this will reduce performance and is not recommended for production runs. - -[Run with the KOKKOS package by editing an input script:] - -Alternatively the effect of the "-sf" or "-pk" switches can be -duplicated by adding the "package kokkos"_package.html or "suffix -kk"_suffix.html commands to your input script. - -The discussion above for building LAMMPS with the KOKKOS package, the mpirun/mpiexec command, and setting -appropriate thread are the same. - -You must still use the "-k on" "command-line -switch"_Section_start.html#start_7 to enable the KOKKOS package, and -specify its additional arguments for hardware options appropriate to -your system, as documented above. - -You can use the "suffix kk"_suffix.html command, or you can explicitly add a -"kk" suffix to individual styles in your input script, e.g. - -pair_style lj/cut/kk 2.5 :pre - -You only need to use the "package kokkos"_package.html command if you -wish to change any of its option defaults, as set by the "-k on" -"command-line switch"_Section_start.html#start_7. - -[Using OpenMP threading and CUDA together (experimental):] - -With the KOKKOS package, both OpenMP multi-threading and GPUs can be used -together in a few special cases. In the Makefile, the KOKKOS_DEVICES variable must -include both "Cuda" and "OpenMP", as is the case for /src/MAKE/OPTIONS/Makefile.kokkos_cuda_mpi - -KOKKOS_DEVICES=Cuda,OpenMP :pre - -The suffix "/kk" is equivalent to "/kk/device", and for Kokkos CUDA, -using the "-sf kk" in the command line gives the default CUDA version everywhere. -However, if the "/kk/host" suffix is added to a specific style in the input -script, the Kokkos OpenMP (CPU) version of that specific style will be used instead. -Set the number of OpenMP threads as "t Nt" and the number of GPUs as "g Ng" - --k on t Nt g Ng :pre - -For example, the command to run with 1 GPU and 8 OpenMP threads is then: - -mpiexec -np 1 lmp_kokkos_cuda_openmpi -in in.lj -k on g 1 t 8 -sf kk :pre - -Conversely, if the "-sf kk/host" is used in the command line and then the -"/kk" or "/kk/device" suffix is added to a specific style in your input script, -then only that specific style will run on the GPU while everything else will -run on the CPU in OpenMP mode. Note that the execution of the CPU and GPU -styles will NOT overlap, except for a special case: - -A kspace style and/or molecular topology (bonds, angles, etc.) running on -the host CPU can overlap with a pair style running on the GPU. First compile -with "--default-stream per-thread" added to CCFLAGS in the Kokkos CUDA Makefile. -Then explicitly use the "/kk/host" suffix for kspace and bonds, angles, etc. -in the input file and the "kk" suffix (equal to "kk/device") on the command line. -Also make sure the environment variable CUDA_LAUNCH_BLOCKING is not set to "1" -so CPU/GPU overlap can occur. - -[Speed-ups to expect:] - -The performance of KOKKOS running in different modes is a function of -your hardware, which KOKKOS-enable styles are used, and the problem -size. - -Generally speaking, the following rules of thumb apply: - -When running on CPUs only, with a single thread per MPI task, -performance of a KOKKOS style is somewhere between the standard -(un-accelerated) styles (MPI-only mode), and those provided by the -USER-OMP package. However the difference between all 3 is small (less -than 20%). :ulb,l - -When running on CPUs only, with multiple threads per MPI task, -performance of a KOKKOS style is a bit slower than the USER-OMP -package. :l - -When running large number of atoms per GPU, KOKKOS is typically faster -than the GPU package. :l - -When running on Intel hardware, KOKKOS is not as fast as -the USER-INTEL package, which is optimized for that hardware. :l -:ule - -See the "Benchmark page"_http://lammps.sandia.gov/bench.html of the -LAMMPS web site for performance of the KOKKOS package on different -hardware. - -[Advanced Kokkos options:] - -There are other allowed options when building with the KOKKOS package. -As above, they can be set either as variables on the make command line -or in Makefile.machine. This is the full list of options, including -those discussed above. Each takes a value shown below. The -default value is listed, which is set in the -/lib/kokkos/Makefile.kokkos file. - -KOKKOS_DEVICES, values = {Serial}, {OpenMP}, {Pthreads}, {Cuda}, default = {OpenMP} -KOKKOS_ARCH, values = {KNC}, {SNB}, {HSW}, {Kepler30}, {Kepler32}, {Kepler35}, {Kepler37}, {Maxwell50}, {Maxwell52}, {Maxwell53}, {Pascal60}, {Pascal61}, {ARMv80}, {ARMv81}, {ARMv81}, {ARMv8-ThunderX}, {BGQ}, {Power7}, {Power8}, {Power9}, {KNL}, {BDW}, {SKX}, default = {none} -KOKKOS_DEBUG, values = {yes}, {no}, default = {no} -KOKKOS_USE_TPLS, values = {hwloc}, {librt}, {experimental_memkind}, default = {none} -KOKKOS_CXX_STANDARD, values = {c++11}, {c++1z}, default = {c++11} -KOKKOS_OPTIONS, values = {aggressive_vectorization}, {disable_profiling}, default = {none} -KOKKOS_CUDA_OPTIONS, values = {force_uvm}, {use_ldg}, {rdc}, {enable_lambda}, default = {enable_lambda} :ul - -KOKKOS_DEVICES sets the parallelization method used for Kokkos code -(within LAMMPS). KOKKOS_DEVICES=Serial means that no threading will be used. -KOKKOS_DEVICES=OpenMP means that OpenMP threading will be -used. KOKKOS_DEVICES=Pthreads means that pthreads will be used. -KOKKOS_DEVICES=Cuda means an NVIDIA GPU running CUDA will be used. - -KOKKOS_ARCH enables compiler switches needed when compiling for a -specific hardware: - -ARMv80 = ARMv8.0 Compatible CPU -ARMv81 = ARMv8.1 Compatible CPU -ARMv8-ThunderX = ARMv8 Cavium ThunderX CPU -SNB = Intel Sandy/Ivy Bridge CPUs -HSW = Intel Haswell CPUs -BDW = Intel Broadwell Xeon E-class CPUs -SKX = Intel Sky Lake Xeon E-class HPC CPUs (AVX512) -KNC = Intel Knights Corner Xeon Phi -KNL = Intel Knights Landing Xeon Phi -Kepler30 = NVIDIA Kepler generation CC 3.0 -Kepler32 = NVIDIA Kepler generation CC 3.2 -Kepler35 = NVIDIA Kepler generation CC 3.5 -Kepler37 = NVIDIA Kepler generation CC 3.7 -Maxwell50 = NVIDIA Maxwell generation CC 5.0 -Maxwell52 = NVIDIA Maxwell generation CC 5.2 -Maxwell53 = NVIDIA Maxwell generation CC 5.3 -Pascal60 = NVIDIA Pascal generation CC 6.0 -Pascal61 = NVIDIA Pascal generation CC 6.1 -BGQ = IBM Blue Gene/Q CPUs -Power8 = IBM POWER8 CPUs -Power9 = IBM POWER9 CPUs :ul - -KOKKOS_USE_TPLS=hwloc binds threads to hardware cores, so they do not -migrate during a simulation. KOKKOS_USE_TPLS=hwloc should always be -used if running with KOKKOS_DEVICES=Pthreads for pthreads. It is not -necessary for KOKKOS_DEVICES=OpenMP for OpenMP, because OpenMP -provides alternative methods via environment variables for binding -threads to hardware cores. More info on binding threads to cores is -given in "Section 5.3"_Section_accelerate.html#acc_3. - -KOKKOS_USE_TPLS=librt enables use of a more accurate timer mechanism -on most Unix platforms. This library is not available on all -platforms. - -KOKKOS_DEBUG is only useful when developing a Kokkos-enabled style -within LAMMPS. KOKKOS_DEBUG=yes enables printing of run-time -debugging information that can be useful. It also enables runtime -bounds checking on Kokkos data structures. - -KOKKOS_CXX_STANDARD and KOKKOS_OPTIONS are typically not changed when building LAMMPS. - -KOKKOS_CUDA_OPTIONS are additional options for CUDA. The LAMMPS KOKKOS package must be compiled -with the {enable_lambda} option when using GPUs. - -[Restrictions:] - -Currently, there are no precision options with the KOKKOS -package. All compilation and computation is performed in double -precision. diff --git a/doc/src/angle_charmm.txt b/doc/src/angle_charmm.txt index 7ff7ef8fd4..8b0e298a43 100644 --- a/doc/src/angle_charmm.txt +++ b/doc/src/angle_charmm.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -51,31 +51,30 @@ internally; hence the units of K are in energy/radian^2. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line [Restrictions:] This angle style can only be used if LAMMPS was built with the -MOLECULE package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info on packages. +MOLECULE package. See the "Build package"_Build_package.html doc page +for more info. [Related commands:] diff --git a/doc/src/angle_class2.txt b/doc/src/angle_class2.txt index d4330139c9..fa5e29582c 100644 --- a/doc/src/angle_class2.txt +++ b/doc/src/angle_class2.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -83,23 +83,22 @@ same value from the Ea formula. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line @@ -124,8 +123,8 @@ The bond-bond and bond-angle terms remain unchanged. This angle style can only be used if LAMMPS was built with the CLASS2 package. For the {class2/p6} style LAMMPS needs to be built with the -USER-MOFFF package. See the "Making LAMMPS"_Section_start.html#start_3 -section for more info on packages. +USER-MOFFF package. See the "Build package"_Build_package.html doc +page for more info. [Related commands:] diff --git a/doc/src/angle_coeff.txt b/doc/src/angle_coeff.txt index 37298ba145..4c217bae7d 100644 --- a/doc/src/angle_coeff.txt +++ b/doc/src/angle_coeff.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -65,9 +65,9 @@ the style to display the formula it computes and coefficients specified by the associated "angle_coeff"_angle_coeff.html command. Note that there are also additional angle styles submitted by users -which are included in the LAMMPS distribution. The list of these with -links to the individual styles are given in the angle section of "this -page"_Section_commands.html#cmd_5. +which are included in the LAMMPS distribution. The full list of all +angle styles is on the "Commands bond"_Commands_bond.html#angle doc +page. "angle_style none"_angle_none.html - turn off angle interactions "angle_style hybrid"_angle_hybrid.html - define multiple styles of angle interactions :ul diff --git a/doc/src/angle_cosine.txt b/doc/src/angle_cosine.txt index c0ce3c9301..80cf8ae8f1 100644 --- a/doc/src/angle_cosine.txt +++ b/doc/src/angle_cosine.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -38,31 +38,30 @@ K (energy) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line [Restrictions:] This angle style can only be used if LAMMPS was built with the -MOLECULE package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info on packages. +MOLECULE package. See the "Build package"_Build_package.html doc page +for more info. [Related commands:] diff --git a/doc/src/angle_cosine_buck6d.txt b/doc/src/angle_cosine_buck6d.txt index 7182ffecc8..54709c1370 100644 --- a/doc/src/angle_cosine_buck6d.txt +++ b/doc/src/angle_cosine_buck6d.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -55,8 +55,8 @@ the "special_bonds"_special_bonds.html 1-3 interactions to be weighted "special_bonds"_special_bonds.html 0.0 weighting of 1-3 interactions. This angle style can only be used if LAMMPS was built with the -USER-MOFFF package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info on packages. +USER-MOFFF package. See the "Build package"_Build_package.html doc +page for more info. [Related commands:] diff --git a/doc/src/angle_cosine_delta.txt b/doc/src/angle_cosine_delta.txt index 830fd6db58..1532e39b31 100644 --- a/doc/src/angle_cosine_delta.txt +++ b/doc/src/angle_cosine_delta.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -43,31 +43,30 @@ internally. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line [Restrictions:] This angle style can only be used if LAMMPS was built with the -MOLECULE package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info on packages. +MOLECULE package. See the "Build package"_Build_package.html doc page +for more info. [Related commands:] diff --git a/doc/src/angle_cosine_periodic.txt b/doc/src/angle_cosine_periodic.txt index b5c53b1b0f..039144797f 100644 --- a/doc/src/angle_cosine_periodic.txt +++ b/doc/src/angle_cosine_periodic.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -21,10 +21,10 @@ angle_coeff * 75.0 1 6 :pre [Description:] The {cosine/periodic} angle style uses the following potential, which -is commonly used in the "DREIDING"_Section_howto.html#howto_4 force -field, particularly for organometallic systems where {n} = 4 might be -used for an octahedral complex and {n} = 3 might be used for a -trigonal center: +is commonly used in the "DREIDING"_Howto_bioFF.html force field, +particularly for organometallic systems where {n} = 4 might be used +for an octahedral complex and {n} = 3 might be used for a trigonal +center: :c,image(Eqs/angle_cosine_periodic.jpg) @@ -51,31 +51,30 @@ geometry. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line [Restrictions:] This angle style can only be used if LAMMPS was built with the -MOLECULE package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info on packages. +MOLECULE package. See the "Build package"_Build_package.html doc page +for more info. [Related commands:] diff --git a/doc/src/angle_cosine_shift.txt b/doc/src/angle_cosine_shift.txt index 6ed9fe2150..3a4efad218 100644 --- a/doc/src/angle_cosine_shift.txt +++ b/doc/src/angle_cosine_shift.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -41,31 +41,29 @@ theta (angle) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line [Restrictions:] This angle style can only be used if LAMMPS was built with the -USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_3 -section for more info on packages. +USER-MISC package. [Related commands:] diff --git a/doc/src/angle_cosine_shift_exp.txt b/doc/src/angle_cosine_shift_exp.txt index 44a68c1087..3091e83885 100644 --- a/doc/src/angle_cosine_shift_exp.txt +++ b/doc/src/angle_cosine_shift_exp.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -53,31 +53,30 @@ A (real number) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line [Restrictions:] This angle style can only be used if LAMMPS was built with the -USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_3 -section for more info on packages. +USER-MISC package. See the "Build package"_Build_package.html doc +page for more info. [Related commands:] diff --git a/doc/src/angle_cosine_squared.txt b/doc/src/angle_cosine_squared.txt index 065cdad542..07fcb1ceb4 100644 --- a/doc/src/angle_cosine_squared.txt +++ b/doc/src/angle_cosine_squared.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -43,31 +43,30 @@ internally. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line [Restrictions:] This angle style can only be used if LAMMPS was built with the -MOLECULE package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info on packages. +MOLECULE package. See the "Build package"_Build_package.html doc page +for more info. [Related commands:] diff --git a/doc/src/angle_dipole.txt b/doc/src/angle_dipole.txt index d91f260d51..cdb11972ec 100644 --- a/doc/src/angle_dipole.txt +++ b/doc/src/angle_dipole.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -71,41 +71,41 @@ gamma0 (degrees) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. [Restrictions:] This angle style can only be used if LAMMPS was built with the -USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_2_3 -section for more info on packages. +USER-MISC package. See the "Build package"_Build_package.html doc +page for more info. NOTE: In the "Angles" section of the data file, the atom ID 'j' -corresponding to the dipole to restrain must come before the atom ID -of the reference atom 'i'. A third atom ID 'k' must also be provided, -although 'k' is just a 'dummy' atom which can be any atom; it may be -useful to choose a convention (e.g., 'k'='i') and adhere to it. For -example, if ID=1 for the dipolar atom to restrain, and ID=2 for the -reference atom, the corresponding line in the "Angles" section of the -data file would read: X X 1 2 2 +defining the direction of the dipole vector to restrain must come +before the atom ID of the reference atom 'i'. A third atom ID 'k' must +also be provided to comply with the requirement of a valid angle +definition. This atom ID k should be chosen to be that of an atom +bonded to atom 'i' to avoid errors with "lost angle atoms" when running +in parallel. Since the LAMMPS code checks for valid angle definitions, +cannot use the same atom ID of either 'i' or 'j' (this was allowed +and recommended with older LAMMPS versions). The "newton" command for intramolecular interactions must be "on" -(which is the default). +(which is the default except when using some accelerator packages). This angle style should not be used with SHAKE. diff --git a/doc/src/angle_fourier.txt b/doc/src/angle_fourier.txt index da39e7cf32..7dc9975793 100644 --- a/doc/src/angle_fourier.txt +++ b/doc/src/angle_fourier.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -39,31 +39,30 @@ C2 (real) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line [Restrictions:] This angle style can only be used if LAMMPS was built with the -USER_MISC package. See the "Making LAMMPS"_Section_start.html#start_3 -section for more info on packages. +USER_MISC package. See the "Build package"_Build_package.html doc +page for more info. [Related commands:] diff --git a/doc/src/angle_fourier_simple.txt b/doc/src/angle_fourier_simple.txt index 5adda6cb32..ae5d308353 100644 --- a/doc/src/angle_fourier_simple.txt +++ b/doc/src/angle_fourier_simple.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -38,31 +38,30 @@ n (real) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line [Restrictions:] This angle style can only be used if LAMMPS was built with the -USER_MISC package. See the "Making LAMMPS"_Section_start.html#start_3 -section for more info on packages. +USER_MISC package. See the "Build package"_Build_package.html doc +page for more info. [Related commands:] diff --git a/doc/src/angle_harmonic.txt b/doc/src/angle_harmonic.txt index 4c74763964..b632f68478 100644 --- a/doc/src/angle_harmonic.txt +++ b/doc/src/angle_harmonic.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -45,31 +45,30 @@ internally; hence the units of K are in energy/radian^2. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line [Restrictions:] This angle style can only be used if LAMMPS was built with the -MOLECULE package. See the "Making LAMMPS"_Section_start.html#start_3 -section for more info on packages. +MOLECULE package. See the "Build package"_Build_package.html doc +page for more info. [Related commands:] diff --git a/doc/src/angle_hybrid.txt b/doc/src/angle_hybrid.txt index bdd3707ccb..0046c161be 100644 --- a/doc/src/angle_hybrid.txt +++ b/doc/src/angle_hybrid.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -76,8 +76,8 @@ for specific angle types. [Restrictions:] This angle style can only be used if LAMMPS was built with the -MOLECULE package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info on packages. +MOLECULE package. See the "Build package"_Build_package.html doc page +for more info. Unlike other angle styles, the hybrid angle style does not store angle coefficient info for individual sub-styles in a "binary restart diff --git a/doc/src/angle_none.txt b/doc/src/angle_none.txt index a4a9b07c78..1eca5cbbec 100644 --- a/doc/src/angle_none.txt +++ b/doc/src/angle_none.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/angle_quartic.txt b/doc/src/angle_quartic.txt index f7640bdfbc..b20a06eb8d 100644 --- a/doc/src/angle_quartic.txt +++ b/doc/src/angle_quartic.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -45,31 +45,30 @@ internally; hence the units of K are in energy/radian^2. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line [Restrictions:] This angle style can only be used if LAMMPS was built with the -USER_MISC package. See the "Making LAMMPS"_Section_start.html#start_3 -section for more info on packages. +USER_MISC package. See the "Build package"_Build_package.html doc +page for more info. [Related commands:] diff --git a/doc/src/angle_sdk.txt b/doc/src/angle_sdk.txt index 0cc535e543..4de1a6755d 100644 --- a/doc/src/angle_sdk.txt +++ b/doc/src/angle_sdk.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -46,8 +46,8 @@ from the pair_style. [Restrictions:] This angle style can only be used if LAMMPS was built with the -USER-CGSDK package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info on packages. +USER-CGSDK package. See the "Build package"_Build_package.html doc +page for more info. [Related commands:] diff --git a/doc/src/angle_style.txt b/doc/src/angle_style.txt index f687e9286c..756cfc0c60 100644 --- a/doc/src/angle_style.txt +++ b/doc/src/angle_style.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -58,9 +58,9 @@ the style to display the formula it computes and coefficients specified by the associated "angle_coeff"_angle_coeff.html command. Note that there are also additional angle styles submitted by users -which are included in the LAMMPS distribution. The list of these with -links to the individual styles are given in the angle section of "this -page"_Section_commands.html#cmd_5. +which are included in the LAMMPS distribution. The full list of all +angle styles are is on the "Commands bond"_Commands_bond.html#angle +doc page. "angle_style none"_angle_none.html - turn off angle interactions "angle_style zero"_angle_zero.html - topology but no interactions @@ -83,10 +83,9 @@ Angle styles can only be set for atom_styles that allow angles to be defined. Most angle styles are part of the MOLECULE package. They are only -enabled if LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info on packages. -The doc pages for individual bond potentials tell if it is part of a -package. +enabled if LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. The doc pages for +individual bond potentials tell if it is part of a package. [Related commands:] diff --git a/doc/src/angle_table.txt b/doc/src/angle_table.txt index bd6e167bd8..6b9187e512 100644 --- a/doc/src/angle_table.txt +++ b/doc/src/angle_table.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -124,31 +124,30 @@ one that matches the specified keyword. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line [Restrictions:] This angle style can only be used if LAMMPS was built with the -MOLECULE package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info on packages. +MOLECULE package. See the "Build package"_Build_package.html doc page +for more info. [Related commands:] diff --git a/doc/src/angle_zero.txt b/doc/src/angle_zero.txt index b8e8ebf953..c6c1958ec8 100644 --- a/doc/src/angle_zero.txt +++ b/doc/src/angle_zero.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/atom_modify.txt b/doc/src/atom_modify.txt index 1dc0fa6bfb..0f0b241b76 100644 --- a/doc/src/atom_modify.txt +++ b/doc/src/atom_modify.txt @@ -3,7 +3,7 @@ Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -58,16 +58,16 @@ simulation so large that IDs cannot be uniquely assigned. For a default LAMMPS build this limit is 2^31 or about 2 billion atoms. However, even in this case, you can use 64-bit atom IDs, allowing 2^63 or about 9e18 atoms, if you build LAMMPS with the - DLAMMPS_BIGBIG -switch. This is described in "Section 2.2"_Section_start.html#start_2 -of the manual. If atom IDs are not used, they must be specified as 0 -for all atoms, e.g. in a data or restart file. +switch. This is described on the "Build_settings"_Build_settings.html +doc page. If atom IDs are not used, they must be specified as 0 for +all atoms, e.g. in a data or restart file. The {map} keyword determines how atoms with specific IDs are found when required. An example are the bond (angle, etc) methods which need to find the local index of an atom with a specific global ID which is a bond (angle, etc) partner. LAMMPS performs this operation efficiently by creating a "map", which is either an {array} or {hash} -table, as descibed below. +table, as described below. When the {map} keyword is not specified in your input script, LAMMPS only creates a map for "atom_styles"_atom_style.html for molecular diff --git a/doc/src/atom_style.txt b/doc/src/atom_style.txt index 49d9dde791..db2e285dc4 100644 --- a/doc/src/atom_style.txt +++ b/doc/src/atom_style.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -15,12 +15,12 @@ atom_style style args :pre style = {angle} or {atomic} or {body} or {bond} or {charge} or {dipole} or \ {dpd} or {edpd} or {mdpd} or {tdpd} or {electron} or {ellipsoid} or \ {full} or {line} or {meso} or {molecular} or {peri} or {smd} or \ - {sphere} or {tri} or {template} or {hybrid} :ulb,l + {sphere} or {spin} or {tri} or {template} or {hybrid} :ulb,l args = none for any style except the following {body} args = bstyle bstyle-args bstyle = style of body particles bstyle-args = additional arguments specific to the bstyle - see the "body"_body.html doc page for details + see the "Howto body"_Howto_body.html doc page for details {tdpd} arg = Nspecies Nspecies = # of chemical species {template} arg = template-ID @@ -38,6 +38,7 @@ atom_style full atom_style body nparticle 2 10 atom_style hybrid charge bond atom_style hybrid charge body nparticle 2 5 +atom_style spin atom_style template myMols atom_style tdpd 2 :pre @@ -89,6 +90,7 @@ quantities. {peri} | mass, volume | mesocopic Peridynamic models | {smd} | volume, kernel diameter, contact radius, mass | solid and fluid SPH particles | {sphere} | diameter, mass, angular velocity | granular models | +{spin} | magnetic moment | system with magnetic particles | {template} | template index, template atom | small molecules with fixed topology | {tri} | corner points, angular momentum | rigid bodies | {wavepacket} | charge, spin, eradius, etag, cs_re, cs_im | AWPMD :tb(c=3,s=|) @@ -104,9 +106,9 @@ output the custom values. All of the above styles define point particles, except the {sphere}, {ellipsoid}, {electron}, {peri}, {wavepacket}, {line}, {tri}, and -{body} styles, which define finite-size particles. See "Section -6.14"_Section_howto.html#howto_14 for an overview of using finite-size -particle models with LAMMPS. +{body} styles, which define finite-size particles. See the "Howto +spherical"_Howto_spherical.html doc page for an overview of using +finite-size particle models with LAMMPS. All of the point-particle styles assign mass to particles on a per-type basis, using the "mass"_mass.html command, The finite-size @@ -175,6 +177,9 @@ used for calculating the field variables (e.g. stress and deformation) and a contact radius for calculating repulsive forces which prevent individual physical bodies from penetrating each other. +For the {spin} style, a magnetic spin is associated to each atom. +Those spins have a norm (their magnetic moment) and a direction. + The {wavepacket} style is similar to {electron}, but the electrons may consist of several Gaussian wave packets, summed up with coefficients cs= (cs_re,cs_im). Each of the wave packets is treated as a separate @@ -219,15 +224,16 @@ the {bstyle} argument. Body particles can represent complex entities, such as surface meshes of discrete points, collections of sub-particles, deformable objects, etc. -The "body"_body.html doc page describes the body styles LAMMPS -currently supports, and provides more details as to the kind of body -particles they represent. For all styles, each body particle stores -moments of inertia and a quaternion 4-vector, so that its orientation -and position can be time integrated due to forces and torques. +The "Howto body"_Howto_body.html doc page describes the body styles +LAMMPS currently supports, and provides more details as to the kind of +body particles they represent. For all styles, each body particle +stores moments of inertia and a quaternion 4-vector, so that its +orientation and position can be time integrated due to forces and +torques. Note that there may be additional arguments required along with the {bstyle} specification, in the atom_style body command. These -arguments are described in the "body"_body.html doc page. +arguments are described on the "Howto body"_Howto_body.html doc page. :line @@ -250,32 +256,32 @@ with another molecular style that stores bond,angle,etc info on a per-atom basis. LAMMPS can be extended with new atom styles as well as new body -styles; see "this section"_Section_modify.html. +styles; see the "Modify"_Modify.html doc page. :line Styles with a {kk} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to -run faster, depending on your available hardware, as discussed in -"Section 5"_Section_accelerate.html of the manual. The -accelerated styles take the same arguments and should produce the same -results, except for round-off and precision issues. +run faster, depending on your available hardware, as discussed in on +the "Speed packages"_Speed_packages.html doc page. The accelerated +styles take the same arguments and should produce the same results, +except for round-off and precision issues. Note that other acceleration packages in LAMMPS, specifically the GPU, USER-INTEL, USER-OMP, and OPT packages do not use accelerated atom styles. The accelerated styles are part of the KOKKOS package. They are only -enabled if LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +enabled if LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. [Restrictions:] @@ -283,8 +289,8 @@ This command cannot be used after the simulation box is defined by a "read_data"_read_data.html or "create_box"_create_box.html command. Many of the styles listed above are only enabled if LAMMPS was built -with a specific package, as listed below. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +with a specific package, as listed below. See the "Build +package"_Build_package.html doc page for more info. The {angle}, {bond}, {full}, {molecular}, and {template} styles are part of the MOLECULE package. @@ -312,6 +318,8 @@ The {meso} style is part of the USER-SPH package for smoothed particle hydrodynamics (SPH). See "this PDF guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in LAMMPS. +The {spin} style is part of the SPIN package. + The {wavepacket} style is part of the USER-AWPMD package for the "antisymmetrized wave packet MD method"_pair_awpmd.html. diff --git a/doc/src/balance.txt b/doc/src/balance.txt index da6f59900d..26e146d89b 100644 --- a/doc/src/balance.txt +++ b/doc/src/balance.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -394,11 +394,11 @@ weights. It assigns the same weight to each particle owned by a processor based on the total computational time spent by that processor. See details below on what time window is used. It uses the same timing information as is used for the "MPI task timing -breakdown"_Section_start.html#start_7, namely, for sections {Pair}, -{Bond}, {Kspace}, and {Neigh}. The time spent in those portions of -the timestep are measured for each MPI rank, summed, then divided by -the number of particles owned by that processor. I.e. the weight is -an effective CPU time/particle averaged over the particles on that +breakdown"_Run_output.html, namely, for sections {Pair}, {Bond}, +{Kspace}, and {Neigh}. The time spent in those portions of the +timestep are measured for each MPI rank, summed, then divided by the +number of particles owned by that processor. I.e. the weight is an +effective CPU time/particle averaged over the particles on that processor. The {factor} setting is applied as an overall scale factor to the diff --git a/doc/src/bond_class2.txt b/doc/src/bond_class2.txt index 9687a63168..4390e3613c 100644 --- a/doc/src/bond_class2.txt +++ b/doc/src/bond_class2.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -44,31 +44,30 @@ K4 (energy/distance^4) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line [Restrictions:] This bond style can only be used if LAMMPS was built with the CLASS2 -package. See the "Making LAMMPS"_Section_start.html#start_3 section -for more info on packages. +package. See the "Build package"_Build_package.html doc page for more +info. [Related commands:] diff --git a/doc/src/bond_coeff.txt b/doc/src/bond_coeff.txt index d93c0b223b..7485fa3d8d 100644 --- a/doc/src/bond_coeff.txt +++ b/doc/src/bond_coeff.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -61,9 +61,8 @@ the style to display the formula it computes and coefficients specified by the associated "bond_coeff"_bond_coeff.html command. Note that here are also additional bond styles submitted by users -which are included in the LAMMPS distribution. The list of these with -links to the individual styles are given in the bond section of "this -page"_Section_commands.html#cmd_5. +which are included in the LAMMPS distribution. The full list of all +bond styles is on the "Commands bond"_Commands_bond.html doc page. "bond_style none"_bond_none.html - turn off bonded interactions "bond_style hybrid"_bond_hybrid.html - define multiple styles of bond interactions :ul diff --git a/doc/src/bond_fene.txt b/doc/src/bond_fene.txt index 9050c3bf5c..9ec4017d00 100644 --- a/doc/src/bond_fene.txt +++ b/doc/src/bond_fene.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -47,31 +47,30 @@ sigma (distance) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line [Restrictions:] -This bond style can only be used if LAMMPS was built with the -MOLECULE package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info on packages. +This bond style can only be used if LAMMPS was built with the MOLECULE +package. See the "Build package"_Build_package.html doc page for more +info. You typically should specify "special_bonds fene"_special_bonds.html or "special_bonds lj/coul 0 1 1"_special_bonds.html to use this bond diff --git a/doc/src/bond_fene_expand.txt b/doc/src/bond_fene_expand.txt index ff687444a9..4d7d2d5438 100644 --- a/doc/src/bond_fene_expand.txt +++ b/doc/src/bond_fene_expand.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -50,31 +50,30 @@ delta (distance) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line [Restrictions:] -This bond style can only be used if LAMMPS was built with the -MOLECULE package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info on packages. +This bond style can only be used if LAMMPS was built with the MOLECULE +package. See the "Build package"_Build_package.html doc page for more +info. You typically should specify "special_bonds fene"_special_bonds.html or "special_bonds lj/coul 0 1 1"_special_bonds.html to use this bond diff --git a/doc/src/bond_gromos.txt b/doc/src/bond_gromos.txt index cc3ff75878..e039e6c411 100644 --- a/doc/src/bond_gromos.txt +++ b/doc/src/bond_gromos.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -40,31 +40,30 @@ r0 (distance) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line [Restrictions:] -This bond style can only be used if LAMMPS was built with the -MOLECULE package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info on packages. +This bond style can only be used if LAMMPS was built with the MOLECULE +package. See the "Build package"_Build_package.html doc page for more +info. [Related commands:] diff --git a/doc/src/bond_harmonic.txt b/doc/src/bond_harmonic.txt index c18a7e0fd4..3afdf4ceba 100644 --- a/doc/src/bond_harmonic.txt +++ b/doc/src/bond_harmonic.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -42,31 +42,30 @@ r0 (distance) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line [Restrictions:] -This bond style can only be used if LAMMPS was built with the -MOLECULE package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info on packages. +This bond style can only be used if LAMMPS was built with the MOLECULE +package. See the "Build package"_Build_package.html doc page for more +info. [Related commands:] diff --git a/doc/src/bond_harmonic_shift.txt b/doc/src/bond_harmonic_shift.txt index bf3b3c115a..23d3dcb5d5 100644 --- a/doc/src/bond_harmonic_shift.txt +++ b/doc/src/bond_harmonic_shift.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -43,31 +43,30 @@ rc (distance) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line [Restrictions:] This bond style can only be used if LAMMPS was built with the -USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_3 -section for more info on packages. +USER-MISC package. See the "Build package"_Build_package.html doc +page for more info. [Related commands:] diff --git a/doc/src/bond_harmonic_shift_cut.txt b/doc/src/bond_harmonic_shift_cut.txt index 1918ce00b6..13ccb5843b 100644 --- a/doc/src/bond_harmonic_shift_cut.txt +++ b/doc/src/bond_harmonic_shift_cut.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -43,31 +43,30 @@ rc (distance) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line [Restrictions:] This bond style can only be used if LAMMPS was built with the -USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_3 -section for more info on packages. +USER-MISC package. See the "Build package"_Build_package.html doc +page for more info. [Related commands:] diff --git a/doc/src/bond_hybrid.txt b/doc/src/bond_hybrid.txt index 400c3e0be4..0996f72ce3 100644 --- a/doc/src/bond_hybrid.txt +++ b/doc/src/bond_hybrid.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -58,9 +58,9 @@ bond types. [Restrictions:] -This bond style can only be used if LAMMPS was built with the -MOLECULE package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info on packages. +This bond style can only be used if LAMMPS was built with the MOLECULE +package. See the "Build package"_Build_package.html doc page for more +info. Unlike other bond styles, the hybrid bond style does not store bond coefficient info for individual sub-styles in a "binary restart diff --git a/doc/src/bond_morse.txt b/doc/src/bond_morse.txt index 4f6a32e341..60fd16e17a 100644 --- a/doc/src/bond_morse.txt +++ b/doc/src/bond_morse.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -41,31 +41,30 @@ r0 (distance) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line [Restrictions:] -This bond style can only be used if LAMMPS was built with the -MOLECULE package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info on packages. +This bond style can only be used if LAMMPS was built with the MOLECULE +package. See the "Build package"_Build_package.html doc page for more +info. [Related commands:] diff --git a/doc/src/bond_none.txt b/doc/src/bond_none.txt index 8cb262a50f..cace1919e1 100644 --- a/doc/src/bond_none.txt +++ b/doc/src/bond_none.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/bond_nonlinear.txt b/doc/src/bond_nonlinear.txt index 434af62506..af51383213 100644 --- a/doc/src/bond_nonlinear.txt +++ b/doc/src/bond_nonlinear.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -41,31 +41,30 @@ lamda (distance) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line [Restrictions:] -This bond style can only be used if LAMMPS was built with the -MOLECULE package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info on packages. +This bond style can only be used if LAMMPS was built with the MOLECULE +package. See the "Build package"_Build_package.html doc page for more +info. [Related commands:] diff --git a/doc/src/bond_oxdna.txt b/doc/src/bond_oxdna.txt index 927fea6403..1944f7027a 100644 --- a/doc/src/bond_oxdna.txt +++ b/doc/src/bond_oxdna.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -62,8 +62,8 @@ The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf. [Restrictions:] This bond style can only be used if LAMMPS was built with the -USER-CGDNA package and the MOLECULE and ASPHERE package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info on packages. +USER-CGDNA package and the MOLECULE and ASPHERE package. See the +"Build package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/bond_quartic.txt b/doc/src/bond_quartic.txt index 4dc7ad4a36..b7b1ee4ce6 100644 --- a/doc/src/bond_quartic.txt +++ b/doc/src/bond_quartic.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -76,31 +76,30 @@ delete_bonds all bond 0 remove :pre Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line [Restrictions:] -This bond style can only be used if LAMMPS was built with the -MOLECULE package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info on packages. +This bond style can only be used if LAMMPS was built with the MOLECULE +package. See the "Build package"_Build_package.html doc page for more +info. The {quartic} style requires that "special_bonds"_special_bonds.html parameters be set to 1,1,1. Three- and four-body interactions (angle, diff --git a/doc/src/bond_style.txt b/doc/src/bond_style.txt index 3bd8afda19..22fae3e346 100644 --- a/doc/src/bond_style.txt +++ b/doc/src/bond_style.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -66,9 +66,8 @@ the style to display the formula it computes and coefficients specified by the associated "bond_coeff"_bond_coeff.html command. Note that there are also additional bond styles submitted by users -which are included in the LAMMPS distribution. The list of these with -links to the individual styles are given in the bond section of "this -page"_Section_commands.html#cmd_5. +which are included in the LAMMPS distribution. The full list of all +bond styles is on the "Commands bond"_Commands_bond.html doc page. "bond_style none"_bond_none.html - turn off bonded interactions "bond_style zero"_bond_zero.html - topology but no interactions @@ -91,10 +90,9 @@ Bond styles can only be set for atom styles that allow bonds to be defined. Most bond styles are part of the MOLECULE package. They are only -enabled if LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info on packages. -The doc pages for individual bond potentials tell if it is part of a -package. +enabled if LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. The doc pages for +individual bond potentials tell if it is part of a package. [Related commands:] diff --git a/doc/src/bond_table.txt b/doc/src/bond_table.txt index 906d3e5d76..fbf6eb5815 100644 --- a/doc/src/bond_table.txt +++ b/doc/src/bond_table.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -121,31 +121,30 @@ one that matches the specified keyword. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line [Restrictions:] -This bond style can only be used if LAMMPS was built with the -MOLECULE package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info on packages. +This bond style can only be used if LAMMPS was built with the MOLECULE +package. See the "Build package"_Build_package.html doc page for more +info. [Related commands:] diff --git a/doc/src/bond_write.txt b/doc/src/bond_write.txt index 4797d06cb1..711bd2c296 100644 --- a/doc/src/bond_write.txt +++ b/doc/src/bond_write.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/bond_zero.txt b/doc/src/bond_zero.txt index b599f291b4..554f26e7f0 100644 --- a/doc/src/bond_zero.txt +++ b/doc/src/bond_zero.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/boundary.txt b/doc/src/boundary.txt index ce638f11b3..f9685433b2 100644 --- a/doc/src/boundary.txt +++ b/doc/src/boundary.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -82,9 +82,9 @@ and xhi faces of the box are planes tilting in the +y direction as y increases. These tilted planes are shrink-wrapped around the atoms to determine the x extent of the box. -See "Section 6.12"_Section_howto.html#howto_12 of the doc pages -for a geometric description of triclinic boxes, as defined by LAMMPS, -and how to transform these parameters to and from other commonly used +See the "Howto triclinic"_Howto_triclinic.html doc page for a +geometric description of triclinic boxes, as defined by LAMMPS, and +how to transform these parameters to and from other commonly used triclinic representations. [Restrictions:] diff --git a/doc/src/box.txt b/doc/src/box.txt index a6207ae993..38c874fb78 100644 --- a/doc/src/box.txt +++ b/doc/src/box.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -30,9 +30,9 @@ For triclinic (non-orthogonal) simulation boxes, the {tilt} keyword allows simulation domains to be created with arbitrary tilt factors, e.g. via the "create_box"_create_box.html or "read_data"_read_data.html commands. Tilt factors determine how -skewed the triclinic box is; see "this -section"_Section_howto.html#howto_12 of the manual for a discussion of -triclinic boxes in LAMMPS. +skewed the triclinic box is; see the "Howto +triclinic"_Howto_triclinic.html doc page for a discussion of triclinic +boxes in LAMMPS. LAMMPS normally requires that no tilt factor can skew the box more than half the distance of the parallel box length, which is the 1st diff --git a/doc/src/change_box.txt b/doc/src/change_box.txt index 2c7a890d4c..adc5d6bdcb 100644 --- a/doc/src/change_box.txt +++ b/doc/src/change_box.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -75,9 +75,9 @@ The "create_box"_create_box.html, "read data"_read_data.html, and simulation box is orthogonal or triclinic and their doc pages explain the meaning of the xy,xz,yz tilt factors. -See "Section 6.12"_Section_howto.html#howto_12 of the doc pages -for a geometric description of triclinic boxes, as defined by LAMMPS, -and how to transform these parameters to and from other commonly used +See the "Howto triclinic"_Howto_triclinic.html doc page for a +geometric description of triclinic boxes, as defined by LAMMPS, and +how to transform these parameters to and from other commonly used triclinic representations. The keywords used in this command are applied sequentially to the @@ -140,8 +140,8 @@ transformation in the sequence. If skew is exceeded before the final transformation this can be avoided by changing the order of the sequence, or breaking the transformation into two or more smaller transformations. For more information on the allowed limits for box -skew see the discussion on triclinic boxes on "this -page"_Section_howto.html#howto_12. +skew see the discussion on triclinic boxes on "Howto +triclinic"_Howto_triclinic.html doc page. :line @@ -258,9 +258,7 @@ command. :line The {ortho} and {triclinic} keywords convert the simulation box to be -orthogonal or triclinic (non-orthogonal). See "this -section"_Section_howto#howto_13 for a discussion of how non-orthogonal -boxes are represented in LAMMPS. +orthogonal or triclinic (non-orthogonal). The simulation box is defined as either orthogonal or triclinic when it is created via the "create_box"_create_box.html, @@ -271,8 +269,8 @@ These keywords allow you to toggle the existing simulation box from orthogonal to triclinic and vice versa. For example, an initial equilibration simulation can be run in an orthogonal box, the box can be toggled to triclinic, and then a "non-equilibrium MD (NEMD) -simulation"_Section_howto.html#howto_13 can be run with deformation -via the "fix deform"_fix_deform.html command. +simulation"_Howto_nemd.html can be run with deformation via the "fix +deform"_fix_deform.html command. If the simulation box is currently triclinic and has non-zero tilt in xy, yz, or xz, then it cannot be converted to an orthogonal box. diff --git a/doc/src/clear.txt b/doc/src/clear.txt index 7ac4da5c8d..c4ad4c4030 100644 --- a/doc/src/clear.txt +++ b/doc/src/clear.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/comm_modify.txt b/doc/src/comm_modify.txt index 3e8d0eca4f..489278523b 100644 --- a/doc/src/comm_modify.txt +++ b/doc/src/comm_modify.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/comm_style.txt b/doc/src/comm_style.txt index 8248d654d3..39eb1d4ef5 100644 --- a/doc/src/comm_style.txt +++ b/doc/src/comm_style.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/commands.txt b/doc/src/commands_list.txt similarity index 96% rename from doc/src/commands.txt rename to doc/src/commands_list.txt index 62b973e3a4..db3ef36ddf 100644 --- a/doc/src/commands.txt +++ b/doc/src/commands_list.txt @@ -56,6 +56,7 @@ Commands :h1 lattice log mass + message min_modify min_style minimize @@ -87,6 +88,9 @@ Commands :h1 restart run run_style + server + server_mc + server_md set shell special_bonds diff --git a/doc/src/compute.txt b/doc/src/compute.txt index c06735d28e..72ea1c1930 100644 --- a/doc/src/compute.txt +++ b/doc/src/compute.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -33,7 +33,7 @@ information about a previous state of the system. Defining a compute does not perform a computation. Instead computes are invoked by other LAMMPS commands as needed, e.g. to calculate a temperature needed for a thermostat fix or to generate thermodynamic or dump file output. -See this "howto section"_Section_howto.html#howto_15 for a summary of +See the "Howto output"_Howto_output.html doc page for a summary of various LAMMPS output options, many of which involve computes. The ID of a compute can only contain alphanumeric characters and @@ -153,21 +153,27 @@ via the "compute_modify"_compute_modify.html command. Computes can be deleted with the "uncompute"_uncompute.html command. -Code for new computes can be added to LAMMPS (see "this -section"_Section_modify.html of the manual) and the results of their +Code for new computes can be added to LAMMPS; see the +"Modify"_Modify.html doc page for details. The results of their calculations accessed in the various ways described above. :line Each compute style has its own doc page which describes its arguments and what it does. Here is an alphabetic list of compute styles -available in LAMMPS. They are also given in more compact form in the -Compute section of "this page"_Section_commands.html#cmd_5. +available in LAMMPS. They are also listed in more compact form on the +"Commands compute"_Commands_compute.html doc page. There are also additional compute styles (not listed here) submitted -by users which are included in the LAMMPS distribution. The list of -these with links to the individual styles are given in the compute -section of "this page"_Section_commands.html#cmd_5. +by users which are included in the LAMMPS distribution. The full list +of all compute styles is on the "Commands +compute"_Commands_compute.html doc page. + +There are also additional accelerated compute styles included in the +LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs. +The individual style names on the "Commands +compute"_Commands_compute.html doc page are followed by one or more of +(g,i,k,o,t) to indicate which accelerated styles exist. "aggregate/atom"_compute_cluster_atom.html - aggregate ID for each atom "angle/local"_compute_bond_local.html - theta and energy of each angle @@ -177,6 +183,7 @@ section of "this page"_Section_commands.html#cmd_5. "bond/local"_compute_bond_local.html - distance and energy of each bond "centro/atom"_compute_centro_atom.html - centro-symmetry parameter for each atom "chunk/atom"_compute_chunk_atom.html - assign chunk IDs to each atom +"chunk/spread/atom"_compute_chunk_spread_atom.html - spreads chunk values to each atom in chunk "cluster/atom"_compute_cluster_atom.html - cluster ID for each atom "cna/atom"_compute_cna_atom.html - common neighbor analysis (CNA) for each atom "com"_compute_com.html - center-of-mass of group of atoms @@ -219,6 +226,7 @@ section of "this page"_Section_commands.html#cmd_5. "property/chunk"_compute_property_chunk.html - extract various per-chunk attributes "rdf"_compute_rdf.html - radial distribution function g(r) histogram of group of atoms "reduce"_compute_reduce.html - combine per-atom quantities into a single global value +"reduce/chunk"_compute_reduce_chunk.html - reduce per-atom quantities within each chunk "reduce/region"_compute_reduce.html - same as compute reduce, within a region "rigid/local"_compute_rigid_local.html - extract rigid body attributes "slice"_compute_slice.html - extract values from global vector or array @@ -243,16 +251,6 @@ section of "this page"_Section_commands.html#cmd_5. "vcm/chunk"_compute_vcm_chunk.html - velocity of center-of-mass for each chunk "voronoi/atom"_compute_voronoi_atom.html - Voronoi volume and neighbors for each atom :ul -There are also additional compute styles submitted by users which are -included in the LAMMPS distribution. The list of these with links to -the individual styles are given in the compute section of "this -page"_Section_commands.html#cmd_5. - -There are also additional accelerated compute styles included in the -LAMMPS distribution for faster performance on CPUs and GPUs. The list -of these with links to the individual styles are given in the pair -section of "this page"_Section_commands.html#cmd_5. - [Restrictions:] none [Related commands:] diff --git a/doc/src/compute_ackland_atom.txt b/doc/src/compute_ackland_atom.txt index 3fd838d957..46db81eb9e 100644 --- a/doc/src/compute_ackland_atom.txt +++ b/doc/src/compute_ackland_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -32,7 +32,7 @@ according to the formulation given in "(Ackland)"_#Ackland. Historically, LAMMPS had two, slightly different implementations of the algorithm from the paper. With the {legacy} keyword, it is possible to switch between the pre-2015 ({legacy yes}) and post-2015 -implemention ({legacy no}). The post-2015 variant is the default. +implementation ({legacy no}). The post-2015 variant is the default. In contrast to the "centro-symmetry parameter"_compute_centro_atom.html this method is stable against @@ -60,14 +60,14 @@ which computes this quantity.- This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -"Section 6.15"_Section_howto.html#howto_15 for an overview of +the "Howto output"_Howto_output.html doc page for an overview of LAMMPS output options. [Restrictions:] This compute is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. The per-atom vector values will be unitless since they are the integers defined above. diff --git a/doc/src/compute_angle.txt b/doc/src/compute_angle.txt index 2c363ce8f6..64eb2f4bb1 100644 --- a/doc/src/compute_angle.txt +++ b/doc/src/compute_angle.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -37,8 +37,8 @@ This compute calculates a global vector of length N where N is the number of sub_styles defined by the "angle_style hybrid"_angle_style.html command, which can be accessed by indices 1-N. These values can be used by any command that uses global scalar -or vector values from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output +or vector values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. The vector values are "extensive" and will be in energy diff --git a/doc/src/compute_angle_local.txt b/doc/src/compute_angle_local.txt index 0ee1d32d7d..8acaec94d5 100644 --- a/doc/src/compute_angle_local.txt +++ b/doc/src/compute_angle_local.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -10,20 +10,27 @@ compute angle/local command :h3 [Syntax:] -compute ID group-ID angle/local value1 value2 ... :pre +compute ID group-ID angle/local value1 value2 ... keyword args ... :pre ID, group-ID are documented in "compute"_compute.html command :ulb,l angle/local = style name of this compute command :l one or more values may be appended :l -value = {theta} or {eng} :l +value = {theta} or {eng} or {v_name} :l {theta} = tabulate angles - {eng} = tabulate angle energies :pre + {eng} = tabulate angle energies + {v_name} = equal-style variable with name (see below) :pre +zero or more keyword/args pairs may be appended :l +keyword = {set} :l + {set} args = theta name + theta = only currently allowed arg + name = name of variable to set with theta :pre :ule [Examples:] compute 1 all angle/local theta -compute 1 all angle/local eng theta :pre +compute 1 all angle/local eng theta +compute 1 all angle/local theta v_cos set theta t :pre [Description:] @@ -36,6 +43,47 @@ The value {theta} is the angle for the 3 atoms in the interaction. The value {eng} is the interaction energy for the angle. +The value {v_name} can be used together with the {set} keyword to +compute a user-specified function of the angle theta. The {name} +specified for the {v_name} value is the name of an "equal-style +variable"_variable.html which should evaluate a formula based on a +variable which will store the angle theta. This other variable must +be an "internal-style variable"_variable.html defined in the input +script; its initial numeric value can be anything. It must be an +internal-style variable, because this command resets its value +directly. The {set} keyword is used to identify the name of this +other variable associated with theta. + +Note that the value of theta for each angle which stored in the +internal variable is in radians, not degrees. + +As an example, these commands can be added to the bench/in.rhodo +script to compute the cosine and cosine^2 of every angle in the system +and output the statistics in various ways: + +variable t internal 0.0 +variable cos equal cos(v_t) +variable cossq equal cos(v_t)*cos(v_t) :pre + +compute 1 all property/local aatom1 aatom2 aatom3 atype +compute 2 all angle/local eng theta v_cos v_cossq set theta t +dump 1 all local 100 tmp.dump c_1[*] c_2[*] :pre + +compute 3 all reduce ave c_2[*] +thermo_style custom step temp press c_3[*] :pre + +fix 10 all ave/histo 10 10 100 -1 1 20 c_2[3] mode vector file tmp.histo :pre + +The "dump local"_dump.html command will output the energy, angle, +cosine(angle), cosine^2(angle) for every angle in the system. The +"thermo_style"_thermo_style.html command will print the average of +those quantities via the "compute reduce"_compute_reduce.html command +with thermo output. And the "fix ave/histo"_fix_ave_histo.html +command will histogram the cosine(angle) values and write them to a +file. + +:line + The local data stored by this command is generated by looping over all the atoms owned on a processor and their angles. An angle will only be included if all 3 atoms in the angle are in the specified compute @@ -65,13 +113,13 @@ dump 1 all local 1000 tmp.dump index c_1\[1\] c_1\[2\] c_1\[3\] c_1\[4\] c_2\[1\ [Output info:] This compute calculates a local vector or local array depending on the -number of keywords. The length of the vector or number of rows in the -array is the number of angles. If a single keyword is specified, a -local vector is produced. If two or more keywords are specified, a +number of values. The length of the vector or number of rows in the +array is the number of angles. If a single value is specified, a +local vector is produced. If two or more values are specified, a local array is produced where the number of columns = the number of -keywords. The vector or array can be accessed by any command that -uses local values from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output +values. The vector or array can be accessed by any command that uses +local values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. The output for {theta} will be in degrees. The output for {eng} will diff --git a/doc/src/compute_angmom_chunk.txt b/doc/src/compute_angmom_chunk.txt index 813da15eea..7e49ff3024 100644 --- a/doc/src/compute_angmom_chunk.txt +++ b/doc/src/compute_angmom_chunk.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -30,10 +30,9 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom to a single chunk (or no chunk). The ID for this command is specified as chunkID. For example, a single chunk could be the atoms in a molecule or atoms in a spatial bin. See the "compute -chunk/atom"_compute_chunk_atom.html doc page and "Section -6.23"_Section_howto.html#howto_23 for details of how chunks can be -defined and examples of how they can be used to measure properties of -a system. +chunk/atom"_compute_chunk_atom.html and "Howto chunk"_Howto_chunk.html +doc pages for details of how chunks can be defined and examples of how +they can be used to measure properties of a system. This compute calculates the 3 components of the angular momentum vector for each chunk, due to the velocity/momentum of the individual @@ -73,8 +72,8 @@ number of chunks {Nchunk} as calculated by the specified "compute chunk/atom"_compute_chunk_atom.html command. The number of columns = 3 for the 3 xyz components of the angular momentum for each chunk. These values can be accessed by any command that uses global array -values from a compute as input. See "Section -6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output +values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. The array values are "intensive". The array values will be in diff --git a/doc/src/compute_basal_atom.txt b/doc/src/compute_basal_atom.txt index b59a3fd4c8..5c28b8e378 100644 --- a/doc/src/compute_basal_atom.txt +++ b/doc/src/compute_basal_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -46,9 +46,8 @@ in examples/USER/misc/basal. This compute calculates a per-atom array with 3 columns, which can be accessed by indices 1-3 by any command that uses per-atom values from -a compute as input. See "Section -6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output -options. +a compute as input. See the "Howto output"_Howto_output.html doc page +for an overview of LAMMPS output options. The per-atom vector values are unitless since the 3 columns represent components of a unit vector. @@ -56,8 +55,8 @@ components of a unit vector. [Restrictions:] This compute is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. The output of this compute will be meaningless unless the atoms are on (or near) hcp lattice sites, since the calculation assumes a diff --git a/doc/src/compute_body_local.txt b/doc/src/compute_body_local.txt index 12ce218853..8ac3f00c55 100644 --- a/doc/src/compute_body_local.txt +++ b/doc/src/compute_body_local.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -32,9 +32,8 @@ Define a computation that calculates properties of individual body sub-particles. The number of datums generated, aggregated across all processors, equals the number of body sub-particles plus the number of non-body particles in the system, modified by the group parameter as -explained below. See "Section 6.14"_Section_howto.html#howto_14 -of the manual and the "body"_body.html doc page for more details on -using body particles. +explained below. See the "Howto body"_Howto_body.html doc page for +more details on using body particles. The local data stored by this command is generated by looping over all the atoms. An atom will only be included if it is in the group. If @@ -58,8 +57,8 @@ group. For a body particle, the {integer} keywords refer to fields calculated by the body style for each sub-particle. The body style, as specified by the "atom_style body"_atom_style.html, determines how many fields -exist and what they are. See the "body"_body.html doc page for -details of the different styles. +exist and what they are. See the "Howto_body"_Howto_body.html doc +page for details of the different styles. Here is an example of how to output body information using the "dump local"_dump.html command with this compute. If fields 1,2,3 for the @@ -78,9 +77,9 @@ array is the number of datums as described above. If a single keyword is specified, a local vector is produced. If two or more keywords are specified, a local array is produced where the number of columns = the number of keywords. The vector or array can be accessed by any -command that uses local values from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output -options. +command that uses local values from a compute as input. See the +"Howto output"_Howto_output.html doc page for an overview of LAMMPS +output options. The "units"_units.html for output values depend on the body style. diff --git a/doc/src/compute_bond.txt b/doc/src/compute_bond.txt index 6c4384b080..a87c510538 100644 --- a/doc/src/compute_bond.txt +++ b/doc/src/compute_bond.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -37,8 +37,8 @@ This compute calculates a global vector of length N where N is the number of sub_styles defined by the "bond_style hybrid"_bond_style.html command, which can be accessed by indices 1-N. These values can be used by any command that uses global scalar or -vector values from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output +vector values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. The vector values are "extensive" and will be in energy diff --git a/doc/src/compute_bond_local.txt b/doc/src/compute_bond_local.txt index 58d96f9ee4..4afd1aec40 100644 --- a/doc/src/compute_bond_local.txt +++ b/doc/src/compute_bond_local.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -10,12 +10,12 @@ compute bond/local command :h3 [Syntax:] -compute ID group-ID bond/local value1 value2 ... :pre +compute ID group-ID bond/local value1 value2 ... keyword args ... :pre ID, group-ID are documented in "compute"_compute.html command :ulb,l bond/local = style name of this compute command :l one or more values may be appended :l -value = {dist} or {engpot} or {force} or {engvib} or {engrot} or {engtrans} or {omega} or {velvib} :l +value = {dist} or {engpot} or {force} or {engvib} or {engrot} or {engtrans} or {omega} or {velvib} or {v_name} :l {dist} = bond distance {engpot} = bond potential energy {force} = bond force :pre @@ -23,13 +23,22 @@ value = {dist} or {engpot} or {force} or {engvib} or {engrot} or {engtrans} or { {engrot} = bond kinetic energy of rotation {engtrans} = bond kinetic energy of translation {omega} = magnitude of bond angular velocity - {velvib} = vibrational velocity along the bond length :pre + {velvib} = vibrational velocity along the bond length + {v_name} = equal-style variable with name (see below) :pre +zero or more keyword/args pairs may be appended :l +keyword = {set} :l + {set} args = dist name + dist = only currently allowed arg + name = name of variable to set with distance (dist) :pre +:ule + :ule [Examples:] compute 1 all bond/local engpot compute 1 all bond/local dist engpot force :pre +compute 1 all angle/local dist v_distsq set dist d :pre [Description:] @@ -38,6 +47,10 @@ interactions. The number of datums generated, aggregated across all processors, equals the number of bonds in the system, modified by the group parameter as explained below. +All these properties are computed for the pair of atoms in a bond, +whether the 2 atoms represent a simple diatomic molecule, or are part +of some larger molecule. + The value {dist} is the current length of the bond. The value {engpot} is the potential energy for the bond, @@ -79,9 +92,41 @@ two atoms in the bond towards each other. A negative value means the 2 atoms are moving toward each other; a positive value means they are moving apart. -Note that all these properties are computed for the pair of atoms in a -bond, whether the 2 atoms represent a simple diatomic molecule, or are -part of some larger molecule. +The value {v_name} can be used together with the {set} keyword to +compute a user-specified function of the bond distance. The {name} +specified for the {v_name} value is the name of an "equal-style +variable"_variable.html which should evaluate a formula based on a +variable which will store the bond distance. This other variable must +be an "internal-style variable"_variable.html defined in the input +script; its initial numeric value can be anything. It must be an +internal-style variable, because this command resets its value +directly. The {set} keyword is used to identify the name of this +other variable associated with theta. + +As an example, these commands can be added to the bench/in.rhodo +script to compute the distance^2 of every bond in the system and +output the statistics in various ways: + +variable d internal 0.0 +variable dsq equal v_d*v_d :pre + +compute 1 all property/local batom1 batom2 btype +compute 2 all bond/local engpot dist v_dsq set dist d +dump 1 all local 100 tmp.dump c_1[*] c_2[*] :pre + +compute 3 all reduce ave c_2[*] +thermo_style custom step temp press c_3[*] :pre + +fix 10 all ave/histo 10 10 100 0 6 20 c_2[3] mode vector file tmp.histo :pre + +The "dump local"_dump.html command will output the energy, distance, +distance^2 for every bond in the system. The +"thermo_style"_thermo_style.html command will print the average of +those quantities via the "compute reduce"_compute_reduce.html command +with thermo output. And the "fix ave/histo"_fix_ave_histo.html +command will histogram the distance^2 values and write them to a file. + +:line The local data stored by this command is generated by looping over all the atoms owned on a processor and their bonds. A bond will only be @@ -111,13 +156,13 @@ dump 1 all local 1000 tmp.dump index c_1\[*\] c_2\[*\] :pre [Output info:] This compute calculates a local vector or local array depending on the -number of keywords. The length of the vector or number of rows in the -array is the number of bonds. If a single keyword is specified, a -local vector is produced. If two or more keywords are specified, a -local array is produced where the number of columns = the number of -keywords. The vector or array can be accessed by any command that -uses local values from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output +number of values. The length of the vector or number of rows in the +array is the number of bonds. If a single value is specified, a local +vector is produced. If two or more values are specified, a local +array is produced where the number of columns = the number of values. +The vector or array can be accessed by any command that uses local +values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. The output for {dist} will be in distance "units"_units.html. The diff --git a/doc/src/compute_centro_atom.txt b/doc/src/compute_centro_atom.txt index 4e4b03d167..183537690f 100644 --- a/doc/src/compute_centro_atom.txt +++ b/doc/src/compute_centro_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -97,8 +97,8 @@ too frequently or to have multiple compute/dump commands, each with a By default, this compute calculates the centrosymmetry value for each atom as a per-atom vector, which can be accessed by any command that -uses per-atom values from a compute as input. See "Section -6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output +uses per-atom values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. If the {axes} keyword setting is {yes}, then a per-atom array is diff --git a/doc/src/compute_chunk_atom.txt b/doc/src/compute_chunk_atom.txt index 3a46f79d16..c29a5600a9 100644 --- a/doc/src/compute_chunk_atom.txt +++ b/doc/src/compute_chunk_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -14,7 +14,7 @@ compute ID group-ID chunk/atom style args keyword values ... :pre ID, group-ID are documented in "compute"_compute.html command :ulb,l chunk/atom = style name of this compute command :l -style = {bin/1d} or {bin/2d} or {bin/3d} or {bin/sphere} or {type} or {molecule} or {compute/fix/variable} +style = {bin/1d} or {bin/2d} or {bin/3d} or {bin/sphere} or {type} or {molecule} or c_ID, c_ID\[I\], f_ID, f_ID\[I\], v_name {bin/1d} args = dim origin delta dim = {x} or {y} or {z} origin = {lower} or {center} or {upper} or coordinate value (distance units) @@ -40,7 +40,7 @@ style = {bin/1d} or {bin/2d} or {bin/3d} or {bin/sphere} or {type} or {molecule} ncbin = # of concentric circle bins between rmin and rmax {type} args = none {molecule} args = none - {compute/fix/variable} = c_ID, c_ID\[I\], f_ID, f_ID\[I\], v_name with no args + c_ID, c_ID\[I\], f_ID, f_ID\[I\], v_name args = none c_ID = per-atom vector calculated by a compute with ID c_ID\[I\] = Ith column of per-atom array calculated by a compute with ID f_ID = per-atom vector calculated by a fix with ID @@ -85,7 +85,8 @@ compute 1 all chunk/atom bin/1d z lower 0.02 units reduced compute 1 all chunk/atom bin/2d z lower 1.0 y 0.0 2.5 compute 1 all chunk/atom molecule region sphere nchunk once ids once compress yes compute 1 all chunk/atom bin/sphere 5 5 5 2.0 5.0 5 discard yes -compute 1 all chunk/atom bin/cylinder z lower 2 10 10 2.0 5.0 3 discard yes :pre +compute 1 all chunk/atom bin/cylinder z lower 2 10 10 2.0 5.0 3 discard yes +compute 1 all chunk/atom c_cluster :pre [Description:] @@ -101,14 +102,13 @@ msd/chunk"_compute_msd_chunk.html. Or they can be used by the "fix ave/chunk"_fix_ave_chunk.html command to sum and time average a variety of per-atom properties over the atoms in each chunk. Or they can simply be accessed by any command that uses per-atom values from a -compute as input, as discussed in "Section -6.15"_Section_howto.html#howto_15. +compute as input, as discussed on the "Howto output"_Howto_output.html +doc page. -See "Section 6.23"_Section_howto.html#howto_23 for an overview of -how this compute can be used with a variety of other commands to -tabulate properties of a simulation. The howto section gives several -examples of input script commands that can be used to calculate -interesting properties. +See the "Howto chunk"_Howto_chunk.html doc page for an overview of how +this compute can be used with a variety of other commands to tabulate +properties of a simulation. The page gives several examples of input +script commands that can be used to calculate interesting properties. Conceptually it is important to realize that this compute does two simple things. First, it sets the value of {Nchunk} = the number of @@ -135,7 +135,6 @@ timesteps it specifies, while it accumulates per-chunk averages. The details are described below. -:line :line The different chunk styles operate as follows. For each style, how it @@ -167,11 +166,11 @@ or the bounds specified by the optional {bounds} keyword. For orthogonal simulation boxes, the bins are layers, pencils, or boxes aligned with the xyz coordinate axes. For triclinic (non-orthogonal) simulation boxes, the bin faces are parallel to the -tilted faces of the simulation box. See "this -section"_Section_howto.html#howto_12 of the manual for a discussion of -the geometry of triclinic boxes in LAMMPS. As described there, a -tilted simulation box has edge vectors a,b,c. In that nomenclature, -bins in the x dimension have faces with normals in the "b" cross "c" +tilted faces of the simulation box. See the "Howto +triclinic"_Howto_triclinic.html doc page for a discussion of the +geometry of triclinic boxes in LAMMPS. As described there, a tilted +simulation box has edge vectors a,b,c. In that nomenclature, bins in +the x dimension have faces with normals in the "b" cross "c" direction. Bins in y have faces normal to the "a" cross "c" direction. And bins in z have faces normal to the "a" cross "b" direction. Note that in order to define the size and position of @@ -275,7 +274,7 @@ previously defined in the input script. If no bracketed integer is appended, the per-atom vector calculated by the compute is used. If a bracketed integer is appended, the Ith column of the per-atom array calculated by the compute is used. Users can also write code for -their own compute styles and "add them to LAMMPS"_Section_modify.html. +their own compute styles and "add them to LAMMPS"_Modify.html. If the style begins with "f_", a fix ID must follow which has been previously defined in the input script. If no bracketed integer is @@ -285,7 +284,7 @@ calculated by the fix is used. Note that some fixes only produce their values on certain timesteps, which must be compatible with the timestep on which this compute accesses the fix, else an error results. Users can also write code for their own fix styles and "add -them to LAMMPS"_Section_modify.html. +them to LAMMPS"_Modify.html. If a value begins with "v_", a variable name for an {atom} or {atomfile} style "variable"_variable.html must follow which has been @@ -295,7 +294,6 @@ invoke other computes, fixes, or variables when they are evaluated, so this is a very general means of generating per-atom quantities to treat as a chunk ID. -:line :line Normally, {Nchunk} = the number of chunks, is re-calculated every time @@ -323,7 +321,6 @@ the same compute chunk/atom compute. However, the time windows they induce for holding {Nchunk} constant must be identical, else an error will be generated. -:line :line The various optional keywords operate as follows. Note that some of @@ -390,8 +387,8 @@ described below, which resets {Nchunk}. The {limit} keyword is then applied to the new {Nchunk} value, exactly as described in the preceding paragraph. Note that in this case, all atoms will end up with chunk IDs <= {Nc}, but their original values (e.g. molecule ID or -compute/fix/variable value) may have been > {Nc}, because of the -compression operation. +compute/fix/variable) may have been > {Nc}, because of the compression +operation. If {compress yes} is set, and the {compress} keyword comes after the {limit} keyword, then the {limit} value of {Nc} is applied first to @@ -626,7 +623,7 @@ cylinder, x for a y-axis cylinder, and x for a z-axis cylinder. This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -"Section 6.15"_Section_howto.html#howto_15 for an overview of +the "Howto output"_Howto_output.html doc page for an overview of LAMMPS output options. The per-atom vector values are unitless chunk IDs, ranging from 1 to diff --git a/doc/src/compute_chunk_spread_atom.txt b/doc/src/compute_chunk_spread_atom.txt new file mode 100644 index 0000000000..f84ef67974 --- /dev/null +++ b/doc/src/compute_chunk_spread_atom.txt @@ -0,0 +1,174 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +compute chunk/spread/atom command :h3 + +[Syntax:] + +compute ID group-ID chunk/spread/atom chunkID input1 input2 ... :pre + +ID, group-ID are documented in "compute"_compute.html command :ulb,l +chunk/spread/atom = style name of this compute command :l +chunkID = ID of "compute chunk/atom"_compute_chunk_atom.html command :l +one or more inputs can be listed :l +input = c_ID, c_ID\[N\], f_ID, f_ID\[N\] :l + c_ID = global vector calculated by a compute with ID + c_ID\[I\] = Ith column of global array calculated by a compute with ID, I can include wildcard (see below) + f_ID = global vector calculated by a fix with ID + f_ID\[I\] = Ith column of global array calculated by a fix with ID, I can include wildcard (see below) :pre +:ule + +[Examples:] + +compute 1 all chunk/spread/atom mychunk c_com[*] c_gyration :pre + +[Description:] + +Define a calculation that "spreads" one or more per-chunk values to +each atom in the chunk. This can be useful for creating a "dump +file"_dump.html where each atom lists info about the chunk it is in, +e.g. for post-processing purposes. It can also be used in "atom-style +variables"_variable.html that need info about the chunk each atom is +in. Examples are given below. + +In LAMMPS, chunks are collections of atoms defined by a "compute +chunk/atom"_compute_chunk_atom.html command, which assigns each atom +to a single chunk (or no chunk). The ID for this command is specified +as chunkID. For example, a single chunk could be the atoms in a +molecule or atoms in a spatial bin. See the "compute +chunk/atom"_compute_chunk_atom.html and "Howto chunk"_Howto_chunk.html +doc pages for details of how chunks can be defined and examples of how +they can be used to measure properties of a system. + +For inputs that are computes, they must be a compute that calculates +per-chunk values. These are computes whose style names end in +"/chunk". + +For inputs that are fixes, they should be a a fix that calculates +per-chunk values. For example, "fix ave/chunk"_fix_ave_chunk.html or +"fix ave/time"_fix_ave_time.html (assuming it is time-averaging +per-chunk data). + +For each atom, this compute accesses its chunk ID from the specified +{chunkID} compute, then accesses the per-chunk value in each input. +Those values are copied to this compute to become the output for that +atom. + +The values generated by this compute will be 0.0 for atoms not in the +specified compute group {group-ID}. They will also be 0.0 if the atom +is not in a chunk, as assigned by the {chunkID} compute. They will +also be 0.0 if the current chunk ID for the atom is out-of-bounds with +respect to the number of chunks stored by a particular input compute +or fix. + +NOTE: LAMMPS does not check that a compute or fix which calculates +per-chunk values uses the same definition of chunks as this compute. +It's up to you to be consistent. Likewise, for a fix input, LAMMPS +does not check that it is per-chunk data. It only checks that the fix +produces a global vector or array. + +:line + +Each listed input is operated on independently. + +If a bracketed index I is used, it can be specified using a wildcard +asterisk with the index to effectively specify multiple values. This +takes the form "*" or "*n" or "n*" or "m*n". If N = the number of +columns in the array, then an asterisk with no numeric values means +all indices from 1 to N. A leading asterisk means all indices from 1 +to n (inclusive). A trailing asterisk means all indices from n to N +(inclusive). A middle asterisk means all indices from m to n +(inclusive). + +Using a wildcard is the same as if the individual columns of the array +had been listed one by one. E.g. these 2 compute chunk/spread/atom +commands are equivalent, since the "compute +com/chunk"_compute_com_chunk.html command creates a per-atom array +with 3 columns: + +compute com all com/chunk mychunk +compute 10 all chunk/spread/atom mychunk c_com\[*\] +compute 10 all chunk/spread/atom mychunk c_com\[1\] c_com\[2\] c_com\[3\] :pre + +:line + +Here is an example of writing a dump file the with the center-of-mass +(COM) for the chunk each atom is in. The commands below can be added +to the bench/in.chain script. + +compute cmol all chunk/atom molecule +compute com all com/chunk cmol +compute comchunk all chunk/spread/atom cmol c_com[*] +dump 1 all custom 50 tmp.dump id mol type x y z c_comchunk[*] +dump_modify 1 sort id :pre + +The same per-chunk data for each atom could be used to define per-atom +forces for the "fix addforce"_fix_addforce.html command. In this +example the forces act to pull atoms of an extended polymer chain +towards its COM in an attractive manner. + +compute prop all property/atom xu yu zu +variable k equal 0.1 +variable fx atom v_k*(c_comchunk\[1\]-c_prop\[1\]) +variable fy atom v_k*(c_comchunk\[2\]-c_prop\[2\]) +variable fz atom v_k*(c_comchunk\[3\]-c_prop\[3\]) +fix 3 all addforce v_fx v_fy v_fz :pre + +Note that "compute property/atom"_compute_property_atom.html is used +to generate unwrapped coordinates for use in the per-atom force +calculation, so that the effect of periodic boundaries is accounted +for properly. + +Over time this applied force could shrink each polymer chain's radius +of gyration in a polymer mixture simulation. Here is output from the +bench/in.chain script. Thermo output is shown for 1000 steps, where +the last column is the average radius of gyration over all 320 chains +in the 32000 atom system: + +compute gyr all gyration/chunk cmol +variable ave equal ave(c_gyr) +thermo_style custom step etotal press v_ave :pre + + 0 22.394765 4.6721833 5.128278 + 100 22.445002 4.8166709 5.0348372 + 200 22.500128 4.8790392 4.9364875 + 300 22.534686 4.9183766 4.8590693 + 400 22.557196 4.9492211 4.7937849 + 500 22.571017 4.9161853 4.7412008 + 600 22.573944 5.0229708 4.6931243 + 700 22.581804 5.0541301 4.6440647 + 800 22.584683 4.9691734 4.6000016 + 900 22.59128 5.0247538 4.5611513 + 1000 22.586832 4.94697 4.5238362 :pre + +:line + +[Output info:] + +This compute calculates a per-atom vector or array, which can be +accessed by any command that uses per-atom values from a compute as +input. See the "Howto output"_Howto_output.html doc page for an +overview of LAMMPS output options. + +The output is a per-atom vector if a single input value is specified, +otherwise a per-atom array is output. The number of columns in the +array is the number of inputs provided. The per-atom values for the +vector or each column of the array will be in whatever +"units"_units.html the corresponding input value is in. + +The vector or array values are "intensive". + +[Restrictions:] none + +[Related commands:] + +"compute chunk/atom"_compute_chunk_atom.html, "fix +ave/chunk"_fix_ave_chunk.html, "compute +reduce/chunk"_compute_reduce_chunk.html + +[Default:] none diff --git a/doc/src/compute_cluster_atom.txt b/doc/src/compute_cluster_atom.txt index 94113de5f2..e6138fe1e8 100644 --- a/doc/src/compute_cluster_atom.txt +++ b/doc/src/compute_cluster_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -84,7 +84,7 @@ the neighbor list. This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -"Section 6.15"_Section_howto.html#howto_15 for an overview of +the "Howto output"_Howto_output.html doc page for an overview of LAMMPS output options. The per-atom vector values will be an ID > 0, as explained above. diff --git a/doc/src/compute_cna_atom.txt b/doc/src/compute_cna_atom.txt index 23289b0132..d69c5e9c46 100644 --- a/doc/src/compute_cna_atom.txt +++ b/doc/src/compute_cna_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -74,7 +74,7 @@ too frequently or to have multiple compute/dump commands, each with a This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -"Section 6.15"_Section_howto.html#howto_15 for an overview of +the "Howto output"_Howto_output.html doc page for an overview of LAMMPS output options. The per-atom vector values will be a number from 0 to 5, as explained diff --git a/doc/src/compute_cnp_atom.txt b/doc/src/compute_cnp_atom.txt index 16a51f5241..95dd59089f 100644 --- a/doc/src/compute_cnp_atom.txt +++ b/doc/src/compute_cnp_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -78,7 +78,7 @@ too frequently or to have multiple compute/dump commands, each with a This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -"Section 6.15"_Section_howto.html#howto_15 for an overview of +the "Howto output"_Howto_output.html doc page for an overview of LAMMPS output options. The per-atom vector values will be real positive numbers. Some typical CNP @@ -95,8 +95,8 @@ FCC dislocation core ~ 11 :pre [Restrictions:] This compute is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/compute_com.txt b/doc/src/compute_com.txt index b0e0c14e42..fdc631a263 100644 --- a/doc/src/compute_com.txt +++ b/doc/src/compute_com.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -41,9 +41,8 @@ image"_set.html command. This compute calculates a global vector of length 3, which can be accessed by indices 1-3 by any command that uses global vector values -from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output -options. +from a compute as input. See the "Howto output"_Howto_output.html doc +page for an overview of LAMMPS output options. The vector values are "intensive". The vector values will be in distance "units"_units.html. diff --git a/doc/src/compute_com_chunk.txt b/doc/src/compute_com_chunk.txt index d497585cb0..b982f0d901 100644 --- a/doc/src/compute_com_chunk.txt +++ b/doc/src/compute_com_chunk.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -30,10 +30,9 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom to a single chunk (or no chunk). The ID for this command is specified as chunkID. For example, a single chunk could be the atoms in a molecule or atoms in a spatial bin. See the "compute -chunk/atom"_compute_chunk_atom.html doc page and "Section -6.23"_Section_howto.html#howto_23 for details of how chunks can be -defined and examples of how they can be used to measure properties of -a system. +chunk/atom"_compute_chunk_atom.html and "Howto chunk"_Howto_chunk.html +doc pages for details of how chunks can be defined and examples of how +they can be used to measure properties of a system. This compute calculates the x,y,z coordinates of the center-of-mass for each chunk, which includes all effects due to atoms passing thru @@ -71,9 +70,8 @@ number of chunks {Nchunk} as calculated by the specified "compute chunk/atom"_compute_chunk_atom.html command. The number of columns = 3 for the x,y,z center-of-mass coordinates of each chunk. These values can be accessed by any command that uses global array values -from a compute as input. See "Section -6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output -options. +from a compute as input. See the "Howto output"_Howto_output.html doc +page for an overview of LAMMPS output options. The array values are "intensive". The array values will be in distance "units"_units.html. diff --git a/doc/src/compute_contact_atom.txt b/doc/src/compute_contact_atom.txt index f0bd62f4e8..efe524263a 100644 --- a/doc/src/compute_contact_atom.txt +++ b/doc/src/compute_contact_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -36,7 +36,7 @@ specified compute group. This compute calculates a per-atom vector, whose values can be accessed by any command that uses per-atom values from a compute as -input. See "Section 6.15"_Section_howto.html#howto_15 for an +input. See the "Howto output"_Howto_output.html doc page for an overview of LAMMPS output options. The per-atom vector values will be a number >= 0.0, as explained diff --git a/doc/src/compute_coord_atom.txt b/doc/src/compute_coord_atom.txt index a88f7ec729..ddc4cc82d3 100644 --- a/doc/src/compute_coord_atom.txt +++ b/doc/src/compute_coord_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -67,7 +67,7 @@ identify crystal-like atoms in a system, as discussed in "ten Wolde"_#tenWolde1. The ID of the previously specified "compute -orientorder/atom"_compute_orientorder/atom command is specified as +orientorder/atom"_compute_orientorder_atom.html command is specified as {orientorderID}. The compute must invoke its {components} option to calculate components of the {Ybar_lm} vector for each atoms, as described in its documentation. Note that orientorder/atom compute @@ -109,9 +109,8 @@ array, with N columns. For {cstyle} orientorder, this compute calculates a per-atom vector. These values can be accessed by any command that uses per-atom values -from a compute as input. See "Section -6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output -options. +from a compute as input. See the "Howto output"_Howto_output.html doc +page for an overview of LAMMPS output options. The per-atom vector or array values will be a number >= 0.0, as explained above. diff --git a/doc/src/compute_damage_atom.txt b/doc/src/compute_damage_atom.txt index 918fbf65ef..2594dfe356 100644 --- a/doc/src/compute_damage_atom.txt +++ b/doc/src/compute_damage_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -44,7 +44,7 @@ group. This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -"Section 6.15"_Section_howto.html#howto_15 for an overview of +the "Howto output"_Howto_output.html doc page for an overview of LAMMPS output options. The per-atom vector values are unitless numbers (damage) >= 0.0. @@ -52,8 +52,8 @@ The per-atom vector values are unitless numbers (damage) >= 0.0. [Restrictions:] This compute is part of the PERI package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/compute_dihedral.txt b/doc/src/compute_dihedral.txt index a3c3dff8d6..aa25f9dd10 100644 --- a/doc/src/compute_dihedral.txt +++ b/doc/src/compute_dihedral.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -37,8 +37,8 @@ This compute calculates a global vector of length N where N is the number of sub_styles defined by the "dihedral_style hybrid"_dihedral_style.html command. which can be accessed by indices 1-N. These values can be used by any command that uses global scalar -or vector values from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output +or vector values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. The vector values are "extensive" and will be in energy diff --git a/doc/src/compute_dihedral_local.txt b/doc/src/compute_dihedral_local.txt index 865e86fddb..951b360f19 100644 --- a/doc/src/compute_dihedral_local.txt +++ b/doc/src/compute_dihedral_local.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -10,18 +10,25 @@ compute dihedral/local command :h3 [Syntax:] -compute ID group-ID dihedral/local value1 value2 ... :pre +compute ID group-ID dihedral/local value1 value2 ... keyword args ... :pre ID, group-ID are documented in "compute"_compute.html command :ulb,l dihedral/local = style name of this compute command :l one or more values may be appended :l -value = {phi} :l - {phi} = tabulate dihedral angles :pre +value = {phi} or {v_name} :l + {phi} = tabulate dihedral angles + {v_name} = equal-style variable with name (see below) :pre +zero or more keyword/args pairs may be appended :l +keyword = {set} :l + {set} args = phi name + phi = only currently allowed arg + name = name of variable to set with phi :pre :ule [Examples:] compute 1 all dihedral/local phi :pre +compute 1 all dihedral/local phi v_cos set phi p :pre [Description:] @@ -33,6 +40,47 @@ by the group parameter as explained below. The value {phi} is the dihedral angle, as defined in the diagram on the "dihedral_style"_dihedral_style.html doc page. +The value {v_name} can be used together with the {set} keyword to +compute a user-specified function of the dihedral angle phi. The +{name} specified for the {v_name} value is the name of an "equal-style +variable"_variable.html which should evaluate a formula based on a +variable which will store the angle phi. This other variable must +be an "internal-style variable"_variable.html defined in the input +script; its initial numeric value can be anything. It must be an +internal-style variable, because this command resets its value +directly. The {set} keyword is used to identify the name of this +other variable associated with phi. + +Note that the value of phi for each angle which stored in the internal +variable is in radians, not degrees. + +As an example, these commands can be added to the bench/in.rhodo +script to compute the cosine and cosine^2 of every dihedral angle in +the system and output the statistics in various ways: + +variable p internal 0.0 +variable cos equal cos(v_p) +variable cossq equal cos(v_p)*cos(v_p) :pre + +compute 1 all property/local datom1 datom2 datom3 datom4 dtype +compute 2 all dihedral/local phi v_cos v_cossq set phi p +dump 1 all local 100 tmp.dump c_1[*] c_2[*] :pre + +compute 3 all reduce ave c_2[*] +thermo_style custom step temp press c_3[*] :pre + +fix 10 all ave/histo 10 10 100 -1 1 20 c_2[2] mode vector file tmp.histo :pre + +The "dump local"_dump.html command will output the angle, +cosine(angle), cosine^2(angle) for every dihedral in the system. The +"thermo_style"_thermo_style.html command will print the average of +those quantities via the "compute reduce"_compute_reduce.html command +with thermo output. And the "fix ave/histo"_fix_ave_histo.html +command will histogram the cosine(angle) values and write them to a +file. + +:line + The local data stored by this command is generated by looping over all the atoms owned on a processor and their dihedrals. A dihedral will only be included if all 4 atoms in the dihedral are in the specified @@ -57,13 +105,13 @@ dump 1 all local 1000 tmp.dump index c_1\[1\] c_1\[2\] c_1\[3\] c_1\[4\] c_1\[5\ [Output info:] This compute calculates a local vector or local array depending on the -number of keywords. The length of the vector or number of rows in the -array is the number of dihedrals. If a single keyword is specified, a -local vector is produced. If two or more keywords are specified, a +number of values. The length of the vector or number of rows in the +array is the number of dihedrals. If a single value is specified, a +local vector is produced. If two or more values are specified, a local array is produced where the number of columns = the number of -keywords. The vector or array can be accessed by any command that -uses local values from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output +values. The vector or array can be accessed by any command that uses +local values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. The output for {phi} will be in degrees. diff --git a/doc/src/compute_dilatation_atom.txt b/doc/src/compute_dilatation_atom.txt index ce00f7f12a..292638bdf5 100644 --- a/doc/src/compute_dilatation_atom.txt +++ b/doc/src/compute_dilatation_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -47,16 +47,17 @@ compute group. [Output info:] This compute calculates a per-atom vector, which can be accessed by -any command that uses per-atom values from a compute as input. See -Section_howto 15 for an overview of LAMMPS output options. +any command that uses per-atom values from a compute as input. See +the "Howto output"_Howto_output.html doc page for an overview of +LAMMPS output options. The per-atom vector values are unitless numbers (theta) >= 0.0. [Restrictions:] This compute is part of the PERI package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/compute_dipole_chunk.txt b/doc/src/compute_dipole_chunk.txt index 75131ffbb1..d45fde9af2 100644 --- a/doc/src/compute_dipole_chunk.txt +++ b/doc/src/compute_dipole_chunk.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -32,10 +32,9 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom to a single chunk (or no chunk). The ID for this command is specified as chunkID. For example, a single chunk could be the atoms in a molecule or atoms in a spatial bin. See the "compute -chunk/atom"_compute_chunk_atom.html doc page and "Section -6.23"_Section_howto.html#howto_23 for details of how chunks can be -defined and examples of how they can be used to measure properties of -a system. +chunk/atom"_compute_chunk_atom.html and "Howto chunk"_Howto_chunk.html +doc pages for details of how chunks can be defined and examples of how +they can be used to measure properties of a system. This compute calculates the x,y,z coordinates of the dipole vector and the total dipole moment for each chunk, which includes all effects @@ -76,8 +75,8 @@ number of chunks {Nchunk} as calculated by the specified "compute chunk/atom"_compute_chunk_atom.html command. The number of columns = 4 for the x,y,z dipole vector components and the total dipole of each chunk. These values can be accessed by any command that uses global -array values from a compute as input. See "Section -6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output +array values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. The array values are "intensive". The array values will be in diff --git a/doc/src/compute_displace_atom.txt b/doc/src/compute_displace_atom.txt index 00e5f696c1..7cea62c7b3 100644 --- a/doc/src/compute_displace_atom.txt +++ b/doc/src/compute_displace_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -85,7 +85,7 @@ dump 1 all custom 100 tmp.dump id type x y z dump_modify 1 append yes thresh c_dsp[4] > ${Dhop} & refresh c_dsp delay 100 :pre -The "dump_modify thresh"_dump_modify.html command will only ouptut +The "dump_modify thresh"_dump_modify.html command will only output atoms that have displaced more than 0.6 Angstroms on each snapshot (assuming metal units). The dump_modify {refresh} option triggers a call to this compute at the end of every dump. @@ -118,9 +118,8 @@ would be empty. This compute calculates a per-atom array with 4 columns, which can be accessed by indices 1-4 by any command that uses per-atom values from -a compute as input. See "Section -6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output -options. +a compute as input. See the "Howto output"_Howto_output.html doc page +for an overview of LAMMPS output options. The per-atom array values will be in distance "units"_units.html. diff --git a/doc/src/compute_dpd.txt b/doc/src/compute_dpd.txt index 0e43feb9d2..eccffee9b8 100644 --- a/doc/src/compute_dpd.txt +++ b/doc/src/compute_dpd.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -40,17 +40,17 @@ where N is the number of particles in the system [Output info:] This compute calculates a global vector of length 5 (U_cond, U_mech, -U_chem, dpdTheta, N_particles), which can be accessed by indices 1-5. See -"this section"_Section_howto.html#howto_15 for an overview of LAMMPS -output options. +U_chem, dpdTheta, N_particles), which can be accessed by indices 1-5. +See the "Howto output"_Howto_output.html doc page for an overview of +LAMMPS output options. The vector values will be in energy and temperature "units"_units.html. [Restrictions:] This command is part of the USER-DPD package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. This command also requires use of the "atom_style dpd"_atom_style.html command. diff --git a/doc/src/compute_dpd_atom.txt b/doc/src/compute_dpd_atom.txt index 0532fc60c6..2f9b4098cf 100644 --- a/doc/src/compute_dpd_atom.txt +++ b/doc/src/compute_dpd_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -34,9 +34,9 @@ particles. [Output info:] This compute calculates a per-particle array with 4 columns (u_cond, -u_mech, u_chem, dpdTheta), which can be accessed by indices 1-4 by any command -that uses per-particle values from a compute as input. See -"Section 6.15"_Section_howto.html#howto_15 for an overview of +u_mech, u_chem, dpdTheta), which can be accessed by indices 1-4 by any +command that uses per-particle values from a compute as input. See +the "Howto output"_Howto_output.html doc page for an overview of LAMMPS output options. The per-particle array values will be in energy (u_cond, u_mech, u_chem) @@ -45,8 +45,8 @@ and temperature (dpdTheta) "units"_units.html. [Restrictions:] This command is part of the USER-DPD package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. This command also requires use of the "atom_style dpd"_atom_style.html command. diff --git a/doc/src/compute_edpd_temp_atom.txt b/doc/src/compute_edpd_temp_atom.txt index 5b8c8ebd67..f3c1418d44 100644 --- a/doc/src/compute_edpd_temp_atom.txt +++ b/doc/src/compute_edpd_temp_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -32,17 +32,17 @@ For more details please see "(Espanol1997)"_#Espanol1997 and [Output info:] This compute calculates a per-atom vector, which can be accessed by -any command that uses per-atom values from a compute as input. See -"Section 6.15"_Section_howto.html#howto_15 for an overview of -LAMMPS output options. +any command that uses per-atom values from a compute as input. See the +"Howto output"_Howto_output.html doc page for an overview of LAMMPS +output options. The per-atom vector values will be in temperature "units"_units.html. [Restrictions:] This compute is part of the USER-MESO package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/compute_entropy_atom.txt b/doc/src/compute_entropy_atom.txt new file mode 100644 index 0000000000..04f0fd0b82 --- /dev/null +++ b/doc/src/compute_entropy_atom.txt @@ -0,0 +1,130 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +compute entropy/atom command :h3 + +[Syntax:] + +compute ID group-ID entropy/atom sigma cutoff keyword value ... :pre + +ID, group-ID are documented in "compute"_compute.html command :l +entropy/atom = style name of this compute command :l +sigma = width of gaussians used in the g(r) smoothing :l +cutoff = cutoff for the g(r) calculation :l +one or more keyword/value pairs may be appended :l +keyword = {avg} or {local} + {avg} values = {yes} or {no} cutoff2 + {yes} = average the pair entropy over neighbors + {no} = do not average the pair entropy over neighbors + cutoff2 = cutoff for the averaging over neighbors + {local} values = {yes} or {no} = use the local density around each atom to normalize the g(r) :pre +:ule + +[Examples:] + +compute 1 all entropy/atom 0.25 5. +compute 1 all entropy/atom 0.25 5. avg yes 5. +compute 1 all entropy/atom 0.125 7.3 avg yes 5.1 local yes :pre + +[Description:] + +Define a computation that calculates the pair entropy fingerprint for +each atom in the group. The fingerprint is useful to distinguish between +ordered and disordered environments, for instance liquid and solid-like +environments, or glassy and crystalline-like environments. Some +applications could be the identification of grain boundaries, a +melt-solid interface, or a solid cluster emerging from the melt. +The advantage of this parameter over others is that no a priori +information about the solid structure is required. + +This parameter for atom i is computed using the following formula from +"(Piaggi)"_#Piaggi and "(Nettleton)"_#Nettleton , + +:c,image(Eqs/pair_entropy.jpg) + +where r is a distance, g(r) is the radial distribution function of atom +i and rho is the density of the system. The g(r) computed for each +atom i can be noisy and therefore it is smoothed using: + +:c,image(Eqs/pair_entropy2.jpg) + +where the sum in j goes through the neighbors of atom i, and sigma is a +parameter to control the smoothing. + +The input parameters are {sigma} the smoothing parameter, and the +{cutoff} for the calculation of g(r). + +If the keyword {avg} has the setting {yes}, then this compute also +averages the parameter over the neighbors of atom i according to: + +:c,image(Eqs/pair_entropy3.jpg) + +where the sum j goes over the neighbors of atom i and N is the number +of neighbors. This procedure provides a sharper distinction between +order and disorder environments. In this case the input parameter +{cutoff2} is the cutoff for the averaging over the neighbors and +must also be specified. + +If the {avg yes} option is used, the effective cutoff of the neighbor +list should be {cutoff}+{cutoff2} and therefore it might be necessary +to increase the skin of the neighbor list with: + +neighbor skin bin :pre + +See "neighbor"_neighbor.html for details. + +If the {local yes} option is used, the g(r) is normalized by the +local density around each atom, that is to say the density around each +atom is the number of neighbors within the neighbor list cutoff divided +by the corresponding volume. This option can be useful when dealing with +inhomogeneous systems such as those that have surfaces. + +Here are typical input parameters for fcc aluminum (lattice +constant 4.05 Angstroms), + +compute 1 all entropy/atom 0.25 5.7 avg yes 3.7 :pre + +and for bcc sodium (lattice constant 4.23 Angstroms), + +compute 1 all entropy/atom 0.25 7.3 avg yes 5.1 :pre + + +[Output info:] + +By default, this compute calculates the pair entropy value for each +atom as a per-atom vector, which can be accessed by any command that +uses per-atom values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output +options. + +The pair entropy values have units of the Boltzmann constant. They are +always negative, and lower values (lower entropy) correspond to more +ordered environments. + +[Restrictions:] + +This compute is part of the USER-MISC package. It is only enabled if +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. + +[Related commands:] + +"compute cna/atom"_compute_cna_atom.html +"compute centro/atom"_compute_centro_atom.html + +[Default:] + +The default values for the optional keywords are avg = no and local = no. + +:line + +:link(Piaggi) +[(Piaggi)] Piaggi and Parrinello, J Chem Phys, 147, 114112 (2017). + +:link(Nettleton) +[(Nettleton)] Nettleton and Green, J Chem Phys, 29, 6 (1958). diff --git a/doc/src/compute_erotate_asphere.txt b/doc/src/compute_erotate_asphere.txt index b9a486c32e..5cdc099782 100644 --- a/doc/src/compute_erotate_asphere.txt +++ b/doc/src/compute_erotate_asphere.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -40,7 +40,7 @@ will be the same as in 3d. This compute calculates a global scalar (the KE). This value can be used by any command that uses a global scalar value from a compute as -input. See "Section 6.15"_Section_howto.html#howto_15 for an +input. See the "Howto output"_Howto_output.html doc page for an overview of LAMMPS output options. The scalar value calculated by this compute is "extensive". The diff --git a/doc/src/compute_erotate_rigid.txt b/doc/src/compute_erotate_rigid.txt index dec0939a43..fa433c1c97 100644 --- a/doc/src/compute_erotate_rigid.txt +++ b/doc/src/compute_erotate_rigid.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -41,9 +41,9 @@ calculation. This compute calculates a global scalar (the summed rotational energy of all the rigid bodies). This value can be used by any command that -uses a global scalar value from a compute as input. See -"Section 6.15"_Section_howto.html#howto_15 for an overview of -LAMMPS output options. +uses a global scalar value from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output +options. The scalar value calculated by this compute is "extensive". The scalar value will be in energy "units"_units.html. @@ -51,8 +51,8 @@ scalar value will be in energy "units"_units.html. [Restrictions:] This compute is part of the RIGID package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/compute_erotate_sphere.txt b/doc/src/compute_erotate_sphere.txt index 41e80b0154..d0c176b50e 100644 --- a/doc/src/compute_erotate_sphere.txt +++ b/doc/src/compute_erotate_sphere.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -35,7 +35,7 @@ as in 3d. This compute calculates a global scalar (the KE). This value can be used by any command that uses a global scalar value from a compute as -input. See "Section 6.15"_Section_howto.html#howto_15 for an +input. See the "Howto output"_Howto_output.html doc page for an overview of LAMMPS output options. The scalar value calculated by this compute is "extensive". The diff --git a/doc/src/compute_erotate_sphere_atom.txt b/doc/src/compute_erotate_sphere_atom.txt index a0081ff6a8..fdd609a0e6 100644 --- a/doc/src/compute_erotate_sphere_atom.txt +++ b/doc/src/compute_erotate_sphere_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -39,7 +39,7 @@ in the specified compute group or for point particles with a radius = This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -"Section 6.15"_Section_howto.html#howto_15 for an overview of +the "Howto output"_Howto_output.html doc page for an overview of LAMMPS output options. The per-atom vector values will be in energy "units"_units.html. diff --git a/doc/src/compute_event_displace.txt b/doc/src/compute_event_displace.txt index 5e3a0c8599..a36cf2c9c4 100644 --- a/doc/src/compute_event_displace.txt +++ b/doc/src/compute_event_displace.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -43,7 +43,7 @@ local atom displacements and may generate "false positives." This compute calculates a global scalar (the flag). This value can be used by any command that uses a global scalar value from a compute as -input. See "Section 6.15"_Section_howto.html#howto_15 for an +input. See the "Howto output"_Howto_output.html doc page for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The @@ -52,8 +52,8 @@ scalar value will be a 0 or 1 as explained above. [Restrictions:] This command can only be used if LAMMPS was built with the REPLICA -package. See the "Making LAMMPS"_Section_start.html#start_3 section -for more info on packages. +package. See the "Build package"_Build_package.html doc +page for more info. [Related commands:] diff --git a/doc/src/compute_fep.txt b/doc/src/compute_fep.txt index 9bbae7b20f..5b3a6915dd 100644 --- a/doc/src/compute_fep.txt +++ b/doc/src/compute_fep.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -219,8 +219,8 @@ unperturbed parameters. The energies include kspace terms if these are used in the simulation. These output results can be used by any command that uses a global -scalar or vector from a compute as input. See "Section -6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output +scalar or vector from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. For example, the computed values can be averaged using "fix ave/time"_fix_ave_time.html. @@ -230,8 +230,8 @@ The values calculated by this compute are "extensive". [Restrictions:] This compute is distributed as the USER-FEP package. It is only -enabled if LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +enabled if LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/compute_global_atom.txt b/doc/src/compute_global_atom.txt index 3136b1fd18..a26dba72b0 100644 --- a/doc/src/compute_global_atom.txt +++ b/doc/src/compute_global_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -67,7 +67,7 @@ this command. This command will then assign the global chunk value to each atom in the chunk, producing a per-atom vector or per-atom array as output. The per-atom values can then be output to a dump file or used by any command that uses per-atom values from a compute as input, -as discussed in "Section 6.15"_Section_howto.html#howto_15. +as discussed on the "Howto output"_Howto_output.html doc page. As a concrete example, these commands will calculate the displacement of each atom from the center-of-mass of the molecule it is in, and @@ -130,7 +130,7 @@ page for details. If no bracketed integer is appended, the per-atom vector calculated by the compute is used. If a bracketed integer is appended, the Ith column of the per-atom array calculated by the compute is used. Users can also write code for their own compute -styles and "add them to LAMMPS"_Section_modify.html. See the +styles and "add them to LAMMPS"_Modify.html. See the discussion above for how I can be specified with a wildcard asterisk to effectively specify multiple values. @@ -143,7 +143,7 @@ references the values, else an error results. If no bracketed integer is appended, the per-atom vector calculated by the fix is used. If a bracketed integer is appended, the Ith column of the per-atom array calculated by the fix is used. Users can also write code for their -own fix style and "add them to LAMMPS"_Section_modify.html. See the +own fix style and "add them to LAMMPS"_Modify.html. See the discussion above for how I can be specified with a wildcard asterisk to effectively specify multiple values. @@ -168,7 +168,7 @@ page for details. If no bracketed integer is appended, the vector calculated by the compute is used. If a bracketed integer is appended, the Ith column of the array calculated by the compute is used. Users can also write code for their own compute styles and "add -them to LAMMPS"_Section_modify.html. See the discussion above for how +them to LAMMPS"_Modify.html. See the discussion above for how I can be specified with a wildcard asterisk to effectively specify multiple values. @@ -181,7 +181,7 @@ global/atom references the values, else an error results. If no bracketed integer is appended, the vector calculated by the fix is used. If a bracketed integer is appended, the Ith column of the array calculated by the fix is used. Users can also write code for their -own fix style and "add them to LAMMPS"_Section_modify.html. See the +own fix style and "add them to LAMMPS"_Modify.html. See the discussion above for how I can be specified with a wildcard asterisk to effectively specify multiple values. @@ -203,7 +203,7 @@ vector. If multiple inputs are specified, this compute produces a per-atom array values, where the number of columns is equal to the number of inputs specified. These values can be used by any command that uses per-atom vector or array values from a compute as input. -See "Section 6.15"_Section_howto.html#howto_15 for an overview of +See the "Howto output"_Howto_output.html doc page for an overview of LAMMPS output options. The per-atom vector or array values will be in whatever units the diff --git a/doc/src/compute_group_group.txt b/doc/src/compute_group_group.txt index f10547339d..cff3687354 100644 --- a/doc/src/compute_group_group.txt +++ b/doc/src/compute_group_group.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -123,8 +123,8 @@ group-group calculations are performed. This compute calculates a global scalar (the energy) and a global vector of length 3 (force), which can be accessed by indices 1-3. These values can be used by any command that uses global scalar or -vector values from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output +vector values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. Both the scalar and vector values calculated by this compute are diff --git a/doc/src/compute_gyration.txt b/doc/src/compute_gyration.txt index dd71431527..4dc883ad0b 100644 --- a/doc/src/compute_gyration.txt +++ b/doc/src/compute_gyration.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -55,8 +55,8 @@ using the "set image"_set.html command. This compute calculates a global scalar (Rg) and a global vector of length 6 (Rg^2 tensor), which can be accessed by indices 1-6. These values can be used by any command that uses a global scalar value or -vector values from a compute as input. See "Section -6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output +vector values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. The scalar and vector values calculated by this compute are diff --git a/doc/src/compute_gyration_chunk.txt b/doc/src/compute_gyration_chunk.txt index 3e338213cf..dcbfc65393 100644 --- a/doc/src/compute_gyration_chunk.txt +++ b/doc/src/compute_gyration_chunk.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -35,10 +35,9 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom to a single chunk (or no chunk). The ID for this command is specified as chunkID. For example, a single chunk could be the atoms in a molecule or atoms in a spatial bin. See the "compute -chunk/atom"_compute_chunk_atom.html doc page and "Section -6.23"_Section_howto.html#howto_23 for details of how chunks can be -defined and examples of how they can be used to measure properties of -a system. +chunk/atom"_compute_chunk_atom.html and "Howto chunk"_Howto_chunk.html +doc pages for details of how chunks can be defined and examples of how +they can be used to measure properties of a system. This compute calculates the radius of gyration Rg for each chunk, which includes all effects due to atoms passing thru periodic @@ -93,8 +92,8 @@ calculated by the specified "compute chunk/atom"_compute_chunk_atom.html command. If the {tensor} keyword is specified, the global array has 6 columns. The vector or array can be accessed by any command that uses global values from a compute as -input. See "this section"_Section_howto.html#howto_15 for an overview -of LAMMPS output options. +input. See the "Howto output"_Howto_output.html doc page for an +overview of LAMMPS output options. All the vector or array values calculated by this compute are "intensive". The vector or array values will be in distance diff --git a/doc/src/compute_heat_flux.txt b/doc/src/compute_heat_flux.txt index 39a1470201..81a2a3f517 100644 --- a/doc/src/compute_heat_flux.txt +++ b/doc/src/compute_heat_flux.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -32,9 +32,9 @@ or to calculate a thermal conductivity using the equilibrium Green-Kubo formalism. For other non-equilibrium ways to compute a thermal conductivity, see -"this section"_Section_howto.html#howto_20. These include use of the -"fix thermal/conductivity"_fix_thermal_conductivity.html command for -the Muller-Plathe method. Or the "fix heat"_fix_heat.html command +the "Howto kappa"_Howto_kappa.html doc page.. These include use of +the "fix thermal/conductivity"_fix_thermal_conductivity.html command +for the Muller-Plathe method. Or the "fix heat"_fix_heat.html command which can add or subtract heat from groups of atoms. The compute takes three arguments which are IDs of other @@ -99,8 +99,8 @@ result should be: average conductivity ~0.29 in W/mK. This compute calculates a global vector of length 6 (total heat flux vector, followed by convective heat flux vector), which can be accessed by indices 1-6. These values can be used by any command that -uses global vector values from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output +uses global vector values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. The vector values calculated by this compute are "extensive", meaning diff --git a/doc/src/compute_hexorder_atom.txt b/doc/src/compute_hexorder_atom.txt index cdf47e0894..082a3cad7a 100644 --- a/doc/src/compute_hexorder_atom.txt +++ b/doc/src/compute_hexorder_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -95,10 +95,9 @@ This compute calculates a per-atom array with 2 columns, giving the real and imaginary parts {qn}, a complex number restricted to the unit disk of the complex plane i.e. Re({qn})^2 + Im({qn})^2 <= 1 . -These values can be accessed by any command that uses -per-atom values from a compute as input. See "Section -6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output -options. +These values can be accessed by any command that uses per-atom values +from a compute as input. See the "Howto output"_Howto_output.html doc +page for an overview of LAMMPS output options. [Restrictions:] none diff --git a/doc/src/compute_improper.txt b/doc/src/compute_improper.txt index f0d2fa400e..867dd48cc1 100644 --- a/doc/src/compute_improper.txt +++ b/doc/src/compute_improper.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -37,8 +37,8 @@ This compute calculates a global vector of length N where N is the number of sub_styles defined by the "improper_style hybrid"_improper_style.html command. which can be accessed by indices 1-N. These values can be used by any command that uses global scalar -or vector values from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output +or vector values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. The vector values are "extensive" and will be in energy diff --git a/doc/src/compute_improper_local.txt b/doc/src/compute_improper_local.txt index 0c289fbf07..f340d5a03f 100644 --- a/doc/src/compute_improper_local.txt +++ b/doc/src/compute_improper_local.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -63,8 +63,8 @@ array is the number of impropers. If a single keyword is specified, a local vector is produced. If two or more keywords are specified, a local array is produced where the number of columns = the number of keywords. The vector or array can be accessed by any command that -uses local values from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output +uses local values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. The output for {chi} will be in degrees. diff --git a/doc/src/compute_inertia_chunk.txt b/doc/src/compute_inertia_chunk.txt index b0dbb12aea..d6cdb3fe79 100644 --- a/doc/src/compute_inertia_chunk.txt +++ b/doc/src/compute_inertia_chunk.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -30,10 +30,9 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom to a single chunk (or no chunk). The ID for this command is specified as chunkID. For example, a single chunk could be the atoms in a molecule or atoms in a spatial bin. See the "compute -chunk/atom"_compute_chunk_atom.html doc page and "Section -6.23"_Section_howto.html#howto_23 for details of how chunks can be -defined and examples of how they can be used to measure properties of -a system. +chunk/atom"_compute_chunk_atom.html and "Howto chunk"_Howto_chunk.html +doc pages for details of how chunks can be defined and examples of how +they can be used to measure properties of a system. This compute calculates the 6 components of the symmetric inertia tensor for each chunk, ordered Ixx,Iyy,Izz,Ixy,Iyz,Ixz. The @@ -72,8 +71,8 @@ number of chunks {Nchunk} as calculated by the specified "compute chunk/atom"_compute_chunk_atom.html command. The number of columns = 6 for the 6 components of the inertia tensor for each chunk, ordered as listed above. These values can be accessed by any command that -uses global array values from a compute as input. See "Section -6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output +uses global array values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. The array values are "intensive". The array values will be in diff --git a/doc/src/compute_ke.txt b/doc/src/compute_ke.txt index caee897162..64ab83db48 100644 --- a/doc/src/compute_ke.txt +++ b/doc/src/compute_ke.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -44,7 +44,7 @@ include different degrees of freedom (translational, rotational, etc). This compute calculates a global scalar (the summed KE). This value can be used by any command that uses a global scalar value from a -compute as input. See "Section 6.15"_Section_howto.html#howto_15 +compute as input. See the "Howto output"_Howto_output.html doc page for an overview of LAMMPS output options. The scalar value calculated by this compute is "extensive". The diff --git a/doc/src/compute_ke_atom.txt b/doc/src/compute_ke_atom.txt index f5431f0569..d288ab0236 100644 --- a/doc/src/compute_ke_atom.txt +++ b/doc/src/compute_ke_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -34,7 +34,7 @@ specified compute group. This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -"Section 6.15"_Section_howto.html#howto_15 for an overview of +the "Howto output"_Howto_output.html doc page for an overview of LAMMPS output options. The per-atom vector values will be in energy "units"_units.html. diff --git a/doc/src/compute_ke_atom_eff.txt b/doc/src/compute_ke_atom_eff.txt index 8228e13f07..29905f81d6 100644 --- a/doc/src/compute_ke_atom_eff.txt +++ b/doc/src/compute_ke_atom_eff.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -57,17 +57,17 @@ electrons) not in the specified compute group. [Output info:] This compute calculates a scalar quantity for each atom, which can be -accessed by any command that uses per-atom computes as input. See -"Section 6.15"_Section_howto.html#howto_15 for an overview of -LAMMPS output options. +accessed by any command that uses per-atom computes as input. See the +"Howto output"_Howto_output.html doc page for an overview of LAMMPS +output options. The per-atom vector values will be in energy "units"_units.html. [Restrictions:] This compute is part of the USER-EFF package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/compute_ke_eff.txt b/doc/src/compute_ke_eff.txt index ac8d7e6c01..fa2c51a032 100644 --- a/doc/src/compute_ke_eff.txt +++ b/doc/src/compute_ke_eff.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -61,7 +61,7 @@ See "compute temp/eff"_compute_temp_eff.html. This compute calculates a global scalar (the KE). This value can be used by any command that uses a global scalar value from a compute as -input. See "Section 6.15"_Section_howto.html#howto_15 for an +input. See the "Howto output"_Howto_output.html doc page for an overview of LAMMPS output options. The scalar value calculated by this compute is "extensive". The @@ -70,8 +70,8 @@ scalar value will be in energy "units"_units.html. [Restrictions:] This compute is part of the USER-EFF package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] none diff --git a/doc/src/compute_ke_rigid.txt b/doc/src/compute_ke_rigid.txt index f79696a77a..ad6baf567f 100644 --- a/doc/src/compute_ke_rigid.txt +++ b/doc/src/compute_ke_rigid.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -40,8 +40,8 @@ calculation. This compute calculates a global scalar (the summed KE of all the rigid bodies). This value can be used by any command that uses a -global scalar value from a compute as input. See "Section -6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output +global scalar value from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. The scalar value calculated by this compute is "extensive". The @@ -50,8 +50,8 @@ scalar value will be in energy "units"_units.html. [Restrictions:] This compute is part of the RIGID package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/compute_meso_e_atom.txt b/doc/src/compute_meso_e_atom.txt index 4e621b4301..0f0cfda2d1 100644 --- a/doc/src/compute_meso_e_atom.txt +++ b/doc/src/compute_meso_e_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -38,7 +38,7 @@ specified compute group. This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -"Section 6.15"_Section_howto.html#howto_15 for an overview of +the "Howto output"_Howto_output.html doc page for an overview of LAMMPS output options. The per-atom vector values will be in energy "units"_units.html. @@ -46,8 +46,8 @@ The per-atom vector values will be in energy "units"_units.html. [Restrictions:] This compute is part of the USER-SPH package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/compute_meso_rho_atom.txt b/doc/src/compute_meso_rho_atom.txt index a017424dd0..5127ad2c48 100644 --- a/doc/src/compute_meso_rho_atom.txt +++ b/doc/src/compute_meso_rho_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -38,7 +38,7 @@ specified compute group. This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -"Section 6.15"_Section_howto.html#howto_15 for an overview of +the "Howto output"_Howto_output.html doc page for an overview of LAMMPS output options. The per-atom vector values will be in mass/volume "units"_units.html. @@ -46,8 +46,8 @@ The per-atom vector values will be in mass/volume "units"_units.html. [Restrictions:] This compute is part of the USER-SPH package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/compute_meso_t_atom.txt b/doc/src/compute_meso_t_atom.txt index 9e81b038f4..f4ab869ec2 100644 --- a/doc/src/compute_meso_t_atom.txt +++ b/doc/src/compute_meso_t_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -40,7 +40,7 @@ specified compute group. This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -"Section 6.15"_Section_howto.html#howto_15 for an overview of +the "Howto output"_Howto_output.html doc page for an overview of LAMMPS output options. The per-atom vector values will be in temperature "units"_units.html. @@ -48,8 +48,8 @@ The per-atom vector values will be in temperature "units"_units.html. [Restrictions:] This compute is part of the USER-SPH package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/compute_modify.txt b/doc/src/compute_modify.txt index 9a2480ec0a..5ba2100fba 100644 --- a/doc/src/compute_modify.txt +++ b/doc/src/compute_modify.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -19,7 +19,7 @@ keyword = {extra/dof} or {extra} or {dynamic/dof} or {dynamic} :l N = # of extra degrees of freedom to subtract {extra} syntax is identical to {extra/dof}, will be disabled at some point {dynamic/dof} value = {yes} or {no} - yes/no = do or do not recompute the number of degrees of freedom (DOF) contributing to the temperature + yes/no = do or do not re-compute the number of degrees of freedom (DOF) contributing to the temperature {dynamic} syntax is identical to {dynamic/dof}, will be disabled at some point :pre :ule diff --git a/doc/src/compute_msd.txt b/doc/src/compute_msd.txt index f806c5e292..b54e05bc64 100644 --- a/doc/src/compute_msd.txt +++ b/doc/src/compute_msd.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -93,9 +93,8 @@ instead of many, which will change the values of msd somewhat. This compute calculates a global vector of length 4, which can be accessed by indices 1-4 by any command that uses global vector values -from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output -options. +from a compute as input. See the "Howto output"_Howto_output.html doc +page for an overview of LAMMPS output options. The vector values are "intensive". The vector values will be in distance^2 "units"_units.html. diff --git a/doc/src/compute_msd_chunk.txt b/doc/src/compute_msd_chunk.txt index 7f31b61ed0..264f38d5fd 100644 --- a/doc/src/compute_msd_chunk.txt +++ b/doc/src/compute_msd_chunk.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -30,10 +30,9 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom to a single chunk (or no chunk). The ID for this command is specified as chunkID. For example, a single chunk could be the atoms in a molecule or atoms in a spatial bin. See the "compute -chunk/atom"_compute_chunk_atom.html doc page and "Section -6.23"_Section_howto.html#howto_23 for details of how chunks can be -defined and examples of how they can be used to measure properties of -a system. +chunk/atom"_compute_chunk_atom.html and "Howto chunk"_Howto_chunk.html +doc pages for details of how chunks can be defined and examples of how +they can be used to measure properties of a system. Four quantities are calculated by this compute for each chunk. The first 3 quantities are the squared dx,dy,dz displacements of the @@ -106,7 +105,7 @@ number of chunks {Nchunk} as calculated by the specified "compute chunk/atom"_compute_chunk_atom.html command. The number of columns = 4 for dx,dy,dz and the total displacement. These values can be accessed by any command that uses global array values from a compute -as input. See "this section"_Section_howto.html#howto_15 for an +as input. See the "Howto output"_Howto_output.html doc page for an overview of LAMMPS output options. The array values are "intensive". The array values will be in diff --git a/doc/src/compute_msd_nongauss.txt b/doc/src/compute_msd_nongauss.txt index 198da999e0..c6e89a1061 100644 --- a/doc/src/compute_msd_nongauss.txt +++ b/doc/src/compute_msd_nongauss.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -57,9 +57,8 @@ NOTEs, which also apply to this compute. This compute calculates a global vector of length 3, which can be accessed by indices 1-3 by any command that uses global vector values -from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output -options. +from a compute as input. See the "Howto output"_Howto_output.html doc +page for an overview of LAMMPS output options. The vector values are "intensive". The first vector value will be in distance^2 "units"_units.html, the second is in distance^4 units, and @@ -67,9 +66,9 @@ the 3rd is dimensionless. [Restrictions:] -This compute is part of the MISC package. It is only enabled if LAMMPS -was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +This compute is part of the MISC package. It is only enabled if +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/compute_omega_chunk.txt b/doc/src/compute_omega_chunk.txt index 46c72d3dcb..84b25ac6f2 100644 --- a/doc/src/compute_omega_chunk.txt +++ b/doc/src/compute_omega_chunk.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -30,10 +30,9 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom to a single chunk (or no chunk). The ID for this command is specified as chunkID. For example, a single chunk could be the atoms in a molecule or atoms in a spatial bin. See the "compute -chunk/atom"_compute_chunk_atom.html doc page and "Section -6.23"_Section_howto.html#howto_23 for details of how chunks can be -defined and examples of how they can be used to measure properties of -a system. +chunk/atom"_compute_chunk_atom.html and "Howto chunk"_Howto_chunk.html +doc pages for details of how chunks can be defined and examples of how +they can be used to measure properties of a system. This compute calculates the 3 components of the angular velocity vector for each chunk, via the formula L = Iw where L is the angular @@ -73,8 +72,8 @@ number of chunks {Nchunk} as calculated by the specified "compute chunk/atom"_compute_chunk_atom.html command. The number of columns = 3 for the 3 xyz components of the angular velocity for each chunk. These values can be accessed by any command that uses global array -values from a compute as input. See "Section -6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output +values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. The array values are "intensive". The array values will be in diff --git a/doc/src/compute_orientorder_atom.txt b/doc/src/compute_orientorder_atom.txt index adf11dcfcf..7327a7b1d3 100644 --- a/doc/src/compute_orientorder_atom.txt +++ b/doc/src/compute_orientorder_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -115,10 +115,9 @@ Re({Ybar_-m+1}) Im({Ybar_-m+1}) ... Re({Ybar_m}) Im({Ybar_m}). This way, the per-atom array will have a total of {nlvalues}+2*(2{l}+1) columns. -These values can be accessed by any command that uses -per-atom values from a compute as input. See "Section -6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output -options. +These values can be accessed by any command that uses per-atom values +from a compute as input. See the "Howto output"_Howto_output.html doc +page for an overview of LAMMPS output options. [Restrictions:] none diff --git a/doc/src/compute_pair.txt b/doc/src/compute_pair.txt index 0602dab81b..b309019e30 100644 --- a/doc/src/compute_pair.txt +++ b/doc/src/compute_pair.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -27,7 +27,9 @@ compute 1 all pair reax :pre Define a computation that extracts additional values calculated by a pair style, and makes them accessible for output or further processing -by other commands. The group specified for this command is ignored. +by other commands. + +NOTE: The group specified for this command is [ignored]. The specified {pstyle} must be a pair style used in your simulation either by itself or as a sub-style in a "pair_style hybrid or @@ -62,9 +64,8 @@ This compute calculates a global scalar which is {epair} or {evdwl} or {ecoul}. If the pair style supports it, it also calculates a global vector of length >= 1, as determined by the pair style. These values can be used by any command that uses global scalar or vector values -from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output -options. +from a compute as input. See the "Howto output"_Howto_output.html doc +page for an overview of LAMMPS output options. The scalar and vector values calculated by this compute are "extensive". diff --git a/doc/src/compute_pair_local.txt b/doc/src/compute_pair_local.txt index 16aaba4667..1460ba18a5 100644 --- a/doc/src/compute_pair_local.txt +++ b/doc/src/compute_pair_local.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -62,7 +62,7 @@ pair styles do not define any additional quantities, so N = 0. An example of ones that do are the "granular pair styles"_pair_gran.html which calculate the tangential force between two particles and return its components and magnitude acting on atom I for N = 1,2,3,4. See -individual pair styles for detils. +individual pair styles for details. The value {dist} will be in distance "units"_units.html. The value {eng} will be in energy "units"_units.html. The values {force}, {fx}, @@ -76,7 +76,7 @@ command for the types of the two atoms is used. For the {radius} setting, the sum of the radii of the two particles is used as a cutoff. For example, this is appropriate for granular particles which only interact when they are overlapping, as computed by "granular pair -styles"_pair_gran.txt. Note that if a granular model defines atom +styles"_pair_gran.html. Note that if a granular model defines atom types such that all particles of a specific type are monodisperse (same diameter), then the two settings are effectively identical. @@ -119,8 +119,8 @@ array is the number of pairs. If a single keyword is specified, a local vector is produced. If two or more keywords are specified, a local array is produced where the number of columns = the number of keywords. The vector or array can be accessed by any command that -uses local values from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output +uses local values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. The output for {dist} will be in distance "units"_units.html. The diff --git a/doc/src/compute_pe.txt b/doc/src/compute_pe.txt index 15f27a8eff..37655dfd48 100644 --- a/doc/src/compute_pe.txt +++ b/doc/src/compute_pe.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -64,9 +64,8 @@ See the "thermo_style" command for more details. This compute calculates a global scalar (the potential energy). This value can be used by any command that uses a global scalar value from -a compute as input. See "Section -6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output -options. +a compute as input. See the "Howto output"_Howto_output.html doc page +for an overview of LAMMPS output options. The scalar value calculated by this compute is "extensive". The scalar value will be in energy "units"_units.html. diff --git a/doc/src/compute_pe_atom.txt b/doc/src/compute_pe_atom.txt index c312c886a6..400621f8df 100644 --- a/doc/src/compute_pe_atom.txt +++ b/doc/src/compute_pe_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -81,7 +81,7 @@ global system energy. This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -"Section 6.15"_Section_howto.html#howto_15 for an overview of +the "Howto output"_Howto_output.html doc page for an overview of LAMMPS output options. The per-atom vector values will be in energy "units"_units.html. diff --git a/doc/src/compute_plasticity_atom.txt b/doc/src/compute_plasticity_atom.txt index 788213fc65..b82179712a 100644 --- a/doc/src/compute_plasticity_atom.txt +++ b/doc/src/compute_plasticity_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -41,16 +41,17 @@ compute group. [Output info:] This compute calculates a per-atom vector, which can be accessed by -any command that uses per-atom values from a compute as input. See -Section_howto 15 for an overview of LAMMPS output options. +any command that uses per-atom values from a compute as input. See +the "Howto output"_Howto_output.html doc page for an overview of +LAMMPS output options. The per-atom vector values are unitless numbers (lambda) >= 0.0. [Restrictions:] This compute is part of the PERI package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/compute_pressure.txt b/doc/src/compute_pressure.txt index f0691ad207..6acbaf7d3d 100644 --- a/doc/src/compute_pressure.txt +++ b/doc/src/compute_pressure.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -105,23 +105,22 @@ where "thermo_temp" is the ID of a similarly defined compute of style Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line @@ -130,8 +129,8 @@ more instructions on how to use the accelerated styles effectively. This compute calculates a global scalar (the pressure) and a global vector of length 6 (pressure tensor), which can be accessed by indices 1-6. These values can be used by any command that uses global scalar -or vector values from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output +or vector values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. The scalar and vector values calculated by this compute are diff --git a/doc/src/compute_pressure_uef.txt b/doc/src/compute_pressure_uef.txt index 5b252b369d..72ed0ba5c4 100644 --- a/doc/src/compute_pressure_uef.txt +++ b/doc/src/compute_pressure_uef.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -27,8 +27,8 @@ compute 2 all pressure/uef my_temp_uef virial :pre This command is used to compute the pressure tensor in the reference frame of the applied flow field when -"fix nvt/uef"_fix_nh_uef.html" or -"fix npt/uef"_fix_nh_uef.html" is used. +"fix nvt/uef"_fix_nh_uef.html or +"fix npt/uef"_fix_nh_uef.html is used. It is not necessary to use this command to compute the scalar value of the pressure. A "compute pressure"_compute_pressure.html may be used for that purpose. @@ -38,9 +38,9 @@ The keywords and output information are documented in [Restrictions:] -This fix is part of the USER-UEF package. It is only enabled if -LAMMPS was built with that package. See the -"Making LAMMPS"_Section_start.html#start_3 section for more info. +This fix is part of the USER-UEF package. It is only enabled if LAMMPS +was built with that package. See the "Build +package"_Build_package.html doc page for more info. This command can only be used when "fix nvt/uef"_fix_nh_uef.html or "fix npt/uef"_fix_nh_uef.html is active. diff --git a/doc/src/compute_property_atom.txt b/doc/src/compute_property_atom.txt index bac19918ba..bc1e3049fa 100644 --- a/doc/src/compute_property_atom.txt +++ b/doc/src/compute_property_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -19,6 +19,7 @@ input = one or more atom attributes :l x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz, vx, vy, vz, fx, fy, fz, q, mux, muy, muz, mu, + sp, spx, spy, spz, fmx, fmy, fmz, radius, diameter, omegax, omegay, omegaz, angmomx, angmomy, angmomz, shapex,shapey, shapez, @@ -46,6 +47,9 @@ input = one or more atom attributes :l q = atom charge mux,muy,muz = orientation of dipole moment of atom mu = magnitude of dipole moment of atom + sp = atomic magnetic spin moment + spx, spy, spz = direction of the atomic magnetic spin + fmx, fmy, fmz = magnetic force radius,diameter = radius,diameter of spherical particle omegax,omegay,omegaz = angular velocity of spherical particle angmomx,angmomy,angmomz = angular momentum of aspherical particle @@ -82,17 +86,18 @@ input = one or more atom attributes :l compute 1 all property/atom xs vx fx mux compute 2 all property/atom type -compute 1 all property/atom ix iy iz :pre +compute 1 all property/atom ix iy iz +compute 3 all property/atom sp spx spy spz :pre [Description:] Define a computation that simply stores atom attributes for each atom in the group. This is useful so that the values can be used by other -"output commands"_Section_howto.html#howto_15 that take computes as -inputs. See for example, the "compute reduce"_compute_reduce.html, -"fix ave/atom"_fix_ave_atom.html, "fix ave/histo"_fix_ave_histo.html, -"fix ave/chunk"_fix_ave_chunk.html, and "atom-style -variable"_variable.html commands. +"output commands"_Howto_output.html that take computes as inputs. See +for example, the "compute reduce"_compute_reduce.html, "fix +ave/atom"_fix_ave_atom.html, "fix ave/histo"_fix_ave_histo.html, "fix +ave/chunk"_fix_ave_chunk.html, and "atom-style variable"_variable.html +commands. The list of possible attributes is the same as that used by the "dump custom"_dump.html command, which describes their meaning, with some @@ -144,14 +149,18 @@ on the number of input values. If a single input is specified, a per-atom vector is produced. If two or more inputs are specified, a per-atom array is produced where the number of columns = the number of inputs. The vector or array can be accessed by any command that uses -per-atom values from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output +per-atom values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. The vector or array values will be in whatever "units"_units.html the corresponding attribute is in, e.g. velocity units for vx, charge units for q, etc. +For the spin quantities, sp is in the units of the Bohr magneton, spx, +spy, and spz are adimensional quantities, and fmx, fmy and fmz are +given in rad.THz. + [Restrictions:] none [Related commands:] diff --git a/doc/src/compute_property_chunk.txt b/doc/src/compute_property_chunk.txt index b9d4944b30..a30b5a1f0a 100644 --- a/doc/src/compute_property_chunk.txt +++ b/doc/src/compute_property_chunk.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -36,15 +36,14 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom to a single chunk (or no chunk). The ID for this command is specified as chunkID. For example, a single chunk could be the atoms in a molecule or atoms in a spatial bin. See the "compute -chunk/atom"_compute_chunk_atom.html doc page and "Section -6.23"_Section_howto.html#howto_23 for details of how chunks can be -defined and examples of how they can be used to measure properties of -a system. +chunk/atom"_compute_chunk_atom.html and "Howto chunk"_Howto_chunk.html +doc pages for details of how chunks can be defined and examples of how +they can be used to measure properties of a system. This compute calculates and stores the specified attributes of chunks as global data so they can be accessed by other "output -commands"_Section_howto.html#howto_15 and used in conjunction with -other commands that generate per-chunk data, such as "compute +commands"_Howto_output.html and used in conjunction with other +commands that generate per-chunk data, such as "compute com/chunk"_compute_com_chunk.html or "compute msd/chunk"_compute_msd_chunk.html. @@ -103,8 +102,8 @@ single input is specified, a global vector is produced. If two or more inputs are specified, a global array is produced where the number of columns = the number of inputs. The vector or array can be accessed by any command that uses global values from a compute as -input. See "this section"_Section_howto.html#howto_15 for an overview -of LAMMPS output options. +input. See the "Howto output"_Howto_output.html doc page for an +overview of LAMMPS output options. The vector or array values are "intensive". The values will be unitless or in the units discussed above. diff --git a/doc/src/compute_property_local.txt b/doc/src/compute_property_local.txt index 39106a39c8..c4ad0afc95 100644 --- a/doc/src/compute_property_local.txt +++ b/doc/src/compute_property_local.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -19,8 +19,8 @@ one or more attributes may be appended :l patom1 patom2 ptype1 ptype2 batom1 batom2 btype aatom1 aatom2 aatom3 atype - datom1 datom2 datom3 dtype - iatom1 iatom2 iatom3 itype :pre + datom1 datom2 datom3 datom4 dtype + iatom1 iatom2 iatom3 iatom4 itype :pre natom1, natom2 = IDs of 2 atoms in each pair (within neighbor cutoff) ntype1, ntype2 = type of 2 atoms in each pair (within neighbor cutoff) @@ -48,10 +48,10 @@ compute 1 all property/local atype aatom2 :pre Define a computation that stores the specified attributes as local data so it can be accessed by other "output -commands"_Section_howto.html#howto_15. If the input attributes refer -to bond information, then the number of datums generated, aggregated -across all processors, equals the number of bonds in the system. -Ditto for pairs, angles, etc. +commands"_Howto_output.html. If the input attributes refer to bond +information, then the number of datums generated, aggregated across +all processors, equals the number of bonds in the system. Ditto for +pairs, angles, etc. If multiple attributes are specified then they must all generate the same amount of information, so that the resulting local array has the @@ -140,8 +140,8 @@ the array is the number of bonds, angles, etc. If a single input is specified, a local vector is produced. If two or more inputs are specified, a local array is produced where the number of columns = the number of inputs. The vector or array can be accessed by any command -that uses local values from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output +that uses local values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. The vector or array values will be integers that correspond to the diff --git a/doc/src/compute_rdf.txt b/doc/src/compute_rdf.txt index e462e85fc0..d11ae9e3bf 100644 --- a/doc/src/compute_rdf.txt +++ b/doc/src/compute_rdf.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -152,7 +152,7 @@ coordinate (center of the bin), Each successive set of 2 columns has the g(r) and coord(r) values for a specific set of {itypeN} versus {jtypeN} interactions, as described above. These values can be used by any command that uses a global values from a compute as input. See -"Section 6.15"_Section_howto.html#howto_15 for an overview of +the "Howto output"_Howto_output.html doc page for an overview of LAMMPS output options. The array values calculated by this compute are all "intensive". @@ -182,7 +182,7 @@ change from zero to one at the location of the spike in g(r). NOTE: compute rdf can handle dynamic groups and systems where atoms are added or removed, but this causes that certain normalization -parameters need to be recomputed in every step and include collective +parameters need to be re-computed in every step and include collective communication operations. This will reduce performance and limit parallel efficiency and scaling. For systems, where only the type of atoms changes (e.g. when using "fix atom/swap"_fix_atom_swap.html), diff --git a/doc/src/compute_reduce.txt b/doc/src/compute_reduce.txt index 07d3c3bda7..0bd2accf3c 100644 --- a/doc/src/compute_reduce.txt +++ b/doc/src/compute_reduce.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -97,9 +97,9 @@ equivalent, since the "compute stress/atom"_compute_stress_atom.html command creates a per-atom array with 6 columns: compute myPress all stress/atom NULL -compute 2 all reduce min myPress\[*\] -compute 2 all reduce min myPress\[1\] myPress\[2\] myPress\[3\] & - myPress\[4\] myPress\[5\] myPress\[6\] :pre +compute 2 all reduce min c_myPress\[*\] +compute 2 all reduce min c_myPress\[1\] c_myPress\[2\] c_myPress\[3\] & + c_myPress\[4\] c_myPress\[5\] c_myPress\[6\] :pre :line @@ -116,7 +116,7 @@ per-atom or local quantities. See the individual is appended, the vector calculated by the compute is used. If a bracketed integer is appended, the Ith column of the array calculated by the compute is used. Users can also write code for their own -compute styles and "add them to LAMMPS"_Section_modify.html. See the +compute styles and "add them to LAMMPS"_Modify.html. See the discussion above for how I can be specified with a wildcard asterisk to effectively specify multiple values. @@ -129,9 +129,9 @@ references the values, else an error results. If no bracketed integer is appended, the vector calculated by the fix is used. If a bracketed integer is appended, the Ith column of the array calculated by the fix is used. Users can also write code for their own fix style and "add -them to LAMMPS"_Section_modify.html. See the discussion above for how -I can be specified with a wildcard asterisk to effectively specify -multiple values. +them to LAMMPS"_Modify.html. See the discussion above for how I can +be specified with a wildcard asterisk to effectively specify multiple +values. If a value begins with "v_", a variable name must follow which has been previously defined in the input script. It must be an @@ -192,7 +192,7 @@ This compute calculates a global scalar if a single input value is specified or a global vector of length N where N is the number of inputs, and which can be accessed by indices 1 to N. These values can be used by any command that uses global scalar or vector values from a -compute as input. See "Section 6.15"_Section_howto.html#howto_15 +compute as input. See the "Howto output"_Howto_output.html doc page for an overview of LAMMPS output options. All the scalar or vector values calculated by this compute are diff --git a/doc/src/compute_reduce_chunk.txt b/doc/src/compute_reduce_chunk.txt new file mode 100644 index 0000000000..3628c0f1ad --- /dev/null +++ b/doc/src/compute_reduce_chunk.txt @@ -0,0 +1,177 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +compute reduce/chunk command :h3 + +[Syntax:] + +compute ID group-ID reduce/chunk chunkID mode input1 input2 ... :pre + +ID, group-ID are documented in "compute"_compute.html command :ulb,l +reduce/chunk = style name of this compute command :l +chunkID = ID of "compute chunk/atom"_compute_chunk_atom.html command :l +mode = {sum} or {min} or {max} :l +one or more inputs can be listed :l +input = c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_ID :l + c_ID = per-atom vector calculated by a compute with ID + c_ID\[I\] = Ith column of per-atom array calculated by a compute with ID, I can include wildcard (see below) + f_ID = per-atom vector calculated by a fix with ID + f_ID\[I\] = Ith column of per-atom array calculated by a fix with ID, I can include wildcard (see below) + v_name = per-atom vector calculated by an atom-style variable with name :pre +:ule + +[Examples:] + +compute 1 all reduce/chunk/atom mychunk min c_cluster :pre + +[Description:] + +Define a calculation that reduces one or more per-atom vectors into +per-chunk values. This can be useful for diagnostic output. Or when +used in conjunction with the "compute +chunk/spread/atom"_compute_chunk_spread_atom.html command it can be +used ot create per-atom values that induce a new set of chunks with a +second "compute chunk/atom"_compute_chunk_atom.html command. An +example is given below. + +In LAMMPS, chunks are collections of atoms defined by a "compute +chunk/atom"_compute_chunk_atom.html command, which assigns each atom +to a single chunk (or no chunk). The ID for this command is specified +as chunkID. For example, a single chunk could be the atoms in a +molecule or atoms in a spatial bin. See the "compute +chunk/atom"_compute_chunk_atom.html and "Howto chunk"_Howto_chunk.html +doc pages for details of how chunks can be defined and examples of how +they can be used to measure properties of a system. + +For each atom, this compute accesses its chunk ID from the specified +{chunkID} compute. The per-atom value from an input contributes +to a per-chunk value corresponding the the chunk ID. + +The reduction operation is specified by the {mode} setting and is +performed over all the per-atom values from the atoms in each chunk. +The {sum} option adds the pre-atom values to a per-chunk total. The +{min} or {max} options find the minimum or maximum value of the +per-atom values for each chunk. + +Note that only atoms in the specified group contribute to the +reduction operation. If the {chunkID} compute returns a 0 for the +chunk ID of an atom (i.e. the atom is not in a chunk defined by the +"compute chunk/atom"_compute_chunk_atom.html command), that atom will +also not contribute to the reduction operation. An input that is a +compute or fix may define its own group which affects the quantities +it returns. For example, a compute with return a zero value for atoms +that are not in the group specified for that compute. + +Each listed input is operated on independently. Each input can be the +result of a "compute"_compute.html or "fix"_fix.html or the evaluation +of an atom-style "variable"_variable.html. + +Note that for values from a compute or fix, the bracketed index I can +be specified using a wildcard asterisk with the index to effectively +specify multiple values. This takes the form "*" or "*n" or "n*" or +"m*n". If N = the size of the vector (for {mode} = scalar) or the +number of columns in the array (for {mode} = vector), then an asterisk +with no numeric values means all indices from 1 to N. A leading +asterisk means all indices from 1 to n (inclusive). A trailing +asterisk means all indices from n to N (inclusive). A middle asterisk +means all indices from m to n (inclusive). + +Using a wildcard is the same as if the individual columns of the array +had been listed one by one. E.g. these 2 compute reduce/chunk +commands are equivalent, since the "compute +property/chunk"_compute_property_chunk.html command creates a per-atom +array with 3 columns: + +compute prop all property/atom vx vy vz +compute 10 all reduce/chunk mychunk max c_prop\[*\] +compute 10 all reduce/chunk mychunk max c_prop\[1\] c_prop\[2\] c_prop\[3\] :pre + +:line + +Here is an example of using this compute, in conjunction with the +compute chunk/spread/atom command to identify self-assembled micelles. +The commands below can be added to the examples/in.micelle script. + +Imagine a collection of polymer chains or small molecules with +hydrophobic end groups. All the hydrophobic (HP) atoms are assigned +to a group called "phobic". + +These commands will assign a unique cluster ID to all HP atoms within +a specified distance of each other. A cluster will contain all HP +atoms in a single molecule, but also the HP atoms in nearby molecules, +e.g. molecules that have clumped to form a micelle due to the +attraction induced by the hydrophobicity. The output of the +chunk/reduce command will be a cluster ID per chunk (molecule). +Molecules with the same cluster ID are in the same micelle. + +group phobic type 4 # specific to in.micelle model +compute cluster phobic cluster/atom 2.0 +compute cmol all chunk/atom molecule +compute reduce phobic reduce/chunk cmol min c_cluster :pre + +This per-chunk info could be output in at least two ways: + +fix 10 all ave/time 1000 1 1000 c_reduce file tmp.phobic mode vector :pre + +compute spread all chunk/spread/atom cmol c_reduce +dump 1 all custom 1000 tmp.dump id type mol x y z c_cluster c_spread +dump_modify 1 sort id :pre + +In the first case, each snapshot in the tmp.phobic file will contain +one line per molecule. Molecules with the same value are in the same +micelle. In the second case each dump snapshot contains all atoms, +each with a final field with the cluster ID of the micelle that the HP +atoms of that atom's molecule belong to. + +The result from compute chunk/spread/atom can be used to define a new +set of chunks, where all the atoms in all the molecules in the same +micelle are assigned to the same chunk, i.e. one chunk per micelle. + +compute micelle all chunk/atom c_spread compress yes :pre + +Further analysis on a per-micelle basis can now be performed using any +of the per-chunk computes listed on the "Howto chunk"_Howto_chunk.html +doc page. E.g. count the number of atoms in each micelle, calculate +its center or mass, shape (moments of intertia), radius of gyration, +etc. + +compute prop all property/chunk micelle count +fix 20 all ave/time 1000 1 1000 c_prop file tmp.micelle mode vector :pre + +Each snapshot in the tmp.micelle file will have one line per micelle +with its count of atoms, plus a first line for a chunk with all the +solvent atoms. By the time 50000 steps have elapsed there are a +handful of large micelles. + +:line + +[Output info:] + +This compute calculates a global vector if a single input value is +specified, otherwise a global array is output. The number of columns +in the array is the number of inputs provided. The length of the +vector or the number of vector elements or array rows = the number of +chunks {Nchunk} as calculated by the specified "compute +chunk/atom"_compute_chunk_atom.html command. The vector or array can +be accessed by any command that uses global values from a compute as +input. See the "Howto output"_Howto_output.html doc page for an +overview of LAMMPS output options. + +The per-atom values for the vector or each column of the array will be +in whatever "units"_units.html the corresponding input value is in. +The vector or array values are "intensive". + +[Restrictions:] none + +[Related commands:] + +"compute chunk/atom"_compute_chunk_atom.html, "compute +reduce"_compute_reduce.html, "compute +chunk/spread/atom"_compute_chunk_spread_atom.html + +[Default:] none diff --git a/doc/src/compute_rigid_local.txt b/doc/src/compute_rigid_local.txt index 077ad57d81..67c6209bdf 100644 --- a/doc/src/compute_rigid_local.txt +++ b/doc/src/compute_rigid_local.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -49,8 +49,8 @@ Define a computation that simply stores rigid body attributes for rigid bodies defined by the "fix rigid/small"_fix_rigid.html command or one of its NVE, NVT, NPT, NPH variants. The data is stored as local data so it can be accessed by other "output -commands"_Section_howto.html#howto_15 that process local data, such as -the "compute reduce"_compute_reduce.html or "dump local"_dump.html +commands"_Howto_output.html that process local data, such as the +"compute reduce"_compute_reduce.html or "dump local"_dump.html commands. Note that this command only works with the "fix @@ -92,7 +92,7 @@ dump 1 all local 1000 tmp.dump index c_1\[1\] c_1\[2\] c_1\[3\] c_1\[4\] c_1\[5\ This section explains the rigid body attributes that can be specified. -The {id} attribute is the atomID of the atom which owns the rigid body, which is +The {id} attribute is the atom-ID of the atom which owns the rigid body, which is assigned by the "fix rigid/small"_fix_rigid.html command. The {mol} attribute is the molecule ID of the rigid body. It should @@ -154,9 +154,9 @@ array is the number of rigid bodies. If a single keyword is specified, a local vector is produced. If two or more keywords are specified, a local array is produced where the number of columns = the number of keywords. The vector or array can be accessed by any -command that uses local values from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output -options. +command that uses local values from a compute as input. See the +"Howto output"_Howto_output.html doc page for an overview of LAMMPS +output options. The vector or array values will be in whatever "units"_units.html the corresponding attribute is in: @@ -175,8 +175,8 @@ inertiax,inertiay,inertiaz = mass*distance^2 units :ul [Restrictions:] This compute is part of the RIGID package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/compute_saed.txt b/doc/src/compute_saed.txt index 020f72f565..b27c36e318 100644 --- a/doc/src/compute_saed.txt +++ b/doc/src/compute_saed.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -143,18 +143,17 @@ the number of reciprocal lattice nodes that are explored by the mesh. The entries of the global vector are the computed diffraction intensities as described above. -The vector can be accessed by any command that uses global values -from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output -options. +The vector can be accessed by any command that uses global values from +a compute as input. See the "Howto output"_Howto_output.html doc page +for an overview of LAMMPS output options. All array values calculated by this compute are "intensive". [Restrictions:] This compute is part of the USER-DIFFRACTION package. It is only -enabled if LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +enabled if LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. The compute_saed command does not work for triclinic cells. diff --git a/doc/src/compute_slice.txt b/doc/src/compute_slice.txt index e89c05a0f9..51031aeab3 100644 --- a/doc/src/compute_slice.txt +++ b/doc/src/compute_slice.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -58,7 +58,7 @@ page for details. If no bracketed integer is appended, the vector calculated by the compute is used. If a bracketed integer is appended, the Ith column of the array calculated by the compute is used. Users can also write code for their own compute styles and "add -them to LAMMPS"_Section_modify.html. +them to LAMMPS"_Modify.html. If a value begins with "f_", a fix ID must follow which has been previously defined in the input script and which generates a global @@ -69,7 +69,7 @@ the values, else an error results. If no bracketed integer is appended, the vector calculated by the fix is used. If a bracketed integer is appended, the Ith column of the array calculated by the fix is used. Users can also write code for their own fix style and "add -them to LAMMPS"_Section_modify.html. +them to LAMMPS"_Modify.html. If an input value begins with "v_", a variable name must follow which has been previously defined in the input script. Only vector-style @@ -94,8 +94,8 @@ specified or a global array with N columns where N is the number of inputs. The length of the vector or the number of rows in the array is equal to the number of values extracted from each input vector. These values can be used by any command that uses global vector or -array values from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output +array values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. The vector or array values calculated by this compute are simply diff --git a/doc/src/compute_smd_contact_radius.txt b/doc/src/compute_smd_contact_radius.txt index 69fe453343..4ab03e3738 100644 --- a/doc/src/compute_smd_contact_radius.txt +++ b/doc/src/compute_smd_contact_radius.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -35,9 +35,9 @@ specified compute group. [Output info:] -This compute calculates a per-particle vector, which can be accessed by -any command that uses per-particle values from a compute as input. See -"Section 6.15"_Section_howto.html#howto_15 for an overview of +This compute calculates a per-particle vector, which can be accessed +by any command that uses per-particle values from a compute as input. +See the "Howto output"_Howto_output.html doc page for an overview of LAMMPS output options. The per-particle vector values will be in distance "units"_units.html. @@ -45,8 +45,8 @@ The per-particle vector values will be in distance "units"_units.html. [Restrictions:] This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/compute_smd_damage.txt b/doc/src/compute_smd_damage.txt index b6c75a3b20..139fb3ec7b 100644 --- a/doc/src/compute_smd_damage.txt +++ b/doc/src/compute_smd_damage.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -28,18 +28,18 @@ See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to use Smooth Mach Dynamics in [Output Info:] -This compute calculates a per-particle vector, which can be accessed by -any command that uses per-particle values from a compute as input. See -"How-to discussions, section 6.15"_Section_howto.html#howto_15 -for an overview of LAMMPS output options. +This compute calculates a per-particle vector, which can be accessed +by any command that uses per-particle values from a compute as input. +See the "Howto output"_Howto_output.html doc page for an overview of +LAMMPS output options. The per-particle values are dimensionless an in the range of zero to one. [Restrictions:] This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 -section for more info. +LAMMPS was built with that package. See the "Build + [Related commands:] diff --git a/doc/src/compute_smd_hourglass_error.txt b/doc/src/compute_smd_hourglass_error.txt index a15b79e64e..5bc3e3a2de 100644 --- a/doc/src/compute_smd_hourglass_error.txt +++ b/doc/src/compute_smd_hourglass_error.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -37,10 +37,10 @@ Mach Dynamics in LAMMPS. [Output Info:] -This compute calculates a per-particle vector, which can be accessed by -any command that uses per-particle values from a compute as input. See -"How-to discussions, section 6.15"_Section_howto.html#howto_15 -for an overview of LAMMPS output options. +This compute calculates a per-particle vector, which can be accessed +by any command that uses per-particle values from a compute as input. +See the "Howto output"_Howto_output.html doc page for an overview of +LAMMPS output options. The per-particle vector values will are dimensionless. See "units"_units.html. @@ -48,8 +48,8 @@ The per-particle vector values will are dimensionless. See [Restrictions:] This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. This quantity will be computed only for particles which interact with tlsph pair style. diff --git a/doc/src/compute_smd_internal_energy.txt b/doc/src/compute_smd_internal_energy.txt index bc6f9e0f20..b9d18ce933 100644 --- a/doc/src/compute_smd_internal_energy.txt +++ b/doc/src/compute_smd_internal_energy.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -31,18 +31,18 @@ Mach Dynamics in LAMMPS. This compute calculates a per-particle vector, which can be accessed by any command that uses per-particle values from a compute as input. -See "How-to discussions, section 6.15"_Section_howto.html#howto_15 for -an overview of LAMMPS output options. +See the "Howto output"_Howto_output.html doc page for an overview of +LAMMPS output options. The per-particle vector values will be given in "units"_units.html of energy. [Restrictions:] This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. This compute -can only be used for particles which interact via the updated -Lagrangian or total Lagrangian SPH pair styles. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. This compute can +only be used for particles which interact via the updated Lagrangian +or total Lagrangian SPH pair styles. [Related Commands:] diff --git a/doc/src/compute_smd_plastic_strain.txt b/doc/src/compute_smd_plastic_strain.txt index af5b164453..d12be7222a 100644 --- a/doc/src/compute_smd_plastic_strain.txt +++ b/doc/src/compute_smd_plastic_strain.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -32,18 +32,18 @@ Mach Dynamics in LAMMPS. This compute calculates a per-particle vector, which can be accessed by any command that uses per-particle values from a compute as input. -See "How-to discussions, section 6.15"_Section_howto.html#howto_15 for -an overview of LAMMPS output options. +See the "Howto output"_Howto_output.html doc page for an overview of +LAMMPS output options. The per-particle values will be given dimensionless. See "units"_units.html. [Restrictions:] This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. This compute -can only be used for particles which interact via the updated -Lagrangian or total Lagrangian SPH pair styles. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. This compute can +only be used for particles which interact via the updated Lagrangian +or total Lagrangian SPH pair styles. [Related commands:] diff --git a/doc/src/compute_smd_plastic_strain_rate.txt b/doc/src/compute_smd_plastic_strain_rate.txt index ba7b3176db..ffc009b2a7 100644 --- a/doc/src/compute_smd_plastic_strain_rate.txt +++ b/doc/src/compute_smd_plastic_strain_rate.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -32,18 +32,18 @@ Mach Dynamics in LAMMPS. This compute calculates a per-particle vector, which can be accessed by any command that uses per-particle values from a compute as input. -See "How-to discussions, section 6.15"_Section_howto.html#howto_15 for -an overview of LAMMPS output options. +See the "Howto output"_Howto_output.html doc page for an overview of +LAMMPS output options. The per-particle values will be given in "units"_units.html of one over time. [Restrictions:] This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. This compute -can only be used for particles which interact via the updated -Lagrangian or total Lagrangian SPH pair styles. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. This compute can +only be used for particles which interact via the updated Lagrangian +or total Lagrangian SPH pair styles. [Related commands:] diff --git a/doc/src/compute_smd_rho.txt b/doc/src/compute_smd_rho.txt index ae50526725..31d7351c92 100644 --- a/doc/src/compute_smd_rho.txt +++ b/doc/src/compute_smd_rho.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -33,16 +33,16 @@ Mach Dynamics in LAMMPS. This compute calculates a per-particle vector, which can be accessed by any command that uses per-particle values from a compute as input. -See "How-to discussions, section 6.15"_Section_howto.html#howto_15 for -an overview of LAMMPS output options. +See the "Howto output"_Howto_output.html doc page for an overview of +LAMMPS output options. The per-particle values will be in "units"_units.html of mass over volume. [Restrictions:] This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/compute_smd_tlsph_defgrad.txt b/doc/src/compute_smd_tlsph_defgrad.txt index 68b5dffa1c..a733a3d6a7 100644 --- a/doc/src/compute_smd_tlsph_defgrad.txt +++ b/doc/src/compute_smd_tlsph_defgrad.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -32,9 +32,8 @@ Mach Dynamics in LAMMPS. This compute outputss a per-particle vector of vectors (tensors), which can be accessed by any command that uses per-particle values -from a compute as input. See "How-to discussions, section -6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output -options. +from a compute as input. See the "Howto output"_Howto_output.html doc +page for an overview of LAMMPS output options. The per-particle vector values will be given dimensionless. See "units"_units.html. The per-particle vector has 10 entries. The first @@ -45,10 +44,10 @@ entry is the determinant of the deformation gradient. [Restrictions:] This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. TThis -compute can only be used for particles which interact via the total -Lagrangian SPH pair style. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. TThis compute can +only be used for particles which interact via the total Lagrangian SPH +pair style. [Related commands:] diff --git a/doc/src/compute_smd_tlsph_dt.txt b/doc/src/compute_smd_tlsph_dt.txt index 560a9b6fd8..e9ff2e739b 100644 --- a/doc/src/compute_smd_tlsph_dt.txt +++ b/doc/src/compute_smd_tlsph_dt.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -25,7 +25,7 @@ Define a computation that outputs the CFL-stable time increment per particle. This time increment is essentially given by the speed of sound, divided by the SPH smoothing length. Because both the speed of sound and the smoothing length typically change during the course of a -simulation, the stable time increment needs to be recomputed every +simulation, the stable time increment needs to be re-computed every time step. This calculation is performed automatically in the relevant SPH pair styles and this compute only serves to make the stable time increment accessible for output purposes. @@ -37,16 +37,16 @@ Mach Dynamics in LAMMPS. This compute calculates a per-particle vector, which can be accessed by any command that uses per-particle values from a compute as input. -See "How-to discussions, section 6.15"_Section_howto.html#howto_15 for -an overview of LAMMPS output options. +See the "Howto output"_Howto_output.html doc page for an overview of +LAMMPS output options. The per-particle values will be given in "units"_units.html of time. [Restrictions:] This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. This compute can only be used for particles interacting with the Total-Lagrangian SPH pair style. diff --git a/doc/src/compute_smd_tlsph_num_neighs.txt b/doc/src/compute_smd_tlsph_num_neighs.txt index 0420d1903d..db977fe676 100644 --- a/doc/src/compute_smd_tlsph_num_neighs.txt +++ b/doc/src/compute_smd_tlsph_num_neighs.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -32,16 +32,16 @@ Mach Dynamics in LAMMPS. This compute calculates a per-particle vector, which can be accessed by any command that uses per-particle values from a compute as input. -See "How-to discussions, section 6.15"_Section_howto.html#howto_15 for -an overview of LAMMPS output options. +See the "Howto output"_Howto_output.html doc page for an overview of +LAMMPS output options. The per-particle values are dimensionless. See "units"_units.html. [Restrictions:] This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. This quantity will be computed only for particles which interact with the Total-Lagrangian pair style. diff --git a/doc/src/compute_smd_tlsph_shape.txt b/doc/src/compute_smd_tlsph_shape.txt index 02bd0c50dd..9c17194ec1 100644 --- a/doc/src/compute_smd_tlsph_shape.txt +++ b/doc/src/compute_smd_tlsph_shape.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -33,9 +33,8 @@ Mach Dynamics in LAMMPS. This compute calculates a per-particle vector of vectors, which can be accessed by any command that uses per-particle values from a compute -as input. See "How-to discussions, section -6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output -options. +as input. See the "Howto output"_Howto_output.html doc page for an +overview of LAMMPS output options. The per-particle vector has 7 entries. The first three entries correspond to the lengths of the ellipsoid's axes and have units of @@ -48,8 +47,8 @@ particle relative to its initial state. [Restrictions:] This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. This quantity will be computed only for particles which interact with the Total-Lagrangian SPH pair style. diff --git a/doc/src/compute_smd_tlsph_strain.txt b/doc/src/compute_smd_tlsph_strain.txt index f25d1b77db..70f996e206 100644 --- a/doc/src/compute_smd_tlsph_strain.txt +++ b/doc/src/compute_smd_tlsph_strain.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -31,9 +31,8 @@ Mach Dynamics in LAMMPS. This compute calculates a per-particle vector of vectors (tensors), which can be accessed by any command that uses per-particle values -from a compute as input. See "How-to discussions, section -6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output -options. +from a compute as input. See the "Howto output"_Howto_output.html doc +page for an overview of LAMMPS output options. The per-particle tensor values will be given dimensionless. See "units"_units.html. @@ -44,8 +43,8 @@ zz, xy, xz, yz components of the symmetric strain tensor. [Restrictions:] This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. This quantity will be computed only for particles which interact with the Total-Lagrangian SPH pair style. diff --git a/doc/src/compute_smd_tlsph_strain_rate.txt b/doc/src/compute_smd_tlsph_strain_rate.txt index 13ca57ac4d..e6d968c523 100644 --- a/doc/src/compute_smd_tlsph_strain_rate.txt +++ b/doc/src/compute_smd_tlsph_strain_rate.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -31,9 +31,8 @@ Mach Dynamics in LAMMPS. This compute calculates a per-particle vector of vectors (tensors), which can be accessed by any command that uses per-particle values -from a compute as input. See "How-to discussions, section -6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output -options. +from a compute as input. See the "Howto output"_Howto_output.html doc +page for an overview of LAMMPS output options. The values will be given in "units"_units.html of one over time. @@ -43,8 +42,8 @@ zz, xy, xz, yz components of the symmetric strain rate tensor. [Restrictions:] This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. This quantity will be computed only for particles which interact with Total-Lagrangian SPH pair style. diff --git a/doc/src/compute_smd_tlsph_stress.txt b/doc/src/compute_smd_tlsph_stress.txt index 5d707d4c2f..8340e88536 100644 --- a/doc/src/compute_smd_tlsph_stress.txt +++ b/doc/src/compute_smd_tlsph_stress.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -29,11 +29,10 @@ Mach Dynamics in LAMMPS. [Output info:] -This compute calculates a per-particle vector of vectors (tensors), which can be -accessed by any command that uses per-particle values from a compute -as input. See -"How-to discussions, section 6.15"_Section_howto.html#howto_15 -for an overview of LAMMPS output options. +This compute calculates a per-particle vector of vectors (tensors), +which can be accessed by any command that uses per-particle values +from a compute as input. See the "Howto output"_Howto_output.html doc +page for an overview of LAMMPS output options. The values will be given in "units"_units.html of pressure. @@ -45,8 +44,8 @@ invariant of the stress tensor, i.e., the von Mises equivalent stress. [Restrictions:] This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. This quantity will be computed only for particles which interact with the Total-Lagrangian SPH pair style. diff --git a/doc/src/compute_smd_triangle_mesh_vertices.txt b/doc/src/compute_smd_triangle_mesh_vertices.txt index 5b0f0afc4c..cd1f8fdd9b 100644 --- a/doc/src/compute_smd_triangle_mesh_vertices.txt +++ b/doc/src/compute_smd_triangle_mesh_vertices.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -31,9 +31,9 @@ Mach Dynamics in LAMMPS. [Output info:] This compute returns a per-particle vector of vectors, which can be -accessed by any command that uses per-particle values from a compute as -input. See "How-to discussions, section 6.15"_Section_howto.html#howto_15 -for an overview of LAMMPS output options. +accessed by any command that uses per-particle values from a compute +as input. See the "Howto output"_Howto_output.html doc page for an +overview of LAMMPS output options. The per-particle vector has nine entries, (x1/y1/z1), (x2/y2/z2), and (x3/y3/z3) corresponding to the first, second, and third vertex of @@ -51,8 +51,8 @@ The values will be given in "units"_units.html of distance. [Restrictions:] This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/compute_smd_ulsph_num_neighs.txt b/doc/src/compute_smd_ulsph_num_neighs.txt index adece93343..5157f17e57 100644 --- a/doc/src/compute_smd_ulsph_num_neighs.txt +++ b/doc/src/compute_smd_ulsph_num_neighs.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -32,7 +32,7 @@ Mach Dynamics in LAMMPS. This compute returns a per-particle vector, which can be accessed by any command that uses per-particle values from a compute as input. -See "Section 6.15"_Section_howto.html#howto_15 for an overview of +See the "Howto output"_Howto_output.html doc page for an overview of LAMMPS output options. The per-particle values will be given dimensionless, see "units"_units.html. @@ -40,10 +40,10 @@ The per-particle values will be given dimensionless, see "units"_units.html. [Restrictions:] This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_2 section for more info. This compute -can only be used for particles which interact with the updated -Lagrangian SPH pair style. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. This compute can +only be used for particles which interact with the updated Lagrangian +SPH pair style. [Related commands:] diff --git a/doc/src/compute_smd_ulsph_strain.txt b/doc/src/compute_smd_ulsph_strain.txt index b7d425b12b..3dc6bd5249 100644 --- a/doc/src/compute_smd_ulsph_strain.txt +++ b/doc/src/compute_smd_ulsph_strain.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -31,7 +31,7 @@ Mach Dynamics in LAMMPS. This compute calculates a per-particle tensor, which can be accessed by any command that uses per-particle values from a compute as input. -See "Section 6.15"_Section_howto.html#howto_15 for an overview of +See the "Howto output"_Howto_output.html doc page for an overview of LAMMPS output options. The per-particle vector has 6 entries, corresponding to the xx, yy, @@ -43,10 +43,10 @@ The per-particle tensor values will be given dimensionless, see [Restrictions:] This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. This compute -can only be used for particles which interact with the updated -Lagrangian SPH pair style. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. This compute can +only be used for particles which interact with the updated Lagrangian +SPH pair style. [Related commands:] diff --git a/doc/src/compute_smd_ulsph_strain_rate.txt b/doc/src/compute_smd_ulsph_strain_rate.txt index e2c349c265..1ade5ac2d5 100644 --- a/doc/src/compute_smd_ulsph_strain_rate.txt +++ b/doc/src/compute_smd_ulsph_strain_rate.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -32,9 +32,8 @@ Mach Dynamics in LAMMPS. This compute calculates a per-particle vector of vectors (tensors), which can be accessed by any command that uses per-particle values -from a compute as input. See "Section -6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output -options. +from a compute as input. See the "Howto output"_Howto_output.html doc +page for an overview of LAMMPS output options. The values will be given in "units"_units.html of one over time. @@ -44,10 +43,11 @@ zz, xy, xz, yz components of the symmetric strain rate tensor. [Restrictions:] This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_2 section for more info. This compute -can only be used for particles which interact with the updated -Lagrangian SPH pair style. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. + +This compute can only be used for particles which interact with the +updated Lagrangian SPH pair style. [Related commands:] diff --git a/doc/src/compute_smd_ulsph_stress.txt b/doc/src/compute_smd_ulsph_stress.txt index 47f903d3b8..ff53e777c5 100644 --- a/doc/src/compute_smd_ulsph_stress.txt +++ b/doc/src/compute_smd_ulsph_stress.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -30,9 +30,8 @@ Mach Dynamics in LAMMPS. This compute calculates a per-particle vector of vectors (tensors), which can be accessed by any command that uses per-particle values -from a compute as input. See "Section -6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output -options. +from a compute as input. See the "Howto output"_Howto_output.html doc +page for an overview of LAMMPS output options. The values will be given in "units"_units.html of pressure. @@ -44,10 +43,10 @@ stress tensor, i.e., the von Mises equivalent stress. [Restrictions:] This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. This compute -can only be used for particles which interact with the updated -Lagrangian SPH pair style. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. This compute can +only be used for particles which interact with the updated Lagrangian +SPH pair style. [Related commands:] diff --git a/doc/src/compute_smd_vol.txt b/doc/src/compute_smd_vol.txt index fc736a5bf5..0edd61f624 100644 --- a/doc/src/compute_smd_vol.txt +++ b/doc/src/compute_smd_vol.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -31,8 +31,8 @@ Mach Dynamics in LAMMPS. This compute calculates a per-particle vector, which can be accessed by any command that uses per-particle values from a compute as input. -See "How-to discussions, section 6.15"_Section_howto.html#howto_15 for -an overview of LAMMPS output options. +See the "Howto output"_Howto_output.html doc page for an overview of +LAMMPS output options. The per-particle vector values will be given in "units"_units.html of volume. @@ -43,8 +43,8 @@ per-particle volumes of the group for which the fix is defined. [Restrictions:] This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/compute_sna_atom.txt b/doc/src/compute_sna_atom.txt index 268e23ac28..95d183937f 100644 --- a/doc/src/compute_sna_atom.txt +++ b/doc/src/compute_sna_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -244,15 +244,14 @@ So the nesting order from inside to outside is bispectrum component, linear then quadratic, vector/tensor component, type. These values can be accessed by any command that uses per-atom values -from a compute as input. See "Section -6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output -options. +from a compute as input. See the "Howto output"_Howto_output.html doc +page for an overview of LAMMPS output options. [Restrictions:] These computes are part of the SNAP package. They are only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/compute_spin.txt b/doc/src/compute_spin.txt new file mode 100644 index 0000000000..e6185a2dd8 --- /dev/null +++ b/doc/src/compute_spin.txt @@ -0,0 +1,78 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +compute spin command :h3 + +[Syntax:] + +compute ID group-ID compute/spin :pre + +ID, group-ID are documented in "compute"_compute.html command +compute/spin = style name of this compute command :ul + +[Examples:] + +compute out_mag all compute/spin :pre + +[Description:] + +Define a computation that calculates magnetic quantities for a system +of atoms having spins. + +This compute calculates 6 magnetic quantities. + +The three first quantities are the x,y and z coordinates of the total magnetization. + +The fourth quantity is the norm of the total magnetization. + +The fifth quantity is the magnetic energy. + +The sixth one is referred to as the spin temperature, according +to the work of "(Nurdin)"_#Nurdin1. + +The simplest way to output the results of the compute spin calculation +is to define some of the quantities as variables, and to use the thermo and +thermo_style commands, for example: + +compute out_mag all compute/spin :pre + +variable mag_z equal c_out_mag\[3\] +variable mag_norm equal c_out_mag\[4\] +variable temp_mag equal c_out_mag\[6\] :pre + +thermo 10 +thermo_style custom step v_mag_z v_mag_norm v_temp_mag :pre + +This series of commands evaluates the total magnetization along z, the norm of +the total magnetization, and the magnetic temperature. Three variables are +assigned to those quantities. The thermo and thermo_style commands print them +every 10 timesteps. + + +[Output info:] + +The array values are "intensive". The array values will be in +metal units ("units"_units.html). + +[Restrictions:] + +The {spin} compute is part of the SPIN package. This compute is only +enabled if LAMMPS was built with this package. See the "Build +package"_Build_package.html doc page for more info. The atom_style +has to be "spin" for this compute to be valid. + +[Related commands:] none + + +[Default:] none + +:line + +:link(Nurdin1) +[(Nurdin)] Nurdin and Schotte Phys Rev E, 61(4), 3579 (2000) + diff --git a/doc/src/compute_stress_atom.txt b/doc/src/compute_stress_atom.txt index 83b1df68e3..222513da61 100644 --- a/doc/src/compute_stress_atom.txt +++ b/doc/src/compute_stress_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -142,9 +142,8 @@ global system pressure. This compute calculates a per-atom array with 6 columns, which can be accessed by indices 1-6 by any command that uses per-atom values from -a compute as input. See "Section -6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output -options. +a compute as input. See the "Howto output"_Howto_output.html doc page +for an overview of LAMMPS output options. The per-atom array values will be in pressure*volume "units"_units.html as discussed above. diff --git a/doc/src/compute_tally.txt b/doc/src/compute_tally.txt index 95ef4a553b..a4a8441f9e 100644 --- a/doc/src/compute_tally.txt +++ b/doc/src/compute_tally.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -76,9 +76,9 @@ Both the scalar and vector values calculated by this compute are [Restrictions:] -This compute is part of the USER-TALLY package. It is only enabled -if LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +This compute is part of the USER-TALLY package. It is only enabled if +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. Not all pair styles can be evaluated in a pairwise mode as required by this compute. For example, 3-body and other many-body potentials, diff --git a/doc/src/compute_tdpd_cc_atom.txt b/doc/src/compute_tdpd_cc_atom.txt index a6a12dc52c..a385bef10b 100644 --- a/doc/src/compute_tdpd_cc_atom.txt +++ b/doc/src/compute_tdpd_cc_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -33,9 +33,9 @@ details see "(Li2015)"_#Li2015a. [Output info:] This compute calculates a per-atom vector, which can be accessed by -any command that uses per-atom values from a compute as input. See -"Section 6.15"_Section_howto.html#howto_15 for an overview of -LAMMPS output options. +any command that uses per-atom values from a compute as input. See the +"Howto output"_Howto_output.html doc page for an overview of LAMMPS +output options. The per-atom vector values will be in the units of chemical species per unit mass. @@ -43,8 +43,8 @@ per unit mass. [Restrictions:] This compute is part of the USER-MESO package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/compute_temp.txt b/doc/src/compute_temp.txt index b88be79e20..757e00c4d2 100644 --- a/doc/src/compute_temp.txt +++ b/doc/src/compute_temp.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -58,8 +58,8 @@ compute thermo_temp all temp :pre See the "thermo_style" command for more details. -See "this howto section"_Section_howto.html#howto_16 of the manual for -a discussion of different ways to compute temperature and perform +See the "Howto thermostat"_Howto_thermostat.html doc page for a +discussion of different ways to compute temperature and perform thermostatting. :line @@ -67,23 +67,22 @@ thermostatting. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line @@ -92,8 +91,8 @@ more instructions on how to use the accelerated styles effectively. This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. These values can be used by any command that uses global scalar or -vector values from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output +vector values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The diff --git a/doc/src/compute_temp_asphere.txt b/doc/src/compute_temp_asphere.txt index 495366b345..eb73891e82 100644 --- a/doc/src/compute_temp_asphere.txt +++ b/doc/src/compute_temp_asphere.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -93,8 +93,8 @@ computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the {extra} option of the "compute_modify"_compute_modify.html command. -See "this howto section"_Section_howto.html#howto_16 of the manual for -a discussion of different ways to compute temperature and perform +See the "Howto thermostat"_Howto_thermostat.html doc page for a +discussion of different ways to compute temperature and perform thermostatting. :line @@ -122,8 +122,8 @@ rotational degrees of freedom. This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. These values can be used by any command that uses global scalar or -vector values from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output +vector values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The @@ -135,8 +135,8 @@ vector values will be in energy "units"_units.html. [Restrictions:] This compute is part of the ASPHERE package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. This compute requires that atoms store angular momentum and a quaternion as defined by the "atom_style ellipsoid"_atom_style.html diff --git a/doc/src/compute_temp_body.txt b/doc/src/compute_temp_body.txt index f72b886cc4..341d6d7f79 100644 --- a/doc/src/compute_temp_body.txt +++ b/doc/src/compute_temp_body.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -75,8 +75,8 @@ computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the {extra} option of the "compute_modify"_compute_modify.html command. -See "this howto section"_Section_howto.html#howto_16 of the manual for -a discussion of different ways to compute temperature and perform +See the "Howto thermostat"_Howto_thermostat.html doc page for a +discussion of different ways to compute temperature and perform thermostatting. :line @@ -104,8 +104,8 @@ rotational degrees of freedom. This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. These values can be used by any command that uses global scalar or -vector values from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output +vector values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The @@ -117,8 +117,8 @@ vector values will be in energy "units"_units.html. [Restrictions:] This compute is part of the BODY package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. This compute requires that atoms store angular momentum and a quaternion as defined by the "atom_style body"_atom_style.html diff --git a/doc/src/compute_temp_chunk.txt b/doc/src/compute_temp_chunk.txt index f877f6ece8..de8c850a70 100644 --- a/doc/src/compute_temp_chunk.txt +++ b/doc/src/compute_temp_chunk.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -52,10 +52,9 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom to a single chunk (or no chunk). The ID for this command is specified as chunkID. For example, a single chunk could be the atoms in a molecule or atoms in a spatial bin. See the "compute -chunk/atom"_compute_chunk_atom.html doc page and "Section -6.23"_Section_howto.html#howto_23 for details of how chunks can be -defined and examples of how they can be used to measure properties of -a system. +chunk/atom"_compute_chunk_atom.html and "Howto chunk"_Howto_chunk.html +doc pages for details of how chunks can be defined and examples of how +they can be used to measure properties of a system. The temperature is calculated by the formula KE = DOF/2 k T, where KE = total kinetic energy of all atoms assigned to chunks (sum of 1/2 m @@ -200,8 +199,8 @@ molecule. This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. These values can be used by any command that uses global scalar or -vector values from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output +vector values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. This compute also optionally calculates a global array, if one or more @@ -210,9 +209,8 @@ of the optional values are specified. The number of rows in the array "compute chunk/atom"_compute_chunk_atom.html command. The number of columns is the number of specified values (1 or more). These values can be accessed by any command that uses global array values from a -compute as input. Again, see "Section -6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output -options. +compute as input. Again, see the "Howto output"_Howto_output.html doc +page for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The vector values are "extensive". The array values are "intensive". diff --git a/doc/src/compute_temp_com.txt b/doc/src/compute_temp_com.txt index c7cc5ec4e2..12df694e38 100644 --- a/doc/src/compute_temp_com.txt +++ b/doc/src/compute_temp_com.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -65,8 +65,8 @@ atoms that include these constraints will be computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the {extra} option of the "compute_modify"_compute_modify.html command. -See "this howto section"_Section_howto.html#howto_16 of the manual for -a discussion of different ways to compute temperature and perform +See the "Howto thermostat"_Howto_thermostat.html doc page for a +discussion of different ways to compute temperature and perform thermostatting. [Output info:] @@ -74,8 +74,8 @@ thermostatting. This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. These values can be used by any command that uses global scalar or -vector values from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output +vector values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The diff --git a/doc/src/compute_temp_cs.txt b/doc/src/compute_temp_cs.txt index 561b787df6..0236319f54 100644 --- a/doc/src/compute_temp_cs.txt +++ b/doc/src/compute_temp_cs.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -28,9 +28,9 @@ Define a computation that calculates the temperature of a system based on the center-of-mass velocity of atom pairs that are bonded to each other. This compute is designed to be used with the adiabatic core/shell model of "(Mitchell and Finchham)"_#MitchellFinchham1. See -"Section 6.25"_Section_howto.html#howto_25 of the manual for an -overview of the model as implemented in LAMMPS. Specifically, this -compute enables correct temperature calculation and thermostatting of +the "Howto coreshell"_Howto_coreshell.html doc page for an overview of +the model as implemented in LAMMPS. Specifically, this compute +enables correct temperature calculation and thermostatting of core/shell pairs where it is desirable for the internal degrees of freedom of the core/shell pairs to not be influenced by a thermostat. A compute of this style can be used by any command that computes a @@ -83,8 +83,9 @@ langevin"_fix_langevin.html. The internal energy of core/shell pairs can be calculated by the "compute temp/chunk"_compute_temp_chunk.html command, if chunks are -defined as core/shell pairs. See "Section -6.25"_Section_howto.html#howto_25 for more discussion on how to do this. +defined as core/shell pairs. See the "Howto +coreshell"_Howto_coreshell.html doc page doc page for more discussion +on how to do this. [Output info:] diff --git a/doc/src/compute_temp_deform.txt b/doc/src/compute_temp_deform.txt index 168b0b3880..26d322589e 100644 --- a/doc/src/compute_temp_deform.txt +++ b/doc/src/compute_temp_deform.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -104,8 +104,8 @@ atoms that include these constraints will be computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the {extra} option of the "compute_modify"_compute_modify.html command. -See "this howto section"_Section_howto.html#howto_16 of the manual for -a discussion of different ways to compute temperature and perform +See the "Howto thermostat"_Howto_thermostat.html doc page for a +discussion of different ways to compute temperature and perform thermostatting. [Output info:] @@ -113,8 +113,8 @@ thermostatting. This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. These values can be used by any command that uses global scalar or -vector values from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output +vector values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The diff --git a/doc/src/compute_temp_deform_eff.txt b/doc/src/compute_temp_deform_eff.txt index d09a0ace2f..4af61dc918 100644 --- a/doc/src/compute_temp_deform_eff.txt +++ b/doc/src/compute_temp_deform_eff.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -48,8 +48,8 @@ component of the electrons is not affected. This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. These values can be used by any command that uses global scalar or -vector values from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output +vector values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The @@ -61,8 +61,8 @@ vector values will be in energy "units"_units.html. [Restrictions:] This compute is part of the USER-EFF package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/compute_temp_drude.txt b/doc/src/compute_temp_drude.txt index 169b8d5880..20d9a5c056 100644 --- a/doc/src/compute_temp_drude.txt +++ b/doc/src/compute_temp_drude.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -22,10 +22,10 @@ compute TDRUDE all temp/drude :pre [Description:] Define a computation that calculates the temperatures of core-Drude -pairs. This compute is designed to be used with the -"thermalized Drude oscillator model"_tutorial_drude.html. Polarizable -models in LAMMPS are described in "this -Section"_Section_howto.html#howto_25. +pairs. This compute is designed to be used with the "thermalized Drude +oscillator model"_Howto_drude.html. Polarizable models in LAMMPS +are described on the "Howto polarizable"_Howto_polarizable.html doc +page. Drude oscillators consist of a core particle and a Drude particle connected by a harmonic bond, and the relative motion of these Drude @@ -57,8 +57,8 @@ kinetic energy of the centers of mass (energy units) kinetic energy of the dipoles (energy units) :ol These values can be used by any command that uses global scalar or -vector values from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output +vector values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. Both the scalar value and the first two values of the vector diff --git a/doc/src/compute_temp_eff.txt b/doc/src/compute_temp_eff.txt index 409319edcb..415cb77595 100644 --- a/doc/src/compute_temp_eff.txt +++ b/doc/src/compute_temp_eff.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -69,8 +69,8 @@ atoms that include these constraints will be computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the {extra} option of the "compute_modify"_compute_modify.html command. -See "this howto section"_Section_howto.html#howto_16 of the manual for -a discussion of different ways to compute temperature and perform +See the "Howto thermostat"_Howto_thermostat.html doc page for a +discussion of different ways to compute temperature and perform thermostatting. [Output info:] @@ -83,8 +83,8 @@ the simulation. [Restrictions:] This compute is part of the USER-EFF package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/compute_temp_partial.txt b/doc/src/compute_temp_partial.txt index fe2420b4e4..14294842a1 100644 --- a/doc/src/compute_temp_partial.txt +++ b/doc/src/compute_temp_partial.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -65,8 +65,8 @@ atoms that include these constraints will be computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the {extra} option of the "compute_modify"_compute_modify.html command. -See "this howto section"_Section_howto.html#howto_16 of the manual for -a discussion of different ways to compute temperature and perform +See the "Howto thermostat"_Howto_thermostat.html doc page for a +discussion of different ways to compute temperature and perform thermostatting. :line @@ -74,23 +74,22 @@ thermostatting. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line @@ -99,8 +98,8 @@ more instructions on how to use the accelerated styles effectively. This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. These values can be used by any command that uses global scalar or -vector values from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output +vector values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The diff --git a/doc/src/compute_temp_profile.txt b/doc/src/compute_temp_profile.txt index 64a6abd283..4ed04ca67e 100644 --- a/doc/src/compute_temp_profile.txt +++ b/doc/src/compute_temp_profile.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -122,8 +122,8 @@ degrees-of-freedom adjustment described in the preceding paragraph, for fixes that constrain molecular motion. It does include the adjustment due to the {extra} option, which is applied to each bin. -See "this howto section"_Section_howto.html#howto_16 of the manual for -a discussion of different ways to compute temperature and perform +See the "Howto thermostat"_Howto_thermostat.html doc page for a +discussion of different ways to compute temperature and perform thermostatting. Using this compute in conjunction with a thermostatting fix, as explained there, will effectively implement a profile-unbiased thermostat (PUT), as described in "(Evans)"_#Evans1. @@ -145,8 +145,8 @@ indices ix,iy,iz = 2,3,4 would map to row M = (iz-1)*10*10 + (iy-1)*10 indices are numbered from 1 to 10 in each dimension. These values can be used by any command that uses global scalar or -vector or array values from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output +vector or array values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The diff --git a/doc/src/compute_temp_ramp.txt b/doc/src/compute_temp_ramp.txt index bc9283469c..15cad9c0cb 100644 --- a/doc/src/compute_temp_ramp.txt +++ b/doc/src/compute_temp_ramp.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -83,8 +83,8 @@ atoms that include these constraints will be computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the {extra} option of the "compute_modify"_compute_modify.html command. -See "this howto section"_Section_howto.html#howto_16 of the manual for -a discussion of different ways to compute temperature and perform +See the "Howto thermostat"_Howto_thermostat.html doc page for a +discussion of different ways to compute temperature and perform thermostatting. [Output info:] @@ -92,8 +92,8 @@ thermostatting. This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. These values can be used by any command that uses global scalar or -vector values from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output +vector values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The diff --git a/doc/src/compute_temp_region.txt b/doc/src/compute_temp_region.txt index 3e4a80db8d..f23901af98 100644 --- a/doc/src/compute_temp_region.txt +++ b/doc/src/compute_temp_region.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -81,8 +81,8 @@ If needed the number of subtracted degrees-of-freedom can be set explicitly using the {extra} option of the "compute_modify"_compute_modify.html command. -See "this howto section"_Section_howto.html#howto_16 of the manual for -a discussion of different ways to compute temperature and perform +See the "Howto thermostat"_Howto_thermostat.html doc page for a +discussion of different ways to compute temperature and perform thermostatting. [Output info:] @@ -90,8 +90,8 @@ thermostatting. This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. These values can be used by any command that uses global scalar or -vector values from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output +vector values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The diff --git a/doc/src/compute_temp_region_eff.txt b/doc/src/compute_temp_region_eff.txt index 8baf2dd46c..f15f3155b0 100644 --- a/doc/src/compute_temp_region_eff.txt +++ b/doc/src/compute_temp_region_eff.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -39,8 +39,8 @@ temp/eff"_compute_temp_eff.html command. This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. These values can be used by any command that uses global scalar or -vector values from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output +vector values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The @@ -52,8 +52,8 @@ vector values will be in energy "units"_units.html. [Restrictions:] This compute is part of the USER-EFF package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/compute_temp_rotate.txt b/doc/src/compute_temp_rotate.txt index 34feca7b6f..8dac0405b4 100644 --- a/doc/src/compute_temp_rotate.txt +++ b/doc/src/compute_temp_rotate.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -64,8 +64,8 @@ atoms that include these constraints will be computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the {extra} option of the "compute_modify"_compute_modify.html command. -See "this howto section"_Section_howto.html#howto_16 of the manual for -a discussion of different ways to compute temperature and perform +See the "Howto thermostat"_Howto_thermostat.html doc page for a +discussion of different ways to compute temperature and perform thermostatting. [Output info:] @@ -73,8 +73,8 @@ thermostatting. This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. These values can be used by any command that uses global scalar or -vector values from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output +vector values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The @@ -86,8 +86,8 @@ vector values will be in energy "units"_units.html. [Restrictions:] This compute is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/compute_temp_sphere.txt b/doc/src/compute_temp_sphere.txt index 9e9dff2cb6..5a55126d12 100644 --- a/doc/src/compute_temp_sphere.txt +++ b/doc/src/compute_temp_sphere.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -79,8 +79,8 @@ computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the {extra} option of the "compute_modify"_compute_modify.html command. -See "this howto section"_Section_howto.html#howto_16 of the manual for -a discussion of different ways to compute temperature and perform +See the "Howto thermostat"_Howto_thermostat.html doc page for a +discussion of different ways to compute temperature and perform thermostatting. :line @@ -108,8 +108,8 @@ rotational degrees of freedom. This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. These values can be used by any command that uses global scalar or -vector values from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output +vector values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The diff --git a/doc/src/compute_temp_uef.txt b/doc/src/compute_temp_uef.txt index acd3a6218d..97e1d6e1ae 100644 --- a/doc/src/compute_temp_uef.txt +++ b/doc/src/compute_temp_uef.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -24,8 +24,8 @@ compute 2 sel temp/uef :pre This command is used to compute the kinetic energy tensor in the reference frame of the applied flow field when -"fix nvt/uef"_fix_nh_uef.html" or -"fix npt/uef"_fix_nh_uef.html" is used. +"fix nvt/uef"_fix_nh_uef.html or +"fix npt/uef"_fix_nh_uef.html is used. It is not necessary to use this command to compute the scalar value of the temperature. A "compute temp"_compute_temp.html may be used for that purpose. @@ -35,9 +35,9 @@ documentation for "compute temp"_compute_temp.html. [Restrictions:] -This fix is part of the USER-UEF package. It is only enabled if -LAMMPS was built with that package. See the -"Making LAMMPS"_Section_start.html#start_3 section for more info. +This fix is part of the USER-UEF package. It is only enabled if LAMMPS +was built with that package. See the "Build +package"_Build_package.html doc page for more info. This command can only be used when "fix nvt/uef"_fix_nh_uef.html or "fix npt/uef"_fix_nh_uef.html is active. diff --git a/doc/src/compute_ti.txt b/doc/src/compute_ti.txt index 733954d146..9057cab476 100644 --- a/doc/src/compute_ti.txt +++ b/doc/src/compute_ti.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -111,9 +111,8 @@ du/dl can be found in the paper by "Eike"_#Eike. This compute calculates a global scalar, namely dUs/dlambda. This value can be used by any command that uses a global scalar value from -a compute as input. See "Section -6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output -options. +a compute as input. See the "Howto output"_Howto_output.html doc page +for an overview of LAMMPS output options. The scalar value calculated by this compute is "extensive". @@ -122,8 +121,8 @@ The scalar value will be in energy "units"_units.html. [Restrictions:] This compute is part of the MISC package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/compute_torque_chunk.txt b/doc/src/compute_torque_chunk.txt index b9f832dd03..6484076b37 100644 --- a/doc/src/compute_torque_chunk.txt +++ b/doc/src/compute_torque_chunk.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -30,10 +30,9 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom to a single chunk (or no chunk). The ID for this command is specified as chunkID. For example, a single chunk could be the atoms in a molecule or atoms in a spatial bin. See the "compute -chunk/atom"_compute_chunk_atom.html doc page and "Section -6.23"_Section_howto.html#howto_23 for details of how chunks can be -defined and examples of how they can be used to measure properties of -a system. +chunk/atom"_compute_chunk_atom.html and "Howto chunk"_Howto_chunk.html +doc pages for details of how chunks can be defined and examples of how +they can be used to measure properties of a system. This compute calculates the 3 components of the torque vector for eqch chunk, due to the forces on the individual atoms in the chunk around @@ -72,7 +71,7 @@ number of chunks {Nchunk} as calculated by the specified "compute chunk/atom"_compute_chunk_atom.html command. The number of columns = 3 for the 3 xyz components of the torque for each chunk. These values can be accessed by any command that uses global array values from a -compute as input. See "Section 6.15"_Section_howto.html#howto_15 +compute as input. See the "Howto output"_Howto_output.html doc page for an overview of LAMMPS output options. The array values are "intensive". The array values will be in diff --git a/doc/src/compute_vacf.txt b/doc/src/compute_vacf.txt index a0d9a3c5f7..70f1e99490 100644 --- a/doc/src/compute_vacf.txt +++ b/doc/src/compute_vacf.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -55,9 +55,8 @@ correctly with time=0 atom velocities from the restart file. This compute calculates a global vector of length 4, which can be accessed by indices 1-4 by any command that uses global vector values -from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output -options. +from a compute as input. See the "Howto output"_Howto_output.html doc +page for an overview of LAMMPS output options. The vector values are "intensive". The vector values will be in velocity^2 "units"_units.html. diff --git a/doc/src/compute_vcm_chunk.txt b/doc/src/compute_vcm_chunk.txt index de02c586bf..7e8ad71208 100644 --- a/doc/src/compute_vcm_chunk.txt +++ b/doc/src/compute_vcm_chunk.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -30,10 +30,9 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom to a single chunk (or no chunk). The ID for this command is specified as chunkID. For example, a single chunk could be the atoms in a molecule or atoms in a spatial bin. See the "compute -chunk/atom"_compute_chunk_atom.html doc page and "Section -6.23"_Section_howto.html#howto_23 for details of how chunks can be -defined and examples of how they can be used to measure properties of -a system. +chunk/atom"_compute_chunk_atom.html and "Howto chunk"_Howto_chunk.html +doc pages for details of how chunks can be defined and examples of how +they can be used to measure properties of a system. This compute calculates the x,y,z components of the center-of-mass velocity for each chunk. This is done by summing mass*velocity for @@ -63,8 +62,8 @@ number of chunks {Nchunk} as calculated by the specified "compute chunk/atom"_compute_chunk_atom.html command. The number of columns = 3 for the x,y,z center-of-mass velocity coordinates of each chunk. These values can be accessed by any command that uses global array -values from a compute as input. See "Section -6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output +values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. The array values are "intensive". The array values will be in diff --git a/doc/src/compute_voronoi_atom.txt b/doc/src/compute_voronoi_atom.txt index a280b2b151..d01f4df712 100644 --- a/doc/src/compute_voronoi_atom.txt +++ b/doc/src/compute_voronoi_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -122,18 +122,16 @@ to locate vacancies (the coordinates are given by the atom coordinates at the time step when the compute was first invoked), while column two data can be used to identify interstitial atoms. -If the {neighbors} value is set to yes, then -this compute creates a local array with 3 columns. There -is one row for each face of each Voronoi cell. The -3 columns are the atom ID of the atom that owns the cell, -the atom ID of the atom in the neighboring cell -(or zero if the face is external), and the area of the face. -The array can be accessed by any command that -uses local values from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output -options. More specifically, the array can be accessed by a -"dump local"_dump.html command to write a file containing -all the Voronoi neighbors in a system: +If the {neighbors} value is set to yes, then this compute creates a +local array with 3 columns. There is one row for each face of each +Voronoi cell. The 3 columns are the atom ID of the atom that owns the +cell, the atom ID of the atom in the neighboring cell (or zero if the +face is external), and the area of the face. The array can be +accessed by any command that uses local values from a compute as +input. See the "Howto output"_Howto_output.html doc page for an +overview of LAMMPS output options. More specifically, the array can be +accessed by a "dump local"_dump.html command to write a file +containing all the Voronoi neighbors in a system: compute 6 all voronoi/atom neighbors yes dump d2 all local 1 dump.neighbors index c_6\[1\] c_6\[2\] c_6\[3\] :pre @@ -186,8 +184,8 @@ columns. In regular dynamic tessellation mode the first column is the Voronoi volume, the second is the neighbor count, as described above (read above for the output data in case the {occupation} keyword is specified). These values can be accessed by any command that uses -per-atom values from a compute as input. See "Section -6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output +per-atom values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. If the {peratom} keyword is set to "no", the per-atom array is still created, but it is not accessible. @@ -214,8 +212,8 @@ The Voronoi face area will be in distance "units"_units.html squared. [Restrictions:] This compute is part of the VORONOI package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. It also requires you have a copy of the Voro++ library built and installed on your system. See instructions on obtaining and diff --git a/doc/src/compute_xrd.txt b/doc/src/compute_xrd.txt index 1a151d63f9..41523f25af 100644 --- a/doc/src/compute_xrd.txt +++ b/doc/src/compute_xrd.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -162,7 +162,7 @@ or degrees) provided with the {2Theta} values. The second column contains the computed diffraction intensities as described above. The array can be accessed by any command that uses global values from -a compute as input. See "this section"_Section_howto.html#howto_15 +a compute as input. See the "Howto output"_Howto_output.html doc page for an overview of LAMMPS output options. All array values calculated by this compute are "intensive". @@ -170,8 +170,8 @@ All array values calculated by this compute are "intensive". [Restrictions:] This compute is part of the USER-DIFFRACTION package. It is only -enabled if LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +enabled if LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. The compute_xrd command does not work for triclinic cells. diff --git a/doc/src/computes.txt b/doc/src/computes.txt index 1b64e2e5b4..6528f78e40 100644 --- a/doc/src/computes.txt +++ b/doc/src/computes.txt @@ -15,6 +15,7 @@ Computes :h1 compute_bond_local compute_centro_atom compute_chunk_atom + compute_chunk_spread_atom compute_cluster_atom compute_cna_atom compute_cnp_atom @@ -31,6 +32,7 @@ Computes :h1 compute_dpd compute_dpd_atom compute_edpd_temp_atom + compute_entropy_atom compute_erotate_asphere compute_erotate_rigid compute_erotate_sphere @@ -71,6 +73,7 @@ Computes :h1 compute_property_local compute_rdf compute_reduce + compute_reduce_chunk compute_rigid_local compute_saed compute_slice @@ -95,6 +98,7 @@ Computes :h1 compute_smd_ulsph_stress compute_smd_vol compute_sna_atom + compute_spin compute_stress_atom compute_tally compute_tdpd_cc_atom diff --git a/doc/src/create_atoms.txt b/doc/src/create_atoms.txt index 5d824ae1ef..d80e2d45f1 100644 --- a/doc/src/create_atoms.txt +++ b/doc/src/create_atoms.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/create_bonds.txt b/doc/src/create_bonds.txt index 6700ed29d3..fbf741d914 100644 --- a/doc/src/create_bonds.txt +++ b/doc/src/create_bonds.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -132,7 +132,7 @@ between 1 and the number of bond types defined. The {single/angle} style creates a single angle of type {atype} between three atoms with IDs {aatom1}, {aatom2}, and {aatom3}. The ordering of the atoms is the same as in the {Angles} section of a data -file read by the "read_data"_read_data command. I.e. the 3 atoms are +file read by the "read_data"_read_data.html command. I.e. the 3 atoms are ordered linearly within the angle; the central atom is {aatom2}. {Atype} must be a value between 1 and the number of angle types defined. @@ -140,7 +140,7 @@ defined. The {single/dihedral} style creates a single dihedral of type {btype} between two atoms with IDs {batom1} and {batom2}. The ordering of the atoms is the same as in the {Dihedrals} section of a data file read by -the "read_data"_read_data command. I.e. the 4 atoms are ordered +the "read_data"_read_data.html command. I.e. the 4 atoms are ordered linearly within the dihedral. {Dtype} must be a value between 1 and the number of dihedral types defined. diff --git a/doc/src/create_box.txt b/doc/src/create_box.txt index f4ef13654c..0993b4f927 100644 --- a/doc/src/create_box.txt +++ b/doc/src/create_box.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -73,9 +73,9 @@ factors that exceed these limits, you can use the "box tilt"_box.html command, with a setting of {large}; a setting of {small} is the default. -See "Section 6.12"_Section_howto.html#howto_12 of the doc pages -for a geometric description of triclinic boxes, as defined by LAMMPS, -and how to transform these parameters to and from other commonly used +See the "Howto triclinic"_Howto_triclinic.html doc page for a +geometric description of triclinic boxes, as defined by LAMMPS, and +how to transform these parameters to and from other commonly used triclinic representations. When a prism region is used, the simulation domain should normally be diff --git a/doc/src/delete_atoms.txt b/doc/src/delete_atoms.txt index 1aa71d341f..a55288e1db 100644 --- a/doc/src/delete_atoms.txt +++ b/doc/src/delete_atoms.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -84,7 +84,7 @@ connectivity that has already been assigned. However, the "reset_ids"_reset_ids.html command can be used after this command to accomplish the same thing. -Note that the re-assignement of IDs is not really a compression, where +Note that the re-assignment of IDs is not really a compression, where gaps in atom IDs are removed by decrementing atom IDs that are larger. Instead the IDs for all atoms are erased, and new IDs are assigned so that the atoms owned by individual processors have consecutive IDs, as diff --git a/doc/src/delete_bonds.txt b/doc/src/delete_bonds.txt index b1137a2288..4e33604696 100644 --- a/doc/src/delete_bonds.txt +++ b/doc/src/delete_bonds.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -140,7 +140,7 @@ enough for a processor to acquire the ghost atoms its needs to compute bond, angle, etc interactions. If deleted bonds (angles, etc) are removed but the 1-2, 1-3, 1-4 -weighting list is not recomputed, this can cause a later "fix +weighting list is not re-computed, this can cause a later "fix shake"_fix_shake.html command to fail due to an atom's bonds being inconsistent with the weighting list. This should only happen if the group used in the fix command includes both atoms in the bond, in diff --git a/doc/src/dielectric.txt b/doc/src/dielectric.txt index e98badf87b..f93be8cc25 100644 --- a/doc/src/dielectric.txt +++ b/doc/src/dielectric.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/dihedral_charmm.txt b/doc/src/dihedral_charmm.txt index 06abe054e4..637a10102d 100644 --- a/doc/src/dihedral_charmm.txt +++ b/doc/src/dihedral_charmm.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -116,23 +116,22 @@ computed. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line @@ -147,8 +146,8 @@ Otherwise non-bonded contributions for these 1-4 pairs will be computed multiple times. These dihedral styles can only be used if LAMMPS was built with the -MOLECULE package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info on packages. +MOLECULE package. See the "Build package"_Build_package.html doc page +for more info. [Related commands:] diff --git a/doc/src/dihedral_class2.txt b/doc/src/dihedral_class2.txt index cb9fc72c22..9936f3768d 100644 --- a/doc/src/dihedral_class2.txt +++ b/doc/src/dihedral_class2.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -141,31 +141,30 @@ r3 (distance) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line [Restrictions:] This dihedral style can only be used if LAMMPS was built with the -CLASS2 package. See the "Making LAMMPS"_Section_start.html#start_3 -section for more info on packages. +CLASS2 package. See the "Build package"_Build_package.html doc +page for more info. [Related commands:] diff --git a/doc/src/dihedral_coeff.txt b/doc/src/dihedral_coeff.txt index 5b43cbbe7f..1db69e40d5 100644 --- a/doc/src/dihedral_coeff.txt +++ b/doc/src/dihedral_coeff.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -74,9 +74,9 @@ the style to display the formula it computes and coefficients specified by the associated "dihedral_coeff"_dihedral_coeff.html command. Note that there are also additional dihedral styles submitted by users -which are included in the LAMMPS distribution. The list of these with -links to the individual styles are given in the dihedral section of -"this page"_Section_commands.html#cmd_5. +which are included in the LAMMPS distribution. The full list of all +dihedral styles is on the "Commands bond"_Commands_bond.html#dihedral +doc page. "dihedral_style none"_dihedral_none.html - turn off dihedral interactions "dihedral_style hybrid"_dihedral_hybrid.html - define multiple styles of dihedral interactions :ul diff --git a/doc/src/dihedral_cosine_shift_exp.txt b/doc/src/dihedral_cosine_shift_exp.txt index 715682affc..e2a46d28d8 100644 --- a/doc/src/dihedral_cosine_shift_exp.txt +++ b/doc/src/dihedral_cosine_shift_exp.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -52,31 +52,30 @@ A (real number) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line [Restrictions:] This dihedral style can only be used if LAMMPS was built with the -USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_3 -section for more info on packages. +USER-MISC package. See the "Build package"_Build_package.html doc +page for more info. [Related commands:] diff --git a/doc/src/dihedral_fourier.txt b/doc/src/dihedral_fourier.txt index 0accbb22bf..3045f6824b 100644 --- a/doc/src/dihedral_fourier.txt +++ b/doc/src/dihedral_fourier.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -44,31 +44,30 @@ dm (degrees) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line [Restrictions:] This angle style can only be used if LAMMPS was built with the -USER_MISC package. See the "Making LAMMPS"_Section_start.html#start_3 -section for more info on packages. +USER_MISC package. See the "Build package"_Build_package.html doc +page for more info. [Related commands:] diff --git a/doc/src/dihedral_harmonic.txt b/doc/src/dihedral_harmonic.txt index d9a48ff384..27bc04f9df 100644 --- a/doc/src/dihedral_harmonic.txt +++ b/doc/src/dihedral_harmonic.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -53,31 +53,30 @@ Some force fields let {n} be positive or negative which corresponds to Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line [Restrictions:] This dihedral style can only be used if LAMMPS was built with the -MOLECULE package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info on packages. +MOLECULE package. See the "Build package"_Build_package.html doc page +for more info. [Related commands:] diff --git a/doc/src/dihedral_helix.txt b/doc/src/dihedral_helix.txt index 1e907557b2..3b3607337b 100644 --- a/doc/src/dihedral_helix.txt +++ b/doc/src/dihedral_helix.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -46,31 +46,30 @@ C (energy) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line [Restrictions:] This dihedral style can only be used if LAMMPS was built with the -MOLECULE package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info on packages. +MOLECULE package. See the "Build package"_Build_package.html doc page +for more info. [Related commands:] diff --git a/doc/src/dihedral_hybrid.txt b/doc/src/dihedral_hybrid.txt index 8cb40eff44..a4a2a2808e 100644 --- a/doc/src/dihedral_hybrid.txt +++ b/doc/src/dihedral_hybrid.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -77,8 +77,8 @@ for specific dihedral types. [Restrictions:] This dihedral style can only be used if LAMMPS was built with the -MOLECULE package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info on packages. +MOLECULE package. See the "Build package"_Build_package.html doc page +for more info. Unlike other dihedral styles, the hybrid dihedral style does not store dihedral coefficient info for individual sub-styles in a "binary diff --git a/doc/src/dihedral_multi_harmonic.txt b/doc/src/dihedral_multi_harmonic.txt index 7d3c2ea083..74f1f6abc6 100644 --- a/doc/src/dihedral_multi_harmonic.txt +++ b/doc/src/dihedral_multi_harmonic.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -40,31 +40,30 @@ A5 (energy) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line [Restrictions:] This dihedral style can only be used if LAMMPS was built with the -MOLECULE package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info on packages. +MOLECULE package. See the "Build package"_Build_package.html doc page +for more info. [Related commands:] diff --git a/doc/src/dihedral_nharmonic.txt b/doc/src/dihedral_nharmonic.txt index 8392d83899..7a8bf6cdb7 100644 --- a/doc/src/dihedral_nharmonic.txt +++ b/doc/src/dihedral_nharmonic.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -40,31 +40,30 @@ An (energy) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line [Restrictions:] This angle style can only be used if LAMMPS was built with the -USER_MISC package. See the "Making LAMMPS"_Section_start.html#start_3 -section for more info on packages. +USER_MISC package. See the "Build package"_Build_package.html doc +page for more info. [Related commands:] diff --git a/doc/src/dihedral_none.txt b/doc/src/dihedral_none.txt index 3ce2aa1729..4c1ff2ea5d 100644 --- a/doc/src/dihedral_none.txt +++ b/doc/src/dihedral_none.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/dihedral_opls.txt b/doc/src/dihedral_opls.txt index d1a6ba3ff2..7fa5d81a14 100644 --- a/doc/src/dihedral_opls.txt +++ b/doc/src/dihedral_opls.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -48,31 +48,30 @@ K4 (energy) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line [Restrictions:] This dihedral style can only be used if LAMMPS was built with the -MOLECULE package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info on packages. +MOLECULE package. See the "Build package"_Build_package.html doc page +for more info. [Related commands:] diff --git a/doc/src/dihedral_quadratic.txt b/doc/src/dihedral_quadratic.txt index ca2f5aed40..dc951e4269 100644 --- a/doc/src/dihedral_quadratic.txt +++ b/doc/src/dihedral_quadratic.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -41,31 +41,30 @@ phi0 (degrees) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line [Restrictions:] This angle style can only be used if LAMMPS was built with the -USER_MISC package. See the "Making LAMMPS"_Section_start.html#start_3 -section for more info on packages. +USER_MISC package. See the "Build package"_Build_package.html doc +page for more info. [Related commands:] diff --git a/doc/src/dihedral_spherical.txt b/doc/src/dihedral_spherical.txt index 7c17fbf5ef..61949174df 100644 --- a/doc/src/dihedral_spherical.txt +++ b/doc/src/dihedral_spherical.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -78,8 +78,8 @@ wn (typically 0.0 or 1.0) :ul [Restrictions:] This dihedral style can only be used if LAMMPS was built with the -USER_MISC package. See the "Making LAMMPS"_Section_start.html#start_3 -section for more info on packages. +USER_MISC package. See the "Build package"_Build_package.html doc +page for more info. [Related commands:] diff --git a/doc/src/dihedral_style.txt b/doc/src/dihedral_style.txt index ca592b29b5..749f74e399 100644 --- a/doc/src/dihedral_style.txt +++ b/doc/src/dihedral_style.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -81,9 +81,9 @@ the style to display the formula it computes and coefficients specified by the associated "dihedral_coeff"_dihedral_coeff.html command. Note that there are also additional dihedral styles submitted by users -which are included in the LAMMPS distribution. The list of these with -links to the individual styles are given in the dihedral section of -"this page"_Section_commands.html#cmd_5. +which are included in the LAMMPS distribution. The full list of all +dihedral styles is on the "Commands bond"_Commands_bond.html#dihedral +doc page. "dihedral_style none"_dihedral_none.html - turn off dihedral interactions "dihedral_style zero"_dihedral_zero.html - topology but no interactions @@ -104,10 +104,9 @@ Dihedral styles can only be set for atom styles that allow dihedrals to be defined. Most dihedral styles are part of the MOLECULE package. They are only -enabled if LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info on packages. -The doc pages for individual dihedral potentials tell if it is part of -a package. +enabled if LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. The doc pages for +individual dihedral potentials tell if it is part of a package. [Related commands:] diff --git a/doc/src/dihedral_table.txt b/doc/src/dihedral_table.txt index 0b88f26a61..3f679f5709 100644 --- a/doc/src/dihedral_table.txt +++ b/doc/src/dihedral_table.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -174,29 +174,28 @@ that matches the specified keyword. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. [Restrictions:] This dihedral style can only be used if LAMMPS was built with the -USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_3 -section for more info on packages. +USER-MISC package. See the "Build package"_Build_package.html doc +page for more info. [Related commands:] diff --git a/doc/src/dihedral_table_cut.txt b/doc/src/dihedral_table_cut.txt index 1c83d4ffa0..b8e0ec64c8 100644 --- a/doc/src/dihedral_table_cut.txt +++ b/doc/src/dihedral_table_cut.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -192,8 +192,8 @@ that matches the specified keyword. [Restrictions:] This dihedral style can only be used if LAMMPS was built with the -USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_3 -section for more info on packages. +USER-MISC package. See the "Build package"_Build_package.html doc +page for more info. [Related commands:] diff --git a/doc/src/dihedral_zero.txt b/doc/src/dihedral_zero.txt index 4d33126eeb..0c9995a563 100644 --- a/doc/src/dihedral_zero.txt +++ b/doc/src/dihedral_zero.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/dimension.txt b/doc/src/dimension.txt index 0531e92acf..b7dde76524 100644 --- a/doc/src/dimension.txt +++ b/doc/src/dimension.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -26,7 +26,7 @@ prior to setting up a simulation box via the "create_box"_create_box.html or "read_data"_read_data.html commands. Restart files also store this setting. -See the discussion in "Section 6"_Section_howto.html for +See the discussion on the "Howto 2d"_Howto_2d.html doc page for additional instructions on how to run 2d simulations. NOTE: Some models in LAMMPS treat particles as finite-size spheres or diff --git a/doc/src/displace_atoms.txt b/doc/src/displace_atoms.txt index 634add196b..b4afd5c3a9 100644 --- a/doc/src/displace_atoms.txt +++ b/doc/src/displace_atoms.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/dump.txt b/doc/src/dump.txt index 438ff1d4e0..8b630cc706 100644 --- a/doc/src/dump.txt +++ b/doc/src/dump.txt @@ -1,8 +1,8 @@ - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -184,10 +184,10 @@ file and in what format. Settings made via the individual values and the file itself. The {atom}, {local}, and {custom} styles create files in a simple text -format that is self-explanatory when viewing a dump file. Many of the -LAMMPS "post-processing tools"_Section_tools.html, including -"Pizza.py"_http://www.sandia.gov/~sjplimp/pizza.html, work with this -format, as does the "rerun"_rerun.html command. +format that is self-explanatory when viewing a dump file. Some of the +LAMMPS post-processing tools described on the "Tools"_Tools.html doc +page, including "Pizza.py"_http://www.sandia.gov/~sjplimp/pizza.html, +work with this format, as does the "rerun"_rerun.html command. For post-processing purposes the {atom}, {local}, and {custom} text files are self-describing in the following sense. @@ -224,12 +224,12 @@ This bounding box is convenient for many visualization programs. The meaning of the 6 character flags for "xx yy zz" is the same as above. Note that the first two numbers on each line are now xlo_bound instead -of xlo, etc, since they represent a bounding box. See "this -section"_Section_howto.html#howto_12 of the doc pages for a geometric -description of triclinic boxes, as defined by LAMMPS, simple formulas -for how the 6 bounding box extents (xlo_bound,xhi_bound,etc) are -calculated from the triclinic parameters, and how to transform those -parameters to and from other commonly used triclinic representations. +of xlo, etc, since they represent a bounding box. See the "Howto +triclinic"_Howto_triclinic.html doc page for a geometric description +of triclinic boxes, as defined by LAMMPS, simple formulas for how the +6 bounding box extents (xlo_bound,xhi_bound,etc) are calculated from +the triclinic parameters, and how to transform those parameters to and +from other commonly used triclinic representations. The "ITEM: ATOMS" line in each snapshot lists column descriptors for the per-atom lines that follow. For example, the descriptors would be @@ -413,10 +413,10 @@ If the filename ends with ".bin", the dump file (or files, if "*" or will be about the same size as a text version, but will typically write out much faster. Of course, when post-processing, you will need to convert it back to text format (see the "binary2txt -tool"_Section_tools.html#binary) or write your own code to read the -binary file. The format of the binary file can be understood by -looking at the tools/binary2txt.cpp file. This option is only -available for the {atom} and {custom} styles. +tool"_Tools.html#binary) or write your own code to read the binary +file. The format of the binary file can be understood by looking at +the tools/binary2txt.cpp file. This option is only available for the +{atom} and {custom} styles. If the filename ends with ".gz", the dump file (or files, if "*" or "%" is also used) is written in gzipped format. A gzipped dump file will @@ -530,7 +530,7 @@ so that each value is 0.0 to 1.0. If the simulation box is triclinic (tilted), then all atom coords will still be between 0.0 and 1.0. I.e. actual unscaled (x,y,z) = xs*A + ys*B + zs*C, where (A,B,C) are the non-orthogonal vectors of the simulation box edges, as discussed -in "Section 6.12"_Section_howto.html#howto_12. +on the "Howto triclinic"_Howto_triclinic.html doc page. Use {xu}, {yu}, {zu} if you want the coordinates "unwrapped" by the image flags for each atom. Unwrapped means that if the atom has @@ -625,32 +625,31 @@ The {d_name} and {i_name} attributes allow to output custom per atom floating point or integer properties that are managed by "fix property/atom"_fix_property_atom.html. -See "Section 10"_Section_modify.html of the manual for information -on how to add new compute and fix styles to LAMMPS to calculate -per-atom quantities which could then be output into dump files. +See the "Modify"_Modify.html doc page for information on how to add +new compute and fix styles to LAMMPS to calculate per-atom quantities +which could then be output into dump files. :line [Restrictions:] To write gzipped dump files, you must either compile LAMMPS with the --DLAMMPS_GZIP option or use the styles from the COMPRESS package -- see the "Making LAMMPS"_Section_start.html#start_2 section of -the documentation. +-DLAMMPS_GZIP option or use the styles from the COMPRESS package. +See the "Build settings"_Build_settings.html doc page for details. -The {atom/gz}, {cfg/gz}, {custom/gz}, and {xyz/gz} styles are part -of the COMPRESS package. They are only enabled if LAMMPS was built -with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +The {atom/gz}, {cfg/gz}, {custom/gz}, and {xyz/gz} styles are part of +the COMPRESS package. They are only enabled if LAMMPS was built with +that package. See the "Build package"_Build_package.html doc page for +more info. The {atom/mpiio}, {cfg/mpiio}, {custom/mpiio}, and {xyz/mpiio} styles are part of the MPIIO package. They are only enabled if LAMMPS was -built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +built with that package. See the "Build package"_Build_package.html +doc page for more info. The {xtc} style is part of the MISC package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/dump_cfg_uef.txt b/doc/src/dump_cfg_uef.txt index e257f9c4f1..16e4aba4c0 100644 --- a/doc/src/dump_cfg_uef.txt +++ b/doc/src/dump_cfg_uef.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -38,9 +38,9 @@ reference frame as the atomic positions. [Restrictions:] -This fix is part of the USER-UEF package. It is only enabled if -LAMMPS was built with that package. See the -"Making LAMMPS"_Section_start.html#start_3 section for more info. +This fix is part of the USER-UEF package. It is only enabled if LAMMPS +was built with that package. See the "Build +package"_Build_package.html doc page for more info. This command can only be used when "fix nvt/uef"_fix_nh_uef.html or "fix npt/uef"_fix_nh_uef.html is active. diff --git a/doc/src/dump_h5md.txt b/doc/src/dump_h5md.txt index 93c87d85b7..9065e8a648 100644 --- a/doc/src/dump_h5md.txt +++ b/doc/src/dump_h5md.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -98,13 +98,13 @@ note above). Only orthogonal domains are currently supported. This is a limitation of the present dump h5md command and not of H5MD itself. The {h5md} dump style is part of the USER-H5MD package. It is only -enabled if LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. It also -requires (i) building the ch5md library provided with LAMMPS (See the -"Making LAMMPS"_Section_start.html#start_3 section for more info.) and -(ii) having the "HDF5"_HDF5_ws library installed (C bindings are -sufficient) on your system. The library ch5md is compiled with the -h5cc wrapper provided by the HDF5 library. +enabled if LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. It also requires +(i) building the ch5md library provided with LAMMPS (See the "Build +package"_Build_package.html doc page for more info.) and (ii) having +the "HDF5"_HDF5_ws library installed (C bindings are sufficient) on +your system. The library ch5md is compiled with the h5cc wrapper +provided by the HDF5 library. :link(HDF5_ws,http://www.hdfgroup.org/HDF5/) diff --git a/doc/src/dump_image.txt b/doc/src/dump_image.txt index 3fa267d2b0..9b56dd95a6 100644 --- a/doc/src/dump_image.txt +++ b/doc/src/dump_image.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -142,8 +142,8 @@ framerate can be set using the "dump_modify"_dump_modify.html command. To write out JPEG and PNG format files, you must build LAMMPS with support for the corresponding JPEG or PNG library. To convert images into movies, LAMMPS has to be compiled with the -DLAMMPS_FFMPEG -flag. See "this section"_Section_start.html#start_2_4 of the manual -for instructions on how to do this. +flag. See the "Build settings"_Build_settings.html doc page for +details. NOTE: Because periodic boundary conditions are enforced only on timesteps when neighbor lists are rebuilt, the coordinates of an atom @@ -356,16 +356,16 @@ is used to define body particles with internal state body style. If this keyword is not used, such particles will be drawn as spheres, the same as if they were regular atoms. -The "body"_body.html doc page describes the body styles LAMMPS -currently supports, and provides more details as to the kind of body -particles they represent and how they are drawn by this dump image -command. For all the body styles, individual atoms can be either a -body particle or a usual point (non-body) particle. Non-body +The "Howto body"_Howto_body.html doc page describes the body styles +LAMMPS currently supports, and provides more details as to the kind of +body particles they represent and how they are drawn by this dump +image command. For all the body styles, individual atoms can be +either a body particle or a usual point (non-body) particle. Non-body particles will be drawn the same way they would be as a regular atom. The {bflag1} and {bflag2} settings are numerical values which are passed to the body style to affect how the drawing of a body particle -is done. See the "body"_body.html doc page for a description of what -these parameters mean for each body style. +is done. See the "Howto body"_Howto_body.html doc page for a +description of what these parameters mean for each body style. The only setting currently allowed for the {color} value is {type}, which will color the body particles according to the atom type of the @@ -606,9 +606,9 @@ supported. :l :line -See "Section 10"_Section_modify.html of the manual for information -on how to add new compute and fix styles to LAMMPS to calculate -per-atom quantities which could then be output into dump files. +See the "Modify"_Modify.html doc page for information on how to add +new compute and fix styles to LAMMPS to calculate per-atom quantities +which could then be output into dump files. :line @@ -624,8 +624,7 @@ building LAMMPS and have the FFmpeg executable available on the machine where LAMMPS is being run. Typically it's name is lowercase, i.e. ffmpeg. -See the "Making LAMMPS"_Section_start.html#start_2_4 section of the -documentation for details on how to compile with optional switches. +See the "Build settings"_Build_settings.html doc page for details. Note that since FFmpeg is run as an external program via a pipe, LAMMPS has limited control over its execution and no knowledge about diff --git a/doc/src/dump_modify.txt b/doc/src/dump_modify.txt index 3230507dc3..72f4935916 100644 --- a/doc/src/dump_modify.txt +++ b/doc/src/dump_modify.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -133,7 +133,6 @@ dump_modify option below is valid for the {atom} style, it is also valid for the {atom/mpiio} style, and similarly for the other styles which allow for use of MPI-IO. -:line :line These keywords apply to various dump styles, including the "dump @@ -486,7 +485,7 @@ to respond to the call from the dump command, and update the appropriate reference positions. This is done be defining an "atom-style variable"_variable.html, {check} in this example, which calculates a Boolean value (0 or 1) for each atom, based on the same -criterion used by dump_modify thresh. +criterion used by dump_modify thresh. See the "compute displace/atom"_compute_displace_atom.html command for more details, including an example of how to produce output that @@ -600,13 +599,13 @@ included.) region foo sphere 10 20 10 15 variable inregion atom rmask(foo) -dump_modify ... thresh v_inregion |^ LAST +dump_modify ... thresh v_inregion |^ LAST :pre This will dump atoms which crossed the boundary of the spherical region since the last dump. variable charge atom "(q > 0.5) || (q < -0.5)" -dump_modify ... thresh v_charge |^ LAST +dump_modify ... thresh v_charge |^ LAST :pre This will dump atoms whose charge has changed from an absolute value less than 1/2 to greater than 1/2 (or vice versa) since the last dump. @@ -629,7 +628,6 @@ the coordinate would be if it had not been wrapped back into the periodic box. Note that these coordinates may thus be far outside the box size stored with the snapshot. -:line :line These keywords apply only to the "dump image"_dump_image.html and @@ -894,7 +892,6 @@ frame rate higher than 24 is not recommended, as it will result in simply dropping the rendered images. It is more efficient to dump images less frequently. -:line :line [Restrictions:] none @@ -917,7 +914,7 @@ flush = yes format = %d and %g for each integer or floating point value image = no label = ENTRIES -maxifiles = -1 +maxfiles = -1 nfile = 1 pad = 0 pbc = no diff --git a/doc/src/dump_molfile.txt b/doc/src/dump_molfile.txt index 7e68490a68..b5f157cf29 100644 --- a/doc/src/dump_molfile.txt +++ b/doc/src/dump_molfile.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -90,8 +90,8 @@ determine the sequence of timesteps on which dump files are written. [Restrictions:] The {molfile} dump style is part of the USER-MOLFILE package. It is -only enabled if LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +only enabled if LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. Molfile plugins provide a consistent programming interface to read and write file formats commonly used in molecular simulations. The @@ -99,7 +99,7 @@ USER-MOLFILE package only provides the interface code, not the plugins. These can be obtained from a VMD installation which has to match the platform that you are using to compile LAMMPS for. By adding plugins to VMD, support for new file formats can be added to LAMMPS (or VMD -or other programs that use them) without having to recompile the +or other programs that use them) without having to re-compile the application itself. The plugins are installed in the directory: /plugins//molfile diff --git a/doc/src/dump_netcdf.txt b/doc/src/dump_netcdf.txt index 70111a36a8..52d757eac5 100644 --- a/doc/src/dump_netcdf.txt +++ b/doc/src/dump_netcdf.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -66,8 +66,8 @@ by "thermo_style"_thermo_style.html. The {netcdf} and {netcdf/mpiio} dump styles are part of the USER-NETCDF package. They are only enabled if LAMMPS was built with -that package. See the "Making LAMMPS"_Section_start.html#start_3 -section for more info. +that package. See the "Build package"_Build_package.html doc page for +more info. :line diff --git a/doc/src/dump_vtk.txt b/doc/src/dump_vtk.txt index d4d28c81fc..7eaa59a795 100644 --- a/doc/src/dump_vtk.txt +++ b/doc/src/dump_vtk.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -156,9 +156,9 @@ write out much faster. The {vtk} style does not support writing of gzipped dump files. -The {vtk} dump style is part of the USER-VTK package. It is -only enabled if LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +The {vtk} dump style is part of the USER-VTK package. It is only +enabled if LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. To use this dump style, you also must link to the VTK library. See the info in lib/vtk/README and insure the Makefile.lammps file in that diff --git a/doc/src/echo.txt b/doc/src/echo.txt index 3141c7a719..3436737faa 100644 --- a/doc/src/echo.txt +++ b/doc/src/echo.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -26,8 +26,8 @@ command to the screen and/or log file as it is read and processed. If an input script has errors, it can be useful to look at echoed output to see the last command processed. -The "command-line switch"_Section_start.html#start_6 -echo can be used -in place of this command. +The "command-line switch"_Run_options.html -echo can be used in place +of this command. [Restrictions:] none diff --git a/doc/src/fix.txt b/doc/src/fix.txt index e54a918cd0..ee0d006fe8 100644 --- a/doc/src/fix.txt +++ b/doc/src/fix.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -30,9 +30,9 @@ Set a fix that will be applied to a group of atoms. In LAMMPS, a timestepping or minimization. Examples include updating of atom positions and velocities due to time integration, controlling temperature, applying constraint forces to atoms, enforcing boundary -conditions, computing diagnostics, etc. There are dozens of fixes -defined in LAMMPS and new ones can be added; see "this -section"_Section_modify.html for a discussion. +conditions, computing diagnostics, etc. There are hundreds of fixes +defined in LAMMPS and new ones can be added; see the +"Modify"_Modify.html doc page for details. Fixes perform their operations at different stages of the timestep. If 2 or more fixes operate at the same stage of the timestep, they are @@ -133,7 +133,7 @@ reduce"_compute_reduce.html command, or histogrammed by the "fix ave/histo"_fix_ave_histo.html command. :l :ule -See this "howto section"_Section_howto.html#howto_15 for a summary of +See the "Howto output"_Howto_output.html doc page for a summary of various LAMMPS output options, many of which involve fixes. The results of fixes that calculate global quantities can be either @@ -151,16 +151,20 @@ for further info. :line -Each fix style has its own documentation page which describes its -arguments and what it does, as listed below. Here is an alphabetic -list of fix styles available in LAMMPS. They are also given in more -compact form in the Fix section of "this -page"_Section_commands.html#cmd_5. +Each fix style has its own doc page which describes its arguments and +what it does, as listed below. Here is an alphabetic list of fix +styles available in LAMMPS. They are also listed in more compact form +on the "Commands fix"_Commands_fix.html doc page. There are also additional fix styles (not listed here) submitted by -users which are included in the LAMMPS distribution. The list of -these with links to the individual styles are given in the fix section -of "this page"_Section_commands.html#cmd_5. +users which are included in the LAMMPS distribution. The full list of +all fix styles is on the "Commands fix"_Commands_fix.html doc page. + +There are also additional accelerated fix styles included in the +LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs. +The individual style names on the "Commands fix"_Commands_fix.html doc +page are followed by one or more of (g,i,k,o,t) to indicate which +accelerated styles exist. "adapt"_fix_adapt.html - change a simulation parameter over time "addforce"_fix_addforce.html - add a force to each atom @@ -305,9 +309,9 @@ of "this page"_Section_commands.html#cmd_5. [Restrictions:] Some fix styles are part of specific packages. They are only enabled -if LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info on packages. -The doc pages for individual fixes tell if it is part of a package. +if LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. The doc pages for +individual fixes tell if it is part of a package. [Related commands:] diff --git a/doc/src/fix_adapt.txt b/doc/src/fix_adapt.txt index 7a34f2ff44..0ca28fb869 100644 --- a/doc/src/fix_adapt.txt +++ b/doc/src/fix_adapt.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -270,10 +270,10 @@ fix 1 center adapt 10 atom diameter v_size :pre No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. For "rRESPA time integration"_run_style.html, this fix changes parameters on the outermost rRESPA level. diff --git a/doc/src/fix_adapt_fep.txt b/doc/src/fix_adapt_fep.txt index 5dd58bc39a..7e30a1d29d 100644 --- a/doc/src/fix_adapt_fep.txt +++ b/doc/src/fix_adapt_fep.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -243,10 +243,10 @@ parameters on the outermost rRESPA level. No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. [Restrictions:] none diff --git a/doc/src/fix_addforce.txt b/doc/src/fix_addforce.txt index b2ac95eabb..4fdf9a41dd 100644 --- a/doc/src/fix_addforce.txt +++ b/doc/src/fix_addforce.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -103,25 +103,25 @@ converge properly. :line -Styles with a suffix are functionally the same as the corresponding -style without the suffix. They have been optimized to run faster, -depending on your available hardware, as discussed in -"Section 5"_Section_accelerate.html of the manual. The -accelerated styles take the same arguments and should produce the same -results, except for round-off and precision issues. +Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line @@ -150,11 +150,11 @@ integrator the fix is adding its forces. Default is the outermost level. This fix computes a global scalar and a global 3-vector of forces, -which can be accessed by various "output -commands"_Section_howto.html#howto_15. The scalar is the potential -energy discussed above. The vector is the total force on the group of -atoms before the forces on individual atoms are changed by the fix. -The scalar and vector values calculated by this fix are "extensive". +which can be accessed by various "output commands"_Howto_output.html. +The scalar is the potential energy discussed above. The vector is the +total force on the group of atoms before the forces on individual +atoms are changed by the fix. The scalar and vector values calculated +by this fix are "extensive". No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. diff --git a/doc/src/fix_addtorque.txt b/doc/src/fix_addtorque.txt index 793ec0e015..0963915e7a 100644 --- a/doc/src/fix_addtorque.txt +++ b/doc/src/fix_addtorque.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -70,11 +70,11 @@ this fix. This allows to set at which level of the "r-RESPA"_run_style.html integrator the fix is adding its torque. Default is the outermost level. This fix computes a global scalar and a global 3-vector, which can be -accessed by various "output commands"_Section_howto.html#howto_15. -The scalar is the potential energy discussed above. The vector is the -total torque on the group of atoms before the forces on individual -atoms are changed by the fix. The scalar and vector values calculated -by this fix are "extensive". +accessed by various "output commands"_Howto_output.html. The scalar +is the potential energy discussed above. The vector is the total +torque on the group of atoms before the forces on individual atoms are +changed by the fix. The scalar and vector values calculated by this +fix are "extensive". No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. @@ -88,8 +88,8 @@ the iteration count during the minimization. [Restrictions:] This fix is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/fix_append_atoms.txt b/doc/src/fix_append_atoms.txt index 27070c9be5..d83f265982 100644 --- a/doc/src/fix_append_atoms.txt +++ b/doc/src/fix_append_atoms.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -87,16 +87,16 @@ define the lattice spacings. No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. [Restrictions:] This fix style is part of the SHOCK package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. The boundary on which atoms are added with append/atoms must be shrink/minimum. The opposite boundary may be any boundary type other diff --git a/doc/src/fix_atc.txt b/doc/src/fix_atc.txt index 49014f0591..6de917e571 100644 --- a/doc/src/fix_atc.txt +++ b/doc/src/fix_atc.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -102,7 +102,13 @@ Note coupling and post-processing can be combined in the same simulations using [Restart, fix_modify, output, run start/stop, minimize info:] -No information about this fix is written to "binary restart files"_restart.html. The "fix_modify"_fix_modify.html options relevant to this fix are listed below. No global scalar or vector or per-atom quantities are stored by this fix for access by various "output commands"_Section_howto.html#howto_15. No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. This fix is not invoked during "energy minimization"_minimize.html. +No information about this fix is written to "binary restart +files"_restart.html. The "fix_modify"_fix_modify.html options +relevant to this fix are listed below. No global scalar or vector or +per-atom quantities are stored by this fix for access by various +"output commands"_Howto_output.html. No parameter of this fix can be +used with the {start/stop} keywords of the "run"_run.html command. +This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] diff --git a/doc/src/fix_atom_swap.txt b/doc/src/fix_atom_swap.txt index bf56277214..22091eca00 100644 --- a/doc/src/fix_atom_swap.txt +++ b/doc/src/fix_atom_swap.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -150,8 +150,8 @@ None of the "fix_modify"_fix_modify.html options are relevant to this fix. This fix computes a global vector of length 2, which can be accessed -by various "output commands"_Section_howto.html#howto_15. The vector -values are the following global cumulative quantities: +by various "output commands"_Howto_output.html. The vector values are +the following global cumulative quantities: 1 = swap attempts 2 = swap successes :ul @@ -165,8 +165,8 @@ minimization"_minimize.html. [Restrictions:] This fix is part of the MC package. It is only enabled if LAMMPS was -built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +built with that package. See the "Build package"_Build_package.html +doc page for more info. [Related commands:] diff --git a/doc/src/fix_ave_atom.txt b/doc/src/fix_ave_atom.txt index 3251125a5d..10deaf64cd 100644 --- a/doc/src/fix_ave_atom.txt +++ b/doc/src/fix_ave_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -38,7 +38,7 @@ fix 1 all ave/atom 10 20 1000 c_my_stress\[*\] :pre Use one or more per-atom vectors as inputs every few timesteps, and average them atom by atom over longer timescales. The resulting per-atom averages can be used by other "output -commands"_Section_howto.html#howto_15 such as the "fix +commands"_Howto_output.html such as the "fix ave/chunk"_fix_ave_chunk.html or "dump custom"_dump.html commands. The group specified with the command means only atoms within the group @@ -124,7 +124,7 @@ appended, the per-atom vector calculated by the compute is used. If a bracketed term containing an index I is appended, the Ith column of the per-atom array calculated by the compute is used. Users can also write code for their own compute styles and "add them to -LAMMPS"_Section_modify.html. See the discussion above for how I can +LAMMPS"_Modify.html. See the discussion above for how I can be specified with a wildcard asterisk to effectively specify multiple values. @@ -136,8 +136,8 @@ the per-atom array calculated by the fix is used. Note that some fixes only produce their values on certain timesteps, which must be compatible with {Nevery}, else an error will result. Users can also write code for their own fix styles and "add them to -LAMMPS"_Section_modify.html. See the discussion above for how I can -be specified with a wildcard asterisk to effectively specify multiple +LAMMPS"_Modify.html. See the discussion above for how I can be +specified with a wildcard asterisk to effectively specify multiple values. If a value begins with "v_", a variable name must follow which has @@ -155,14 +155,14 @@ No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global scalar or vector quantities are stored by this fix for access by various "output -commands"_Section_howto.html#howto_15. +commands"_Howto_output.html. This fix produces a per-atom vector or array which can be accessed by -various "output commands"_Section_howto.html#howto_15. A vector is -produced if only a single quantity is averaged by this fix. If two or -more quantities are averaged, then an array of values is produced. -The per-atom values can only be accessed on timesteps that are -multiples of {Nfreq} since that is when averaging is performed. +various "output commands"_Howto_output.html. A vector is produced if +only a single quantity is averaged by this fix. If two or more +quantities are averaged, then an array of values is produced. The +per-atom values can only be accessed on timesteps that are multiples +of {Nfreq} since that is when averaging is performed. No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. This fix is not invoked during "energy diff --git a/doc/src/fix_ave_chunk.txt b/doc/src/fix_ave_chunk.txt index a8691d3767..d331e51295 100644 --- a/doc/src/fix_ave_chunk.txt +++ b/doc/src/fix_ave_chunk.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -85,17 +85,17 @@ fix 1 flow ave/chunk 100 10 1000 cc1 vx vz norm sample file vel.profile :pre Use one or more per-atom vectors as inputs every few timesteps, sum the values over the atoms in each chunk at each timestep, then average the per-chunk values over longer timescales. The resulting chunk -averages can be used by other "output -commands"_Section_howto.html#howto_15 such as "thermo_style -custom"_thermo_style.html, and can also be written to a file. +averages can be used by other "output commands"_Howto_output.html such +as "thermo_style custom"_thermo_style.html, and can also be written to +a file. In LAMMPS, chunks are collections of atoms defined by a "compute chunk/atom"_compute_chunk_atom.html command, which assigns each atom to a single chunk (or no chunk). The ID for this command is specified as chunkID. For example, a single chunk could be the atoms in a molecule or atoms in a spatial bin. See the "compute -chunk/atom"_compute_chunk_atom.html doc page and "Section -6.23"_Section_howto.html#howto_23 for details of how chunks can be +chunk/atom"_compute_chunk_atom.html doc page and the "Howto +chunk"_Howto_chunk.html doc page for details of how chunks can be defined and examples of how they can be used to measure properties of a system. @@ -263,7 +263,7 @@ previously defined in the input script. If no bracketed integer is appended, the per-atom vector calculated by the compute is used. If a bracketed integer is appended, the Ith column of the per-atom array calculated by the compute is used. Users can also write code for -their own compute styles and "add them to LAMMPS"_Section_modify.html. +their own compute styles and "add them to LAMMPS"_Modify.html. See the discussion above for how I can be specified with a wildcard asterisk to effectively specify multiple values. @@ -274,7 +274,7 @@ bracketed integer is appended, the Ith column of the per-atom array calculated by the fix is used. Note that some fixes only produce their values on certain timesteps, which must be compatible with {Nevery}, else an error results. Users can also write code for their -own fix styles and "add them to LAMMPS"_Section_modify.html. See the +own fix styles and "add them to LAMMPS"_Modify.html. See the discussion above for how I can be specified with a wildcard asterisk to effectively specify multiple values. @@ -456,20 +456,19 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. This fix computes a global array of values which can be accessed by -various "output commands"_Section_howto.html#howto_15. The values can -only be accessed on timesteps that are multiples of {Nfreq} since that -is when averaging is performed. The global array has # of rows = -the number of chunks {Nchunk} as calculated by the specified "compute +various "output commands"_Howto_output.html. The values can only be +accessed on timesteps that are multiples of {Nfreq} since that is when +averaging is performed. The global array has # of rows = the number +of chunks {Nchunk} as calculated by the specified "compute chunk/atom"_compute_chunk_atom.html command. The # of columns = M+1+Nvalues, where M = 1 to 4, depending on whether the optional -columns for OrigID and CoordN are used, as explained above. -Following the optional columns, the next column contains the count of -atoms in the chunk, and the remaining columns are the Nvalue -quantities. When the array is accessed with a row I that exceeds the -current number of chunks, than a 0.0 is returned by the fix instead of -an error, since the number of chunks can vary as a simulation runs -depending on how that value is computed by the compute chunk/atom -command. +columns for OrigID and CoordN are used, as explained above. Following +the optional columns, the next column contains the count of atoms in +the chunk, and the remaining columns are the Nvalue quantities. When +the array is accessed with a row I that exceeds the current number of +chunks, than a 0.0 is returned by the fix instead of an error, since +the number of chunks can vary as a simulation runs depending on how +that value is computed by the compute chunk/atom command. The array values calculated by this fix are treated as "intensive", since they are typically already normalized by the count of atoms in diff --git a/doc/src/fix_ave_correlate.txt b/doc/src/fix_ave_correlate.txt index 371f2f66a8..22e8768f1d 100644 --- a/doc/src/fix_ave_correlate.txt +++ b/doc/src/fix_ave_correlate.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -68,7 +68,7 @@ calculate time correlations between them at varying time intervals, and average the correlation data over longer timescales. The resulting correlation values can be time integrated by "variables"_variable.html or used by other "output -commands"_Section_howto.html#howto_15 such as "thermo_style +commands"_Howto_output.html such as "thermo_style custom"_thermo_style.html, and can also be written to a file. See the "fix ave/correlate/long"_fix_ave_correlate_long.html command for an alternate method for computing correlation functions efficiently over @@ -176,7 +176,7 @@ output"_thermo_style.html or other fixes such as "fix nvt"_fix_nh.html or "fix temp/rescale"_fix_temp_rescale.html. See the doc pages for these commands which give the IDs of these computes. Users can also write code for their own compute styles and "add them to -LAMMPS"_Section_modify.html. +LAMMPS"_Modify.html. If a value begins with "f_", a fix ID must follow which has been previously defined in the input script. If no bracketed term is @@ -189,7 +189,7 @@ values. Note that some fixes only produce their values on certain timesteps, which must be compatible with {Nevery}, else an error will result. Users can also write code for their own fix styles and "add them to -LAMMPS"_Section_modify.html. +LAMMPS"_Modify.html. If a value begins with "v_", a variable name must follow which has been previously defined in the input script. Only equal-style or @@ -313,16 +313,15 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. This fix computes a global array of values which can be accessed by -various "output commands"_Section_howto.html#howto_15. The values can -only be accessed on timesteps that are multiples of {Nfreq} since that -is when averaging is performed. The global array has # of rows = -{Nrepeat} and # of columns = Npair+2. The first column has the time -delta (in timesteps) between the pairs of input values used to -calculate the correlation, as described above. The 2nd column has the -number of samples contributing to the correlation average, as -described above. The remaining Npair columns are for I,J pairs of the -N input values, as determined by the {type} keyword, as described -above. +various "output commands"_Howto_output.html. The values can only be +accessed on timesteps that are multiples of {Nfreq} since that is when +averaging is performed. The global array has # of rows = {Nrepeat} +and # of columns = Npair+2. The first column has the time delta (in +timesteps) between the pairs of input values used to calculate the +correlation, as described above. The 2nd column has the number of +samples contributing to the correlation average, as described above. +The remaining Npair columns are for I,J pairs of the N input values, +as determined by the {type} keyword, as described above. For {type} = {auto}, the Npair = N columns are ordered: C11, C22, ..., CNN. :ulb,l diff --git a/doc/src/fix_ave_correlate_long.txt b/doc/src/fix_ave_correlate_long.txt index 7b4bc53701..d94bf8af7b 100644 --- a/doc/src/fix_ave_correlate_long.txt +++ b/doc/src/fix_ave_correlate_long.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -120,8 +120,8 @@ the run command. This fix is not invoked during energy minimization. [Restrictions:] This compute is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/fix_ave_histo.txt b/doc/src/fix_ave_histo.txt index 043f0e22be..f1da130ff7 100644 --- a/doc/src/fix_ave_histo.txt +++ b/doc/src/fix_ave_histo.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -69,10 +69,9 @@ fix 1 all ave/histo/weight 1 1 1 10 100 2000 c_XRD\[1\] c_XRD\[2\] :pre Use one or more values as inputs every few timesteps to create a single histogram. The histogram can then be averaged over longer timescales. The resulting histogram can be used by other "output -commands"_Section_howto.html#howto_15, and can also be written to a -file. The fix ave/histo/weight command has identical syntax to fix -ave/histo, except that exactly two values must be specified. See -details below. +commands"_Howto_output.html, and can also be written to a file. The +fix ave/histo/weight command has identical syntax to fix ave/histo, +except that exactly two values must be specified. See details below. The group specified with this command is ignored for global and local input values. For per-atom input values, only atoms in the group @@ -183,11 +182,11 @@ Note that there is a "compute reduce"_compute_reduce.html command which can sum per-atom quantities into a global scalar or vector which can thus be accessed by fix ave/histo. Or it can be a compute defined not in your input script, but by "thermodynamic -output"_thermo_style.html or other fixes such as "fix -nvt"_fix_nh.html or "fix temp/rescale"_fix_temp_rescale.html. See -the doc pages for these commands which give the IDs of these computes. -Users can also write code for their own compute styles and "add them -to LAMMPS"_Section_modify.html. +output"_thermo_style.html or other fixes such as "fix nvt"_fix_nh.html +or "fix temp/rescale"_fix_temp_rescale.html. See the doc pages for +these commands which give the IDs of these computes. Users can also +write code for their own compute styles and "add them to +LAMMPS"_Modify.html. If a value begins with "f_", a fix ID must follow which has been previously defined in the input script. If {mode} = scalar, then if @@ -204,7 +203,7 @@ values. Note that some fixes only produce their values on certain timesteps, which must be compatible with {Nevery}, else an error will result. Users can also write code for their own fix styles and "add them to -LAMMPS"_Section_modify.html. +LAMMPS"_Modify.html. If a value begins with "v_", a variable name must follow which has been previously defined in the input script. If {mode} = scalar, then @@ -320,10 +319,10 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. This fix produces a global vector and global array which can be -accessed by various "output commands"_Section_howto.html#howto_15. -The values can only be accessed on timesteps that are multiples of -{Nfreq} since that is when a histogram is generated. The global -vector has 4 values: +accessed by various "output commands"_Howto_output.html. The values +can only be accessed on timesteps that are multiples of {Nfreq} since +that is when a histogram is generated. The global vector has 4 +values: 1 = total counts in the histogram 2 = values that were not histogrammed (see {beyond} keyword) diff --git a/doc/src/fix_ave_time.txt b/doc/src/fix_ave_time.txt index 266e3f0e38..a53e318d3f 100644 --- a/doc/src/fix_ave_time.txt +++ b/doc/src/fix_ave_time.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -64,7 +64,7 @@ fix 1 all ave/time 1 100 1000 f_indent f_indent\[1\] file temp.indent off 1 :pre Use one or more global values as inputs every few timesteps, and average them over longer timescales. The resulting averages can be -used by other "output commands"_Section_howto.html#howto_15 such as +used by other "output commands"_Howto_output.html such as "thermo_style custom"_thermo_style.html, and can also be written to a file. Note that if no time averaging is done, this command can be used as a convenient way to simply output one or more global values to @@ -168,7 +168,7 @@ output"_thermo_style.html or other fixes such as "fix nvt"_fix_nh.html or "fix temp/rescale"_fix_temp_rescale.html. See the doc pages for these commands which give the IDs of these computes. Users can also write code for their own compute styles and "add them -to LAMMPS"_Section_modify.html. +to LAMMPS"_Modify.html. If a value begins with "f_", a fix ID must follow which has been previously defined in the input script. If {mode} = scalar, then if @@ -184,7 +184,7 @@ specify multiple values. Note that some fixes only produce their values on certain timesteps, which must be compatible with {Nevery}, else an error will result. Users can also write code for their own fix styles and "add them to -LAMMPS"_Section_modify.html. +LAMMPS"_Modify.html. If a value begins with "v_", a variable name must follow which has been previously defined in the input script. If {mode} = scalar, then @@ -305,10 +305,9 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. This fix produces a global scalar or global vector or global array -which can be accessed by various "output -commands"_Section_howto.html#howto_15. The values can only be -accessed on timesteps that are multiples of {Nfreq} since that is when -averaging is performed. +which can be accessed by various "output commands"_Howto_output.html. +The values can only be accessed on timesteps that are multiples of +{Nfreq} since that is when averaging is performed. A scalar is produced if only a single input value is averaged and {mode} = scalar. A vector is produced if multiple input values are diff --git a/doc/src/fix_aveforce.txt b/doc/src/fix_aveforce.txt index 5d7dec3e6a..8c759864c6 100644 --- a/doc/src/fix_aveforce.txt +++ b/doc/src/fix_aveforce.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -63,25 +63,25 @@ to it. :line -Styles with a suffix are functionally the same as the corresponding -style without the suffix. They have been optimized to run faster, -depending on your available hardware, as discussed in -"Section 5"_Section_accelerate.html of the manual. The -accelerated styles take the same arguments and should produce the same -results, except for round-off and precision issues. +Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line @@ -95,10 +95,10 @@ fix. This allows to set at which level of the "r-RESPA"_run_style.html integrator the fix is adding its forces. Default is the outermost level. This fix computes a global 3-vector of forces, which can be accessed -by various "output commands"_Section_howto.html#howto_15. This is the -total force on the group of atoms before the forces on individual -atoms are changed by the fix. The vector values calculated by this -fix are "extensive". +by various "output commands"_Howto_output.html. This is the total +force on the group of atoms before the forces on individual atoms are +changed by the fix. The vector values calculated by this fix are +"extensive". No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. diff --git a/doc/src/fix_balance.txt b/doc/src/fix_balance.txt index f148e6f996..2de17cdd2a 100644 --- a/doc/src/fix_balance.txt +++ b/doc/src/fix_balance.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -357,8 +357,8 @@ number of particles (or total weight) on any processor to the average number of particles (or total weight) per processor. These quantities can be accessed by various "output -commands"_Section_howto.html#howto_15. The scalar and vector values -calculated by this fix are "intensive". +commands"_Howto_output.html. The scalar and vector values calculated +by this fix are "intensive". No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. This fix is not invoked during "energy diff --git a/doc/src/fix_bocs.txt b/doc/src/fix_bocs.txt index f53b7c785c..b7d4e7badf 100644 --- a/doc/src/fix_bocs.txt +++ b/doc/src/fix_bocs.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -56,7 +56,7 @@ value and its corresponding pressure correction. The volumes in the file should be uniformly spaced. Both the volumes and the pressure corrections should be provided in the proper units, e.g. if you are using {units real}, the volumes should all be in cubic angstroms, and the pressure corrections -should all be in atomspheres. Furthermore, the table should start/end at a +should all be in atmospheres. Furthermore, the table should start/end at a volume considerably smaller/larger than you expect your system to sample during the simulation. If the system ever reaches a volume outside of the range provided, the simulation will stop. @@ -85,8 +85,8 @@ XXXX_press, where XXXX is the ID given to the fix bocs command (in the example, the ID of the fix bocs command is 1 ). This fix is part of the USER-BOCS package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related:] diff --git a/doc/src/fix_bond_break.txt b/doc/src/fix_bond_break.txt index 83364b9efb..59fea8f45b 100644 --- a/doc/src/fix_bond_break.txt +++ b/doc/src/fix_bond_break.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -116,8 +116,8 @@ are relevant to this fix. This fix computes two statistics which it stores in a global vector of length 2, which can be accessed by various "output -commands"_Section_howto.html#howto_15. The vector values calculated -by this fix are "intensive". +commands"_Howto_output.html. The vector values calculated by this fix +are "intensive". These are the 2 quantities: @@ -131,8 +131,8 @@ minimization"_minimize.html. [Restrictions:] This fix is part of the MC package. It is only enabled if LAMMPS was -built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +built with that package. See the "Build package"_Build_package.html +doc page for more info. [Related commands:] diff --git a/doc/src/fix_bond_create.txt b/doc/src/fix_bond_create.txt index c0045ac0f0..02655577fd 100644 --- a/doc/src/fix_bond_create.txt +++ b/doc/src/fix_bond_create.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -211,8 +211,8 @@ are relevant to this fix. This fix computes two statistics which it stores in a global vector of length 2, which can be accessed by various "output -commands"_Section_howto.html#howto_15. The vector values calculated -by this fix are "intensive". +commands"_Howto_output.html. The vector values calculated by this fix +are "intensive". These are the 2 quantities: @@ -226,8 +226,8 @@ minimization"_minimize.html. [Restrictions:] This fix is part of the MC package. It is only enabled if LAMMPS was -built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +built with that package. See the "Build package"_Build_package.html +doc page for more info. [Related commands:] diff --git a/doc/src/fix_bond_react.txt b/doc/src/fix_bond_react.txt index f85ef9bc1a..8e7cb1bdae 100644 --- a/doc/src/fix_bond_react.txt +++ b/doc/src/fix_bond_react.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -34,7 +34,7 @@ react = mandatory argument indicating new reaction specification :l Rmax = bonding pair atoms must be separated by less than Rmax to initiate reaction (distance units) :l template-ID(pre-reacted) = ID of a molecule template containing pre-reaction topology :l template-ID(post-reacted) = ID of a molecule template containing post-reaction topology :l - map_file = name of file specifying corresponding atomIDs in the pre- and post-reacted templates :l + map_file = name of file specifying corresponding atom-IDs in the pre- and post-reacted templates :l zero or more individual keyword/value pairs may be appended to each react argument :l individual_keyword = {prob} or {stabilize_steps} :l {prob} values = fraction seed @@ -125,13 +125,13 @@ template. If both these conditions are met, the reaction site is modified to match the post-reaction template. A bonding atom pair will be identified if several conditions are met. -First, a pair of atoms within the specified react-group-ID of type -typei and typej must separated by a distance between {Rmin} and +First, a pair of atoms I,J within the specified react-group-ID of type +itype and jtype must separated by a distance between {Rmin} and {Rmax}. It is possible that multiple bonding atom pairs are identified: if the bonding atoms in the pre-reacted template are not 1-2, 1-3, or 1-4 neighbors, the closest bonding atom partner is set as its bonding partner; otherwise, the farthest potential partner is -chosen. Then, if both an atomi and atomj have each other as their +chosen. Then, if both an atom I and atom J have each other as their nearest bonding partners, these two atoms are identified as the bonding atom pair of the reaction site. Once this unique bonding atom pair is identified for each reaction, there could two or more @@ -298,9 +298,8 @@ relevant to this fix. This fix computes one statistic for each {react} argument that it stores in a global vector, of length 'number of react arguments', that -can be accessed by various "output -commands"_Section_howto.html#howto_15. The vector values calculated by -this fix are "intensive". +can be accessed by various "output commands"_Howto_output.html. The +vector values calculated by this fix are "intensive". These is 1 quantity for each react argument: @@ -313,8 +312,8 @@ minimization"_minimize.html. [Restrictions:] This fix is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] @@ -324,7 +323,7 @@ bond/break"_fix_bond_break.html, "fix bond/swap"_fix_bond_swap.html, [Default:] -The option defaults are stabilization = no, stabilize_steps = 60 +The option defaults are stabilization = no, prob = 1.0, stabilize_steps = 60 :line diff --git a/doc/src/fix_bond_swap.txt b/doc/src/fix_bond_swap.txt index ca7069e247..3c90bb53f6 100644 --- a/doc/src/fix_bond_swap.txt +++ b/doc/src/fix_bond_swap.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -150,13 +150,13 @@ the Boltzmann criterion. This fix computes two statistical quantities as a global 2-vector of output, which can be accessed by various "output -commands"_Section_howto.html#howto_15. The first component of the -vector is the cumulative number of swaps performed by all processors. -The second component of the vector is the cumulative number of swaps -attempted (whether accepted or rejected). Note that a swap "attempt" -only occurs when swap partners meeting the criteria described above -are found on a particular timestep. The vector values calculated by -this fix are "intensive". +commands"_Howto_output.html. The first component of the vector is the +cumulative number of swaps performed by all processors. The second +component of the vector is the cumulative number of swaps attempted +(whether accepted or rejected). Note that a swap "attempt" only +occurs when swap partners meeting the criteria described above are +found on a particular timestep. The vector values calculated by this +fix are "intensive". No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. This fix is not invoked during "energy @@ -165,8 +165,8 @@ minimization"_minimize.html. [Restrictions:] This fix is part of the MC package. It is only enabled if LAMMPS was -built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +built with that package. See the "Build package"_Build_package.html +doc page for more info. The settings of the "special_bond" command must be 0,1,1 in order to use this fix, which is typical of bead-spring chains with FENE or diff --git a/doc/src/fix_box_relax.txt b/doc/src/fix_box_relax.txt index e3d75ee858..29ebeaeef3 100644 --- a/doc/src/fix_box_relax.txt +++ b/doc/src/fix_box_relax.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -126,8 +126,6 @@ minimizer from the new adjusted box size/shape, since that creates a new objective function valid for the new box size/shape. Repeat as necessary until the box size/shape has reached its new equilibrium. -:line -:line :line The {couple} keyword allows two or three of the diagonal components of @@ -315,17 +313,15 @@ specified by the {press} keyword will be unaffected by the {temp} setting. This fix computes a global scalar which can be accessed by various -"output commands"_Section_howto.html#howto_15. The scalar is the -pressure-volume energy, plus the strain energy, if it exists, -as described above. -The energy values reported at the -end of a minimization run under "Minimization stats" include this -energy, and so differ from what LAMMPS normally reports as potential -energy. This fix does not support the "fix_modify"_fix_modify.html -{energy} option, because that would result in double-counting of the -fix energy in the minimization energy. Instead, the fix energy can be -explicitly added to the potential energy using one of these two -variants: +"output commands"_Howto_output.html. The scalar is the pressure-volume +energy, plus the strain energy, if it exists, as described above. The +energy values reported at the end of a minimization run under +"Minimization stats" include this energy, and so differ from what +LAMMPS normally reports as potential energy. This fix does not support +the "fix_modify"_fix_modify.html {energy} option, because that would +result in double-counting of the fix energy in the minimization +energy. Instead, the fix energy can be explicitly added to the +potential energy using one of these two variants: variable emin equal pe+f_1 :pre diff --git a/doc/src/fix_client_md.txt b/doc/src/fix_client_md.txt new file mode 100644 index 0000000000..77f6b82c5e --- /dev/null +++ b/doc/src/fix_client_md.txt @@ -0,0 +1,106 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +fix client/md command :h3 + +[Syntax:] + +fix ID group-ID client/md :pre + +ID, group-ID are documented in "fix"_fix.html command +client/md = style name of this fix command :ul + +[Examples:] + +fix 1 all client/md :pre + +[Description:] + +This fix style enables LAMMPS to run as a "client" code and +communicate each timestep with a separate "server" code to perform an +MD simulation together. + +The "Howto client/server"_Howto_client_server.html doc page gives an +overview of client/server coupling of LAMMPS with another code where +one code is the "client" and sends request messages to a "server" +code. The server responds to each request with a reply message. This +enables the two codes to work in tandem to perform a simulation. + +When using this fix, LAMMPS (as the client code) passes the current +coordinates of all particles to the server code each timestep, which +computes their interaction, and returns the energy, forces, and virial +for the interacting particles to LAMMPS, so it can complete the +timestep. + +The server code could be a quantum code, or another classical MD code +which encodes a force field (pair_style in LAMMPS lingo) which LAMMPS +does not have. In the quantum case, this fix is a mechanism for +running {ab initio} MD with quantum forces. + +The group associated with this fix is ignored. + +The protocol and "units"_units.html for message format and content +that LAMMPS exchanges with the server code is defined on the "server +md"_server_md.html doc page. + +Note that when using LAMMPS as an MD client, your LAMMPS input script +should not normally contain force field commands, like a +"pair_style"_pair_style.html, "bond_style"_bond_style.html, or +"kspace_style"_kspace_style.html commmand. However it is possible for +a server code to only compute a portion of the full force-field, while +LAMMPS computes the remaining part. Your LAMMPS script can also +specify boundary conditions or force constraints in the usual way, +which will be added to the per-atom forces returned by the server +code. + +See the examples/message dir for example scripts where LAMMPS is both +the "client" and/or "server" code for this kind of client/server MD +simulation. The examples/message/README file explains how to launch +LAMMPS and another code in tandem to perform a coupled simulation. + +:line + +[Restart, fix_modify, output, run start/stop, minimize info:] + +No information about this fix is written to "binary restart +files"_restart.html. + +The "fix_modify"_fix_modify.html {energy} option is supported by this +fix to add the potential energy computed by the server application to +the system's potential energy as part of "thermodynamic +output"_thermo_style.html. + +The "fix_modify"_fix_modify.html {virial} option is supported by this +fix to add the server application's contribution to the system's +virial as part of "thermodynamic output"_thermo_style.html. The +default is {virial yes} + +This fix computes a global scalar which can be accessed by various +"output commands"_Howto_output.html. The scalar is the potential +energy discussed above. The scalar value calculated by this fix is +"extensive". + +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. + +[Restrictions:] + +This fix is part of the MESSAGE package. It is only enabled if LAMMPS +was built with that package. See the "Build +package"_Build_package.html doc page for more info. + +A script that uses this command must also use the +"message"_message.html command to setup the messaging protocol with +the other server code. + +[Related commands:] + +"message"_message.html, "server"_server.html + +[Default:] none diff --git a/doc/src/fix_cmap.txt b/doc/src/fix_cmap.txt index f8de2b4efe..ef48e8b51c 100644 --- a/doc/src/fix_cmap.txt +++ b/doc/src/fix_cmap.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -103,9 +103,9 @@ the system's virial as part of "thermodynamic output"_thermo_style.html. The default is {virial yes} This fix computes a global scalar which can be accessed by various -"output commands"_Section_howto.html#howto_15. The scalar is the -potential energy discussed above. The scalar value calculated by this -fix is "extensive". +"output commands"_Howto_output.html. The scalar is the potential +energy discussed above. The scalar value calculated by this fix is +"extensive". No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. @@ -125,8 +125,8 @@ To function as expected this fix command must be issued {before} a "read_restart"_read_restart.html command. This fix can only be used if LAMMPS was built with the MOLECULE -package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info on packages. +package. See the "Build package"_Build_package.html doc page for more +info. [Related commands:] diff --git a/doc/src/fix_colvars.txt b/doc/src/fix_colvars.txt index e48dedacd9..3a64840bdc 100644 --- a/doc/src/fix_colvars.txt +++ b/doc/src/fix_colvars.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -99,15 +99,15 @@ to the system's potential energy as part of "thermodynamic output"_thermo_style.html. This fix computes a global scalar which can be accessed by various -"output commands"_Section_howto.html#howto_15. The scalar is the -cumulative energy change due to this fix. The scalar value -calculated by this fix is "extensive". +"output commands"_Howto_output.html. The scalar is the cumulative +energy change due to this fix. The scalar value calculated by this +fix is "extensive". [Restrictions:] This fix is part of the USER-COLVARS package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. There can only be one colvars fix active at a time. Since the interface communicates only the minimum amount of information and colvars module diff --git a/doc/src/fix_controller.txt b/doc/src/fix_controller.txt index cfb26138fd..7458f1bcfa 100644 --- a/doc/src/fix_controller.txt +++ b/doc/src/fix_controller.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -139,7 +139,7 @@ for details. If no bracketed integer is appended, the scalar calculated by the compute is used. If a bracketed integer is appended, the Ith value of the vector calculated by the compute is used. Users can also write code for their own compute styles and "add -them to LAMMPS"_Section_modify.html. +them to LAMMPS"_Modify.html. If {pvar} begins with "f_", a fix ID must follow which has been previously defined in the input script and which generates a global @@ -150,7 +150,7 @@ references the values, or else an error results. If no bracketed integer is appended, the scalar calculated by the fix is used. If a bracketed integer is appended, the Ith value of the vector calculated by the fix is used. Users can also write code for their own fix style and "add -them to LAMMPS"_Section_modify.html. +them to LAMMPS"_Modify.html. If {pvar} begins with "v_", a variable name must follow which has been previously defined in the input script. Only equal-style variables @@ -180,9 +180,9 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. This fix produces a global vector with 3 values which can be accessed -by various "output commands"_Section_howto.html#howto_15. The values -can be accessed on any timestep, though they are only updated on -timesteps that are a multiple of {Nevery}. +by various "output commands"_Howto_output.html. The values can be +accessed on any timestep, though they are only updated on timesteps +that are a multiple of {Nevery}. The three values are the most recent updates made to the control variable by each of the 3 terms in the PID equation above. The first diff --git a/doc/src/fix_deform.txt b/doc/src/fix_deform.txt index c870c73bdc..d35c3065a2 100644 --- a/doc/src/fix_deform.txt +++ b/doc/src/fix_deform.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -94,7 +94,7 @@ nvt/sllod"_fix_nvt_sllod.html and "compute temp/deform"_compute_temp_deform.html commands for more details. Note that simulation of a continuously extended system (extensional flow) can be modeled using the "USER-UEF -package"_Section_packages.html#USER-UEF and its "fix +package"_Packages_details.html#PKG-USER-UEF and its "fix commands"_fix_nh_uef.html. For the {x}, {y}, {z} parameters, the associated dimension cannot be @@ -550,33 +550,31 @@ command if you want to include lattice spacings in a variable formula. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. [Restart, fix_modify, output, run start/stop, minimize info:] This fix will restore the initial box settings from "binary restart files"_restart.html, which allows the fix to be properly continue deformation, when using the start/stop options of the "run"_run.html -command. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. +command. None of the "fix_modify"_fix_modify.html options are +relevant to this fix. No global or per-atom quantities are stored by +this fix for access by various "output commands"_Howto_output.html. This fix can perform deformation over multiple runs, using the {start} and {stop} keywords of the "run"_run.html command. See the diff --git a/doc/src/fix_deposit.txt b/doc/src/fix_deposit.txt index 477c14ea89..265f43bd4b 100644 --- a/doc/src/fix_deposit.txt +++ b/doc/src/fix_deposit.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -116,8 +116,8 @@ side = {in}. NOTE: LAMMPS checks that the specified region is wholly inside the simulation box. It can do this correctly for orthonormal simulation -boxes. However for "triclinic boxes"_Section_howto.html#howto_12, it -only tests against the larger orthonormal box that bounds the tilted +boxes. However for "triclinic boxes"_Howto_triclinic.html, it only +tests against the larger orthonormal box that bounds the tilted simulation box. If the specified region includes volume outside the tilted box, then an insertion will likely fail, leading to a "lost atoms" error. Thus for triclinic boxes you should insure the @@ -263,16 +263,16 @@ operation of the fix continues in an uninterrupted fashion. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored by this fix for -access by various "output commands"_Section_howto.html#howto_15. No -parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy +access by various "output commands"_Howto_output.html. No parameter +of this fix can be used with the {start/stop} keywords of the +"run"_run.html command. This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] This fix is part of the MISC package. It is only enabled if LAMMPS -was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +was built with that package. See the "Build +package"_Build_package.html doc page for more info. The specified insertion region cannot be a "dynamic" region, as defined by the "region"_region.html command. diff --git a/doc/src/fix_dpd_energy.txt b/doc/src/fix_dpd_energy.txt index 1c10d954d6..5e8e295de9 100644 --- a/doc/src/fix_dpd_energy.txt +++ b/doc/src/fix_dpd_energy.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -50,31 +50,30 @@ examples/USER/dpd directory. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line [Restrictions:] This command is part of the USER-DPD package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. This fix must be used with an additional fix that specifies time integration, e.g. "fix nve"_fix_nve.html. diff --git a/doc/src/fix_dpd_source.txt b/doc/src/fix_dpd_source.txt index b6decc657c..691cfe86f1 100644 --- a/doc/src/fix_dpd_source.txt +++ b/doc/src/fix_dpd_source.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -63,16 +63,16 @@ cuboid domain to apply the source flux to. No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. [Restrictions:] This fix is part of the USER-MESO package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. Fix {edpd/source} must be used with the "pair_style edpd"_pair_meso.html command. Fix {tdpd/source} must be used with the diff --git a/doc/src/fix_drag.txt b/doc/src/fix_drag.txt index 235d3d38b5..92e68d13a4 100644 --- a/doc/src/fix_drag.txt +++ b/doc/src/fix_drag.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -47,9 +47,9 @@ fix. This allows to set at which level of the "r-RESPA"_run_style.html integrator the fix is adding its forces. Default is the outermost level. This fix computes a global 3-vector of forces, which can be accessed -by various "output commands"_Section_howto.html#howto_15. This is the -total force on the group of atoms by the drag force. The vector -values calculated by this fix are "extensive". +by various "output commands"_Howto_output.html. This is the total +force on the group of atoms by the drag force. The vector values +calculated by this fix are "extensive". No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. This fix is not invoked during "energy diff --git a/doc/src/fix_drude.txt b/doc/src/fix_drude.txt index faa354b314..80eb79201b 100644 --- a/doc/src/fix_drude.txt +++ b/doc/src/fix_drude.txt @@ -3,7 +3,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -25,10 +25,10 @@ fix 1 all drude C C N C N D D D :pre [Description:] Assign each atom type in the system to be one of 3 kinds of atoms -within the Drude polarization model. This fix is designed to be -used with the "thermalized Drude oscillator -model"_tutorial_drude.html. Polarizable models in LAMMPS -are described in "this Section"_Section_howto.html#howto_25. +within the Drude polarization model. This fix is designed to be used +with the "thermalized Drude oscillator model"_Howto_drude.html. +Polarizable models in LAMMPS are described on the "Howto +polarizable"_Howto_polarizable.html doc page. The three possible types can be designated with an integer (0,1,2) or capital letter (N,C,D): diff --git a/doc/src/fix_drude_transform.txt b/doc/src/fix_drude_transform.txt index 2e094d528c..8864cc4eb6 100644 --- a/doc/src/fix_drude_transform.txt +++ b/doc/src/fix_drude_transform.txt @@ -9,7 +9,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -34,8 +34,8 @@ Transform the coordinates of Drude oscillators from real to reduced and back for thermalizing the Drude oscillators as described in "(Lamoureux)"_#Lamoureux1 using a Nose-Hoover thermostat. This fix is designed to be used with the "thermalized Drude oscillator -model"_tutorial_drude.html. Polarizable models in LAMMPS are -described in "this Section"_Section_howto.html#howto_25. +model"_Howto_drude.html. Polarizable models in LAMMPS are described +on the "Howto polarizable"_Howto_polarizable.html doc page. Drude oscillators are a pair of atoms representing a single polarizable atom. Ideally, the mass of Drude particles would vanish diff --git a/doc/src/fix_dt_reset.txt b/doc/src/fix_dt_reset.txt index 7605395ca0..0c5a4493ae 100644 --- a/doc/src/fix_dt_reset.txt +++ b/doc/src/fix_dt_reset.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -14,7 +14,7 @@ fix ID group-ID dt/reset N Tmin Tmax Xmax keyword values ... :pre ID, group-ID are documented in "fix"_fix.html command dt/reset = style name of this fix command -N = recompute dt every N timesteps +N = re-compute dt every N timesteps Tmin = minimum dt allowed which can be NULL (time units) Tmax = maximum dt allowed which can be NULL (time units) Xmax = maximum distance for an atom to move in one timestep (distance units) @@ -82,8 +82,8 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. This fix computes a global scalar which can be accessed by various -"output commands"_Section_howto.html#howto_15. The scalar stores -the last timestep on which the timestep was reset to a new value. +"output commands"_Howto_output.html. The scalar stores the last +timestep on which the timestep was reset to a new value. The scalar value calculated by this fix is "intensive". diff --git a/doc/src/fix_efield.txt b/doc/src/fix_efield.txt index 5d2b86fe4b..cecfb6e6a3 100644 --- a/doc/src/fix_efield.txt +++ b/doc/src/fix_efield.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -134,11 +134,10 @@ fix. This allows to set at which level of the "r-RESPA"_run_style.html integrator the fix adding its forces. Default is the outermost level. This fix computes a global scalar and a global 3-vector of forces, -which can be accessed by various "output -commands"_Section_howto.html#howto_15. The scalar is the potential -energy discussed above. The vector is the total force added to the -group of atoms. The scalar and vector values calculated by this fix -are "extensive". +which can be accessed by various "output commands"_Howto_output.html. +The scalar is the potential energy discussed above. The vector is the +total force added to the group of atoms. The scalar and vector values +calculated by this fix are "extensive". No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. @@ -157,8 +156,8 @@ system (the quantity being minimized), you MUST enable the [Restrictions:] This fix is part of the MISC package. It is only enabled if LAMMPS -was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/fix_ehex.txt b/doc/src/fix_ehex.txt index 40752a811f..75651e21a4 100644 --- a/doc/src/fix_ehex.txt +++ b/doc/src/fix_ehex.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -156,8 +156,8 @@ minimization"_minimize.html. [Restrictions:] This fix is part of the RIGID package. It is only enabled if LAMMPS -was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/fix_enforce2d.txt b/doc/src/fix_enforce2d.txt index 5d04e96677..17ac8146fd 100644 --- a/doc/src/fix_enforce2d.txt +++ b/doc/src/fix_enforce2d.txt @@ -2,11 +2,12 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line fix enforce2d command :h3 +fix enforce2d/kk command :h3 [Syntax:] @@ -27,25 +28,25 @@ not move from their initial z coordinate. :line -Styles with a suffix are functionally the same as the corresponding -style without the suffix. They have been optimized to run faster, -depending on your available hardware, as discussed in -"Section 5"_Section_accelerate.html of the manual. The -accelerated styles take the same arguments and should produce the same -results, except for round-off and precision issues. +Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line @@ -54,9 +55,9 @@ more instructions on how to use the accelerated styles effectively. No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. The forces due to this fix are imposed during an energy minimization, invoked by the "minimize"_minimize.html command. diff --git a/doc/src/fix_eos_cv.txt b/doc/src/fix_eos_cv.txt index 4c97304335..b2ac0eb6b9 100644 --- a/doc/src/fix_eos_cv.txt +++ b/doc/src/fix_eos_cv.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -39,8 +39,8 @@ possible. [Restrictions:] This command is part of the USER-DPD package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. This command also requires use of the "atom_style dpd"_atom_style.html command. diff --git a/doc/src/fix_eos_table.txt b/doc/src/fix_eos_table.txt index 42778d7978..53b3204372 100644 --- a/doc/src/fix_eos_table.txt +++ b/doc/src/fix_eos_table.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -99,8 +99,8 @@ one that matches the specified keyword. [Restrictions:] This command is part of the USER-DPD package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. This command also requires use of the "atom_style dpd"_atom_style.html command. diff --git a/doc/src/fix_eos_table_rx.txt b/doc/src/fix_eos_table_rx.txt index 0c87874347..1a2daa0bc6 100644 --- a/doc/src/fix_eos_table_rx.txt +++ b/doc/src/fix_eos_table_rx.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -156,31 +156,30 @@ no 0.93 0.00 0.000 -1.76 :pre Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line [Restrictions:] This command is part of the USER-DPD package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. This command also requires use of the "atom_style dpd"_atom_style.html command. diff --git a/doc/src/fix_evaporate.txt b/doc/src/fix_evaporate.txt index ed6c6d0377..59dab43d9a 100644 --- a/doc/src/fix_evaporate.txt +++ b/doc/src/fix_evaporate.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -73,9 +73,9 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. This fix computes a global scalar, which can be accessed by various -"output commands"_Section_howto.html#howto_15. The scalar is the -cumulative number of deleted atoms. The scalar value calculated by -this fix is "intensive". +"output commands"_Howto_output.html. The scalar is the cumulative +number of deleted atoms. The scalar value calculated by this fix is +"intensive". No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. This fix is not invoked during "energy @@ -84,8 +84,8 @@ minimization"_minimize.html. [Restrictions:] This fix is part of the MISC package. It is only enabled if LAMMPS -was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/fix_external.txt b/doc/src/fix_external.txt index b28d33446f..dd7f7914e9 100644 --- a/doc/src/fix_external.txt +++ b/doc/src/fix_external.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -31,11 +31,10 @@ fix 1 all external pf/array 10 :pre [Description:] This fix allows external programs that are running LAMMPS through its -"library interface"_Section_howto.html#howto_19 to modify certain -LAMMPS properties on specific timesteps, similar to the way other -fixes do. The external driver can be a "C/C++ or Fortran -program"_Section_howto.html#howto_19 or a "Python -script"_Section_python.html. +"library interface"_Howto_library.html to modify certain LAMMPS +properties on specific timesteps, similar to the way other fixes do. +The external driver can be a "C/C++ or Fortran +program"_Howto_library.html or a "Python script"_Python_head.html. :line @@ -137,9 +136,8 @@ external program to the system's virial as part of "thermodynamic output"_thermo_style.html. The default is {virial yes} This fix computes a global scalar which can be accessed by various -"output commands"_Section_howto.html#howto_15. The scalar is the -potential energy discussed above. The scalar stored by this fix -is "extensive". +"output commands"_Howto_output.html. The scalar is the potential +energy discussed above. The scalar stored by this fix is "extensive". No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. diff --git a/doc/src/fix_filter_corotate.txt b/doc/src/fix_filter_corotate.txt index b782d285c7..4868761d42 100644 --- a/doc/src/fix_filter_corotate.txt +++ b/doc/src/fix_filter_corotate.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -47,7 +47,7 @@ this can significantly accelerate the simulation. The filter computes a cluster decomposition of the molecular structure following the criteria indicated by the options a, b, t and m. This process is similar to the approach in "fix shake"_fix_shake.html, -however, the clusters are not kept contrained. Instead, the position +however, the clusters are not kept constrained. Instead, the position is slightly modified only for the computation of long-range forces. A good cluster decomposition constitutes in building clusters which contain the fastest covalent bonds inside clusters. @@ -63,16 +63,15 @@ No information about these fixes is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to these fixes. No global or per-atom quantities are stored by these fixes for access by various "output -commands"_Section_howto.html#howto_15. No parameter of these fixes -can be used with the {start/stop} keywords of the "run"_run.html -command. These fixes are not invoked during "energy -minimization"_minimize.html. +commands"_Howto_output.html. No parameter of these fixes can be used +with the {start/stop} keywords of the "run"_run.html command. These +fixes are not invoked during "energy minimization"_minimize.html. [Restrictions:] This fix is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. Currently, it does not support "molecule templates"_molecule.html. diff --git a/doc/src/fix_flow_gauss.txt b/doc/src/fix_flow_gauss.txt index efa58ea65f..46a9477aa2 100644 --- a/doc/src/fix_flow_gauss.txt +++ b/doc/src/fix_flow_gauss.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -111,8 +111,8 @@ flow/gauss fixes, one that specifies {fix_modify respa 3} and one with [Restart, fix_modify, output, run start/stop, minimize info:] This fix is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. No information about this fix is written to "binary restart files"_restart.html. @@ -128,11 +128,11 @@ integrator the fix computes and adds the external acceleration. Default is the outermost level. This fix computes a global scalar and a global 3-vector of forces, -which can be accessed by various "output -commands"_Section_howto.html#howto_15. The scalar is the negative of the -work done on the system, see above discussion. The vector is the total force -that this fix applied to the group of atoms on the current timestep. -The scalar and vector values calculated by this fix are "extensive". +which can be accessed by various "output commands"_Howto_output.html. +The scalar is the negative of the work done on the system, see above +discussion. The vector is the total force that this fix applied to +the group of atoms on the current timestep. The scalar and vector +values calculated by this fix are "extensive". No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. diff --git a/doc/src/fix_freeze.txt b/doc/src/fix_freeze.txt index a63ee4cb32..89f2dd8179 100644 --- a/doc/src/fix_freeze.txt +++ b/doc/src/fix_freeze.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -31,25 +31,25 @@ using "fix setforce"_fix_setforce.html. :line -Styles with a suffix are functionally the same as the corresponding -style without the suffix. They have been optimized to run faster, -depending on your available hardware, as discussed in -"Section 5"_Section_accelerate.html of the manual. The -accelerated styles take the same arguments and should produce the same -results, except for round-off and precision issues. +Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line @@ -60,10 +60,10 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. This fix computes a global 3-vector of forces, which can be accessed -by various "output commands"_Section_howto.html#howto_15. This is the -total force on the group of atoms before the forces on individual -atoms are changed by the fix. The vector values calculated by this -fix are "extensive". +by various "output commands"_Howto_output.html. This is the total +force on the group of atoms before the forces on individual atoms are +changed by the fix. The vector values calculated by this fix are +"extensive". No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. This fix is not invoked during "energy @@ -72,8 +72,8 @@ minimization"_minimize.html. [Restrictions:] This fix is part of the GRANULAR package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. There can only be a single freeze fix defined. This is because other the "granular pair styles"_pair_gran.html treat frozen particles diff --git a/doc/src/fix_gcmc.txt b/doc/src/fix_gcmc.txt index 38f0fb95ce..6b9a02eeca 100644 --- a/doc/src/fix_gcmc.txt +++ b/doc/src/fix_gcmc.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -349,7 +349,7 @@ in the context of NVT dynamics. NOTE: If the density of the cell is initially very small or zero, and increases to a much larger density after a period of equilibration, then certain quantities that are only calculated once at the start -(kspace parameters, tail corrections) may no longer be accurate. The +(kspace parameters) may no longer be accurate. The solution is to start a new simulation after the equilibrium density has been reached. @@ -382,8 +382,8 @@ None of the "fix_modify"_fix_modify.html options are relevant to this fix. This fix computes a global vector of length 8, which can be accessed -by various "output commands"_Section_howto.html#howto_15. The vector -values are the following global cumulative quantities: +by various "output commands"_Howto_output.html. The vector values are +the following global cumulative quantities: 1 = translation attempts 2 = translation successes @@ -403,8 +403,8 @@ minimization"_minimize.html. [Restrictions:] This fix is part of the MC package. It is only enabled if LAMMPS was -built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +built with that package. See the "Build package"_Build_package.html +doc page for more info. Do not set "neigh_modify once yes" or else this fix will never be called. Reneighboring is required. diff --git a/doc/src/fix_gld.txt b/doc/src/fix_gld.txt index 1425f62e13..97c3d0e408 100644 --- a/doc/src/fix_gld.txt +++ b/doc/src/fix_gld.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -126,7 +126,7 @@ sense, a restarted simulation should produce the same behavior. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored by this fix for -access by various "output commands"_Section_howto.html#howto_15. +access by various "output commands"_Howto_output.html. This fix can ramp its target temperature over multiple runs, using the {start} and {stop} keywords of the "run"_run.html command. See the @@ -137,8 +137,8 @@ This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] This fix is part of the MISC package. It is only enabled if LAMMPS -was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/fix_gle.txt b/doc/src/fix_gle.txt index 6568060f0c..70a8e7f342 100644 --- a/doc/src/fix_gle.txt +++ b/doc/src/fix_gle.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -116,9 +116,9 @@ system's potential energy as part of "thermodynamic output"_thermo_style.html. This fix computes a global scalar which can be accessed by various -"output commands"_Section_howto.html#howto_15. The scalar is the -cumulative energy change due to this fix. The scalar value -calculated by this fix is "extensive". +"output commands"_Howto_output.html. The scalar is the cumulative +energy change due to this fix. The scalar value calculated by this +fix is "extensive". [Restrictions:] @@ -132,9 +132,9 @@ In order to perform constant-pressure simulations please use "fix npt"_fix_nh.html, to avoid duplicate integration of the equations of motion. -This fix is part of the USER-MISC package. It is only enabled if LAMMPS -was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +This fix is part of the USER-MISC package. It is only enabled if +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/fix_gravity.txt b/doc/src/fix_gravity.txt index dae8ac5ed0..ea596c8668 100644 --- a/doc/src/fix_gravity.txt +++ b/doc/src/fix_gravity.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -90,23 +90,22 @@ field. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line @@ -125,11 +124,11 @@ fix. This allows to set at which level of the "r-RESPA"_run_style.html integrator the fix is adding its forces. Default is the outermost level. This fix computes a global scalar which can be accessed by various -"output commands"_Section_howto.html#howto_15. This scalar is the -gravitational potential energy of the particles in the defined field, -namely mass * (g dot x) for each particles, where x and mass are the -particles position and mass, and g is the gravitational field. The -scalar value calculated by this fix is "extensive". +"output commands"_Howto_output.html. This scalar is the gravitational +potential energy of the particles in the defined field, namely mass * +(g dot x) for each particles, where x and mass are the particles +position and mass, and g is the gravitational field. The scalar value +calculated by this fix is "extensive". No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. This fix is not invoked during "energy diff --git a/doc/src/fix_grem.txt b/doc/src/fix_grem.txt index 661f68ed99..e096d4bd3c 100644 --- a/doc/src/fix_grem.txt +++ b/doc/src/fix_grem.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -91,8 +91,8 @@ by this fix to add the rescaled kinetic pressure as part of [Restrictions:] This fix is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/fix_halt.txt b/doc/src/fix_halt.txt index 08043eb5fb..ec117518d2 100644 --- a/doc/src/fix_halt.txt +++ b/doc/src/fix_halt.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -133,10 +133,10 @@ files. No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. [Restrictions:] none diff --git a/doc/src/fix_heat.txt b/doc/src/fix_heat.txt index 23db87dac2..6db7592609 100644 --- a/doc/src/fix_heat.txt +++ b/doc/src/fix_heat.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -108,12 +108,11 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. This fix computes a global scalar which can be accessed by various -"output commands"_Section_howto.html#howto_15. This scalar is the -most recent value by which velocites were scaled. The scalar value -calculated by this fix is "intensive". If {eflux} is specified as -an atom-style variable, this fix computes the average value by which -the velocities were scaled for all of the atoms that had their -velocities scaled. +"output commands"_Howto_output.html. This scalar is the most recent +value by which velocites were scaled. The scalar value calculated by +this fix is "intensive". If {eflux} is specified as an atom-style +variable, this fix computes the average value by which the velocities +were scaled for all of the atoms that had their velocities scaled. No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. This fix is not invoked during "energy diff --git a/doc/src/fix_imd.txt b/doc/src/fix_imd.txt index b275612819..a58cfdb3d3 100644 --- a/doc/src/fix_imd.txt +++ b/doc/src/fix_imd.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -136,15 +136,15 @@ No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global scalar or vector or per-atom quantities are stored by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. +commands"_Howto_output.html. No parameter of this fix can be used +with the {start/stop} keywords of the "run"_run.html command. This +fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] This fix is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. When used in combination with VMD, a topology or coordinate file has to be loaded, which matches (in number and ordering of atoms) the diff --git a/doc/src/fix_indent.txt b/doc/src/fix_indent.txt index c9a791ae4e..9931793c0b 100644 --- a/doc/src/fix_indent.txt +++ b/doc/src/fix_indent.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -180,8 +180,8 @@ integrator the fix is adding its forces. Default is the outermost level. This fix computes a global scalar energy and a global 3-vector of forces (on the indenter), which can be accessed by various "output -commands"_Section_howto.html#howto_15. The scalar and vector values -calculated by this fix are "extensive". +commands"_Howto_output.html. The scalar and vector values calculated +by this fix are "extensive". The forces due to this fix are imposed during an energy minimization, invoked by the "minimize"_minimize.html command. Note that if you diff --git a/doc/src/fix_ipi.txt b/doc/src/fix_ipi.txt index 07e8025d77..64486a9cc7 100644 --- a/doc/src/fix_ipi.txt +++ b/doc/src/fix_ipi.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -63,7 +63,7 @@ electrostatics, or that contain parameters that depend on box size: all of these options will be initialized based on the cell size in the LAMMPS-side initial configuration and kept constant during the run. This is required to e.g. obtain reproducible and conserved forces. -If the cell varies too wildly, it may be advisable to reinitialize +If the cell varies too wildly, it may be advisable to re-initialize these interactions at each call. This behavior can be requested by setting the {reset} switch. @@ -81,9 +81,9 @@ define an external potential acting on the atoms that are moved by i-PI. This fix is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. Because of -the use of UNIX domain sockets, this fix will only work in a UNIX +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. Because of the +use of UNIX domain sockets, this fix will only work in a UNIX environment. [Related commands:] diff --git a/doc/src/fix_langevin.txt b/doc/src/fix_langevin.txt index 93c73f5a5d..e97c7c3c37 100644 --- a/doc/src/fix_langevin.txt +++ b/doc/src/fix_langevin.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -101,7 +101,7 @@ should not normally be used on atoms that also have their temperature controlled by another fix - e.g. by "fix nvt"_fix_nh.html or "fix temp/rescale"_fix_temp_rescale.html commands. -See "this howto section"_Section_howto.html#howto_16 of the manual for +See the "Howto thermostat"_Howto_thermostat.html doc page for a discussion of different ways to compute temperature and perform thermostatting. @@ -264,23 +264,22 @@ generates an average temperature of 220 K, instead of 300 K. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line @@ -306,10 +305,10 @@ output"_thermo_style.html. Note that use of this option requires setting the {tally} keyword to {yes}. This fix computes a global scalar which can be accessed by various -"output commands"_Section_howto.html#howto_15. The scalar is the -cumulative energy change due to this fix. The scalar value -calculated by this fix is "extensive". Note that calculation of this -quantity requires setting the {tally} keyword to {yes}. +"output commands"_Howto_output.html. The scalar is the cumulative +energy change due to this fix. The scalar value calculated by this +fix is "extensive". Note that calculation of this quantity requires +setting the {tally} keyword to {yes}. This fix can ramp its target temperature over multiple runs, using the {start} and {stop} keywords of the "run"_run.html command. See the diff --git a/doc/src/fix_langevin_drude.txt b/doc/src/fix_langevin_drude.txt index c85ff24c96..19a3f87ffc 100644 --- a/doc/src/fix_langevin_drude.txt +++ b/doc/src/fix_langevin_drude.txt @@ -9,7 +9,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -44,8 +44,9 @@ fix 1 all langevin/drude 298.15 100.0 19377 5.0 10.0 83451 zero yes :pre Apply two Langevin thermostats as described in "(Jiang)"_#Jiang1 for thermalizing the reduced degrees of freedom of Drude oscillators. This link describes how to use the "thermalized Drude oscillator -model"_tutorial_drude.html in LAMMPS and polarizable models in LAMMPS -are discussed in "this Section"_Section_howto.html#howto_25. +model"_Howto_drude.html in LAMMPS and polarizable models in LAMMPS +are discussed on the "Howto polarizable"_Howto_polarizable.html doc +page. Drude oscillators are a way to simulate polarizables atoms, by splitting them into a core and a Drude particle bound by a harmonic @@ -99,8 +100,8 @@ Likewise, this fix should not normally be used on atoms that also have their temperature controlled by another fix - e.g. by "fix nvt"_fix_nh.html or "fix temp/rescale"_fix_temp_rescale.html commands. -See "this howto section"_Section_howto.html#howto_16 of the manual for -a discussion of different ways to compute temperature and perform +See the "Howto thermostat"_Howto_thermostat.html doc page for a +discussion of different ways to compute temperature and perform thermostating. :line diff --git a/doc/src/fix_langevin_eff.txt b/doc/src/fix_langevin_eff.txt index 4a50bfae54..e55e40c6c8 100644 --- a/doc/src/fix_langevin_eff.txt +++ b/doc/src/fix_langevin_eff.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -79,10 +79,10 @@ output"_thermo_style.html. Note that use of this option requires setting the {tally} keyword to {yes}. This fix computes a global scalar which can be accessed by various -"output commands"_Section_howto.html#howto_15. The scalar is the -cumulative energy change due to this fix. The scalar value -calculated by this fix is "extensive". Note that calculation of this -quantity requires setting the {tally} keyword to {yes}. +"output commands"_Howto_output.html. The scalar is the cumulative +energy change due to this fix. The scalar value calculated by this +fix is "extensive". Note that calculation of this quantity requires +setting the {tally} keyword to {yes}. This fix can ramp its target temperature over multiple runs, using the {start} and {stop} keywords of the "run"_run.html command. See the @@ -93,8 +93,8 @@ This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] none This fix is part of the USER-EFF package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/fix_langevin_spin.txt b/doc/src/fix_langevin_spin.txt new file mode 100644 index 0000000000..d4836706e2 --- /dev/null +++ b/doc/src/fix_langevin_spin.txt @@ -0,0 +1,102 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +fix langevin/spin command :h3 + +[Syntax:] + +fix ID group-ID langevin/spin T Tdamp seed :pre + +ID, group-ID are documented in "fix"_fix.html command :ulb,l +langevin/spin = style name of this fix command :l +T = desired temperature of the bath (temperature units, K in metal units) :l +Tdamp = transverse magnetic damping parameter (adim) :l +seed = random number seed to use for white noise (positive integer) :l +:ule + +[Examples:] + +fix 2 all langevin/spin 300.0 0.01 21 :pre + +[Description:] + +Apply a Langevin thermostat as described in "(Mayergoyz)"_#Mayergoyz1 to the +magnetic spins associated to the atoms. +Used with "fix nve/spin"_fix_nve_spin.html, this command performs +Brownian dynamics (BD). +A random torque and a transverse dissipation are applied to each spin i according to +the following stochastic differential equation: + +:c,image(Eqs/fix_langevin_spin_sLLG.jpg) + +with lambda the transverse damping, and eta a random vector. +This equation is referred to as the stochastic Landau-Lifshitz-Gilbert (sLLG) +equation. + +The components of eta are drawn from a Gaussian probability law. Their amplitude +is defined as a proportion of the temperature of the external thermostat T (in K +in metal units). + +More details about this implementation are reported in "(Tranchida)"_#Tranchida2. + +Note: due to the form of the sLLG equation, this fix has to be defined just +before the nve/spin fix (and after all other magnetic fixes). +As an example: + +fix 1 all precession/spin zeeman 0.01 0.0 0.0 1.0 +fix 2 all langevin/spin 300.0 0.01 21 +fix 3 all nve/spin lattice yes :pre + +is correct, but defining a force/spin command after the langevin/spin command +would give an error message. + +Note: The random # {seed} must be a positive integer. A Marsaglia random +number generator is used. Each processor uses the input seed to +generate its own unique seed and its own stream of random numbers. +Thus the dynamics of the system will not be identical on two runs on +different numbers of processors. + +:line + +[Restart, fix_modify, output, run start/stop, minimize info:] + +No information about this fix is written to "binary restart +files"_restart.html. Because the state of the random number generator +is not saved in restart files, this means you cannot do "exact" +restarts with this fix, where the simulation continues on the same as +if no restart had taken place. However, in a statistical sense, a +restarted simulation should produce the same behavior. + +This fix is not invoked during "energy minimization"_minimize.html. + +[Restrictions:] + +The {langevin/spin} fix is part of the SPIN package. This style is +only enabled if LAMMPS was built with this package. See the "Build +package"_Build_package.html doc page for more info. + +The numerical integration has to be performed with {fix nve/spin} +when {fix langevin/spin} is enabled. + +This fix has to be the last defined magnetic fix before the time +integration fix (e.g. {fix nve/spin}). + +[Related commands:] + +"fix nve/spin"_fix_nve_spin.html, "fix precession/spin"_fix_precession_spin.html + +[Default:] none + +:line + +:link(Mayergoyz1) +[(Mayergoyz)] I.D. Mayergoyz, G. Bertotti, C. Serpico (2009). Elsevier (2009) + +:link(Tranchida2) +[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson, +Journal of Computational Physics, (2018). diff --git a/doc/src/fix_latte.txt b/doc/src/fix_latte.txt index 4edd610546..c97095bcfc 100644 --- a/doc/src/fix_latte.txt +++ b/doc/src/fix_latte.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -44,7 +44,7 @@ Once LAMMPS is built with the LATTE package, you can run the example input scripts for molecular dynamics or energy minimization that are found in examples/latte. -A step-by-step tutorial can be follwed at: "LAMMPS-LATTE +A step-by-step tutorial can be followed at: "LAMMPS-LATTE tutorial"_https://github.com/lanl/LATTE/wiki/Using-LATTE-through-LAMMPS The {peID} argument is not yet supported by fix latte, so it must be @@ -118,9 +118,9 @@ of "thermodynamic output"_thermo_style.html. The default is {virial yes} This fix computes a global scalar which can be accessed by various -"output commands"_Section_howto.html#howto_15. The scalar is the -potential energy discussed above. The scalar value calculated by this -fix is "extensive". +"output commands"_Howto_output.html. The scalar is the potential +energy discussed above. The scalar value calculated by this fix is +"extensive". No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. @@ -136,11 +136,11 @@ quantity being minimized), you MUST enable the [Restrictions:] This fix is part of the LATTE package. It is only enabled if LAMMPS -was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +was built with that package. See the "Build +package"_Build_package.html doc page for more info. -You must use metal units, as set by the "units"_units command to use -this fix. +You must use metal units, as set by the "units"_units.html command to +use this fix. LATTE does not currently compute per-atom energy or per-atom virial contributions. So they will not show up as part of the calculations @@ -154,8 +154,8 @@ doing 99% or more of the work to compute quantum-accurate forces. NOTE: NEB calculations can be done using this fix using multiple replicas and running LAMMPS in parallel. However, each replica must be run on a single MPI task. For details, see the "neb"_neb.html -command and -partition command-line explained in "Section -2.6"_Section_start.html#start_6 of the manual. +command doc page and the "-partition command-line +switch"_Run_options.html [Related commands:] none diff --git a/doc/src/fix_lb_fluid.txt b/doc/src/fix_lb_fluid.txt index fc6203b0f2..d9012d8cb3 100644 --- a/doc/src/fix_lb_fluid.txt +++ b/doc/src/fix_lb_fluid.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -187,7 +187,7 @@ NOTE: Care must be taken when choosing both a value for dx, and a simulation domain size. This fix uses the same subdivision of the simulation domain among processors as the main LAMMPS program. In order to uniformly cover the simulation domain with lattice sites, the -lengths of the individual LAMMPS subdomains must all be evenly +lengths of the individual LAMMPS sub-domains must all be evenly divisible by dx. If the simulation domain size is cubic, with equal lengths in all dimensions, and the default value for dx is used, this will automatically be satisfied. @@ -299,16 +299,16 @@ is written to the main LAMMPS "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored by this fix for -access by various "output commands"_Section_howto.html#howto_15. No -parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy +access by various "output commands"_Howto_output.html. No parameter +of this fix can be used with the {start/stop} keywords of the +"run"_run.html command. This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] This fix is part of the USER-LB package. It is only enabled if LAMMPS -was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +was built with that package. See the "Build +package"_Build_package.html doc page for more info. This fix can only be used with an orthogonal simulation domain. diff --git a/doc/src/fix_lb_momentum.txt b/doc/src/fix_lb_momentum.txt index 97965e870d..408978f64c 100644 --- a/doc/src/fix_lb_momentum.txt +++ b/doc/src/fix_lb_momentum.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -49,10 +49,10 @@ dimension. No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can be -used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. [Restrictions:] @@ -61,8 +61,8 @@ Can only be used if a lattice-Boltzmann fluid has been created via the command. This fix is part of the USER-LB package. It is only enabled if LAMMPS -was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/fix_lb_pc.txt b/doc/src/fix_lb_pc.txt index d2b6aafaab..05b5eb20a2 100644 --- a/doc/src/fix_lb_pc.txt +++ b/doc/src/fix_lb_pc.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -34,16 +34,16 @@ algorithm if the force coupling constant has been set by default. No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can be -used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. [Restrictions:] This fix is part of the USER-LB package. It is only enabled if LAMMPS -was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +was built with that package. See the "Build +package"_Build_package.html doc page for more info. Can only be used if a lattice-Boltzmann fluid has been created via the "fix lb/fluid"_fix_lb_fluid.html command, and must come after this diff --git a/doc/src/fix_lb_rigid_pc_sphere.txt b/doc/src/fix_lb_rigid_pc_sphere.txt index 468ebe1ff5..ddaa552ecc 100644 --- a/doc/src/fix_lb_rigid_pc_sphere.txt +++ b/doc/src/fix_lb_rigid_pc_sphere.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -80,12 +80,12 @@ assumes the constituent atoms are point particles); see No information about the {rigid} and {rigid/nve} fixes are written to "binary restart files"_restart.html. -Similar to the "fix rigid"_fix_rigid.html command: The rigid -fix computes a global scalar which can be accessed by various "output -commands"_Section_howto.html#howto_15. The scalar value calculated by -these fixes is "intensive". The scalar is the current temperature of -the collection of rigid bodies. This is averaged over all rigid -bodies and their translational and rotational degrees of freedom. The +Similar to the "fix rigid"_fix_rigid.html command: The rigid fix +computes a global scalar which can be accessed by various "output +commands"_Howto_output.html. The scalar value calculated by these +fixes is "intensive". The scalar is the current temperature of the +collection of rigid bodies. This is averaged over all rigid bodies +and their translational and rotational degrees of freedom. The translational energy of a rigid body is 1/2 m v^2, where m = total mass of the body and v = the velocity of its center of mass. The rotational energy of a rigid body is 1/2 I w^2, where I = the moment @@ -94,17 +94,17 @@ of freedom constrained by the {force} and {torque} keywords are removed from this calculation. All of these fixes compute a global array of values which can be -accessed by various "output commands"_Section_howto.html#howto_15. -The number of rows in the array is equal to the number of rigid -bodies. The number of columns is 15. Thus for each rigid body, 15 -values are stored: the xyz coords of the center of mass (COM), the xyz -components of the COM velocity, the xyz components of the force acting -on the COM, the xyz components of the torque acting on the COM, and -the xyz image flags of the COM, which have the same meaning as image -flags for atom positions (see the "dump" command). The force and -torque values in the array are not affected by the {force} and -{torque} keywords in the fix rigid command; they reflect values before -any changes are made by those keywords. +accessed by various "output commands"_Howto_output.html. The number +of rows in the array is equal to the number of rigid bodies. The +number of columns is 15. Thus for each rigid body, 15 values are +stored: the xyz coords of the center of mass (COM), the xyz components +of the COM velocity, the xyz components of the force acting on the +COM, the xyz components of the torque acting on the COM, and the xyz +image flags of the COM, which have the same meaning as image flags for +atom positions (see the "dump" command). The force and torque values +in the array are not affected by the {force} and {torque} keywords in +the fix rigid command; they reflect values before any changes are made +by those keywords. The ordering of the rigid bodies (by row in the array) is as follows. For the {single} keyword there is just one rigid body. For the @@ -122,8 +122,8 @@ of the "run"_run.html command. These fixes are not invoked during [Restrictions:] This fix is part of the USER-LB package. It is only enabled if LAMMPS -was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +was built with that package. See the "Build +package"_Build_package.html doc page for more info. Can only be used if a lattice-Boltzmann fluid has been created via the "fix lb/fluid"_fix_lb_fluid.html command, and must come after this diff --git a/doc/src/fix_lb_viscous.txt b/doc/src/fix_lb_viscous.txt index fcc69d2b43..ba91a2cd54 100644 --- a/doc/src/fix_lb_viscous.txt +++ b/doc/src/fix_lb_viscous.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -57,9 +57,9 @@ As described in the "fix viscous"_fix_viscous.html documentation: "No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. The forces due to this fix are imposed during an energy minimization, invoked by the "minimize"_minimize.html command. This fix should only @@ -70,8 +70,8 @@ for details." [Restrictions:] This fix is part of the USER-LB package. It is only enabled if LAMMPS -was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +was built with that package. See the "Build +package"_Build_package.html doc page for more info. Can only be used if a lattice-Boltzmann fluid has been created via the "fix lb/fluid"_fix_lb_fluid.html command, and must come after this diff --git a/doc/src/fix_lineforce.txt b/doc/src/fix_lineforce.txt index 65672fc5a5..3114ed6250 100644 --- a/doc/src/fix_lineforce.txt +++ b/doc/src/fix_lineforce.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -35,9 +35,9 @@ it should continue to move along the line thereafter. No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. The forces due to this fix are imposed during an energy minimization, invoked by the "minimize"_minimize.html command. diff --git a/doc/src/fix_manifoldforce.txt b/doc/src/fix_manifoldforce.txt index 5fc25167a7..a25b9f0b2e 100644 --- a/doc/src/fix_manifoldforce.txt +++ b/doc/src/fix_manifoldforce.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -24,10 +24,14 @@ fix constrain all manifoldforce sphere 5.0 [Description:] -This fix subtracts each time step from the force the component along the normal of the specified "manifold"_manifolds.html. -This can be used in combination with "minimize"_minimize.html to remove overlap between particles while -keeping them (roughly) constrained to the given manifold, e.g. to set up a run with "fix nve/manifold/rattle"_fix_nve_manifold_rattle.html. -I have found that only {hftn} and {quickmin} with a very small time step perform adequately though. +This fix subtracts each time step from the force the component along +the normal of the specified "manifold"_Howto_manifold.html. This can be +used in combination with "minimize"_minimize.html to remove overlap +between particles while keeping them (roughly) constrained to the +given manifold, e.g. to set up a run with "fix +nve/manifold/rattle"_fix_nve_manifold_rattle.html. I have found that +only {hftn} and {quickmin} with a very small time step perform +adequately though. :line @@ -36,26 +40,27 @@ I have found that only {hftn} and {quickmin} with a very small time step perform No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. -This fix is invoked during "energy minimization"_minimize.html. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is invoked during "energy +minimization"_minimize.html. :line [Restrictions:] -This fix is part of the USER-MANIFOLD package. It is only enabled if LAMMPS -was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 -section for more info. +This fix is part of the USER-MANIFOLD package. It is only enabled if +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. -Only use this with {min_style hftn} or {min_style quickmin}. If not, the constraints -will not be satisfied very well at all. A warning is generated if the {min_style} is -incompatible but no error. +Only use this with {min_style hftn} or {min_style quickmin}. If not, +the constraints will not be satisfied very well at all. A warning is +generated if the {min_style} is incompatible but no error. :line [Related commands:] -"fix nve/manifold/rattle"_fix_nve_manifold_rattle.html, "fix nvt/manifold/rattle"_fix_nvt_manifold_rattle.html +"fix nve/manifold/rattle"_fix_nve_manifold_rattle.html, "fix +nvt/manifold/rattle"_fix_nvt_manifold_rattle.html diff --git a/doc/src/fix_meso.txt b/doc/src/fix_meso.txt index 85f5838dd2..8c0ce5a9b7 100644 --- a/doc/src/fix_meso.txt +++ b/doc/src/fix_meso.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -34,16 +34,16 @@ LAMMPS. No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. [Restrictions:] This fix is part of the USER-SPH package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/fix_meso_stationary.txt b/doc/src/fix_meso_stationary.txt index 5b83573bc8..1a546efec0 100644 --- a/doc/src/fix_meso_stationary.txt +++ b/doc/src/fix_meso_stationary.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -35,16 +35,16 @@ LAMMPS. No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. [Restrictions:] This fix is part of the USER-SPH package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/fix_modify.txt b/doc/src/fix_modify.txt index 308bba1ac3..f50747948a 100644 --- a/doc/src/fix_modify.txt +++ b/doc/src/fix_modify.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -21,7 +21,7 @@ keyword = {temp} or {press} or {energy} or {virial} or {respa} or {dynamic/dof} {virial} value = {yes} or {no} {respa} value = {1} to {max respa level} or {0} (for outermost level) {dynamic/dof} value = {yes} or {no} - yes/no = do or do not recompute the number of degrees of freedom (DOF) contributing to the temperature + yes/no = do or do not re-compute the number of degrees of freedom (DOF) contributing to the temperature {bodyforces} value = {early} or {late} early/late = compute rigid-body forces/torques early or late in the timestep :pre :ule diff --git a/doc/src/fix_momentum.txt b/doc/src/fix_momentum.txt index bcf4465fb8..aeedad0719 100644 --- a/doc/src/fix_momentum.txt +++ b/doc/src/fix_momentum.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -61,33 +61,32 @@ initial velocities with zero aggregate linear and/or angular momentum. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. [Restart, fix_modify, output, run start/stop, minimize info:] No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. [Restrictions:] none diff --git a/doc/src/fix_move.txt b/doc/src/fix_move.txt index 7cb40ad132..08f38d0ed6 100644 --- a/doc/src/fix_move.txt +++ b/doc/src/fix_move.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -203,10 +203,9 @@ None of the "fix_modify"_fix_modify.html options are relevant to this fix. This fix produces a per-atom array which can be accessed by various -"output commands"_Section_howto.html#howto_15. The number of columns -for each atom is 3, and the columns store the original unwrapped x,y,z -coords of each atom. The per-atom values can be accessed on any -timestep. +"output commands"_Howto_output.html. The number of columns for each +atom is 3, and the columns store the original unwrapped x,y,z coords +of each atom. The per-atom values can be accessed on any timestep. No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. This fix is not invoked during "energy diff --git a/doc/src/fix_mscg.txt b/doc/src/fix_mscg.txt index 7d16967955..1ad7804127 100644 --- a/doc/src/fix_mscg.txt +++ b/doc/src/fix_mscg.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -103,8 +103,8 @@ dihedrals a bead can have in the coarse-grained model. [Restrictions:] This fix is part of the MSCG package. It is only enabled if LAMMPS was -built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +built with that package. See the "Build package"_Build_package.html +doc page for more info. The MS-CG library uses C++11, which may not be supported by older compilers. The MS-CG library also has some additional numeric library diff --git a/doc/src/fix_msst.txt b/doc/src/fix_msst.txt index 310692669a..e31f61e5f7 100644 --- a/doc/src/fix_msst.txt +++ b/doc/src/fix_msst.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -156,14 +156,14 @@ thermo_style custom step temp ke pe lz pzz etotal v_dhug v_dray v_lgr_vel v_ These fixes compute a global scalar and a global vector of 4 quantities, which can be accessed by various "output -commands"_Section_howto.html#howto_15. The scalar values calculated -by this fix are "extensive"; the vector values are "intensive". +commands"_Howto_output.html. The scalar values calculated by this fix +are "extensive"; the vector values are "intensive". [Restrictions:] This fix style is part of the SHOCK package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. All cell dimensions must be periodic. This fix can not be used with a triclinic cell. The MSST fix has been tested only for the group-ID diff --git a/doc/src/fix_mvv_dpd.txt b/doc/src/fix_mvv_dpd.txt index fb3c6fe888..507f271469 100644 --- a/doc/src/fix_mvv_dpd.txt +++ b/doc/src/fix_mvv_dpd.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -69,16 +69,16 @@ addition to position and velocity, and must be used with the No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. [Restrictions:] This fix is part of the USER-MESO package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/fix_neb.txt b/doc/src/fix_neb.txt index 5d18c39d99..521dfff12b 100644 --- a/doc/src/fix_neb.txt +++ b/doc/src/fix_neb.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -43,9 +43,9 @@ Add nudging forces to atoms in the group for a multi-replica simulation run via the "neb"_neb.html command to perform a nudged elastic band (NEB) calculation for finding the transition state. Hi-level explanations of NEB are given with the "neb"_neb.html command -and in "Section_howto 5"_Section_howto.html#howto_5 of the manual. -The fix neb command must be used with the "neb" command and defines -how inter-replica nudging forces are computed. A NEB calculation is +and on the "Howto replica"_Howto_replica.html doc page. The fix neb +command must be used with the "neb" command and defines how +inter-replica nudging forces are computed. A NEB calculation is divided in two stages. In the first stage n replicas are relaxed toward a MEP until convergence. In the second stage, the climbing image scheme (see "(Henkelman2)"_#Henkelman2) is enabled, so that the @@ -168,7 +168,7 @@ The difference between these two {estyle} options is as follows. When {estyle} is specified as {last/efirst}, no change is made to the inter-replica force applied to the intermediate replicas (neither first or last). If the initial path is too far from the MEP, an -intermediate repilica may relax "faster" and reach a lower energy than +intermediate replica may relax "faster" and reach a lower energy than the last replica. In this case the intermediate replica will be relaxing toward its own local minima. This behavior can be prevented by specifying {estyle} as {last/efirst/middle} which will alter the @@ -192,9 +192,9 @@ target energy. No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. The forces due to this fix are imposed during an energy minimization, as invoked by the "minimize"_minimize.html command via the @@ -203,8 +203,8 @@ as invoked by the "minimize"_minimize.html command via the [Restrictions:] This command can only be used if LAMMPS was built with the REPLICA -package. See the "Making LAMMPS"_Section_start.html#start_3 section -for more info on packages. +package. See the "Build package"_Build_package.html doc +page for more info. [Related commands:] diff --git a/doc/src/fix_nh.txt b/doc/src/fix_nh.txt index 41d0e6438f..644ced4bdc 100644 --- a/doc/src/fix_nh.txt +++ b/doc/src/fix_nh.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -386,9 +386,10 @@ have their temperature controlled by another fix - e.g. by "fix langevin"_fix_nh.html or "fix temp/rescale"_fix_temp_rescale.html commands. -See "this howto section"_Section_howto.html#howto_16 of the manual for -a discussion of different ways to compute temperature and perform -thermostatting and barostatting. +See the "Howto thermostat"_Howto_thermostat.html and "Howto +barostat"_Howto_barostat.html doc pages for a discussion of different +ways to compute temperature and perform thermostatting and +barostatting. :line @@ -484,23 +485,22 @@ the various ways to do this. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line @@ -538,9 +538,9 @@ and barostatting to the system's potential energy as part of "thermodynamic output"_thermo_style.html. These fixes compute a global scalar and a global vector of quantities, -which can be accessed by various "output -commands"_Section_howto.html#howto_15. The scalar value calculated by -these fixes is "extensive"; the vector values are "intensive". +which can be accessed by various "output commands"_Howto_output.html. +The scalar value calculated by these fixes is "extensive"; the vector +values are "intensive". The scalar is the cumulative energy change due to the fix. diff --git a/doc/src/fix_nh_eff.txt b/doc/src/fix_nh_eff.txt index 1731f1f331..d7c0457708 100644 --- a/doc/src/fix_nh_eff.txt +++ b/doc/src/fix_nh_eff.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -101,8 +101,8 @@ for details. [Restrictions:] This fix is part of the USER-EFF package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. Other restriction discussed on the doc page for the "fix nvt, npt, and nph"_fix_nh.html commands also apply. diff --git a/doc/src/fix_nh_uef.txt b/doc/src/fix_nh_uef.txt index bde1818371..dc05948de3 100644 --- a/doc/src/fix_nh_uef.txt +++ b/doc/src/fix_nh_uef.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -174,7 +174,7 @@ This fix can be used with the "fix_modify"_fix_modify.html {temp} and {press} options. The temperature and pressure computes used must be of type {temp/uef} and {pressure/uef}. -This fix computes the same global scalar and vecor quantities as "fix +This fix computes the same global scalar and vector quantities as "fix npt"_fix_nh.html. The fix is not invoked during "energy minimization"_minimize.html. @@ -182,8 +182,8 @@ The fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] This fix is part of the USER-UEF package. It is only enabled if LAMMPS -was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +was built with that package. See the "Build +package"_Build_package.html doc page for more info. Due to requirements of the boundary conditions, when the {strain} keyword is set to zero (or unset), the initial simulation box must be diff --git a/doc/src/fix_nph_asphere.txt b/doc/src/fix_nph_asphere.txt index 8c35b6a1a7..5cabf930e7 100644 --- a/doc/src/fix_nph_asphere.txt +++ b/doc/src/fix_nph_asphere.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -81,23 +81,22 @@ It also means that changing attributes of {thermo_temp} or Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. [Restart, fix_modify, output, run start/stop, minimize info:] @@ -133,8 +132,8 @@ This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] This fix is part of the ASPHERE package. It is only enabled if LAMMPS -was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +was built with that package. See the "Build +package"_Build_package.html doc page for more info. This fix requires that atoms store torque and angular momentum and a quaternion as defined by the "atom_style ellipsoid"_atom_style.html diff --git a/doc/src/fix_nph_body.txt b/doc/src/fix_nph_body.txt index 1e590f1cb3..e04c240de9 100644 --- a/doc/src/fix_nph_body.txt +++ b/doc/src/fix_nph_body.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -80,23 +80,22 @@ It also means that changing attributes of {thermo_temp} or Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. [Restart, fix_modify, output, run start/stop, minimize info:] @@ -132,8 +131,8 @@ This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] This fix is part of the BODY package. It is only enabled if LAMMPS -was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +was built with that package. See the "Build +package"_Build_package.html doc page for more info. This fix requires that atoms store torque and angular momentum and a quaternion as defined by the "atom_style body"_atom_style.html diff --git a/doc/src/fix_nph_sphere.txt b/doc/src/fix_nph_sphere.txt index 62b45edfd7..f94c057c93 100644 --- a/doc/src/fix_nph_sphere.txt +++ b/doc/src/fix_nph_sphere.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -90,23 +90,22 @@ It also means that changing attributes of {thermo_temp} or Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. [Restart, fix_modify, output, run start/stop, minimize info:] diff --git a/doc/src/fix_nphug.txt b/doc/src/fix_nphug.txt index 292e46f94a..855a4c9ae4 100644 --- a/doc/src/fix_nphug.txt +++ b/doc/src/fix_nphug.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -140,23 +140,22 @@ It also means that changing attributes of {thermo_temp} or Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line @@ -193,9 +192,9 @@ included in the definition of internal energy E when calculating the value of Delta in the above equation. These fixes compute a global scalar and a global vector of quantities, -which can be accessed by various "output -commands"_Section_howto.html#howto_15. The scalar value calculated by -these fixes is "extensive"; the vector values are "intensive". +which can be accessed by various "output commands"_Howto_output.html. +The scalar value calculated by these fixes is "extensive"; the vector +values are "intensive". The scalar is the cumulative energy change due to the fix. @@ -209,8 +208,8 @@ shock calculated from the RH conditions. They have units of distance/time. [Restrictions:] This fix style is part of the SHOCK package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. All the usual restrictions for "fix npt"_fix_nh.html apply, plus the additional ones mentioned above. diff --git a/doc/src/fix_npt_asphere.txt b/doc/src/fix_npt_asphere.txt index 5f3979e36e..194f4ff499 100644 --- a/doc/src/fix_npt_asphere.txt +++ b/doc/src/fix_npt_asphere.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -105,23 +105,22 @@ thermal degrees of freedom, and the bias is added back in. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. [Restart, fix_modify, output, run start/stop, minimize info:] @@ -158,8 +157,8 @@ This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] This fix is part of the ASPHERE package. It is only enabled if LAMMPS -was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +was built with that package. See the "Build +package"_Build_package.html doc page for more info. This fix requires that atoms store torque and angular momentum and a quaternion as defined by the "atom_style ellipsoid"_atom_style.html diff --git a/doc/src/fix_npt_body.txt b/doc/src/fix_npt_body.txt index d89bf19db2..1d608137b6 100644 --- a/doc/src/fix_npt_body.txt +++ b/doc/src/fix_npt_body.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -104,23 +104,22 @@ thermal degrees of freedom, and the bias is added back in. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. [Restart, fix_modify, output, run start/stop, minimize info:] @@ -157,8 +156,8 @@ This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] This fix is part of the BODY package. It is only enabled if LAMMPS -was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +was built with that package. See the "Build +package"_Build_package.html doc page for more info. This fix requires that atoms store torque and angular momentum and a quaternion as defined by the "atom_style body"_atom_style.html diff --git a/doc/src/fix_npt_sphere.txt b/doc/src/fix_npt_sphere.txt index c4cf2cb08d..6ebb68e176 100644 --- a/doc/src/fix_npt_sphere.txt +++ b/doc/src/fix_npt_sphere.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -115,23 +115,22 @@ thermal degrees of freedom, and the bias is added back in. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. [Restart, fix_modify, output, run start/stop, minimize info:] diff --git a/doc/src/fix_nve.txt b/doc/src/fix_nve.txt index c04c17858e..2347f957ae 100644 --- a/doc/src/fix_nve.txt +++ b/doc/src/fix_nve.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -34,23 +34,22 @@ ensemble. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line @@ -59,10 +58,10 @@ more instructions on how to use the accelerated styles effectively. No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. [Restrictions:] none diff --git a/doc/src/fix_nve_asphere.txt b/doc/src/fix_nve_asphere.txt index 1f31fb9679..bd9e4ae873 100644 --- a/doc/src/fix_nve_asphere.txt +++ b/doc/src/fix_nve_asphere.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -35,41 +35,40 @@ assumes point particles and only updates their position and velocity. No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. :line Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line [Restrictions:] This fix is part of the ASPHERE package. It is only enabled if LAMMPS -was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +was built with that package. See the "Build +package"_Build_package.html doc page for more info. This fix requires that atoms store torque and angular momentum and a quaternion as defined by the "atom_style ellipsoid"_atom_style.html diff --git a/doc/src/fix_nve_asphere_noforce.txt b/doc/src/fix_nve_asphere_noforce.txt index 5f1b271546..c0598e8839 100644 --- a/doc/src/fix_nve_asphere_noforce.txt +++ b/doc/src/fix_nve_asphere_noforce.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -29,7 +29,7 @@ angular momenta are used to update their positions and orientation. This is useful as an implicit time integrator for Fast Lubrication Dynamics, since the velocity and angular momentum are updated by the -"pair_style lubricuteU"_pair_lubricateU.txt command. +"pair_style lubricuteU"_pair_lubricateU.html command. :line @@ -38,16 +38,16 @@ Dynamics, since the velocity and angular momentum are updated by the No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. [Restrictions:] This fix is part of the ASPHERE package. It is only enabled if LAMMPS -was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +was built with that package. See the "Build +package"_Build_package.html doc page for more info. This fix requires that atoms store torque and angular momentum and a quaternion as defined by the "atom_style ellipsoid"_atom_style.html diff --git a/doc/src/fix_nve_body.txt b/doc/src/fix_nve_body.txt index 604b5391cd..1a9efb5e13 100644 --- a/doc/src/fix_nve_body.txt +++ b/doc/src/fix_nve_body.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -24,9 +24,9 @@ fix 1 all nve/body :pre Perform constant NVE integration to update position, velocity, orientation, and angular velocity for body particles in the group each timestep. V is volume; E is energy. This creates a system trajectory -consistent with the microcanonical ensemble. See "Section -6.14"_Section_howto.html#howto_14 of the manual and the "body"_body.html -doc page for more details on using body particles. +consistent with the microcanonical ensemble. See the "Howto +body"_Howto_body.html doc page for more details on using body +particles. This fix differs from the "fix nve"_fix_nve.html command, which assumes point particles and only updates their position and velocity. @@ -36,16 +36,16 @@ assumes point particles and only updates their position and velocity. No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. [Restrictions:] This fix is part of the BODY package. It is only enabled if LAMMPS -was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +was built with that package. See the "Build +package"_Build_package.html doc page for more info. This fix requires that atoms store torque and angular momentum and a quaternion as defined by the "atom_style body"_atom_style.html diff --git a/doc/src/fix_nve_dot.txt b/doc/src/fix_nve_dot.txt index 0e0c8f8ecf..06140c2d37 100644 --- a/doc/src/fix_nve_dot.txt +++ b/doc/src/fix_nve_dot.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -44,8 +44,8 @@ A technical report with more information on this integrator can be found [Restrictions:] These pair styles can only be used if LAMMPS was built with the -"USER-CGDNA"_#USER-CGDNA package and the MOLECULE and ASPHERE package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info on packages. +"USER-CGDNA"_Package_details.html#PKG-USER-CGDNA package and the MOLECULE and ASPHERE package. +See the "Build package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/fix_nve_dotc_langevin.txt b/doc/src/fix_nve_dotc_langevin.txt index 93d875bca5..7339f251ad 100644 --- a/doc/src/fix_nve_dotc_langevin.txt +++ b/doc/src/fix_nve_dotc_langevin.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -122,8 +122,8 @@ A technical report with more information on this integrator can be found [Restrictions:] These pair styles can only be used if LAMMPS was built with the -"USER-CGDNA"_#USER-CGDNA package and the MOLECULE and ASPHERE package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info on packages. +"USER-CGDNA"_Package_details.html#PKG-USER-CGDNA package and the MOLECULE and ASPHERE package. +See the "Build package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/fix_nve_eff.txt b/doc/src/fix_nve_eff.txt index 156f184dac..556b95deba 100644 --- a/doc/src/fix_nve_eff.txt +++ b/doc/src/fix_nve_eff.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -35,16 +35,16 @@ of electrons are also updated. No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. [Restrictions:] This fix is part of the USER-EFF package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/fix_nve_limit.txt b/doc/src/fix_nve_limit.txt index 2ecec83e9c..8c8c66a0da 100644 --- a/doc/src/fix_nve_limit.txt +++ b/doc/src/fix_nve_limit.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -63,14 +63,14 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. This fix computes a global scalar which can be accessed by various -"output commands"_Section_howto.html#howto_15. The scalar is the -count of how many updates of atom's velocity/position were limited by -the maximum distance criterion. This should be roughly the number of -atoms so affected, except that updates occur at both the beginning and -end of a timestep in a velocity Verlet timestepping algorithm. This -is a cumulative quantity for the current run, but is re-initialized to -zero each time a run is performed. The scalar value calculated by -this fix is "extensive". +"output commands"_Howto_output.html. The scalar is the count of how +many updates of atom's velocity/position were limited by the maximum +distance criterion. This should be roughly the number of atoms so +affected, except that updates occur at both the beginning and end of a +timestep in a velocity Verlet timestepping algorithm. This is a +cumulative quantity for the current run, but is re-initialized to zero +each time a run is performed. The scalar value calculated by this fix +is "extensive". No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. This fix is not invoked during "energy diff --git a/doc/src/fix_nve_line.txt b/doc/src/fix_nve_line.txt index ac5206aa5c..896e3b810d 100644 --- a/doc/src/fix_nve_line.txt +++ b/doc/src/fix_nve_line.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -24,9 +24,9 @@ fix 1 all nve/line :pre Perform constant NVE integration to update position, velocity, orientation, and angular velocity for line segment particles in the group each timestep. V is volume; E is energy. This creates a system -trajectory consistent with the microcanonical ensemble. See -"Section 6.14"_Section_howto.html#howto_14 of the manual for an -overview of using line segment particles. +trajectory consistent with the microcanonical ensemble. See "Howto +spherical"_Howto_spherical.html doc page for an overview of using line +segment particles. This fix differs from the "fix nve"_fix_nve.html command, which assumes point particles and only updates their position and velocity. @@ -36,16 +36,16 @@ assumes point particles and only updates their position and velocity. No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. [Restrictions:] This fix is part of the ASPHERE package. It is only enabled if LAMMPS -was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +was built with that package. See the "Build +package"_Build_package.html doc page for more info. This fix requires that particles be line segments as defined by the "atom_style line"_atom_style.html command. diff --git a/doc/src/fix_nve_manifold_rattle.txt b/doc/src/fix_nve_manifold_rattle.txt index e032a7e1cc..5301ea603c 100644 --- a/doc/src/fix_nve_manifold_rattle.txt +++ b/doc/src/fix_nve_manifold_rattle.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -40,7 +40,7 @@ the dynamics of particles constrained to curved surfaces can be studied. If combined with "fix langevin"_fix_langevin.html, this generates Brownian motion of particles constrained to a curved surface. For a list of currently supported manifolds and their -parameters, see "manifolds"_manifolds.html. +parameters, see the "Howto manifold"_Howto_manifold.html doc page. Note that the particles must initially be close to the manifold in question. If not, RATTLE will not be able to iterate until the @@ -68,18 +68,18 @@ conserved. No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. :line [Restrictions:] This fix is part of the USER-MANIFOLD package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. :line diff --git a/doc/src/fix_nve_noforce.txt b/doc/src/fix_nve_noforce.txt index a0dbcc80f1..da8d16bbb7 100644 --- a/doc/src/fix_nve_noforce.txt +++ b/doc/src/fix_nve_noforce.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -40,10 +40,10 @@ fcm() group function to compute the total force on the group of atoms. No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. [Restrictions:] none diff --git a/doc/src/fix_nve_sphere.txt b/doc/src/fix_nve_sphere.txt index 21dc6cba8a..818940a9bd 100644 --- a/doc/src/fix_nve_sphere.txt +++ b/doc/src/fix_nve_sphere.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -65,23 +65,22 @@ moment of inertia, as used in the time integration. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line @@ -90,10 +89,10 @@ more instructions on how to use the accelerated styles effectively. No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. [Restrictions:] diff --git a/doc/src/fix_nve_spin.txt b/doc/src/fix_nve_spin.txt new file mode 100644 index 0000000000..08f0eab61d --- /dev/null +++ b/doc/src/fix_nve_spin.txt @@ -0,0 +1,76 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +fix nve/spin command :h3 + +[Syntax:] + +fix ID group-ID nve/spin keyword values :pre + +ID, group-ID are documented in "fix"_fix.html command :ulb,l +nve/spin = style name of this fix command :l +keyword = {lattice} :l + {lattice} value = {no} or {yes} :pre +:ule + +[Examples:] + +fix 3 all nve/spin lattice yes +fix 1 all nve/spin lattice no :pre + +[Description:] + +Perform a symplectic integration for the spin or spin-lattice system. + +The {lattice} keyword defines if the spins are integrated on a lattice +of fixed atoms (lattice = no), or if atoms are moving (lattice = yes). + +By default (lattice = yes), a spin-lattice integration is performed. + +The {nve/spin} fix applies a Suzuki-Trotter decomposition to +the equations of motion of the spin lattice system, following the scheme: + +:c,image(Eqs/fix_integration_spin_stdecomposition.jpg) + +according to the implementation reported in "(Omelyan)"_#Omelyan1. + +A sectoring method enables this scheme for parallel calculations. +The implementation of this sectoring algorithm is reported +in "(Tranchida)"_#Tranchida1. + +:line + +[Restrictions:] + +This fix style can only be used if LAMMPS was built with the SPIN +package. See the "Build package"_Build_package.html doc page for more +info. + +To use the spin algorithm, it is necessary to define a map with +the atom_modify command. Typically, by adding the command: + +atom_modify map array :pre + +before you create the simulation box. Note that the keyword "hash" +instead of "array" is also valid. + +[Related commands:] + +"atom_style spin"_atom_style.html, "fix nve"_fix_nve.html + +[Default:] none + +:line + +:link(Omelyan1) +[(Omelyan)] Omelyan, Mryglod, and Folk. Phys. Rev. Lett. +86(5), 898. (2001). + +:link(Tranchida1) +[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson, +Journal of Computational Physics, (2018). diff --git a/doc/src/fix_nve_tri.txt b/doc/src/fix_nve_tri.txt index cee27e2fa4..c14907ca02 100644 --- a/doc/src/fix_nve_tri.txt +++ b/doc/src/fix_nve_tri.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -23,10 +23,10 @@ fix 1 all nve/tri :pre Perform constant NVE integration to update position, velocity, orientation, and angular momentum for triangular particles in the -group each timestep. V is volume; E is energy. This creates a -system trajectory consistent with the microcanonical ensemble. See -"Section 6.14"_Section_howto.html#howto_14 of the manual for an -overview of using triangular particles. +group each timestep. V is volume; E is energy. This creates a system +trajectory consistent with the microcanonical ensemble. See the +"Howto spherical"_Howto_spherical.html doc page for an overview of +using triangular particles. This fix differs from the "fix nve"_fix_nve.html command, which assumes point particles and only updates their position and velocity. @@ -36,16 +36,16 @@ assumes point particles and only updates their position and velocity. No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. [Restrictions:] This fix is part of the ASPHERE package. It is only enabled if LAMMPS -was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +was built with that package. See the "Build +package"_Build_package.html doc page for more info. This fix requires that particles be triangles as defined by the "atom_style tri"_atom_style.html command. diff --git a/doc/src/fix_nvk.txt b/doc/src/fix_nvk.txt index 49fd8217ab..98f63487b7 100644 --- a/doc/src/fix_nvk.txt +++ b/doc/src/fix_nvk.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -42,10 +42,10 @@ energy prior to this fix. No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. [Restrictions:] @@ -54,9 +54,9 @@ the simulation box. Therefore, the group must be set to all. This fix has not yet been implemented to work with the RESPA integrator. -This fix is part of the USER-MISC package. It is only enabled if LAMMPS -was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +This fix is part of the USER-MISC package. It is only enabled if +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] none diff --git a/doc/src/fix_nvt_asphere.txt b/doc/src/fix_nvt_asphere.txt index 21b900f16a..a2187f8495 100644 --- a/doc/src/fix_nvt_asphere.txt +++ b/doc/src/fix_nvt_asphere.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -86,23 +86,22 @@ thermal degrees of freedom, and the bias is added back in. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. [Restart, fix_modify, output, run start/stop, minimize info:] @@ -134,8 +133,8 @@ This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] This fix is part of the ASPHERE package. It is only enabled if LAMMPS -was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +was built with that package. See the "Build +package"_Build_package.html doc page for more info. This fix requires that atoms store torque and angular momentum and a quaternion as defined by the "atom_style ellipsoid"_atom_style.html diff --git a/doc/src/fix_nvt_body.txt b/doc/src/fix_nvt_body.txt index 6a5e09ba7f..62c7cfecf8 100644 --- a/doc/src/fix_nvt_body.txt +++ b/doc/src/fix_nvt_body.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -85,23 +85,22 @@ thermal degrees of freedom, and the bias is added back in. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. [Restart, fix_modify, output, run start/stop, minimize info:] @@ -133,8 +132,8 @@ This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] This fix is part of the BODY package. It is only enabled if LAMMPS -was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +was built with that package. See the "Build +package"_Build_package.html doc page for more info. This fix requires that atoms store torque and angular momentum and a quaternion as defined by the "atom_style body"_atom_style.html diff --git a/doc/src/fix_nvt_manifold_rattle.txt b/doc/src/fix_nvt_manifold_rattle.txt index a620648a46..0c4b81aa32 100644 --- a/doc/src/fix_nvt_manifold_rattle.txt +++ b/doc/src/fix_nvt_manifold_rattle.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -27,8 +27,6 @@ keyword = {temp} or {tchain} or {every} N = length of thermostat chain (1 = single thermostat) {every} value = N N = print info about iteration every N steps. N = 0 means no output :pre - - :ule [Examples:] @@ -37,9 +35,13 @@ fix 1 all nvt/manifold/rattle 1e-4 10 cylinder 3.0 temp 1.0 1.0 10.0 [Description:] -This fix combines the RATTLE-based "(Andersen)"_#Andersen2 time integrator of "fix nve/manifold/rattle"_fix_nve_manifold_rattle.html "(Paquay)"_#Paquay3 with a Nose-Hoover-chain thermostat to sample the -canonical ensemble of particles constrained to a curved surface (manifold). This sampling does suffer from discretization bias of O(dt). -For a list of currently supported manifolds and their parameters, see "manifolds"_manifolds.html +This fix combines the RATTLE-based "(Andersen)"_#Andersen2 time +integrator of "fix nve/manifold/rattle"_fix_nve_manifold_rattle.html +"(Paquay)"_#Paquay3 with a Nose-Hoover-chain thermostat to sample the +canonical ensemble of particles constrained to a curved surface +(manifold). This sampling does suffer from discretization bias of +O(dt). For a list of currently supported manifolds and their +parameters, see the "Howto manifold"_Howto_manifold.html doc page. :line @@ -48,27 +50,25 @@ For a list of currently supported manifolds and their parameters, see "manifolds No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. :line - [Restrictions:] -This fix is part of the USER-MANIFOLD package. It is only enabled if LAMMPS -was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 -section for more info. +This fix is part of the USER-MANIFOLD package. It is only enabled if +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. :line - [Related commands:] -"fix nve/manifold/rattle"_fix_nvt_manifold_rattle.html, "fix manifoldforce"_fix_manifoldforce.html -[Default:] every = 0 +"fix nve/manifold/rattle"_fix_nvt_manifold_rattle.html, "fix +manifoldforce"_fix_manifoldforce.html [Default:] every = 0 :line diff --git a/doc/src/fix_nvt_sllod.txt b/doc/src/fix_nvt_sllod.txt index 392dbc281c..97a864a231 100644 --- a/doc/src/fix_nvt_sllod.txt +++ b/doc/src/fix_nvt_sllod.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -109,23 +109,22 @@ thermal degrees of freedom, and the bias is added back in. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. [Restart, fix_modify, output, run start/stop, minimize info:] diff --git a/doc/src/fix_nvt_sllod_eff.txt b/doc/src/fix_nvt_sllod_eff.txt index 408eb1da01..5cba15c8cf 100644 --- a/doc/src/fix_nvt_sllod_eff.txt +++ b/doc/src/fix_nvt_sllod_eff.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -69,8 +69,8 @@ This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] This fix is part of the USER-EFF package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. This fix works best without Nose-Hoover chain thermostats, i.e. using tchain = 1. Setting tchain to larger values can result in poor diff --git a/doc/src/fix_nvt_sphere.txt b/doc/src/fix_nvt_sphere.txt index ecf0922b79..75222e0de8 100644 --- a/doc/src/fix_nvt_sphere.txt +++ b/doc/src/fix_nvt_sphere.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -96,23 +96,22 @@ thermal degrees of freedom, and the bias is added back in. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. [Restart, fix_modify, output, run start/stop, minimize info:] diff --git a/doc/src/fix_oneway.txt b/doc/src/fix_oneway.txt index 2d85c581eb..433ceb50f2 100644 --- a/doc/src/fix_oneway.txt +++ b/doc/src/fix_oneway.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -43,10 +43,10 @@ membrane, or as an implementation of Maxwell's demon. No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. [Restrictions:] none diff --git a/doc/src/fix_orient.txt b/doc/src/fix_orient.txt index 20ff94866e..9d8e4e8628 100644 --- a/doc/src/fix_orient.txt +++ b/doc/src/fix_orient.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -135,14 +135,14 @@ fixes. This allows to set at which level of the "r-RESPA"_run_style.html integrator a fix is adding its forces. Default is the outermost level. This fix calculates a global scalar which can be accessed by various -"output commands"_Section_howto.html#howto_15. The scalar is the -potential energy change due to this fix. The scalar value calculated -by this fix is "extensive". +"output commands"_Howto_output.html. The scalar is the potential +energy change due to this fix. The scalar value calculated by this +fix is "extensive". This fix also calculates a per-atom array which can be accessed by -various "output commands"_Section_howto.html#howto_15. The array -stores the order parameter Xi and normalized order parameter (0 to 1) -for each atom. The per-atom values can be accessed on any timestep. +various "output commands"_Howto_output.html. The array stores the +order parameter Xi and normalized order parameter (0 to 1) for each +atom. The per-atom values can be accessed on any timestep. No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. This fix is not invoked during "energy @@ -151,8 +151,8 @@ minimization"_minimize.html. [Restrictions:] This fix is part of the MISC package. It is only enabled if LAMMPS -was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +was built with that package. See the "Build +package"_Build_package.html doc page for more info. This fix should only be used with fcc or bcc lattices. diff --git a/doc/src/fix_phonon.txt b/doc/src/fix_phonon.txt index aad6c2bfaa..0c449899df 100644 --- a/doc/src/fix_phonon.txt +++ b/doc/src/fix_phonon.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -150,7 +150,7 @@ fix. You can use it to change the temperature compute from thermo_temp to the one that reflects the true temperature of atoms in the group. No global scalar or vector or per-atom quantities are stored by this -fix for access by various "output commands"_Section_howto.html#howto_15. +fix for access by various "output commands"_Howto_output.html. Instead, this fix outputs its initialization information (including mapping information) and the calculated dynamical matrices to the file @@ -171,11 +171,11 @@ temperature of the system should not exceed the melting temperature to keep the system in its solid state. This fix is part of the USER-PHONON package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. -This fix requires LAMMPS be built with an FFT library. See the -"Making LAMMPS"_Section_start.html#start_2 section for more info. +This fix requires LAMMPS be built with an FFT library. See the "Build +settings"_Build_settings.html doc page for details. [Related commands:] diff --git a/doc/src/fix_pimd.txt b/doc/src/fix_pimd.txt index 38022e4c7d..a826244973 100644 --- a/doc/src/fix_pimd.txt +++ b/doc/src/fix_pimd.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -103,14 +103,13 @@ is appropriate for most situations. The PIMD algorithm in LAMMPS is implemented as a hyper-parallel scheme as described in "(Calhoun)"_#Calhoun. In LAMMPS this is done by using -"multi-replica feature"_Section_howto.html#howto_5 in LAMMPS, where -each quasi-particle system is stored and simulated on a separate -partition of processors. The following diagram illustrates this -approach. The original system with 2 ring polymers is shown in red. -Since each ring has 4 quasi-beads (imaginary time slices), there are 4 -replicas of the system, each running on one of the 4 partitions of -processors. Each replica (shown in green) owns one quasi-bead in each -ring. +"multi-replica feature"_Howto_replica.html in LAMMPS, where each +quasi-particle system is stored and simulated on a separate partition +of processors. The following diagram illustrates this approach. The +original system with 2 ring polymers is shown in red. Since each ring +has 4 quasi-beads (imaginary time slices), there are 4 replicas of the +system, each running on one of the 4 partitions of processors. Each +replica (shown in green) owns one quasi-bead in each ring. :c,image(JPG/pimd.jpg) @@ -137,8 +136,8 @@ read_restart system_$\{ibead\}.restart2 :pre [Restrictions:] This fix is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. A PIMD simulation can be initialized with a single data file read via the "read_data"_read_data.html command. However, this means all diff --git a/doc/src/fix_planeforce.txt b/doc/src/fix_planeforce.txt index 67956c8b6d..ffe1952e31 100644 --- a/doc/src/fix_planeforce.txt +++ b/doc/src/fix_planeforce.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -35,9 +35,9 @@ should continue to move in the plane thereafter. No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. The forces due to this fix are imposed during an energy minimization, invoked by the "minimize"_minimize.html command. diff --git a/doc/src/fix_poems.txt b/doc/src/fix_poems.txt index 03abc058b8..52ab0ca44d 100644 --- a/doc/src/fix_poems.txt +++ b/doc/src/fix_poems.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -114,17 +114,17 @@ early or late in a timestep, i.e. at the post-force stage or at the final-integrate stage, respectively. No global or per-atom quantities are stored by this fix for access by -various "output commands"_Section_howto.html#howto_15. No parameter -of this fix can be used with the {start/stop} keywords of the -"run"_run.html command. This fix is not invoked during "energy +various "output commands"_Howto_output.html. No parameter of this fix +can be used with the {start/stop} keywords of the "run"_run.html +command. This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] This fix is part of the POEMS package. It is only enabled if LAMMPS was built with that package, which also requires the POEMS library be -built and linked with LAMMPS. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +built and linked with LAMMPS. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/fix_pour.txt b/doc/src/fix_pour.txt index 54f78287e0..65f01c00fb 100644 --- a/doc/src/fix_pour.txt +++ b/doc/src/fix_pour.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -237,16 +237,16 @@ appropriately. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored by this fix for -access by various "output commands"_Section_howto.html#howto_15. No -parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy +access by various "output commands"_Howto_output.html. No parameter +of this fix can be used with the {start/stop} keywords of the +"run"_run.html command. This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] This fix is part of the GRANULAR package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. For 3d simulations, a gravity fix in the -z direction must be defined for use in conjunction with this fix. For 2d simulations, gravity diff --git a/doc/src/fix_precession_spin.txt b/doc/src/fix_precession_spin.txt new file mode 100644 index 0000000000..d58cd622b0 --- /dev/null +++ b/doc/src/fix_precession_spin.txt @@ -0,0 +1,87 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +fix precession/spin command :h3 + +[Syntax:] + +fix ID group precession/spin style args :pre + +ID, group are documented in "fix"_fix.html command :ulb,l +precession/spin = style name of this fix command :l +style = {zeeman} or {anisotropy} :l + {zeeman} args = H x y z + H = intensity of the magnetic field (in Tesla) + x y z = vector direction of the field + {anisotropy} args = K x y z + K = intensity of the magnetic anisotropy (in eV) + x y z = vector direction of the anisotropy :pre +:ule + +[Examples:] + +fix 1 all precession/spin zeeman 0.1 0.0 0.0 1.0 +fix 1 all precession/spin anisotropy 0.001 0.0 0.0 1.0 +fix 1 all precession/spin zeeman 0.1 0.0 0.0 1.0 anisotropy 0.001 0.0 0.0 1.0 :pre + +[Description:] + +Impose a force torque to each magnetic spin in the group. + +Style {zeeman} is used for the simulation of the interaction +between the magnetic spins in the defined group and an external +magnetic field: + +:c,image(Eqs/force_spin_zeeman.jpg) + +with mu0 the vacuum permeability, muB the Bohr magneton (muB = 5.788 eV/T +in metal units). + +Style {anisotropy} is used to simulate an easy axis or an easy plane +for the magnetic spins in the defined group: + +:c,image(Eqs/force_spin_aniso.jpg) + +with n defining the direction of the anisotropy, and K (in eV) its intensity. +If K>0, an easy axis is defined, and if K<0, an easy plane is defined. + +In both cases, the choice of (x y z) imposes the vector direction for the force. +Only the direction of the vector is important; it's length is ignored. + +Both styles can be combined within one single command line. + +:line + +[Restart, fix_modify, output, run start/stop, minimize info:] + +By default, the energy associated to this fix is not added to the potential +energy of the system. +The "fix_modify"_fix_modify.html {energy} option is supported by this fix +to add this magnetic potential energy to the potential energy of the system, + +fix 1 all precession/spin zeeman 1.0 0.0 0.0 1.0 +fix_modify 1 energy yes :pre + +This fix computes a global scalar which can be accessed by various +"output commands"_Howto_output.html. + +No information about this fix is written to "binary restart +files"_restart.html. + +[Restrictions:] + +The {precession/spin} style is part of the SPIN package. This style +is only enabled if LAMMPS was built with this package, and if the +atom_style "spin" was declared. See the "Build +package"_Build_package.html doc page for more info. + +[Related commands:] + +"atom_style spin"_atom_style.html + +[Default:] none diff --git a/doc/src/fix_press_berendsen.txt b/doc/src/fix_press_berendsen.txt index 9c9da8ec7b..7f47a29ba3 100644 --- a/doc/src/fix_press_berendsen.txt +++ b/doc/src/fix_press_berendsen.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -58,9 +58,8 @@ to control the temperature, such as "fix nvt"_fix_nh.html or "fix langevin"_fix_langevin.html or "fix temp/berendsen"_fix_temp_berendsen.html. -See "this howto section"_Section_howto.html#howto_16 of the manual for -a discussion of different ways to compute temperature and perform -thermostatting and barostatting. +See the "Howto baroostat"_Howto_barostat.html doc page for a +discussion of different ways to perform barostatting. :line @@ -196,7 +195,7 @@ pressure. LAMMPS will warn you if you choose to compute temperature on a subset of atoms. No global or per-atom quantities are stored by this fix for access by -various "output commands"_Section_howto.html#howto_15. +various "output commands"_Howto_output.html. This fix can ramp its target pressure over multiple runs, using the {start} and {stop} keywords of the "run"_run.html command. See the diff --git a/doc/src/fix_print.txt b/doc/src/fix_print.txt index cf3b542833..d23c1103d3 100644 --- a/doc/src/fix_print.txt +++ b/doc/src/fix_print.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -73,10 +73,10 @@ where ID is replaced with the fix-ID. No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. [Restrictions:] none diff --git a/doc/src/fix_property_atom.txt b/doc/src/fix_property_atom.txt index 10bb89c94c..8a70cd8213 100644 --- a/doc/src/fix_property_atom.txt +++ b/doc/src/fix_property_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -194,24 +194,24 @@ dump 1 all custom 100 tmp.dump id x y z c_1\[1\] c_1\[2\] :pre If you wish to add new "pair styles"_pair_style.html, "fixes"_fix.html, or "computes"_compute.html that use the per-atom -properties defined by this fix, see "Section -modify"_Section_modify.html#mod_1 of the manual which has some details -on how the properties can be accessed from added classes. +properties defined by this fix, see the "Modify atom"_Modify_atom.html +doc page which has details on how the properties can be accessed from +added classes. :line :link(isotopes) -Example for using per-atom masses with TIP4P water to study isotope -effects. When setting up simulations with the "TIP4P pair -styles"_Section_howto.html#howto_8 for water, you have to provide -exactly one atom type each to identify the water oxygen and hydrogen +Example for using per-atom masses with TIP4P water to +study isotope effects. When setting up simulations with the "TIP4P +pair styles"_Howto_tip4p.html for water, you have to provide exactly +one atom type each to identify the water oxygen and hydrogen atoms. Since the atom mass is normally tied to the atom type, this makes it impossible to study multiple isotopes in the same simulation. With {fix property/atom rmass} however, the per-type masses are replaced by per-atom masses. Asumming you have a working input deck -for regular TIP4P water, where water oxygen is atom type 1 and -water hydrogen is atom type 2, the following lines of input script -convert this to using per-atom masses: +for regular TIP4P water, where water oxygen is atom type 1 and water +hydrogen is atom type 2, the following lines of input script convert +this to using per-atom masses: fix Isotopes all property/atom rmass ghost yes set type 1 mass 15.9994 @@ -247,12 +247,12 @@ command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. -None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. +None of the "fix_modify"_fix_modify.html options are relevant to this +fix. No global or per-atom quantities are stored by this fix for +access by various "output commands"_Howto_output.html. No parameter +of this fix can be used with the {start/stop} keywords of the +"run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. [Restrictions:] none diff --git a/doc/src/fix_python_invoke.txt b/doc/src/fix_python_invoke.txt index 787940d9eb..2a0124e6bf 100644 --- a/doc/src/fix_python_invoke.txt +++ b/doc/src/fix_python_invoke.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -62,9 +62,9 @@ case not work or in the worst case result in undefined behavior. [Restrictions:] -This fix is part of the PYTHON package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +This fix is part of the PYTHON package. It is only enabled if LAMMPS +was built with that package. See the "Build +package"_Build_package.html doc page for more info. Building LAMMPS with the PYTHON package will link LAMMPS with the Python library on your system. Settings to enable this are in the diff --git a/doc/src/fix_python_move.txt b/doc/src/fix_python_move.txt index f10f607a9b..c64ee788af 100644 --- a/doc/src/fix_python_move.txt +++ b/doc/src/fix_python_move.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -83,16 +83,16 @@ Examples for how to do this are in the {examples/python} folder. No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. [Restrictions:] This pair style is part of the PYTHON package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/fix_qbmsst.txt b/doc/src/fix_qbmsst.txt index 2c116fb0f8..546d8c0813 100644 --- a/doc/src/fix_qbmsst.txt +++ b/doc/src/fix_qbmsst.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -179,18 +179,18 @@ thermo_style custom step temp ke pe lz pzz etotal v_dhug v_dray v_lgr_vel v_ The global scalar under the entry f_fix_id is the quantity of thermo energy as an extra part of etot. This global scalar and the vector of 5 quantities can be accessed by various "output -commands"_Section_howto.html#howto_15. It is worth noting that the -temp keyword under the "thermo_style"_thermo_style.html command print -the instantaneous classical temperature Tcl as -described in the command "fix qtb"_fix_qtb.html. +commands"_Howto_output.html. It is worth noting that the temp keyword +under the "thermo_style"_thermo_style.html command print the +instantaneous classical temperature Tcl as described +in the command "fix qtb"_fix_qtb.html. :line [Restrictions:] This fix style is part of the USER-QTB package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. All cell dimensions must be periodic. This fix can not be used with a triclinic cell. The QBMSST fix has been tested only for the group-ID diff --git a/doc/src/fix_qeq.txt b/doc/src/fix_qeq.txt index 194361e990..46d2dd918c 100644 --- a/doc/src/fix_qeq.txt +++ b/doc/src/fix_qeq.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -179,17 +179,16 @@ parameters. See the examples/qeq directory for some examples. No information about these fixes is written to "binary restart files"_restart.html. No global scalar or vector or per-atom quantities are stored by these fixes for access by various "output -commands"_Section_howto.html#howto_15. No parameter of these fixes -can be used with the {start/stop} keywords of the "run"_run.html -command. +commands"_Howto_output.html. No parameter of these fixes can be used +with the {start/stop} keywords of the "run"_run.html command. Thexe fixes are invoked during "energy minimization"_minimize.html. [Restrictions:] These fixes are part of the QEQ package. They are only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/fix_qeq_comb.txt b/doc/src/fix_qeq_comb.txt index 7f82404127..714d03f602 100644 --- a/doc/src/fix_qeq_comb.txt +++ b/doc/src/fix_qeq_comb.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -62,23 +62,22 @@ equilibration calculation is written to the specified file. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line @@ -93,9 +92,9 @@ integrator the fix is performing charge equilibration. Default is the outermost level. This fix produces a per-atom vector which can be accessed by various -"output commands"_Section_howto.html#howto_15. The vector stores the -gradient of the charge on each atom. The per-atom values be accessed -on any timestep. +"output commands"_Howto_output.html. The vector stores the gradient +of the charge on each atom. The per-atom values be accessed on any +timestep. No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. diff --git a/doc/src/fix_qeq_reax.txt b/doc/src/fix_qeq_reax.txt index 18450c7cd5..b62d46d9de 100644 --- a/doc/src/fix_qeq_reax.txt +++ b/doc/src/fix_qeq_reax.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -70,8 +70,8 @@ the {qeq/reax/omp} style. Otherwise they are processed separately. No information about this fix is written to "binary restart files"_restart.html. No global scalar or vector or per-atom quantities are stored by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. +commands"_Howto_output.html. No parameter of this fix can be used +with the {start/stop} keywords of the "run"_run.html command. This fix is invoked during "energy minimization"_minimize.html. @@ -80,31 +80,30 @@ This fix is invoked during "energy minimization"_minimize.html. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line [Restrictions:] This fix is part of the USER-REAXC package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. This fix does not correctly handle interactions involving multiple periodic images of the same atom. Hence, it should not diff --git a/doc/src/fix_qmmm.txt b/doc/src/fix_qmmm.txt index 1b4a850a42..2dbf935f93 100644 --- a/doc/src/fix_qmmm.txt +++ b/doc/src/fix_qmmm.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -46,16 +46,16 @@ No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global scalar or vector or per-atom quantities are stored by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. +commands"_Howto_output.html. No parameter of this fix can be used +with the {start/stop} keywords of the "run"_run.html command. This +fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] This fix is part of the USER-QMMM package. It is only enabled if LAMMPS was built with that package. It also requires building a -library provided with LAMMPS. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +library provided with LAMMPS. See the "Build +package"_Build_package.html doc page for more info. The fix is only functional when LAMMPS is built as a library and linked with a compatible QM program and a QM/MM frontend into a QM/MM diff --git a/doc/src/fix_qtb.txt b/doc/src/fix_qtb.txt index 07a6af39ba..c412146604 100644 --- a/doc/src/fix_qtb.txt +++ b/doc/src/fix_qtb.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -155,8 +155,8 @@ This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] This fix style is part of the USER-QTB package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. :line diff --git a/doc/src/fix_reax_bonds.txt b/doc/src/fix_reax_bonds.txt index 3f8f237de1..06d30d871a 100644 --- a/doc/src/fix_reax_bonds.txt +++ b/doc/src/fix_reax_bonds.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -62,32 +62,32 @@ version, but will also take longer to write. No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. :line Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section_accelerate"_Section_accelerate.html +hardware, as discussed in "Speed"_Speed.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Speed"_Speed.html of the manual for more instructions on how to use the accelerated styles effectively. :line @@ -101,8 +101,8 @@ which also requires the REAX library be built and linked with LAMMPS. The fix reax/c/bonds command requires that the "pair_style reax/c"_pair_reaxc.html be invoked. This fix is part of the USER-REAXC package. It is only enabled if LAMMPS was built with that -package. See the "Making LAMMPS"_Section_start.html#start_3 section -for more info. +package. See the "Build package"_Build_package.html doc page for more +info. To write gzipped bond files, you must compile LAMMPS with the -DLAMMPS_GZIP option. diff --git a/doc/src/fix_reaxc_species.txt b/doc/src/fix_reaxc_species.txt index 7c920791f7..980384ff34 100644 --- a/doc/src/fix_reaxc_species.txt +++ b/doc/src/fix_reaxc_species.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -116,8 +116,8 @@ are relevant to this fix. This fix computes both a global vector of length 2 and a per-atom vector, either of which can be accessed by various "output -commands"_Section_howto.html#howto_15. The values in the global -vector are "intensive". +commands"_Howto_output.html. The values in the global vector are +"intensive". The 2 values in the global vector are as follows: @@ -139,34 +139,34 @@ minimization"_minimize.html. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section_accelerate"_Section_accelerate.html +hardware, as discussed in "Speed"_Speed.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Speed"_Speed.html of the manual for more instructions on how to use the accelerated styles effectively. :line [Restrictions:] -The fix species currently only works with -"pair_style reax/c"_pair_reaxc.html and it requires that the "pair_style +The fix species currently only works with "pair_style +reax/c"_pair_reaxc.html and it requires that the "pair_style reax/c"_pair_reaxc.html be invoked. This fix is part of the USER-REAXC package. It is only enabled if LAMMPS was built with that -package. See the "Making LAMMPS"_Section_start.html#start_3 section -for more info. +package. See the "Build package"_Build_package.html doc page for more +info. To write gzipped species files, you must compile LAMMPS with the -DLAMMPS_GZIP option. diff --git a/doc/src/fix_recenter.txt b/doc/src/fix_recenter.txt index 342bed4251..cfac756cd1 100644 --- a/doc/src/fix_recenter.txt +++ b/doc/src/fix_recenter.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -94,13 +94,13 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. This fix computes a global scalar which can be accessed by various -"output commands"_Section_howto.html#howto_15. The scalar is the -distance the group is moved by fix recenter. +"output commands"_Howto_output.html. The scalar is the distance the +group is moved by fix recenter. This fix also computes global 3-vector which can be accessed by -various "output commands"_Section_howto.html#howto_15. The 3 -quantities in the vector are xyz components of displacement applied to -the group of atoms by the fix. +various "output commands"_Howto_output.html. The 3 quantities in the +vector are xyz components of displacement applied to the group of +atoms by the fix. The scalar and vector values calculated by this fix are "extensive". diff --git a/doc/src/fix_restrain.txt b/doc/src/fix_restrain.txt index 9de63defb7..2edc7e3296 100644 --- a/doc/src/fix_restrain.txt +++ b/doc/src/fix_restrain.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -187,8 +187,8 @@ added forces to be included in the total potential energy of the system (the quantity being minimized), you MUST enable the "fix_modify"_fix_modify.html {energy} option for this fix. -This fix computes a global scalar and a global vector of length 3, which -can be accessed by various "output commands"_Section_howto.html#howto_15. +This fix computes a global scalar and a global vector of length 3, +which can be accessed by various "output commands"_Howto_output.html. The scalar is the total potential energy for {all} the restraints as discussed above. The vector values are the sum of contributions to the following individual categories: diff --git a/doc/src/fix_rhok.txt b/doc/src/fix_rhok.txt index 2db920ac4b..f013ebfae1 100644 --- a/doc/src/fix_rhok.txt +++ b/doc/src/fix_rhok.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -11,7 +11,7 @@ fix rhok command :h3 fix ID group-ID rhok nx ny nz K a :pre ID, group-ID are documented in "fix"_fix.html command -nx, ny, nz = k-vektor of collective density field +nx, ny, nz = k-vector of collective density field K = spring constant of bias potential a = anchor point of bias potential :ul @@ -40,8 +40,8 @@ An example of using the interface pinning method is located in the [Restrictions:] This fix is part of the MISC package. It is only enabled if LAMMPS -was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/fix_rigid.txt b/doc/src/fix_rigid.txt index ec7ed4f2b1..5d65856735 100644 --- a/doc/src/fix_rigid.txt +++ b/doc/src/fix_rigid.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -241,19 +241,17 @@ molecule ID = 0) surrounding rigid bodies, this may not be what you want. Thus you should be careful to use a fix group that only includes atoms you want to be part of rigid bodies. -Bodystyle {custom} is similar to bodystyle {molecule}, however some -custom properties are used to group atoms into rigid bodies. The -special case for molecule/body ID = 0 is not available. Possible -custom properties are an integer property associated with atoms through -"fix property/atom"_fix_property_atom.html or an atom style variable -or an atomfile style variable. For the latter two, the variable value -will be rounded to an integer and then rigid bodies defined from -those values. - -For bodystyle {group}, each of the listed groups is treated as a -separate rigid body. Only atoms that are also in the fix group are -included in each rigid body. This option is only allowed for the -{rigid} styles. +Bodystyle {custom} is similar to bodystyle {molecule} except that it +is more flexible in using other per-atom properties to define the sets +of atoms that form rigid bodies. An integer vector defined by the +"fix property/atom"_fix_property_atom.html command can be used. Or an +"atom-style or atomfile-style variable"_variable.html can be used; the +floating-point value produced by the variable is rounded to an +integer. As with bondstyle {molecule}, each set of atoms in the fix +groups with the same integer value is treated as a different rigid +body. Since fix property/atom vectors and atom-style variables +produce values for all atoms, you should be careful to use a fix group +that only includes atoms you want to be part of rigid bodies. NOTE: To compute the initial center-of-mass position and other properties of each rigid body, the image flags for each atom in the @@ -444,11 +442,11 @@ couple none :pre The keyword/value option pairs are used in the following ways. The {reinit} keyword determines, whether the rigid body properties -are reinitialized between run commands. With the option {yes} (the +are re-initialized between run commands. With the option {yes} (the default) this is done, with the option {no} this is not done. Turning -off the reinitialization can be helpful to protect rigid bodies against +off the re-initialization can be helpful to protect rigid bodies against unphysical manipulations between runs or when properties cannot be -easily recomputed (e.g. when read from a file). When using the {infile} +easily re-computed (e.g. when read from a file). When using the {infile} keyword, the {reinit} option is automatically set to {no}. The {langevin} and {temp} and {tparam} keywords perform thermostatting @@ -692,23 +690,22 @@ rigid/nvt. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line @@ -748,29 +745,29 @@ computed early or late in a timestep, i.e. at the post-force stage or at the final-integrate stage or the timestep, respectively. The 2 NVE rigid fixes compute a global scalar which can be accessed by -various "output commands"_Section_howto.html#howto_15. The scalar -value calculated by these fixes is "intensive". The scalar is the -current temperature of the collection of rigid bodies. This is -averaged over all rigid bodies and their translational and rotational -degrees of freedom. The translational energy of a rigid body is 1/2 m -v^2, where m = total mass of the body and v = the velocity of its -center of mass. The rotational energy of a rigid body is 1/2 I w^2, -where I = the moment of inertia tensor of the body and w = its angular -velocity. Degrees of freedom constrained by the {force} and {torque} -keywords are removed from this calculation, but only for the {rigid} -and {rigid/nve} fixes. +various "output commands"_Howto_output.html. The scalar value +calculated by these fixes is "intensive". The scalar is the current +temperature of the collection of rigid bodies. This is averaged over +all rigid bodies and their translational and rotational degrees of +freedom. The translational energy of a rigid body is 1/2 m v^2, where +m = total mass of the body and v = the velocity of its center of mass. +The rotational energy of a rigid body is 1/2 I w^2, where I = the +moment of inertia tensor of the body and w = its angular velocity. +Degrees of freedom constrained by the {force} and {torque} keywords +are removed from this calculation, but only for the {rigid} and +{rigid/nve} fixes. The 6 NVT, NPT, NPH rigid fixes compute a global scalar which can be -accessed by various "output commands"_Section_howto.html#howto_15. -The scalar value calculated by these fixes is "extensive". The scalar -is the cumulative energy change due to the thermostatting and -barostatting the fix performs. +accessed by various "output commands"_Howto_output.html. The scalar +value calculated by these fixes is "extensive". The scalar is the +cumulative energy change due to the thermostatting and barostatting +the fix performs. All of the {rigid} styles (not the {rigid/small} styles) compute a global array of values which can be accessed by various "output -commands"_Section_howto.html#howto_15. Similar information about the -bodies defined by the {rigid/small} styles can be accessed via the -"compute rigid/local"_compute_rigid_local.html command. +commands"_Howto_output.html. Similar information about the bodies +defined by the {rigid/small} styles can be accessed via the "compute +rigid/local"_compute_rigid_local.html command. The number of rows in the array is equal to the number of rigid bodies. The number of columns is 15. Thus for each rigid body, 15 @@ -809,8 +806,8 @@ of the "run"_run.html command. These fixes are not invoked during [Restrictions:] These fixes are all part of the RIGID package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. Assigning a temperature via the "velocity create"_velocity.html command to a system with "rigid bodies"_fix_rigid.html may not have diff --git a/doc/src/fix_rx.txt b/doc/src/fix_rx.txt index 0810a34740..ad42c577aa 100644 --- a/doc/src/fix_rx.txt +++ b/doc/src/fix_rx.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -186,31 +186,30 @@ read_data data.dpd fix foo_SPECIES NULL Species Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line [Restrictions:] This command is part of the USER-DPD package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. This command also requires use of the "atom_style dpd"_atom_style.html command. diff --git a/doc/src/fix_saed_vtk.txt b/doc/src/fix_saed_vtk.txt index 814e17b8e9..60708cd696 100644 --- a/doc/src/fix_saed_vtk.txt +++ b/doc/src/fix_saed_vtk.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_setforce.txt b/doc/src/fix_setforce.txt index f5be0f93a5..4b9abba52f 100644 --- a/doc/src/fix_setforce.txt +++ b/doc/src/fix_setforce.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -65,28 +65,28 @@ to it. :line -Styles with a r {kk} suffix are functionally the same as the -corresponding style without the suffix. They have been optimized to -run faster, depending on your available hardware, as discussed in -"Section 5"_Section_accelerate.html of the manual. The -accelerated styles take the same arguments and should produce the same -results, except for round-off and precision issues. +Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. The region keyword is also supported by Kokkos, but a Kokkos-enabled region must be used. See the region "region"_region.html command for more information. These accelerated styles are part of the r Kokkos package. They are -only enabled if LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +only enabled if LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line @@ -103,10 +103,10 @@ so that setforce values are not counted multiple times. Default is to to override forces at the outermost level. This fix computes a global 3-vector of forces, which can be accessed -by various "output commands"_Section_howto.html#howto_15. This is the -total force on the group of atoms before the forces on individual -atoms are changed by the fix. The vector values calculated by this -fix are "extensive". +by various "output commands"_Howto_output.html. This is the total +force on the group of atoms before the forces on individual atoms are +changed by the fix. The vector values calculated by this fix are +"extensive". No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. diff --git a/doc/src/fix_shake.txt b/doc/src/fix_shake.txt index 46452a1f7e..77bb5794f6 100644 --- a/doc/src/fix_shake.txt +++ b/doc/src/fix_shake.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -145,25 +145,25 @@ info of atoms in the molecule. :line -Styles with a suffix are functionally the same as the corresponding -style without the suffix. They have been optimized to run faster, -depending on your available hardware, as discussed in -"Section 5"_Section_accelerate.html of the manual. The -accelerated styles take the same arguments and should produce the same -results, except for round-off and precision issues. +Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line @@ -195,16 +195,15 @@ No information about these fixes is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to these fixes. No global or per-atom quantities are stored by these fixes for access by various "output -commands"_Section_howto.html#howto_15. No parameter of these fixes -can be used with the {start/stop} keywords of the "run"_run.html -command. These fixes are not invoked during "energy -minimization"_minimize.html. +commands"_Howto_output.html. No parameter of these fixes can be used +with the {start/stop} keywords of the "run"_run.html command. These +fixes are not invoked during "energy minimization"_minimize.html. [Restrictions:] These fixes are part of the RIGID package. They are only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. For computational efficiency, there can only be one shake or rattle fix defined in a simulation. diff --git a/doc/src/fix_shardlow.txt b/doc/src/fix_shardlow.txt index 24726d8610..c1be146fa6 100644 --- a/doc/src/fix_shardlow.txt +++ b/doc/src/fix_shardlow.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -56,31 +56,30 @@ examples/USER/dpd directory. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line [Restrictions:] This command is part of the USER-DPD package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. This fix is currently limited to orthogonal simulation cell geometries. diff --git a/doc/src/fix_smd.txt b/doc/src/fix_smd.txt index cb4a40f0fd..774842c7cf 100644 --- a/doc/src/fix_smd.txt +++ b/doc/src/fix_smd.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -77,7 +77,7 @@ normalized. But since it represents the {absolute} displacement of group-ID2 relative to the fix group, (1,1,0) is a different spring than (-1,-1,0). For each vector component, the displacement can be described with the {auto} parameter. In this case the direction is -recomputed in every step, which can be useful for steering a local +re-computed in every step, which can be useful for steering a local process where the whole object undergoes some other change. When the relative positions and distance between the two groups are not in equilibrium, the same spring force described above is applied to atoms @@ -111,12 +111,12 @@ this fix. This allows to set at which level of the "r-RESPA"_run_style.html integrator the fix is adding its forces. Default is the outermost level. This fix computes a vector list of 7 quantities, which can be accessed -by various "output commands"_Section_howto.html#howto_15. The -quantities in the vector are in this order: the x-, y-, and -z-component of the pulling force, the total force in direction of the -pull, the equilibrium distance of the spring, the distance between the -two reference points, and finally the accumulated PMF (the sum of -pulling forces times displacement). +by various "output commands"_Howto_output.html. The quantities in the +vector are in this order: the x-, y-, and z-component of the pulling +force, the total force in direction of the pull, the equilibrium +distance of the spring, the distance between the two reference points, +and finally the accumulated PMF (the sum of pulling forces times +displacement). The force is the total force on the group of atoms by the spring. In the case of the {couple} style, it is the force on the fix group @@ -130,8 +130,8 @@ minimization"_minimize.html. [Restrictions:] This fix is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/fix_smd_adjust_dt.txt b/doc/src/fix_smd_adjust_dt.txt index 86b7363300..3535ddfcc2 100644 --- a/doc/src/fix_smd_adjust_dt.txt +++ b/doc/src/fix_smd_adjust_dt.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -25,18 +25,23 @@ fix 1 all smd/adjust_dt 0.1 :pre [Description:] -The fix calculates a new stable time increment for use with the SMD time integrators. +The fix calculates a new stable time increment for use with the SMD +time integrators. -The stable time increment is based on multiple conditions. For the SPH pair styles, a -CFL criterion (Courant, Friedrichs & Lewy, 1928) is evaluated, which determines the speed of -sound cannot propagate further than a typical spacing between particles within a single time step to ensure -no information is lost. For the contact pair styles, a linear analysis of the pair potential determines a -stable maximum time step. +The stable time increment is based on multiple conditions. For the SPH +pair styles, a CFL criterion (Courant, Friedrichs & Lewy, 1928) is +evaluated, which determines the speed of sound cannot propagate +further than a typical spacing between particles within a single time +step to ensure no information is lost. For the contact pair styles, a +linear analysis of the pair potential determines a stable maximum time +step. -This fix inquires the minimum stable time increment across all particles contained in the group for which this -fix is defined. An additional safety factor {s_fact} is applied to the time increment. +This fix inquires the minimum stable time increment across all +particles contained in the group for which this fix is defined. An +additional safety factor {s_fact} is applied to the time increment. -See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to use Smooth Mach Dynamics in LAMMPS. +See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to use Smooth Mach +Dynamics in LAMMPS. [Restart, fix_modify, output, run start/stop, minimize info:] @@ -45,8 +50,8 @@ Currently, no part of USER-SMD supports restarting nor minimization. [Restrictions:] This fix is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 -section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/fix_smd_integrate_tlsph.txt b/doc/src/fix_smd_integrate_tlsph.txt index 17c9c0f400..029605ff7f 100644 --- a/doc/src/fix_smd_integrate_tlsph.txt +++ b/doc/src/fix_smd_integrate_tlsph.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -27,22 +27,26 @@ fix 1 all smd/integrate_tlsph limit_velocity 1000 :pre [Description:] -The fix performs explicit time integration for particles which interact according with the Total-Lagrangian SPH pair style. +The fix performs explicit time integration for particles which +interact according with the Total-Lagrangian SPH pair style. -See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth Mach Dynamics in LAMMPS. +See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth Mach +Dynamics in LAMMPS. -The {limit_velocity} keyword will control the velocity, scaling the norm of -the velocity vector to max_vel in case it exceeds this velocity limit. +The {limit_velocity} keyword will control the velocity, scaling the +norm of the velocity vector to max_vel in case it exceeds this +velocity limit. [Restart, fix_modify, output, run start/stop, minimize info:] -Currently, no part of USER-SMD supports restarting nor minimization. This fix has no outputs. +Currently, no part of USER-SMD supports restarting nor +minimization. This fix has no outputs. [Restrictions:] This fix is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 -section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/fix_smd_integrate_ulsph.txt b/doc/src/fix_smd_integrate_ulsph.txt index 28e38c7f97..a99574cc85 100644 --- a/doc/src/fix_smd_integrate_ulsph.txt +++ b/doc/src/fix_smd_integrate_ulsph.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -24,7 +24,6 @@ adjust_radius values = adjust_radius_factor min_nn max_nn limit_velocity values = max_velocity max_velocity = maximum allowed velocity. - [Examples:] fix 1 all smd/integrate_ulsph adjust_radius 1.02 25 50 @@ -32,28 +31,33 @@ fix 1 all smd/integrate_ulsph limit_velocity 1000 :pre [Description:] -The fix performs explicit time integration for particles which interact with the updated Lagrangian SPH pair style. -See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth Mach Dynamics in LAMMPS. +The fix performs explicit time integration for particles which +interact with the updated Lagrangian SPH pair style. -The {adjust_radius} keyword activates dynamic adjustment of the per-particle SPH smoothing kernel radius such that the number of neighbors per particles remains -within the interval {min_nn} to {max_nn}. The parameter {adjust_radius_factor} determines the amount of adjustment per timestep. Typical values are -{adjust_radius_factor} =1.02, {min_nn} =15, and {max_nn} =20. +See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth Mach +Dynamics in LAMMPS. + +The {adjust_radius} keyword activates dynamic adjustment of the +per-particle SPH smoothing kernel radius such that the number of +neighbors per particles remains within the interval {min_nn} to +{max_nn}. The parameter {adjust_radius_factor} determines the amount +of adjustment per timestep. Typical values are {adjust_radius_factor} +=1.02, {min_nn} =15, and {max_nn} =20. The {limit_velocity} keyword will control the velocity, scaling the norm of the velocity vector to max_vel in case it exceeds this velocity limit. [Restart, fix_modify, output, run start/stop, minimize info:] -Currently, no part of USER-SMD supports restarting nor minimization. This fix has no outputs. +Currently, no part of USER-SMD supports restarting nor +minimization. This fix has no outputs. [Restrictions:] This fix is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 -section for more info. - -[Related commands:] - +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. +[Related commands:] none [Default:] none diff --git a/doc/src/fix_smd_move_triangulated_surface.txt b/doc/src/fix_smd_move_triangulated_surface.txt index 2cba001267..2a998ba8c6 100644 --- a/doc/src/fix_smd_move_triangulated_surface.txt +++ b/doc/src/fix_smd_move_triangulated_surface.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -25,7 +25,6 @@ keyword = {*LINEAR} or {*WIGGLE} or {*ROTATE} :l Px,Py,Pz = origin point of axis of rotation (distance units) Rx,Ry,Rz = axis of rotation vector period = period of rotation (time units) :pre - :ule [Examples:] @@ -36,9 +35,11 @@ fix 2 tool smd/move_tri_surf *ROTATE 0 0 0 5 2 1 :pre [Description:] -This fix applies only to rigid surfaces read from .STL files via fix "smd/wall_surface"_fix_smd_wall_surface.html . -It updates position and velocity for the particles in the group each timestep without regard to forces on the particles. -The rigid surfaces can thus be moved along simple trajectories during the simulation. +This fix applies only to rigid surfaces read from .STL files via fix +"smd/wall_surface"_fix_smd_wall_surface.html . It updates position +and velocity for the particles in the group each timestep without +regard to forces on the particles. The rigid surfaces can thus be +moved along simple trajectories during the simulation. The {*LINEAR} style moves particles with the specified constant velocity vector V = (Vx,Vy,Vz). This style also sets the velocity of each particle @@ -49,27 +50,30 @@ Particles are moved along (vx, vy, vz) with constant velocity until a displacement of max_travel is reached. Then, the velocity vector is reversed. This process is repeated. -The {*ROTATE} style rotates particles around a rotation axis R = (Rx,Ry,Rz) that -goes through a point P = (Px,Py,Pz). The period of the rotation is also -specified. This style also sets the velocity of each particle to (omega cross -Rperp) where omega is its angular velocity around the rotation axis and -Rperp is a perpendicular vector from the rotation axis to the particle. +The {*ROTATE} style rotates particles around a rotation axis R = +(Rx,Ry,Rz) that goes through a point P = (Px,Py,Pz). The period of the +rotation is also specified. This style also sets the velocity of each +particle to (omega cross Rperp) where omega is its angular velocity +around the rotation axis and Rperp is a perpendicular vector from the +rotation axis to the particle. -See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth Mach Dynamics in LAMMPS. +See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth Mach +Dynamics in LAMMPS. [Restart, fix_modify, output, run start/stop, minimize info:] -Currently, no part of USER-SMD supports restarting nor minimization. This fix has no outputs. +Currently, no part of USER-SMD supports restarting nor +minimization. This fix has no outputs. [Restrictions:] This fix is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 -section for more info. - +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] -"smd/triangle_mesh_vertices"_compute_smd_triangle_mesh_vertices.html, "smd/wall_surface"_fix_smd_wall_surface.html +"smd/triangle_mesh_vertices"_compute_smd_triangle_mesh_vertices.html, +"smd/wall_surface"_fix_smd_wall_surface.html [Default:] none diff --git a/doc/src/fix_smd_setvel.txt b/doc/src/fix_smd_setvel.txt index f93a7d0965..b170eff860 100644 --- a/doc/src/fix_smd_setvel.txt +++ b/doc/src/fix_smd_setvel.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -66,9 +66,9 @@ None of the "fix_modify"_fix_modify.html options are relevant to this fix. This fix computes a global 3-vector of forces, which can be accessed -by various "output commands"_Section_howto.html#howto_15. This is the -total force on the group of atoms. The vector values calculated by this -fix are "extensive". +by various "output commands"_Howto_output.html. This is the total +force on the group of atoms. The vector values calculated by this fix +are "extensive". No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. @@ -76,8 +76,8 @@ the "run"_run.html command. [Restrictions:] This fix is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 -section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] none diff --git a/doc/src/fix_smd_wall_surface.txt b/doc/src/fix_smd_wall_surface.txt index feb65b2312..dc3625e95e 100644 --- a/doc/src/fix_smd_wall_surface.txt +++ b/doc/src/fix_smd_wall_surface.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -17,9 +17,7 @@ smd/wall_surface = style name of this fix command :l arg = {file} :l {file} = file name of a triangular mesh in stl format :pre type = particle type to be given to the new particles created by this fix :l -mol-ID = molecule-ID to be given to the new particles created by this fix (must be >= 65535) :l - -:ule +mol-ID = molecule-ID to be given to the new particles created by this fix (must be >= 65535) :l,ule [Examples:] @@ -27,32 +25,47 @@ fix stl_surf all smd/wall_surface tool.stl 2 65535 :pre [Description:] -This fix creates reads a triangulated surface from a file in .STL format. -For each triangle, a new particle is created which stores the barycenter of the triangle and the vertex positions. -The radius of the new particle is that of the minimum circle which encompasses the triangle vertices. +This fix creates reads a triangulated surface from a file in .STL +format. For each triangle, a new particle is created which stores the +barycenter of the triangle and the vertex positions. The radius of +the new particle is that of the minimum circle which encompasses the +triangle vertices. -The triangulated surface can be used as a complex rigid wall via the "smd/tri_surface"_pair_smd_triangulated_surface.html pair style. -It is possible to move the triangulated surface via the "smd/move_tri_surf"_fix_smd_move_triangulated_surface.html fix style. +The triangulated surface can be used as a complex rigid wall via the +"smd/tri_surface"_pair_smd_triangulated_surface.html pair style. It +is possible to move the triangulated surface via the +"smd/move_tri_surf"_fix_smd_move_triangulated_surface.html fix style. -Immediately after a .STL file has been read, the simulation needs to be run for 0 timesteps in order to properly register the new particles -in the system. See the "funnel_flow" example in the USER-SMD examples directory. +Immediately after a .STL file has been read, the simulation needs to +be run for 0 timesteps in order to properly register the new particles +in the system. See the "funnel_flow" example in the USER-SMD examples +directory. -See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to use Smooth Mach Dynamics in LAMMPS. +See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to use Smooth Mach +Dynamics in LAMMPS. [Restart, fix_modify, output, run start/stop, minimize info:] -Currently, no part of USER-SMD supports restarting nor minimization. This fix has no outputs. +Currently, no part of USER-SMD supports restarting nor +minimization. This fix has no outputs. [Restrictions:] This fix is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 -section for more info. The molecule ID given to the particles created by this fix have to be equal to or larger than 65535. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. -Within each .STL file, only a single triangulated object must be present, even though the STL format allows for the possibility of multiple objects in one file. +The molecule ID given to the particles created by this fix have to be +equal to or larger than 65535. + +Within each .STL file, only a single triangulated object must be +present, even though the STL format allows for the possibility of +multiple objects in one file. [Related commands:] -"smd/triangle_mesh_vertices"_compute_smd_triangle_mesh_vertices.html, "smd/move_tri_surf"_fix_smd_move_triangulated_surface.html, "smd/tri_surface"_pair_smd_triangulated_surface.html +"smd/triangle_mesh_vertices"_compute_smd_triangle_mesh_vertices.html, +"smd/move_tri_surf"_fix_smd_move_triangulated_surface.html, +"smd/tri_surface"_pair_smd_triangulated_surface.html [Default:] none diff --git a/doc/src/fix_spring.txt b/doc/src/fix_spring.txt index 014a43aacc..690fc3e67c 100644 --- a/doc/src/fix_spring.txt +++ b/doc/src/fix_spring.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -105,19 +105,19 @@ fix. This allows to set at which level of the "r-RESPA"_run_style.html integrator the fix is adding its forces. Default is the outermost level. This fix computes a global scalar which can be accessed by various -"output commands"_Section_howto.html#howto_15. The scalar is the -spring energy = 0.5 * K * r^2. +"output commands"_Howto_output.html. The scalar is the spring energy += 0.5 * K * r^2. This fix also computes global 4-vector which can be accessed by -various "output commands"_Section_howto.html#howto_15. The first 3 -quantities in the vector are xyz components of the total force added -to the group of atoms by the spring. In the case of the {couple} -style, it is the force on the fix group (group-ID) or the negative of -the force on the 2nd group (group-ID2). The 4th quantity in the -vector is the magnitude of the force added by the spring, as a -positive value if (r-R0) > 0 and a negative value if (r-R0) < 0. This -sign convention can be useful when using the spring force to compute a -potential of mean force (PMF). +various "output commands"_Howto_output.html. The first 3 quantities +in the vector are xyz components of the total force added to the group +of atoms by the spring. In the case of the {couple} style, it is the +force on the fix group (group-ID) or the negative of the force on the +2nd group (group-ID2). The 4th quantity in the vector is the +magnitude of the force added by the spring, as a positive value if +(r-R0) > 0 and a negative value if (r-R0) < 0. This sign convention +can be useful when using the spring force to compute a potential of +mean force (PMF). The scalar and vector values calculated by this fix are "extensive". diff --git a/doc/src/fix_spring_chunk.txt b/doc/src/fix_spring_chunk.txt index 7630a009dd..9d4e8afd09 100644 --- a/doc/src/fix_spring_chunk.txt +++ b/doc/src/fix_spring_chunk.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -60,8 +60,8 @@ fix. This allows to set at which level of the "r-RESPA"_run_style.html integrator the fix is adding its forces. Default is the outermost level. This fix computes a global scalar which can be accessed by various -"output commands"_Section_howto.html#howto_15. The scalar is the -energy of all the springs, i.e. 0.5 * K * r^2 per-spring. +"output commands"_Howto_output.html. The scalar is the energy of all +the springs, i.e. 0.5 * K * r^2 per-spring. The scalar value calculated by this fix is "extensive". diff --git a/doc/src/fix_spring_rg.txt b/doc/src/fix_spring_rg.txt index bff6b38e7e..b252163958 100644 --- a/doc/src/fix_spring_rg.txt +++ b/doc/src/fix_spring_rg.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -51,10 +51,10 @@ the time the fix is specified, and that value is used as the target. No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. The "fix_modify"_fix_modify.html {respa} option is supported by this fix. This allows to set at which level of the "r-RESPA"_run_style.html diff --git a/doc/src/fix_spring_self.txt b/doc/src/fix_spring_self.txt index 68961a1512..0ac1d5eecb 100644 --- a/doc/src/fix_spring_self.txt +++ b/doc/src/fix_spring_self.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -57,10 +57,10 @@ this fix. This allows to set at which level of the "r-RESPA"_run_style.html integrator the fix is adding its forces. Default is the outermost level. This fix computes a global scalar which can be accessed by various -"output commands"_Section_howto.html#howto_15. The scalar is an -energy which is the sum of the spring energy for each atom, where the -per-atom energy is 0.5 * K * r^2. The scalar value calculated by this -fix is "extensive". +"output commands"_Howto_output.html. The scalar is an energy which is +the sum of the spring energy for each atom, where the per-atom energy +is 0.5 * K * r^2. The scalar value calculated by this fix is +"extensive". No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. diff --git a/doc/src/fix_srd.txt b/doc/src/fix_srd.txt index 4e190234fd..557eee1cfc 100644 --- a/doc/src/fix_srd.txt +++ b/doc/src/fix_srd.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -341,11 +341,11 @@ are relevant to this fix. This fix tabulates several SRD statistics which are stored in a vector of length 12, which can be accessed by various "output -commands"_Section_howto.html#howto_15. The vector values calculated -by this fix are "intensive", meaning they do not scale with the size -of the simulation. Technically, the first 8 do scale with the size of -the simulation, but treating them as intensive means they are not -scaled when printed as part of thermodynamic output. +commands"_Howto_output.html. The vector values calculated by this fix +are "intensive", meaning they do not scale with the size of the +simulation. Technically, the first 8 do scale with the size of the +simulation, but treating them as intensive means they are not scaled +when printed as part of thermodynamic output. These are the 12 quantities. All are values for the current timestep, except for quantity 5 and the last three, each of which are @@ -371,8 +371,8 @@ minimization"_minimize.html. [Restrictions:] This command can only be used if LAMMPS was built with the SRD -package. See the "Making LAMMPS"_Section_start.html#start_3 section -for more info on packages. +package. See the "Build package"_Build_package.html doc +page for more info. [Related commands:] diff --git a/doc/src/fix_store_force.txt b/doc/src/fix_store_force.txt index c988431f9d..33ebc962d5 100644 --- a/doc/src/fix_store_force.txt +++ b/doc/src/fix_store_force.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -26,7 +26,7 @@ timestep when the fix is invoked, as described below. This is useful for storing forces before constraints or other boundary conditions are computed which modify the forces, so that unmodified forces can be "written to a dump file"_dump.html or accessed by other "output -commands"_Section_howto.html#howto_15 that use per-atom quantities. +commands"_Howto_output.html that use per-atom quantities. This fix is invoked at the point in the velocity-Verlet timestepping immediately after "pair"_pair_style.html, "bond"_bond_style.html, @@ -54,9 +54,9 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. This fix produces a per-atom array which can be accessed by various -"output commands"_Section_howto.html#howto_15. The number of columns -for each atom is 3, and the columns store the x,y,z forces on each -atom. The per-atom values be accessed on any timestep. +"output commands"_Howto_output.html. The number of columns for each +atom is 3, and the columns store the x,y,z forces on each atom. The +per-atom values be accessed on any timestep. No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. This fix is not invoked during "energy diff --git a/doc/src/fix_store_state.txt b/doc/src/fix_store_state.txt index df694fb97b..df05adc5b9 100644 --- a/doc/src/fix_store_state.txt +++ b/doc/src/fix_store_state.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -68,8 +68,7 @@ Define a fix that stores attributes for each atom in the group at the time the fix is defined. If {N} is 0, then the values are never updated, so this is a way of archiving an atom attribute at a given time for future use in a calculation or output. See the discussion of -"output commands"_Section_howto.html#howto_15 that take fixes as -inputs. +"output commands"_Howto_output.html that take fixes as inputs. If {N} is not zero, then the attributes will be updated every {N} steps. @@ -108,9 +107,8 @@ fix. If a single input is specified, this fix produces a per-atom vector. If multiple inputs are specified, a per-atom array is produced where the number of columns for each atom is the number of inputs. These -can be accessed by various "output -commands"_Section_howto.html#howto_15. The per-atom values be -accessed on any timestep. +can be accessed by various "output commands"_Howto_output.html. The +per-atom values be accessed on any timestep. No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. This fix is not invoked during "energy diff --git a/doc/src/fix_surface_global.txt b/doc/src/fix_surface_global.txt index b470babab7..2ee045141a 100644 --- a/doc/src/fix_surface_global.txt +++ b/doc/src/fix_surface_global.txt @@ -2,11 +2,11 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line -fix wall/surface/globale command :h3 +fix wall/surface/global command :h3 [Description:] diff --git a/doc/src/fix_temp_berendsen.txt b/doc/src/fix_temp_berendsen.txt index 6944860e14..c1f1626782 100644 --- a/doc/src/fix_temp_berendsen.txt +++ b/doc/src/fix_temp_berendsen.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -68,8 +68,8 @@ be used on atoms that also have their temperature controlled by another fix - e.g. by "fix nvt"_fix_nh.html or "fix langevin"_fix_langevin.html commands. -See "this howto section"_Section_howto.html#howto_16 of the manual for -a discussion of different ways to compute temperature and perform +See the "Howto thermostat"_Howto_thermostat.html doc page for a +discussion of different ways to compute temperature and perform thermostatting. This fix computes a temperature each timestep. To do this, the fix @@ -126,9 +126,9 @@ system's potential energy as part of "thermodynamic output"_thermo_style.html. This fix computes a global scalar which can be accessed by various -"output commands"_Section_howto.html#howto_15. The scalar is the -cumulative energy change due to this fix. The scalar value -calculated by this fix is "extensive". +"output commands"_Howto_output.html. The scalar is the cumulative +energy change due to this fix. The scalar value calculated by this +fix is "extensive". This fix can ramp its target temperature over multiple runs, using the {start} and {stop} keywords of the "run"_run.html command. See the diff --git a/doc/src/fix_temp_csvr.txt b/doc/src/fix_temp_csvr.txt index 4129ad73c8..e50f821bfe 100644 --- a/doc/src/fix_temp_csvr.txt +++ b/doc/src/fix_temp_csvr.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -76,8 +76,8 @@ normally be used on atoms that also have their temperature controlled by another fix - e.g. by "fix nvt"_fix_nh.html or "fix langevin"_fix_langevin.html commands. -See "this howto section"_Section_howto.html#howto_16 of the manual for -a discussion of different ways to compute temperature and perform +See the "Howto thermostat"_Howto_thermostat.html doc page for a +discussion of different ways to compute temperature and perform thermostatting. These fixes compute a temperature each timestep. To do this, the fix @@ -135,9 +135,9 @@ the {start} and {stop} keywords of the "run"_run.html command. See the These fixes are not invoked during "energy minimization"_minimize.html. These fixes compute a global scalar which can be accessed by various -"output commands"_Section_howto.html#howto_15. The scalar is the -cumulative energy change due to the fix. The scalar value -calculated by this fix is "extensive". +"output commands"_Howto_output.html. The scalar is the cumulative +energy change due to the fix. The scalar value calculated by this fix +is "extensive". [Restrictions:] diff --git a/doc/src/fix_temp_rescale.txt b/doc/src/fix_temp_rescale.txt index eff25297c1..5640317f1c 100644 --- a/doc/src/fix_temp_rescale.txt +++ b/doc/src/fix_temp_rescale.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -75,8 +75,8 @@ be used on atoms that also have their temperature controlled by another fix - e.g. by "fix nvt"_fix_nh.html or "fix langevin"_fix_langevin.html commands. -See "this howto section"_Section_howto.html#howto_16 of the manual for -a discussion of different ways to compute temperature and perform +See the "Howto thermostat"_Howto_thermostat.html doc page for a +discussion of different ways to compute temperature and perform thermostatting. This fix computes a temperature each timestep. To do this, the fix @@ -133,9 +133,9 @@ system's potential energy as part of "thermodynamic output"_thermo_style.html. This fix computes a global scalar which can be accessed by various -"output commands"_Section_howto.html#howto_15. The scalar is the -cumulative energy change due to this fix. The scalar value -calculated by this fix is "extensive". +"output commands"_Howto_output.html. The scalar is the cumulative +energy change due to this fix. The scalar value calculated by this +fix is "extensive". This fix can ramp its target temperature over multiple runs, using the {start} and {stop} keywords of the "run"_run.html command. See the diff --git a/doc/src/fix_temp_rescale_eff.txt b/doc/src/fix_temp_rescale_eff.txt index f87c1a2192..83b360df85 100644 --- a/doc/src/fix_temp_rescale_eff.txt +++ b/doc/src/fix_temp_rescale_eff.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -51,9 +51,9 @@ system's potential energy as part of "thermodynamic output"_thermo_style.html. This fix computes a global scalar which can be accessed by various -"output commands"_Section_howto.html#howto_15. The scalar is the -cumulative energy change due to this fix. The scalar value -calculated by this fix is "extensive". +"output commands"_Howto_output.html. The scalar is the cumulative +energy change due to this fix. The scalar value calculated by this +fix is "extensive". This fix can ramp its target temperature over multiple runs, using the {start} and {stop} keywords of the "run"_run.html command. See the @@ -64,8 +64,8 @@ This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] This fix is part of the USER-EFF package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/fix_tfmc.txt b/doc/src/fix_tfmc.txt index 3c81d62ee0..2d4f003607 100644 --- a/doc/src/fix_tfmc.txt +++ b/doc/src/fix_tfmc.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -125,8 +125,8 @@ This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] This fix is part of the MC package. It is only enabled if LAMMPS was -built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +built with that package. See the "Build package"_Build_package.html +doc page for more info. This fix is not compatible with "fix shake"_fix_shake.html. diff --git a/doc/src/fix_thermal_conductivity.txt b/doc/src/fix_thermal_conductivity.txt index 0353c095b2..2ab32b25f0 100644 --- a/doc/src/fix_thermal_conductivity.txt +++ b/doc/src/fix_thermal_conductivity.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -108,9 +108,9 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. This fix computes a global scalar which can be accessed by various -"output commands"_Section_howto.html#howto_15. The scalar is the -cumulative kinetic energy transferred between the bottom and middle -of the simulation box (in the {edim} direction) is stored as a scalar +"output commands"_Howto_output.html. The scalar is the cumulative +kinetic energy transferred between the bottom and middle of the +simulation box (in the {edim} direction) is stored as a scalar quantity by this fix. This quantity is zeroed when the fix is defined and accumulates thereafter, once every N steps. The units of the quantity are energy; see the "units"_units.html command for details. @@ -123,8 +123,8 @@ minimization"_minimize.html. [Restrictions:] This fix is part of the MISC package. It is only enabled if LAMMPS -was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +was built with that package. See the "Build +package"_Build_package.html doc page for more info. Swaps conserve both momentum and kinetic energy, even if the masses of the swapped atoms are not equal. Thus you should not need to diff --git a/doc/src/fix_ti_spring.txt b/doc/src/fix_ti_spring.txt index 191f9e7c6b..290ee95b9a 100644 --- a/doc/src/fix_ti_spring.txt +++ b/doc/src/fix_ti_spring.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -121,13 +121,12 @@ fix to add the energy stored in the per-atom springs to the system's potential energy as part of "thermodynamic output"_thermo_style.html. This fix computes a global scalar and a global vector quantities which -can be accessed by various "output -commands"_Section_howto.html#howto_15. The scalar is an energy which -is the sum of the spring energy for each atom, where the per-atom -energy is 0.5 * k * r^2. The vector has 2 positions, the first one is -the coupling parameter lambda and the second one is the time -derivative of lambda. The scalar and vector values calculated by this -fix are "extensive". +can be accessed by various "output commands"_Howto_output.html. The +scalar is an energy which is the sum of the spring energy for each +atom, where the per-atom energy is 0.5 * k * r^2. The vector has 2 +positions, the first one is the coupling parameter lambda and the +second one is the time derivative of lambda. The scalar and vector +values calculated by this fix are "extensive". No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. @@ -147,8 +146,8 @@ this fix. [Restrictions:] This fix is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Default:] diff --git a/doc/src/fix_tmd.txt b/doc/src/fix_tmd.txt index 71d8d2c767..73e95ba9fe 100644 --- a/doc/src/fix_tmd.txt +++ b/doc/src/fix_tmd.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -90,8 +90,7 @@ For more information about TMD, see "(Schlitter1)"_#Schlitter1 and No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. +by this fix for access by various "output commands"_Howto_output.html. This fix can ramp its rho parameter over multiple runs, using the {start} and {stop} keywords of the "run"_run.html command. See the @@ -111,8 +110,8 @@ are not multiple competing holonomic constraints applied to the same atoms. To read gzipped target files, you must compile LAMMPS with the --DLAMMPS_GZIP option - see the "Making -LAMMPS"_Section_start.html#start_2 section of the documentation. +-DLAMMPS_GZIP option. See the "Build settings"_Build_settings.html +doc page for details. [Related commands:] none diff --git a/doc/src/fix_ttm.txt b/doc/src/fix_ttm.txt index 48dfd254a0..85407f2466 100644 --- a/doc/src/fix_ttm.txt +++ b/doc/src/fix_ttm.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -272,18 +272,17 @@ None of the "fix_modify"_fix_modify.html options are relevant to these fixes. Both fixes compute 2 output quantities stored in a vector of length 2, -which can be accessed by various "output -commands"_Section_howto.html#howto_15. The first quantity is the -total energy of the electronic subsystem. The second quantity is the -energy transferred from the electronic to the atomic subsystem on that -timestep. Note that the velocity verlet integrator applies the fix ttm -forces to the atomic subsystem as two half-step velocity updates: one -on the current timestep and one on the subsequent timestep. -Consequently, the change in the atomic subsystem energy is lagged by -half a timestep relative to the change in the electronic subsystem -energy. As a result of this, users may notice slight fluctuations in -the sum of the atomic and electronic subsystem energies reported at -the end of the timestep. +which can be accessed by various "output commands"_Howto_output.html. +The first quantity is the total energy of the electronic +subsystem. The second quantity is the energy transferred from the +electronic to the atomic subsystem on that timestep. Note that the +velocity verlet integrator applies the fix ttm forces to the atomic +subsystem as two half-step velocity updates: one on the current +timestep and one on the subsequent timestep. Consequently, the change +in the atomic subsystem energy is lagged by half a timestep relative +to the change in the electronic subsystem energy. As a result of this, +users may notice slight fluctuations in the sum of the atomic and +electronic subsystem energies reported at the end of the timestep. The vector values calculated are "extensive". @@ -296,8 +295,7 @@ of the "run"_run.html command. The fixes are not invoked during Fix {ttm} is part of the MISC package. It is only enabled if LAMMPS was built with that package. Fix {ttm/mod} is part of the USER-MISC package. It is only enabled if LAMMPS was built with that package. -See the "Making LAMMPS"_Section_start.html#start_3 section for more -info. +See the "Build package"_Build_package.html doc page for more info. These fixes can only be used for 3d simulations and orthogonal simulation boxes. You must also use periodic diff --git a/doc/src/fix_tune_kspace.txt b/doc/src/fix_tune_kspace.txt index 60a34a26c9..147bb1eb3d 100644 --- a/doc/src/fix_tune_kspace.txt +++ b/doc/src/fix_tune_kspace.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -79,9 +79,9 @@ minimization"_minimize.html. [Restrictions:] -This fix is part of the KSPACE package. It is only enabled if LAMMPS was -built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +This fix is part of the KSPACE package. It is only enabled if LAMMPS +was built with that package. See the "Build +package"_Build_package.html doc page for more info. Do not set "neigh_modify once yes" or else this fix will never be called. Reneighboring is required. diff --git a/doc/src/fix_vector.txt b/doc/src/fix_vector.txt index 47b3cfc67a..e1bfbe5738 100644 --- a/doc/src/fix_vector.txt +++ b/doc/src/fix_vector.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -37,7 +37,7 @@ simply store them. For a single specified value, the values are stored as a global vector of growing length. For multiple specified values, they are stored as rows in a global array, whose number of rows is growing. The resulting vector or array can be used by other -"output commands"_Section_howto.html#howto_15. +"output commands"_Howto_output.html. One way to to use this command is to accumulate a vector that is time-integrated using the "variable trap()"_variable.html function. @@ -94,7 +94,7 @@ output"_thermo_style.html or other fixes such as "fix nvt"_fix_nh.html or "fix temp/rescale"_fix_temp_rescale.html. See the doc pages for these commands which give the IDs of these computes. Users can also write code for their own compute styles and "add them to -LAMMPS"_Section_modify.html. +LAMMPS"_Modify.html. If a value begins with "f_", a fix ID must follow which has been previously defined in the input script. If no bracketed term is @@ -105,7 +105,7 @@ calculated by the fix is used. Note that some fixes only produce their values on certain timesteps, which must be compatible with {Nevery}, else an error will result. Users can also write code for their own fix styles and "add them to -LAMMPS"_Section_modify.html. +LAMMPS"_Modify.html. If a value begins with "v_", a variable name must follow which has been previously defined in the input script. An equal-style or @@ -127,9 +127,8 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. This fix produces a global vector or global array which can be -accessed by various "output commands"_Section_howto.html#howto_15. -The values can only be accessed on timesteps that are multiples of -{Nevery}. +accessed by various "output commands"_Howto_output.html. The values +can only be accessed on timesteps that are multiples of {Nevery}. A vector is produced if only a single input value is specified. An array is produced if multiple input values are specified. diff --git a/doc/src/fix_viscosity.txt b/doc/src/fix_viscosity.txt index f6603be624..d86b13d055 100644 --- a/doc/src/fix_viscosity.txt +++ b/doc/src/fix_viscosity.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -100,13 +100,12 @@ accurately infer a viscosity and should try increasing the Nevery parameter. An alternative method for calculating a viscosity is to run a NEMD -simulation, as described in "Section -6.13"_Section_howto.html#howto_13 of the manual. NEMD simulations -deform the simulation box via the "fix deform"_fix_deform.html -command. Thus they cannot be run on a charged system using a "PPPM -solver"_kspace_style.html since PPPM does not currently support -non-orthogonal boxes. Using fix viscosity keeps the box orthogonal; -thus it does not suffer from this limitation. +simulation, as described on the "Howto nemd"_Howto_nemd.html doc page. +NEMD simulations deform the simulation box via the "fix +deform"_fix_deform.html command. Thus they cannot be run on a charged +system using a "PPPM solver"_kspace_style.html since PPPM does not +currently support non-orthogonal boxes. Using fix viscosity keeps the +box orthogonal; thus it does not suffer from this limitation. [Restart, fix_modify, output, run start/stop, minimize info:] @@ -115,13 +114,13 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. This fix computes a global scalar which can be accessed by various -"output commands"_Section_howto.html#howto_15. The scalar is the -cumulative momentum transferred between the bottom and middle of the -simulation box (in the {pdim} direction) is stored as a scalar -quantity by this fix. This quantity is zeroed when the fix is defined -and accumulates thereafter, once every N steps. The units of the -quantity are momentum = mass*velocity. The scalar value calculated by -this fix is "intensive". +"output commands"_Howto_output.html. The scalar is the cumulative +momentum transferred between the bottom and middle of the simulation +box (in the {pdim} direction) is stored as a scalar quantity by this +fix. This quantity is zeroed when the fix is defined and accumulates +thereafter, once every N steps. The units of the quantity are +momentum = mass*velocity. The scalar value calculated by this fix is +"intensive". No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. This fix is not invoked during "energy @@ -130,8 +129,8 @@ minimization"_minimize.html. [Restrictions:] This fix is part of the MISC package. It is only enabled if LAMMPS -was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +was built with that package. See the "Build +package"_Build_package.html doc page for more info. Swaps conserve both momentum and kinetic energy, even if the masses of the swapped atoms are not equal. Thus you should not need to diff --git a/doc/src/fix_viscous.txt b/doc/src/fix_viscous.txt index 9c30e40249..c5a3ede0b2 100644 --- a/doc/src/fix_viscous.txt +++ b/doc/src/fix_viscous.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -82,9 +82,9 @@ easily be used as a thermostat. No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. The "fix_modify"_fix_modify.html {respa} option is supported by this fix. This allows to set at which level of the "r-RESPA"_run_style.html diff --git a/doc/src/fix_wall.txt b/doc/src/fix_wall.txt index e814c89a07..162e32c68c 100644 --- a/doc/src/fix_wall.txt +++ b/doc/src/fix_wall.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -263,14 +263,14 @@ integrator the fix is adding its forces. Default is the outermost level. This fix computes a global scalar energy and a global vector of forces, which can be accessed by various "output -commands"_Section_howto.html#howto_15. Note that the scalar energy is -the sum of interactions with all defined walls. If you want the -energy on a per-wall basis, you need to use multiple fix wall -commands. The length of the vector is equal to the number of walls -defined by the fix. Each vector value is the normal force on a -specific wall. Note that an outward force on a wall will be a -negative value for {lo} walls and a positive value for {hi} walls. -The scalar and vector values calculated by this fix are "extensive". +commands"_Howto_output.html. Note that the scalar energy is the sum +of interactions with all defined walls. If you want the energy on a +per-wall basis, you need to use multiple fix wall commands. The +length of the vector is equal to the number of walls defined by the +fix. Each vector value is the normal force on a specific wall. Note +that an outward force on a wall will be a negative value for {lo} +walls and a positive value for {hi} walls. The scalar and vector +values calculated by this fix are "extensive". No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. @@ -288,23 +288,22 @@ option for this fix. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/fix_wall_body_polygon.txt b/doc/src/fix_wall_body_polygon.txt new file mode 100644 index 0000000000..45cbb2841d --- /dev/null +++ b/doc/src/fix_wall_body_polygon.txt @@ -0,0 +1,104 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +fix wall/body/polygon command :h3 + +[Syntax:] + +fix ID group-ID wall/body/polygon k_n c_n c_t wallstyle args keyword values ... :pre + +ID, group-ID are documented in "fix"_fix.html command :ulb,l +wall/body/polygon = style name of this fix command :l +k_n = normal repulsion strength (force/distance or pressure units) :l +c_n = normal damping coefficient (force/distance or pressure units) :l +c_t = tangential damping coefficient (force/distance or pressure units) :l +wallstyle = {xplane} or {yplane} or {zplane} or {zcylinder} :l +args = list of arguments for a particular style :l + {xplane} or {yplane} args = lo hi + lo,hi = position of lower and upper plane (distance units), either can be NULL) + {zcylinder} args = radius + radius = cylinder radius (distance units) :pre +zero or more keyword/value pairs may be appended to args :l +keyword = {wiggle} :l + {wiggle} values = dim amplitude period + dim = {x} or {y} or {z} + amplitude = size of oscillation (distance units) + period = time of oscillation (time units) :pre +:ule + +[Examples:] + +fix 1 all wall/body/polygon 1000.0 20.0 5.0 xplane -10.0 10.0 + +[Description:] + +This fix is for use with 2d models of body particles of style +{rounded/polygon}. It bounds the simulation domain with wall(s). All +particles in the group interact with the wall when they are close +enough to touch it. The nature of the interaction between the wall +and the polygon particles is the same as that between the polygon +particles themselves, which is similar to a Hookean potential. See +the "Howto body"_Howto_body.html doc page for more details on using +body particles. + +The parameters {k_n}, {c_n}, {c_t} have the same meaning and units as +those specified with the "pair_style +body/rounded/polygon"_pair_body_rounded_polygon.html command. + +The {wallstyle} can be planar or cylindrical. The 2 planar options +specify a pair of walls in a dimension. Wall positions are given by +{lo} and {hi}. Either of the values can be specified as NULL if a +single wall is desired. For a {zcylinder} wallstyle, the cylinder's +axis is at x = y = 0.0, and the radius of the cylinder is specified. + +Optionally, the wall can be moving, if the {wiggle} keyword is +appended. + +For the {wiggle} keyword, the wall oscillates sinusoidally, similar to +the oscillations of particles which can be specified by the "fix +move"_fix_move.html command. This is useful in packing simulations of +particles. The arguments to the {wiggle} keyword specify a dimension +for the motion, as well as it's {amplitude} and {period}. Note that +if the dimension is in the plane of the wall, this is effectively a +shearing motion. If the dimension is perpendicular to the wall, it is +more of a shaking motion. A {zcylinder} wall can only be wiggled in +the z dimension. + +Each timestep, the position of a wiggled wall in the appropriate {dim} +is set according to this equation: + +position = coord + A - A cos (omega * delta) :pre + +where {coord} is the specified initial position of the wall, {A} is +the {amplitude}, {omega} is 2 PI / {period}, and {delta} is the time +elapsed since the fix was specified. The velocity of the wall is set +to the derivative of this expression. + +[Restart, fix_modify, output, run start/stop, minimize info:] + +None of the "fix_modify"_fix_modify.html options are relevant to this +fix. No global or per-atom quantities are stored by this fix for +access by various "output commands"_Howto_output.html. No parameter +of this fix can be used with the {start/stop} keywords of the +"run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. + +[Restrictions:] + +This fix is part of the BODY package. It is only enabled if LAMMPS +was built with that package. See the "Build +package"_Build_package.html doc page for more info. + +Any dimension (xy) that has a wall must be non-periodic. + +[Related commands:] + +"atom_style body"_atom_style.html, "pair_style +body/rounded/polygon"_pair_body_rounded_polygon.html + +[Default:] none diff --git a/doc/src/fix_wall_body_polyhedron.txt b/doc/src/fix_wall_body_polyhedron.txt new file mode 100644 index 0000000000..231ab1f0fe --- /dev/null +++ b/doc/src/fix_wall_body_polyhedron.txt @@ -0,0 +1,103 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +fix wall/body/polyhedron command :h3 + +[Syntax:] + +fix ID group-ID wall/body/polyhedron k_n c_n c_t wallstyle args keyword values ... :pre + +ID, group-ID are documented in "fix"_fix.html command :ulb,l +wall/body/polyhedron = style name of this fix command :l +k_n = normal repulsion strength (force/distance units or pressure units - see discussion below) :l +c_n = normal damping coefficient (force/distance units or pressure units - see discussion below) :l +c_t = tangential damping coefficient (force/distance units or pressure units - see discussion below) :l +wallstyle = {xplane} or {yplane} or {zplane} or {zcylinder} :l +args = list of arguments for a particular style :l + {xplane} or {yplane} args = lo hi + lo,hi = position of lower and upper plane (distance units), either can be NULL) + {zcylinder} args = radius + radius = cylinder radius (distance units) :pre +zero or more keyword/value pairs may be appended to args :l +keyword = {wiggle} :l + {wiggle} values = dim amplitude period + dim = {x} or {y} or {z} + amplitude = size of oscillation (distance units) + period = time of oscillation (time units) :pre +:ule + +[Examples:] + +fix 1 all wall/body/polyhedron 1000.0 20.0 5.0 xplane -10.0 10.0 + +[Description:] + +This fix is for use with 3d models of body particles of style +{rounded/polyhedron}. It bounds the simulation domain with wall(s). +All particles in the group interact with the wall when they are close +enough to touch it. The nature of the interaction between the wall +and the polygon particles is the same as that between the polygon +particles themselves, which is similar to a Hookean potential. See +the "Howto body"_Howto_body.html doc page for more details on using +body particles. + +The parameters {k_n}, {c_n}, {c_t} have the same meaning and units as +those specified with the "pair_style +body/rounded/polyhedron"_pair_body_rounded_polyhedron.html command. + +The {wallstyle} can be planar or cylindrical. The 3 planar options +specify a pair of walls in a dimension. Wall positions are given by +{lo} and {hi}. Either of the values can be specified as NULL if a +single wall is desired. For a {zcylinder} wallstyle, the cylinder's +axis is at x = y = 0.0, and the radius of the cylinder is specified. + +Optionally, the wall can be moving, if the {wiggle} keyword is appended. + +For the {wiggle} keyword, the wall oscillates sinusoidally, similar to +the oscillations of particles which can be specified by the "fix +move"_fix_move.html command. This is useful in packing simulations of +particles. The arguments to the {wiggle} keyword specify a dimension +for the motion, as well as it's {amplitude} and {period}. Note that +if the dimension is in the plane of the wall, this is effectively a +shearing motion. If the dimension is perpendicular to the wall, it is +more of a shaking motion. A {zcylinder} wall can only be wiggled in +the z dimension. + +Each timestep, the position of a wiggled wall in the appropriate {dim} +is set according to this equation: + +position = coord + A - A cos (omega * delta) :pre + +where {coord} is the specified initial position of the wall, {A} is +the {amplitude}, {omega} is 2 PI / {period}, and {delta} is the time +elapsed since the fix was specified. The velocity of the wall is set +to the derivative of this expression. + +[Restart, fix_modify, output, run start/stop, minimize info:] + +None of the "fix_modify"_fix_modify.html options are relevant to this +fix. No global or per-atom quantities are stored by this fix for +access by various "output commands"_Howto_output.html. No parameter +of this fix can be used with the {start/stop} keywords of the +"run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. + +[Restrictions:] + +This fix is part of the BODY package. It is only enabled if LAMMPS +was built with that package. See the "Build +package"_Build_package.html doc page for more info. + +Any dimension (xyz) that has a wall must be non-periodic. + +[Related commands:] + +"atom_style body"_atom_style.html, "pair_style +body/rounded/polyhedron"_pair_body_rounded_polyhedron.html + +[Default:] none diff --git a/doc/src/fix_wall_ees.txt b/doc/src/fix_wall_ees.txt index f141a19405..4cc91f5222 100644 --- a/doc/src/fix_wall_ees.txt +++ b/doc/src/fix_wall_ees.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -97,8 +97,8 @@ of using this fix in the examples/USER/misc/ees/ directory. [Restrictions:] This fix is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. This fix requires that atoms be ellipsoids as defined by the "atom_style ellipsoid"_atom_style.html command. diff --git a/doc/src/fix_wall_gran.txt b/doc/src/fix_wall_gran.txt index 5f1679604e..0ea5b194eb 100644 --- a/doc/src/fix_wall_gran.txt +++ b/doc/src/fix_wall_gran.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -148,16 +148,16 @@ uninterrupted fashion. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored by this fix for -access by various "output commands"_Section_howto.html#howto_15. No -parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy +access by various "output commands"_Howto_output.html. No parameter +of this fix can be used with the {start/stop} keywords of the +"run"_run.html command. This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] This fix is part of the GRANULAR package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. Any dimension (xyz) that has a granular wall must be non-periodic. diff --git a/doc/src/fix_wall_gran_region.txt b/doc/src/fix_wall_gran_region.txt index 92fb042194..50d744b305 100644 --- a/doc/src/fix_wall_gran_region.txt +++ b/doc/src/fix_wall_gran_region.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -180,16 +180,16 @@ region with a different region ID. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored by this fix for -access by various "output commands"_Section_howto.html#howto_15. No -parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy +access by various "output commands"_Howto_output.html. No parameter +of this fix can be used with the {start/stop} keywords of the +"run"_run.html command. This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] This fix is part of the GRANULAR package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/fix_wall_piston.txt b/doc/src/fix_wall_piston.txt index 4d7756c237..b1968e0d49 100644 --- a/doc/src/fix_wall_piston.txt +++ b/doc/src/fix_wall_piston.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -91,16 +91,16 @@ define the lattice spacings. No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. [Restrictions:] This fix style is part of the SHOCK package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. The face that has the wall/piston must be boundary type 's' (shrink-wrapped). The opposing face can be diff --git a/doc/src/fix_wall_reflect.txt b/doc/src/fix_wall_reflect.txt index 954ec65bf6..d43cafbf09 100644 --- a/doc/src/fix_wall_reflect.txt +++ b/doc/src/fix_wall_reflect.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -51,7 +51,7 @@ corresponding component of its velocity is flipped. When used in conjunction with "fix nve"_fix_nve.html and "run_style verlet"_run_style.html, the resultant time-integration algorithm is equivalent to the primitive splitting algorithm (PSA) described by -"Bond"_#Bond. Because each reflection event divides +"Bond"_#Bond1. Because each reflection event divides the corresponding timestep asymmetrically, energy conservation is only satisfied to O(dt), rather than to O(dt^2) as it would be for velocity-Verlet integration without reflective walls. @@ -130,23 +130,22 @@ position = c0 + A (1 - cos(omega*delta)) :pre Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line @@ -155,10 +154,10 @@ more instructions on how to use the accelerated styles effectively. No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. [Restrictions:] @@ -180,5 +179,5 @@ error. :line -:link(Bond) +:link(Bond1) [(Bond)] Bond and Leimkuhler, SIAM J Sci Comput, 30, p 134 (2007). diff --git a/doc/src/fix_wall_region.txt b/doc/src/fix_wall_region.txt index 9700545dc9..559a2f0d89 100644 --- a/doc/src/fix_wall_region.txt +++ b/doc/src/fix_wall_region.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -156,12 +156,11 @@ integrator the fix is adding its forces. Default is the outermost level. This fix computes a global scalar energy and a global 3-length vector of forces, which can be accessed by various "output -commands"_Section_howto.html#howto_15. The scalar energy is the sum -of energy interactions for all particles interacting with the wall -represented by the region surface. The 3 vector quantities are the -x,y,z components of the total force acting on the wall due to the -particles. The scalar and vector values calculated by this fix are -"extensive". +commands"_Howto_output.html. The scalar energy is the sum of energy +interactions for all particles interacting with the wall represented +by the region surface. The 3 vector quantities are the x,y,z +components of the total force acting on the wall due to the particles. +The scalar and vector values calculated by this fix are "extensive". No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. diff --git a/doc/src/fix_wall_srd.txt b/doc/src/fix_wall_srd.txt index c465896d37..3a50c45ab7 100644 --- a/doc/src/fix_wall_srd.txt +++ b/doc/src/fix_wall_srd.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -166,9 +166,9 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. This fix computes a global array of values which can be accessed by -various "output commands"_Section_howto.html#howto_15. The number of -rows in the array is equal to the number of walls defined by the fix. -The number of columns is 3, for the x,y,z components of force on each +various "output commands"_Howto_output.html. The number of rows in +the array is equal to the number of walls defined by the fix. The +number of columns is 3, for the x,y,z components of force on each wall. Note that an outward normal force on a wall will be a negative value diff --git a/doc/src/fixes.txt b/doc/src/fixes.txt index 79c2f75b8b..f2f257b134 100644 --- a/doc/src/fixes.txt +++ b/doc/src/fixes.txt @@ -26,6 +26,7 @@ Fixes :h1 fix_bond_swap fix_bond_react fix_box_relax + fix_client_md fix_cmap fix_colvars fix_controller @@ -61,6 +62,7 @@ Fixes :h1 fix_langevin fix_langevin_drude fix_langevin_eff + fix_langevin_spin fix_latte fix_lb_fluid fix_lb_momentum @@ -99,6 +101,7 @@ Fixes :h1 fix_nve_manifold_rattle fix_nve_noforce fix_nve_sphere + fix_nve_spin fix_nve_tri fix_nvk fix_nvt_asphere @@ -114,6 +117,7 @@ Fixes :h1 fix_planeforce fix_poems fix_pour + fix_precession_spin fix_press_berendsen fix_print fix_property_atom @@ -165,6 +169,8 @@ Fixes :h1 fix_viscosity fix_viscous fix_wall + fix_wall_body_polygon + fix_wall_body_polyhedron fix_wall_ees fix_wall_gran fix_wall_gran_region diff --git a/doc/src/group.txt b/doc/src/group.txt index dddb0459e3..8472677372 100644 --- a/doc/src/group.txt +++ b/doc/src/group.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/group2ndx.txt b/doc/src/group2ndx.txt index 94d188399b..ed9bcb003a 100644 --- a/doc/src/group2ndx.txt +++ b/doc/src/group2ndx.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -54,8 +54,8 @@ This command requires that atoms have atom IDs, since this is the information that is written to the index file. These commands are part of the USER-COLVARS package. They are only -enabled if LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +enabled if LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/if.txt b/doc/src/if.txt index 52fad5aea7..513e451034 100644 --- a/doc/src/if.txt +++ b/doc/src/if.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -65,9 +65,9 @@ above. NOTE: If a command itself requires a quoted argument (e.g. a "print"_print.html command), then double and single quotes can be used and nested in the usual manner, as in the examples above and below. -See "Section 3.2"_Section_commands.html#cmd_2 of the manual for -more details on using quotes in arguments. Only one of level of -nesting is allowed, but that should be sufficient for most use cases. +The "Commands parse"_Commands_parse.html doc page has more details on +using quotes in arguments. Only one of level of nesting is allowed, +but that should be sufficient for most use cases. Note that by using the line continuation character "&", the if command can be spread across many lines, though it is still a single command: diff --git a/doc/src/improper_class2.txt b/doc/src/improper_class2.txt index 14ec6258de..704944920e 100644 --- a/doc/src/improper_class2.txt +++ b/doc/src/improper_class2.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -87,31 +87,30 @@ radians internally; hence the units of M are in energy/radian^2. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line [Restrictions:] This improper style can only be used if LAMMPS was built with the -CLASS2 package. See the "Making LAMMPS"_Section_start.html#start_3 -section for more info on packages. +CLASS2 package. See the "Build package"_Build_package.html doc +page for more info. [Related commands:] diff --git a/doc/src/improper_coeff.txt b/doc/src/improper_coeff.txt index 5c01a23ae9..8ed65f9535 100644 --- a/doc/src/improper_coeff.txt +++ b/doc/src/improper_coeff.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -67,9 +67,9 @@ the style to display the formula it computes and coefficients specified by the associated "improper_coeff"_improper_coeff.html command. Note that there are also additional improper styles submitted by users -which are included in the LAMMPS distribution. The list of these with -links to the individual styles are given in the improper section of -"this page"_Section_commands.html#cmd_5. +which are included in the LAMMPS distribution. The full list of all +improper styles is on the "Commands bond"_Commands_bond.html#improper +doc page. "improper_style none"_improper_none.html - turn off improper interactions "improper_style hybrid"_improper_hybrid.html - define multiple styles of improper interactions :ul diff --git a/doc/src/improper_cossq.txt b/doc/src/improper_cossq.txt index 138a6a1650..8bd02afb84 100644 --- a/doc/src/improper_cossq.txt +++ b/doc/src/improper_cossq.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -53,31 +53,30 @@ X0 (degrees) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line [Restrictions:] This improper style can only be used if LAMMPS was built with the -USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_3 -section for more info on packages. +USER-MISC package. See the "Build package"_Build_package.html doc +page for more info. [Related commands:] diff --git a/doc/src/improper_cvff.txt b/doc/src/improper_cvff.txt index 5f69eccc60..d57fddc512 100644 --- a/doc/src/improper_cvff.txt +++ b/doc/src/improper_cvff.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -54,31 +54,30 @@ n (0,1,2,3,4,6) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line [Restrictions:] This improper style can only be used if LAMMPS was built with the -MOLECULE package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info on packages. +MOLECULE package. See the "Build package"_Build_package.html doc page +for more info. [Related commands:] diff --git a/doc/src/improper_distance.txt b/doc/src/improper_distance.txt index 7d49d17c97..bfd92f57ec 100644 --- a/doc/src/improper_distance.txt +++ b/doc/src/improper_distance.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -48,8 +48,8 @@ K_4 (energy/distance^4) :ul [Restrictions:] This improper style can only be used if LAMMPS was built with the -USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_3 -section for more info on packages. +USER-MISC package. See the "Build package"_Build_package.html doc +page for more info. [Related commands:] diff --git a/doc/src/improper_fourier.txt b/doc/src/improper_fourier.txt index f9062da207..8b2021dccd 100644 --- a/doc/src/improper_fourier.txt +++ b/doc/src/improper_fourier.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -48,31 +48,30 @@ all (integer >= 0) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line [Restrictions:] This angle style can only be used if LAMMPS was built with the -USER_MISC package. See the "Making LAMMPS"_Section_start.html#start_3 -section for more info on packages. +USER_MISC package. See the "Build package"_Build_package.html doc +page for more info. [Related commands:] diff --git a/doc/src/improper_harmonic.txt b/doc/src/improper_harmonic.txt index bb17e5a641..1e9e7172f9 100644 --- a/doc/src/improper_harmonic.txt +++ b/doc/src/improper_harmonic.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -58,31 +58,30 @@ internally; hence the units of K are in energy/radian^2. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line [Restrictions:] This improper style can only be used if LAMMPS was built with the -MOLECULE package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info on packages. +MOLECULE package. See the "Build package"_Build_package.html doc page +for more info. [Related commands:] diff --git a/doc/src/improper_hybrid.txt b/doc/src/improper_hybrid.txt index 0c2beaef18..929eec43e1 100644 --- a/doc/src/improper_hybrid.txt +++ b/doc/src/improper_hybrid.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -55,8 +55,8 @@ types. [Restrictions:] This improper style can only be used if LAMMPS was built with the -MOLECULE package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info on packages. +MOLECULE package. See the "Build package"_Build_package.html doc page +for more info. Unlike other improper styles, the hybrid improper style does not store improper coefficient info for individual sub-styles in a "binary diff --git a/doc/src/improper_inversion_harmonic.txt b/doc/src/improper_inversion_harmonic.txt index 34683ca2bb..43ffdeb8e9 100644 --- a/doc/src/improper_inversion_harmonic.txt +++ b/doc/src/improper_inversion_harmonic.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -52,8 +52,8 @@ in between. [Restrictions:] This improper style can only be used if LAMMPS was built with the -USER-MOFFF package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info on packages. +USER-MOFFF package. See the "Build package"_Build_package.html doc +page for more info. [Related commands:] diff --git a/doc/src/improper_none.txt b/doc/src/improper_none.txt index af9964c743..f97af101fc 100644 --- a/doc/src/improper_none.txt +++ b/doc/src/improper_none.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/improper_ring.txt b/doc/src/improper_ring.txt index c02d392474..8a2ee29e17 100644 --- a/doc/src/improper_ring.txt +++ b/doc/src/improper_ring.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -57,31 +57,30 @@ theta0 (degrees) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line [Restrictions:] This improper style can only be used if LAMMPS was built with the -USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_3 -section for more info on packages. +USER-MISC package. See the "Build package"_Build_package.html doc +page for more info. [Related commands:] diff --git a/doc/src/improper_style.txt b/doc/src/improper_style.txt index 861701590f..ef0c524d14 100644 --- a/doc/src/improper_style.txt +++ b/doc/src/improper_style.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -60,9 +60,9 @@ specified by the associated "improper_coeff"_improper_coeff.html command. Note that there are also additional improper styles submitted by users -which are included in the LAMMPS distribution. The list of these with -links to the individual styles are given in the improper section of -"this page"_Section_commands.html#cmd_5. +which are included in the LAMMPS distribution. The full list of all +improper styles is on the "Commands bond"_Commands_bond.html#improper +doc page. "improper_style none"_improper_none.html - turn off improper interactions "improper_style zero"_improper_zero.html - topology but no interactions @@ -81,10 +81,9 @@ Improper styles can only be set for atom_style choices that allow impropers to be defined. Most improper styles are part of the MOLECULE package. They are only -enabled if LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info on packages. -The doc pages for individual improper potentials tell if it is part of -a package. +enabled if LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. The doc pages for +individual improper potentials tell if it is part of a package. [Related commands:] diff --git a/doc/src/improper_umbrella.txt b/doc/src/improper_umbrella.txt index d6df9ee6cc..6c29ec7ac5 100644 --- a/doc/src/improper_umbrella.txt +++ b/doc/src/improper_umbrella.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -22,7 +22,7 @@ improper_coeff 1 100.0 180.0 :pre The {umbrella} improper style uses the following potential, which is commonly referred to as a classic inversion and used in the -"DREIDING"_Section_howto.html#howto_4 force field: +"DREIDING"_Howto_bioFF.html force field: :c,image(Eqs/improper_umbrella.jpg) @@ -51,31 +51,30 @@ omega0 (degrees) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line [Restrictions:] This improper style can only be used if LAMMPS was built with the -MOLECULE package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info on packages. +MOLECULE package. See the "Build package"_Build_package.html doc page +for more info. [Related commands:] diff --git a/doc/src/improper_zero.txt b/doc/src/improper_zero.txt index 2a298573d5..f3f3485b57 100644 --- a/doc/src/improper_zero.txt +++ b/doc/src/improper_zero.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/include.txt b/doc/src/include.txt index 95d08db352..c114056313 100644 --- a/doc/src/include.txt +++ b/doc/src/include.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/info.txt b/doc/src/info.txt index d5b5bd97b9..99211de4fb 100644 --- a/doc/src/info.txt +++ b/doc/src/info.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/jump.txt b/doc/src/jump.txt index 4e3799f7b1..2e26d32c40 100644 --- a/doc/src/jump.txt +++ b/doc/src/jump.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -40,15 +40,14 @@ lmp_g++ < in.script :pre since the SELF option invokes the C-library rewind() call, which may not be supported for stdin on some systems or by some MPI implementations. This can be worked around by using the "-in -command-line argument"_Section_start.html#start_6, e.g. +command-line switch"_Run_options.html, e.g. lmp_g++ -in in.script :pre -or by using the "-var command-line -argument"_Section_start.html#start_6 to pass the script name as a -variable to the input script. In the latter case, a -"variable"_variable.html called "fname" could be used in place of -SELF, e.g. +or by using the "-var command-line switch"_Run_options.html to pass +the script name as a variable to the input script. In the latter +case, a "variable"_variable.html called "fname" could be used in place +of SELF, e.g. lmp_g++ -var fname in.script < in.script :pre diff --git a/doc/src/kspace_modify.txt b/doc/src/kspace_modify.txt index 6d27bb7076..41973601d7 100644 --- a/doc/src/kspace_modify.txt +++ b/doc/src/kspace_modify.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -13,47 +13,53 @@ kspace_modify command :h3 kspace_modify keyword value ... :pre one or more keyword/value pairs may be listed :ulb,l -keyword = {mesh} or {order} or {order/disp} or {mix/disp} or {overlap} or {minorder} or {force} or {gewald} or {gewald/disp} or {slab} or (nozforce} or {compute} or {cutoff/adjust} or {fftbench} or {collective} or {diff} or {kmax/ewald} or {force/disp/real} or {force/disp/kspace} or {splittol} or {disp/auto}:l - {mesh} value = x y z - x,y,z = grid size in each dimension for long-range Coulombics - {mesh/disp} value = x y z - x,y,z = grid size in each dimension for 1/r^6 dispersion - {order} value = N - N = extent of Gaussian for PPPM or MSM mapping of charge to grid - {order/disp} value = N - N = extent of Gaussian for PPPM mapping of dispersion term to grid - {mix/disp} value = {pair} or {geom} or {none} - {overlap} = {yes} or {no} = whether the grid stencil for PPPM is allowed to overlap into more than the nearest-neighbor processor - {minorder} value = M - M = min allowed extent of Gaussian when auto-adjusting to minimize grid communication +keyword = {collective} or {compute} or {cutoff/adjust} or {diff} or {disp/auto} or {fftbench} or {force/disp/kspace} or {force/disp/real} or {force} or {gewald/disp} or {gewald} or {kmax/ewald} or {mesh} or {minorder} or {mix/disp} or {order/disp} or {order} or {overlap} or {scafacos} or {slab} or {splittol} :l + {collective} value = {yes} or {no} + {compute} value = {yes} or {no} + {cutoff/adjust} value = {yes} or {no} + {diff} value = {ad} or {ik} = 2 or 4 FFTs for PPPM in smoothed or non-smoothed mode + {disp/auto} value = yes or no + {fftbench} value = {yes} or {no} + {force/disp/real} value = accuracy (force units) + {force/disp/kspace} value = accuracy (force units) {force} value = accuracy (force units) {gewald} value = rinv (1/distance units) rinv = G-ewald parameter for Coulombics {gewald/disp} value = rinv (1/distance units) rinv = G-ewald parameter for dispersion + {kmax/ewald} value = kx ky kz + kx,ky,kz = number of Ewald sum kspace vectors in each dimension + {mesh} value = x y z + x,y,z = grid size in each dimension for long-range Coulombics + {mesh/disp} value = x y z + x,y,z = grid size in each dimension for 1/r^6 dispersion + {minorder} value = M + M = min allowed extent of Gaussian when auto-adjusting to minimize grid communication + {mix/disp} value = {pair} or {geom} or {none} + {order} value = N + N = extent of Gaussian for PPPM or MSM mapping of charge to grid + {order/disp} value = N + N = extent of Gaussian for PPPM mapping of dispersion term to grid + {overlap} = {yes} or {no} = whether the grid stencil for PPPM is allowed to overlap into more than the nearest-neighbor processor + {pressure/scalar} value = {yes} or {no} + {scafacos} values = option value1 value2 ... + option = {tolerance} + value = {energy} or {energy_rel} or {field} or {field_rel} or {potential} or {potential_rel} + option = {fmm_tuning} + value = {0} or {1} {slab} value = volfactor or {nozforce} volfactor = ratio of the total extended volume used in the 2d approximation compared with the volume of the simulation domain {nozforce} turns off kspace forces in the z direction - {compute} value = {yes} or {no} - {cutoff/adjust} value = {yes} or {no} - {pressure/scalar} value = {yes} or {no} - {fftbench} value = {yes} or {no} - {collective} value = {yes} or {no} - {diff} value = {ad} or {ik} = 2 or 4 FFTs for PPPM in smoothed or non-smoothed mode - {kmax/ewald} value = kx ky kz - kx,ky,kz = number of Ewald sum kspace vectors in each dimension - {force/disp/real} value = accuracy (force units) - {force/disp/kspace} value = accuracy (force units) {splittol} value = tol - tol = relative size of two eigenvalues (see discussion below) - {disp/auto} value = yes or no :pre + tol = relative size of two eigenvalues (see discussion below) :pre :ule [Examples:] kspace_modify mesh 24 24 30 order 6 -kspace_modify slab 3.0 :pre +kspace_modify slab 3.0 +kspace_modify scafacos tolerance energy :pre [Description:] @@ -61,6 +67,132 @@ Set parameters used by the kspace solvers defined by the "kspace_style"_kspace_style.html command. Not all parameters are relevant to all kspace styles. +:line + +The {collective} keyword applies only to PPPM. It is set to {no} by +default, except on IBM BlueGene machines. If this option is set to +{yes}, LAMMPS will use MPI collective operations to remap data for +3d-FFT operations instead of the default point-to-point communication. +This is faster on IBM BlueGene machines, and may also be faster on +other machines if they have an efficient implementation of MPI +collective operations and adequate hardware. + +:line + +The {compute} keyword allows Kspace computations to be turned off, +even though a "kspace_style"_kspace_style.html is defined. This is +not useful for running a real simulation, but can be useful for +debugging purposes or for computing only partial forces that do not +include the Kspace contribution. You can also do this by simply not +defining a "kspace_style"_kspace_style.html, but a Kspace-compatible +"pair_style"_pair_style.html requires a kspace style to be defined. +This keyword gives you that option. + +:line + +The {cutoff/adjust} keyword applies only to MSM. If this option is +turned on, the Coulombic cutoff will be automatically adjusted at the +beginning of the run to give the desired estimated error. Other +cutoffs such as LJ will not be affected. If the grid is not set using +the {mesh} command, this command will also attempt to use the optimal +grid that minimizes cost using an estimate given by +"(Hardy)"_#Hardy1. Note that this cost estimate is not exact, somewhat +experimental, and still may not yield the optimal parameters. + +:line + +The {diff} keyword specifies the differentiation scheme used by the +PPPM method to compute forces on particles given electrostatic +potentials on the PPPM mesh. The {ik} approach is the default for +PPPM and is the original formulation used in "(Hockney)"_#Hockney1. It +performs differentiation in Kspace, and uses 3 FFTs to transfer each +component of the computed fields back to real space for total of 4 +FFTs per timestep. + +The analytic differentiation {ad} approach uses only 1 FFT to transfer +information back to real space for a total of 2 FFTs per timestep. It +then performs analytic differentiation on the single quantity to +generate the 3 components of the electric field at each grid point. +This is sometimes referred to as "smoothed" PPPM. This approach +requires a somewhat larger PPPM mesh to achieve the same accuracy as +the {ik} method. Currently, only the {ik} method (default) can be +used for a triclinic simulation cell with PPPM. The {ad} method is +always used for MSM. + +NOTE: Currently, not all PPPM styles support the {ad} option. Support +for those PPPM variants will be added later. + +:line + +The {disp/auto} option controls whether the pppm/disp is allowed to +generate PPPM parameters automatically. If set to {no}, parameters have +to be specified using the {gewald/disp}, {mesh/disp}, +{force/disp/real} or {force/disp/kspace} keywords, or +the code will stop with an error message. When this option is set to +{yes}, the error message will not appear and the simulation will start. +For a typical application, using the automatic parameter generation +will provide simulations that are either inaccurate or slow. Using this +option is thus not recommended. For guidelines on how to obtain good +parameters, see the "How-To"_Howto_dispersion.html discussion. + +:line + +The {fftbench} keyword applies only to PPPM. It is off by default. If +this option is turned on, LAMMPS will perform a short FFT benchmark +computation and report its timings, and will thus finish a some seconds +later than it would if this option were off. + +:line + +The {force/disp/real} and {force/disp/kspace} keywords set the force +accuracy for the real and space computations for the dispersion part +of pppm/disp. As shown in "(Isele-Holder)"_#Isele-Holder1, optimal +performance and accuracy in the results is obtained when these values +are different. + +:line + +The {force} keyword overrides the relative accuracy parameter set by +the "kspace_style"_kspace_style.html command with an absolute +accuracy. The accuracy determines the RMS error in per-atom forces +calculated by the long-range solver and is thus specified in force +units. A negative value for the accuracy setting means to use the +relative accuracy parameter. The accuracy setting is used in +conjunction with the pairwise cutoff to determine the number of +K-space vectors for style {ewald}, the FFT grid size for style +{pppm}, or the real space grid size for style {msm}. + +:line + +The {gewald} keyword sets the value of the Ewald or PPPM G-ewald +parameter for charge as {rinv} in reciprocal distance units. Without +this setting, LAMMPS chooses the parameter automatically as a function +of cutoff, precision, grid spacing, etc. This means it can vary from +one simulation to the next which may not be desirable for matching a +KSpace solver to a pre-tabulated pairwise potential. This setting can +also be useful if Ewald or PPPM fails to choose a good grid spacing +and G-ewald parameter automatically. If the value is set to 0.0, +LAMMPS will choose the G-ewald parameter automatically. MSM does not +use the {gewald} parameter. + +:line + +The {gewald/disp} keyword sets the value of the Ewald or PPPM G-ewald +parameter for dispersion as {rinv} in reciprocal distance units. It +has the same meaning as the {gewald} setting for Coulombics. + +:line + +The {kmax/ewald} keyword sets the number of kspace vectors in each +dimension for kspace style {ewald}. The three values must be positive +integers, or else (0,0,0), which unsets the option. When this option +is not set, the Ewald sum scheme chooses its own kspace vectors, +consistent with the user-specified accuracy and pairwise cutoff. In +any case, if kspace style {ewald} is invoked, the values used are +printed to the screen and the log file at the start of the run. + +:line + The {mesh} keyword sets the grid size for kspace style {pppm} or {msm}. In the case of PPPM, this is the FFT mesh, and each dimension must be factorizable into powers of 2, 3, and 5. In the case of MSM, @@ -70,6 +202,8 @@ or MSM solver chooses its own grid size, consistent with the user-specified accuracy and pairwise cutoff. Values for x,y,z of 0,0,0 unset the option. +:line + The {mesh/disp} keyword sets the grid size for kspace style {pppm/disp}. This is the FFT mesh for long-range dispersion and ach dimension must be factorizable into powers of 2, 3, and 5. When this @@ -77,39 +211,7 @@ option is not set, the PPPM solver chooses its own grid size, consistent with the user-specified accuracy and pairwise cutoff. Values for x,y,z of 0,0,0 unset the option. -The {order} keyword determines how many grid spacings an atom's charge -extends when it is mapped to the grid in kspace style {pppm} or {msm}. -The default for this parameter is 5 for PPPM and 8 for MSM, which -means each charge spans 5 or 8 grid cells in each dimension, -respectively. For the LAMMPS implementation of MSM, the order can -range from 4 to 10 and must be even. For PPPM, the minimum allowed -setting is 2 and the maximum allowed setting is 7. The larger the -value of this parameter, the smaller that LAMMPS will set the grid -size, to achieve the requested accuracy. Conversely, the smaller the -order value, the larger the grid size will be. Note that there is an -inherent trade-off involved: a small grid will lower the cost of FFTs -or MSM direct sum, but a larger order parameter will increase the cost -of interpolating charge/fields to/from the grid. - -The {order/disp} keyword determines how many grid spacings an atom's -dispersion term extends when it is mapped to the grid in kspace style -{pppm/disp}. It has the same meaning as the {order} setting for -Coulombics. - -The {overlap} keyword can be used in conjunction with the {minorder} -keyword with the PPPM styles to adjust the amount of communication -that occurs when values on the FFT grid are exchanged between -processors. This communication is distinct from the communication -inherent in the parallel FFTs themselves, and is required because -processors interpolate charge and field values using grid point values -owned by neighboring processors (i.e. ghost point communication). If -the {overlap} keyword is set to {yes} then this communication is -allowed to extend beyond nearest-neighbor processors, e.g. when using -lots of processors on a small problem. If it is set to {no} then the -communication will be limited to nearest-neighbor processors and the -{order} setting will be reduced if necessary, as explained by the -{minorder} keyword discussion. The {overlap} keyword is always set to -{yes} in MSM. +:line The {minorder} keyword allows LAMMPS to reduce the {order} setting if necessary to keep the communication of ghost grid point limited to @@ -126,6 +228,42 @@ error if the grid communication is non-nearest-neighbor and {overlap} is set to {no}. The {minorder} keyword is not currently supported in MSM. +:line + +The {mix/disp} keyword selects the mixing rule for the dispersion +coefficients. With {pair}, the dispersion coefficients of unlike +types are computed as indicated with "pair_modify"_pair_modify.html. +With {geom}, geometric mixing is enforced on the dispersion +coefficients in the kspace coefficients. When using the arithmetic +mixing rule, this will speed-up the simulations but introduces some +error in the force computations, as shown in "(Wennberg)"_#Wennberg. +With {none}, it is assumed that no mixing rule is +applicable. Splitting of the dispersion coefficients will be performed +as described in "(Isele-Holder)"_#Isele-Holder1. + +This splitting can be influenced with the {splittol} keywords. Only +the eigenvalues that are larger than tol compared to the largest +eigenvalues are included. Using this keywords the original matrix of +dispersion coefficients is approximated. This leads to faster +computations, but the accuracy in the reciprocal space computations of +the dispersion part is decreased. + +:line + +The {order} keyword determines how many grid spacings an atom's charge +extends when it is mapped to the grid in kspace style {pppm} or {msm}. +The default for this parameter is 5 for PPPM and 8 for MSM, which +means each charge spans 5 or 8 grid cells in each dimension, +respectively. For the LAMMPS implementation of MSM, the order can +range from 4 to 10 and must be even. For PPPM, the minimum allowed +setting is 2 and the maximum allowed setting is 7. The larger the +value of this parameter, the smaller that LAMMPS will set the grid +size, to achieve the requested accuracy. Conversely, the smaller the +order value, the larger the grid size will be. Note that there is an +inherent trade-off involved: a small grid will lower the cost of FFTs +or MSM direct sum, but a larger order parameter will increase the cost +of interpolating charge/fields to/from the grid. + The PPPM order parameter may be reset by LAMMPS when it sets up the FFT grid if the implied grid stencil extends beyond the grid cells owned by neighboring processors. Typically this will only occur when @@ -134,30 +272,102 @@ be generated indicating the order parameter is being reduced to allow LAMMPS to run the problem. Automatic adjustment of the order parameter is not supported in MSM. -The {force} keyword overrides the relative accuracy parameter set by -the "kspace_style"_kspace_style.html command with an absolute -accuracy. The accuracy determines the RMS error in per-atom forces -calculated by the long-range solver and is thus specified in force -units. A negative value for the accuracy setting means to use the -relative accuracy parameter. The accuracy setting is used in -conjunction with the pairwise cutoff to determine the number of -K-space vectors for style {ewald}, the FFT grid size for style -{pppm}, or the real space grid size for style {msm}. +:line -The {gewald} keyword sets the value of the Ewald or PPPM G-ewald -parameter for charge as {rinv} in reciprocal distance units. Without -this setting, LAMMPS chooses the parameter automatically as a function -of cutoff, precision, grid spacing, etc. This means it can vary from -one simulation to the next which may not be desirable for matching a -KSpace solver to a pre-tabulated pairwise potential. This setting can -also be useful if Ewald or PPPM fails to choose a good grid spacing -and G-ewald parameter automatically. If the value is set to 0.0, -LAMMPS will choose the G-ewald parameter automatically. MSM does not -use the {gewald} parameter. +The {order/disp} keyword determines how many grid spacings an atom's +dispersion term extends when it is mapped to the grid in kspace style +{pppm/disp}. It has the same meaning as the {order} setting for +Coulombics. -The {gewald/disp} keyword sets the value of the Ewald or PPPM G-ewald -parameter for dispersion as {rinv} in reciprocal distance units. It -has the same meaning as the {gewald} setting for Coulombics. +:line + +The {overlap} keyword can be used in conjunction with the {minorder} +keyword with the PPPM styles to adjust the amount of communication +that occurs when values on the FFT grid are exchanged between +processors. This communication is distinct from the communication +inherent in the parallel FFTs themselves, and is required because +processors interpolate charge and field values using grid point values +owned by neighboring processors (i.e. ghost point communication). If +the {overlap} keyword is set to {yes} then this communication is +allowed to extend beyond nearest-neighbor processors, e.g. when using +lots of processors on a small problem. If it is set to {no} then the +communication will be limited to nearest-neighbor processors and the +{order} setting will be reduced if necessary, as explained by the +{minorder} keyword discussion. The {overlap} keyword is always set to +{yes} in MSM. + +:line + +The {pressure/scalar} keyword applies only to MSM. If this option is +turned on, only the scalar pressure (i.e. (Pxx + Pyy + Pzz)/3.0) will +be computed, which can be used, for example, to run an isotropic barostat. +Computing the full pressure tensor with MSM is expensive, and this option +provides a faster alternative. The scalar pressure is computed using a +relationship between the Coulombic energy and pressure "(Hummer)"_#Hummer +instead of using the virial equation. This option cannot be used to access +individual components of the pressure tensor, to compute per-atom virial, +or with suffix kspace/pair styles of MSM, like OMP or GPU. + +:line + +The {scafacos} keyword is used for settings that are passed to the +ScaFaCoS library when using "kspace_style scafacos"_kspace_style.html. + +The {tolerance} option affects how the {accuracy} specified with the +"kspace_style"_kspace_style.html command is interpreted by ScaFaCoS. +The following values may be used: + +energy = absolute accuracy in total Coulomic energy +energy_rel = relative accuracy in total Coulomic energy +potential = absolute accuracy in total Coulomic potential +potential_rel = relative accuracy in total Coulomic potential +field = absolute accuracy in electric field +field_rel = relative accuracy in electric field :ul + +The values with suffix _rel indicate the tolerance is a relative +tolerance; the other values impose an absolute tolerance on the given +quantity. Absoulte tolerance in this case means, that for a given +quantity q and a given absolute tolerance of t_a the result should +be between q-t_a and q+t_a. For a relative tolerance t_r the relative +error should not be greater than t_r, i.e. abs(1 - (result/q)) < t_r. +As a consequence of this, the tolerance type should be checked, when +performing computations with a high absolute field / energy. E.g. +if the total energy in the system is 1000000.0 an absolute tolerance +of 1e-3 would mean that the result has to be between 999999.999 and +1000000.001, which would be equivalent to a relative tolerance of +1e-9. + +The energy and energy_rel values, set a tolerance based on the total +Coulomic energy of the system. The potential and potential_rel set a +tolerance based on the per-atom Coulomic energy. The field and +field_rel tolerance types set a tolerance based on the electric field +values computed by ScaFaCoS. Since per-atom forces are derived from +the per-atom electric field, this effectively sets a tolerance on the +forces, simimlar to other LAMMPS KSpace styles, as explained on the +"kspace_style"_kspace_style.html doc page. + +Note that not all ScaFaCoS solvers support all tolerance types. +These are the allowed values for each method: + +fmm = energy and energy_rel +p2nfft = field (1d-,2d-,3d-periodic systems) or potential (0d-periodic) +p3m = field +ewald = field +direct = has no tolerance tuning :ul + +If the tolerance type is not changed, the default values for the +tolerance type are the first values in the above list, e.g. energy +is the default tolerance type for the fmm solver. + +The {fmm_tuning} option is only relevant when using the FMM method. +It activates (value=1) or deactivates (value=0) an internal tuning +mechanism for the FMM solver. The tuning operation runs sequentially +and can be very time-consuming. Usually it is not needed for systems +with a homogenous charge distribution. The default for this option is +therefore {0}. The FMM internal tuning is performed once, when the +solver is set up. + +:line The {slab} keyword allows an Ewald or PPPM solver to be used for a systems that are periodic in x,y but non-periodic in z - a @@ -191,92 +401,7 @@ the "fix efield"_fix_efield.html command, it will not give the correct dielectric constant due to the Yeh/Berkowitz "(Yeh)"_#Yeh correction not being compatible with how "fix efield"_fix_efield.html works. -The {compute} keyword allows Kspace computations to be turned off, -even though a "kspace_style"_kspace_style.html is defined. This is -not useful for running a real simulation, but can be useful for -debugging purposes or for computing only partial forces that do not -include the Kspace contribution. You can also do this by simply not -defining a "kspace_style"_kspace_style.html, but a Kspace-compatible -"pair_style"_pair_style.html requires a kspace style to be defined. -This keyword gives you that option. - -The {cutoff/adjust} keyword applies only to MSM. If this option is -turned on, the Coulombic cutoff will be automatically adjusted at the -beginning of the run to give the desired estimated error. Other -cutoffs such as LJ will not be affected. If the grid is not set using -the {mesh} command, this command will also attempt to use the optimal -grid that minimizes cost using an estimate given by -"(Hardy)"_#Hardy1. Note that this cost estimate is not exact, somewhat -experimental, and still may not yield the optimal parameters. - -The {pressure/scalar} keyword applies only to MSM. If this option is -turned on, only the scalar pressure (i.e. (Pxx + Pyy + Pzz)/3.0) will -be computed, which can be used, for example, to run an isotropic barostat. -Computing the full pressure tensor with MSM is expensive, and this option -provides a faster alternative. The scalar pressure is computed using a -relationship between the Coulombic energy and pressure "(Hummer)"_#Hummer -instead of using the virial equation. This option cannot be used to access -individual components of the pressure tensor, to compute per-atom virial, -or with suffix kspace/pair styles of MSM, like OMP or GPU. - -The {fftbench} keyword applies only to PPPM. It is off by default. If -this option is turned on, LAMMPS will perform a short FFT benchmark -computation and report its timings, and will thus finish a some seconds -later than it would if this option were off. - -The {collective} keyword applies only to PPPM. It is set to {no} by -default, except on IBM BlueGene machines. If this option is set to -{yes}, LAMMPS will use MPI collective operations to remap data for -3d-FFT operations instead of the default point-to-point communication. -This is faster on IBM BlueGene machines, and may also be faster on -other machines if they have an efficient implementation of MPI -collective operations and adequate hardware. - -The {diff} keyword specifies the differentiation scheme used by the -PPPM method to compute forces on particles given electrostatic -potentials on the PPPM mesh. The {ik} approach is the default for -PPPM and is the original formulation used in "(Hockney)"_#Hockney1. It -performs differentiation in Kspace, and uses 3 FFTs to transfer each -component of the computed fields back to real space for total of 4 -FFTs per timestep. - -The analytic differentiation {ad} approach uses only 1 FFT to transfer -information back to real space for a total of 2 FFTs per timestep. It -then performs analytic differentiation on the single quantity to -generate the 3 components of the electric field at each grid point. -This is sometimes referred to as "smoothed" PPPM. This approach -requires a somewhat larger PPPM mesh to achieve the same accuracy as -the {ik} method. Currently, only the {ik} method (default) can be -used for a triclinic simulation cell with PPPM. The {ad} method is -always used for MSM. - -NOTE: Currently, not all PPPM styles support the {ad} option. Support -for those PPPM variants will be added later. - -The {kmax/ewald} keyword sets the number of kspace vectors in each -dimension for kspace style {ewald}. The three values must be positive -integers, or else (0,0,0), which unsets the option. When this option -is not set, the Ewald sum scheme chooses its own kspace vectors, -consistent with the user-specified accuracy and pairwise cutoff. In -any case, if kspace style {ewald} is invoked, the values used are -printed to the screen and the log file at the start of the run. - -With the {mix/disp} keyword one can select the mixing rule for the -dispersion coefficients. With {pair}, the dispersion coefficients of -unlike types are computed as indicated with -"pair_modify"_pair_modify.html. With {geom}, geometric mixing is -enforced on the dispersion coefficients in the kspace -coefficients. When using the arithmetic mixing rule, this will -speed-up the simulations but introduces some error in the force -computations, as shown in "(Wennberg)"_#Wennberg. With {none}, it is -assumed that no mixing rule is applicable. Splitting of the dispersion -coefficients will be performed as described in -"(Isele-Holder)"_#Isele-Holder1. This splitting can be influenced with -the {splittol} keywords. Only the eigenvalues that are larger than tol -compared to the largest eigenvalues are included. Using this keywords -the original matrix of dispersion coefficients is approximated. This -leads to faster computations, but the accuracy in the reciprocal space -computations of the dispersion part is decreased. +:line The {force/disp/real} and {force/disp/kspace} keywords set the force accuracy for the real and space computations for the dispersion part @@ -285,15 +410,17 @@ performance and accuracy in the results is obtained when these values are different. The {disp/auto} option controls whether the pppm/disp is allowed to -generate PPPM parameters automatically. If set to {no}, parameters have -to be specified using the {gewald/disp}, {mesh/disp}, -{force/disp/real} or {force/disp/kspace} keywords, or -the code will stop with an error message. When this option is set to -{yes}, the error message will not appear and the simulation will start. -For a typical application, using the automatic parameter generation -will provide simulations that are either inaccurate or slow. Using this -option is thus not recommended. For guidelines on how to obtain good -parameters, see the "How-To"_Section_howto.html#howto_24 discussion. +generate PPPM parameters automatically. If set to {no}, parameters +have to be specified using the {gewald/disp}, {mesh/disp}, +{force/disp/real} or {force/disp/kspace} keywords, or the code will +stop with an error message. When this option is set to {yes}, the +error message will not appear and the simulation will start. For a +typical application, using the automatic parameter generation will +provide simulations that are either inaccurate or slow. Using this +option is thus not recommended. For guidelines on how to obtain good +parameters, see the "Howto dispersion"_Howto_dispersion.html doc page. + +:line [Restrictions:] none @@ -306,10 +433,12 @@ parameters, see the "How-To"_Section_howto.html#howto_24 discussion. The option defaults are mesh = mesh/disp = 0 0 0, order = order/disp = 5 (PPPM), order = 10 (MSM), minorder = 2, overlap = yes, force = -1.0, gewald = gewald/disp = 0.0, slab = 1.0, compute = yes, cutoff/adjust = -yes (MSM), pressure/scalar = yes (MSM), fftbench = no (PPPM), diff = ik -(PPPM), mix/disp = pair, force/disp/real = -1.0, force/disp/kspace = -1.0, -split = 0, tol = 1.0e-6, and disp/auto = no. For pppm/intel, order = -order/disp = 7. +yes (MSM), pressure/scalar = yes (MSM), fftbench = no (PPPM), diff = +ik (PPPM), mix/disp = pair, force/disp/real = -1.0, force/disp/kspace += -1.0, split = 0, tol = 1.0e-6, and disp/auto = no. For pppm/intel, +order = order/disp = 7. For scafacos settings, the scafacos tolerance +option depends on the method chosen, as documented above. The +scafacos fmm_tuning default = 0. :line diff --git a/doc/src/kspace_style.txt b/doc/src/kspace_style.txt index 4f27c9aa78..6d8a289470 100644 --- a/doc/src/kspace_style.txt +++ b/doc/src/kspace_style.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -12,7 +12,7 @@ kspace_style command :h3 kspace_style style value :pre -style = {none} or {ewald} or {ewald/disp} or {ewald/omp} or {pppm} or {pppm/cg} or {pppm/disp} or {pppm/tip4p} or {pppm/stagger} or {pppm/disp/tip4p} or {pppm/gpu} or {pppm/kk} or {pppm/omp} or {pppm/cg/omp} or {pppm/tip4p/omp} or {msm} or {msm/cg} or {msm/omp} or {msm/cg/omp} :ulb,l +style = {none} or {ewald} or {ewald/disp} or {ewald/omp} or {pppm} or {pppm/cg} or {pppm/disp} or {pppm/tip4p} or {pppm/stagger} or {pppm/disp/tip4p} or {pppm/gpu} or {pppm/kk} or {pppm/omp} or {pppm/cg/omp} or {pppm/tip4p/omp} or {msm} or {msm/cg} or {msm/omp} or {msm/cg/omp} or {scafacos} :ulb,l {none} value = none {ewald} value = accuracy accuracy = desired relative error in forces @@ -22,7 +22,7 @@ style = {none} or {ewald} or {ewald/disp} or {ewald/omp} or {pppm} or {pppm/cg} accuracy = desired relative error in forces {pppm} value = accuracy accuracy = desired relative error in forces - {pppm/cg} value = accuracy (smallq) + {pppm/cg} values = accuracy (smallq) accuracy = desired relative error in forces smallq = cutoff for charges to be considered (optional) (charge units) {pppm/disp} value = accuracy @@ -56,7 +56,10 @@ style = {none} or {ewald} or {ewald/disp} or {ewald/omp} or {pppm} or {pppm/cg} accuracy = desired relative error in forces {msm/cg/omp} value = accuracy (smallq) accuracy = desired relative error in forces - smallq = cutoff for charges to be considered (optional) (charge units) :pre + smallq = cutoff for charges to be considered (optional) (charge units) + {scafacos} values = method accuracy + method = fmm or p2nfft or ewald or direct + accuracy = desired relative error in forces :pre :ule [Examples:] @@ -64,6 +67,7 @@ style = {none} or {ewald} or {ewald/disp} or {ewald/omp} or {pppm} or {pppm/cg} kspace_style pppm 1.0e-4 kspace_style pppm/cg 1.0e-5 1.0e-6 kspace style msm 1.0e-4 +kspace style scafacos fmm 1.0e-4 kspace_style none :pre [Description:] @@ -145,8 +149,8 @@ speedup in the KSpace time (8x less mesh points, 2x more expensive). However, for low relative accuracy, the staggered PPPM mesh size may be essentially the same as for regular PPPM, which means the method will be up to 2x slower in the KSpace time (simply 2x more expensive). -For more details and timings, see -"Section 5"_Section_accelerate.html. +For more details and timings, see the "Speed tips"_Speed_tips.html doc +page. NOTE: Using {pppm/stagger} may not give the same increase in the accuracy of energy and pressure as it does in forces, so some caution @@ -161,15 +165,16 @@ similar to the {ewald/disp} style. The 1/r^6 capability means that Lennard-Jones or Buckingham potentials can be used without a cutoff, i.e. they become full long-range potentials. -For these styles, you will possibly want to adjust the default choice of -parameters by using the "kspace_modify"_kspace_modify.html command. +For these styles, you will possibly want to adjust the default choice +of parameters by using the "kspace_modify"_kspace_modify.html command. This can be done by either choosing the Ewald and grid parameters, or by specifying separate accuracies for the real and kspace -calculations. When not making any settings, the simulation will stop with -an error message. Further information on the influence of the parameters -and how to choose them is described in "(Isele-Holder)"_#Isele-Holder2012, -"(Isele-Holder2)"_#Isele-Holder2013 and the -"How-To"_Section_howto.html#howto_24 discussion. +calculations. When not making any settings, the simulation will stop +with an error message. Further information on the influence of the +parameters and how to choose them is described in +"(Isele-Holder)"_#Isele-Holder2012, +"(Isele-Holder2)"_#Isele-Holder2013 and the "Howto +dispersion"_Howto_dispersion.html doc page. :line @@ -179,9 +184,9 @@ lo-level Makefile. This setting also changes some of the PPPM operations (e.g. mapping charge to mesh and interpolating electric fields to particles) to be performed in single precision. This option can speed-up long-range calculations, particularly in parallel or on -GPUs. The use of the -DFFT_SINGLE flag is discussed in "this -section"_Section_start.html#start_2_4 of the manual. MSM does not -currently support the -DFFT_SINGLE compiler switch. +GPUs. The use of the -DFFT_SINGLE flag is discussed on the "Build +settings"_Build_settings.html doc page. MSM does not currently support +the -DFFT_SINGLE compiler switch. :line @@ -210,6 +215,63 @@ pressure simulation with MSM will cause the code to run slower. :line +The {scafacos} style is a wrapper on the "ScaFaCoS Coulomb solver +library"_http://www.scafacos.de which provides a variety of solver +methods which can be used with LAMMPS. The paper by "(Who)"_#Who2012 +gives an overview of ScaFaCoS. + +ScaFaCoS was developed by a consortium of German research facilities +with a BMBF (German Ministry of Science and Education) funded project +in 2009-2012. Participants of the consortium were the Universities of +Bonn, Chemnitz, Stuttgart, and Wuppertal as well as the +Forschungszentrum Juelich. + +The library is available for download at "http://scafacos.de" or can +be cloned from the git-repository +"git://github.com/scafacos/scafacos.git". + +In order to use this KSpace style, you must download and build the +ScaFaCoS library, then build LAMMPS with the USER-SCAFACOS package +installed package which links LAMMPS to the ScaFaCoS library. +See details on "this page"_Section_packages.html#USER-SCAFACOS. + +NOTE: Unlike other KSpace solvers in LAMMPS, ScaFaCoS computes all +Coulombic interactions, both short- and long-range. Thus you should +NOT use a Coulmbic pair style when using kspace_style scafacos. This +also means the total Coulombic energy (short- and long-range) will be +tallied for "thermodynamic output"_thermo_style.html command as part +of the {elong} keyword; the {ecoul} keyword will be zero. + +NOTE: See the current restriction below about use of ScaFaCoS in +LAMMPS with molecular charged systems or the TIP4P water model. + +The specified {method} determines which ScaFaCoS algorithm is used. +These are the ScaFaCoS methods currently available from LAMMPS: + +{fmm} = Fast Multi-Pole method +{p2nfft} = FFT-based Coulomb solver +{ewald} = Ewald summation +{direct} = direct O(N^2) summation +{p3m} = PPPM :ul + +We plan to support additional ScaFaCoS solvers from LAMMPS in the +future. For an overview of the included solvers, refer to +"(Sutmann)"_#Sutmann2013 + +The specified {accuracy} is similar to the accuracy setting for other +LAMMPS KSpace styles, but is passed to ScaFaCoS, which can interpret +it in different ways for different methods it supports. Within the +ScaFaCoS library the {accuracy} is treated as a tolerance level +(either absolute or relative) for the chosen quantity, where the +quantity can be either the Columic field values, the per-atom Columic +energy or the total Columic energy. To select from these options, see +the "kspace_modify scafacos accuracy"_kspace_modify.html doc page. + +The "kspace_modify scafacos"_kspace_modify.html command also explains +other ScaFaCoS options currently exposed to LAMMPS. + +:line + The specified {accuracy} determines the relative RMS error in per-atom forces calculated by the long-range solver. It is set as a dimensionless number, relative to the force that two unit point @@ -267,10 +329,9 @@ relative RMS error. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. More specifically, the {pppm/gpu} style performs charge assignment and force interpolation calculations on the GPU. These processes are @@ -286,13 +347,13 @@ The {pppm/kk} style also performs charge assignment and force interpolation calculations on the GPU while the FFTs themselves are calculated on the CPU in non-threaded mode. -These accelerated styles are part of the GPU, USER-INTEL, -KOKKOS, USER-OMP, and OPT packages respectively. They are only -enabled if LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, +USER-OMP, and OPT packages respectively. They are only enabled if +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line @@ -308,9 +369,9 @@ triclinic simulation cells may not yet be supported by suffix versions of these styles. All of the kspace styles are part of the KSPACE package. They are -only enabled if LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. Note that -the KSPACE package is installed by default. +only enabled if LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. Note that the +KSPACE package is installed by default. For MSM, a simulation must be 3d and one can use any combination of periodic, non-periodic, or shrink-wrapped boundaries (specified using @@ -321,12 +382,24 @@ dimensions. The only exception is if the slab option is set with "kspace_modify"_kspace_modify.html, in which case the xy dimensions must be periodic and the z dimension must be non-periodic. +The scafacos KSpace style will only be enabled if LAMMPS is built with +the USER-SCAFACOS package. See the "Build package"_Build_package.html +doc page for more info. + +The use of ScaFaCos in LAMMPS does not yet support molecular charged +systems where the short-range Coulombic interactions between atoms in +the same bond/angle/dihedral are weighted by the +"special_bonds"_special_bonds.html command. Likewise it does not +support the "TIP4P water style" where a fictitious charge site is +introduced in each water molecule. + [Related commands:] "kspace_modify"_kspace_modify.html, "pair_style lj/cut/coul/long"_pair_lj.html, "pair_style lj/charmm/coul/long"_pair_charmm.html, "pair_style -lj/long/coul/long"_pair_lj_long.html, "pair_style buck/coul/long"_pair_buck.html +lj/long/coul/long"_pair_lj_long.html, "pair_style +buck/coul/long"_pair_buck.html [Default:] @@ -384,5 +457,12 @@ Evaluation of Forces for the Simulation of Biomolecules, University of Illinois at Urbana-Champaign, (2006). :link(Hardy2009) -[(Hardy2)] Hardy, Stone, Schulten, Parallel Computing 35 (2009) -164-177. +[(Hardy2)] Hardy, Stone, Schulten, Parallel Computing, 35, 164-177 +(2009). + +:link(Sutmann2013) +[(Sutmann)] Sutmann, Arnold, Fahrenberger, et. al., Physical review / E 88(6), 063308 (2013) + +:link(Who2012) +[(Who)] Who, Author2, Author3, J of Long Range Solvers, 35, 164-177 +(2012). diff --git a/doc/src/label.txt b/doc/src/label.txt index c6a573141b..adab44188c 100644 --- a/doc/src/label.txt +++ b/doc/src/label.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/lammps.book b/doc/src/lammps.book index 0764c593f7..751622ffc0 100644 --- a/doc/src/lammps.book +++ b/doc/src/lammps.book @@ -1,34 +1,135 @@ #HTMLDOC 1.8.28 -t pdf14 -f "../Manual.pdf" --book --toclevels 4 --no-numbered --toctitle "Table of Contents" --title --textcolor #000000 --linkcolor #0000ff --linkstyle plain --bodycolor #ffffff --size Universal --left 1.00in --right 0.50in --top 0.50in --bottom 0.50in --header .t. --header1 ... --footer ..1 --nup 1 --tocheader .t. --tocfooter ..i --portrait --color --no-pscommands --no-xrxcomments --compression=9 --jpeg=0 --fontsize 11.0 --fontspacing 1.2 --headingfont Sans --bodyfont Serif --headfootsize 11.0 --headfootfont Sans-Bold --charset iso-8859-15 --links --embedfonts --pagemode document --pagelayout single --firstpage c1 --pageeffect none --pageduration 10 --effectduration 1.0 --no-encryption --permissions all --owner-password "" --user-password "" --browserwidth 680 --no-strict --no-overflow Manual.html -Section_intro.html -Section_start.html -Section_commands.html -Section_packages.html -Section_accelerate.html -accelerate_gpu.html -accelerate_intel.html -accelerate_kokkos.html -accelerate_omp.html -accelerate_opt.html -Section_howto.html -Section_example.html -Section_perf.html -Section_tools.html -Section_modify.html -Section_python.html -Section_errors.html -Section_history.html - -lammps_tutorials.html -tutorial_bash_on_windows.html -tutorial_drude.html -tutorial_github.html -tutorial_pylammps.html - -lammps_support.html -body.html -manifolds.html +Intro.html +Intro_overview.html +Manual_version.html +Intro_features.html +Intro_nonfeatures.html +Intro_opensource.html +Intro_authors.html +Intro_website.html +Install.html +Install_linux.html +Install_mac.html +Install_windows.html +Install_tarball.html +Install_git.html +Install_svn.html +Install_patch.html +Build.html +Build_cmake.html +Build_make.html +Build_link.html +Build_basics.html +Build_settings.html +Build_package.html +Build_extras.html +Build_windows.html +Run_head.html +Run_basics.html +Run_options.html +Run_output.html +Run_windows.html +Commands.html +Commands_input.html +Commands_parse.html +Commands_structure.html +Commands_category.html +Commands_all.html +Commands_fix.html +Commands_compute.html +Commands_pair.html +Commands_bond.html +Commands_kspace.html +Packages.html +Packages_standard.html +Packages_user.html +Packages_details.html +Speed.html +Speed_bench.html +Speed_measure.html +Speed_tips.html +Speed_packages.html +Speed_gpu.html +Speed_intel.html +Speed_kokkos.html +Speed_omp.html +Speed_opt.html +Speed_compare.html +Howto.html +Howto_github.html +Howto_pylammps.html +Howto_bash.html +Howto_restart.html +Howto_viz.html +Howto_multiple.html +Howto_replica.html +Howto_library.html +Howto_couple.html +Howto_client_server.html +Howto_output.html +Howto_chunk.html +Howto_2d.html +Howto_triclinic.html +Howto_walls.html +Howto_nemd.html +Howto_granular.html +Howto_spherical.html +Howto_dispersion.html +Howto_temperature.html +Howto_thermostat.html +Howto_barostat.html +Howto_elastic.html +Howto_kappa.html +Howto_viscosity.html +Howto_diffusion.html +Howto_bioFF.html +Howto_tip3p.html +Howto_tip4p.html +Howto_spc.html +Howto_body.html +Howto_polarizable.html +Howto_coreshell.html +Howto_drude.html +Howto_drude2.html +Howto_manifold.html +Howto_spins.html +Examples.html +Tools.html +Modify.html +Modify_overview.html +Modify_contribute.html +Modify_atom.html +Modify_pair.html +Modify_bond.html +Modify_compute.html +Modify_fix.html +Modify_command.html +Modify_dump.html +Modify_kspace.html +Modify_min.html +Modify_region.html +Modify_body.html +Modify_thermo.html +Modify_variable.html +Python_head.html +Python_overview.html +Python_run.html +Python_shlib.html +Python_install.html +Python_mpi.html +Python_test.html +Python_library.html +Python_pylammps.html +Python_examples.html +Python_call.html +Errors.html +Errors_common.html +Errors_bugs.html +Errors_messages.html +Errors_warnings.html +Manual_build.html lammps_commands.html atom_modify.html @@ -67,6 +168,7 @@ label.html lattice.html log.html mass.html +message.html min_modify.html min_style.html minimize.html @@ -94,6 +196,9 @@ reset_timestep.html restart.html run.html run_style.html +server.html +server_mc.html +server_md.html set.html shell.html special_bonds.html @@ -141,6 +246,7 @@ fix_bond_create.html fix_bond_react.html fix_bond_swap.html fix_box_relax.html +fix_client_md.html fix_cmap.html fix_colvars.html fix_controller.html @@ -176,6 +282,7 @@ fix_ipi.html fix_langevin.html fix_langevin_drude.html fix_langevin_eff.html +fix_langevin_spin.html fix_latte.html fix_lb_fluid.html fix_lb_momentum.html @@ -213,6 +320,7 @@ fix_nve_line.html fix_nve_manifold_rattle.html fix_nve_noforce.html fix_nve_sphere.html +fix_nve_spin.html fix_nve_tri.html fix_nvk.html fix_nvt_asphere.html @@ -229,6 +337,7 @@ fix_pimd.html fix_planeforce.html fix_poems.html fix_pour.html +fix_precession_spin.html fix_press_berendsen.html fix_print.html fix_property_atom.html @@ -280,6 +389,8 @@ fix_vector.html fix_viscosity.html fix_viscous.html fix_wall.html +fix_wall_body_polygon.html +fix_wall_body_polyhedron.html fix_wall_ees.html fix_wall_gran.html fix_wall_gran_region.html @@ -301,6 +412,7 @@ compute_bond.html compute_bond_local.html compute_centro_atom.html compute_chunk_atom.html +compute_chunk_spread_atom.html compute_cluster_atom.html compute_cna_atom.html compute_cnp_atom.html @@ -317,6 +429,7 @@ compute_displace_atom.html compute_dpd.html compute_dpd_atom.html compute_edpd_temp_atom.html +compute_entropy_atom.html compute_erotate_asphere.html compute_erotate_rigid.html compute_erotate_sphere.html @@ -357,6 +470,7 @@ compute_property_chunk.html compute_property_local.html compute_rdf.html compute_reduce.html +compute_reduce_chunk.html compute_rigid_local.html compute_saed.html compute_slice.html @@ -381,6 +495,7 @@ compute_smd_ulsph_strain_rate.html compute_smd_ulsph_stress.html compute_smd_vol.html compute_sna_atom.html +compute_spin.html compute_stress_atom.html compute_tally.html compute_tdpd_cc_atom.html @@ -417,10 +532,12 @@ pair_write.html pair_adp.html pair_agni.html pair_airebo.html +pair_atm.html pair_awpmd.html pair_beck.html -pair_body.html +pair_body_nparticle.html pair_body_rounded_polygon.html +pair_body_rounded_polyhedron.html pair_bop.html pair_born.html pair_brownian.html @@ -506,6 +623,10 @@ pair_sph_lj.html pair_sph_rhosum.html pair_sph_taitwater.html pair_sph_taitwater_morris.html +pair_spin_dmi.html +pair_spin_exchange.html +pair_spin_magelec.html +pair_spin_neel.html pair_srp.html pair_sw.html pair_table.html diff --git a/doc/src/lammps_support.txt b/doc/src/lammps_support.txt deleted file mode 100644 index fa460ce6c2..0000000000 --- a/doc/src/lammps_support.txt +++ /dev/null @@ -1,7 +0,0 @@ - -Supporting Information :h1 - -This section of the manual contains supporting information that -is not documenting individual commands but general concepts and -supporting information about entities like body particles or -manifolds. diff --git a/doc/src/lammps_tutorials.txt b/doc/src/lammps_tutorials.txt deleted file mode 100644 index 5ceda65b60..0000000000 --- a/doc/src/lammps_tutorials.txt +++ /dev/null @@ -1,6 +0,0 @@ - -Tutorials :h2 - -The following pages contain some in-depth tutorials for -selected topics, that did not fit into any other place -in the manual. diff --git a/doc/src/lattice.txt b/doc/src/lattice.txt index 7a90df1f5d..6f16dc5432 100644 --- a/doc/src/lattice.txt +++ b/doc/src/lattice.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/log.txt b/doc/src/log.txt index 92bb12e6db..d526158a3c 100644 --- a/doc/src/log.txt +++ b/doc/src/log.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -33,9 +33,8 @@ be a variable, so that different processors do not attempt to write to the same log file. The file "log.lammps" is the default log file for a LAMMPS run. The -name of the initial log file can also be set by the command-line -switch -log. See "Section 2.6"_Section_start.html#start_6 for -details. +name of the initial log file can also be set by the "-log command-line +switch"_Run_options.html. [Restrictions:] none diff --git a/doc/src/mass.txt b/doc/src/mass.txt index 4b75132ccf..c693963044 100644 --- a/doc/src/mass.txt +++ b/doc/src/mass.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/message.txt b/doc/src/message.txt new file mode 100644 index 0000000000..cca1a5b369 --- /dev/null +++ b/doc/src/message.txt @@ -0,0 +1,162 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Command_all.html) + +:line + +message command :h3 + +[Syntax:] + +message which protocol mode arg :pre + +which = {client} or {server} :ulb,l +protocol = {md} or {mc} :l +mode = {file} or {zmq} or {mpi/one} or {mpi/two} :l + {file} arg = filename + filename = file used for message exchanges + {zmq} arg = socket-ID + socket-ID for client = localhost:5555, see description below + socket-ID for server = *:5555, see description below + {mpi/one} arg = none + {mpi/two} arg = filename + filename = file used to establish communication bewteen 2 MPI jobs :pre +:ule + +[Examples:] + +message client md file tmp.couple +message server md file tmp.couple :pre + +message client md zmq localhost:5555 +message server md zmq *:5555 :pre + +message client md mpi/one +message server md mpi/one :pre + +message client md mpi/two tmp.couple +message server md mpi/two tmp.couple :pre + +[Description:] + +Establish a messaging protocol between LAMMPS and another code for the +purpose of client/server coupling. + +The "Howto client/server"_Howto_client_server.html doc page gives an +overview of client/server coupling of LAMMPS with another code where +one code is the "client" and sends request messages to a "server" +code. The server responds to each request with a reply message. This +enables the two codes to work in tandem to perform a simulation. + +:line + +The {which} argument defines LAMMPS to be the client or the server. + +:line + +The {protocol} argument defines the format and content of messages +that will be exchanged between the two codes. The current options +are: + +md = run dynamics with another code +mc = perform Monte Carlo moves with another code :ul + +For protocol {md}, LAMMPS can be either a client or server. See the +"server md"_server_md.html doc page for details on the protocol. + +For protocol {mc}, LAMMPS can be the server. See the "server +mc"_server_mc.html doc page for details on the protocol. + +:line + +The {mode} argument specifies how messages are exchanged between the +client and server codes. Both codes must use the same mode and use +consistent parameters. + +For mode {file}, the 2 codes communicate via binary files. They must +use the same filename, which is actually a file prefix. Several files +with that prefix will be created and deleted as a simulation runs. +The filename can include a path. Both codes must be able to access +the path/file in a common filesystem. + +For mode {zmq}, the 2 codes communicate via a socket on the server +code's machine. Support for socket messaging is provided by the +open-source "ZeroMQ library"_http://zeromq.org, which must be +installed on your system. The client specifies an IP address (IPv4 +format) or the DNS name of the machine the server code is running on, +followed by a 4-digit port ID for the socket, separated by a colon. +E.g. + +localhost:5555 # client and server running on same machine +192.168.1.1:5555 # server is 192.168.1.1 +deptbox.uni.edu:5555 # server is deptbox.uni.edu :pre + +The server specifes "*:5555" where "*" represents all available +interfaces on the server's machine, and the port ID must match +what the client specifies. + +NOTE: What are allowed port IDs? + +NOTE: Additional explanation is needed here about how to use the {zmq} +mode on a parallel machine, e.g. a cluster with many nodes. + +For mode {mpi/one}, the 2 codes communicate via MPI and are launched +by the same mpirun command, e.g. with this syntax for OpenMPI: + +mpirun -np 2 lmp_mpi -mpicolor 0 -in in.client -log log.client : -np 4 othercode args # LAMMPS is client +mpirun -np 2 othercode args : -np 4 lmp_mpi -mpicolor 1 -in in.server # LAMMPS is server :pre + +Note the use of the "-mpicolor color" command-line argument with +LAMMPS. See the "command-line args"_Run_options.html doc page for +further explanation. + +For mode {mpi/two}, the 2 codes communicate via MPI, but are launched +be 2 separate mpirun commands. The specified {filename} argument is a +file the 2 MPI processes will use to exchange info so that an MPI +inter-communicator can be established to enable the 2 codes to send +MPI messages to each other. Both codes must be able to access the +path/file in a common filesystem. + +:line + +Normally, the message command should be used at the top of a LAMMPS +input script. It performs an initial handshake with the other code to +setup messaging and to verify that both codes are using the same +message protocol and mode. Assuming both codes are launched at +(nearly) the same time, the other code should perform the same kind of +initialization. + +If LAMMPS is the client code, it will begin sending messages when a +LAMMPS client command begins its operation. E.g. for the "fix +client/md"_fix_client_md.html command, it is when a "run"_run.html +command is executed. + +If LAMMPS is the server code, it will begin receiving messages when +the "server"_server.html command is invoked. + +A fix client command will terminate its messaging with the server when +LAMMPS ends, or the fix is deleted via the "unfix"_unfix command. The +server command will terminate its messaging with the client when the +client signals it. Then the remainder of the LAMMPS input script will +be processed. + +If both codes do something similar, this means a new round of +client/server messaging can be initiated after termination by re-using +a 2nd message command in your LAMMPS input script, followed by a new +fix client or server command. + +:line + +[Restrictions:] + +This command is part of the MESSAGE package. It is only enabled if +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. + +[Related commands:] + +"server"_server.html, "fix client/md"_fix_client_md.html + +[Default:] none diff --git a/doc/src/min_modify.txt b/doc/src/min_modify.txt index 73d142f5fa..9408eea167 100644 --- a/doc/src/min_modify.txt +++ b/doc/src/min_modify.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/min_style.txt b/doc/src/min_style.txt index 245ac5864c..4948a34864 100644 --- a/doc/src/min_style.txt +++ b/doc/src/min_style.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line min_style command :h3 diff --git a/doc/src/minimize.txt b/doc/src/minimize.txt index a3f2c5d0bf..910fc7f821 100644 --- a/doc/src/minimize.txt +++ b/doc/src/minimize.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/molecule.txt b/doc/src/molecule.txt index cd9ecce42c..88c6292d8b 100644 --- a/doc/src/molecule.txt +++ b/doc/src/molecule.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -176,9 +176,8 @@ LAMMPS uses this info to properly exclude or weight bonded pairwise interactions between bonded atoms. See the "special_bonds"_special_bonds.html command for more details. One reason to list the special bond info explicitly is for the -"thermalized Drude oscillator model"_tutorial_drude.html which treats -the bonds between nuclear cores and Drude electrons in a different -manner. +"thermalized Drude oscillator model"_Howto_drude.html which treats the +bonds between nuclear cores and Drude electrons in a different manner. NOTE: Whether a section is required depends on how the molecule template is used by other LAMMPS commands. For example, to add a diff --git a/doc/src/neb.txt b/doc/src/neb.txt index 56f075c301..75d199e0b4 100644 --- a/doc/src/neb.txt +++ b/doc/src/neb.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -50,15 +50,14 @@ follows the discussion in these 4 papers: "(HenkelmanA)"_#HenkelmanA, "(HenkelmanB)"_#HenkelmanB, "(Nakano)"_#Nakano3 and "(Maras)"_#Maras2. Each replica runs on a partition of one or more processors. Processor -partitions are defined at run-time using the -partition command-line -switch; see "Section 2.6"_Section_start.html#start_6 of the manual. -Note that if you have MPI installed, you can run a multi-replica -simulation with more replicas (partitions) than you have physical -processors, e.g you can run a 10-replica simulation on just one or two -processors. You will simply not get the performance speed-up you -would see with one or more physical processors per replica. See -"Section 6.5"_Section_howto.html#howto_5 of the manual for further -discussion. +partitions are defined at run-time using the "-partition command-line +switch"_Run_options.html. Note that if you have MPI installed, you +can run a multi-replica simulation with more replicas (partitions) +than you have physical processors, e.g you can run a 10-replica +simulation on just one or two processors. You will simply not get the +performance speed-up you would see with one or more physical +processors per replica. See the "Howto replica"_Howto_replica.html +doc page for further discussion. NOTE: As explained below, a NEB calculation perfoms a damped dynamics minimization across all the replicas. The minimizer uses whatever @@ -339,9 +338,9 @@ energy gradient of image i. ReplicaForce is the two-norm of the 3N-length force vector (including nudging forces) for replica i. MaxAtomForce is the maximum force component of any atom in replica i. -When a NEB calculation does not converge properly, the suplementary +When a NEB calculation does not converge properly, the supplementary information can help understanding what is going wrong. For instance -when the path angle becomes accute the definition of tangent used in +when the path angle becomes accute, the definition of tangent used in the NEB calculation is questionable and the NEB cannot may diverge "(Maras)"_#Maras2. @@ -396,8 +395,8 @@ image. [Restrictions:] This command can only be used if LAMMPS was built with the REPLICA -package. See the "Making LAMMPS"_Section_start.html#start_3 section -for more info on packages. +package. See the "Build package"_Build_package.html doc +page for more info. :line diff --git a/doc/src/neigh_modify.txt b/doc/src/neigh_modify.txt index c4544cb29b..6c4218cff5 100644 --- a/doc/src/neigh_modify.txt +++ b/doc/src/neigh_modify.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/neighbor.txt b/doc/src/neighbor.txt index 062f79a5bb..3e590eaff1 100644 --- a/doc/src/neighbor.txt +++ b/doc/src/neighbor.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -65,8 +65,8 @@ stored in the list. When a run is finished, counts of the number of neighbors stored in the pairwise list and the number of times neighbor lists were built -are printed to the screen and log file. See "this -section"_Section_start.html#start_7 for details. +are printed to the screen and log file. See the "Run +output"_Run_output.html doc page for details. [Restrictions:] none diff --git a/doc/src/newton.txt b/doc/src/newton.txt index a3e7f4fa91..fd7b536920 100644 --- a/doc/src/newton.txt +++ b/doc/src/newton.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/next.txt b/doc/src/next.txt index 08f73b896c..aefb2ca594 100644 --- a/doc/src/next.txt +++ b/doc/src/next.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -70,11 +70,11 @@ incrementing is done, using a single lock file for all variables. The next value (for each variable) is assigned to whichever processor partition executes the command first. All processors in the partition are assigned the same value(s). Running LAMMPS on multiple partitions -of processors via the "-partition" command-line switch is described in -"this section"_Section_start.html#start_6 of the manual. {Universe}- -and {uloop}-style variables are incremented using the files -"tmp.lammps.variable" and "tmp.lammps.variable.lock" which you will -see in your directory during and after such a LAMMPS run. +of processors via the "-partition command-line +switch"_Run_options.html. {Universe}- and {uloop}-style variables are +incremented using the files "tmp.lammps.variable" and +"tmp.lammps.variable.lock" which you will see in your directory during +and after such a LAMMPS run. Here is an example of running a series of simulations using the next command with an {index}-style variable. If this input script is named diff --git a/doc/src/package.txt b/doc/src/package.txt index 5c698934e8..65117ba3c3 100644 --- a/doc/src/package.txt +++ b/doc/src/package.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -33,8 +33,10 @@ args = arguments specific to the style :l last = ID of last GPU to be used on each node {tpa} value = Nthreads Nthreads = # of GPU threads used per atom - {device} value = device_type - device_type = {kepler} or {fermi} or {cypress} or {generic} + {device} value = device_type or platform_id:device_type or platform_id:custom,val1,val2,val3,..,val13 + platform_id = numerical OpenCL platform id (default: -1) + device_type = {kepler} or {fermi} or {cypress} or {intel} or {phi} or {generic} or {custom} + val1,val2,... = custom OpenCL tune parameters (see below for details) {blocksize} value = size size = thread block size for pair force computation {intel} args = NPhi keyword value ... @@ -82,6 +84,9 @@ args = arguments specific to the style :l no = perform communication pack/unpack in non-KOKKOS mode host = perform pack/unpack on host (e.g. with OpenMP threading) device = perform pack/unpack on device (e.g. on GPU) + {gpu/direct} = {off} or {on} + off = do not use GPU-direct + on = use GPU-direct (default) {omp} args = Nthreads keyword value ... Nthread = # of OpenMP threads to associate with each MPI process zero or more keyword/value pairs may be appended @@ -96,6 +101,9 @@ args = arguments specific to the style :l package gpu 1 package gpu 1 split 0.75 package gpu 2 split -1.0 +package gpu 1 device kepler +package gpu 1 device 2:generic +package gpu 1 device custom,32,4,8,256,11,128,256,128,32,64,8,128,128 package kokkos neigh half comm device package omp 0 neigh no package omp 4 @@ -116,8 +124,8 @@ their initialization, before a simulation is defined. This command can also be specified from the command-line when launching LAMMPS, using the "-pk" "command-line -switch"_Section_start.html#start_6. The syntax is exactly the same as -when used in an input script. +switch"_Run_options.html. The syntax is exactly the same as when used +in an input script. Note that all of the accelerator packages require the package command to be specified (except the OPT package), if the package is to be used @@ -127,26 +135,25 @@ a default version of the command is typically invoked by other accelerator settings. The KOKKOS package requires a "-k on" "command-line -switch"_Section_start.html#start_6 respectively, which invokes a -"package kokkos" command with default settings. +switch"_Run_options.html respectively, which invokes a "package +kokkos" command with default settings. For the GPU, USER-INTEL, and USER-OMP packages, if a "-sf gpu" or "-sf -intel" or "-sf omp" "command-line switch"_Section_start.html#start_6 -is used to auto-append accelerator suffixes to various styles in the -input script, then those switches also invoke a "package gpu", -"package intel", or "package omp" command with default settings. +intel" or "-sf omp" "command-line switch"_Run_options.html is used to +auto-append accelerator suffixes to various styles in the input +script, then those switches also invoke a "package gpu", "package +intel", or "package omp" command with default settings. NOTE: A package command for a particular style can be invoked multiple -times when a simulation is setup, e.g. by the "-c on", "-k on", "-sf", -and "-pk" "command-line switches"_Section_start.html#start_6, and by -using this command in an input script. Each time it is used all of -the style options are set, either to default values or to specified -settings. I.e. settings from previous invocations do not persist -across multiple invocations. +times when a simulation is setup, e.g. by the "-c on, -k on, -sf, and +-pk command-line switches"_Run_options.html, and by using this command +in an input script. Each time it is used all of the style options are +set, either to default values or to specified settings. I.e. settings +from previous invocations do not persist across multiple invocations. -See the "Section 5.3"_Section_accelerate.html#acc_3 section of the -manual for more details about using the various accelerator packages -for speeding up LAMMPS simulations. +See the "Speed packages"_Speed_packages.html doc page for more details +about using the various accelerator packages for speeding up LAMMPS +simulations. :line @@ -244,12 +251,40 @@ the value can improve performance. The number of threads per atom must be a power of 2 and currently cannot be greater than 32. The {device} keyword can be used to tune parameters optimized for a -specific accelerator, when using OpenCL. For CUDA, the {device} -keyword is ignored. Currently, the device type is limited to NVIDIA -Kepler, NVIDIA Fermi, AMD Cypress, or a generic device. More devices -may be added later. The default device type can be specified when -building LAMMPS with the GPU library, via settings in the -lib/gpu/Makefile that is used. +specific accelerator and platform when using OpenCL. OpenCL supports +the concept of a [platform], which represents one or more devices that +share the same driver (e.g. there would be a different platform for +GPUs from different vendors or for CPU based accelerator support). +In LAMMPS only one platform can be active at a time and by default +the first platform with an accelerator is selected. This is equivalent +to using a platform ID of -1. The platform ID is a number corresponding +to the output of the ocl_get_devices tool. The platform ID is passed +to the GPU library, by prefixing the {device} keyword with that number +separated by a colon. For CUDA, the {device} keyword is ignored. +Currently, the device tuning support is limited to NVIDIA Kepler, NVIDIA +Fermi, AMD Cypress, Intel x86_64 CPU, Intel Xeon Phi, or a generic device. +More devices may be added later. The default device type can be +specified when building LAMMPS with the GPU library, via setting a +variable in the lib/gpu/Makefile that is used. + +In addition, a device type {custom} is available, which is followed by +13 comma separated numbers, which allows to set those tweakable parameters +from the package command. It can be combined with the (colon separated) +platform id. The individual settings are: + +MEM_THREADS +THREADS_PER_ATOM +THREADS_PER_CHARGE +BLOCK_PAIR +MAX_SHARED_TYPES +BLOCK_NBOR_BUILD +BLOCK_BIO_PAIR +BLOCK_ELLIPSE +WARP_SIZE +PPPM_BLOCK_1D +BLOCK_CELL_2D +BLOCK_CELL_ID +MAX_BIO_SHARED_TYPES :ul The {blocksize} keyword allows you to tweak the number of threads used per thread block. This number should be a multiple of 32 (for GPUs) @@ -305,10 +340,10 @@ value via their package commands, but there is only a single global {Nthreads} value used by OpenMP. Thus if both package commands are invoked, you should insure the two values are consistent. If they are not, the last one invoked will take precedence, for both packages. -Also note that if the "-sf hybrid intel omp" "command-line -switch"_"_Section_start.html#start_6 is used, it invokes a "package -intel" command, followed by a "package omp" command, both with a -setting of {Nthreads} = 0. +Also note that if the "-sf hybrid intel omp command-line +switch"_Run_options.html is used, it invokes a "package intel" +command, followed by a "package omp" command, both with a setting of +{Nthreads} = 0. The {mode} keyword determines the precision mode to use for computing pair style forces, either on the CPU or on the coprocessor, @@ -328,7 +363,7 @@ specified with the OMP_NUM_THREADS environment variable or the {omp} keyword). The extra thread is dedicated for performing part of the "PPPM solver"_kspace_style.html computations and communications. This can improve parallel performance on processors supporting -Simultaneous Multithreading (SMT) such as Hyperthreading on Intel +Simultaneous Multithreading (SMT) such as Hyper-Threading (HT) on Intel processors. In this mode, one additional thread is generated per MPI process. LAMMPS will generate a warning in the case that more threads are used than available in SMT hardware on a node. If the PPPM solver @@ -447,15 +482,15 @@ The value options for all 3 keywords are {no} or {host} or {device}. A value of {no} means to use the standard non-KOKKOS method of packing/unpacking data for the communication. A value of {host} means to use the host, typically a multi-core CPU, and perform the -packing/unpacking in parallel with threads. A value of {device} means -to use the device, typically a GPU, to perform the packing/unpacking -operation. +packing/unpacking in parallel with threads. A value of {device} +means to use the device, typically a GPU, to perform the +packing/unpacking operation. The optimal choice for these keywords depends on the input script and the hardware used. The {no} value is useful for verifying that the -Kokkos-based {host} and {device} values are working correctly. It may -also be the fastest choice when using Kokkos styles in MPI-only mode -(i.e. with a thread count of 1). +Kokkos-based {host} and {device} values are working correctly. +It may also be the fastest choice when using Kokkos styles in +MPI-only mode (i.e. with a thread count of 1). When running on CPUs or Xeon Phi, the {host} and {device} values work identically. When using GPUs, the {device} value will typically be @@ -471,6 +506,18 @@ typically faster to let the host handle communication, by using the {host} value. Using {host} instead of {no} will enable use of multiple threads to pack/unpack communicated data. +The {gpu/direct} keyword chooses whether GPU-direct will be used. When +this keyword is set to {on}, buffers in GPU memory are passed directly +through MPI send/receive calls. This reduces overhead of first copying +the data to the host CPU. However GPU-direct is not supported on all +systems, which can lead to segmentation faults and would require +using a value of {off}. If LAMMPS can safely detect that GPU-direct is +not available (currently only possible with OpenMPI v2.0.0 or later), +then the {gpu/direct} keyword is automatically set to {off} by default. +When the {gpu/direct} keyword is set to {off} while any of the {comm} +keywords are set to {device}, the value for these {comm} keywords will +be automatically changed to {host}. + :line The {omp} style invokes settings associated with the use of the @@ -535,58 +582,58 @@ This command cannot be used after the simulation box is defined by a "read_data"_read_data.html or "create_box"_create_box.html command. The gpu style of this command can only be invoked if LAMMPS was built -with the GPU package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +with the GPU package. See the "Build package"_Build_package.html doc +page for more info. The intel style of this command can only be invoked if LAMMPS was -built with the USER-INTEL package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +built with the USER-INTEL package. See the "Build +package"_Build_package.html doc page for more info. The kk style of this command can only be invoked if LAMMPS was built -with the KOKKOS package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +with the KOKKOS package. See the "Build package"_Build_package.html +doc page for more info. The omp style of this command can only be invoked if LAMMPS was built -with the USER-OMP package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +with the USER-OMP package. See the "Build package"_Build_package.html +doc page for more info. [Related commands:] -"suffix"_suffix.html, "-pk" "command-line -setting"_Section_start.html#start_6 +"suffix"_suffix.html, "-pk command-line switch"_Run_options.html [Default:] For the GPU package, the default is Ngpu = 1 and the option defaults are neigh = yes, newton = off, binsize = 0.0, split = 1.0, gpuID = 0 to Ngpu-1, tpa = 1, and device = not used. These settings are made -automatically if the "-sf gpu" "command-line -switch"_Section_start.html#start_6 is used. If it is not used, you -must invoke the package gpu command in your input script or via the -"-pk gpu" "command-line switch"_Section_start.html#start_6. +automatically if the "-sf gpu" "command-line switch"_Run_options.html +is used. If it is not used, you must invoke the package gpu command +in your input script or via the "-pk gpu" "command-line +switch"_Run_options.html. For the USER-INTEL package, the default is Nphi = 1 and the option defaults are omp = 0, mode = mixed, lrt = no, balance = -1, tpc = 4, tptask = 240. The default ghost option is determined by the pair style being used. This value is output to the screen in the offload report at the end of each run. Note that all of these settings, -except "omp" and "mode", are ignored if LAMMPS was not built with -Xeon Phi coprocessor support. These settings are made automatically -if the "-sf intel" "command-line switch"_Section_start.html#start_6 -is used. If it is not used, you must invoke the package intel -command in your input script or or via the "-pk intel" "command-line -switch"_Section_start.html#start_6. +except "omp" and "mode", are ignored if LAMMPS was not built with Xeon +Phi coprocessor support. These settings are made automatically if the +"-sf intel" "command-line switch"_Run_options.html is used. If it is +not used, you must invoke the package intel command in your input +script or or via the "-pk intel" "command-line +switch"_Run_options.html. -For the KOKKOS package, the option defaults neigh = full, -neigh/qeq = full, newton = off, binsize = 0.0, and comm = device. -These settings are made automatically by the required "-k on" "command-line -switch"_Section_start.html#start_6. You can change them bu using the -package kokkos command in your input script or via the "-pk kokkos" -"command-line switch"_Section_start.html#start_6. +For the KOKKOS package, the option defaults neigh = full, neigh/qeq = +full, newton = off, binsize = 0.0, and comm = device, gpu/direct = on. +When LAMMPS can safely detect, that GPU-direct is not available, the +default value of gpu/direct becomes "off". +These settings are made automatically by the required "-k on" +"command-line switch"_Run_options.html. You can change them by +using the package kokkos command in your input script or via the +"-pk kokkos command-line switch"_Run_options.html. For the OMP package, the default is Nthreads = 0 and the option defaults are neigh = yes. These settings are made automatically if -the "-sf omp" "command-line switch"_Section_start.html#start_6 is -used. If it is not used, you must invoke the package omp command in -your input script or via the "-pk omp" "command-line -switch"_Section_start.html#start_6. +the "-sf omp" "command-line switch"_Run_options.html is used. If it +is not used, you must invoke the package omp command in your input +script or via the "-pk omp" "command-line switch"_Run_options.html. diff --git a/doc/src/pair_adp.txt b/doc/src/pair_adp.txt index 9d2a48dcbc..fc888ffbff 100644 --- a/doc/src/pair_adp.txt +++ b/doc/src/pair_adp.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -125,23 +125,22 @@ array tabulated with a scaling by r. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_agni.txt b/doc/src/pair_agni.txt index 402e537dad..74aef41255 100644 --- a/doc/src/pair_agni.txt +++ b/doc/src/pair_agni.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -58,23 +58,23 @@ and input files are provided in the examples/USER/misc/agni directory. :line Styles with {omp} suffix is functionally the same as the corresponding -style without the suffix. They have been optimized to run faster, depending -on your available hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated style takes the same arguments and -should produce the same results, except for round-off and precision -issues. +style without the suffix. They have been optimized to run faster, +depending on your available hardware, as discussed on the "Speed +packages"_Speed_packages.html doc page. The accelerated style takes +the same arguments and should produce the same results, except for +round-off and precision issues. -The accelerated style is part of the USER-OMP. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +The accelerated style is part of the USER-OMP. They are only enabled +if LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated style explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line @@ -96,13 +96,14 @@ This pair style can only be used via the {pair} keyword of the [Restrictions:] -Currently, only elemental systems are implemented. Also, the method only -provides access to the forces and not energies or stresses. However, one -can access the energy via thermodynamic integration of the forces as -discussed in "(Botu3)"_#Botu2016construct. This pair style is part -of the USER-MISC package. It is only enabled if LAMMPS was built with -that package. See the "Making LAMMPS"_Section_start.html#start_3 section -for more info. +Currently, only elemental systems are implemented. Also, the method +only provides access to the forces and not energies or +stresses. However, one can access the energy via thermodynamic +integration of the forces as discussed in +"(Botu3)"_#Botu2016construct. This pair style is part of the +USER-MISC package. It is only enabled if LAMMPS was built with that +package. See the "Build package"_Build_package.html doc page for more +info. The AGNI force field files provided with LAMMPS (see the potentials directory) are parameterized for metal "units"_units.html. diff --git a/doc/src/pair_airebo.txt b/doc/src/pair_airebo.txt index 1aa017f278..c090a39af7 100644 --- a/doc/src/pair_airebo.txt +++ b/doc/src/pair_airebo.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -176,23 +176,22 @@ thermo_style custom step temp epair v_REBO v_LJ v_TORSION :pre Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line @@ -213,8 +212,8 @@ These pair styles can only be used via the {pair} keyword of the [Restrictions:] These pair styles are part of the MANYBODY package. They are only -enabled if LAMMPS was built with that package. See the -"Making LAMMPS"_Section_start.html#start_3 section for more info. +enabled if LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. These pair potentials require the "newton"_newton.html setting to be "on" for pair interactions. diff --git a/doc/src/pair_atm.txt b/doc/src/pair_atm.txt new file mode 100644 index 0000000000..63a450c51a --- /dev/null +++ b/doc/src/pair_atm.txt @@ -0,0 +1,164 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +pair_style atm command :h3 + +[Syntax:] + +pair_style atm cutoff cutoff_triple :pre + +cutoff = cutoff for each pair in 3-body interaction (distance units) +cutoff_triple = additional cutoff applied to product of 3 pairwise distances (distance units) :ul + +[Examples:] + +pair_style atm 4.5 2.5 +pair_coeff * * * 0.072 :pre + +pair_style hybrid/overlay lj/cut 6.5 atm 4.5 2.5 +pair_coeff * * lj/cut 1.0 1.0 +pair_coeff 1 1 atm 1 0.064 +pair_coeff 1 1 atm 2 0.080 +pair_coeff 1 2 atm 2 0.100 +pair_coeff 2 2 atm 2 0.125 :pre + +[Description:] + +The {atm} style computes a 3-body "Axilrod-Teller-Muto"_#Axilrod +potential for the energy E of a system of atoms as + +:c,image(Eqs/pair_atm.jpg) + +where nu is the three-body interaction strength. The distances +between pairs of atoms r12, r23, r31 and the angles gamma1, gamma2, +gamma3 are as shown in this diagram: + +:c,image(JPG/pair_atm_dia.jpg) + +Note that for the interaction between a triplet of atoms I,J,K, there +is no "central" atom. The interaction is symmetric with respect to +permutation of the three atoms. Thus the nu value is +the same for all those permutations of the atom types of I,J,K +and needs to be specified only once, as discussed below. + +The {atm} potential is typically used in combination with a two-body +potential using the "pair_style hybrid/overlay"_pair_hybrid.html +command as in the example above. + +The potential for a triplet of atom is calculated only if all 3 +distances r12, r23, r31 between the 3 atoms satisfy rIJ < cutoff. +In addition, the product of the 3 distances r12*r23*r31 < +cutoff_triple^3 is required, which excludes from calculation the +triplets with small contribution to the interaction. + +The following coefficients must be defined for each pair of atoms +types via the "pair_coeff"_pair_coeff.html command as in the examples +above, or in the restart files read by the +"read_restart"_read_restart.html commands: + +K = atom type of the third atom (1 to Ntypes) +nu = prefactor (energy/distance^9 units) :ul + +K can be specified in one of two ways. An explicit numeric value can +be used, as in the 2nd example above. J <= K is required. LAMMPS +sets the coefficients for the other 5 symmetric interactions to the +same values. E.g. if I = 1, J = 2, K = 3, then these 6 values are set +to the specified nu: nu123, nu132, nu213, nu231, nu312, nu321. This +enforces the symmetry discussed above. + +A wildcard asterisk can be used for K to set the coefficients for +multiple triplets of atom types. This takes the form "*" or "*n" or +"n*" or "m*n". If N = the number of atom types, then an asterisk with +no numeric values means all types from 1 to N. A leading asterisk +means all types from 1 to n (inclusive). A trailing asterisk means +all types from n to N (inclusive). A middle asterisk means all types +from m to n (inclusive). Note that only type triplets with J <= K are +considered; if asterisks imply type triplets where K < J, they are +ignored. + +Note that a pair_coeff command can override a previous setting for the +same I,J,K triplet. For example, these commands set nu for all I,J.K +triplets, then overwrite nu for just the I,J,K = 2,3,4 triplet: + +pair_coeff * * * 0.25 +pair_coeff 2 3 4 0.1 :pre + +Note that for a simulation with a single atom type, only a single +entry is required, e.g. + +pair_coeff 1 1 1 0.25 :pre + +For a simulation with two atom types, four pair_coeff commands will +specify all possible nu values: + +pair_coeff 1 1 1 nu1 +pair_coeff 1 1 2 nu2 +pair_coeff 1 2 2 nu3 +pair_coeff 2 2 2 nu4 :pre + +For a simulation with three atom types, ten pair_coeff commands will +specify all possible nu values: + +pair_coeff 1 1 1 nu1 +pair_coeff 1 1 2 nu2 +pair_coeff 1 1 3 nu3 +pair_coeff 1 2 2 nu4 +pair_coeff 1 2 3 nu5 +pair_coeff 1 3 3 nu6 +pair_coeff 2 2 2 nu7 +pair_coeff 2 2 3 nu8 +pair_coeff 2 3 3 nu9 +pair_coeff 3 3 3 nu10 :pre + +By default the nu value for all triplets is set to 0.0. Thus it is +not required to provide pair_coeff commands that enumerate triplet +interactions for all K types. If some I,J,K combination is not +speficied, then there will be no 3-body ATM interactions for that +combination and all its permutations. However, as with all pair +styles, it is required to specify a pair_coeff command for all I,J +combinations, else an error will result. + +:line + +[Mixing, shift, table, tail correction, restart, rRESPA info]: + +This pair styles do not support the "pair_modify"_pair_modify.html +mix, shift, table, and tail options. + +This pair style writes its information to "binary restart +files"_restart.html, so pair_style and pair_coeff commands do not need +to be specified in an input script that reads a restart file. +However, if the {atm} potential is used in combination with other +potentials using the "pair_style hybrid/overlay"_pair_hybrid.html +command then pair_coeff commands need to be re-specified +in the restart input script. + +This pair style can only be used via the {pair} keyword of the +"run_style respa"_run_style.html command. It does not support the +{inner}, {middle}, {outer} keywords. + +:line + +[Restrictions:] + +This pair style is part of the MANYBODY package. It is only enabled +if LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. + +[Related commands:] + +"pair_coeff"_pair_coeff.html + +[Default:] none + +:line + +:link(Axilrod) +[(Axilrod)] +Axilrod and Teller, J Chem Phys, 11, 299 (1943); +Muto, Nippon Sugaku-Buturigakkwaishi 17, 629 (1943). diff --git a/doc/src/pair_awpmd.txt b/doc/src/pair_awpmd.txt index fe0e3c952a..ec87101d0d 100644 --- a/doc/src/pair_awpmd.txt +++ b/doc/src/pair_awpmd.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_beck.txt b/doc/src/pair_beck.txt index e160f09b3d..af60041ff9 100644 --- a/doc/src/pair_beck.txt +++ b/doc/src/pair_beck.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -51,23 +51,22 @@ Rc is used. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_body.txt b/doc/src/pair_body_nparticle.txt similarity index 84% rename from doc/src/pair_body.txt rename to doc/src/pair_body_nparticle.txt index 7899da832b..158eb68ca8 100644 --- a/doc/src/pair_body.txt +++ b/doc/src/pair_body_nparticle.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -10,29 +10,28 @@ pair_style body command :h3 [Syntax:] -pair_style body cutoff :pre +pair_style body/nparticle cutoff :pre cutoff = global cutoff for interactions (distance units) [Examples:] -pair_style body 3.0 +pair_style body/nparticle 3.0 pair_coeff * * 1.0 1.0 pair_coeff 1 1 1.0 1.5 2.5 :pre [Description:] -Style {body} is for use with body particles and calculates pairwise -body/body interactions as well as interactions between body and -point-particles. See "Section 6.14"_Section_howto.html#howto_14 -of the manual and the "body"_body.html doc page for more details on -using body particles. +Style {body/nparticle} is for use with body particles and calculates +pairwise body/body interactions as well as interactions between body +and point-particles. See the "Howto body"_Howto_body.html doc page +for more details on using body particles. This pair style is designed for use with the "nparticle" body style, which is specified as an argument to the "atom-style body" command. -See the "body"_body.html doc page for more details about the body -styles LAMMPS supports. The "nparticle" style treats a body particle -as a rigid body composed of N sub-particles. +See the "Howto body"_Howto_body.html doc page for more details about +the body styles LAMMPS supports. The "nparticle" style treats a body +particle as a rigid body composed of N sub-particles. The coordinates of a body particle are its center-of-mass (COM). If the COMs of a pair of body particles are within the cutoff (global or @@ -104,8 +103,8 @@ This pair style can only be used via the {pair} keyword of the [Restrictions:] This style is part of the BODY package. It is only enabled if LAMMPS -was built with that package. See the "Making -LAMMPS"_Section_start.html#start_2_3 section for more info. +was built with that package. See the "Build +package"_Build_package.html doc page for more info. Defining particles to be bodies so they participate in body/body or body/particle interactions requires the use of the "atom_style diff --git a/doc/src/pair_body_rounded_polygon.txt b/doc/src/pair_body_rounded_polygon.txt index b6dc2e37b5..fc07d8fadd 100644 --- a/doc/src/pair_body_rounded_polygon.txt +++ b/doc/src/pair_body_rounded_polygon.txt @@ -2,18 +2,132 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line pair_style body/rounded/polygon command :h3 +[Syntax:] + +pair_style body/rounded/polygon c_n c_t mu delta_ua cutoff :pre + +c_n = normal damping coefficient +c_t = tangential damping coefficient +mu = normal friction coefficient during gross sliding +delta_ua = multiple contact scaling factor +cutoff = global separation cutoff for interactions (distance units), see below for definition :pre + +[Examples:] + +pair_style body/rounded/polygon 20.0 5.0 0.0 1.0 0.5 +pair_coeff * * 100.0 1.0 +pair_coeff 1 1 100.0 1.0 :pre + [Description:] -Note: This feature is not yet implemented. +Style {body/rounded/polygon} is for use with 2d models of body +particles of style {rounded/polygon}. It calculates pairwise +body/body interactions which can include body particles modeled as +1-vertex circular disks with a specified diameter. See the "Howto +body"_Howto_body.html doc page for more details on using body +rounded/polygon particles. + +This pairwise interaction between rounded polygons is described in +"Fraige"_#pair-Fraige, where a polygon does not have sharp corners, +but is rounded at its vertices by circles centered on each vertex with +a specified diameter. The edges of the polygon are defined between +pairs of adjacent vertices. The circle diameter for each polygon is +specified in the data file read by the "read data"_read_data.html +command. This is a 2d discrete element model (DEM) which allows for +multiple contact points. + +Note that when two particles interact, the effective surface of each +polygon particle is displaced outward from each of its vertices and +edges by half its circle diameter (as in the diagram below of a gray +and yellow square particle). The interaction forces and energies +between two particles are defined with respect to the separation of +their respective rounded surfaces, not by the separation of the +vertices and edges themselves. + +This means that the specified cutoff in the pair_style command is the +cutoff distance, r_c, for the surface separation, \delta_n (see figure +below). This is the distance at which two particles no longer +interact. If r_c is specified as 0.0, then it is a contact-only +interaction. I.e. the two particles must overlap in order to exert a +repulsive force on each other. If r_c > 0.0, then the force between +two particles will be attractive for surface separations from 0 to +r_c, and repulsive once the particles overlap. + +Note that unlike for other pair styles, the specified cutoff is not +the distance between the centers of two particles at which they stop +interacting. This center-to-center distance depends on the shape and +size of the two particles and their relative orientation. LAMMPS +takes that into account when computing the surface separation distance +and applying the r_c cutoff. + +The forces between vertex-vertex, vertex-edge, and edge-edge overlaps +are given by: + +:c,image(Eqs/pair_body_rounded.jpg) + +:c,image(JPG/pair_body_rounded.jpg) + +Note that F_n and F_t are functions of the surface separation \delta_n += d - (R_i + R_j). In this model, when (R_i + R_j) < d < (R_i + R_j) ++ r_c, that is, 0 < \delta_n < r_c, the cohesive region of the two +surfaces overlap and the two surfaces are attractive to each other. + +In "Fraige"_#pair-Fraige, the tangential friction force between two +particles that are in contact is modeled differently prior to gross +sliding (i.e. static friction) and during gross-sliding (kinetic +friction). The latter takes place when the tangential deformation +exceeds the Coulomb frictional limit. In the current implementation, +however, we do not take into account frictional history, i.e. we do +not keep track of how many time steps the two particles have been in +contact nor calculate the tangential deformation. Instead, we assume +that gross sliding takes place as soon as two particles are in +contact. + +The following coefficients must be defined for each pair of atom types +via the "pair_coeff"_pair_coeff.html command as in the examples above, +or in the data file read by the "read_data"_read_data.html command: + +k_n (energy/distance^2 units) +k_na (energy/distance^2 units) :ul + +Effectively, k_n and k_na are the slopes of the red lines in the plot +above for force versus surface separation, for \delta_n < 0 and 0 < +\delta_n < r_c respectively. + +[Mixing, shift, table, tail correction, restart, rRESPA info]: + +This pair style does not support the "pair_modify"_pair_modify.html +mix, shift, table, and tail options. + +This pair style does not write its information to "binary restart +files"_restart.html. Thus, you need to re-specify the pair_style and +pair_coeff commands in an input script that reads a restart file. + +This pair style can only be used via the {pair} keyword of the +"run_style respa"_run_style.html command. It does not support the +{inner}, {middle}, {outer} keywords. + +[Restrictions:] + +These pair styles are part of the BODY package. They are only enabled +if LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. + +This pair style requires the "newton"_newton.html setting to be "on" +for pair interactions. [Related commands:] -"pair_style body"_pair_body.html +"pair_coeff"_pair_coeff.html [Default:] none + +:link(pair-Fraige) +[(Fraige)] F. Y. Fraige, P. A. Langston, A. J. Matchett, J. Dodds, +Particuology, 6, 455 (2008). diff --git a/doc/src/pair_body_rounded_polyhedron.txt b/doc/src/pair_body_rounded_polyhedron.txt new file mode 100644 index 0000000000..e650e5138a --- /dev/null +++ b/doc/src/pair_body_rounded_polyhedron.txt @@ -0,0 +1,129 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +pair_style body/rounded/polyhedron command :h3 + +[Syntax:] + +pair_style body/rounded/polyhedron c_n c_t mu delta_ua cutoff :pre + +c_n = normal damping coefficient +c_t = tangential damping coefficient +mu = normal friction coefficient during gross sliding +delta_ua = multiple contact scaling factor +cutoff = global separation cutoff for interactions (distance units), see below for definition :pre + +[Examples:] + +pair_style body/rounded/polyhedron 20.0 5.0 0.0 1.0 0.5 +pair_coeff * * 100.0 1.0 +pair_coeff 1 1 100.0 1.0 :pre + +[Description:] + +Style {body/rounded/polygon} is for use with 3d models of body +particles of style {rounded/polyhedron}. It calculates pairwise +body/body interactions which can include body particles modeled as +1-vertex spheres with a specified diameter. See the "Howto +body"_Howto_body.html doc page for more details on using body +rounded/polyhedron particles. + +This pairwise interaction between the rounded polyhedra is described +in "Wang"_#pair-Wang, where a polyhedron does not have sharp corners +and edges, but is rounded at its vertices and edges by spheres +centered on each vertex with a specified diameter. The edges if the +polyhedron are defined between pairs of adjacent vertices. Its faces +are defined by a loop of edges. The sphere diameter for each polygon +is specified in the data file read by the "read data"_read_data.html +command. This is a discrete element model (DEM) which allows for +multiple contact points. + +Note that when two particles interact, the effective surface of each +polyhedron particle is displaced outward from each of its vertices, +edges, and faces by half its sphere diameter. The interaction forces +and energies between two particles are defined with respect to the +separation of their respective rounded surfaces, not by the separation +of the vertices, edges, and faces themselves. + +This means that the specified cutoff in the pair_style command is the +cutoff distance, r_c, for the surface separation, \delta_n (see figure +below). This is the distance at which two particles no longer +interact. If r_c is specified as 0.0, then it is a contact-only +interaction. I.e. the two particles must overlap in order to exert a +repulsive force on each other. If r_c > 0.0, then the force between +two particles will be attractive for surface separations from 0 to +r_c, and repulsive once the particles overlap. + +Note that unlike for other pair styles, the specified cutoff is not +the distance between the centers of two particles at which they stop +interacting. This center-to-center distance depends on the shape and +size of the two particles and their relative orientation. LAMMPS +takes that into account when computing the surface separation distance +and applying the r_c cutoff. + +The forces between vertex-vertex, vertex-edge, vertex-face, edge-edge, +and edge-face overlaps are given by: + +:c,image(Eqs/pair_body_rounded.jpg) + +:c,image(JPG/pair_body_rounded.jpg) + +In "Wang"_#pair-Wang, the tangential friction force between two +particles that are in contact is modeled differently prior to gross +sliding (i.e. static friction) and during gross-sliding (kinetic +friction). The latter takes place when the tangential deformation +exceeds the Coulomb frictional limit. In the current implementation, +however, we do not take into account frictional history, i.e. we do +not keep track of how many time steps the two particles have been in +contact nor calculate the tangential deformation. Instead, we assume +that gross sliding takes place as soon as two particles are in +contact. + +The following coefficients must be defined for each pair of atom types +via the "pair_coeff"_pair_coeff.html command as in the examples above, +or in the data file read by the "read_data"_read_data.html command: + +k_n (energy/distance^2 units) +k_na (energy/distance^2 units) :ul + +Effectively, k_n and k_na are the slopes of the red lines in the plot +above for force versus surface separation, for \delta_n < 0 and 0 < +\delta_n < r_c respectively. + +[Mixing, shift, table, tail correction, restart, rRESPA info]: + +This pair style does not support the "pair_modify"_pair_modify.html +mix, shift, table, and tail options. + +This pair style does not write its information to "binary restart +files"_restart.html. Thus, you need to re-specify the pair_style and +pair_coeff commands in an input script that reads a restart file. + +This pair style can only be used via the {pair} keyword of the +"run_style respa"_run_style.html command. It does not support the +{inner}, {middle}, {outer} keywords. + +[Restrictions:] + +These pair styles are part of the BODY package. They are only enabled +if LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. + +This pair style requires the "newton"_newton.html setting to be "on" +for pair interactions. + +[Related commands:] + +"pair_coeff"_pair_coeff.html + +[Default:] none + +:link(pair-Wang) +[(Wang)] J. Wang, H. S. Yu, P. A. Langston, F. Y. Fraige, Granular +Matter, 13, 1 (2011). + diff --git a/doc/src/pair_bop.txt b/doc/src/pair_bop.txt index 2a611e4bd0..f9b4262f0c 100644 --- a/doc/src/pair_bop.txt +++ b/doc/src/pair_bop.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -382,9 +382,8 @@ This pair style can only be used via the {pair} keyword of the [Restrictions:] These pair styles are part of the MANYBODY package. They are only -enabled if LAMMPS was built with that package. -See the "Making LAMMPS"_Section_start.html#start_3 section for more -info. +enabled if LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. These pair potentials require the "newtion"_newton.html setting to be "on" for pair interactions. diff --git a/doc/src/pair_born.txt b/doc/src/pair_born.txt index f867107426..195d3e6669 100644 --- a/doc/src/pair_born.txt +++ b/doc/src/pair_born.txt @@ -3,7 +3,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -108,10 +108,10 @@ The {born/coul/dsf} style computes the Coulomb contribution with the damped shifted force model as in the "coul/dsf"_pair_coul.html style. Style {born/coul/long/cs} is identical to {born/coul/long} except that -a term is added for the "core/shell model"_Section_howto.html#howto_25 -to allow charges on core and shell particles to be separated by r = -0.0. The same correction is introduced for the {born/coul/dsf/cs} -style which is identical to {born/coul/dsf}. And likewise for +a term is added for the "core/shell model"_Howto_coreshell.html to +allow charges on core and shell particles to be separated by r = 0.0. +The same correction is introduced for the {born/coul/dsf/cs} style +which is identical to {born/coul/dsf}. And likewise for {born/coul/wolf/cs} style which is identical to {born/coul/wolf}. Note that these potentials are related to the "Buckingham @@ -145,23 +145,22 @@ pair_style command. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line @@ -194,8 +193,8 @@ respa"_run_style.html command. They do not support the {inner}, [Restrictions:] The {born/coul/long} style is part of the KSPACE package. It is only -enabled if LAMMPS was built with that package. See the -"Making LAMMPS"_Section_start.html#start_3 section for more info. +enabled if LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/pair_brownian.txt b/doc/src/pair_brownian.txt index 79b71e91c7..52720daa23 100644 --- a/doc/src/pair_brownian.txt +++ b/doc/src/pair_brownian.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -74,21 +74,21 @@ must be specified. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "this section"_Section_accelerate.html of +hardware, as discussed in "this section"_Speed.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "this section"_Section_accelerate.html of the manual for more +See "this section"_Speed.html of the manual for more instructions on how to use the accelerated styles effectively. :line @@ -122,8 +122,8 @@ This pair style can only be used via the {pair} keyword of the [Restrictions:] These styles are part of the COLLOID package. They are only enabled -if LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +if LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. Only spherical monodisperse particles are allowed for pair_style brownian. diff --git a/doc/src/pair_buck.txt b/doc/src/pair_buck.txt index d18b39d5d9..5b1688e868 100644 --- a/doc/src/pair_buck.txt +++ b/doc/src/pair_buck.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -93,9 +93,8 @@ used as the cutoff for the A,C terms, and the second is the cutoff for the Coulombic term. Style {buck/coul/long/cs} is identical to {buck/coul/long} except that -a term is added for the "core/shell model"_Section_howto.html#howto_25 -to allow charges on core and shell particles to be separated by r = -0.0. +a term is added for the "core/shell model"_Howto_coreshell.html to +allow charges on core and shell particles to be separated by r = 0.0. Note that these potentials are related to the "Born-Mayer-Huggins potential"_pair_born.html. @@ -140,23 +139,22 @@ pair_style command. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line @@ -188,8 +186,8 @@ respa"_run_style.html command. They do not support the {inner}, The {buck/coul/long} style is part of the KSPACE package. The {buck/coul/long/cs} style is part of the CORESHELL package. They are -only enabled if LAMMPS was built with that package. See the -"Making LAMMPS"_Section_start.html#start_3 section for more info. +only enabled if LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/pair_buck6d_coul_gauss.txt b/doc/src/pair_buck6d_coul_gauss.txt index 879972772b..d9780e0320 100644 --- a/doc/src/pair_buck6d_coul_gauss.txt +++ b/doc/src/pair_buck6d_coul_gauss.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -52,18 +52,18 @@ The latter corrects for artifacts occurring at short distances which become an issue for soft vdW potentials. The {buck6d} styles include a smoothing function which is invoked -according to the global smooting parameter within the specified +according to the global smoothing parameter within the specified cutoff. Hereby a parameter of i.e. 0.9 invokes the smoothing within 90% of the cutoff. No smoothing is applied at a value of 1.0. For the {gauss/dsf} style this smoothing is only applicable for the dispersion damped Buckingham potential. For the {gauss/long} styles the smoothing function can also be invoked for the real -space coulomb interactions which enforce continous energies and +space coulomb interactions which enforce continuous energies and forces at the cutoff. Both styles {buck6d/coul/gauss/dsf} and {buck6d/coul/gauss/long} evaluate a Coulomb potential using spherical Gaussian type charge -distributions which effectively dampen electrostatic ineractions +distributions which effectively dampen electrostatic interactions for high charges at close distances. The electrostatic potential is thus evaluated as: @@ -122,9 +122,9 @@ to be specified in an input script that reads a restart file. [Restrictions:] -These styles are part of the USER-MOFFF package. They are only enabled -if LAMMPS was built with that package. See the -"Making LAMMPS"_Section_start.html#start_3 section for more info. +These styles are part of the USER-MOFFF package. They are only +enabled if LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/pair_buck_long.txt b/doc/src/pair_buck_long.txt index 05e760e1b2..7f3a959ad6 100644 --- a/doc/src/pair_buck_long.txt +++ b/doc/src/pair_buck_long.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -102,23 +102,22 @@ global Coulombic cutoff is allowed. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line @@ -154,9 +153,9 @@ details. [Restrictions:] This style is part of the KSPACE package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. Note that -the KSPACE package is installed by default. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. Note that the +KSPACE package is installed by default. [Related commands:] diff --git a/doc/src/pair_charmm.txt b/doc/src/pair_charmm.txt index 75a8e4bff9..dfc87e1bce 100644 --- a/doc/src/pair_charmm.txt +++ b/doc/src/pair_charmm.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -184,23 +184,22 @@ the pair_style command. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line @@ -246,9 +245,9 @@ details. All the styles with {coul/charmm} or {coul/charmmfsh} styles are part of the MOLECULE package. All the styles with {coul/long} style are part of the KSPACE package. They are only enabled if LAMMPS was built -with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. Note that -the MOLECULE and KSPACE packages are installed by default. +with those packages. See the "Build package"_Build_package.html doc +page for more info. Note that the MOLECULE and KSPACE packages are +installed by default. [Related commands:] diff --git a/doc/src/pair_class2.txt b/doc/src/pair_class2.txt index 36fae5068b..5fc42e78f9 100644 --- a/doc/src/pair_class2.txt +++ b/doc/src/pair_class2.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -102,23 +102,22 @@ cutoff distance. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line @@ -155,8 +154,8 @@ support the {inner}, {middle}, {outer} keywords. [Restrictions:] These styles are part of the CLASS2 package. They are only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/pair_coeff.txt b/doc/src/pair_coeff.txt index fe9238f423..88f95b5b2c 100644 --- a/doc/src/pair_coeff.txt +++ b/doc/src/pair_coeff.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -111,9 +111,8 @@ Windows: :line The alphabetic list of pair styles defined in LAMMPS is given on the -"pair_style"_pair_style.html doc page. They are also given in more -compact form in the pair section of "this -page"_Section_commands.html#cmd_5. +"pair_style"_pair_style.html doc page. They are also listed in more +compact form on the "Commands pair"_Commands_pair.html doc page. Click on the style to display the formula it computes, arguments specified in the pair_style command, and coefficients specified by the @@ -121,15 +120,15 @@ associated "pair_coeff"_pair_coeff.html command. Note that there are also additional pair styles (not listed on the "pair_style"_pair_style.html doc page) submitted by users which are -included in the LAMMPS distribution. The list of these with links to -the individual styles are given in the pair section of "this -page"_Section_commands.html#cmd_5. +included in the LAMMPS distribution. The full list of all pair styles +is on the "Commands pair"_Commands_pair.html doc page. There are also additional accelerated pair styles (not listed on the "pair_style"_pair_style.html doc page) included in the LAMMPS -distribution for faster performance on CPUs and GPUs. The list of -these with links to the individual styles are given in the pair -section of "this page"_Section_commands.html#cmd_5. +distribution for faster performance on CPUs, GPUs, and KNLs. The +individual style names on the "Commands pair"_Commands_pair.html doc +page are followed by one or more of (g,i,k,o,t) to indicate which +accelerated styles exist. :line diff --git a/doc/src/pair_colloid.txt b/doc/src/pair_colloid.txt index 83b15b358b..e8a44e1cba 100644 --- a/doc/src/pair_colloid.txt +++ b/doc/src/pair_colloid.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -127,23 +127,22 @@ commands for efficiency: "neighbor multi"_neighbor.html and Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line @@ -178,8 +177,8 @@ This pair style can only be used via the {pair} keyword of the [Restrictions:] This style is part of the COLLOID package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. Normally, this pair style should be used with finite-size particles which have a diameter, e.g. see the "atom_style diff --git a/doc/src/pair_comb.txt b/doc/src/pair_comb.txt index f5461b1cbc..45ce3a3b76 100644 --- a/doc/src/pair_comb.txt +++ b/doc/src/pair_comb.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -112,23 +112,22 @@ nor file {ffield.comb3} with style {comb}. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line @@ -155,9 +154,9 @@ These pair styles can only be used via the {pair} keyword of the [Restrictions:] -These pair styles are part of the MANYBODY package. It is only enabled -if LAMMPS was built with that package. See -the "Making LAMMPS"_Section_start.html#start_3 section for more info. +These pair styles are part of the MANYBODY package. It is only +enabled if LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. These pair styles requires the "newton"_newton.html setting to be "on" for pair interactions. diff --git a/doc/src/pair_coul.txt b/doc/src/pair_coul.txt index aa3a008bd3..bc0d76a071 100644 --- a/doc/src/pair_coul.txt +++ b/doc/src/pair_coul.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -205,9 +205,9 @@ pairwise interactions within this distance are computed directly; interactions outside that distance are computed in reciprocal space. Style {coul/long/cs} is identical to {coul/long} except that a term is -added for the "core/shell model"_Section_howto.html#howto_25 to allow -charges on core and shell particles to be separated by r = 0.0. The -same correction is introduced for the {coul/wolf/cs} style which is +added for the "core/shell model"_Howto_coreshell.html to allow charges +on core and shell particles to be separated by r = 0.0. The same +correction is introduced for the {coul/wolf/cs} style which is identical to {coul/wolf}. Styles {tip4p/cut} and {tip4p/long} implement the coulomb part of @@ -226,16 +226,16 @@ is to enable LAMMPS to "find" the 2 H atoms associated with each O atom. For example, if the atom ID of an O atom in a TIP4P water molecule is 500, then its 2 H atoms must have IDs 501 and 502. -See the "howto section"_Section_howto.html#howto_8 for more -information on how to use the TIP4P pair styles and lists of -parameters to set. Note that the neighbor list cutoff for Coulomb -interactions is effectively extended by a distance 2*qdist when using -the TIP4P pair style, to account for the offset distance of the -fictitious charges on O atoms in water molecules. Thus it is -typically best in an efficiency sense to use a LJ cutoff >= Coulomb -cutoff + 2*qdist, to shrink the size of the neighbor list. This leads -to slightly larger cost for the long-range calculation, so you can -test the trade-off for your model. +See the "Howto tip4p"_Howto_tip4p.html doc page for more information +on how to use the TIP4P pair styles and lists of parameters to set. +Note that the neighbor list cutoff for Coulomb interactions is +effectively extended by a distance 2*qdist when using the TIP4P pair +style, to account for the offset distance of the fictitious charges on +O atoms in water molecules. Thus it is typically best in an +efficiency sense to use a LJ cutoff >= Coulomb cutoff + 2*qdist, to +shrink the size of the neighbor list. This leads to slightly larger +cost for the long-range calculation, so you can test the trade-off for +your model. :line @@ -268,23 +268,22 @@ command. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line @@ -320,7 +319,7 @@ This pair style can only be used via the {pair} keyword of the The {coul/long}, {coul/msm} and {tip4p/long} styles are part of the KSPACE package. The {coul/long/cs} style is part of the CORESHELL package. They are only enabled if LAMMPS was built with that package. -See the "Making LAMMPS"_Section_start.html#start_3 section for more info. +See the "Build package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/pair_coul_diel.txt b/doc/src/pair_coul_diel.txt index f651cb4b5e..7708287db9 100644 --- a/doc/src/pair_coul_diel.txt +++ b/doc/src/pair_coul_diel.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -67,7 +67,8 @@ The global cutoff (r_c) specified in the pair_style command is used. [Mixing, shift, table, tail correction, restart, rRESPA info]: -This pair style does not support parameter mixing. Coefficients must be given explicitly for each type of particle pairs. +This pair style does not support parameter mixing. Coefficients must +be given explicitly for each type of particle pairs. This pair style supports the "pair_modify"_pair_modify.html shift option for the energy of the Gauss-potential portion of the pair @@ -86,9 +87,9 @@ This pair style can only be used via the {pair} keyword of the [Restrictions:] -This style is part of the "user-misc" package. It is only enabled -if LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_2_3 section for more info. +This style is part of the "USER-MISC" package. It is only enabled if +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/pair_coul_shield.txt b/doc/src/pair_coul_shield.txt index c6eb7bf7a1..8b88d07ece 100644 --- a/doc/src/pair_coul_shield.txt +++ b/doc/src/pair_coul_shield.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -69,9 +69,9 @@ This pair style can only be used via the {pair} keyword of the [Restrictions:] -This style is part of the USER-MISC package. It is only enabled -if LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_2_3 section for more info. +This style is part of the USER-MISC package. It is only enabled if +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/pair_cs.txt b/doc/src/pair_cs.txt index c1084c6087..8bd4abed68 100644 --- a/doc/src/pair_cs.txt +++ b/doc/src/pair_cs.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -54,8 +54,8 @@ pair_coeff 1 1 480.0 0.25 0.00 1.05 0.50 :pre These pair styles are designed to be used with the adiabatic core/shell model of "(Mitchell and Finchham)"_#MitchellFinchham2. See -"Section 6.25"_Section_howto.html#howto_25 of the manual for an -overview of the model as implemented in LAMMPS. +the "Howto coreshell"_Howto_coreshell.html doc page for an overview of +the model as implemented in LAMMPS. The styles with a {coul/long} term are identical to the "pair_style born/coul/long"_pair_born.html and "pair_style @@ -100,8 +100,8 @@ core/shell pair. [Restrictions:] These pair styles are part of the CORESHELL package. They are only -enabled if LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +enabled if LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/pair_dipole.txt b/doc/src/pair_dipole.txt index 2516e5eae4..dcb2448949 100644 --- a/doc/src/pair_dipole.txt +++ b/doc/src/pair_dipole.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -186,23 +186,22 @@ type pair. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line @@ -241,12 +240,12 @@ This pair style can only be used via the {pair} keyword of the The {lj/cut/dipole/cut}, {lj/cut/dipole/long}, and {lj/long/dipole/long} styles are part of the DIPOLE package. They are -only enabled if LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +only enabled if LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. The {lj/sf/dipole/sf} style is part of the USER-MISC package. It is -only enabled if LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +only enabled if LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. Using dipole pair styles with {electron} "units"_units.html is not currently supported. diff --git a/doc/src/pair_dpd.txt b/doc/src/pair_dpd.txt index 9e29e93430..55ae298682 100644 --- a/doc/src/pair_dpd.txt +++ b/doc/src/pair_dpd.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -110,23 +110,22 @@ random force. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_dpd_fdt.txt b/doc/src/pair_dpd_fdt.txt index 867f3f2315..4f2459588a 100644 --- a/doc/src/pair_dpd_fdt.txt +++ b/doc/src/pair_dpd_fdt.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -129,31 +129,30 @@ significantly larger timesteps to be taken. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line [Restrictions:] These commands are part of the USER-DPD package. They are only -enabled if LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +enabled if LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. Pair styles {dpd/fdt} and {dpd/fdt/energy} require use of the "comm_modify vel yes"_comm_modify.html option so that velocites are diff --git a/doc/src/pair_dsmc.txt b/doc/src/pair_dsmc.txt index 9e24100ab7..8b1ceab858 100644 --- a/doc/src/pair_dsmc.txt +++ b/doc/src/pair_dsmc.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -16,7 +16,7 @@ max_cell_size = global maximum cell size for DSMC interactions (distance units) seed = random # seed (positive integer) weighting = macroparticle weighting Tref = reference temperature (temperature units) -Nrecompute = recompute v*sigma_max every this many timesteps (timesteps) +Nrecompute = re-compute v*sigma_max every this many timesteps (timesteps) Nsample = sample this many times in recomputing v*sigma_max :ul [Examples:] @@ -130,8 +130,8 @@ This pair style can only be used via the {pair} keyword of the [Restrictions:] This style is part of the MC package. It is only enabled if LAMMPS -was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/pair_eam.txt b/doc/src/pair_eam.txt index 03e77f53ab..6c3793cb61 100644 --- a/doc/src/pair_eam.txt +++ b/doc/src/pair_eam.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -371,22 +371,21 @@ are listed. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for more +See the "Speed packages"_Speed_packages.html doc page for more instructions on how to use the accelerated styles effectively. :line @@ -414,14 +413,9 @@ The eam pair styles can only be used via the {pair} keyword of the [Restrictions:] -All of these styles except the {eam/cd} style are part of the MANYBODY -package. They are only enabled if LAMMPS was built with that package. -See the "Making LAMMPS"_Section_start.html#start_3 section for more info. - -The {eam/cd} style is part of the USER-MISC package and also requires -the MANYBODY package. It is only enabled if LAMMPS was built with -those packages. See the "Making LAMMPS"_Section_start.html#start_3 -section for more info. +All of these styles are part of the MANYBODY package. They are only +enabled if LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/pair_edip.txt b/doc/src/pair_edip.txt index e5b1420b59..053d43b2ba 100644 --- a/doc/src/pair_edip.txt +++ b/doc/src/pair_edip.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -109,23 +109,22 @@ the EDIP package. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line @@ -148,8 +147,8 @@ This pair style can only be used via the {pair} keyword of the [Restrictions:] This pair style can only be used if LAMMPS was built with the -USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_3 -section for more info on packages. +USER-MISC package. See the "Build package"_Build_package.html doc +page for more info. This pair style requires the "newton"_newton.html setting to be "on" for pair interactions. diff --git a/doc/src/pair_eff.txt b/doc/src/pair_eff.txt index ee7dc99932..a665654af0 100644 --- a/doc/src/pair_eff.txt +++ b/doc/src/pair_eff.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -280,8 +280,8 @@ These pair styles can only be used via the {pair} keyword of the These pair styles will only be enabled if LAMMPS is built with the USER-EFF package. It will only be enabled if LAMMPS was built with -that package. See the "Making LAMMPS"_Section_start.html#start_3 -section for more info. +that package. See the "Build package"_Build_package.html doc page for +more info. These pair styles require that particles store electron attributes such as radius, radial velocity, and radial force, as defined by the diff --git a/doc/src/pair_eim.txt b/doc/src/pair_eim.txt index 75ad2d4683..5f9dcd4c5c 100644 --- a/doc/src/pair_eim.txt +++ b/doc/src/pair_eim.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -136,23 +136,22 @@ needs. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_exp6_rx.txt b/doc/src/pair_exp6_rx.txt index 7eafa23543..790674644d 100644 --- a/doc/src/pair_exp6_rx.txt +++ b/doc/src/pair_exp6_rx.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -153,31 +153,30 @@ pair interaction. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line [Restrictions:] This command is part of the USER-DPD package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/pair_extep.txt b/doc/src/pair_extep.txt index 9a784e2501..3acad1132d 100644 --- a/doc/src/pair_extep.txt +++ b/doc/src/pair_extep.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_gauss.txt b/doc/src/pair_gauss.txt index f6f46a2de8..ef924b1ef0 100644 --- a/doc/src/pair_gauss.txt +++ b/doc/src/pair_gauss.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -84,23 +84,22 @@ is used. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch7_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line @@ -168,8 +167,8 @@ thermo_style custom step temp epair v_occ :pre [Restrictions:] The {gauss/cut} style is part of the "user-misc" package. It is only -enabled if LAMMPS is build with that package. See the "Making of -LAMMPS"_Section_start.html#start_3 section for more info. +enabled if LAMMPS is build with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/pair_gayberne.txt b/doc/src/pair_gayberne.txt index c923578586..426352dc4c 100644 --- a/doc/src/pair_gayberne.txt +++ b/doc/src/pair_gayberne.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -133,23 +133,22 @@ pair_coeff sigma to 1.0 as well. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line @@ -185,8 +184,8 @@ This pair style can only be used via the {pair} keyword of the [Restrictions:] The {gayberne} style is part of the ASPHERE package. It is only -enabled if LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +enabled if LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. These pair style require that atoms store torque and a quaternion to represent their orientation, as defined by the diff --git a/doc/src/pair_gran.txt b/doc/src/pair_gran.txt index d7e87af013..e06d410084 100644 --- a/doc/src/pair_gran.txt +++ b/doc/src/pair_gran.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -179,23 +179,22 @@ potential. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line @@ -233,8 +232,8 @@ pair/local"_compute_pair_local.html command, as {p1}, {p2}, ..., [Restrictions:] All the granular pair styles are part of the GRANULAR package. It is -only enabled if LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +only enabled if LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. These pair styles require that atoms store torque and angular velocity (omega) as defined by the "atom_style"_atom_style.html. They also diff --git a/doc/src/pair_gromacs.txt b/doc/src/pair_gromacs.txt index ec84a2d57a..6a36a036c9 100644 --- a/doc/src/pair_gromacs.txt +++ b/doc/src/pair_gromacs.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -91,23 +91,22 @@ cutoff(s) specified in the pair_style command. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_gw.txt b/doc/src/pair_gw.txt index 8f1251cf1f..ff85955dc0 100644 --- a/doc/src/pair_gw.txt +++ b/doc/src/pair_gw.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -96,8 +96,8 @@ This pair style can only be used via the {pair} keyword of the [Restrictions:] This pair style is part of the MANYBODY package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. This pair style requires the "newton"_newton.html setting to be "on" for pair interactions. diff --git a/doc/src/pair_hbond_dreiding.txt b/doc/src/pair_hbond_dreiding.txt index d3cf90ec14..d4bdcd9258 100644 --- a/doc/src/pair_hbond_dreiding.txt +++ b/doc/src/pair_hbond_dreiding.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -33,8 +33,8 @@ pair_coeff 1 2 hbond/dreiding/morse 3 i 3.88 1.7241379 2.9 2 9 11 90 :pre [Description:] The {hbond/dreiding} styles compute the Acceptor-Hydrogen-Donor (AHD) -3-body hydrogen bond interaction for the -"DREIDING"_Section_howto.html#howto_4 force field, given by: +3-body hydrogen bond interaction for the "DREIDING"_Howto_bioFF.html +force field, given by: :c,image(Eqs/pair_hbond_dreiding.jpg) @@ -65,8 +65,8 @@ potential for the Donor-Acceptor interactions. "(Liu)"_#Liu showed that the Morse form gives improved results for Dendrimer simulations, when n = 2. -See this "howto section"_Section_howto.html#howto_4 of the manual for -more information on the DREIDING forcefield. +See the "Howto bioFF"_Howto_bioFF.html doc page for more information +on the DREIDING forcefield. NOTE: Because the Dreiding hydrogen bond potential is only one portion of an overall force field which typically includes other pairwise @@ -166,23 +166,22 @@ optional parameters. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_hybrid.txt b/doc/src/pair_hybrid.txt index d37dedc709..6e68e820a8 100644 --- a/doc/src/pair_hybrid.txt +++ b/doc/src/pair_hybrid.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -315,8 +315,8 @@ off C/C interaction, i.e. by setting the appropriate coefficients to Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. Since the {hybrid} and {hybrid/overlay} styles delegate computation to the individual sub-styles, the suffix versions of the {hybrid} and @@ -324,18 +324,18 @@ the individual sub-styles, the suffix versions of the {hybrid} and to all sub-styles, if those versions exist. Otherwise the non-accelerated version will be used. -The individual accelerated sub-styles are part of the GPU, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the -"Making LAMMPS"_Section_start.html#start_3 section for more info. +The individual accelerated sub-styles are part of the GPU, USER-OMP +and OPT packages, respectively. They are only enabled if LAMMPS was +built with those packages. See the "Build package"_Build_package.html +doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_ilp_graphene_hbn.txt b/doc/src/pair_ilp_graphene_hbn.txt index d5d8a29fbe..b7d1c2cdb1 100644 --- a/doc/src/pair_ilp_graphene_hbn.txt +++ b/doc/src/pair_ilp_graphene_hbn.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -42,6 +42,7 @@ cutoff (up to third derivative) for interatomic separations larger than r_c "(Maaravi)"_#Maaravi2. The definitons of each parameter in the above equation can be found in "(Leven1)"_#Leven1 and "(Maaravi)"_#Maaravi2. + It is important to include all the pairs to build the neighbor list for calculating the normals. @@ -63,7 +64,7 @@ Angstrom. Using different cutoff or taper function should be careful. NOTE: Two new sets of parameters of ILP for two-dimensional hexagonal Materials are presented in "(Ouyang)"_#Ouyang. These parameters provide a good description in both short- and long-range interaction regimes. -While the old ILP parameters published in "(Leven)"_#Leven and "(Maaravi)"_#Maaravi2 are +While the old ILP parameters published in "(Leven2)"_#Leven2 and "(Maaravi)"_#Maaravi2 are only suitable for long-range interaction regime. This feature is essential for simulations in high pressure regime (i.e., the interlayer distance is smaller than the equilibrium distance). The benchmark tests and comparison of these parameters can be found in "(Ouyang)"_#Ouyang. @@ -86,8 +87,8 @@ that reads a restart file. [Restrictions:] This fix is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. This pair potential requires the newton setting to be {on} for pair interactions. diff --git a/doc/src/pair_kim.txt b/doc/src/pair_kim.txt index c5d910e27c..e1bde4f10e 100644 --- a/doc/src/pair_kim.txt +++ b/doc/src/pair_kim.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -46,8 +46,8 @@ are included in the KIM library by default, in the "What is in the KIM API source package?" section. To use this pair style, you must first download and install the KIM -API library from the "OpenKIM website"_https://openkim.org. The "KIM -section of Section packages"_Section_packages.html#KIM has +API library from the "OpenKIM website"_https://openkim.org. The KIM +section of the "Packages details"_Packages_details.html doc page has instructions on how to do this with a simple make command, when building LAMMPS. @@ -126,8 +126,8 @@ This pair style can only be used via the {pair} keyword of the [Restrictions:] This pair style is part of the KIM package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. This current version of pair_style kim is compatible with the kim-api package version 1.6.0 and higher. diff --git a/doc/src/pair_kolmogorov_crespi_full.txt b/doc/src/pair_kolmogorov_crespi_full.txt index 09f0aaaed0..1fe87dd7ee 100644 --- a/doc/src/pair_kolmogorov_crespi_full.txt +++ b/doc/src/pair_kolmogorov_crespi_full.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -81,8 +81,8 @@ that reads a restart file. [Restrictions:] This fix is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. This pair potential requires the newton setting to be {on} for pair interactions. @@ -109,4 +109,4 @@ units. [(Kolmogorov)] A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005) :link(Ouyang1) -[(Ouyang)] W. Ouyang, D. Mandelli, M. Urbakh and O. Hod, Nano Lett. 18, 6009-6016 (2018). +[(Ouyang)] W. Ouyang, D. Mandelli, M. Urbakh and O. Hod, Nano Lett. 18, 6009-6016 (2018). \ No newline at end of file diff --git a/doc/src/pair_kolmogorov_crespi_z.txt b/doc/src/pair_kolmogorov_crespi_z.txt index 97f132eacd..912fca1657 100644 --- a/doc/src/pair_kolmogorov_crespi_z.txt +++ b/doc/src/pair_kolmogorov_crespi_z.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -30,7 +30,7 @@ which is to take all normals along the z-axis. :c,image(Eqs/pair_kolmogorov_crespi_z.jpg) -It is important to have a suffiently large cutoff to ensure smooth forces. +It is important to have a sufficiently large cutoff to ensure smooth forces. Energies are shifted so that they go continously to zero at the cutoff assuming that the exponential part of {Vij} (first term) decays sufficiently fast. This shift is achieved by the last term in the equation for {Vij} above. @@ -51,8 +51,8 @@ Other interactions can be set to zero using pair_style {none}. [Restrictions:] This fix is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/pair_lcbop.txt b/doc/src/pair_lcbop.txt index 148a1d47a0..21c809bf6a 100644 --- a/doc/src/pair_lcbop.txt +++ b/doc/src/pair_lcbop.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -72,8 +72,8 @@ This pair style can only be used via the {pair} keyword of the [Restrictions:] This pair styles is part of the MANYBODY package. It is only enabled -if LAMMPS was built with that package. See -the "Making LAMMPS"_Section_start.html#start_3 section for more info. +if LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. This pair potential requires the "newton"_newton.html setting to be "on" for pair interactions. diff --git a/doc/src/pair_line_lj.txt b/doc/src/pair_line_lj.txt index 44cfeb48e9..ca5ececa56 100644 --- a/doc/src/pair_line_lj.txt +++ b/doc/src/pair_line_lj.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -130,8 +130,8 @@ This pair style can only be used via the {pair} keyword of the [Restrictions:] This style is part of the ASPHERE package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. Defining particles to be line segments so they participate in line/line or line/particle interactions requires the use the diff --git a/doc/src/pair_list.txt b/doc/src/pair_list.txt index 653e8b0c2d..9500a4c508 100644 --- a/doc/src/pair_list.txt +++ b/doc/src/pair_list.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -130,8 +130,8 @@ atom J (assuming the images are within the cutoff distance), but only with the nearest image. This style is part of the USER-MISC package. It is only enabled if -LAMMPS is build with that package. See the "Making of -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS is build with that package. See the "Build +package"_Build_package.html doc page on for more info. [Related commands:] diff --git a/doc/src/pair_lj.txt b/doc/src/pair_lj.txt index e297d479bc..b5a5726182 100644 --- a/doc/src/pair_lj.txt +++ b/doc/src/pair_lj.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -185,9 +185,9 @@ distance are computed directly; interactions outside that distance are computed in reciprocal space. Style {lj/cut/coul/long/cs} is identical to {lj/cut/coul/long} except -that a term is added for the "core/shell -model"_Section_howto.html#howto_25 to allow charges on core and shell -particles to be separated by r = 0.0. +that a term is added for the "core/shell model"_Howto_coreshell.html +to allow charges on core and shell particles to be separated by r = +0.0. Style {coul/wolf} adds a Coulombic pairwise interaction via the Wolf summation method, described in "Wolf"_#Wolf1, given by: @@ -223,16 +223,16 @@ is to enable LAMMPS to "find" the 2 H atoms associated with each O atom. For example, if the atom ID of an O atom in a TIP4P water molecule is 500, then its 2 H atoms must have IDs 501 and 502. -See the "howto section"_Section_howto.html#howto_8 for more -information on how to use the TIP4P pair styles and lists of -parameters to set. Note that the neighbor list cutoff for Coulomb -interactions is effectively extended by a distance 2*qdist when using -the TIP4P pair style, to account for the offset distance of the -fictitious charges on O atoms in water molecules. Thus it is -typically best in an efficiency sense to use a LJ cutoff >= Coulomb -cutoff + 2*qdist, to shrink the size of the neighbor list. This leads -to slightly larger cost for the long-range calculation, so you can -test the trade-off for your model. +See the "Howto tip4p"_Howto_tip4p.html doc page for more information +on how to use the TIP4P pair styles and lists of parameters to set. +Note that the neighbor list cutoff for Coulomb interactions is +effectively extended by a distance 2*qdist when using the TIP4P pair +style, to account for the offset distance of the fictitious charges on +O atoms in water molecules. Thus it is typically best in an +efficiency sense to use a LJ cutoff >= Coulomb cutoff + 2*qdist, to +shrink the size of the neighbor list. This leads to slightly larger +cost for the long-range calculation, so you can test the trade-off for +your model. For all of the {lj/cut} pair styles, the following coefficients must be defined for each pair of atoms types via the @@ -269,23 +269,22 @@ pair_style command. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line @@ -327,9 +326,9 @@ See the "run_style"_run_style.html command for details. The {lj/cut/coul/long} and {lj/cut/tip4p/long} styles are part of the KSPACE package. The {lj/cut/tip4p/cut} style is part of the MOLECULE package. These styles are only enabled if LAMMPS was built with those -packages. See the "Making LAMMPS"_Section_start.html#start_3 section -for more info. Note that the KSPACE and MOLECULE packages are -installed by default. +packages. See the "Build package"_Build_package.html doc page for +more info. Note that the KSPACE and MOLECULE packages are installed +by default. [Related commands:] diff --git a/doc/src/pair_lj96.txt b/doc/src/pair_lj96.txt index 83f6ec063d..19369adc66 100644 --- a/doc/src/pair_lj96.txt +++ b/doc/src/pair_lj96.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -49,23 +49,22 @@ cutoff specified in the pair_style command is used. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_lj_cubic.txt b/doc/src/pair_lj_cubic.txt index 4ca8c3c141..0a56672d28 100644 --- a/doc/src/pair_lj_cubic.txt +++ b/doc/src/pair_lj_cubic.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -63,23 +63,22 @@ located at rmin = 2^(1/6)*sigma. In the above example, sigma = Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_lj_expand.txt b/doc/src/pair_lj_expand.txt index e0838426f6..d26c88e4f7 100644 --- a/doc/src/pair_lj_expand.txt +++ b/doc/src/pair_lj_expand.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -53,23 +53,22 @@ optional. If not specified, the global LJ cutoff is used. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_lj_long.txt b/doc/src/pair_lj_long.txt index 6be4562d18..2bc2b656ac 100644 --- a/doc/src/pair_lj_long.txt +++ b/doc/src/pair_lj_long.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -90,7 +90,7 @@ is to enable LAMMPS to "find" the 2 H atoms associated with each O atom. For example, if the atom ID of an O atom in a TIP4P water molecule is 500, then its 2 H atoms must have IDs 501 and 502. -See the "howto section"_Section_howto.html#howto_8 for more +See the the "Howto tip4p"_Howto_tip4p.html doc page for more information on how to use the TIP4P pair style. Note that the neighbor list cutoff for Coulomb interactions is effectively extended by a distance 2*qdist when using the TIP4P pair style, to account for @@ -156,23 +156,22 @@ specified in the pair_style command. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line @@ -210,9 +209,9 @@ different levels of the rRESPA hierarchy. See the [Restrictions:] These styles are part of the KSPACE package. They are only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. Note that -the KSPACE package is installed by default. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. Note that the +KSPACE package is installed by default. [Related commands:] diff --git a/doc/src/pair_lj_smooth.txt b/doc/src/pair_lj_smooth.txt index b1678cad58..0c66dd0f66 100644 --- a/doc/src/pair_lj_smooth.txt +++ b/doc/src/pair_lj_smooth.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -62,23 +62,22 @@ specified, the global values for Rin and Rc are used. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_lj_smooth_linear.txt b/doc/src/pair_lj_smooth_linear.txt index 5f7c226cee..9c509515c0 100644 --- a/doc/src/pair_lj_smooth_linear.txt +++ b/doc/src/pair_lj_smooth_linear.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -49,23 +49,22 @@ LJ cutoff specified in the pair_style command is used. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_lj_soft.txt b/doc/src/pair_lj_soft.txt index 2ef133da55..9bcc83fa66 100644 --- a/doc/src/pair_lj_soft.txt +++ b/doc/src/pair_lj_soft.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -207,23 +207,22 @@ directory tree, under examples/USER/fep. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line @@ -262,7 +261,7 @@ similar substyle can be used via the All of the plain {soft} pair styles are part of the USER-FEP package. The {long} styles also requires the KSPACE package to be installed. They are only enabled if LAMMPS was built with those packages. See -the "Making LAMMPS"_Section_start.html#start_3 section for more info. +the "Build package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/pair_lubricate.txt b/doc/src/pair_lubricate.txt index b39c7545c7..83a67d0300 100644 --- a/doc/src/pair_lubricate.txt +++ b/doc/src/pair_lubricate.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -143,21 +143,21 @@ must be specified. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "this section"_Section_accelerate.html of +hardware, as discussed in "this section"_Speed.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "this section"_Section_accelerate.html of the manual for more +See "this section"_Speed.html of the manual for more instructions on how to use the accelerated styles effectively. :line @@ -191,8 +191,8 @@ This pair style can only be used via the {pair} keyword of the [Restrictions:] These styles are part of the COLLOID package. They are only enabled -if LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_2_3 section for more info. +if LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. Only spherical monodisperse particles are allowed for pair_style lubricate. diff --git a/doc/src/pair_lubricateU.txt b/doc/src/pair_lubricateU.txt index 720a8539b8..bfc7c36013 100644 --- a/doc/src/pair_lubricateU.txt +++ b/doc/src/pair_lubricateU.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -179,8 +179,8 @@ This pair style can only be used via the {pair} keyword of the [Restrictions:] These styles are part of the COLLOID package. They are only enabled -if LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_2_3 section for more info. +if LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. Currently, these pair styles assume that all other types of forces/torques on the particles have been already been computed when diff --git a/doc/src/pair_mdf.txt b/doc/src/pair_mdf.txt index ca06f1bf8e..8a1551dded 100644 --- a/doc/src/pair_mdf.txt +++ b/doc/src/pair_mdf.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -148,8 +148,8 @@ See the "run_style"_run_style.html command for details. [Restrictions:] These pair styles can only be used if LAMMPS was built with the -USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_3 -section for more info on packages. +USER-MISC package. See the "Build package"_Build_package.html doc +page for more info. [Related commands:] diff --git a/doc/src/pair_meam.txt b/doc/src/pair_meam.txt index c7449428bd..0b1c1ac767 100644 --- a/doc/src/pair_meam.txt +++ b/doc/src/pair_meam.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -352,14 +352,14 @@ This pair style can only be used via the {pair} keyword of the [Restrictions:] -The {meam} style is part of the MEAM package. It is only enabled if LAMMPS -was built with that package, which also requires the MEAM library be -built and linked with LAMMPS. -The {meam/c} style is provided in the USER-MEAMC package. It is only enabled -if LAMMPS was built with that package. In contrast to the {meam} style, -{meam/c} does not require a separate library to be compiled and it can be +The {meam} style is part of the MEAM package. It is only enabled if +LAMMPS was built with that package, which also requires the MEAM +library be built and linked with LAMMPS. The {meam/c} style is +provided in the USER-MEAMC package. It is only enabled if LAMMPS was +built with that package. In contrast to the {meam} style, {meam/c} +does not require a separate library to be compiled and it can be instantiated multiple times in a "hybrid"_pair_hybrid.html pair style. -See the "Making LAMMPS"_Section_start.html#start_3 section for more info. +See the "Build package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/pair_meam_spline.txt b/doc/src/pair_meam_spline.txt index 6653b397a0..df5db81264 100644 --- a/doc/src/pair_meam_spline.txt +++ b/doc/src/pair_meam_spline.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -106,23 +106,22 @@ MEAM files. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line @@ -148,8 +147,8 @@ This pair style requires the "newton"_newton.html setting to be "on" for pair interactions. This pair style is only enabled if LAMMPS was built with the USER-MISC -package. See the "Making LAMMPS"_Section_start.html#start_3 section -for more info. +package. See the "Build package"_Build_package.html doc page for more +info. [Related commands:] diff --git a/doc/src/pair_meam_sw_spline.txt b/doc/src/pair_meam_sw_spline.txt index fa731799dd..2e8c26658a 100644 --- a/doc/src/pair_meam_sw_spline.txt +++ b/doc/src/pair_meam_sw_spline.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -111,8 +111,9 @@ support the {inner}, {middle}, {outer} keywords. This pair style requires the "newton"_newton.html setting to be "on" for pair interactions. -This pair style is only enabled if LAMMPS was built with the USER-MISC package. -See the "Making LAMMPS"_Section_start.html#start_3 section for more info. +This pair style is only enabled if LAMMPS was built with the USER-MISC +package. See the "Build package"_Build_package.html doc page for more +info. [Related commands:] diff --git a/doc/src/pair_meso.txt b/doc/src/pair_meso.txt index bcdf717d68..005498d8bf 100644 --- a/doc/src/pair_meso.txt +++ b/doc/src/pair_meso.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -245,8 +245,8 @@ that reads a restart file. The pair styles {edpd}, {mdpd}, {mdpd/rhosum} and {tdpd} are part of the USER-MESO package. It is only enabled if LAMMPS was built with -that package. See the "Making LAMMPS"_Section_start.html#start_3 -section for more info. +that package. See the "Build package"_Build_package.html doc page for +more info. [Related commands:] diff --git a/doc/src/pair_mgpt.txt b/doc/src/pair_mgpt.txt index f8b0c9f071..bd55d529b8 100644 --- a/doc/src/pair_mgpt.txt +++ b/doc/src/pair_mgpt.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -159,8 +159,8 @@ This pair style can only be used via the {pair} keyword of the [Restrictions:] This pair style is part of the USER-MGPT package and is only enabled -if LAMMPS is built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +if LAMMPS is built with that package. See the "Build +package"_Build_package.html doc page for more info. The MGPT potentials require the "newtion"_newton.html setting to be "on" for pair style interactions. diff --git a/doc/src/pair_mie.txt b/doc/src/pair_mie.txt index ad602db9f1..818e37272b 100644 --- a/doc/src/pair_mie.txt +++ b/doc/src/pair_mie.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_modify.txt b/doc/src/pair_modify.txt index 34dbb5bc3d..c043fde5a7 100644 --- a/doc/src/pair_modify.txt +++ b/doc/src/pair_modify.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_momb.txt b/doc/src/pair_momb.txt index 77c4f184d9..f1989f56f4 100644 --- a/doc/src/pair_momb.txt +++ b/doc/src/pair_momb.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -50,8 +50,8 @@ Rr (distance units, typically sum of atomic vdW radii) :ul [Restrictions:] This style is part of the USER-MISC package. It is only enabled if -LAMMPS is built with that package. See the "Making of -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS is built with that package. See the "Build +package"_Build_package.html doc page on for more info. [Related commands:] diff --git a/doc/src/pair_morse.txt b/doc/src/pair_morse.txt index 3eb5ac5afe..68894f6913 100644 --- a/doc/src/pair_morse.txt +++ b/doc/src/pair_morse.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -101,23 +101,22 @@ cutoff is used. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line @@ -149,12 +148,12 @@ These pair styles can only be used via the {pair} keyword of the [Restrictions:] The {morse/smooth/linear} pair style is only enabled if LAMMPS was -built with the USER-MISC package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +built with the USER-MISC package. See the "Build +package"_Build_package.html doc page for more info. The {morse/soft} pair style is only enabled if LAMMPS was built with -the USER-FEP package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +the USER-FEP package. See the "Build package"_Build_package.html doc +page for more info. [Related commands:] diff --git a/doc/src/pair_multi_lucy.txt b/doc/src/pair_multi_lucy.txt index 38fd1ede4a..0b3a430417 100644 --- a/doc/src/pair_multi_lucy.txt +++ b/doc/src/pair_multi_lucy.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -177,8 +177,8 @@ This pair style can only be used via the {pair} keyword of the [Restrictions:] This command is part of the USER-DPD package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/pair_multi_lucy_rx.txt b/doc/src/pair_multi_lucy_rx.txt index 57abcf4a4c..819a15b624 100644 --- a/doc/src/pair_multi_lucy_rx.txt +++ b/doc/src/pair_multi_lucy_rx.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -204,31 +204,30 @@ This pair style can only be used via the {pair} keyword of the Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line [Restrictions:] This command is part of the USER-DPD package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/pair_nb3b_harmonic.txt b/doc/src/pair_nb3b_harmonic.txt index 2395707fb4..6a119d74e1 100644 --- a/doc/src/pair_nb3b_harmonic.txt +++ b/doc/src/pair_nb3b_harmonic.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -92,31 +92,30 @@ a particular simulation; LAMMPS ignores those entries. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line [Restrictions:] This pair style can only be used if LAMMPS was built with the MANYBODY -package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info on packages. +package. See the "Build package"_Build_package.html doc page for more +info. [Related commands:] diff --git a/doc/src/pair_nm.txt b/doc/src/pair_nm.txt index 81cea1a38d..a42dfa3c98 100644 --- a/doc/src/pair_nm.txt +++ b/doc/src/pair_nm.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -133,29 +133,28 @@ the "run_style respa"_run_style.html command. They do not support the Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. [Restrictions:] These pair styles are part of the MISC package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/pair_none.txt b/doc/src/pair_none.txt index f4e9525198..960dc05d97 100644 --- a/doc/src/pair_none.txt +++ b/doc/src/pair_none.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_oxdna.txt b/doc/src/pair_oxdna.txt index f272d15a86..b24e3c07df 100644 --- a/doc/src/pair_oxdna.txt +++ b/doc/src/pair_oxdna.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -82,8 +82,8 @@ The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf. [Restrictions:] These pair styles can only be used if LAMMPS was built with the -USER-CGDNA package and the MOLECULE and ASPHERE package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info on packages. +USER-CGDNA package and the MOLECULE and ASPHERE package. See the +"Build package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/pair_oxdna2.txt b/doc/src/pair_oxdna2.txt index 1b55031b2c..c5662abdeb 100644 --- a/doc/src/pair_oxdna2.txt +++ b/doc/src/pair_oxdna2.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -88,8 +88,8 @@ The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf. [Restrictions:] These pair styles can only be used if LAMMPS was built with the -USER-CGDNA package and the MOLECULE and ASPHERE package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info on packages. +USER-CGDNA package and the MOLECULE and ASPHERE package. See the +"Build package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/pair_peri.txt b/doc/src/pair_peri.txt index deca093e3b..b6baa4edc5 100644 --- a/doc/src/pair_peri.txt +++ b/doc/src/pair_peri.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -139,23 +139,22 @@ details please see the description in "(Mtchell2011a)". Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line @@ -183,8 +182,8 @@ These pair styles can only be used via the {pair} keyword of the [Restrictions:] All of these styles are part of the PERI package. They are only -enabled if LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +enabled if LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/pair_polymorphic.txt b/doc/src/pair_polymorphic.txt index c088e8bb22..7460044043 100644 --- a/doc/src/pair_polymorphic.txt +++ b/doc/src/pair_polymorphic.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -191,8 +191,8 @@ input script. If using read_data, atomic masses must be defined in the atomic structure data file. This pair style is part of the MANYBODY package. It is only enabled if -LAMMPS was built with that package. See the -"Making LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. This pair potential requires the "newtion"_newton.html setting to be "on" for pair interactions. diff --git a/doc/src/pair_python.txt b/doc/src/pair_python.txt index 2f8ed7a27c..e8baf14d2e 100644 --- a/doc/src/pair_python.txt +++ b/doc/src/pair_python.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -29,7 +29,7 @@ The {python} pair style provides a way to define pairwise additive potential functions as python script code that is loaded into LAMMPS from a python file which must contain specific python class definitions. This allows to rapidly evaluate different potential functions without -having to modify and recompile LAMMPS. Due to python being an +having to modify and re-compile LAMMPS. Due to python being an interpreted language, however, the performance of this pair style is going to be significantly slower (often between 20x and 100x) than corresponding compiled code. This penalty can be significantly reduced @@ -98,7 +98,7 @@ verify, that the potential definition in the python class and in the LAMMPS input match. Here is an example for a single type Lennard-Jones potential class -{LJCutMelt} in reducted units, which defines an atom type {lj} for +{LJCutMelt} in reduced units, which defines an atom type {lj} for which the parameters epsilon and sigma are both 1.0: class LJCutMelt(LAMMPSPairPotential): @@ -204,8 +204,8 @@ This pair style can only be used via the {pair} keyword of the [Restrictions:] This pair style is part of the PYTHON package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/pair_quip.txt b/doc/src/pair_quip.txt index 9436b0c4ed..1f794d0c84 100644 --- a/doc/src/pair_quip.txt +++ b/doc/src/pair_quip.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -74,8 +74,8 @@ This pair style can only be used via the {pair} keyword of the [Restrictions:] This pair style is part of the USER-QUIP package. It is only enabled -if LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +if LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. QUIP potentials are parametrized in electron-volts and Angstroms and therefore should be used with LAMMPS metal "units"_units.html. diff --git a/doc/src/pair_reax.txt b/doc/src/pair_reax.txt index 1d13f93706..a3b84955cd 100644 --- a/doc/src/pair_reax.txt +++ b/doc/src/pair_reax.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_reaxc.txt b/doc/src/pair_reaxc.txt index 39759b3111..e63f4a90ee 100644 --- a/doc/src/pair_reaxc.txt +++ b/doc/src/pair_reaxc.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -50,11 +50,11 @@ as a package. The {reax/c/kk} style is a Kokkos version of the ReaxFF potential that is derived from the {reax/c} style. The Kokkos version can run on GPUs and can also use OpenMP multithreading. For more information about the -Kokkos package, see "Section 4"_Section_packages.html#kokkos and -"Section 5.3.3"_accelerate_kokkos.html. One important consideration -when using the {reax/c/kk} style is the choice of either half or full -neighbor lists. This setting can be changed using the Kokkos -"package"_package.html command. +Kokkos package, see "Packages details"_Packages_details.html and +"Speed kokkos"_Speed_kokkos.html doc pages. One important +consideration when using the {reax/c/kk} style is the choice of either +half or full neighbor lists. This setting can be changed using the +Kokkos "package"_package.html command. The {reax/c} style differs from the "pair_style reax"_pair_reax.html command in the lo-level implementation details. The {reax} style is a @@ -303,31 +303,30 @@ This pair style can only be used via the {pair} keyword of the Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line [Restrictions:] This pair style is part of the USER-REAXC package. It is only enabled -if LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +if LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. The ReaxFF potential files provided with LAMMPS in the potentials directory are parameterized for real "units"_units.html. You can use diff --git a/doc/src/pair_resquared.txt b/doc/src/pair_resquared.txt index 9ad95eb5fc..5e760be495 100644 --- a/doc/src/pair_resquared.txt +++ b/doc/src/pair_resquared.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -145,23 +145,22 @@ specified in the pair_style command is used. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line @@ -204,8 +203,8 @@ command"_run_style.html. [Restrictions:] This style is part of the ASPHERE package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. This pair style requires that atoms be ellipsoids as defined by the "atom_style ellipsoid"_atom_style.html command. diff --git a/doc/src/pair_sdk.txt b/doc/src/pair_sdk.txt index 360136a4ea..b977aefe88 100644 --- a/doc/src/pair_sdk.txt +++ b/doc/src/pair_sdk.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -85,23 +85,22 @@ pair_style command. Styles with a {gpu}, {intel}, {kk}, {omp} or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP, and OPT packages respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line @@ -134,11 +133,11 @@ respa"_run_style.html command. [Restrictions:] -All of the lj/sdk pair styles are part of the USER-CGSDK package. -The {lj/sdk/coul/long} style also requires the KSPACE package to be -built (which is enabled by default). They are only enabled if LAMMPS -was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +All of the lj/sdk pair styles are part of the USER-CGSDK package. The +{lj/sdk/coul/long} style also requires the KSPACE package to be built +(which is enabled by default). They are only enabled if LAMMPS was +built with that package. See the "Build package"_Build_package.html +doc page for more info. [Related commands:] diff --git a/doc/src/pair_smd_hertz.txt b/doc/src/pair_smd_hertz.txt index eeaa3387a4..2581c84dc9 100644 --- a/doc/src/pair_smd_hertz.txt +++ b/doc/src/pair_smd_hertz.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -19,32 +19,36 @@ pair_coeff 1 1 [Description:] -The {smd/hertz} style calculates contact forces between SPH particles belonging to different physical bodies. +The {smd/hertz} style calculates contact forces between SPH particles +belonging to different physical bodies. -The contact forces are calculated using a Hertz potential, which evaluates the overlap between two particles -(whose spatial extents are defined via its contact radius). -The effect is that a particles cannot penetrate into each other. -The parameter has units of pressure and should equal roughly one half -of the Young's modulus (or bulk modulus in the case of fluids) of the material model associated with the SPH particles. +The contact forces are calculated using a Hertz potential, which +evaluates the overlap between two particles (whose spatial extents are +defined via its contact radius). The effect is that a particles +cannot penetrate into each other. The parameter +has units of pressure and should equal roughly one half of the Young's +modulus (or bulk modulus in the case of fluids) of the material model +associated with the SPH particles. -The parameter {scale_factor} can be used to scale the particles' contact radii. This can be useful to control how close -particles can approach each other. Usually, {scale_factor} =1.0. +The parameter {scale_factor} can be used to scale the particles' +contact radii. This can be useful to control how close particles can +approach each other. Usually, {scale_factor} =1.0. :line [Mixing, shift, table, tail correction, restart, rRESPA info]: -No mixing is performed automatically. -Currently, no part of USER-SMD supports restarting nor minimization. -rRESPA does not apply to this pair style. +No mixing is performed automatically. Currently, no part of USER-SMD +supports restarting nor minimization. rRESPA does not apply to this +pair style. :line [Restrictions:] This fix is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 -section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/pair_smd_tlsph.txt b/doc/src/pair_smd_tlsph.txt index f73acf74ee..44b0c6cae8 100644 --- a/doc/src/pair_smd_tlsph.txt +++ b/doc/src/pair_smd_tlsph.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -16,10 +16,11 @@ pair_style smd/tlsph args :pre pair_style smd/tlsph - [Description:] -The {smd/tlsph} style computes particle interactions according to continuum mechanics constitutive laws and a Total-Lagrangian Smooth-Particle Hydrodynamics algorithm. +The {smd/tlsph} style computes particle interactions according to +continuum mechanics constitutive laws and a Total-Lagrangian +Smooth-Particle Hydrodynamics algorithm. This pair style is invoked with the following command: @@ -27,35 +28,40 @@ pair_style smd/tlsph pair_coeff i j *COMMON rho0 E nu Q1 Q2 hg Cp & *END :pre -Here, {i} and {j} denote the {LAMMPS} particle types for which this pair style is -defined. Note that {i} and {j} must be equal, i.e., no {tlsph} cross interactions -between different particle types are allowed. -In contrast to the usual {LAMMPS} {pair coeff} definitions, which are given solely a -number of floats and integers, the {tlsph} {pair coeff} definition is organised using -keywords. These keywords mark the beginning of different sets of parameters for particle properties, -material constitutive models, and damage models. The {pair coeff} line must be terminated with -the {*END} keyword. The use the line continuation operator {&} is recommended. A typical -invocation of the {tlsph} for a solid body would consist of an equation of state for computing -the pressure (the diagonal components of the stress tensor), and a material model to compute shear -stresses (the off-diagonal components of the stress tensor). Damage and failure models can also be added. +Here, {i} and {j} denote the {LAMMPS} particle types for which this +pair style is defined. Note that {i} and {j} must be equal, i.e., no +{tlsph} cross interactions between different particle types are +allowed. In contrast to the usual {LAMMPS} {pair coeff} definitions, +which are given solely a number of floats and integers, the {tlsph} +{pair coeff} definition is organised using keywords. These keywords +mark the beginning of different sets of parameters for particle +properties, material constitutive models, and damage models. The {pair +coeff} line must be terminated with the {*END} keyword. The use the +line continuation operator {&} is recommended. A typical invocation of +the {tlsph} for a solid body would consist of an equation of state for +computing the pressure (the diagonal components of the stress tensor), +and a material model to compute shear stresses (the off-diagonal +components of the stress tensor). Damage and failure models can also +be added. -Please see the "SMD user guide"_PDF/SMD_LAMMPS_userguide.pdf for a complete listing of the possible keywords and material models. +Please see the "SMD user guide"_PDF/SMD_LAMMPS_userguide.pdf for a +complete listing of the possible keywords and material models. :line [Mixing, shift, table, tail correction, restart, rRESPA info]: -No mixing is performed automatically. -Currently, no part of USER-SMD supports restarting nor minimization. -rRESPA does not apply to this pair style. +No mixing is performed automatically. Currently, no part of USER-SMD +supports restarting nor minimization. rRESPA does not apply to this +pair style. :line [Restrictions:] This fix is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 -section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/pair_smd_triangulated_surface.txt b/doc/src/pair_smd_triangulated_surface.txt index c32bf3a22e..9eb5e311b8 100644 --- a/doc/src/pair_smd_triangulated_surface.txt +++ b/doc/src/pair_smd_triangulated_surface.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -19,17 +19,21 @@ pair_coeff 1 1 [Description:] -The {smd/tri_surface} style calculates contact forces between SPH particles and a rigid wall boundary defined via the +The {smd/tri_surface} style calculates contact forces between SPH +particles and a rigid wall boundary defined via the "smd/wall_surface"_fix_smd_wall_surface.html fix. -The contact forces are calculated using a Hertz potential, which evaluates the overlap between a particle -(whose spatial extents are defined via its contact radius) and the triangle. -The effect is that a particle cannot penetrate into the triangular surface. -The parameter has units of pressure and should equal roughly one half -of the Young's modulus (or bulk modulus in the case of fluids) of the material model associated with the SPH particle +The contact forces are calculated using a Hertz potential, which +evaluates the overlap between a particle (whose spatial extents are +defined via its contact radius) and the triangle. The effect is that +a particle cannot penetrate into the triangular surface. The +parameter has units of pressure and should equal +roughly one half of the Young's modulus (or bulk modulus in the case +of fluids) of the material model associated with the SPH particle -The parameter {scale_factor} can be used to scale the particles' contact radii. This can be useful to control how close -particles can approach the triangulated surface. Usually, {scale_factor} =1.0. +The parameter {scale_factor} can be used to scale the particles' +contact radii. This can be useful to control how close particles can +approach the triangulated surface. Usually, {scale_factor} =1.0. :line @@ -44,8 +48,8 @@ rRESPA does not apply to this pair style. [Restrictions:] This fix is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 -section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/pair_smd_ulsph.txt b/doc/src/pair_smd_ulsph.txt index 268fe78d02..f28dd9043c 100644 --- a/doc/src/pair_smd_ulsph.txt +++ b/doc/src/pair_smd_ulsph.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -17,11 +17,13 @@ keyword = {*DENSITY_SUMMATION} or {*DENSITY_CONTINUITY} and {*VELOCITY_GRADIENT} [Examples:] -pair_style smd/ulsph *DENSITY_CONTINUITY *VELOCITY_GRADIENT *NO_GRADIENT_CORRECTION +pair_style smd/ulsph *DENSITY_CONTINUITY *VELOCITY_GRADIENT *NO_GRADIENT_CORRECTION :pre [Description:] -The {smd/ulsph} style computes particle interactions according to continuum mechanics constitutive laws and an updated Lagrangian Smooth-Particle Hydrodynamics algorithm. +The {smd/ulsph} style computes particle interactions according to +continuum mechanics constitutive laws and an updated Lagrangian +Smooth-Particle Hydrodynamics algorithm. This pair style is invoked similar to the following command: @@ -29,37 +31,45 @@ pair_style smd/ulsph *DENSITY_CONTINUITY *VELOCITY_GRADIENT *NO_GRADIENT_CORRECT pair_coeff i j *COMMON rho0 c0 Q1 Cp hg & *END :pre -Here, {i} and {j} denote the {LAMMPS} particle types for which this pair style is -defined. Note that {i} and {j} can be different, i.e., {ulsph} cross interactions -between different particle types are allowed. However, {i}--{i} respectively {j}--{j} pair_coeff lines have to precede a cross interaction. -In contrast to the usual {LAMMPS} {pair coeff} definitions, which are given solely a -number of floats and integers, the {ulsph} {pair coeff} definition is organised using -keywords. These keywords mark the beginning of different sets of parameters for particle properties, -material constitutive models, and damage models. The {pair coeff} line must be terminated with -the {*END} keyword. The use the line continuation operator {&} is recommended. A typical -invocation of the {ulsph} for a solid body would consist of an equation of state for computing -the pressure (the diagonal components of the stress tensor), and a material model to compute shear -stresses (the off-diagonal components of the stress tensor). +Here, {i} and {j} denote the {LAMMPS} particle types for which this +pair style is defined. Note that {i} and {j} can be different, i.e., +{ulsph} cross interactions between different particle types are +allowed. However, {i}--{i} respectively {j}--{j} pair_coeff lines have +to precede a cross interaction. In contrast to the usual {LAMMPS} +{pair coeff} definitions, which are given solely a number of floats +and integers, the {ulsph} {pair coeff} definition is organised using +keywords. These keywords mark the beginning of different sets of +parameters for particle properties, material constitutive models, and +damage models. The {pair coeff} line must be terminated with the +{*END} keyword. The use the line continuation operator {&} is +recommended. A typical invocation of the {ulsph} for a solid body +would consist of an equation of state for computing the pressure (the +diagonal components of the stress tensor), and a material model to +compute shear stresses (the off-diagonal components of the stress +tensor). -Note that the use of *GRADIENT_CORRECTION can lead to severe numerical instabilities. For a general fluid simulation, *NO_GRADIENT_CORRECTION is recommended. +Note that the use of *GRADIENT_CORRECTION can lead to severe numerical +instabilities. For a general fluid simulation, *NO_GRADIENT_CORRECTION +is recommended. -Please see the "SMD user guide"_PDF/SMD_LAMMPS_userguide.pdf for a complete listing of the possible keywords and material models. +Please see the "SMD user guide"_PDF/SMD_LAMMPS_userguide.pdf for a +complete listing of the possible keywords and material models. :line [Mixing, shift, table, tail correction, restart, rRESPA info]: -No mixing is performed automatically. -Currently, no part of USER-SMD supports restarting nor minimization. -rRESPA does not apply to this pair style. +No mixing is performed automatically. Currently, no part of USER-SMD +supports restarting nor minimization. rRESPA does not apply to this +pair style. :line [Restrictions:] This fix is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 -section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/pair_smtbq.txt b/doc/src/pair_smtbq.txt index c8d6b21b3f..e81411678a 100644 --- a/doc/src/pair_smtbq.txt +++ b/doc/src/pair_smtbq.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -219,8 +219,8 @@ This pair style can only be used via the {pair} keyword of the [Restriction:] This pair style is part of the USER-SMTBQ package and is only enabled -if LAMMPS is built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +if LAMMPS is built with that package. See the "Build +package"_Build_package.html doc page for more info. This potential requires using atom type 1 for oxygen and atom type higher than 1 for metal atoms. diff --git a/doc/src/pair_snap.txt b/doc/src/pair_snap.txt index 27dcf6082b..6f8cc3d8a8 100644 --- a/doc/src/pair_snap.txt +++ b/doc/src/pair_snap.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -175,31 +175,30 @@ This pair style can only be used via the {pair} keyword of the Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line [Restrictions:] -This style is part of the SNAP package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +This style is part of the SNAP package. It is only enabled if LAMMPS +was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/pair_soft.txt b/doc/src/pair_soft.txt index 08fa88c477..ca0266f34a 100644 --- a/doc/src/pair_soft.txt +++ b/doc/src/pair_soft.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -82,23 +82,22 @@ variables. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_sph_heatconduction.txt b/doc/src/pair_sph_heatconduction.txt index 2387056a1b..78a9cf2b63 100644 --- a/doc/src/pair_sph_heatconduction.txt +++ b/doc/src/pair_sph_heatconduction.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -53,8 +53,8 @@ respa"_run_style.html command. It does not support the {inner}, [Restrictions:] This pair style is part of the USER-SPH package. It is only enabled -if LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +if LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/pair_sph_idealgas.txt b/doc/src/pair_sph_idealgas.txt index 957f901425..59513e7a73 100644 --- a/doc/src/pair_sph_idealgas.txt +++ b/doc/src/pair_sph_idealgas.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -60,8 +60,8 @@ respa"_run_style.html command. It does not support the {inner}, [Restrictions:] This pair style is part of the USER-SPH package. It is only enabled -if LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +if LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/pair_sph_lj.txt b/doc/src/pair_sph_lj.txt index ef89c4ad3e..43e77f1aae 100644 --- a/doc/src/pair_sph_lj.txt +++ b/doc/src/pair_sph_lj.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -60,8 +60,8 @@ As noted above, the Lennard-Jones parameters epsilon and sigma are set to unity. This pair style is part of the USER-SPH package. It is only enabled -if LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +if LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/pair_sph_rhosum.txt b/doc/src/pair_sph_rhosum.txt index 352e717f76..9069176f29 100644 --- a/doc/src/pair_sph_rhosum.txt +++ b/doc/src/pair_sph_rhosum.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -54,8 +54,8 @@ respa"_run_style.html command. It does not support the {inner}, [Restrictions:] This pair style is part of the USER-SPH package. It is only enabled -if LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +if LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/pair_sph_taitwater.txt b/doc/src/pair_sph_taitwater.txt index 9177ca80b8..dcb9e39603 100644 --- a/doc/src/pair_sph_taitwater.txt +++ b/doc/src/pair_sph_taitwater.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -63,8 +63,8 @@ respa"_run_style.html command. It does not support the {inner}, [Restrictions:] This pair style is part of the USER-SPH package. It is only enabled -if LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +if LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/pair_sph_taitwater_morris.txt b/doc/src/pair_sph_taitwater_morris.txt index e6c5a6bb20..b88707d1af 100644 --- a/doc/src/pair_sph_taitwater_morris.txt +++ b/doc/src/pair_sph_taitwater_morris.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -62,8 +62,8 @@ respa"_run_style.html command. It does not support the {inner}, [Restrictions:] This pair style is part of the USER-SPH package. It is only enabled -if LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +if LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/pair_spin_dmi.txt b/doc/src/pair_spin_dmi.txt new file mode 100644 index 0000000000..bd605bd064 --- /dev/null +++ b/doc/src/pair_spin_dmi.txt @@ -0,0 +1,91 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +pair_style spin/dmi command :h3 + +[Syntax:] + +pair_style spin/dmi cutoff :pre + +cutoff = global cutoff pair (distance in metal units) :ulb,l + +:ule + +[Examples:] + +pair_style spin/dmi 4.0 +pair_coeff * * dmi 2.6 0.001 1.0 0.0 0.0 +pair_coeff 1 2 dmi 4.0 0.00109 0.0 0.0 1.0 :pre + +[Description:] + +Style {spin/dmi} computes the Dzyaloshinskii-Moriya (DM) interaction +between pairs of magnetic spins. +According to the expression reported in "(Rohart)"_#Rohart, one has +the following DM energy: + +:c,image(Eqs/pair_spin_dmi_interaction.jpg) + +where si and sj are two neighboring magnetic spins of two particles, +eij = (ri - rj)/|ri-rj| is the unit vector between sites i and j, +and D is the DM vector defining the intensity (in eV) and the direction +of the interaction. + +In "(Rohart)"_#Rohart, D is defined as the direction normal to the film oriented +from the high spin-orbit layer to the magnetic ultrathin film. + +The application of a spin-lattice Poisson bracket to this energy (as described +in "(Tranchida)"_#Tranchida5) allows to derive a magnetic torque omega, and a +mechanical force F (for spin-lattice calculations only) for each magnetic +particle i: + +:c,image(Eqs/pair_spin_dmi_forces.jpg) + +More details about the derivation of these torques/forces are reported in +"(Tranchida)"_#Tranchida5. + +For the {spin/dmi} pair style, the following coefficients must be defined for +each pair of atoms types via the "pair_coeff"_pair_coeff.html command as in +the examples above, or in the data file or restart files read by the +"read_data"_read_data.html or "read_restart"_read_restart.html commands, and +set in the following order: + +rc (distance units) +|D| (energy units) +Dx, Dy, Dz (direction of D) :ul + +Note that rc is the radius cutoff of the considered DM interaction, |D| is +the norm of the DM vector (in eV), and Dx, Dy and Dz define its direction. + +None of those coefficients is optional. If not specified, the {spin/dmi} +pair style cannot be used. + +:line + +[Restrictions:] + +All the {pair/spin} styles are part of the SPIN package. These styles +are only enabled if LAMMPS was built with this package, and if the +atom_style "spin" was declared. See the "Build +package"_Build_package.html doc page for more info. + +[Related commands:] + +"atom_style spin"_atom_style.html, "pair_coeff"_pair_coeff.html, +"pair_eam"_pair_eam.html, + +[Default:] none + +:line + +:link(Rohart) +[(Rohart)] Rohart and Thiaville, +Physical Review B, 88(18), 184422. (2013). +:link(Tranchida5) +[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson, +Journal of Computational Physics, (2018). diff --git a/doc/src/pair_spin_exchange.txt b/doc/src/pair_spin_exchange.txt new file mode 100644 index 0000000000..2f158704a9 --- /dev/null +++ b/doc/src/pair_spin_exchange.txt @@ -0,0 +1,98 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +pair_style spin/exchange command :h3 + +[Syntax:] + +pair_style spin/exchange cutoff :pre + +cutoff = global cutoff pair (distance in metal units) :ulb,l + +:ule + +[Examples:] + +pair_style spin/exchange 4.0 +pair_coeff * * exchange 4.0 0.0446928 0.003496 1.4885 +pair_coeff 1 2 exchange 6.0 -0.01575 0.0 1.965 :pre + +[Description:] + +Style {spin/exchange} computes the exchange interaction between +pairs of magnetic spins: + +:c,image(Eqs/pair_spin_exchange_interaction.jpg) + +where si and sj are two neighboring magnetic spins of two particles, +rij = ri - rj is the inter-atomic distance between the two particles, +and J(rij) is a function defining the intensity and the sign of the exchange +interaction for different neighboring shells. This function is defined as: + +:c,image(Eqs/pair_spin_exchange_function.jpg) + +where a, b and d are the three constant coefficients defined in the associated +"pair_coeff" command (see below for more explanations). + +The coefficients a, b, and d need to be fitted so that the function above matches with +the value of the exchange interaction for the N neighbor shells taken into account. +Examples and more explanations about this function and its parametrization are reported +in "(Tranchida)"_#Tranchida3. + +From this exchange interaction, each spin i will be submitted +to a magnetic torque omega, and its associated atom can be submitted to a +force F for spin-lattice calculations (see "fix_nve_spin"_fix_nve_spin.html), +such as: + +:c,image(Eqs/pair_spin_exchange_forces.jpg) + +with h the Planck constant (in metal units), and eij = (ri - rj)/|ri-rj| the unit +vector between sites i and j. + +More details about the derivation of these torques/forces are reported in +"(Tranchida)"_#Tranchida3. + +For the {spin/exchange} pair style, the following coefficients must be defined +for each pair of atoms types via the "pair_coeff"_pair_coeff.html command as in +the examples above, or in the data file or restart files read by the +"read_data"_read_data.html or "read_restart"_read_restart.html commands, and +set in the following order: + +rc (distance units) +a (energy units) +b (adim parameter) +d (distance units) :ul + +Note that rc is the radius cutoff of the considered exchange interaction, +and a, b and d are the three coefficients performing the parametrization +of the function J(rij) defined above. + +None of those coefficients is optional. If not specified, the +{spin/exchange} pair style cannot be used. + +:line + +[Restrictions:] + +All the {pair/spin} styles are part of the SPIN package. These styles +are only enabled if LAMMPS was built with this package, and if the +atom_style "spin" was declared. See the "Build +package"_Build_package.html doc page for more info. + +[Related commands:] + +"atom_style spin"_atom_style.html, "pair_coeff"_pair_coeff.html, +"pair_eam"_pair_eam.html, + +[Default:] none + +:line + +:link(Tranchida3) +[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson, +Journal of Computational Physics, (2018). diff --git a/doc/src/pair_spin_magelec.txt b/doc/src/pair_spin_magelec.txt new file mode 100644 index 0000000000..f552c56a4b --- /dev/null +++ b/doc/src/pair_spin_magelec.txt @@ -0,0 +1,73 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +pair_style spin/me command :h3 + +[Syntax:] + +pair_style spin/me cutoff :pre + +cutoff = global cutoff pair (distance in metal units) :ulb,l + +:ule + +[Examples:] + +pair_style spin/me 4.5 +pair_coeff * * me 4.5 0.00109 1.0 1.0 1.0 :pre + +[Description:] + +Style {spin/me} computes a magneto-electric interaction between +pairs of magnetic spins. According to the derivation reported in +"(Katsura)"_#Katsura1, this interaction is defined as: + +:c,image(Eqs/pair_spin_me_interaction.jpg) + +where si and sj are neighboring magnetic spins of two particles, +eij = (ri - rj)/|ri-rj| is the normalized separation vector between the +two particles, and E is an electric polarization vector. +The norm and direction of E are giving the intensity and the +direction of a screened dielectric atomic polarization (in eV). + +From this magneto-electric interaction, each spin i will be submitted +to a magnetic torque omega, and its associated atom can be submitted to a +force F for spin-lattice calculations (see "fix_nve_spin"_fix_nve_spin.html), +such as: + +:c,image(Eqs/pair_spin_me_forces.jpg) + +with h the Planck constant (in metal units). + +More details about the derivation of these torques/forces are reported in +"(Tranchida)"_#Tranchida4. + +:line + +[Restrictions:] + +All the {pair/spin} styles are part of the SPIN package. These styles +are only enabled if LAMMPS was built with this package, and if the +atom_style "spin" was declared. See the "Build +package"_Build_package.html doc page for more info. + +[Related commands:] + +"atom_style spin"_atom_style.html, "pair_coeff"_pair_coeff.html, +"pair_spin_exchange"_pair_spin_exchange.html, "pair_eam"_pair_eam.html, + +[Default:] none + +:line + +:link(Katsura1) +[(Katsura)] H. Katsura, N. Nagaosa, A.V. Balatsky. Phys. Rev. Lett., 95(5), 057205. (2005) + +:link(Tranchida4) +[(Tranchida)] Tranchida, Plimpton, Thibaudeau, and Thompson, +Journal of Computational Physics, (2018). diff --git a/doc/src/pair_spin_neel.txt b/doc/src/pair_spin_neel.txt new file mode 100644 index 0000000000..fe3bb1ad14 --- /dev/null +++ b/doc/src/pair_spin_neel.txt @@ -0,0 +1,81 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +pair_style spin/neel command :h3 + +[Syntax:] + +pair_style spin/neel cutoff :pre + +cutoff = global cutoff pair (distance in metal units) :ulb,l + +:ule + +[Examples:] + +pair_style spin/neel 4.0 +pair_coeff * * neel 4.0 0.0048 0.234 1.168 2.6905 0.705 0.652 +pair_coeff 1 2 neel 4.0 0.0048 0.234 1.168 0.0 0.0 1.0 :pre + +[Description:] + +Style {spin/neel} computes the Neel pair anisotropy model +between pairs of magnetic spins: + +:c,image(Eqs/pair_spin_neel_interaction.jpg) + +where si and sj are two neighboring magnetic spins of two particles, +rij = ri - rj is the inter-atomic distance between the two particles, +eij = (ri - rj)/|ri-rj| is their normalized separation vector +and g1, q1 and q2 are three functions defining the intensity of the +dipolar and quadrupolar contributions, with: + +:c,image(Eqs/pair_spin_neel_functions.jpg) + +With the functions g(rij) and q(rij) defined and fitted according to the same +Bethe-Slater function used to fit the exchange interaction: + +:c,image(Eqs/pair_spin_exchange_function.jpg) + +where a, b and d are the three constant coefficients defined in the associated +"pair_coeff" command. + +The coefficients a, b, and d need to be fitted so that the function above matches with +the values of the magneto-elastic constant of the materials at stake. + +Examples and more explanations about this function and its parametrization are reported +in "(Tranchida)"_#Tranchida6. More examples of parametrization will be provided in +future work. + +From this DM interaction, each spin i will be submitted to a magnetic torque +omega and its associated atom to a force F (for spin-lattice calculations only). + +More details about the derivation of these torques/forces are reported in +"(Tranchida)"_#Tranchida6. + +:line + +[Restrictions:] + +All the {pair/spin} styles are part of the SPIN package. These styles +are only enabled if LAMMPS was built with this package, and if the +atom_style "spin" was declared. See the "Build +package"_Build_package.html doc page for more info. + +[Related commands:] + +"atom_style spin"_atom_style.html, "pair_coeff"_pair_coeff.html, +"pair_eam"_pair_eam.html, + +[Default:] none + +:line + +:link(Tranchida6) +[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson, +Journal of Computational Physics, (2018). diff --git a/doc/src/pair_srp.txt b/doc/src/pair_srp.txt index e7f1e00d10..e784ac3d17 100644 --- a/doc/src/pair_srp.txt +++ b/doc/src/pair_srp.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_style.txt b/doc/src/pair_style.txt index 475761add7..9dfead300e 100644 --- a/doc/src/pair_style.txt +++ b/doc/src/pair_style.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -78,22 +78,22 @@ previously specified pair_coeff values. :line Here is an alphabetic list of pair styles defined in LAMMPS. They are -also given in more compact form in the pair section of "this -page"_Section_commands.html#cmd_5. +also listed in more compact form on the "Commands +pair"_Commands_pair.html doc page. Click on the style to display the formula it computes, arguments specified in the pair_style command, and coefficients specified by the associated "pair_coeff"_pair_coeff.html command. There are also additional pair styles (not listed here) submitted by -users which are included in the LAMMPS distribution. The list of -these with links to the individual styles are given in the pair -section of "this page"_Section_commands.html#cmd_5. +users which are included in the LAMMPS distribution. The full list of +all pair styles is on the "Commands pair"_Commands_pair.html doc page. There are also additional accelerated pair styles (not listed here) -included in the LAMMPS distribution for faster performance on CPUs and -GPUs. The list of these with links to the individual styles are given -in the pair section of "this page"_Section_commands.html#cmd_5. +included in the LAMMPS distribution for faster performance on CPUs, +GPUs, and KNLs. The individual style names on the "Commands +pair"_Commands_pair.html doc page are followed by one or more of +(g,i,k,o,t) to indicate which accelerated styles exist. "pair_style none"_pair_none.html - turn off pairwise interactions "pair_style hybrid"_pair_hybrid.html - multiple styles of pairwise interactions @@ -103,8 +103,9 @@ in the pair section of "this page"_Section_commands.html#cmd_5. "pair_style adp"_pair_adp.html - angular dependent potential (ADP) of Mishin "pair_style airebo"_pair_airebo.html - AIREBO potential of Stuart "pair_style airebo/morse"_pair_airebo.html - AIREBO with Morse instead of LJ +"pair_style atm"_pair_atm.html - Axilrod-Teller-Muto potential "pair_style beck"_pair_beck.html - Beck potential -"pair_style body"_pair_body.html - interactions between body particles +"pair_style body/nparticle"_pair_body_nparticle.html - interactions between body particles "pair_style bop"_pair_bop.html - BOP potential of Pettifor "pair_style born"_pair_born.html - Born-Mayer-Huggins potential "pair_style born/coul/long"_pair_born.html - Born-Mayer-Huggins with long-range Coulombics @@ -218,10 +219,9 @@ This command must be used before any coefficients are set by the "read_restart"_read_restart.html commands. Some pair styles are part of specific packages. They are only enabled -if LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info on packages. -The doc pages for individual pair potentials tell if it is part of a -package. +if LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. The doc pages for +individual pair potentials tell if it is part of a package. [Related commands:] diff --git a/doc/src/pair_sw.txt b/doc/src/pair_sw.txt index 4932fe55d3..ff83316419 100644 --- a/doc/src/pair_sw.txt +++ b/doc/src/pair_sw.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -144,28 +144,27 @@ taken from the ij and ik pairs (sigma, a, gamma) Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. When using the USER-INTEL package with this style, there is an additional 5 to 10 percent performance improvement when the Stillinger-Weber parameters p and q are set to 4 and 0 respectively. These parameters are common for modeling silicon and water. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line @@ -192,8 +191,8 @@ This pair style can only be used via the {pair} keyword of the [Restrictions:] This pair style is part of the MANYBODY package. It is only enabled -if LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +if LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. This pair style requires the "newton"_newton.html setting to be "on" for pair interactions. diff --git a/doc/src/pair_table.txt b/doc/src/pair_table.txt index b99491b477..22c63a1f32 100644 --- a/doc/src/pair_table.txt +++ b/doc/src/pair_table.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -217,23 +217,22 @@ one that matches the specified keyword. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_table_rx.txt b/doc/src/pair_table_rx.txt index cd3a7ef31b..9b9a6abff8 100644 --- a/doc/src/pair_table_rx.txt +++ b/doc/src/pair_table_rx.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -227,31 +227,30 @@ This pair style can only be used via the {pair} keyword of the Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line [Restrictions:] This command is part of the USER-DPD package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/pair_tersoff.txt b/doc/src/pair_tersoff.txt index 918e889924..20744bc2a9 100644 --- a/doc/src/pair_tersoff.txt +++ b/doc/src/pair_tersoff.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -179,23 +179,22 @@ defined in various papers. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line @@ -222,8 +221,8 @@ This pair style can only be used via the {pair} keyword of the [Restrictions:] This pair style is part of the MANYBODY package. It is only enabled -if LAMMPS was built with that package. See -the "Making LAMMPS"_Section_start.html#start_3 section for more info. +if LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. This pair style requires the "newton"_newton.html setting to be "on" for pair interactions. diff --git a/doc/src/pair_tersoff_mod.txt b/doc/src/pair_tersoff_mod.txt index e0c2b5a5cb..2df23045a3 100644 --- a/doc/src/pair_tersoff_mod.txt +++ b/doc/src/pair_tersoff_mod.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -131,23 +131,22 @@ for SiSiSi means Si bonded to a Si with another Si atom influencing the bond. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line @@ -170,8 +169,8 @@ This pair style can only be used via the {pair} keyword of the [Restrictions:] This pair style is part of the MANYBODY package. It is only enabled -if LAMMPS was built with that package. See -the "Making LAMMPS"_Section_start.html#start_3 section for more info. +if LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. This pair style requires the "newton"_newton.html setting to be "on" for pair interactions. diff --git a/doc/src/pair_tersoff_zbl.txt b/doc/src/pair_tersoff_zbl.txt index 21d57e4e88..5f03ffd94e 100644 --- a/doc/src/pair_tersoff_zbl.txt +++ b/doc/src/pair_tersoff_zbl.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -189,23 +189,22 @@ providing the base ZBL implementation. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line @@ -232,8 +231,8 @@ This pair style can only be used via the {pair} keyword of the [Restrictions:] This pair style is part of the MANYBODY package. It is only enabled -if LAMMPS was built with that package. See -the "Making LAMMPS"_Section_start.html#start_3 section for more info. +if LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. This pair style requires the "newton"_newton.html setting to be "on" for pair interactions. diff --git a/doc/src/pair_thole.txt b/doc/src/pair_thole.txt index 41a4059cee..c7a304ca41 100644 --- a/doc/src/pair_thole.txt +++ b/doc/src/pair_thole.txt @@ -9,7 +9,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -45,8 +45,8 @@ pair_style lj/cut/thole/long 2.6 12.0 :pre The {thole} pair styles are meant to be used with force fields that include explicit polarization through Drude dipoles. This link describes how to use the "thermalized Drude oscillator -model"_tutorial_drude.html in LAMMPS and polarizable models in LAMMPS -are discussed in "this Section"_Section_howto.html#howto_25. +model"_Howto_drude.html in LAMMPS and polarizable models in LAMMPS are +discussed on the "Howto polarizable"_Howto_polarizable.html doc page. The {thole} pair style should be used as a sub-style within in the "pair_hybrid/overlay"_pair_hybrid.html command, in conjunction with a @@ -130,23 +130,22 @@ the {pair_style} command line. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. [Mixing]: @@ -162,8 +161,8 @@ are defined using [Restrictions:] These pair styles are part of the USER-DRUDE package. They are only -enabled if LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +enabled if LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. This pair_style should currently not be used with the "charmm dihedral style"_dihedral_charmm.html if the latter has non-zero 1-4 weighting diff --git a/doc/src/pair_tri_lj.txt b/doc/src/pair_tri_lj.txt index 42a5bbdfe2..98bb4e284e 100644 --- a/doc/src/pair_tri_lj.txt +++ b/doc/src/pair_tri_lj.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -101,8 +101,8 @@ This pair style can only be used via the {pair} keyword of the [Restrictions:] This style is part of the ASPHERE package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. Defining particles to be triangles so they participate in tri/tri or tri/particle interactions requires the use the "atom_style diff --git a/doc/src/pair_ufm.txt b/doc/src/pair_ufm.txt index 88a22864cc..787c60a1bd 100644 --- a/doc/src/pair_ufm.txt +++ b/doc/src/pair_ufm.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -69,23 +69,22 @@ NOTE: The thermodynamic integration procedure can be performed with this potenti Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_vashishta.txt b/doc/src/pair_vashishta.txt index d9c66d45c0..01d089b4de 100644 --- a/doc/src/pair_vashishta.txt +++ b/doc/src/pair_vashishta.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -171,23 +171,22 @@ two-body parameters from the CCC and CSiSi entries. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line @@ -214,8 +213,8 @@ This pair style can only be used via the {pair} keyword of the [Restrictions:] These pair style are part of the MANYBODY package. They is only -enabled if LAMMPS was built with that package. See the -"Making LAMMPS"_Section_start.html#start_3 section for more info. +enabled if LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. These pair styles requires the "newton"_newton.html setting to be "on" for pair interactions. diff --git a/doc/src/pair_write.txt b/doc/src/pair_write.txt index 9f5970fcbc..48ad76e76e 100644 --- a/doc/src/pair_write.txt +++ b/doc/src/pair_write.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_yukawa.txt b/doc/src/pair_yukawa.txt index e7c063ded9..154fd3e836 100644 --- a/doc/src/pair_yukawa.txt +++ b/doc/src/pair_yukawa.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -49,23 +49,22 @@ cutoff is used. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_yukawa_colloid.txt b/doc/src/pair_yukawa_colloid.txt index 2037a9451f..b36c4c235c 100644 --- a/doc/src/pair_yukawa_colloid.txt +++ b/doc/src/pair_yukawa_colloid.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -80,23 +80,22 @@ yukawa/colloid cutoff is used. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line @@ -130,8 +129,8 @@ This pair style can only be used via the {pair} keyword of the [Restrictions:] This style is part of the COLLOID package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. This pair style requires that atoms be finite-size spheres with a diameter, as defined by the "atom_style sphere"_atom_style.html diff --git a/doc/src/pair_zbl.txt b/doc/src/pair_zbl.txt index 1984cd831f..4c8dfb5455 100644 --- a/doc/src/pair_zbl.txt +++ b/doc/src/pair_zbl.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -71,23 +71,22 @@ copper. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_zero.txt b/doc/src/pair_zero.txt index e58b33c75f..b324003bd1 100644 --- a/doc/src/pair_zero.txt +++ b/doc/src/pair_zero.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pairs.txt b/doc/src/pairs.txt index 202aaa9c0f..d535798482 100644 --- a/doc/src/pairs.txt +++ b/doc/src/pairs.txt @@ -8,10 +8,12 @@ Pair Styles :h1 pair_adp pair_agni pair_airebo + pair_atm pair_awpmd pair_beck - pair_body + pair_body_nparticle pair_body_rounded_polygon + pair_body_rounded_polyhedron pair_bop pair_born pair_brownian @@ -97,6 +99,10 @@ Pair Styles :h1 pair_sph_rhosum pair_sph_taitwater pair_sph_taitwater_morris + pair_spin_dmi + pair_spin_exchange + pair_spin_magelec + pair_spin_neel pair_srp pair_sw pair_table diff --git a/doc/src/partition.txt b/doc/src/partition.txt index 610eee99b3..86673c226b 100644 --- a/doc/src/partition.txt +++ b/doc/src/partition.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -26,9 +26,8 @@ partition yes 6* fix all nvt temp 1.0 1.0 0.1 :pre [Description:] This command invokes the specified command on a subset of the -partitions of processors you have defined via the -partition -command-line switch. See "Section 2.6"_Section_start.html#start_6 -for an explanation of the switch. +partitions of processors you have defined via the "-partition +command-line switch"_Run_options.html. Normally, every input script command in your script is invoked by every partition. This behavior can be modified by defining world- or @@ -49,7 +48,7 @@ argument. Partitions are numbered from 1 to Np, where Np is the number of partitions specified by the "-partition command-line -switch"_Section_start.html#start_6. +switch"_Run_options.html. {N} can be specified in one of two ways. An explicit numeric value can be used, as in the 1st example above. Or a wild-card asterisk can diff --git a/doc/src/prd.txt b/doc/src/prd.txt index 3c0305e316..f71f285336 100644 --- a/doc/src/prd.txt +++ b/doc/src/prd.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -62,15 +62,15 @@ timescale spanned by the multiple simulations, while waiting for an event to occur. Each replica runs on a partition of one or more processors. Processor -partitions are defined at run-time using the -partition command-line -switch; see "Section 2.6"_Section_start.html#start_6 of the manual. -Note that if you have MPI installed, you can run a multi-replica -simulation with more replicas (partitions) than you have physical -processors, e.g you can run a 10-replica simulation on one or two -processors. However for PRD, this makes little sense, since running a -replica on virtual instead of physical processors,offers no effective -parallel speed-up in searching for infrequent events. See "Section -6.5"_Section_howto.html#howto_5 of the manual for further discussion. +partitions are defined at run-time using the "-partition command-line +switch"_Run_options.html. Note that if you have MPI installed, you +can run a multi-replica simulation with more replicas (partitions) +than you have physical processors, e.g you can run a 10-replica +simulation on one or two processors. However for PRD, this makes +little sense, since running a replica on virtual instead of physical +processors,offers no effective parallel speed-up in searching for +infrequent events. See the "Howto replica"_Howto_replica.html doc +page for further discussion. When a PRD simulation is performed, it is assumed that each replica is running the same model, though LAMMPS does not check for this. @@ -285,8 +285,8 @@ value for the first event in the new run will be slightly off. [Restrictions:] This command can only be used if LAMMPS was built with the REPLICA -package. See the "Making LAMMPS"_Section_start.html#start_3 section -for more info on packages. +package. See the "Build package"_Build_package.html doc +page for more info. The {N} and {t_correlate} settings must be integer multiples of {t_event}. diff --git a/doc/src/print.txt b/doc/src/print.txt index 77e0c7cfd3..476d4104fa 100644 --- a/doc/src/print.txt +++ b/doc/src/print.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/processors.txt b/doc/src/processors.txt index e54b2cede3..b9bd927f96 100644 --- a/doc/src/processors.txt +++ b/doc/src/processors.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -81,11 +81,11 @@ communication costs due to the high surface area of each processor's sub-domain. Also note that if multiple partitions are being used then P is the -number of processors in this partition; see "this -section"_Section_start.html#start_6 for an explanation of the --partition command-line switch. Also note that you can prefix the -processors command with the "partition"_partition.html command to -easily specify different Px,Py,Pz values for different partitions. +number of processors in this partition; see the "-partition +command-line switch"_Run_options.html doc page for details. Also note +that you can prefix the processors command with the +"partition"_partition.html command to easily specify different +Px,Py,Pz values for different partitions. You can use the "partition"_partition.html command to specify different processor grids for different partitions, e.g. @@ -249,7 +249,7 @@ partition {Precv} which is enforced when each is setting up their own mapping of their processors to the simulation box. Each of {Psend} and {Precv} must be integers from 1 to Np, where Np is the number of partitions you have defined via the "-partition command-line -switch"_Section_start.html#start_6. +switch"_Run_options.html. A "dependency" means that the sending partition will create its regular 3d grid as Px by Py by Pz and after it has done this, it will @@ -286,8 +286,8 @@ processors and their mapping to the 3d grid to the specified file processors in the manner you desired, which can be tricky to figure out, especially when running on multiple partitions or on, a multicore machine or when the processor ranks were reordered by use of the -"-reorder command-line switch"_Section_start.html#start_6 or due to -use of MPI-specific launch options such as a config file. +"-reorder command-line switch"_Run_options.html or due to use of +MPI-specific launch options such as a config file. If you have multiple partitions you should insure that each one writes to a different file, e.g. using a "world-style variable"_variable.html @@ -300,11 +300,11 @@ The IDs are the processor's rank in this simulation (the world), the universe (of multiple simulations), and the original MPI communicator used to instantiate LAMMPS, respectively. The world and universe IDs will only be different if you are running on more than one partition; -see the "-partition command-line switch"_Section_start.html#start_6. -The universe and original IDs will only be different if you used the -"-reorder command-line switch"_Section_start.html#start_6 to reorder -the processors differently than their rank in the original -communicator LAMMPS was instantiated with. +see the "-partition command-line switch"_Run_options.html. The +universe and original IDs will only be different if you used the +"-reorder command-line switch"_Run_options.html to reorder the +processors differently than their rank in the original communicator +LAMMPS was instantiated with. I,J,K are the indices of the processor in the regular 3d grid, each from 1 to Nd, where Nd is the number of processors in that dimension @@ -332,7 +332,8 @@ The {part} keyword (for the receiving partition) only works with the [Related commands:] -"partition"_partition.html, "-reorder command-line switch"_Section_start.html#start_6 +"partition"_partition.html, "-reorder command-line +switch"_Run_options.html [Default:] diff --git a/doc/src/python.txt b/doc/src/python.txt index 1ac2b48528..54d18d2f60 100644 --- a/doc/src/python.txt +++ b/doc/src/python.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -99,10 +99,9 @@ They can be substituted for directly in an input script. Or they can be passed to various commands as arguments, so that the variable is evaluated during a simulation run. -A broader overview of how Python can be used with LAMMPS is -given in "Section 11"_Section_python.html. There is an -examples/python directory which illustrates use of the python -command. +A broader overview of how Python can be used with LAMMPS is given on +the "Python"_Python_head.html doc page. There is an examples/python +directory which illustrates use of the python command. :line @@ -200,9 +199,9 @@ The {here} keyword does the same thing, except that the Python code follows as a single argument to the {here} keyword. This can be done using triple quotes as delimiters, as in the examples above. This allows Python code to be listed verbatim in your input script, with -proper indentation, blank lines, and comments, as desired. See -"Section 3.2"_Section_commands.html#cmd_2, for an explanation of how -triple quotes can be used as part of input script syntax. +proper indentation, blank lines, and comments, as desired. See the +"Commands parse"_Commands_parse.html doc page, for an explanation of +how triple quotes can be used as part of input script syntax. The {exists} keyword takes no argument. It means that Python code containing the required Python function defined by the {func} setting, @@ -331,9 +330,9 @@ to the screen and log file. Note that since the LAMMPS print command itself takes a string in quotes as its argument, the Python string must be delimited with a different style of quotes. -"Section 11.7"_Section_python.html#py_7 describes the syntax for how -Python wraps the various functions included in the LAMMPS library -interface. +The "Pytnon library"_Python_library.html doc page describes the syntax +for how Python wraps the various functions included in the LAMMPS +library interface. A more interesting example is in the examples/python/in.python script which loads and runs the following function from examples/python/funcs.py: @@ -470,8 +469,8 @@ sys.exit() in the except clause). [Restrictions:] This command is part of the PYTHON package. It is only enabled if -LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. Building LAMMPS with the PYTHON package will link LAMMPS with the Python library on your system. Settings to enable this are in the @@ -484,15 +483,16 @@ building LAMMPS. LAMMPS must also be built as a shared library and your Python function must be able to to load the Python module in python/lammps.py that wraps the LAMMPS library interface. These are the same steps required to use Python by itself to wrap LAMMPS. -Details on these steps are explained in "Section -python"_Section_python.html. Note that it is important that the -stand-alone LAMMPS executable and the LAMMPS shared library be -consistent (built from the same source code files) in order for this -to work. If the two have been built at different times using -different source files, problems may occur. +Details on these steps are explained on the "Python"_Python_head.html +doc page. Note that it is important that the stand-alone LAMMPS +executable and the LAMMPS shared library be consistent (built from the +same source code files) in order for this to work. If the two have +been built at different times using different source files, problems +may occur. [Related commands:] -"shell"_shell.html, "variable"_variable.html, "fix python/invoke"_fix_python_invoke.html +"shell"_shell.html, "variable"_variable.html, "fix +python/invoke"_fix_python_invoke.html [Default:] none diff --git a/doc/src/quit.txt b/doc/src/quit.txt index 843d3de7f3..802df97711 100644 --- a/doc/src/quit.txt +++ b/doc/src/quit.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/read_data.txt b/doc/src/read_data.txt index fd297e36c1..6aa30d9e63 100644 --- a/doc/src/read_data.txt +++ b/doc/src/read_data.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -63,8 +63,8 @@ simulation. The file can be ASCII text or a gzipped text file atom coordinates; see the "read_restart"_read_restart.html and "create_atoms"_create_atoms.html commands for alternative methods. Also see the explanation of the "-restart command-line -switch"_Section_start.html#start_6 which can convert a restart file to -a data file. +switch"_Run_options.html which can convert a restart file to a data +file. This command can be used multiple times to add new atoms and their properties to an existing system by using the {add}, {offset}, and @@ -124,14 +124,14 @@ bond atoms or bad dynamics. The three choices for the {add} argument affect how the atom IDs and molecule IDs of atoms in the data file are treated. If {append} is specified, atoms in the data file are added to the current system, -with their atom IDs reset so that an atomID = M in the data file -becomes atomID = N+M, where N is the largest atom ID in the current +with their atom IDs reset so that an atom-ID = M in the data file +becomes atom-ID = N+M, where N is the largest atom ID in the current system. This rule is applied to all occurrences of atom IDs in the data file, e.g. in the Velocity or Bonds section. This is also done for molecule IDs, if the atom style does support molecule IDs or they are enabled via fix property/atom. If {IDoffset} is specified, then {IDoffset} is a numeric value is given, e.g. 1000, so that an -atomID = M in the data file becomes atomID = 1000+M. For systems +atom-ID = M in the data file becomes atom-ID = 1000+M. For systems with enabled molecule IDs, another numerical argument {MOLoffset} is required representing the equivalent offset for molecule IDs. If {merge} is specified, the data file atoms @@ -139,7 +139,7 @@ are added to the current system without changing their IDs. They are assumed to merge (without duplication) with the currently defined atoms. It is up to you to insure there are no multiply defined atom IDs, as LAMMPS only performs an incomplete check that this is the case -by insuring the resulting max atomID >= the number of atoms. For +by insuring the resulting max atom-ID >= the number of atoms. For molecule IDs, there is no check done at all. The {offset} and {shift} keywords can only be used if the {add} @@ -322,9 +322,9 @@ with tilt factors that exceed these limits, you can use the "box tilt"_box.html command, with a setting of {large}; a setting of {small} is the default. -See "Section 6.12"_Section_howto.html#howto_12 of the doc pages -for a geometric description of triclinic boxes, as defined by LAMMPS, -and how to transform these parameters to and from other commonly used +See the "Howto triclinic"_Howto_triclinic.html doc page for a +geometric description of triclinic boxes, as defined by LAMMPS, and +how to transform these parameters to and from other commonly used triclinic representations. When a triclinic system is used, the simulation domain should normally @@ -772,9 +772,9 @@ the "bodies" keyword. Each body can have a variable number of integer and/or floating-point values. The number and meaning of the values is defined by the body -style, as described in the "body"_body.html doc page. The body style -is given as an argument to the "atom_style body"_atom_style.html -command. +style, as described in the "Howto body"_Howto_body.html doc page. The +body style is given as an argument to the "atom_style +body"_atom_style.html command. The Ninteger and Ndouble values determine how many integer and floating-point values are specified for this particle. Ninteger and @@ -1153,8 +1153,8 @@ Translational velocities can also be set by the [Restrictions:] To read gzipped data files, you must compile LAMMPS with the --DLAMMPS_GZIP option - see the "Making -LAMMPS"_Section_start.html#start_2 section of the documentation. +-DLAMMPS_GZIP option. See the "Build settings"_Build_settings.html +doc page for details. [Related commands:] diff --git a/doc/src/read_dump.txt b/doc/src/read_dump.txt index 23f6274582..db9cfca825 100644 --- a/doc/src/read_dump.txt +++ b/doc/src/read_dump.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -282,11 +282,11 @@ conditions are applied to remap an atom back into the simulation box. NOTE: If you get a warning about inconsistent image flags after reading in a dump snapshot, it means one or more pairs of bonded atoms -now have inconsistent image flags. As discussed in "Section -errors"_Section_errors.html this may or may not cause problems for -subsequent simulations, One way this can happen is if you read image -flag fields from the dump file but do not also use the dump file box -parameters. +now have inconsistent image flags. As discussed on the "Errors +common"_Errors_common.html doc page this may or may not cause problems +for subsequent simulations. One way this can happen is if you read +image flag fields from the dump file but do not also use the dump file +box parameters. LAMMPS knows how to compute unscaled and remapped coordinates for the snapshot column labels discussed above, e.g. {x}, {xs}, {xu}, {xsu}. @@ -311,12 +311,12 @@ needed to generate absolute, unscaled coordinates. [Restrictions:] To read gzipped dump files, you must compile LAMMPS with the --DLAMMPS_GZIP option - see the "Making -LAMMPS"_Section_start.html#start_2 section of the documentation. +-DLAMMPS_GZIP option. See the "Build settings"_Build_settings.html +doc page for details. The {molfile} dump file formats are part of the USER-MOLFILE package. They are only enabled if LAMMPS was built with that packages. See the -"Making LAMMPS"_Section_start.html#start_3 section for more info. +"Build package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/read_restart.txt b/doc/src/read_restart.txt index a5a2bfcc97..08cb6a2e6c 100644 --- a/doc/src/read_restart.txt +++ b/doc/src/read_restart.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -76,13 +76,11 @@ different than if the run had continued. These pair styles include If a restarted run is immediately different than the run which produced the restart file, it could be a LAMMPS bug, so consider -"reporting it"_Section_errors.html#err_2 if you think the behavior is -wrong. +"reporting it"_Errors_bugs.html if you think the behavior is a bug. Because restart files are binary, they may not be portable to other machines. In this case, you can use the "-restart command-line -switch"_Section_start.html#start_6 to convert a restart file to a data -file. +switch"_Run_options.html to convert a restart file to a data file. Similar to how restart files are written (see the "write_restart"_write_restart.html and "restart"_restart.html diff --git a/doc/src/region.txt b/doc/src/region.txt index 5039e4a516..acc85dcebb 100644 --- a/doc/src/region.txt +++ b/doc/src/region.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -186,9 +186,9 @@ functions, and include "thermo_style"_thermo_style.html command keywords for the simulation box parameters and timestep and elapsed time. Thus it is easy to specify a time-dependent radius. -See "Section 6.12"_Section_howto.html#howto_12 of the doc pages -for a geometric description of triclinic boxes, as defined by LAMMPS, -and how to transform these parameters to and from other commonly used +See the "Howto tricilinc"_Howto_triclinic.html doc page for a +geometric description of triclinic boxes, as defined by LAMMPS, and +how to transform these parameters to and from other commonly used triclinic representations. The {union} style creates a region consisting of the volume of all the @@ -358,28 +358,28 @@ sub-regions can be defined with the {open} keyword. :line -Styles with a {kk} suffix are functionally the same as the -corresponding style without the suffix. They have been optimized to -run faster, depending on your available hardware, as discussed in -"Section 5"_Section_accelerate.html of the manual. The -accelerated styles take the same arguments and should produce the same -results, except for round-off and precision issues. +Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. The code using the region (such as a fix or compute) must also be supported by Kokkos or no acceleration will occur. Currently, only {block} style regions are supported by Kokkos. These accelerated styles are part of the Kokkos package. They are -only enabled if LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +only enabled if LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/replicate.txt b/doc/src/replicate.txt index 08523ecdd8..79a481746e 100644 --- a/doc/src/replicate.txt +++ b/doc/src/replicate.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -14,7 +14,7 @@ replicate nx ny nz {keyword} :pre nx,ny,nz = replication factors in each dimension :ulb optional {keyword} = {bbox} :l - {bbox} = only check atoms in replicas that overlap with a processor's subdomain :ule + {bbox} = only check atoms in replicas that overlap with a processor's sub-domain :ule [Examples:] @@ -46,7 +46,7 @@ image flags that differ by 1. This will allow the bond to be unwrapped appropriately. The optional keyword {bbox} uses a bounding box to only check atoms -in replicas that overlap with a processor's subdomain when assigning +in replicas that overlap with a processor's sub-domain when assigning atoms to processors, and thus can result in substantial speedups for calculations using a large number of processors. It does require temporarily using more memory. diff --git a/doc/src/rerun.txt b/doc/src/rerun.txt index edf94cc711..71ad464bb0 100644 --- a/doc/src/rerun.txt +++ b/doc/src/rerun.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -189,8 +189,8 @@ every 1000 steps, then you will only see thermodynamic output every [Restrictions:] To read gzipped dump files, you must compile LAMMPS with the --DLAMMPS_GZIP option - see the "Making -LAMMPS"_Section_start.html#start_2 section of the documentation. +-DLAMMPS_GZIP option. See the "Build settings"_Build_settings.html +doc page for details. [Related commands:] diff --git a/doc/src/reset_ids.txt b/doc/src/reset_ids.txt index 8655a9d54f..8b217c7b1c 100644 --- a/doc/src/reset_ids.txt +++ b/doc/src/reset_ids.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -23,7 +23,7 @@ for bond, angle, dihedral, improper topology data. This will create a set of IDs that are numbered contiguously from 1 to N for a N atoms system. -This can be useful to do after perfoming a "delete_atoms" command for +This can be useful to do after performing a "delete_atoms" command for a molecular system. The delete_atoms compress yes option will not perform this operation due to the existence of bond topology. It can also be useful to do after any simulation which has lost atoms, diff --git a/doc/src/reset_timestep.txt b/doc/src/reset_timestep.txt index 79a5812ca1..0d518655fb 100644 --- a/doc/src/reset_timestep.txt +++ b/doc/src/reset_timestep.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/restart.txt b/doc/src/restart.txt index 7c39ae1404..e0fae3909d 100644 --- a/doc/src/restart.txt +++ b/doc/src/restart.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -49,7 +49,7 @@ as it writes successive restart files. Note that you can specify the restart command twice, once with a single filename and once with two filenames. This would allow you, for example, to write out archival restart files every 100000 steps -using a single filenname, and more frequent temporary restart files +using a single filename, and more frequent temporary restart files every 1000 steps, using two filenames. Using restart 0 will turn off both modes of output. @@ -125,8 +125,7 @@ Restart files can be read by a "read_restart"_read_restart.html command to restart a simulation from a particular state. Because the file is binary (to enable exact restarts), it may not be readable on another machine. In this case, you can use the "-r command-line -switch"_Section_start.html#start_6 to convert a restart file to a data -file. +switch"_Run_options.html to convert a restart file to a data file. NOTE: Although the purpose of restart files is to enable restarting a simulation from where it left off, not all information about a diff --git a/doc/src/run.txt b/doc/src/run.txt index 311560d66b..c7c73463d9 100644 --- a/doc/src/run.txt +++ b/doc/src/run.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -126,11 +126,10 @@ and interleaving commands in your input script. For example, a be redefined, e.g. to reset a thermostat temperature. Or this could be useful for invoking a command you have added to LAMMPS that wraps some other code (e.g. as a library) to perform a computation -periodically during a long LAMMPS run. See "this -section"_Section_modify.html of the documentation for info about how -to add new commands to LAMMPS. See "this -section"_Section_howto.html#howto_10 of the documentation for ideas -about how to couple LAMMPS to other codes. +periodically during a long LAMMPS run. See the "Modify"_Modify.html +doc page for info about how to add new commands to LAMMPS. See the +"Howto couple"_Howto_couple.html doc page for ideas about how to +couple LAMMPS to other codes. With the {every} option, N total steps are simulated, in shorter runs of M steps each. After each M-length run, the specified commands are diff --git a/doc/src/run_style.txt b/doc/src/run_style.txt index ba836a07dd..9defd1314e 100644 --- a/doc/src/run_style.txt +++ b/doc/src/run_style.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -69,8 +69,8 @@ The {verlet} style is a standard velocity-Verlet integrator. The {verlet/split} style is also a velocity-Verlet integrator, but it splits the force calculation within each timestep over 2 partitions of -processors. See "Section 2.6"_Section_start.html#start_6 for an -explanation of the -partition command-line switch. +processors. See the "-partition command-line switch"_Run_options.html +for info on how to run LAMMPS with multiple partitions. Specifically, this style performs all computation except the "kspace_style"_kspace_style.html portion of the force field on the 1st @@ -115,17 +115,17 @@ When you run in 2-partition mode with the {verlet/split} style, the thermodynamic data for the entire simulation will be output to the log and screen file of the 1st partition, which are log.lammps.0 and screen.0 by default; see the "-plog and -pscreen command-line -switches"_Section_start.html#start_6 to change this. The log and -screen file for the 2nd partition will not contain thermodynamic -output beyond the 1st timestep of the run. +switches"_Run_options.html to change this. The log and screen file +for the 2nd partition will not contain thermodynamic output beyond the +1st timestep of the run. -See "Section 5"_Section_accelerate.html of the manual for -performance details of the speed-up offered by the {verlet/split} -style. One important performance consideration is the assignment of -logical processors in the 2 partitions to the physical cores of a -parallel machine. The "processors"_processors.html command has -options to support this, and strategies are discussed in -"Section 5"_Section_accelerate.html of the manual. +See the "Speed packages"_Speed_packages.html doc page for performance +details of the speed-up offered by the {verlet/split} style. One +important performance consideration is the assignment of logical +processors in the 2 partitions to the physical cores of a parallel +machine. The "processors"_processors.html command has options to +support this, and strategies are discussed in "Section +5"_Speed.html of the manual. :line @@ -138,13 +138,19 @@ iterations of level 1 for a single iteration of level 2, N2 is the iterations of level 2 per iteration of level 3, etc. N-1 looping parameters must be specified. -The "timestep"_timestep.html command sets the timestep for the -outermost rRESPA level. Thus if the example command above for a -4-level rRESPA had an outer timestep of 4.0 fmsec, the inner timestep -would be 8x smaller or 0.5 fmsec. All other LAMMPS commands that -specify number of timesteps (e.g. "neigh_modify"_neigh_modify.html -parameters, "dump"_dump.html every N timesteps, etc) refer to the -outermost timesteps. +Thus with a 4-level respa setting of "2 2 2" for the 3 loop factors, +you could choose to have bond interactions computed 8x per large +timestep, angle interactions computed 4x, pair interactions computed +2x, and long-range interactions once per large timestep. + +The "timestep"_timestep.html command sets the large timestep for the +outermost rRESPA level. Thus if the 3 loop factors are "2 2 2" for +4-level rRESPA, and the outer timestep is set to 4.0 fmsec, then the +inner timestep would be 8x smaller or 0.5 fmsec. All other LAMMPS +commands that specify number of timesteps (e.g. "thermo"_thermo.html +for thermo output every N steps, "neigh_modify +delay/every"_neigh_modify.html parameters, "dump"_dump.html every N +steps, etc) refer to the outermost timesteps. The rRESPA keywords enable you to specify at what level of the hierarchy various forces will be computed. If not specified, the @@ -167,11 +173,17 @@ have their force go ramped to 0.0 so the overlap with the next regime compute forces for all pairs from 5.0 outward, with those from 5.0 to 6.0 having their value ramped in an inverse manner. -Only some pair potentials support the use of the {inner} and {middle} -and {outer} keywords. If not, only the {pair} keyword can be used -with that pair style, meaning all pairwise forces are computed at the -same rRESPA level. See the doc pages for individual pair styles for -details.i +Note that you can use {inner} and {outer} without using {middle} to +split the pairwise computations into two portions instead of three. +Unless you are using a very long pairwise cutoff, a 2-way split is +often faster than a 3-way split, since it avoids too much duplicate +computation of pairwise interactions near the intermediate cutoffs. + +Also note that only a few pair potentials support the use of the +{inner} and {middle} and {outer} keywords. If not, only the {pair} +keyword can be used with that pair style, meaning all pairwise forces +are computed at the same rRESPA level. See the doc pages for +individual pair styles for details. Another option for using pair potentials with rRESPA is with the {hybrid} keyword, which requires the use of the "pair_style hybrid or @@ -238,42 +250,54 @@ roughly a 1.5 fold speedup over the {verlet} style with SHAKE and a For non-biomolecular simulations, the {respa} style can be advantageous if there is a clear separation of time scales - fast and -slow modes in the simulation. Even a LJ system can benefit from -rRESPA if the interactions are divided by the inner, middle and outer -keywords. A 2-fold or more speedup can be obtained while maintaining -good energy conservation. In real units, for a pure LJ fluid at -liquid density, with a sigma of 3.0 angstroms, and epsilon of 0.1 -Kcal/mol, the following settings seem to work well: +slow modes in the simulation. For example, a system of slowly-moving +charged polymer chains could be setup as follows: + +timestep 4.0 +run_style respa 2 8 :pre + +This is two-level rRESPA with an 8x difference between the short and +long timesteps. The bonds, angles, dihedrals will be computed every +0.5 fs (assuming real units), while the pair and kspace interactions +will be computed once every 4 fs. These are the default settings for +each kind of interaction, so no additional keywords are necessary. + +Even a LJ system can benefit from rRESPA if the interactions are +divided by the inner, middle and outer keywords. A 2-fold or more +speedup can be obtained while maintaining good energy conservation. +In real units, for a pure LJ fluid at liquid density, with a sigma of +3.0 angstroms, and epsilon of 0.1 Kcal/mol, the following settings +seem to work well: timestep 36.0 run_style respa 3 3 4 inner 1 3.0 4.0 middle 2 6.0 7.0 outer 3 :pre :line -The {respa/omp} styles is a variant of {respa} adapted for use with +The {respa/omp} style is a variant of {respa} adapted for use with pair, bond, angle, dihedral, improper, or kspace styles with an {omp} -suffix. It is functionally equivalent to {respa} but performs additional -operations required for managing {omp} styles. For more on {omp} styles -see the "Section 5"_Section_accelerate.html of the manual. -Accelerated styles take the same arguments and should produce the same -results, except for round-off and precision issues. +suffix. It is functionally equivalent to {respa} but performs +additional operations required for managing {omp} styles. For more on +{omp} styles see the "Speed omp"_Speed_omp.html doc page. Accelerated +styles take the same arguments and should produce the same results, +except for round-off and precision issues. -You can specify {respa/omp} explicitly in your input script, or -you can use the "-suffix command-line switch"_Section_start.html#start_6 -when you invoke LAMMPS, or you can use the "suffix"_suffix.html -command in your input script. +You can specify {respa/omp} explicitly in your input script, or you +can use the "-suffix command-line switch"_Run_options.html when you +invoke LAMMPS, or you can use the "suffix"_suffix.html command in your +input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line [Restrictions:] The {verlet/split} style can only be used if LAMMPS was built with the -REPLICA package. Correspondingly the {respa/omp} style is available only -if the USER-OMP package was included. See the "Making LAMMPS"_Section_start.html#start_3 -section for more info on packages. +REPLICA package. Correspondingly the {respa/omp} style is available +only if the USER-OMP package was included. See the "Build +package"_Build_package.html doc page for more info. Whenever using rRESPA, the user should experiment with trade-offs in speed and accuracy for their system, and verify that they are @@ -287,6 +311,17 @@ conserving energy to adequate precision. run_style verlet :pre +For run_style respa, the default assignment of interactions +to rRESPA levels is as follows: + +bond forces = level 1 (innermost loop) +angle forces = same level as bond forces +dihedral forces = same level as angle forces +improper forces = same level as dihedral forces +pair forces = level N (outermost level) +kspace forces = same level as pair forces +inner, middle, outer forces = no default :ul + :line :link(Tuckerman3) diff --git a/doc/src/server.txt b/doc/src/server.txt new file mode 100644 index 0000000000..86fb68d012 --- /dev/null +++ b/doc/src/server.txt @@ -0,0 +1,71 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +server command :h3 + +[Syntax:] + +server protocol :pre + +protocol = {md} or {mc} :ul + +[Examples:] + +server md :pre + +[Description:] + +This command starts LAMMPS running in "server" mode, where it receives +messages from a separate "client" code and responds by sending a reply +message back to the client. The specified {protocol} determines the +format and content of messages LAMMPS expects to receive and how it +responds. + +The "Howto client/server"_Howto_client_server.html doc page gives an +overview of client/server coupling of LAMMPS with another code where +one code is the "client" and sends request messages to a "server" +code. The server responds to each request with a reply message. This +enables the two codes to work in tandem to perform a simulation. + +When this command is invoked, LAMMPS will run in server mode in an +endless loop, waiting for messages from the client code. The client +signals when it is done sending messages to LAMMPS, at which point the +loop will exit, and the remainder of the LAMMPS script will be +processed. + +The {protocol} argument defines the format and content of messages +that will be exchanged between the two codes. The current options +are: + +"md"_server_md.html = run dynamics with another code +"mc"_server_mc.html = perform Monte Carlo moves with another code :ul + +For protocol {md}, LAMMPS can be either a client (via the "fix +client/md"_fix_client_md.html command) or server. See the "server +md"_server_md.html doc page for details on the protocol. + +For protocol {mc}, LAMMPS can be the server. See the "server +mc"_server_mc.html doc page for details on the protocol. + +:line + +[Restrictions:] + +This command is part of the MESSAGE package. It is only enabled if +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. + +A script that uses this command must also use the +"message"_message.html command to setup the messaging protocol with +the other client code. + +[Related commands:] + +"message"_message.html, "fix client/md"_fix_client_md.html + +[Default:] none diff --git a/doc/src/server_mc.txt b/doc/src/server_mc.txt new file mode 100644 index 0000000000..58ca415be3 --- /dev/null +++ b/doc/src/server_mc.txt @@ -0,0 +1,116 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +server mc command :h3 + +[Syntax:] + +server mc :pre + +mc = the protocol argument to the "server"_server.html command + +[Examples:] + +server mc :pre + +[Description:] + +This command starts LAMMPS running in "server" mode, where it will +expect messages from a separate "client" code that match the {mc} +protocol for format and content explained below. For each message +LAMMPS receives it will send a message back to the client. + +The "Howto client/server"_Howto_client_server.html doc page gives an +overview of client/server coupling of LAMMPS with another code where +one code is the "client" and sends request messages to a "server" +code. The server responds to each request with a reply message. This +enables the two codes to work in tandem to perform a simulation. + +When this command is invoked, LAMMPS will run in server mode in an +endless loop, waiting for messages from the client code. The client +signals when it is done sending messages to LAMMPS, at which point the +loop will exit, and the remainder of the LAMMPS script will be +processed. + +The "server"_server.html doc page gives other options for using LAMMPS +See an example of how this command is used in +examples/COUPLE/lammps_mc/in.server. + +:line + +When using this command, LAMMPS (as the server code) receives +instructions from a Monte Carlo (MC) driver to displace random atoms, +compute the energy before and after displacement, and run dynamics to +equilibrate the system. + +The MC driver performs the random displacements on random atoms, +accepts or rejects the move in an MC sense, and orchestrates the MD +runs. + +The format and content of the exchanged messages are explained here in +a conceptual sense. Python-style pseudo code for the library calls to +the CSlib is shown, which performs the actual message exchange between +the two codes. See the "CSlib website"_http://cslib.sandia.gov doc +pages for more details on the actual library syntax. The "cs" object +in this pseudo code is a pointer to an instance of the CSlib. + +See the src/MESSAGE/server_mc.cpp file for details on how LAMMPS uses +these messages. See the examples/COUPLE/lammmps_mc/mc.cpp file for an +example of how an MC driver code can use these messages. + +Define NATOMS=1, EINIT=2, DISPLACE=3, ACCEPT=4, RUN=5. + +[Client sends one of these kinds of message]: + +cs->send(NATOMS,0) # msgID = 1 with no fields :pre + +cs->send(EINIT,0) # msgID = 2 with no fields :pre + +cs->send(DISPLACE,2) # msgID = 3 with 2 fields +cs->pack_int(1,ID) # 1st field = ID of atom to displace +cs->pack(2,3,xnew) # 2nd field = new xyz coords of displaced atom :pre + +cs->send(ACCEPT,1) # msgID = 4 with 1 field +cs->pack_int(1,flag) # 1st field = accept/reject flag :pre + +cs->send(RUN,1) # msgID = 5 with 1 field +cs->pack_int(1,nsteps) # 1st field = # of timesteps to run MD :pre + +[Server replies]: + +cs->send(NATOMS,1) # msgID = 1 with 1 field +cs->pack_int(1,natoms) # 1st field = number of atoms :pre + +cs->send(EINIT,2) # msgID = 2 with 2 fields +cs->pack_double(1,poteng) # 1st field = potential energy of system +cs->pack(2,3*natoms,x) # 2nd field = 3N coords of Natoms :pre + +cs->send(DISPLACE,1) # msgID = 3 with 1 field +cs->pack_double(1,poteng) # 1st field = new potential energy of system :pre + +cs->send(ACCEPT,0) # msgID = 4 with no fields :pre + +cs->send(RUN,0) # msgID = 5 with no fields :pre + +:line + +[Restrictions:] + +This command is part of the MESSAGE package. It is only enabled if +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. + +A script that uses this command must also use the +"message"_message.html command to setup the messaging protocol with +the other client code. + +[Related commands:] + +"message"_message.html + +[Default:] none diff --git a/doc/src/server_md.txt b/doc/src/server_md.txt new file mode 100644 index 0000000000..753542dc75 --- /dev/null +++ b/doc/src/server_md.txt @@ -0,0 +1,149 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +server md command :h3 + +[Syntax:] + +server md :pre + +md = the protocol argument to the "server"_server.html command + +[Examples:] + +server md :pre + +[Description:] + +This command starts LAMMPS running in "server" mode, where it will +expect messages from a separate "client" code that match the {md} +protocol for format and content explained below. For each message +LAMMPS receives it will send a message back to the client. + +The "Howto client/server"_Howto_client_server.html doc page gives an +overview of client/server coupling of LAMMPS with another code where +one code is the "client" and sends request messages to a "server" +code. The server responds to each request with a reply message. This +enables the two codes to work in tandem to perform a simulation. + +When this command is invoked, LAMMPS will run in server mode in an +endless loop, waiting for messages from the client code. The client +signals when it is done sending messages to LAMMPS, at which point the +loop will exit, and the remainder of the LAMMPS script will be +processed. + +The "server"_server.html doc page gives other options for using LAMMPS +in server mode. See an example of how this command is used in +examples/message/in.message.server. + +:line + +When using this command, LAMMPS (as the server code) receives the +current coordinates of all particles from the client code each +timestep, computes their interaction, and returns the energy, forces, +and pressure for the interacting particles to the client code, so it +can complete the timestep. This command could also be used with a +client code that performs energy minimization, using the server to +compute forces and energy each iteration of its minimizer. + +When using the "fix client/md"_fix_client_md.html command, LAMMPS (as +the client code) does the timestepping and receives needed energy, +forces, and pressure values from the server code. + +The format and content of the exchanged messages are explained here in +a conceptual sense. Python-style pseudo code for the library calls to +the CSlib is shown, which performs the actual message exchange between +the two codes. See the "CSlib website"_http://cslib.sandia.gov doc +pages for more details on the actual library syntax. The "cs" object +in this pseudo code is a pointer to an instance of the CSlib. + +See the src/MESSAGE/server_md.cpp and src/MESSAGE/fix_client_md.cpp +files for details on how LAMMPS uses these messages. See the +examples/COUPLE/lammps_vasp/vasp_wrapper.py file for an example of how +a quantum code (VASP) can use use these messages. + +The following pseudo-code uses these values, defined as enums. + +Define: + +SETUP=1, STEP=2 +DIM=1, PERIODICITY=2, ORIGIN=3, BOX=4, NATOMS=5, NTYPES=6, TYPES=7, COORDS=8, UNITS-9, CHARGE=10 +FORCES=1, ENERGY=2, PRESSURE=3, ERROR=4 :pre + +[Client sends 2 kinds of messages]: + +# required fields: DIM, PERIODICTY, ORIGIN, BOX, NATOMS, NTYPES, TYPES, COORDS +# optional fields: UNITS, CHARGE :pre + +cs->send(SETUP,nfields) # msgID with nfields :pre + +cs->pack_int(DIM,dim) # dimension (2,3) of simulation +cs->pack(PERIODICITY,3,xyz) # periodicity flags in 3 dims +cs->pack(ORIGIN,3,origin) # lower-left corner of simulation box +cs->pack(BOX,9,box) # 3 edge vectors of simulation box +cs->pack_int(NATOMS,natoms) # total number of atoms +cs->pack_int(NTYPES,ntypes) # number of atom types +cs->pack(TYPES,natoms,type) # vector of per-atom types +cs->pack(COORDS,3*natoms,x) # vector of 3N atom coords +cs->pack_string(UNITS,units) # units = "lj", "real", "metal", etc +cs->pack(CHARGE,natoms,q) # vector of per-atom charge :pre + +# required fields: COORDS +# optional fields: ORIGIN, BOX :pre + +cs->send(STEP,nfields) # msgID with nfields :pre + +cs->pack(COORDS,3*natoms,x) # vector of 3N atom coords +cs->pack(ORIGIN,3,origin) # lower-left corner of simulation box +cs->pack(BOX,9,box) # 3 edge vectors of simulation box :pre + +[Server replies to either kind of message]: + +# required fields: FORCES, ENERGY, PRESSURE +# optional fields: ERROR :pre + +cs->send(msgID,nfields) # msgID with nfields +cs->pack(FORCES,3*Natoms,f) # vector of 3N forces on atoms +cs->pack(ENERGY,1,poteng) # total potential energy of system +cs->pack(PRESSURE,6,press) # global pressure tensor (6-vector) +cs->pack_int(ERROR,flag) # server had an error (e.g. DFT non-convergence) :pre + +:line + +The units for various quantities that are sent and received iva +messages are defined for atomic-scale simulations in the table below. +The client and server codes (including LAMMPS) can use internal units +different than these (e.g. "real units"_units.html in LAMMPS), so long +as they convert to these units for meesaging. + +COORDS, ORIGIN, BOX = Angstroms +CHARGE = multiple of electron charge (1.0 is a proton) +ENERGY = eV +FORCES = eV/Angstrom +PRESSURE = bars :ul + +Note that these are "metal units"_units.html in LAMMPS. + +If you wish to run LAMMPS in another its non-atomic units, e.g. "lj +units"_units.html, then the client and server should exchange a UNITS +message as indicated above, and both the client and server should +agree on the units for the data they exchange. + +:line + +[Restrictions:] + +This command is part of the MESSAGE package. It is only enabled if +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. + +[Related commands:] + +"message"_message.html, "fix client/md"_fix_client_md.html + +[Default:] none diff --git a/doc/src/set.txt b/doc/src/set.txt index 4757d1c575..b83ad54f4e 100644 --- a/doc/src/set.txt +++ b/doc/src/set.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -17,6 +17,7 @@ ID = atom ID range or type range or mol ID range or group ID or region ID :l one or more keyword/value pairs may be appended :l keyword = {type} or {type/fraction} or {mol} or {x} or {y} or {z} or \ {charge} or {dipole} or {dipole/random} or {quat} or \ + {spin} or {spin/random} or {quat} or \ {quat/random} or {diameter} or {shape} or \ {length} or {tri} or {theta} or {theta/random} or \ {angmom} or {omega} or \ @@ -35,6 +36,8 @@ keyword = {type} or {type/fraction} or {mol} or {x} or {y} or {z} or \ value can be an atom-style variable (see below) {x},{y},{z} value = atom coordinate (distance units) value can be an atom-style variable (see below) + {vx},{vy},{vz} value = atom velocity (velocity units) + value can be an atom-style variable (see below) {charge} value = atomic charge (charge units) value can be an atom-style variable (see below) {dipole} values = x y z @@ -43,6 +46,13 @@ keyword = {type} or {type/fraction} or {mol} or {x} or {y} or {z} or \ {dipole/random} value = seed Dlen seed = random # seed (positive integer) for dipole moment orientations Dlen = magnitude of dipole moment (dipole units) + {spin} values = g x y z + g = magnitude of magnetic spin vector (in Bohr magneton's unit) + x,y,z = orientation of magnetic spin vector + any of x,y,z can be an atom-style variable (see below) + {spin/random} value = seed Dlen + seed = random # seed (positive integer) for magnetic spin orientations + Dlen = magnitude of magnetic spin vector (in Bohr magneton's unit) {quat} values = a b c theta a,b,c = unit vector to rotate particle around via right-hand rule theta = rotation angle (degrees) @@ -119,6 +129,7 @@ set type 3 charge 0.5 set type 1*3 charge 0.5 set atom * charge v_atomfile set atom 100*200 x 0.5 y 1.0 +set atom 100 vx 0.0 vy 0.0 vz -1.0 set atom 1492 type 3 :pre [Description:] @@ -217,7 +228,8 @@ IDs. Keywords {x}, {y}, {z}, and {charge} set the coordinates or charge of all selected atoms. For {charge}, the "atom style"_atom_style.html -being used must support the use of atomic charge. +being used must support the use of atomic charge. Keywords {vx}, {vy}, +and {vz} set the velocities of all selected atoms. Keyword {dipole} uses the specified x,y,z values as components of a vector to set as the orientation of the dipole moment vectors of the @@ -232,6 +244,15 @@ the orientation of a particular atom is the same, regardless of how many processors are being used. This keyword does not allow use of an atom-style variable. +Keyword {spin} uses the specified g value to set the magnitude of the +magnetic spin vectors, and the x,y,z values as components of a vector +to set as the orientation of the magnetic spin vectors of the selected +atoms. + +Keyword {spin/random} randomizes the orientation of the magnetic spin +vectors for the selected atoms and sets the magnitude of each to the +specified {Dlen} value. + Keyword {quat} uses the specified values to create a quaternion (4-vector) that represents the orientation of the selected atoms. The particles must define a quaternion for their orientation diff --git a/doc/src/shell.txt b/doc/src/shell.txt index 205164f874..d274f498e5 100644 --- a/doc/src/shell.txt +++ b/doc/src/shell.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/special_bonds.txt b/doc/src/special_bonds.txt index 1021c4856b..283aad6c2d 100644 --- a/doc/src/special_bonds.txt +++ b/doc/src/special_bonds.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -64,7 +64,7 @@ e.g. when using the "pair_style hybrid"_pair_hybrid.html command. Thus LAMMPS ignores special_bonds settings when manybody potentials are calculated. Please note, that the existence of explicit bonds for atoms that are described by a manybody potential will alter the -neigborlist and thus can render the computation of those interactions +neighbor list and thus can render the computation of those interactions invalid, since those pairs are not only used to determine direct pairwise interactions but also neighbors of neighbors and more. The recommended course of action is to remove such bonds, or - if @@ -110,7 +110,7 @@ simulation. The two exceptions to this rule are (a) if the {angle} or {dihedral} keywords are set to {yes} (see below), or (b) if the "delete_bonds"_delete_bonds.html command is used with the {special} -option that recomputes the 1-2,1-3,1-4 topologies after bonds are +option that re-computes the 1-2,1-3,1-4 topologies after bonds are deleted; see the "delete_bonds"_delete_bonds.html command for more details. diff --git a/doc/src/suffix.txt b/doc/src/suffix.txt index 74f69b6dfe..62e41ed29a 100644 --- a/doc/src/suffix.txt +++ b/doc/src/suffix.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -28,16 +28,16 @@ suffix kk :pre This command allows you to use variants of various styles if they exist. In that respect it operates the same as the "-suffix -command-line switch"_Section_start.html#start_6. It also has options -to turn off or back on any suffix setting made via the command line. +command-line switch"_Run_options.html. It also has options to turn +off or back on any suffix setting made via the command line. The specified style can be {gpu}, {intel}, {kk}, {omp}, {opt} or {hybrid}. These refer to optional packages that LAMMPS can be built -with, as described in "this section of the -manual"_Section_start.html#start_3. The "gpu" style corresponds to -the GPU package, the "intel" style to the USER-INTEL package, the "kk" -style to the KOKKOS package, the "omp" style to the USER-OMP package, -and the "opt" style to the OPT package. +with, as described on the "Build package"_Build_package.html doc page. +The "gpu" style corresponds to the GPU package, the "intel" style to +the USER-INTEL package, the "kk" style to the KOKKOS package, the +"omp" style to the USER-OMP package, and the "opt" style to the OPT +package. These are the variants these packages provide: @@ -105,6 +105,6 @@ input script. [Related commands:] -"Command-line switch -suffix"_Section_start.html#start_6 +"-suffix command-line switch"_Run_options.html [Default:] none diff --git a/doc/src/tad.txt b/doc/src/tad.txt index f5e7c6d653..9b34a68636 100644 --- a/doc/src/tad.txt +++ b/doc/src/tad.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -92,9 +92,8 @@ restricts you to having exactly one processor per replica. For more information, see the documentation for the "neb"_neb.html command. In the current LAMMPS implementation of TAD, all the non-NEB TAD operations are performed on the first partition, while the other -partitions remain idle. See "Section -6.5"_Section_howto.html#howto_5 of the manual for further discussion of -multi-replica simulations. +partitions remain idle. See the "Howto replica"_Howto_replica.html doc +page for further discussion of multi-replica simulations. A TAD run has several stages, which are repeated each time an event is performed. The logic for a TAD run is as follows: @@ -272,8 +271,8 @@ are always monotonically increasing. [Restrictions:] This command can only be used if LAMMPS was built with the REPLICA -package. See the "Making LAMMPS"_Section_start.html#start_3 section -for more info on packages. +package. See the "Build package"_Build_package.html doc +page for more info. {N} setting must be integer multiple of {t_event}. diff --git a/doc/src/temper.txt b/doc/src/temper.txt index b1c47c8076..edd578fbc9 100644 --- a/doc/src/temper.txt +++ b/doc/src/temper.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -31,15 +31,14 @@ Run a parallel tempering or replica exchange simulation using multiple replicas (ensembles) of a system. Two or more replicas must be used. Each replica runs on a partition of one or more processors. Processor -partitions are defined at run-time using the -partition command-line -switch; see "Section 2.6"_Section_start.html#start_6 of the -manual. Note that if you have MPI installed, you can run a -multi-replica simulation with more replicas (partitions) than you have -physical processors, e.g you can run a 10-replica simulation on one or -two processors. You will simply not get the performance speed-up you -would see with one or more physical processors per replica. See "this -section"_Section_howto.html#howto_5 of the manual for further -discussion. +partitions are defined at run-time using the "-partition command-line +switch"_Run_options.html. Note that if you have MPI installed, you +can run a multi-replica simulation with more replicas (partitions) +than you have physical processors, e.g you can run a 10-replica +simulation on one or two processors. You will simply not get the +performance speed-up you would see with one or more physical +processors per replica. See the "Howto replica"_Howto_replica.html +doc page for further discussion. Each replica's temperature is controlled at a different value by a fix with {fix-ID} that controls temperature. Most thermostat fix styles @@ -69,9 +68,8 @@ rejected based on a Boltzmann-weighted Metropolis criterion which uses As a tempering run proceeds, multiple log files and screen output files are created, one per replica. By default these files are named log.lammps.M and screen.M where M is the replica number from 0 to N-1, -with N = # of replicas. See the "section on command-line -switches"_Section_start.html#start_6 for info on how to change these -names. +with N = # of replicas. See the "-log and -screen command-line +swiches"_Run_options.html for info on how to change these names. The main screen and log file (log.lammps) will list information about which temperature is assigned to each replica at each thermodynamic @@ -139,8 +137,8 @@ example above with $w as the last argument. [Restrictions:] This command can only be used if LAMMPS was built with the REPLICA -package. See the "Making LAMMPS"_Section_start.html#start_3 section -for more info on packages. +package. See the "Build package"_Build_package.html doc +page for more info. [Related commands:] diff --git a/doc/src/temper_grem.txt b/doc/src/temper_grem.txt index 6145c8704c..7d22e46403 100644 --- a/doc/src/temper_grem.txt +++ b/doc/src/temper_grem.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -94,8 +94,8 @@ identical to "temper"_temper.html. [Restrictions:] This command can only be used if LAMMPS was built with the USER-MISC -package. See the "Making LAMMPS"_Section_start.html#start_3 section -for more info on packages. +package. See the "Build package"_Build_package.html doc +page for more info. This command must be used with "fix grem"_fix_grem.html. diff --git a/doc/src/temper_npt.txt b/doc/src/temper_npt.txt index 4ad49f9e33..50ac5615f6 100644 --- a/doc/src/temper_npt.txt +++ b/doc/src/temper_npt.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line temper/npt command :h3 @@ -48,8 +48,8 @@ on how the parallel tempering is handled in general. [Restrictions:] This command can only be used if LAMMPS was built with the USER-MISC -package. See the "Making LAMMPS"_Section_start.html#start_3 section -for more info on packages. +package. See the "Build package"_Build_package.html doc page for more +info. This command should be used with a fix that maintains the isothermal-isobaric (NPT) ensemble. diff --git a/doc/src/thermo.txt b/doc/src/thermo.txt index 1d5d34995c..5f12f98707 100644 --- a/doc/src/thermo.txt +++ b/doc/src/thermo.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/thermo_modify.txt b/doc/src/thermo_modify.txt index e9aca0f20a..ca2957de77 100644 --- a/doc/src/thermo_modify.txt +++ b/doc/src/thermo_modify.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/thermo_style.txt b/doc/src/thermo_style.txt index 6102169ee3..4d294c1df7 100644 --- a/doc/src/thermo_style.txt +++ b/doc/src/thermo_style.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -108,12 +108,11 @@ Style {custom} is the most general setting and allows you to specify which of the keywords listed above you want printed on each thermodynamic timestep. Note that the keywords c_ID, f_ID, v_name are references to "computes"_compute.html, "fixes"_fix.html, and -equal-style "variables"_variable.html that have been defined -elsewhere in the input script or can even be new styles which users -have added to LAMMPS (see the "Section 10"_Section_modify.html -section of the documentation). Thus the {custom} style provides a -flexible means of outputting essentially any desired quantity as a -simulation proceeds. +equal-style "variables"_variable.html that have been defined elsewhere +in the input script or can even be new styles which users have added +to LAMMPS. See the "Modify"_Modify.html doc page for details on the +latter. Thus the {custom} style provides a flexible means of +outputting essentially any desired quantity as a simulation proceeds. All styles except {custom} have {vol} appended to their list of outputs if the simulation box volume changes during the simulation. @@ -254,9 +253,9 @@ proceed for the maximum number of allowed iterations. The {part} keyword is useful for multi-replica or multi-partition simulations to indicate which partition this output and this file corresponds to, or for use in a "variable"_variable.html to append to -a filename for output specific to this partition. See "Section -2.6"_Section_start.html#start_6 of the manual for details on running -in multi-partition mode. +a filename for output specific to this partition. See discussion of +the "-partition command-line switch"_Run_options.html for details on +running in multi-partition mode. The {timeremain} keyword returns the remaining seconds when a timeout has been configured via the "timer timeout"_timer.html command. @@ -287,11 +286,11 @@ takes place. The keywords {cella}, {cellb}, {cellc}, {cellalpha}, {cellbeta}, {cellgamma}, correspond to the usual crystallographic quantities that -define the periodic unit cell of a crystal. See "this -section"_Section_howto.html#howto_12 of the doc pages for a geometric -description of triclinic periodic cells, including a precise definition -of these quantities in terms of the internal LAMMPS cell dimensions -{lx}, {ly}, {lz}, {yz}, {xz}, {xy}. +define the periodic unit cell of a crystal. See the "Howto +triclinic"_Howto_triclinic.html doc page for a geometric description +of triclinic periodic cells, including a precise definition of these +quantities in terms of the internal LAMMPS cell dimensions {lx}, {ly}, +{lz}, {yz}, {xz}, {xy}. :line diff --git a/doc/src/timer.txt b/doc/src/timer.txt index 768c3e1353..4025af9ea6 100644 --- a/doc/src/timer.txt +++ b/doc/src/timer.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -39,8 +39,8 @@ During a simulation run LAMMPS collects information about how much time is spent in different sections of the code and thus can provide information for determining performance and load imbalance problems. This can be done at different levels of detail and accuracy. For more -information about the timing output, see this "discussion of screen -output in Section 2.7"_Section_start.html#start_7. +information about the timing output, see the "Run +output"_Run_output.html doc page. The {off} setting will turn all time measurements off. The {loop} setting will only measure the total time for a run and not collect any diff --git a/doc/src/timestep.txt b/doc/src/timestep.txt index 639ad6f311..ee0ace05b9 100644 --- a/doc/src/timestep.txt +++ b/doc/src/timestep.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/tutorials.txt b/doc/src/tutorials.txt deleted file mode 100644 index 338439ac8e..0000000000 --- a/doc/src/tutorials.txt +++ /dev/null @@ -1,15 +0,0 @@ -Tutorials :h1 - - diff --git a/doc/src/uncompute.txt b/doc/src/uncompute.txt index 49b46781d7..4c788d4722 100644 --- a/doc/src/uncompute.txt +++ b/doc/src/uncompute.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/undump.txt b/doc/src/undump.txt index a2a371aca5..cc3d8b9103 100644 --- a/doc/src/undump.txt +++ b/doc/src/undump.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/unfix.txt b/doc/src/unfix.txt index dcc4499b20..9608b39c7e 100644 --- a/doc/src/unfix.txt +++ b/doc/src/unfix.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/units.txt b/doc/src/units.txt index 0b856dcc68..8df8fe6810 100644 --- a/doc/src/units.txt +++ b/doc/src/units.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/variable.txt b/doc/src/variable.txt index 717c77c079..a8d50503ac 100644 --- a/doc/src/variable.txt +++ b/doc/src/variable.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -124,8 +124,8 @@ provide, so that the variable gets its value from the evaluation of the Python code. Variables of style {internal} are used by a few commands which set their value directly. -NOTE: As discussed in "Section 3.2"_Section_commands.html#cmd_2 of the -manual, an input script can use "immediate" variables, specified as +NOTE: As discussed on the "Commands parse"_Commands_parse.html doc +page, an input script can use "immediate" variables, specified as $(formula) with parenthesis, where the formula has the same syntax as equal-style variables described on this page. This is a convenient way to evaluate a formula immediately without using the variable @@ -178,9 +178,8 @@ This means variables can NOT be re-defined in an input script (with two exceptions, read further). This is to allow an input script to be processed multiple times without resetting the variables; see the "jump"_jump.html or "include"_include.html commands. It also means -that using the "command-line switch"_Section_start.html#start_6 -var -will override a corresponding index variable setting in the input -script. +that using the "command-line switch"_Run_options.html -var will +override a corresponding index variable setting in the input script. There are two exceptions to this rule. First, variables of style {string}, {getenv}, {internal}, {equal}, {vector}, {atom}, and @@ -198,7 +197,7 @@ the same thing. :line -"This section"_Section_commands.html#cmd_2 of the manual explains how +The "Commands parse"_Commands_parse.html doc page explains how occurrences of a variable name in an input script line are replaced by the variable's string. The variable name can be referenced as $x if the name "x" is a single character, or as $\{LoopVar\} if the name @@ -247,8 +246,7 @@ string is assigned. All processors assign the same string to the variable. {Index} style variables with a single string value can also be set by -using the command-line switch -var; see "this -section"_Section_start.html#start_6 for details. +using the "command-line switch -var"_Run_options.html. The {loop} style is identical to the {index} style except that the strings are the integers from 1 to N inclusive, if only one argument N @@ -263,32 +261,31 @@ inclusive, and the string N1 is initially assigned to the variable. N1 <= N2 and N2 >= 0 is required. For the {world} style, one or more strings are specified. There must -be one string for each processor partition or "world". See "this -section"_Section_start.html#start_6 of the manual for information on -running LAMMPS with multiple partitions via the "-partition" -command-line switch. This variable command assigns one string to each -world. All processors in the world are assigned the same string. The -next command cannot be used with {equal} style variables, since there -is only one value per world. This style of variable is useful when -you wish to run different simulations on different partitions, or when -performing a parallel tempering simulation (see the +be one string for each processor partition or "world". LAMMPS can be +run with multiple partitions via the "-partition command-line +switch"_Run_options.html. This variable command assigns one string to +each world. All processors in the world are assigned the same string. +The next command cannot be used with {equal} style variables, since +there is only one value per world. This style of variable is useful +when you wish to run different simulations on different partitions, or +when performing a parallel tempering simulation (see the "temper"_temper.html command), to assign different temperatures to different partitions. For the {universe} style, one or more strings are specified. There must be at least as many strings as there are processor partitions or -"worlds". See "this page"_Section_start.html#start_6 for information -on running LAMMPS with multiple partitions via the "-partition" -command-line switch. This variable command initially assigns one -string to each world. When a "next"_next.html command is encountered -using this variable, the first processor partition to encounter it, is -assigned the next available string. This continues until all the -variable strings are consumed. Thus, this command can be used to run -50 simulations on 8 processor partitions. The simulations will be run -one after the other on whatever partition becomes available, until -they are all finished. {Universe} style variables are incremented -using the files "tmp.lammps.variable" and "tmp.lammps.variable.lock" -which you will see in your directory during such a LAMMPS run. +"worlds". LAMMPS can be run with multiple partitions via the +"-partition command-line switch"_Run_options.html. This variable +command initially assigns one string to each world. When a +"next"_next.html command is encountered using this variable, the first +processor partition to encounter it, is assigned the next available +string. This continues until all the variable strings are consumed. +Thus, this command can be used to run 50 simulations on 8 processor +partitions. The simulations will be run one after the other on +whatever partition becomes available, until they are all finished. +{Universe} style variables are incremented using the files +"tmp.lammps.variable" and "tmp.lammps.variable.lock" which you will +see in your directory during such a LAMMPS run. The {uloop} style is identical to the {universe} style except that the strings are the integers from 1 to N. This allows generation of long @@ -312,8 +309,8 @@ If you simply wish to print a variable value with desired precision to the screen or logfile via the "print"_print.html or "fix print"_fix_print.html commands, you can also do this by specifying an "immediate" variable with a trailing colon and format string, as part -of the string argument of those commands. This is explained in -"Section 3.2"_Section_commands.html#cmd_2. +of the string argument of those commands. This is explained on the +"Commands parse"_Commands_parse.html doc page. For the {getenv} style, a single string is assigned to the variable which should be the name of an environment variable. When the @@ -1119,24 +1116,23 @@ Vectors" discussion above. If you want an equal-style variable to be evaluated immediately, it may be the case that you do not need to define a variable at all. See -"Section 3.2"_Section_commands.html#cmd_2 of the manual, which -describes the use of "immediate" variables in an input script, -specified as $(formula) with parenthesis, where the formula has the -same syntax as equal-style variables described on this page. This -effectively evaluates a formula immediately without using the variable -command to define a named variable. +the "Commands parse"_Commands_parse.html doc page for info on how to +use "immediate" variables in an input script, specified as $(formula) +with parenthesis, where the formula has the same syntax as equal-style +variables described on this page. This effectively evaluates a +formula immediately without using the variable command to define a +named variable. More generally, there is a difference between referencing a variable with a leading $ sign (e.g. $x or $\{abc\}) versus with a leading "v_" (e.g. v_x or v_abc). The former can be used in any input script command, including a variable command. The input script parser evaluates the reference variable immediately and substitutes its value -into the command. As explained in "Section -3.2"_Section_commands.html#cmd_2 for "Parsing rules", you can also use -un-named "immediate" variables for this purpose. For example, a -string like this $((xlo+xhi)/2+sqrt(v_area)) in an input script -command evaluates the string between the parenthesis as an equal-style -variable formula. +into the command. As explained on the "Commands +parse"_Commands_parse.html doc page, you can also use un-named +"immediate" variables for this purpose. For example, a string like +this $((xlo+xhi)/2+sqrt(v_area)) in an input script command evaluates +the string between the parenthesis as an equal-style variable formula. Referencing a variable with a leading "v_" is an optional or required kind of argument for some commands (e.g. the "fix @@ -1180,10 +1176,9 @@ quotes if it contains variables preceded by $ signs. For example, variable vratio equal "$\{vfinal\}/$\{v0\}" :pre -This is because the quotes prevent variable substitution (see "this -section"_Section_commands.html#cmd_2 on parsing input script -commands), and thus an error will occur when the formula for "vratio" -is evaluated later. +This is because the quotes prevent variable substitution (explained on +the "Commands parse"_Commands_parse.html doc page), and thus an error +will occur when the formula for "vratio" is evaluated later. :line diff --git a/doc/src/velocity.txt b/doc/src/velocity.txt index b8299a5acf..96d3fa6dc4 100644 --- a/doc/src/velocity.txt +++ b/doc/src/velocity.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -139,10 +139,9 @@ if rot = yes, the angular momentum is zeroed. If specified, the {temp} keyword is used by {create} and {scale} to specify a "compute"_compute.html that calculates temperature in a desired way, e.g. by first subtracting out a velocity bias, as -discussed in "Section 6.16"_Section_howto.html#howto_16 of the doc -pages. If this keyword is not specified, {create} and {scale} -calculate temperature using a compute that is defined internally as -follows: +discussed on the "Howto thermostat"_Howto_thermostat.html doc page. +If this keyword is not specified, {create} and {scale} calculate +temperature using a compute that is defined internally as follows: compute velocity_temp group-ID temp :pre @@ -161,11 +160,11 @@ The {bias} keyword with a {yes} setting is used by {create} and If the temperature compute also calculates a velocity bias, the the bias is subtracted from atom velocities before the {create} and {scale} operations are performed. After the operations, the bias is -added back to the atom velocities. See "Section -6.16"_Section_howto.html#howto_16 of the doc pages for more discussion -of temperature computes with biases. Note that the velocity bias is -only applied to atoms in the temperature compute specified with the -{temp} keyword. +added back to the atom velocities. See the "Howto +thermostat"_Howto_thermostat.html doc page for more discussion of +temperature computes with biases. Note that the velocity bias is only +applied to atoms in the temperature compute specified with the {temp} +keyword. As an example, assume atoms are currently streaming in a flow direction (which could be separately initialized with the {ramp} diff --git a/doc/src/write_coeff.txt b/doc/src/write_coeff.txt index 764e119a9d..5dc4b331de 100644 --- a/doc/src/write_coeff.txt +++ b/doc/src/write_coeff.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/write_data.txt b/doc/src/write_data.txt index c76f20319c..b6002b5252 100644 --- a/doc/src/write_data.txt +++ b/doc/src/write_data.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -60,7 +60,7 @@ If you want to do more exact restarts, using binary files, see the "restart"_restart.html, "write_restart"_write_restart.html, and "read_restart"_read_restart.html commands. You can also convert binary restart files to text data files, after a simulation has run, -using the "-r command-line switch"_Section_start.html#start_6. +using the "-r command-line switch"_Run_options.html. NOTE: Only limited information about a simulation is stored in a data file. For example, no information about atom "groups"_group.html and diff --git a/doc/src/write_dump.txt b/doc/src/write_dump.txt index 840716085f..e676979001 100644 --- a/doc/src/write_dump.txt +++ b/doc/src/write_dump.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/write_restart.txt b/doc/src/write_restart.txt index ff3b652dba..c393c7f735 100644 --- a/doc/src/write_restart.txt +++ b/doc/src/write_restart.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -66,8 +66,7 @@ Restart files can be read by a "read_restart"_read_restart.html command to restart a simulation from a particular state. Because the file is binary (to enable exact restarts), it may not be readable on another machine. In this case, you can use the "-r command-line -switch"_Section_start.html#start_6 to convert a restart file to a data -file. +switch"_Run_options.html to convert a restart file to a data file. NOTE: Although the purpose of restart files is to enable restarting a simulation from where it left off, not all information about a diff --git a/doc/utils/converters/lammpsdoc/lammps_filters.py b/doc/utils/converters/lammpsdoc/lammps_filters.py index 11460185db..7b1481ceb9 100644 --- a/doc/utils/converters/lammpsdoc/lammps_filters.py +++ b/doc/utils/converters/lammpsdoc/lammps_filters.py @@ -64,7 +64,7 @@ def filter_file_header_until_first_horizontal_line(content): common_links = "\n.. _lws: http://lammps.sandia.gov\n" \ ".. _ld: Manual.html\n" \ - ".. _lc: Section_commands.html#comm\n" + ".. _lc: Commands_all.html\n" if first_hr >= 0: return content[first_hr+len(hr):].lstrip() + common_links diff --git a/doc/utils/converters/lammpsdoc/txt2html.py b/doc/utils/converters/lammpsdoc/txt2html.py index 79a75d72f6..ed9f47a4e4 100755 --- a/doc/utils/converters/lammpsdoc/txt2html.py +++ b/doc/utils/converters/lammpsdoc/txt2html.py @@ -662,14 +662,15 @@ class TxtConverter: parser = self.get_argument_parser() parsed_args = parser.parse_args(args) - write_to_files = len(parsed_args.files) > 1 + write_to_files = parsed_args.output_dir or (len(parsed_args.files) > 1) for filename in parsed_args.files: if parsed_args.skip_files and filename in parsed_args.skip_files: continue with open(filename, 'r') as f: - print("Converting", filename, "...", file=err) + if parsed_args.verbose: + print("Converting", filename, "...", file=err) content = f.read() converter = self.create_converter(parsed_args) @@ -683,7 +684,10 @@ class TxtConverter: result = msg if write_to_files: - output_filename = self.get_output_filename(filename) + if parsed_args.output_dir: + output_filename = os.path.join(parsed_args.output_dir, os.path.basename(self.get_output_filename(filename))) + else: + output_filename = self.get_output_filename(filename) with open(output_filename, "w+t") as outfile: outfile.write(result) else: @@ -698,6 +702,8 @@ class Txt2HtmlConverter(TxtConverter): 'HTML file. useful when set of HTML files' ' will be converted to PDF') parser.add_argument('-x', metavar='file-to-skip', dest='skip_files', action='append') + parser.add_argument('--verbose', '-v', dest='verbose', action='store_true') + parser.add_argument('--output-directory', '-o', dest='output_dir') parser.add_argument('--generate-title', dest='create_title', action='store_true', help='add HTML head page' 'title based on first ' 'h1,h2,h3,h4... element') diff --git a/doc/utils/converters/lammpsdoc/txt2rst.py b/doc/utils/converters/lammpsdoc/txt2rst.py index 17d0916157..8119ad3a78 100755 --- a/doc/utils/converters/lammpsdoc/txt2rst.py +++ b/doc/utils/converters/lammpsdoc/txt2rst.py @@ -395,6 +395,8 @@ class Txt2RstConverter(TxtConverter): parser = argparse.ArgumentParser(description='converts a text file with simple formatting & markup into ' 'Restructured Text for Sphinx.') parser.add_argument('-x', metavar='file-to-skip', dest='skip_files', action='append') + parser.add_argument('--verbose', '-v', dest='verbose', action='store_true') + parser.add_argument('--output-directory', '-o', dest='output_dir') parser.add_argument('files', metavar='file', nargs='+', help='one or more files to convert') return parser diff --git a/doc/utils/converters/tests/test_lammps_filters.py b/doc/utils/converters/tests/test_lammps_filters.py index 6c25c23a79..8d2fa2e577 100644 --- a/doc/utils/converters/tests/test_lammps_filters.py +++ b/doc/utils/converters/tests/test_lammps_filters.py @@ -47,7 +47,7 @@ class TestStructuralFilters(unittest.TestCase): self.assertEqual("Title\n\n" "\n.. _lws: http://lammps.sandia.gov\n" ".. _ld: Manual.html\n" - ".. _lc: Section_commands.html#comm\n", s) + ".. _lc: Commands_all.html\n", s) def test_filter_multiple_horizontal_rules(self): s = self.txt2rst.convert(":hline\n" diff --git a/doc/utils/requirements.txt b/doc/utils/requirements.txt new file mode 100644 index 0000000000..2806c16498 --- /dev/null +++ b/doc/utils/requirements.txt @@ -0,0 +1 @@ +Sphinx diff --git a/doc/utils/sphinx-config/_themes/lammps_theme/breadcrumbs.html b/doc/utils/sphinx-config/_themes/lammps_theme/breadcrumbs.html index 39ee684a0b..1eb53c70a2 100644 --- a/doc/utils/sphinx-config/_themes/lammps_theme/breadcrumbs.html +++ b/doc/utils/sphinx-config/_themes/lammps_theme/breadcrumbs.html @@ -18,7 +18,7 @@ View page source {% endif %} Website - Commands + Commands {% endif %} diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index fb08e4e97e..febd5c20a0 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -260,6 +260,8 @@ Caro cartesian Cates cbecker +ccache +ccmake CCu cd cdeam @@ -286,6 +288,9 @@ cgs Chalopin Champaign charmm +charmmfsw +charmmfsh +charmm CHARMM checkmark checkqeq @@ -308,6 +313,8 @@ Clebsch Clermont clo Clovertown +cmake +CMake cmap Cmax cmdlist @@ -410,6 +417,7 @@ Cval cvar cvff cwiggle +cygwin Cygwin Cyrot cyrstals @@ -585,6 +593,7 @@ ehanced ehex eHEX Ei +Eigen Eigensolve Eike eim @@ -713,7 +722,10 @@ fhg Fi figshare Fij -filenname +filename +filenames +Filename +Filenames fileper Fincham Finchham @@ -1385,6 +1397,7 @@ Mikami Militzer Minary mincap +mingw minima minimizations minimizer @@ -1456,6 +1469,7 @@ Mtotal Muccioli Mukherjee Mulders +multi multibody Multibody multicenter @@ -2489,6 +2503,7 @@ velocites Verlag verlet Verlet +versa ves vhi vibrational @@ -2566,6 +2581,7 @@ whitespace Wi Wicaksono wih +wildcard Wirnsberger wirtes witin diff --git a/doc/utils/txt2html/txt2html b/doc/utils/txt2html/txt2html new file mode 100755 index 0000000000..023631eac1 Binary files /dev/null and b/doc/utils/txt2html/txt2html differ diff --git a/examples/COUPLE/README b/examples/COUPLE/README index 83e7463531..0e611befbd 100644 --- a/examples/COUPLE/README +++ b/examples/COUPLE/README @@ -10,6 +10,7 @@ See these sections of the LAMMPS manaul for details: 2.5 Building LAMMPS as a library (doc/Section_start.html#start_5) 6.10 Coupling LAMMPS to other codes (doc/Section_howto.html#howto_10) +6.29 Using LAMMPS in client/server mode (doc/Section_howto.html#howto_29) In all of the examples included here, LAMMPS must first be built as a library. Basically, in the src dir you type one of @@ -33,9 +34,13 @@ These are the sub-directories included in this directory: simple simple example of driver code calling LAMMPS as a lib multiple example of driver code calling multiple instances of LAMMPS +lammps_mc client/server coupling of Monte Carlo client + with LAMMPS server for energy evaluation lammps_quest MD with quantum forces, coupling to Quest DFT code lammps_spparks grain-growth Monte Carlo with strain via MD, coupling to SPPARKS kinetic MC code +lammps_vasp client/server coupling of LAMMPS client with + VASP quantum DFT as server for quantum forces library collection of useful inter-code communication routines fortran a simple wrapper on the LAMMPS library API that can be called from Fortran diff --git a/examples/COUPLE/lammps_mc/Makefile b/examples/COUPLE/lammps_mc/Makefile new file mode 100644 index 0000000000..c75bd08c73 --- /dev/null +++ b/examples/COUPLE/lammps_mc/Makefile @@ -0,0 +1,33 @@ +# Makefile for MC + +SHELL = /bin/sh + +SRC = mc.cpp random_park.cpp +OBJ = $(SRC:.cpp=.o) + +# change this line for your machine to path for CSlib src dir + +CSLIB = /home/sjplimp/lammps/lib/message/cslib/src + +# compiler/linker settings + +CC = g++ +CCFLAGS = -g -O3 -I$(CSLIB) +LINK = g++ +LINKFLAGS = -g -O -L$(CSLIB) + +# targets + +mc: $(OBJ) +# first line if built the CSlib within lib/message with ZMQ support +# second line if built the CSlib without ZMQ support + $(LINK) $(LINKFLAGS) $(OBJ) -lcsnompi -lzmq -o mc +# $(LINK) $(LINKFLAGS) $(OBJ) -lcsnompi -o mc + +clean: + @rm -f *.o mc + +# rules + +%.o:%.cpp + $(CC) $(CCFLAGS) -c $< diff --git a/examples/COUPLE/lammps_mc/README b/examples/COUPLE/lammps_mc/README new file mode 100644 index 0000000000..c201a6351c --- /dev/null +++ b/examples/COUPLE/lammps_mc/README @@ -0,0 +1,128 @@ +Sample Monte Carlo (MC) wrapper on LAMMPS via client/server coupling + +See the MESSAGE package (doc/Section_messages.html#MESSAGE) +and Section_howto.html#howto10 for more details on how +client/server coupling works in LAMMPS. + +In this dir, the mc.cpp/h files are a standalone "client" MC code. It +should be run on a single processor, though it could become a parallel +program at some point. LAMMPS is also run as a standalone executable +as a "server" on as many processors as desired using its "server mc" +command; see it's doc page for details. + +Messages are exchanged between MC and LAMMPS via a client/server +library (CSlib), which is included in the LAMMPS distribution in +lib/message. As explained below you can choose to exchange data +between the two programs either via files or sockets (ZMQ). If the MC +program became parallel, data could also be exchanged via MPI. + +The MC code makes simple MC moves, by displacing a single random atom +by a small random amount. It uses LAMMPS to calculate the energy +change, and to run dynamics between MC moves. + +---------------- + +Build LAMMPS with its MESSAGE package installed: + +See the Build extras doc page and its MESSAGE package +section for details. + +CMake: + +-D PKG_MESSAGE=yes # include the MESSAGE package +-D MESSAGE_ZMQ=value # build with ZeroMQ support, value = no (default) or yes + +Traditional make: + +% cd lammps/lib/message +% python Install.py -m -z # build CSlib with MPI and ZMQ support +% cd lammps/src +% make yes-message +% make mpi + +You can leave off the -z if you do not have ZMQ on your system. + +---------------- + +Build the MC client code + +The source files for the MC code are in this dir. It links with the +CSlib library in lib/message/cslib. + +You must first build the CSlib in serial mode, e.g. + +% cd lammps/lib/message/cslib/src +% make lib # build serial and parallel lib with ZMQ support +% make lib zmq=no # build serial and parallel lib without ZMQ support + +Then edit the Makefile in this dir. The CSLIB variable should be the +path to where the LAMMPS lib/message/cslib/src dir is on your system. +If you built the CSlib without ZMQ support you will also need to +comment/uncomment one line. Then you can just type + +% make + +and you should get an "mc" executable. + +---------------- + +To run in client/server mode: + +Both the client (MC) and server (LAMMPS) must use the same messaging +mode, namely file or zmq. This is an argument to the MC code; it can +be selected by setting the "mode" variable when you run LAMMPS. The +default mode = file. + +Here we assume LAMMPS was built to run in parallel, and the MESSAGE +package was installed with socket (ZMQ) support. This means either of +the messaging modes can be used and LAMMPS can be run in serial or +parallel. The MC code is always run in serial. + +When you run, the server should print out thermodynamic info +for every MD run it performs (between MC moves). The client +will print nothing until the simulation ends, then it will +print stats about the accepted MC moves. + +The examples below are commands you should use in two different +terminal windows. The order of the two commands (client or server +launch) does not matter. You can run them both in the same window if +you append a "&" character to the first one to run it in the +background. + +-------------- + +File mode of messaging: + +% mpirun -np 1 mc in.mc file tmp.couple +% mpirun -np 1 lmp_mpi -v mode file < in.mc.server + +% mpirun -np 1 mc in.mc file tmp.couple +% mpirun -np 4 lmp_mpi -v mode file < in.mc.server + +ZMQ mode of messaging: + +% mpirun -np 1 mc in.mc zmq localhost:5555 +% mpirun -np 1 lmp_mpi -v mode zmq < in.mc.server + +% mpirun -np 1 mc in.mc zmq localhost:5555 +% mpirun -np 4 lmp_mpi -v mode zmq < in.mc.server + +-------------- + +The input script for the MC program is in.mc. You can edit it to run +longer simulations. + +500 nsteps = total # of steps of MD +100 ndynamics = # of MD steps between MC moves +0.1 delta = displacement size of MC move +1.0 temperature = used in MC Boltzman factor +12345 seed = random number seed + +-------------- + +The problem size that LAMMPS is computing the MC energy for and +running dynamics on is set by the x,y,z variables in the LAMMPS +in.mc.server script. The default size is 500 particles. You can +adjust the size as follows: + +lmp_mpi -v x 10 -v y 10 -v z 20 # 8000 particles diff --git a/examples/COUPLE/lammps_mc/in.mc b/examples/COUPLE/lammps_mc/in.mc new file mode 100644 index 0000000000..85052d09f1 --- /dev/null +++ b/examples/COUPLE/lammps_mc/in.mc @@ -0,0 +1,7 @@ +# MC params + +500 nsteps +100 ndynamics +0.1 delta +1.0 temperature +12345 seed diff --git a/examples/COUPLE/lammps_mc/in.mc.server b/examples/COUPLE/lammps_mc/in.mc.server new file mode 100644 index 0000000000..8b10bb0f7b --- /dev/null +++ b/examples/COUPLE/lammps_mc/in.mc.server @@ -0,0 +1,36 @@ +# 3d Lennard-Jones Monte Carlo server script + +variable mode index file + +if "${mode} == file" then & + "message server mc file tmp.couple" & +elif "${mode} == zmq" & + "message server mc zmq *:5555" & + +variable x index 5 +variable y index 5 +variable z index 5 + +units lj +atom_style atomic +atom_modify map yes + +lattice fcc 0.8442 +region box block 0 $x 0 $y 0 $z +create_box 1 box +create_atoms 1 box +mass 1 1.0 + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 20 check no + +velocity all create 1.44 87287 loop geom + +fix 1 all nve + +thermo 50 + +server mc diff --git a/examples/COUPLE/lammps_mc/log.28Aug18.file.g++.1 b/examples/COUPLE/lammps_mc/log.28Aug18.file.g++.1 new file mode 100644 index 0000000000..0d67c89cf1 --- /dev/null +++ b/examples/COUPLE/lammps_mc/log.28Aug18.file.g++.1 @@ -0,0 +1,254 @@ +LAMMPS (22 Aug 2018) +# 3d Lennard-Jones Monte Carlo server script + +variable mode index file + +if "${mode} == file" then "message server mc file tmp.couple" elif "${mode} == zmq" "message server mc zmq *:5555" +message server mc file tmp.couple +variable x index 5 +variable y index 5 +variable z index 5 + +units lj +atom_style atomic +atom_modify map yes + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 $x 0 $y 0 $z +region box block 0 5 0 $y 0 $z +region box block 0 5 0 5 0 $z +region box block 0 5 0 5 0 5 +create_box 1 box +Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 500 atoms + Time spent = 0.000649929 secs +mass 1 1.0 + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 20 check no + +velocity all create 1.44 87287 loop geom + +fix 1 all nve + +thermo 50 + +server mc +run 0 +Neighbor list info ... + update every 20 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.44 -6.7733681 0 -4.6176881 -5.0221006 +Loop time of 2.14577e-06 on 1 procs for 0 steps with 500 atoms + +93.2% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 2.146e-06 | | |100.00 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1956 ave 1956 max 1956 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 19500 ave 19500 max 19500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 19500 +Ave neighs/atom = 39 +Neighbor list builds = 0 +Dangerous builds not checked +run 0 +Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.44 -6.7723127 0 -4.6166327 -5.015531 +Loop time of 2.14577e-06 on 1 procs for 0 steps with 500 atoms + +93.2% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 2.146e-06 | | |100.00 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1956 ave 1956 max 1956 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 19501 ave 19501 max 19501 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 19501 +Ave neighs/atom = 39.002 +Neighbor list builds = 0 +Dangerous builds not checked +Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.44 -6.7723127 0 -4.6166327 -5.015531 + 50 0.70239211 -5.6763152 0 -4.6248342 0.59544428 + 100 0.7565013 -5.757431 0 -4.6249485 0.21982657 +run 0 +Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes +Step Temp E_pair E_mol TotEng Press + 100 0.7565013 -5.7565768 0 -4.6240944 0.22436405 +Loop time of 1.90735e-06 on 1 procs for 0 steps with 500 atoms + +157.3% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.907e-06 | | |100.00 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1939 ave 1939 max 1939 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 18757 ave 18757 max 18757 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 18757 +Ave neighs/atom = 37.514 +Neighbor list builds = 0 +Dangerous builds not checked +Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes +Step Temp E_pair E_mol TotEng Press + 100 0.7565013 -5.757431 0 -4.6249485 0.21982657 + 150 0.76110797 -5.7664315 0 -4.6270529 0.16005254 + 200 0.73505651 -5.7266069 0 -4.6262273 0.34189744 +run 0 +Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes +Step Temp E_pair E_mol TotEng Press + 200 0.73505651 -5.7181381 0 -4.6177585 0.37629943 +Loop time of 2.14577e-06 on 1 procs for 0 steps with 500 atoms + +139.8% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 2.146e-06 | | |100.00 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1899 ave 1899 max 1899 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 18699 ave 18699 max 18699 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 18699 +Ave neighs/atom = 37.398 +Neighbor list builds = 0 +Dangerous builds not checked +Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes +Step Temp E_pair E_mol TotEng Press + 200 0.73505651 -5.7266069 0 -4.6262273 0.34189744 + 250 0.73052476 -5.7206316 0 -4.627036 0.39287516 + 300 0.76300831 -5.7675007 0 -4.6252773 0.16312925 +run 0 +Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes +Step Temp E_pair E_mol TotEng Press + 300 0.76300831 -5.768304 0 -4.6260806 0.15954325 +Loop time of 2.14577e-06 on 1 procs for 0 steps with 500 atoms + +139.8% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 2.146e-06 | | |100.00 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1903 ave 1903 max 1903 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 18715 ave 18715 max 18715 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 18715 +Ave neighs/atom = 37.43 +Neighbor list builds = 0 +Dangerous builds not checked +Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes +Step Temp E_pair E_mol TotEng Press + 300 0.76300831 -5.768304 0 -4.6260806 0.15954325 + 350 0.72993309 -5.7193261 0 -4.6266162 0.3358374 + 400 0.72469448 -5.713463 0 -4.6285954 0.44859547 +run 0 +Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes +Step Temp E_pair E_mol TotEng Press + 400 0.72469448 -5.7077332 0 -4.6228655 0.47669832 +Loop time of 1.90735e-06 on 1 procs for 0 steps with 500 atoms + +157.3% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.907e-06 | | |100.00 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1899 ave 1899 max 1899 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 18683 ave 18683 max 18683 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 18683 +Ave neighs/atom = 37.366 +Neighbor list builds = 0 +Dangerous builds not checked +Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes +Step Temp E_pair E_mol TotEng Press + 400 0.72469448 -5.713463 0 -4.6285954 0.44859547 + 450 0.75305735 -5.7518283 0 -4.6245015 0.34658587 + 500 0.73092571 -5.7206337 0 -4.6264379 0.43715809 +Total wall time: 0:00:02 diff --git a/examples/COUPLE/lammps_mc/log.28Aug18.file.g++.4 b/examples/COUPLE/lammps_mc/log.28Aug18.file.g++.4 new file mode 100644 index 0000000000..2ae51d2461 --- /dev/null +++ b/examples/COUPLE/lammps_mc/log.28Aug18.file.g++.4 @@ -0,0 +1,254 @@ +LAMMPS (22 Aug 2018) +# 3d Lennard-Jones Monte Carlo server script + +variable mode index file + +if "${mode} == file" then "message server mc file tmp.couple" elif "${mode} == zmq" "message server mc zmq *:5555" +message server mc file tmp.couple +variable x index 5 +variable y index 5 +variable z index 5 + +units lj +atom_style atomic +atom_modify map yes + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 $x 0 $y 0 $z +region box block 0 5 0 $y 0 $z +region box block 0 5 0 5 0 $z +region box block 0 5 0 5 0 5 +create_box 1 box +Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 500 atoms + Time spent = 0.000592947 secs +mass 1 1.0 + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 20 check no + +velocity all create 1.44 87287 loop geom + +fix 1 all nve + +thermo 50 + +server mc +run 0 +Neighbor list info ... + update every 20 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.44 -6.7733681 0 -4.6176881 -5.0221006 +Loop time of 3.8147e-06 on 4 procs for 0 steps with 500 atoms + +59.0% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 3.815e-06 | | |100.00 + +Nlocal: 125 ave 125 max 125 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 1099 ave 1099 max 1099 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 4875 ave 4875 max 4875 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 19500 +Ave neighs/atom = 39 +Neighbor list builds = 0 +Dangerous builds not checked +run 0 +Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.44 -6.7723127 0 -4.6166327 -5.015531 +Loop time of 3.03984e-06 on 4 procs for 0 steps with 500 atoms + +106.9% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 3.04e-06 | | |100.00 + +Nlocal: 125 ave 125 max 125 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 1099 ave 1099 max 1099 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 4875.25 ave 4885 max 4866 min +Histogram: 1 0 0 0 2 0 0 0 0 1 + +Total # of neighbors = 19501 +Ave neighs/atom = 39.002 +Neighbor list builds = 0 +Dangerous builds not checked +Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.44 -6.7723127 0 -4.6166327 -5.015531 + 50 0.70210225 -5.6759068 0 -4.6248598 0.59609192 + 100 0.75891559 -5.7611234 0 -4.6250267 0.20841608 +run 0 +Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes +Step Temp E_pair E_mol TotEng Press + 100 0.75891559 -5.7609392 0 -4.6248426 0.20981291 +Loop time of 3.75509e-06 on 4 procs for 0 steps with 500 atoms + +113.2% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 3.755e-06 | | |100.00 + +Nlocal: 125 ave 126 max 124 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 1085.25 ave 1089 max 1079 min +Histogram: 1 0 0 0 0 1 0 0 0 2 +Neighs: 4690.25 ave 4996 max 4401 min +Histogram: 1 0 0 1 0 1 0 0 0 1 + +Total # of neighbors = 18761 +Ave neighs/atom = 37.522 +Neighbor list builds = 0 +Dangerous builds not checked +Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes +Step Temp E_pair E_mol TotEng Press + 100 0.75891559 -5.7609392 0 -4.6248426 0.20981291 + 150 0.75437991 -5.7558622 0 -4.6265555 0.20681722 + 200 0.73111257 -5.7193748 0 -4.6248993 0.35230715 +run 0 +Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes +Step Temp E_pair E_mol TotEng Press + 200 0.73111257 -5.7143906 0 -4.6199151 0.37126023 +Loop time of 2.563e-06 on 4 procs for 0 steps with 500 atoms + +117.1% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 2.563e-06 | | |100.00 + +Nlocal: 125 ave 126 max 123 min +Histogram: 1 0 0 0 0 0 1 0 0 2 +Nghost: 1068.5 ave 1076 max 1063 min +Histogram: 2 0 0 0 0 0 1 0 0 1 +Neighs: 4674.75 ave 4938 max 4419 min +Histogram: 1 0 0 0 1 1 0 0 0 1 + +Total # of neighbors = 18699 +Ave neighs/atom = 37.398 +Neighbor list builds = 0 +Dangerous builds not checked +Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes +Step Temp E_pair E_mol TotEng Press + 200 0.73111257 -5.7193748 0 -4.6248993 0.35230715 + 250 0.73873144 -5.7312505 0 -4.6253696 0.33061033 + 300 0.76392796 -5.7719207 0 -4.6283206 0.18197874 +run 0 +Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes +Step Temp E_pair E_mol TotEng Press + 300 0.76392796 -5.7725589 0 -4.6289588 0.17994628 +Loop time of 3.99351e-06 on 4 procs for 0 steps with 500 atoms + +93.9% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 3.994e-06 | | |100.00 + +Nlocal: 125 ave 128 max 121 min +Histogram: 1 0 0 0 0 1 0 1 0 1 +Nghost: 1069 ave 1080 max 1055 min +Histogram: 1 0 0 0 0 0 2 0 0 1 +Neighs: 4672 ave 4803 max 4600 min +Histogram: 2 0 0 1 0 0 0 0 0 1 + +Total # of neighbors = 18688 +Ave neighs/atom = 37.376 +Neighbor list builds = 0 +Dangerous builds not checked +Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes +Step Temp E_pair E_mol TotEng Press + 300 0.76392796 -5.7725589 0 -4.6289588 0.17994628 + 350 0.71953041 -5.7041632 0 -4.6270261 0.44866153 + 400 0.7319047 -5.7216051 0 -4.6259438 0.46321355 +run 0 +Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes +Step Temp E_pair E_mol TotEng Press + 400 0.7319047 -5.7158168 0 -4.6201554 0.49192039 +Loop time of 3.57628e-06 on 4 procs for 0 steps with 500 atoms + +111.8% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 3.576e-06 | | |100.00 + +Nlocal: 125 ave 132 max 118 min +Histogram: 1 0 0 0 0 2 0 0 0 1 +Nghost: 1057.5 ave 1068 max 1049 min +Histogram: 1 0 0 1 1 0 0 0 0 1 +Neighs: 4685.75 ave 5045 max 4229 min +Histogram: 1 0 0 1 0 0 0 0 0 2 + +Total # of neighbors = 18743 +Ave neighs/atom = 37.486 +Neighbor list builds = 0 +Dangerous builds not checked +Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes +Step Temp E_pair E_mol TotEng Press + 400 0.7319047 -5.7216051 0 -4.6259438 0.46321355 + 450 0.74503154 -5.7405318 0 -4.6252196 0.33211879 + 500 0.70570501 -5.6824439 0 -4.6260035 0.62020788 +Total wall time: 0:00:02 diff --git a/examples/COUPLE/lammps_mc/log.28Aug18.zmq.g++.1 b/examples/COUPLE/lammps_mc/log.28Aug18.zmq.g++.1 new file mode 100644 index 0000000000..0565487bc6 --- /dev/null +++ b/examples/COUPLE/lammps_mc/log.28Aug18.zmq.g++.1 @@ -0,0 +1,254 @@ +LAMMPS (22 Aug 2018) +# 3d Lennard-Jones Monte Carlo server script + +variable mode index file + +if "${mode} == file" then "message server mc file tmp.couple" elif "${mode} == zmq" "message server mc zmq *:5555" +message server mc zmq *:5555 +variable x index 5 +variable y index 5 +variable z index 5 + +units lj +atom_style atomic +atom_modify map yes + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 $x 0 $y 0 $z +region box block 0 5 0 $y 0 $z +region box block 0 5 0 5 0 $z +region box block 0 5 0 5 0 5 +create_box 1 box +Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 500 atoms + Time spent = 0.000741005 secs +mass 1 1.0 + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 20 check no + +velocity all create 1.44 87287 loop geom + +fix 1 all nve + +thermo 50 + +server mc +run 0 +Neighbor list info ... + update every 20 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.44 -6.7733681 0 -4.6176881 -5.0221006 +Loop time of 1.90735e-06 on 1 procs for 0 steps with 500 atoms + +52.4% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.907e-06 | | |100.00 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1956 ave 1956 max 1956 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 19500 ave 19500 max 19500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 19500 +Ave neighs/atom = 39 +Neighbor list builds = 0 +Dangerous builds not checked +run 0 +Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.44 -6.7723127 0 -4.6166327 -5.015531 +Loop time of 1.90735e-06 on 1 procs for 0 steps with 500 atoms + +52.4% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.907e-06 | | |100.00 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1956 ave 1956 max 1956 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 19501 ave 19501 max 19501 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 19501 +Ave neighs/atom = 39.002 +Neighbor list builds = 0 +Dangerous builds not checked +Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.44 -6.7723127 0 -4.6166327 -5.015531 + 50 0.70239211 -5.6763152 0 -4.6248342 0.59544428 + 100 0.7565013 -5.757431 0 -4.6249485 0.21982657 +run 0 +Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes +Step Temp E_pair E_mol TotEng Press + 100 0.7565013 -5.7565768 0 -4.6240944 0.22436405 +Loop time of 1.19209e-06 on 1 procs for 0 steps with 500 atoms + +83.9% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.192e-06 | | |100.00 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1939 ave 1939 max 1939 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 18757 ave 18757 max 18757 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 18757 +Ave neighs/atom = 37.514 +Neighbor list builds = 0 +Dangerous builds not checked +Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes +Step Temp E_pair E_mol TotEng Press + 100 0.7565013 -5.757431 0 -4.6249485 0.21982657 + 150 0.76110797 -5.7664315 0 -4.6270529 0.16005254 + 200 0.73505651 -5.7266069 0 -4.6262273 0.34189744 +run 0 +Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes +Step Temp E_pair E_mol TotEng Press + 200 0.73505651 -5.7181381 0 -4.6177585 0.37629943 +Loop time of 9.53674e-07 on 1 procs for 0 steps with 500 atoms + +209.7% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 9.537e-07 | | |100.00 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1899 ave 1899 max 1899 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 18699 ave 18699 max 18699 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 18699 +Ave neighs/atom = 37.398 +Neighbor list builds = 0 +Dangerous builds not checked +Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes +Step Temp E_pair E_mol TotEng Press + 200 0.73505651 -5.7266069 0 -4.6262273 0.34189744 + 250 0.73052476 -5.7206316 0 -4.627036 0.39287516 + 300 0.76300831 -5.7675007 0 -4.6252773 0.16312925 +run 0 +Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes +Step Temp E_pair E_mol TotEng Press + 300 0.76300831 -5.768304 0 -4.6260806 0.15954325 +Loop time of 9.53674e-07 on 1 procs for 0 steps with 500 atoms + +104.9% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 9.537e-07 | | |100.00 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1903 ave 1903 max 1903 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 18715 ave 18715 max 18715 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 18715 +Ave neighs/atom = 37.43 +Neighbor list builds = 0 +Dangerous builds not checked +Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes +Step Temp E_pair E_mol TotEng Press + 300 0.76300831 -5.768304 0 -4.6260806 0.15954325 + 350 0.72993309 -5.7193261 0 -4.6266162 0.3358374 + 400 0.72469448 -5.713463 0 -4.6285954 0.44859547 +run 0 +Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes +Step Temp E_pair E_mol TotEng Press + 400 0.72469448 -5.7077332 0 -4.6228655 0.47669832 +Loop time of 9.53674e-07 on 1 procs for 0 steps with 500 atoms + +209.7% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 9.537e-07 | | |100.00 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1899 ave 1899 max 1899 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 18683 ave 18683 max 18683 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 18683 +Ave neighs/atom = 37.366 +Neighbor list builds = 0 +Dangerous builds not checked +Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes +Step Temp E_pair E_mol TotEng Press + 400 0.72469448 -5.713463 0 -4.6285954 0.44859547 + 450 0.75305735 -5.7518283 0 -4.6245015 0.34658587 + 500 0.73092571 -5.7206337 0 -4.6264379 0.43715809 +Total wall time: 0:00:00 diff --git a/examples/COUPLE/lammps_mc/log.28Aug18.zmq.g++.4 b/examples/COUPLE/lammps_mc/log.28Aug18.zmq.g++.4 new file mode 100644 index 0000000000..e74d03235d --- /dev/null +++ b/examples/COUPLE/lammps_mc/log.28Aug18.zmq.g++.4 @@ -0,0 +1,254 @@ +LAMMPS (22 Aug 2018) +# 3d Lennard-Jones Monte Carlo server script + +variable mode index file + +if "${mode} == file" then "message server mc file tmp.couple" elif "${mode} == zmq" "message server mc zmq *:5555" +message server mc zmq *:5555 +variable x index 5 +variable y index 5 +variable z index 5 + +units lj +atom_style atomic +atom_modify map yes + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 $x 0 $y 0 $z +region box block 0 5 0 $y 0 $z +region box block 0 5 0 5 0 $z +region box block 0 5 0 5 0 5 +create_box 1 box +Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 500 atoms + Time spent = 0.000576019 secs +mass 1 1.0 + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 20 check no + +velocity all create 1.44 87287 loop geom + +fix 1 all nve + +thermo 50 + +server mc +run 0 +Neighbor list info ... + update every 20 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.44 -6.7733681 0 -4.6176881 -5.0221006 +Loop time of 4.76837e-06 on 4 procs for 0 steps with 500 atoms + +89.1% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 4.768e-06 | | |100.00 + +Nlocal: 125 ave 125 max 125 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 1099 ave 1099 max 1099 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 4875 ave 4875 max 4875 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 19500 +Ave neighs/atom = 39 +Neighbor list builds = 0 +Dangerous builds not checked +run 0 +Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.44 -6.7723127 0 -4.6166327 -5.015531 +Loop time of 3.45707e-06 on 4 procs for 0 steps with 500 atoms + +94.0% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 3.457e-06 | | |100.00 + +Nlocal: 125 ave 125 max 125 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 1099 ave 1099 max 1099 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 4875.25 ave 4885 max 4866 min +Histogram: 1 0 0 0 2 0 0 0 0 1 + +Total # of neighbors = 19501 +Ave neighs/atom = 39.002 +Neighbor list builds = 0 +Dangerous builds not checked +Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.44 -6.7723127 0 -4.6166327 -5.015531 + 50 0.70210225 -5.6759068 0 -4.6248598 0.59609192 + 100 0.75891559 -5.7611234 0 -4.6250267 0.20841608 +run 0 +Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes +Step Temp E_pair E_mol TotEng Press + 100 0.75891559 -5.7609392 0 -4.6248426 0.20981291 +Loop time of 3.03984e-06 on 4 procs for 0 steps with 500 atoms + +115.1% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 3.04e-06 | | |100.00 + +Nlocal: 125 ave 126 max 124 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 1085.25 ave 1089 max 1079 min +Histogram: 1 0 0 0 0 1 0 0 0 2 +Neighs: 4690.25 ave 4996 max 4401 min +Histogram: 1 0 0 1 0 1 0 0 0 1 + +Total # of neighbors = 18761 +Ave neighs/atom = 37.522 +Neighbor list builds = 0 +Dangerous builds not checked +Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes +Step Temp E_pair E_mol TotEng Press + 100 0.75891559 -5.7609392 0 -4.6248426 0.20981291 + 150 0.75437991 -5.7558622 0 -4.6265555 0.20681722 + 200 0.73111257 -5.7193748 0 -4.6248993 0.35230715 +run 0 +Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes +Step Temp E_pair E_mol TotEng Press + 200 0.73111257 -5.7143906 0 -4.6199151 0.37126023 +Loop time of 2.38419e-06 on 4 procs for 0 steps with 500 atoms + +125.8% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 2.384e-06 | | |100.00 + +Nlocal: 125 ave 126 max 123 min +Histogram: 1 0 0 0 0 0 1 0 0 2 +Nghost: 1068.5 ave 1076 max 1063 min +Histogram: 2 0 0 0 0 0 1 0 0 1 +Neighs: 4674.75 ave 4938 max 4419 min +Histogram: 1 0 0 0 1 1 0 0 0 1 + +Total # of neighbors = 18699 +Ave neighs/atom = 37.398 +Neighbor list builds = 0 +Dangerous builds not checked +Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes +Step Temp E_pair E_mol TotEng Press + 200 0.73111257 -5.7193748 0 -4.6248993 0.35230715 + 250 0.73873144 -5.7312505 0 -4.6253696 0.33061033 + 300 0.76392796 -5.7719207 0 -4.6283206 0.18197874 +run 0 +Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes +Step Temp E_pair E_mol TotEng Press + 300 0.76392796 -5.7725589 0 -4.6289588 0.17994628 +Loop time of 2.44379e-06 on 4 procs for 0 steps with 500 atoms + +112.5% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 2.444e-06 | | |100.00 + +Nlocal: 125 ave 128 max 121 min +Histogram: 1 0 0 0 0 1 0 1 0 1 +Nghost: 1069 ave 1080 max 1055 min +Histogram: 1 0 0 0 0 0 2 0 0 1 +Neighs: 4672 ave 4803 max 4600 min +Histogram: 2 0 0 1 0 0 0 0 0 1 + +Total # of neighbors = 18688 +Ave neighs/atom = 37.376 +Neighbor list builds = 0 +Dangerous builds not checked +Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes +Step Temp E_pair E_mol TotEng Press + 300 0.76392796 -5.7725589 0 -4.6289588 0.17994628 + 350 0.71953041 -5.7041632 0 -4.6270261 0.44866153 + 400 0.7319047 -5.7216051 0 -4.6259438 0.46321355 +run 0 +Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes +Step Temp E_pair E_mol TotEng Press + 400 0.7319047 -5.7158168 0 -4.6201554 0.49192039 +Loop time of 2.14577e-06 on 4 procs for 0 steps with 500 atoms + +139.8% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 2.146e-06 | | |100.00 + +Nlocal: 125 ave 132 max 118 min +Histogram: 1 0 0 0 0 2 0 0 0 1 +Nghost: 1057.5 ave 1068 max 1049 min +Histogram: 1 0 0 1 1 0 0 0 0 1 +Neighs: 4685.75 ave 5045 max 4229 min +Histogram: 1 0 0 1 0 0 0 0 0 2 + +Total # of neighbors = 18743 +Ave neighs/atom = 37.486 +Neighbor list builds = 0 +Dangerous builds not checked +Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes +Step Temp E_pair E_mol TotEng Press + 400 0.7319047 -5.7216051 0 -4.6259438 0.46321355 + 450 0.74503154 -5.7405318 0 -4.6252196 0.33211879 + 500 0.70570501 -5.6824439 0 -4.6260035 0.62020788 +Total wall time: 0:00:00 diff --git a/examples/COUPLE/lammps_mc/mc.cpp b/examples/COUPLE/lammps_mc/mc.cpp new file mode 100644 index 0000000000..7c2e2ce039 --- /dev/null +++ b/examples/COUPLE/lammps_mc/mc.cpp @@ -0,0 +1,263 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov +------------------------------------------------------------------------- */ + +// MC code used with LAMMPS in client/server mode +// MC is the client, LAMMPS is the server + +// Syntax: mc infile mode modearg +// mode = file, zmq +// modearg = filename for file, localhost:5555 for zmq + +#include +#include +#include +#include +#include "mc.h" +#include "random_park.h" + +#include "cslib.h" +using namespace CSLIB_NS; + +void error(const char *); +CSlib *cs_create(char *, char *); + +#define MAXLINE 256 + +/* ---------------------------------------------------------------------- */ + +// main program + +int main(int narg, char **arg) +{ + if (narg != 4) { + error("Syntax: mc infile mode modearg"); + exit(1); + } + + // initialize CSlib + + CSlib *cs = cs_create(arg[2],arg[3]); + + // create MC class and perform run + + MC *mc = new MC(arg[1],cs); + mc->run(); + + // final MC stats + + int naccept = mc->naccept; + int nattempt = mc->nattempt; + + printf("------ MC stats ------\n"); + printf("MC attempts = %d\n",nattempt); + printf("MC accepts = %d\n",naccept); + printf("Acceptance ratio = %g\n",1.0*naccept/nattempt); + + // clean up + + delete cs; + delete mc; +} + +/* ---------------------------------------------------------------------- */ + +void error(const char *str) +{ + printf("ERROR: %s\n",str); + exit(1); +} + +/* ---------------------------------------------------------------------- */ + +CSlib *cs_create(char *mode, char *arg) +{ + CSlib *cs = new CSlib(0,mode,arg,NULL); + + // initial handshake to agree on protocol + + cs->send(0,1); + cs->pack_string(1,(char *) "mc"); + + int msgID,nfield; + int *fieldID,*fieldtype,*fieldlen; + msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen); + + return cs; +} + +// ---------------------------------------------------------------------- +// MC class +// ---------------------------------------------------------------------- + +MC::MC(char *mcfile, void *cs_caller) +//MC::MC(char *mcfile, CSlib *cs_caller) +{ + cs_void = cs_caller; + + // setup MC params + + options(mcfile); + + // random # generator + + random = new RanPark(seed); +} + +/* ---------------------------------------------------------------------- */ + +MC::~MC() +{ + free(x); + delete random; +} + +/* ---------------------------------------------------------------------- */ + +void MC::run() +{ + int iatom,accept,msgID,nfield; + double pe_initial,pe_final,edelta; + double dx,dy,dz; + double xold[3],xnew[3]; + int *fieldID,*fieldtype,*fieldlen; + + enum{NATOMS=1,EINIT,DISPLACE,ACCEPT,RUN}; + + CSlib *cs = (CSlib *) cs_void; + + // one-time request for atom count from MD + // allocate 1d coord buffer + + cs->send(NATOMS,0); + + msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen); + natoms = cs->unpack_int(1); + + x = (double *) malloc(3*natoms*sizeof(double)); + + // loop over MC moves + + naccept = nattempt = 0; + + for (int iloop = 0; iloop < nloop; iloop++) { + + // request current energy from MD + // recv energy, coords from MD + + cs->send(EINIT,0); + + msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen); + pe_initial = cs->unpack_double(1); + double *x = (double *) cs->unpack(2); + + // perform simple MC event + // displace a single atom by random amount + + iatom = (int) natoms*random->uniform(); + xold[0] = x[3*iatom+0]; + xold[1] = x[3*iatom+1]; + xold[2] = x[3*iatom+2]; + + dx = 2.0*delta*random->uniform() - delta; + dy = 2.0*delta*random->uniform() - delta; + dz = 2.0*delta*random->uniform() - delta; + + xnew[0] = xold[0] + dx; + xnew[1] = xold[1] + dx; + xnew[2] = xold[2] + dx; + + // send atom ID and its new coords to MD + // recv new energy + + cs->send(DISPLACE,2); + cs->pack_int(1,iatom+1); + cs->pack(2,4,3,xnew); + + msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen); + pe_final = cs->unpack_double(1); + + // decide whether to accept/reject MC event + + if (pe_final <= pe_initial) accept = 1; + else if (temperature == 0.0) accept = 0; + else if (random->uniform() > + exp(natoms*(pe_initial-pe_final)/temperature)) accept = 0; + else accept = 1; + + nattempt++; + if (accept) naccept++; + + // send accept (1) or reject (0) flag to MD + + cs->send(ACCEPT,1); + cs->pack_int(1,accept); + + msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen); + + // send dynamics timesteps + + cs->send(RUN,1); + cs->pack_int(1,ndynamics); + + msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen); + } + + // send exit message to MD + + cs->send(-1,0); + msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen); +} + +/* ---------------------------------------------------------------------- */ + +void MC::options(char *filename) +{ + // default params + + nsteps = 0; + ndynamics = 100; + delta = 0.1; + temperature = 1.0; + seed = 12345; + + // read and parse file + + FILE *fp = fopen(filename,"r"); + if (fp == NULL) error("Could not open MC file"); + + char line[MAXLINE]; + char *keyword,*value; + char *eof = fgets(line,MAXLINE,fp); + + while (eof) { + if (line[0] == '#') { // comment line + eof = fgets(line,MAXLINE,fp); + continue; + } + + value = strtok(line," \t\n\r\f"); + if (value == NULL) { // blank line + eof = fgets(line,MAXLINE,fp); + continue; + } + + keyword = strtok(NULL," \t\n\r\f"); + if (keyword == NULL) error("Missing keyword in MC file"); + + if (strcmp(keyword,"nsteps") == 0) nsteps = atoi(value); + else if (strcmp(keyword,"ndynamics") == 0) ndynamics = atoi(value); + else if (strcmp(keyword,"delta") == 0) delta = atof(value); + else if (strcmp(keyword,"temperature") == 0) temperature = atof(value); + else if (strcmp(keyword,"seed") == 0) seed = atoi(value); + else error("Unknown param in MC file"); + + eof = fgets(line,MAXLINE,fp); + } + + // derived params + + nloop = nsteps/ndynamics; +} diff --git a/examples/COUPLE/lammps_mc/mc.h b/examples/COUPLE/lammps_mc/mc.h new file mode 100644 index 0000000000..e9d88523fc --- /dev/null +++ b/examples/COUPLE/lammps_mc/mc.h @@ -0,0 +1,40 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov +------------------------------------------------------------------------- */ + +#ifndef MC_H +#define MC_H + +/* ---------------------------------------------------------------------- */ + +class MC { + public: + int naccept; // # of accepted MC events + int nattempt; // # of attempted MC events + + MC(char *, void *); + ~MC(); + void run(); + + private: + int nsteps; // total # of MD steps + int ndynamics; // steps in one short dynamics run + int nloop; // nsteps/ndynamics + int natoms; // # of MD atoms + + double delta; // MC displacement distance + double temperature; // MC temperature for Boltzmann criterion + double *x; // atom coords as 3N 1d vector + double energy; // global potential energy + + int seed; // RNG seed + class RanPark *random; + + void *cs_void; // messaging library + + void options(char *); +}; + +#endif diff --git a/examples/COUPLE/lammps_mc/random_park.cpp b/examples/COUPLE/lammps_mc/random_park.cpp new file mode 100644 index 0000000000..61ac18c6c0 --- /dev/null +++ b/examples/COUPLE/lammps_mc/random_park.cpp @@ -0,0 +1,72 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +// Park/Miller RNG + +#include +#include "random_park.h" +//#include "error.h" + +#define IA 16807 +#define IM 2147483647 +#define AM (1.0/IM) +#define IQ 127773 +#define IR 2836 + +/* ---------------------------------------------------------------------- */ + +RanPark::RanPark(int seed_init) +{ + //if (seed_init <= 0) + // error->one(FLERR,"Invalid seed for Park random # generator"); + seed = seed_init; + save = 0; +} + +/* ---------------------------------------------------------------------- + uniform RN +------------------------------------------------------------------------- */ + +double RanPark::uniform() +{ + int k = seed/IQ; + seed = IA*(seed-k*IQ) - IR*k; + if (seed < 0) seed += IM; + double ans = AM*seed; + return ans; +} + +/* ---------------------------------------------------------------------- + gaussian RN +------------------------------------------------------------------------- */ + +double RanPark::gaussian() +{ + double first,v1,v2,rsq,fac; + + if (!save) { + do { + v1 = 2.0*uniform()-1.0; + v2 = 2.0*uniform()-1.0; + rsq = v1*v1 + v2*v2; + } while ((rsq >= 1.0) || (rsq == 0.0)); + fac = sqrt(-2.0*log(rsq)/rsq); + second = v1*fac; + first = v2*fac; + save = 1; + } else { + first = second; + save = 0; + } + return first; +} diff --git a/examples/COUPLE/lammps_mc/random_park.h b/examples/COUPLE/lammps_mc/random_park.h new file mode 100644 index 0000000000..0dc2081768 --- /dev/null +++ b/examples/COUPLE/lammps_mc/random_park.h @@ -0,0 +1,28 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifndef RANPARK_H +#define RANPARK_H + +class RanPark { + public: + RanPark(int); + double uniform(); + double gaussian(); + + private: + int seed,save; + double second; +}; + +#endif diff --git a/examples/COUPLE/lammps_vasp/INCAR b/examples/COUPLE/lammps_vasp/INCAR new file mode 100644 index 0000000000..ac2358e5fb --- /dev/null +++ b/examples/COUPLE/lammps_vasp/INCAR @@ -0,0 +1,53 @@ +# Startparameter for this run: + NWRITE = 2 write-flag & timer + PREC = normal normal or accurate (medium, high low for compatibility) + ISTART = 0 job : 0-new 1-cont 2-samecut + ICHARG = 2 charge: 1-file 2-atom 10-const + ISPIN = 1 spin polarized calculation? + LSORBIT = F spin-orbit coupling + INIWAV = 1 electr: 0-lowe 1-rand 2-diag + +# Electronic Relaxation 1 + ENCUT = 600.0 eV #Plane wave energy cutoff + ENINI = 600.0 initial cutoff + NELM = 100; NELMIN= 2; NELMDL= -5 # of ELM steps + EDIFF = 0.1E-05 stopping-criterion for ELM +# Ionic relaxation + EDIFFG = 0.1E-02 stopping-criterion for IOM + NSW = 0 number of steps for IOM + NBLOCK = 1; KBLOCK = 1 inner block; outer block + IBRION = -1 ionic relax: 0-MD 1-quasi-New 2-CG #No ion relaxation with -1 + NFREE = 0 steps in history (QN), initial steepest desc. (CG) + ISIF = 2 stress and relaxation # 2: F-yes Sts-yes RlxIon-yes cellshape-no cellvol-no + IWAVPR = 10 prediction: 0-non 1-charg 2-wave 3-comb # 10: TMPCAR stored in memory rather than file + + POTIM = 0.5000 time-step for ionic-motion + TEBEG = 3500.0; TEEND = 3500.0 temperature during run # Finite Temperature variables if AI-MD is on + SMASS = -3.00 Nose mass-parameter (am) + estimated Nose-frequenzy (Omega) = 0.10E-29 period in steps =****** mass= -0.366E-27a.u. + PSTRESS= 0.0 pullay stress + +# DOS related values: + EMIN = 10.00; EMAX =-10.00 energy-range for DOS + EFERMI = 0.00 + ISMEAR = 0; SIGMA = 0.10 broadening in eV -4-tet -1-fermi 0-gaus + +# Electronic relaxation 2 (details) + IALGO = 48 algorithm + +# Write flags + LWAVE = T write WAVECAR + LCHARG = T write CHGCAR + LVTOT = F write LOCPOT, total local potential + LVHAR = F write LOCPOT, Hartree potential only + LELF = F write electronic localiz. function (ELF) + +# Dipole corrections + LMONO = F monopole corrections only (constant potential shift) + LDIPOL = F correct potential (dipole corrections) + IDIPOL = 0 1-x, 2-y, 3-z, 4-all directions + EPSILON= 1.0000000 bulk dielectric constant + +# Exchange correlation treatment: + GGA = -- GGA type + diff --git a/examples/COUPLE/lammps_vasp/KPOINTS b/examples/COUPLE/lammps_vasp/KPOINTS new file mode 100644 index 0000000000..322509da30 --- /dev/null +++ b/examples/COUPLE/lammps_vasp/KPOINTS @@ -0,0 +1,6 @@ +K-Points + 0 +Monkhorst Pack + 15 15 15 + 0 0 0 + diff --git a/examples/COUPLE/lammps_vasp/POSCAR_W b/examples/COUPLE/lammps_vasp/POSCAR_W new file mode 100644 index 0000000000..aba5df54a0 --- /dev/null +++ b/examples/COUPLE/lammps_vasp/POSCAR_W @@ -0,0 +1,11 @@ +W unit cell +1.0 +3.16 0.00000000 0.00000000 +0.00000000 3.16 0.00000000 +0.00000000 0.00000000 3.16 +W +2 +Direct + 0.00000000 0.00000000 0.00000000 + 0.50000000 0.50000000 0.50000000 + diff --git a/examples/COUPLE/lammps_vasp/README b/examples/COUPLE/lammps_vasp/README new file mode 100644 index 0000000000..e942d52535 --- /dev/null +++ b/examples/COUPLE/lammps_vasp/README @@ -0,0 +1,149 @@ +Sample LAMMPS MD wrapper on VASP quantum DFT via client/server +coupling + +See the MESSAGE package (doc/Section_messages.html#MESSAGE) and +Section_howto.html#howto10 for more details on how client/server +coupling works in LAMMPS. + +In this dir, the vasp_wrap.py is a wrapper on the VASP quantum DFT +code so it can work as a "server" code which LAMMPS drives as a +"client" code to perform ab initio MD. LAMMPS performs the MD +timestepping, sends VASP a current set of coordinates each timestep, +VASP computes forces and energy and virial and returns that info to +LAMMPS. + +Messages are exchanged between MC and LAMMPS via a client/server +library (CSlib), which is included in the LAMMPS distribution in +lib/message. As explained below you can choose to exchange data +between the two programs either via files or sockets (ZMQ). If the +vasp_wrap.py program became parallel, or the CSlib library calls were +integrated into VASP directly, then data could also be exchanged via +MPI. + +---------------- + +Build LAMMPS with its MESSAGE package installed: + +See the Build extras doc page and its MESSAGE package +section for details. + +CMake: + +-D PKG_MESSAGE=yes # include the MESSAGE package +-D MESSAGE_ZMQ=value # build with ZeroMQ support, value = no (default) or yes + +Traditional make: + +cd lammps/lib/message +python Install.py -m -z # build CSlib with MPI and ZMQ support +cd lammps/src +make yes-message +make mpi + +You can leave off the -z if you do not have ZMQ on your system. + +---------------- + +Build the CSlib in a form usable by the vasp_wrapper.py script: + +% cd lammps/lib/message/cslib/src +% make shlib # build serial and parallel shared lib with ZMQ support +% make shlib zmq=no # build serial and parallel shared lib w/out ZMQ support + +This will make a shared library versions of the CSlib, which Python +requires. Python must be able to find both the cslib.py script and +the libcsnompi.so library in your lammps/lib/message/cslib/src +directory. If it is not able to do this, you will get an error when +you run vasp_wrapper.py. + +You can do this by augmenting two environment variables, either +from the command line, or in your shell start-up script. +Here is the sample syntax for the csh or tcsh shells: + +setenv PYTHONPATH ${PYTHONPATH}:/home/sjplimp/lammps/lib/message/cslib/src +setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/lib/message/cslib/src + +---------------- + +Prepare to use VASP and the vasp_wrapper.py script + +You can run the vasp_wrap.py script as-is to test that the coupling +between it and LAMMPS is functional. This will use the included +vasprun.xml file output by a previous VASP run. + +But note that the as-is version of vasp_wrap.py will not attempt to +run VASP. + +To do this, you must edit the 1st vaspcmd line at the top of +vasp_wrapper.py to be the launch command needed to run VASP on your +system. It can be a command to run VASP in serial or in parallel, +e.g. an mpirun command. Then comment out the 2nd vaspcmd line +immediately following it. + +Insure you have the necessary VASP input files in this +directory, suitable for the VASP calculation you want to perform: + +INCAR +KPOINTS +POSCAR_template +POTCAR + +Examples of all but the POTCAR file are provided. As explained below, +POSCAR_W is an input file for a 2-atom unit cell of tungsten and can +be used to test the LAMMPS/VASP coupling. The POTCAR file is a +proprietary VASP file, so use one from your VASP installation. + +Note that the POSCAR_template file should be matched to the LAMMPS +input script (# of atoms and atom types, box size, etc). The provided +POSCAR_W matches in.client.W. + +Once you run VASP yourself, the vasprun.xml file will be overwritten. + +---------------- + +To run in client/server mode: + +NOTE: The vasp_wrap.py script must be run with Python version 2, not +3. This is because it used the CSlib python wrapper, which only +supports version 2. We plan to upgrade CSlib to support Python 3. + +Both the client (LAMMPS) and server (vasp_wrap.py) must use the same +messaging mode, namely file or zmq. This is an argument to the +vasp_wrap.py code; it can be selected by setting the "mode" variable +when you run LAMMPS. The default mode = file. + +Here we assume LAMMPS was built to run in parallel, and the MESSAGE +package was installed with socket (ZMQ) support. This means either of +the messaging modes can be used and LAMMPS can be run in serial or +parallel. The vasp_wrap.py code is always run in serial, but it +launches VASP from Python via an mpirun command which can run VASP +itself in parallel. + +When you run, the server should print out thermodynamic info every +timestep which corresponds to the forces and virial computed by VASP. +VASP will also generate output files each timestep. The vasp_wrapper.py +script could be generalized to archive these. + +The examples below are commands you should use in two different +terminal windows. The order of the two commands (client or server +launch) does not matter. You can run them both in the same window if +you append a "&" character to the first one to run it in the +background. + +-------------- + +File mode of messaging: + +% mpirun -np 1 lmp_mpi -v mode file < in.client.W +% python vasp_wrap.py file POSCAR_W + +% mpirun -np 2 lmp_mpi -v mode file < in.client.W +% python vasp_wrap.py file POSCAR_W + +ZMQ mode of messaging: + +% mpirun -np 1 lmp_mpi -v mode zmq < in.client.W +% python vasp_wrap.py zmq POSCAR_W + +% mpirun -np 2 lmp_mpi -v mode zmq < in.client.W +% python vasp_wrap.py zmq POSCAR_W diff --git a/examples/COUPLE/lammps_vasp/data.W b/examples/COUPLE/lammps_vasp/data.W new file mode 100644 index 0000000000..8accd9ca79 --- /dev/null +++ b/examples/COUPLE/lammps_vasp/data.W @@ -0,0 +1,15 @@ +LAMMPS W data file + +2 atoms + +1 atom types + +0.0 3.16 xlo xhi +0.0 3.16 ylo yhi +0.0 3.16 zlo zhi + +Atoms + +1 1 0.000 0.000 0.000 +2 1 1.58 1.58 1.58 + diff --git a/examples/COUPLE/lammps_vasp/in.client.W b/examples/COUPLE/lammps_vasp/in.client.W new file mode 100644 index 0000000000..3eaf99dcbb --- /dev/null +++ b/examples/COUPLE/lammps_vasp/in.client.W @@ -0,0 +1,34 @@ +# small W unit cell for use with VASP + +variable mode index file + +if "${mode} == file" then & + "message client md file tmp.couple" & +elif "${mode} == zmq" & + "message client md zmq localhost:5555" & + +variable x index 1 +variable y index 1 +variable z index 1 + +units metal +atom_style atomic +atom_modify sort 0 0.0 map yes + +read_data data.W +mass 1 183.85 + +replicate $x $y $z + +velocity all create 300.0 87287 loop geom + +neighbor 0.3 bin +neigh_modify delay 0 every 10 check no + +fix 1 all nve +fix 2 all client/md +fix_modify 2 energy yes + +thermo 1 +run 3 + diff --git a/examples/COUPLE/lammps_vasp/log.client.output b/examples/COUPLE/lammps_vasp/log.client.output new file mode 100644 index 0000000000..fa8f4f920a --- /dev/null +++ b/examples/COUPLE/lammps_vasp/log.client.output @@ -0,0 +1,76 @@ +LAMMPS (22 Aug 2018) +# small W unit cell for use with VASP + +variable mode index file + +if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" +message client md zmq localhost:5555 +variable x index 1 +variable y index 1 +variable z index 1 + +units metal +atom_style atomic +atom_modify sort 0 0.0 map yes + +read_data data.W + orthogonal box = (0 0 0) to (3.16 3.16 3.16) + 1 by 1 by 2 MPI processor grid + reading atoms ... + 2 atoms +mass 1 183.85 + +replicate $x $y $z +replicate 1 $y $z +replicate 1 1 $z +replicate 1 1 1 + orthogonal box = (0 0 0) to (3.16 3.16 3.16) + 1 by 1 by 2 MPI processor grid + 2 atoms + Time spent = 0.000148058 secs + +velocity all create 300.0 87287 loop geom + +neighbor 0.3 bin +neigh_modify delay 0 every 10 check no + +fix 1 all nve +fix 2 all client/md +fix_modify 2 energy yes + +thermo 1 +run 3 +Per MPI rank memory allocation (min/avg/max) = 1.8 | 1.8 | 1.8 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 300 0 0 -48.030793 -78159.503 + 1 298.24318 0 0 -48.03102 -78167.19 + 2 296.85584 0 0 -48.031199 -78173.26 + 3 295.83795 0 0 -48.031331 -78177.714 +Loop time of 0.457491 on 2 procs for 3 steps with 2 atoms + +Performance: 0.567 ns/day, 42.360 hours/ns, 6.558 timesteps/s +50.1% CPU use with 2 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 1.3828e-05 | 2.9922e-05 | 4.6015e-05 | 0.0 | 0.01 +Output | 7.5817e-05 | 9.3937e-05 | 0.00011206 | 0.0 | 0.02 +Modify | 0.45735 | 0.45736 | 0.45736 | 0.0 | 99.97 +Other | | 1.204e-05 | | | 0.00 + +Nlocal: 1 ave 1 max 1 min +Histogram: 2 0 0 0 0 0 0 0 0 0 +Nghost: 4 ave 4 max 4 min +Histogram: 2 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds not checked + +Total wall time: 0:01:21 diff --git a/examples/COUPLE/lammps_vasp/vasp_wrap.py b/examples/COUPLE/lammps_vasp/vasp_wrap.py new file mode 100644 index 0000000000..1e2c52aa46 --- /dev/null +++ b/examples/COUPLE/lammps_vasp/vasp_wrap.py @@ -0,0 +1,300 @@ +#!/usr/bin/env python + +# ---------------------------------------------------------------------- +# LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator +# http://lammps.sandia.gov, Sandia National Laboratories +# Steve Plimpton, sjplimp@sandia.gov +# ---------------------------------------------------------------------- + +# Syntax: vasp_wrap.py file/zmq POSCARfile + +# wrapper on VASP to act as server program using CSlib +# receives message with list of coords from client +# creates VASP inputs +# invokes VASP to calculate self-consistent energy of that config +# reads VASP outputs +# sends message with energy, forces, pressure to client + +# NOTES: +# check to insure basic VASP input files are in place? +# could archive VASP input/output in special filenames or dirs? +# need to check that POTCAR file is consistent with atom ordering? +# could make syntax for launching VASP more flexible +# e.g. command-line arg for # of procs +# detect if VASP had an error and return ERROR field, e.g. non-convergence ?? + +from __future__ import print_function +import sys + +version = sys.version_info[0] +if version == 3: + sys.exit("The CSlib python wrapper does not yet support python 3") + +import subprocess +import xml.etree.ElementTree as ET +from cslib import CSlib + +# comment out 2nd line once 1st line is correct for your system + +vaspcmd = "srun -N 1 --ntasks-per-node=4 " + \ + "-n 4 /projects/vasp/2017-build/cts1/vasp5.4.4/vasp_tfermi/bin/vasp_std" +vaspcmd = "touch tmp" + +# enums matching FixClientMD class in LAMMPS + +SETUP,STEP = range(1,2+1) +DIM,PERIODICITY,ORIGIN,BOX,NATOMS,NTYPES,TYPES,COORDS,UNITS,CHARGE = range(1,10+1) +FORCES,ENERGY,VIRIAL,ERROR = range(1,4+1) + +# ------------------------------------- +# functions + +# error message and exit + +def error(txt): + print("ERROR:",txt) + sys.exit(1) + +# ------------------------------------- +# read initial VASP POSCAR file to setup problem +# return natoms,ntypes,box + +def vasp_setup(poscar): + + ps = open(poscar,'r').readlines() + + # box size + + words = ps[2].split() + xbox = float(words[0]) + words = ps[3].split() + ybox = float(words[1]) + words = ps[4].split() + zbox = float(words[2]) + box = [xbox,ybox,zbox] + + ntypes = 0 + natoms = 0 + words = ps[6].split() + for word in words: + if word == '#': break + ntypes += 1 + natoms += int(word) + + return natoms,ntypes,box + +# ------------------------------------- +# write a new POSCAR file for VASP + +def poscar_write(poscar,natoms,ntypes,types,coords,box): + + psold = open(poscar,'r').readlines() + psnew = open("POSCAR",'w') + + # header, including box size + + psnew.write(psold[0]) + psnew.write(psold[1]) + psnew.write("%g %g %g\n" % (box[0],box[1],box[2])) + psnew.write("%g %g %g\n" % (box[3],box[4],box[5])) + psnew.write("%g %g %g\n" % (box[6],box[7],box[8])) + psnew.write(psold[5]) + psnew.write(psold[6]) + + # per-atom coords + # grouped by types + + psnew.write("Cartesian\n") + + for itype in range(1,ntypes+1): + for i in range(natoms): + if types[i] != itype: continue + x = coords[3*i+0] + y = coords[3*i+1] + z = coords[3*i+2] + aline = " %g %g %g\n" % (x,y,z) + psnew.write(aline) + + psnew.close() + +# ------------------------------------- +# read a VASP output vasprun.xml file +# uses ElementTree module +# see https://docs.python.org/2/library/xml.etree.elementtree.html + +def vasprun_read(): + tree = ET.parse('vasprun.xml') + root = tree.getroot() + + #fp = open("vasprun.xml","r") + #root = ET.parse(fp) + + scsteps = root.findall('calculation/scstep') + energy = scsteps[-1].find('energy') + for child in energy: + if child.attrib["name"] == "e_0_energy": + eout = float(child.text) + + fout = [] + sout = [] + + varrays = root.findall('calculation/varray') + for varray in varrays: + if varray.attrib["name"] == "forces": + forces = varray.findall("v") + for line in forces: + fxyz = line.text.split() + fxyz = [float(value) for value in fxyz] + fout += fxyz + if varray.attrib["name"] == "stress": + tensor = varray.findall("v") + stensor = [] + for line in tensor: + sxyz = line.text.split() + sxyz = [float(value) for value in sxyz] + stensor.append(sxyz) + sxx = stensor[0][0] + syy = stensor[1][1] + szz = stensor[2][2] + # symmetrize off-diagonal components + sxy = 0.5 * (stensor[0][1] + stensor[1][0]) + sxz = 0.5 * (stensor[0][2] + stensor[2][0]) + syz = 0.5 * (stensor[1][2] + stensor[2][1]) + sout = [sxx,syy,szz,sxy,sxz,syz] + + #fp.close() + + return eout,fout,sout + +# ------------------------------------- +# main program + +# command-line args + +if len(sys.argv) != 3: + print("Syntax: python vasp_wrap.py file/zmq POSCARfile") + sys.exit(1) + +mode = sys.argv[1] +poscar_template = sys.argv[2] + +if mode == "file": cs = CSlib(1,mode,"tmp.couple",None) +elif mode == "zmq": cs = CSlib(1,mode,"*:5555",None) +else: + print("Syntax: python vasp_wrap.py file/zmq POSCARfile") + sys.exit(1) + +natoms,ntypes,box = vasp_setup(poscar_template) + +# initial message for MD protocol + +msgID,nfield,fieldID,fieldtype,fieldlen = cs.recv() +if msgID != 0: error("Bad initial client/server handshake") +protocol = cs.unpack_string(1) +if protocol != "md": error("Mismatch in client/server protocol") +cs.send(0,0) + +# endless server loop + +while 1: + + # recv message from client + # msgID = 0 = all-done message + + msgID,nfield,fieldID,fieldtype,fieldlen = cs.recv() + if msgID < 0: break + + # SETUP receive at beginning of each run + # required fields: DIM, PERIODICTY, ORIGIN, BOX, + # NATOMS, NTYPES, TYPES, COORDS + # optional fields: others in enum above, but VASP ignores them + + if msgID == SETUP: + + origin = [] + box = [] + natoms_recv = ntypes_recv = 0 + types = [] + coords = [] + + for field in fieldID: + if field == DIM: + dim = cs.unpack_int(DIM) + if dim != 3: error("VASP only performs 3d simulations") + elif field == PERIODICITY: + periodicity = cs.unpack(PERIODICITY,1) + if not periodicity[0] or not periodicity[1] or not periodicity[2]: + error("VASP wrapper only currently supports fully periodic systems") + elif field == ORIGIN: + origin = cs.unpack(ORIGIN,1) + elif field == BOX: + box = cs.unpack(BOX,1) + elif field == NATOMS: + natoms_recv = cs.unpack_int(NATOMS) + if natoms != natoms_recv: + error("VASP wrapper mis-match in number of atoms") + elif field == NTYPES: + ntypes_recv = cs.unpack_int(NTYPES) + if ntypes != ntypes_recv: + error("VASP wrapper mis-match in number of atom types") + elif field == TYPES: + types = cs.unpack(TYPES,1) + elif field == COORDS: + coords = cs.unpack(COORDS,1) + + if not origin or not box or not natoms or not ntypes or \ + not types or not coords: + error("Required VASP wrapper setup field not received"); + + # STEP receive at each timestep of run or minimization + # required fields: COORDS + # optional fields: ORIGIN, BOX + + elif msgID == STEP: + + coords = [] + + for field in fieldID: + if field == COORDS: + coords = cs.unpack(COORDS,1) + elif field == ORIGIN: + origin = cs.unpack(ORIGIN,1) + elif field == BOX: + box = cs.unpack(BOX,1) + + if not coords: error("Required VASP wrapper step field not received"); + + else: error("VASP wrapper received unrecognized message") + + # create POSCAR file + + poscar_write(poscar_template,natoms,ntypes,types,coords,box) + + # invoke VASP + + print("\nLaunching VASP ...") + print(vaspcmd) + subprocess.check_output(vaspcmd,stderr=subprocess.STDOUT,shell=True) + + # process VASP output + + energy,forces,virial = vasprun_read() + + # convert VASP kilobars to bars + + for i,value in enumerate(virial): virial[i] *= 1000.0 + + # return forces, energy, pressure to client + + cs.send(msgID,3); + cs.pack(FORCES,4,3*natoms,forces) + cs.pack_double(ENERGY,energy) + cs.pack(VIRIAL,4,6,virial) + +# final reply to client + +cs.send(0,0) + +# clean-up + +del cs diff --git a/examples/COUPLE/lammps_vasp/vasprun.xml b/examples/COUPLE/lammps_vasp/vasprun.xml new file mode 100644 index 0000000000..0f15c871b4 --- /dev/null +++ b/examples/COUPLE/lammps_vasp/vasprun.xml @@ -0,0 +1,12329 @@ + + + + vasp + 5.4.4.18Apr17-6-g9f103f2a35 + (build Aug 01 2017 10:32:50) complex parallel + LinuxIFC + 2017 12 19 + 15:22:45 + + + 0 + normal normal or accurate (medium, h + 48 + F + 1 + 2 + 1 + 100 + -5 + 2 + -1 + 0 + 0.00000100 + 0.00100000 + 0 + 2 + 10 + 1 + 1 + 600.00000000 + 600.00000000 + 0.50000000 + 3500.00000000 + 3500.00000000 + -3.00000000 + 10.00000000 + -10.00000000 + 0.00000000 + 0 + 0.10000000 + 2 + 0.00000000 + T + T + F + F + F + -1 0 0 0 + 100 + -- GGA type + F + F + 0 + 1.00000000 + + + + + 3.66961100 0.00000000 0.00000000 + 0.00000000 3.55744000 0.00000000 + 0.00000000 0.00000000 3.17678100 + + 41.47103646 + + 0.27250845 0.00000000 0.00000000 + 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0.00000000 0.00000000 + 0.00000000 0.28110102 0.00000000 + 0.00000000 0.00000000 0.31478405 + + + + 0.00000000 0.00000000 0.00000000 + 0.00000000 0.50000000 0.50000000 + 0.50000000 0.00000000 0.50000000 + 0.50000000 0.50000000 0.00000000 + + + diff --git a/examples/DIFFUSE/README b/examples/DIFFUSE/README index df2a675f73..e78ca2eacf 100644 --- a/examples/DIFFUSE/README +++ b/examples/DIFFUSE/README @@ -47,7 +47,7 @@ compute the diffusion coefficient. You can see that both measures give roughly the same answer and rapidly become roughly constant for the 100K step simulation. -Dcoeff = 0.36 +Dcoeff = 0.33 (2) in.vacf.2d @@ -58,4 +58,4 @@ that point in time, converted into the diffusion coefficient. You can see the VACF approach gives a more noise, fluctuating value for the diffusion coefficient, compared to the MSD approach. -Dcoeff = 0.25 to 0.45 +Dcoeff = ~0.25 diff --git a/examples/DIFFUSE/log.13Oct16.msd.2d.g++.8 b/examples/DIFFUSE/log.13Oct16.msd.2d.g++.8 deleted file mode 100644 index 473aa56527..0000000000 --- a/examples/DIFFUSE/log.13Oct16.msd.2d.g++.8 +++ /dev/null @@ -1,245 +0,0 @@ -LAMMPS (13 Oct 2016) -# sample LAMMPS input script for diffusion of 2d LJ liquid -# mean-squared displacement via compute msd - -# settings - -variable x equal 40 -variable y equal 40 - -variable rho equal 0.6 -variable t equal 1.0 -variable rc equal 2.5 - -# problem setup - -units lj -dimension 2 -atom_style atomic -neigh_modify delay 0 every 1 - -lattice sq2 ${rho} -lattice sq2 0.6 -Lattice spacing in x,y,z = 1.82574 1.82574 1.82574 -region simbox block 0 $x 0 $y -0.1 0.1 -region simbox block 0 40 0 $y -0.1 0.1 -region simbox block 0 40 0 40 -0.1 0.1 -create_box 1 simbox -Created orthogonal box = (0 0 -0.182574) to (73.0297 73.0297 0.182574) - 4 by 2 by 1 MPI processor grid -create_atoms 1 box -Created 3200 atoms - -pair_style lj/cut ${rc} -pair_style lj/cut 2.5 -pair_coeff * * 1 1 - -mass * 1.0 -velocity all create $t 97287 -velocity all create 1 97287 - -fix 1 all nve -fix 2 all langevin $t $t 0.1 498094 -fix 2 all langevin 1 $t 0.1 498094 -fix 2 all langevin 1 1 0.1 498094 -fix 3 all enforce2d - -# equilibration run - -thermo 1000 -run 5000 -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4 -> bins = 53 53 1 -Memory usage per processor = 2.478 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1 -1.56492 0 -0.5652325 -1.5346995 - 1000 0.97537833 -1.5723957 0 -0.5973222 0.92877783 - 2000 0.99008371 -1.5748206 0 -0.58504633 1.0809416 - 3000 1.0111412 -1.5848987 0 -0.57407352 1.0174297 - 4000 1.0055417 -1.5857581 0 -0.58053054 0.95647691 - 5000 0.97069905 -1.5851114 0 -0.61471567 0.90108287 -Loop time of 0.554412 on 8 procs for 5000 steps with 3200 atoms - -Performance: 3896017.421 tau/day, 9018.559 timesteps/s -98.9% CPU use with 8 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.23992 | 0.24608 | 0.25161 | 0.7 | 44.39 -Neigh | 0.063106 | 0.064417 | 0.066279 | 0.4 | 11.62 -Comm | 0.072465 | 0.085066 | 0.094837 | 2.3 | 15.34 -Output | 0.00013208 | 0.00013691 | 0.00014591 | 0.0 | 0.02 -Modify | 0.11441 | 0.11621 | 0.11769 | 0.3 | 20.96 -Other | | 0.04251 | | | 7.67 - -Nlocal: 400 ave 406 max 394 min -Histogram: 1 1 0 1 0 2 1 0 1 1 -Nghost: 202.5 ave 212 max 191 min -Histogram: 1 0 0 0 3 1 0 2 0 1 -Neighs: 2800.88 ave 2903 max 2690 min -Histogram: 1 1 0 0 1 2 1 0 1 1 - -Total # of neighbors = 22407 -Ave neighs/atom = 7.00219 -Neighbor list builds = 599 -Dangerous builds = 0 - -unfix 2 - -# data gathering run - -reset_timestep 0 - -# factor of 4 in 2 variables is for 2d - -compute msd all msd com yes -variable twopoint equal c_msd[4]/4/(step*dt+1.0e-6) -fix 9 all vector 10 c_msd[4] -variable fitslope equal slope(f_9)/4/(10*dt) - -thermo_style custom step temp c_msd[4] v_twopoint v_fitslope - -# only need to run for 10K steps to make a good 100-frame movie - -#dump 1 all custom 1 tmp.dump id type vx vy vz - -#dump 2 all image 100 image.*.jpg type type zoom 1.6 adiam 1.2 - -thermo 1000 -run 100000 -Memory usage per processor = 2.853 Mbytes -Step Temp c_msd[4] v_twopoint v_fitslope - 0 0.97069905 0 0 5e+20 - 1000 0.98138076 4.0484996 0.20242494 0.18046446 - 2000 0.97606079 9.2121392 0.23030346 0.2091528 - 3000 0.97924866 14.815034 0.24691721 0.22619184 - 4000 0.98568451 20.516817 0.25646019 0.23715506 - 5000 0.97551815 27.33922 0.27339219 0.24709999 - 6000 0.98482252 34.37734 0.28647782 0.25735178 - 7000 0.9672559 41.696689 0.29783348 0.26654059 - 8000 0.9836541 48.340277 0.30212673 0.27440308 - 9000 0.99087147 56.042692 0.31134828 0.28113047 - 10000 0.99663166 63.69663 0.31848314 0.28767921 - 11000 0.97776688 71.144109 0.32338231 0.29344527 - 12000 0.98246011 78.301774 0.32625739 0.29849471 - 13000 0.98788732 85.061923 0.32716124 0.3026655 - 14000 0.96872483 91.1658 0.32559214 0.30601023 - 15000 0.98955796 97.278388 0.32426129 0.3084275 - 16000 0.99855196 104.23997 0.3257499 0.31049883 - 17000 0.98600861 110.66055 0.3254722 0.31220348 - 18000 0.98696963 116.90111 0.32472531 0.31352676 - 19000 0.9881192 124.21305 0.32687644 0.31480062 - 20000 0.98527319 131.09874 0.32774685 0.31596198 - 21000 0.99015191 137.89263 0.32831579 0.31705324 - 22000 0.97972418 146.68982 0.33338595 0.31833889 - 23000 0.98911012 155.1264 0.33723129 0.31979515 - 24000 0.98810498 162.88634 0.33934653 0.32131187 - 25000 0.96961962 170.37907 0.34075814 0.32276215 - 26000 0.99118408 179.26511 0.34474059 0.32427111 - 27000 0.98515159 185.90764 0.3442734 0.32574529 - 28000 0.98951677 192.12183 0.34307469 0.32700292 - 29000 0.9832026 196.99457 0.33964581 0.32799023 - 30000 0.98449493 203.48475 0.33914124 0.3287171 - 31000 0.96585993 210.06193 0.33880956 0.32935775 - 32000 0.98758117 218.94174 0.34209646 0.33001591 - 33000 0.98875584 225.96489 0.34237104 0.33072947 - 34000 0.98007229 233.5792 0.34349882 0.3314385 - 35000 0.98415295 241.98148 0.34568783 0.33216634 - 36000 0.98101154 250.30876 0.34765106 0.33295272 - 37000 0.97606878 258.2127 0.34893608 0.33377673 - 38000 0.97220293 266.40464 0.35053242 0.33459273 - 39000 0.979783 272.8578 0.34981769 0.33539728 - 40000 0.98375673 279.87598 0.34984497 0.33609699 - 41000 0.97506523 288.07676 0.35131312 0.33677708 - 42000 0.97106749 296.11647 0.3525196 0.33751312 - 43000 0.97717259 304.46747 0.35403194 0.33823441 - 44000 0.98541435 312.57228 0.35519578 0.3389771 - 45000 0.97678287 321.82674 0.35758527 0.33973306 - 46000 0.98169719 329.78197 0.35845866 0.34051748 - 47000 0.99471466 337.11283 0.35863066 0.34127239 - 48000 0.98332437 346.0754 0.3604952 0.34202442 - 49000 0.98126947 356.11859 0.36338631 0.34282132 - 50000 0.98809751 365.65248 0.36565248 0.34368171 - 51000 0.95919516 373.91833 0.36658659 0.34454516 - 52000 0.98097913 381.26492 0.36660089 0.34538506 - 53000 0.97774072 388.81031 0.36680218 0.34618232 - 54000 0.99096915 395.56767 0.36626636 0.3469296 - 55000 0.97652739 401.72735 0.36520668 0.34760374 - 56000 0.99185306 407.28834 0.3636503 0.34819906 - 57000 0.96289342 414.75298 0.3638184 0.34871992 - 58000 0.97871716 424.69443 0.36611588 0.34927986 - 59000 0.98637393 433.14205 0.36706953 0.34986296 - 60000 0.98009845 438.14533 0.36512111 0.35040349 - 61000 0.99416712 446.08007 0.3656394 0.35088379 - 62000 0.97612483 450.90846 0.36363585 0.35132647 - 63000 0.97786531 455.36749 0.36140277 0.35167458 - 64000 0.99080668 458.04873 0.35785057 0.3519105 - 65000 0.97952497 461.31241 0.3548557 0.3520506 - 66000 0.98095955 463.91727 0.35145248 0.35207764 - 67000 0.98370788 468.93 0.34994776 0.35204043 - 68000 0.96931818 471.07765 0.34638063 0.35192685 - 69000 0.98512552 474.59146 0.34390685 0.35174053 - 70000 0.98065743 478.66071 0.3419005 0.35149002 - 71000 0.98971283 482.57357 0.33984054 0.35119434 - 72000 0.99890324 485.32018 0.3370279 0.35084345 - 73000 0.98649924 490.19497 0.33574998 0.35043722 - 74000 0.98723422 496.04991 0.33516886 0.35003351 - 75000 1.0025633 501.6313 0.33442087 0.34962094 - 76000 0.97859959 505.97813 0.33288035 0.34921013 - 77000 0.97973006 510.55334 0.33152814 0.3487692 - 78000 0.9903944 515.06966 0.33017286 0.34830833 - 79000 0.96847518 518.76483 0.32833217 0.3478214 - 80000 0.99171112 524.18127 0.32761329 0.34733349 - 81000 0.97202573 529.09959 0.32660468 0.3468315 - 82000 0.99368438 535.80271 0.32670897 0.34633058 - 83000 0.97932483 543.08233 0.32715803 0.34586259 - 84000 0.99078651 547.57861 0.32593965 0.34540839 - 85000 0.98973457 552.24581 0.32485048 0.34493584 - 86000 0.9835873 557.3493 0.32404029 0.34446152 - 87000 0.97180564 564.93434 0.32467491 0.34400358 - 88000 0.99743353 571.39837 0.32465817 0.3435667 - 89000 0.98993437 577.81703 0.32461631 0.3431411 - 90000 0.9926071 583.39378 0.32410765 0.342724 - 91000 0.98800458 591.08741 0.3247733 0.34232767 - 92000 0.98501879 596.10133 0.32396811 0.34193949 - 93000 0.98810082 604.02652 0.32474544 0.3415681 - 94000 0.97563748 609.43676 0.32416849 0.341209 - 95000 0.97283448 615.15754 0.32376713 0.34084828 - 96000 0.9883071 622.30912 0.32411933 0.34049871 - 97000 0.97717678 628.84457 0.32414669 0.34016355 - 98000 0.97190208 634.37377 0.32366009 0.3398341 - 99000 0.98687379 640.66666 0.32356902 0.33950845 - 100000 0.97559757 646.96406 0.32348203 0.33919036 -Loop time of 9.58779 on 8 procs for 100000 steps with 3200 atoms - -Performance: 4505729.040 tau/day, 10429.928 timesteps/s -99.4% CPU use with 8 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 4.8572 | 4.9363 | 4.9822 | 1.7 | 51.49 -Neigh | 1.3583 | 1.376 | 1.3991 | 1.2 | 14.35 -Comm | 1.5192 | 1.7079 | 1.8264 | 7.2 | 17.81 -Output | 0.0085125 | 0.0086059 | 0.0089455 | 0.1 | 0.09 -Modify | 0.77663 | 0.7903 | 0.81378 | 1.3 | 8.24 -Other | | 0.7686 | | | 8.02 - -Nlocal: 400 ave 413 max 391 min -Histogram: 2 1 0 2 0 0 1 1 0 1 -Nghost: 204.75 ave 213 max 197 min -Histogram: 1 1 0 1 0 3 0 1 0 1 -Neighs: 2800.62 ave 2959 max 2661 min -Histogram: 1 1 1 2 0 0 0 1 1 1 - -Total # of neighbors = 22405 -Ave neighs/atom = 7.00156 -Neighbor list builds = 12728 -Dangerous builds = 0 -Total wall time: 0:00:10 diff --git a/examples/DIFFUSE/log.3Aug18.msd.2d.g++.8 b/examples/DIFFUSE/log.3Aug18.msd.2d.g++.8 new file mode 100644 index 0000000000..113da9040d --- /dev/null +++ b/examples/DIFFUSE/log.3Aug18.msd.2d.g++.8 @@ -0,0 +1,251 @@ +LAMMPS (2 Aug 2018) +# sample LAMMPS input script for diffusion of 2d LJ liquid +# mean-squared displacement via compute msd + +# settings + +variable x equal 40 +variable y equal 40 + +variable rho equal 0.6 +variable t equal 1.0 +variable rc equal 2.5 + +# problem setup + +units lj +dimension 2 +atom_style atomic +neigh_modify delay 0 every 1 + +lattice sq2 ${rho} +lattice sq2 0.6 +Lattice spacing in x,y,z = 1.82574 1.82574 1.82574 +region simbox block 0 $x 0 $y -0.1 0.1 +region simbox block 0 40 0 $y -0.1 0.1 +region simbox block 0 40 0 40 -0.1 0.1 +create_box 1 simbox +Created orthogonal box = (0 0 -0.182574) to (73.0297 73.0297 0.182574) + 4 by 2 by 1 MPI processor grid +create_atoms 1 box +Created 3200 atoms + Time spent = 0.000706911 secs + +pair_style lj/cut ${rc} +pair_style lj/cut 2.5 +pair_coeff * * 1 1 + +mass * 1.0 +velocity all create $t 97287 +velocity all create 1 97287 + +fix 1 all nve +fix 2 all langevin $t $t 0.1 498094 +fix 2 all langevin 1 $t 0.1 498094 +fix 2 all langevin 1 1 0.1 498094 +fix 3 all enforce2d + +# equilibration run + +thermo 1000 +run 5000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 53 53 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.052 | 3.052 | 3.052 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1 -1.56492 0 -0.5652325 -1.5346995 + 1000 0.97537833 -1.5723957 0 -0.5973222 0.92877783 + 2000 0.99008371 -1.5748206 0 -0.58504633 1.0809416 + 3000 1.0111412 -1.5848987 0 -0.57407352 1.0174297 + 4000 1.0055417 -1.5857581 0 -0.58053054 0.95647691 + 5000 0.97069905 -1.5851114 0 -0.61471567 0.90108287 +Loop time of 0.667446 on 8 procs for 5000 steps with 3200 atoms + +Performance: 3236214.756 tau/day, 7491.238 timesteps/s +99.9% CPU use with 8 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.22913 | 0.24877 | 0.28382 | 3.6 | 37.27 +Neigh | 0.064419 | 0.071256 | 0.080013 | 1.7 | 10.68 +Comm | 0.103 | 0.14054 | 0.17204 | 5.5 | 21.06 +Output | 0.00010705 | 0.00013995 | 0.00021911 | 0.0 | 0.02 +Modify | 0.13457 | 0.14973 | 0.16887 | 2.6 | 22.43 +Other | | 0.05701 | | | 8.54 + +Nlocal: 400 ave 406 max 394 min +Histogram: 1 1 0 1 0 2 1 0 1 1 +Nghost: 202.5 ave 212 max 191 min +Histogram: 1 0 0 0 3 1 0 2 0 1 +Neighs: 2800.88 ave 2903 max 2690 min +Histogram: 1 1 0 0 1 2 1 0 1 1 + +Total # of neighbors = 22407 +Ave neighs/atom = 7.00219 +Neighbor list builds = 599 +Dangerous builds = 0 + +unfix 2 + +# data gathering run + +reset_timestep 0 + +# factor of 4 in 2 variables is for 2d + +compute msd all msd com yes +variable twopoint equal c_msd[4]/4/(step*dt+1.0e-6) +fix 9 all vector 10 c_msd[4] +variable fitslope equal slope(f_9)/4/(10*dt) + +thermo_style custom step temp c_msd[4] v_twopoint v_fitslope + +# only need to run for 10K steps to make a good 100-frame movie + +#dump 1 all custom 1 tmp.dump id type vx vy vz + +#dump 2 all image 100 image.*.jpg type type zoom 1.6 adiam 1.2 + +thermo 1000 +run 100000 +Per MPI rank memory allocation (min/avg/max) = 3.427 | 3.427 | 3.427 Mbytes +Step Temp c_msd[4] v_twopoint v_fitslope + 0 0.97069905 0 0 5e+20 + 1000 0.98138076 4.0484996 0.20242494 0.20685564 + 2000 0.97606079 9.2121392 0.23030346 0.23687918 + 3000 0.97924866 14.815034 0.24691721 0.25405247 + 4000 0.98568451 20.516817 0.25646019 0.26353644 + 5000 0.97551815 27.33922 0.27339219 0.27544492 + 6000 0.98482252 34.37734 0.28647782 0.28966619 + 7000 0.9672559 41.696689 0.29783348 0.30165524 + 8000 0.9836541 48.340277 0.30212673 0.31085371 + 9000 0.99087147 56.042692 0.31134828 0.31811489 + 10000 0.99663166 63.69663 0.31848314 0.32589374 + 11000 0.97776688 71.144109 0.32338231 0.33219745 + 12000 0.98246011 78.301774 0.32625739 0.33723 + 13000 0.98788732 85.061923 0.32716124 0.34053027 + 14000 0.96872483 91.1658 0.32559214 0.34231162 + 15000 0.98955796 97.278388 0.32426129 0.34229511 + 16000 0.99855196 104.23997 0.3257499 0.34217252 + 17000 0.98600861 110.66055 0.3254722 0.34172446 + 18000 0.98696963 116.90111 0.32472531 0.3408227 + 19000 0.9881192 124.21305 0.32687644 0.34036538 + 20000 0.98527319 131.09874 0.32774685 0.34003478 + 21000 0.99015191 137.89263 0.32831579 0.33987868 + 22000 0.97972418 146.68982 0.33338595 0.34060035 + 23000 0.98911012 155.1264 0.33723129 0.34201036 + 24000 0.98810498 162.88634 0.33934653 0.34371488 + 25000 0.96961962 170.37907 0.34075814 0.34531409 + 26000 0.99118408 179.26511 0.34474059 0.34717195 + 27000 0.98515159 185.90764 0.3442734 0.34898035 + 28000 0.98951677 192.12183 0.34307469 0.35021808 + 29000 0.9832026 196.99457 0.33964581 0.35075459 + 30000 0.98449493 203.48475 0.33914124 0.35066186 + 31000 0.96585993 210.06193 0.33880956 0.35046715 + 32000 0.98758117 218.94174 0.34209646 0.35046623 + 33000 0.98875584 225.96489 0.34237104 0.35073944 + 34000 0.98007229 233.5792 0.34349882 0.35109188 + 35000 0.98415295 241.98148 0.34568783 0.35157879 + 36000 0.98101154 250.30876 0.34765106 0.3523013 + 37000 0.97606878 258.2127 0.34893608 0.35318097 + 38000 0.97220293 266.40464 0.35053242 0.3540743 + 39000 0.979783 272.8578 0.34981769 0.35496561 + 40000 0.98375673 279.87598 0.34984497 0.35558182 + 41000 0.97506523 288.07676 0.35131312 0.35618259 + 42000 0.97106749 296.11647 0.3525196 0.35698571 + 43000 0.97717259 304.46747 0.35403194 0.3577736 + 44000 0.98541435 312.57228 0.35519578 0.35865003 + 45000 0.97678287 321.82674 0.35758527 0.35958623 + 46000 0.98169719 329.78197 0.35845866 0.36062236 + 47000 0.99471466 337.11283 0.35863066 0.36158322 + 48000 0.98332437 346.0754 0.3604952 0.36255042 + 49000 0.98126947 356.11859 0.36338631 0.3636628 + 50000 0.98809751 365.65248 0.36565248 0.36496809 + 51000 0.95919516 373.91833 0.36658659 0.36628073 + 52000 0.98097913 381.26492 0.36660089 0.36752237 + 53000 0.97774072 388.81031 0.36680218 0.36863962 + 54000 0.99096915 395.56767 0.36626636 0.36961521 + 55000 0.97652739 401.72735 0.36520668 0.37038579 + 56000 0.99185306 407.28834 0.3636503 0.37094092 + 57000 0.96289342 414.75298 0.3638184 0.37130039 + 58000 0.97871716 424.69443 0.36611588 0.37180428 + 59000 0.98637393 433.14205 0.36706953 0.37239862 + 60000 0.98009845 438.14533 0.36512111 0.37288487 + 61000 0.99416712 446.08007 0.3656394 0.37321496 + 62000 0.97612483 450.90846 0.36363585 0.37345792 + 63000 0.97786531 455.36749 0.36140277 0.37344803 + 64000 0.99080668 458.04873 0.35785057 0.37313914 + 65000 0.97952497 461.31241 0.3548557 0.3725875 + 66000 0.98095955 463.91727 0.35145248 0.37174735 + 67000 0.98370788 468.93 0.34994776 0.37076942 + 68000 0.96931818 471.07765 0.34638063 0.36961868 + 69000 0.98512552 474.59146 0.34390685 0.36830908 + 70000 0.98065743 478.66071 0.3419005 0.36686789 + 71000 0.98971283 482.57357 0.33984054 0.36535224 + 72000 0.99890324 485.32018 0.3370279 0.36373174 + 73000 0.98649924 490.19497 0.33574998 0.36200692 + 74000 0.98723422 496.04991 0.33516886 0.36034919 + 75000 1.0025633 501.6313 0.33442087 0.35872052 + 76000 0.97859959 505.97813 0.33288035 0.35714939 + 77000 0.97973006 510.55334 0.33152814 0.35553808 + 78000 0.9903944 515.06966 0.33017286 0.35391584 + 79000 0.96847518 518.76483 0.32833217 0.35226287 + 80000 0.99171112 524.18127 0.32761329 0.35065267 + 81000 0.97202573 529.09959 0.32660468 0.34904364 + 82000 0.99368438 535.80271 0.32670897 0.34747913 + 83000 0.97932483 543.08233 0.32715803 0.34605097 + 84000 0.99078651 547.57861 0.32593965 0.34469765 + 85000 0.98973457 552.24581 0.32485048 0.34332115 + 86000 0.9835873 557.3493 0.32404029 0.34197018 + 87000 0.97180564 564.93434 0.32467491 0.34069702 + 88000 0.99743353 571.39837 0.32465817 0.33951258 + 89000 0.98993437 577.81703 0.32461631 0.33838511 + 90000 0.9926071 583.39378 0.32410765 0.33730429 + 91000 0.98800458 591.08741 0.3247733 0.33630505 + 92000 0.98501879 596.10133 0.32396811 0.33534725 + 93000 0.98810082 604.02652 0.32474544 0.33445545 + 94000 0.97563748 609.43676 0.32416849 0.33361404 + 95000 0.97283448 615.15754 0.32376713 0.33278044 + 96000 0.9883071 622.30912 0.32411933 0.33199212 + 97000 0.97717678 628.84457 0.32414669 0.33125729 + 98000 0.97190208 634.37377 0.32366009 0.33054877 + 99000 0.98687379 640.66666 0.32356902 0.32986014 + 100000 0.97559757 646.96406 0.32348203 0.32920186 +Loop time of 7.61838 on 8 procs for 100000 steps with 3200 atoms + +Performance: 5670494.518 tau/day, 13126.145 timesteps/s +100.0% CPU use with 8 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 3.5458 | 3.6709 | 3.8234 | 4.3 | 48.19 +Neigh | 1.1363 | 1.1513 | 1.1753 | 1.0 | 15.11 +Comm | 1.5901 | 1.7017 | 1.8664 | 6.9 | 22.34 +Output | 0.0041966 | 0.0043583 | 0.0050626 | 0.4 | 0.06 +Modify | 0.63816 | 0.65537 | 0.68918 | 2.0 | 8.60 +Other | | 0.4348 | | | 5.71 + +Nlocal: 400 ave 413 max 391 min +Histogram: 2 1 0 2 0 0 1 1 0 1 +Nghost: 204.75 ave 213 max 197 min +Histogram: 1 1 0 1 0 3 0 1 0 1 +Neighs: 2800.62 ave 2959 max 2661 min +Histogram: 1 1 1 2 0 0 0 1 1 1 + +Total # of neighbors = 22405 +Ave neighs/atom = 7.00156 +Neighbor list builds = 12728 +Dangerous builds = 0 +Total wall time: 0:00:08 diff --git a/examples/DIFFUSE/log.13Oct16.vacf.2d.g++.8 b/examples/DIFFUSE/log.3Aug18.vacf.2d.g++.8 similarity index 84% rename from examples/DIFFUSE/log.13Oct16.vacf.2d.g++.8 rename to examples/DIFFUSE/log.3Aug18.vacf.2d.g++.8 index 458315bc29..80c57ada9c 100644 --- a/examples/DIFFUSE/log.13Oct16.vacf.2d.g++.8 +++ b/examples/DIFFUSE/log.3Aug18.vacf.2d.g++.8 @@ -1,4 +1,4 @@ -LAMMPS (13 Oct 2016) +LAMMPS (2 Aug 2018) # sample LAMMPS input script for diffusion of 2d LJ liquid # mean-squared displacement via compute msd @@ -29,6 +29,7 @@ Created orthogonal box = (0 0 -0.182574) to (73.0297 73.0297 0.182574) 4 by 2 by 1 MPI processor grid create_atoms 1 box Created 3200 atoms + Time spent = 0.000712872 secs pair_style lj/cut ${rc} pair_style lj/cut 2.5 @@ -49,13 +50,18 @@ fix 3 all enforce2d thermo 1000 run 5000 Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 2.8 ghost atom cutoff = 2.8 - binsize = 1.4 -> bins = 53 53 1 -Memory usage per processor = 2.478 Mbytes + binsize = 1.4, bins = 53 53 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.052 | 3.052 | 3.052 Mbytes Step Temp E_pair E_mol TotEng Press 0 1 -1.56492 0 -0.5652325 -1.5346995 1000 0.97537833 -1.5723957 0 -0.5973222 0.92877783 @@ -63,20 +69,20 @@ Step Temp E_pair E_mol TotEng Press 3000 1.0111412 -1.5848987 0 -0.57407352 1.0174297 4000 1.0055417 -1.5857581 0 -0.58053054 0.95647691 5000 0.97069905 -1.5851114 0 -0.61471567 0.90108287 -Loop time of 0.557588 on 8 procs for 5000 steps with 3200 atoms +Loop time of 0.648098 on 8 procs for 5000 steps with 3200 atoms -Performance: 3873826.669 tau/day, 8967.191 timesteps/s -99.1% CPU use with 8 MPI tasks x no OpenMP threads +Performance: 3332829.949 tau/day, 7714.884 timesteps/s +99.9% CPU use with 8 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.23784 | 0.24683 | 0.25594 | 1.0 | 44.27 -Neigh | 0.062975 | 0.06439 | 0.0662 | 0.4 | 11.55 -Comm | 0.083826 | 0.092564 | 0.1035 | 2.1 | 16.60 -Output | 0.00011778 | 0.00012615 | 0.00014257 | 0.1 | 0.02 -Modify | 0.11466 | 0.11648 | 0.1187 | 0.4 | 20.89 -Other | | 0.0372 | | | 6.67 +Pair | 0.22614 | 0.24602 | 0.27481 | 2.8 | 37.96 +Neigh | 0.066875 | 0.07135 | 0.077825 | 1.2 | 11.01 +Comm | 0.098293 | 0.12744 | 0.1569 | 5.6 | 19.66 +Output | 0.0001049 | 0.00012228 | 0.00014496 | 0.0 | 0.02 +Modify | 0.13725 | 0.14919 | 0.16903 | 2.4 | 23.02 +Other | | 0.05398 | | | 8.33 Nlocal: 400 ave 406 max 394 min Histogram: 1 1 0 1 0 2 1 0 1 1 @@ -114,7 +120,7 @@ thermo_style custom step temp c_vacf[4] v_vacf thermo 1000 run 100000 -Memory usage per processor = 2.853 Mbytes +Per MPI rank memory allocation (min/avg/max) = 3.427 | 3.427 | 3.427 Mbytes Step Temp c_vacf[4] v_vacf 0 0.97069905 1.9407914 0 1000 0.98138076 0.029239763 0.22157396 @@ -217,20 +223,20 @@ Step Temp c_vacf[4] v_vacf 98000 0.97190208 0.015065013 0.20906937 99000 0.98687379 -0.036869401 0.22993959 100000 0.97559757 0.045464091 0.23369283 -Loop time of 10.8346 on 8 procs for 100000 steps with 3200 atoms +Loop time of 8.16691 on 8 procs for 100000 steps with 3200 atoms -Performance: 3987213.825 tau/day, 9229.662 timesteps/s -99.5% CPU use with 8 MPI tasks x no OpenMP threads +Performance: 5289636.190 tau/day, 12244.528 timesteps/s +100.0% CPU use with 8 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 4.8486 | 4.9469 | 5.0248 | 2.8 | 45.66 -Neigh | 1.3613 | 1.374 | 1.3916 | 0.8 | 12.68 -Comm | 1.8181 | 1.9534 | 2.0665 | 5.7 | 18.03 -Output | 0.016565 | 0.016701 | 0.017039 | 0.1 | 0.15 -Modify | 1.8395 | 1.9053 | 1.9704 | 2.8 | 17.59 -Other | | 0.6383 | | | 5.89 +Pair | 3.5668 | 3.6612 | 3.7867 | 4.0 | 44.83 +Neigh | 1.1409 | 1.1555 | 1.1804 | 1.4 | 14.15 +Comm | 1.581 | 1.711 | 1.8239 | 7.1 | 20.95 +Output | 0.016626 | 0.016831 | 0.017569 | 0.2 | 0.21 +Modify | 1.225 | 1.2594 | 1.3008 | 2.0 | 15.42 +Other | | 0.363 | | | 4.45 Nlocal: 400 ave 413 max 391 min Histogram: 2 1 0 2 0 0 1 1 0 1 @@ -243,4 +249,4 @@ Total # of neighbors = 22405 Ave neighs/atom = 7.00156 Neighbor list builds = 12728 Dangerous builds = 0 -Total wall time: 0:00:11 +Total wall time: 0:00:08 diff --git a/examples/README b/examples/README index a8dfe63d92..3c9c299819 100644 --- a/examples/README +++ b/examples/README @@ -59,6 +59,7 @@ sub-directories: accelerate: use of all the various accelerator packages airebo: polyethylene with AIREBO potential +atm: Axilrod-Teller-Muto potential balance: dynamic load balancing, 2d system body: body particles, 2d system cmap: CMAP 5-body contributions to CHARMM force field @@ -82,6 +83,7 @@ kim: use of potentials in Knowledge Base for Interatomic Models (KIM) latte: use of LATTE density-functional tight-binding quantum code meam: MEAM test for SiC and shear (same as shear examples) melt: rapid melt of 3d LJ system +message: client/server coupling of 2 codes micelle: self-assembly of small lipid-like molecules into 2d bilayers min: energy minimization of 2d LJ melt mscg: parameterize a multi-scale coarse-graining (MSCG) model diff --git a/examples/SPIN/README b/examples/SPIN/README new file mode 100644 index 0000000000..5ad252e7f2 --- /dev/null +++ b/examples/SPIN/README @@ -0,0 +1,20 @@ +This directory contains examples and applications of the SPIN package +===================================================================== + +- the iron, cobalt_hcp, cobalt_fcc and nickel directories provide +examples of spin-lattice calculations. + +- the bfo repository provides an example of spin dynamics calculation +performed on a fixed lattice, and applied to the multiferroic +material bismuth-oxide. + +- the read_restart directory provides examples allowing to write or +read data files, and restart magneto-mechanical simulations. + +- vizualization of the dump files can be achieved using Ovito or +VMD. See the vmd repository for help vizualizing results with VMD. + +** Note, the aim of this repository is mainly to provide users with +examples. Better values and tuning of the magnetic and mechanical +interactions can be achieved for more accurate materials +simulations. ** diff --git a/examples/SPIN/bfo/in.spin.bfo b/examples/SPIN/bfo/in.spin.bfo new file mode 100644 index 0000000000..de23ba87ba --- /dev/null +++ b/examples/SPIN/bfo/in.spin.bfo @@ -0,0 +1,56 @@ +# layer sc iron atoms (in the [001] plane) in bismuth oxide + +clear +units metal +atom_style spin + +dimension 3 +boundary p p f + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice sc 3.96 +region box block 0.0 34.0 0.0 34.0 0.0 5.0 +create_box 1 box +create_atoms 1 box + +# setting mass, mag. moments, and interactions for bfo + +mass 1 1.0 + +set group all spin/random 11 2.50 + +#pair_style hybrid/overlay spin/exchange 6.0 spin/magelec 4.5 +pair_style hybrid/overlay spin/exchange 6.0 spin/magelec 4.5 spin/dmi 4.5 +pair_coeff * * spin/exchange exchange 6.0 -0.01575 0.0 1.965 +pair_coeff * * spin/magelec magelec 4.5 0.000109 1.0 1.0 1.0 +pair_coeff * * spin/dmi dmi 4.5 0.00005 1.0 1.0 1.0 + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +fix 1 all precession/spin anisotropy 0.0000033 0.0 0.0 1.0 +fix 2 all langevin/spin 0.0 0.1 21 +fix 3 all nve/spin lattice no + +timestep 0.0002 + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +#thermo_style custom step time v_magnorm v_emag temp etotal +thermo_style custom step time v_magnorm pe ke v_emag temp etotal +thermo 10 + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 100 all custom 1 dump_bfo.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] + +run 2000 diff --git a/examples/SPIN/bfo/log.11May18.spin.bfo.g++.1 b/examples/SPIN/bfo/log.11May18.spin.bfo.g++.1 new file mode 100644 index 0000000000..8e9eb82d1f --- /dev/null +++ b/examples/SPIN/bfo/log.11May18.spin.bfo.g++.1 @@ -0,0 +1,212 @@ +LAMMPS (11 May 2018) +# layer sc iron atoms (in the [001] plane) in bismuth oxide + +clear +units metal +atom_style spin + +dimension 3 +boundary p p f + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice sc 3.96 +Lattice spacing in x,y,z = 3.96 3.96 3.96 +region box block 0.0 34.0 0.0 34.0 0.0 5.0 +create_box 1 box +Created orthogonal box = (0 0 0) to (134.64 134.64 19.8) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 5780 atoms + Time spent = 0.0013566 secs + +# setting mass, mag. moments, and interactions for bfo + +mass 1 1.0 + +set group all spin/random 11 2.50 + 5780 settings made for spin/random + +pair_style hybrid/overlay spin/exchange 6.0 spin/magelec 4.5 +pair_coeff * * spin/exchange exchange 6.0 -0.01575 0.0 1.965 +pair_coeff * * spin/magelec magelec 4.5 0.000109 1.0 1.0 1.0 + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +fix 1 all precession/spin anisotropy 0.0000033 0.0 0.0 1.0 +fix 2 all langevin/spin 0.0 0.1 21 +fix 3 all nve/spin lattice no + +timestep 0.0002 + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo_style custom step time v_magnorm v_emag temp etotal +thermo 50 + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 100 all custom 1 dump_bfo.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] + +run 5000 +Neighbor list info ... + update every 10 steps, delay 20 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.1 + ghost atom cutoff = 6.1 + binsize = 3.05, bins = 45 45 7 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair spin/magelec, perpetual, copy from (1) + attributes: full, newton on + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 7.272 | 7.272 | 7.272 Mbytes +Step Time v_magnorm v_emag Temp TotEng + 0 0 0.010071723 -0.13298298 0 -0.12034311 + 50 0.01 0.0098643821 -1.3898985 0 -1.3772103 + 100 0.02 0.0096526211 -2.6381677 0 -2.6254222 + 150 0.03 0.0094342235 -3.8784006 0 -3.8656019 + 200 0.04 0.0092074832 -5.111441 0 -5.0986001 + 250 0.05 0.0089713115 -6.3380611 0 -6.3251904 + 300 0.06 0.0087256081 -7.5587787 0 -7.5458894 + 350 0.07 0.0084715548 -8.7738491 0 -8.7609521 + 400 0.08 0.008211486 -9.9833855 0 -9.9704932 + 450 0.09 0.0079483243 -11.18751 0 -11.174637 + 500 0.1 0.0076849713 -12.386462 0 -12.37362 + 550 0.11 0.007424064 -13.580633 0 -13.567832 + 600 0.12 0.0071680699 -14.770519 0 -14.757759 + 650 0.13 0.0069192726 -15.956579 0 -15.943853 + 700 0.14 0.0066793495 -17.139049 0 -17.126343 + 750 0.15 0.0064488038 -18.317803 0 -18.305099 + 800 0.16 0.0062267571 -19.492336 0 -19.479616 + 850 0.17 0.0060112235 -20.661925 0 -20.649176 + 900 0.18 0.0057995251 -21.825931 0 -21.813141 + 950 0.19 0.0055886511 -22.98413 0 -22.971297 + 1000 0.2 0.0053757923 -24.136967 0 -24.124095 + 1050 0.21 0.0051592263 -25.285621 0 -25.272717 + 1100 0.22 0.0049391661 -26.431928 0 -26.419004 + 1150 0.23 0.0047179149 -27.578212 0 -27.565281 + 1200 0.24 0.0044991004 -28.727051 0 -28.714128 + 1250 0.25 0.0042864034 -29.880967 0 -29.868062 + 1300 0.26 0.0040824475 -31.042054 0 -31.029173 + 1350 0.27 0.0038883007 -32.21165 0 -32.198795 + 1400 0.28 0.0037036595 -33.390159 0 -33.377326 + 1450 0.29 0.0035274815 -34.577121 0 -34.564302 + 1500 0.3 0.0033587207 -35.771483 0 -35.758672 + 1550 0.31 0.0031969501 -36.971996 0 -36.95919 + 1600 0.32 0.0030429081 -38.177601 0 -38.164801 + 1650 0.33 0.0028989804 -39.387757 0 -39.374962 + 1700 0.34 0.0027692024 -40.602665 0 -40.589873 + 1750 0.35 0.0026581403 -41.823341 0 -41.81054 + 1800 0.36 0.0025686991 -43.05145 0 -43.038628 + 1850 0.37 0.002500124 -44.288966 0 -44.276111 + 1900 0.38 0.0024477804 -45.537752 0 -45.52486 + 1950 0.39 0.0024050049 -46.799255 0 -46.786336 + 2000 0.4 0.0023657031 -48.074388 0 -48.061466 + 2050 0.41 0.0023260844 -49.363587 0 -49.350695 + 2100 0.42 0.0022848329 -50.666866 0 -50.654039 + 2150 0.43 0.0022419759 -51.983781 0 -51.971055 + 2200 0.44 0.0021972506 -53.31336 0 -53.300764 + 2250 0.45 0.0021488322 -54.654121 0 -54.641676 + 2300 0.46 0.0020929483 -56.004207 0 -55.991918 + 2350 0.47 0.0020244601 -57.361586 0 -57.349442 + 2400 0.48 0.001938225 -58.72428 0 -58.712247 + 2450 0.49 0.0018309419 -60.09064 0 -60.078671 + 2500 0.5 0.0017030436 -61.459658 0 -61.447705 + 2550 0.51 0.0015599449 -62.831213 0 -62.819237 + 2600 0.52 0.0014117554 -64.206088 0 -64.194074 + 2650 0.53 0.0012709942 -65.585701 0 -65.573657 + 2700 0.54 0.0011490452 -66.971565 0 -66.959515 + 2750 0.55 0.001053009 -68.364663 0 -68.352635 + 2800 0.56 0.00098415327 -69.765002 0 -69.753017 + 2850 0.57 0.00093809306 -71.171532 0 -71.159598 + 2900 0.58 0.00090656933 -72.58234 0 -72.570459 + 2950 0.59 0.00088069677 -73.994931 0 -73.983099 + 3000 0.6 0.00085472643 -75.406507 0 -75.39472 + 3050 0.61 0.00082842902 -76.814319 0 -76.802575 + 3100 0.62 0.00080642618 -78.216074 0 -78.204373 + 3150 0.63 0.00079463972 -79.610246 0 -79.598589 + 3200 0.64 0.0007962304 -80.996103 0 -80.984494 + 3250 0.65 0.00080980411 -82.37346 0 -82.361903 + 3300 0.66 0.00083070982 -83.742356 0 -83.730855 + 3350 0.67 0.00085389185 -85.102808 0 -85.091374 + 3400 0.68 0.00087624091 -86.454619 0 -86.443259 + 3450 0.69 0.00089741986 -87.797089 0 -87.785814 + 3500 0.7 0.00091910796 -89.12875 0 -89.117567 + 3550 0.71 0.00094318459 -90.447312 0 -90.436232 + 3600 0.72 0.00096989367 -91.750008 0 -91.739046 + 3650 0.73 0.00099713096 -93.034224 0 -93.023402 + 3700 0.74 0.0010212995 -94.298186 0 -94.287529 + 3750 0.75 0.0010391164 -95.5414 0 -95.530926 + 3800 0.76 0.0010491462 -96.764626 0 -96.754338 + 3850 0.77 0.0010521238 -97.969346 0 -97.95923 + 3900 0.78 0.0010500324 -99.156875 0 -99.146899 + 3950 0.79 0.0010447043 -100.32743 0 -100.31756 + 4000 0.8 0.0010368986 -101.4796 0 -101.46978 + 4050 0.81 0.0010263632 -102.61044 0 -102.60064 + 4100 0.82 0.0010126933 -103.71619 0 -103.70639 + 4150 0.83 0.00099631895 -104.79338 0 -104.78358 + 4200 0.84 0.0009789075 -105.8398 0 -105.82998 + 4250 0.85 0.00096287608 -106.85496 0 -106.84515 + 4300 0.86 0.00095034023 -107.84011 0 -107.83029 + 4350 0.87 0.00094219078 -108.7976 0 -108.78778 + 4400 0.88 0.00093779428 -109.73016 0 -109.72031 + 4450 0.89 0.0009354459 -110.63996 0 -110.63008 + 4500 0.9 0.00093342614 -111.52805 0 -111.51812 + 4550 0.91 0.0009311077 -112.39417 0 -112.38416 + 4600 0.92 0.00092926689 -113.23706 0 -113.22697 + 4650 0.93 0.00092921566 -114.05512 0 -114.04495 + 4700 0.94 0.00093142598 -114.84701 0 -114.83675 + 4750 0.95 0.00093479851 -115.61197 0 -115.60164 + 4800 0.96 0.0009369799 -116.3499 0 -116.33951 + 4850 0.97 0.00093516768 -117.06128 0 -117.05084 + 4900 0.98 0.00092684411 -117.74695 0 -117.73645 + 4950 0.99 0.00091046222 -118.40798 0 -118.39742 + 5000 1 0.00088619957 -119.04554 0 -119.03492 +Loop time of 128.304 on 1 procs for 5000 steps with 5780 atoms + +Performance: 0.673 ns/day, 35.640 hours/ns, 38.970 timesteps/s +99.6% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 24.227 | 24.227 | 24.227 | 0.0 | 18.88 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.081048 | 0.081048 | 0.081048 | 0.0 | 0.06 +Output | 39.796 | 39.796 | 39.796 | 0.0 | 31.02 +Modify | 64.112 | 64.112 | 64.112 | 0.0 | 49.97 +Other | | 0.08788 | | | 0.07 + +Nlocal: 5780 ave 5780 max 5780 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1065 ave 1065 max 1065 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 92480 ave 92480 max 92480 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 92480 +Ave neighs/atom = 16 +Neighbor list builds = 0 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:02:08 diff --git a/examples/SPIN/bfo/log.11May18.spin.bfo.g++.4 b/examples/SPIN/bfo/log.11May18.spin.bfo.g++.4 new file mode 100644 index 0000000000..c0f96b8195 --- /dev/null +++ b/examples/SPIN/bfo/log.11May18.spin.bfo.g++.4 @@ -0,0 +1,212 @@ +LAMMPS (11 May 2018) +# layer sc iron atoms (in the [001] plane) in bismuth oxide + +clear +units metal +atom_style spin + +dimension 3 +boundary p p f + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice sc 3.96 +Lattice spacing in x,y,z = 3.96 3.96 3.96 +region box block 0.0 34.0 0.0 34.0 0.0 5.0 +create_box 1 box +Created orthogonal box = (0 0 0) to (134.64 134.64 19.8) + 2 by 2 by 1 MPI processor grid +create_atoms 1 box +Created 5780 atoms + Time spent = 0.000355959 secs + +# setting mass, mag. moments, and interactions for bfo + +mass 1 1.0 + +set group all spin/random 11 2.50 + 5780 settings made for spin/random + +pair_style hybrid/overlay spin/exchange 6.0 spin/magelec 4.5 +pair_coeff * * spin/exchange exchange 6.0 -0.01575 0.0 1.965 +pair_coeff * * spin/magelec magelec 4.5 0.000109 1.0 1.0 1.0 + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +fix 1 all precession/spin anisotropy 0.0000033 0.0 0.0 1.0 +fix 2 all langevin/spin 0.0 0.1 21 +fix 3 all nve/spin lattice no + +timestep 0.0002 + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo_style custom step time v_magnorm v_emag temp etotal +thermo 50 + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 100 all custom 1 dump_bfo.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] + +run 5000 +Neighbor list info ... + update every 10 steps, delay 20 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.1 + ghost atom cutoff = 6.1 + binsize = 3.05, bins = 45 45 7 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair spin/magelec, perpetual, copy from (1) + attributes: full, newton on + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 6.862 | 6.862 | 6.862 Mbytes +Step Time v_magnorm v_emag Temp TotEng + 0 0 0.010071723 -0.13298298 0 -0.12034311 + 50 0.01 0.0098643821 -1.3898985 0 -1.3772103 + 100 0.02 0.009652621 -2.6381677 0 -2.6254222 + 150 0.03 0.0094342234 -3.8784007 0 -3.8656019 + 200 0.04 0.009207483 -5.1114411 0 -5.0986001 + 250 0.05 0.0089713114 -6.3380611 0 -6.3251904 + 300 0.06 0.0087256079 -7.5587787 0 -7.5458894 + 350 0.07 0.0084715546 -8.7738491 0 -8.7609521 + 400 0.08 0.0082114858 -9.9833855 0 -9.9704932 + 450 0.09 0.0079483242 -11.18751 0 -11.174637 + 500 0.1 0.0076849711 -12.386462 0 -12.37362 + 550 0.11 0.0074240638 -13.580633 0 -13.567832 + 600 0.12 0.0071680697 -14.770519 0 -14.757759 + 650 0.13 0.0069192724 -15.956579 0 -15.943853 + 700 0.14 0.0066793493 -17.139049 0 -17.126343 + 750 0.15 0.0064488035 -18.317803 0 -18.305099 + 800 0.16 0.0062267569 -19.492336 0 -19.479616 + 850 0.17 0.0060112233 -20.661925 0 -20.649176 + 900 0.18 0.005799525 -21.825931 0 -21.813141 + 950 0.19 0.0055886511 -22.98413 0 -22.971297 + 1000 0.2 0.0053757923 -24.136967 0 -24.124095 + 1050 0.21 0.0051592265 -25.285621 0 -25.272717 + 1100 0.22 0.0049391664 -26.431928 0 -26.419004 + 1150 0.23 0.0047179153 -27.578212 0 -27.565281 + 1200 0.24 0.0044991009 -28.727051 0 -28.714128 + 1250 0.25 0.0042864039 -29.880967 0 -29.868062 + 1300 0.26 0.004082448 -31.042054 0 -31.029174 + 1350 0.27 0.0038883012 -32.21165 0 -32.198795 + 1400 0.28 0.0037036599 -33.390159 0 -33.377326 + 1450 0.29 0.0035274817 -34.577121 0 -34.564302 + 1500 0.3 0.0033587208 -35.771483 0 -35.758672 + 1550 0.31 0.0031969501 -36.971996 0 -36.95919 + 1600 0.32 0.0030429079 -38.177601 0 -38.164801 + 1650 0.33 0.0028989801 -39.387757 0 -39.374962 + 1700 0.34 0.0027692022 -40.602666 0 -40.589873 + 1750 0.35 0.0026581401 -41.823341 0 -41.81054 + 1800 0.36 0.002568699 -43.05145 0 -43.038628 + 1850 0.37 0.0025001242 -44.288966 0 -44.276111 + 1900 0.38 0.0024477808 -45.537752 0 -45.52486 + 1950 0.39 0.0024050056 -46.799255 0 -46.786336 + 2000 0.4 0.002365704 -48.074388 0 -48.061466 + 2050 0.41 0.0023260854 -49.363587 0 -49.350695 + 2100 0.42 0.002284834 -50.666866 0 -50.654039 + 2150 0.43 0.0022419771 -51.983781 0 -51.971055 + 2200 0.44 0.0021972518 -53.31336 0 -53.300764 + 2250 0.45 0.0021488333 -54.654121 0 -54.641676 + 2300 0.46 0.0020929494 -56.004207 0 -55.991918 + 2350 0.47 0.0020244612 -57.361586 0 -57.349441 + 2400 0.48 0.0019382262 -58.72428 0 -58.712247 + 2450 0.49 0.001830943 -60.090639 0 -60.078671 + 2500 0.5 0.0017030446 -61.459658 0 -61.447704 + 2550 0.51 0.0015599459 -62.831213 0 -62.819237 + 2600 0.52 0.0014117562 -64.206088 0 -64.194074 + 2650 0.53 0.001270995 -65.5857 0 -65.573657 + 2700 0.54 0.001149046 -66.971565 0 -66.959515 + 2750 0.55 0.0010530098 -68.364663 0 -68.352635 + 2800 0.56 0.00098415418 -69.765002 0 -69.753017 + 2850 0.57 0.00093809402 -71.171532 0 -71.159598 + 2900 0.58 0.00090657031 -72.58234 0 -72.570459 + 2950 0.59 0.00088069773 -73.994931 0 -73.983099 + 3000 0.6 0.00085472731 -75.406507 0 -75.39472 + 3050 0.61 0.00082842975 -76.814319 0 -76.802575 + 3100 0.62 0.00080642669 -78.216074 0 -78.204373 + 3150 0.63 0.00079464 -79.610246 0 -79.59859 + 3200 0.64 0.00079623049 -80.996103 0 -80.984494 + 3250 0.65 0.00080980416 -82.373461 0 -82.361903 + 3300 0.66 0.00083070997 -83.742356 0 -83.730856 + 3350 0.67 0.00085389223 -85.102809 0 -85.091374 + 3400 0.68 0.00087624159 -86.454619 0 -86.44326 + 3450 0.69 0.00089742086 -87.79709 0 -87.785815 + 3500 0.7 0.00091910931 -89.12875 0 -89.117568 + 3550 0.71 0.00094318635 -90.447312 0 -90.436233 + 3600 0.72 0.00096989594 -91.750008 0 -91.739047 + 3650 0.73 0.00099713386 -93.034224 0 -93.023403 + 3700 0.74 0.0010213031 -94.298186 0 -94.287529 + 3750 0.75 0.0010391209 -95.541401 0 -95.530926 + 3800 0.76 0.0010491514 -96.764626 0 -96.754339 + 3850 0.77 0.0010521296 -97.969347 0 -97.959231 + 3900 0.78 0.0010500386 -99.156876 0 -99.146899 + 3950 0.79 0.0010447106 -100.32743 0 -100.31756 + 4000 0.8 0.0010369046 -101.4796 0 -101.46978 + 4050 0.81 0.0010263688 -102.61044 0 -102.60064 + 4100 0.82 0.0010126985 -103.71619 0 -103.70639 + 4150 0.83 0.00099632366 -104.79338 0 -104.78358 + 4200 0.84 0.00097891183 -105.8398 0 -105.82998 + 4250 0.85 0.00096288003 -106.85496 0 -106.84515 + 4300 0.86 0.00095034371 -107.84011 0 -107.83029 + 4350 0.87 0.00094219371 -108.7976 0 -108.78778 + 4400 0.88 0.00093779663 -109.73016 0 -109.72031 + 4450 0.89 0.00093544766 -110.63996 0 -110.63008 + 4500 0.9 0.00093342739 -111.52805 0 -111.51812 + 4550 0.91 0.00093110855 -112.39417 0 -112.38416 + 4600 0.92 0.00092926746 -113.23706 0 -113.22697 + 4650 0.93 0.00092921608 -114.05512 0 -114.04495 + 4700 0.94 0.0009314263 -114.84701 0 -114.83675 + 4750 0.95 0.0009347987 -115.61197 0 -115.60164 + 4800 0.96 0.00093697985 -116.3499 0 -116.33951 + 4850 0.97 0.00093516726 -117.06128 0 -117.05084 + 4900 0.98 0.00092684316 -117.74695 0 -117.73645 + 4950 0.99 0.00091046061 -118.40798 0 -118.39742 + 5000 1 0.00088619727 -119.04554 0 -119.03492 +Loop time of 37.142 on 4 procs for 5000 steps with 5780 atoms + +Performance: 2.326 ns/day, 10.317 hours/ns, 134.619 timesteps/s +98.7% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 6.2804 | 6.3487 | 6.4569 | 2.7 | 17.09 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.15385 | 0.27957 | 0.36215 | 14.6 | 0.75 +Output | 10.573 | 10.784 | 10.994 | 4.8 | 29.03 +Modify | 19.48 | 19.707 | 19.925 | 3.7 | 53.06 +Other | | 0.02255 | | | 0.06 + +Nlocal: 1445 ave 1445 max 1445 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 555 ave 555 max 555 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 23120 ave 23120 max 23120 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 92480 +Ave neighs/atom = 16 +Neighbor list builds = 0 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:37 diff --git a/examples/SPIN/cobalt_fcc/Co_PurjaPun_2012.eam.alloy b/examples/SPIN/cobalt_fcc/Co_PurjaPun_2012.eam.alloy new file mode 100644 index 0000000000..3af058baf7 --- /dev/null +++ b/examples/SPIN/cobalt_fcc/Co_PurjaPun_2012.eam.alloy @@ -0,0 +1,6006 @@ +Cobalt EAM potential: G. P. Purja Pun and Y. Mishin, Phys. Rev. B xx, 004100 (2012) (in press) +Data below r = 1.5 A is extrapolated. F(Rho) data not extrapolated. +Created on Wed Sep 26 17:29:54 2012 +1 Co +10000 4.788742913000000e-04 10000 6.499539000000001e-04 6.499539000000000e+00 +27 5.893320000000000e+01 2.507000000000000e+00 hcp + -1.680303080000000e-02 -1.879913964471138e-02 -2.091739081044659e-02 -2.303564197615629e-02 -2.503175082079116e-02 + -2.681996612041136e-02 -2.846010103933253e-02 -3.003179469400266e-02 -3.154842562124295e-02 -3.300931506782415e-02 + -3.442381570000001e-02 -3.580233366714632e-02 -3.714945763166951e-02 -3.846832763111274e-02 -3.976210669053554e-02 + -4.103374908125148e-02 -4.228535107207521e-02 -4.351872320172212e-02 -4.473539109100971e-02 -4.593674531110434e-02 + -4.712392115246503e-02 -4.829795108118731e-02 -4.945971154662068e-02 -5.061001094949964e-02 -5.174954151284258e-02 + -5.287894548568519e-02 -5.399878139884967e-02 -5.510957102742049e-02 -5.621177284174523e-02 -5.730581735016625e-02 + -5.839208651773948e-02 -5.947094067448531e-02 -6.054270215356945e-02 -6.160767623453070e-02 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2.671593859185241e-07 2.498478511400059e-07 2.333896726605378e-07 2.177564985206194e-07 2.029204500538344e-07 + 1.888541210793108e-07 1.755305458522738e-07 1.629232393506973e-07 1.510062144201093e-07 1.397539174372155e-07 + 1.291412703741045e-07 1.191437050672961e-07 1.097370923617762e-07 1.008977778162274e-07 9.260259669902208e-08 + 8.482883141984319e-08 7.755426670738778e-08 7.075715683240311e-08 6.441620467100832e-08 5.851063608240125e-08 + 5.302013495440350e-08 4.792483459927075e-08 4.320538955913144e-08 3.884291294265582e-08 3.481898425658018e-08 + 3.111569527451850e-08 2.771559342817648e-08 2.460171067137196e-08 2.175758348333717e-08 1.916719757773861e-08 + 1.681503457183268e-08 1.468607978947252e-08 1.276576812429566e-08 1.104003874048358e-08 9.495328649625366e-09 + 8.118528715645258e-09 6.897042498203040e-09 5.818760232281117e-09 4.872032311209139e-09 4.045732447740840e-09 + 3.329210679517489e-09 2.712284881132093e-09 2.185301687016959e-09 1.739076161987666e-09 1.364901589086205e-09 + 1.054599065845252e-09 8.004535320102697e-10 5.952414597054672e-10 4.322622496028902e-10 3.052766304104823e-10 + 2.085502003918036e-10 1.368642901349301e-10 8.546164059834664e-11 5.010215808832263e-11 2.705311520847365e-11 + 1.304599438344934e-11 5.339090781311160e-12 1.692041320615927e-12 3.321208355096226e-13 6.781366937015517e-15 diff --git a/examples/SPIN/cobalt_fcc/exchange_fit_fcc_co/exchange_fcc_cobalt.dat b/examples/SPIN/cobalt_fcc/exchange_fit_fcc_co/exchange_fcc_cobalt.dat new file mode 100644 index 0000000000..dce45c090d --- /dev/null +++ b/examples/SPIN/cobalt_fcc/exchange_fit_fcc_co/exchange_fcc_cobalt.dat @@ -0,0 +1,5 @@ +2.503 0.01476 +3.54 0.001497 +4.33 0.001578 +5.01 -0.001224 +5.597 0.000354 diff --git a/examples/SPIN/cobalt_fcc/exchange_fit_fcc_co/exchange_fit.py b/examples/SPIN/cobalt_fcc/exchange_fit_fcc_co/exchange_fit.py new file mode 100644 index 0000000000..09be6db3e4 --- /dev/null +++ b/examples/SPIN/cobalt_fcc/exchange_fit_fcc_co/exchange_fit.py @@ -0,0 +1,32 @@ +#Program fitting the exchange interaction +#Model curve: Bethe-Slater function +import numpy as np, pylab, tkinter +import matplotlib.pyplot as plt +from scipy.optimize import curve_fit +from decimal import * + +print("Loop begin") + +#Definition of the Bethe-Slater function +def func(x,a,b,c): + return 4*a*((x/c)**2)*(1-b*(x/c)**2)*np.exp(-(x/c)**2) + +#Exchange coeff table (data to fit) +rdata, Jdata = np.loadtxt('exchange_fcc_cobalt.dat', usecols=(0,1), unpack=True) +plt.plot(rdata, Jdata, 'b-', label='data') + +#Perform the fit +popt, pcov = curve_fit(func, rdata, Jdata, bounds=(0, [500.,5.,5.])) +plt.plot(rdata, func(rdata, *popt), 'r--', label='fit') + +#Print the fitted params +print("Parameters: a={:.10} (in meV), b={:.10} (adim), c={:.10} (in Ang)".format(*popt)) + +#Ploting the result +plt.xlabel('r_ij') +pylab.xlim([0,6.5]) +plt.ylabel('J_ij') +plt.legend() +plt.show() + +print("Loop end") diff --git a/examples/SPIN/cobalt_fcc/in.spin.cobalt_fcc b/examples/SPIN/cobalt_fcc/in.spin.cobalt_fcc new file mode 100644 index 0000000000..fd6833727b --- /dev/null +++ b/examples/SPIN/cobalt_fcc/in.spin.cobalt_fcc @@ -0,0 +1,63 @@ +# fcc cobalt in a 3d periodic box + +clear +units metal +atom_style spin + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice fcc 3.54 +region box block 0.0 5.0 0.0 5.0 0.0 5.0 +create_box 1 box +create_atoms 1 box + +# setting mass, mag. moments, and interactions for fcc cobalt + +mass 1 58.93 + +#set group all spin/random 31 1.72 +set group all spin 1.72 0.0 0.0 1.0 +velocity all create 100 4928459 rot yes dist gaussian + +pair_style hybrid/overlay eam/alloy spin/exchange 4.0 +pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co +pair_coeff * * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885 + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +fix 1 all precession/spin zeeman 1.0 0.0 0.0 1.0 +fix_modify 1 energy yes + +fix 2 all langevin/spin 0.0 0.0 21 + +fix 3 all nve/spin lattice yes +timestep 0.0001 + +# compute and output options + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +thermo_style custom f_1 + +variable magx equal c_out_mag[1] +variable magy equal c_out_mag[2] +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo_style custom step time f_1 v_magx v_magy v_magnorm v_emag temp etotal +thermo 50 + +#compute outsp all property/atom spx spy spz sp fmx fmy fmz +#dump 100 all custom 1 dump_cobalt_fcc.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] + +run 1000 diff --git a/examples/SPIN/cobalt_fcc/log.11May18.spin.cobalt_fcc.g++.1 b/examples/SPIN/cobalt_fcc/log.11May18.spin.cobalt_fcc.g++.1 new file mode 100644 index 0000000000..d832b0001a --- /dev/null +++ b/examples/SPIN/cobalt_fcc/log.11May18.spin.cobalt_fcc.g++.1 @@ -0,0 +1,142 @@ +LAMMPS (11 May 2018) +# fcc cobalt in a 3d periodic box + +clear +units metal +atom_style spin + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice fcc 3.54 +Lattice spacing in x,y,z = 3.54 3.54 3.54 +region box block 0.0 5.0 0.0 5.0 0.0 5.0 +create_box 1 box +Created orthogonal box = (0 0 0) to (17.7 17.7 17.7) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 500 atoms + Time spent = 0.000651121 secs + +# setting mass, mag. moments, and interactions for fcc cobalt + +mass 1 58.93 + +#set group all spin/random 31 1.72 +set group all spin 1.72 0.0 0.0 1.0 + 500 settings made for spin +velocity all create 100 4928459 rot yes dist gaussian + +pair_style hybrid/overlay eam/alloy spin/exchange 4.0 +pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co +pair_coeff * * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885 + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +fix 1 all precession/spin zeeman 1.0 0.0 0.0 1.0 +fix_modify 1 energy yes + +fix 2 all langevin/spin 0.0 0.0 21 + +fix 3 all nve/spin lattice yes +timestep 0.0001 + +# compute and output options + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +thermo_style custom f_1 + +variable magx equal c_out_mag[1] +variable magy equal c_out_mag[2] +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo_style custom step time f_1 v_magx v_magy v_magnorm v_emag temp etotal +thermo 50 + +#compute outsp all property/atom spx spy spz sp fmx fmy fmz +#dump 100 all custom 1 dump_cobalt_fcc.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] + +run 1000 +Neighbor list info ... + update every 10 steps, delay 20 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.59954 + ghost atom cutoff = 6.59954 + binsize = 3.29977, bins = 6 6 6 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair eam/alloy, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.218 | 5.218 | 5.218 Mbytes +Step Time f_1 v_magx v_magy v_magnorm v_emag Temp TotEng + 0 0 0.049785486 0 0 1 -187.94116 100.00543 -2372.4636 + 50 0.005 0.049785486 0 0 1 -187.94112 95.094679 -2372.4636 + 100 0.01 0.049785486 0 0 1 -187.94071 81.578321 -2372.4636 + 150 0.015 0.049785486 0 0 1 -187.93912 62.802727 -2372.4636 + 200 0.02 0.049785486 0 0 1 -187.93551 43.35108 -2372.4636 + 250 0.025 0.049785486 0 0 1 -187.92942 27.749821 -2372.4636 + 300 0.03 0.049785486 0 0 1 -187.92118 19.149389 -2372.4636 + 350 0.035 0.049785486 0 0 1 -187.91199 18.453387 -2372.4636 + 400 0.04 0.049785486 0 0 1 -187.90364 24.249423 -2372.4636 + 450 0.045 0.049785486 0 0 1 -187.89806 33.548008 -2372.4636 + 500 0.05 0.049785486 0 0 1 -187.89668 42.973172 -2372.4636 + 550 0.055 0.049785486 0 0 1 -187.9 49.902539 -2372.4636 + 600 0.06 0.049785486 0 0 1 -187.90735 53.166772 -2372.4636 + 650 0.065 0.049785486 0 0 1 -187.91706 53.153416 -2372.4636 + 700 0.07 0.049785486 0 0 1 -187.92692 51.377187 -2372.4636 + 750 0.075 0.049785486 0 0 1 -187.9348 49.725449 -2372.4636 + 800 0.08 0.049785486 0 0 1 -187.93921 49.663576 -2372.4636 + 850 0.085 0.049785486 0 0 1 -187.93974 51.681567 -2372.4636 + 900 0.09 0.049785486 0 0 1 -187.937 55.166554 -2372.4636 + 950 0.095 0.049785486 0 0 1 -187.93239 58.718232 -2372.4636 + 1000 0.1 0.049785486 0 0 1 -187.92755 60.75567 -2372.4636 +Loop time of 4.1303 on 1 procs for 1000 steps with 500 atoms + +Performance: 2.092 ns/day, 11.473 hours/ns, 242.113 timesteps/s +99.9% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.142 | 2.142 | 2.142 | 0.0 | 51.86 +Neigh | 0.0094573 | 0.0094573 | 0.0094573 | 0.0 | 0.23 +Comm | 0.023293 | 0.023293 | 0.023293 | 0.0 | 0.56 +Output | 0.00031972 | 0.00031972 | 0.00031972 | 0.0 | 0.01 +Modify | 1.9488 | 1.9488 | 1.9488 | 0.0 | 47.18 +Other | | 0.006488 | | | 0.16 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1956 ave 1956 max 1956 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 24065 ave 24065 max 24065 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 48130 ave 48130 max 48130 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 48130 +Ave neighs/atom = 96.26 +Neighbor list builds = 6 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:04 diff --git a/examples/SPIN/cobalt_fcc/log.11May18.spin.cobalt_fcc.g++.4 b/examples/SPIN/cobalt_fcc/log.11May18.spin.cobalt_fcc.g++.4 new file mode 100644 index 0000000000..358d7cfc7a --- /dev/null +++ b/examples/SPIN/cobalt_fcc/log.11May18.spin.cobalt_fcc.g++.4 @@ -0,0 +1,142 @@ +LAMMPS (11 May 2018) +# fcc cobalt in a 3d periodic box + +clear +units metal +atom_style spin + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice fcc 3.54 +Lattice spacing in x,y,z = 3.54 3.54 3.54 +region box block 0.0 5.0 0.0 5.0 0.0 5.0 +create_box 1 box +Created orthogonal box = (0 0 0) to (17.7 17.7 17.7) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 500 atoms + Time spent = 0.000240088 secs + +# setting mass, mag. moments, and interactions for fcc cobalt + +mass 1 58.93 + +#set group all spin/random 31 1.72 +set group all spin 1.72 0.0 0.0 1.0 + 500 settings made for spin +velocity all create 100 4928459 rot yes dist gaussian + +pair_style hybrid/overlay eam/alloy spin/exchange 4.0 +pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co +pair_coeff * * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885 + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +fix 1 all precession/spin zeeman 1.0 0.0 0.0 1.0 +fix_modify 1 energy yes + +fix 2 all langevin/spin 0.0 0.0 21 + +fix 3 all nve/spin lattice yes +timestep 0.0001 + +# compute and output options + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +thermo_style custom f_1 + +variable magx equal c_out_mag[1] +variable magy equal c_out_mag[2] +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo_style custom step time f_1 v_magx v_magy v_magnorm v_emag temp etotal +thermo 50 + +#compute outsp all property/atom spx spy spz sp fmx fmy fmz +#dump 100 all custom 1 dump_cobalt_fcc.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] + +run 1000 +Neighbor list info ... + update every 10 steps, delay 20 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.59954 + ghost atom cutoff = 6.59954 + binsize = 3.29977, bins = 6 6 6 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair eam/alloy, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.163 | 5.163 | 5.163 Mbytes +Step Time f_1 v_magx v_magy v_magnorm v_emag Temp TotEng + 0 0 0.049785486 0 0 1 -187.94116 100.00543 -2372.4636 + 50 0.005 0.049785486 0 0 1 -187.94101 95.174807 -2372.4636 + 100 0.01 0.049785486 0 0 1 -187.94029 81.854304 -2372.4636 + 150 0.015 0.049785486 0 0 1 -187.93834 63.270938 -2372.4636 + 200 0.02 0.049785486 0 0 1 -187.93446 43.867262 -2372.4636 + 250 0.025 0.049785486 0 0 1 -187.92831 28.075261 -2372.4636 + 300 0.03 0.049785486 0 0 1 -187.92031 19.046222 -2372.4636 + 350 0.035 0.049785486 0 0 1 -187.91161 17.79071 -2372.4636 + 400 0.04 0.049785486 0 0 1 -187.9039 23.079994 -2372.4636 + 450 0.045 0.049785486 0 0 1 -187.89895 32.127316 -2372.4636 + 500 0.05 0.049785486 0 0 1 -187.89801 41.709644 -2372.4636 + 550 0.055 0.049785486 0 0 1 -187.90146 49.246292 -2372.4636 + 600 0.06 0.049785486 0 0 1 -187.90859 53.465535 -2372.4636 + 650 0.065 0.049785486 0 0 1 -187.91778 54.522857 -2372.4636 + 700 0.07 0.049785486 0 0 1 -187.9269 53.635521 -2372.4636 + 750 0.075 0.049785486 0 0 1 -187.93396 52.419678 -2372.4636 + 800 0.08 0.049785486 0 0 1 -187.9376 52.176558 -2372.4636 + 850 0.085 0.049785486 0 0 1 -187.93744 53.380592 -2372.4636 + 900 0.09 0.049785486 0 0 1 -187.93412 55.551378 -2372.4636 + 950 0.095 0.049785486 0 0 1 -187.92902 57.540047 -2372.4636 + 1000 0.1 0.049785486 0 0 1 -187.92378 58.088674 -2372.4636 +Loop time of 1.71411 on 4 procs for 1000 steps with 500 atoms + +Performance: 5.041 ns/day, 4.761 hours/ns, 583.392 timesteps/s +97.7% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.54717 | 0.57392 | 0.58784 | 2.1 | 33.48 +Neigh | 0.0023484 | 0.0025793 | 0.0026793 | 0.3 | 0.15 +Comm | 0.058548 | 0.073335 | 0.10006 | 5.9 | 4.28 +Output | 0.00042272 | 0.00079203 | 0.0018559 | 0.0 | 0.05 +Modify | 1.0577 | 1.0611 | 1.0625 | 0.2 | 61.90 +Other | | 0.00239 | | | 0.14 + +Nlocal: 125 ave 133 max 116 min +Histogram: 1 0 0 0 0 2 0 0 0 1 +Nghost: 1099 ave 1108 max 1091 min +Histogram: 1 0 0 0 2 0 0 0 0 1 +Neighs: 6032.5 ave 6417 max 5489 min +Histogram: 1 0 0 0 0 0 1 1 0 1 +FullNghs: 12065 ave 13062 max 10970 min +Histogram: 1 0 0 0 0 2 0 0 0 1 + +Total # of neighbors = 48260 +Ave neighs/atom = 96.52 +Neighbor list builds = 6 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:01 diff --git a/examples/SPIN/cobalt_hcp/Co_PurjaPun_2012.eam.alloy b/examples/SPIN/cobalt_hcp/Co_PurjaPun_2012.eam.alloy new file mode 120000 index 0000000000..6a47c9eebe --- /dev/null +++ b/examples/SPIN/cobalt_hcp/Co_PurjaPun_2012.eam.alloy @@ -0,0 +1 @@ +../cobalt_fcc/Co_PurjaPun_2012.eam.alloy \ No newline at end of file diff --git a/examples/SPIN/cobalt_hcp/exchange_fit_hcp_co/exchange_fit.py b/examples/SPIN/cobalt_hcp/exchange_fit_hcp_co/exchange_fit.py new file mode 100644 index 0000000000..fa7dba417e --- /dev/null +++ b/examples/SPIN/cobalt_hcp/exchange_fit_hcp_co/exchange_fit.py @@ -0,0 +1,32 @@ +#Program fitting the exchange interaction +#Model curve: Bethe-Slater function +import numpy as np, pylab, tkinter +import matplotlib.pyplot as plt +from scipy.optimize import curve_fit +from decimal import * + +print("Loop begin") + +#Definition of the Bethe-Slater function +def func(x,a,b,c): + return 4*a*((x/c)**2)*(1-b*(x/c)**2)*np.exp(-(x/c)**2) + +#Exchange coeff table (data to fit) +rdata, Jdata = np.loadtxt('exchange_hcp_co.dat', usecols=(0,1), unpack=True) +plt.plot(rdata, Jdata, 'b-', label='data') + +#Perform the fit +popt, pcov = curve_fit(func, rdata, Jdata, bounds=(0, [500.,5.,5.])) +plt.plot(rdata, func(rdata, *popt), 'r--', label='fit') + +#Print the fitted params +print("Parameters: a={:.10} (in meV), b={:.10} (adim), c={:.10} (in Ang)".format(*popt)) + +#Ploting the result +plt.xlabel('r_ij') +pylab.xlim([0,6.5]) +plt.ylabel('J_ij') +plt.legend() +plt.show() + +print("Loop end") diff --git a/examples/SPIN/cobalt_hcp/exchange_fit_hcp_co/exchange_hcp_co.dat b/examples/SPIN/cobalt_hcp/exchange_fit_hcp_co/exchange_hcp_co.dat new file mode 100644 index 0000000000..0968fa3edb --- /dev/null +++ b/examples/SPIN/cobalt_hcp/exchange_fit_hcp_co/exchange_hcp_co.dat @@ -0,0 +1,9 @@ +2.25569176882662 73.37931034482759 +2.3817863397548162 47.99999999999999 +2.4518388791593697 34.39080459770115 +2.507880910683012 31.816091954022987 +2.5359019264448337 28.137931034482747 +2.5779334500875657 25.011494252873554 +2.6339754816112086 19.126436781609186 +2.760070052539404 13.241379310344826 +3.5446584938704033 6.068965517241367 diff --git a/examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp b/examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp new file mode 100644 index 0000000000..35aa1df86c --- /dev/null +++ b/examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp @@ -0,0 +1,59 @@ +# hcp cobalt in a 3d periodic box + +clear +units metal +atom_style spin + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice hcp 2.5071 +region box block 0.0 5.0 0.0 5.0 0.0 5.0 +create_box 1 box +create_atoms 1 box + +# setting mass, mag. moments, and interactions for hcp cobalt + +mass 1 58.93 + +set group all spin/random 31 1.72 +#set group all spin 1.72 0.0 0.0 1.0 +velocity all create 100 4928459 rot yes dist gaussian + +#pair_style hybrid/overlay eam/alloy spin/exchange 4.0 spin/neel 4.0 +pair_style hybrid/overlay eam/alloy spin/exchange 4.0 +pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co +pair_coeff * * spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567 +#pair_coeff * * spin/neel neel 4.0 0.0048 0.234 1.168 2.6905 0.705 0.652 + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +#fix 1 all precession/spin zeeman 1.0 0.0 0.0 1.0 +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 +fix 2 all langevin/spin 0.0 0.0 21 +fix 3 all nve/spin lattice yes + +timestep 0.0001 + + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo_style custom step time v_magnorm v_emag temp etotal +thermo 10 + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 100 all custom 1 dump_cobalt_hcp.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] + +run 20000 diff --git a/examples/SPIN/cobalt_hcp/log.11May18.spin.cobalt_hcp.g++.1 b/examples/SPIN/cobalt_hcp/log.11May18.spin.cobalt_hcp.g++.1 new file mode 100644 index 0000000000..4bb513de18 --- /dev/null +++ b/examples/SPIN/cobalt_hcp/log.11May18.spin.cobalt_hcp.g++.1 @@ -0,0 +1,318 @@ +LAMMPS (11 May 2018) +# hcp cobalt in a 3d periodic box + +clear +units metal +atom_style spin + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice hcp 2.5071 +Lattice spacing in x,y,z = 2.5071 4.34242 4.09408 +region box block 0.0 5.0 0.0 5.0 0.0 5.0 +create_box 1 box +Created orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 500 atoms + Time spent = 0.000801802 secs + +# setting mass, mag. moments, and interactions for hcp cobalt + +mass 1 58.93 + +#set group all spin/random 31 1.72 +set group all spin 1.72 0.0 0.0 1.0 + 500 settings made for spin +velocity all create 100 4928459 rot yes dist gaussian + +#pair_style hybrid/overlay eam/alloy spin/exchange 4.0 spin/neel 4.0 +pair_style hybrid/overlay eam/alloy spin/exchange 4.0 +pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co +pair_coeff * * spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567 +#pair_coeff * * spin/neel neel 4.0 0.0048 0.234 1.168 2.6905 0.705 0.652 + + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +fix 1 all precession/spin zeeman 1.0 0.0 0.0 1.0 +fix 2 all langevin/spin 0.0 0.0 21 +fix 3 all nve/spin lattice yes + +timestep 0.0001 + + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo_style custom step time v_magnorm v_emag temp etotal +thermo 10 + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 100 all custom 1 dump_cobalt_hcp.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] + +run 2000 +Neighbor list info ... + update every 10 steps, delay 20 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.59954 + ghost atom cutoff = 6.59954 + binsize = 3.29977, bins = 4 7 7 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair eam/alloy, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 7.401 | 7.401 | 7.401 Mbytes +Step Time v_magnorm v_emag Temp TotEng + 0 0 1 -187.29499 100.00543 -2375.8943 + 10 0.001 1 -187.29714 99.845593 -2375.8943 + 20 0.002 1 -187.30356 99.367234 -2375.8943 + 30 0.003 1 -187.31419 98.573996 -2375.8943 + 40 0.004 1 -187.32896 97.472027 -2375.8943 + 50 0.005 1 -187.34772 96.069944 -2375.8943 + 60 0.006 1 -187.37032 94.378764 -2375.8943 + 70 0.007 1 -187.39656 92.411827 -2375.8943 + 80 0.008 1 -187.4262 90.184697 -2375.8943 + 90 0.009 1 -187.459 87.715037 -2375.8943 + 100 0.01 1 -187.49466 85.022479 -2375.8943 + 110 0.011 1 -187.53289 82.128462 -2375.8943 + 120 0.012 1 -187.57334 79.05606 -2375.8943 + 130 0.013 1 -187.61568 75.82979 -2375.8943 + 140 0.014 1 -187.65953 72.475403 -2375.8943 + 150 0.015 1 -187.70453 69.019658 -2375.8943 + 160 0.016 1 -187.75028 65.490086 -2375.8943 + 170 0.017 1 -187.79642 61.914735 -2375.8943 + 180 0.018 1 -187.84254 58.321911 -2375.8943 + 190 0.019 1 -187.88828 54.739907 -2375.8943 + 200 0.02 1 -187.93324 51.196728 -2375.8943 + 210 0.021 1 -187.97708 47.719812 -2375.8943 + 220 0.022 1 -188.01947 44.335762 -2375.8943 + 230 0.023 1 -188.06003 41.07007 -2375.8943 + 240 0.024 1 -188.09853 37.946852 -2375.8944 + 250 0.025 1 -188.13457 34.988599 -2375.8944 + 260 0.026 1 -188.16795 32.215943 -2375.8944 + 270 0.027 1 -188.19851 29.647465 -2375.8944 + 280 0.028 1 -188.22593 27.299481 -2375.8944 + 290 0.029 1 -188.25011 25.185896 -2375.8944 + 300 0.03 1 -188.27095 23.318075 -2375.8945 + 310 0.031 1 -188.2883 21.70475 -2375.8945 + 320 0.032 1 -188.30213 20.35194 -2375.8945 + 330 0.033 1 -188.31251 19.262946 -2375.8945 + 340 0.034 1 -188.31928 18.438347 -2375.8945 + 350 0.035 1 -188.32258 17.876036 -2375.8945 + 360 0.036 1 -188.32249 17.571322 -2375.8945 + 370 0.037 1 -188.31913 17.517032 -2375.8945 + 380 0.038 1 -188.31264 17.703653 -2375.8945 + 390 0.039 1 -188.30321 18.119513 -2375.8945 + 400 0.04 1 -188.29102 18.750969 -2375.8945 + 410 0.041 1 -188.2763 19.582631 -2375.8945 + 420 0.042 1 -188.25929 20.597597 -2375.8945 + 430 0.043 1 -188.24025 21.777699 -2375.8945 + 440 0.044 1 -188.21945 23.103765 -2375.8945 + 450 0.045 1 -188.19719 24.555878 -2375.8946 + 460 0.046 1 -188.17368 26.113643 -2375.8946 + 470 0.047 1 -188.1493 27.756439 -2375.8946 + 480 0.048 1 -188.12429 29.463677 -2375.8946 + 490 0.049 1 -188.09895 31.21504 -2375.8946 + 500 0.05 1 -188.07354 32.990713 -2375.8946 + 510 0.051 1 -188.04832 34.771601 -2375.8945 + 520 0.052 1 -188.02358 36.539517 -2375.8945 + 530 0.053 1 -187.99951 38.27736 -2375.8945 + 540 0.054 1 -187.97636 39.969275 -2375.8945 + 550 0.055 1 -187.95437 41.600775 -2375.8945 + 560 0.056 1 -187.93364 43.158863 -2375.8944 + 570 0.057 1 -187.9144 44.632119 -2375.8944 + 580 0.058 1 -187.89669 46.010765 -2375.8944 + 590 0.059 1 -187.88074 47.286714 -2375.8944 + 600 0.06 1 -187.86658 48.453573 -2375.8944 + 610 0.061 1 -187.85422 49.506668 -2375.8943 + 620 0.062 1 -187.84377 50.443021 -2375.8943 + 630 0.063 1 -187.8352 51.261297 -2375.8943 + 640 0.064 1 -187.8285 51.961764 -2375.8943 + 650 0.065 1 -187.8236 52.54622 -2375.8943 + 660 0.066 1 -187.8205 53.017899 -2375.8943 + 670 0.067 1 -187.81909 53.381374 -2375.8943 + 680 0.068 1 -187.81926 53.64244 -2375.8943 + 690 0.069 1 -187.82092 53.807997 -2375.8943 + 700 0.07 1 -187.82391 53.885909 -2375.8943 + 710 0.071 1 -187.82814 53.884865 -2375.8943 + 720 0.072 1 -187.83339 53.814238 -2375.8943 + 730 0.073 1 -187.83952 53.68392 -2375.8943 + 740 0.074 1 -187.84635 53.504185 -2375.8943 + 750 0.075 1 -187.85375 53.285525 -2375.8943 + 760 0.076 1 -187.86153 53.038494 -2375.8943 + 770 0.077 1 -187.86952 52.773567 -2375.8943 + 780 0.078 1 -187.87758 52.500994 -2375.8943 + 790 0.079 1 -187.88549 52.230655 -2375.8943 + 800 0.08 1 -187.89313 51.971933 -2375.8943 + 810 0.081 1 -187.90035 51.733593 -2375.8943 + 820 0.082 1 -187.90702 51.523671 -2375.8943 + 830 0.083 1 -187.91302 51.349376 -2375.8943 + 840 0.084 1 -187.91824 51.217006 -2375.8943 + 850 0.085 1 -187.9226 51.131875 -2375.8943 + 860 0.086 1 -187.92602 51.098259 -2375.8943 + 870 0.087 1 -187.92844 51.119356 -2375.8943 + 880 0.088 1 -187.92979 51.197261 -2375.8943 + 890 0.089 1 -187.93011 51.332955 -2375.8943 + 900 0.09 1 -187.92937 51.526314 -2375.8943 + 910 0.091 1 -187.92757 51.77613 -2375.8943 + 920 0.092 1 -187.92475 52.080145 -2375.8943 + 930 0.093 1 -187.92096 52.435106 -2375.8943 + 940 0.094 1 -187.91624 52.836825 -2375.8943 + 950 0.095 1 -187.91068 53.280251 -2375.8943 + 960 0.096 1 -187.90435 53.759559 -2375.8943 + 970 0.097 1 -187.89734 54.268246 -2375.8943 + 980 0.098 1 -187.88981 54.799223 -2375.8943 + 990 0.099 1 -187.88185 55.344928 -2375.8943 + 1000 0.1 1 -187.87357 55.897438 -2375.8943 + 1010 0.101 1 -187.86511 56.448585 -2375.8943 + 1020 0.102 1 -187.8566 56.990069 -2375.8943 + 1030 0.103 1 -187.84817 57.513575 -2375.8943 + 1040 0.104 1 -187.83995 58.010887 -2375.8943 + 1050 0.105 1 -187.83208 58.474004 -2375.8943 + 1060 0.106 1 -187.8247 58.89524 -2375.8943 + 1070 0.107 1 -187.81789 59.267328 -2375.8943 + 1080 0.108 1 -187.81177 59.583518 -2375.8943 + 1090 0.109 1 -187.80646 59.837665 -2375.8943 + 1100 0.11 1 -187.80204 60.024306 -2375.8943 + 1110 0.111 1 -187.79861 60.138734 -2375.8943 + 1120 0.112 1 -187.79625 60.177056 -2375.8943 + 1130 0.113 1 -187.79497 60.136244 -2375.8943 + 1140 0.114 1 -187.79485 60.014176 -2375.8943 + 1150 0.115 1 -187.7959 59.809665 -2375.8943 + 1160 0.116 1 -187.79811 59.52248 -2375.8943 + 1170 0.117 1 -187.80157 59.153353 -2375.8943 + 1180 0.118 1 -187.80618 58.703971 -2375.8943 + 1190 0.119 1 -187.81193 58.176956 -2375.8943 + 1200 0.12 1 -187.81879 57.575849 -2375.8943 + 1210 0.121 1 -187.82668 56.905072 -2375.8943 + 1220 0.122 1 -187.83554 56.169878 -2375.8943 + 1230 0.123 1 -187.84528 55.376297 -2375.8943 + 1240 0.124 1 -187.85581 54.53107 -2375.8943 + 1250 0.125 1 -187.86702 53.641573 -2375.8943 + 1260 0.126 1 -187.8788 52.715739 -2375.8943 + 1270 0.127 1 -187.89103 51.761969 -2375.8943 + 1280 0.128 1 -187.90358 50.789036 -2375.8943 + 1290 0.129 1 -187.91632 49.805988 -2375.8943 + 1300 0.13 1 -187.92911 48.822045 -2375.8943 + 1310 0.131 1 -187.94182 47.846491 -2375.8943 + 1320 0.132 1 -187.95428 46.888574 -2375.8943 + 1330 0.133 1 -187.96643 45.957394 -2375.8943 + 1340 0.134 1 -187.9781 45.061794 -2375.8943 + 1350 0.135 1 -187.9892 44.210263 -2375.8943 + 1360 0.136 1 -187.99955 43.410832 -2375.8943 + 1370 0.137 1 -188.00907 42.670979 -2375.8943 + 1380 0.138 1 -188.01767 41.997547 -2375.8943 + 1390 0.139 1 -188.02525 41.396655 -2375.8943 + 1400 0.14 1 -188.03177 40.873631 -2375.8944 + 1410 0.141 1 -188.03711 40.432952 -2375.8944 + 1420 0.142 1 -188.04124 40.078172 -2375.8944 + 1430 0.143 1 -188.04413 39.811902 -2375.8944 + 1440 0.144 1 -188.04575 39.635775 -2375.8944 + 1450 0.145 1 -188.04607 39.550435 -2375.8943 + 1460 0.146 1 -188.04515 39.555512 -2375.8943 + 1470 0.147 1 -188.04298 39.649651 -2375.8943 + 1480 0.148 1 -188.03961 39.830523 -2375.8943 + 1490 0.149 1 -188.03508 40.094865 -2375.8943 + 1500 0.15 1 -188.02944 40.438519 -2375.8943 + 1510 0.151 1 -188.02275 40.856491 -2375.8943 + 1520 0.152 1 -188.01515 41.343019 -2375.8943 + 1530 0.153 1 -188.00671 41.891643 -2375.8943 + 1540 0.154 1 -187.99753 42.495295 -2375.8943 + 1550 0.155 1 -187.98772 43.14639 -2375.8943 + 1560 0.156 1 -187.9774 43.836918 -2375.8943 + 1570 0.157 1 -187.9667 44.558553 -2375.8943 + 1580 0.158 1 -187.95576 45.302751 -2375.8943 + 1590 0.159 1 -187.94466 46.060862 -2375.8943 + 1600 0.16 1 -187.93356 46.824226 -2375.8943 + 1610 0.161 1 -187.92257 47.584289 -2375.8943 + 1620 0.162 1 -187.91183 48.332703 -2375.8943 + 1630 0.163 1 -187.90145 49.061422 -2375.8943 + 1640 0.164 1 -187.89155 49.762798 -2375.8943 + 1650 0.165 1 -187.88222 50.429671 -2375.8943 + 1660 0.166 1 -187.87357 51.055445 -2375.8943 + 1670 0.167 1 -187.86569 51.634167 -2375.8943 + 1680 0.168 1 -187.85864 52.160588 -2375.8943 + 1690 0.169 1 -187.85249 52.630219 -2375.8943 + 1700 0.17 1 -187.8473 53.039377 -2375.8943 + 1710 0.171 1 -187.84311 53.385221 -2375.8943 + 1720 0.172 1 -187.83994 53.665778 -2375.8943 + 1730 0.173 1 -187.83781 53.879954 -2375.8943 + 1740 0.174 1 -187.83671 54.027539 -2375.8943 + 1750 0.175 1 -187.83663 54.109201 -2375.8943 + 1760 0.176 1 -187.83753 54.126472 -2375.8943 + 1770 0.177 1 -187.83941 54.081708 -2375.8943 + 1780 0.178 1 -187.8422 53.97806 -2375.8943 + 1790 0.179 1 -187.84584 53.819424 -2375.8943 + 1800 0.18 1 -187.85025 53.610389 -2375.8943 + 1810 0.181 1 -187.85535 53.356163 -2375.8943 + 1820 0.182 1 -187.86105 53.06251 -2375.8943 + 1830 0.183 1 -187.86723 52.735671 -2375.8943 + 1840 0.184 1 -187.87384 52.382262 -2375.8943 + 1850 0.185 1 -187.88075 52.009201 -2375.8943 + 1860 0.186 1 -187.88784 51.623613 -2375.8943 + 1870 0.187 1 -187.89501 51.232726 -2375.8943 + 1880 0.188 1 -187.90214 50.843782 -2375.8943 + 1890 0.189 1 -187.90912 50.463929 -2375.8943 + 1900 0.19 1 -187.91585 50.100133 -2375.8943 + 1910 0.191 1 -187.92222 49.759075 -2375.8943 + 1920 0.192 1 -187.92814 49.447064 -2375.8943 + 1930 0.193 1 -187.93351 49.169949 -2375.8943 + 1940 0.194 1 -187.93826 48.933036 -2375.8943 + 1950 0.195 1 -187.94232 48.741013 -2375.8943 + 1960 0.196 1 -187.94561 48.597888 -2375.8943 + 1970 0.197 1 -187.94809 48.506926 -2375.8943 + 1980 0.198 1 -187.94972 48.470605 -2375.8943 + 1990 0.199 1 -187.95047 48.490576 -2375.8943 + 2000 0.2 1 -187.95033 48.567643 -2375.8943 +Loop time of 10.5391 on 1 procs for 2000 steps with 500 atoms + +Performance: 1.640 ns/day, 14.638 hours/ns, 189.770 timesteps/s +99.6% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 4.9958 | 4.9958 | 4.9958 | 0.0 | 47.40 +Neigh | 0.020741 | 0.020741 | 0.020741 | 0.0 | 0.20 +Comm | 0.05899 | 0.05899 | 0.05899 | 0.0 | 0.56 +Output | 1.1598 | 1.1598 | 1.1598 | 0.0 | 11.00 +Modify | 4.2885 | 4.2885 | 4.2885 | 0.0 | 40.69 +Other | | 0.01522 | | | 0.14 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 2444 ave 2444 max 2444 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 27041 ave 27041 max 27041 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 54082 ave 54082 max 54082 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 54082 +Ave neighs/atom = 108.164 +Neighbor list builds = 12 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:10 diff --git a/examples/SPIN/cobalt_hcp/log.11May18.spin.cobalt_hcp.g++.4 b/examples/SPIN/cobalt_hcp/log.11May18.spin.cobalt_hcp.g++.4 new file mode 100644 index 0000000000..4e7e6b1b97 --- /dev/null +++ b/examples/SPIN/cobalt_hcp/log.11May18.spin.cobalt_hcp.g++.4 @@ -0,0 +1,318 @@ +LAMMPS (11 May 2018) +# hcp cobalt in a 3d periodic box + +clear +units metal +atom_style spin + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice hcp 2.5071 +Lattice spacing in x,y,z = 2.5071 4.34242 4.09408 +region box block 0.0 5.0 0.0 5.0 0.0 5.0 +create_box 1 box +Created orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 500 atoms + Time spent = 0.000241518 secs + +# setting mass, mag. moments, and interactions for hcp cobalt + +mass 1 58.93 + +#set group all spin/random 31 1.72 +set group all spin 1.72 0.0 0.0 1.0 + 500 settings made for spin +velocity all create 100 4928459 rot yes dist gaussian + +#pair_style hybrid/overlay eam/alloy spin/exchange 4.0 spin/neel 4.0 +pair_style hybrid/overlay eam/alloy spin/exchange 4.0 +pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co +pair_coeff * * spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567 +#pair_coeff * * spin/neel neel 4.0 0.0048 0.234 1.168 2.6905 0.705 0.652 + + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +fix 1 all precession/spin zeeman 1.0 0.0 0.0 1.0 +fix 2 all langevin/spin 0.0 0.0 21 +fix 3 all nve/spin lattice yes + +timestep 0.0001 + + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo_style custom step time v_magnorm v_emag temp etotal +thermo 10 + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 100 all custom 1 dump_cobalt_hcp.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] + +run 2000 +Neighbor list info ... + update every 10 steps, delay 20 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.59954 + ghost atom cutoff = 6.59954 + binsize = 3.29977, bins = 4 7 7 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair eam/alloy, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 7.313 | 7.314 | 7.314 Mbytes +Step Time v_magnorm v_emag Temp TotEng + 0 0 1 -187.29499 100.00543 -2375.8943 + 10 0.001 1 -187.29721 99.841045 -2375.8943 + 20 0.002 1 -187.30385 99.349208 -2375.8943 + 30 0.003 1 -187.31485 98.533905 -2375.8943 + 40 0.004 1 -187.33011 97.401749 -2375.8943 + 50 0.005 1 -187.34949 95.961938 -2375.8943 + 60 0.006 1 -187.37283 94.22618 -2375.8943 + 70 0.007 1 -187.39992 92.208606 -2375.8943 + 80 0.008 1 -187.43051 89.92566 -2375.8943 + 90 0.009 1 -187.46434 87.39597 -2375.8943 + 100 0.01 1 -187.5011 84.640195 -2375.8943 + 110 0.011 1 -187.54047 81.680862 -2375.8943 + 120 0.012 1 -187.5821 78.542172 -2375.8943 + 130 0.013 1 -187.62564 75.249797 -2375.8943 + 140 0.014 1 -187.67069 71.830656 -2375.8943 + 150 0.015 1 -187.71686 68.312673 -2375.8943 + 160 0.016 1 -187.76377 64.724523 -2375.8943 + 170 0.017 1 -187.81099 61.095365 -2375.8943 + 180 0.018 1 -187.85814 57.454566 -2375.8943 + 190 0.019 1 -187.90481 53.831412 -2375.8943 + 200 0.02 1 -187.95061 50.254822 -2375.8943 + 210 0.021 1 -187.99517 46.753056 -2375.8943 + 220 0.022 1 -188.03812 43.353428 -2375.8943 + 230 0.023 1 -188.07913 40.082023 -2375.8943 + 240 0.024 1 -188.11787 36.963429 -2375.8943 + 250 0.025 1 -188.15409 34.020481 -2375.8943 + 260 0.026 1 -188.1875 31.27403 -2375.8943 + 270 0.027 1 -188.21782 28.74271 -2375.8943 + 280 0.028 1 -188.2449 26.44276 -2375.8943 + 290 0.029 1 -188.26857 24.387875 -2375.8943 + 300 0.03 1 -188.28877 22.589076 -2375.8944 + 310 0.031 1 -188.30529 21.054615 -2375.8944 + 320 0.032 1 -188.31814 19.789913 -2375.8944 + 330 0.033 1 -188.3273 18.797563 -2375.8944 + 340 0.034 1 -188.33284 18.077336 -2375.8944 + 350 0.035 1 -188.33478 17.626237 -2375.8945 + 360 0.036 1 -188.33319 17.438611 -2375.8945 + 370 0.037 1 -188.32824 17.506247 -2375.8945 + 380 0.038 1 -188.32007 17.818564 -2375.8945 + 390 0.039 1 -188.30888 18.362769 -2375.8945 + 400 0.04 1 -188.2949 19.124086 -2375.8945 + 410 0.041 1 -188.27837 20.085983 -2375.8945 + 420 0.042 1 -188.25957 21.230423 -2375.8945 + 430 0.043 1 -188.23868 22.538112 -2375.8945 + 440 0.044 1 -188.21604 23.988778 -2375.8945 + 450 0.045 1 -188.19195 25.561447 -2375.8945 + 460 0.046 1 -188.16672 27.234703 -2375.8945 + 470 0.047 1 -188.14064 28.986964 -2375.8946 + 480 0.048 1 -188.11402 30.796738 -2375.8946 + 490 0.049 1 -188.08713 32.642869 -2375.8945 + 500 0.05 1 -188.06032 34.504776 -2375.8945 + 510 0.051 1 -188.03383 36.362662 -2375.8945 + 520 0.052 1 -188.00793 38.197721 -2375.8945 + 530 0.053 1 -187.98284 39.992314 -2375.8945 + 540 0.054 1 -187.95884 41.730127 -2375.8945 + 550 0.055 1 -187.93612 43.396298 -2375.8945 + 560 0.056 1 -187.91489 44.97754 -2375.8945 + 570 0.057 1 -187.89524 46.462224 -2375.8945 + 580 0.058 1 -187.87735 47.840443 -2375.8945 + 590 0.059 1 -187.8613 49.104064 -2375.8945 + 600 0.06 1 -187.84719 50.246744 -2375.8945 + 610 0.061 1 -187.83509 51.26393 -2375.8944 + 620 0.062 1 -187.82506 52.152839 -2375.8944 + 630 0.063 1 -187.81706 52.912413 -2375.8944 + 640 0.064 1 -187.81109 53.543272 -2375.8944 + 650 0.065 1 -187.80708 54.047636 -2375.8944 + 660 0.066 1 -187.80499 54.429234 -2375.8944 + 670 0.067 1 -187.8047 54.693202 -2375.8944 + 680 0.068 1 -187.80613 54.845965 -2375.8944 + 690 0.069 1 -187.80914 54.895106 -2375.8944 + 700 0.07 1 -187.81356 54.849238 -2375.8944 + 710 0.071 1 -187.81923 54.71786 -2375.8943 + 720 0.072 1 -187.82608 54.511181 -2375.8943 + 730 0.073 1 -187.83388 54.239987 -2375.8943 + 740 0.074 1 -187.84244 53.91548 -2375.8943 + 750 0.075 1 -187.85158 53.549112 -2375.8943 + 760 0.076 1 -187.86112 53.152433 -2375.8943 + 770 0.077 1 -187.87086 52.736925 -2375.8943 + 780 0.078 1 -187.88063 52.313858 -2375.8943 + 790 0.079 1 -187.89026 51.894138 -2375.8943 + 800 0.08 1 -187.89958 51.488169 -2375.8943 + 810 0.081 1 -187.90842 51.105725 -2375.8943 + 820 0.082 1 -187.91663 50.755829 -2375.8943 + 830 0.083 1 -187.92411 50.446651 -2375.8943 + 840 0.084 1 -187.93071 50.185404 -2375.8943 + 850 0.085 1 -187.93637 49.978262 -2375.8943 + 860 0.086 1 -187.94099 49.830307 -2375.8943 + 870 0.087 1 -187.9445 49.745473 -2375.8943 + 880 0.088 1 -187.94685 49.726517 -2375.8943 + 890 0.089 1 -187.94802 49.774999 -2375.8943 + 900 0.09 1 -187.94799 49.891282 -2375.8943 + 910 0.091 1 -187.94678 50.074549 -2375.8943 + 920 0.092 1 -187.94441 50.322833 -2375.8943 + 930 0.093 1 -187.94093 50.633063 -2375.8943 + 940 0.094 1 -187.93639 51.001126 -2375.8943 + 950 0.095 1 -187.93089 51.421938 -2375.8943 + 960 0.096 1 -187.9245 51.889531 -2375.8943 + 970 0.097 1 -187.91733 52.397148 -2375.8943 + 980 0.098 1 -187.9095 52.937345 -2375.8943 + 990 0.099 1 -187.90113 53.502108 -2375.8943 + 1000 0.1 1 -187.89236 54.082966 -2375.8943 + 1010 0.101 1 -187.88332 54.671115 -2375.8943 + 1020 0.102 1 -187.87415 55.257545 -2375.8943 + 1030 0.103 1 -187.86501 55.833162 -2375.8943 + 1040 0.104 1 -187.85602 56.388915 -2375.8943 + 1050 0.105 1 -187.84734 56.915918 -2375.8943 + 1060 0.106 1 -187.83909 57.405575 -2375.8943 + 1070 0.107 1 -187.83143 57.849686 -2375.8943 + 1080 0.108 1 -187.82446 58.240564 -2375.8943 + 1090 0.109 1 -187.8183 58.571132 -2375.8943 + 1100 0.11 1 -187.81306 58.835016 -2375.8943 + 1110 0.111 1 -187.80883 59.026633 -2375.8943 + 1120 0.112 1 -187.8057 59.141258 -2375.8943 + 1130 0.113 1 -187.80372 59.17509 -2375.8943 + 1140 0.114 1 -187.80295 59.125305 -2375.8943 + 1150 0.115 1 -187.80341 58.990092 -2375.8943 + 1160 0.116 1 -187.80515 58.76868 -2375.8943 + 1170 0.117 1 -187.80814 58.461352 -2375.8943 + 1180 0.118 1 -187.81244 58.069457 -2375.8943 + 1190 0.119 1 -187.81794 57.595377 -2375.8944 + 1200 0.12 1 -187.82458 57.042514 -2375.8944 + 1210 0.121 1 -187.83233 56.415256 -2375.8944 + 1220 0.122 1 -187.84112 55.718931 -2375.8944 + 1230 0.123 1 -187.85086 54.959744 -2375.8944 + 1240 0.124 1 -187.86145 54.144707 -2375.8944 + 1250 0.125 1 -187.87277 53.281562 -2375.8944 + 1260 0.126 1 -187.88471 52.378686 -2375.8944 + 1270 0.127 1 -187.89713 51.445 -2375.8944 + 1280 0.128 1 -187.9099 50.489858 -2375.8944 + 1290 0.129 1 -187.92288 49.522943 -2375.8944 + 1300 0.13 1 -187.93591 48.554147 -2375.8944 + 1310 0.131 1 -187.94886 47.593456 -2375.8944 + 1320 0.132 1 -187.96157 46.650829 -2375.8944 + 1330 0.133 1 -187.97391 45.736073 -2375.8944 + 1340 0.134 1 -187.98573 44.858733 -2375.8944 + 1350 0.135 1 -187.99691 44.027964 -2375.8944 + 1360 0.136 1 -188.00731 43.252426 -2375.8944 + 1370 0.137 1 -188.01678 42.540178 -2375.8943 + 1380 0.138 1 -188.02529 41.898568 -2375.8943 + 1390 0.139 1 -188.0327 41.334152 -2375.8943 + 1400 0.14 1 -188.03894 40.852606 -2375.8943 + 1410 0.141 1 -188.04396 40.45866 -2375.8944 + 1420 0.142 1 -188.04768 40.156041 -2375.8944 + 1430 0.143 1 -188.05007 39.947416 -2375.8944 + 1440 0.144 1 -188.05107 39.834367 -2375.8944 + 1450 0.145 1 -188.0507 39.817378 -2375.8944 + 1460 0.146 1 -188.04898 39.895828 -2375.8944 + 1470 0.147 1 -188.04595 40.068005 -2375.8945 + 1480 0.148 1 -188.04164 40.331129 -2375.8945 + 1490 0.149 1 -188.03603 40.681394 -2375.8945 + 1500 0.15 1 -188.02929 41.114003 -2375.8945 + 1510 0.151 1 -188.02148 41.623259 -2375.8945 + 1520 0.152 1 -188.0127 42.20263 -2375.8945 + 1530 0.153 1 -188.00302 42.844846 -2375.8945 + 1540 0.154 1 -187.99255 43.541977 -2375.8945 + 1550 0.155 1 -187.98148 44.285554 -2375.8945 + 1560 0.156 1 -187.96989 45.066666 -2375.8945 + 1570 0.157 1 -187.95793 45.876084 -2375.8945 + 1580 0.158 1 -187.94574 46.704378 -2375.8945 + 1590 0.159 1 -187.93346 47.542032 -2375.8945 + 1600 0.16 1 -187.92122 48.379564 -2375.8945 + 1610 0.161 1 -187.90916 49.207642 -2375.8945 + 1620 0.162 1 -187.89742 50.0172 -2375.8945 + 1630 0.163 1 -187.88613 50.799541 -2375.8945 + 1640 0.164 1 -187.87536 51.546446 -2375.8944 + 1650 0.165 1 -187.86531 52.250265 -2375.8944 + 1660 0.166 1 -187.85604 52.904001 -2375.8944 + 1670 0.167 1 -187.84765 53.501394 -2375.8944 + 1680 0.168 1 -187.84021 54.036987 -2375.8944 + 1690 0.169 1 -187.83379 54.506178 -2375.8944 + 1700 0.17 1 -187.82846 54.905273 -2375.8944 + 1710 0.171 1 -187.82424 55.231514 -2375.8944 + 1720 0.172 1 -187.82117 55.483104 -2375.8944 + 1730 0.173 1 -187.81922 55.659221 -2375.8944 + 1740 0.174 1 -187.81843 55.760007 -2375.8944 + 1750 0.175 1 -187.81881 55.786556 -2375.8944 + 1760 0.176 1 -187.82029 55.740888 -2375.8944 + 1770 0.177 1 -187.82284 55.625916 -2375.8944 + 1780 0.178 1 -187.82639 55.445397 -2375.8944 + 1790 0.179 1 -187.83088 55.203871 -2375.8944 + 1800 0.18 1 -187.83623 54.906597 -2375.8944 + 1810 0.181 1 -187.84235 54.559471 -2375.8944 + 1820 0.182 1 -187.84913 54.168949 -2375.8944 + 1830 0.183 1 -187.85646 53.741952 -2375.8943 + 1840 0.184 1 -187.86424 53.28578 -2375.8943 + 1850 0.185 1 -187.87239 52.807988 -2375.8943 + 1860 0.186 1 -187.88077 52.3163 -2375.8943 + 1870 0.187 1 -187.88925 51.81851 -2375.8943 + 1880 0.188 1 -187.89772 51.322368 -2375.8943 + 1890 0.189 1 -187.90605 50.835483 -2375.8943 + 1900 0.19 1 -187.91415 50.365218 -2375.8943 + 1910 0.191 1 -187.92189 49.9186 -2375.8943 + 1920 0.192 1 -187.92917 49.502222 -2375.8943 + 1930 0.193 1 -187.93591 49.122167 -2375.8943 + 1940 0.194 1 -187.94198 48.783928 -2375.8943 + 1950 0.195 1 -187.94737 48.492348 -2375.8943 + 1960 0.196 1 -187.95199 48.25154 -2375.8943 + 1970 0.197 1 -187.95576 48.064862 -2375.8943 + 1980 0.198 1 -187.95866 47.934875 -2375.8943 + 1990 0.199 1 -187.96065 47.863314 -2375.8943 + 2000 0.2 1 -187.96171 47.851079 -2375.8943 +Loop time of 4.40076 on 4 procs for 2000 steps with 500 atoms + +Performance: 3.927 ns/day, 6.112 hours/ns, 454.467 timesteps/s +96.2% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.2934 | 1.3683 | 1.432 | 4.2 | 31.09 +Neigh | 0.005039 | 0.0053418 | 0.0054908 | 0.2 | 0.12 +Comm | 0.12642 | 0.1922 | 0.26891 | 11.6 | 4.37 +Output | 0.39256 | 0.40875 | 0.43431 | 2.5 | 9.29 +Modify | 2.395 | 2.4202 | 2.4352 | 1.0 | 54.99 +Other | | 0.006007 | | | 0.14 + +Nlocal: 125 ave 130 max 122 min +Histogram: 1 1 0 1 0 0 0 0 0 1 +Nghost: 1324 ave 1330 max 1316 min +Histogram: 1 0 0 1 0 0 0 0 0 2 +Neighs: 6747 ave 6959 max 6652 min +Histogram: 2 1 0 0 0 0 0 0 0 1 +FullNghs: 13494 ave 14060 max 13186 min +Histogram: 2 0 0 1 0 0 0 0 0 1 + +Total # of neighbors = 53976 +Ave neighs/atom = 107.952 +Neighbor list builds = 12 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:04 diff --git a/examples/SPIN/iron/Fe_Mishin2006.eam.alloy b/examples/SPIN/iron/Fe_Mishin2006.eam.alloy new file mode 100644 index 0000000000..69231bb7ee --- /dev/null +++ b/examples/SPIN/iron/Fe_Mishin2006.eam.alloy @@ -0,0 +1,15009 @@ +comment 1 +comment 2 +Converted by Ganga P Purja Pun using C++ code on Mon Nov 3 10:48:17 2014 +1 Fe +5001 2.400000000000000e-03 5001 1.134673400048920e-03 5.673367000244601e+00 +26 5.584700000000000e+01 2.855300000000000e+00 BCC + 0.000000000000000e+00 + -2.338738741480766e-02 + -4.628214468925276e-02 + -6.912258036387915e-02 + -9.175603963501618e-02 + -1.141497214000000e-01 + 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-7.315906671893518e-07 + -6.171385461507109e-07 + -5.166657190198488e-07 + -4.289874671965282e-07 + -3.529682224298676e-07 + -2.875261969469119e-07 + -2.316338735426513e-07 + -1.843129441850586e-07 + -1.446395043479685e-07 + -1.117434618507405e-07 + -8.480406305106530e-08 + -6.305553831873507e-08 + -4.578544870958251e-08 + -3.233089380928512e-08 + -2.208448022054805e-08 + -1.449165750478591e-08 + -9.047683233008124e-09 + -5.303766739728543e-09 + -2.863504097386866e-09 + -1.380623394721897e-09 + -5.650641971230870e-10 + -1.790372475752245e-10 + -3.511990521548007e-11 + -8.192061809269277e-13 + 0.000000000000000e+00 diff --git a/examples/SPIN/iron/exchange_fit_bcc_iron/exchange_bcc_iron.dat b/examples/SPIN/iron/exchange_fit_bcc_iron/exchange_bcc_iron.dat new file mode 100644 index 0000000000..58134f2444 --- /dev/null +++ b/examples/SPIN/iron/exchange_fit_bcc_iron/exchange_bcc_iron.dat @@ -0,0 +1,5 @@ +2.4824 0.01948336 +2.8665 0.01109 +4.0538 -0.0002176 +4.753 -0.001714 +4.965 -0.001986 diff --git a/examples/SPIN/iron/exchange_fit_bcc_iron/exchange_fit.py b/examples/SPIN/iron/exchange_fit_bcc_iron/exchange_fit.py new file mode 100644 index 0000000000..ccf84fc233 --- /dev/null +++ b/examples/SPIN/iron/exchange_fit_bcc_iron/exchange_fit.py @@ -0,0 +1,32 @@ +#Program fitting the exchange interaction +#Model curve: Bethe-Slater function +import numpy as np, pylab, tkinter +import matplotlib.pyplot as plt +from scipy.optimize import curve_fit +from decimal import * + +print("Loop begin") + +#Definition of the Bethe-Slater function +def func(x,a,b,c): + return 4*a*((x/c)**2)*(1-b*(x/c)**2)*np.exp(-(x/c)**2) + +#Exchange coeff table (data to fit) +rdata, Jdata = np.loadtxt('exchange_bcc_iron.dat', usecols=(0,1), unpack=True) +plt.plot(rdata, Jdata, 'b-', label='data') + +#Perform the fit +popt, pcov = curve_fit(func, rdata, Jdata, bounds=(0, [500.,5.,5.])) +plt.plot(rdata, func(rdata, *popt), 'r--', label='fit') + +#Print the fitted params +print("Parameters: a={:.10} (in meV), b={:.10} (adim), c={:.10} (in Ang)".format(*popt)) + +#Ploting the result +plt.xlabel('r_ij') +pylab.xlim([0,6.5]) +plt.ylabel('J_ij') +plt.legend() +plt.show() + +print("Loop end") diff --git a/examples/SPIN/iron/fe_dd.dat b/examples/SPIN/iron/fe_dd.dat new file mode 100644 index 0000000000..a4b4c9a0d7 --- /dev/null +++ b/examples/SPIN/iron/fe_dd.dat @@ -0,0 +1,19 @@ + 6 8 + Optimal parameter set + 1 4.100199340884814 F + 2 1.565647547483517 F + 1 0.9332056681088162 T 3.000000000000000 + 2 -1.162558782567700 T 2.866666666666670 + 3 -0.3502026949249225 T 2.733333333333330 + 4 0.4287820835430028 T 2.600000000000000 + 5 4.907925057809273 T 2.400000000000000 + 6 -5.307049068415304 T 2.300000000000000 + 1 -0.1960674387419232 F 4.100000000000000 + 2 0.3687525935422963 F 3.800000000000000 + 3 -1.505333614924853 F 3.500000000000000 + 4 4.948907078156191 T 3.200000000000000 + 5 -4.894613262753399 T 2.900000000000000 + 6 3.468897724782442 T 2.600000000000000 + 7 -1.792218099820337 T 2.400000000000000 + 8 80.22069592246987 T 2.300000000000000 + diff --git a/examples/SPIN/iron/in.spin.iron b/examples/SPIN/iron/in.spin.iron new file mode 100644 index 0000000000..c2d5082cb6 --- /dev/null +++ b/examples/SPIN/iron/in.spin.iron @@ -0,0 +1,56 @@ +# bcc iron in a 3d periodic box + +clear +units metal +atom_style spin + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice bcc 2.8665 +region box block 0.0 5.0 0.0 5.0 0.0 5.0 +create_box 1 box +create_atoms 1 box + +# setting mass, mag. moments, and interactions for bcc iron + +mass 1 55.845 + +set group all spin/random 31 2.2 +velocity all create 100 4928459 rot yes dist gaussian + +pair_style hybrid/overlay eam/alloy spin/exchange 3.5 +pair_coeff * * eam/alloy Fe_Mishin2006.eam.alloy Fe +pair_coeff * * spin/exchange exchange 3.4 0.02726 0.2171 1.841 + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 +fix 2 all langevin/spin 0.0 0.0 21 + +fix 3 all nve/spin lattice yes +timestep 0.0001 + +# compute and output options + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo_style custom step time v_magnorm v_tmag temp v_emag ke pe etotal +thermo 50 + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 100 all custom 1 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] + +run 50000 diff --git a/examples/SPIN/iron/log.11May18.spin.iron.g++.1 b/examples/SPIN/iron/log.11May18.spin.iron.g++.1 new file mode 100644 index 0000000000..1b27478002 --- /dev/null +++ b/examples/SPIN/iron/log.11May18.spin.iron.g++.1 @@ -0,0 +1,1115 @@ +LAMMPS (11 May 2018) +# bcc iron in a 3d periodic box + +clear +units metal +atom_style spin + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice bcc 2.8665 +Lattice spacing in x,y,z = 2.8665 2.8665 2.8665 +region box block 0.0 5.0 0.0 5.0 0.0 5.0 +create_box 1 box +Created orthogonal box = (0 0 0) to (14.3325 14.3325 14.3325) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 250 atoms + Time spent = 0.000727415 secs + +# setting mass, mag. moments, and interactions for bcc iron + +mass 1 55.845 + +set group all spin/random 31 2.2 + 250 settings made for spin/random +velocity all create 100 4928459 rot yes dist gaussian + +pair_style hybrid/overlay eam/alloy spin/exchange 3.5 +pair_coeff * * eam/alloy Fe_Mishin2006.eam.alloy Fe +pair_coeff * * spin/exchange exchange 3.4 0.02726 0.2171 1.841 + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 +fix 2 all langevin/spin 0.0 0.0 21 + +fix 3 all nve/spin lattice yes +timestep 0.0001 + +# compute and output options + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo_style custom step time v_magnorm v_tmag temp v_emag ke pe etotal +thermo 50 + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 100 all custom 1 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] + +run 50000 +Neighbor list info ... + update every 10 steps, delay 20 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.77337 + ghost atom cutoff = 5.77337 + binsize = 2.88668, bins = 5 5 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair eam/alloy, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 7.319 | 7.319 | 7.319 Mbytes +Step Time v_magnorm v_tmag Temp v_emag KinEng PotEng TotEng + 0 0 0.076456975 9109.0924 100.00358 -0.85791269 3.2186929 -1070.8579 -1067.6392 + 50 0.005 0.076456974 9316.7659 96.663685 -0.86504718 3.1111957 -1070.7504 -1067.6392 + 100 0.01 0.076456983 9488.3743 86.965803 -0.88035771 2.7990619 -1070.4383 -1067.6392 + 150 0.015 0.076456973 9589.0566 72.421197 -0.8996913 2.3309324 -1069.9702 -1067.6392 + 200 0.02 0.076456944 9415.3095 55.633188 -0.921682 1.7905973 -1069.4298 -1067.6392 + 250 0.025 0.076456953 8878.9394 39.802206 -0.94649004 1.2810649 -1068.9203 -1067.6392 + 300 0.03 0.076457027 8203.3388 27.882295 -0.97253854 0.8974133 -1068.5366 -1067.6392 + 350 0.035 0.076457103 7720.309 21.776538 -0.99708692 0.70089477 -1068.3401 -1067.6392 + 400 0.04 0.076457117 7531.0683 21.857102 -1.0190244 0.70348778 -1068.3427 -1067.6392 + 450 0.045 0.076457072 7479.8073 26.959407 -1.0389343 0.86770942 -1068.5069 -1067.6392 + 500 0.05 0.076457001 7461.6683 34.92521 -1.0582008 1.124095 -1068.7633 -1067.6392 + 550 0.055 0.076456962 7396.1112 43.405912 -1.0785156 1.397053 -1069.0363 -1067.6392 + 600 0.06 0.076456997 7121.894 50.544844 -1.102048 1.626825 -1069.2661 -1067.6392 + 650 0.065 0.076457079 6683.4805 55.261218 -1.1296588 1.7786252 -1069.4179 -1067.6392 + 700 0.07 0.076457136 6313.6896 57.25083 -1.1595102 1.8426624 -1069.4819 -1067.6392 + 750 0.075 0.076457132 6199.0363 56.934336 -1.1893875 1.8324758 -1069.4717 -1067.6392 + 800 0.08 0.076457116 6265.997 55.266343 -1.2181223 1.7787901 -1069.418 -1067.6392 + 850 0.085 0.076457116 6326.5886 53.376453 -1.2443326 1.7179626 -1069.3572 -1067.6392 + 900 0.09 0.076457121 6336.1261 52.279557 -1.2676425 1.6826581 -1069.3219 -1067.6392 + 950 0.095 0.076457122 6288.4204 52.667743 -1.2902335 1.6951522 -1069.3344 -1067.6392 + 1000 0.1 0.076457135 6122.1622 54.684094 -1.314147 1.76005 -1069.3993 -1067.6392 + 1050 0.105 0.076457155 5830.2219 57.880399 -1.3392396 1.8629256 -1069.5022 -1067.6392 + 1100 0.11 0.076457162 5477.4214 61.505616 -1.3662331 1.979606 -1069.6188 -1067.6392 + 1150 0.115 0.076457195 5194.1423 64.810972 -1.3984474 2.0859914 -1069.7252 -1067.6392 + 1200 0.12 0.076457219 5096.2484 67.147472 -1.438326 2.1611935 -1069.8004 -1067.6392 + 1250 0.125 0.076457214 5180.7444 67.957533 -1.4822383 2.1872659 -1069.8265 -1067.6392 + 1300 0.13 0.076457208 5332.4483 66.96652 -1.5226303 2.1553694 -1069.7946 -1067.6392 + 1350 0.135 0.076457225 5441.1287 64.471602 -1.5553539 2.0750686 -1069.7143 -1067.6392 + 1400 0.14 0.076457244 5466.8622 61.292592 -1.5804721 1.9727496 -1069.612 -1067.6392 + 1450 0.145 0.07645724 5403.309 58.518161 -1.6006864 1.8834524 -1069.5227 -1067.6392 + 1500 0.15 0.076457224 5275.2171 57.1713 -1.6196756 1.8401027 -1069.4793 -1067.6392 + 1550 0.155 0.076457217 5122.7481 57.878063 -1.6407322 1.8628504 -1069.5021 -1067.6392 + 1600 0.16 0.076457217 4968.5049 60.639452 -1.6657935 1.9517278 -1069.591 -1067.6392 + 1650 0.165 0.076457208 4850.1861 64.668839 -1.690847 2.0814168 -1069.7206 -1067.6392 + 1700 0.17 0.076457217 4809.0194 68.693586 -1.7087416 2.2109564 -1069.8502 -1067.6392 + 1750 0.175 0.076457274 4835.8611 71.611033 -1.7188587 2.3048567 -1069.9441 -1067.6392 + 1800 0.18 0.076457318 4929.7428 72.815077 -1.7280248 2.3436098 -1069.9828 -1067.6392 + 1850 0.185 0.076457279 5036.6365 72.102335 -1.7426092 2.3206696 -1069.9599 -1067.6392 + 1900 0.19 0.076457222 5116.2436 69.579977 -1.7638235 2.2394856 -1069.8787 -1067.6392 + 1950 0.195 0.076457228 5207.2334 65.715745 -1.7895824 2.1151122 -1069.7543 -1067.6392 + 2000 0.2 0.076457288 5216.0413 61.340972 -1.8174915 1.9743068 -1069.6135 -1067.6392 + 2050 0.205 0.076457267 5023.1601 57.468628 -1.8456914 1.8496724 -1069.4889 -1067.6392 + 2100 0.21 0.076457198 4748.7818 55.033266 -1.8742291 1.7712884 -1069.4105 -1067.6392 + 2150 0.215 0.076457199 4558.1302 54.573806 -1.9035225 1.7565003 -1069.3957 -1067.6392 + 2200 0.22 0.076457185 4483.1644 56.074241 -1.9322669 1.804793 -1069.444 -1067.6392 + 2250 0.225 0.076457114 4430.1583 59.0552 -1.9577399 1.9007374 -1069.54 -1067.6392 + 2300 0.23 0.076457092 4353.7973 62.874849 -1.9801275 2.0236758 -1069.6629 -1067.6392 + 2350 0.235 0.076457145 4303.5275 66.892738 -2.0022129 2.1529947 -1069.7922 -1067.6392 + 2400 0.24 0.076457171 4258.6889 70.426826 -2.0233072 2.2667421 -1069.906 -1067.6392 + 2450 0.245 0.076457169 4178.5775 72.910422 -2.0405304 2.3466785 -1069.9859 -1067.6392 + 2500 0.25 0.07645717 4114.786 74.106367 -2.0531755 2.3851709 -1070.0244 -1067.6392 + 2550 0.255 0.076457136 4067.5017 74.169349 -2.0634674 2.3871981 -1070.0264 -1067.6392 + 2600 0.26 0.076457099 4045.3324 73.586199 -2.0755814 2.3684289 -1070.0077 -1067.6392 + 2650 0.265 0.076457099 4137.898 72.914235 -2.0913646 2.3468012 -1069.986 -1067.6392 + 2700 0.27 0.076457106 4332.063 72.583192 -2.1091075 2.3361464 -1069.9754 -1067.6392 + 2750 0.275 0.07645709 4465.1953 72.814559 -2.125099 2.3435931 -1069.9828 -1067.6392 + 2800 0.28 0.076457051 4516.5192 73.652154 -2.1371914 2.3705517 -1070.0098 -1067.6392 + 2850 0.285 0.076457019 4555.5962 75.060211 -2.1489378 2.4158711 -1070.0551 -1067.6392 + 2900 0.29 0.076457069 4544.2734 76.844795 -2.1667679 2.4733094 -1070.1125 -1067.6392 + 2950 0.295 0.076457172 4460.2109 78.48171 -2.1924421 2.5259948 -1070.1652 -1067.6392 + 3000 0.3 0.076457219 4323.2746 79.20682 -2.2209955 2.549333 -1070.1886 -1067.6392 + 3050 0.305 0.076457213 4155.688 78.543529 -2.2505299 2.5279844 -1070.1672 -1067.6392 + 3100 0.31 0.076457203 3969.6188 76.554785 -2.2858382 2.4639752 -1070.1032 -1067.6392 + 3150 0.315 0.076457187 3761.432 73.396149 -2.3245055 2.362312 -1070.0015 -1067.6392 + 3200 0.32 0.076457142 3602.8035 69.313196 -2.3577056 2.230899 -1069.8701 -1067.6392 + 3250 0.325 0.076457116 3505.707 65.032482 -2.3836874 2.0931209 -1069.7324 -1067.6392 + 3300 0.33 0.07645716 3424.8795 61.551539 -2.4057167 1.9810841 -1069.6203 -1067.6392 + 3350 0.335 0.076457236 3335.9672 59.709703 -2.4251844 1.9218031 -1069.561 -1067.6392 + 3400 0.34 0.076457298 3238.0186 60.026953 -2.4425501 1.9320141 -1069.5712 -1067.6392 + 3450 0.345 0.076457297 3185.0674 62.613739 -2.4593531 2.0152718 -1069.6545 -1067.6392 + 3500 0.35 0.07645723 3197.4087 67.011871 -2.4756907 2.1568291 -1069.7961 -1067.6392 + 3550 0.355 0.076457177 3216.1428 72.316209 -2.4911379 2.3275533 -1069.9668 -1067.6392 + 3600 0.36 0.076457165 3241.0326 77.550071 -2.5083858 2.4960092 -1070.1352 -1067.6392 + 3650 0.365 0.076457168 3309.6874 81.877688 -2.5306273 2.6352969 -1070.2745 -1067.6392 + 3700 0.37 0.07645718 3350.748 84.764646 -2.5595247 2.7282159 -1070.3674 -1067.6392 + 3750 0.375 0.07645721 3368.085 86.031781 -2.5938559 2.7689996 -1070.4082 -1067.6392 + 3800 0.38 0.076457208 3425.3173 85.733048 -2.6266899 2.7593847 -1070.3986 -1067.6392 + 3850 0.385 0.076457165 3420.4429 84.240647 -2.6514805 2.7113506 -1070.3506 -1067.6392 + 3900 0.39 0.076457146 3323.0403 82.320886 -2.6700966 2.6495616 -1070.2888 -1067.6392 + 3950 0.395 0.076457179 3273.2625 80.780607 -2.6892405 2.5999865 -1070.2392 -1067.6392 + 4000 0.4 0.076457229 3313.2671 79.92769 -2.709641 2.5725347 -1070.2118 -1067.6392 + 4050 0.405 0.076457272 3381.1117 79.663389 -2.7291493 2.564028 -1070.2033 -1067.6392 + 4100 0.41 0.07645731 3373.3005 79.895158 -2.7514856 2.5714877 -1070.2107 -1067.6392 + 4150 0.415 0.076457296 3279.6989 80.402828 -2.7788004 2.5878274 -1070.2271 -1067.6392 + 4200 0.42 0.076457251 3197.0478 80.770336 -2.8064773 2.599656 -1070.2389 -1067.6392 + 4250 0.425 0.076457243 3160.9065 80.756747 -2.8307967 2.5992186 -1070.2385 -1067.6392 + 4300 0.43 0.076457282 3173.9599 80.446488 -2.852192 2.5892326 -1070.2285 -1067.6392 + 4350 0.435 0.076457289 3185.8003 80.110494 -2.8726607 2.5784184 -1070.2177 -1067.6392 + 4400 0.44 0.076457262 3166.3054 80.045036 -2.8936787 2.5763116 -1070.2155 -1067.6392 + 4450 0.445 0.076457226 3177.4332 80.500194 -2.9171408 2.5909612 -1070.2302 -1067.6392 + 4500 0.45 0.076457174 3238.8362 81.573722 -2.9447352 2.6255135 -1070.2647 -1067.6392 + 4550 0.455 0.07645714 3277.7104 83.104228 -2.975052 2.6747741 -1070.314 -1067.6392 + 4600 0.46 0.076457157 3224.8571 84.845473 -3.0065552 2.7308174 -1070.37 -1067.6392 + 4650 0.465 0.076457215 3112.9952 86.608217 -3.03972 2.7875527 -1070.4268 -1067.6392 + 4700 0.47 0.076457254 3001.141 88.18732 -3.074928 2.8383773 -1070.4776 -1067.6392 + 4750 0.475 0.076457235 2904.0735 89.204263 -3.1082127 2.8711084 -1070.5103 -1067.6392 + 4800 0.48 0.076457195 2832.0276 89.24571 -3.134302 2.8724424 -1070.5117 -1067.6392 + 4850 0.485 0.076457172 2833.7453 88.206351 -3.1541802 2.8389899 -1070.4782 -1067.6392 + 4900 0.49 0.076457184 2941.993 86.310712 -3.1725372 2.7779773 -1070.4172 -1067.6392 + 4950 0.495 0.076457228 3082.4825 84.029047 -3.1931038 2.7045401 -1070.3438 -1067.6392 + 5000 0.5 0.07645727 3155.7095 81.99875 -3.2175967 2.6391934 -1070.2784 -1067.6392 + 5050 0.505 0.076457297 3162.1875 80.72053 -3.2420203 2.5980529 -1070.2373 -1067.6392 + 5100 0.51 0.076457279 3133.3889 80.483768 -3.2606472 2.5904325 -1070.2297 -1067.6392 + 5150 0.515 0.076457223 3144.6361 81.566513 -3.2759117 2.6252815 -1070.2645 -1067.6392 + 5200 0.52 0.076457166 3156.8183 84.062018 -3.2944729 2.7056013 -1070.3448 -1067.6392 + 5250 0.525 0.076457128 3059.9886 87.694328 -3.3209415 2.82251 -1070.4617 -1067.6392 + 5300 0.53 0.076457126 2891.6506 91.782947 -3.3547324 2.9541054 -1070.5933 -1067.6392 + 5350 0.535 0.076457151 2751.9451 95.417928 -3.3914125 3.0711001 -1070.7103 -1067.6392 + 5400 0.54 0.07645725 2681.0265 97.845096 -3.4276651 3.1492204 -1070.7885 -1067.6392 + 5450 0.545 0.076457325 2657.0871 98.736021 -3.4632111 3.1778955 -1070.8171 -1067.6392 + 5500 0.55 0.076457263 2653.1919 98.075727 -3.4957627 3.1566434 -1070.7959 -1067.6392 + 5550 0.555 0.076457185 2644.2053 96.114963 -3.5208827 3.0935347 -1070.7328 -1067.6392 + 5600 0.56 0.076457195 2622.4174 93.525807 -3.5389264 3.0102007 -1070.6494 -1067.6392 + 5650 0.565 0.07645725 2616.3851 91.264369 -3.5558733 2.9374145 -1070.5766 -1067.6392 + 5700 0.57 0.076457256 2608.2454 90.135397 -3.5771374 2.9010777 -1070.5403 -1067.6392 + 5750 0.575 0.076457193 2573.217 90.456889 -3.6030061 2.9114252 -1070.5507 -1067.6392 + 5800 0.58 0.076457145 2565.3325 92.099499 -3.6318265 2.9642939 -1070.6035 -1067.6392 + 5850 0.585 0.076457161 2566.2763 94.62532 -3.6627041 3.0455894 -1070.6848 -1067.6392 + 5900 0.59 0.076457186 2564.6814 97.321391 -3.6927592 3.1323645 -1070.7716 -1067.6392 + 5950 0.595 0.076457195 2570.6317 99.384979 -3.7170023 3.1987827 -1070.838 -1067.6392 + 6000 0.6 0.076457206 2556.8466 100.3814 -3.7363622 3.2308533 -1070.8701 -1067.6392 + 6050 0.605 0.076457195 2521.7989 100.35237 -3.7587516 3.2299188 -1070.8692 -1067.6392 + 6100 0.61 0.076457175 2476.1857 99.370382 -3.7869326 3.1983129 -1070.8375 -1067.6392 + 6150 0.615 0.076457178 2397.2805 97.465979 -3.8168635 3.1370182 -1070.7763 -1067.6392 + 6200 0.62 0.07645713 2286.8528 94.931714 -3.8450242 3.0554509 -1070.6947 -1067.6392 + 6250 0.625 0.076457116 2250.5238 92.438461 -3.8722441 2.9752036 -1070.6144 -1067.6392 + 6300 0.63 0.076457156 2338.521 90.714356 -3.9006124 2.9197119 -1070.5589 -1067.6392 + 6350 0.635 0.07645717 2433.0115 90.142291 -3.9291158 2.9012996 -1070.5405 -1067.6392 + 6400 0.64 0.076457159 2467.5348 90.771111 -3.9562691 2.9215387 -1070.5608 -1067.6392 + 6450 0.645 0.076457107 2475.8592 92.488016 -3.9828131 2.9767986 -1070.616 -1067.6392 + 6500 0.65 0.0764571 2489.7418 95.127451 -4.0122141 3.0617508 -1070.701 -1067.6392 + 6550 0.655 0.076457169 2500.4747 98.171693 -4.0419177 3.1597321 -1070.799 -1067.6392 + 6600 0.66 0.076457208 2530.7924 100.74938 -4.0631997 3.242697 -1070.8819 -1067.6392 + 6650 0.665 0.076457205 2539.1274 102.26227 -4.0743158 3.2913904 -1070.9306 -1067.6392 + 6700 0.67 0.076457193 2456.6296 102.74328 -4.083416 3.3068723 -1070.9461 -1067.6392 + 6750 0.675 0.076457138 2387.5795 102.56259 -4.0973623 3.3010567 -1070.9403 -1067.6392 + 6800 0.68 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0.076457037 2130.7469 112.46016 -4.5932603 3.6196176 -1071.2589 -1067.6392 + 8000 0.8 0.076457043 2075.0145 110.59865 -4.6198672 3.5597035 -1071.1989 -1067.6392 + 8050 0.805 0.076457061 2007.4917 108.6927 -4.6506917 3.4983589 -1071.1376 -1067.6392 + 8100 0.81 0.076457077 1991.5702 107.59433 -4.6877068 3.4630069 -1071.1022 -1067.6392 + 8150 0.815 0.07645708 2031.0743 107.95739 -4.7305236 3.4746923 -1071.1139 -1067.6392 + 8200 0.82 0.076457089 2054.3404 109.99515 -4.7756305 3.5402792 -1071.1795 -1067.6392 + 8250 0.825 0.076457091 2082.2542 113.4122 -4.8195703 3.6502597 -1071.2895 -1067.6392 + 8300 0.83 0.076457089 2137.8944 117.42257 -4.8606167 3.7793367 -1071.4186 -1067.6392 + 8350 0.835 0.076457127 2145.0506 120.77123 -4.8931181 3.8871159 -1071.5263 -1067.6392 + 8400 0.84 0.076457184 2101.9996 122.34334 -4.9126837 3.9377155 -1071.5769 -1067.6392 + 8450 0.845 0.076457201 2057.1092 121.73484 -4.921619 3.9181301 -1071.5574 -1067.6392 + 8500 0.85 0.076457149 2005.1132 119.2385 -4.9251343 3.8377838 -1071.477 -1067.6392 + 8550 0.855 0.076457098 1942.6247 115.64537 -4.9291799 3.722136 -1071.3614 -1067.6392 + 8600 0.86 0.076457115 1910.1502 111.98317 -4.9396222 3.6042654 -1071.2435 -1067.6392 + 8650 0.865 0.076457185 1943.3663 109.19353 -4.9603011 3.5144784 -1071.1537 -1067.6392 + 8700 0.87 0.076457254 2019.4182 107.80177 -4.9898541 3.4696837 -1071.1089 -1067.6392 + 8750 0.875 0.076457249 2073.1225 107.76716 -5.0205034 3.4685697 -1071.1078 -1067.6392 + 8800 0.88 0.076457175 2088.6545 108.72646 -5.0437829 3.4994455 -1071.1387 -1067.6392 + 8850 0.885 0.076457093 2077.5406 110.36499 -5.0572565 3.5521827 -1071.1914 -1067.6392 + 8900 0.89 0.076457088 2039.5392 112.51291 -5.0650529 3.6213154 -1071.2605 -1067.6392 + 8950 0.895 0.076457167 2016.6853 114.99374 -5.0744542 3.7011627 -1071.3404 -1067.6392 + 9000 0.9 0.076457241 2000.3012 117.47475 -5.0917242 3.781016 -1071.4202 -1067.6392 + 9050 0.905 0.076457226 1957.0091 119.35854 -5.1139655 3.8416472 -1071.4809 -1067.6392 + 9100 0.91 0.076457166 1923.1545 120.23087 -5.1350957 3.869724 -1071.509 -1067.6392 + 9150 0.915 0.076457128 1933.618 120.11319 -5.1511544 3.8659364 -1071.5052 -1067.6392 + 9200 0.92 0.076457114 1961.4473 119.3017 -5.1596749 3.8398178 -1071.4791 -1067.6392 + 9250 0.925 0.076457136 1962.1 118.34889 -5.1642618 3.8091509 -1071.4484 -1067.6392 + 9300 0.93 0.076457156 1942.9357 117.84262 -5.1720815 3.7928561 -1071.4321 -1067.6392 + 9350 0.935 0.076457138 1911.4886 118.10075 -5.1877615 3.8011641 -1071.4404 -1067.6392 + 9400 0.94 0.076457123 1890.6033 118.99959 -5.2079977 3.830094 -1071.4693 -1067.6392 + 9450 0.945 0.076457145 1911.9879 120.23989 -5.2265042 3.8700141 -1071.5092 -1067.6392 + 9500 0.95 0.076457172 1944.8053 121.67513 -5.2423826 3.9162086 -1071.5554 -1067.6392 + 9550 0.955 0.076457175 1950.6137 123.16708 -5.2566963 3.9642282 -1071.6035 -1067.6392 + 9600 0.96 0.076457174 1953.467 124.46943 -5.2686278 4.0061451 -1071.6454 -1067.6392 + 9650 0.965 0.076457174 1991.321 125.52237 -5.2816008 4.0400348 -1071.6793 -1067.6392 + 9700 0.97 0.076457153 2064.4494 126.48746 -5.3037304 4.0710971 -1071.7103 -1067.6392 + 9750 0.975 0.076457119 2117.0576 127.38593 -5.3401962 4.100015 -1071.7392 -1067.6392 + 9800 0.98 0.076457147 2129.8396 127.90735 -5.38872 4.1167973 -1071.756 -1067.6392 + 9850 0.985 0.076457201 2114.5902 127.47883 -5.4369444 4.103005 -1071.7422 -1067.6392 + 9900 0.99 0.076457216 2054.2807 125.71916 -5.4695662 4.0463688 -1071.6856 -1067.6392 + 9950 0.995 0.076457168 1984.2158 123.01154 -5.4834672 3.9592219 -1071.5985 -1067.6392 + 10000 1 0.076457131 1962.6658 120.32305 -5.4872199 3.8726906 -1071.5119 -1067.6392 + 10050 1.005 0.076457159 1973.2973 118.61523 -5.4922129 3.8177233 -1071.457 -1067.6392 + 10100 1.01 0.076457216 1957.9424 118.36973 -5.5066432 3.8098215 -1071.4491 -1067.6392 + 10150 1.015 0.076457197 1942.1125 119.27525 -5.5290592 3.8389666 -1071.4782 -1067.6392 + 10200 1.02 0.076457142 1978.3009 120.6949 -5.5571675 3.8846591 -1071.5239 -1067.6392 + 10250 1.025 0.076457171 2058.9652 122.05983 -5.5914809 3.9285903 -1071.5678 -1067.6392 + 10300 1.03 0.07645722 2104.5325 122.92754 -5.6303584 3.9565181 -1071.5958 -1067.6392 + 10350 1.035 0.07645723 2072.9687 123.15237 -5.6697758 3.9637547 -1071.603 -1067.6392 + 10400 1.04 0.076457234 2012.912 123.02584 -5.7067292 3.9596822 -1071.5989 -1067.6392 + 10450 1.045 0.076457242 1971.6903 123.23438 -5.7426231 3.9663941 -1071.6056 -1067.6392 + 10500 1.05 0.0764573 1932.8929 124.43675 -5.7779702 4.0050935 -1071.6443 -1067.6392 + 10550 1.055 0.076457357 1892.1027 126.80016 -5.8082237 4.0811614 -1071.7204 -1067.6392 + 10600 1.06 0.076457317 1911.4422 130.09167 -5.8347562 4.1871012 -1071.8263 -1067.6392 + 10650 1.065 0.076457251 1994.4648 133.74505 -5.8634891 4.3046881 -1071.9439 -1067.6392 + 10700 1.07 0.076457242 2058.3043 136.94864 -5.8957766 4.4077983 -1072.047 -1067.6392 + 10750 1.075 0.076457284 2065.4421 138.83647 -5.9266133 4.4685595 -1072.1078 -1067.6392 + 10800 1.08 0.076457341 2054.3284 138.84647 -5.9519915 4.4688815 -1072.1081 -1067.6392 + 10850 1.085 0.076457339 2019.0718 136.8565 -5.9690783 4.4048328 -1072.0441 -1067.6392 + 10900 1.09 0.076457316 1950.5439 133.30535 -5.9772058 4.290536 -1071.9298 -1067.6392 + 10950 1.095 0.076457386 1880.7681 129.31046 -5.9839906 4.1619576 -1071.8012 -1067.6392 + 11000 1.1 0.076457422 1858.5762 126.17301 -5.9991286 4.0609761 -1071.7002 -1067.6392 + 11050 1.105 0.076457344 1895.8864 124.66179 -6.0225804 4.0123366 -1071.6516 -1067.6392 + 11100 1.11 0.076457251 1940.5442 124.88033 -6.0460181 4.0193704 -1071.6586 -1067.6392 + 11150 1.115 0.076457202 1961.4346 126.74742 -6.0683173 4.0794642 -1071.7187 -1067.6392 + 11200 1.12 0.076457268 1940.4836 129.91024 -6.0923522 4.1812618 -1071.8205 -1067.6392 + 11250 1.125 0.07645736 1893.8666 133.48134 -6.1129806 4.2962004 -1071.9354 -1067.6392 + 11300 1.13 0.076457404 1883.0365 136.68921 -6.127246 4.3994482 -1072.0387 -1067.6392 + 11350 1.135 0.076457466 1882.1011 139.1981 -6.1379481 4.480199 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0.076457169 953.72078 306.60692 -17.937745 9.8683816 -1077.5076 -1067.6392 + 46650 4.665 0.07645714 969.19209 304.86187 -17.945815 9.8122157 -1077.4514 -1067.6392 + 46700 4.67 0.076457121 982.50268 307.98161 -17.974576 9.9126272 -1077.5519 -1067.6392 + 46750 4.675 0.076457149 974.5768 314.91384 -18.000917 10.135746 -1077.775 -1067.6392 + 46800 4.68 0.076457222 954.17186 322.2853 -18.003497 10.373003 -1078.0122 -1067.6392 + 46850 4.685 0.076457263 943.539 327.31716 -17.991456 10.534957 -1078.1742 -1067.6392 + 46900 4.69 0.076457272 943.2156 329.68269 -17.979619 10.611093 -1078.2503 -1067.6392 + 46950 4.695 0.076457248 943.45366 330.93325 -17.974243 10.651343 -1078.2906 -1067.6392 + 47000 4.7 0.076457135 949.24404 332.85406 -17.979019 10.713166 -1078.3524 -1067.6392 + 47050 4.705 0.076457109 948.38347 335.49431 -17.990033 10.798145 -1078.4374 -1067.6392 + 47100 4.71 0.076457108 930.57759 336.79293 -18.000912 10.839942 -1078.4792 -1067.6392 + 47150 4.715 0.076457061 927.62433 334.90723 -18.010023 10.779249 -1078.4185 -1067.6392 + 47200 4.72 0.076457026 952.31461 330.77819 -18.012971 10.646353 -1078.2856 -1067.6392 + 47250 4.725 0.076457029 970.41647 328.26943 -18.01237 10.565606 -1078.2048 -1067.6392 + 47300 4.73 0.07645704 968.2995 329.56928 -18.014991 10.607443 -1078.2467 -1067.6392 + 47350 4.735 0.076457096 954.1138 332.31723 -18.02454 10.695888 -1078.3351 -1067.6392 + 47400 4.74 0.07645714 968.01812 333.90938 -18.038354 10.747133 -1078.3864 -1067.6392 + 47450 4.745 0.076457183 1006.2574 334.70242 -18.050106 10.772657 -1078.4119 -1067.6392 + 47500 4.75 0.076457147 1037.4547 335.39669 -18.062338 10.795003 -1078.4342 -1067.6392 + 47550 4.755 0.076457004 1027.5546 333.98227 -18.07862 10.749479 -1078.3887 -1067.6392 + 47600 4.76 0.076457078 986.81013 328.40773 -18.100384 10.570058 -1078.2093 -1067.6392 + 47650 4.765 0.076457236 980.12421 319.46388 -18.120191 10.282193 -1077.9214 -1067.6392 + 47700 4.77 0.076457087 973.75413 310.20532 -18.133538 9.984199 -1077.6234 -1067.6392 + 47750 4.775 0.076456955 944.49227 304.05996 -18.150575 9.7864056 -1077.4256 -1067.6392 + 47800 4.78 0.076457043 934.26558 302.74055 -18.16342 9.7439395 -1077.3832 -1067.6392 + 47850 4.785 0.076457163 946.5867 306.50326 -18.158739 9.8650453 -1077.5043 -1067.6392 + 47900 4.79 0.076457207 956.86274 314.93949 -18.15119 10.136572 -1077.7758 -1067.6392 + 47950 4.795 0.07645715 958.82327 326.06488 -18.164425 10.494651 -1078.1339 -1067.6392 + 48000 4.8 0.076457039 947.13341 336.0645 -18.196245 10.816497 -1078.4557 -1067.6392 + 48050 4.805 0.076457079 939.87276 341.25341 -18.222449 10.983506 -1078.6227 -1067.6392 + 48100 4.81 0.076457027 941.59608 340.87478 -18.232947 10.971319 -1078.6106 -1067.6392 + 48150 4.815 0.076456851 947.69448 337.06143 -18.235444 10.848584 -1078.4878 -1067.6392 + 48200 4.82 0.076456923 945.0083 331.93845 -18.226235 10.683697 -1078.3229 -1067.6392 + 48250 4.825 0.076457065 955.23353 326.88598 -18.206503 10.521079 -1078.1603 -1067.6392 + 48300 4.83 0.076457035 976.25082 323.10993 -18.198786 10.399544 -1078.0388 -1067.6392 + 48350 4.835 0.076456918 980.22652 320.95231 -18.21424 10.330099 -1077.9693 -1067.6392 + 48400 4.84 0.07645681 991.61794 319.56431 -18.236887 10.285425 -1077.9247 -1067.6392 + 48450 4.845 0.076456811 1004.3973 319.00657 -18.259638 10.267474 -1077.9067 -1067.6392 + 48500 4.85 0.076456872 1011.2382 320.78368 -18.281738 10.324672 -1077.9639 -1067.6392 + 48550 4.855 0.076456865 1011.4359 325.48338 -18.293785 10.475935 -1078.1152 -1067.6392 + 48600 4.86 0.076456844 1005.7488 332.46822 -18.305193 10.700748 -1078.34 -1067.6392 + 48650 4.865 0.076456876 989.87609 340.85827 -18.332595 10.970788 -1078.61 -1067.6392 + 48700 4.87 0.07645693 968.07155 348.89288 -18.372402 11.229388 -1078.8686 -1067.6392 + 48750 4.875 0.076456873 954.48433 354.07093 -18.412323 11.396048 -1079.0353 -1067.6392 + 48800 4.88 0.076456838 951.82821 354.8518 -18.445418 11.421181 -1079.0604 -1067.6392 + 48850 4.885 0.076456946 955.18291 351.65785 -18.473652 11.318381 -1078.9576 -1067.6392 + 48900 4.89 0.076457014 961.21122 345.9779 -18.498732 11.135567 -1078.7748 -1067.6392 + 48950 4.895 0.076456863 971.60448 338.99359 -18.517002 10.910772 -1078.55 -1067.6392 + 49000 4.9 0.076456715 983.55102 331.29604 -18.525123 10.66302 -1078.3022 -1067.6392 + 49050 4.905 0.076456793 965.60848 324.24302 -18.535514 10.436013 -1078.0752 -1067.6392 + 49100 4.91 0.076456864 944.53951 319.79955 -18.557009 10.292997 -1077.9322 -1067.6392 + 49150 4.915 0.076456768 947.20225 319.09103 -18.582911 10.270192 -1077.9094 -1067.6392 + 49200 4.92 0.076456734 944.86084 321.47471 -18.607567 10.346913 -1077.9861 -1067.6392 + 49250 4.925 0.076456851 940.6342 324.66116 -18.626242 10.449471 -1078.0887 -1067.6392 + 49300 4.93 0.076456872 950.6162 326.9518 -18.64032 10.523198 -1078.1624 -1067.6392 + 49350 4.935 0.076456643 952.42705 328.08816 -18.649274 10.559772 -1078.199 -1067.6392 + 49400 4.94 0.076456451 940.33548 329.05106 -18.66058 10.590764 -1078.23 -1067.6392 + 49450 4.945 0.076456558 946.93554 331.05799 -18.683544 10.655358 -1078.2946 -1067.6392 + 49500 4.95 0.076456719 968.13429 334.1178 -18.710726 10.753841 -1078.3931 -1067.6392 + 49550 4.955 0.076456712 989.14725 337.02333 -18.733226 10.847357 -1078.4866 -1067.6392 + 49600 4.96 0.076456681 986.97561 338.47429 -18.752155 10.894058 -1078.5333 -1067.6392 + 49650 4.965 0.076456692 980.18259 338.36307 -18.779369 10.890478 -1078.5297 -1067.6392 + 49700 4.97 0.076456776 962.29895 337.41689 -18.815353 10.860024 -1078.4993 -1067.6392 + 49750 4.975 0.076456852 943.47442 335.97999 -18.836611 10.813777 -1078.453 -1067.6392 + 49800 4.98 0.076456829 951.10385 334.29845 -18.839995 10.759655 -1078.3989 -1067.6392 + 49850 4.985 0.076456797 968.57767 333.00568 -18.84792 10.718046 -1078.3573 -1067.6392 + 49900 4.99 0.076456886 973.40031 332.98155 -18.860429 10.71727 -1078.3565 -1067.6392 + 49950 4.995 0.076456914 964.32242 335.13156 -18.853933 10.786469 -1078.4257 -1067.6392 + 50000 5 0.076456921 972.52311 340.63067 -18.841947 10.963463 -1078.6027 -1067.6392 +Loop time of 90.4316 on 1 procs for 50000 steps with 250 atoms + +Performance: 4.777 ns/day, 5.024 hours/ns, 552.904 timesteps/s +99.3% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 37.302 | 37.302 | 37.302 | 0.0 | 41.25 +Neigh | 0.386 | 0.386 | 0.386 | 0.0 | 0.43 +Comm | 0.7718 | 0.7718 | 0.7718 | 0.0 | 0.85 +Output | 15.35 | 15.35 | 15.35 | 0.0 | 16.97 +Modify | 36.465 | 36.465 | 36.465 | 0.0 | 40.32 +Other | | 0.1579 | | | 0.17 + +Nlocal: 250 ave 250 max 250 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1327 ave 1327 max 1327 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 7747 ave 7747 max 7747 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 15494 ave 15494 max 15494 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 15494 +Ave neighs/atom = 61.976 +Neighbor list builds = 614 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:01:30 diff --git a/examples/SPIN/iron/log.11May18.spin.iron.g++.4 b/examples/SPIN/iron/log.11May18.spin.iron.g++.4 new file mode 100644 index 0000000000..1467f8e2c5 --- /dev/null +++ b/examples/SPIN/iron/log.11May18.spin.iron.g++.4 @@ -0,0 +1,1115 @@ +LAMMPS (11 May 2018) +# bcc iron in a 3d periodic box + +clear +units metal +atom_style spin + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice bcc 2.8665 +Lattice spacing in x,y,z = 2.8665 2.8665 2.8665 +region box block 0.0 5.0 0.0 5.0 0.0 5.0 +create_box 1 box +Created orthogonal box = (0 0 0) to (14.3325 14.3325 14.3325) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 250 atoms + Time spent = 0.00023818 secs + +# setting mass, mag. moments, and interactions for bcc iron + +mass 1 55.845 + +set group all spin/random 31 2.2 + 250 settings made for spin/random +velocity all create 100 4928459 rot yes dist gaussian + +pair_style hybrid/overlay eam/alloy spin/exchange 3.5 +pair_coeff * * eam/alloy Fe_Mishin2006.eam.alloy Fe +pair_coeff * * spin/exchange exchange 3.4 0.02726 0.2171 1.841 + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 +fix 2 all langevin/spin 0.0 0.0 21 + +fix 3 all nve/spin lattice yes +timestep 0.0001 + +# compute and output options + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo_style custom step time v_magnorm v_tmag temp v_emag ke pe etotal +thermo 50 + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 100 all custom 1 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] + +run 50000 +Neighbor list info ... + update every 10 steps, delay 20 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.77337 + ghost atom cutoff = 5.77337 + binsize = 2.88668, bins = 5 5 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair eam/alloy, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 7.265 | 7.265 | 7.265 Mbytes +Step Time v_magnorm v_tmag Temp v_emag KinEng PotEng TotEng + 0 0 0.076456975 9109.0924 100.00358 -0.85791269 3.2186929 -1070.8579 -1067.6392 + 50 0.005 0.076456995 9402.4007 96.298333 -0.85659448 3.0994366 -1070.7387 -1067.6392 + 100 0.01 0.076457028 9589.1846 86.330828 -0.87003341 2.7786247 -1070.4179 -1067.6392 + 150 0.015 0.076457074 9673.9268 71.603402 -0.89006992 2.3046111 -1069.9438 -1067.6392 + 200 0.02 0.076457106 9509.1148 54.648817 -0.91124541 1.7589146 -1069.3981 -1067.6392 + 250 0.025 0.076457128 9004.27 38.599515 -0.93187522 1.2423553 -1068.8816 -1067.6392 + 300 0.03 0.076457157 8353.4371 26.383018 -0.95082226 0.8491579 -1068.4884 -1067.6392 + 350 0.035 0.076457207 7911.1316 20.01039 -0.96826468 0.64404992 -1068.2833 -1067.6392 + 400 0.04 0.076457243 7775.9492 20.097682 -0.98706373 0.64685949 -1068.2861 -1067.6392 + 450 0.045 0.076457231 7737.1225 25.687511 -1.0095684 0.82677249 -1068.466 -1067.6392 + 500 0.05 0.076457204 7676.9809 34.604697 -1.0349855 1.113779 -1068.753 -1067.6392 + 550 0.055 0.076457196 7550.2809 44.251809 -1.0609123 1.4242788 -1069.0635 -1067.6392 + 600 0.06 0.076457188 7209.7657 52.475202 -1.0880854 1.6889551 -1069.3282 -1067.6392 + 650 0.065 0.07645718 6691.1787 57.926479 -1.1179657 1.8644087 -1069.5036 -1067.6392 + 700 0.07 0.076457185 6276.4003 60.030548 -1.1469999 1.9321298 -1069.5714 -1067.6392 + 750 0.075 0.07645719 6149.9253 59.122504 -1.1721939 1.9029037 -1069.5421 -1067.6392 + 800 0.08 0.076457195 6207.0587 56.349146 -1.1949365 1.813641 -1069.4529 -1067.6392 + 850 0.085 0.076457199 6328.4635 53.154464 -1.2164642 1.7108177 -1069.35 -1067.6392 + 900 0.09 0.076457199 6456.2716 50.837416 -1.2366018 1.6362417 -1069.2755 -1067.6392 + 950 0.095 0.076457222 6495.1064 50.234549 -1.2539657 1.6168379 -1069.2561 -1067.6392 + 1000 0.1 0.076457266 6416.775 51.592727 -1.2671834 1.6605519 -1069.2998 -1067.6392 + 1050 0.105 0.076457256 6305.9015 54.719414 -1.2794824 1.7611868 -1069.4004 -1067.6392 + 1100 0.11 0.076457222 6165.987 59.01343 -1.2960617 1.8993931 -1069.5386 -1067.6392 + 1150 0.115 0.076457194 5941.7807 63.475298 -1.317859 2.0430017 -1069.6822 -1067.6392 + 1200 0.12 0.076457182 5692.0982 67.036713 -1.3432854 2.1576286 -1069.7969 -1067.6392 + 1250 0.125 0.076457217 5543.1736 68.917405 -1.3719994 2.2181602 -1069.8574 -1067.6392 + 1300 0.13 0.076457263 5507.9968 68.753418 -1.4042339 2.2128821 -1069.8521 -1067.6392 + 1350 0.135 0.076457286 5500.7848 66.608286 -1.4385667 2.1438394 -1069.7831 -1067.6392 + 1400 0.14 0.076457254 5523.456 62.967429 -1.4712143 2.0266556 -1069.6659 -1067.6392 + 1450 0.145 0.076457188 5501.5777 58.75732 -1.4990458 1.89115 -1069.5304 -1067.6392 + 1500 0.15 0.076457175 5324.4931 55.246308 -1.5236774 1.7781453 -1069.4174 -1067.6392 + 1550 0.155 0.076457234 5025.5908 53.607297 -1.5492947 1.7253925 -1069.3646 -1067.6392 + 1600 0.16 0.076457297 4742.9546 54.443418 -1.5785798 1.7523036 -1069.3915 -1067.6392 + 1650 0.165 0.076457321 4558.083 57.572305 -1.6113848 1.8530093 -1069.4922 -1067.6392 + 1700 0.17 0.076457304 4479.4352 62.073307 -1.6443595 1.9978776 -1069.6371 -1067.6392 + 1750 0.175 0.076457272 4520.5577 66.677964 -1.6742729 2.146082 -1069.7853 -1067.6392 + 1800 0.18 0.076457253 4659.9114 70.277293 -1.7021557 2.2619292 -1069.9012 -1067.6392 + 1850 0.185 0.076457257 4734.1597 72.135028 -1.7307798 2.3217219 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-18.839015 10.080004 -1077.7192 -1067.6392 + 49700 4.97 0.076457431 960.65868 314.4735 -18.863274 10.121574 -1077.7608 -1067.6392 + 49750 4.975 0.076457515 966.54445 320.68235 -18.880959 10.32141 -1077.9606 -1067.6392 + 49800 4.98 0.076457498 965.47876 331.30789 -18.90627 10.663401 -1078.3026 -1067.6392 + 49850 4.985 0.076457382 964.05595 343.93887 -18.938996 11.069939 -1078.7092 -1067.6392 + 49900 4.99 0.076457357 944.93024 354.89734 -18.970612 11.422646 -1079.0619 -1067.6392 + 49950 4.995 0.076457532 918.77322 361.48317 -18.987516 11.634616 -1079.2739 -1067.6392 + 50000 5 0.07645762 900.51128 363.08297 -18.994661 11.686107 -1079.3253 -1067.6392 +Loop time of 52.5523 on 4 procs for 50000 steps with 250 atoms + +Performance: 8.220 ns/day, 2.920 hours/ns, 951.434 timesteps/s +94.1% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 10.242 | 10.478 | 10.799 | 6.3 | 19.94 +Neigh | 0.10368 | 0.10776 | 0.11329 | 1.1 | 0.21 +Comm | 2.4492 | 2.7097 | 2.8852 | 11.0 | 5.16 +Output | 5.5737 | 5.9107 | 6.2742 | 11.8 | 11.25 +Modify | 32.833 | 33.256 | 33.661 | 5.2 | 63.28 +Other | | 0.09063 | | | 0.17 + +Nlocal: 62.5 ave 66 max 57 min +Histogram: 1 0 0 0 0 1 0 0 1 1 +Nghost: 772 ave 785 max 755 min +Histogram: 1 0 0 0 0 0 2 0 0 1 +Neighs: 1931 ave 2025 max 1751 min +Histogram: 1 0 0 0 0 0 1 0 0 2 +FullNghs: 3862 ave 4082 max 3518 min +Histogram: 1 0 0 0 0 1 0 0 1 1 + +Total # of neighbors = 15448 +Ave neighs/atom = 61.792 +Neighbor list builds = 614 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:52 diff --git a/examples/SPIN/nickel/Ni99.eam.alloy b/examples/SPIN/nickel/Ni99.eam.alloy new file mode 100644 index 0000000000..458f550462 --- /dev/null +++ b/examples/SPIN/nickel/Ni99.eam.alloy @@ -0,0 +1,30006 @@ + Ni EAM from Phys. Rev. B 59, 3393 (1999) in the LAMMPS setfl format. + Conversion by C. A. Becker from Y. Mishin files. + 14 February 2009. http://www.ctcms.nist.gov/potentials + 1 Ni +10000 0.2000000000000000E-03 10000 0.5803750000000001E-03 0.5803750000000000E+01 + 28 0.5871000000E+02 0.3520000000E+01 fcc + -0.3097002992599740E-10 + -0.6727670264584218E-03 + -0.1347243064545615E-02 + -0.2023426205791608E-02 + -0.2701314510756404E-02 + -0.3380906040000000E-02 + -0.4062198854082398E-02 + -0.4745191013563596E-02 + -0.5429880579003596E-02 + -0.6116265610962398E-02 + -0.6804344169999999E-02 + -0.7494114316748643E-02 + -0.8185574112129526E-02 + -0.8878721617136087E-02 + -0.9573554892761765E-02 + -0.1027007200000000E-01 + -0.1096827099948303E-01 + -0.1166814995039830E-01 + -0.1236970691157206E-01 + -0.1307293994183054E-01 + -0.1377784710000000E-01 + -0.1448442644595924E-01 + -0.1519267604379728E-01 + -0.1590259395865570E-01 + -0.1661417825567608E-01 + -0.1732742700000000E-01 + -0.1804233825508002E-01 + -0.1875891007761259E-01 + -0.1947714052260515E-01 + -0.2019702764506515E-01 + 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a/examples/SPIN/nickel/exchange_fit_fcc_ni/exchange_fcc_ni2.dat b/examples/SPIN/nickel/exchange_fit_fcc_ni/exchange_fcc_ni2.dat new file mode 100644 index 0000000000..4e5aa47659 --- /dev/null +++ b/examples/SPIN/nickel/exchange_fit_fcc_ni/exchange_fcc_ni2.dat @@ -0,0 +1,5 @@ +2.495 8.3 +3.524 -3.99 +4.31 0.998 +4.99 -0.955 +5.56 0.213 diff --git a/examples/SPIN/nickel/exchange_fit_fcc_ni/exchange_fit.py b/examples/SPIN/nickel/exchange_fit_fcc_ni/exchange_fit.py new file mode 100644 index 0000000000..4046fa45f7 --- /dev/null +++ b/examples/SPIN/nickel/exchange_fit_fcc_ni/exchange_fit.py @@ -0,0 +1,33 @@ +# program fitting the exchange interaction +# model curve: Bethe-Slater function +import numpy as np, pylab, tkinter +import matplotlib.pyplot as plt +from scipy.optimize import curve_fit +from decimal import * + +print("Loop begin") + +# definition of the Bethe-Slater function +def func(x,a,b,c): + return 4*a*((x/c)**2)*(1-b*(x/c)**2)*np.exp(-(x/c)**2) + +# exchange coeff table (data to fit) +rdata, Jdata = np.loadtxt('exchange_fcc_ni.dat', usecols=(0,1), unpack=True) +plt.plot(rdata, Jdata, 'b-', label='data') + +# perform the fit +popt, pcov = curve_fit(func, rdata, Jdata, bounds=([0.0,-1.0,0.0], [100.,5.,5.])) +plt.plot(rdata, func(rdata, *popt), 'r--', label='fit') + +# print the fitted parameters +print("Parameters: a={:.10} (in meV), b={:.10} (adim), c={:.10} (in Ang)".format(*popt)) + +# ploting the result +plt.xlabel('r_ij') +pylab.xlim([0.0,6.5]) +#pylab.ylim([-2.0,10.0]) +plt.ylabel('J_ij') +plt.legend() +plt.show() + +print("Loop end") diff --git a/examples/SPIN/nickel/in.spin.nickel b/examples/SPIN/nickel/in.spin.nickel new file mode 100644 index 0000000000..ba447b077f --- /dev/null +++ b/examples/SPIN/nickel/in.spin.nickel @@ -0,0 +1,58 @@ +# fcc nickel in a 3d periodic box + +clear +units metal +atom_style spin + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice fcc 3.524 +region box block 0.0 5.0 0.0 5.0 0.0 5.0 +create_box 1 box +create_atoms 1 box + +# setting mass, mag. moments, and interactions for cobalt + +mass 1 58.69 + +set group all spin/random 31 0.63 +#set group all spin 0.63 0.0 0.0 1.0 +velocity all create 100 4928459 rot yes dist gaussian + +pair_style hybrid/overlay eam/alloy spin/exchange 4.0 +pair_coeff * * eam/alloy Ni99.eam.alloy Ni +pair_coeff * * spin/exchange exchange 4.0 0.50 0.2280246862 1.229983475 + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 +fix 2 all langevin/spin 0.0 0.0 21 + +fix 3 all nve/spin lattice yes +timestep 0.0001 + +# compute and output options + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo_style custom step time v_magnorm v_emag temp v_tmag etotal +thermo 50 + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 50 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] + +run 2000 + diff --git a/examples/SPIN/nickel/log.11May18.spin.nickel.g++.1 b/examples/SPIN/nickel/log.11May18.spin.nickel.g++.1 new file mode 100644 index 0000000000..82f54f4e6b --- /dev/null +++ b/examples/SPIN/nickel/log.11May18.spin.nickel.g++.1 @@ -0,0 +1,157 @@ +LAMMPS (11 May 2018) +# fcc nickel in a 3d periodic box + +clear +units metal +atom_style spin + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice fcc 3.524 +Lattice spacing in x,y,z = 3.524 3.524 3.524 +region box block 0.0 5.0 0.0 5.0 0.0 5.0 +create_box 1 box +Created orthogonal box = (0 0 0) to (17.62 17.62 17.62) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 500 atoms + Time spent = 0.000804186 secs + +# setting mass, mag. moments, and interactions for cobalt + +mass 1 58.69 + +set group all spin/random 31 0.63 + 500 settings made for spin/random +#set group all spin 0.63 0.0 0.0 1.0 +velocity all create 100 4928459 rot yes dist gaussian + +pair_style hybrid/overlay eam/alloy spin/exchange 4.0 +pair_coeff * * eam/alloy Ni99.eam.alloy Ni +pair_coeff * * spin/exchange exchange 4.0 0.50 0.2280246862 1.229983475 + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 +fix 2 all langevin/spin 0.0 0.0 21 + +fix 3 all nve/spin lattice yes +timestep 0.0001 + +# compute and output options + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo_style custom step time v_magnorm v_emag temp v_tmag etotal +thermo 50 + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 50 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] + +run 2000 +Neighbor list info ... + update every 10 steps, delay 20 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.90375 + ghost atom cutoff = 5.90375 + binsize = 2.95187, bins = 6 6 6 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair eam/alloy, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 7.384 | 7.384 | 7.384 Mbytes +Step Time v_magnorm v_emag Temp v_tmag TotEng + 0 0 0.028733803 0.40997576 100.03408 -9550.1342 -2218.1018 + 50 0.005 0.028733807 0.070491717 101.47879 -56307.038 -2218.1018 + 100 0.01 0.028733815 -0.70937134 101.7311 5851.6355 -2218.1018 + 150 0.015 0.028733823 -1.853981 99.63039 2395.8677 -2218.1018 + 200 0.02 0.028733828 -3.2679239 94.850105 1482.3486 -2218.1018 + 250 0.025 0.028733824 -4.863967 88.444584 1100.7396 -2218.1018 + 300 0.03 0.028733807 -6.5763457 82.689581 899.56642 -2218.1018 + 350 0.035 0.028733783 -8.3489158 80.108798 768.64457 -2218.1018 + 400 0.04 0.028733763 -10.120216 82.374947 670.03091 -2218.1018 + 450 0.045 0.028733755 -11.828932 89.814597 593.77931 -2218.1018 + 500 0.05 0.028733762 -13.423712 101.39613 535.03371 -2218.1018 + 550 0.055 0.028733783 -14.866724 115.07399 489.92024 -2218.1018 + 600 0.06 0.028733801 -16.135279 128.57849 458.66654 -2218.1018 + 650 0.065 0.028733804 -17.222838 140.22402 440.11437 -2218.1018 + 700 0.07 0.028733795 -18.154813 149.61295 425.91356 -2218.1018 + 750 0.075 0.028733781 -18.996903 157.5814 412.82654 -2218.1018 + 800 0.08 0.028733768 -19.804249 164.92075 407.77954 -2218.1018 + 850 0.085 0.028733752 -20.579151 171.67278 406.84726 -2218.1018 + 900 0.09 0.028733728 -21.294277 177.67238 399.69633 -2218.1018 + 950 0.095 0.028733715 -21.943945 183.2621 389.92281 -2218.1018 + 1000 0.1 0.02873374 -22.551277 188.99284 383.19592 -2218.1018 + 1050 0.105 0.028733783 -23.120147 194.51391 375.87245 -2218.1018 + 1100 0.11 0.028733792 -23.602325 198.18631 365.37753 -2218.1018 + 1150 0.115 0.028733774 -23.976048 199.04022 354.04863 -2218.1018 + 1200 0.12 0.02873376 -24.31575 198.41999 346.40397 -2218.1018 + 1250 0.125 0.028733759 -24.718347 198.3669 343.1701 -2218.1018 + 1300 0.13 0.028733765 -25.189073 199.57949 336.90052 -2218.1018 + 1350 0.135 0.028733774 -25.650252 201.45897 329.07023 -2218.1018 + 1400 0.14 0.028733785 -26.042702 203.6926 327.97373 -2218.1018 + 1450 0.145 0.028733791 -26.373965 206.80469 327.38747 -2218.1018 + 1500 0.15 0.028733791 -26.691802 211.43923 322.75885 -2218.1018 + 1550 0.155 0.028733794 -27.021573 217.10969 315.55781 -2218.1018 + 1600 0.16 0.028733792 -27.344066 222.16052 310.6743 -2218.1018 + 1650 0.165 0.028733788 -27.640017 225.28449 310.49671 -2218.1018 + 1700 0.17 0.028733803 -27.907241 226.37676 310.9389 -2218.1018 + 1750 0.175 0.028733828 -28.143477 226.31095 313.28034 -2218.1018 + 1800 0.18 0.028733833 -28.363397 226.43633 317.31668 -2218.1018 + 1850 0.185 0.028733811 -28.58153 227.36287 318.98645 -2218.1018 + 1900 0.19 0.028733796 -28.785208 228.39889 316.9972 -2218.1018 + 1950 0.195 0.028733826 -28.9724 228.84666 309.8027 -2218.1018 + 2000 0.2 0.02873386 -29.175039 228.918 297.88519 -2218.1018 +Loop time of 10.033 on 1 procs for 2000 steps with 500 atoms + +Performance: 1.722 ns/day, 13.935 hours/ns, 199.342 timesteps/s +99.4% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 3.909 | 3.909 | 3.909 | 0.0 | 38.96 +Neigh | 0.031031 | 0.031031 | 0.031031 | 0.0 | 0.31 +Comm | 0.046559 | 0.046559 | 0.046559 | 0.0 | 0.46 +Output | 2.4087 | 2.4087 | 2.4087 | 0.0 | 24.01 +Modify | 3.625 | 3.625 | 3.625 | 0.0 | 36.13 +Other | | 0.01268 | | | 0.13 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1956 ave 1956 max 1956 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 19508 ave 19508 max 19508 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 39016 ave 39016 max 39016 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 39016 +Ave neighs/atom = 78.032 +Neighbor list builds = 21 +Dangerous builds = 0 + + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:10 diff --git a/examples/SPIN/nickel/log.11May18.spin.nickel.g++.4 b/examples/SPIN/nickel/log.11May18.spin.nickel.g++.4 new file mode 100644 index 0000000000..373271459f --- /dev/null +++ b/examples/SPIN/nickel/log.11May18.spin.nickel.g++.4 @@ -0,0 +1,157 @@ +LAMMPS (11 May 2018) +# fcc nickel in a 3d periodic box + +clear +units metal +atom_style spin + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice fcc 3.524 +Lattice spacing in x,y,z = 3.524 3.524 3.524 +region box block 0.0 5.0 0.0 5.0 0.0 5.0 +create_box 1 box +Created orthogonal box = (0 0 0) to (17.62 17.62 17.62) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 500 atoms + Time spent = 0.000523567 secs + +# setting mass, mag. moments, and interactions for cobalt + +mass 1 58.69 + +set group all spin/random 31 0.63 + 500 settings made for spin/random +#set group all spin 0.63 0.0 0.0 1.0 +velocity all create 100 4928459 rot yes dist gaussian + +pair_style hybrid/overlay eam/alloy spin/exchange 4.0 +pair_coeff * * eam/alloy Ni99.eam.alloy Ni +pair_coeff * * spin/exchange exchange 4.0 0.50 0.2280246862 1.229983475 + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 +fix 2 all langevin/spin 0.0 0.0 21 + +fix 3 all nve/spin lattice yes +timestep 0.0001 + +# compute and output options + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo_style custom step time v_magnorm v_emag temp v_tmag etotal +thermo 50 + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 50 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] + +run 2000 +Neighbor list info ... + update every 10 steps, delay 20 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.90375 + ghost atom cutoff = 5.90375 + binsize = 2.95187, bins = 6 6 6 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair eam/alloy, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 7.298 | 7.298 | 7.298 Mbytes +Step Time v_magnorm v_emag Temp v_tmag TotEng + 0 0 0.028733803 0.40997576 100.03408 -9550.1342 -2218.1018 + 50 0.005 0.028733805 0.25324083 98.741633 -15727.749 -2218.1018 + 100 0.01 0.028733812 -0.37320751 97.073875 11244.373 -2218.1018 + 150 0.015 0.028733819 -1.3971549 94.073447 3250.0517 -2218.1018 + 200 0.02 0.028733825 -2.7238372 89.419944 1838.752 -2218.1018 + 250 0.025 0.028733829 -4.2684428 84.07494 1304.3675 -2218.1018 + 300 0.03 0.028733824 -5.9636712 80.06368 1025.7815 -2218.1018 + 350 0.035 0.02873381 -7.7386326 79.366702 844.49729 -2218.1018 + 400 0.04 0.028733802 -9.5148059 83.052751 715.20758 -2218.1018 + 450 0.045 0.028733806 -11.234935 91.282747 621.75552 -2218.1018 + 500 0.05 0.02873381 -12.875184 103.49836 550.04479 -2218.1018 + 550 0.055 0.028733808 -14.413473 118.16526 495.70417 -2218.1018 + 600 0.06 0.028733803 -15.812466 132.83837 461.35805 -2218.1018 + 650 0.065 0.028733808 -17.061311 145.41049 444.38951 -2218.1018 + 700 0.07 0.028733818 -18.181903 154.83414 438.85866 -2218.1018 + 750 0.075 0.028733823 -19.176259 160.58645 436.90462 -2218.1018 + 800 0.08 0.028733825 -20.035157 163.02829 429.73193 -2218.1018 + 850 0.085 0.028733825 -20.806548 164.4197 419.73763 -2218.1018 + 900 0.09 0.028733829 -21.571419 167.8571 411.59699 -2218.1018 + 950 0.095 0.028733825 -22.365879 175.00875 402.66175 -2218.1018 + 1000 0.1 0.028733821 -23.133464 184.68305 391.05824 -2218.1018 + 1050 0.105 0.028733833 -23.770507 193.83795 379.23354 -2218.1018 + 1100 0.11 0.02873385 -24.249882 200.5039 372.08521 -2218.1018 + 1150 0.115 0.028733864 -24.630489 204.46984 367.92135 -2218.1018 + 1200 0.12 0.028733877 -24.956281 205.96624 363.72367 -2218.1018 + 1250 0.125 0.028733884 -25.227332 205.18503 361.09236 -2218.1018 + 1300 0.13 0.028733877 -25.43568 202.76969 359.10924 -2218.1018 + 1350 0.135 0.028733868 -25.588748 199.85462 358.69556 -2218.1018 + 1400 0.14 0.028733866 -25.723582 197.99165 360.27856 -2218.1018 + 1450 0.145 0.028733851 -25.866283 198.30283 360.46623 -2218.1018 + 1500 0.15 0.028733812 -26.014569 200.95517 354.66722 -2218.1018 + 1550 0.155 0.02873379 -26.192673 205.95485 348.37935 -2218.1018 + 1600 0.16 0.028733795 -26.444059 212.87557 345.53576 -2218.1018 + 1650 0.165 0.028733838 -26.75551 219.86449 338.9224 -2218.1018 + 1700 0.17 0.028733868 -27.068513 224.47868 327.81241 -2218.1018 + 1750 0.175 0.028733862 -27.344118 225.62318 319.85486 -2218.1018 + 1800 0.18 0.028733849 -27.57563 224.07463 320.07064 -2218.1018 + 1850 0.185 0.028733852 -27.774274 221.70618 323.12599 -2218.1018 + 1900 0.19 0.028733864 -27.967999 220.53947 322.9504 -2218.1018 + 1950 0.195 0.028733863 -28.173041 221.61407 318.63401 -2218.1018 + 2000 0.2 0.028733853 -28.362177 224.22281 310.55185 -2218.1018 +Loop time of 3.95094 on 4 procs for 2000 steps with 500 atoms + +Performance: 4.374 ns/day, 5.487 hours/ns, 506.208 timesteps/s +98.1% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.0289 | 1.0467 | 1.0811 | 2.0 | 26.49 +Neigh | 0.0079527 | 0.0081946 | 0.0084369 | 0.2 | 0.21 +Comm | 0.094456 | 0.13311 | 0.15138 | 6.2 | 3.37 +Output | 0.69702 | 0.71998 | 0.74483 | 2.1 | 18.22 +Modify | 2.0107 | 2.0383 | 2.0598 | 1.3 | 51.59 +Other | | 0.004668 | | | 0.12 + +Nlocal: 125 ave 132 max 120 min +Histogram: 2 0 0 0 0 1 0 0 0 1 +Nghost: 1099 ave 1104 max 1092 min +Histogram: 1 0 0 0 1 0 0 0 0 2 +Neighs: 4876.5 ave 5100 max 4721 min +Histogram: 2 0 0 0 0 1 0 0 0 1 +FullNghs: 9753 ave 10296 max 9362 min +Histogram: 2 0 0 0 0 1 0 0 0 1 + +Total # of neighbors = 39012 +Ave neighs/atom = 78.024 +Neighbor list builds = 21 +Dangerous builds = 0 + + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:04 diff --git a/examples/SPIN/read_restart/Co_PurjaPun_2012.eam.alloy b/examples/SPIN/read_restart/Co_PurjaPun_2012.eam.alloy new file mode 120000 index 0000000000..6a47c9eebe --- /dev/null +++ b/examples/SPIN/read_restart/Co_PurjaPun_2012.eam.alloy @@ -0,0 +1 @@ +../cobalt_fcc/Co_PurjaPun_2012.eam.alloy \ No newline at end of file diff --git a/examples/SPIN/read_restart/Norm_randXY_8x8x32.data b/examples/SPIN/read_restart/Norm_randXY_8x8x32.data new file mode 100644 index 0000000000..d239bb6ca0 --- /dev/null +++ b/examples/SPIN/read_restart/Norm_randXY_8x8x32.data @@ -0,0 +1,8207 @@ +LAMMPS data file via write_data, version 4 May 2017, timestep = 0 + +8192 atoms +1 atom types + +0.0000000000000000e+00 2.8320000000000000e+01 xlo xhi +0.0000000000000000e+00 2.8320000000000000e+01 ylo yhi +0.0000000000000000e+00 1.1328000000000000e+02 zlo zhi + +Masses + +1 58.93 + +Atoms # spin + +1 1 1.72 0.0 0.0 0.0 0.52887 -0.848703 1.0 +2 1 1.72 1.77 1.77 0.0 -0.745115 -0.666936 1.0 +3 1 1.72 1.77 0.0 1.77 -0.989437 -0.144964 1.0 +4 1 1.72 0.0 1.77 1.77 0.999926 -0.0121449 1.0 +5 1 1.72 3.54 0.0 0.0 0.377063 -0.926188 1.0 +6 1 1.72 5.31 1.77 0.0 0.412944 0.910756 1.0 +7 1 1.72 5.31 0.0 1.77 -0.999979 0.00650985 1.0 +8 1 1.72 3.54 1.77 1.77 0.535453 -0.844565 1.0 +9 1 1.72 7.0799999 0.0 0.0 -0.986135 0.165942 1.0 +10 1 1.72 8.8500004 1.77 0.0 -0.37352 -0.927622 1.0 +11 1 1.72 8.8500004 0.0 1.77 -0.926878 0.375363 1.0 +12 1 1.72 7.0799999 1.77 1.77 -0.690063 -0.72375 1.0 +13 1 1.72 10.6199999 0.0 0.0 -0.7204 -0.693559 1.0 +14 1 1.72 12.3900004 1.77 0.0 -0.832046 -0.554707 1.0 +15 1 1.72 12.3900004 0.0 1.77 0.23719 0.971463 1.0 +16 1 1.72 10.6199999 1.77 1.77 0.456617 -0.889663 1.0 +17 1 1.72 14.1599999 0.0 0.0 -0.661715 0.749755 1.0 +18 1 1.72 15.9300004 1.77 0.0 -0.847309 -0.531099 1.0 +19 1 1.72 15.9300004 0.0 1.77 -0.956536 0.291614 1.0 +20 1 1.72 14.1599999 1.77 1.77 -0.770778 -0.637104 1.0 +21 1 1.72 17.7000008 0.0 0.0 -0.896558 -0.442927 1.0 +22 1 1.72 19.4699993 1.77 0.0 0.557673 0.830061 1.0 +23 1 1.72 19.4699993 0.0 1.77 0.983224 0.182403 1.0 +24 1 1.72 17.7000008 1.77 1.77 -0.939201 0.343368 1.0 +25 1 1.72 21.2399998 0.0 0.0 0.894393 0.447281 1.0 +26 1 1.72 23.0100002 1.77 0.0 0.484661 0.874702 1.0 +27 1 1.72 23.0100002 0.0 1.77 0.525609 -0.850726 1.0 +28 1 1.72 21.2399998 1.77 1.77 0.551899 0.833911 1.0 +29 1 1.72 24.7800007 0.0 0.0 -0.307979 0.951393 1.0 +30 1 1.72 26.5499993 1.77 0.0 -0.993353 -0.115107 1.0 +31 1 1.72 26.5499993 0.0 1.77 0.786777 -0.617237 1.0 +32 1 1.72 24.7800007 1.77 1.77 -0.646691 0.762752 1.0 +33 1 1.72 0.0 3.54 0.0 0.119106 -0.992881 1.0 +34 1 1.72 1.77 5.31 0.0 0.719383 0.694614 1.0 +35 1 1.72 1.77 3.54 1.77 -0.704699 0.709506 1.0 +36 1 1.72 0.0 5.31 1.77 0.795511 -0.605939 1.0 +37 1 1.72 3.54 3.54 0.0 -0.97 -0.243107 1.0 +38 1 1.72 5.31 5.31 0.0 0.976076 0.217428 1.0 +39 1 1.72 5.31 3.54 1.77 0.735471 -0.677556 1.0 +40 1 1.72 3.54 5.31 1.77 -0.319137 -0.947708 1.0 +41 1 1.72 7.0799999 3.54 0.0 -0.610942 0.791675 1.0 +42 1 1.72 8.8500004 5.31 0.0 -0.679543 0.733635 1.0 +43 1 1.72 8.8500004 3.54 1.77 0.983607 -0.180324 1.0 +44 1 1.72 7.0799999 5.31 1.77 -0.217118 -0.976145 1.0 +45 1 1.72 10.6199999 3.54 0.0 -0.997762 0.0668716 1.0 +46 1 1.72 12.3900004 5.31 0.0 0.275194 -0.961389 1.0 +47 1 1.72 12.3900004 3.54 1.77 -0.828419 -0.560108 1.0 +48 1 1.72 10.6199999 5.31 1.77 0.118246 -0.992984 1.0 +49 1 1.72 14.1599999 3.54 0.0 0.737418 0.675437 1.0 +50 1 1.72 15.9300004 5.31 0.0 0.723539 -0.690283 1.0 +51 1 1.72 15.9300004 3.54 1.77 0.445177 0.895443 1.0 +52 1 1.72 14.1599999 5.31 1.77 -0.0224847 -0.999747 1.0 +53 1 1.72 17.7000008 3.54 0.0 -0.0340097 0.999422 1.0 +54 1 1.72 19.4699993 5.31 0.0 -0.842076 -0.539358 1.0 +55 1 1.72 19.4699993 3.54 1.77 0.628732 -0.777622 1.0 +56 1 1.72 17.7000008 5.31 1.77 -0.710873 -0.70332 1.0 +57 1 1.72 21.2399998 3.54 0.0 -0.997492 0.0707798 1.0 +58 1 1.72 23.0100002 5.31 0.0 -0.643338 -0.765582 1.0 +59 1 1.72 23.0100002 3.54 1.77 -0.891542 0.452938 1.0 +60 1 1.72 21.2399998 5.31 1.77 -0.576343 -0.817208 1.0 +61 1 1.72 24.7800007 3.54 0.0 0.915658 -0.401959 1.0 +62 1 1.72 26.5499993 5.31 0.0 -0.674018 -0.738715 1.0 +63 1 1.72 26.5499993 3.54 1.77 -0.92775 -0.373203 1.0 +64 1 1.72 24.7800007 5.31 1.77 -0.336441 0.941705 1.0 +65 1 1.72 0.0 7.0799999 0.0 0.499974 0.86604 1.0 +66 1 1.72 1.77 8.8500004 0.0 -0.582403 0.8129 1.0 +67 1 1.72 1.77 7.0799999 1.77 0.46326 -0.886222 1.0 +68 1 1.72 0.0 8.8500004 1.77 0.812676 -0.582716 1.0 +69 1 1.72 3.54 7.0799999 0.0 0.572515 0.819894 1.0 +70 1 1.72 5.31 8.8500004 0.0 -0.765807 -0.64307 1.0 +71 1 1.72 5.31 7.0799999 1.77 0.474871 0.880056 1.0 +72 1 1.72 3.54 8.8500004 1.77 -0.975682 -0.219192 1.0 +73 1 1.72 7.0799999 7.0799999 0.0 -0.810957 0.585105 1.0 +74 1 1.72 8.8500004 8.8500004 0.0 -0.877575 0.479439 1.0 +75 1 1.72 8.8500004 7.0799999 1.77 0.824057 -0.566506 1.0 +76 1 1.72 7.0799999 8.8500004 1.77 0.297271 0.954793 1.0 +77 1 1.72 10.6199999 7.0799999 0.0 -0.681778 -0.731559 1.0 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109.7399979 0.547786 0.836619 1.0 +8090 1 1.72 23.0100002 15.9300004 109.7399979 -0.810246 0.58609 1.0 +8091 1 1.72 23.0100002 14.1599999 111.5100022 -0.0396045 -0.999215 1.0 +8092 1 1.72 21.2399998 15.9300004 111.5100022 0.999244 0.0388725 1.0 +8093 1 1.72 24.7800007 14.1599999 109.7399979 -0.995393 -0.0958841 1.0 +8094 1 1.72 26.5499993 15.9300004 109.7399979 0.707666 -0.706547 1.0 +8095 1 1.72 26.5499993 14.1599999 111.5100022 -0.857797 0.513989 1.0 +8096 1 1.72 24.7800007 15.9300004 111.5100022 0.688346 0.725383 1.0 +8097 1 1.72 0.0 17.7000008 109.7399979 0.453695 0.891157 1.0 +8098 1 1.72 1.77 19.4699993 109.7399979 -0.869991 0.493068 1.0 +8099 1 1.72 1.77 17.7000008 111.5100022 -0.828945 0.55933 1.0 +8100 1 1.72 0.0 19.4699993 111.5100022 -0.578312 -0.815815 1.0 +8101 1 1.72 3.54 17.7000008 109.7399979 -0.474111 -0.880465 1.0 +8102 1 1.72 5.31 19.4699993 109.7399979 -0.953145 0.302515 1.0 +8103 1 1.72 5.31 17.7000008 111.5100022 -0.662482 0.749078 1.0 +8104 1 1.72 3.54 19.4699993 111.5100022 -0.673709 0.738997 1.0 +8105 1 1.72 7.0799999 17.7000008 109.7399979 0.703708 0.71049 1.0 +8106 1 1.72 8.8500004 19.4699993 109.7399979 -0.962777 0.270298 1.0 +8107 1 1.72 8.8500004 17.7000008 111.5100022 -0.409325 0.912389 1.0 +8108 1 1.72 7.0799999 19.4699993 111.5100022 0.992278 0.12403 1.0 +8109 1 1.72 10.6199999 17.7000008 109.7399979 -0.256869 -0.966446 1.0 +8110 1 1.72 12.3900004 19.4699993 109.7399979 -0.81811 0.575062 1.0 +8111 1 1.72 12.3900004 17.7000008 111.5100022 0.944442 -0.328678 1.0 +8112 1 1.72 10.6199999 19.4699993 111.5100022 -0.790776 0.612106 1.0 +8113 1 1.72 14.1599999 17.7000008 109.7399979 0.99885 0.047945 1.0 +8114 1 1.72 15.9300004 19.4699993 109.7399979 -0.75767 0.652638 1.0 +8115 1 1.72 15.9300004 17.7000008 111.5100022 0.104479 -0.994527 1.0 +8116 1 1.72 14.1599999 19.4699993 111.5100022 -0.366155 -0.930554 1.0 +8117 1 1.72 17.7000008 17.7000008 109.7399979 -0.100712 0.994916 1.0 +8118 1 1.72 19.4699993 19.4699993 109.7399979 0.20119 -0.979552 1.0 +8119 1 1.72 19.4699993 17.7000008 111.5100022 0.7043 -0.709902 1.0 +8120 1 1.72 17.7000008 19.4699993 111.5100022 0.995221 -0.0976515 1.0 +8121 1 1.72 21.2399998 17.7000008 109.7399979 0.0913868 0.995815 1.0 +8122 1 1.72 23.0100002 19.4699993 109.7399979 -0.783334 0.6216 1.0 +8123 1 1.72 23.0100002 17.7000008 111.5100022 0.762993 0.646407 1.0 +8124 1 1.72 21.2399998 19.4699993 111.5100022 0.969106 -0.246644 1.0 +8125 1 1.72 24.7800007 17.7000008 109.7399979 -0.99318 -0.116594 1.0 +8126 1 1.72 26.5499993 19.4699993 109.7399979 0.751321 -0.659937 1.0 +8127 1 1.72 26.5499993 17.7000008 111.5100022 -0.41311 -0.910681 1.0 +8128 1 1.72 24.7800007 19.4699993 111.5100022 -0.231533 0.972827 1.0 +8129 1 1.72 0.0 21.2399998 109.7399979 -0.638342 -0.769753 1.0 +8130 1 1.72 1.77 23.0100002 109.7399979 -0.358386 -0.933574 1.0 +8131 1 1.72 1.77 21.2399998 111.5100022 0.0433983 -0.999058 1.0 +8132 1 1.72 0.0 23.0100002 111.5100022 -0.986115 -0.166067 1.0 +8133 1 1.72 3.54 21.2399998 109.7399979 0.996583 0.082601 1.0 +8134 1 1.72 5.31 23.0100002 109.7399979 -0.865815 0.500364 1.0 +8135 1 1.72 5.31 21.2399998 111.5100022 0.446465 0.894801 1.0 +8136 1 1.72 3.54 23.0100002 111.5100022 0.701589 -0.712582 1.0 +8137 1 1.72 7.0799999 21.2399998 109.7399979 0.994388 0.105798 1.0 +8138 1 1.72 8.8500004 23.0100002 109.7399979 0.779675 0.626184 1.0 +8139 1 1.72 8.8500004 21.2399998 111.5100022 -0.913378 0.407112 1.0 +8140 1 1.72 7.0799999 23.0100002 111.5100022 -0.974435 0.22467 1.0 +8141 1 1.72 10.6199999 21.2399998 109.7399979 0.0180628 0.999837 1.0 +8142 1 1.72 12.3900004 23.0100002 109.7399979 -0.393018 0.919531 1.0 +8143 1 1.72 12.3900004 21.2399998 111.5100022 0.171283 -0.985222 1.0 +8144 1 1.72 10.6199999 23.0100002 111.5100022 0.853928 0.520391 1.0 +8145 1 1.72 14.1599999 21.2399998 109.7399979 -0.893534 -0.448996 1.0 +8146 1 1.72 15.9300004 23.0100002 109.7399979 0.783901 0.620886 1.0 +8147 1 1.72 15.9300004 21.2399998 111.5100022 -0.636441 0.771326 1.0 +8148 1 1.72 14.1599999 23.0100002 111.5100022 -0.62653 0.779398 1.0 +8149 1 1.72 17.7000008 21.2399998 109.7399979 -0.426717 -0.904385 1.0 +8150 1 1.72 19.4699993 23.0100002 109.7399979 0.150477 -0.988614 1.0 +8151 1 1.72 19.4699993 21.2399998 111.5100022 0.993032 -0.117843 1.0 +8152 1 1.72 17.7000008 23.0100002 111.5100022 -0.858474 -0.512857 1.0 +8153 1 1.72 21.2399998 21.2399998 109.7399979 0.671527 -0.74098 1.0 +8154 1 1.72 23.0100002 23.0100002 109.7399979 0.724398 -0.689382 1.0 +8155 1 1.72 23.0100002 21.2399998 111.5100022 -0.533734 -0.845652 1.0 +8156 1 1.72 21.2399998 23.0100002 111.5100022 0.446337 0.894865 1.0 +8157 1 1.72 24.7800007 21.2399998 109.7399979 0.100506 -0.994936 1.0 +8158 1 1.72 26.5499993 23.0100002 109.7399979 0.663547 -0.748135 1.0 +8159 1 1.72 26.5499993 21.2399998 111.5100022 -0.838999 0.544134 1.0 +8160 1 1.72 24.7800007 23.0100002 111.5100022 -0.412355 -0.911023 1.0 +8161 1 1.72 0.0 24.7800007 109.7399979 -0.768577 -0.639757 1.0 +8162 1 1.72 1.77 26.5499993 109.7399979 0.876973 -0.480539 1.0 +8163 1 1.72 1.77 24.7800007 111.5100022 0.940988 0.33844 1.0 +8164 1 1.72 0.0 26.5499993 111.5100022 -0.739484 -0.673174 1.0 +8165 1 1.72 3.54 24.7800007 109.7399979 0.463964 0.885854 1.0 +8166 1 1.72 5.31 26.5499993 109.7399979 0.834599 0.550857 1.0 +8167 1 1.72 5.31 24.7800007 111.5100022 -0.414423 -0.910084 1.0 +8168 1 1.72 3.54 26.5499993 111.5100022 0.209991 0.977703 1.0 +8169 1 1.72 7.0799999 24.7800007 109.7399979 -0.200071 -0.979781 1.0 +8170 1 1.72 8.8500004 26.5499993 109.7399979 -0.593916 0.804527 1.0 +8171 1 1.72 8.8500004 24.7800007 111.5100022 -0.976341 -0.216238 1.0 +8172 1 1.72 7.0799999 26.5499993 111.5100022 0.892014 -0.452008 1.0 +8173 1 1.72 10.6199999 24.7800007 109.7399979 0.262541 0.964921 1.0 +8174 1 1.72 12.3900004 26.5499993 109.7399979 -0.541535 -0.840678 1.0 +8175 1 1.72 12.3900004 24.7800007 111.5100022 0.789328 0.613972 1.0 +8176 1 1.72 10.6199999 26.5499993 111.5100022 0.500046 0.865999 1.0 +8177 1 1.72 14.1599999 24.7800007 109.7399979 0.353277 0.935519 1.0 +8178 1 1.72 15.9300004 26.5499993 109.7399979 0.604788 0.796387 1.0 +8179 1 1.72 15.9300004 24.7800007 111.5100022 0.840508 -0.541799 1.0 +8180 1 1.72 14.1599999 26.5499993 111.5100022 0.296351 -0.955079 1.0 +8181 1 1.72 17.7000008 24.7800007 109.7399979 -0.957237 0.289304 1.0 +8182 1 1.72 19.4699993 26.5499993 109.7399979 0.344119 -0.938926 1.0 +8183 1 1.72 19.4699993 24.7800007 111.5100022 -0.989355 -0.145521 1.0 +8184 1 1.72 17.7000008 26.5499993 111.5100022 0.787109 0.616813 1.0 +8185 1 1.72 21.2399998 24.7800007 109.7399979 -0.321766 0.946819 1.0 +8186 1 1.72 23.0100002 26.5499993 109.7399979 -0.647284 -0.762249 1.0 +8187 1 1.72 23.0100002 24.7800007 111.5100022 -0.999094 0.0425548 1.0 +8188 1 1.72 21.2399998 26.5499993 111.5100022 -0.33438 0.942438 1.0 +8189 1 1.72 24.7800007 24.7800007 109.7399979 0.960667 -0.277704 1.0 +8190 1 1.72 26.5499993 26.5499993 109.7399979 0.822147 -0.569276 1.0 +8191 1 1.72 26.5499993 24.7800007 111.5100022 0.915832 -0.401561 1.0 +8192 1 1.72 24.7800007 26.5499993 111.5100022 -0.746316 -0.665592 1.0 diff --git a/examples/SPIN/read_restart/in.spin.read_data b/examples/SPIN/read_restart/in.spin.read_data new file mode 100644 index 0000000000..80de036661 --- /dev/null +++ b/examples/SPIN/read_restart/in.spin.read_data @@ -0,0 +1,45 @@ +units metal +dimension 3 +boundary p p p + +atom_style spin + +# necessary for the serial algorithm (sametag) +atom_modify map array +read_data Norm_randXY_8x8x32.data + +mass 1 58.93 + +pair_style hybrid/overlay eam/alloy spin/exchange 4.0 +pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co +pair_coeff * * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885 + +neighbor 1.0 bin +neigh_modify every 1 check no delay 0 + +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 +fix 2 all langevin/spin 0.0 0.0 21 + +fix 3 all nve/spin lattice yes +timestep 0.0001 + +# define outputs and computes + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo 10 +thermo_style custom step time v_magnorm v_emag v_tmag temp etotal +thermo_modify format float %20.15g + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 10 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] + +run 100 diff --git a/examples/SPIN/read_restart/in.spin.restart b/examples/SPIN/read_restart/in.spin.restart new file mode 100644 index 0000000000..a1198ccf93 --- /dev/null +++ b/examples/SPIN/read_restart/in.spin.restart @@ -0,0 +1,49 @@ +# start a spin-lattice simulation from a data file +units metal +atom_style spin + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +read_restart restart_hcp_cobalt.equil + +# setting mass, mag. moments, and interactions + +mass 1 58.93 + +pair_style hybrid/overlay eam/alloy spin/exchange 4.0 +pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co +pair_coeff * * spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567 + +neighbor 1.0 bin +neigh_modify every 1 check no delay 0 + +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 +fix 2 all langevin/spin 0.0 0.0 21 + +fix 3 all nve/spin lattice yes +timestep 0.0001 + +# define outputs + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo 10 +thermo_style custom step time v_magnorm v_emag v_tmag temp etotal +thermo_modify format float %20.15g + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] + +run 100 diff --git a/examples/SPIN/read_restart/in.spin.write_restart b/examples/SPIN/read_restart/in.spin.write_restart new file mode 100644 index 0000000000..84fea24611 --- /dev/null +++ b/examples/SPIN/read_restart/in.spin.write_restart @@ -0,0 +1,55 @@ +# fcc cobalt in a 3d periodic box + +units metal +atom_style spin + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice hcp 2.5071 +region box block 0.0 5.0 0.0 5.0 0.0 5.0 +create_box 1 box +create_atoms 1 box + +# setting mass, mag. moments, and interactions for cobalt + +mass 1 58.93 + +set group all spin/random 31 1.72 + +pair_style spin/exchange 4.0 +pair_coeff * * exchange 4.0 0.3593 1.135028015e-05 1.064568567 + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 +fix 2 all langevin/spin 100.0 0.01 21 + +fix 3 all nve/spin lattice no +timestep 0.0001 + +# compute and output options + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo_style custom step time v_magnorm v_emag temp etotal +thermo 100 + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] + +run 1000 +write_restart restart_hcp_cobalt.equil + diff --git a/examples/SPIN/read_restart/log.11May18.spin.read_data.g++.1 b/examples/SPIN/read_restart/log.11May18.spin.read_data.g++.1 new file mode 100644 index 0000000000..405be50bd9 --- /dev/null +++ b/examples/SPIN/read_restart/log.11May18.spin.read_data.g++.1 @@ -0,0 +1,112 @@ +LAMMPS (11 May 2018) +units metal +dimension 3 +boundary p p p + +atom_style spin + +# necessary for the serial algorithm (sametag) +atom_modify map array +read_data Norm_randXY_8x8x32.data + orthogonal box = (0 0 0) to (28.32 28.32 113.28) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 8192 atoms + +mass 1 58.93 + +pair_style hybrid/overlay eam/alloy spin/exchange 4.0 +pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co +pair_coeff * * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885 + +neighbor 1.0 bin +neigh_modify every 1 check no delay 0 + +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 +fix 2 all langevin/spin 0.0 0.0 21 + +fix 3 all nve/spin lattice yes +timestep 0.0001 + +# define outputs and computes + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo 10 +thermo_style custom step time v_magnorm v_emag v_tmag temp etotal +thermo_modify format float %20.15g + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 10 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] + +run 100 +Neighbor list info ... + update every 1 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7.49954 + ghost atom cutoff = 7.49954 + binsize = 3.74977, bins = 8 8 31 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair eam/alloy, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 18.68 | 18.68 | 18.68 Mbytes +Step Time v_magnorm v_emag v_tmag Temp TotEng + 0 0 0.980832325249102 -2984.9466433509 51.7121203365409 0 -38881.8459242429 + 10 0.001 0.980832325038224 -2984.94800197308 52.2550760237226 0.00128259392155095 -38881.8459243688 + 20 0.002 0.980832322622779 -2984.95196908579 53.4253029071033 0.0050206854169363 -38881.8459246487 + 30 0.003 0.980832317889283 -2984.95826684048 55.1488791221993 0.0109316238061975 -38881.8459250502 + 40 0.004 0.980832310888481 -2984.96649810512 57.3217709603901 0.0186091353316915 -38881.8459255204 + 50 0.005 0.980832301939686 -2984.97619813381 59.8271487572311 0.0275752699737783 -38881.8459260027 + 60 0.006 0.980832291654664 -2984.98688847988 62.5518654049861 0.0373348857300743 -38881.8459264498 + 70 0.007 0.980832280861627 -2984.99812400566 65.3978892661935 0.0474235455824994 -38881.845926824 + 80 0.008 0.980832270462785 -2985.00952679611 68.286219599829 0.0574425858114516 -38881.8459271072 + 90 0.009 0.980832261284587 -2985.02080458573 71.1539714621652 0.0670788260497413 -38881.8459272915 + 100 0.01 0.980832253960703 -2985.03175506188 73.9486358176052 0.0761100787140068 -38881.8459273845 +Loop time of 12.4286 on 1 procs for 100 steps with 8192 atoms + +Performance: 0.070 ns/day, 345.239 hours/ns, 8.046 timesteps/s +99.6% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 4.0123 | 4.0123 | 4.0123 | 0.0 | 32.28 +Neigh | 3.005 | 3.005 | 3.005 | 0.0 | 24.18 +Comm | 0.041798 | 0.041798 | 0.041798 | 0.0 | 0.34 +Output | 1.8465 | 1.8465 | 1.8465 | 0.0 | 14.86 +Modify | 3.5157 | 3.5157 | 3.5157 | 0.0 | 28.29 +Other | | 0.007261 | | | 0.06 + +Nlocal: 8192 ave 8192 max 8192 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 14621 ave 14621 max 14621 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 573440 ave 573440 max 573440 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 1.14688e+06 ave 1.14688e+06 max 1.14688e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 1146880 +Ave neighs/atom = 140 +Neighbor list builds = 100 +Dangerous builds not checked + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:12 diff --git a/examples/SPIN/read_restart/log.11May18.spin.read_data.g++.4 b/examples/SPIN/read_restart/log.11May18.spin.read_data.g++.4 new file mode 100644 index 0000000000..56fed35307 --- /dev/null +++ b/examples/SPIN/read_restart/log.11May18.spin.read_data.g++.4 @@ -0,0 +1,112 @@ +LAMMPS (11 May 2018) +units metal +dimension 3 +boundary p p p + +atom_style spin + +# necessary for the serial algorithm (sametag) +atom_modify map array +read_data Norm_randXY_8x8x32.data + orthogonal box = (0 0 0) to (28.32 28.32 113.28) + 1 by 1 by 4 MPI processor grid + reading atoms ... + 8192 atoms + +mass 1 58.93 + +pair_style hybrid/overlay eam/alloy spin/exchange 4.0 +pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co +pair_coeff * * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885 + +neighbor 1.0 bin +neigh_modify every 1 check no delay 0 + +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 +fix 2 all langevin/spin 0.0 0.0 21 + +fix 3 all nve/spin lattice yes +timestep 0.0001 + +# define outputs and computes + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo 10 +thermo_style custom step time v_magnorm v_emag v_tmag temp etotal +thermo_modify format float %20.15g + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 10 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] + +run 100 +Neighbor list info ... + update every 1 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7.49954 + ghost atom cutoff = 7.49954 + binsize = 3.74977, bins = 8 8 31 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair eam/alloy, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 7.883 | 7.994 | 8.25 Mbytes +Step Time v_magnorm v_emag v_tmag Temp TotEng + 0 0 0.980832325249103 -2984.9466433509 51.7121203365411 0 -38881.8459242507 + 10 0.001 0.980832325329477 -2984.94800197307 52.2550778515409 0.00128259391683994 -38881.8459243698 + 20 0.002 0.980832324654401 -2984.95196908569 53.4253110612179 0.00502068532291255 -38881.8459246487 + 30 0.003 0.98083232312993 -2984.95826683995 55.148898005011 0.0109316232931419 -38881.84592505 + 40 0.004 0.980832320808156 -2984.9664981035 57.3218040934977 0.0186091337978305 -38881.8459255198 + 50 0.005 0.980832317596783 -2984.97619813016 59.827198436387 0.0275752665472358 -38881.8459260035 + 60 0.006 0.980832313514709 -2984.98688847322 62.5519331668858 0.037334879488755 -38881.84592645 + 70 0.007 0.980832309220414 -2984.99812399537 65.3979760533737 0.0474235360022736 -38881.8459268243 + 80 0.008 0.980832304490479 -2985.00952678209 68.2863250613635 0.0574425728014485 -38881.8459271068 + 90 0.009 0.980832299379824 -2985.02080456789 71.1540940309591 0.0670788096168283 -38881.8459272917 + 100 0.01 0.980832294622694 -2985.03175503971 73.9487734241296 0.0761100584457276 -38881.8459273851 +Loop time of 3.6612 on 4 procs for 100 steps with 8192 atoms + +Performance: 0.236 ns/day, 101.700 hours/ns, 27.313 timesteps/s +98.8% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.0622 | 1.076 | 1.0936 | 1.1 | 29.39 +Neigh | 0.77462 | 0.79542 | 0.81798 | 1.9 | 21.73 +Comm | 0.024701 | 0.066122 | 0.10261 | 11.1 | 1.81 +Output | 0.50304 | 0.51253 | 0.52111 | 0.9 | 14.00 +Modify | 1.2006 | 1.2082 | 1.2205 | 0.7 | 33.00 +Other | | 0.002962 | | | 0.08 + +Nlocal: 2048 ave 2095 max 1981 min +Histogram: 1 0 0 0 0 0 2 0 0 1 +Nghost: 5765 ave 5832 max 5718 min +Histogram: 1 0 0 2 0 0 0 0 0 1 +Neighs: 143360 ave 146361 max 139058 min +Histogram: 1 0 0 0 0 0 1 1 0 1 +FullNghs: 286720 ave 293300 max 277340 min +Histogram: 1 0 0 0 0 0 2 0 0 1 + +Total # of neighbors = 1146880 +Ave neighs/atom = 140 +Neighbor list builds = 100 +Dangerous builds not checked + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:03 diff --git a/examples/SPIN/read_restart/log.11May18.spin.restart.g++.1 b/examples/SPIN/read_restart/log.11May18.spin.restart.g++.1 new file mode 100644 index 0000000000..16eb7c3f5e --- /dev/null +++ b/examples/SPIN/read_restart/log.11May18.spin.restart.g++.1 @@ -0,0 +1,117 @@ +LAMMPS (11 May 2018) +# start a spin-lattice simulation from a data file +units metal +atom_style spin + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +read_restart restart_hcp_cobalt.equil + restoring atom style spin from restart + orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704) + 1 by 1 by 1 MPI processor grid + restoring pair style spin/exchange from restart + 500 atoms + +# setting mass, mag. moments, and interactions + +mass 1 58.93 + +pair_style hybrid/overlay eam/alloy spin/exchange 4.0 +pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co +pair_coeff * * spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567 + +neighbor 1.0 bin +neigh_modify every 1 check no delay 0 + +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 +fix 2 all langevin/spin 0.0 0.0 21 + +fix 3 all nve/spin lattice yes +timestep 0.0001 + +# define outputs + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo 10 +thermo_style custom step time v_magnorm v_emag v_tmag temp etotal +thermo_modify format float %20.15g + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] + +run 100 +Neighbor list info ... + update every 1 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7.49954 + ghost atom cutoff = 7.49954 + binsize = 3.74977, bins = 4 6 6 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair eam/alloy, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 6.315 | 6.315 | 6.315 Mbytes +Step Time v_magnorm v_emag v_tmag Temp TotEng + 1000 0 0.106120063678768 -11.8110267448938 5244.87332482316 0 -2206.81097898043 + 1010 0.001 0.106120047478105 -11.8198467887534 5263.87502105137 0.136650312456579 -2206.81097929055 + 1020 0.002 0.106120026430373 -11.8460960518731 5267.29822866382 0.542282409605327 -2206.81098022997 + 1030 0.003 0.106120005015917 -11.8891434078861 5252.95323564256 1.204018338139 -2206.81098172551 + 1040 0.004 0.106119988532653 -11.9479778701641 5220.88508622311 2.10120884995911 -2206.81098371047 + 1050 0.005 0.10611998133687 -12.021242685853 5172.58549378915 3.20622445795757 -2206.81098610701 + 1060 0.006 0.10611998489458 -12.107271344148 5110.57395203849 4.48535975411235 -2206.81098879725 + 1070 0.007 0.106119996964771 -12.204156761765 5038.48903231346 5.9003121044977 -2206.81099161183 + 1080 0.008 0.106120013042521 -12.3098695046152 4961.0327167967 7.4104497466856 -2206.81099434653 + 1090 0.009 0.106120029236234 -12.4224157835754 4883.3210922213 8.97568980540163 -2206.81099680117 + 1100 0.01 0.106120044071404 -12.5400036896932 4809.88136080052 10.559459821976 -2206.81099883104 +Loop time of 0.833234 on 1 procs for 100 steps with 500 atoms + +Performance: 1.037 ns/day, 23.145 hours/ns, 120.014 timesteps/s +99.7% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.26558 | 0.26558 | 0.26558 | 0.0 | 31.87 +Neigh | 0.21352 | 0.21352 | 0.21352 | 0.0 | 25.62 +Comm | 0.0057988 | 0.0057988 | 0.0057988 | 0.0 | 0.70 +Output | 0.12463 | 0.12463 | 0.12463 | 0.0 | 14.96 +Modify | 0.22275 | 0.22275 | 0.22275 | 0.0 | 26.73 +Other | | 0.0009537 | | | 0.11 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 2534 ave 2534 max 2534 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 36500 ave 36500 max 36500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 73000 ave 73000 max 73000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 73000 +Ave neighs/atom = 146 +Neighbor list builds = 100 +Dangerous builds not checked + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:00 diff --git a/examples/SPIN/read_restart/log.11May18.spin.restart.g++.4 b/examples/SPIN/read_restart/log.11May18.spin.restart.g++.4 new file mode 100644 index 0000000000..f93605a10a --- /dev/null +++ b/examples/SPIN/read_restart/log.11May18.spin.restart.g++.4 @@ -0,0 +1,118 @@ +LAMMPS (11 May 2018) +# start a spin-lattice simulation from a data file +units metal +atom_style spin + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +read_restart restart_hcp_cobalt.equil +WARNING: Restart file used different # of processors (../read_restart.cpp:723) + restoring atom style spin from restart + orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704) + 1 by 2 by 2 MPI processor grid + restoring pair style spin/exchange from restart + 500 atoms + +# setting mass, mag. moments, and interactions + +mass 1 58.93 + +pair_style hybrid/overlay eam/alloy spin/exchange 4.0 +pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co +pair_coeff * * spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567 + +neighbor 1.0 bin +neigh_modify every 1 check no delay 0 + +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 +fix 2 all langevin/spin 0.0 0.0 21 + +fix 3 all nve/spin lattice yes +timestep 0.0001 + +# define outputs + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo 10 +thermo_style custom step time v_magnorm v_emag v_tmag temp etotal +thermo_modify format float %20.15g + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] + +run 100 +Neighbor list info ... + update every 1 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7.49954 + ghost atom cutoff = 7.49954 + binsize = 3.74977, bins = 4 6 6 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair eam/alloy, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 6.203 | 6.203 | 6.203 Mbytes +Step Time v_magnorm v_emag v_tmag Temp TotEng + 1000 0 0.106120063678768 -11.8110267448939 5244.87332482316 0 -2206.81097898003 + 1010 0.001 0.106120030254187 -11.8198467883806 5263.87550015043 0.136650306637598 -2206.81097929055 + 1020 0.002 0.106119996655714 -11.8460960476455 5267.299198699 0.542282344092749 -2206.81098022997 + 1030 0.003 0.106119967407682 -11.8891433919665 5252.95473019843 1.20401809237154 -2206.81098172552 + 1040 0.004 0.106119960016585 -11.9479778326021 5220.88686874944 2.10120827278397 -2206.81098371049 + 1050 0.005 0.106119961252471 -12.0212426191481 5172.58712301374 3.20622343988728 -2206.81098610703 + 1060 0.006 0.106119967598995 -12.1072712483404 5110.57504803718 4.48535830705751 -2206.81098879724 + 1070 0.007 0.106119967669058 -12.2041566468564 5038.48927079832 5.90031039867811 -2206.81099161179 + 1080 0.008 0.106119969263395 -12.3098693905406 4961.03212459716 7.41044810751949 -2206.8109943465 + 1090 0.009 0.106119960964075 -12.4224156966204 4883.31968289062 8.97568865379831 -2206.81099680112 + 1100 0.01 0.106119945605273 -12.5400036591612 4809.87930844463 10.5594596175303 -2206.81099883101 +Loop time of 0.304678 on 4 procs for 100 steps with 500 atoms + +Performance: 2.836 ns/day, 8.463 hours/ns, 328.215 timesteps/s +98.0% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.071445 | 0.073018 | 0.074151 | 0.4 | 23.97 +Neigh | 0.054448 | 0.055709 | 0.057528 | 0.5 | 18.28 +Comm | 0.0061178 | 0.0074609 | 0.0090766 | 1.2 | 2.45 +Output | 0.037489 | 0.038586 | 0.039952 | 0.5 | 12.66 +Modify | 0.12826 | 0.12954 | 0.13065 | 0.3 | 42.52 +Other | | 0.0003686 | | | 0.12 + +Nlocal: 125 ave 129 max 120 min +Histogram: 1 0 0 0 1 0 0 1 0 1 +Nghost: 1387 ave 1392 max 1383 min +Histogram: 1 0 1 0 0 1 0 0 0 1 +Neighs: 9125 ave 9428 max 8740 min +Histogram: 1 0 0 1 0 0 0 0 1 1 +FullNghs: 18250 ave 18834 max 17520 min +Histogram: 1 0 0 0 1 0 0 1 0 1 + +Total # of neighbors = 73000 +Ave neighs/atom = 146 +Neighbor list builds = 100 +Dangerous builds not checked + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:00 diff --git a/examples/SPIN/read_restart/log.11May18.spin.write_restart.g++.1 b/examples/SPIN/read_restart/log.11May18.spin.write_restart.g++.1 new file mode 100644 index 0000000000..c3be90cb50 --- /dev/null +++ b/examples/SPIN/read_restart/log.11May18.spin.write_restart.g++.1 @@ -0,0 +1,119 @@ +LAMMPS (11 May 2018) +# fcc cobalt in a 3d periodic box + +units metal +atom_style spin + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice hcp 2.5071 +Lattice spacing in x,y,z = 2.5071 4.34242 4.09408 +region box block 0.0 5.0 0.0 5.0 0.0 5.0 +create_box 1 box +Created orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 500 atoms + Time spent = 0.00027585 secs + +# setting mass, mag. moments, and interactions for cobalt + +mass 1 58.93 + +set group all spin/random 31 1.72 + 500 settings made for spin/random + +pair_style spin/exchange 4.0 +pair_coeff * * exchange 4.0 0.3593 1.135028015e-05 1.064568567 + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 +fix 2 all langevin/spin 100.0 0.01 21 + +fix 3 all nve/spin lattice no +timestep 0.0001 + +# compute and output options + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo_style custom step time v_magnorm v_emag temp etotal +thermo 100 + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] + +run 1000 +Neighbor list info ... + update every 10 steps, delay 20 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 4.1 + ghost atom cutoff = 4.1 + binsize = 2.05, bins = 7 11 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 6.446 | 6.446 | 6.446 Mbytes +Step Time v_magnorm v_emag Temp TotEng + 0 0 0.076558814 1.7982359 0 1.7982359 + 100 0.01 0.079107243 0.56368447 0 0.56368447 + 200 0.02 0.08225862 -0.42421042 0 -0.42421042 + 300 0.03 0.08397714 -1.4964948 0 -1.4964948 + 400 0.04 0.084704989 -2.6740652 0 -2.6740652 + 500 0.05 0.087486342 -4.2043382 0 -4.2043382 + 600 0.06 0.09187261 -5.6687169 0 -5.6687169 + 700 0.07 0.096925249 -6.937499 0 -6.937499 + 800 0.08 0.098988236 -8.2456715 0 -8.2456715 + 900 0.09 0.10434092 -10.111953 0 -10.111953 + 1000 0.1 0.10612006 -11.811027 0 -11.811027 +Loop time of 2.60215 on 1 procs for 1000 steps with 500 atoms + +Performance: 3.320 ns/day, 7.228 hours/ns, 384.297 timesteps/s +99.0% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.35178 | 0.35178 | 0.35178 | 0.0 | 13.52 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.014421 | 0.014421 | 0.014421 | 0.0 | 0.55 +Output | 1.2046 | 1.2046 | 1.2046 | 0.0 | 46.29 +Modify | 1.0274 | 1.0274 | 1.0274 | 0.0 | 39.48 +Other | | 0.004006 | | | 0.15 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1221 ave 1221 max 1221 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 10000 ave 10000 max 10000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 10000 +Ave neighs/atom = 20 +Neighbor list builds = 0 +Dangerous builds = 0 +write_restart restart_hcp_cobalt.equil + + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:02 diff --git a/examples/SPIN/read_restart/log.11May18.spin.write_restart.g++.4 b/examples/SPIN/read_restart/log.11May18.spin.write_restart.g++.4 new file mode 100644 index 0000000000..e54299b9dd --- /dev/null +++ b/examples/SPIN/read_restart/log.11May18.spin.write_restart.g++.4 @@ -0,0 +1,119 @@ +LAMMPS (11 May 2018) +# fcc cobalt in a 3d periodic box + +units metal +atom_style spin + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice hcp 2.5071 +Lattice spacing in x,y,z = 2.5071 4.34242 4.09408 +region box block 0.0 5.0 0.0 5.0 0.0 5.0 +create_box 1 box +Created orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 500 atoms + Time spent = 0.000257969 secs + +# setting mass, mag. moments, and interactions for cobalt + +mass 1 58.93 + +set group all spin/random 31 1.72 + 500 settings made for spin/random + +pair_style spin/exchange 4.0 +pair_coeff * * exchange 4.0 0.3593 1.135028015e-05 1.064568567 + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 +fix 2 all langevin/spin 100.0 0.01 21 + +fix 3 all nve/spin lattice no +timestep 0.0001 + +# compute and output options + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo_style custom step time v_magnorm v_emag temp etotal +thermo 100 + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] + +run 1000 +Neighbor list info ... + update every 10 steps, delay 20 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 4.1 + ghost atom cutoff = 4.1 + binsize = 2.05, bins = 7 11 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 6.367 | 6.367 | 6.367 Mbytes +Step Time v_magnorm v_emag Temp TotEng + 0 0 0.076558814 1.7982359 0 1.7982359 + 100 0.01 0.081414414 0.70545723 0 0.70545723 + 200 0.02 0.084519539 -0.33171078 0 -0.33171078 + 300 0.03 0.089334139 -1.3988283 0 -1.3988283 + 400 0.04 0.092873722 -2.8519371 0 -2.8519371 + 500 0.05 0.0970839 -4.1531164 0 -4.1531164 + 600 0.06 0.099626132 -5.7993765 0 -5.7993765 + 700 0.07 0.10467169 -7.3011333 0 -7.3011333 + 800 0.08 0.10893493 -8.6918141 0 -8.6918141 + 900 0.09 0.11389657 -10.236174 0 -10.236174 + 1000 0.1 0.1180057 -11.896933 0 -11.896933 +Loop time of 1.05012 on 4 procs for 1000 steps with 500 atoms + +Performance: 8.228 ns/day, 2.917 hours/ns, 952.272 timesteps/s +98.1% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.08972 | 0.090456 | 0.091872 | 0.3 | 8.61 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.016958 | 0.018047 | 0.019791 | 0.8 | 1.72 +Output | 0.36286 | 0.37483 | 0.38975 | 1.6 | 35.69 +Modify | 0.55131 | 0.56541 | 0.57702 | 1.3 | 53.84 +Other | | 0.001374 | | | 0.13 + +Nlocal: 125 ave 125 max 125 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 597.5 ave 600 max 595 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 2500 ave 2500 max 2500 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 10000 +Ave neighs/atom = 20 +Neighbor list builds = 0 +Dangerous builds = 0 +write_restart restart_hcp_cobalt.equil + + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:01 diff --git a/examples/SPIN/vmd/prepare_vmd.sh b/examples/SPIN/vmd/prepare_vmd.sh new file mode 100755 index 0000000000..fa62c6e109 --- /dev/null +++ b/examples/SPIN/vmd/prepare_vmd.sh @@ -0,0 +1,91 @@ +#!/bin/bash +# example prepare_vmd.sh /home/jtranch/Documents/lammps/src/dump_VSRSV.lammpstrj +# you will get a return file + +echo "vmd script for file $1 is preparing..." + +timestamp(){ + date +%s +} + +TS=$(timestamp) +FILE=view_${TS}.vmd + +cat >${FILE} <] [resolution ] [radius ] [filled ]"} + # defaults + set scale 2.0 + set res 50 + set radius 0.1 + set filled yes + + if {[llength \$args] < 3} { + error "wrong # args: should be \$usage" + } + set mol [lindex \$args 0] + set center [lindex \$args 1] + set vector [lindex \$args 2] + if {[llength \$center] != 3 || [llength \$vector] != 3} { + error "wrong type of args: should be \$usage" + } + + foreach {flag value} [lrange \$args 3 end] { + switch -glob \$flag { + scale {set scale \$value} + res* {set res \$value} + rad* {set radius \$value} + fill* {set filled \$value} + default {error "unknown option '\$flag': should be \$usage" } + } + } + + set vechalf [vecscale [expr \$scale * 0.5] \$vector] + return [list \\ + [graphics \$mol color yellow]\\ + [graphics \$mol cylinder [vecsub \$center \$vechalf]\\ + [vecadd \$center [vecscale 0.7 \$vechalf]] \\ + radius \$radius resolution \$res filled \$filled] \\ + [graphics \$mol color orange]\\ + [graphics \$mol cone [vecadd \$center [vecscale 0.6 \$vechalf]] \\ + [vecadd \$center \$vechalf] radius [expr \$radius * 2.5] \\ + resolution \$res]] +} + +proc vmd_draw_spin {args} { + global molid + graphics \$molid delete all + set frame [molinfo \$molid get frame] + set natoms [molinfo \$molid get numatoms] + for {set i 0} {\$i < \$natoms} {incr i} { + set sel [atomselect top "index \$i"] + set coords [lindex [\$sel get {x y z}] \$molid] + set velocities [lindex [\$sel get {vx vy vz}] \$molid] + draw vector \$coords \$velocities + set uvx [lindex [\$sel get {vx}] \$molid] + set uvy [lindex [\$sel get {vy}] \$molid] + set uvz [lindex [\$sel get {vz}] \$molid] + \$sel set user [vecadd [vecadd [vecscale \$uvy \$uvy] [vecscale \$uvz \$uvz] ] [vecscale \$uvx \$uvx]] + \$sel set user \$uvy + #draw vector \$coords {0.0 uvy 0.0} + } + #pbc box -color 3 +} + +proc enable_trace {} { + global vmd_frame + trace variable vmd_frame([molinfo top]) w vmd_draw_spin +} + +set molid [mol addfile {$1} type {lammpstrj} autobonds off first 0 last -1 step 1 waitfor all] +scale by 0.5 +animate style Loop +enable_trace +EOF +echo "$FILE is ready..." diff --git a/examples/SPIN/vmd/vmd_nano.vmd b/examples/SPIN/vmd/vmd_nano.vmd new file mode 100644 index 0000000000..f9e3454270 --- /dev/null +++ b/examples/SPIN/vmd/vmd_nano.vmd @@ -0,0 +1,79 @@ +proc vmd_draw_arrow {mol start end} { + set middle [vecadd $start [vecscale 0.9 [vecsub $end $start]]] + graphics $mol cylinder $start $middle radius 0.05 + graphics $mol cone $middle $end radius 0.01 color 3 +} + +proc vmd_draw_vector {args} { + set usage {"draw vector {x1 y1 z1} {x2 y2 z2} [scale ] [resolution ] [radius ] [filled ]"} + # defaults + set scale 2.0 + set res 50 + set radius 0.1 + set filled yes + + if {[llength $args] < 3} { + error "wrong # args: should be $usage" + } + set mol [lindex $args 0] + set center [lindex $args 1] + set vector [lindex $args 2] + if {[llength $center] != 3 || [llength $vector] != 3} { + error "wrong type of args: should be $usage" + } + + foreach {flag value} [lrange $args 3 end] { + switch -glob $flag { + scale {set scale $value} + res* {set res $value} + rad* {set radius $value} + fill* {set filled $value} + default {error "unknown option '$flag': should be $usage" } + } + } + + set vechalf [vecscale [expr $scale * 0.5] $vector] + return [list \ + [graphics $mol color yellow]\ + [graphics $mol cylinder [vecsub $center $vechalf]\ + [vecadd $center [vecscale 0.7 $vechalf]] \ + radius $radius resolution $res filled $filled] \ + [graphics $mol color orange]\ + [graphics $mol cone [vecadd $center [vecscale 0.6 $vechalf]] \ + [vecadd $center $vechalf] radius [expr $radius * 2.5] \ + resolution $res]] +} + +proc vmd_draw_spin {args} { + global molid + graphics $molid delete all + set frame [molinfo $molid get frame] + set natoms [molinfo $molid get numatoms] + for {set i 0} {$i < $natoms} {incr i} { + set sel [atomselect top "index $i"] +# set sel [atomselect top "index 1200"] + set coords [lindex [$sel get {x y z}] $molid] + set velocities [lindex [$sel get {vx vy vz}] $molid] + draw vector $coords $velocities + set uvx [lindex [$sel get {vx}] $molid] + set uvy [lindex [$sel get {vy}] $molid] + set uvz [lindex [$sel get {vz}] $molid] + $sel set user [vecadd [vecadd [vecscale $uvy $uvy] [vecscale $uvz $uvz] ] [vecscale $uvx $uvx]] + $sel set user $uvy + #draw vector $coords {0.0 uvy 0.0} + } + #pbc box -color 3 +} + +proc enable_trace {} { + global vmd_frame + trace variable vmd_frame([molinfo top]) w vmd_draw_spin + } + +set molid [mol addfile {/home/jtranch/Documents/lammps/src/dump.lammpstrj} type {lammpstrj} autobonds off first 0 last -1 step 1 waitfor all] +scale by 0.5 +animate style Loop +enable_trace + + + diff --git a/examples/USER/diffraction/BulkNi.in b/examples/USER/diffraction/BulkNi.in index a18163175c..8315e57750 100644 --- a/examples/USER/diffraction/BulkNi.in +++ b/examples/USER/diffraction/BulkNi.in @@ -17,10 +17,11 @@ atom_modify sort 0 0 compute XRD all xrd 1.541838 Ni 2Theta 40 80 c 2 2 2 LP 1 echo -compute SAED all saed 0.0251 Ni Kmax 0.85 Zone 1 0 0 c 0.025 0.025 0.025 & - dR_Ewald 0.05 echo manual +compute SAED all saed 0.0251 Ni Kmax 0.85 & + Zone 0 0 0 c 0.025 0.025 0.025 & + dR_Ewald 0.01 echo manual -fix 1 all ave/histo 1 1 1 40 80 200 c_XRD[1] c_XRD[2] & +fix 1 all ave/histo/weight 1 1 1 40 80 200 c_XRD[1] c_XRD[2] & mode vector file $A.hist.xrd fix 2 all saed/vtk 1 1 1 c_SAED file $A_001.saed diff --git a/examples/USER/diffraction/Output/BulkNi.in b/examples/USER/diffraction/Output/BulkNi.in deleted file mode 100644 index 8315e57750..0000000000 --- a/examples/USER/diffraction/Output/BulkNi.in +++ /dev/null @@ -1,35 +0,0 @@ -variable A string bulkNi -log $A.log - -boundary p p p - -units metal -timestep 0.001 - -lattice fcc 3.52 -region box block 0 20 0 20 0 20 -create_box 1 box -create_atoms 1 box - -pair_style none -mass * 58.71 -atom_modify sort 0 0 - -compute XRD all xrd 1.541838 Ni 2Theta 40 80 c 2 2 2 LP 1 echo - -compute SAED all saed 0.0251 Ni Kmax 0.85 & - Zone 0 0 0 c 0.025 0.025 0.025 & - dR_Ewald 0.01 echo manual - -fix 1 all ave/histo/weight 1 1 1 40 80 200 c_XRD[1] c_XRD[2] & - mode vector file $A.hist.xrd - -fix 2 all saed/vtk 1 1 1 c_SAED file $A_001.saed - -dump 1 all custom 1 $A.dump id x y z -run 0 - -unfix 1 -unfix 2 -uncompute XRD -uncompute SAED diff --git a/examples/USER/misc/entropy/Na_MendelevM_2014.eam.fs b/examples/USER/misc/entropy/Na_MendelevM_2014.eam.fs new file mode 100644 index 0000000000..76ecae7b44 --- /dev/null +++ b/examples/USER/misc/entropy/Na_MendelevM_2014.eam.fs @@ -0,0 +1,6006 @@ +Source: M.I. 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4.0580253230452010e+00 -3.0945361122357586e+00 -8.8323796705297763e-01 +4089 7.2248060554373073e+00 9.0480655644191388e-01 -9.6284911590930766e-01 +2593 3.2503133857492319e+00 -4.1972151630470256e+00 -1.7952974231313504e-01 diff --git a/examples/USER/misc/entropy/in.entropy b/examples/USER/misc/entropy/in.entropy new file mode 100644 index 0000000000..2c25dac320 --- /dev/null +++ b/examples/USER/misc/entropy/in.entropy @@ -0,0 +1,34 @@ +echo both + +units metal +atom_style full + +read_data data.interface +mass 1 22.98977 + +neigh_modify delay 10 every 1 +pair_style eam/fs +pair_coeff * * Na_MendelevM_2014.eam.fs Na +timestep 0.002 +thermo 500 + +neighbor 4. bin + +# Define computes +# Global density, no average +compute 1 all entropy/atom 0.25 7.75 +# Local density, no average +compute 2 all entropy/atom 0.25 7.75 local yes +# Global density, average over neighbors +compute 3 all entropy/atom 0.25 7.75 avg yes 5. +# Local density, average over neighbors +compute 4 all entropy/atom 0.25 7.75 avg yes 5. local yes + +dump myDump all custom 500 dump.interface id type x y z c_1 c_2 c_3 c_4 + + +fix 1 all nph x 1. 1. 10. +fix 2 all temp/csvr 350. 350. 0.1 64582 + +run 1000 + diff --git a/examples/USER/misc/entropy/log.entropy b/examples/USER/misc/entropy/log.entropy new file mode 100644 index 0000000000..c380c62a73 --- /dev/null +++ b/examples/USER/misc/entropy/log.entropy @@ -0,0 +1,124 @@ +LAMMPS (30 Mar 2018) + +units metal +atom_style full + +read_data data.interface +Reading data file ... + triclinic box = (0 0 0) to (138.4 34.57 34.57) with tilt (0 0 0) + 4 by 1 by 1 MPI processor grid + reading atoms ... + 4096 atoms + reading velocities ... + 4096 velocities +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors +mass 1 22.98977 + +neigh_modify delay 10 every 1 +pair_style eam/fs +pair_coeff * * Na_MendelevM_2014.eam.fs Na +timestep 0.002 +thermo 500 + +neighbor 4. bin + +# Define computes +# Global density, no average +compute 1 all entropy/atom 0.25 7.75 +# Local density, no average +compute 2 all entropy/atom 0.25 7.75 local yes +# Global density, average over neighbors +compute 3 all entropy/atom 0.25 7.75 avg yes 5. +# Local density, average over neighbors +compute 4 all entropy/atom 0.25 7.75 avg yes 5. local yes + +dump myDump all custom 500 dump.interface id type x y z c_1 c_2 c_3 c_4 + + +fix 1 all nph x 1. 1. 10. +fix 2 all temp/csvr 350. 350. 0.1 64582 + +run 1000 +WARNING: More than one compute entropy/atom (../compute_entropy_atom.cpp:138) +WARNING: More than one compute entropy/atom (../compute_entropy_atom.cpp:138) +WARNING: More than one compute entropy/atom (../compute_entropy_atom.cpp:138) +WARNING: More than one compute entropy/atom (../compute_entropy_atom.cpp:138) +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 13.2 + ghost atom cutoff = 13.2 + binsize = 6.6, bins = 21 6 6 + 5 neighbor lists, perpetual/occasional/extra = 5 0 0 + (1) pair eam/fs, perpetual + attributes: half, newton on + pair build: half/bin/newton/tri + stencil: half/bin/3d/newton/tri + bin: standard + (2) compute entropy/atom, perpetual + attributes: full, newton on, ghost + pair build: full/bin/ghost + stencil: full/ghost/bin/3d + bin: standard + (3) compute entropy/atom, perpetual, copy from (2) + attributes: full, newton on, ghost + pair build: copy + stencil: none + bin: none + (4) compute entropy/atom, perpetual, copy from (2) + attributes: full, newton on, ghost + pair build: copy + stencil: none + bin: none + (5) compute entropy/atom, perpetual, copy from (2) + attributes: full, newton on, ghost + pair build: copy + stencil: none + bin: none +Setting up Verlet run ... + Unit style : metal + Current step : 0 + Time step : 0.002 +Per MPI rank memory allocation (min/avg/max) = 25.68 | 25.69 | 25.69 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 346.29871 -4285.222 0 -4101.9191 594.65353 165399.75 + 500 359.33758 -4285.247 0 -4095.0423 471.98587 165847.18 + 1000 348.99659 -4276.2274 0 -4091.4964 149.27188 166966.18 +Loop time of 5.3437 on 4 procs for 1000 steps with 4096 atoms + +Performance: 32.337 ns/day, 0.742 hours/ns, 187.136 timesteps/s +99.8% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 4.2832 | 4.3257 | 4.3839 | 1.8 | 80.95 +Bond | 0.00018309 | 0.00019825 | 0.00021418 | 0.0 | 0.00 +Neigh | 0.42195 | 0.42512 | 0.42739 | 0.3 | 7.96 +Comm | 0.051679 | 0.1101 | 0.14916 | 10.8 | 2.06 +Output | 0.40909 | 0.4091 | 0.40911 | 0.0 | 7.66 +Modify | 0.060869 | 0.061921 | 0.06327 | 0.4 | 1.16 +Other | | 0.01161 | | | 0.22 + +Nlocal: 1024 ave 1040 max 1001 min +Histogram: 1 0 0 0 0 0 2 0 0 1 +Nghost: 4614.25 ave 4700 max 4540 min +Histogram: 1 1 0 0 0 0 0 1 0 1 +Neighs: 121747 ave 126398 max 116931 min +Histogram: 1 0 0 1 0 0 1 0 0 1 +FullNghs: 243494 ave 252523 max 233842 min +Histogram: 1 0 0 1 0 0 1 0 0 1 + +Total # of neighbors = 973974 +Ave neighs/atom = 237.787 +Ave special neighs/atom = 0 +Neighbor list builds = 13 +Dangerous builds = 0 + +Total wall time: 0:00:05 diff --git a/examples/USER/scafacos/data.NaCl b/examples/USER/scafacos/data.NaCl new file mode 100644 index 0000000000..2fd6077983 --- /dev/null +++ b/examples/USER/scafacos/data.NaCl @@ -0,0 +1,25 @@ +LAMMPS Description + +8 atoms + +2 atom types + +0 1 xlo xhi +0 1 ylo yhi +0 1 zlo zhi + +Masses + +1 22.98976928 +2 35.45 + +Atoms + +1 2 1 0.25 0.25 0.25 +2 1 -1 0.75 0.25 0.25 +3 1 -1 0.25 0.75 0.25 +4 2 1 0.75 0.75 0.25 +5 1 -1 0.25 0.25 0.75 +6 2 1 0.75 0.25 0.75 +7 2 1 0.25 0.75 0.75 +8 1 -1 0.75 0.75 0.75 diff --git a/examples/USER/scafacos/data.cloud_wall b/examples/USER/scafacos/data.cloud_wall new file mode 100644 index 0000000000..1592ec666a --- /dev/null +++ b/examples/USER/scafacos/data.cloud_wall @@ -0,0 +1,316 @@ +LAMMPS Description + +300 atoms + +1 atom types + +0 10 xlo xhi +0 10 ylo yhi +0 10 zlo zhi + +Masses + +1 1.0 + +Atoms + +1 1 1 0 0 4.5 +2 1 -1 0 0 5.5 +3 1 1 0 1 4.5 +4 1 -1 0 1 5.5 +5 1 1 0 2 4.5 +6 1 -1 0 2 5.5 +7 1 1 0 3 4.5 +8 1 -1 0 3 5.5 +9 1 1 0 4 4.5 +10 1 -1 0 4 5.5 +11 1 1 0 5 4.5 +12 1 -1 0 5 5.5 +13 1 1 0 6 4.5 +14 1 -1 0 6 5.5 +15 1 1 0 7 4.5 +16 1 -1 0 7 5.5 +17 1 1 0 8 4.5 +18 1 -1 0 8 5.5 +19 1 1 0 9 4.5 +20 1 -1 0 9 5.5 +21 1 1 1 0 4.5 +22 1 -1 1 0 5.5 +23 1 1 1 1 4.5 +24 1 -1 1 1 5.5 +25 1 1 1 2 4.5 +26 1 -1 1 2 5.5 +27 1 1 1 3 4.5 +28 1 -1 1 3 5.5 +29 1 1 1 4 4.5 +30 1 -1 1 4 5.5 +31 1 1 1 5 4.5 +32 1 -1 1 5 5.5 +33 1 1 1 6 4.5 +34 1 -1 1 6 5.5 +35 1 1 1 7 4.5 +36 1 -1 1 7 5.5 +37 1 1 1 8 4.5 +38 1 -1 1 8 5.5 +39 1 1 1 9 4.5 +40 1 -1 1 9 5.5 +41 1 1 2 0 4.5 +42 1 -1 2 0 5.5 +43 1 1 2 1 4.5 +44 1 -1 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0.428803 0.104119 0.797 +799 1 1 0.104847 0.571066 0.798 +800 1 1 0.89442 0.429066 0.799 +801 1 1 0.897285 0.546527 0.8 +802 1 -1 0.103462 0.45356 0.801 +803 1 -1 0.453648 0.895787 0.802 +804 1 1 0.546264 0.104968 0.803 +805 1 1 0.746143 0.811444 0.804 +806 1 -1 0.254333 0.189158 0.805 +807 1 1 0.189764 0.745189 0.806 +808 1 1 0.809628 0.255293 0.807 +809 1 1 0.843889 0.692033 0.808 +810 1 1 0.156796 0.308349 0.809 +811 1 1 0.308734 0.842516 0.81 +812 1 1 0.69088 0.158176 0.811 +813 1 -1 0.606516 0.875913 0.812 +814 1 -1 0.393702 0.124858 0.813 +815 1 1 0.125632 0.606079 0.814 +816 1 1 0.873589 0.394142 0.815 +817 1 1 0.868666 0.619287 0.816 +818 1 -1 0.132112 0.380965 0.817 +819 1 1 0.381218 0.867106 0.818 +820 1 -1 0.618528 0.13368 0.819 +821 1 1 0.674837 0.842099 0.82 +822 1 1 0.325543 0.158644 0.821 +823 1 1 0.159392 0.674075 0.822 +824 1 -1 0.839856 0.326309 0.823 +825 1 -1 0.789881 0.746967 0.824 +826 1 1 0.210768 0.253586 0.825 +827 1 -1 0.254142 0.788579 0.826 +828 1 -1 0.745299 0.212077 0.827 +829 1 1 0.530071 0.87618 0.828 +830 1 1 0.469999 0.124688 0.829 +831 1 1 0.125562 0.529931 0.83 +832 1 1 0.87356 0.470139 0.831 +833 1 1 0.873015 0.525215 0.832 +834 1 -1 0.127873 0.474845 0.833 +835 1 -1 0.474905 0.871233 0.834 +836 1 1 0.525034 0.129665 0.835 +837 1 1 0.74357 0.778887 0.836 +838 1 1 0.257029 0.221799 0.837 +839 1 1 0.222488 0.742369 0.838 +840 1 -1 0.776819 0.258236 0.839 +841 1 -1 0.828467 0.662818 0.84 +842 1 1 0.172367 0.337595 0.841 +843 1 1 0.33801 0.826796 0.842 +844 1 -1 0.661572 0.174047 0.843 +845 1 -1 0.615933 0.843836 0.844 +846 1 -1 0.384371 0.157064 0.845 +847 1 -1 0.15797 0.615324 0.846 +848 1 -1 0.841119 0.384983 0.847 +849 1 -1 0.846597 0.593631 0.848 +850 1 1 0.154342 0.406623 0.849 +851 1 1 0.406878 0.844715 0.85 +852 1 -1 0.592866 0.156234 0.851 +853 1 1 0.676921 0.807888 0.852 +854 1 -1 0.323575 0.192974 0.853 +855 1 -1 0.193841 0.675927 0.854 +856 1 1 0.805288 0.324574 0.855 +857 1 1 0.7781 0.714299 0.856 +858 1 1 0.222705 0.286322 0.857 +859 1 -1 0.286946 0.776485 0.858 +860 1 1 0.712426 0.22433 0.859 +861 1 1 0.544587 0.84411 0.86 +862 1 -1 0.455547 0.156921 0.861 +863 1 1 0.157959 0.544319 0.862 +864 1 1 0.840997 0.455816 0.863 +865 1 1 0.838095 0.55653 0.864 +866 1 1 0.162955 0.443645 0.865 +867 1 1 0.443822 0.835988 0.866 +868 1 -1 0.556 0.165075 0.867 +869 1 -1 0.6966 0.775544 0.868 +870 1 -1 0.304033 0.225344 0.869 +871 1 -1 0.226237 0.69533 0.87 +872 1 -1 0.772865 0.305311 0.871 +873 1 1 0.783348 0.677002 0.872 +874 1 1 0.217599 0.32359 0.873 +875 1 -1 0.324185 0.781448 0.874 +876 1 -1 0.675216 0.219511 0.875 +877 1 -1 0.574184 0.821124 0.876 +878 1 -1 0.426074 0.179991 0.877 +879 1 -1 0.181113 0.573667 0.878 +880 1 -1 0.817759 0.426594 0.879 +881 1 1 0.803899 0.61509 0.88 +882 1 1 0.197198 0.385326 0.881 +883 1 1 0.385744 0.801698 0.882 +884 1 -1 0.613835 0.199413 0.883 +885 1 -1 0.631562 0.791951 0.884 +886 1 1 0.368932 0.209146 0.885 +887 1 1 0.21025 0.630571 0.886 +888 1 -1 0.78864 0.36993 0.887 +889 1 -1 0.729733 0.716052 0.888 +890 1 1 0.271166 0.284793 0.889 +891 1 -1 0.285644 0.727929 0.89 +892 1 1 0.713499 0.272982 0.891 +893 1 1 0.509521 0.810234 0.892 +894 1 -1 0.490518 0.191032 0.893 +895 1 -1 0.192307 0.509443 0.894 +896 1 -1 0.806409 0.490597 0.895 +897 1 1 0.804979 0.513107 0.896 +898 1 1 0.196321 0.486949 0.897 +899 1 -1 0.487005 0.802369 0.898 +900 1 -1 0.512939 0.198949 0.899 +901 1 -1 0.702828 0.721045 0.9 +902 1 -1 0.298077 0.279941 0.901 +903 1 1 0.280934 0.701012 0.902 +904 1 -1 0.718067 0.299905 0.903 +905 1 1 0.767075 0.624318 0.904 +906 1 1 0.234173 0.376263 0.905 +907 1 -1 0.376848 0.764571 0.906 +908 1 -1 0.622563 0.236695 0.907 +909 1 1 0.599038 0.771528 0.908 +910 1 1 0.401448 0.229803 0.909 +911 1 -1 0.231144 0.598063 0.91 +912 1 -1 0.767505 0.40243 0.911 +913 1 -1 0.775222 0.567148 0.912 +914 1 -1 0.226196 0.433198 0.913 +915 1 -1 0.433547 0.772375 0.914 +916 1 -1 0.566102 0.229065 0.915 +917 1 1 0.644063 0.737044 0.916 +918 1 1 0.356719 0.264243 0.917 +919 1 -1 0.265539 0.642493 0.918 +920 1 1 0.733153 0.358301 0.919 +921 1 1 0.718892 0.660269 0.92 +922 1 1 0.282362 0.340649 0.921 +923 1 1 0.341575 0.716374 0.922 +924 1 1 0.657491 0.284901 0.923 +925 1 1 0.540491 0.761886 0.924 +926 1 1 0.459755 0.239702 0.925 +927 1 1 0.241303 0.539998 0.926 +928 1 -1 0.757082 0.460252 0.927 +929 1 1 0.755918 0.536358 0.928 +930 1 1 0.245728 0.463875 0.929 +931 1 -1 0.464111 0.75261 0.93 +932 1 -1 0.53565 0.249066 0.931 +933 1 -1 0.651203 0.70128 0.932 +934 1 -1 0.349833 0.300098 0.933 +935 1 -1 0.301489 0.649122 0.934 +936 1 1 0.697107 0.351933 0.935 +937 1 1 0.7107 0.624538 0.936 +938 1 1 0.290841 0.376373 0.937 +939 1 1 0.377293 0.707603 0.938 +940 1 -1 0.621778 0.293968 0.939 +941 1 1 0.559117 0.730011 0.94 +942 1 1 0.441347 0.271792 0.941 +943 1 1 0.273614 0.558185 0.942 +944 1 -1 0.724545 0.442288 0.943 +945 1 1 0.716953 0.576129 0.944 +946 1 1 0.284879 0.424514 0.945 +947 1 1 0.425164 0.713269 0.946 +948 1 1 0.574179 0.288603 0.947 +949 1 1 0.596159 0.700124 0.948 +950 1 1 0.40472 0.301705 0.949 +951 1 -1 0.303556 0.594391 0.95 +952 1 1 0.694572 0.406509 0.951 +953 1 1 0.659268 0.642582 0.952 +954 1 1 0.342317 0.358837 0.953 +955 1 -1 0.360273 0.656078 0.954 +956 1 -1 0.638272 0.345546 0.955 +957 1 1 0.51132 0.704782 0.956 +958 1 -1 0.488803 0.297452 0.957 +959 1 -1 0.299717 0.511072 0.958 +960 1 1 0.697988 0.489055 0.959 +961 1 1 0.69513 0.51801 0.96 +962 1 -1 0.307224 0.482207 0.961 +963 1 1 0.482427 0.690387 0.962 +964 1 -1 0.517349 0.312037 0.963 +965 1 1 0.619063 0.643276 0.964 +966 1 -1 0.382542 0.358654 0.965 +967 1 -1 0.360616 0.615828 0.966 +968 1 1 0.63739 0.385829 0.967 +969 1 1 0.655724 0.582012 0.968 +970 1 1 0.346649 0.419238 0.969 +971 1 -1 0.42051 0.650935 0.97 +972 1 1 0.578194 0.351525 0.971 +973 1 1 0.548857 0.657572 0.972 +974 1 1 0.451999 0.345188 0.973 +975 1 -1 0.348003 0.547128 0.974 +976 1 1 0.649121 0.453763 0.975 +977 1 -1 0.646729 0.543528 0.976 +978 1 -1 0.356287 0.457366 0.977 +979 1 -1 0.458282 0.640626 0.978 +980 1 1 0.54078 0.362537 0.979 +981 1 -1 0.566752 0.623062 0.98 +982 1 -1 0.434905 0.379993 0.981 +983 1 -1 0.383134 0.563391 0.982 +984 1 -1 0.613631 0.438364 0.983 +985 1 -1 0.59748 0.579004 0.984 +986 1 1 0.405567 0.423466 0.985 +987 1 -1 0.426024 0.591277 0.986 +988 1 -1 0.571322 0.411999 0.987 +989 1 1 0.511337 0.608293 0.988 +990 1 1 0.48914 0.396264 0.989 +991 1 -1 0.401042 0.51036 0.99 +992 1 1 0.593927 0.490167 0.991 +993 1 1 0.587477 0.516843 0.992 +994 1 1 0.418131 0.484237 0.993 +995 1 1 0.485399 0.575834 0.994 +996 1 -1 0.513336 0.430738 0.995 +997 1 -1 0.535388 0.552265 0.996 +998 1 -1 0.469337 0.454714 0.997 +999 1 1 0.463006 0.525048 0.998 +1000 1 -1 0.526172 0.482279 0.999 diff --git a/examples/USER/scafacos/in.scafacos b/examples/USER/scafacos/in.scafacos new file mode 100644 index 0000000000..9a1f0f321e --- /dev/null +++ b/examples/USER/scafacos/in.scafacos @@ -0,0 +1,37 @@ +# Point dipoles in a 2d box + +units lj +atom_style full + +read_data data.NaCl + +replicate 8 8 8 + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos p3m 0.001 +kspace_style scafacos tolerance field + +timestep 0.005 +thermo 10 + +run 100 diff --git a/examples/USER/scafacos/in.scafacos.cw.ewald b/examples/USER/scafacos/in.scafacos.cw.ewald new file mode 100644 index 0000000000..55ebd0e7b3 --- /dev/null +++ b/examples/USER/scafacos/in.scafacos.cw.ewald @@ -0,0 +1,31 @@ + +units lj +atom_style charge + +read_data data.cloud_wall + +velocity all set 0.0 0.0 0.0 mom no + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve +kspace_style scafacos ewald 0.001 +kspace_modify scafacos tolerance field + +timestep 0.005 + +thermo_style custom step atoms cpu temp pe ke etotal ecoul press + +run_style verlet + +#dump simple all custom 1000 id x y z vx vy vz +#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass +#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass +#dump_modify dmpvtk pad 7 + +thermo 10 +run 100 diff --git a/examples/USER/scafacos/in.scafacos.cw.fmm b/examples/USER/scafacos/in.scafacos.cw.fmm new file mode 100644 index 0000000000..c63e241d63 --- /dev/null +++ b/examples/USER/scafacos/in.scafacos.cw.fmm @@ -0,0 +1,37 @@ +units lj +atom_style charge + +read_data data.cloud_wall + +velocity all set 0.0 0.0 0.0 mom no + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +kspace_style scafacos fmm 1.0e-3 +kspace_modify scafacos tolerance energy_rel +kspace_modify scafacos fmm_tuning 1 + +timestep 0.005 + +thermo_style custom step atoms cpu temp pe ke etotal ecoul press + +run_style verlet + +#dump simple all custom 1000 id x y z vx vy vz +#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass +#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass +#dump_modify dmpvtk pad 7 + +thermo 10 +run 100 diff --git a/examples/USER/scafacos/in.scafacos.cw.p2nfft b/examples/USER/scafacos/in.scafacos.cw.p2nfft new file mode 100644 index 0000000000..96be1b7d3c --- /dev/null +++ b/examples/USER/scafacos/in.scafacos.cw.p2nfft @@ -0,0 +1,31 @@ + +units lj +atom_style charge + +read_data data.cloud_wall + +velocity all set 0.0 0.0 0.0 mom no + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve +kspace_style scafacos p2nfft 0.001 +kspace_modify scafacos tolerance field + +timestep 0.005 + +thermo_style custom step atoms cpu temp pe ke etotal ecoul press + +run_style verlet + +#dump simple all custom 1000 id x y z vx vy vz +#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass +#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass +#dump_modify dmpvtk pad 7 + +thermo 10 +run 100 diff --git a/examples/USER/scafacos/in.scafacos.cw.p3m b/examples/USER/scafacos/in.scafacos.cw.p3m new file mode 100644 index 0000000000..50ff1a64a8 --- /dev/null +++ b/examples/USER/scafacos/in.scafacos.cw.p3m @@ -0,0 +1,31 @@ + +units lj +atom_style charge + +read_data data.cloud_wall + +velocity all set 0.0 0.0 0.0 mom no + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve +kspace_style scafacos p3m 0.001 +kspace_modify scafacos tolerance field + +timestep 0.005 + +thermo_style custom step atoms cpu temp pe ke etotal ecoul press + +run_style verlet + +#dump simple all custom 1000 id x y z vx vy vz +#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass +#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass +#dump_modify dmpvtk pad 7 + +thermo 10 +run 100 diff --git a/examples/USER/scafacos/in.scafacos.ewald b/examples/USER/scafacos/in.scafacos.ewald new file mode 100644 index 0000000000..6c26c71884 --- /dev/null +++ b/examples/USER/scafacos/in.scafacos.ewald @@ -0,0 +1,37 @@ +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.NaCl + +replicate 8 8 8 + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos ewald 0.001 +kspace_modify scafacos tolerance field + +timestep 0.005 +thermo 10 + +run 100 diff --git a/examples/USER/scafacos/in.scafacos.fmm b/examples/USER/scafacos/in.scafacos.fmm new file mode 100644 index 0000000000..054188ede2 --- /dev/null +++ b/examples/USER/scafacos/in.scafacos.fmm @@ -0,0 +1,37 @@ +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.NaCl + +replicate 8 8 8 + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos fmm 0.001 +kspace_modify scafacos tolerance energy + +timestep 0.005 +thermo 10 + +run 100 diff --git a/examples/USER/scafacos/in.scafacos.hsph.direct b/examples/USER/scafacos/in.scafacos.hsph.direct new file mode 100644 index 0000000000..3688b5157c --- /dev/null +++ b/examples/USER/scafacos/in.scafacos.hsph.direct @@ -0,0 +1,34 @@ +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.hammersley_sphere +change_box all boundary f f f + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos direct 0.001 + +timestep 0.005 +thermo 1 +run 20 diff --git a/examples/USER/scafacos/in.scafacos.hsph.fmm b/examples/USER/scafacos/in.scafacos.hsph.fmm new file mode 100644 index 0000000000..48a60a4b8b --- /dev/null +++ b/examples/USER/scafacos/in.scafacos.hsph.fmm @@ -0,0 +1,37 @@ +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.hammersley_sphere +change_box all boundary f f f + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos fmm 0.001 +kspace_modify scafacos tolerance energy_rel +kspace_modify scafacos fmm_tuning 1 + +timestep 0.005 +thermo 1 + +run 20 diff --git a/examples/USER/scafacos/in.scafacos.hsph.p2nfft b/examples/USER/scafacos/in.scafacos.hsph.p2nfft new file mode 100644 index 0000000000..a91f8f91c7 --- /dev/null +++ b/examples/USER/scafacos/in.scafacos.hsph.p2nfft @@ -0,0 +1,36 @@ +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.hammersley_sphere +change_box all boundary f f f + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos p2nfft 0.001 +kspace_modify scafacos tolerance potential + +timestep 0.005 +thermo 1 + +run 20 diff --git a/examples/USER/scafacos/in.scafacos.p2nfft b/examples/USER/scafacos/in.scafacos.p2nfft new file mode 100644 index 0000000000..7fa2ccdd9e --- /dev/null +++ b/examples/USER/scafacos/in.scafacos.p2nfft @@ -0,0 +1,37 @@ +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.NaCl + +replicate 8 8 8 + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos p2nfft 0.001 +kspace_modify scafacos tolerance field + +timestep 0.005 +thermo 10 + +run 100 diff --git a/examples/USER/scafacos/in.scafacos.p3m b/examples/USER/scafacos/in.scafacos.p3m new file mode 100644 index 0000000000..874b1d151a --- /dev/null +++ b/examples/USER/scafacos/in.scafacos.p3m @@ -0,0 +1,37 @@ +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.NaCl + +replicate 8 8 8 + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos p3m 0.001 +kspace_modify scafacos tolerance field + +timestep 0.005 +thermo 10 + +run 100 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.ewald.16 b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.ewald.16 new file mode 100644 index 0000000000..20d3faaf7f --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.ewald.16 @@ -0,0 +1,92 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task + +units lj +atom_style charge + +read_data data.cloud_wall + orthogonal box = (0 0 0) to (10 10 10) + 2 by 2 by 4 MPI processor grid + reading atoms ... + 300 atoms + +velocity all set 0.0 0.0 0.0 mom no + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve +kspace_style scafacos ewald 0.001 +kspace_modify scafacos tolerance field + +timestep 0.005 + +thermo_style custom step atoms cpu temp pe ke etotal ecoul press + +run_style verlet + +#dump simple all custom 1000 id x y z vx vy vz +#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass +#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass +#dump_modify dmpvtk pad 7 + +thermo 10 +run 100 +Setting up ScaFaCoS with solver ewald ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 10 10 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.313 | 3.501 | 3.689 Mbytes +Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press + 0 300 0 0 0.49647271 0 0.49647271 0 0 + 10 300 0.051135063 0.014582562 0.44286522 0.02180093 0.46466616 0 0.0043601861 + 20 300 0.10210872 0.058693359 0.37869251 0.087746571 0.46643909 0 0.017549314 + 30 300 0.15278506 0.13468789 0.26730177 0.2013584 0.46866017 0 0.040271679 + 40 300 0.19430375 0.50949535 0.083356437 0.76169555 0.84505198 0 0.15233911 + 50 300 0.23220921 1.1731116 -0.055261984 1.7538018 1.6985399 0 0.35076037 + 60 300 0.27002859 1.3589639 -0.33351524 2.031651 1.6981358 0 0.4063302 + 70 300 0.30781388 1.6482648 -0.76570045 2.4641559 1.6984554 0 0.49283118 + 80 300 0.34566283 2.8640899 -2.4038488 4.2818144 1.8779656 0 0.85636288 + 90 300 0.38424087 93.168442 -2.5911448 139.28682 136.69568 0 27.857364 + 100 300 0.42331123 94.146897 -1.3480439 140.74961 139.40157 0 28.149922 +Loop time of 0.423331 on 16 procs for 100 steps with 300 atoms + +Performance: 102047.913 tau/day, 236.222 timesteps/s +99.2% CPU use with 16 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.5988e-05 | 3.6508e-05 | 5.5075e-05 | 0.0 | 0.01 +Kspace | 0.41852 | 0.41925 | 0.41976 | 0.1 | 99.04 +Neigh | 0.00023413 | 0.00056887 | 0.0012875 | 0.0 | 0.13 +Comm | 0.0019519 | 0.0022772 | 0.0027158 | 0.5 | 0.54 +Output | 0.00028276 | 0.00030752 | 0.0003624 | 0.0 | 0.07 +Modify | 8.3685e-05 | 0.0001286 | 0.00018764 | 0.0 | 0.03 +Other | | 0.000758 | | | 0.18 + +Nlocal: 18.75 ave 39 max 6 min +Histogram: 6 1 1 0 1 2 2 1 1 1 +Nghost: 122.812 ave 195 max 63 min +Histogram: 8 0 0 0 0 0 0 1 3 4 +Neighs: 160.625 ave 598 max 13 min +Histogram: 8 2 1 1 1 0 0 2 0 1 + +Total # of neighbors = 2570 +Ave neighs/atom = 8.56667 +Neighbor list builds = 23 +Dangerous builds = 16 +Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.ewald.8 b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.ewald.8 new file mode 100644 index 0000000000..d26138522a --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.ewald.8 @@ -0,0 +1,92 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task + +units lj +atom_style charge + +read_data data.cloud_wall + orthogonal box = (0 0 0) to (10 10 10) + 2 by 2 by 2 MPI processor grid + reading atoms ... + 300 atoms + +velocity all set 0.0 0.0 0.0 mom no + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve +kspace_style scafacos ewald 0.001 +kspace_modify scafacos tolerance field + +timestep 0.005 + +thermo_style custom step atoms cpu temp pe ke etotal ecoul press + +run_style verlet + +#dump simple all custom 1000 id x y z vx vy vz +#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass +#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass +#dump_modify dmpvtk pad 7 + +thermo 10 +run 100 +Setting up ScaFaCoS with solver ewald ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 10 10 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.317 | 3.317 | 3.317 Mbytes +Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press + 0 300 0 0 0.49647271 0 0.49647271 0 0 + 10 300 0.057411432 0.014718629 0.45088339 0.02200435 0.47288774 0 0.00440087 + 20 300 0.11482716 0.05922597 0.38470912 0.088542825 0.47325194 0 0.017708565 + 30 300 0.17278481 0.13587829 0.27058048 0.20313804 0.47371852 0 0.040627608 + 40 300 0.23021507 0.51353118 0.088432648 0.76772911 0.85616176 0 0.15354582 + 50 300 0.28812647 1.1760001 -0.058088247 1.7581201 1.7000319 0 0.35162403 + 60 300 0.34651113 1.3627885 -0.33736672 2.0373688 1.7000021 0 0.40747376 + 70 300 0.40509939 1.6529365 -0.77082139 2.4711401 1.7003187 0 0.49422802 + 80 300 0.46342874 2.9569837 -2.4624654 4.4206907 1.9582253 0 0.88413814 + 90 300 0.52329254 81.642726 -2.5370215 122.05588 119.51885 0 24.411175 + 100 300 0.58335209 85.047974 -1.128107 127.14672 126.01861 0 25.429344 +Loop time of 0.583369 on 8 procs for 100 steps with 300 atoms + +Performance: 74052.598 tau/day, 171.418 timesteps/s +99.7% CPU use with 8 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 4.0531e-05 | 4.6492e-05 | 4.8876e-05 | 0.0 | 0.01 +Kspace | 0.57805 | 0.5785 | 0.57893 | 0.0 | 99.17 +Neigh | 0.00062275 | 0.00091892 | 0.0013313 | 0.0 | 0.16 +Comm | 0.002604 | 0.0028289 | 0.0031538 | 0.3 | 0.48 +Output | 0.0002265 | 0.0002434 | 0.00029039 | 0.0 | 0.04 +Modify | 0.00016117 | 0.00017747 | 0.00019884 | 0.0 | 0.03 +Other | | 0.00065 | | | 0.11 + +Nlocal: 37.5 ave 46 max 31 min +Histogram: 2 0 0 2 1 0 2 0 0 1 +Nghost: 203.875 ave 212 max 192 min +Histogram: 1 0 1 0 0 2 1 0 0 3 +Neighs: 321.625 ave 599 max 112 min +Histogram: 1 2 0 1 1 0 1 1 0 1 + +Total # of neighbors = 2573 +Ave neighs/atom = 8.57667 +Neighbor list builds = 23 +Dangerous builds = 16 +Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.1 b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.1 new file mode 100644 index 0000000000..714ce85a5f --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.1 @@ -0,0 +1,99 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +units lj +atom_style charge + +read_data data.cloud_wall + orthogonal box = (0 0 0) to (10 10 10) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 300 atoms + +velocity all set 0.0 0.0 0.0 mom no + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +kspace_style scafacos fmm 1.0e-3 +kspace_modify scafacos tolerance energy_rel +kspace_modify scafacos fmm_tuning 1 +ScaFaCoS setting fmm inhomogen tuning ... + +timestep 0.005 + +thermo_style custom step atoms cpu temp pe ke etotal ecoul press + +run_style verlet + +#dump simple all custom 1000 id x y z vx vy vz +#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass +#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass +#dump_modify dmpvtk pad 7 + +thermo 10 +run 100 +Setting up ScaFaCoS with solver fmm ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 10 10 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.34 | 3.34 | 3.34 Mbytes +Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press + 0 300 0 0 0.49646402 0 0.49646402 0 0.016548801 + 10 300 0.063865185 0.015455559 0.47335833 0.02310606 0.49646439 0 0.020399823 + 20 300 0.12760854 0.06229069 0.40334177 0.093124582 0.49646635 0 0.032069642 + 30 300 0.19143319 0.14310163 0.28254277 0.21393694 0.49647971 0 0.05220548 + 40 300 0.25553131 0.52929788 0.089669015 0.79130033 0.88096934 0 0.16124903 + 50 300 0.31961966 1.1963022 -0.082792461 1.7884718 1.7056794 0 0.35493462 + 60 300 0.38388991 1.3928167 -0.37659239 2.082261 1.7056686 0 0.40389911 + 70 300 0.44797421 1.7069009 -0.84571914 2.5518169 1.7060978 0 0.48217274 + 80 300 0.50961447 15.358343 -3.368063 22.960722 19.592659 0 4.4798757 + 90 300 0.57181501 42.280432 -2.1623864 63.209247 61.04686 0 12.56977 + 100 300 0.63501096 41.48079 -0.89904529 62.013782 61.114736 0 12.372788 +Loop time of 0.635022 on 1 procs for 100 steps with 300 atoms + +Performance: 68029.122 tau/day, 157.475 timesteps/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 9.0837e-05 | 9.0837e-05 | 9.0837e-05 | 0.0 | 0.01 +Kspace | 0.62877 | 0.62877 | 0.62877 | 0.0 | 99.01 +Neigh | 0.0035319 | 0.0035319 | 0.0035319 | 0.0 | 0.56 +Comm | 0.0010211 | 0.0010211 | 0.0010211 | 0.0 | 0.16 +Output | 0.00014758 | 0.00014758 | 0.00014758 | 0.0 | 0.02 +Modify | 0.0010428 | 0.0010428 | 0.0010428 | 0.0 | 0.16 +Other | | 0.0004218 | | | 0.07 + +Nlocal: 300 ave 300 max 300 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 374 ave 374 max 374 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 2459 ave 2459 max 2459 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 2459 +Ave neighs/atom = 8.19667 +Neighbor list builds = 15 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.16 b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.16 new file mode 100644 index 0000000000..c9c1e0d155 --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.16 @@ -0,0 +1,99 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +units lj +atom_style charge + +read_data data.cloud_wall + orthogonal box = (0 0 0) to (10 10 10) + 2 by 2 by 4 MPI processor grid + reading atoms ... + 300 atoms + +velocity all set 0.0 0.0 0.0 mom no + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +kspace_style scafacos fmm 1.0e-3 +kspace_modify scafacos tolerance energy_rel +kspace_modify scafacos fmm_tuning 1 +ScaFaCoS setting fmm inhomogen tuning ... + +timestep 0.005 + +thermo_style custom step atoms cpu temp pe ke etotal ecoul press + +run_style verlet + +#dump simple all custom 1000 id x y z vx vy vz +#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass +#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass +#dump_modify dmpvtk pad 7 + +thermo 10 +run 100 +Setting up ScaFaCoS with solver fmm ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 10 10 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.313 | 3.501 | 3.689 Mbytes +Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press + 0 300 0 0 0.49646402 0 0.49646402 0 0.016548801 + 10 300 0.023007393 0.015455559 0.47335833 0.02310606 0.49646439 0 0.020399823 + 20 300 0.045746088 0.06229069 0.40334177 0.093124582 0.49646635 0 0.032069642 + 30 300 0.068123341 0.14310163 0.28254277 0.21393694 0.49647971 0 0.05220548 + 40 300 0.090359211 0.52929788 0.089669015 0.79130033 0.88096934 0 0.16124903 + 50 300 0.11304998 1.1963022 -0.082792461 1.7884718 1.7056794 0 0.35493462 + 60 300 0.13585806 1.3928167 -0.37659239 2.082261 1.7056686 0 0.40389911 + 70 300 0.15867376 1.7069009 -0.84571914 2.5518169 1.7060978 0 0.48217274 + 80 300 0.18324137 15.358343 -3.368063 22.960722 19.592659 0 4.4798757 + 90 300 0.20960689 42.280432 -2.1623864 63.209247 61.04686 0 12.56977 + 100 300 0.23539281 41.48079 -0.89904529 62.013782 61.114736 0 12.372788 +Loop time of 0.235411 on 16 procs for 100 steps with 300 atoms + +Performance: 183509.107 tau/day, 424.790 timesteps/s +97.9% CPU use with 16 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 3.2425e-05 | 4.4718e-05 | 6.1274e-05 | 0.0 | 0.02 +Kspace | 0.23097 | 0.23143 | 0.2318 | 0.1 | 98.31 +Neigh | 0.00015116 | 0.00035347 | 0.00075746 | 0.0 | 0.15 +Comm | 0.0020316 | 0.002282 | 0.0025339 | 0.3 | 0.97 +Output | 0.00034404 | 0.00037053 | 0.00042701 | 0.0 | 0.16 +Modify | 9.3937e-05 | 0.00014532 | 0.00018811 | 0.0 | 0.06 +Other | | 0.0007878 | | | 0.33 + +Nlocal: 18.75 ave 36 max 6 min +Histogram: 4 3 1 0 0 1 2 1 2 2 +Nghost: 127 ave 196 max 71 min +Histogram: 8 0 0 0 0 0 0 1 6 1 +Neighs: 153.688 ave 491 max 10 min +Histogram: 8 1 1 1 1 1 0 0 0 3 + +Total # of neighbors = 2459 +Ave neighs/atom = 8.19667 +Neighbor list builds = 15 +Dangerous builds = 0 +Total wall time: 0:00:01 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.2 b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.2 new file mode 100644 index 0000000000..1a9bc77146 --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.2 @@ -0,0 +1,99 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +units lj +atom_style charge + +read_data data.cloud_wall + orthogonal box = (0 0 0) to (10 10 10) + 1 by 1 by 2 MPI processor grid + reading atoms ... + 300 atoms + +velocity all set 0.0 0.0 0.0 mom no + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +kspace_style scafacos fmm 1.0e-3 +kspace_modify scafacos tolerance energy_rel +kspace_modify scafacos fmm_tuning 1 +ScaFaCoS setting fmm inhomogen tuning ... + +timestep 0.005 + +thermo_style custom step atoms cpu temp pe ke etotal ecoul press + +run_style verlet + +#dump simple all custom 1000 id x y z vx vy vz +#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass +#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass +#dump_modify dmpvtk pad 7 + +thermo 10 +run 100 +Setting up ScaFaCoS with solver fmm ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 10 10 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.354 | 3.354 | 3.355 Mbytes +Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press + 0 300 0 0 0.49646402 0 0.49646402 0 0.016548801 + 10 300 0.038181543 0.015455559 0.47335833 0.02310606 0.49646439 0 0.020399823 + 20 300 0.076276302 0.06229069 0.40334177 0.093124582 0.49646635 0 0.032069642 + 30 300 0.11437607 0.14310163 0.28254277 0.21393694 0.49647971 0 0.05220548 + 40 300 0.15244293 0.52929788 0.089669015 0.79130033 0.88096934 0 0.16124903 + 50 300 0.19081283 1.1963022 -0.082792461 1.7884718 1.7056794 0 0.35493462 + 60 300 0.22923493 1.3928167 -0.37659239 2.082261 1.7056686 0 0.40389911 + 70 300 0.26754427 1.7069009 -0.84571914 2.5518169 1.7060978 0 0.48217274 + 80 300 0.30721259 15.358343 -3.368063 22.960722 19.592659 0 4.4798757 + 90 300 0.34865618 42.280432 -2.1623864 63.209247 61.04686 0 12.56977 + 100 300 0.39100981 41.48079 -0.89904529 62.013782 61.114736 0 12.372788 +Loop time of 0.391022 on 2 procs for 100 steps with 300 atoms + +Performance: 110479.760 tau/day, 255.740 timesteps/s +99.6% CPU use with 2 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 8.0109e-05 | 8.1539e-05 | 8.297e-05 | 0.0 | 0.02 +Kspace | 0.38534 | 0.38582 | 0.3863 | 0.1 | 98.67 +Neigh | 0.0014851 | 0.0019699 | 0.0024548 | 1.1 | 0.50 +Comm | 0.0019314 | 0.0020101 | 0.0020888 | 0.2 | 0.51 +Output | 0.00014496 | 0.00017297 | 0.00020099 | 0.0 | 0.04 +Modify | 0.0005033 | 0.00052273 | 0.00054216 | 0.0 | 0.13 +Other | | 0.0004461 | | | 0.11 + +Nlocal: 150 ave 159 max 141 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Nghost: 392 ave 395 max 389 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Neighs: 1229.5 ave 1773 max 686 min +Histogram: 1 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 2459 +Ave neighs/atom = 8.19667 +Neighbor list builds = 15 +Dangerous builds = 0 +Total wall time: 0:00:01 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.4 b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.4 new file mode 100644 index 0000000000..eae3f2b840 --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.4 @@ -0,0 +1,99 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +units lj +atom_style charge + +read_data data.cloud_wall + orthogonal box = (0 0 0) to (10 10 10) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 300 atoms + +velocity all set 0.0 0.0 0.0 mom no + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +kspace_style scafacos fmm 1.0e-3 +kspace_modify scafacos tolerance energy_rel +kspace_modify scafacos fmm_tuning 1 +ScaFaCoS setting fmm inhomogen tuning ... + +timestep 0.005 + +thermo_style custom step atoms cpu temp pe ke etotal ecoul press + +run_style verlet + +#dump simple all custom 1000 id x y z vx vy vz +#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass +#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass +#dump_modify dmpvtk pad 7 + +thermo 10 +run 100 +Setting up ScaFaCoS with solver fmm ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 10 10 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.333 | 3.333 | 3.333 Mbytes +Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press + 0 300 0 0 0.49646402 0 0.49646402 0 0.016548801 + 10 300 0.029414415 0.015455559 0.47335833 0.02310606 0.49646439 0 0.020399823 + 20 300 0.058616877 0.06229069 0.40334177 0.093124582 0.49646635 0 0.032069642 + 30 300 0.087769508 0.14310163 0.28254277 0.21393694 0.49647971 0 0.05220548 + 40 300 0.1168611 0.52929788 0.089669015 0.79130033 0.88096934 0 0.16124903 + 50 300 0.14482284 1.1963022 -0.082792461 1.7884718 1.7056794 0 0.35493462 + 60 300 0.17198443 1.3928167 -0.37659239 2.082261 1.7056686 0 0.40389911 + 70 300 0.19868851 1.7069009 -0.84571914 2.5518169 1.7060978 0 0.48217274 + 80 300 0.22835517 15.358343 -3.368063 22.960722 19.592659 0 4.4798757 + 90 300 0.26023602 42.280432 -2.1623864 63.209247 61.04686 0 12.56977 + 100 300 0.29043221 41.48079 -0.89904529 62.013782 61.114736 0 12.372788 +Loop time of 0.290448 on 4 procs for 100 steps with 300 atoms + +Performance: 148735.741 tau/day, 344.296 timesteps/s +99.0% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 5.9605e-05 | 6.187e-05 | 6.4135e-05 | 0.0 | 0.02 +Kspace | 0.28551 | 0.28584 | 0.28604 | 0.0 | 98.41 +Neigh | 0.00077796 | 0.0010615 | 0.0013225 | 0.7 | 0.37 +Comm | 0.002372 | 0.0024325 | 0.002497 | 0.1 | 0.84 +Output | 0.00025368 | 0.0002659 | 0.00029516 | 0.0 | 0.09 +Modify | 0.00030279 | 0.00031865 | 0.00033021 | 0.0 | 0.11 +Other | | 0.0004706 | | | 0.16 + +Nlocal: 75 ave 81 max 70 min +Histogram: 2 0 0 0 0 0 0 1 0 1 +Nghost: 282.5 ave 290 max 274 min +Histogram: 1 0 0 1 0 0 0 0 1 1 +Neighs: 614.75 ave 981 max 285 min +Histogram: 1 1 0 0 0 0 0 1 0 1 + +Total # of neighbors = 2459 +Ave neighs/atom = 8.19667 +Neighbor list builds = 15 +Dangerous builds = 0 +Total wall time: 0:00:01 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.8 b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.8 new file mode 100644 index 0000000000..feb7e2a5a6 --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.8 @@ -0,0 +1,99 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +units lj +atom_style charge + +read_data data.cloud_wall + orthogonal box = (0 0 0) to (10 10 10) + 2 by 2 by 2 MPI processor grid + reading atoms ... + 300 atoms + +velocity all set 0.0 0.0 0.0 mom no + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +kspace_style scafacos fmm 1.0e-3 +kspace_modify scafacos tolerance energy_rel +kspace_modify scafacos fmm_tuning 1 +ScaFaCoS setting fmm inhomogen tuning ... + +timestep 0.005 + +thermo_style custom step atoms cpu temp pe ke etotal ecoul press + +run_style verlet + +#dump simple all custom 1000 id x y z vx vy vz +#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass +#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass +#dump_modify dmpvtk pad 7 + +thermo 10 +run 100 +Setting up ScaFaCoS with solver fmm ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 10 10 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.317 | 3.317 | 3.317 Mbytes +Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press + 0 300 0 0 0.49646402 0 0.49646402 0 0.016548801 + 10 300 0.026465416 0.015455559 0.47335833 0.02310606 0.49646439 0 0.020399823 + 20 300 0.057377338 0.06229069 0.40334177 0.093124582 0.49646635 0 0.032069642 + 30 300 0.088356495 0.14310163 0.28254277 0.21393694 0.49647971 0 0.05220548 + 40 300 0.11900806 0.52929788 0.089669015 0.79130033 0.88096934 0 0.16124903 + 50 300 0.15157914 1.1963022 -0.082792461 1.7884718 1.7056794 0 0.35493462 + 60 300 0.18608141 1.3928167 -0.37659239 2.082261 1.7056686 0 0.40389911 + 70 300 0.21956491 1.7069009 -0.84571914 2.5518169 1.7060978 0 0.48217274 + 80 300 0.24269128 15.358343 -3.368063 22.960722 19.592659 0 4.4798757 + 90 300 0.26847005 42.280432 -2.1623864 63.209247 61.04686 0 12.56977 + 100 300 0.29283834 41.48079 -0.89904529 62.013782 61.114736 0 12.372788 +Loop time of 0.292855 on 8 procs for 100 steps with 300 atoms + +Performance: 147513.337 tau/day, 341.466 timesteps/s +98.4% CPU use with 8 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 4.7207e-05 | 5.5045e-05 | 6.9618e-05 | 0.0 | 0.02 +Kspace | 0.28739 | 0.28773 | 0.2881 | 0.0 | 98.25 +Neigh | 0.00040698 | 0.00060901 | 0.00082922 | 0.0 | 0.21 +Comm | 0.0029533 | 0.0031788 | 0.0034056 | 0.3 | 1.09 +Output | 0.00029063 | 0.00030866 | 0.00035119 | 0.0 | 0.11 +Modify | 0.00018978 | 0.00022188 | 0.00026703 | 0.0 | 0.08 +Other | | 0.0007486 | | | 0.26 + +Nlocal: 37.5 ave 45 max 31 min +Histogram: 1 1 1 1 1 0 1 0 1 1 +Nghost: 200 ave 209 max 189 min +Histogram: 1 0 0 0 1 4 0 0 0 2 +Neighs: 307.375 ave 514 max 115 min +Histogram: 2 1 0 1 1 0 0 0 1 2 + +Total # of neighbors = 2459 +Ave neighs/atom = 8.19667 +Neighbor list builds = 15 +Dangerous builds = 0 +Total wall time: 0:00:01 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.1 b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.1 new file mode 100644 index 0000000000..f47f24edee --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.1 @@ -0,0 +1,92 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task + +units lj +atom_style charge + +read_data data.cloud_wall + orthogonal box = (0 0 0) to (10 10 10) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 300 atoms + +velocity all set 0.0 0.0 0.0 mom no + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve +kspace_style scafacos p2nfft 0.001 +kspace_modify scafacos tolerance field + +timestep 0.005 + +thermo_style custom step atoms cpu temp pe ke etotal ecoul press + +run_style verlet + +#dump simple all custom 1000 id x y z vx vy vz +#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass +#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass +#dump_modify dmpvtk pad 7 + +thermo 10 +run 100 +Setting up ScaFaCoS with solver p2nfft ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 10 10 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.34 | 3.34 | 3.34 Mbytes +Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press + 0 300 0 0 0.49683273 0 0.49683273 0 0.016561091 + 10 300 0.071435928 0.015479312 0.47369009 0.023141571 0.49683166 0 0.020417984 + 20 300 0.14302707 0.062386358 0.40356181 0.093267605 0.49682941 0 0.032105581 + 30 300 0.21480989 0.14331637 0.2825636 0.21425798 0.49682157 0 0.052270382 + 40 300 0.28638172 0.53041843 0.089505208 0.79297556 0.88248077 0 0.16157862 + 50 300 0.35810781 1.1948397 -0.083317439 1.7862853 1.7029679 0 0.35447982 + 60 300 0.42993116 1.3915614 -0.37745551 2.0803842 1.7029287 0 0.40349499 + 70 300 0.50181961 1.7061978 -0.84746071 2.5507657 1.703305 0 0.48190445 + 80 300 0.57404566 20.692093 -3.32971 30.93468 27.60497 0 6.0759456 + 90 300 0.64724708 48.999403 -2.1632167 73.254107 71.090891 0 14.578714 + 100 300 0.72128963 51.199785 -0.81127924 76.543678 75.732399 0 15.281693 +Loop time of 0.721302 on 1 procs for 100 steps with 300 atoms + +Performance: 59891.733 tau/day, 138.638 timesteps/s +100.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 8.893e-05 | 8.893e-05 | 8.893e-05 | 0.0 | 0.01 +Kspace | 0.71502 | 0.71502 | 0.71502 | 0.0 | 99.13 +Neigh | 0.0035415 | 0.0035415 | 0.0035415 | 0.0 | 0.49 +Comm | 0.001024 | 0.001024 | 0.001024 | 0.0 | 0.14 +Output | 0.00015044 | 0.00015044 | 0.00015044 | 0.0 | 0.02 +Modify | 0.0010409 | 0.0010409 | 0.0010409 | 0.0 | 0.14 +Other | | 0.0004385 | | | 0.06 + +Nlocal: 300 ave 300 max 300 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 381 ave 381 max 381 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 2461 ave 2461 max 2461 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 2461 +Ave neighs/atom = 8.20333 +Neighbor list builds = 15 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.16 b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.16 new file mode 100644 index 0000000000..d6e7cbea37 --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.16 @@ -0,0 +1,92 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task + +units lj +atom_style charge + +read_data data.cloud_wall + orthogonal box = (0 0 0) to (10 10 10) + 2 by 2 by 4 MPI processor grid + reading atoms ... + 300 atoms + +velocity all set 0.0 0.0 0.0 mom no + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve +kspace_style scafacos p2nfft 0.001 +kspace_modify scafacos tolerance field + +timestep 0.005 + +thermo_style custom step atoms cpu temp pe ke etotal ecoul press + +run_style verlet + +#dump simple all custom 1000 id x y z vx vy vz +#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass +#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass +#dump_modify dmpvtk pad 7 + +thermo 10 +run 100 +Setting up ScaFaCoS with solver p2nfft ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 10 10 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.313 | 3.501 | 3.689 Mbytes +Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press + 0 300 0 0 0.49683273 0 0.49683273 0 0.016561091 + 10 300 0.015678644 0.015479312 0.47369009 0.023141571 0.49683166 0 0.020417984 + 20 300 0.031283855 0.062386358 0.40356181 0.093267605 0.49682941 0 0.032105581 + 30 300 0.046878099 0.14331637 0.2825636 0.21425798 0.49682157 0 0.052270382 + 40 300 0.062416077 0.53041843 0.089505208 0.79297556 0.88248077 0 0.16157862 + 50 300 0.078029871 1.1948397 -0.083317439 1.7862853 1.7029679 0 0.35447982 + 60 300 0.093806505 1.3915614 -0.37745551 2.0803842 1.7029287 0 0.40349499 + 70 300 0.1096344 1.7061978 -0.84746071 2.5507657 1.703305 0 0.48190445 + 80 300 0.12532592 20.692093 -3.32971 30.93468 27.60497 0 6.0759456 + 90 300 0.14175463 48.999403 -2.1632167 73.254107 71.090891 0 14.578714 + 100 300 0.15838337 51.199785 -0.81127924 76.543678 75.732399 0 15.281693 +Loop time of 0.158406 on 16 procs for 100 steps with 300 atoms + +Performance: 272716.448 tau/day, 631.288 timesteps/s +99.4% CPU use with 16 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.718e-05 | 3.7491e-05 | 5.6744e-05 | 0.0 | 0.02 +Kspace | 0.15435 | 0.15482 | 0.15516 | 0.1 | 97.74 +Neigh | 0.00014806 | 0.0003508 | 0.00074744 | 0.0 | 0.22 +Comm | 0.0016866 | 0.0019967 | 0.0023787 | 0.5 | 1.26 +Output | 0.00027871 | 0.00033027 | 0.00038028 | 0.0 | 0.21 +Modify | 8.0347e-05 | 0.00011933 | 0.00016522 | 0.0 | 0.08 +Other | | 0.0007506 | | | 0.47 + +Nlocal: 18.75 ave 33 max 6 min +Histogram: 2 6 0 0 0 0 2 1 2 3 +Nghost: 128.875 ave 198 max 71 min +Histogram: 7 1 0 0 0 0 0 1 5 2 +Neighs: 153.812 ave 490 max 14 min +Histogram: 8 0 3 0 1 1 0 0 1 2 + +Total # of neighbors = 2461 +Ave neighs/atom = 8.20333 +Neighbor list builds = 15 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.2 b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.2 new file mode 100644 index 0000000000..fb863797f3 --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.2 @@ -0,0 +1,92 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task + +units lj +atom_style charge + +read_data data.cloud_wall + orthogonal box = (0 0 0) to (10 10 10) + 1 by 1 by 2 MPI processor grid + reading atoms ... + 300 atoms + +velocity all set 0.0 0.0 0.0 mom no + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve +kspace_style scafacos p2nfft 0.001 +kspace_modify scafacos tolerance field + +timestep 0.005 + +thermo_style custom step atoms cpu temp pe ke etotal ecoul press + +run_style verlet + +#dump simple all custom 1000 id x y z vx vy vz +#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass +#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass +#dump_modify dmpvtk pad 7 + +thermo 10 +run 100 +Setting up ScaFaCoS with solver p2nfft ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 10 10 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.354 | 3.354 | 3.355 Mbytes +Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press + 0 300 0 0 0.49683273 0 0.49683273 0 0.016561091 + 10 300 0.044083834 0.015479312 0.47369009 0.023141571 0.49683166 0 0.020417984 + 20 300 0.088379145 0.062386358 0.40356181 0.093267605 0.49682941 0 0.032105581 + 30 300 0.13264704 0.14331637 0.2825636 0.21425798 0.49682157 0 0.052270382 + 40 300 0.17687225 0.53041843 0.089505208 0.79297556 0.88248077 0 0.16157862 + 50 300 0.22116137 1.1948397 -0.083317439 1.7862853 1.7029679 0 0.35447982 + 60 300 0.26515126 1.3915614 -0.37745551 2.0803842 1.7029287 0 0.40349499 + 70 300 0.30891085 1.7061978 -0.84746071 2.5507657 1.703305 0 0.48190445 + 80 300 0.35292292 20.692093 -3.32971 30.93468 27.60497 0 6.0759456 + 90 300 0.39845228 48.999403 -2.1632167 73.254107 71.090891 0 14.578714 + 100 300 0.44492316 51.199785 -0.81127924 76.543678 75.732399 0 15.281693 +Loop time of 0.444937 on 2 procs for 100 steps with 300 atoms + +Performance: 97092.373 tau/day, 224.751 timesteps/s +100.0% CPU use with 2 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 7.7248e-05 | 7.844e-05 | 7.9632e-05 | 0.0 | 0.02 +Kspace | 0.43932 | 0.43979 | 0.44026 | 0.1 | 98.84 +Neigh | 0.0014915 | 0.0019662 | 0.0024409 | 1.1 | 0.44 +Comm | 0.0019331 | 0.0019941 | 0.0020552 | 0.1 | 0.45 +Output | 0.00013781 | 0.00016308 | 0.00018835 | 0.0 | 0.04 +Modify | 0.00050378 | 0.00050449 | 0.00050521 | 0.0 | 0.11 +Other | | 0.0004425 | | | 0.10 + +Nlocal: 150 ave 157 max 143 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Nghost: 399 ave 402 max 396 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Neighs: 1230.5 ave 1756 max 705 min +Histogram: 1 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 2461 +Ave neighs/atom = 8.20333 +Neighbor list builds = 15 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.4 b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.4 new file mode 100644 index 0000000000..d5a07e0324 --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.4 @@ -0,0 +1,92 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task + +units lj +atom_style charge + +read_data data.cloud_wall + orthogonal box = (0 0 0) to (10 10 10) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 300 atoms + +velocity all set 0.0 0.0 0.0 mom no + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve +kspace_style scafacos p2nfft 0.001 +kspace_modify scafacos tolerance field + +timestep 0.005 + +thermo_style custom step atoms cpu temp pe ke etotal ecoul press + +run_style verlet + +#dump simple all custom 1000 id x y z vx vy vz +#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass +#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass +#dump_modify dmpvtk pad 7 + +thermo 10 +run 100 +Setting up ScaFaCoS with solver p2nfft ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 10 10 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.333 | 3.333 | 3.333 Mbytes +Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press + 0 300 0 0 0.49683273 0 0.49683273 0 0.016561091 + 10 300 0.02743125 0.015479312 0.47369009 0.023141571 0.49683166 0 0.020417984 + 20 300 0.05494833 0.062386358 0.40356181 0.093267605 0.49682941 0 0.032105581 + 30 300 0.082517862 0.14331637 0.2825636 0.21425798 0.49682157 0 0.052270382 + 40 300 0.11015558 0.53041843 0.089505208 0.79297556 0.88248077 0 0.16157862 + 50 300 0.13790298 1.1948397 -0.083317439 1.7862853 1.7029679 0 0.35447982 + 60 300 0.1660006 1.3915614 -0.37745551 2.0803842 1.7029287 0 0.40349499 + 70 300 0.1937964 1.7061978 -0.84746071 2.5507657 1.703305 0 0.48190445 + 80 300 0.22181106 20.692093 -3.32971 30.93468 27.60497 0 6.0759456 + 90 300 0.25105524 48.999403 -2.1632167 73.254107 71.090891 0 14.578714 + 100 300 0.28086019 51.199785 -0.81127924 76.543678 75.732399 0 15.281693 +Loop time of 0.280875 on 4 procs for 100 steps with 300 atoms + +Performance: 153805.254 tau/day, 356.031 timesteps/s +99.7% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 5.6744e-05 | 6.0022e-05 | 6.4135e-05 | 0.0 | 0.02 +Kspace | 0.27651 | 0.27682 | 0.27714 | 0.0 | 98.56 +Neigh | 0.00079465 | 0.001082 | 0.0014107 | 0.8 | 0.39 +Comm | 0.0019372 | 0.002014 | 0.0020835 | 0.1 | 0.72 +Output | 0.00018406 | 0.00019914 | 0.00023413 | 0.0 | 0.07 +Modify | 0.0002749 | 0.00028563 | 0.00029325 | 0.0 | 0.10 +Other | | 0.0004173 | | | 0.15 + +Nlocal: 75 ave 81 max 69 min +Histogram: 1 0 0 0 1 1 0 0 0 1 +Nghost: 287 ave 296 max 278 min +Histogram: 1 0 1 0 0 0 0 1 0 1 +Neighs: 615.25 ave 964 max 286 min +Histogram: 1 1 0 0 0 0 0 1 0 1 + +Total # of neighbors = 2461 +Ave neighs/atom = 8.20333 +Neighbor list builds = 15 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.8 b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.8 new file mode 100644 index 0000000000..a6f9228673 --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.8 @@ -0,0 +1,92 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task + +units lj +atom_style charge + +read_data data.cloud_wall + orthogonal box = (0 0 0) to (10 10 10) + 2 by 2 by 2 MPI processor grid + reading atoms ... + 300 atoms + +velocity all set 0.0 0.0 0.0 mom no + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve +kspace_style scafacos p2nfft 0.001 +kspace_modify scafacos tolerance field + +timestep 0.005 + +thermo_style custom step atoms cpu temp pe ke etotal ecoul press + +run_style verlet + +#dump simple all custom 1000 id x y z vx vy vz +#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass +#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass +#dump_modify dmpvtk pad 7 + +thermo 10 +run 100 +Setting up ScaFaCoS with solver p2nfft ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 10 10 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.317 | 3.317 | 3.317 Mbytes +Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press + 0 300 0 0 0.49683273 0 0.49683273 0 0.016561091 + 10 300 0.01961565 0.015479312 0.47369009 0.023141571 0.49683166 0 0.020417984 + 20 300 0.039346695 0.062386358 0.40356181 0.093267605 0.49682941 0 0.032105581 + 30 300 0.059037447 0.14331637 0.2825636 0.21425798 0.49682157 0 0.052270382 + 40 300 0.078732729 0.53041843 0.089505208 0.79297556 0.88248077 0 0.16157862 + 50 300 0.098586798 1.1948397 -0.083317439 1.7862853 1.7029679 0 0.35447982 + 60 300 0.11857247 1.3915614 -0.37745551 2.0803842 1.7029287 0 0.40349499 + 70 300 0.1385541 1.7061978 -0.84746071 2.5507657 1.703305 0 0.48190445 + 80 300 0.15850091 20.692093 -3.32971 30.93468 27.60497 0 6.0759456 + 90 300 0.17892075 48.999403 -2.1632167 73.254107 71.090891 0 14.578714 + 100 300 0.19964767 51.199785 -0.81127924 76.543678 75.732399 0 15.281693 +Loop time of 0.199664 on 8 procs for 100 steps with 300 atoms + +Performance: 216363.074 tau/day, 500.840 timesteps/s +99.4% CPU use with 8 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 4.5061e-05 | 4.7535e-05 | 5.3167e-05 | 0.0 | 0.02 +Kspace | 0.19551 | 0.19584 | 0.19611 | 0.0 | 98.08 +Neigh | 0.00041366 | 0.00060952 | 0.00082064 | 0.0 | 0.31 +Comm | 0.0021496 | 0.0022282 | 0.0024025 | 0.2 | 1.12 +Output | 0.0002346 | 0.00024167 | 0.00027847 | 0.0 | 0.12 +Modify | 0.00016665 | 0.00017652 | 0.0001924 | 0.0 | 0.09 +Other | | 0.0005245 | | | 0.26 + +Nlocal: 37.5 ave 42 max 33 min +Histogram: 2 1 0 1 0 0 1 0 1 2 +Nghost: 202.25 ave 212 max 194 min +Histogram: 1 0 2 1 0 2 0 1 0 1 +Neighs: 307.625 ave 505 max 129 min +Histogram: 3 0 0 1 1 0 0 0 1 2 + +Total # of neighbors = 2461 +Ave neighs/atom = 8.20333 +Neighbor list builds = 15 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.g++.ewald.1 b/examples/USER/scafacos/log.08Aug18.scafacos.g++.ewald.1 new file mode 100644 index 0000000000..13212ede0c --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.g++.ewald.1 @@ -0,0 +1,102 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.NaCl + orthogonal box = (0 0 0) to (1 1 1) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 8 atoms + +replicate 8 8 8 + orthogonal box = (0 0 0) to (8 8 8) + 1 by 1 by 1 MPI processor grid + 4096 atoms + Time spent = 0.000498772 secs + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos ewald 0.001 +kspace_modify scafacos tolerance field + +timestep 0.005 +thermo 10 + +run 100 +Setting up ScaFaCoS with solver ewald ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 8 8 8 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.813 | 5.813 | 5.813 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -1.7475938 0 0.50185691 11.99707 + 10 1.500011 -1.747529 0 0.50193816 11.997158 + 20 1.5000023 -1.7475152 0 0.50193898 11.997089 + 30 1.4999308 -1.747404 0 0.50194285 11.996517 + 40 1.4997722 -1.7471622 0 0.50194686 11.995248 + 50 1.4995835 -1.746878 0 0.50194808 11.993739 + 60 1.4996054 -1.7469114 0 0.50194749 11.993914 + 70 1.5004341 -1.7481558 0 0.50194592 12.000543 + 80 1.5033218 -1.7524875 0 0.50194458 12.023638 + 90 1.5108306 -1.7637462 0 0.50194636 12.083694 + 100 1.5292479 -1.7913449 0 0.50196695 12.230996 +Loop time of 1121.22 on 1 procs for 100 steps with 4096 atoms + +Performance: 38.530 tau/day, 0.089 timesteps/s +100.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0015197 | 0.0015197 | 0.0015197 | 0.0 | 0.00 +Kspace | 1121.2 | 1121.2 | 1121.2 | 0.0 |100.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.013699 | 0.013699 | 0.013699 | 0.0 | 0.00 +Output | 0.00038314 | 0.00038314 | 0.00038314 | 0.0 | 0.00 +Modify | 0.011126 | 0.011126 | 0.011126 | 0.0 | 0.00 +Other | | 0.00418 | | | 0.00 + +Nlocal: 4096 ave 4096 max 4096 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 9728 ave 9728 max 9728 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 524288 ave 524288 max 524288 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 524288 +Ave neighs/atom = 128 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:18:57 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.g++.ewald.16 b/examples/USER/scafacos/log.08Aug18.scafacos.g++.ewald.16 new file mode 100644 index 0000000000..2fc46da3cd --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.g++.ewald.16 @@ -0,0 +1,102 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.NaCl + orthogonal box = (0 0 0) to (1 1 1) + 2 by 2 by 4 MPI processor grid + reading atoms ... + 8 atoms + +replicate 8 8 8 + orthogonal box = (0 0 0) to (8 8 8) + 2 by 2 by 4 MPI processor grid + 4096 atoms + Time spent = 0.000462294 secs + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos ewald 0.001 +kspace_modify scafacos tolerance field + +timestep 0.005 +thermo 10 + +run 100 +Setting up ScaFaCoS with solver ewald ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 8 8 8 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.501 | 3.501 | 3.501 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -1.7475938 0 0.50185691 -nan + 10 1.500011 -1.747529 0 0.50193816 -nan + 20 1.5000023 -1.7475152 0 0.50193898 -nan + 30 1.4999308 -1.747404 0 0.50194285 -nan + 40 1.4997722 -1.7471622 0 0.50194686 -nan + 50 1.4995835 -1.746878 0 0.50194808 -nan + 60 1.4996054 -1.7469114 0 0.50194749 -nan + 70 1.5004341 -1.7481558 0 0.50194592 -nan + 80 1.5033218 -1.7524875 0 0.50194458 -nan + 90 1.5108306 -1.7637462 0 0.50194636 -nan + 100 1.5292479 -1.7913449 0 0.50196695 -nan +Loop time of 80.2777 on 16 procs for 100 steps with 4096 atoms + +Performance: 538.132 tau/day, 1.246 timesteps/s +99.8% CPU use with 16 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0003705 | 0.00039807 | 0.00048542 | 0.0 | 0.00 +Kspace | 80.262 | 80.263 | 80.264 | 0.0 | 99.98 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.010191 | 0.011419 | 0.012416 | 0.6 | 0.01 +Output | 0.00028253 | 0.00033158 | 0.0004065 | 0.0 | 0.00 +Modify | 0.00082541 | 0.0008464 | 0.00087833 | 0.0 | 0.00 +Other | | 0.001511 | | | 0.00 + +Nlocal: 256 ave 256 max 256 min +Histogram: 16 0 0 0 0 0 0 0 0 0 +Nghost: 2816 ave 2816 max 2816 min +Histogram: 16 0 0 0 0 0 0 0 0 0 +Neighs: 32768 ave 32768 max 32768 min +Histogram: 16 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 524288 +Ave neighs/atom = 128 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:01:22 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.g++.ewald.2 b/examples/USER/scafacos/log.08Aug18.scafacos.g++.ewald.2 new file mode 100644 index 0000000000..b6bf41de24 --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.g++.ewald.2 @@ -0,0 +1,102 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.NaCl + orthogonal box = (0 0 0) to (1 1 1) + 1 by 1 by 2 MPI processor grid + reading atoms ... + 8 atoms + +replicate 8 8 8 + orthogonal box = (0 0 0) to (8 8 8) + 1 by 1 by 2 MPI processor grid + 4096 atoms + Time spent = 0.000344753 secs + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos ewald 0.001 +kspace_modify scafacos tolerance field + +timestep 0.005 +thermo 10 + +run 100 +Setting up ScaFaCoS with solver ewald ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 8 8 8 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.574 | 4.574 | 4.574 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -1.7475938 0 0.50185691 11.99707 + 10 1.500011 -1.747529 0 0.50193816 11.997158 + 20 1.5000023 -1.7475152 0 0.50193898 11.997089 + 30 1.4999308 -1.747404 0 0.50194285 11.996517 + 40 1.4997722 -1.7471622 0 0.50194686 11.995248 + 50 1.4995835 -1.746878 0 0.50194808 11.993739 + 60 1.4996054 -1.7469114 0 0.50194749 11.993914 + 70 1.5004341 -1.7481558 0 0.50194592 12.000543 + 80 1.5033218 -1.7524875 0 0.50194458 12.023638 + 90 1.5108306 -1.7637462 0 0.50194636 12.083694 + 100 1.5292479 -1.7913449 0 0.50196695 12.230996 +Loop time of 566.796 on 2 procs for 100 steps with 4096 atoms + +Performance: 76.218 tau/day, 0.176 timesteps/s +100.0% CPU use with 2 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0010231 | 0.0010413 | 0.0010595 | 0.1 | 0.00 +Kspace | 566.77 | 566.77 | 566.77 | 0.0 | 99.99 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.019707 | 0.01982 | 0.019932 | 0.1 | 0.00 +Output | 0.0002656 | 0.00029266 | 0.00031972 | 0.0 | 0.00 +Modify | 0.0055575 | 0.0055707 | 0.0055838 | 0.0 | 0.00 +Other | | 0.002497 | | | 0.00 + +Nlocal: 2048 ave 2048 max 2048 min +Histogram: 2 0 0 0 0 0 0 0 0 0 +Nghost: 7168 ave 7168 max 7168 min +Histogram: 2 0 0 0 0 0 0 0 0 0 +Neighs: 262144 ave 262144 max 262144 min +Histogram: 2 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 524288 +Ave neighs/atom = 128 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:09:38 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.g++.ewald.4 b/examples/USER/scafacos/log.08Aug18.scafacos.g++.ewald.4 new file mode 100644 index 0000000000..26c1953afa --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.g++.ewald.4 @@ -0,0 +1,102 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.NaCl + orthogonal box = (0 0 0) to (1 1 1) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 8 atoms + +replicate 8 8 8 + orthogonal box = (0 0 0) to (8 8 8) + 1 by 2 by 2 MPI processor grid + 4096 atoms + Time spent = 0.000261068 secs + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos ewald 0.001 +kspace_modify scafacos tolerance field + +timestep 0.005 +thermo 10 + +run 100 +Setting up ScaFaCoS with solver ewald ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 8 8 8 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.008 | 4.008 | 4.008 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -1.7475938 0 0.50185691 -nan + 10 1.500011 -1.747529 0 0.50193816 -nan + 20 1.5000023 -1.7475152 0 0.50193898 -nan + 30 1.4999308 -1.747404 0 0.50194285 -nan + 40 1.4997722 -1.7471622 0 0.50194686 -nan + 50 1.4995835 -1.746878 0 0.50194808 -nan + 60 1.4996054 -1.7469114 0 0.50194749 -nan + 70 1.5004341 -1.7481558 0 0.50194592 -nan + 80 1.5033218 -1.7524875 0 0.50194458 -nan + 90 1.5108306 -1.7637462 0 0.50194636 -nan + 100 1.5292479 -1.7913449 0 0.50196695 -nan +Loop time of 295.996 on 4 procs for 100 steps with 4096 atoms + +Performance: 145.948 tau/day, 0.338 timesteps/s +99.9% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.00071096 | 0.00071985 | 0.00072813 | 0.0 | 0.00 +Kspace | 295.98 | 295.98 | 295.98 | 0.0 | 99.99 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.013666 | 0.013736 | 0.013795 | 0.0 | 0.00 +Output | 0.00023484 | 0.00025135 | 0.00029254 | 0.0 | 0.00 +Modify | 0.0029099 | 0.002973 | 0.0030224 | 0.1 | 0.00 +Other | | 0.001821 | | | 0.00 + +Nlocal: 1024 ave 1024 max 1024 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 5120 ave 5120 max 5120 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 131072 ave 131072 max 131072 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 524288 +Ave neighs/atom = 128 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:05:02 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.g++.ewald.8 b/examples/USER/scafacos/log.08Aug18.scafacos.g++.ewald.8 new file mode 100644 index 0000000000..4a1a5b91ed --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.g++.ewald.8 @@ -0,0 +1,102 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.NaCl + orthogonal box = (0 0 0) to (1 1 1) + 2 by 2 by 2 MPI processor grid + reading atoms ... + 8 atoms + +replicate 8 8 8 + orthogonal box = (0 0 0) to (8 8 8) + 2 by 2 by 2 MPI processor grid + 4096 atoms + Time spent = 0.000232935 secs + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos ewald 0.001 +kspace_modify scafacos tolerance field + +timestep 0.005 +thermo 10 + +run 100 +Setting up ScaFaCoS with solver ewald ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 8 8 8 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.508 | 3.508 | 3.508 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -1.7475938 0 0.50185691 -nan + 10 1.500011 -1.747529 0 0.50193816 -nan + 20 1.5000023 -1.7475152 0 0.50193898 -nan + 30 1.4999308 -1.747404 0 0.50194285 -nan + 40 1.4997722 -1.7471622 0 0.50194686 -nan + 50 1.4995835 -1.746878 0 0.50194808 -nan + 60 1.4996054 -1.7469114 0 0.50194749 -nan + 70 1.5004341 -1.7481558 0 0.50194592 -nan + 80 1.5033218 -1.7524875 0 0.50194458 -nan + 90 1.5108306 -1.7637462 0 0.50194636 -nan + 100 1.5292479 -1.7913449 0 0.50196695 -nan +Loop time of 154.44 on 8 procs for 100 steps with 4096 atoms + +Performance: 279.720 tau/day, 0.647 timesteps/s +99.9% CPU use with 8 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.00049257 | 0.00051311 | 0.00059295 | 0.0 | 0.00 +Kspace | 154.42 | 154.42 | 154.42 | 0.0 | 99.99 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.012076 | 0.013177 | 0.014308 | 0.8 | 0.01 +Output | 0.00025177 | 0.00028065 | 0.00030136 | 0.0 | 0.00 +Modify | 0.0015776 | 0.0017182 | 0.0018268 | 0.2 | 0.00 +Other | | 0.001309 | | | 0.00 + +Nlocal: 512 ave 512 max 512 min +Histogram: 8 0 0 0 0 0 0 0 0 0 +Nghost: 3584 ave 3584 max 3584 min +Histogram: 8 0 0 0 0 0 0 0 0 0 +Neighs: 65536 ave 65536 max 65536 min +Histogram: 8 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 524288 +Ave neighs/atom = 128 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:02:38 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.g++.fmm.1 b/examples/USER/scafacos/log.08Aug18.scafacos.g++.fmm.1 new file mode 100644 index 0000000000..598585ae95 --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.g++.fmm.1 @@ -0,0 +1,102 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.NaCl + orthogonal box = (0 0 0) to (1 1 1) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 8 atoms + +replicate 8 8 8 + orthogonal box = (0 0 0) to (8 8 8) + 1 by 1 by 1 MPI processor grid + 4096 atoms + Time spent = 0.000518799 secs + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos fmm 0.001 +kspace_modify scafacos tolerance energy + +timestep 0.005 +thermo 10 + +run 100 +Setting up ScaFaCoS with solver fmm ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 8 8 8 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.813 | 5.813 | 5.813 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -1.7475646 0 0.50188608 10.44368 + 10 1.5000016 -1.7475671 0 0.50188602 10.44369 + 20 1.4999827 -1.7475388 0 0.50188592 10.443564 + 30 1.4999016 -1.7474173 0 0.5018858 10.443023 + 40 1.4997356 -1.7471685 0 0.50188572 10.441917 + 50 1.4995414 -1.7468771 0 0.5018858 10.440623 + 60 1.4995587 -1.7469027 0 0.50188622 10.440739 + 70 1.5003837 -1.7481389 0 0.50188727 10.446238 + 80 1.5032684 -1.7524625 0 0.50188958 10.465466 + 90 1.5107749 -1.763714 0 0.50189507 10.515502 + 100 1.52919 -1.791306 0 0.50191895 10.638261 +Loop time of 34.7058 on 1 procs for 100 steps with 4096 atoms + +Performance: 1244.749 tau/day, 2.881 timesteps/s +100.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0015228 | 0.0015228 | 0.0015228 | 0.0 | 0.00 +Kspace | 34.675 | 34.675 | 34.675 | 0.0 | 99.91 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.013741 | 0.013741 | 0.013741 | 0.0 | 0.04 +Output | 0.00041246 | 0.00041246 | 0.00041246 | 0.0 | 0.00 +Modify | 0.01107 | 0.01107 | 0.01107 | 0.0 | 0.03 +Other | | 0.004232 | | | 0.01 + +Nlocal: 4096 ave 4096 max 4096 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 9728 ave 9728 max 9728 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 524288 ave 524288 max 524288 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 524288 +Ave neighs/atom = 128 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:35 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.g++.fmm.16 b/examples/USER/scafacos/log.08Aug18.scafacos.g++.fmm.16 new file mode 100644 index 0000000000..4bd0c3d4f3 --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.g++.fmm.16 @@ -0,0 +1,102 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.NaCl + orthogonal box = (0 0 0) to (1 1 1) + 2 by 2 by 4 MPI processor grid + reading atoms ... + 8 atoms + +replicate 8 8 8 + orthogonal box = (0 0 0) to (8 8 8) + 2 by 2 by 4 MPI processor grid + 4096 atoms + Time spent = 0.000400543 secs + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos fmm 0.001 +kspace_modify scafacos tolerance energy + +timestep 0.005 +thermo 10 + +run 100 +Setting up ScaFaCoS with solver fmm ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 8 8 8 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.501 | 3.501 | 3.501 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -1.7475646 0 0.50188608 10.44368 + 10 1.5000016 -1.7475671 0 0.50188602 10.44369 + 20 1.4999827 -1.7475388 0 0.50188592 10.443564 + 30 1.4999016 -1.7474173 0 0.5018858 10.443023 + 40 1.4997356 -1.7471685 0 0.50188572 10.441917 + 50 1.4995414 -1.7468771 0 0.5018858 10.440623 + 60 1.4995587 -1.7469027 0 0.50188622 10.440739 + 70 1.5003837 -1.7481389 0 0.50188727 10.446238 + 80 1.5032684 -1.7524625 0 0.50188958 10.465466 + 90 1.5107749 -1.763714 0 0.50189507 10.515502 + 100 1.52919 -1.791306 0 0.50191895 10.638261 +Loop time of 4.23774 on 16 procs for 100 steps with 4096 atoms + +Performance: 10194.102 tau/day, 23.597 timesteps/s +99.6% CPU use with 16 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.00038028 | 0.00040729 | 0.00046206 | 0.0 | 0.01 +Kspace | 4.2206 | 4.2211 | 4.2216 | 0.0 | 99.61 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.011439 | 0.012491 | 0.013172 | 0.4 | 0.29 +Output | 0.00042915 | 0.000489 | 0.00061274 | 0.0 | 0.01 +Modify | 0.00093102 | 0.00099151 | 0.0010982 | 0.0 | 0.02 +Other | | 0.002255 | | | 0.05 + +Nlocal: 256 ave 256 max 256 min +Histogram: 16 0 0 0 0 0 0 0 0 0 +Nghost: 2816 ave 2816 max 2816 min +Histogram: 16 0 0 0 0 0 0 0 0 0 +Neighs: 32768 ave 32768 max 32768 min +Histogram: 16 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 524288 +Ave neighs/atom = 128 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:06 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.g++.fmm.2 b/examples/USER/scafacos/log.08Aug18.scafacos.g++.fmm.2 new file mode 100644 index 0000000000..50dcc99393 --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.g++.fmm.2 @@ -0,0 +1,102 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.NaCl + orthogonal box = (0 0 0) to (1 1 1) + 1 by 1 by 2 MPI processor grid + reading atoms ... + 8 atoms + +replicate 8 8 8 + orthogonal box = (0 0 0) to (8 8 8) + 1 by 1 by 2 MPI processor grid + 4096 atoms + Time spent = 0.0003407 secs + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos fmm 0.001 +kspace_modify scafacos tolerance energy + +timestep 0.005 +thermo 10 + +run 100 +Setting up ScaFaCoS with solver fmm ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 8 8 8 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.574 | 4.574 | 4.574 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -1.7475646 0 0.50188608 10.44368 + 10 1.5000016 -1.7475671 0 0.50188602 10.44369 + 20 1.4999827 -1.7475388 0 0.50188592 10.443564 + 30 1.4999016 -1.7474173 0 0.5018858 10.443023 + 40 1.4997356 -1.7471685 0 0.50188572 10.441917 + 50 1.4995414 -1.7468771 0 0.5018858 10.440623 + 60 1.4995587 -1.7469027 0 0.50188622 10.440739 + 70 1.5003837 -1.7481389 0 0.50188727 10.446238 + 80 1.5032684 -1.7524625 0 0.50188958 10.465466 + 90 1.5107749 -1.763714 0 0.50189507 10.515502 + 100 1.52919 -1.791306 0 0.50191895 10.638261 +Loop time of 17.9401 on 2 procs for 100 steps with 4096 atoms + +Performance: 2408.014 tau/day, 5.574 timesteps/s +99.9% CPU use with 2 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0010042 | 0.0010235 | 0.0010428 | 0.1 | 0.01 +Kspace | 17.912 | 17.912 | 17.912 | 0.0 | 99.84 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.018252 | 0.018528 | 0.018804 | 0.2 | 0.10 +Output | 0.00034094 | 0.00035989 | 0.00037885 | 0.0 | 0.00 +Modify | 0.0055602 | 0.0056567 | 0.0057533 | 0.1 | 0.03 +Other | | 0.002716 | | | 0.02 + +Nlocal: 2048 ave 2048 max 2048 min +Histogram: 2 0 0 0 0 0 0 0 0 0 +Nghost: 7168 ave 7168 max 7168 min +Histogram: 2 0 0 0 0 0 0 0 0 0 +Neighs: 262144 ave 262144 max 262144 min +Histogram: 2 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 524288 +Ave neighs/atom = 128 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:19 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.g++.fmm.4 b/examples/USER/scafacos/log.08Aug18.scafacos.g++.fmm.4 new file mode 100644 index 0000000000..27fdfcedcb --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.g++.fmm.4 @@ -0,0 +1,102 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.NaCl + orthogonal box = (0 0 0) to (1 1 1) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 8 atoms + +replicate 8 8 8 + orthogonal box = (0 0 0) to (8 8 8) + 1 by 2 by 2 MPI processor grid + 4096 atoms + Time spent = 0.000270367 secs + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos fmm 0.001 +kspace_modify scafacos tolerance energy + +timestep 0.005 +thermo 10 + +run 100 +Setting up ScaFaCoS with solver fmm ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 8 8 8 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.008 | 4.008 | 4.008 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -1.7475646 0 0.50188608 10.44368 + 10 1.5000016 -1.7475671 0 0.50188602 10.44369 + 20 1.4999827 -1.7475388 0 0.50188592 10.443564 + 30 1.4999016 -1.7474173 0 0.5018858 10.443023 + 40 1.4997356 -1.7471685 0 0.50188572 10.441917 + 50 1.4995414 -1.7468771 0 0.5018858 10.440623 + 60 1.4995587 -1.7469027 0 0.50188622 10.440739 + 70 1.5003837 -1.7481389 0 0.50188727 10.446238 + 80 1.5032684 -1.7524625 0 0.50188958 10.465466 + 90 1.5107749 -1.763714 0 0.50189507 10.515502 + 100 1.52919 -1.791306 0 0.50191895 10.638261 +Loop time of 10.0781 on 4 procs for 100 steps with 4096 atoms + +Performance: 4286.533 tau/day, 9.923 timesteps/s +99.9% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.00071096 | 0.00073177 | 0.00075269 | 0.0 | 0.01 +Kspace | 10.056 | 10.057 | 10.057 | 0.0 | 99.79 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.01492 | 0.015036 | 0.015207 | 0.1 | 0.15 +Output | 0.00036311 | 0.00039428 | 0.00046515 | 0.0 | 0.00 +Modify | 0.002944 | 0.0030704 | 0.0033708 | 0.3 | 0.03 +Other | | 0.002214 | | | 0.02 + +Nlocal: 1024 ave 1024 max 1024 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 5120 ave 5120 max 5120 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 131072 ave 131072 max 131072 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 524288 +Ave neighs/atom = 128 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:11 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.g++.fmm.8 b/examples/USER/scafacos/log.08Aug18.scafacos.g++.fmm.8 new file mode 100644 index 0000000000..02a5528c59 --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.g++.fmm.8 @@ -0,0 +1,102 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.NaCl + orthogonal box = (0 0 0) to (1 1 1) + 2 by 2 by 2 MPI processor grid + reading atoms ... + 8 atoms + +replicate 8 8 8 + orthogonal box = (0 0 0) to (8 8 8) + 2 by 2 by 2 MPI processor grid + 4096 atoms + Time spent = 0.000236988 secs + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos fmm 0.001 +kspace_modify scafacos tolerance energy + +timestep 0.005 +thermo 10 + +run 100 +Setting up ScaFaCoS with solver fmm ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 8 8 8 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.508 | 3.508 | 3.508 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -1.7475646 0 0.50188608 10.44368 + 10 1.5000016 -1.7475671 0 0.50188602 10.44369 + 20 1.4999827 -1.7475388 0 0.50188592 10.443564 + 30 1.4999016 -1.7474173 0 0.5018858 10.443023 + 40 1.4997356 -1.7471685 0 0.50188572 10.441917 + 50 1.4995414 -1.7468771 0 0.5018858 10.440623 + 60 1.4995587 -1.7469027 0 0.50188622 10.440739 + 70 1.5003837 -1.7481389 0 0.50188727 10.446238 + 80 1.5032684 -1.7524625 0 0.50188958 10.465466 + 90 1.5107749 -1.763714 0 0.50189507 10.515502 + 100 1.52919 -1.791306 0 0.50191895 10.638261 +Loop time of 5.96037 on 8 procs for 100 steps with 4096 atoms + +Performance: 7247.876 tau/day, 16.777 timesteps/s +99.8% CPU use with 8 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.00049591 | 0.0005368 | 0.00056005 | 0.0 | 0.01 +Kspace | 5.94 | 5.941 | 5.9419 | 0.0 | 99.68 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.013702 | 0.014631 | 0.015768 | 0.6 | 0.25 +Output | 0.00044751 | 0.00048846 | 0.00058961 | 0.0 | 0.01 +Modify | 0.0016675 | 0.0017205 | 0.0017893 | 0.1 | 0.03 +Other | | 0.001971 | | | 0.03 + +Nlocal: 512 ave 512 max 512 min +Histogram: 8 0 0 0 0 0 0 0 0 0 +Nghost: 3584 ave 3584 max 3584 min +Histogram: 8 0 0 0 0 0 0 0 0 0 +Neighs: 65536 ave 65536 max 65536 min +Histogram: 8 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 524288 +Ave neighs/atom = 128 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:07 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.g++.p2nfft.1 b/examples/USER/scafacos/log.08Aug18.scafacos.g++.p2nfft.1 new file mode 100644 index 0000000000..1876a0e52b --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.g++.p2nfft.1 @@ -0,0 +1,102 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.NaCl + orthogonal box = (0 0 0) to (1 1 1) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 8 atoms + +replicate 8 8 8 + orthogonal box = (0 0 0) to (8 8 8) + 1 by 1 by 1 MPI processor grid + 4096 atoms + Time spent = 0.00049448 secs + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos p2nfft 0.001 +kspace_modify scafacos tolerance field + +timestep 0.005 +thermo 10 + +run 100 +Setting up ScaFaCoS with solver p2nfft ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 8 8 8 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.813 | 5.813 | 5.813 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -1.7477245 0 0.50172614 10.443537 + 10 1.5000176 -1.7475898 0 0.50188725 10.443798 + 20 1.5000161 -1.7475262 0 0.50194874 10.443843 + 30 1.4999486 -1.7474019 0 0.50197176 10.443413 + 40 1.4997889 -1.7471525 0 0.50198161 10.442357 + 50 1.4995945 -1.7468614 0 0.50198122 10.441061 + 60 1.499609 -1.7468813 0 0.50198309 10.44116 + 70 1.5004314 -1.7481179 0 0.50197962 10.446638 + 80 1.5033149 -1.7524495 0 0.50197233 10.46585 + 90 1.5108219 -1.7637095 0 0.50197005 10.515883 + 100 1.529239 -1.7913105 0 0.501988 10.638649 +Loop time of 18.1113 on 1 procs for 100 steps with 4096 atoms + +Performance: 2385.257 tau/day, 5.521 timesteps/s +100.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0014985 | 0.0014985 | 0.0014985 | 0.0 | 0.01 +Kspace | 18.079 | 18.079 | 18.079 | 0.0 | 99.82 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.014229 | 0.014229 | 0.014229 | 0.0 | 0.08 +Output | 0.0004642 | 0.0004642 | 0.0004642 | 0.0 | 0.00 +Modify | 0.011227 | 0.011227 | 0.011227 | 0.0 | 0.06 +Other | | 0.004455 | | | 0.02 + +Nlocal: 4096 ave 4096 max 4096 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 9728 ave 9728 max 9728 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 524288 ave 524288 max 524288 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 524288 +Ave neighs/atom = 128 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:21 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.g++.p2nfft.16 b/examples/USER/scafacos/log.08Aug18.scafacos.g++.p2nfft.16 new file mode 100644 index 0000000000..6e6e8f6e94 --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.g++.p2nfft.16 @@ -0,0 +1,102 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.NaCl + orthogonal box = (0 0 0) to (1 1 1) + 2 by 2 by 4 MPI processor grid + reading atoms ... + 8 atoms + +replicate 8 8 8 + orthogonal box = (0 0 0) to (8 8 8) + 2 by 2 by 4 MPI processor grid + 4096 atoms + Time spent = 0.000361443 secs + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos p2nfft 0.001 +kspace_modify scafacos tolerance field + +timestep 0.005 +thermo 10 + +run 100 +Setting up ScaFaCoS with solver p2nfft ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 8 8 8 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.501 | 3.501 | 3.501 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -1.7477245 0 0.50172614 10.443537 + 10 1.5000176 -1.7475898 0 0.50188725 10.443798 + 20 1.5000161 -1.7475262 0 0.50194874 10.443843 + 30 1.4999486 -1.7474019 0 0.50197176 10.443413 + 40 1.4997889 -1.7471525 0 0.50198161 10.442357 + 50 1.4995945 -1.7468614 0 0.50198122 10.441061 + 60 1.499609 -1.7468813 0 0.50198309 10.44116 + 70 1.5004314 -1.7481179 0 0.50197962 10.446638 + 80 1.5033149 -1.7524495 0 0.50197233 10.46585 + 90 1.5108219 -1.7637095 0 0.50197005 10.515883 + 100 1.529239 -1.7913105 0 0.501988 10.638649 +Loop time of 1.56685 on 16 procs for 100 steps with 4096 atoms + +Performance: 27571.239 tau/day, 63.822 timesteps/s +99.8% CPU use with 16 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.00036407 | 0.00040755 | 0.00047517 | 0.0 | 0.03 +Kspace | 1.5521 | 1.553 | 1.5536 | 0.0 | 99.12 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.009537 | 0.010175 | 0.011894 | 0.6 | 0.65 +Output | 0.000319 | 0.00039139 | 0.00052881 | 0.0 | 0.02 +Modify | 0.00086999 | 0.00097834 | 0.0010362 | 0.0 | 0.06 +Other | | 0.001859 | | | 0.12 + +Nlocal: 256 ave 256 max 256 min +Histogram: 16 0 0 0 0 0 0 0 0 0 +Nghost: 2816 ave 2816 max 2816 min +Histogram: 16 0 0 0 0 0 0 0 0 0 +Neighs: 32768 ave 32768 max 32768 min +Histogram: 16 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 524288 +Ave neighs/atom = 128 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:01 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.g++.p2nfft.2 b/examples/USER/scafacos/log.08Aug18.scafacos.g++.p2nfft.2 new file mode 100644 index 0000000000..72a53c48ff --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.g++.p2nfft.2 @@ -0,0 +1,102 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.NaCl + orthogonal box = (0 0 0) to (1 1 1) + 1 by 1 by 2 MPI processor grid + reading atoms ... + 8 atoms + +replicate 8 8 8 + orthogonal box = (0 0 0) to (8 8 8) + 1 by 1 by 2 MPI processor grid + 4096 atoms + Time spent = 0.0003438 secs + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos p2nfft 0.001 +kspace_modify scafacos tolerance field + +timestep 0.005 +thermo 10 + +run 100 +Setting up ScaFaCoS with solver p2nfft ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 8 8 8 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.574 | 4.574 | 4.574 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -1.7477245 0 0.50172614 10.443537 + 10 1.5000176 -1.7475898 0 0.50188725 10.443798 + 20 1.5000161 -1.7475262 0 0.50194874 10.443843 + 30 1.4999486 -1.7474019 0 0.50197176 10.443413 + 40 1.4997889 -1.7471525 0 0.50198161 10.442357 + 50 1.4995945 -1.7468614 0 0.50198122 10.441061 + 60 1.499609 -1.7468813 0 0.50198309 10.44116 + 70 1.5004314 -1.7481179 0 0.50197962 10.446638 + 80 1.5033149 -1.7524495 0 0.50197233 10.46585 + 90 1.5108219 -1.7637095 0 0.50197005 10.515883 + 100 1.529239 -1.7913105 0 0.501988 10.638649 +Loop time of 9.38943 on 2 procs for 100 steps with 4096 atoms + +Performance: 4600.920 tau/day, 10.650 timesteps/s +99.9% CPU use with 2 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0010064 | 0.0010065 | 0.0010066 | 0.0 | 0.01 +Kspace | 9.3602 | 9.3603 | 9.3604 | 0.0 | 99.69 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.019444 | 0.01968 | 0.019916 | 0.2 | 0.21 +Output | 0.00033355 | 0.00035357 | 0.0003736 | 0.0 | 0.00 +Modify | 0.0055819 | 0.0056176 | 0.0056534 | 0.0 | 0.06 +Other | | 0.002495 | | | 0.03 + +Nlocal: 2048 ave 2048 max 2048 min +Histogram: 2 0 0 0 0 0 0 0 0 0 +Nghost: 7168 ave 7168 max 7168 min +Histogram: 2 0 0 0 0 0 0 0 0 0 +Neighs: 262144 ave 262144 max 262144 min +Histogram: 2 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 524288 +Ave neighs/atom = 128 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:11 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.g++.p2nfft.4 b/examples/USER/scafacos/log.08Aug18.scafacos.g++.p2nfft.4 new file mode 100644 index 0000000000..bf4494df8b --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.g++.p2nfft.4 @@ -0,0 +1,102 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.NaCl + orthogonal box = (0 0 0) to (1 1 1) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 8 atoms + +replicate 8 8 8 + orthogonal box = (0 0 0) to (8 8 8) + 1 by 2 by 2 MPI processor grid + 4096 atoms + Time spent = 0.000260592 secs + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos p2nfft 0.001 +kspace_modify scafacos tolerance field + +timestep 0.005 +thermo 10 + +run 100 +Setting up ScaFaCoS with solver p2nfft ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 8 8 8 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.008 | 4.008 | 4.008 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -1.7477245 0 0.50172614 10.443537 + 10 1.5000176 -1.7475898 0 0.50188725 10.443798 + 20 1.5000161 -1.7475262 0 0.50194874 10.443843 + 30 1.4999486 -1.7474019 0 0.50197176 10.443413 + 40 1.4997889 -1.7471525 0 0.50198161 10.442357 + 50 1.4995945 -1.7468614 0 0.50198122 10.441061 + 60 1.499609 -1.7468813 0 0.50198309 10.44116 + 70 1.5004314 -1.7481179 0 0.50197962 10.446638 + 80 1.5033149 -1.7524495 0 0.50197233 10.46585 + 90 1.5108219 -1.7637095 0 0.50197005 10.515883 + 100 1.529239 -1.7913105 0 0.501988 10.638649 +Loop time of 5.09997 on 4 procs for 100 steps with 4096 atoms + +Performance: 8470.643 tau/day, 19.608 timesteps/s +99.8% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.00069928 | 0.00071001 | 0.00073647 | 0.0 | 0.01 +Kspace | 5.0795 | 5.0796 | 5.0797 | 0.0 | 99.60 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.014101 | 0.014216 | 0.014331 | 0.1 | 0.28 +Output | 0.00030541 | 0.00033581 | 0.00039625 | 0.0 | 0.01 +Modify | 0.0030217 | 0.0030621 | 0.0030868 | 0.0 | 0.06 +Other | | 0.002036 | | | 0.04 + +Nlocal: 1024 ave 1024 max 1024 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 5120 ave 5120 max 5120 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 131072 ave 131072 max 131072 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 524288 +Ave neighs/atom = 128 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:05 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.g++.p2nfft.8 b/examples/USER/scafacos/log.08Aug18.scafacos.g++.p2nfft.8 new file mode 100644 index 0000000000..b5e889dfc1 --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.g++.p2nfft.8 @@ -0,0 +1,102 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.NaCl + orthogonal box = (0 0 0) to (1 1 1) + 2 by 2 by 2 MPI processor grid + reading atoms ... + 8 atoms + +replicate 8 8 8 + orthogonal box = (0 0 0) to (8 8 8) + 2 by 2 by 2 MPI processor grid + 4096 atoms + Time spent = 0.000324488 secs + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos p2nfft 0.001 +kspace_modify scafacos tolerance field + +timestep 0.005 +thermo 10 + +run 100 +Setting up ScaFaCoS with solver p2nfft ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 8 8 8 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.508 | 3.508 | 3.508 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -1.7477245 0 0.50172614 10.443537 + 10 1.5000176 -1.7475898 0 0.50188725 10.443798 + 20 1.5000161 -1.7475262 0 0.50194874 10.443843 + 30 1.4999486 -1.7474019 0 0.50197176 10.443413 + 40 1.4997889 -1.7471525 0 0.50198161 10.442357 + 50 1.4995945 -1.7468614 0 0.50198122 10.441061 + 60 1.499609 -1.7468813 0 0.50198309 10.44116 + 70 1.5004314 -1.7481179 0 0.50197962 10.446638 + 80 1.5033149 -1.7524495 0 0.50197233 10.46585 + 90 1.5108219 -1.7637095 0 0.50197005 10.515883 + 100 1.529239 -1.7913105 0 0.501988 10.638649 +Loop time of 2.88506 on 8 procs for 100 steps with 4096 atoms + +Performance: 14973.700 tau/day, 34.661 timesteps/s +99.6% CPU use with 8 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.000489 | 0.00051507 | 0.00052857 | 0.0 | 0.02 +Kspace | 2.8657 | 2.866 | 2.8664 | 0.0 | 99.34 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.014354 | 0.014851 | 0.015097 | 0.2 | 0.51 +Output | 0.00037169 | 0.00042769 | 0.00054169 | 0.0 | 0.01 +Modify | 0.0015774 | 0.0016578 | 0.0018044 | 0.2 | 0.06 +Other | | 0.001645 | | | 0.06 + +Nlocal: 512 ave 512 max 512 min +Histogram: 8 0 0 0 0 0 0 0 0 0 +Nghost: 3584 ave 3584 max 3584 min +Histogram: 8 0 0 0 0 0 0 0 0 0 +Neighs: 65536 ave 65536 max 65536 min +Histogram: 8 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 524288 +Ave neighs/atom = 128 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:03 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.g++.p3m.2 b/examples/USER/scafacos/log.08Aug18.scafacos.g++.p3m.2 new file mode 100644 index 0000000000..e69de29bb2 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.direct.1 b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.direct.1 new file mode 100644 index 0000000000..b0a47e4f98 --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.direct.1 @@ -0,0 +1,105 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.hammersley_shphere + orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 1000 atoms +change_box all boundary f f f + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos direct 0.001 + +timestep 0.005 +thermo 1 +run 20 +Setting up ScaFaCoS with solver direct ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 102 102 102 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 10.3 | 10.3 | 10.3 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -0.62417787 0 1.6235721 0.0015678854 + 1 18.780041 -10.770002 0 17.371889 0.016718957 + 2 65.289192 -11.084705 0 86.751149 0.060353634 + 3 121.92987 -7.0625759 0 175.64933 0.11404974 + 4 185.78164 -5.8777512 0 272.51604 0.17462195 + 5 286.36222 -4.382053 0 424.73173 0.26918926 + 6 481.42206 -4.3095567 0 717.1014 0.45274088 + 7 488.59167 -3.8685194 0 728.2861 0.45956866 + 8 497.85287 -3.0417966 0 742.99073 0.46838116 + 9 499.61615 -3.419003 0 745.2558 0.46983345 + 10 502.63684 -2.8360961 0 750.36521 0.47280809 + 11 504.4846 -2.7628105 0 753.20736 0.47462793 + 12 506.54485 -2.8460356 0 756.21142 0.47651441 + 13 508.27211 -2.730935 0 758.91482 0.47813752 + 14 510.57045 -2.6094877 0 762.48033 0.48031431 + 15 513.14798 -2.7150827 0 766.23717 0.48275229 + 16 515.78124 -2.3961811 0 770.50201 0.48526333 + 17 515.70265 -2.2982683 0 770.48215 0.48526617 + 18 515.7081 -2.1515983 0 770.63699 0.48530393 + 19 515.74906 -2.0581436 0 770.79182 0.48530977 + 20 515.70883 -1.8922577 0 770.89742 0.48527105 +Loop time of 0.465839 on 1 procs for 20 steps with 1000 atoms + +Performance: 18547.165 tau/day, 42.933 timesteps/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.00021982 | 0.00021982 | 0.00021982 | 0.0 | 0.05 +Kspace | 0.3218 | 0.3218 | 0.3218 | 0.0 | 69.08 +Neigh | 0.14249 | 0.14249 | 0.14249 | 0.0 | 30.59 +Comm | 0.00014853 | 0.00014853 | 0.00014853 | 0.0 | 0.03 +Output | 0.00026131 | 0.00026131 | 0.00026131 | 0.0 | 0.06 +Modify | 0.00055146 | 0.00055146 | 0.00055146 | 0.0 | 0.12 +Other | | 0.0003715 | | | 0.08 + +Nlocal: 1000 ave 1000 max 1000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 247817 ave 247817 max 247817 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 247817 +Ave neighs/atom = 247.817 +Neighbor list builds = 19 +Dangerous builds = 18 +Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.direct.2 b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.direct.2 new file mode 100644 index 0000000000..1ffab0ca6a --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.direct.2 @@ -0,0 +1,105 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.hammersley_shphere + orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5) + 1 by 1 by 2 MPI processor grid + reading atoms ... + 1000 atoms +change_box all boundary f f f + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos direct 0.001 + +timestep 0.005 +thermo 1 +run 20 +Setting up ScaFaCoS with solver direct ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 102 102 102 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 6.48 | 6.861 | 7.243 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -0.62417787 0 1.6235721 0.0015678854 + 1 18.780041 -10.770002 0 17.371889 0.016718957 + 2 65.289192 -11.084705 0 86.751149 0.060353634 + 3 121.92987 -7.0625759 0 175.64933 0.11404974 + 4 185.78164 -5.8777512 0 272.51604 0.17462195 + 5 286.36222 -4.382053 0 424.73173 0.26918926 + 6 481.42206 -4.3095567 0 717.1014 0.45274088 + 7 488.59167 -3.8685194 0 728.2861 0.45956866 + 8 497.85287 -3.0417966 0 742.99073 0.46838116 + 9 499.61615 -3.419003 0 745.2558 0.46983345 + 10 502.63684 -2.8360961 0 750.36521 0.47280809 + 11 504.4846 -2.7628105 0 753.20736 0.47462793 + 12 506.54485 -2.8460356 0 756.21142 0.47651441 + 13 508.27211 -2.730935 0 758.91482 0.47813752 + 14 510.57045 -2.6094877 0 762.48033 0.48031431 + 15 513.14798 -2.7150827 0 766.23717 0.48275229 + 16 515.78124 -2.3961811 0 770.50201 0.48526333 + 17 515.70265 -2.2982683 0 770.48215 0.48526617 + 18 515.7081 -2.1515983 0 770.63699 0.48530393 + 19 515.74906 -2.0581436 0 770.79182 0.48530977 + 20 515.70883 -1.8922577 0 770.89742 0.48527105 +Loop time of 0.284007 on 2 procs for 20 steps with 1000 atoms + +Performance: 30421.778 tau/day, 70.421 timesteps/s +99.1% CPU use with 2 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.00022578 | 0.00022626 | 0.00022674 | 0.0 | 0.08 +Kspace | 0.18253 | 0.20503 | 0.22752 | 5.0 | 72.19 +Neigh | 0.05363 | 0.076239 | 0.098848 | 8.2 | 26.84 +Comm | 0.0014737 | 0.0016443 | 0.0018148 | 0.4 | 0.58 +Output | 0.000247 | 0.00032353 | 0.00040007 | 0.0 | 0.11 +Modify | 0.00029159 | 0.00029731 | 0.00030303 | 0.0 | 0.10 +Other | | 0.0002506 | | | 0.09 + +Nlocal: 500 ave 516 max 484 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Nghost: 456.5 ave 475 max 438 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Neighs: 123908 ave 172139 max 75678 min +Histogram: 1 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 247817 +Ave neighs/atom = 247.817 +Neighbor list builds = 19 +Dangerous builds = 18 +Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.direct.4 b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.direct.4 new file mode 100644 index 0000000000..1235c0a3cd --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.direct.4 @@ -0,0 +1,105 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.hammersley_shphere + orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 1000 atoms +change_box all boundary f f f + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos direct 0.001 + +timestep 0.005 +thermo 1 +run 20 +Setting up ScaFaCoS with solver direct ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 102 102 102 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.837 | 5.123 | 5.6 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -0.62417787 0 1.6235721 0.0015678854 + 1 18.780041 -10.770002 0 17.371889 0.016718957 + 2 65.289192 -11.084705 0 86.751149 0.060353634 + 3 121.92987 -7.0625759 0 175.64933 0.11404974 + 4 185.78164 -5.8777512 0 272.51604 0.17462195 + 5 286.36222 -4.382053 0 424.73173 0.26918926 + 6 481.42206 -4.3095567 0 717.1014 0.45274088 + 7 488.59167 -3.8685194 0 728.2861 0.45956866 + 8 497.85287 -3.0417966 0 742.99073 0.46838116 + 9 499.61615 -3.419003 0 745.2558 0.46983345 + 10 502.63684 -2.8360961 0 750.36521 0.47280809 + 11 504.4846 -2.7628105 0 753.20736 0.47462793 + 12 506.54485 -2.8460356 0 756.21142 0.47651441 + 13 508.27211 -2.730935 0 758.91482 0.47813752 + 14 510.57045 -2.6094877 0 762.48033 0.48031431 + 15 513.14798 -2.7150827 0 766.23717 0.48275229 + 16 515.78124 -2.3961811 0 770.50201 0.48526333 + 17 515.70265 -2.2982683 0 770.48215 0.48526617 + 18 515.7081 -2.1515983 0 770.63699 0.48530393 + 19 515.74906 -2.0581436 0 770.79182 0.48530977 + 20 515.70883 -1.8922577 0 770.89742 0.48527105 +Loop time of 0.161335 on 4 procs for 20 steps with 1000 atoms + +Performance: 53553.228 tau/day, 123.966 timesteps/s +99.5% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.00022721 | 0.00023353 | 0.000247 | 0.0 | 0.14 +Kspace | 0.10295 | 0.11808 | 0.13377 | 3.5 | 73.19 +Neigh | 0.023849 | 0.039717 | 0.055031 | 6.1 | 24.62 +Comm | 0.0023148 | 0.0025774 | 0.0028391 | 0.4 | 1.60 +Output | 0.00029063 | 0.00038403 | 0.00050664 | 0.0 | 0.24 +Modify | 0.00015664 | 0.00015944 | 0.00016165 | 0.0 | 0.10 +Other | | 0.0001805 | | | 0.11 + +Nlocal: 250 ave 259 max 238 min +Histogram: 1 0 0 1 0 0 0 0 0 2 +Nghost: 672.25 ave 683 max 663 min +Histogram: 2 0 0 0 0 0 0 0 1 1 +Neighs: 61954.2 ave 97157 max 25016 min +Histogram: 1 0 0 1 0 0 1 0 0 1 + +Total # of neighbors = 247817 +Ave neighs/atom = 247.817 +Neighbor list builds = 19 +Dangerous builds = 18 +Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.direct.8 b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.direct.8 new file mode 100644 index 0000000000..e72ade73b5 --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.direct.8 @@ -0,0 +1,105 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.hammersley_shphere + orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5) + 2 by 2 by 2 MPI processor grid + reading atoms ... + 1000 atoms +change_box all boundary f f f + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos direct 0.001 + +timestep 0.005 +thermo 1 +run 20 +Setting up ScaFaCoS with solver direct ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 102 102 102 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.164 | 4.26 | 4.546 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -0.62417787 0 1.6235721 0.0015678854 + 1 18.780041 -10.770002 0 17.371889 0.016718957 + 2 65.289192 -11.084705 0 86.751149 0.060353634 + 3 121.92987 -7.0625759 0 175.64933 0.11404974 + 4 185.78164 -5.8777512 0 272.51604 0.17462195 + 5 286.36222 -4.382053 0 424.73173 0.26918926 + 6 481.42206 -4.3095567 0 717.1014 0.45274088 + 7 488.59167 -3.8685194 0 728.2861 0.45956866 + 8 497.85287 -3.0417966 0 742.99073 0.46838116 + 9 499.61615 -3.419003 0 745.2558 0.46983345 + 10 502.63684 -2.8360961 0 750.36521 0.47280809 + 11 504.4846 -2.7628105 0 753.20736 0.47462793 + 12 506.54485 -2.8460356 0 756.21142 0.47651441 + 13 508.27211 -2.730935 0 758.91482 0.47813752 + 14 510.57045 -2.6094877 0 762.48033 0.48031431 + 15 513.14798 -2.7150827 0 766.23717 0.48275229 + 16 515.78124 -2.3961811 0 770.50201 0.48526333 + 17 515.70265 -2.2982683 0 770.48215 0.48526617 + 18 515.7081 -2.1515983 0 770.63699 0.48530393 + 19 515.74906 -2.0581436 0 770.79182 0.48530977 + 20 515.70883 -1.8922577 0 770.89742 0.48527105 +Loop time of 0.0883947 on 8 procs for 20 steps with 1000 atoms + +Performance: 97743.448 tau/day, 226.258 timesteps/s +99.2% CPU use with 8 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0002284 | 0.00024167 | 0.00029922 | 0.0 | 0.27 +Kspace | 0.055725 | 0.063153 | 0.071883 | 2.4 | 71.44 +Neigh | 0.012251 | 0.021348 | 0.029026 | 4.3 | 24.15 +Comm | 0.0025573 | 0.0029825 | 0.0034359 | 0.5 | 3.37 +Output | 0.00034451 | 0.00044149 | 0.00057721 | 0.0 | 0.50 +Modify | 7.8917e-05 | 8.437e-05 | 8.9407e-05 | 0.0 | 0.10 +Other | | 0.0001439 | | | 0.16 + +Nlocal: 125 ave 133 max 113 min +Histogram: 2 0 0 0 0 1 1 0 2 2 +Nghost: 773.625 ave 788 max 764 min +Histogram: 1 1 2 1 1 0 0 0 1 1 +Neighs: 30977.1 ave 50690 max 10447 min +Histogram: 1 1 1 0 1 1 0 0 2 1 + +Total # of neighbors = 247817 +Ave neighs/atom = 247.817 +Neighbor list builds = 19 +Dangerous builds = 18 +Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.fmm.1 b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.fmm.1 new file mode 100644 index 0000000000..4bef247e26 --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.fmm.1 @@ -0,0 +1,109 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.hammersley_shphere + orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 1000 atoms +change_box all boundary f f f + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos fmm 0.001 +kspace_modify scafacos tolerance energy_rel +kspace_modify scafacos fmm_tuning 1 +ScaFaCoS setting fmm inhomogen tuning ... + +timestep 0.005 +thermo 1 + +run 20 +Setting up ScaFaCoS with solver fmm ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 102 102 102 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 10.3 | 10.3 | 10.3 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -0.62417141 0 1.6235786 0.0015676581 + 1 18.780412 -10.770009 0 17.372438 0.016719188 + 2 65.294131 -11.084501 0 86.758754 0.06035827 + 3 121.92555 -7.0612033 0 175.64423 0.1140457 + 4 185.71165 -5.8781334 0 272.41077 0.17455524 + 5 286.28339 -4.3800108 0 424.61565 0.26911306 + 6 481.28097 -4.3052012 0 716.89433 0.45262045 + 7 487.26022 -3.8672741 0 726.29216 0.45830216 + 8 493.65478 -3.0242687 0 736.71742 0.46443761 + 9 495.66203 -3.4336343 0 739.31592 0.46613014 + 10 498.41831 -2.8837072 0 743.99613 0.46887706 + 11 499.20944 -2.7724783 0 745.29287 0.46966875 + 12 500.97345 -2.8281484 0 747.88057 0.47126462 + 13 507.46412 -2.7752775 0 757.65971 0.47728761 + 14 525.35729 -2.5749814 0 784.67292 0.49422171 + 15 563.9578 -2.9982381 0 842.09253 0.53043696 + 16 645.47602 -2.5519203 0 964.69389 0.60730795 + 17 647.09276 -2.2568468 0 967.41166 0.60891914 + 18 647.12596 -2.2791003 0 967.43915 0.60900309 + 19 647.24862 -2.2495226 0 967.65253 0.60908339 + 20 647.51175 -2.0239179 0 968.27244 0.60932598 +Loop time of 0.797289 on 1 procs for 20 steps with 1000 atoms + +Performance: 10836.721 tau/day, 25.085 timesteps/s +100.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.00022364 | 0.00022364 | 0.00022364 | 0.0 | 0.03 +Kspace | 0.6524 | 0.6524 | 0.6524 | 0.0 | 81.83 +Neigh | 0.14312 | 0.14312 | 0.14312 | 0.0 | 17.95 +Comm | 0.00020337 | 0.00020337 | 0.00020337 | 0.0 | 0.03 +Output | 0.00036621 | 0.00036621 | 0.00036621 | 0.0 | 0.05 +Modify | 0.00058126 | 0.00058126 | 0.00058126 | 0.0 | 0.07 +Other | | 0.0003934 | | | 0.05 + +Nlocal: 1000 ave 1000 max 1000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 244342 ave 244342 max 244342 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 244342 +Ave neighs/atom = 244.342 +Neighbor list builds = 19 +Dangerous builds = 18 +Total wall time: 0:00:01 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.fmm.2 b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.fmm.2 new file mode 100644 index 0000000000..e8e614004d --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.fmm.2 @@ -0,0 +1,109 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.hammersley_shphere + orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5) + 1 by 1 by 2 MPI processor grid + reading atoms ... + 1000 atoms +change_box all boundary f f f + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos fmm 0.001 +kspace_modify scafacos tolerance energy_rel +kspace_modify scafacos fmm_tuning 1 +ScaFaCoS setting fmm inhomogen tuning ... + +timestep 0.005 +thermo 1 + +run 20 +Setting up ScaFaCoS with solver fmm ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 102 102 102 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 6.48 | 6.861 | 7.243 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -0.62417141 0 1.6235786 0.0015676581 + 1 18.780412 -10.770009 0 17.372438 0.016719188 + 2 65.294131 -11.084501 0 86.758754 0.06035827 + 3 121.92555 -7.0612033 0 175.64423 0.1140457 + 4 185.71165 -5.8781334 0 272.41077 0.17455524 + 5 286.28339 -4.3800108 0 424.61565 0.26911306 + 6 481.28097 -4.3052012 0 716.89433 0.45262045 + 7 487.26022 -3.8672741 0 726.29216 0.45830216 + 8 493.65478 -3.0242687 0 736.71742 0.46443761 + 9 495.66203 -3.4336343 0 739.31592 0.46613014 + 10 498.41831 -2.8837072 0 743.99613 0.46887706 + 11 499.20944 -2.7724783 0 745.29287 0.46966875 + 12 500.97345 -2.8281484 0 747.88057 0.47126462 + 13 507.46412 -2.7752775 0 757.65971 0.47728761 + 14 525.35729 -2.5749814 0 784.67292 0.49422171 + 15 563.9578 -2.9982381 0 842.09253 0.53043696 + 16 645.47602 -2.5519203 0 964.69389 0.60730795 + 17 647.09276 -2.2568468 0 967.41166 0.60891914 + 18 647.12596 -2.2791003 0 967.43915 0.60900309 + 19 647.24862 -2.2495226 0 967.65253 0.60908339 + 20 647.51175 -2.0239179 0 968.27244 0.60932598 +Loop time of 0.701186 on 2 procs for 20 steps with 1000 atoms + +Performance: 12321.981 tau/day, 28.523 timesteps/s +99.7% CPU use with 2 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.00022388 | 0.00022912 | 0.00023437 | 0.0 | 0.03 +Kspace | 0.60189 | 0.62405 | 0.64621 | 2.8 | 89.00 +Neigh | 0.051681 | 0.073973 | 0.096265 | 8.2 | 10.55 +Comm | 0.0016983 | 0.0018919 | 0.0020854 | 0.4 | 0.27 +Output | 0.00034356 | 0.00044572 | 0.00054789 | 0.0 | 0.06 +Modify | 0.00031281 | 0.0003171 | 0.00032139 | 0.0 | 0.05 +Other | | 0.0002786 | | | 0.04 + +Nlocal: 500 ave 509 max 491 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Nghost: 455.5 ave 467 max 444 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Neighs: 122171 ave 171834 max 72508 min +Histogram: 1 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 244342 +Ave neighs/atom = 244.342 +Neighbor list builds = 19 +Dangerous builds = 18 +Total wall time: 0:00:01 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.fmm.4 b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.fmm.4 new file mode 100644 index 0000000000..e3f5bf44c9 --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.fmm.4 @@ -0,0 +1,109 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.hammersley_shphere + orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 1000 atoms +change_box all boundary f f f + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos fmm 0.001 +kspace_modify scafacos tolerance energy_rel +kspace_modify scafacos fmm_tuning 1 +ScaFaCoS setting fmm inhomogen tuning ... + +timestep 0.005 +thermo 1 + +run 20 +Setting up ScaFaCoS with solver fmm ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 102 102 102 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.837 | 5.123 | 5.6 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -0.62417141 0 1.6235786 0.0015676581 + 1 18.780412 -10.770009 0 17.372438 0.016719188 + 2 65.294131 -11.084501 0 86.758754 0.06035827 + 3 121.92555 -7.0612033 0 175.64423 0.1140457 + 4 185.71165 -5.8781334 0 272.41077 0.17455524 + 5 286.28339 -4.3800108 0 424.61565 0.26911306 + 6 481.28097 -4.3052012 0 716.89433 0.45262045 + 7 487.26022 -3.8672741 0 726.29216 0.45830216 + 8 493.65478 -3.0242687 0 736.71742 0.46443761 + 9 495.66203 -3.4336343 0 739.31592 0.46613014 + 10 498.41831 -2.8837072 0 743.99613 0.46887706 + 11 499.20944 -2.7724783 0 745.29287 0.46966875 + 12 500.97345 -2.8281484 0 747.88057 0.47126462 + 13 507.46412 -2.7752775 0 757.65971 0.47728761 + 14 525.35729 -2.5749814 0 784.67292 0.49422171 + 15 563.9578 -2.9982381 0 842.09253 0.53043696 + 16 645.47602 -2.5519203 0 964.69389 0.60730795 + 17 647.09276 -2.2568468 0 967.41166 0.60891914 + 18 647.12596 -2.2791003 0 967.43915 0.60900309 + 19 647.24862 -2.2495226 0 967.65253 0.60908339 + 20 647.51175 -2.0239179 0 968.27244 0.60932598 +Loop time of 0.666895 on 4 procs for 20 steps with 1000 atoms + +Performance: 12955.555 tau/day, 29.990 timesteps/s +99.5% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0002284 | 0.00024879 | 0.00025725 | 0.0 | 0.04 +Kspace | 0.6085 | 0.62278 | 0.6386 | 1.6 | 93.38 +Neigh | 0.023998 | 0.040044 | 0.054552 | 6.2 | 6.00 +Comm | 0.0025489 | 0.0028656 | 0.0031898 | 0.4 | 0.43 +Output | 0.0004077 | 0.00053912 | 0.00071406 | 0.0 | 0.08 +Modify | 0.00017953 | 0.00018525 | 0.00020218 | 0.0 | 0.03 +Other | | 0.0002366 | | | 0.04 + +Nlocal: 250 ave 259 max 240 min +Histogram: 1 0 0 0 0 2 0 0 0 1 +Nghost: 668.75 ave 679 max 657 min +Histogram: 1 0 0 0 0 1 1 0 0 1 +Neighs: 61085.5 ave 95363 max 24964 min +Histogram: 1 0 0 1 0 0 0 1 0 1 + +Total # of neighbors = 244342 +Ave neighs/atom = 244.342 +Neighbor list builds = 19 +Dangerous builds = 18 +Total wall time: 0:00:01 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.fmm.8 b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.fmm.8 new file mode 100644 index 0000000000..22d1140813 --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.fmm.8 @@ -0,0 +1,109 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.hammersley_shphere + orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5) + 2 by 2 by 2 MPI processor grid + reading atoms ... + 1000 atoms +change_box all boundary f f f + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos fmm 0.001 +kspace_modify scafacos tolerance energy_rel +kspace_modify scafacos fmm_tuning 1 +ScaFaCoS setting fmm inhomogen tuning ... + +timestep 0.005 +thermo 1 + +run 20 +Setting up ScaFaCoS with solver fmm ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 102 102 102 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.164 | 4.26 | 4.546 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -0.62417141 0 1.6235786 0.0015676581 + 1 18.780412 -10.770009 0 17.372438 0.016719188 + 2 65.294131 -11.084501 0 86.758754 0.06035827 + 3 121.92555 -7.0612033 0 175.64423 0.1140457 + 4 185.71165 -5.8781334 0 272.41077 0.17455524 + 5 286.28339 -4.3800108 0 424.61565 0.26911306 + 6 481.28097 -4.3052012 0 716.89433 0.45262045 + 7 487.26022 -3.8672741 0 726.29216 0.45830216 + 8 493.65478 -3.0242687 0 736.71742 0.46443761 + 9 495.66203 -3.4336343 0 739.31592 0.46613014 + 10 498.41831 -2.8837072 0 743.99613 0.46887706 + 11 499.20944 -2.7724783 0 745.29287 0.46966875 + 12 500.97345 -2.8281484 0 747.88057 0.47126462 + 13 507.46412 -2.7752775 0 757.65971 0.47728761 + 14 525.35729 -2.5749814 0 784.67292 0.49422171 + 15 563.9578 -2.9982381 0 842.09253 0.53043696 + 16 645.47602 -2.5519203 0 964.69389 0.60730795 + 17 647.09276 -2.2568468 0 967.41166 0.60891914 + 18 647.12596 -2.2791003 0 967.43915 0.60900309 + 19 647.24862 -2.2495226 0 967.65253 0.60908339 + 20 647.51175 -2.0239179 0 968.27244 0.60932598 +Loop time of 0.569395 on 8 procs for 20 steps with 1000 atoms + +Performance: 15174.000 tau/day, 35.125 timesteps/s +99.3% CPU use with 8 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.00021982 | 0.00023353 | 0.0002408 | 0.0 | 0.04 +Kspace | 0.53679 | 0.54466 | 0.55292 | 0.8 | 95.66 +Neigh | 0.011844 | 0.02033 | 0.028357 | 4.2 | 3.57 +Comm | 0.0028894 | 0.0031579 | 0.0034704 | 0.4 | 0.55 +Output | 0.0005579 | 0.00067073 | 0.0008719 | 0.0 | 0.12 +Modify | 0.0001018 | 0.00011405 | 0.00012612 | 0.0 | 0.02 +Other | | 0.0002268 | | | 0.04 + +Nlocal: 125 ave 137 max 111 min +Histogram: 1 1 0 0 0 2 2 1 0 1 +Nghost: 768.875 ave 788 max 761 min +Histogram: 4 0 2 0 0 0 1 0 0 1 +Neighs: 30542.8 ave 48077 max 10011 min +Histogram: 1 1 1 0 1 1 0 0 0 3 + +Total # of neighbors = 244342 +Ave neighs/atom = 244.342 +Neighbor list builds = 19 +Dangerous builds = 18 +Total wall time: 0:00:01 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.p2nfft.1 b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.p2nfft.1 new file mode 100644 index 0000000000..f8a85c6c6b --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.p2nfft.1 @@ -0,0 +1,107 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.hammersley_shphere + orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 1000 atoms +change_box all boundary f f f + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos p2nfft 0.001 +kspace_modify scafacos tolerance potential + +timestep 0.005 +thermo 1 + +run 20 +Setting up ScaFaCoS with solver p2nfft ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 102 102 102 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 10.3 | 10.3 | 10.3 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -0.62417787 0 1.6235721 0.0015678854 + 1 18.780041 -10.770002 0 17.371889 0.016718957 + 2 65.289192 -11.084705 0 86.751149 0.060353634 + 3 121.92987 -7.0625759 0 175.64933 0.11404974 + 4 185.78164 -5.8777511 0 272.51603 0.17462194 + 5 286.36221 -4.3820531 0 424.73172 0.26918925 + 6 481.42203 -4.3095567 0 717.10136 0.45274086 + 7 488.59165 -3.8685193 0 728.28607 0.45956865 + 8 497.85288 -3.0417938 0 742.99075 0.46838117 + 9 499.61619 -3.4190063 0 745.25585 0.46983349 + 10 502.63691 -2.8360951 0 750.36531 0.47280815 + 11 504.4847 -2.7628089 0 753.20751 0.47462802 + 12 506.54494 -2.8460319 0 756.21157 0.4765145 + 13 508.2722 -2.7309328 0 758.91497 0.47813761 + 14 510.57053 -2.6094792 0 762.48045 0.48031438 + 15 513.14804 -2.7150819 0 766.23726 0.48275234 + 16 515.78127 -2.3961749 0 770.50206 0.48526336 + 17 515.70267 -2.2982581 0 770.48219 0.48526619 + 18 515.70813 -2.1516075 0 770.63702 0.48530395 + 19 515.74908 -2.0581483 0 770.79185 0.48530979 + 20 515.70881 -1.892235 0 770.89742 0.48527104 +Loop time of 1.06008 on 1 procs for 20 steps with 1000 atoms + +Performance: 8150.306 tau/day, 18.866 timesteps/s +100.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.00022078 | 0.00022078 | 0.00022078 | 0.0 | 0.02 +Kspace | 0.91611 | 0.91611 | 0.91611 | 0.0 | 86.42 +Neigh | 0.14232 | 0.14232 | 0.14232 | 0.0 | 13.43 +Comm | 0.00015092 | 0.00015092 | 0.00015092 | 0.0 | 0.01 +Output | 0.00033736 | 0.00033736 | 0.00033736 | 0.0 | 0.03 +Modify | 0.00056243 | 0.00056243 | 0.00056243 | 0.0 | 0.05 +Other | | 0.0003803 | | | 0.04 + +Nlocal: 1000 ave 1000 max 1000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 247817 ave 247817 max 247817 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 247817 +Ave neighs/atom = 247.817 +Neighbor list builds = 19 +Dangerous builds = 18 +Total wall time: 0:00:01 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.p2nfft.2 b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.p2nfft.2 new file mode 100644 index 0000000000..bd7e7fee1f --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.p2nfft.2 @@ -0,0 +1,107 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.hammersley_shphere + orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5) + 1 by 1 by 2 MPI processor grid + reading atoms ... + 1000 atoms +change_box all boundary f f f + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos p2nfft 0.001 +kspace_modify scafacos tolerance potential + +timestep 0.005 +thermo 1 + +run 20 +Setting up ScaFaCoS with solver p2nfft ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 102 102 102 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 6.48 | 6.861 | 7.243 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -0.62417787 0 1.6235721 0.0015678854 + 1 18.780041 -10.770002 0 17.371889 0.016718957 + 2 65.289192 -11.084705 0 86.751149 0.060353634 + 3 121.92987 -7.0625759 0 175.64933 0.11404974 + 4 185.78164 -5.8777511 0 272.51603 0.17462194 + 5 286.36221 -4.3820531 0 424.73172 0.26918925 + 6 481.42203 -4.3095567 0 717.10136 0.45274086 + 7 488.59165 -3.8685193 0 728.28607 0.45956865 + 8 497.85288 -3.0417938 0 742.99075 0.46838117 + 9 499.61619 -3.4190063 0 745.25585 0.46983349 + 10 502.63691 -2.8360951 0 750.36531 0.47280815 + 11 504.4847 -2.7628089 0 753.20751 0.47462802 + 12 506.54494 -2.8460319 0 756.21157 0.4765145 + 13 508.2722 -2.7309328 0 758.91497 0.47813761 + 14 510.57053 -2.6094792 0 762.48045 0.48031438 + 15 513.14804 -2.7150819 0 766.23726 0.48275234 + 16 515.78127 -2.3961749 0 770.50206 0.48526336 + 17 515.70267 -2.2982581 0 770.48219 0.48526619 + 18 515.70813 -2.1516075 0 770.63702 0.48530395 + 19 515.74908 -2.0581483 0 770.79185 0.48530979 + 20 515.70881 -1.892235 0 770.89742 0.48527104 +Loop time of 0.701267 on 2 procs for 20 steps with 1000 atoms + +Performance: 12320.557 tau/day, 28.520 timesteps/s +99.6% CPU use with 2 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0002265 | 0.00022769 | 0.00022888 | 0.0 | 0.03 +Kspace | 0.60195 | 0.62374 | 0.64554 | 2.8 | 88.95 +Neigh | 0.05268 | 0.074592 | 0.096504 | 8.0 | 10.64 +Comm | 0.0015199 | 0.0016934 | 0.0018668 | 0.4 | 0.24 +Output | 0.00031519 | 0.00041544 | 0.0005157 | 0.0 | 0.06 +Modify | 0.00029492 | 0.00030565 | 0.00031638 | 0.0 | 0.04 +Other | | 0.000288 | | | 0.04 + +Nlocal: 500 ave 516 max 484 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Nghost: 456.5 ave 475 max 438 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Neighs: 123908 ave 172139 max 75678 min +Histogram: 1 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 247817 +Ave neighs/atom = 247.817 +Neighbor list builds = 19 +Dangerous builds = 18 +Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.p2nfft.4 b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.p2nfft.4 new file mode 100644 index 0000000000..8a7e591f9a --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.p2nfft.4 @@ -0,0 +1,107 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.hammersley_shphere + orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 1000 atoms +change_box all boundary f f f + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos p2nfft 0.001 +kspace_modify scafacos tolerance potential + +timestep 0.005 +thermo 1 + +run 20 +Setting up ScaFaCoS with solver p2nfft ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 102 102 102 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.837 | 5.123 | 5.6 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -0.62417787 0 1.6235721 0.0015678854 + 1 18.780041 -10.770002 0 17.371889 0.016718957 + 2 65.289192 -11.084705 0 86.751149 0.060353634 + 3 121.92987 -7.0625759 0 175.64933 0.11404974 + 4 185.78164 -5.8777511 0 272.51603 0.17462194 + 5 286.36221 -4.3820531 0 424.73172 0.26918925 + 6 481.42203 -4.3095567 0 717.10136 0.45274086 + 7 488.59165 -3.8685193 0 728.28607 0.45956865 + 8 497.85288 -3.0417938 0 742.99075 0.46838117 + 9 499.61619 -3.4190063 0 745.25585 0.46983349 + 10 502.63691 -2.8360951 0 750.36531 0.47280815 + 11 504.4847 -2.7628089 0 753.20751 0.47462802 + 12 506.54494 -2.8460319 0 756.21157 0.4765145 + 13 508.2722 -2.7309328 0 758.91497 0.47813761 + 14 510.57053 -2.6094792 0 762.48045 0.48031438 + 15 513.14804 -2.7150819 0 766.23726 0.48275234 + 16 515.78127 -2.3961749 0 770.50206 0.48526336 + 17 515.70267 -2.2982581 0 770.48219 0.48526619 + 18 515.70813 -2.1516075 0 770.63702 0.48530395 + 19 515.74908 -2.0581483 0 770.79185 0.48530979 + 20 515.70881 -1.892235 0 770.89742 0.48527104 +Loop time of 0.427495 on 4 procs for 20 steps with 1000 atoms + +Performance: 20210.785 tau/day, 46.784 timesteps/s +99.7% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0002327 | 0.00023341 | 0.00023437 | 0.0 | 0.05 +Kspace | 0.36897 | 0.38411 | 0.39988 | 1.9 | 89.85 +Neigh | 0.023831 | 0.039796 | 0.055124 | 6.1 | 9.31 +Comm | 0.0022776 | 0.0025444 | 0.0028152 | 0.4 | 0.60 +Output | 0.00033784 | 0.0004344 | 0.00057077 | 0.0 | 0.10 +Modify | 0.00016117 | 0.00016713 | 0.00017095 | 0.0 | 0.04 +Other | | 0.0002093 | | | 0.05 + +Nlocal: 250 ave 259 max 238 min +Histogram: 1 0 0 1 0 0 0 0 0 2 +Nghost: 672.25 ave 683 max 663 min +Histogram: 2 0 0 0 0 0 0 0 1 1 +Neighs: 61954.2 ave 97157 max 25016 min +Histogram: 1 0 0 1 0 0 1 0 0 1 + +Total # of neighbors = 247817 +Ave neighs/atom = 247.817 +Neighbor list builds = 19 +Dangerous builds = 18 +Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.p2nfft.8 b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.p2nfft.8 new file mode 100644 index 0000000000..13922c09ac --- /dev/null +++ b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.p2nfft.8 @@ -0,0 +1,107 @@ +LAMMPS (2 Aug 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.hammersley_shphere + orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5) + 2 by 2 by 2 MPI processor grid + reading atoms ... + 1000 atoms +change_box all boundary f f f + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos p2nfft 0.001 +kspace_modify scafacos tolerance potential + +timestep 0.005 +thermo 1 + +run 20 +Setting up ScaFaCoS with solver p2nfft ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 102 102 102 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.164 | 4.26 | 4.546 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -0.62417787 0 1.6235721 0.0015678854 + 1 18.780041 -10.770002 0 17.371889 0.016718957 + 2 65.289192 -11.084705 0 86.751149 0.060353634 + 3 121.92987 -7.0625759 0 175.64933 0.11404974 + 4 185.78164 -5.8777511 0 272.51603 0.17462194 + 5 286.36221 -4.3820531 0 424.73172 0.26918925 + 6 481.42203 -4.3095567 0 717.10136 0.45274086 + 7 488.59165 -3.8685193 0 728.28607 0.45956865 + 8 497.85288 -3.0417938 0 742.99075 0.46838117 + 9 499.61619 -3.4190063 0 745.25585 0.46983349 + 10 502.63691 -2.8360951 0 750.36531 0.47280815 + 11 504.4847 -2.7628089 0 753.20751 0.47462802 + 12 506.54494 -2.8460319 0 756.21157 0.4765145 + 13 508.2722 -2.7309328 0 758.91497 0.47813761 + 14 510.57053 -2.6094792 0 762.48045 0.48031438 + 15 513.14804 -2.7150819 0 766.23726 0.48275234 + 16 515.78127 -2.3961749 0 770.50206 0.48526336 + 17 515.70267 -2.2982581 0 770.48219 0.48526619 + 18 515.70813 -2.1516075 0 770.63702 0.48530395 + 19 515.74908 -2.0581483 0 770.79185 0.48530979 + 20 515.70881 -1.892235 0 770.89742 0.48527104 +Loop time of 0.242145 on 8 procs for 20 steps with 1000 atoms + +Performance: 35681.038 tau/day, 82.595 timesteps/s +99.2% CPU use with 8 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0002315 | 0.00023672 | 0.00024652 | 0.0 | 0.10 +Kspace | 0.20915 | 0.21666 | 0.22564 | 1.3 | 89.48 +Neigh | 0.012218 | 0.021341 | 0.029026 | 4.3 | 8.81 +Comm | 0.0028954 | 0.0031248 | 0.0033553 | 0.3 | 1.29 +Output | 0.00039291 | 0.00049406 | 0.00066066 | 0.0 | 0.20 +Modify | 8.7976e-05 | 9.2953e-05 | 9.7752e-05 | 0.0 | 0.04 +Other | | 0.0001938 | | | 0.08 + +Nlocal: 125 ave 133 max 113 min +Histogram: 2 0 0 0 0 1 1 0 2 2 +Nghost: 773.625 ave 788 max 764 min +Histogram: 1 1 2 1 1 0 0 0 1 1 +Neighs: 30977.1 ave 50690 max 10447 min +Histogram: 1 1 1 0 1 1 0 0 2 1 + +Total # of neighbors = 247817 +Ave neighs/atom = 247.817 +Neighbor list builds = 19 +Dangerous builds = 18 +Total wall time: 0:00:00 diff --git a/examples/atm/in.atm b/examples/atm/in.atm new file mode 100644 index 0000000000..131528dce3 --- /dev/null +++ b/examples/atm/in.atm @@ -0,0 +1,31 @@ +# Axilrod-Teller-Muto potential example + +variable x index 1 +variable y index 1 +variable z index 1 + +variable xx equal 10*$x +variable yy equal 10*$y +variable zz equal 10*$z + +units lj +atom_style atomic + +lattice fcc 0.65 +region box block 0 ${xx} 0 ${yy} 0 ${zz} +create_box 1 box +create_atoms 1 box + +pair_style hybrid/overlay lj/cut 4.5 atm 4.5 2.5 +pair_coeff * * lj/cut 1.0 1.0 +pair_coeff * * atm * 0.072 + +mass * 1.0 +velocity all create 1.033 12345678 loop geom + +fix 1 all nvt temp 1.033 1.033 0.05 + +timestep 0.002 +thermo 5 + +run 25 diff --git a/examples/atm/log.27Aug18.g++.1 b/examples/atm/log.27Aug18.g++.1 new file mode 100644 index 0000000000..46215e108c --- /dev/null +++ b/examples/atm/log.27Aug18.g++.1 @@ -0,0 +1,100 @@ +LAMMPS (22 Aug 2018) +# Axilrod-Teller-Muto potential example + +variable x index 1 +variable y index 1 +variable z index 1 + +variable xx equal 10*$x +variable xx equal 10*1 +variable yy equal 10*$y +variable yy equal 10*1 +variable zz equal 10*$z +variable zz equal 10*1 + +units lj +atom_style atomic + +lattice fcc 0.65 +Lattice spacing in x,y,z = 1.83252 1.83252 1.83252 +region box block 0 ${xx} 0 ${yy} 0 ${zz} +region box block 0 10 0 ${yy} 0 ${zz} +region box block 0 10 0 10 0 ${zz} +region box block 0 10 0 10 0 10 +create_box 1 box +Created orthogonal box = (0 0 0) to (18.3252 18.3252 18.3252) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 4000 atoms + Time spent = 0.00139618 secs + +pair_style hybrid/overlay lj/cut 4.5 atm 4.5 2.5 +pair_coeff * * lj/cut 1.0 1.0 +pair_coeff * * atm * 0.072 + +mass * 1.0 +velocity all create 1.033 12345678 loop geom + +fix 1 all nvt temp 1.033 1.033 0.05 + +timestep 0.002 +thermo 5 + +run 25 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 4.8 + ghost atom cutoff = 4.8 + binsize = 2.4, bins = 8 8 8 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair lj/cut, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair atm, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 11.47 | 11.47 | 11.47 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.033 -4.8404387 0 -3.291326 -4.1332095 + 5 1.0337247 -4.8402263 0 -3.290027 -4.1207962 + 10 1.0355935 -4.8425889 0 -3.2895869 -4.0870158 + 15 1.0376519 -4.84599 0 -3.2899013 -4.0278711 + 20 1.0382257 -4.8478854 0 -3.2909361 -3.9368052 + 25 1.0347886 -4.84473 0 -3.2929351 -3.8044469 +Loop time of 15.95 on 1 procs for 25 steps with 4000 atoms + +Performance: 270.846 tau/day, 1.567 timesteps/s +100.0% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 15.946 | 15.946 | 15.946 | 0.0 | 99.97 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.0015042 | 0.0015042 | 0.0015042 | 0.0 | 0.01 +Output | 0.00013781 | 0.00013781 | 0.00013781 | 0.0 | 0.00 +Modify | 0.0017776 | 0.0017776 | 0.0017776 | 0.0 | 0.01 +Other | | 0.0006771 | | | 0.00 + +Nlocal: 4000 ave 4000 max 4000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 10895 ave 10895 max 10895 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 640000 ave 640000 max 640000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 1.28e+06 ave 1.28e+06 max 1.28e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 1280000 +Ave neighs/atom = 320 +Neighbor list builds = 0 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:16 diff --git a/examples/atm/log.27Aug18.g++.4 b/examples/atm/log.27Aug18.g++.4 new file mode 100644 index 0000000000..d84f17ee2b --- /dev/null +++ b/examples/atm/log.27Aug18.g++.4 @@ -0,0 +1,100 @@ +LAMMPS (22 Aug 2018) +# Axilrod-Teller-Muto potential example + +variable x index 1 +variable y index 1 +variable z index 1 + +variable xx equal 10*$x +variable xx equal 10*1 +variable yy equal 10*$y +variable yy equal 10*1 +variable zz equal 10*$z +variable zz equal 10*1 + +units lj +atom_style atomic + +lattice fcc 0.65 +Lattice spacing in x,y,z = 1.83252 1.83252 1.83252 +region box block 0 ${xx} 0 ${yy} 0 ${zz} +region box block 0 10 0 ${yy} 0 ${zz} +region box block 0 10 0 10 0 ${zz} +region box block 0 10 0 10 0 10 +create_box 1 box +Created orthogonal box = (0 0 0) to (18.3252 18.3252 18.3252) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 4000 atoms + Time spent = 0.000900984 secs + +pair_style hybrid/overlay lj/cut 4.5 atm 4.5 2.5 +pair_coeff * * lj/cut 1.0 1.0 +pair_coeff * * atm * 0.072 + +mass * 1.0 +velocity all create 1.033 12345678 loop geom + +fix 1 all nvt temp 1.033 1.033 0.05 + +timestep 0.002 +thermo 5 + +run 25 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 4.8 + ghost atom cutoff = 4.8 + binsize = 2.4, bins = 8 8 8 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair lj/cut, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair atm, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.532 | 5.532 | 5.532 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.033 -4.8404387 0 -3.291326 -4.1332095 + 5 1.0337247 -4.8402263 0 -3.290027 -4.1207962 + 10 1.0355935 -4.8425889 0 -3.2895869 -4.0870158 + 15 1.0376519 -4.84599 0 -3.2899013 -4.0278711 + 20 1.0382257 -4.8478854 0 -3.2909361 -3.9368052 + 25 1.0347886 -4.84473 0 -3.2929351 -3.8044469 +Loop time of 4.34636 on 4 procs for 25 steps with 4000 atoms + +Performance: 993.935 tau/day, 5.752 timesteps/s +99.6% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 3.9977 | 4.1036 | 4.209 | 4.9 | 94.41 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.13588 | 0.24134 | 0.34722 | 20.4 | 5.55 +Output | 0.00013757 | 0.00015104 | 0.00016761 | 0.0 | 0.00 +Modify | 0.00087953 | 0.00091547 | 0.00095582 | 0.0 | 0.02 +Other | | 0.0003656 | | | 0.01 + +Nlocal: 1000 ave 1000 max 1000 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 5835 ave 5835 max 5835 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 160000 ave 160000 max 160000 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 320000 ave 320000 max 320000 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 1280000 +Ave neighs/atom = 320 +Neighbor list builds = 0 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:04 diff --git a/examples/body/data.cubes b/examples/body/data.cubes new file mode 100644 index 0000000000..c1323ca350 --- /dev/null +++ b/examples/body/data.cubes @@ -0,0 +1,76 @@ +LAMMPS data file for polygons: cubes, moment of inertia I = m edge^2/ 6 +2 atoms +2 bodies +1 atom types +0 6 xlo xhi +0 6 ylo yhi +0 6 zlo zhi + +Atoms + +1 1 1 1 1.5 1.5 1.5 +2 1 1 1 4.0 4.0 4.0 + +Bodies + +1 3 79 +8 12 6 +0.667 0.667 0.667 0 0 0 +1 1 1 +1 -1 1 +-1 -1 1 +-1 1 1 +1 1 -1 +1 -1 -1 +-1 -1 -1 +-1 1 -1 +0 1 +1 2 +2 3 +3 0 +4 5 +5 6 +6 7 +7 4 +0 4 +1 5 +2 6 +3 7 +0 1 2 3 +4 5 6 7 +0 1 5 4 +1 2 6 5 +2 3 7 6 +3 0 4 7 +0.5 +2 3 79 +8 12 6 +0.667 0.667 0.667 0 0 0 +1 1 1 +1 -1 1 +-1 -1 1 +-1 1 1 +1 1 -1 +1 -1 -1 +-1 -1 -1 +-1 1 -1 +0 1 +1 2 +2 3 +3 0 +4 5 +5 6 +6 7 +7 4 +0 4 +1 5 +2 6 +3 7 +0 1 2 3 +4 5 6 7 +0 1 5 4 +1 2 6 5 +2 3 7 6 +3 0 4 7 +0.5 + diff --git a/examples/body/data.squares b/examples/body/data.squares new file mode 100755 index 0000000000..6b198fd422 --- /dev/null +++ b/examples/body/data.squares @@ -0,0 +1,32 @@ +LAMMPS data file for polygons: squares of edge length L: Izz = 1/6mL^2 +2 atoms +2 bodies +1 atom types +0 12 xlo xhi +0 12 ylo yhi +-0.5 0.5 zlo zhi + +Atoms + +1 1 1 1 4 5 0 +2 1 1 1 9 6 0 + +Bodies + +1 1 19 +4 +1 1 2.67 0 0 0 +-2 -2 0 +-2 2 0 +2 2 0 +2 -2 0 +0.5 +2 1 19 +4 +1 1 2.67 0 0 0 +-2 -2 0 +-2 2 0 +2 2 0 +2 -2 0 +0.5 + diff --git a/examples/body/in.body b/examples/body/in.body index 5879ed5e45..815b853154 100644 --- a/examples/body/in.body +++ b/examples/body/in.body @@ -8,7 +8,7 @@ read_data data.body velocity all create 1.44 87287 loop geom -pair_style body 5.0 +pair_style body/nparticle 5.0 pair_coeff * * 1.0 1.0 neighbor 0.5 bin diff --git a/examples/body/in.cubes b/examples/body/in.cubes new file mode 100644 index 0000000000..a22599fe96 --- /dev/null +++ b/examples/body/in.cubes @@ -0,0 +1,53 @@ +# 3d rounded cubes + +variable r index 3 +variable steps index 10000 + +units lj +dimension 3 + +atom_style body rounded/polyhedron 1 10 + +read_data data.cubes + +replicate $r $r $r + +velocity all create 1.2 187287 dist gaussian mom yes rot yes + +variable cut_inner equal 0.5 +variable k_n equal 100 +variable k_na equal 1 +variable c_n equal 20 +variable c_t equal 5 +variable mu equal 0 +variable A_ua equal 1 + +pair_style body/rounded/polyhedron ${c_n} ${c_t} ${mu} ${A_ua} ${cut_inner} +pair_coeff * * ${k_n} ${k_na} + +comm_modify vel yes + +neighbor 0.5 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.001 + +#fix 1 all nve/body +fix 1 all nvt/body temp 1.2 1.2 0.1 +#fix 1 all npt/body temp 1.2 1.2 0.1 iso 0.002 0.02 1.0 + +compute p2 all pressure 1_temp + +#compute 1 all body/local id 1 2 3 +#dump 1 all local 1000 dump.* index c_1[1] c_1[2] c_1[3] c_1[4] + +#dump 2 all image 1000 image.*.jpg type type & +# zoom 1.5 adiam 1.5 body type 0 0 view 60 15 +#dump_modify 2 pad 6 + +thermo_style custom step ke pe etotal c_p2 c_1_temp + +thermo 1000 + +run ${steps} + diff --git a/examples/body/in.pour3d b/examples/body/in.pour3d new file mode 100644 index 0000000000..bcba950e59 --- /dev/null +++ b/examples/body/in.pour3d @@ -0,0 +1,57 @@ +# pouring 3d rounded polyhedron bodies + +variable steps index 6000 + +units lj +boundary p p fm +comm_modify vel yes + +atom_style body rounded/polyhedron 1 8 +atom_modify map array + +region reg block 0 50 0 50 0 50 units box +create_box 4 reg + +variable cut_inner equal 0.5 +variable k_n equal 100 +variable k_na equal 5 +variable c_n equal 20 +variable c_t equal 5 +variable mu equal 0 +variable A_ua equal 1 + +pair_style body/rounded/polyhedron ${c_n} ${c_t} ${mu} ${A_ua} ${cut_inner} +pair_coeff * * ${k_n} ${k_na} + +neighbor 0.5 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.001 + +fix 1 all nve/body +fix 2 all gravity 1.0 spherical 0.0 -180.0 + +molecule object molecule.cube molecule.tetra toff 1 & + molecule.rod3d toff 2 molecule.point3d toff 3 + +region slab block 5 45 5 45 25 35 units box +fix ins all pour 500 0 4767548 vol 0.4 10 region slab mol object & + molfrac 0.25 0.25 0.25 0.25 + +fix 4 all wall/body/polyhedron 2000 50 50 zplane 0.0 NULL + +#compute 1 all body/local type 1 2 3 +#dump 1 all local 1000 dump.polyhedron index c_1[1] c_1[2] c_1[3] c_1[4] +#dump 10 all custom 1000 tmp.dump id type x y z radius + +thermo_style custom step atoms ke pe etotal press + +thermo 1000 + +#dump 2 all image 500 image.*.jpg type type & +# zoom 1.5 adiam 1.5 body type 0 0 view 75 15 +#dump_modify 2 pad 6 + +run ${steps} + + diff --git a/examples/body/in.squares b/examples/body/in.squares new file mode 100755 index 0000000000..3b05b5cead --- /dev/null +++ b/examples/body/in.squares @@ -0,0 +1,55 @@ +# 2d rounded polygon bodies + +variable r index 4 +variable steps index 100000 +variable T index 0.5 +variable P index 0.1 +variable seed index 980411 + +units lj +dimension 2 + +atom_style body rounded/polygon 1 6 +atom_modify map array +read_data data.squares + +replicate $r $r 1 + +velocity all create $T ${seed} dist gaussian mom yes rot yes + +variable cut_inner equal 0.5 +variable k_n equal 100 +variable k_na equal 2 +variable c_n equal 1 +variable c_t equal 1 +variable mu equal 0.1 +variable delta_ua equal 0.5 + +pair_style body/rounded/polygon ${c_n} ${c_t} ${mu} ${delta_ua} ${cut_inner} +pair_coeff * * ${k_n} ${k_na} + +comm_modify vel yes + +neighbor 0.5 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.001 + +#fix 1 all nve/body +#fix 1 all nvt/body temp $T $T 1.0 +fix 1 all npt/body temp $T $T 1.0 x 0.001 $P 1.0 & + y 0.001 $P 1.0 couple xy fixedpoint 0 0 0 + +fix 2 all enforce2d + +#compute 1 all body/local id 1 2 3 +#dump 1 all local 100000 dump.polygon.* index c_1[1] c_1[2] c_1[3] c_1[4] + +thermo_style custom step ke pe etotal press +thermo 1000 + +#dump 2 all image 10000 image.*.jpg type type zoom 2.0 & +# adiam 1.5 body type 0 0 +#dump_modify 2 pad 6 + +run ${steps} diff --git a/examples/body/in.wall2d b/examples/body/in.wall2d new file mode 100755 index 0000000000..04e7f31cb6 --- /dev/null +++ b/examples/body/in.wall2d @@ -0,0 +1,57 @@ +# 2d rounded polygon bodies + +variable r index 4 +variable steps index 100000 +variable T index 0.5 +variable P index 0.1 +variable seed index 980411 + +units lj +dimension 2 + +atom_style body rounded/polygon 1 6 +atom_modify map array +read_data data.squares + +replicate $r $r 1 + +velocity all create $T ${seed} dist gaussian mom yes rot yes + +change_box all boundary p f p + +variable cut_inner equal 0.5 +variable k_n equal 100 +variable k_na equal 2 +variable c_n equal 0.1 +variable c_t equal 0.1 +variable mu equal 0.1 +variable delta_ua equal 0.5 + +pair_style body/rounded/polygon ${c_n} ${c_t} ${mu} ${delta_ua} ${cut_inner} +pair_coeff * * ${k_n} ${k_na} + +comm_modify vel yes + +neighbor 0.5 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.001 + +#fix 1 all nve/body +#fix 1 all nvt/body temp $T $T 1.0 +fix 1 all npt/body temp $T $T 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0 + +fix 2 all enforce2d +fix 3 all wall/body/polygon 2000 50 50 yplane 0.0 48.0 + +#compute 1 all body/local id 1 2 3 +#dump 1 all local 100000 dump.polygon.* index c_1[1] c_1[2] c_1[3] c_1[4] + +thermo_style custom step ke pe etotal press +thermo 1000 + +#dump 2 all image 10000 image.*.jpg type type zoom 2.0 & +# adiam 1.5 body type 0 0 +#dump_modify 2 pad 6 + +run ${steps} diff --git a/examples/body/log.9Jul18.body.cubes.g++.1 b/examples/body/log.9Jul18.body.cubes.g++.1 new file mode 100644 index 0000000000..c9a799c0b5 --- /dev/null +++ b/examples/body/log.9Jul18.body.cubes.g++.1 @@ -0,0 +1,125 @@ +LAMMPS (29 Jun 2018) +# 3d rounded cubes + +variable r index 3 +variable steps index 10000 + +units lj +dimension 3 + +atom_style body rounded/polyhedron 1 10 + +read_data data.cubes + orthogonal box = (0 0 0) to (6 6 6) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 2 atoms + 2 bodies + +replicate $r $r $r +replicate 3 $r $r +replicate 3 3 $r +replicate 3 3 3 + orthogonal box = (0 0 0) to (18 18 18) + 1 by 1 by 1 MPI processor grid + 54 atoms + Time spent = 0.000217915 secs + +velocity all create 1.2 187287 dist gaussian mom yes rot yes + +variable cut_inner equal 0.5 +variable k_n equal 100 +variable k_na equal 1 +variable c_n equal 20 +variable c_t equal 5 +variable mu equal 0 +variable A_ua equal 1 + +pair_style body/rounded/polyhedron ${c_n} ${c_t} ${mu} ${A_ua} ${cut_inner} +pair_style body/rounded/polyhedron 20 ${c_t} ${mu} ${A_ua} ${cut_inner} +pair_style body/rounded/polyhedron 20 5 ${mu} ${A_ua} ${cut_inner} +pair_style body/rounded/polyhedron 20 5 0 ${A_ua} ${cut_inner} +pair_style body/rounded/polyhedron 20 5 0 1 ${cut_inner} +pair_style body/rounded/polyhedron 20 5 0 1 0.5 +pair_coeff * * ${k_n} ${k_na} +pair_coeff * * 100 ${k_na} +pair_coeff * * 100 1 + +comm_modify vel yes + +neighbor 0.5 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.001 + +#fix 1 all nve/body +fix 1 all nvt/body temp 1.2 1.2 0.1 +#fix 1 all npt/body temp 1.2 1.2 0.1 iso 0.002 0.02 1.0 + +compute p2 all pressure 1_temp + +#compute 1 all body/local id 1 2 3 +#dump 1 all local 1000 dump.* index c_1[1] c_1[2] c_1[3] c_1[4] + +#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 adiam 1.5 body type 0 0 view 60 15 +#dump_modify 2 pad 6 + +thermo_style custom step ke pe etotal c_p2 c_1_temp + +thermo 1000 + +run ${steps} +run 10000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 3.9641 + ghost atom cutoff = 3.9641 + binsize = 1.98205, bins = 10 10 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair body/rounded/polyhedron, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.952 | 4.952 | 4.952 Mbytes +Step KinEng PotEng TotEng c_p2 c_1_temp + 0 1.7666667 0 1.7666667 0.01090535 0.59439252 + 1000 3.1462962 0.17392649 3.3202227 0.02361912 1.1654694 + 2000 2.9311648 0.13836102 3.0695258 0.021748224 1.1950624 + 3000 3.090491 0.16511199 3.255603 0.018691142 1.23672 + 4000 2.7401565 0.17792155 2.9180781 0.015093853 1.1180839 + 5000 3.0880849 0.17587085 3.2639557 0.030563042 1.2831154 + 6000 3.2180776 0.19732251 3.4154001 0.028338151 1.258839 + 7000 2.9514882 0.25088882 3.202377 0.025296925 1.1746326 + 8000 3.0101226 0.28825968 3.2983823 0.027273454 1.2138056 + 9000 3.0164253 0.1901733 3.2065986 0.033228915 1.3095914 + 10000 2.3780401 0.34082434 2.7188644 0.031838531 1.0208679 +Loop time of 38.5686 on 1 procs for 10000 steps with 54 atoms + +Performance: 22401.653 tau/day, 259.278 timesteps/s +100.0% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 38.426 | 38.426 | 38.426 | 0.0 | 99.63 +Neigh | 0.0043154 | 0.0043154 | 0.0043154 | 0.0 | 0.01 +Comm | 0.047616 | 0.047616 | 0.047616 | 0.0 | 0.12 +Output | 0.00017595 | 0.00017595 | 0.00017595 | 0.0 | 0.00 +Modify | 0.082948 | 0.082948 | 0.082948 | 0.0 | 0.22 +Other | | 0.007761 | | | 0.02 + +Nlocal: 54 ave 54 max 54 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 96 ave 96 max 96 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 100 ave 100 max 100 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 100 +Ave neighs/atom = 1.85185 +Neighbor list builds = 268 +Dangerous builds = 0 + +Total wall time: 0:00:38 diff --git a/examples/body/log.9Jul18.body.cubes.g++.4 b/examples/body/log.9Jul18.body.cubes.g++.4 new file mode 100644 index 0000000000..e2407e9725 --- /dev/null +++ b/examples/body/log.9Jul18.body.cubes.g++.4 @@ -0,0 +1,125 @@ +LAMMPS (29 Jun 2018) +# 3d rounded cubes + +variable r index 3 +variable steps index 10000 + +units lj +dimension 3 + +atom_style body rounded/polyhedron 1 10 + +read_data data.cubes + orthogonal box = (0 0 0) to (6 6 6) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 2 atoms + 2 bodies + +replicate $r $r $r +replicate 3 $r $r +replicate 3 3 $r +replicate 3 3 3 + orthogonal box = (0 0 0) to (18 18 18) + 1 by 2 by 2 MPI processor grid + 54 atoms + Time spent = 0.00103807 secs + +velocity all create 1.2 187287 dist gaussian mom yes rot yes + +variable cut_inner equal 0.5 +variable k_n equal 100 +variable k_na equal 1 +variable c_n equal 20 +variable c_t equal 5 +variable mu equal 0 +variable A_ua equal 1 + +pair_style body/rounded/polyhedron ${c_n} ${c_t} ${mu} ${A_ua} ${cut_inner} +pair_style body/rounded/polyhedron 20 ${c_t} ${mu} ${A_ua} ${cut_inner} +pair_style body/rounded/polyhedron 20 5 ${mu} ${A_ua} ${cut_inner} +pair_style body/rounded/polyhedron 20 5 0 ${A_ua} ${cut_inner} +pair_style body/rounded/polyhedron 20 5 0 1 ${cut_inner} +pair_style body/rounded/polyhedron 20 5 0 1 0.5 +pair_coeff * * ${k_n} ${k_na} +pair_coeff * * 100 ${k_na} +pair_coeff * * 100 1 + +comm_modify vel yes + +neighbor 0.5 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.001 + +#fix 1 all nve/body +fix 1 all nvt/body temp 1.2 1.2 0.1 +#fix 1 all npt/body temp 1.2 1.2 0.1 iso 0.002 0.02 1.0 + +compute p2 all pressure 1_temp + +#compute 1 all body/local id 1 2 3 +#dump 1 all local 1000 dump.* index c_1[1] c_1[2] c_1[3] c_1[4] + +#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 adiam 1.5 body type 0 0 view 60 15 +#dump_modify 2 pad 6 + +thermo_style custom step ke pe etotal c_p2 c_1_temp + +thermo 1000 + +run ${steps} +run 10000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 3.9641 + ghost atom cutoff = 3.9641 + binsize = 1.98205, bins = 10 10 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair body/rounded/polyhedron, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.879 | 5.068 | 5.256 Mbytes +Step KinEng PotEng TotEng c_p2 c_1_temp + 0 1.7666667 0 1.7666667 0.01090535 0.59439252 + 1000 3.1462962 0.17392649 3.3202227 0.02361912 1.1654694 + 2000 2.9311648 0.13836102 3.0695258 0.021748224 1.1950624 + 3000 3.090491 0.16511199 3.255603 0.018691142 1.23672 + 4000 2.7401565 0.17792155 2.9180781 0.015093853 1.1180839 + 5000 3.0880849 0.17587085 3.2639557 0.030563042 1.2831154 + 6000 3.2180776 0.19732251 3.4154001 0.028338151 1.258839 + 7000 2.9514882 0.25088882 3.202377 0.025296925 1.1746326 + 8000 3.0101226 0.28825968 3.2983823 0.027273454 1.2138056 + 9000 3.0164253 0.1901733 3.2065986 0.033228915 1.3095914 + 10000 2.3780401 0.34082434 2.7188644 0.031838531 1.0208679 +Loop time of 20.5306 on 4 procs for 10000 steps with 54 atoms + +Performance: 42083.509 tau/day, 487.078 timesteps/s +100.0% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 7.5288 | 10.878 | 19.952 | 159.0 | 52.98 +Neigh | 0.0014424 | 0.0016552 | 0.0021195 | 0.7 | 0.01 +Comm | 0.50623 | 9.5805 | 12.93 | 169.4 | 46.66 +Output | 0.00011921 | 0.00014341 | 0.00021386 | 0.0 | 0.00 +Modify | 0.044663 | 0.047684 | 0.05382 | 1.6 | 0.23 +Other | | 0.023 | | | 0.11 + +Nlocal: 13.5 ave 17 max 9 min +Histogram: 1 0 0 1 0 0 0 0 1 1 +Nghost: 63.5 ave 68 max 58 min +Histogram: 1 0 0 1 0 0 0 0 0 2 +Neighs: 25 ave 38 max 6 min +Histogram: 1 0 0 0 0 1 0 0 1 1 + +Total # of neighbors = 100 +Ave neighs/atom = 1.85185 +Neighbor list builds = 268 +Dangerous builds = 0 + +Total wall time: 0:00:20 diff --git a/examples/body/log.9Jul18.body.pour3d.g++.1 b/examples/body/log.9Jul18.body.pour3d.g++.1 new file mode 100644 index 0000000000..213dd2e18f --- /dev/null +++ b/examples/body/log.9Jul18.body.pour3d.g++.1 @@ -0,0 +1,138 @@ +LAMMPS (29 Jun 2018) +# pouring 3d rounded polyhedron bodies + +variable steps index 6000 + +units lj +boundary p p fm +comm_modify vel yes + +atom_style body rounded/polyhedron 1 8 +atom_modify map array + +region reg block 0 50 0 50 0 50 units box +create_box 4 reg +Created orthogonal box = (0 0 0) to (50 50 50) + 1 by 1 by 1 MPI processor grid + +variable cut_inner equal 0.5 +variable k_n equal 100 +variable k_na equal 5 +variable c_n equal 20 +variable c_t equal 5 +variable mu equal 0 +variable A_ua equal 1 + +pair_style body/rounded/polyhedron ${c_n} ${c_t} ${mu} ${A_ua} ${cut_inner} +pair_style body/rounded/polyhedron 20 ${c_t} ${mu} ${A_ua} ${cut_inner} +pair_style body/rounded/polyhedron 20 5 ${mu} ${A_ua} ${cut_inner} +pair_style body/rounded/polyhedron 20 5 0 ${A_ua} ${cut_inner} +pair_style body/rounded/polyhedron 20 5 0 1 ${cut_inner} +pair_style body/rounded/polyhedron 20 5 0 1 0.5 +pair_coeff * * ${k_n} ${k_na} +pair_coeff * * 100 ${k_na} +pair_coeff * * 100 5 + +neighbor 0.5 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.001 + +fix 1 all nve/body +fix 2 all gravity 1.0 spherical 0.0 -180.0 + +molecule object molecule.cube molecule.tetra toff 1 molecule.rod3d toff 2 molecule.point3d toff 3 +Read molecule object: + 1 atoms with max type 1 + 0 bonds with max type 0 + 0 angles with max type 0 + 0 dihedrals with max type 0 + 0 impropers with max type 0 +Read molecule object: + 1 atoms with max type 2 + 0 bonds with max type 0 + 0 angles with max type 0 + 0 dihedrals with max type 0 + 0 impropers with max type 0 +Read molecule object: + 1 atoms with max type 3 + 0 bonds with max type 0 + 0 angles with max type 0 + 0 dihedrals with max type 0 + 0 impropers with max type 0 +Read molecule object: + 1 atoms with max type 4 + 0 bonds with max type 0 + 0 angles with max type 0 + 0 dihedrals with max type 0 + 0 impropers with max type 0 + +region slab block 5 45 5 45 25 35 units box +fix ins all pour 500 0 4767548 vol 0.4 10 region slab mol object molfrac 0.25 0.25 0.25 0.25 +Particle insertion: 134 every 4472 steps, 500 by step 13417 + +fix 4 all wall/body/polyhedron 2000 50 50 zplane 0.0 NULL + +#compute 1 all body/local type 1 2 3 +#dump 1 all local 1000 dump.polyhedron index c_1[1] c_1[2] c_1[3] c_1[4] +#dump 10 all custom 1000 tmp.dump id type x y z radius + +thermo_style custom step atoms ke pe etotal press + +thermo 1000 + +#dump 2 all image 500 image.*.jpg type type # zoom 1.5 adiam 1.5 body type 0 0 view 75 15 +#dump_modify 2 pad 6 + +run ${steps} +run 6000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5 + ghost atom cutoff = 5 + binsize = 2.5, bins = 20 20 20 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair body/rounded/polyhedron, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 0.5065 | 0.5065 | 0.5065 Mbytes +Step Atoms KinEng PotEng TotEng Press + 0 0 -0 0 0 0 + 1000 134 -0 0.00083010524 0.00083010524 -2.1515152e-06 + 2000 134 -0 -0.00069962476 -0.00069962476 -1.4170663e-08 + 3000 134 -0 -0.00069962687 -0.00069962687 -4.1478181e-11 + 4000 134 -0 -0.00069962687 -0.00069962687 -1.2141026e-13 + 5000 268 -0 0.014969705 0.014969705 3.0797164e-05 + 6000 268 -0 0.042467887 0.042467887 0.00056148005 +Loop time of 0.634737 on 1 procs for 6000 steps with 268 atoms + +Performance: 816716.196 tau/day, 9452.734 timesteps/s +100.0% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.41391 | 0.41391 | 0.41391 | 0.0 | 65.21 +Neigh | 0.010547 | 0.010547 | 0.010547 | 0.0 | 1.66 +Comm | 0.0030921 | 0.0030921 | 0.0030921 | 0.0 | 0.49 +Output | 0.00011492 | 0.00011492 | 0.00011492 | 0.0 | 0.02 +Modify | 0.19736 | 0.19736 | 0.19736 | 0.0 | 31.09 +Other | | 0.009719 | | | 1.53 + +Nlocal: 268 ave 268 max 268 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 3 ave 3 max 3 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 68 ave 68 max 68 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 68 +Ave neighs/atom = 0.253731 +Neighbor list builds = 168 +Dangerous builds = 0 + + +Total wall time: 0:00:00 diff --git a/examples/body/log.9Jul18.body.squares.g++.1 b/examples/body/log.9Jul18.body.squares.g++.1 new file mode 100644 index 0000000000..7b539797bd --- /dev/null +++ b/examples/body/log.9Jul18.body.squares.g++.1 @@ -0,0 +1,221 @@ +LAMMPS (29 Jun 2018) +# 2d rounded polygon bodies + +variable r index 4 +variable steps index 100000 +variable T index 0.5 +variable P index 0.1 +variable seed index 980411 + +units lj +dimension 2 + +atom_style body rounded/polygon 1 6 +atom_modify map array +read_data data.squares + orthogonal box = (0 0 -0.5) to (12 12 0.5) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 2 atoms + 2 bodies + +replicate $r $r 1 +replicate 4 $r 1 +replicate 4 4 1 + orthogonal box = (0 0 -0.5) to (48 48 0.5) + 1 by 1 by 1 MPI processor grid + 32 atoms + Time spent = 0.00020504 secs + +velocity all create $T ${seed} dist gaussian mom yes rot yes +velocity all create 0.5 ${seed} dist gaussian mom yes rot yes +velocity all create 0.5 980411 dist gaussian mom yes rot yes + +variable cut_inner equal 0.5 +variable k_n equal 100 +variable k_na equal 2 +variable c_n equal 1 +variable c_t equal 1 +variable mu equal 0.1 +variable delta_ua equal 0.5 + +pair_style body/rounded/polygon ${c_n} ${c_t} ${mu} ${delta_ua} ${cut_inner} +pair_style body/rounded/polygon 1 ${c_t} ${mu} ${delta_ua} ${cut_inner} +pair_style body/rounded/polygon 1 1 ${mu} ${delta_ua} ${cut_inner} +pair_style body/rounded/polygon 1 1 0.1 ${delta_ua} ${cut_inner} +pair_style body/rounded/polygon 1 1 0.1 0.5 ${cut_inner} +pair_style body/rounded/polygon 1 1 0.1 0.5 0.5 +pair_coeff * * ${k_n} ${k_na} +pair_coeff * * 100 ${k_na} +pair_coeff * * 100 2 + +comm_modify vel yes + +neighbor 0.5 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.001 + +#fix 1 all nve/body +#fix 1 all nvt/body temp $T $T 1.0 +fix 1 all npt/body temp $T $T 1.0 x 0.001 $P 1.0 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0 +fix 1 all npt/body temp 0.5 $T 1.0 x 0.001 $P 1.0 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0 +fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 $P 1.0 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0 +fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0 +fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0 y 0.001 0.1 1.0 couple xy fixedpoint 0 0 0 + +fix 2 all enforce2d + +#compute 1 all body/local id 1 2 3 +#dump 1 all local 100000 dump.polygon.* index c_1[1] c_1[2] c_1[3] c_1[4] + +thermo_style custom step ke pe etotal press +thermo 1000 + +#dump 2 all image 10000 image.*.jpg type type zoom 2.0 # adiam 1.5 body type 0 0 +#dump_modify 2 pad 6 + +run ${steps} +run 100000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.15685 + ghost atom cutoff = 6.15685 + binsize = 3.07843, bins = 16 16 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair body/rounded/polygon, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.781 | 4.781 | 4.781 Mbytes +Step KinEng PotEng TotEng Press + 0 0.484375 0.25 0.734375 0.0067274306 + 1000 0.39423376 0.0017918048 0.39602557 0.0021941612 + 2000 0.42284177 0.01346585 0.43630762 0.0029377883 + 3000 0.58154405 0.011321689 0.59286574 0.003667871 + 4000 0.73518304 0.034603175 0.76978621 0.0018689207 + 5000 0.84367476 0.025292163 0.86896692 0.0089161373 + 6000 0.70803236 0.0085631016 0.71659546 0.0045552895 + 7000 0.56206452 0.10453031 0.66659483 0.010255161 + 8000 0.64538994 0.088817673 0.73420761 0.0037633655 + 9000 0.90540819 0.063696004 0.96910419 0.0077673359 + 10000 0.68632042 0.093265016 0.77958544 0.0057864838 + 11000 0.59118074 0.025654748 0.61683549 0.012518759 + 12000 0.67522767 0.038176401 0.71340407 0.01741153 + 13000 0.7644843 0.10429844 0.86878274 0.013161339 + 14000 0.56152694 0.067836655 0.62936359 0.016852121 + 15000 0.41895506 0.019513348 0.43846841 0.015225695 + 16000 0.55799421 0.1564559 0.71445011 0.011703561 + 17000 0.59391964 0.034450221 0.62836986 0.026215002 + 18000 0.75911858 0.030885726 0.7900043 0.018396366 + 19000 0.64417995 0.12110912 0.76528907 0.010247952 + 20000 0.57751435 0.16965651 0.74717086 0.023392323 + 21000 0.7613368 0.13405354 0.89539034 0.021498982 + 22000 0.57676692 0.18011879 0.75688571 0.024469161 + 23000 0.54043723 0.11842026 0.65885749 0.019799067 + 24000 0.62276061 0.038967924 0.66172853 0.019080086 + 25000 0.53157536 0.11651937 0.64809473 0.017019298 + 26000 0.72213293 0.039012448 0.76114538 0.015434904 + 27000 0.62157832 0.13697494 0.75855326 0.028711011 + 28000 0.41323738 0.16301101 0.57624839 0.041792632 + 29000 0.45774328 0.17569066 0.63343394 0.019975231 + 30000 0.78901796 0.099791386 0.88880934 0.024116947 + 31000 0.85205397 0.11977547 0.97182945 0.026667489 + 32000 0.37137095 0.1232622 0.49463315 0.00087637364 + 33000 0.26860871 0.26056381 0.52917252 0.036110517 + 34000 0.3018636 0.21336905 0.51523265 0.040315549 + 35000 0.39915129 0.28245957 0.68161085 0.034876856 + 36000 0.25761236 0.2352705 0.49288286 0.022772767 + 37000 0.1071233 0.31692858 0.42405188 0.017994666 + 38000 0.083729577 0.28473145 0.36846103 -0.0045370431 + 39000 0.070355565 0.26682083 0.33717639 0.017921556 + 40000 0.075894079 0.20077896 0.27667304 0.014873186 + 41000 0.05891028 0.15989064 0.21880092 0.025547873 + 42000 0.1225107 0.16583605 0.28834675 0.038842785 + 43000 0.17049189 0.14323991 0.3137318 0.029550161 + 44000 0.26823939 0.15208257 0.42032196 0.028113612 + 45000 0.10172203 0.1729706 0.27469264 -0.013769913 + 46000 0.14841355 0.19085074 0.33926429 -0.00073741985 + 47000 0.27654927 0.19097937 0.46752864 0.04021431 + 48000 0.53432331 0.080769923 0.61509323 0.029932845 + 49000 0.69111634 0.13064951 0.82176585 0.028985406 + 50000 0.24520806 0.18317453 0.42838258 0.05179746 + 51000 0.23541368 0.14281364 0.37822732 0.071884238 + 52000 0.25464996 0.095730242 0.3503802 0.034488204 + 53000 0.53677633 0.1058745 0.64265084 0.059932498 + 54000 0.32970921 0.27979128 0.60950049 0.062869716 + 55000 0.49094054 0.096735015 0.58767556 0.04728005 + 56000 0.54398249 0.2216472 0.76562969 0.056712022 + 57000 0.60869068 0.2338422 0.84253288 0.077143302 + 58000 0.72175509 0.18687368 0.90862877 0.019357656 + 59000 0.79442757 0.092502981 0.88693055 0.066882632 + 60000 0.6810555 0.077699385 0.75875488 0.095975173 + 61000 0.63178834 0.05071143 0.68249977 0.043586668 + 62000 0.76589344 0.044615704 0.81050914 0.085718411 + 63000 0.84815889 0.030527848 0.87868674 0.053072795 + 64000 0.7309043 0.051938637 0.78284294 0.058887766 + 65000 0.62498816 0.034474465 0.65946262 0.068446407 + 66000 0.69817494 0.068546004 0.76672094 0.062634433 + 67000 0.86444275 0.010184259 0.87462701 0.073635055 + 68000 0.77820319 0.0079319524 0.78613515 0.090330925 + 69000 0.56938919 0.0092629332 0.57865213 0.061838729 + 70000 0.61870712 0.010047381 0.6287545 0.066501338 + 71000 0.71651803 0.0088366199 0.72535465 0.079136316 + 72000 0.76278925 0.008828151 0.77161741 0.063672771 + 73000 0.75447428 0.0083985526 0.76287283 0.078256913 + 74000 0.66185251 0.0091910052 0.67104351 0.069840511 + 75000 0.58458829 0.0097671568 0.59435544 0.076123422 + 76000 0.7487564 0.0100022 0.7587586 0.076171741 + 77000 0.89505465 0.009250681 0.90430533 0.074921699 + 78000 0.73738164 0.0092029279 0.74658457 0.078835344 + 79000 0.65735281 0.010099528 0.66745233 0.077940627 + 80000 0.70247542 0.010306464 0.71278189 0.079560093 + 81000 0.74839505 0.010199092 0.75859415 0.080835104 + 82000 0.75193767 0.010274058 0.76221173 0.081086684 + 83000 0.71392598 0.010495573 0.72442156 0.082746145 + 84000 0.58498928 0.011027388 0.59601667 0.08356465 + 85000 0.59022869 0.011729474 0.60195817 0.084519397 + 86000 0.81753578 0.011208964 0.82874475 0.085490261 + 87000 0.83480682 0.010542579 0.8453494 0.086268527 + 88000 0.67322538 0.011170734 0.68439611 0.08751623 + 89000 0.62637389 0.012033316 0.6384072 0.088548094 + 90000 0.92828557 0.011750388 0.94003596 0.089199823 + 91000 0.96072564 0.010324509 0.97105015 0.090204803 + 92000 0.72105071 0.011484152 0.73253486 0.09140819 + 93000 0.65762527 0.012558219 0.67018349 0.092453474 + 94000 0.73991591 0.01261909 0.752535 0.093373477 + 95000 0.91791653 0.011980455 0.92989699 0.094182136 + 96000 0.76562561 0.011807085 0.7774327 0.095323684 + 97000 0.57292104 0.013610205 0.58653124 0.096505977 + 98000 0.68141076 0.013863204 0.69527396 0.097380069 + 99000 0.82390969 0.013002341 0.83691203 0.098235926 + 100000 0.77639728 0.012989342 0.78938662 0.099274147 +Loop time of 3.88899 on 1 procs for 100000 steps with 32 atoms + +Performance: 2221655.884 tau/day, 25713.610 timesteps/s +99.9% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 3.056 | 3.056 | 3.056 | 0.0 | 78.58 +Neigh | 0.0051048 | 0.0051048 | 0.0051048 | 0.0 | 0.13 +Comm | 0.091444 | 0.091444 | 0.091444 | 0.0 | 2.35 +Output | 0.0011995 | 0.0011995 | 0.0011995 | 0.0 | 0.03 +Modify | 0.69909 | 0.69909 | 0.69909 | 0.0 | 17.98 +Other | | 0.03616 | | | 0.93 + +Nlocal: 32 ave 32 max 32 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 21 ave 21 max 21 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 57 ave 57 max 57 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 57 +Ave neighs/atom = 1.78125 +Neighbor list builds = 1445 +Dangerous builds = 0 +Total wall time: 0:00:03 diff --git a/examples/body/log.9Jul18.body.squares.g++.4 b/examples/body/log.9Jul18.body.squares.g++.4 new file mode 100644 index 0000000000..56d7734b7b --- /dev/null +++ b/examples/body/log.9Jul18.body.squares.g++.4 @@ -0,0 +1,221 @@ +LAMMPS (29 Jun 2018) +# 2d rounded polygon bodies + +variable r index 4 +variable steps index 100000 +variable T index 0.5 +variable P index 0.1 +variable seed index 980411 + +units lj +dimension 2 + +atom_style body rounded/polygon 1 6 +atom_modify map array +read_data data.squares + orthogonal box = (0 0 -0.5) to (12 12 0.5) + 2 by 2 by 1 MPI processor grid + reading atoms ... + 2 atoms + 2 bodies + +replicate $r $r 1 +replicate 4 $r 1 +replicate 4 4 1 + orthogonal box = (0 0 -0.5) to (48 48 0.5) + 2 by 2 by 1 MPI processor grid + 32 atoms + Time spent = 0.000324011 secs + +velocity all create $T ${seed} dist gaussian mom yes rot yes +velocity all create 0.5 ${seed} dist gaussian mom yes rot yes +velocity all create 0.5 980411 dist gaussian mom yes rot yes + +variable cut_inner equal 0.5 +variable k_n equal 100 +variable k_na equal 2 +variable c_n equal 1 +variable c_t equal 1 +variable mu equal 0.1 +variable delta_ua equal 0.5 + +pair_style body/rounded/polygon ${c_n} ${c_t} ${mu} ${delta_ua} ${cut_inner} +pair_style body/rounded/polygon 1 ${c_t} ${mu} ${delta_ua} ${cut_inner} +pair_style body/rounded/polygon 1 1 ${mu} ${delta_ua} ${cut_inner} +pair_style body/rounded/polygon 1 1 0.1 ${delta_ua} ${cut_inner} +pair_style body/rounded/polygon 1 1 0.1 0.5 ${cut_inner} +pair_style body/rounded/polygon 1 1 0.1 0.5 0.5 +pair_coeff * * ${k_n} ${k_na} +pair_coeff * * 100 ${k_na} +pair_coeff * * 100 2 + +comm_modify vel yes + +neighbor 0.5 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.001 + +#fix 1 all nve/body +#fix 1 all nvt/body temp $T $T 1.0 +fix 1 all npt/body temp $T $T 1.0 x 0.001 $P 1.0 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0 +fix 1 all npt/body temp 0.5 $T 1.0 x 0.001 $P 1.0 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0 +fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 $P 1.0 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0 +fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0 +fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0 y 0.001 0.1 1.0 couple xy fixedpoint 0 0 0 + +fix 2 all enforce2d + +#compute 1 all body/local id 1 2 3 +#dump 1 all local 100000 dump.polygon.* index c_1[1] c_1[2] c_1[3] c_1[4] + +thermo_style custom step ke pe etotal press +thermo 1000 + +#dump 2 all image 10000 image.*.jpg type type zoom 2.0 # adiam 1.5 body type 0 0 +#dump_modify 2 pad 6 + +run ${steps} +run 100000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.15685 + ghost atom cutoff = 6.15685 + binsize = 3.07843, bins = 16 16 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair body/rounded/polygon, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.774 | 4.774 | 4.774 Mbytes +Step KinEng PotEng TotEng Press + 0 0.484375 0.25 0.734375 0.0067274306 + 1000 0.39423376 0.0017918048 0.39602557 0.0021941612 + 2000 0.42284177 0.01346585 0.43630762 0.0029377883 + 3000 0.58154405 0.011321689 0.59286574 0.003667871 + 4000 0.73518304 0.034603175 0.76978621 0.0018689207 + 5000 0.84367476 0.025292163 0.86896692 0.0089161373 + 6000 0.70803236 0.0085631016 0.71659546 0.0045552895 + 7000 0.56206452 0.10453031 0.66659483 0.010255161 + 8000 0.64538994 0.088817673 0.73420761 0.0037633655 + 9000 0.90540819 0.063696004 0.96910419 0.0077673359 + 10000 0.68632042 0.093265016 0.77958544 0.0057864837 + 11000 0.59118074 0.025654748 0.61683549 0.012518759 + 12000 0.67522767 0.038176401 0.71340407 0.01741153 + 13000 0.7644843 0.10429844 0.86878274 0.013161339 + 14000 0.56152694 0.067836656 0.6293636 0.016852113 + 15000 0.41895505 0.019513353 0.43846841 0.015225696 + 16000 0.55799443 0.15645637 0.7144508 0.011703646 + 17000 0.59385248 0.03451986 0.62837234 0.025482966 + 18000 0.75902169 0.031103586 0.79012527 0.018263354 + 19000 0.64266826 0.12535314 0.76802141 0.014884119 + 20000 0.57836261 0.16581188 0.74417449 0.024667165 + 21000 0.78281936 0.11877527 0.90159464 -0.0090089213 + 22000 0.5312006 0.13300874 0.66420934 0.025797278 + 23000 0.56458861 0.084369128 0.64895774 0.024630917 + 24000 0.65126875 0.06122992 0.71249867 0.034377198 + 25000 0.55173441 0.15694886 0.70868327 0.021634086 + 26000 0.59121615 0.17071182 0.76192797 0.024758366 + 27000 0.6394843 0.17442949 0.81391378 0.034919937 + 28000 0.31144221 0.41243036 0.72387256 0.074115225 + 29000 0.13516917 0.3075419 0.44271107 0.023861298 + 30000 0.14094934 0.24407203 0.38502137 0.037030438 + 31000 0.26313749 0.087395422 0.35053291 0.042347005 + 32000 0.51602457 0.063012079 0.57903664 0.018550299 + 33000 0.55628829 0.200213 0.75650129 0.026507686 + 34000 0.97399408 0.082504517 1.0564986 0.037889878 + 35000 0.64710533 0.17662002 0.82372535 0.058295508 + 36000 0.45769083 0.08241194 0.54010277 0.014957415 + 37000 0.72850105 0.053874061 0.78237512 0.037194593 + 38000 0.44177995 0.28939498 0.73117493 0.045194029 + 39000 0.46828451 0.077630686 0.54591519 0.089849009 + 40000 0.46786451 0.092828423 0.56069294 0.028042052 + 41000 0.71861856 0.097085715 0.81570427 0.036473296 + 42000 0.74121021 0.10553127 0.84674148 0.054058843 + 43000 0.62945489 0.12770673 0.75716161 0.047267994 + 44000 0.49900638 0.085150056 0.58415644 0.054798793 + 45000 0.70199572 0.063415877 0.7654116 0.038363546 + 46000 0.49513142 0.10649384 0.60162526 0.059392561 + 47000 0.3858898 0.079458749 0.46534855 0.051825764 + 48000 0.62585854 0.028585902 0.65444444 0.054074424 + 49000 0.65934482 0.51865062 1.1779954 -0.035272836 + 50000 0.5420438 0.082056756 0.62410056 0.031187494 + 51000 0.36685223 0.14224019 0.50909241 0.073790397 + 52000 0.19044627 0.15368389 0.34413016 0.059034266 + 53000 0.26847678 0.075693324 0.3441701 0.032276915 + 54000 0.3593711 0.19034549 0.54971659 0.070827883 + 55000 0.21659198 0.1929074 0.40949939 0.035916364 + 56000 0.28242715 0.12313241 0.40555956 0.062083926 + 57000 0.34067475 0.14711992 0.48779467 0.059321458 + 58000 0.4842796 0.16143425 0.64571385 0.059048247 + 59000 0.84438871 0.076546849 0.92093556 0.048046901 + 60000 0.92794849 0.054331626 0.98228012 0.058392272 + 61000 0.6916736 0.076168342 0.76784194 0.058654987 + 62000 0.63317965 0.094506389 0.72768604 0.061044719 + 63000 0.63317266 0.038785593 0.67195825 0.097236147 + 64000 0.81696668 0.121811 0.93877769 0.064935373 + 65000 0.82644758 0.25188344 1.078331 0.093352359 + 66000 0.64975019 0.17930857 0.82905876 0.058805254 + 67000 0.63487678 0.16877059 0.80364737 0.070254696 + 68000 0.79140717 0.11631004 0.9077172 0.064646394 + 69000 0.85687272 0.057835331 0.91470805 0.071057291 + 70000 0.67785976 0.040686768 0.71854653 0.074687222 + 71000 0.60594577 0.032193155 0.63813893 0.069349268 + 72000 0.77586745 0.024068533 0.79993598 0.083394193 + 73000 0.88877625 0.025746326 0.91452258 0.081511105 + 74000 0.73507888 0.036574786 0.77165367 0.075360233 + 75000 0.68787782 0.042098622 0.72997644 0.068651098 + 76000 0.72515745 0.04360868 0.76876613 0.069594624 + 77000 0.77580944 0.041826702 0.81763614 0.071937144 + 78000 0.76640394 0.039285046 0.80568899 0.074274921 + 79000 0.62504309 0.039593585 0.66463667 0.076443295 + 80000 0.60001642 0.043468215 0.64348464 0.094547719 + 81000 0.82175037 0.045608873 0.86735924 0.080186295 + 82000 0.85783276 0.042692576 0.90052534 0.081576548 + 83000 0.71367707 0.042172193 0.75584926 0.08256625 + 84000 0.68532406 0.044724759 0.73004882 0.083672013 + 85000 0.72576789 0.046982462 0.77275035 0.084789331 + 86000 0.75597701 0.04765086 0.80362787 0.085758056 + 87000 0.74190598 0.047629096 0.78953507 0.086679976 + 88000 0.60967704 0.049906172 0.65958321 0.085526191 + 89000 0.54490288 0.054768238 0.59967112 0.090604027 + 90000 0.75398341 0.057153453 0.81113686 0.091900858 + 91000 0.84577472 0.052753512 0.89852823 0.091913909 + 92000 0.7176235 0.050677427 0.76830093 0.092032507 + 93000 0.61699446 0.054097013 0.67109147 0.092071275 + 94000 0.76330752 0.057398618 0.82070614 0.092435043 + 95000 0.98754458 0.053801311 1.0413459 0.093526707 + 96000 0.7405897 0.052135628 0.79272533 0.095011929 + 97000 0.65587599 0.057011962 0.71288795 0.096692123 + 98000 0.72345634 0.060700171 0.78415651 0.097510345 + 99000 0.88283624 0.061795247 0.94463149 0.09799633 + 100000 0.86303812 0.058912988 0.92195111 0.09892993 +Loop time of 2.80074 on 4 procs for 100000 steps with 32 atoms + +Performance: 3084895.573 tau/day, 35704.810 timesteps/s +99.9% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.81169 | 0.89466 | 0.97669 | 8.4 | 31.94 +Neigh | 0.0017524 | 0.0018129 | 0.0018773 | 0.1 | 0.06 +Comm | 0.91307 | 0.99193 | 1.0691 | 7.3 | 35.42 +Output | 0.00076914 | 0.00093722 | 0.0013936 | 0.0 | 0.03 +Modify | 0.75335 | 0.75779 | 0.76346 | 0.4 | 27.06 +Other | | 0.1536 | | | 5.48 + +Nlocal: 8 ave 10 max 4 min +Histogram: 1 0 0 0 0 0 1 0 0 2 +Nghost: 17.25 ave 19 max 15 min +Histogram: 1 0 1 0 0 0 0 0 0 2 +Neighs: 13.5 ave 21 max 5 min +Histogram: 1 0 0 0 1 0 1 0 0 1 + +Total # of neighbors = 54 +Ave neighs/atom = 1.6875 +Neighbor list builds = 1443 +Dangerous builds = 0 +Total wall time: 0:00:02 diff --git a/examples/body/log.9Jul18.body.wall2d.g++.1 b/examples/body/log.9Jul18.body.wall2d.g++.1 new file mode 100644 index 0000000000..f22c366380 --- /dev/null +++ b/examples/body/log.9Jul18.body.wall2d.g++.1 @@ -0,0 +1,223 @@ +LAMMPS (29 Jun 2018) +# 2d rounded polygon bodies + +variable r index 4 +variable steps index 100000 +variable T index 0.5 +variable P index 0.1 +variable seed index 980411 + +units lj +dimension 2 + +atom_style body rounded/polygon 1 6 +atom_modify map array +read_data data.squares + orthogonal box = (0 0 -0.5) to (12 12 0.5) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 2 atoms + 2 bodies + +replicate $r $r 1 +replicate 4 $r 1 +replicate 4 4 1 + orthogonal box = (0 0 -0.5) to (48 48 0.5) + 1 by 1 by 1 MPI processor grid + 32 atoms + Time spent = 0.00029707 secs + +velocity all create $T ${seed} dist gaussian mom yes rot yes +velocity all create 0.5 ${seed} dist gaussian mom yes rot yes +velocity all create 0.5 980411 dist gaussian mom yes rot yes + +change_box all boundary p f p + +variable cut_inner equal 0.5 +variable k_n equal 100 +variable k_na equal 2 +variable c_n equal 0.1 +variable c_t equal 0.1 +variable mu equal 0.1 +variable delta_ua equal 0.5 + +pair_style body/rounded/polygon ${c_n} ${c_t} ${mu} ${delta_ua} ${cut_inner} +pair_style body/rounded/polygon 0.1 ${c_t} ${mu} ${delta_ua} ${cut_inner} +pair_style body/rounded/polygon 0.1 0.1 ${mu} ${delta_ua} ${cut_inner} +pair_style body/rounded/polygon 0.1 0.1 0.1 ${delta_ua} ${cut_inner} +pair_style body/rounded/polygon 0.1 0.1 0.1 0.5 ${cut_inner} +pair_style body/rounded/polygon 0.1 0.1 0.1 0.5 0.5 +pair_coeff * * ${k_n} ${k_na} +pair_coeff * * 100 ${k_na} +pair_coeff * * 100 2 + +comm_modify vel yes + +neighbor 0.5 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.001 + +#fix 1 all nve/body +#fix 1 all nvt/body temp $T $T 1.0 +fix 1 all npt/body temp $T $T 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0 +fix 1 all npt/body temp 0.5 $T 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0 +fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0 +fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0 fixedpoint 0 0 0 + +fix 2 all enforce2d +fix 3 all wall/body/polygon 2000 50 50 yplane 0.0 48.0 + +#compute 1 all body/local id 1 2 3 +#dump 1 all local 100000 dump.polygon.* index c_1[1] c_1[2] c_1[3] c_1[4] + +thermo_style custom step ke pe etotal press +thermo 1000 + +#dump 2 all image 10000 image.*.jpg type type zoom 2.0 # adiam 1.5 body type 0 0 +#dump_modify 2 pad 6 + +run ${steps} +run 100000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.15685 + ghost atom cutoff = 6.15685 + binsize = 3.07843, bins = 16 16 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair body/rounded/polygon, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.771 | 4.771 | 4.771 Mbytes +Step KinEng PotEng TotEng Press + 0 0.484375 0.25 0.734375 0.0067274306 + 1000 0.49241101 0.0031318767 0.49554289 0.017768281 + 2000 0.56118632 0.0026068888 0.56379321 0.003410416 + 3000 0.75565115 0.025578366 0.78122951 0.0071862988 + 4000 0.72298647 0.093150646 0.81613712 0.003190158 + 5000 0.51684166 0.049164868 0.56600653 0.0096960168 + 6000 0.56627905 0.048132853 0.6144119 0.020733586 + 7000 0.58122129 0.018223718 0.59944501 0.0038160759 + 8000 0.64297977 0.025934821 0.66891459 0.0041091784 + 9000 0.41748404 0.0077890042 0.42527305 0.0039270065 + 10000 0.35738377 0.078487805 0.43587158 3.9079782e-05 + 11000 0.41529308 0.13619284 0.55148592 -0.0067482285 + 12000 0.43274718 0.071315497 0.50406268 0.007006378 + 13000 0.4748331 0.069904647 0.54473775 0.0010384372 + 14000 0.6287791 0.12721033 0.75598943 0.0047792448 + 15000 0.4692413 0.12344005 0.59268136 0.018033616 + 16000 0.43157074 0.14306789 0.57463862 0.042356676 + 17000 0.53085999 0.22126296 0.75212294 0.027509646 + 18000 0.52688968 0.13225282 0.6591425 0.0021558013 + 19000 0.55032328 0.12513047 0.67545375 0.025036251 + 20000 0.48465097 0.1431055 0.62775647 0.017193781 + 21000 0.53166734 0.21928574 0.75095307 0.011564317 + 22000 0.62177353 0.09296159 0.71473512 0.017660922 + 23000 0.6972939 0.12434123 0.82163514 0.024432327 + 24000 0.42767372 0.22152311 0.64919684 -0.013712449 + 25000 0.4816037 0.19272865 0.67433236 0.052386055 + 26000 0.72642579 0.19697046 0.92339625 0.020407694 + 27000 0.39649144 0.15058326 0.5470747 0.023705766 + 28000 0.44896324 0.18500106 0.6339643 -0.0089410286 + 29000 0.5565759 0.11085772 0.66743362 0.048437166 + 30000 0.58173584 0.21773281 0.79946865 0.0057357773 + 31000 0.49199415 0.23601982 0.72801397 0.046744152 + 32000 0.55665496 0.20542161 0.76207658 -0.0038756805 + 33000 0.62730739 0.24460524 0.87191263 0.045330682 + 34000 0.58107044 0.16395278 0.74502322 -0.0049496051 + 35000 0.56838849 0.21842922 0.78681771 0.0062086036 + 36000 0.45910273 0.28464172 0.74374445 -0.011700747 + 37000 0.37092037 0.27646862 0.647389 0.022305679 + 38000 0.7278047 0.30674438 1.0345491 0.07698342 + 39000 0.5132923 0.27395066 0.78724295 0.026898634 + 40000 0.62348649 0.24424644 0.86773293 0.039403899 + 41000 0.3658401 0.15512326 0.52096337 0.022559003 + 42000 0.4912253 0.35712978 0.84835508 -0.010336341 + 43000 0.70225957 0.36314638 1.0654059 0.004148866 + 44000 0.56958157 0.25488927 0.82447084 0.067537066 + 45000 0.45854352 0.30149439 0.76003791 -0.017002401 + 46000 0.62787247 0.34567995 0.97355242 0.11894801 + 47000 0.61348914 0.29378625 0.90727539 0.067873976 + 48000 0.71301829 0.34135284 1.0543711 0.021077736 + 49000 0.53520804 0.30593196 0.84113999 0.0059257647 + 50000 0.44966403 0.35370793 0.80337195 0.0020395669 + 51000 0.5236113 0.32296924 0.84658054 -0.051011506 + 52000 0.53905573 0.351771 0.89082672 0.013720106 + 53000 0.55978158 0.41293947 0.97272106 0.068558589 + 54000 0.52170459 0.2718066 0.7935112 0.0093138985 + 55000 0.61078876 0.43353897 1.0443277 0.045377392 + 56000 0.51300655 0.33182278 0.84482933 -0.018418487 + 57000 0.54882822 0.38380093 0.93262915 0.10249946 + 58000 0.72106212 0.45361279 1.1746749 0.030313481 + 59000 0.55871447 0.63823029 1.1969448 0.019079703 + 60000 0.49395192 0.58283102 1.0767829 0.0179349 + 61000 0.45991079 0.62540573 1.0853165 0.074398804 + 62000 0.4655788 0.60862262 1.0742014 0.11472976 + 63000 0.55634524 0.63069255 1.1870378 -0.0025676135 + 64000 0.57688903 0.45435264 1.0312417 0.0083813852 + 65000 0.57168922 0.42217005 0.99385927 0.044931269 + 66000 0.6206044 0.46727538 1.0878798 0.019686229 + 67000 0.61037155 0.41840109 1.0287726 0.0195109 + 68000 0.63848598 0.41305347 1.0515395 0.072940144 + 69000 0.49244916 0.3834095 0.87585866 0.07963677 + 70000 0.41847062 0.51907975 0.93755037 0.18447904 + 71000 0.45198986 0.52973709 0.98172695 0.078419371 + 72000 0.47064262 0.37808165 0.84872427 -0.00046308054 + 73000 0.6690143 0.37549359 1.0445079 0.061208432 + 74000 0.60444955 0.33779636 0.94224592 -0.068840321 + 75000 0.61762382 0.3916421 1.0092659 0.16253292 + 76000 0.63657961 0.50277989 1.1393595 0.013857508 + 77000 0.52524028 0.43597896 0.96121924 -0.03296482 + 78000 0.43803533 0.33172284 0.76975817 0.078763029 + 79000 0.67156089 0.55272177 1.2242827 0.080822223 + 80000 0.68678238 0.46061627 1.1473987 0.0027036992 + 81000 0.64956678 0.44959229 1.0991591 0.11201483 + 82000 0.51060477 0.43508342 0.9456882 0.028000608 + 83000 0.59550548 0.69026083 1.2857663 -0.0015809004 + 84000 0.64222145 0.38768816 1.0299096 0.014153173 + 85000 0.7661229 0.43445261 1.2005755 0.048034534 + 86000 0.60025257 0.53027929 1.1305319 0.0056865157 + 87000 0.46220939 0.47470035 0.93690974 0.075311946 + 88000 0.54123847 0.62899839 1.1702369 0.13260162 + 89000 0.61212272 0.6114241 1.2235468 0.033284822 + 90000 0.63924773 0.6916249 1.3308726 0.045088296 + 91000 0.49316865 0.51037033 1.003539 0.023203598 + 92000 0.57572123 0.43496319 1.0106844 0.297092 + 93000 0.65187559 0.56815972 1.2200353 0.1538215 + 94000 0.64107331 0.58948521 1.2305585 0.031117778 + 95000 0.64584158 0.6364688 1.2823104 0.096154676 + 96000 0.60509093 0.601487 1.2065779 0.03457172 + 97000 0.68837218 0.77974186 1.468114 0.17801164 + 98000 0.62725266 0.64137144 1.2686241 0.17449001 + 99000 0.46861221 0.67000291 1.1386151 0.2429588 + 100000 0.5879119 0.7140612 1.3019731 0.064634257 +Loop time of 2.50594 on 1 procs for 100000 steps with 32 atoms + +Performance: 3447804.126 tau/day, 39905.140 timesteps/s +100.0% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.5639 | 1.5639 | 1.5639 | 0.0 | 62.41 +Neigh | 0.0086911 | 0.0086911 | 0.0086911 | 0.0 | 0.35 +Comm | 0.058926 | 0.058926 | 0.058926 | 0.0 | 2.35 +Output | 0.0012379 | 0.0012379 | 0.0012379 | 0.0 | 0.05 +Modify | 0.83537 | 0.83537 | 0.83537 | 0.0 | 33.34 +Other | | 0.03781 | | | 1.51 + +Nlocal: 32 ave 32 max 32 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 20 ave 20 max 20 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 57 ave 57 max 57 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 57 +Ave neighs/atom = 1.78125 +Neighbor list builds = 2705 +Dangerous builds = 0 +Total wall time: 0:00:02 diff --git a/examples/body/log.9Jul18.body.wall2d.g++.4 b/examples/body/log.9Jul18.body.wall2d.g++.4 new file mode 100644 index 0000000000..7239fd4dcd --- /dev/null +++ b/examples/body/log.9Jul18.body.wall2d.g++.4 @@ -0,0 +1,223 @@ +LAMMPS (29 Jun 2018) +# 2d rounded polygon bodies + +variable r index 4 +variable steps index 100000 +variable T index 0.5 +variable P index 0.1 +variable seed index 980411 + +units lj +dimension 2 + +atom_style body rounded/polygon 1 6 +atom_modify map array +read_data data.squares + orthogonal box = (0 0 -0.5) to (12 12 0.5) + 2 by 2 by 1 MPI processor grid + reading atoms ... + 2 atoms + 2 bodies + +replicate $r $r 1 +replicate 4 $r 1 +replicate 4 4 1 + orthogonal box = (0 0 -0.5) to (48 48 0.5) + 2 by 2 by 1 MPI processor grid + 32 atoms + Time spent = 0.000386 secs + +velocity all create $T ${seed} dist gaussian mom yes rot yes +velocity all create 0.5 ${seed} dist gaussian mom yes rot yes +velocity all create 0.5 980411 dist gaussian mom yes rot yes + +change_box all boundary p f p + +variable cut_inner equal 0.5 +variable k_n equal 100 +variable k_na equal 2 +variable c_n equal 0.1 +variable c_t equal 0.1 +variable mu equal 0.1 +variable delta_ua equal 0.5 + +pair_style body/rounded/polygon ${c_n} ${c_t} ${mu} ${delta_ua} ${cut_inner} +pair_style body/rounded/polygon 0.1 ${c_t} ${mu} ${delta_ua} ${cut_inner} +pair_style body/rounded/polygon 0.1 0.1 ${mu} ${delta_ua} ${cut_inner} +pair_style body/rounded/polygon 0.1 0.1 0.1 ${delta_ua} ${cut_inner} +pair_style body/rounded/polygon 0.1 0.1 0.1 0.5 ${cut_inner} +pair_style body/rounded/polygon 0.1 0.1 0.1 0.5 0.5 +pair_coeff * * ${k_n} ${k_na} +pair_coeff * * 100 ${k_na} +pair_coeff * * 100 2 + +comm_modify vel yes + +neighbor 0.5 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.001 + +#fix 1 all nve/body +#fix 1 all nvt/body temp $T $T 1.0 +fix 1 all npt/body temp $T $T 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0 +fix 1 all npt/body temp 0.5 $T 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0 +fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0 +fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0 fixedpoint 0 0 0 + +fix 2 all enforce2d +fix 3 all wall/body/polygon 2000 50 50 yplane 0.0 48.0 + +#compute 1 all body/local id 1 2 3 +#dump 1 all local 100000 dump.polygon.* index c_1[1] c_1[2] c_1[3] c_1[4] + +thermo_style custom step ke pe etotal press +thermo 1000 + +#dump 2 all image 10000 image.*.jpg type type zoom 2.0 # adiam 1.5 body type 0 0 +#dump_modify 2 pad 6 + +run ${steps} +run 100000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.15685 + ghost atom cutoff = 6.15685 + binsize = 3.07843, bins = 16 16 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair body/rounded/polygon, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.773 | 4.773 | 4.773 Mbytes +Step KinEng PotEng TotEng Press + 0 0.484375 0.25 0.734375 0.0067274306 + 1000 0.49241101 0.0031318767 0.49554289 0.017768281 + 2000 0.56118632 0.0026068888 0.56379321 0.003410416 + 3000 0.75565115 0.025578366 0.78122951 0.0071862988 + 4000 0.72298647 0.093150646 0.81613712 0.003190158 + 5000 0.51684166 0.049164868 0.56600653 0.0096960168 + 6000 0.56627905 0.048132853 0.6144119 0.020733586 + 7000 0.58122129 0.018223718 0.59944501 0.0038160759 + 8000 0.64297977 0.025934821 0.66891459 0.0041091784 + 9000 0.41748404 0.0077890042 0.42527305 0.0039270065 + 10000 0.35738377 0.078487805 0.43587158 3.9079865e-05 + 11000 0.41529307 0.13619284 0.55148591 -0.0067482285 + 12000 0.43274718 0.071315527 0.50406271 0.007006369 + 13000 0.4748324 0.069905666 0.54473807 0.0010385254 + 14000 0.62603727 0.098905625 0.7249429 0.0048876764 + 15000 0.44512086 0.10415235 0.54927321 0.01902062 + 16000 0.47460177 0.18053316 0.65513493 0.045013976 + 17000 0.52742676 0.10110706 0.62853382 0.013615471 + 18000 0.46111734 0.096118795 0.55723613 0.0073676834 + 19000 0.59668439 0.13652292 0.73320731 0.029403553 + 20000 0.46840192 0.11611719 0.58451911 -0.00034412499 + 21000 0.53550533 0.096457461 0.6319628 0.0019785732 + 22000 0.46599715 0.13206373 0.59806087 0.031970672 + 23000 0.49280776 0.20404726 0.69685501 0.03657433 + 24000 0.60901688 0.18255214 0.79156902 0.044955017 + 25000 0.47345185 0.13671357 0.61016542 0.020313539 + 26000 0.47653832 0.12448225 0.60102057 0.01878099 + 27000 0.50008212 0.24740634 0.74748845 0.021862639 + 28000 0.41627204 0.2519463 0.66821834 0.054683701 + 29000 0.55608273 0.23100212 0.78708485 -0.0043318497 + 30000 0.53884537 0.3001584 0.83900377 -0.012838186 + 31000 0.53036238 0.2300328 0.76039518 -0.0061688449 + 32000 0.42666792 0.20536256 0.63203048 0.045305282 + 33000 0.62908185 0.1652033 0.79428515 0.0072777588 + 34000 0.47028154 0.388736 0.85901754 0.04332288 + 35000 0.54602322 0.2775624 0.82358562 0.02898206 + 36000 0.59860544 0.21824655 0.81685199 0.0025936194 + 37000 0.62467827 0.11983499 0.74451326 0.050052743 + 38000 0.72594229 0.36584781 1.0917901 0.04280621 + 39000 0.51129656 0.23859043 0.74988699 0.050817447 + 40000 0.53263836 0.24212889 0.77476725 0.036245922 + 41000 0.50288088 0.36668283 0.86956371 0.018381415 + 42000 0.46653688 0.21974887 0.68628574 0.012661062 + 43000 0.61738785 0.32131037 0.93869821 0.012709433 + 44000 0.56603903 0.26515554 0.83119457 0.03315102 + 45000 0.56231638 0.32111693 0.88343331 0.06079756 + 46000 0.7096208 0.2570131 0.96663391 0.048770468 + 47000 0.588755 0.1880748 0.7768298 0.035962604 + 48000 0.56296339 0.25783519 0.82079858 0.053019928 + 49000 0.419885 0.42328618 0.84317118 0.038105269 + 50000 0.63073351 0.41426285 1.0449964 0.0015271048 + 51000 0.59357935 0.184222 0.77780136 0.015996218 + 52000 0.60608471 0.36247533 0.96856003 0.10984665 + 53000 0.5227842 0.27686739 0.79965159 0.02761699 + 54000 0.39435923 0.34197355 0.73633278 0.061183263 + 55000 0.46748455 0.34230903 0.80979358 0.077441382 + 56000 0.59819827 0.29212061 0.89031889 0.043772353 + 57000 0.61682559 0.32788566 0.94471124 0.03992069 + 58000 0.52702478 0.24891506 0.77593984 0.058480883 + 59000 0.66925719 0.4109031 1.0801603 0.072434423 + 60000 0.66807714 0.39233068 1.0604078 0.082370324 + 61000 0.5724275 0.43308567 1.0055132 0.0072945426 + 62000 0.49433556 0.38453743 0.87887299 0.0036097443 + 63000 0.57575143 0.54067119 1.1164226 0.073339638 + 64000 0.68045383 0.38246533 1.0629192 0.025314593 + 65000 0.59843527 0.42928622 1.0277215 -0.030096445 + 66000 0.60274797 0.50186417 1.1046121 0.069797184 + 67000 0.47450407 0.52689807 1.0014021 0.008758012 + 68000 0.5514135 0.64113187 1.1925454 0.093863314 + 69000 0.52008074 0.45749565 0.97757639 -0.066061381 + 70000 0.69042662 0.50416006 1.1945867 0.014128617 + 71000 0.63925854 0.35153425 0.9907928 -0.01134957 + 72000 0.52088835 0.47626986 0.99715821 0.10198133 + 73000 0.46333852 0.5515537 1.0148922 0.00060582772 + 74000 0.53481418 0.50409531 1.0389095 0.00919451 + 75000 0.67182749 0.50380162 1.1756291 0.043301985 + 76000 0.70492289 0.4112122 1.1161351 0.14880484 + 77000 0.59781817 0.50197661 1.0997948 -0.057111711 + 78000 0.51677429 0.4348232 0.95159749 -0.0074619446 + 79000 0.50663297 0.55000424 1.0566372 0.0052071216 + 80000 0.59392006 0.48394003 1.0778601 -0.018990234 + 81000 0.66323593 0.40358336 1.0668193 -0.02961345 + 82000 0.61596979 0.49177944 1.1077492 0.1314853 + 83000 0.63917554 0.61656584 1.2557414 0.11908351 + 84000 0.49305291 0.46161646 0.95466937 0.033558488 + 85000 0.52552044 0.54250555 1.068026 0.13015174 + 86000 0.55140914 0.38924725 0.94065638 0.047412499 + 87000 0.60952504 0.52603688 1.1355619 0.039230066 + 88000 0.50119735 0.547539 1.0487364 0.019659933 + 89000 0.40331401 0.50331134 0.90662535 -0.056906034 + 90000 0.47067839 0.51306911 0.9837475 0.11918166 + 91000 0.45564995 0.38693455 0.8425845 0.12040045 + 92000 0.64163032 0.34232532 0.98395564 0.0057051641 + 93000 0.70375593 0.53646186 1.2402178 0.16044241 + 94000 0.53378112 0.51971406 1.0534952 0.11389004 + 95000 0.47055342 0.50396004 0.97451346 0.079424215 + 96000 0.59543473 0.40204536 0.99748009 0.096813093 + 97000 0.64821917 0.50051728 1.1487365 0.054071312 + 98000 0.55723937 0.4945909 1.0518303 0.047316424 + 99000 0.56044424 0.50773312 1.0681774 0.0149959 + 100000 0.68254229 0.32704484 1.0095871 0.0069212661 +Loop time of 2.20043 on 4 procs for 100000 steps with 32 atoms + +Performance: 3926501.701 tau/day, 45445.622 timesteps/s +100.0% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.41008 | 0.41366 | 0.41719 | 0.4 | 18.80 +Neigh | 0.0027823 | 0.0030481 | 0.0034747 | 0.5 | 0.14 +Comm | 0.74581 | 0.7675 | 0.78684 | 2.0 | 34.88 +Output | 0.00082111 | 0.0010884 | 0.0016899 | 1.1 | 0.05 +Modify | 0.83828 | 0.85329 | 0.86656 | 1.4 | 38.78 +Other | | 0.1618 | | | 7.36 + +Nlocal: 8 ave 9 max 7 min +Histogram: 1 0 0 0 0 2 0 0 0 1 +Nghost: 12.75 ave 14 max 12 min +Histogram: 2 0 0 0 0 1 0 0 0 1 +Neighs: 11 ave 19 max 5 min +Histogram: 1 0 0 2 0 0 0 0 0 1 + +Total # of neighbors = 44 +Ave neighs/atom = 1.375 +Neighbor list builds = 2663 +Dangerous builds = 0 +Total wall time: 0:00:02 diff --git a/examples/body/molecule.cube b/examples/body/molecule.cube new file mode 100644 index 0000000000..2a8a7bca50 --- /dev/null +++ b/examples/body/molecule.cube @@ -0,0 +1,52 @@ +# 3d polygon body: cubes, moment of inertia I = m edge^2/ 6 + +1 atoms +3 79 body + +Coords + +1 0 0 0 + +Types + +1 1 + +Masses + +1 1.0 + +Body Integers + +8 12 6 + +Body Doubles + +0.667 0.667 0.667 0 0 0 +1 1 1 +1 -1 1 +-1 -1 1 +-1 1 1 +1 1 -1 +1 -1 -1 +-1 -1 -1 +-1 1 -1 +0 1 +1 2 +2 3 +3 0 +4 5 +5 6 +6 7 +7 4 +0 4 +1 5 +2 6 +3 7 +0 1 2 3 +4 5 6 7 +0 1 5 4 +1 2 6 5 +2 3 7 6 +3 0 4 7 +0.5 + diff --git a/examples/body/molecule.point3d b/examples/body/molecule.point3d new file mode 100644 index 0000000000..d22bfbe6fa --- /dev/null +++ b/examples/body/molecule.point3d @@ -0,0 +1,26 @@ +# 2d polygon body: disks Izz = 1/2 m radius^2 + +1 atoms +3 10 body + +Coords + +1 0 0 0 + +Types + +1 1 + +Masses + +1 1.0 + +Body Integers + +1 0 0 + +Body Doubles + +1 1 1.125 0 0 0 +0 0 0 +3.0 diff --git a/examples/body/molecule.rod3d b/examples/body/molecule.rod3d new file mode 100644 index 0000000000..1c8a0a8cd3 --- /dev/null +++ b/examples/body/molecule.rod3d @@ -0,0 +1,27 @@ +# 2d polygon body: rods Izz = 1/12 m length^2 + +1 atoms +3 13 body + +Coords + +1 0 0 0 + +Types + +1 1 + +Masses + +1 1.0 + +Body Integers + +2 1 0 + +Body Doubles + +1 1 1.333 0 0 0 +-2 0 0 +2 0 0 +0.5 diff --git a/examples/body/molecule.tetra b/examples/body/molecule.tetra new file mode 100644 index 0000000000..d67ec906c6 --- /dev/null +++ b/examples/body/molecule.tetra @@ -0,0 +1,39 @@ +# 3d polygon body: regular tetrahedra, moment of inertia I = m edge^2/ 20 + +1 atoms +3 47 body + +Coords + +1 0 0 0 + +Types + +1 1 + +Masses + +1 1.0 + +Body Integers + +4 6 4 + +Body Doubles + +0.4 0.4 0.4 0 0 0 +1 1 1 +1 -1 -1 +-1 1 -1 +-1 -1 1 +0 1 +0 2 +0 3 +1 2 +2 3 +3 1 +0 1 2 -1 +0 1 3 -1 +0 2 3 -1 +1 2 3 -1 +0.5 diff --git a/examples/latte/in.latte.water.ch4.consecutive.md b/examples/latte/in.latte.multiple similarity index 100% rename from examples/latte/in.latte.water.ch4.consecutive.md rename to examples/latte/in.latte.multiple diff --git a/examples/latte/latte.in b/examples/latte/latte.in index de905f411e..f927313457 100644 --- a/examples/latte/latte.in +++ b/examples/latte/latte.in @@ -9,7 +9,7 @@ LATTE INPUT FILE #General controls CONTROL{ - xControl= 1 + XCONTROL= 1 BASISTYPE= NONORTHO PARAMPATH= "./TBparam" KBT= 0.0 diff --git a/examples/latte/log.21Jun18.latte.multiple.g++.1 b/examples/latte/log.21Jun18.latte.multiple.g++.1 new file mode 100644 index 0000000000..2c624e4371 --- /dev/null +++ b/examples/latte/log.21Jun18.latte.multiple.g++.1 @@ -0,0 +1,171 @@ +LAMMPS (22 Jun 2018) +units metal +atom_style full +atom_modify sort 0 0.0 # turn off sorting of the coordinates + +read_data data.water + orthogonal box = (0 0 0) to (6.267 6.267 6.267) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 24 atoms + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + +# initialize system + +velocity all create 0.0 87287 loop geom + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.00025 + +fix 1 all nve +fix 2 all latte NULL +fix_modify 2 energy yes + +thermo_style custom step temp pe etotal press + +# dynamics + +thermo 10 +run 10 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 7 7 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.629 | 5.629 | 5.629 Mbytes +Step Temp PotEng TotEng Press + 0 0 -104.95596 -104.95596 48235.442 + 10 336.53107 -105.96027 -104.95977 97996.851 +Loop time of 0.912921 on 1 procs for 10 steps with 24 atoms + +Performance: 0.237 ns/day, 101.436 hours/ns, 10.954 timesteps/s +6614.5% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 4.3392e-05 | 4.3392e-05 | 4.3392e-05 | 0.0 | 0.00 +Bond | 3.8862e-05 | 3.8862e-05 | 3.8862e-05 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.00036955 | 0.00036955 | 0.00036955 | 0.0 | 0.04 +Output | 9.799e-05 | 9.799e-05 | 9.799e-05 | 0.0 | 0.01 +Modify | 0.91199 | 0.91199 | 0.91199 | 0.0 | 99.90 +Other | | 0.0003812 | | | 0.04 + +Nlocal: 24 ave 24 max 24 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 71 ave 71 max 71 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 37 ave 37 max 37 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 37 +Ave neighs/atom = 1.54167 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + +# Clear up previus calculation + +clear + +# simple CH4 molecule with LATTE + +units metal +atom_style full +atom_modify sort 0 0.0 # turn off sorting of the coordinates + +read_data data.ch4 + triclinic box = (0 0 0) to (19.523 12.758 11.692) with tilt (0 0 0) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 5 atoms + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + +# initialize system + +velocity all create 0.0 87287 loop geom + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.00025 + +fix 1 all nve + +fix 2 all latte NULL +fix_modify 2 energy yes + +thermo_style custom step temp pe etotal press + +# dynamics + +thermo 10 +run 10 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 20 13 12 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton/tri + stencil: half/bin/3d/newton/tri + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.651 | 5.651 | 5.651 Mbytes +Step Temp PotEng TotEng Press + 0 0 -23.980353 -23.980353 348.02716 + 10 19.123149 -23.990297 -23.98041 18.774332 +Loop time of 0.0415399 on 1 procs for 10 steps with 5 atoms + +Performance: 5.200 ns/day, 4.616 hours/ns, 240.732 timesteps/s +6674.9% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 5.722e-06 | 5.722e-06 | 5.722e-06 | 0.0 | 0.01 +Bond | 7.6294e-06 | 7.6294e-06 | 7.6294e-06 | 0.0 | 0.02 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 1.8358e-05 | 1.8358e-05 | 1.8358e-05 | 0.0 | 0.04 +Output | 2.0981e-05 | 2.0981e-05 | 2.0981e-05 | 0.0 | 0.05 +Modify | 0.041394 | 0.041394 | 0.041394 | 0.0 | 99.65 +Other | | 9.322e-05 | | | 0.22 + +Nlocal: 5 ave 5 max 5 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 7 ave 7 max 7 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 10 ave 10 max 10 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 10 +Ave neighs/atom = 2 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + +Total wall time: 0:00:01 diff --git a/examples/message/README b/examples/message/README new file mode 100644 index 0000000000..6cd99d5c09 --- /dev/null +++ b/examples/message/README @@ -0,0 +1,117 @@ +This dir contains scripts that demonstrate how to use LAMMPS as both a +client and server code to run a simple MD simulation. LAMMPS as a +client performs the MD timestepping. LAMMPS as a server provides the +energy and forces between interacting particles. Every timestep the +LAMMPS client sends a message to the LAMMPS server and receives a +response message in return. + +Another code could replace LAMMPS as the client, e.g. another MD code +which wants to use a LAMMPS potential. Another code could replace +LAMMPS as the server, e.g. a quantum code computing quantum forces, so +that ab initio MD could be performed. See an example of the latter in +examples/COUPLE/lammps_vasp. + +See the doc pages for the "MESSAGE package" +(Package_details.html#PKG-MESSAGE) and "Howto client/server" +(Howto_client_server.html) for more details on how client/server +coupling works in LAMMPS. + +-------------- + +Note that you can adjust the problem size run by these scripts by +setting "x,y,z" variables when you run LAMMPS. The default problem size +is x = y = z = 5, which is 500 particles. + +lmp_mpi -v x 10 -v y 10 -v z 20 # 8000 particles + +This applies to either in.message or in.message.client + +You can also run the in.message scripts with an NPT integrator +instead of NVE, if you comment/uncomment the correct lines. + +The client and server script define a "mode" variable +which can be set to file, zmq, mpi/one, or mpi/two, +as illustrated below. + +-------------- + +To run this problem in the traditional way (no client/server coupling) +do one of these: + +% lmp_serial < in.message +% mpirun -np 4 lmp_mpi < in.message + +Or run with in.message.tilt. + +-------------- + +To run in client/server mode: + +Both the client and server script must use the same messaging mode. +This can be selected by setting the "mode" variable when you run +LAMMPS. The default mode = file. The other options for the mode +variable are zmq, mpione, mpitwo. + +Here we assume LAMMPS was built to run in parallel, and the MESSAGE +package was installed with socket (ZMQ) support. This means any of +the 4 messaging modes can be used. + +The next sections illustrate how to launch LAMMPS twice, once as a +client, once as a server, for each of the messaging modes. + +In all cases, the client should print out thermodynamic info for 50 +steps. The server should print out setup info, print nothing until +the client exits, at which point the server should also exit. + +The examples below show launching LAMMPS twice from the same window +(or batch script), using the "&" character to launch the first time in +the background. For all modes except {mpi/one}, you could also launch +twice in separate windows on your desktop machine. It does not matter +whether you launch the client or server first. + +In these examples either the client or server can be run on one or +more processors. If running in a non-MPI mode (file or zmq) you can +launch LAMMPS on a single processor without using mpirun. + +IMPORTANT: If you run in mpi/two mode, you must launch LAMMPS both +times via mpirun, even if one or both of them runs on a single +processor. This is so that MPI can figure out how to connect both MPI +processes together to exchange MPI messages between them. + +-------------- + +NOTE: the Script.sh file has comands to perform all the +runs listed below. + +-------------- + +File or ZMQ or mpi/two modes of messaging: + +% mpirun -np 1 lmp_mpi -v mode file -log log.client < in.message.client & +% mpirun -np 2 lmp_mpi -v mode file -log log.server < in.message.server + +% mpirun -np 4 lmp_mpi -v mode zmq -log log.client < in.message.client & +% mpirun -np 1 lmp_mpi -v mode zmq -log log.server < in.message.server + +% mpirun -np 2 lmp_mpi -v mode mpitwo -log log.client < in.message.client & +% mpirun -np 4 lmp_mpi -v mode mpitwo -log log.server < in.message.server + +Or run with in.message.tilt.client/server. +Don't run the tilt files with the "file" mode; they run too slow. + +-------------- + +Mpi/one mode of messaging: + +Launch LAMMPS twice in a single mpirun command: + +% mpirun -np 2 lmp_mpi -mpicolor 0 -in in.message.client -v mode mpione -log log.client : -np 4 lmp_mpi -mpicolor 1 -in in.message.server -v mode mpione -log log.server + +Or run with in.message.tilt.client/server. + +The two -np values determine how many procs the client and the server +run on. + +A LAMMPS executable run in this manner must use the -mpicolor color +command-line option as its first option, where color is set to one +integer value for the 1st app, and another value for the 2nd app. diff --git a/examples/message/Script.sh b/examples/message/Script.sh new file mode 100644 index 0000000000..fdcd6f1188 --- /dev/null +++ b/examples/message/Script.sh @@ -0,0 +1,55 @@ +# sample launch script + +# message on 1 proc each + +mpirun -np 1 lmp_mpi -log log.message.g++.1 < in.message + +mpirun -np 1 lmp_mpi -v mode file -log log.message.client.file.g++.1 < in.message.client & +mpirun -np 1 lmp_mpi -v mode file -log log.message.server.file.g++.1 < in.message.server + +mpirun -np 1 lmp_mpi -v mode zmq -log log.message.client.zmq.g++.1 < in.message.client & +mpirun -np 1 lmp_mpi -v mode zmq -log log.message.server.zmq.g++.1 < in.message.server + +mpirun -np 1 lmp_mpi -v mode mpitwo -log log.message.client.mpitwo.g++.1 < in.message.client & +mpirun -np 1 lmp_mpi -v mode mpitwo -log log.message.server.mpitwo.g++.1 < in.message.server + +mpirun -np 1 lmp_mpi -m 0 -in in.message.client -v mode mpione -log log.message.client.mpione.g++.1 : -np 1 lmp_mpi -m 1 -in in.message.server -v mode mpione -log log.message.server.mpione.g++.1 + +# message on 2/4 procs each + +mpirun -np 4 lmp_mpi -log log.message.g++.4 < in.message + +mpirun -np 2 lmp_mpi -v mode file -log log.message.client.file.g++.2 < in.message.client & +mpirun -np 4 lmp_mpi -v mode file -log log.message.server.file.g++.4 < in.message.server + +mpirun -np 2 lmp_mpi -v mode zmq -log log.message.client.zmq.g++.2 < in.message.client & +mpirun -np 4 lmp_mpi -v mode zmq -log log.message.server.zmq.g++.4 < in.message.server + +mpirun -np 2 lmp_mpi -v mode mpitwo -log log.message.client.mpitwo.g++.2 < in.message.client & +mpirun -np 4 lmp_mpi -v mode mpitwo -log log.message.server.mpitwo.g++.4 < in.message.server + +mpirun -np 2 lmp_mpi -m 0 -in in.message.client -v mode mpione -log log.message.client.mpione.g++.2 : -np 4 lmp_mpi -m 1 -in in.message.server -v mode mpione -log log.message.server.mpione.g++.4 + +# message.tilt on 1 proc each + +mpirun -np 1 lmp_mpi -log log.message.tilt.g++.1 < in.message.tilt + +mpirun -np 1 lmp_mpi -v mode zmq -log log.message.tilt.client.zmq.g++.1 < in.message.tilt.client & +mpirun -np 1 lmp_mpi -v mode zmq -log log.message.tilt.server.zmq.g++.1 < in.message.tilt.server + +mpirun -np 1 lmp_mpi -v mode mpitwo -log log.message.tilt.client.mpitwo.g++.1 < in.message.tilt.client & +mpirun -np 1 lmp_mpi -v mode mpitwo -log log.message.tilt.server.mpitwo.g++.1 < in.message.tilt.server + +mpirun -np 1 lmp_mpi -m 0 -in in.message.tilt.client -v mode mpione -log log.message.tilt.client.mpione.g++.1 : -np 1 lmp_mpi -m 1 -in in.message.tilt.server -v mode mpione -log log.message.tilt.server.mpione.g++.1 + +# message.tilt on 2/4 procs each + +mpirun -np 1 lmp_mpi -log log.message.tilt.g++.4 < in.message.tilt + +mpirun -np 2 lmp_mpi -v mode zmq -log log.message.tilt.client.zmq.g++.2 < in.message.tilt.client & +mpirun -np 4 lmp_mpi -v mode zmq -log log.message.tilt.server.zmq.g++.4 < in.message.tilt.server + +mpirun -np 2 lmp_mpi -v mode mpitwo -log log.message.tilt.client.mpitwo.g++.2 < in.message.tilt.client & +mpirun -np 4 lmp_mpi -v mode mpitwo -log log.message.tilt.server.mpitwo.g++.4 < in.message.tilt.server + +mpirun -np 2 lmp_mpi -m 0 -in in.message.tilt.client -v mode mpione -log log.message.tilt.client.mpione.g++.2 : -np 4 lmp_mpi -m 1 -in in.message.tilt.server -v mode mpione -log log.message.tilt.server.mpione.g++.4 diff --git a/examples/message/in.message b/examples/message/in.message new file mode 100644 index 0000000000..7fbbffc355 --- /dev/null +++ b/examples/message/in.message @@ -0,0 +1,29 @@ +# 3d Lennard-Jones melt - no client/server mode + +variable x index 5 +variable y index 5 +variable z index 5 + +units lj +atom_style atomic + +lattice fcc 0.8442 +region box block 0 $x 0 $y 0 $z +create_box 1 box +create_atoms 1 box +mass 1 1.0 + +velocity all create 1.44 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve +# same with NPT +#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0 + +thermo 10 +run 50 diff --git a/examples/message/in.message.client b/examples/message/in.message.client new file mode 100644 index 0000000000..f1ec644a80 --- /dev/null +++ b/examples/message/in.message.client @@ -0,0 +1,41 @@ +# 3d Lennard-Jones melt - client script + +variable mode index file + +if "${mode} == file" then & + "message client md file tmp.couple" & +elif "${mode} == zmq" & + "message client md zmq localhost:5555" & +elif "${mode} == mpione" & + "message client md mpi/one" & +elif "${mode} == mpitwo" & + "message client md mpi/two tmp.couple" + +variable x index 5 +variable y index 5 +variable z index 5 + +units lj +atom_style atomic +atom_modify sort 0 0.0 map yes + +lattice fcc 0.8442 +region box block 0 $x 0 $y 0 $z +create_box 1 box +create_atoms 1 box +mass 1 1.0 + +velocity all create 1.44 87287 loop geom + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve +# same with NPT +#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0 + +fix 2 all client/md +fix_modify 2 energy yes + +thermo 10 +run 50 diff --git a/examples/message/in.message.server b/examples/message/in.message.server new file mode 100644 index 0000000000..2fedd2ae00 --- /dev/null +++ b/examples/message/in.message.server @@ -0,0 +1,29 @@ +# 3d Lennard-Jones melt - server script + +variable mode index file + +if "${mode} == file" then & + "message server md file tmp.couple" & +elif "${mode} == zmq" & + "message server md zmq *:5555" & +elif "${mode} == mpione" & + "message server md mpi/one" & +elif "${mode} == mpitwo" & + "message server md mpi/two tmp.couple" + +units lj +atom_style atomic +atom_modify map yes + +lattice fcc 0.8442 +region box block 0 1 0 1 0 1 +create_box 1 box +mass * 1.0 # masses not used by server + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +server md diff --git a/examples/message/in.message.tilt b/examples/message/in.message.tilt new file mode 100644 index 0000000000..51126eae1e --- /dev/null +++ b/examples/message/in.message.tilt @@ -0,0 +1,30 @@ +# 2d NEMD simulation - no client/server mode + +units lj +atom_style atomic +dimension 2 + +lattice sq2 0.8442 +region box prism 0 10 0 8 -0.5 0.5 0 0 0 +create_box 2 box +create_atoms 1 box +mass * 1.0 + +velocity all create 1.44 87287 loop geom + +region slice block 4 6 INF INF INF INF +set region slice type 2 + +pair_style lj/cut 2.5 +pair_coeff * * 1.0 1.0 1.0 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1 +fix 2 all deform 1 xy erate 0.01 remap v + +thermo_style custom step temp epair etotal press xy + +thermo 1000 +run 50000 diff --git a/examples/message/in.message.tilt.client b/examples/message/in.message.tilt.client new file mode 100644 index 0000000000..b55bc6585b --- /dev/null +++ b/examples/message/in.message.tilt.client @@ -0,0 +1,42 @@ +# 2d NEMD simulation - client script + +variable mode index file + +if "${mode} == file" then & + "message client md file tmp.couple" & +elif "${mode} == zmq" & + "message client md zmq localhost:5555" & +elif "${mode} == mpione" & + "message client md mpi/one" & +elif "${mode} == mpitwo" & + "message client md mpi/two tmp.couple" + +units lj +atom_style atomic +dimension 2 +atom_modify sort 0 0.0 map yes + +lattice sq2 0.8442 +region box prism 0 10 0 8 -0.5 0.5 0 0 0 +create_box 2 box +create_atoms 1 box +mass * 1.0 + +velocity all create 1.44 87287 loop geom + +region slice block 4 6 INF INF INF INF +set region slice type 2 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1 +fix 2 all deform 1 xy erate 0.01 remap v + +fix 3 all client/md +fix_modify 3 energy yes + +thermo_style custom step temp epair etotal press xy + +thermo 1000 +run 50000 diff --git a/examples/message/in.message.tilt.server b/examples/message/in.message.tilt.server new file mode 100644 index 0000000000..ba211ed15f --- /dev/null +++ b/examples/message/in.message.tilt.server @@ -0,0 +1,31 @@ +# 3d Lennard-Jones melt - server script + +variable mode index file + +if "${mode} == file" then & + "message server md file tmp.couple" & +elif "${mode} == zmq" & + "message server md zmq *:5555" & +elif "${mode} == mpione" & + "message server md mpi/one" & +elif "${mode} == mpitwo" & + "message server md mpi/two tmp.couple" + +units lj +atom_style atomic +dimension 2 +atom_modify map yes + +lattice sq2 0.8442 +region box prism 0 10 0 8 -0.5 0.5 0 0 0 +create_box 2 box +create_atoms 1 box +mass * 1.0 # masses not used by server + +pair_style lj/cut 2.5 +pair_coeff * * 1.0 1.0 1.0 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +server md diff --git a/examples/message/log.28Aug18.message.client.file.g++.1 b/examples/message/log.28Aug18.message.client.file.g++.1 new file mode 100644 index 0000000000..bca1d37dd5 --- /dev/null +++ b/examples/message/log.28Aug18.message.client.file.g++.1 @@ -0,0 +1,79 @@ +LAMMPS (22 Aug 2018) +# 3d Lennard-Jones melt - client script + +variable mode index file + +if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple" +message client md file tmp.couple + +variable x index 5 +variable y index 5 +variable z index 5 + +units lj +atom_style atomic +atom_modify sort 0 0.0 map yes + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 $x 0 $y 0 $z +region box block 0 5 0 $y 0 $z +region box block 0 5 0 5 0 $z +region box block 0 5 0 5 0 5 +create_box 1 box +Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 500 atoms + Time spent = 0.000752926 secs +mass 1 1.0 + +velocity all create 1.44 87287 loop geom + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve +# same with NPT +#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0 + +fix 2 all client/md +fix_modify 2 energy yes + +thermo 10 +run 50 +Per MPI rank memory allocation (min/avg/max) = 2.303 | 2.303 | 2.303 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.44 0 0 -4.6176881 -5.0221006 + 10 1.1347688 0 0 -4.6166043 -2.6072847 + 20 0.628166 0 0 -4.62213 1.0186262 + 30 0.73767593 0 0 -4.6254647 0.49629637 + 40 0.69517962 0 0 -4.6253506 0.69303877 + 50 0.70150496 0 0 -4.6259832 0.59551518 +Loop time of 5.0251 on 1 procs for 50 steps with 500 atoms + +Performance: 4298.421 tau/day, 9.950 timesteps/s +0.1% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 9.7752e-06 | 9.7752e-06 | 9.7752e-06 | 0.0 | 0.00 +Comm | 0.00014925 | 0.00014925 | 0.00014925 | 0.0 | 0.00 +Output | 0.00023127 | 0.00023127 | 0.00023127 | 0.0 | 0.00 +Modify | 5.0242 | 5.0242 | 5.0242 | 0.0 | 99.98 +Other | | 0.0004668 | | | 0.01 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 4 +Dangerous builds = 0 +Total wall time: 0:00:05 diff --git a/examples/message/log.28Aug18.message.client.file.g++.2 b/examples/message/log.28Aug18.message.client.file.g++.2 new file mode 100644 index 0000000000..1c868dde37 --- /dev/null +++ b/examples/message/log.28Aug18.message.client.file.g++.2 @@ -0,0 +1,79 @@ +LAMMPS (22 Aug 2018) +# 3d Lennard-Jones melt - client script + +variable mode index file + +if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple" +message client md file tmp.couple + +variable x index 5 +variable y index 5 +variable z index 5 + +units lj +atom_style atomic +atom_modify sort 0 0.0 map yes + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 $x 0 $y 0 $z +region box block 0 5 0 $y 0 $z +region box block 0 5 0 5 0 $z +region box block 0 5 0 5 0 5 +create_box 1 box +Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798) + 1 by 1 by 2 MPI processor grid +create_atoms 1 box +Created 500 atoms + Time spent = 0.000613928 secs +mass 1 1.0 + +velocity all create 1.44 87287 loop geom + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve +# same with NPT +#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0 + +fix 2 all client/md +fix_modify 2 energy yes + +thermo 10 +run 50 +Per MPI rank memory allocation (min/avg/max) = 2.302 | 2.302 | 2.302 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.44 0 0 -4.6176881 -5.0221006 + 10 1.1347688 0 0 -4.6166043 -2.6072847 + 20 0.628166 0 0 -4.62213 1.0186262 + 30 0.73767593 0 0 -4.6254647 0.49629637 + 40 0.69517962 0 0 -4.6253506 0.69303877 + 50 0.70150496 0 0 -4.6259832 0.59551518 +Loop time of 5.02384 on 2 procs for 50 steps with 500 atoms + +Performance: 4299.499 tau/day, 9.953 timesteps/s +50.1% CPU use with 2 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 1.9073e-06 | 3.3379e-06 | 4.7684e-06 | 0.0 | 0.00 +Comm | 0.00020742 | 0.00021136 | 0.00021529 | 0.0 | 0.00 +Output | 0.00026989 | 0.00048053 | 0.00069118 | 0.0 | 0.01 +Modify | 5.0171 | 5.0199 | 5.0228 | 0.1 | 99.92 +Other | | 0.003203 | | | 0.06 + +Nlocal: 250 ave 255 max 245 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Nghost: 0 ave 0 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 4 +Dangerous builds = 0 +Total wall time: 0:00:05 diff --git a/examples/message/log.28Aug18.message.client.mpione.g++.1 b/examples/message/log.28Aug18.message.client.mpione.g++.1 new file mode 100644 index 0000000000..78bee72fdf --- /dev/null +++ b/examples/message/log.28Aug18.message.client.mpione.g++.1 @@ -0,0 +1,79 @@ +LAMMPS (22 Aug 2018) +# 3d Lennard-Jones melt - client script + +variable mode index file + +if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple" +message client md mpi/one + +variable x index 5 +variable y index 5 +variable z index 5 + +units lj +atom_style atomic +atom_modify sort 0 0.0 map yes + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 $x 0 $y 0 $z +region box block 0 5 0 $y 0 $z +region box block 0 5 0 5 0 $z +region box block 0 5 0 5 0 5 +create_box 1 box +Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 500 atoms + Time spent = 0.000540018 secs +mass 1 1.0 + +velocity all create 1.44 87287 loop geom + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve +# same with NPT +#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0 + +fix 2 all client/md +fix_modify 2 energy yes + +thermo 10 +run 50 +Per MPI rank memory allocation (min/avg/max) = 2.303 | 2.303 | 2.303 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.44 0 0 -4.6176881 -5.0221006 + 10 1.1347688 0 0 -4.6166043 -2.6072847 + 20 0.628166 0 0 -4.62213 1.0186262 + 30 0.73767593 0 0 -4.6254647 0.49629637 + 40 0.69517962 0 0 -4.6253506 0.69303877 + 50 0.70150496 0 0 -4.6259832 0.59551518 +Loop time of 0.0403891 on 1 procs for 50 steps with 500 atoms + +Performance: 534798.272 tau/day, 1237.959 timesteps/s +99.9% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 4.7684e-06 | 4.7684e-06 | 4.7684e-06 | 0.0 | 0.01 +Comm | 6.3181e-05 | 6.3181e-05 | 6.3181e-05 | 0.0 | 0.16 +Output | 9.5367e-05 | 9.5367e-05 | 9.5367e-05 | 0.0 | 0.24 +Modify | 0.040053 | 0.040053 | 0.040053 | 0.0 | 99.17 +Other | | 0.0001726 | | | 0.43 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 4 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/message/log.28Aug18.message.client.mpione.g++.2 b/examples/message/log.28Aug18.message.client.mpione.g++.2 new file mode 100644 index 0000000000..7d7af866e3 --- /dev/null +++ b/examples/message/log.28Aug18.message.client.mpione.g++.2 @@ -0,0 +1,79 @@ +LAMMPS (22 Aug 2018) +# 3d Lennard-Jones melt - client script + +variable mode index file + +if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple" +message client md mpi/one + +variable x index 5 +variable y index 5 +variable z index 5 + +units lj +atom_style atomic +atom_modify sort 0 0.0 map yes + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 $x 0 $y 0 $z +region box block 0 5 0 $y 0 $z +region box block 0 5 0 5 0 $z +region box block 0 5 0 5 0 5 +create_box 1 box +Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798) + 1 by 1 by 2 MPI processor grid +create_atoms 1 box +Created 500 atoms + Time spent = 0.000475883 secs +mass 1 1.0 + +velocity all create 1.44 87287 loop geom + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve +# same with NPT +#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0 + +fix 2 all client/md +fix_modify 2 energy yes + +thermo 10 +run 50 +Per MPI rank memory allocation (min/avg/max) = 2.302 | 2.302 | 2.302 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.44 0 0 -4.6176881 -5.0221006 + 10 1.1347688 0 0 -4.6166043 -2.6072847 + 20 0.628166 0 0 -4.62213 1.0186262 + 30 0.73767593 0 0 -4.6254647 0.49629637 + 40 0.69517962 0 0 -4.6253506 0.69303877 + 50 0.70150496 0 0 -4.6259832 0.59551518 +Loop time of 0.0208495 on 2 procs for 50 steps with 500 atoms + +Performance: 1035997.740 tau/day, 2398.143 timesteps/s +99.1% CPU use with 2 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 3.0994e-06 | 4.53e-06 | 5.9605e-06 | 0.0 | 0.02 +Comm | 0.00012422 | 0.00012457 | 0.00012493 | 0.0 | 0.60 +Output | 5.7697e-05 | 7.987e-05 | 0.00010204 | 0.0 | 0.38 +Modify | 0.020463 | 0.020464 | 0.020466 | 0.0 | 98.15 +Other | | 0.0001761 | | | 0.84 + +Nlocal: 250 ave 255 max 245 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Nghost: 0 ave 0 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 4 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/message/log.28Aug18.message.client.mpitwo.g++.1 b/examples/message/log.28Aug18.message.client.mpitwo.g++.1 new file mode 100644 index 0000000000..ee97e7bd1a --- /dev/null +++ b/examples/message/log.28Aug18.message.client.mpitwo.g++.1 @@ -0,0 +1,79 @@ +LAMMPS (22 Aug 2018) +# 3d Lennard-Jones melt - client script + +variable mode index file + +if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple" +message client md mpi/two tmp.couple + +variable x index 5 +variable y index 5 +variable z index 5 + +units lj +atom_style atomic +atom_modify sort 0 0.0 map yes + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 $x 0 $y 0 $z +region box block 0 5 0 $y 0 $z +region box block 0 5 0 5 0 $z +region box block 0 5 0 5 0 5 +create_box 1 box +Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 500 atoms + Time spent = 0.000603914 secs +mass 1 1.0 + +velocity all create 1.44 87287 loop geom + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve +# same with NPT +#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0 + +fix 2 all client/md +fix_modify 2 energy yes + +thermo 10 +run 50 +Per MPI rank memory allocation (min/avg/max) = 2.303 | 2.303 | 2.303 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.44 0 0 -4.6176881 -5.0221006 + 10 1.1347688 0 0 -4.6166043 -2.6072847 + 20 0.628166 0 0 -4.62213 1.0186262 + 30 0.73767593 0 0 -4.6254647 0.49629637 + 40 0.69517962 0 0 -4.6253506 0.69303877 + 50 0.70150496 0 0 -4.6259832 0.59551518 +Loop time of 0.069119 on 1 procs for 50 steps with 500 atoms + +Performance: 312504.627 tau/day, 723.390 timesteps/s +42.0% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 7.1526e-06 | 7.1526e-06 | 7.1526e-06 | 0.0 | 0.01 +Comm | 0.0001049 | 0.0001049 | 0.0001049 | 0.0 | 0.15 +Output | 0.00014019 | 0.00014019 | 0.00014019 | 0.0 | 0.20 +Modify | 0.068602 | 0.068602 | 0.068602 | 0.0 | 99.25 +Other | | 0.0002651 | | | 0.38 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 4 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/message/log.28Aug18.message.client.mpitwo.g++.2 b/examples/message/log.28Aug18.message.client.mpitwo.g++.2 new file mode 100644 index 0000000000..72db0198d5 --- /dev/null +++ b/examples/message/log.28Aug18.message.client.mpitwo.g++.2 @@ -0,0 +1,79 @@ +LAMMPS (22 Aug 2018) +# 3d Lennard-Jones melt - client script + +variable mode index file + +if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple" +message client md mpi/two tmp.couple + +variable x index 5 +variable y index 5 +variable z index 5 + +units lj +atom_style atomic +atom_modify sort 0 0.0 map yes + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 $x 0 $y 0 $z +region box block 0 5 0 $y 0 $z +region box block 0 5 0 5 0 $z +region box block 0 5 0 5 0 5 +create_box 1 box +Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798) + 1 by 1 by 2 MPI processor grid +create_atoms 1 box +Created 500 atoms + Time spent = 0.000667095 secs +mass 1 1.0 + +velocity all create 1.44 87287 loop geom + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve +# same with NPT +#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0 + +fix 2 all client/md +fix_modify 2 energy yes + +thermo 10 +run 50 +Per MPI rank memory allocation (min/avg/max) = 2.302 | 2.302 | 2.302 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.44 0 0 -4.6176881 -5.0221006 + 10 1.1347688 0 0 -4.6166043 -2.6072847 + 20 0.628166 0 0 -4.62213 1.0186262 + 30 0.73767593 0 0 -4.6254647 0.49629637 + 40 0.69517962 0 0 -4.6253506 0.69303877 + 50 0.70150496 0 0 -4.6259832 0.59551518 +Loop time of 0.0190214 on 2 procs for 50 steps with 500 atoms + +Performance: 1135563.588 tau/day, 2628.619 timesteps/s +58.5% CPU use with 2 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 1.9073e-06 | 2.861e-06 | 3.8147e-06 | 0.0 | 0.02 +Comm | 0.00017238 | 0.00017989 | 0.0001874 | 0.0 | 0.95 +Output | 0.00012803 | 0.00015497 | 0.00018191 | 0.0 | 0.81 +Modify | 0.018065 | 0.018181 | 0.018297 | 0.1 | 95.58 +Other | | 0.0005029 | | | 2.64 + +Nlocal: 250 ave 255 max 245 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Nghost: 0 ave 0 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 4 +Dangerous builds = 0 +Total wall time: 0:00:01 diff --git a/examples/message/log.28Aug18.message.client.zmq.g++.1 b/examples/message/log.28Aug18.message.client.zmq.g++.1 new file mode 100644 index 0000000000..23fa70c1be --- /dev/null +++ b/examples/message/log.28Aug18.message.client.zmq.g++.1 @@ -0,0 +1,79 @@ +LAMMPS (22 Aug 2018) +# 3d Lennard-Jones melt - client script + +variable mode index file + +if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple" +message client md zmq localhost:5555 + +variable x index 5 +variable y index 5 +variable z index 5 + +units lj +atom_style atomic +atom_modify sort 0 0.0 map yes + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 $x 0 $y 0 $z +region box block 0 5 0 $y 0 $z +region box block 0 5 0 5 0 $z +region box block 0 5 0 5 0 5 +create_box 1 box +Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 500 atoms + Time spent = 0.000734091 secs +mass 1 1.0 + +velocity all create 1.44 87287 loop geom + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve +# same with NPT +#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0 + +fix 2 all client/md +fix_modify 2 energy yes + +thermo 10 +run 50 +Per MPI rank memory allocation (min/avg/max) = 2.303 | 2.303 | 2.303 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.44 0 0 -4.6176881 -5.0221006 + 10 1.1347688 0 0 -4.6166043 -2.6072847 + 20 0.628166 0 0 -4.62213 1.0186262 + 30 0.73767593 0 0 -4.6254647 0.49629637 + 40 0.69517962 0 0 -4.6253506 0.69303877 + 50 0.70150496 0 0 -4.6259832 0.59551518 +Loop time of 0.0778341 on 1 procs for 50 steps with 500 atoms + +Performance: 277513.222 tau/day, 642.392 timesteps/s +11.4% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 7.8678e-06 | 7.8678e-06 | 7.8678e-06 | 0.0 | 0.01 +Comm | 8.3685e-05 | 8.3685e-05 | 8.3685e-05 | 0.0 | 0.11 +Output | 0.00011373 | 0.00011373 | 0.00011373 | 0.0 | 0.15 +Modify | 0.07734 | 0.07734 | 0.07734 | 0.0 | 99.37 +Other | | 0.0002885 | | | 0.37 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 4 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/message/log.28Aug18.message.client.zmq.g++.2 b/examples/message/log.28Aug18.message.client.zmq.g++.2 new file mode 100644 index 0000000000..7833befd21 --- /dev/null +++ b/examples/message/log.28Aug18.message.client.zmq.g++.2 @@ -0,0 +1,79 @@ +LAMMPS (22 Aug 2018) +# 3d Lennard-Jones melt - client script + +variable mode index file + +if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple" +message client md zmq localhost:5555 + +variable x index 5 +variable y index 5 +variable z index 5 + +units lj +atom_style atomic +atom_modify sort 0 0.0 map yes + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 $x 0 $y 0 $z +region box block 0 5 0 $y 0 $z +region box block 0 5 0 5 0 $z +region box block 0 5 0 5 0 5 +create_box 1 box +Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798) + 1 by 1 by 2 MPI processor grid +create_atoms 1 box +Created 500 atoms + Time spent = 0.000570059 secs +mass 1 1.0 + +velocity all create 1.44 87287 loop geom + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve +# same with NPT +#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0 + +fix 2 all client/md +fix_modify 2 energy yes + +thermo 10 +run 50 +Per MPI rank memory allocation (min/avg/max) = 2.302 | 2.302 | 2.302 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.44 0 0 -4.6176881 -5.0221006 + 10 1.1347688 0 0 -4.6166043 -2.6072847 + 20 0.628166 0 0 -4.62213 1.0186262 + 30 0.73767593 0 0 -4.6254647 0.49629637 + 40 0.69517962 0 0 -4.6253506 0.69303877 + 50 0.70150496 0 0 -4.6259832 0.59551518 +Loop time of 0.0416595 on 2 procs for 50 steps with 500 atoms + +Performance: 518489.499 tau/day, 1200.207 timesteps/s +56.5% CPU use with 2 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 2.861e-06 | 3.3379e-06 | 3.8147e-06 | 0.0 | 0.01 +Comm | 0.00013399 | 0.00013685 | 0.00013971 | 0.0 | 0.33 +Output | 8.6784e-05 | 0.00011206 | 0.00013733 | 0.0 | 0.27 +Modify | 0.040948 | 0.04103 | 0.041112 | 0.0 | 98.49 +Other | | 0.0003769 | | | 0.90 + +Nlocal: 250 ave 255 max 245 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Nghost: 0 ave 0 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 4 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/message/log.28Aug18.message.g++.1 b/examples/message/log.28Aug18.message.g++.1 new file mode 100644 index 0000000000..c06af4e0d1 --- /dev/null +++ b/examples/message/log.28Aug18.message.g++.1 @@ -0,0 +1,85 @@ +LAMMPS (22 Aug 2018) +# 3d Lennard-Jones melt - no client/server mode + +variable x index 5 +variable y index 5 +variable z index 5 + +units lj +atom_style atomic + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 $x 0 $y 0 $z +region box block 0 5 0 $y 0 $z +region box block 0 5 0 5 0 $z +region box block 0 5 0 5 0 5 +create_box 1 box +Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 500 atoms + Time spent = 0.000682831 secs +mass 1 1.0 + +velocity all create 1.44 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve +# same with NPT +#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0 + +thermo 10 +run 50 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.143 | 3.143 | 3.143 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.44 -6.7733681 0 -4.6176881 -5.0221006 + 10 1.1347688 -6.3153532 0 -4.6166043 -2.6072847 + 20 0.628166 -5.5624945 0 -4.62213 1.0186262 + 30 0.73767593 -5.7297655 0 -4.6254647 0.49629637 + 40 0.69517962 -5.6660345 0 -4.6253506 0.69303877 + 50 0.70150496 -5.6761362 0 -4.6259832 0.59551518 +Loop time of 0.039681 on 1 procs for 50 steps with 500 atoms + +Performance: 544341.699 tau/day, 1260.050 timesteps/s +99.2% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.029993 | 0.029993 | 0.029993 | 0.0 | 75.59 +Neigh | 0.0073051 | 0.0073051 | 0.0073051 | 0.0 | 18.41 +Comm | 0.0012736 | 0.0012736 | 0.0012736 | 0.0 | 3.21 +Output | 0.00012803 | 0.00012803 | 0.00012803 | 0.0 | 0.32 +Modify | 0.00053287 | 0.00053287 | 0.00053287 | 0.0 | 1.34 +Other | | 0.000448 | | | 1.13 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1946 ave 1946 max 1946 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 18820 ave 18820 max 18820 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 18820 +Ave neighs/atom = 37.64 +Neighbor list builds = 4 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/message/log.28Aug18.message.g++.4 b/examples/message/log.28Aug18.message.g++.4 new file mode 100644 index 0000000000..695b51f166 --- /dev/null +++ b/examples/message/log.28Aug18.message.g++.4 @@ -0,0 +1,85 @@ +LAMMPS (22 Aug 2018) +# 3d Lennard-Jones melt - no client/server mode + +variable x index 5 +variable y index 5 +variable z index 5 + +units lj +atom_style atomic + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 $x 0 $y 0 $z +region box block 0 5 0 $y 0 $z +region box block 0 5 0 5 0 $z +region box block 0 5 0 5 0 5 +create_box 1 box +Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 500 atoms + Time spent = 0.000656843 secs +mass 1 1.0 + +velocity all create 1.44 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve +# same with NPT +#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0 + +thermo 10 +run 50 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.109 | 3.109 | 3.109 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.44 -6.7733681 0 -4.6176881 -5.0221006 + 10 1.1347688 -6.3153532 0 -4.6166043 -2.6072847 + 20 0.628166 -5.5624945 0 -4.62213 1.0186262 + 30 0.73767593 -5.7297655 0 -4.6254647 0.49629637 + 40 0.69517962 -5.6660345 0 -4.6253506 0.69303877 + 50 0.70150496 -5.6761362 0 -4.6259832 0.59551518 +Loop time of 0.0131519 on 4 procs for 50 steps with 500 atoms + +Performance: 1642350.242 tau/day, 3801.737 timesteps/s +97.9% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.006074 | 0.0065379 | 0.0072589 | 0.6 | 49.71 +Neigh | 0.0014219 | 0.0015552 | 0.0017018 | 0.3 | 11.82 +Comm | 0.003546 | 0.0043943 | 0.0049584 | 0.8 | 33.41 +Output | 0.000108 | 0.00012845 | 0.00016999 | 0.0 | 0.98 +Modify | 0.00014353 | 0.00014949 | 0.00015569 | 0.0 | 1.14 +Other | | 0.0003865 | | | 2.94 + +Nlocal: 125 ave 128 max 121 min +Histogram: 1 0 0 0 1 0 0 0 1 1 +Nghost: 1091 ave 1094 max 1089 min +Histogram: 1 0 1 0 1 0 0 0 0 1 +Neighs: 4705 ave 4849 max 4648 min +Histogram: 2 1 0 0 0 0 0 0 0 1 + +Total # of neighbors = 18820 +Ave neighs/atom = 37.64 +Neighbor list builds = 4 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/message/log.28Aug18.message.server.file.g++.1 b/examples/message/log.28Aug18.message.server.file.g++.1 new file mode 100644 index 0000000000..cf1418d3c5 --- /dev/null +++ b/examples/message/log.28Aug18.message.server.file.g++.1 @@ -0,0 +1,44 @@ +LAMMPS (22 Aug 2018) +# 3d Lennard-Jones melt - server script + +variable mode index file + +if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple" +message server md file tmp.couple + +units lj +atom_style atomic +atom_modify map yes + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (1.6796 1.6796 1.6796) + 1 by 1 by 1 MPI processor grid +mass * 1.0 # masses not used by server + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +server md + 1 by 1 by 1 MPI processor grid +WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Server MD calls = 51 +Server MD reneighborings 5 +Total wall time: 0:00:05 diff --git a/examples/message/log.28Aug18.message.server.file.g++.4 b/examples/message/log.28Aug18.message.server.file.g++.4 new file mode 100644 index 0000000000..c233bad692 --- /dev/null +++ b/examples/message/log.28Aug18.message.server.file.g++.4 @@ -0,0 +1,44 @@ +LAMMPS (22 Aug 2018) +# 3d Lennard-Jones melt - server script + +variable mode index file + +if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple" +message server md file tmp.couple + +units lj +atom_style atomic +atom_modify map yes + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (1.6796 1.6796 1.6796) + 1 by 2 by 2 MPI processor grid +mass * 1.0 # masses not used by server + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +server md + 1 by 2 by 2 MPI processor grid +WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Server MD calls = 51 +Server MD reneighborings 5 +Total wall time: 0:00:05 diff --git a/examples/message/log.28Aug18.message.server.mpione.g++.1 b/examples/message/log.28Aug18.message.server.mpione.g++.1 new file mode 100644 index 0000000000..81e04aa923 --- /dev/null +++ b/examples/message/log.28Aug18.message.server.mpione.g++.1 @@ -0,0 +1,44 @@ +LAMMPS (22 Aug 2018) +# 3d Lennard-Jones melt - server script + +variable mode index file + +if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple" +message server md mpi/one + +units lj +atom_style atomic +atom_modify map yes + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (1.6796 1.6796 1.6796) + 1 by 1 by 1 MPI processor grid +mass * 1.0 # masses not used by server + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +server md + 1 by 1 by 1 MPI processor grid +WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Server MD calls = 51 +Server MD reneighborings 5 +Total wall time: 0:00:00 diff --git a/examples/message/log.28Aug18.message.server.mpione.g++.4 b/examples/message/log.28Aug18.message.server.mpione.g++.4 new file mode 100644 index 0000000000..a185cb1c29 --- /dev/null +++ b/examples/message/log.28Aug18.message.server.mpione.g++.4 @@ -0,0 +1,44 @@ +LAMMPS (22 Aug 2018) +# 3d Lennard-Jones melt - server script + +variable mode index file + +if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple" +message server md mpi/one + +units lj +atom_style atomic +atom_modify map yes + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (1.6796 1.6796 1.6796) + 1 by 2 by 2 MPI processor grid +mass * 1.0 # masses not used by server + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +server md + 1 by 2 by 2 MPI processor grid +WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Server MD calls = 51 +Server MD reneighborings 5 +Total wall time: 0:00:00 diff --git a/examples/message/log.28Aug18.message.server.mpitwo.g++.1 b/examples/message/log.28Aug18.message.server.mpitwo.g++.1 new file mode 100644 index 0000000000..973a08eb6a --- /dev/null +++ b/examples/message/log.28Aug18.message.server.mpitwo.g++.1 @@ -0,0 +1,44 @@ +LAMMPS (22 Aug 2018) +# 3d Lennard-Jones melt - server script + +variable mode index file + +if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple" +message server md mpi/two tmp.couple + +units lj +atom_style atomic +atom_modify map yes + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (1.6796 1.6796 1.6796) + 1 by 1 by 1 MPI processor grid +mass * 1.0 # masses not used by server + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +server md + 1 by 1 by 1 MPI processor grid +WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Server MD calls = 51 +Server MD reneighborings 5 +Total wall time: 0:00:00 diff --git a/examples/message/log.28Aug18.message.server.mpitwo.g++.4 b/examples/message/log.28Aug18.message.server.mpitwo.g++.4 new file mode 100644 index 0000000000..9e76e52d90 --- /dev/null +++ b/examples/message/log.28Aug18.message.server.mpitwo.g++.4 @@ -0,0 +1,44 @@ +LAMMPS (22 Aug 2018) +# 3d Lennard-Jones melt - server script + +variable mode index file + +if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple" +message server md mpi/two tmp.couple + +units lj +atom_style atomic +atom_modify map yes + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (1.6796 1.6796 1.6796) + 1 by 2 by 2 MPI processor grid +mass * 1.0 # masses not used by server + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +server md + 1 by 2 by 2 MPI processor grid +WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Server MD calls = 51 +Server MD reneighborings 5 +Total wall time: 0:00:00 diff --git a/examples/message/log.28Aug18.message.server.zmq.g++.1 b/examples/message/log.28Aug18.message.server.zmq.g++.1 new file mode 100644 index 0000000000..ce5729878b --- /dev/null +++ b/examples/message/log.28Aug18.message.server.zmq.g++.1 @@ -0,0 +1,44 @@ +LAMMPS (22 Aug 2018) +# 3d Lennard-Jones melt - server script + +variable mode index file + +if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple" +message server md zmq *:5555 + +units lj +atom_style atomic +atom_modify map yes + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (1.6796 1.6796 1.6796) + 1 by 1 by 1 MPI processor grid +mass * 1.0 # masses not used by server + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +server md + 1 by 1 by 1 MPI processor grid +WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Server MD calls = 51 +Server MD reneighborings 5 +Total wall time: 0:00:00 diff --git a/examples/message/log.28Aug18.message.server.zmq.g++.4 b/examples/message/log.28Aug18.message.server.zmq.g++.4 new file mode 100644 index 0000000000..b3201da4da --- /dev/null +++ b/examples/message/log.28Aug18.message.server.zmq.g++.4 @@ -0,0 +1,44 @@ +LAMMPS (22 Aug 2018) +# 3d Lennard-Jones melt - server script + +variable mode index file + +if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple" +message server md zmq *:5555 + +units lj +atom_style atomic +atom_modify map yes + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 1 0 1 0 1 +create_box 1 box +Created orthogonal box = (0 0 0) to (1.6796 1.6796 1.6796) + 1 by 2 by 2 MPI processor grid +mass * 1.0 # masses not used by server + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +server md + 1 by 2 by 2 MPI processor grid +WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Server MD calls = 51 +Server MD reneighborings 5 +Total wall time: 0:00:00 diff --git a/examples/message/log.28Aug18.message.tilt.client.mpione.g++.1 b/examples/message/log.28Aug18.message.tilt.client.mpione.g++.1 new file mode 100644 index 0000000000..a290ec307b --- /dev/null +++ b/examples/message/log.28Aug18.message.tilt.client.mpione.g++.1 @@ -0,0 +1,130 @@ +LAMMPS (22 Aug 2018) +# 2d NEMD simulation - client script + +variable mode index file + +if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple" +message client md mpi/one + +units lj +atom_style atomic +dimension 2 +atom_modify sort 0 0.0 map yes + +lattice sq2 0.8442 +Lattice spacing in x,y,z = 1.53919 1.53919 1.53919 +region box prism 0 10 0 8 -0.5 0.5 0 0 0 +create_box 2 box +Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 160 atoms + Time spent = 0.000485897 secs +mass * 1.0 + +velocity all create 1.44 87287 loop geom + +region slice block 4 6 INF INF INF INF +set region slice type 2 + 40 settings made for type + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1 +fix 2 all deform 1 xy erate 0.01 remap v + +fix 3 all client/md +fix_modify 3 energy yes + +thermo_style custom step temp epair etotal press xy + +thermo 1000 +run 50000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 0 + ghost atom cutoff = 0 + binsize = 15.3919, bins = 1 1 1 + 0 neighbor lists, perpetual/occasional/extra = 0 0 0 +Per MPI rank memory allocation (min/avg/max) = 2.308 | 2.308 | 2.308 Mbytes +Step Temp E_pair TotEng Press Xy + 0 1.44 0 1.431 1.2080502 0 + 1000 1.0086399 0 1.3760711 6.8772078 0.61567613 + 2000 1.0707188 0 1.3744107 6.628097 1.2313523 + 3000 1.0627515 0 1.310096 6.1647179 1.8470284 + 4000 0.94091054 0 1.268976 6.4723215 2.4627045 + 5000 1.0218949 0 1.2430242 5.6945977 3.0783806 + 6000 0.98649481 0 1.1997565 5.2870413 3.6940568 + 7000 0.9047957 0 1.1461262 5.9291636 4.3097329 + 8000 0.85697614 0 1.0437412 5.0652097 4.925409 + 9000 0.84208329 0 1.109218 6.1749808 5.5410852 + 10000 0.86418108 0 1.1594773 6.2581867 6.1567613 + 11000 0.95136356 0 1.1650901 5.8389085 6.7724374 + 12000 0.94571583 0 1.2210342 6.2498816 7.3881135 + 13000 0.95994288 0 1.2172042 5.9608165 -7.3881135 + 14000 0.99053999 0 1.2925597 6.9994446 -6.7724374 + 15000 1.0316726 0 1.3346023 6.6902672 -6.1567613 + 16000 0.99537481 0 1.3227696 7.0301123 -5.5410852 + 17000 1.0306843 0 1.3101457 6.4750102 -4.925409 + 18000 1.071154 0 1.2947547 5.695888 -4.3097329 + 19000 0.97120752 0 1.3035465 7.3945362 -3.6940568 + 20000 0.97198994 0 1.2244663 6.0047605 -3.0783806 + 21000 0.97943545 0 1.2393394 6.3871012 -2.4627045 + 22000 0.98550707 0 1.1768148 5.019967 -1.8470284 + 23000 0.96920052 0 1.1730698 5.7944947 -1.2313523 + 24000 0.94069959 0 1.184119 5.8434876 -0.61567613 + 25000 0.91569312 0 1.1642118 5.668997 0 + 26000 0.98882932 0 1.1999248 5.0115507 0.61567613 + 27000 0.8972608 0 1.2556546 7.0837158 1.2313523 + 28000 0.93554756 0 1.2221911 5.9302841 1.8470284 + 29000 0.97894608 0 1.2168736 5.5766766 2.4627045 + 30000 0.97877055 0 1.2575839 6.4308887 3.0783806 + 31000 1.0002387 0 1.2338069 5.3873124 3.6940568 + 32000 0.89608618 0 1.2382021 6.7892204 4.3097329 + 33000 0.87439302 0 1.2252635 7.078134 4.925409 + 34000 1.076102 0 1.2991393 5.5556892 5.5410852 + 35000 1.0018689 0 1.272105 6.1320483 6.1567613 + 36000 0.93327214 0 1.2428039 7.0030867 6.7724374 + 37000 1.0770236 0 1.3002931 5.4996076 7.3881135 + 38000 0.98715132 0 1.215562 5.5958335 -7.3881135 + 39000 0.95028417 0 1.2566706 6.4133713 -6.7724374 + 40000 1.0445585 0 1.241151 5.3589806 -6.1567613 + 41000 0.93799713 0 1.2109086 6.4957845 -5.5410852 + 42000 0.99231038 0 1.2228781 5.9363471 -4.925409 + 43000 0.97913815 0 1.1854842 5.8837987 -4.3097329 + 44000 0.86748838 0 1.1616201 6.8991278 -3.6940568 + 45000 0.96284421 0 1.1549383 5.1226785 -3.0783806 + 46000 0.98701623 0 1.170581 4.9719567 -2.4627045 + 47000 0.92618683 0 1.2146576 6.7100075 -1.8470284 + 48000 1.0092593 0 1.2523988 5.7067864 -1.2313523 + 49000 1.0187472 0 1.271608 5.3355092 -0.61567613 + 50000 1.0194881 0 1.2831094 6.2449759 0 +Loop time of 1.74559 on 1 procs for 50000 steps with 160 atoms + +Performance: 12374053.445 tau/day, 28643.642 timesteps/s +100.0% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0.0020533 | 0.0020533 | 0.0020533 | 0.0 | 0.12 +Comm | 0.015517 | 0.015517 | 0.015517 | 0.0 | 0.89 +Output | 0.00052404 | 0.00052404 | 0.00052404 | 0.0 | 0.03 +Modify | 1.6784 | 1.6784 | 1.6784 | 0.0 | 96.15 +Other | | 0.04905 | | | 2.81 + +Nlocal: 160 ave 160 max 160 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 5270 +Dangerous builds = 0 +Total wall time: 0:00:01 diff --git a/examples/message/log.28Aug18.message.tilt.client.mpione.g++.2 b/examples/message/log.28Aug18.message.tilt.client.mpione.g++.2 new file mode 100644 index 0000000000..0089732355 --- /dev/null +++ b/examples/message/log.28Aug18.message.tilt.client.mpione.g++.2 @@ -0,0 +1,130 @@ +LAMMPS (22 Aug 2018) +# 2d NEMD simulation - client script + +variable mode index file + +if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple" +message client md mpi/one + +units lj +atom_style atomic +dimension 2 +atom_modify sort 0 0.0 map yes + +lattice sq2 0.8442 +Lattice spacing in x,y,z = 1.53919 1.53919 1.53919 +region box prism 0 10 0 8 -0.5 0.5 0 0 0 +create_box 2 box +Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0) + 2 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 160 atoms + Time spent = 0.000453949 secs +mass * 1.0 + +velocity all create 1.44 87287 loop geom + +region slice block 4 6 INF INF INF INF +set region slice type 2 + 40 settings made for type + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1 +fix 2 all deform 1 xy erate 0.01 remap v + +fix 3 all client/md +fix_modify 3 energy yes + +thermo_style custom step temp epair etotal press xy + +thermo 1000 +run 50000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 0 + ghost atom cutoff = 0 + binsize = 15.3919, bins = 1 1 1 + 0 neighbor lists, perpetual/occasional/extra = 0 0 0 +Per MPI rank memory allocation (min/avg/max) = 2.308 | 2.308 | 2.308 Mbytes +Step Temp E_pair TotEng Press Xy + 0 1.44 0 1.431 1.2080502 0 + 1000 1.0876599 0 1.3637783 6.063363 0.61567613 + 2000 1.0722996 0 1.4108622 7.0518942 1.2313523 + 3000 1.0580774 0 1.3845895 6.0395275 1.8470284 + 4000 1.0068006 0 1.3804387 7.0944598 2.4627045 + 5000 0.95391814 0 1.2578438 6.1878831 3.0783806 + 6000 0.93492945 0 1.2711287 7.0440517 3.6940568 + 7000 0.94107853 0 1.2384371 6.1438077 4.3097329 + 8000 0.89711744 0 1.145748 6.3558305 4.925409 + 9000 0.90190304 0 1.0860684 4.957098 5.5410852 + 10000 0.84255749 0 1.0376892 5.2351795 6.1567613 + 11000 0.90250882 0 1.0497695 4.3844838 6.7724374 + 12000 0.83461274 0 1.0281949 5.1534361 7.3881135 + 13000 0.80315331 0 1.0226333 5.757222 -7.3881135 + 14000 0.81820939 0 0.99276466 4.6943725 -6.7724374 + 15000 0.8239631 0 1.0408289 5.1669006 -6.1567613 + 16000 0.88908894 0 1.1554855 6.3510278 -5.5410852 + 17000 0.98268136 0 1.2086981 5.6302847 -4.925409 + 18000 1.0098162 0 1.3687676 7.5243587 -4.3097329 + 19000 1.0795086 0 1.4562691 7.639418 -3.6940568 + 20000 1.1932155 0 1.5278988 7.0668432 -3.0783806 + 21000 1.2424296 0 1.6048792 7.959585 -2.4627045 + 22000 1.297169 0 1.7421262 8.9432388 -1.8470284 + 23000 1.2863494 0 1.7236774 8.3584973 -1.2313523 + 24000 1.4084347 0 1.7370339 7.2729078 -0.61567613 + 25000 1.3339728 0 1.6883255 7.529098 0 + 26000 1.1483243 0 1.5155578 7.3869994 0.61567613 + 27000 1.1372606 0 1.4368323 7.0580136 1.2313523 + 28000 1.0518579 0 1.355311 6.478857 1.8470284 + 29000 1.0581145 0 1.2535509 5.3697479 2.4627045 + 30000 0.93612564 0 1.185532 5.5520142 3.0783806 + 31000 0.94387516 0 1.1716454 5.8655485 3.6940568 + 32000 0.83953515 0 1.0737746 5.5551953 4.3097329 + 33000 0.84862926 0 1.0564042 5.7795428 4.925409 + 34000 0.83621877 0 1.079387 5.7514243 5.5410852 + 35000 0.86938506 0 1.031783 4.5897825 6.1567613 + 36000 0.88990609 0 1.0807597 5.3751744 6.7724374 + 37000 0.89534631 0 1.1238882 5.2400355 7.3881135 + 38000 0.98545003 0 1.2121125 5.7783854 -7.3881135 + 39000 0.96737778 0 1.2472934 6.1139 -6.7724374 + 40000 1.0664194 0 1.2956811 5.7353661 -6.1567613 + 41000 1.0681494 0 1.3269435 6.3102722 -5.5410852 + 42000 1.0875422 0 1.3963739 7.1208066 -4.925409 + 43000 1.0968173 0 1.3388062 6.1704339 -4.3097329 + 44000 1.1182109 0 1.3773214 7.0872686 -3.6940568 + 45000 1.1243261 0 1.432186 6.884782 -3.0783806 + 46000 1.039713 0 1.4389721 7.5585257 -2.4627045 + 47000 1.0816108 0 1.4100361 6.4611126 -1.8470284 + 48000 0.97637127 0 1.3605389 7.3992744 -1.2313523 + 49000 1.0361978 0 1.2721873 5.8166109 -0.61567613 + 50000 0.92367087 0 1.1875669 6.4685214 0 +Loop time of 2.82785 on 2 procs for 50000 steps with 160 atoms + +Performance: 7638300.565 tau/day, 17681.251 timesteps/s +100.0% CPU use with 2 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0.0011888 | 0.0012611 | 0.0013335 | 0.2 | 0.04 +Comm | 0.024838 | 0.025075 | 0.025312 | 0.1 | 0.89 +Output | 0.0003581 | 0.00052559 | 0.00069308 | 0.0 | 0.02 +Modify | 2.7209 | 2.7263 | 2.7318 | 0.3 | 96.41 +Other | | 0.07465 | | | 2.64 + +Nlocal: 80 ave 80 max 80 min +Histogram: 2 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 5257 +Dangerous builds = 0 +Total wall time: 0:00:02 diff --git a/examples/message/log.28Aug18.message.tilt.client.mpitwo.g++.1 b/examples/message/log.28Aug18.message.tilt.client.mpitwo.g++.1 new file mode 100644 index 0000000000..814b3df1aa --- /dev/null +++ b/examples/message/log.28Aug18.message.tilt.client.mpitwo.g++.1 @@ -0,0 +1,130 @@ +LAMMPS (22 Aug 2018) +# 2d NEMD simulation - client script + +variable mode index file + +if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple" +message client md mpi/two tmp.couple + +units lj +atom_style atomic +dimension 2 +atom_modify sort 0 0.0 map yes + +lattice sq2 0.8442 +Lattice spacing in x,y,z = 1.53919 1.53919 1.53919 +region box prism 0 10 0 8 -0.5 0.5 0 0 0 +create_box 2 box +Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 160 atoms + Time spent = 0.000543118 secs +mass * 1.0 + +velocity all create 1.44 87287 loop geom + +region slice block 4 6 INF INF INF INF +set region slice type 2 + 40 settings made for type + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1 +fix 2 all deform 1 xy erate 0.01 remap v + +fix 3 all client/md +fix_modify 3 energy yes + +thermo_style custom step temp epair etotal press xy + +thermo 1000 +run 50000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 0 + ghost atom cutoff = 0 + binsize = 15.3919, bins = 1 1 1 + 0 neighbor lists, perpetual/occasional/extra = 0 0 0 +Per MPI rank memory allocation (min/avg/max) = 2.308 | 2.308 | 2.308 Mbytes +Step Temp E_pair TotEng Press Xy + 0 1.44 0 1.431 1.2080502 0 + 1000 1.0086399 0 1.3760711 6.8772078 0.61567613 + 2000 1.0707188 0 1.3744107 6.628097 1.2313523 + 3000 1.0627515 0 1.310096 6.1647179 1.8470284 + 4000 0.94091054 0 1.268976 6.4723215 2.4627045 + 5000 1.0218949 0 1.2430242 5.6945977 3.0783806 + 6000 0.98649481 0 1.1997565 5.2870413 3.6940568 + 7000 0.9047957 0 1.1461262 5.9291636 4.3097329 + 8000 0.85697614 0 1.0437412 5.0652097 4.925409 + 9000 0.84208329 0 1.109218 6.1749808 5.5410852 + 10000 0.86418108 0 1.1594773 6.2581867 6.1567613 + 11000 0.95136356 0 1.1650901 5.8389085 6.7724374 + 12000 0.94571583 0 1.2210342 6.2498816 7.3881135 + 13000 0.95994288 0 1.2172042 5.9608165 -7.3881135 + 14000 0.99053999 0 1.2925597 6.9994446 -6.7724374 + 15000 1.0316726 0 1.3346023 6.6902672 -6.1567613 + 16000 0.99537481 0 1.3227696 7.0301123 -5.5410852 + 17000 1.0306843 0 1.3101457 6.4750102 -4.925409 + 18000 1.071154 0 1.2947547 5.695888 -4.3097329 + 19000 0.97120752 0 1.3035465 7.3945362 -3.6940568 + 20000 0.97198994 0 1.2244663 6.0047605 -3.0783806 + 21000 0.97943545 0 1.2393394 6.3871012 -2.4627045 + 22000 0.98550707 0 1.1768148 5.019967 -1.8470284 + 23000 0.96920052 0 1.1730698 5.7944947 -1.2313523 + 24000 0.94069959 0 1.184119 5.8434876 -0.61567613 + 25000 0.91569312 0 1.1642118 5.668997 0 + 26000 0.98882932 0 1.1999248 5.0115507 0.61567613 + 27000 0.8972608 0 1.2556546 7.0837158 1.2313523 + 28000 0.93554756 0 1.2221911 5.9302841 1.8470284 + 29000 0.97894608 0 1.2168736 5.5766766 2.4627045 + 30000 0.97877055 0 1.2575839 6.4308887 3.0783806 + 31000 1.0002387 0 1.2338069 5.3873124 3.6940568 + 32000 0.89608618 0 1.2382021 6.7892204 4.3097329 + 33000 0.87439302 0 1.2252635 7.078134 4.925409 + 34000 1.076102 0 1.2991393 5.5556892 5.5410852 + 35000 1.0018689 0 1.272105 6.1320483 6.1567613 + 36000 0.93327214 0 1.2428039 7.0030867 6.7724374 + 37000 1.0770236 0 1.3002931 5.4996076 7.3881135 + 38000 0.98715132 0 1.215562 5.5958335 -7.3881135 + 39000 0.95028417 0 1.2566706 6.4133713 -6.7724374 + 40000 1.0445585 0 1.241151 5.3589806 -6.1567613 + 41000 0.93799713 0 1.2109086 6.4957845 -5.5410852 + 42000 0.99231038 0 1.2228781 5.9363471 -4.925409 + 43000 0.97913815 0 1.1854842 5.8837987 -4.3097329 + 44000 0.86748838 0 1.1616201 6.8991278 -3.6940568 + 45000 0.96284421 0 1.1549383 5.1226785 -3.0783806 + 46000 0.98701623 0 1.170581 4.9719567 -2.4627045 + 47000 0.92618683 0 1.2146576 6.7100075 -1.8470284 + 48000 1.0092593 0 1.2523988 5.7067864 -1.2313523 + 49000 1.0187472 0 1.271608 5.3355092 -0.61567613 + 50000 1.0194881 0 1.2831094 6.2449759 0 +Loop time of 4.80282 on 1 procs for 50000 steps with 160 atoms + +Performance: 4497356.047 tau/day, 10410.546 timesteps/s +50.2% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0.0032325 | 0.0032325 | 0.0032325 | 0.0 | 0.07 +Comm | 0.033613 | 0.033613 | 0.033613 | 0.0 | 0.70 +Output | 0.00089812 | 0.00089812 | 0.00089812 | 0.0 | 0.02 +Modify | 4.6706 | 4.6706 | 4.6706 | 0.0 | 97.25 +Other | | 0.09449 | | | 1.97 + +Nlocal: 160 ave 160 max 160 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 5270 +Dangerous builds = 0 +Total wall time: 0:00:04 diff --git a/examples/message/log.28Aug18.message.tilt.client.mpitwo.g++.2 b/examples/message/log.28Aug18.message.tilt.client.mpitwo.g++.2 new file mode 100644 index 0000000000..7c172d3727 --- /dev/null +++ b/examples/message/log.28Aug18.message.tilt.client.mpitwo.g++.2 @@ -0,0 +1,130 @@ +LAMMPS (22 Aug 2018) +# 2d NEMD simulation - client script + +variable mode index file + +if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple" +message client md mpi/two tmp.couple + +units lj +atom_style atomic +dimension 2 +atom_modify sort 0 0.0 map yes + +lattice sq2 0.8442 +Lattice spacing in x,y,z = 1.53919 1.53919 1.53919 +region box prism 0 10 0 8 -0.5 0.5 0 0 0 +create_box 2 box +Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0) + 2 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 160 atoms + Time spent = 0.000574827 secs +mass * 1.0 + +velocity all create 1.44 87287 loop geom + +region slice block 4 6 INF INF INF INF +set region slice type 2 + 40 settings made for type + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1 +fix 2 all deform 1 xy erate 0.01 remap v + +fix 3 all client/md +fix_modify 3 energy yes + +thermo_style custom step temp epair etotal press xy + +thermo 1000 +run 50000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 0 + ghost atom cutoff = 0 + binsize = 15.3919, bins = 1 1 1 + 0 neighbor lists, perpetual/occasional/extra = 0 0 0 +Per MPI rank memory allocation (min/avg/max) = 2.308 | 2.308 | 2.308 Mbytes +Step Temp E_pair TotEng Press Xy + 0 1.44 0 1.431 1.2080502 0 + 1000 1.0876599 0 1.3637783 6.063363 0.61567613 + 2000 1.0722996 0 1.4108622 7.0518942 1.2313523 + 3000 1.0580774 0 1.3845895 6.0395275 1.8470284 + 4000 1.0068006 0 1.3804387 7.0944598 2.4627045 + 5000 0.95391814 0 1.2578438 6.1878831 3.0783806 + 6000 0.93492945 0 1.2711287 7.0440517 3.6940568 + 7000 0.94107853 0 1.2384371 6.1438077 4.3097329 + 8000 0.89711744 0 1.145748 6.3558305 4.925409 + 9000 0.90190304 0 1.0860684 4.957098 5.5410852 + 10000 0.84255749 0 1.0376892 5.2351795 6.1567613 + 11000 0.90250882 0 1.0497695 4.3844838 6.7724374 + 12000 0.83461274 0 1.0281949 5.1534361 7.3881135 + 13000 0.80315331 0 1.0226333 5.757222 -7.3881135 + 14000 0.81820939 0 0.99276466 4.6943725 -6.7724374 + 15000 0.8239631 0 1.0408289 5.1669006 -6.1567613 + 16000 0.88908894 0 1.1554855 6.3510278 -5.5410852 + 17000 0.98268136 0 1.2086981 5.6302847 -4.925409 + 18000 1.0098162 0 1.3687676 7.5243587 -4.3097329 + 19000 1.0795086 0 1.4562691 7.639418 -3.6940568 + 20000 1.1932155 0 1.5278988 7.0668432 -3.0783806 + 21000 1.2424296 0 1.6048792 7.959585 -2.4627045 + 22000 1.297169 0 1.7421262 8.9432388 -1.8470284 + 23000 1.2863494 0 1.7236774 8.3584973 -1.2313523 + 24000 1.4084347 0 1.7370339 7.2729078 -0.61567613 + 25000 1.3339728 0 1.6883255 7.529098 0 + 26000 1.1483243 0 1.5155578 7.3869994 0.61567613 + 27000 1.1372606 0 1.4368323 7.0580136 1.2313523 + 28000 1.0518579 0 1.355311 6.478857 1.8470284 + 29000 1.0581145 0 1.2535509 5.3697479 2.4627045 + 30000 0.93612564 0 1.185532 5.5520142 3.0783806 + 31000 0.94387516 0 1.1716454 5.8655485 3.6940568 + 32000 0.83953515 0 1.0737746 5.5551953 4.3097329 + 33000 0.84862926 0 1.0564042 5.7795428 4.925409 + 34000 0.83621877 0 1.079387 5.7514243 5.5410852 + 35000 0.86938506 0 1.031783 4.5897825 6.1567613 + 36000 0.88990609 0 1.0807597 5.3751744 6.7724374 + 37000 0.89534631 0 1.1238882 5.2400355 7.3881135 + 38000 0.98545003 0 1.2121125 5.7783854 -7.3881135 + 39000 0.96737778 0 1.2472934 6.1139 -6.7724374 + 40000 1.0664194 0 1.2956811 5.7353661 -6.1567613 + 41000 1.0681494 0 1.3269435 6.3102722 -5.5410852 + 42000 1.0875422 0 1.3963739 7.1208066 -4.925409 + 43000 1.0968173 0 1.3388062 6.1704339 -4.3097329 + 44000 1.1182109 0 1.3773214 7.0872686 -3.6940568 + 45000 1.1243261 0 1.432186 6.884782 -3.0783806 + 46000 1.039713 0 1.4389721 7.5585257 -2.4627045 + 47000 1.0816108 0 1.4100361 6.4611126 -1.8470284 + 48000 0.97637127 0 1.3605389 7.3992744 -1.2313523 + 49000 1.0361978 0 1.2721873 5.8166109 -0.61567613 + 50000 0.92367087 0 1.1875669 6.4685214 0 +Loop time of 5.66536 on 2 procs for 50000 steps with 160 atoms + +Performance: 3812643.232 tau/day, 8825.563 timesteps/s +48.1% CPU use with 2 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0.0012836 | 0.0015377 | 0.0017917 | 0.6 | 0.03 +Comm | 0.037211 | 0.037922 | 0.038633 | 0.4 | 0.67 +Output | 0.00052023 | 0.00073683 | 0.00095344 | 0.0 | 0.01 +Modify | 5.5101 | 5.5105 | 5.511 | 0.0 | 97.27 +Other | | 0.1146 | | | 2.02 + +Nlocal: 80 ave 80 max 80 min +Histogram: 2 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 5257 +Dangerous builds = 0 +Total wall time: 0:00:06 diff --git a/examples/message/log.28Aug18.message.tilt.client.zmq.g++.1 b/examples/message/log.28Aug18.message.tilt.client.zmq.g++.1 new file mode 100644 index 0000000000..f5e2f220cd --- /dev/null +++ b/examples/message/log.28Aug18.message.tilt.client.zmq.g++.1 @@ -0,0 +1,130 @@ +LAMMPS (22 Aug 2018) +# 2d NEMD simulation - client script + +variable mode index file + +if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple" +message client md zmq localhost:5555 + +units lj +atom_style atomic +dimension 2 +atom_modify sort 0 0.0 map yes + +lattice sq2 0.8442 +Lattice spacing in x,y,z = 1.53919 1.53919 1.53919 +region box prism 0 10 0 8 -0.5 0.5 0 0 0 +create_box 2 box +Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 160 atoms + Time spent = 0.000530005 secs +mass * 1.0 + +velocity all create 1.44 87287 loop geom + +region slice block 4 6 INF INF INF INF +set region slice type 2 + 40 settings made for type + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1 +fix 2 all deform 1 xy erate 0.01 remap v + +fix 3 all client/md +fix_modify 3 energy yes + +thermo_style custom step temp epair etotal press xy + +thermo 1000 +run 50000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 0 + ghost atom cutoff = 0 + binsize = 15.3919, bins = 1 1 1 + 0 neighbor lists, perpetual/occasional/extra = 0 0 0 +Per MPI rank memory allocation (min/avg/max) = 2.308 | 2.308 | 2.308 Mbytes +Step Temp E_pair TotEng Press Xy + 0 1.44 0 1.431 1.2080502 0 + 1000 1.0086399 0 1.3760711 6.8772078 0.61567613 + 2000 1.0707188 0 1.3744107 6.628097 1.2313523 + 3000 1.0627515 0 1.310096 6.1647179 1.8470284 + 4000 0.94091054 0 1.268976 6.4723215 2.4627045 + 5000 1.0218949 0 1.2430242 5.6945977 3.0783806 + 6000 0.98649481 0 1.1997565 5.2870413 3.6940568 + 7000 0.9047957 0 1.1461262 5.9291636 4.3097329 + 8000 0.85697614 0 1.0437412 5.0652097 4.925409 + 9000 0.84208329 0 1.109218 6.1749808 5.5410852 + 10000 0.86418108 0 1.1594773 6.2581867 6.1567613 + 11000 0.95136356 0 1.1650901 5.8389085 6.7724374 + 12000 0.94571583 0 1.2210342 6.2498816 7.3881135 + 13000 0.95994288 0 1.2172042 5.9608165 -7.3881135 + 14000 0.99053999 0 1.2925597 6.9994446 -6.7724374 + 15000 1.0316726 0 1.3346023 6.6902672 -6.1567613 + 16000 0.99537481 0 1.3227696 7.0301123 -5.5410852 + 17000 1.0306843 0 1.3101457 6.4750102 -4.925409 + 18000 1.071154 0 1.2947547 5.695888 -4.3097329 + 19000 0.97120752 0 1.3035465 7.3945362 -3.6940568 + 20000 0.97198994 0 1.2244663 6.0047605 -3.0783806 + 21000 0.97943545 0 1.2393394 6.3871012 -2.4627045 + 22000 0.98550707 0 1.1768148 5.019967 -1.8470284 + 23000 0.96920052 0 1.1730698 5.7944947 -1.2313523 + 24000 0.94069959 0 1.184119 5.8434876 -0.61567613 + 25000 0.91569312 0 1.1642118 5.668997 0 + 26000 0.98882932 0 1.1999248 5.0115507 0.61567613 + 27000 0.8972608 0 1.2556546 7.0837158 1.2313523 + 28000 0.93554756 0 1.2221911 5.9302841 1.8470284 + 29000 0.97894608 0 1.2168736 5.5766766 2.4627045 + 30000 0.97877055 0 1.2575839 6.4308887 3.0783806 + 31000 1.0002387 0 1.2338069 5.3873124 3.6940568 + 32000 0.89608618 0 1.2382021 6.7892204 4.3097329 + 33000 0.87439302 0 1.2252635 7.078134 4.925409 + 34000 1.076102 0 1.2991393 5.5556892 5.5410852 + 35000 1.0018689 0 1.272105 6.1320483 6.1567613 + 36000 0.93327214 0 1.2428039 7.0030867 6.7724374 + 37000 1.0770236 0 1.3002931 5.4996076 7.3881135 + 38000 0.98715132 0 1.215562 5.5958335 -7.3881135 + 39000 0.95028417 0 1.2566706 6.4133713 -6.7724374 + 40000 1.0445585 0 1.241151 5.3589806 -6.1567613 + 41000 0.93799713 0 1.2109086 6.4957845 -5.5410852 + 42000 0.99231038 0 1.2228781 5.9363471 -4.925409 + 43000 0.97913815 0 1.1854842 5.8837987 -4.3097329 + 44000 0.86748838 0 1.1616201 6.8991278 -3.6940568 + 45000 0.96284421 0 1.1549383 5.1226785 -3.0783806 + 46000 0.98701623 0 1.170581 4.9719567 -2.4627045 + 47000 0.92618683 0 1.2146576 6.7100075 -1.8470284 + 48000 1.0092593 0 1.2523988 5.7067864 -1.2313523 + 49000 1.0187472 0 1.271608 5.3355092 -0.61567613 + 50000 1.0194881 0 1.2831094 6.2449759 0 +Loop time of 12.9652 on 1 procs for 50000 steps with 160 atoms + +Performance: 1666000.147 tau/day, 3856.482 timesteps/s +23.2% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0.0018659 | 0.0018659 | 0.0018659 | 0.0 | 0.01 +Comm | 0.020679 | 0.020679 | 0.020679 | 0.0 | 0.16 +Output | 0.00052547 | 0.00052547 | 0.00052547 | 0.0 | 0.00 +Modify | 12.871 | 12.871 | 12.871 | 0.0 | 99.28 +Other | | 0.07062 | | | 0.54 + +Nlocal: 160 ave 160 max 160 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 5270 +Dangerous builds = 0 +Total wall time: 0:00:12 diff --git a/examples/message/log.28Aug18.message.tilt.client.zmq.g++.2 b/examples/message/log.28Aug18.message.tilt.client.zmq.g++.2 new file mode 100644 index 0000000000..8fc570f5da --- /dev/null +++ b/examples/message/log.28Aug18.message.tilt.client.zmq.g++.2 @@ -0,0 +1,130 @@ +LAMMPS (22 Aug 2018) +# 2d NEMD simulation - client script + +variable mode index file + +if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple" +message client md zmq localhost:5555 + +units lj +atom_style atomic +dimension 2 +atom_modify sort 0 0.0 map yes + +lattice sq2 0.8442 +Lattice spacing in x,y,z = 1.53919 1.53919 1.53919 +region box prism 0 10 0 8 -0.5 0.5 0 0 0 +create_box 2 box +Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0) + 2 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 160 atoms + Time spent = 0.000673056 secs +mass * 1.0 + +velocity all create 1.44 87287 loop geom + +region slice block 4 6 INF INF INF INF +set region slice type 2 + 40 settings made for type + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1 +fix 2 all deform 1 xy erate 0.01 remap v + +fix 3 all client/md +fix_modify 3 energy yes + +thermo_style custom step temp epair etotal press xy + +thermo 1000 +run 50000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 0 + ghost atom cutoff = 0 + binsize = 15.3919, bins = 1 1 1 + 0 neighbor lists, perpetual/occasional/extra = 0 0 0 +Per MPI rank memory allocation (min/avg/max) = 2.308 | 2.308 | 2.308 Mbytes +Step Temp E_pair TotEng Press Xy + 0 1.44 0 1.431 1.2080502 0 + 1000 1.0876599 0 1.3637783 6.063363 0.61567613 + 2000 1.0722996 0 1.4108622 7.0518942 1.2313523 + 3000 1.0580774 0 1.3845895 6.0395275 1.8470284 + 4000 1.0068006 0 1.3804387 7.0944598 2.4627045 + 5000 0.95391814 0 1.2578438 6.1878831 3.0783806 + 6000 0.93492945 0 1.2711287 7.0440517 3.6940568 + 7000 0.94107853 0 1.2384371 6.1438077 4.3097329 + 8000 0.89711744 0 1.145748 6.3558305 4.925409 + 9000 0.90190304 0 1.0860684 4.957098 5.5410852 + 10000 0.84255749 0 1.0376892 5.2351795 6.1567613 + 11000 0.90250882 0 1.0497695 4.3844838 6.7724374 + 12000 0.83461274 0 1.0281949 5.1534361 7.3881135 + 13000 0.80315331 0 1.0226333 5.757222 -7.3881135 + 14000 0.81820939 0 0.99276466 4.6943725 -6.7724374 + 15000 0.8239631 0 1.0408289 5.1669006 -6.1567613 + 16000 0.88908894 0 1.1554855 6.3510278 -5.5410852 + 17000 0.98268136 0 1.2086981 5.6302847 -4.925409 + 18000 1.0098162 0 1.3687676 7.5243587 -4.3097329 + 19000 1.0795086 0 1.4562691 7.639418 -3.6940568 + 20000 1.1932155 0 1.5278988 7.0668432 -3.0783806 + 21000 1.2424296 0 1.6048792 7.959585 -2.4627045 + 22000 1.297169 0 1.7421262 8.9432388 -1.8470284 + 23000 1.2863494 0 1.7236774 8.3584973 -1.2313523 + 24000 1.4084347 0 1.7370339 7.2729078 -0.61567613 + 25000 1.3339728 0 1.6883255 7.529098 0 + 26000 1.1483243 0 1.5155578 7.3869994 0.61567613 + 27000 1.1372606 0 1.4368323 7.0580136 1.2313523 + 28000 1.0518579 0 1.355311 6.478857 1.8470284 + 29000 1.0581145 0 1.2535509 5.3697479 2.4627045 + 30000 0.93612564 0 1.185532 5.5520142 3.0783806 + 31000 0.94387516 0 1.1716454 5.8655485 3.6940568 + 32000 0.83953515 0 1.0737746 5.5551953 4.3097329 + 33000 0.84862926 0 1.0564042 5.7795428 4.925409 + 34000 0.83621877 0 1.079387 5.7514243 5.5410852 + 35000 0.86938506 0 1.031783 4.5897825 6.1567613 + 36000 0.88990609 0 1.0807597 5.3751744 6.7724374 + 37000 0.89534631 0 1.1238882 5.2400355 7.3881135 + 38000 0.98545003 0 1.2121125 5.7783854 -7.3881135 + 39000 0.96737778 0 1.2472934 6.1139 -6.7724374 + 40000 1.0664194 0 1.2956811 5.7353661 -6.1567613 + 41000 1.0681494 0 1.3269435 6.3102722 -5.5410852 + 42000 1.0875422 0 1.3963739 7.1208066 -4.925409 + 43000 1.0968173 0 1.3388062 6.1704339 -4.3097329 + 44000 1.1182109 0 1.3773214 7.0872686 -3.6940568 + 45000 1.1243261 0 1.432186 6.884782 -3.0783806 + 46000 1.039713 0 1.4389721 7.5585257 -2.4627045 + 47000 1.0816108 0 1.4100361 6.4611126 -1.8470284 + 48000 0.97637127 0 1.3605389 7.3992744 -1.2313523 + 49000 1.0361978 0 1.2721873 5.8166109 -0.61567613 + 50000 0.92367087 0 1.1875669 6.4685214 0 +Loop time of 13.6129 on 2 procs for 50000 steps with 160 atoms + +Performance: 1586733.497 tau/day, 3672.994 timesteps/s +59.3% CPU use with 2 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0.0015125 | 0.0015551 | 0.0015976 | 0.1 | 0.01 +Comm | 0.026598 | 0.028413 | 0.030227 | 1.1 | 0.21 +Output | 0.00046492 | 0.00063884 | 0.00081277 | 0.0 | 0.00 +Modify | 13.465 | 13.483 | 13.501 | 0.5 | 99.04 +Other | | 0.0994 | | | 0.73 + +Nlocal: 80 ave 80 max 80 min +Histogram: 2 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 5257 +Dangerous builds = 0 +Total wall time: 0:00:13 diff --git a/examples/message/log.28Aug18.message.tilt.g++.1 b/examples/message/log.28Aug18.message.tilt.g++.1 new file mode 100644 index 0000000000..3f7cfc9da0 --- /dev/null +++ b/examples/message/log.28Aug18.message.tilt.g++.1 @@ -0,0 +1,129 @@ +LAMMPS (22 Aug 2018) +# 2d NEMD simulation - no client/server mode + +units lj +atom_style atomic +dimension 2 + +lattice sq2 0.8442 +Lattice spacing in x,y,z = 1.53919 1.53919 1.53919 +region box prism 0 10 0 8 -0.5 0.5 0 0 0 +create_box 2 box +Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 160 atoms + Time spent = 0.000437021 secs +mass * 1.0 + +velocity all create 1.44 87287 loop geom + +region slice block 4 6 INF INF INF INF +set region slice type 2 + 40 settings made for type + +pair_style lj/cut 2.5 +pair_coeff * * 1.0 1.0 1.0 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1 +fix 2 all deform 1 xy erate 0.01 remap v + +thermo_style custom step temp epair etotal press xy + +thermo 1000 +run 50000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.3 + ghost atom cutoff = 1.3 + binsize = 0.65, bins = 24 19 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton/tri + stencil: half/bin/2d/newton/tri + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.065 | 3.065 | 3.065 Mbytes +Step Temp E_pair TotEng Press Xy + 0 1.44 0 1.431 1.2080502 0 + 1000 1.1326992 0.25863754 1.3842573 6.0588079 0.61567613 + 2000 1.0158438 0.33502643 1.3445212 7.2638652 1.2313523 + 3000 1.0968167 0.3149227 1.4048843 7.0653223 1.8470284 + 4000 1.0070993 0.40611915 1.4069241 7.7283521 2.4627045 + 5000 1.1153133 0.2674828 1.3758254 6.2949171 3.0783806 + 6000 1.0170665 0.25843673 1.2691466 6.049412 3.6940568 + 7000 1.0224605 0.20974914 1.2258193 5.5104976 4.3097329 + 8000 0.96149374 0.24035439 1.1958388 5.4179146 4.925409 + 9000 0.87759014 0.2590493 1.1311545 5.8711239 5.5410852 + 10000 0.83791968 0.23477897 1.0674617 5.666904 6.1567613 + 11000 0.87702487 0.22958877 1.1011322 5.9068062 6.7724374 + 12000 0.81507294 0.26375817 1.0737369 5.9166925 7.3881135 + 13000 0.85655284 0.24676491 1.0979643 5.6918734 -7.3881135 + 14000 0.84369293 0.27818471 1.1166046 6.4146184 -6.7724374 + 15000 0.90052173 0.19836095 1.0932544 5.2690913 -6.1567613 + 16000 0.83836874 0.26921637 1.1023453 5.9579526 -5.5410852 + 17000 0.90492897 0.21933098 1.1186041 5.6042194 -4.925409 + 18000 0.90113412 0.24880908 1.1443111 6.0634846 -4.3097329 + 19000 1.0160445 0.17252962 1.1822239 5.3149334 -3.6940568 + 20000 0.96217234 0.2414377 1.1975965 5.476653 -3.0783806 + 21000 0.98229664 0.27569118 1.2518485 5.9340174 -2.4627045 + 22000 1.0551763 0.26997615 1.3185576 6.2094112 -1.8470284 + 23000 1.051999 0.34076639 1.3861904 7.082385 -1.2313523 + 24000 1.1350071 0.23701844 1.3649317 6.1829742 -0.61567613 + 25000 1.0946409 0.33366032 1.4214597 7.1907559 0 + 26000 1.1511799 0.24626808 1.3902531 5.8469984 0.61567613 + 27000 1.1009203 0.25653085 1.3505704 6.1504287 1.2313523 + 28000 1.0521302 0.2876798 1.3332342 5.9906187 1.8470284 + 29000 1.0518465 0.21853 1.2638025 5.6577549 2.4627045 + 30000 0.97264625 0.28758145 1.2541487 6.5769804 3.0783806 + 31000 1.0133579 0.31575837 1.3227828 6.6650893 3.6940568 + 32000 1.0714324 0.28757036 1.3523063 6.2682059 4.3097329 + 33000 1.0739451 0.28062459 1.3478575 6.6862746 4.925409 + 34000 1.0056867 0.38289586 1.382297 7.1120131 5.5410852 + 35000 1.0911349 0.26370939 1.3480247 6.1476048 6.1567613 + 36000 1.0618618 0.28269593 1.3379211 6.9414608 6.7724374 + 37000 1.0704991 0.29974994 1.3635585 7.0834346 7.3881135 + 38000 1.1087507 0.2682201 1.3700411 5.8506019 -7.3881135 + 39000 1.1303733 0.22362416 1.3469326 5.2500269 -6.7724374 + 40000 1.0174248 0.28956571 1.3006316 6.4491571 -6.1567613 + 41000 0.95981887 0.29162143 1.2454414 6.4658646 -5.5410852 + 42000 0.88302144 0.30432252 1.1818251 6.7401923 -4.925409 + 43000 0.93164419 0.25110308 1.1769245 5.9067383 -4.3097329 + 44000 0.98352598 0.23322873 1.2106077 5.5606585 -3.6940568 + 45000 1.0247245 0.26503082 1.2833508 6.533394 -3.0783806 + 46000 0.93004532 0.32277782 1.2470104 6.4689179 -2.4627045 + 47000 1.0653176 0.29185413 1.3505135 6.9534569 -1.8470284 + 48000 1.0401524 0.3420245 1.3756759 6.8016042 -1.2313523 + 49000 1.0023407 0.31833091 1.314407 6.7385662 -0.61567613 + 50000 1.0566272 0.28657142 1.3365947 6.261203 0 +Loop time of 1.15672 on 1 procs for 50000 steps with 160 atoms + +Performance: 18673426.371 tau/day, 43225.524 timesteps/s +99.8% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.19267 | 0.19267 | 0.19267 | 0.0 | 16.66 +Neigh | 0.15156 | 0.15156 | 0.15156 | 0.0 | 13.10 +Comm | 0.044569 | 0.044569 | 0.044569 | 0.0 | 3.85 +Output | 0.00057936 | 0.00057936 | 0.00057936 | 0.0 | 0.05 +Modify | 0.71051 | 0.71051 | 0.71051 | 0.0 | 61.42 +Other | | 0.05684 | | | 4.91 + +Nlocal: 160 ave 160 max 160 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 71 ave 71 max 71 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 362 ave 362 max 362 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 362 +Ave neighs/atom = 2.2625 +Neighbor list builds = 5256 +Dangerous builds = 0 +Total wall time: 0:00:01 diff --git a/examples/message/log.28Aug18.message.tilt.g++.4 b/examples/message/log.28Aug18.message.tilt.g++.4 new file mode 100644 index 0000000000..74061463f6 --- /dev/null +++ b/examples/message/log.28Aug18.message.tilt.g++.4 @@ -0,0 +1,129 @@ +LAMMPS (22 Aug 2018) +# 2d NEMD simulation - no client/server mode + +units lj +atom_style atomic +dimension 2 + +lattice sq2 0.8442 +Lattice spacing in x,y,z = 1.53919 1.53919 1.53919 +region box prism 0 10 0 8 -0.5 0.5 0 0 0 +create_box 2 box +Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 160 atoms + Time spent = 0.000396967 secs +mass * 1.0 + +velocity all create 1.44 87287 loop geom + +region slice block 4 6 INF INF INF INF +set region slice type 2 + 40 settings made for type + +pair_style lj/cut 2.5 +pair_coeff * * 1.0 1.0 1.0 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1 +fix 2 all deform 1 xy erate 0.01 remap v + +thermo_style custom step temp epair etotal press xy + +thermo 1000 +run 50000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.3 + ghost atom cutoff = 1.3 + binsize = 0.65, bins = 24 19 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton/tri + stencil: half/bin/2d/newton/tri + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.065 | 3.065 | 3.065 Mbytes +Step Temp E_pair TotEng Press Xy + 0 1.44 0 1.431 1.2080502 0 + 1000 1.1326992 0.25863754 1.3842573 6.0588079 0.61567613 + 2000 1.0158438 0.33502643 1.3445212 7.2638652 1.2313523 + 3000 1.0968167 0.3149227 1.4048843 7.0653223 1.8470284 + 4000 1.0070993 0.40611915 1.4069241 7.7283521 2.4627045 + 5000 1.1153133 0.2674828 1.3758254 6.2949171 3.0783806 + 6000 1.0170665 0.25843673 1.2691466 6.049412 3.6940568 + 7000 1.0224605 0.20974914 1.2258193 5.5104976 4.3097329 + 8000 0.96149374 0.24035439 1.1958388 5.4179146 4.925409 + 9000 0.87759014 0.2590493 1.1311545 5.8711239 5.5410852 + 10000 0.83791968 0.23477897 1.0674617 5.666904 6.1567613 + 11000 0.87702487 0.22958877 1.1011322 5.9068062 6.7724374 + 12000 0.81507294 0.26375817 1.0737369 5.9166925 7.3881135 + 13000 0.85655284 0.24676491 1.0979643 5.6918734 -7.3881135 + 14000 0.84369293 0.27818471 1.1166046 6.4146184 -6.7724374 + 15000 0.90052173 0.19836095 1.0932544 5.2690913 -6.1567613 + 16000 0.83836874 0.26921637 1.1023453 5.9579526 -5.5410852 + 17000 0.90492897 0.21933098 1.1186041 5.6042194 -4.925409 + 18000 0.90113412 0.24880908 1.1443111 6.0634846 -4.3097329 + 19000 1.0160445 0.17252962 1.1822239 5.3149334 -3.6940568 + 20000 0.96217234 0.2414377 1.1975965 5.476653 -3.0783806 + 21000 0.98229664 0.27569118 1.2518485 5.9340174 -2.4627045 + 22000 1.0551763 0.26997615 1.3185576 6.2094112 -1.8470284 + 23000 1.051999 0.34076639 1.3861904 7.082385 -1.2313523 + 24000 1.1350071 0.23701844 1.3649317 6.1829742 -0.61567613 + 25000 1.0946409 0.33366032 1.4214597 7.1907559 0 + 26000 1.1511799 0.24626808 1.3902531 5.8469984 0.61567613 + 27000 1.1009203 0.25653085 1.3505704 6.1504287 1.2313523 + 28000 1.0521302 0.2876798 1.3332342 5.9906187 1.8470284 + 29000 1.0518465 0.21853 1.2638025 5.6577549 2.4627045 + 30000 0.97264625 0.28758145 1.2541487 6.5769804 3.0783806 + 31000 1.0133579 0.31575837 1.3227828 6.6650893 3.6940568 + 32000 1.0714324 0.28757036 1.3523063 6.2682059 4.3097329 + 33000 1.0739451 0.28062459 1.3478575 6.6862746 4.925409 + 34000 1.0056867 0.38289586 1.382297 7.1120131 5.5410852 + 35000 1.0911349 0.26370939 1.3480247 6.1476048 6.1567613 + 36000 1.0618618 0.28269593 1.3379211 6.9414608 6.7724374 + 37000 1.0704991 0.29974994 1.3635585 7.0834346 7.3881135 + 38000 1.1087507 0.2682201 1.3700411 5.8506019 -7.3881135 + 39000 1.1303733 0.22362416 1.3469326 5.2500269 -6.7724374 + 40000 1.0174248 0.28956571 1.3006316 6.4491571 -6.1567613 + 41000 0.95981887 0.29162143 1.2454414 6.4658646 -5.5410852 + 42000 0.88302144 0.30432252 1.1818251 6.7401923 -4.925409 + 43000 0.93164419 0.25110308 1.1769245 5.9067383 -4.3097329 + 44000 0.98352598 0.23322873 1.2106077 5.5606585 -3.6940568 + 45000 1.0247245 0.26503082 1.2833508 6.533394 -3.0783806 + 46000 0.93004532 0.32277782 1.2470104 6.4689179 -2.4627045 + 47000 1.0653176 0.29185413 1.3505135 6.9534569 -1.8470284 + 48000 1.0401524 0.3420245 1.3756759 6.8016042 -1.2313523 + 49000 1.0023407 0.31833091 1.314407 6.7385662 -0.61567613 + 50000 1.0566272 0.28657142 1.3365947 6.261203 0 +Loop time of 0.92653 on 1 procs for 50000 steps with 160 atoms + +Performance: 23312793.646 tau/day, 53964.800 timesteps/s +100.0% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.15063 | 0.15063 | 0.15063 | 0.0 | 16.26 +Neigh | 0.11869 | 0.11869 | 0.11869 | 0.0 | 12.81 +Comm | 0.035839 | 0.035839 | 0.035839 | 0.0 | 3.87 +Output | 0.00064468 | 0.00064468 | 0.00064468 | 0.0 | 0.07 +Modify | 0.57422 | 0.57422 | 0.57422 | 0.0 | 61.98 +Other | | 0.0465 | | | 5.02 + +Nlocal: 160 ave 160 max 160 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 71 ave 71 max 71 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 362 ave 362 max 362 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 362 +Ave neighs/atom = 2.2625 +Neighbor list builds = 5256 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/message/log.28Aug18.message.tilt.server.mpione.g++.1 b/examples/message/log.28Aug18.message.tilt.server.mpione.g++.1 new file mode 100644 index 0000000000..428ff346ad --- /dev/null +++ b/examples/message/log.28Aug18.message.tilt.server.mpione.g++.1 @@ -0,0 +1,48 @@ +LAMMPS (22 Aug 2018) +# 3d Lennard-Jones melt - server script + +variable mode index file + +if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple" +message server md mpi/one + +units lj +atom_style atomic +dimension 2 +atom_modify map yes + +lattice sq2 0.8442 +Lattice spacing in x,y,z = 1.53919 1.53919 1.53919 +region box prism 0 10 0 8 -0.5 0.5 0 0 0 +create_box 2 box +Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 160 atoms + Time spent = 0.000438929 secs +mass * 1.0 # masses not used by server + +pair_style lj/cut 2.5 +pair_coeff * * 1.0 1.0 1.0 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +server md + 1 by 1 by 1 MPI processor grid +WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.3 + ghost atom cutoff = 1.3 + binsize = 0.65, bins = 24 19 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton/tri + stencil: half/bin/2d/newton/tri + bin: standard +Server MD calls = 50001 +Server MD reneighborings 5073 +Total wall time: 0:00:01 diff --git a/examples/message/log.28Aug18.message.tilt.server.mpione.g++.4 b/examples/message/log.28Aug18.message.tilt.server.mpione.g++.4 new file mode 100644 index 0000000000..3da50163ed --- /dev/null +++ b/examples/message/log.28Aug18.message.tilt.server.mpione.g++.4 @@ -0,0 +1,48 @@ +LAMMPS (22 Aug 2018) +# 3d Lennard-Jones melt - server script + +variable mode index file + +if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple" +message server md mpi/one + +units lj +atom_style atomic +dimension 2 +atom_modify map yes + +lattice sq2 0.8442 +Lattice spacing in x,y,z = 1.53919 1.53919 1.53919 +region box prism 0 10 0 8 -0.5 0.5 0 0 0 +create_box 2 box +Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0) + 2 by 2 by 1 MPI processor grid +create_atoms 1 box +Created 160 atoms + Time spent = 0.000455141 secs +mass * 1.0 # masses not used by server + +pair_style lj/cut 2.5 +pair_coeff * * 1.0 1.0 1.0 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +server md + 2 by 2 by 1 MPI processor grid +WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.3 + ghost atom cutoff = 1.3 + binsize = 0.65, bins = 24 19 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton/tri + stencil: half/bin/2d/newton/tri + bin: standard +Server MD calls = 50001 +Server MD reneighborings 5066 +Total wall time: 0:00:02 diff --git a/examples/message/log.28Aug18.message.tilt.server.mpitwo.g++.1 b/examples/message/log.28Aug18.message.tilt.server.mpitwo.g++.1 new file mode 100644 index 0000000000..fc29a6da63 --- /dev/null +++ b/examples/message/log.28Aug18.message.tilt.server.mpitwo.g++.1 @@ -0,0 +1,48 @@ +LAMMPS (22 Aug 2018) +# 3d Lennard-Jones melt - server script + +variable mode index file + +if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple" +message server md mpi/two tmp.couple + +units lj +atom_style atomic +dimension 2 +atom_modify map yes + +lattice sq2 0.8442 +Lattice spacing in x,y,z = 1.53919 1.53919 1.53919 +region box prism 0 10 0 8 -0.5 0.5 0 0 0 +create_box 2 box +Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 160 atoms + Time spent = 0.000521898 secs +mass * 1.0 # masses not used by server + +pair_style lj/cut 2.5 +pair_coeff * * 1.0 1.0 1.0 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +server md + 1 by 1 by 1 MPI processor grid +WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.3 + ghost atom cutoff = 1.3 + binsize = 0.65, bins = 24 19 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton/tri + stencil: half/bin/2d/newton/tri + bin: standard +Server MD calls = 50001 +Server MD reneighborings 5073 +Total wall time: 0:00:04 diff --git a/examples/message/log.28Aug18.message.tilt.server.mpitwo.g++.4 b/examples/message/log.28Aug18.message.tilt.server.mpitwo.g++.4 new file mode 100644 index 0000000000..758b84fe9d --- /dev/null +++ b/examples/message/log.28Aug18.message.tilt.server.mpitwo.g++.4 @@ -0,0 +1,48 @@ +LAMMPS (22 Aug 2018) +# 3d Lennard-Jones melt - server script + +variable mode index file + +if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple" +message server md mpi/two tmp.couple + +units lj +atom_style atomic +dimension 2 +atom_modify map yes + +lattice sq2 0.8442 +Lattice spacing in x,y,z = 1.53919 1.53919 1.53919 +region box prism 0 10 0 8 -0.5 0.5 0 0 0 +create_box 2 box +Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0) + 2 by 2 by 1 MPI processor grid +create_atoms 1 box +Created 160 atoms + Time spent = 0.000378847 secs +mass * 1.0 # masses not used by server + +pair_style lj/cut 2.5 +pair_coeff * * 1.0 1.0 1.0 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +server md + 2 by 2 by 1 MPI processor grid +WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.3 + ghost atom cutoff = 1.3 + binsize = 0.65, bins = 24 19 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton/tri + stencil: half/bin/2d/newton/tri + bin: standard +Server MD calls = 50001 +Server MD reneighborings 5066 +Total wall time: 0:00:06 diff --git a/examples/message/log.28Aug18.message.tilt.server.zmq.g++.1 b/examples/message/log.28Aug18.message.tilt.server.zmq.g++.1 new file mode 100644 index 0000000000..78526ba748 --- /dev/null +++ b/examples/message/log.28Aug18.message.tilt.server.zmq.g++.1 @@ -0,0 +1,48 @@ +LAMMPS (22 Aug 2018) +# 3d Lennard-Jones melt - server script + +variable mode index file + +if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple" +message server md zmq *:5555 + +units lj +atom_style atomic +dimension 2 +atom_modify map yes + +lattice sq2 0.8442 +Lattice spacing in x,y,z = 1.53919 1.53919 1.53919 +region box prism 0 10 0 8 -0.5 0.5 0 0 0 +create_box 2 box +Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 160 atoms + Time spent = 0.000557184 secs +mass * 1.0 # masses not used by server + +pair_style lj/cut 2.5 +pair_coeff * * 1.0 1.0 1.0 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +server md + 1 by 1 by 1 MPI processor grid +WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.3 + ghost atom cutoff = 1.3 + binsize = 0.65, bins = 24 19 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton/tri + stencil: half/bin/2d/newton/tri + bin: standard +Server MD calls = 50001 +Server MD reneighborings 5073 +Total wall time: 0:00:12 diff --git a/examples/message/log.28Aug18.message.tilt.server.zmq.g++.4 b/examples/message/log.28Aug18.message.tilt.server.zmq.g++.4 new file mode 100644 index 0000000000..b1ad768470 --- /dev/null +++ b/examples/message/log.28Aug18.message.tilt.server.zmq.g++.4 @@ -0,0 +1,48 @@ +LAMMPS (22 Aug 2018) +# 3d Lennard-Jones melt - server script + +variable mode index file + +if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple" +message server md zmq *:5555 + +units lj +atom_style atomic +dimension 2 +atom_modify map yes + +lattice sq2 0.8442 +Lattice spacing in x,y,z = 1.53919 1.53919 1.53919 +region box prism 0 10 0 8 -0.5 0.5 0 0 0 +create_box 2 box +Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0) + 2 by 2 by 1 MPI processor grid +create_atoms 1 box +Created 160 atoms + Time spent = 0.000586987 secs +mass * 1.0 # masses not used by server + +pair_style lj/cut 2.5 +pair_coeff * * 1.0 1.0 1.0 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +server md + 2 by 2 by 1 MPI processor grid +WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.3 + ghost atom cutoff = 1.3 + binsize = 0.65, bins = 24 19 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton/tri + stencil: half/bin/2d/newton/tri + bin: standard +Server MD calls = 50001 +Server MD reneighborings 5066 +Total wall time: 0:00:13 diff --git a/lib/README b/lib/README index 3c8f46dd0a..12c27b2a39 100644 --- a/lib/README +++ b/lib/README @@ -35,6 +35,8 @@ linalg set of BLAS and LAPACK routines needed by USER-ATC package from Axel Kohlmeyer (Temple U) meam modified embedded atom method (MEAM) potential, MEAM package from Greg Wagner (Sandia) +message client/server communication library via MPI, sockets, files + from Steve Plimpton (Sandia) molfile hooks to VMD molfile plugins, used by the USER-MOLFILE package from Axel Kohlmeyer (Temple U) and the VMD development team mscg hooks to the MSCG library, used by fix_mscg command diff --git a/lib/gpu/Install.py b/lib/gpu/Install.py index 13d7ad157e..d1024c0085 100644 --- a/lib/gpu/Install.py +++ b/lib/gpu/Install.py @@ -23,15 +23,17 @@ optionally copies Makefile.auto to a new Makefile.osuffix -m = use Makefile.machine as starting point, copy to Makefile.auto default machine = linux + default for -h, -a, -p, -e settings are those in -m Makefile -h = set CUDA_HOME variable in Makefile.auto to hdir hdir = path to NVIDIA Cuda software, e.g. /usr/local/cuda -a = set CUDA_ARCH variable in Makefile.auto to arch - use arch = 20 for Tesla C2050/C2070 (Fermi) (deprecated as of CUDA 8.0) - or GeForce GTX 580 or similar - use arch = 30 for Tesla K10 (Kepler) - use arch = 35 for Tesla K40 (Kepler) or GeForce GTX Titan or similar - use arch = 37 for Tesla dual K80 (Kepler) - use arch = 60 for Tesla P100 (Pascal) + use arch = sm_20 for Fermi (C2050/C2070, deprecated as of CUDA 8.0) + or GeForce GTX 580 or similar + use arch = sm_30 for Kepler (K10) + use arch = sm_35 for Kepler (K40) or GeForce GTX Titan or similar + use arch = sm_37 for Kepler (dual K80) + use arch = sm_60 for Pascal (P100) + use arch = sm_70 for Volta -p = set CUDA_PRECISION variable in Makefile.auto to precision use precision = double or mixed or single -e = set EXTRAMAKE variable in Makefile.auto to Makefile.lammps.esuffix @@ -46,7 +48,7 @@ Examples: make lib-gpu args="-b" # build GPU lib with default Makefile.linux make lib-gpu args="-m xk7 -p single -o xk7.single" # create new Makefile.xk7.single, altered for single-precision -make lib-gpu args="-m mpi -a 35 -p single -o mpi.mixed -b" # create new Makefile.mpi.mixed, also build GPU lib with these settings +make lib-gpu args="-m mpi -a sm_35 -p single -o mpi.mixed -b" # create new Makefile.mpi.mixed, also build GPU lib with these settings """ # print error message or help @@ -127,7 +129,7 @@ for line in lines: if hflag and words[0] == "CUDA_HOME" and words[1] == '=': line = line.replace(words[2],hdir) if aflag and words[0] == "CUDA_ARCH" and words[1] == '=': - line = line.replace(words[2],"-arch=sm_%s" % arch) + line = line.replace(words[2],"-arch=%s" % arch) if pflag and words[0] == "CUDA_PRECISION" and words[1] == '=': line = line.replace(words[2],precstr) if eflag and words[0] == "EXTRAMAKE" and words[1] == '=': diff --git a/lib/gpu/Makefile.linux b/lib/gpu/Makefile.linux index ed5b6092d3..9580bfd4ae 100644 --- a/lib/gpu/Makefile.linux +++ b/lib/gpu/Makefile.linux @@ -13,8 +13,8 @@ endif NVCC = nvcc -# Tesla CUDA -CUDA_ARCH = -arch=sm_21 +# older CUDA +#CUDA_ARCH = -arch=sm_21 # newer CUDA #CUDA_ARCH = -arch=sm_13 # older CUDA diff --git a/lib/gpu/Nvidia.makefile_multi b/lib/gpu/Nvidia.makefile_multi index 5fb35cce3c..94cfd4af6b 100644 --- a/lib/gpu/Nvidia.makefile_multi +++ b/lib/gpu/Nvidia.makefile_multi @@ -79,7 +79,10 @@ OBJS = $(OBJ_DIR)/lal_atom.o $(OBJ_DIR)/lal_ans.o \ $(OBJ_DIR)/lal_lj_cubic.o $(OBJ_DIR)/lal_lj_cubic_ext.o \ $(OBJ_DIR)/lal_ufm.o $(OBJ_DIR)/lal_ufm_ext.o \ $(OBJ_DIR)/lal_dipole_long_lj.o $(OBJ_DIR)/lal_dipole_long_lj_ext.o \ - $(OBJ_DIR)/lal_lj_expand_coul_long.o $(OBJ_DIR)/lal_lj_expand_coul_long_ext.o + $(OBJ_DIR)/lal_lj_expand_coul_long.o $(OBJ_DIR)/lal_lj_expand_coul_long_ext.o \ + $(OBJ_DIR)/lal_coul_long_cs.o $(OBJ_DIR)/lal_coul_long_cs_ext.o \ + $(OBJ_DIR)/lal_born_coul_long_cs.o $(OBJ_DIR)/lal_born_coul_long_cs_ext.o \ + $(OBJ_DIR)/lal_born_coul_wolf_cs.o $(OBJ_DIR)/lal_born_coul_wolf_cs_ext.o CBNS = $(OBJ_DIR)/device.cubin $(OBJ_DIR)/device_cubin.h \ $(OBJ_DIR)/atom.cubin $(OBJ_DIR)/atom_cubin.h \ @@ -137,7 +140,10 @@ CBNS = $(OBJ_DIR)/device.cubin $(OBJ_DIR)/device_cubin.h \ $(OBJ_DIR)/lj_cubic.cubin $(OBJ_DIR)/lj_cubic_cubin.h \ $(OBJ_DIR)/ufm.cubin $(OBJ_DIR)/ufm_cubin.h \ $(OBJ_DIR)/dipole_long_lj.cubin $(OBJ_DIR)/dipole_long_lj_cubin.h \ - $(OBJ_DIR)/lj_expand_coul_long.cubin $(OBJ_DIR)/lj_expand_coul_long_cubin.h + $(OBJ_DIR)/lj_expand_coul_long.cubin $(OBJ_DIR)/lj_expand_coul_long_cubin.h \ + $(OBJ_DIR)/coul_long_cs.cubin $(OBJ_DIR)/coul_long_cs_cubin.h \ + $(OBJ_DIR)/born_coul_long_cs.cubin $(OBJ_DIR)/born_coul_long_cs_cubin.h \ + $(OBJ_DIR)/born_coul_wolf_cs.cubin $(OBJ_DIR)/born_coul_wolf_cs_cubin.h all: $(OBJ_DIR) $(GPU_LIB) $(EXECS) @@ -837,6 +843,42 @@ $(OBJ_DIR)/lal_lj_expand_coul_long.o: $(ALL_H) lal_lj_expand_coul_long.h lal_lj_ $(OBJ_DIR)/lal_lj_expand_coul_long_ext.o: $(ALL_H) lal_lj_expand_coul_long.h lal_lj_expand_coul_long_ext.cpp lal_base_charge.h $(CUDR) -o $@ -c lal_lj_expand_coul_long_ext.cpp -I$(OBJ_DIR) +$(OBJ_DIR)/coul_long_cs.cubin: lal_coul_long_cs.cu lal_precision.h lal_preprocessor.h + $(CUDA) --fatbin -DNV_KERNEL -o $@ lal_coul_long_cs.cu + +$(OBJ_DIR)/coul_long_cs_cubin.h: $(OBJ_DIR)/coul_long_cs.cubin $(OBJ_DIR)/coul_long_cs.cubin + $(BIN2C) -c -n coul_long_cs $(OBJ_DIR)/coul_long_cs.cubin > $(OBJ_DIR)/coul_long_cs_cubin.h + +$(OBJ_DIR)/lal_coul_long_cs.o: $(ALL_H) lal_coul_long_cs.h lal_coul_long_cs.cpp $(OBJ_DIR)/coul_long_cs_cubin.h $(OBJ_DIR)/lal_base_charge.o $(OBJ_DIR)/lal_coul_long.o + $(CUDR) -o $@ -c lal_coul_long_cs.cpp -I$(OBJ_DIR) + +$(OBJ_DIR)/lal_coul_long_cs_ext.o: $(ALL_H) lal_coul_long_cs.h lal_coul_long_cs_ext.cpp lal_coul_long.h + $(CUDR) -o $@ -c lal_coul_long_cs_ext.cpp -I$(OBJ_DIR) + +$(OBJ_DIR)/born_coul_long_cs.cubin: lal_born_coul_long_cs.cu lal_precision.h lal_preprocessor.h + $(CUDA) --fatbin -DNV_KERNEL -o $@ lal_born_coul_long_cs.cu + +$(OBJ_DIR)/born_coul_long_cs_cubin.h: $(OBJ_DIR)/born_coul_long_cs.cubin $(OBJ_DIR)/born_coul_long_cs.cubin + $(BIN2C) -c -n born_coul_long_cs $(OBJ_DIR)/born_coul_long_cs.cubin > $(OBJ_DIR)/born_coul_long_cs_cubin.h + +$(OBJ_DIR)/lal_born_coul_long_cs.o: $(ALL_H) lal_born_coul_long_cs.h lal_born_coul_long_cs.cpp $(OBJ_DIR)/born_coul_long_cs_cubin.h $(OBJ_DIR)/lal_base_charge.o $(OBJ_DIR)/lal_born_coul_long.o + $(CUDR) -o $@ -c lal_born_coul_long_cs.cpp -I$(OBJ_DIR) + +$(OBJ_DIR)/lal_born_coul_long_cs_ext.o: $(ALL_H) lal_born_coul_long_cs.h lal_born_coul_long_cs_ext.cpp lal_born_coul_long.h + $(CUDR) -o $@ -c lal_born_coul_long_cs_ext.cpp -I$(OBJ_DIR) + +$(OBJ_DIR)/born_coul_wolf_cs.cubin: lal_born_coul_wolf_cs.cu lal_precision.h lal_preprocessor.h + $(CUDA) --fatbin -DNV_KERNEL -o $@ lal_born_coul_wolf_cs.cu + +$(OBJ_DIR)/born_coul_wolf_cs_cubin.h: $(OBJ_DIR)/born_coul_wolf_cs.cubin $(OBJ_DIR)/born_coul_wolf_cs.cubin + $(BIN2C) -c -n born_coul_wolf_cs $(OBJ_DIR)/born_coul_wolf_cs.cubin > $(OBJ_DIR)/born_coul_wolf_cs_cubin.h + +$(OBJ_DIR)/lal_born_coul_wolf_cs.o: $(ALL_H) lal_born_coul_wolf_cs.h lal_born_coul_wolf_cs.cpp $(OBJ_DIR)/born_coul_wolf_cs_cubin.h $(OBJ_DIR)/lal_base_charge.o $(OBJ_DIR)/lal_born_coul_wolf.o + $(CUDR) -o $@ -c lal_born_coul_wolf_cs.cpp -I$(OBJ_DIR) + +$(OBJ_DIR)/lal_born_coul_wolf_cs_ext.o: $(ALL_H) lal_born_coul_wolf_cs.h lal_born_coul_wolf_cs_ext.cpp lal_born_coul_wolf.h + $(CUDR) -o $@ -c lal_born_coul_wolf_cs_ext.cpp -I$(OBJ_DIR) + $(BIN_DIR)/nvc_get_devices: ./geryon/ucl_get_devices.cpp $(NVD_H) $(CUDR) -o $@ ./geryon/ucl_get_devices.cpp -DUCL_CUDADR $(CUDA_LIB) -lcuda diff --git a/lib/gpu/geryon/nvd_device.h b/lib/gpu/geryon/nvd_device.h index 2d2a751f85..42f176bcbf 100644 --- a/lib/gpu/geryon/nvd_device.h +++ b/lib/gpu/geryon/nvd_device.h @@ -48,7 +48,18 @@ struct NVDProperties { int minor; CUDA_INT_TYPE totalGlobalMem; int multiProcessorCount; - CUdevprop_st p; + + int maxThreadsPerBlock; + int maxThreadsDim[3]; + int maxGridSize[3]; + int sharedMemPerBlock; + int totalConstantMemory; + int SIMDWidth; + int memPitch; + int regsPerBlock; + int clockRate; + int textureAlign; + int kernelExecTimeoutEnabled; int integrated; int canMapHostMemory; @@ -210,18 +221,18 @@ class UCL_Device { inline double clock_rate() { return clock_rate(_device); } /// Clock rate in GHz inline double clock_rate(const int i) - { return _properties[i].p.clockRate*1e-6;} + { return _properties[i].clockRate*1e-6;} /// Get the maximum number of threads per block inline size_t group_size() { return group_size(_device); } /// Get the maximum number of threads per block inline size_t group_size(const int i) - { return _properties[i].p.maxThreadsPerBlock; } + { return _properties[i].maxThreadsPerBlock; } /// Return the maximum memory pitch in bytes for current device inline size_t max_pitch() { return max_pitch(_device); } /// Return the maximum memory pitch in bytes - inline size_t max_pitch(const int i) { return _properties[i].p.memPitch; } + inline size_t max_pitch(const int i) { return _properties[i].memPitch; } /// Returns false if accelerator cannot be shared by multiple processes /** If it cannot be determined, true is returned **/ @@ -260,6 +271,9 @@ class UCL_Device { /// List all devices along with all properties inline void print_all(std::ostream &out); + /// Select the platform that has accelerators (for compatibility with OpenCL) + inline int set_platform_accelerator(int pid=-1) { return UCL_SUCCESS; } + private: int _device, _num_devices; std::vector _properties; @@ -272,49 +286,54 @@ class UCL_Device { UCL_Device::UCL_Device() { CU_SAFE_CALL_NS(cuInit(0)); CU_SAFE_CALL_NS(cuDeviceGetCount(&_num_devices)); - for (int dev=0; dev<_num_devices; ++dev) { - CUdevice m; - CU_SAFE_CALL_NS(cuDeviceGet(&m,dev)); + for (int i=0; i<_num_devices; ++i) { + CUdevice dev; + CU_SAFE_CALL_NS(cuDeviceGet(&dev,i)); int major, minor; - CU_SAFE_CALL_NS(cuDeviceComputeCapability(&major,&minor,m)); + CU_SAFE_CALL_NS(cuDeviceGetAttribute(&major, CU_DEVICE_ATTRIBUTE_COMPUTE_CAPABILITY_MAJOR, dev)); + CU_SAFE_CALL_NS(cuDeviceGetAttribute(&minor, CU_DEVICE_ATTRIBUTE_COMPUTE_CAPABILITY_MINOR, dev)); if (major==9999) continue; - _properties.push_back(NVDProperties()); - _properties.back().device_id=dev; - _properties.back().major=major; - _properties.back().minor=minor; + NVDProperties prop; + prop.device_id = i; + prop.major=major; + prop.minor=minor; char namecstr[1024]; - CU_SAFE_CALL_NS(cuDeviceGetName(namecstr,1024,m)); - _properties.back().name=namecstr; + CU_SAFE_CALL_NS(cuDeviceGetName(namecstr,1024,dev)); + prop.name=namecstr; + + CU_SAFE_CALL_NS(cuDeviceTotalMem(&prop.totalGlobalMem,dev)); + CU_SAFE_CALL_NS(cuDeviceGetAttribute(&prop.multiProcessorCount, CU_DEVICE_ATTRIBUTE_MULTIPROCESSOR_COUNT, dev)); + + CU_SAFE_CALL_NS(cuDeviceGetAttribute(&prop.maxThreadsPerBlock, CU_DEVICE_ATTRIBUTE_MAX_THREADS_PER_BLOCK, dev)); + CU_SAFE_CALL_NS(cuDeviceGetAttribute(&prop.maxThreadsDim[0], CU_DEVICE_ATTRIBUTE_MAX_BLOCK_DIM_X, dev)); + CU_SAFE_CALL_NS(cuDeviceGetAttribute(&prop.maxThreadsDim[1], CU_DEVICE_ATTRIBUTE_MAX_BLOCK_DIM_Y, dev)); + CU_SAFE_CALL_NS(cuDeviceGetAttribute(&prop.maxThreadsDim[2], CU_DEVICE_ATTRIBUTE_MAX_BLOCK_DIM_Z, dev)); + CU_SAFE_CALL_NS(cuDeviceGetAttribute(&prop.maxGridSize[0], CU_DEVICE_ATTRIBUTE_MAX_GRID_DIM_X, dev)); + CU_SAFE_CALL_NS(cuDeviceGetAttribute(&prop.maxGridSize[1], CU_DEVICE_ATTRIBUTE_MAX_GRID_DIM_Y, dev)); + CU_SAFE_CALL_NS(cuDeviceGetAttribute(&prop.maxGridSize[2], CU_DEVICE_ATTRIBUTE_MAX_GRID_DIM_Z, dev)); + CU_SAFE_CALL_NS(cuDeviceGetAttribute(&prop.sharedMemPerBlock, CU_DEVICE_ATTRIBUTE_MAX_SHARED_MEMORY_PER_BLOCK, dev)); + CU_SAFE_CALL_NS(cuDeviceGetAttribute(&prop.totalConstantMemory, CU_DEVICE_ATTRIBUTE_TOTAL_CONSTANT_MEMORY, dev)); + CU_SAFE_CALL_NS(cuDeviceGetAttribute(&prop.SIMDWidth, CU_DEVICE_ATTRIBUTE_WARP_SIZE, dev)); + CU_SAFE_CALL_NS(cuDeviceGetAttribute(&prop.memPitch, CU_DEVICE_ATTRIBUTE_MAX_PITCH, dev)); + CU_SAFE_CALL_NS(cuDeviceGetAttribute(&prop.regsPerBlock, CU_DEVICE_ATTRIBUTE_MAX_REGISTERS_PER_BLOCK, dev)); + CU_SAFE_CALL_NS(cuDeviceGetAttribute(&prop.clockRate, CU_DEVICE_ATTRIBUTE_CLOCK_RATE, dev)); + CU_SAFE_CALL_NS(cuDeviceGetAttribute(&prop.textureAlign, CU_DEVICE_ATTRIBUTE_TEXTURE_ALIGNMENT, dev)); - CU_SAFE_CALL_NS(cuDeviceTotalMem(&_properties.back().totalGlobalMem,m)); - CU_SAFE_CALL_NS(cuDeviceGetAttribute(&_properties.back().multiProcessorCount, - CU_DEVICE_ATTRIBUTE_MULTIPROCESSOR_COUNT, - m)); - CU_SAFE_CALL_NS(cuDeviceGetProperties(&_properties.back().p,m)); #if CUDA_VERSION >= 2020 - CU_SAFE_CALL_NS(cuDeviceGetAttribute( - &_properties.back().kernelExecTimeoutEnabled, - CU_DEVICE_ATTRIBUTE_KERNEL_EXEC_TIMEOUT,dev)); - CU_SAFE_CALL_NS(cuDeviceGetAttribute( - &_properties.back().integrated, - CU_DEVICE_ATTRIBUTE_INTEGRATED, dev)); - CU_SAFE_CALL_NS(cuDeviceGetAttribute( - &_properties.back().canMapHostMemory, - CU_DEVICE_ATTRIBUTE_CAN_MAP_HOST_MEMORY, dev)); - CU_SAFE_CALL_NS(cuDeviceGetAttribute(&_properties.back().computeMode, - CU_DEVICE_ATTRIBUTE_COMPUTE_MODE,dev)); + CU_SAFE_CALL_NS(cuDeviceGetAttribute(&prop.kernelExecTimeoutEnabled, CU_DEVICE_ATTRIBUTE_KERNEL_EXEC_TIMEOUT,dev)); + CU_SAFE_CALL_NS(cuDeviceGetAttribute(&prop.integrated, CU_DEVICE_ATTRIBUTE_INTEGRATED, dev)); + CU_SAFE_CALL_NS(cuDeviceGetAttribute(&prop.canMapHostMemory, CU_DEVICE_ATTRIBUTE_CAN_MAP_HOST_MEMORY, dev)); + CU_SAFE_CALL_NS(cuDeviceGetAttribute(&prop.computeMode, CU_DEVICE_ATTRIBUTE_COMPUTE_MODE,dev)); #endif #if CUDA_VERSION >= 3010 - CU_SAFE_CALL_NS(cuDeviceGetAttribute( - &_properties.back().concurrentKernels, - CU_DEVICE_ATTRIBUTE_CONCURRENT_KERNELS, dev)); - CU_SAFE_CALL_NS(cuDeviceGetAttribute( - &_properties.back().ECCEnabled, - CU_DEVICE_ATTRIBUTE_ECC_ENABLED, dev)); + CU_SAFE_CALL_NS(cuDeviceGetAttribute(&prop.concurrentKernels, CU_DEVICE_ATTRIBUTE_CONCURRENT_KERNELS, dev)); + CU_SAFE_CALL_NS(cuDeviceGetAttribute(&prop.ECCEnabled, CU_DEVICE_ATTRIBUTE_ECC_ENABLED, dev)); #endif + + _properties.push_back(prop); } _device=-1; _cq.push_back(CUstream()); @@ -390,27 +409,27 @@ void UCL_Device::print_all(std::ostream &out) { << cores(i) << std::endl; #endif out << " Total amount of constant memory: " - << _properties[i].p.totalConstantMemory << " bytes\n"; + << _properties[i].totalConstantMemory << " bytes\n"; out << " Total amount of local/shared memory per block: " - << _properties[i].p.sharedMemPerBlock << " bytes\n"; + << _properties[i].sharedMemPerBlock << " bytes\n"; out << " Total number of registers available per block: " - << _properties[i].p.regsPerBlock << std::endl; + << _properties[i].regsPerBlock << std::endl; out << " Warp size: " - << _properties[i].p.SIMDWidth << std::endl; + << _properties[i].SIMDWidth << std::endl; out << " Maximum number of threads per block: " - << _properties[i].p.maxThreadsPerBlock << std::endl; + << _properties[i].maxThreadsPerBlock << std::endl; out << " Maximum group size (# of threads per block) " - << _properties[i].p.maxThreadsDim[0] << " x " - << _properties[i].p.maxThreadsDim[1] << " x " - << _properties[i].p.maxThreadsDim[2] << std::endl; + << _properties[i].maxThreadsDim[0] << " x " + << _properties[i].maxThreadsDim[1] << " x " + << _properties[i].maxThreadsDim[2] << std::endl; out << " Maximum item sizes (# threads for each dim) " - << _properties[i].p.maxGridSize[0] << " x " - << _properties[i].p.maxGridSize[1] << " x " - << _properties[i].p.maxGridSize[2] << std::endl; + << _properties[i].maxGridSize[0] << " x " + << _properties[i].maxGridSize[1] << " x " + << _properties[i].maxGridSize[2] << std::endl; out << " Maximum memory pitch: " << max_pitch(i) << " bytes\n"; out << " Texture alignment: " - << _properties[i].p.textureAlign << " bytes\n"; + << _properties[i].textureAlign << " bytes\n"; out << " Clock rate: " << clock_rate(i) << " GHz\n"; #if CUDA_VERSION >= 2020 diff --git a/lib/gpu/geryon/ocl_device.h b/lib/gpu/geryon/ocl_device.h index 2b2367545e..14455e38a5 100644 --- a/lib/gpu/geryon/ocl_device.h +++ b/lib/gpu/geryon/ocl_device.h @@ -165,8 +165,8 @@ class UCL_Device { /// Get the current OpenCL device name inline std::string name() { return name(_device); } /// Get the OpenCL device name - inline std::string name(const int i) - { return std::string(_properties[i].name); } + inline std::string name(const int i) { + return std::string(_properties[i].name); } /// Get a string telling the type of the current device inline std::string device_type_name() { return device_type_name(_device); } @@ -281,7 +281,7 @@ class UCL_Device { inline cl_device_id & cl_device() { return _cl_device; } /// Select the platform that has accelerators - inline void set_platform_accelerator(int pid=-1); + inline int set_platform_accelerator(int pid=-1); private: int _num_platforms; // Number of platforms @@ -324,6 +324,7 @@ UCL_Device::~UCL_Device() { void UCL_Device::clear() { _properties.clear(); + _cl_devices.clear(); if (_device>-1) { for (size_t i=0; i<_cq.size(); i++) { CL_DESTRUCT_CALL(clReleaseCommandQueue(_cq.back())); @@ -520,8 +521,6 @@ int UCL_Device::device_type(const int i) { // Set the CUDA device to the specified device number int UCL_Device::set(int num) { - clear(); - cl_device_id *device_list = new cl_device_id[_num_devices]; cl_uint n; CL_SAFE_CALL(clGetDeviceIDs(_cl_platform,CL_DEVICE_TYPE_ALL,_num_devices, @@ -612,7 +611,7 @@ void UCL_Device::print_all(std::ostream &out) { // Select the platform that is associated with accelerators // if pid < 0, select the first platform -void UCL_Device::set_platform_accelerator(int pid) { +int UCL_Device::set_platform_accelerator(int pid) { if (pid < 0) { int found = 0; for (int n=0; n<_num_platforms; n++) { @@ -625,10 +624,11 @@ void UCL_Device::set_platform_accelerator(int pid) { break; } } - if (found) break; + if (found) return UCL_SUCCESS; } + return UCL_ERROR; } else { - set_platform(pid); + return set_platform(pid); } } diff --git a/lib/gpu/geryon/ocl_timer.h b/lib/gpu/geryon/ocl_timer.h index 66b79dcab1..bdfec64f54 100644 --- a/lib/gpu/geryon/ocl_timer.h +++ b/lib/gpu/geryon/ocl_timer.h @@ -38,8 +38,8 @@ namespace ucl_opencl { /// Class for timing OpenCL events class UCL_Timer { public: - inline UCL_Timer() : _total_time(0.0f), _initialized(false) { } - inline UCL_Timer(UCL_Device &dev) : _total_time(0.0f), _initialized(false) + inline UCL_Timer() : _total_time(0.0f), _initialized(false), has_measured_time(false) { } + inline UCL_Timer(UCL_Device &dev) : _total_time(0.0f), _initialized(false), has_measured_time(false) { init(dev); } inline ~UCL_Timer() { clear(); } @@ -49,11 +49,10 @@ class UCL_Timer { inline void clear() { if (_initialized) { CL_DESTRUCT_CALL(clReleaseCommandQueue(_cq)); - clReleaseEvent(start_event); - clReleaseEvent(stop_event); _initialized=false; _total_time=0.0; } + has_measured_time = false; } /// Initialize default command queue for timing @@ -66,25 +65,39 @@ class UCL_Timer { _cq=cq; clRetainCommandQueue(_cq); _initialized=true; + has_measured_time = false; } /// Start timing on default command queue - inline void start() { UCL_OCL_MARKER(_cq,&start_event); } + inline void start() { + UCL_OCL_MARKER(_cq,&start_event); + has_measured_time = false; + } /// Stop timing on default command queue - inline void stop() { UCL_OCL_MARKER(_cq,&stop_event); } + inline void stop() { + UCL_OCL_MARKER(_cq,&stop_event); + has_measured_time = true; + } /// Block until the start event has been reached on device - inline void sync_start() - { CL_SAFE_CALL(clWaitForEvents(1,&start_event)); } + inline void sync_start() { + CL_SAFE_CALL(clWaitForEvents(1,&start_event)); + has_measured_time = false; + } /// Block until the stop event has been reached on device - inline void sync_stop() - { CL_SAFE_CALL(clWaitForEvents(1,&stop_event)); } + inline void sync_stop() { + CL_SAFE_CALL(clWaitForEvents(1,&stop_event)); + has_measured_time = true; + } /// Set the time elapsed to zero (not the total_time) - inline void zero() - { UCL_OCL_MARKER(_cq,&start_event); UCL_OCL_MARKER(_cq,&stop_event); } + inline void zero() { + has_measured_time = false; + UCL_OCL_MARKER(_cq,&start_event); + UCL_OCL_MARKER(_cq,&stop_event); + } /// Set the total time to zero inline void zero_total() { _total_time=0.0; } @@ -99,6 +112,7 @@ class UCL_Timer { /// Return the time (ms) of last start to stop - Forces synchronization inline double time() { + if(!has_measured_time) return 0.0; cl_ulong tstart,tend; CL_SAFE_CALL(clWaitForEvents(1,&stop_event)); CL_SAFE_CALL(clGetEventProfilingInfo(stop_event, @@ -107,6 +121,9 @@ class UCL_Timer { CL_SAFE_CALL(clGetEventProfilingInfo(start_event, CL_PROFILING_COMMAND_END, sizeof(cl_ulong), &tstart, NULL)); + clReleaseEvent(start_event); + clReleaseEvent(stop_event); + has_measured_time = false; return (tend-tstart)*t_factor; } @@ -123,8 +140,9 @@ class UCL_Timer { cl_event start_event, stop_event; cl_command_queue _cq; double _total_time; - bool _initialized; double t_factor; + bool _initialized; + bool has_measured_time; }; } // namespace diff --git a/lib/gpu/lal_atom.h b/lib/gpu/lal_atom.h index f6a0b109f2..57880d7ca9 100644 --- a/lib/gpu/lal_atom.h +++ b/lib/gpu/lal_atom.h @@ -322,10 +322,12 @@ class Atom { // Copy charges to device asynchronously inline void add_q_data() { + time_q.start(); if (_q_avail==false) { q.update_device(_nall,true); _q_avail=true; } + time_q.stop(); } // Cast quaternions to write buffer @@ -347,10 +349,12 @@ class Atom { // Copy quaternions to device /** Copies nall()*4 elements **/ inline void add_quat_data() { + time_quat.start(); if (_quat_avail==false) { quat.update_device(_nall*4,true); _quat_avail=true; } + time_quat.stop(); } /// Cast velocities and tags to write buffer diff --git a/lib/gpu/lal_device.cpp b/lib/gpu/lal_device.cpp index 0ea128a5b3..6b4d0ab2a5 100644 --- a/lib/gpu/lal_device.cpp +++ b/lib/gpu/lal_device.cpp @@ -34,8 +34,8 @@ using namespace LAMMPS_AL; template DeviceT::Device() : _init_count(0), _device_init(false), - _gpu_mode(GPU_FORCE), _first_device(0), - _last_device(0), _compiled(false) { + _gpu_mode(GPU_FORCE), _first_device(0), + _last_device(0), _platform_id(-1), _compiled(false) { } template @@ -67,6 +67,17 @@ int DeviceT::init_device(MPI_Comm world, MPI_Comm replica, const int first_gpu, _particle_split=p_split; _cell_size=cell_size; _block_pair=block_pair; + // support selecting platform though "package device" keyword. + // "0:generic" will select platform 0 and tune for generic device + // "1:fermi" will select platform 1 and tune for Nvidia Fermi gpu + if (ocl_vendor) { + char *sep = NULL; + if ((sep = strstr(ocl_vendor,":"))) { + *sep = '\0'; + _platform_id = atoi(ocl_vendor); + ocl_vendor = sep+1; + } + } // Get the rank/size within the world MPI_Comm_rank(_comm_world,&_world_me); @@ -119,8 +130,16 @@ int DeviceT::init_device(MPI_Comm world, MPI_Comm replica, const int first_gpu, // Time on the device only if 1 proc per gpu _time_device=true; + +#if 0 + // XXX: the following setting triggers a memory leak with OpenCL and MPI + // setting _time_device=true for all processes doesn't seem to be a + // problem with either (no segfault, no (large) memory leak. + // thus keeping this disabled for now. may need to review later. + // 2018-07-23 if (_procs_per_gpu>1) _time_device=false; +#endif // Set up a per device communicator MPI_Comm_split(node_comm,my_gpu,0,&_comm_gpu); @@ -135,6 +154,9 @@ int DeviceT::init_device(MPI_Comm world, MPI_Comm replica, const int first_gpu, return -7; #endif + if (gpu->set_platform_accelerator(_platform_id)!=UCL_SUCCESS) + return -12; + if (gpu->set(my_gpu)!=UCL_SUCCESS) return -6; @@ -191,13 +213,15 @@ int DeviceT::set_ocl_params(char *ocl_vendor) { _ocl_vendor_string="-DUSE_OPENCL"; int token_count=0; std::string params[13]; - char *pch = strtok(ocl_vendor,"\" "); + char *pch = strtok(ocl_vendor,","); + pch = strtok(NULL,","); + if (pch == NULL) return -11; while (pch != NULL) { if (token_count==13) return -11; params[token_count]=pch; token_count++; - pch = strtok(NULL,"\" "); + pch = strtok(NULL,","); } _ocl_vendor_string+=" -DMEM_THREADS="+params[0]+ " -DTHREADS_PER_ATOM="+params[1]+ @@ -656,7 +680,7 @@ int DeviceT::compile_kernels() { dev_program=new UCL_Program(*gpu); int success=dev_program->load_string(device,compile_string().c_str()); if (success!=UCL_SUCCESS) - return -4; + return -6; k_zero.set_function(*dev_program,"kernel_zero"); k_info.set_function(*dev_program,"kernel_info"); _compiled=true; diff --git a/lib/gpu/lal_device.h b/lib/gpu/lal_device.h index 95e9f2a430..695b0a62f9 100644 --- a/lib/gpu/lal_device.h +++ b/lib/gpu/lal_device.h @@ -292,7 +292,7 @@ class Device { MPI_Comm _comm_world, _comm_replica, _comm_gpu; int _procs_per_gpu, _gpu_rank, _world_me, _world_size, _replica_me, _replica_size; - int _gpu_mode, _first_device, _last_device, _nthreads; + int _gpu_mode, _first_device, _last_device, _platform_id, _nthreads; double _particle_split; double _cpu_full; double _ptx_arch; diff --git a/lib/gpu/lal_neighbor.cpp b/lib/gpu/lal_neighbor.cpp index 04e08c3e9c..3e128bcf57 100644 --- a/lib/gpu/lal_neighbor.cpp +++ b/lib/gpu/lal_neighbor.cpp @@ -127,10 +127,10 @@ void Neighbor::alloc(bool &success) { dev_packed.clear(); success=success && (dev_packed.alloc((_max_nbors+2)*_max_atoms,*dev, _packed_permissions)==UCL_SUCCESS); - dev_acc.clear(); - success=success && (dev_acc.alloc(_max_atoms,*dev, + dev_ilist.clear(); + success=success && (dev_ilist.alloc(_max_atoms,*dev, UCL_READ_WRITE)==UCL_SUCCESS); - _c_bytes+=dev_packed.row_bytes()+dev_acc.row_bytes(); + _c_bytes+=dev_packed.row_bytes()+dev_ilist.row_bytes(); } if (_max_host>0) { nbor_host.clear(); @@ -197,7 +197,7 @@ void Neighbor::clear() { host_packed.clear(); host_acc.clear(); - dev_acc.clear(); + dev_ilist.clear(); dev_nbor.clear(); nbor_host.clear(); dev_packed.clear(); @@ -281,7 +281,7 @@ void Neighbor::get_host(const int inum, int *ilist, int *numj, } UCL_D_Vec acc_view; acc_view.view_offset(inum,dev_nbor,inum*2); - ucl_copy(acc_view,host_acc,true); + ucl_copy(acc_view,host_acc,inum*2,true); UCL_H_Vec host_view; host_view.alloc(_max_atoms,*dev,UCL_READ_WRITE); @@ -289,7 +289,7 @@ void Neighbor::get_host(const int inum, int *ilist, int *numj, int i=ilist[ii]; host_view[i] = ii; } - ucl_copy(dev_acc,host_view,true); + ucl_copy(dev_ilist,host_view,true); time_nbor.stop(); @@ -364,7 +364,7 @@ void Neighbor::get_host3(const int inum, const int nlist, int *ilist, int *numj, } UCL_D_Vec acc_view; acc_view.view_offset(inum,dev_nbor,inum*2); - ucl_copy(acc_view,host_acc,true); + ucl_copy(acc_view,host_acc,inum*2,true); time_nbor.stop(); if (_use_packing==false) { diff --git a/lib/gpu/lal_neighbor.h b/lib/gpu/lal_neighbor.h index 05168834c6..996deaff6d 100644 --- a/lib/gpu/lal_neighbor.h +++ b/lib/gpu/lal_neighbor.h @@ -110,7 +110,7 @@ class Neighbor { } if (_time_device) { time_nbor.add_to_total(); - time_kernel.add_to_total(); + if (_use_packing==false) time_kernel.add_to_total(); if (_gpu_nbor==2) { time_hybrid1.add_to_total(); time_hybrid2.add_to_total(); @@ -200,7 +200,7 @@ class Neighbor { /// Host storage for nbor counts (row 1) & accumulated neighbor counts (row2) UCL_H_Vec host_acc; /// Device storage for accessing atom indices from the neighbor list (3-body) - UCL_D_Vec dev_acc; + UCL_D_Vec dev_ilist; // ----------------- Data for GPU Neighbor Calculation --------------- diff --git a/lib/gpu/lal_preprocessor.h b/lib/gpu/lal_preprocessor.h index 69a8e61bd4..566a451c21 100644 --- a/lib/gpu/lal_preprocessor.h +++ b/lib/gpu/lal_preprocessor.h @@ -119,6 +119,8 @@ #define BLOCK_ELLIPSE 128 #define MAX_SHARED_TYPES 11 +#if (__CUDACC_VER_MAJOR__ < 9) + #ifdef _SINGLE_SINGLE #define shfl_xor __shfl_xor #else @@ -132,6 +134,25 @@ ucl_inline double shfl_xor(double var, int laneMask, int width) { } #endif +#else + +#ifdef _SINGLE_SINGLE +ucl_inline double shfl_xor(double var, int laneMask, int width) { + return __shfl_xor_sync(0xffffffff, var, laneMask, width); +} +#else +ucl_inline double shfl_xor(double var, int laneMask, int width) { + int2 tmp; + tmp.x = __double2hiint(var); + tmp.y = __double2loint(var); + tmp.x = __shfl_xor_sync(0xffffffff,tmp.x,laneMask,width); + tmp.y = __shfl_xor_sync(0xffffffff,tmp.y,laneMask,width); + return __hiloint2double(tmp.x,tmp.y); +} +#endif + +#endif + #endif #endif diff --git a/lib/gpu/lal_sw.cpp b/lib/gpu/lal_sw.cpp index 24984e4878..46b6382a60 100644 --- a/lib/gpu/lal_sw.cpp +++ b/lib/gpu/lal_sw.cpp @@ -243,7 +243,7 @@ void SWT::loop(const bool _eflag, const bool _vflag, const int evatom) { this->k_three_end_vatom.run(&this->atom->x, &sw1, &sw2, &sw3, &map, &elem2param, &_nelements, &this->nbor->dev_nbor, &this->_nbor_data->begin(), - &this->nbor->dev_acc, &this->dev_short_nbor, + &this->nbor->dev_ilist, &this->dev_short_nbor, &end_ans->force, &end_ans->engv, &eflag, &vflag, &ainum, &nbor_pitch, &this->_threads_per_atom, &this->_gpu_nbor); @@ -252,7 +252,7 @@ void SWT::loop(const bool _eflag, const bool _vflag, const int evatom) { this->k_three_end.run(&this->atom->x, &sw1, &sw2, &sw3, &map, &elem2param, &_nelements, &this->nbor->dev_nbor, &this->_nbor_data->begin(), - &this->nbor->dev_acc, &this->dev_short_nbor, + &this->nbor->dev_ilist, &this->dev_short_nbor, &end_ans->force, &end_ans->engv, &eflag, &vflag, &ainum, &nbor_pitch, &this->_threads_per_atom, &this->_gpu_nbor); diff --git a/lib/gpu/lal_sw.cu b/lib/gpu/lal_sw.cu index 517de70691..3b6de5a683 100644 --- a/lib/gpu/lal_sw.cu +++ b/lib/gpu/lal_sw.cu @@ -544,7 +544,7 @@ __kernel void k_sw_three_end(const __global numtyp4 *restrict x_, const int nelements, const __global int * dev_nbor, const __global int * dev_packed, - const __global int * dev_acc, + const __global int * dev_ilist, const __global int * dev_short_nbor, __global acctyp4 *restrict ans, __global acctyp *restrict engv, @@ -614,13 +614,13 @@ __kernel void k_sw_three_end(const __global numtyp4 *restrict x_, int nbor_k,numk; if (dev_nbor==dev_packed) { if (gpu_nbor) nbor_k=j+nbor_pitch; - else nbor_k=dev_acc[j]+nbor_pitch; + else nbor_k=dev_ilist[j]+nbor_pitch; numk=dev_nbor[nbor_k]; nbor_k+=nbor_pitch+fast_mul(j,t_per_atom-1); k_end=nbor_k+fast_mul(numk/t_per_atom,n_stride)+(numk & (t_per_atom-1)); nbor_k+=offset_k; } else { - nbor_k=dev_acc[j]+nbor_pitch; + nbor_k=dev_ilist[j]+nbor_pitch; numk=dev_nbor[nbor_k]; nbor_k+=nbor_pitch; nbor_k=dev_nbor[nbor_k]; @@ -698,7 +698,7 @@ __kernel void k_sw_three_end_vatom(const __global numtyp4 *restrict x_, const int nelements, const __global int * dev_nbor, const __global int * dev_packed, - const __global int * dev_acc, + const __global int * dev_ilist, const __global int * dev_short_nbor, __global acctyp4 *restrict ans, __global acctyp *restrict engv, @@ -768,13 +768,13 @@ __kernel void k_sw_three_end_vatom(const __global numtyp4 *restrict x_, int nbor_k,numk; if (dev_nbor==dev_packed) { if (gpu_nbor) nbor_k=j+nbor_pitch; - else nbor_k=dev_acc[j]+nbor_pitch; + else nbor_k=dev_ilist[j]+nbor_pitch; numk=dev_nbor[nbor_k]; nbor_k+=nbor_pitch+fast_mul(j,t_per_atom-1); k_end=nbor_k+fast_mul(numk/t_per_atom,n_stride)+(numk & (t_per_atom-1)); nbor_k+=offset_k; } else { - nbor_k=dev_acc[j]+nbor_pitch; + nbor_k=dev_ilist[j]+nbor_pitch; numk=dev_nbor[nbor_k]; nbor_k+=nbor_pitch; nbor_k=dev_nbor[nbor_k]; diff --git a/lib/gpu/lal_tersoff.cpp b/lib/gpu/lal_tersoff.cpp index a63d286d9c..ef55b98a2d 100644 --- a/lib/gpu/lal_tersoff.cpp +++ b/lib/gpu/lal_tersoff.cpp @@ -272,7 +272,7 @@ void TersoffT::loop(const bool _eflag, const bool _vflag, const int evatom) { &map, &elem2param, &_nelements, &_nparams, &_zetaij, &this->nbor->dev_nbor, &this->_nbor_data->begin(), &this->dev_short_nbor, - &_eflag, &this->_ainum, &nbor_pitch, &this->_threads_per_atom); + &eflag, &this->_ainum, &nbor_pitch, &this->_threads_per_atom); ainum=this->ans->inum(); nbor_pitch=this->nbor->nbor_pitch(); @@ -311,7 +311,7 @@ void TersoffT::loop(const bool _eflag, const bool _vflag, const int evatom) { this->k_three_end_vatom.run(&this->atom->x, &ts1, &ts2, &ts4, &cutsq, &map, &elem2param, &_nelements, &_nparams, &_zetaij, &this->nbor->dev_nbor, &this->_nbor_data->begin(), - &this->nbor->dev_acc, &this->dev_short_nbor, + &this->nbor->dev_ilist, &this->dev_short_nbor, &end_ans->force, &end_ans->engv, &eflag, &vflag, &ainum, &nbor_pitch, &this->_threads_per_atom, &this->_gpu_nbor); @@ -320,7 +320,7 @@ void TersoffT::loop(const bool _eflag, const bool _vflag, const int evatom) { this->k_three_end.run(&this->atom->x, &ts1, &ts2, &ts4, &cutsq, &map, &elem2param, &_nelements, &_nparams, &_zetaij, &this->nbor->dev_nbor, &this->_nbor_data->begin(), - &this->nbor->dev_acc, &this->dev_short_nbor, + &this->nbor->dev_ilist, &this->dev_short_nbor, &end_ans->force, &end_ans->engv, &eflag, &vflag, &ainum, &nbor_pitch, &this->_threads_per_atom, &this->_gpu_nbor); } diff --git a/lib/gpu/lal_tersoff.cu b/lib/gpu/lal_tersoff.cu index cec0ccc443..836f05660d 100644 --- a/lib/gpu/lal_tersoff.cu +++ b/lib/gpu/lal_tersoff.cu @@ -696,7 +696,7 @@ __kernel void k_tersoff_three_end(const __global numtyp4 *restrict x_, const __global acctyp4 *restrict zetaij, const __global int * dev_nbor, const __global int * dev_packed, - const __global int * dev_acc, + const __global int * dev_ilist, const __global int * dev_short_nbor, __global acctyp4 *restrict ans, __global acctyp *restrict engv, @@ -777,13 +777,13 @@ __kernel void k_tersoff_three_end(const __global numtyp4 *restrict x_, int nbor_k,numk; if (dev_nbor==dev_packed) { if (gpu_nbor) nbor_k=j+nbor_pitch; - else nbor_k=dev_acc[j]+nbor_pitch; + else nbor_k=dev_ilist[j]+nbor_pitch; numk=dev_nbor[nbor_k]; nbor_k+=nbor_pitch+fast_mul(j,t_per_atom-1); k_end=nbor_k+fast_mul(numk/t_per_atom,n_stride)+(numk & (t_per_atom-1)); nbor_k+=offset_k; } else { - nbor_k=dev_acc[j]+nbor_pitch; + nbor_k=dev_ilist[j]+nbor_pitch; numk=dev_nbor[nbor_k]; nbor_k+=nbor_pitch; nbor_k=dev_nbor[nbor_k]; @@ -941,7 +941,7 @@ __kernel void k_tersoff_three_end_vatom(const __global numtyp4 *restrict x_, const __global acctyp4 *restrict zetaij, const __global int * dev_nbor, const __global int * dev_packed, - const __global int * dev_acc, + const __global int * dev_ilist, const __global int * dev_short_nbor, __global acctyp4 *restrict ans, __global acctyp *restrict engv, @@ -1022,13 +1022,13 @@ __kernel void k_tersoff_three_end_vatom(const __global numtyp4 *restrict x_, int nbor_k,numk; if (dev_nbor==dev_packed) { if (gpu_nbor) nbor_k=j+nbor_pitch; - else nbor_k=dev_acc[j]+nbor_pitch; + else nbor_k=dev_ilist[j]+nbor_pitch; numk=dev_nbor[nbor_k]; nbor_k+=nbor_pitch+fast_mul(j,t_per_atom-1); k_end=nbor_k+fast_mul(numk/t_per_atom,n_stride)+(numk & (t_per_atom-1)); nbor_k+=offset_k; } else { - nbor_k=dev_acc[j]+nbor_pitch; + nbor_k=dev_ilist[j]+nbor_pitch; numk=dev_nbor[nbor_k]; nbor_k+=nbor_pitch; nbor_k=dev_nbor[nbor_k]; diff --git a/lib/gpu/lal_tersoff_mod.cpp b/lib/gpu/lal_tersoff_mod.cpp index c37c07f1a1..3cbb488cab 100644 --- a/lib/gpu/lal_tersoff_mod.cpp +++ b/lib/gpu/lal_tersoff_mod.cpp @@ -272,7 +272,7 @@ void TersoffMT::loop(const bool _eflag, const bool _vflag, const int evatom) { &map, &elem2param, &_nelements, &_nparams, &_zetaij, &this->nbor->dev_nbor, &this->_nbor_data->begin(), &this->dev_short_nbor, - &_eflag, &this->_ainum, &nbor_pitch, &this->_threads_per_atom); + &eflag, &this->_ainum, &nbor_pitch, &this->_threads_per_atom); ainum=this->ans->inum(); nbor_pitch=this->nbor->nbor_pitch(); @@ -311,7 +311,7 @@ void TersoffMT::loop(const bool _eflag, const bool _vflag, const int evatom) { this->k_three_end_vatom.run(&this->atom->x, &ts1, &ts2, &ts4, &ts5, &cutsq, &map, &elem2param, &_nelements, &_nparams, &_zetaij, &this->nbor->dev_nbor, &this->_nbor_data->begin(), - &this->nbor->dev_acc, &this->dev_short_nbor, + &this->nbor->dev_ilist, &this->dev_short_nbor, &end_ans->force, &end_ans->engv, &eflag, &vflag, &ainum, &nbor_pitch, &this->_threads_per_atom, &this->_gpu_nbor); @@ -320,7 +320,7 @@ void TersoffMT::loop(const bool _eflag, const bool _vflag, const int evatom) { this->k_three_end.run(&this->atom->x, &ts1, &ts2, &ts4, &ts5, &cutsq, &map, &elem2param, &_nelements, &_nparams, &_zetaij, &this->nbor->dev_nbor, &this->_nbor_data->begin(), - &this->nbor->dev_acc, &this->dev_short_nbor, + &this->nbor->dev_ilist, &this->dev_short_nbor, &end_ans->force, &end_ans->engv, &eflag, &vflag, &ainum, &nbor_pitch, &this->_threads_per_atom, &this->_gpu_nbor); } diff --git a/lib/gpu/lal_tersoff_mod.cu b/lib/gpu/lal_tersoff_mod.cu index 576359b514..dfb94c4145 100644 --- a/lib/gpu/lal_tersoff_mod.cu +++ b/lib/gpu/lal_tersoff_mod.cu @@ -272,7 +272,7 @@ __kernel void k_tersoff_mod_zeta(const __global numtyp4 *restrict x_, if (iinbor->dev_nbor, &this->_nbor_data->begin(), &this->dev_short_nbor, - &_eflag, &this->_ainum, &nbor_pitch, &this->_threads_per_atom); + &eflag, &this->_ainum, &nbor_pitch, &this->_threads_per_atom); ainum=this->ans->inum(); nbor_pitch=this->nbor->nbor_pitch(); @@ -337,7 +337,7 @@ void TersoffZT::loop(const bool _eflag, const bool _vflag, const int evatom) { this->k_three_end_vatom.run(&this->atom->x, &ts1, &ts2, &ts4, &cutsq, &map, &elem2param, &_nelements, &_nparams, &_zetaij, &this->nbor->dev_nbor, &this->_nbor_data->begin(), - &this->nbor->dev_acc, &this->dev_short_nbor, + &this->nbor->dev_ilist, &this->dev_short_nbor, &end_ans->force, &end_ans->engv, &eflag, &vflag, &ainum, &nbor_pitch, &this->_threads_per_atom, &this->_gpu_nbor); @@ -346,7 +346,7 @@ void TersoffZT::loop(const bool _eflag, const bool _vflag, const int evatom) { this->k_three_end.run(&this->atom->x, &ts1, &ts2, &ts4, &cutsq, &map, &elem2param, &_nelements, &_nparams, &_zetaij, &this->nbor->dev_nbor, &this->_nbor_data->begin(), - &this->nbor->dev_acc, &this->dev_short_nbor, + &this->nbor->dev_ilist, &this->dev_short_nbor, &end_ans->force, &end_ans->engv, &eflag, &vflag, &ainum, &nbor_pitch, &this->_threads_per_atom, &this->_gpu_nbor); } diff --git a/lib/gpu/lal_tersoff_zbl.cu b/lib/gpu/lal_tersoff_zbl.cu index e8bb017f59..73ff51c704 100644 --- a/lib/gpu/lal_tersoff_zbl.cu +++ b/lib/gpu/lal_tersoff_zbl.cu @@ -278,7 +278,7 @@ __kernel void k_tersoff_zbl_zeta(const __global numtyp4 *restrict x_, if (iik_three_end_vatom.run(&this->atom->x, ¶m1, ¶m2, ¶m3, ¶m4, ¶m5, &map, &elem2param, &_nelements, &this->nbor->dev_nbor, &this->_nbor_data->begin(), - &this->nbor->dev_acc, &this->dev_short_nbor, + &this->nbor->dev_ilist, &this->dev_short_nbor, &end_ans->force, &end_ans->engv, &eflag, &vflag, &ainum, &nbor_pitch, &this->_threads_per_atom, &this->_gpu_nbor); } else { @@ -286,7 +286,7 @@ void VashishtaT::loop(const bool _eflag, const bool _vflag, const int evatom) { this->k_three_end.run(&this->atom->x, ¶m1, ¶m2, ¶m3, ¶m4, ¶m5, &map, &elem2param, &_nelements, &this->nbor->dev_nbor, &this->_nbor_data->begin(), - &this->nbor->dev_acc, &this->dev_short_nbor, + &this->nbor->dev_ilist, &this->dev_short_nbor, &end_ans->force, &end_ans->engv, &eflag, &vflag, &ainum, &nbor_pitch, &this->_threads_per_atom, &this->_gpu_nbor); } diff --git a/lib/gpu/lal_vashishta.cu b/lib/gpu/lal_vashishta.cu index d2e8bb1496..0da46c3b53 100644 --- a/lib/gpu/lal_vashishta.cu +++ b/lib/gpu/lal_vashishta.cu @@ -554,7 +554,7 @@ __kernel void k_vashishta_three_end(const __global numtyp4 *restrict x_, const int nelements, const __global int * dev_nbor, const __global int * dev_packed, - const __global int * dev_acc, + const __global int * dev_ilist, const __global int * dev_short_nbor, __global acctyp4 *restrict ans, __global acctyp *restrict engv, @@ -623,13 +623,13 @@ __kernel void k_vashishta_three_end(const __global numtyp4 *restrict x_, int nbor_k,numk; if (dev_nbor==dev_packed) { if (gpu_nbor) nbor_k=j+nbor_pitch; - else nbor_k=dev_acc[j]+nbor_pitch; + else nbor_k=dev_ilist[j]+nbor_pitch; numk=dev_nbor[nbor_k]; nbor_k+=nbor_pitch+fast_mul(j,t_per_atom-1); k_end=nbor_k+fast_mul(numk/t_per_atom,n_stride)+(numk & (t_per_atom-1)); nbor_k+=offset_k; } else { - nbor_k=dev_acc[j]+nbor_pitch; + nbor_k=dev_ilist[j]+nbor_pitch; numk=dev_nbor[nbor_k]; nbor_k+=nbor_pitch; nbor_k=dev_nbor[nbor_k]; @@ -709,7 +709,7 @@ __kernel void k_vashishta_three_end_vatom(const __global numtyp4 *restrict x_, const int nelements, const __global int * dev_nbor, const __global int * dev_packed, - const __global int * dev_acc, + const __global int * dev_ilist, const __global int * dev_short_nbor, __global acctyp4 *restrict ans, __global acctyp *restrict engv, @@ -778,13 +778,13 @@ __kernel void k_vashishta_three_end_vatom(const __global numtyp4 *restrict x_, int nbor_k,numk; if (dev_nbor==dev_packed) { if (gpu_nbor) nbor_k=j+nbor_pitch; - else nbor_k=dev_acc[j]+nbor_pitch; + else nbor_k=dev_ilist[j]+nbor_pitch; numk=dev_nbor[nbor_k]; nbor_k+=nbor_pitch+fast_mul(j,t_per_atom-1); k_end=nbor_k+fast_mul(numk/t_per_atom,n_stride)+(numk & (t_per_atom-1)); nbor_k+=offset_k; } else { - nbor_k=dev_acc[j]+nbor_pitch; + nbor_k=dev_ilist[j]+nbor_pitch; numk=dev_nbor[nbor_k]; nbor_k+=nbor_pitch; nbor_k=dev_nbor[nbor_k]; diff --git a/lib/kokkos/cmake/kokkos_settings.cmake b/lib/kokkos/cmake/kokkos_settings.cmake index 21c9d75a96..58b30ba24d 100644 --- a/lib/kokkos/cmake/kokkos_settings.cmake +++ b/lib/kokkos/cmake/kokkos_settings.cmake @@ -158,7 +158,7 @@ if (NOT "${KOKKOS_INTERNAL_PATHS}" STREQUAL "") set(KOKKOS_SETTINGS ${KOKKOS_SETTINGS} ${KOKKOS_INTERNAL_PATHS}) endif() if (NOT "${KOKKOS_INTERNAL_ADDTOPATH}" STREQUAL "") - set(KOKKOS_SETTINGS ${KOKKOS_SETTINGS} "PATH=\"${KOKKOS_INTERNAL_ADDTOPATH}:$ENV{PATH}\"") + set(KOKKOS_SETTINGS ${KOKKOS_SETTINGS} "PATH=${KOKKOS_INTERNAL_ADDTOPATH}:$ENV{PATH}") endif() if (CMAKE_CXX_STANDARD) diff --git a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_View.hpp b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_View.hpp index 49b11f3ae0..11aa695f08 100644 --- a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_View.hpp +++ b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_View.hpp @@ -292,7 +292,8 @@ public: #if ! defined( KOKKOS_ENABLE_CUDA_LDG_INTRINSIC ) if ( 0 == r ) { - Kokkos::abort("Cuda const random access View using Cuda texture memory requires Kokkos to allocate the View's memory"); + //Kokkos::abort("Cuda const random access View using Cuda texture memory requires Kokkos to allocate the View's memory"); + return handle_type(); } #endif diff --git a/lib/latte/Install.py b/lib/latte/Install.py index 82936ecda4..3b211858dd 100644 --- a/lib/latte/Install.py +++ b/lib/latte/Install.py @@ -4,7 +4,7 @@ # used to automate the steps described in the README file in this dir from __future__ import print_function -import sys,os,re,subprocess +import sys,os,re,subprocess,hashlib # help message @@ -24,7 +24,7 @@ specify one or more options, order does not matter -b = download and build the LATTE library -p = specify folder of existing LATTE installation -m = copy Makefile.lammps.suffix to Makefile.lammps - -v = set version of LATTE library to download and set up (default = 1.1.1) + -v = set version of LATTE library to download and set up (default = 1.2.1) Example: @@ -36,6 +36,13 @@ make lib-latte args="-p $HOME/latte" # use existing LATTE installation version = '1.2.1' +# known checksums for different LATTE versions. used to validate the download. +checksums = { \ + '1.1.0' : '533635721ee222d0ed2925a18fb5b294', \ + '1.2.0' : '68bf0db879da5e068a71281020239ae7', \ + '1.2.1' : '85ac414fdada2d04619c8f936344df14', \ + } + # print error message or help def error(str=None): @@ -91,6 +98,17 @@ def geturl(url,fname): error("Failed to download source code with 'curl' or 'wget'") return +def checkmd5sum(md5sum,fname): + with open(fname,'rb') as fh: + m = hashlib.md5() + while True: + data = fh.read(81920) + if not data: + break + m.update(data) + fh.close() + return m.hexdigest() == md5sum + # parse args args = sys.argv[1:] @@ -144,7 +162,12 @@ if buildflag: print("Downloading LATTE ...") geturl(url,"LATTE.tar.gz") - print("Unpacking LATTE zipfile ...") + # verify downloaded archive integrity via md5 checksum, if known. + if version in checksums: + if not checkmd5sum(checksums[version],'LATTE.tar.gz'): + error("Checksum for LATTE library does not match") + + print("Unpacking LATTE ...") if os.path.exists(lattedir): cmd = 'rm -rf "%s"' % lattedir subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) @@ -162,7 +185,7 @@ if buildflag: # create 3 links in lib/latte to LATTE dirs # do this -b or -p is set - + if buildflag or pathflag: print("Creating links to LATTE files") if os.path.isfile("includelink") or os.path.islink("includelink"): diff --git a/lib/latte/Makefile.lammps.ifort b/lib/latte/Makefile.lammps.ifort index 0491bdd8a5..90010210af 100644 --- a/lib/latte/Makefile.lammps.ifort +++ b/lib/latte/Makefile.lammps.ifort @@ -4,9 +4,9 @@ latte_SYSINC = latte_SYSLIB = ../../lib/latte/filelink.o \ - -llatte -lifcore -lsvml -lompstub -limf -lmkl_intel_lp64 \ - -lmkl_intel_thread -lmkl_core -lmkl_intel_thread -lpthread \ - -openmp -O0 + -llatte -lifport -lifcore -lsvml -lompstub -limf \ + -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core \ + -lmkl_intel_thread -lpthread -openmp latte_SYSPATH = -openmp -L${MKLROOT}/lib/intel64 -lmkl_lapack95_lp64 \ -L/opt/intel/composer_xe_2013_sp1.2.144/compiler/lib/intel64 diff --git a/lib/message/Install.py b/lib/message/Install.py new file mode 100644 index 0000000000..d3f31c986f --- /dev/null +++ b/lib/message/Install.py @@ -0,0 +1,118 @@ +#!/usr/bin/env python + +# Install.py tool to build the CSlib library +# used to automate the steps described in the README file in this dir + +from __future__ import print_function +import sys,os,re,subprocess + +# help message + +help = """ +Syntax from src dir: make lib-message args="-m" + or: make lib-message args="-s -z" +Syntax from lib dir: python Install.py -m + or: python Install.py -s -z + +specify zero or more options, order does not matter + + -m = parallel build of CSlib library + -s = serial build of CSlib library + -z = build CSlib library with ZMQ socket support, default = no ZMQ support + +Example: + +make lib-message args="-m -z" # build parallel CSlib with ZMQ support +make lib-message args="-s" # build serial CSlib with no ZMQ support +""" + +# print error message or help + +def error(str=None): + if not str: print(help) + else: print("ERROR",str) + sys.exit() + +# expand to full path name +# process leading '~' or relative path + +def fullpath(path): + return os.path.abspath(os.path.expanduser(path)) + +def which(program): + def is_exe(fpath): + return os.path.isfile(fpath) and os.access(fpath, os.X_OK) + + fpath, fname = os.path.split(program) + if fpath: + if is_exe(program): + return program + else: + for path in os.environ["PATH"].split(os.pathsep): + path = path.strip('"') + exe_file = os.path.join(path, program) + if is_exe(exe_file): + return exe_file + + return None + +# parse args + +args = sys.argv[1:] +nargs = len(args) +if nargs == 0: error() + +mpiflag = False +serialflag = False +zmqflag = False + +iarg = 0 +while iarg < nargs: + if args[iarg] == "-m": + mpiflag = True + iarg += 1 + elif args[iarg] == "-s": + serialflag = True + iarg += 1 + elif args[iarg] == "-z": + zmqflag = True + iarg += 1 + else: error() + +if (not mpiflag and not serialflag): + error("Must use either -m or -s flag") + +if (mpiflag and serialflag): + error("Cannot use -m and -s flag at the same time") + +# build CSlib +# copy resulting lib to cslib/src/libmessage.a +# copy appropriate Makefile.lammps.* to Makefile.lammps + +print("Building CSlib ...") +srcdir = fullpath("./cslib/src") + +if mpiflag and zmqflag: + cmd = "cd %s; make lib_parallel" % srcdir +elif mpiflag and not zmqflag: + cmd = "cd %s; make lib_parallel zmq=no" % srcdir +elif not mpiflag and zmqflag: + cmd = "cd %s; make lib_serial" % srcdir +elif not mpiflag and not zmqflag: + cmd = "cd %s; make lib_serial zmq=no" % srcdir + +print(cmd) +txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) +print(txt.decode('UTF-8')) + +if mpiflag: cmd = "cd %s; cp libcsmpi.a libmessage.a" % srcdir +else: cmd = "cd %s; cp libcsnompi.a libmessage.a" % srcdir +print(cmd) +txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) +print(txt.decode('UTF-8')) + +if zmqflag: cmd = "cp Makefile.lammps.zmq Makefile.lammps" +else: cmd = "cp Makefile.lammps.nozmq Makefile.lammps" +print(cmd) +txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) +print(txt.decode('UTF-8')) diff --git a/lib/message/Makefile.lammps.nozmq b/lib/message/Makefile.lammps.nozmq new file mode 100644 index 0000000000..1bb10cc988 --- /dev/null +++ b/lib/message/Makefile.lammps.nozmq @@ -0,0 +1,5 @@ +# Settings that the LAMMPS build will import when this package library is used + +message_SYSINC = +message_SYSLIB = +message_SYSPATH = diff --git a/lib/message/Makefile.lammps.zmq b/lib/message/Makefile.lammps.zmq new file mode 100644 index 0000000000..759f2ce04b --- /dev/null +++ b/lib/message/Makefile.lammps.zmq @@ -0,0 +1,5 @@ +# Settings that the LAMMPS build will import when this package library is used + +message_SYSINC = +message_SYSLIB = -lzmq +message_SYSPATH = diff --git a/lib/message/README b/lib/message/README new file mode 100644 index 0000000000..dafb94e9ef --- /dev/null +++ b/lib/message/README @@ -0,0 +1,51 @@ +This directory contains the CSlib library which is required +to use the MESSAGE package and its client/server commands +in a LAMMPS input script. + +The CSlib libary is included in the LAMMPS distribution. A fuller +version including documentation and test programs is available at +http://cslib.sandia.gov. It was developed by Steve Plimpton at Sandia +National Laboratories. + +You can type "make lib-message" from the src directory to see help on +how to build this library via make commands, or you can do the same +thing by typing "python Install.py" from within this directory, or you +can do it manually by following the instructions below. + +The CSlib can be optionally built with support for sockets using +the open-source ZeroMQ (ZMQ) library. If it is not installed +on your system, it is easy to download and install. + +Go to the ZMQ website for details: http://zeromq.org + +----------------- + +Instructions: + +1. Compile CSlib from within cslib/src with one of the following: + % make lib_parallel # build parallel library with ZMQ socket support + % make lib_serial # build serial library with ZMQ support + % make lib_parallel zmq=no # build parallel lib with no ZMQ support + % make lib_serial zmq=no # build serial lib with no ZMQ support + +2. Copy the produced cslib/src/libcsmpi.a or libscnompi.a file to + cslib/src/libmessage.a + +3. Copy either lib/message/Makefile.lammps.zmq or Makefile.lammps.nozmq + to lib/message/Makefile.lammps, depending on whether you + build the library with ZMQ support or not. + If your ZMQ library is not in a place your shell path finds, + you can set the INCLUDE and PATH variables in Makefile.lammps + to point to the dirs where the ZMQ include and library files are. + +----------------- + +When these steps are complete you can build LAMMPS +with the MESSAGAE package installed: + +% cd lammps/src +% make yes-message +% make mpi (or whatever target you wish) + +Note that if you download and unpack a new LAMMPS tarball, you will +need to re-build the CSlib in this dir. diff --git a/lib/message/cslib/LICENSE b/lib/message/cslib/LICENSE new file mode 100644 index 0000000000..7a36e21daf --- /dev/null +++ b/lib/message/cslib/LICENSE @@ -0,0 +1,32 @@ +Program: CSlib client/server coupling library + +Copyright 2018 National Technology & Engineering Solutions of Sandia, +LLC (NTESS). Under the terms of Contract DE-NA0003525 with NTESS, the +U.S. Government retains certain rights in this software. This +software is distributed under the modified Berkeley Software +Distribution (BSD) License. + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + +* Redistributions of source code must retain the above copyright notice, + this list of conditions and the following disclaimer. + +* Redistributions in binary form must reproduce the above copyright notice, + this list of conditions and the following disclaimer in the documentation + and/or other materials provided with the distribution. + +* Neither the name of Sandia Corporation nor the names of contributors + to this software may be used to endorse or promote products derived + from this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' +AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHORS OR CONTRIBUTORS BE LIABLE FOR +ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. diff --git a/lib/message/cslib/README b/lib/message/cslib/README new file mode 100644 index 0000000000..37f4a97d54 --- /dev/null +++ b/lib/message/cslib/README @@ -0,0 +1,23 @@ +This is the the Client/Server messaging library (CSlib). + +Only the source directory and license file are included here as part +of the LAMMPS distribution. The full CSlib distribution, including +documentation and test codes, can be found at the website: +http://cslib.sandia.gov (as of Aug 2018). + +The contact author is + +Steve Plimpton +Sandia National Laboratories +sjplimp@sandia.gov +http://www.sandia.gov/~sjplimp + +The CSlib is distributed as open-source code under the modified +Berkeley Software Distribution (BSD) License. See the accompanying +LICENSE file. + +This directory contains the following: + +README this file +LICENSE GNU LGPL license +src source files for library diff --git a/lib/message/cslib/src/Makefile b/lib/message/cslib/src/Makefile new file mode 100644 index 0000000000..83cf902220 --- /dev/null +++ b/lib/message/cslib/src/Makefile @@ -0,0 +1,107 @@ +# Makefile for CSlib = client/server messaging library +# type "make help" for options + +SHELL = /bin/sh + +# ---------------------------------------- +# should only need to change this section +# compiler/linker settings +# ---------------------------------------- + +CC = g++ +CCFLAGS = -g -O3 -DZMQ_$(ZMQ) -DMPI_$(MPI) +SHFLAGS = -fPIC +ARCHIVE = ar +ARCHFLAGS = -rc +SHLIBFLAGS = -shared + +# files + +LIB = libcsmpi.a +SHLIB = libcsmpi.so +SRC = $(wildcard *.cpp) +INC = $(wildcard *.h) +OBJ = $(SRC:.cpp=.o) + +# build with ZMQ support or not + +zmq = yes +ZMQ = $(shell echo $(zmq) | tr a-z A-Z) + +ifeq ($(ZMQ),YES) + ZMQLIB = -lzmq +else + CCFLAGS += -I./STUBS_ZMQ +endif + +# build with MPI support or not + +mpi = yes +MPI = $(shell echo $(mpi) | tr a-z A-Z) + +ifeq ($(MPI),YES) + CC = mpicxx +else + CCFLAGS += -I./STUBS_MPI + LIB = libcsnompi.a + SHLIB = libcsnompi.so +endif + +# targets + +shlib: shlib_parallel shlib_serial + +lib: lib_parallel lib_serial + +all: shlib lib + +help: + @echo 'make default = shlib' + @echo 'make shlib build 2 shared CSlibs: parallel & serial' + @echo 'make lib build 2 static CSlibs: parallel & serial' + @echo 'make all build 4 CSlibs: shlib and lib' + @echo 'make shlib_parallel build shared parallel CSlib' + @echo 'make shlib_serial build shared serial CSlib' + @echo 'make lib_parallel build static parallel CSlib' + @echo 'make lib_serial build static serial CSlib' + @echo 'make ... zmq=no build w/out ZMQ support' + @echo 'make clean remove all *.o files' + @echo 'make clean-all remove *.o and lib files' + @echo 'make tar create a tarball, 2 levels up' + +shlib_parallel: + $(MAKE) clean + $(MAKE) shared zmq=$(zmq) mpi=yes + +shlib_serial: + $(MAKE) clean + $(MAKE) shared zmq=$(zmq) mpi=no + +lib_parallel: + $(MAKE) clean + $(MAKE) static zmq=$(zmq) mpi=yes + +lib_serial: + $(MAKE) clean + $(MAKE) static zmq=$(zmq) mpi=no + +static: $(OBJ) + $(ARCHIVE) $(ARCHFLAGS) $(LIB) $(OBJ) + +shared: $(OBJ) + $(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) -o $(SHLIB) $(OBJ) $(ZMQLIB) + +clean: + @rm -f *.o *.pyc + +clean-all: + @rm -f *.o *.pyc lib*.a lib*.so + +tar: + cd ../..; tar cvf cslib.tar cslib/README cslib/LICENSE \ + cslib/doc cslib/src cslib/test + +# rules + +%.o:%.cpp + $(CC) $(CCFLAGS) $(SHFLAGS) -c $< diff --git a/lib/message/cslib/src/STUBS_MPI/mpi.h b/lib/message/cslib/src/STUBS_MPI/mpi.h new file mode 100644 index 0000000000..2919e4c3a2 --- /dev/null +++ b/lib/message/cslib/src/STUBS_MPI/mpi.h @@ -0,0 +1,96 @@ +/* ---------------------------------------------------------------------- + CSlib - Client/server library for code coupling + http://cslib.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright 2018 National Technology & Engineering Solutions of + Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with + NTESS, the U.S. Government retains certain rights in this software. + This software is distributed under the modified Berkeley Software + Distribution (BSD) License. + + See the README file in the top-level CSlib directory. +------------------------------------------------------------------------- */ + +// MPI constants and dummy functions + +#ifndef MPI_DUMMY_H +#define MPI_DUMMY_H + +#include +#include +#include + +namespace CSLIB_NS { + +typedef int MPI_Comm; +typedef int MPI_Fint; +typedef int MPI_Datatype; +typedef int MPI_Status; +typedef int MPI_Op; +typedef int MPI_Info; + +#define MPI_COMM_WORLD 0 +#define MPI_MAX_PORT_NAME 0 +#define MPI_INFO_NULL 0 +#define MPI_INT 1 +#define MPI_LONG_LONG 2 +#define MPI_FLOAT 3 +#define MPI_DOUBLE 4 +#define MPI_CHAR 5 +#define MPI_SUM 0 + +static void MPI_Init(int *, char ***) {} +static MPI_Comm MPI_Comm_f2c(MPI_Comm world) {return world;} +static void MPI_Comm_rank(MPI_Comm, int *) {} +static void MPI_Comm_size(MPI_Comm, int *) {} + +static void MPI_Open_port(MPI_Info, char *) {} +static void MPI_Close_port(const char *) {} +static void MPI_Comm_accept(const char *, MPI_Info, int, + MPI_Comm, MPI_Comm *) {} +static void MPI_Comm_connect(const char *, MPI_Info, int, + MPI_Comm, MPI_Comm *) {} + +static void MPI_Comm_split(MPI_Comm, int, int, MPI_Comm *) {} +static void MPI_Comm_free(MPI_Comm *) {} + +static void MPI_Send(const void *, int, MPI_Datatype, int, int, MPI_Comm) {} +static void MPI_Recv(void *, int, MPI_Datatype, int, int, + MPI_Comm, MPI_Status *) {} + +static void MPI_Allreduce(const void *in, void *out, int, MPI_Datatype type, + MPI_Op op, MPI_Comm) +{ + if (type == MPI_INT) *((int *) out) = *((int *) in); +} +static void MPI_Scan(const void *in, void *out, int, MPI_Datatype intype, + MPI_Op op,MPI_Comm) +{ + if (intype == MPI_INT) *((int *) out) = *((int *) in); +} + +static void MPI_Bcast(void *, int, MPI_Datatype, int, MPI_Comm) {} +static void MPI_Allgather(const void *in, int incount, MPI_Datatype intype, + void *out, int, MPI_Datatype, MPI_Comm) +{ + // assuming incount = 1 + if (intype == MPI_INT) *((int *) out) = *((int *) in); +} +static void MPI_Allgatherv(const void *in, int incount, MPI_Datatype intype, + void *out, const int *, const int *, + MPI_Datatype, MPI_Comm) +{ + if (intype == MPI_INT) memcpy(out,in,incount*sizeof(int)); + else if (intype == MPI_LONG_LONG) memcpy(out,in,incount*sizeof(int64_t)); + else if (intype == MPI_FLOAT) memcpy(out,in,incount*sizeof(float)); + else if (intype == MPI_DOUBLE) memcpy(out,in,incount*sizeof(double)); + else if (intype == MPI_CHAR) memcpy(out,in,incount*sizeof(char)); +} + +static void MPI_Abort(MPI_Comm, int) {exit(1);} +static void MPI_Finalize() {} + +} + +#endif diff --git a/lib/message/cslib/src/STUBS_ZMQ/zmq.h b/lib/message/cslib/src/STUBS_ZMQ/zmq.h new file mode 100644 index 0000000000..2f02eb4035 --- /dev/null +++ b/lib/message/cslib/src/STUBS_ZMQ/zmq.h @@ -0,0 +1,36 @@ +/* ---------------------------------------------------------------------- + CSlib - Client/server library for code coupling + http://cslib.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright 2018 National Technology & Engineering Solutions of + Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with + NTESS, the U.S. Government retains certain rights in this software. + This software is distributed under the modified Berkeley Software + Distribution (BSD) License. + + See the README file in the top-level CSlib directory. +------------------------------------------------------------------------- */ + +// ZMQ constants and dummy functions + +#ifndef ZMQ_DUMMY_H +#define ZMQ_DUMMY_H + +namespace CSLIB_NS { + +#define ZMQ_REQ 0 +#define ZMQ_REP 0 + +static void *zmq_ctx_new() {return NULL;} +static void *zmq_connect(void *, char *) {return NULL;} +static int zmq_bind(void *, char *) {return 0;} +static void *zmq_socket(void *,int) {return NULL;} +static void zmq_close(void *) {} +static void zmq_ctx_destroy(void *) {} +static void zmq_send(void *, void *, int, int) {} +static void zmq_recv(void *, void *, int, int) {} + +}; + +#endif diff --git a/lib/message/cslib/src/cslib.cpp b/lib/message/cslib/src/cslib.cpp new file mode 100644 index 0000000000..874333607e --- /dev/null +++ b/lib/message/cslib/src/cslib.cpp @@ -0,0 +1,768 @@ +/* ---------------------------------------------------------------------- + CSlib - Client/server library for code coupling + http://cslib.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright 2018 National Technology & Engineering Solutions of + Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with + NTESS, the U.S. Government retains certain rights in this software. + This software is distributed under the modified Berkeley Software + Distribution (BSD) License. + + See the README file in the top-level CSlib directory. +------------------------------------------------------------------------- */ + +#include +#include +#include +#include +#include + +#include "cslib.h" +#include "msg_file.h" +#include "msg_zmq.h" +#include "msg_mpi_one.h" +#include "msg_mpi_two.h" + +using namespace CSLIB_NS; + +#define MAXTYPE 5 // # of defined field data types + +/* ---------------------------------------------------------------------- */ + +CSlib::CSlib(int csflag, const char *mode, const void *ptr, const void *pcomm) +{ + if (pcomm) myworld = (uint64_t) *((MPI_Comm *) pcomm); + else myworld = 0; + +#ifdef MPI_NO + if (pcomm) + error_all("constructor(): CSlib invoked with MPI_Comm " + "but built w/out MPI support"); +#endif +#ifdef MPI_YES // NOTE: this could be OK to allow ?? + // would allow a parallel app to invoke CSlib + // in parallel and/or in serial + if (!pcomm) + error_all("constructor(): CSlib invoked w/out MPI_Comm " + "but built with MPI support"); +#endif + + client = server = 0; + if (csflag == 0) client = 1; + else if (csflag == 1) server = 1; + else error_all("constructor(): Invalid client/server arg"); + + if (pcomm == NULL) { + me = 0; + nprocs = 1; + + if (strcmp(mode,"file") == 0) msg = new MsgFile(csflag,ptr); + else if (strcmp(mode,"zmq") == 0) msg = new MsgZMQ(csflag,ptr); + else if (strcmp(mode,"mpi/one") == 0) + error_all("constructor(): No mpi/one mode for serial lib usage"); + else if (strcmp(mode,"mpi/two") == 0) + error_all("constructor(): No mpi/two mode for serial lib usage"); + else error_all("constructor(): Unknown mode"); + + } else if (pcomm) { + MPI_Comm world = (MPI_Comm) myworld; + MPI_Comm_rank(world,&me); + MPI_Comm_size(world,&nprocs); + + if (strcmp(mode,"file") == 0) msg = new MsgFile(csflag,ptr,world); + else if (strcmp(mode,"zmq") == 0) msg = new MsgZMQ(csflag,ptr,world); + else if (strcmp(mode,"mpi/one") == 0) msg = new MsgMPIOne(csflag,ptr,world); + else if (strcmp(mode,"mpi/two") == 0) msg = new MsgMPITwo(csflag,ptr,world); + else error_all("constructor(): Unknown mode"); + } + + maxfield = 0; + fieldID = fieldtype = fieldlen = fieldoffset = NULL; + maxheader = 0; + header = NULL; + maxbuf = 0; + buf = NULL; + + recvcounts = displs = NULL; + maxglobal = 0; + allids = NULL; + maxfieldbytes = 0; + fielddata = NULL; + + pad = "\0\0\0\0\0\0\0"; // just length 7 since will have trailing NULL + + nsend = nrecv = 0; +} + +/* ---------------------------------------------------------------------- */ + +CSlib::~CSlib() +{ + deallocate_fields(); + sfree(header); + sfree(buf); + + sfree(recvcounts); + sfree(displs); + sfree(allids); + sfree(fielddata); + + delete msg; +} + +/* ---------------------------------------------------------------------- */ + +void CSlib::send(int msgID_caller, int nfield_caller) +{ + if (nfield_caller < 0) error_all("send(): Invalid nfield"); + + msgID = msgID_caller; + nfield = nfield_caller; + allocate_fields(); + + fieldcount = 0; + nbuf = 0; + + if (fieldcount == nfield) send_message(); +} + +/* ---------------------------------------------------------------------- */ + +void CSlib::pack_int(int id, int value) +{ + pack(id,1,1,&value); +} + +/* ---------------------------------------------------------------------- */ + +void CSlib::pack_int64(int id, int64_t value) +{ + pack(id,2,1,&value); +} + +/* ---------------------------------------------------------------------- */ + +void CSlib::pack_float(int id, float value) +{ + pack(id,3,1,&value); +} + +/* ---------------------------------------------------------------------- */ + +void CSlib::pack_double(int id, double value) +{ + pack(id,4,1,&value); +} + +/* ---------------------------------------------------------------------- */ + +void CSlib::pack_string(int id, char *value) +{ + pack(id,5,strlen(value)+1,value); +} + +/* ---------------------------------------------------------------------- */ + +void CSlib::pack(int id, int ftype, int flen, void *data) +{ + if (find_field(id,fieldcount) >= 0) + error_all("pack(): Reuse of field ID"); + if (ftype < 1 || ftype > MAXTYPE) error_all("pack(): Invalid ftype"); + if (flen < 0) error_all("pack(): Invalid flen"); + + fieldID[fieldcount] = id; + fieldtype[fieldcount] = ftype; + fieldlen[fieldcount] = flen; + + int nbytes,nbytesround; + onefield(ftype,flen,nbytes,nbytesround); + + memcpy(&buf[nbuf],data,nbytes); + memcpy(&buf[nbuf+nbytes],pad,nbytesround-nbytes); + nbuf += nbytesround; + + fieldcount++; + if (fieldcount == nfield) send_message(); +} + +/* ---------------------------------------------------------------------- */ + +void CSlib::pack_parallel(int id, int ftype, + int nlocal, int *ids, int nper, void *data) +{ + int i,j,k,m; + + if (find_field(id,fieldcount) >= 0) + error_all("pack_parallel(): Reuse of field ID"); + if (ftype < 1 || ftype > MAXTYPE) error_all("pack_parallel(): Invalid ftype"); + if (nlocal < 0) error_all("pack_parallel(): Invalid nlocal"); + if (nper < 1) error_all("pack_parallel(): Invalid nper"); + + MPI_Comm world = (MPI_Comm) myworld; + + // NOTE: check for overflow of maxglobal and flen + + int nglobal; + MPI_Allreduce(&nlocal,&nglobal,1,MPI_INT,MPI_SUM,world); + int flen = nper*nglobal; + + fieldID[fieldcount] = id; + fieldtype[fieldcount] = ftype; + fieldlen[fieldcount] = flen; + + // nlocal datums, each of nper length, from all procs + // final data in buf = datums for all natoms, ordered by ids + + if (recvcounts == NULL) { + recvcounts = (int *) smalloc(nprocs*sizeof(int)); + displs = (int *) smalloc(nprocs*sizeof(int)); + } + + MPI_Allgather(&nlocal,1,MPI_INT,recvcounts,1,MPI_INT,world); + + displs[0] = 0; + for (int iproc = 1; iproc < nprocs; iproc++) + displs[iproc] = displs[iproc-1] + recvcounts[iproc-1]; + + if (ids && nglobal > maxglobal) { + sfree(allids); + maxglobal = nglobal; + // NOTE: maxglobal*sizeof(int) could overflow int + allids = (int *) smalloc(maxglobal*sizeof(int)); + } + + MPI_Allgatherv(ids,nlocal,MPI_INT,allids, + recvcounts,displs,MPI_INT,world); + + int nlocalsize = nper*nlocal; + MPI_Allgather(&nlocalsize,1,MPI_INT,recvcounts,1,MPI_INT,world); + + displs[0] = 0; + for (int iproc = 1; iproc < nprocs; iproc++) + displs[iproc] = displs[iproc-1] + recvcounts[iproc-1]; + + int nbytes,nbytesround; + onefield(ftype,flen,nbytes,nbytesround); + + if (ftype == 1) { + int *alldata; + if (ids) { + if (nbytes > maxfieldbytes) { + sfree(fielddata); + maxfieldbytes = nbytes; + fielddata = (char *) smalloc(maxfieldbytes); + } + alldata = (int *) fielddata; + } else alldata = (int *) &buf[nbuf]; + MPI_Allgatherv(data,nlocalsize,MPI_INT,alldata, + recvcounts,displs,MPI_INT,world); + if (ids) { + int *bufptr = (int *) &buf[nbuf]; + m = 0; + for (i = 0; i < nglobal; i++) { + j = (allids[i]-1) * nper; + if (nper == 1) bufptr[j] = alldata[m++]; + else + for (k = 0; k < nper; k++) + bufptr[j++] = alldata[m++]; + } + } + + } else if (ftype == 2) { + int64_t *alldata; + if (ids) { + if (nbytes > maxfieldbytes) { + sfree(fielddata); + maxfieldbytes = nbytes; + fielddata = (char *) smalloc(maxfieldbytes); + } + alldata = (int64_t *) fielddata; + } else alldata = (int64_t *) &buf[nbuf]; + // NOTE: may be just MPI_LONG on some machines + MPI_Allgatherv(data,nlocalsize,MPI_LONG_LONG,alldata, + recvcounts,displs,MPI_LONG_LONG,world); + if (ids) { + int64_t *bufptr = (int64_t *) &buf[nbuf]; + m = 0; + for (i = 0; i < nglobal; i++) { + j = (allids[i]-1) * nper; + if (nper == 1) bufptr[j] = alldata[m++]; + else + for (k = 0; k < nper; k++) + bufptr[j++] = alldata[m++]; + } + } + + } else if (ftype == 3) { + float *alldata; + if (ids) { + if (nbytes > maxfieldbytes) { + sfree(fielddata); + maxfieldbytes = nbytes; + fielddata = (char *) smalloc(maxfieldbytes); + } + alldata = (float *) fielddata; + } else alldata = (float *) &buf[nbuf]; + MPI_Allgatherv(data,nlocalsize,MPI_FLOAT,alldata, + recvcounts,displs,MPI_FLOAT,world); + if (ids) { + float *bufptr = (float *) &buf[nbuf]; + m = 0; + for (i = 0; i < nglobal; i++) { + j = (allids[i]-1) * nper; + if (nper == 1) bufptr[j] = alldata[m++]; + else + for (k = 0; k < nper; k++) + bufptr[j++] = alldata[m++]; + } + } + + } else if (ftype == 4) { + double *alldata; + if (ids) { + if (nbytes > maxfieldbytes) { + sfree(fielddata); + maxfieldbytes = nbytes; + fielddata = (char *) smalloc(maxfieldbytes); + } + alldata = (double *) fielddata; + } else alldata = (double *) &buf[nbuf]; + MPI_Allgatherv(data,nlocalsize,MPI_DOUBLE,alldata, + recvcounts,displs,MPI_DOUBLE,world); + if (ids) { + double *bufptr = (double *) &buf[nbuf]; + m = 0; + for (i = 0; i < nglobal; i++) { + j = (allids[i]-1) * nper; + if (nper == 1) bufptr[j] = alldata[m++]; + else + for (k = 0; k < nper; k++) + bufptr[j++] = alldata[m++]; + } + } + + /* eventually ftype = BYTE, but not yet + } else if (ftype == 5) { + char *alldata; + if (ids) { + if (nbytes > maxfieldbytes) { + sfree(fielddata); + maxfieldbytes = nbytes; + fielddata = (char *) smalloc(maxfieldbytes); + } + alldata = (char *) fielddata; + } else alldata = (char *) &buf[nbuf]; + MPI_Allgatherv(data,nlocalsize,MPI_CHAR,alldata, + recvcounts,displs,MPI_CHAR,world); + if (ids) { + char *bufptr = (char *) &buf[nbuf]; + m = 0; + for (i = 0; i < nglobal; i++) { + j = (allids[i]-1) * nper; + memcpy(&bufptr[j],&alldata[m],nper); + m += nper; + } + } + */ + } + + memcpy(&buf[nbuf+nbytes],pad,nbytesround-nbytes); + nbuf += nbytesround; + + fieldcount++; + if (fieldcount == nfield) send_message(); +} + +/* ---------------------------------------------------------------------- */ + +void CSlib::send_message() +{ + // setup header message + + int m = 0; + header[m++] = msgID; + header[m++] = nfield; + for (int ifield = 0; ifield < nfield; ifield++) { + header[m++] = fieldID[ifield]; + header[m++] = fieldtype[ifield]; + header[m++] = fieldlen[ifield]; + } + + msg->send(nheader,header,nbuf,buf); + nsend++; +} + +/* ---------------------------------------------------------------------- */ + +int CSlib::recv(int &nfield_caller, int *&fieldID_caller, + int *&fieldtype_caller, int *&fieldlen_caller) +{ + msg->recv(maxheader,header,maxbuf,buf); + nrecv++; + + // unpack header message + + int m = 0; + msgID = header[m++]; + nfield = header[m++]; + allocate_fields(); + + int nbytes,nbytesround; + + nbuf = 0; + for (int ifield = 0; ifield < nfield; ifield++) { + fieldID[ifield] = header[m++]; + fieldtype[ifield] = header[m++]; + fieldlen[ifield] = header[m++]; + fieldoffset[ifield] = nbuf; + onefield(fieldtype[ifield],fieldlen[ifield],nbytes,nbytesround); + nbuf += nbytesround; + } + + // return message parameters + + nfield_caller = nfield; + fieldID_caller = fieldID; + fieldtype_caller = fieldtype; + fieldlen_caller = fieldlen; + + return msgID; +} + +/* ---------------------------------------------------------------------- */ + +int CSlib::unpack_int(int id) +{ + int ifield = find_field(id,nfield); + if (ifield < 0) error_all("unpack_int(): Unknown field ID"); + if (fieldtype[ifield] != 1) error_all("unpack_int(): Mis-match of ftype"); + if (fieldlen[ifield] != 1) error_all("unpack_int(): Flen is not 1"); + + int *ptr = (int *) unpack(id); + return *ptr; +} + +/* ---------------------------------------------------------------------- */ + +int64_t CSlib::unpack_int64(int id) +{ + int ifield = find_field(id,nfield); + if (ifield < 0) error_all("unpack_int64(): Unknown field ID"); + if (fieldtype[ifield] != 2) error_all("unpack_int64(): Mis-match of ftype"); + if (fieldlen[ifield] != 1) error_all("unpack_int64(): Flen is not 1"); + + int64_t *ptr = (int64_t *) unpack(id); + return *ptr; +} + +/* ---------------------------------------------------------------------- */ + +float CSlib::unpack_float(int id) +{ + int ifield = find_field(id,nfield); + if (ifield < 0) error_all("unpack_float(): Unknown field ID"); + if (fieldtype[ifield] != 3) error_all("unpack_float(): Mis-match of ftype"); + if (fieldlen[ifield] != 1) error_all("unpack_float(): Flen is not 1"); + + float *ptr = (float *) unpack(id); + return *ptr; +} + +/* ---------------------------------------------------------------------- */ + +double CSlib::unpack_double(int id) +{ + int ifield = find_field(id,nfield); + if (ifield < 0) error_all("unpack_double(): Unknown field ID"); + if (fieldtype[ifield] != 4) error_all("unpack_double(): Mis-match of ftype"); + if (fieldlen[ifield] != 1) error_all("unpack_double(): Flen is not 1"); + + double *ptr = (double *) unpack(id); + return *ptr; +} + +/* ---------------------------------------------------------------------- */ + +char *CSlib::unpack_string(int id) +{ + int ifield = find_field(id,nfield); + if (ifield < 0) error_all("unpack_string(): Unknown field ID"); + if (fieldtype[ifield] != 5) error_all("unpack_string(): Mis-match of ftype"); + + char *ptr = (char *) unpack(id); + return ptr; +} + +/* ---------------------------------------------------------------------- */ + +void *CSlib::unpack(int id) +{ + int ifield = find_field(id,nfield); + if (ifield < 0) error_all("unpack(): Unknown field ID"); + return &buf[fieldoffset[ifield]]; +} + +/* ---------------------------------------------------------------------- */ + +void CSlib::unpack(int id, void *data) +{ + int ifield = find_field(id,nfield); + if (ifield < 0) error_all("unpack(): Unknown field ID"); + + int ftype = fieldtype[ifield]; + int nbytes = fieldlen[ifield]; + if (ftype == 1) nbytes *= sizeof(int); + else if (ftype == 2) nbytes *= sizeof(int64_t); + else if (ftype == 3) nbytes *= sizeof(float); + else if (ftype == 4) nbytes *= sizeof(double); + memcpy(data,&buf[fieldoffset[ifield]],nbytes); +} + +/* ---------------------------------------------------------------------- */ + +void CSlib::unpack_parallel(int id, int nlocal, int *ids, int nper, void *data) +{ + int i,j,k,m; + + int ifield = find_field(id,nfield); + if (ifield < 0) error_all("unpack_parallel(): Unknown field ID"); + if (nlocal < 0) error_all("unpack_parallel(): Invalid nlocal"); + if (nper < 1) error_all("pack_parallel(): Invalid nper"); + + MPI_Comm world = (MPI_Comm) myworld; + + int upto; + if (!ids) { + MPI_Scan(&nlocal,&upto,1,MPI_INT,MPI_SUM,world); + upto -= nlocal; + } + + if (fieldtype[ifield] == 1) { + int *local = (int *) data; + int *global = (int *) &buf[fieldoffset[ifield]]; + if (!ids) memcpy(local,&global[nper*upto],nper*nlocal*sizeof(int)); + else { + m = 0; + for (i = 0; i < nlocal; i++) { + j = (ids[i]-1) * nper; + if (nper == 1) local[m++] = global[j]; + else + for (k = 0; k < nper; k++) + local[m++] = global[j++]; + } + } + + } else if (fieldtype[ifield] == 2) { + int64_t *local = (int64_t *) data; + int64_t *global = (int64_t *) &buf[fieldoffset[ifield]]; + if (!ids) memcpy(local,&global[nper*upto],nper*nlocal*sizeof(int64_t)); + else { + m = 0; + for (i = 0; i < nlocal; i++) { + j = (ids[i]-1) * nper; + if (nper == 1) local[m++] = global[j]; + else + for (k = 0; k < nper; k++) + local[m++] = global[j++]; + } + } + + } else if (fieldtype[ifield] == 3) { + float *local = (float *) data; + float *global = (float *) &buf[fieldoffset[ifield]]; + if (!ids) memcpy(local,&global[nper*upto],nper*nlocal*sizeof(float)); + else { + m = 0; + for (i = 0; i < nlocal; i++) { + j = (ids[i]-1) * nper; + if (nper == 1) local[m++] = global[j]; + else + for (k = 0; k < nper; k++) + local[m++] = global[j++]; + } + } + + } else if (fieldtype[ifield] == 4) { + double *local = (double *) data; + double *global = (double *) &buf[fieldoffset[ifield]]; + if (!ids) memcpy(local,&global[nper*upto],nper*nlocal*sizeof(double)); + else { + m = 0; + for (i = 0; i < nlocal; i++) { + j = (ids[i]-1) * nper; + if (nper == 1) local[m++] = global[j]; + else + for (k = 0; k < nper; k++) + local[m++] = global[j++]; + } + } + + /* eventually ftype = BYTE, but not yet + } else if (fieldtype[ifield] == 5) { + char *local = (char *) data; + char *global = (char *) &buf[fieldoffset[ifield]]; + if (!ids) memcpy(local,&global[nper*upto],nper*nlocal*sizeof(char)); + else { + m = 0; + for (i = 0; i < nlocal; i++) { + j = (ids[i]-1) * nper; + memcpy(&local[m],&global[j],nper); + m += nper; + } + } + */ + } +} + +/* ---------------------------------------------------------------------- */ + +int CSlib::extract(int flag) +{ + if (flag == 1) return nsend; + if (flag == 2) return nrecv; + error_all("extract(): Invalid flag"); + return 0; +} + +/* ---------------------------------------------------------------------- */ + +void CSlib::onefield(int ftype, int flen, int &nbytes, int &nbytesround) +{ + int64_t bigbytes,bigbytesround; + int64_t biglen = flen; + + if (ftype == 1) bigbytes = biglen * sizeof(int); + else if (ftype == 2) bigbytes = biglen * sizeof(int64_t); + else if (ftype == 3) bigbytes = biglen * sizeof(float); + else if (ftype == 4) bigbytes = biglen * sizeof(double); + else if (ftype == 5) bigbytes = biglen * sizeof(char); + bigbytesround = roundup(bigbytes,8); + + if (nbuf + bigbytesround > INT_MAX) + error_all("pack(): Message size exceeds 32-bit integer limit"); + + nbytes = (int) bigbytes; + nbytesround = (int) bigbytesround; + if (nbuf + nbytesround > maxbuf) { + maxbuf = nbuf + nbytesround; + buf = (char *) srealloc(buf,maxbuf); + } +} + +/* ---------------------------------------------------------------------- */ + +int CSlib::find_field(int id, int n) +{ + int ifield; + for (ifield = 0; ifield < n; ifield++) + if (id == fieldID[ifield]) return ifield; + return -1; +} + +/* ---------------------------------------------------------------------- */ + +void CSlib::allocate_fields() +{ + int64_t bigbytes = (2 + 3*((int64_t) nfield)) * sizeof(int); + if (bigbytes > INT_MAX) + error_all("send(): Message header size exceeds 32-bit integer limit"); + + nheader = 2; + nheader += 3 * nfield; + + if (nfield > maxfield) { + deallocate_fields(); + maxfield = nfield; + fieldID = new int[maxfield]; + fieldtype = new int[maxfield]; + fieldlen = new int[maxfield]; + fieldoffset = new int[maxfield]; + } + + if (nheader > maxheader) { + sfree(header); + maxheader = nheader; + header = (int *) smalloc(maxheader*sizeof(int)); + } +} + +/* ---------------------------------------------------------------------- */ + +void CSlib::deallocate_fields() +{ + delete [] fieldID; + delete [] fieldtype; + delete [] fieldlen; + delete [] fieldoffset; +} + +/* ---------------------------------------------------------------------- */ + +void *CSlib::smalloc(int nbytes) +{ + if (nbytes == 0) return NULL; + void *ptr = malloc(nbytes); + if (ptr == NULL) { + char str[128]; + sprintf(str,"malloc(): Failed to allocate %d bytes",nbytes); + error_one(str); + } + return ptr; +} + +/* ---------------------------------------------------------------------- */ + +void *CSlib::srealloc(void *ptr, int nbytes) +{ + if (nbytes == 0) { + sfree(ptr); + return NULL; + } + + ptr = realloc(ptr,nbytes); + if (ptr == NULL) { + char str[128]; + sprintf(str,"realloc(): Failed to reallocate %d bytes",nbytes); + error_one(str); + } + return ptr; +} + +/* ---------------------------------------------------------------------- */ + +void CSlib::sfree(void *ptr) +{ + if (ptr == NULL) return; + free(ptr); +} + +/* ---------------------------------------------------------------------- */ + +void CSlib::error_all(const char *str) +{ + if (me == 0) printf("CSlib ERROR: %s\n",str); + MPI_Comm world = (MPI_Comm) myworld; + MPI_Abort(world,1); +} + +/* ---------------------------------------------------------------------- */ + +void CSlib::error_one(const char *str) +{ + printf("CSlib ERROR: %s\n",str); + MPI_Comm world = (MPI_Comm) myworld; + MPI_Abort(world,1); +} + +/* ---------------------------------------------------------------------- + round N up to multiple of nalign and return it + NOTE: see mapreduce/src/keyvalue.cpp for doing this as uint64_t +------------------------------------------------------------------------- */ + +int64_t CSlib::roundup(int64_t n, int nalign) +{ + if (n % nalign == 0) return n; + n = (n/nalign + 1) * nalign; + return n; +} diff --git a/lib/message/cslib/src/cslib.h b/lib/message/cslib/src/cslib.h new file mode 100644 index 0000000000..b4da968026 --- /dev/null +++ b/lib/message/cslib/src/cslib.h @@ -0,0 +1,87 @@ +/* ---------------------------------------------------------------------- + CSlib - Client/server library for code coupling + http://cslib.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright 2018 National Technology & Engineering Solutions of + Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with + NTESS, the U.S. Government retains certain rights in this software. + This software is distributed under the modified Berkeley Software + Distribution (BSD) License. + + See the README file in the top-level CSlib directory. +------------------------------------------------------------------------- */ + +#ifndef CSLIB_H +#define CSLIB_H + +#include + +namespace CSLIB_NS { + +class CSlib { + public: + int nsend,nrecv; + + CSlib(int, const char *, const void *, const void *); + ~CSlib(); + + void send(int, int); + + void pack_int(int, int); + void pack_int64(int, int64_t); + void pack_float(int, float); + void pack_double(int, double); + void pack_string(int, char *); + void pack(int, int, int, void *); + void pack_parallel(int, int, int, int *, int, void *); + + int recv(int &, int *&, int *&, int *&); + + int unpack_int(int); + int64_t unpack_int64(int); + float unpack_float(int); + double unpack_double(int); + char *unpack_string(int); + void *unpack(int); + void unpack(int, void *); + void unpack_parallel(int, int, int *, int, void *); + + int extract(int); + + private: + uint64_t myworld; // really MPI_Comm, but avoids use of mpi.h in this file + // so apps can include this file w/ no MPI on system + int me,nprocs; + int client,server; + int nfield,maxfield; + int msgID,fieldcount; + int nheader,maxheader; + int nbuf,maxbuf; + int maxglobal,maxfieldbytes; + int *fieldID,*fieldtype,*fieldlen,*fieldoffset; + int *header; + int *recvcounts,*displs; // nprocs size for Allgathers + int *allids; // nglobal size for pack_parallel() + char *buf; // maxbuf size for msg with all fields + char *fielddata; // maxfieldbytes size for one global field + const char *pad; + + class Msg *msg; + + void send_message(); + void onefield(int, int, int &, int &); + int find_field(int, int); + void allocate_fields(); + void deallocate_fields(); + int64_t roundup(int64_t, int); + void *smalloc(int); + void *srealloc(void *, int); + void sfree(void *); + void error_all(const char *); + void error_one(const char *); +}; + +} + +#endif diff --git a/lib/message/cslib/src/cslib.py b/lib/message/cslib/src/cslib.py new file mode 100644 index 0000000000..0ba3516255 --- /dev/null +++ b/lib/message/cslib/src/cslib.py @@ -0,0 +1,362 @@ +# ------------------------------------------------------------------------ +# CSlib - Client/server library for code coupling +# http://cslib.sandia.gov, Sandia National Laboratories +# Steve Plimpton, sjplimp@sandia.gov +# +# Copyright 2018 National Technology & Engineering Solutions of +# Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with +# NTESS, the U.S. Government retains certain rights in this software. +# This software is distributed under the modified Berkeley Software +# Distribution (BSD) License. +# +# See the README file in the top-level CSlib directory. +# ------------------------------------------------------------------------- + +# Python wrapper on CSlib library via ctypes + +# ctypes and Numpy data types: +# 32-bit int = c_int = np.intc = np.int32 +# 64-bit int = c_longlong = np.int64 +# 32-bit floating point = c_float = np.float32 +# 64-bit floating point = c_double = np.float = np.float64 + +import sys,traceback +from ctypes import * + +# Numpy and mpi4py packages may not exist + +try: + import numpy as np + numpyflag = 1 +except: + numpyflag = 0 + +try: + from mpi4py import MPI + mpi4pyflag = 1 +except: + mpi4pyflag = 0 + +# wrapper class + +class CSlib: + + # instantiate CSlib thru its C-interface + + def __init__(self,csflag,mode,ptr,comm): + + # load libcslib.so + + try: + if comm: self.lib = CDLL("libcsmpi.so",RTLD_GLOBAL) + else: self.lib = CDLL("libcsnompi.so",RTLD_GLOBAL) + except: + etype,value,tb = sys.exc_info() + traceback.print_exception(etype,value,tb) + raise OSError,"Could not load CSlib dynamic library" + + # define ctypes API for each library method + + self.lib.cslib_open.argtypes = [c_int,c_char_p,c_void_p,c_void_p, + POINTER(c_void_p)] + self.lib.cslib_open.restype = None + + self.lib.cslib_close.argtypes = [c_void_p] + self.lib.cslib_close.restype = None + + self.lib.cslib_send.argtypes = [c_void_p,c_int,c_int] + self.lib.cslib_send.restype = None + + self.lib.cslib_pack_int.argtypes = [c_void_p,c_int,c_int] + self.lib.cslib_pack_int.restype = None + + self.lib.cslib_pack_int64.argtypes = [c_void_p,c_int,c_longlong] + self.lib.cslib_pack_int64.restype = None + + self.lib.cslib_pack_float.argtypes = [c_void_p,c_int,c_float] + self.lib.cslib_pack_float.restype = None + + self.lib.cslib_pack_double.argtypes = [c_void_p,c_int,c_double] + self.lib.cslib_pack_double.restype = None + + self.lib.cslib_pack_string.argtypes = [c_void_p,c_int,c_char_p] + self.lib.cslib_pack_string.restype = None + + self.lib.cslib_pack.argtypes = [c_void_p,c_int,c_int,c_int,c_void_p] + self.lib.cslib_pack.restype = None + + self.lib.cslib_pack_parallel.argtypes = [c_void_p,c_int,c_int,c_int, + POINTER(c_int),c_int,c_void_p] + self.lib.cslib_pack_parallel.restype = None + + self.lib.cslib_recv.argtypes = [c_void_p,POINTER(c_int), + POINTER(POINTER(c_int)), + POINTER(POINTER(c_int)), + POINTER(POINTER(c_int))] + self.lib.cslib_recv.restype = c_int + + self.lib.cslib_unpack_int.argtypes = [c_void_p,c_int] + self.lib.cslib_unpack_int.restype = c_int + + self.lib.cslib_unpack_int64.argtypes = [c_void_p,c_int] + self.lib.cslib_unpack_int64.restype = c_longlong + + self.lib.cslib_unpack_float.argtypes = [c_void_p,c_int] + self.lib.cslib_unpack_float.restype = c_float + + self.lib.cslib_unpack_double.argtypes = [c_void_p,c_int] + self.lib.cslib_unpack_double.restype = c_double + + self.lib.cslib_unpack_string.argtypes = [c_void_p,c_int] + self.lib.cslib_unpack_string.restype = c_char_p + + # override return in unpack() + self.lib.cslib_unpack.argtypes = [c_void_p,c_int] + self.lib.cslib_unpack.restype = c_void_p + + self.lib.cslib_unpack_data.argtypes = [c_void_p,c_int,c_void_p] + self.lib.cslib_unpack_data.restype = None + + # override last arg in unpack_parallel() + self.lib.cslib_unpack_parallel.argtypes = [c_void_p,c_int,c_int, + POINTER(c_int),c_int,c_void_p] + self.lib.cslib_unpack_parallel.restype = None + + self.lib.cslib_extract.argtypes = [c_void_p,c_int] + self.lib.cslib_extract.restype = c_int + + # create an instance of CSlib with or w/out MPI communicator + + self.cs = c_void_p() + + if not comm: + self.lib.cslib_open(csflag,mode,ptr,None,byref(self.cs)) + elif not mpi4pyflag: + print "Cannot pass MPI communicator to CSlib w/out mpi4py package" + sys.exit() + else: + address = MPI._addressof(comm) + comm_ptr = c_void_p(address) + if mode == "mpi/one": + address = MPI._addressof(ptr) + ptrcopy = c_void_p(address) + else: ptrcopy = ptr + self.lib.cslib_open(csflag,mode,ptrcopy,comm_ptr,byref(self.cs)) + + # destroy instance of CSlib + + def __del__(self): + if self.cs: self.lib.cslib_close(self.cs) + + def close(self): + self.lib.cslib_close(self.cs) + self.lib = None + + # send a message + + def send(self,msgID,nfield): + self.nfield = nfield + self.lib.cslib_send(self.cs,msgID,nfield) + + # pack one field of message + + def pack_int(self,id,value): + self.lib.cslib_pack_int(self.cs,id,value) + + def pack_int64(self,id,value): + self.lib.cslib_pack_int64(self.cs,id,value) + + def pack_float(self,id,value): + self.lib.cslib_pack_float(self.cs,id,value) + + def pack_double(self,id,value): + self.lib.cslib_pack_double(self.cs,id,value) + + def pack_string(self,id,value): + self.lib.cslib_pack_string(self.cs,id,value) + + def pack(self,id,ftype,flen,data): + cdata = self.data_convert(ftype,flen,data) + self.lib.cslib_pack(self.cs,id,ftype,flen,cdata) + + def pack_parallel(self,id,ftype,nlocal,ids,nper,data): + cids = self.data_convert(1,nlocal,ids) + cdata = self.data_convert(ftype,nper*nlocal,data) + self.lib.cslib_pack_parallel(self.cs,id,ftype,nlocal,cids,nper,cdata) + + # convert input data to a ctypes vector to pass to CSlib + + def data_convert(self,ftype,flen,data): + + # tflag = type of data + # tflag = 1 if data is list or tuple + # tflag = 2 if data is Numpy array + # tflag = 3 if data is ctypes vector + # same usage of tflag as in unpack function + + txttype = str(type(data)) + if "numpy" in txttype: tflag = 2 + elif "c_" in txttype: tflag = 3 + else: tflag = 1 + + # create ctypes vector out of data to pass to lib + # cdata = ctypes vector to return + # NOTE: error check on ftype and tflag everywhere, also flen + + if ftype == 1: + if tflag == 1: cdata = (flen * c_int)(*data) + elif tflag == 2: cdata = data.ctypes.data_as(POINTER(c_int)) + elif tflag == 3: cdata = data + elif ftype == 2: + if tflag == 1: cdata = (flen * c_longlong)(*data) + elif tflag == 2: cdata = data.ctypes.data_as(POINTER(c_longlong)) + elif tflag == 3: cdata = data + elif ftype == 3: + if tflag == 1: cdata = (flen * c_float)(*data) + elif tflag == 2: cdata = data.ctypes.data_as(POINTER(c_float)) + elif tflag == 3: cdata = data + elif ftype == 4: + if tflag == 1: cdata = (flen * c_double)(*data) + elif tflag == 2: cdata = data.ctypes.data_as(POINTER(c_double)) + elif tflag == 3: cdata = data + + return cdata + + # receive a message + + def recv(self): + self.lib.cslib_recv.restype = c_int + nfield = c_int() + fieldID = POINTER(c_int)() + fieldtype = POINTER(c_int)() + fieldlen = POINTER(c_int)() + msgID = self.lib.cslib_recv(self.cs,byref(nfield), + byref(fieldID),byref(fieldtype),byref(fieldlen)) + + # copy returned C args to native Python int and lists + # store them in class so unpack() methods can access the info + + self.nfield = nfield = nfield.value + self.fieldID = fieldID[:nfield] + self.fieldtype = fieldtype[:nfield] + self.fieldlen = fieldlen[:nfield] + + return msgID,self.nfield,self.fieldID,self.fieldtype,self.fieldlen + + # unpack one field of message + # tflag = type of data to return + # 3 = ctypes vector is default, since no conversion required + + def unpack_int(self,id): + return self.lib.cslib_unpack_int(self.cs,id) + + def unpack_int64(self,id): + return self.lib.cslib_unpack_int64(self.cs,id) + + def unpack_float(self,id): + return self.lib.cslib_unpack_float(self.cs,id) + + def unpack_double(self,id): + return self.lib.cslib_unpack_double(self.cs,id) + + def unpack_string(self,id): + return self.lib.cslib_unpack_string(self.cs,id) + + def unpack(self,id,tflag=3): + index = self.fieldID.index(id) + + # reset data type of return so can morph by tflag + # cannot do this for the generic c_void_p returned by CSlib + + if self.fieldtype[index] == 1: + self.lib.cslib_unpack.restype = POINTER(c_int) + elif self.fieldtype[index] == 2: + self.lib.cslib_unpack.restype = POINTER(c_longlong) + elif self.fieldtype[index] == 3: + self.lib.cslib_unpack.restype = POINTER(c_float) + elif self.fieldtype[index] == 4: + self.lib.cslib_unpack.restype = POINTER(c_double) + #elif self.fieldtype[index] == 5: + # self.lib.cslib_unpack.restype = POINTER(c_char) + + cdata = self.lib.cslib_unpack(self.cs,id) + + # tflag = user-requested type of data to return + # tflag = 1 to return data as list + # tflag = 2 to return data as Numpy array + # tflag = 3 to return data as ctypes vector + # same usage of tflag as in pack functions + # tflag = 2,3 should NOT perform a data copy + + if tflag == 1: + data = cdata[:self.fieldlen[index]] + elif tflag == 2: + if numpyflag == 0: + print "Cannot return Numpy array w/out numpy package" + sys.exit() + data = np.ctypeslib.as_array(cdata,shape=(self.fieldlen[index],)) + elif tflag == 3: + data = cdata + + return data + + # handle data array like pack() or unpack_parallel() ?? + + def unpack_data(self,id,tflag=3): + index = self.fieldID.index(id) + + # unpack one field of message in parallel + # tflag = type of data to return + # 3 = ctypes vector is default, since no conversion required + # NOTE: allow direct use of user array (e.g. Numpy), if user provides data arg? + # as opposed to creating this cdata + # does that make any performance difference ? + # e.g. should we allow CSlib to populate an existing Numpy array's memory + + def unpack_parallel(self,id,nlocal,ids,nper,tflag=3): + cids = self.data_convert(1,nlocal,ids) + + # allocate memory for the returned data + # pass cdata ptr to the memory to CSlib unpack_parallel() + # this resets data type of last unpack_parallel() arg + + index = self.fieldID.index(id) + if self.fieldtype[index] == 1: cdata = (nper*nlocal * c_int)() + elif self.fieldtype[index] == 2: cdata = (nlocal*nper * c_longlong)() + elif self.fieldtype[index] == 3: cdata = (nlocal*nper * c_float)() + elif self.fieldtype[index] == 4: cdata = (nlocal*nper * c_double)() + #elif self.fieldtype[index] == 5: cdata = (nlocal*nper * c_char)() + + self.lib.cslib_unpack_parallel(self.cs,id,nlocal,cids,nper,cdata) + + # tflag = user-requested type of data to return + # tflag = 1 to return data as list + # tflag = 2 to return data as Numpy array + # tflag = 3 to return data as ctypes vector + # same usage of tflag as in pack functions + + if tflag == 1: + data = cdata[:nper*nlocal] + elif tflag == 2: + if numpyflag == 0: + print "Cannot return Numpy array w/out numpy package" + sys.exit() + # NOTE: next line gives ctypes warning for fieldtype = 2 = 64-bit int + # not sure why, reported as bug between ctypes and Numpy here: + # https://stackoverflow.com/questions/4964101/pep-3118- + # warning-when-using-ctypes-array-as-numpy-array + # but why not same warning when just using unpack() ?? + # in Python these lines give same warning: + # >>> import ctypes,numpy + # >>> a = (10 * ctypes.c_longlong)() + # >>> b = numpy.ctypeslib.as_array(a) + data = np.ctypeslib.as_array(cdata,shape=(nlocal*nper,)) + elif tflag == 3: + data = cdata + + return data + + # extract a library value + + def extract(self,flag): + return self.lib.cslib_extract(self.cs,flag) diff --git a/lib/message/cslib/src/cslib_wrap.cpp b/lib/message/cslib/src/cslib_wrap.cpp new file mode 100644 index 0000000000..c2d69eaf0d --- /dev/null +++ b/lib/message/cslib/src/cslib_wrap.cpp @@ -0,0 +1,239 @@ +/* ---------------------------------------------------------------------- + CSlib - Client/server library for code coupling + http://cslib.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright 2018 National Technology & Engineering Solutions of + Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with + NTESS, the U.S. Government retains certain rights in this software. + This software is distributed under the modified Berkeley Software + Distribution (BSD) License. + + See the README file in the top-level CSlib directory. +------------------------------------------------------------------------- */ + +// C style library interface to CSlib class + +#include +#include +#include +#include +#include + +#include "cslib_wrap.h" +#include "cslib.h" + +using namespace CSLIB_NS; + +// ---------------------------------------------------------------------- + +void cslib_open(int csflag, const char *mode, const void *ptr, + const void *pcomm, void **csptr) +{ + CSlib *cs = new CSlib(csflag,mode,ptr,pcomm); + *csptr = (void *) cs; +} + +// ---------------------------------------------------------------------- + +void cslib_open_fortran(int csflag, const char *mode, const char *str, + const void *pcomm, void **csptr) +{ + MPI_Comm ccomm; + void *pccomm = NULL; + + if (pcomm) { + MPI_Fint *fcomm = (MPI_Fint *) pcomm; + ccomm = MPI_Comm_f2c(*fcomm); + pccomm = &ccomm; + } + + CSlib *cs = new CSlib(csflag,mode,str,pccomm); + *csptr = (void *) cs; +} + +// ---------------------------------------------------------------------- + +void cslib_open_fortran_mpi_one(int csflag, const char *mode, + const void *pboth, const void *pcomm, + void **csptr) +{ + MPI_Comm ccomm,cboth; + void *pccomm,*pcboth; + + MPI_Fint *fcomm = (MPI_Fint *) pcomm; + ccomm = MPI_Comm_f2c(*fcomm); + pccomm = &ccomm; + + MPI_Fint *fboth = (MPI_Fint *) pboth; + cboth = MPI_Comm_f2c(*fboth); + pcboth = &cboth; + + CSlib *cs = new CSlib(csflag,mode,pcboth,pccomm); + *csptr = (void *) cs; +} + +// ---------------------------------------------------------------------- + +void cslib_close(void *ptr) +{ + CSlib *cs = (CSlib *) ptr; + delete cs; +} + +// ---------------------------------------------------------------------- + +void cslib_send(void *ptr, int msgID, int nfield) +{ + CSlib *cs = (CSlib *) ptr; + cs->send(msgID,nfield); +} + +// ---------------------------------------------------------------------- + +void cslib_pack_int(void *ptr, int id, int value) +{ + CSlib *cs = (CSlib *) ptr; + cs->pack_int(id,value); +} + +// ---------------------------------------------------------------------- + +void cslib_pack_int64(void *ptr, int id, int64_t value) +{ + CSlib *cs = (CSlib *) ptr; + cs->pack_int64(id,value); +} + +// ---------------------------------------------------------------------- + +void cslib_pack_float(void *ptr, int id, float value) +{ + CSlib *cs = (CSlib *) ptr; + cs->pack_float(id,value); +} + +// ---------------------------------------------------------------------- + +void cslib_pack_double(void *ptr, int id, double value) +{ + CSlib *cs = (CSlib *) ptr; + cs->pack_double(id,value); +} + +// ---------------------------------------------------------------------- + +void cslib_pack_string(void *ptr, int id, char *value) +{ + CSlib *cs = (CSlib *) ptr; + cs->pack_string(id,value); +} + +// ---------------------------------------------------------------------- + +void cslib_pack(void *ptr, int id, int ftype, int flen, void *data) +{ + CSlib *cs = (CSlib *) ptr; + cs->pack(id,ftype,flen,data); +} + +// ---------------------------------------------------------------------- + +void cslib_pack_parallel(void *ptr, int id, int ftype, + int nlocal, int *ids, int nper, void *data) +{ + CSlib *cs = (CSlib *) ptr; + cs->pack_parallel(id,ftype,nlocal,ids,nper,data); +} + +// ---------------------------------------------------------------------- + +int cslib_recv(void *ptr, int *nfield_caller, + int **fieldID_caller, int **fieldtype_caller, + int **fieldlen_caller) +{ + CSlib *cs = (CSlib *) ptr; + + int nfield; + int *fieldID,*fieldtype,*fieldlen; + int msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen); + + *nfield_caller = nfield; + *fieldID_caller = fieldID; + *fieldtype_caller = fieldtype; + *fieldlen_caller = fieldlen; + + return msgID; +} + +// ---------------------------------------------------------------------- + +int cslib_unpack_int(void *ptr, int id) +{ + CSlib *cs = (CSlib *) ptr; + return cs->unpack_int(id); +} +// ---------------------------------------------------------------------- + +int64_t cslib_unpack_int64(void *ptr, int id) +{ + CSlib *cs = (CSlib *) ptr; + return cs->unpack_int64(id); +} + +// ---------------------------------------------------------------------- + +float cslib_unpack_float(void *ptr, int id) +{ + CSlib *cs = (CSlib *) ptr; + return cs->unpack_float(id); +} + +// ---------------------------------------------------------------------- + +double cslib_unpack_double(void *ptr, int id) +{ + CSlib *cs = (CSlib *) ptr; + return cs->unpack_double(id); +} + +// ---------------------------------------------------------------------- + +char *cslib_unpack_string(void *ptr, int id) +{ + CSlib *cs = (CSlib *) ptr; + return cs->unpack_string(id); +} + +// ---------------------------------------------------------------------- + +void *cslib_unpack(void *ptr, int id) +{ + CSlib *cs = (CSlib *) ptr; + return cs->unpack(id); +} + +// ---------------------------------------------------------------------- + +void cslib_unpack_data(void *ptr, int id, void *data) +{ + CSlib *cs = (CSlib *) ptr; + cs->unpack(id,data); +} + +// ---------------------------------------------------------------------- + +void cslib_unpack_parallel(void *ptr, int id, int nlocal, int *ids, + int nper, void *data) +{ + CSlib *cs = (CSlib *) ptr; + cs->unpack_parallel(id,nlocal,ids,nper,data); +} + +// ---------------------------------------------------------------------- + +int cslib_extract(void *ptr, int flag) +{ + CSlib *cs = (CSlib *) ptr; + return cs->extract(flag); +} diff --git a/lib/message/cslib/src/cslib_wrap.f90 b/lib/message/cslib/src/cslib_wrap.f90 new file mode 100644 index 0000000000..cd2e058b78 --- /dev/null +++ b/lib/message/cslib/src/cslib_wrap.f90 @@ -0,0 +1,147 @@ +! ISO_C_binding wrapper on CSlib C interface + +module cslib_wrap + +interface + subroutine cslib_open_fortran(csflag,mode,str,pcomm,ptr) bind(c) + use iso_c_binding + integer(c_int), value :: csflag + character(c_char) :: mode(*),str(*) + type(c_ptr), value :: pcomm + type(c_ptr) :: ptr + end subroutine cslib_open_fortran + + subroutine cslib_open_fortran_mpi_one(csflag,mode,pboth,pcomm,ptr) bind(c) + use iso_c_binding + integer(c_int), value :: csflag + character(c_char) :: mode(*) + type(c_ptr), value :: pboth,pcomm + type(c_ptr) :: ptr + end subroutine cslib_open_fortran_mpi_one + + subroutine cslib_close(ptr) bind(c) + use iso_c_binding + type(c_ptr), value :: ptr + end subroutine cslib_close + + subroutine cslib_send(ptr,msgID,nfield) bind(c) + use iso_c_binding + type(c_ptr), value :: ptr + integer(c_int), value :: msgID,nfield + end subroutine cslib_send + + subroutine cslib_pack_int(ptr,id,value) bind(c) + use iso_c_binding + type(c_ptr), value :: ptr + integer(c_int), value :: id + integer(c_int), value :: value + end subroutine cslib_pack_int + + subroutine cslib_pack_int64(ptr,id,value) bind(c) + use iso_c_binding + type(c_ptr), value :: ptr + integer(c_int), value :: id + integer(c_int64_t), value :: value + end subroutine cslib_pack_int64 + + subroutine cslib_pack_float(ptr,id,value) bind(c) + use iso_c_binding + type(c_ptr), value :: ptr + integer(c_int), value :: id + real(c_float), value :: value + end subroutine cslib_pack_float + + subroutine cslib_pack_double(ptr,id,value) bind(c) + use iso_c_binding + type(c_ptr), value :: ptr + integer(c_int), value :: id + real(c_double), value :: value + end subroutine cslib_pack_double + + subroutine cslib_pack_string(ptr,id,value) bind(c) + use iso_c_binding + type(c_ptr), value :: ptr + integer(c_int), value :: id + character(c_char) :: value(*) + end subroutine cslib_pack_string + + subroutine cslib_pack(ptr,id,ftype,flen,data) bind(c) + use iso_c_binding + type(c_ptr), value :: ptr + integer(c_int), value :: id,ftype,flen + type(c_ptr), value :: data + end subroutine cslib_pack + + subroutine cslib_pack_parallel(ptr,id,ftype,nlocal,ids,nper,data) bind(c) + use iso_c_binding + type(c_ptr), value :: ptr + integer(c_int), value :: id,ftype,nlocal,nper + type(c_ptr), value :: ids,data + end subroutine cslib_pack_parallel + + function cslib_recv(ptr,nfield,fieldID,fieldtype,fieldlen) bind(c) + use iso_c_binding + integer(c_int) :: cslib_recv + type(c_ptr), value :: ptr + integer(c_int) :: nfield + type(c_ptr) :: fieldID,fieldtype,fieldlen + end function cslib_recv + + function cslib_unpack_int(ptr,id) bind(c) + use iso_c_binding + integer(c_int) :: cslib_unpack_int + type(c_ptr), value :: ptr + integer(c_int), value :: id + end function cslib_unpack_int + + function cslib_unpack_int64(ptr,id) bind(c) + use iso_c_binding + integer(c_int64_t) :: cslib_unpack_int64 + type(c_ptr), value :: ptr + integer(c_int), value :: id + end function cslib_unpack_int64 + + function cslib_unpack_float(ptr,id) bind(c) + use iso_c_binding + real(c_float) :: cslib_unpack_float + type(c_ptr), value :: ptr + integer(c_int), value :: id + end function cslib_unpack_float + + function cslib_unpack_double(ptr,id) bind(c) + use iso_c_binding + real(c_double) :: cslib_unpack_double + type(c_ptr), value :: ptr + integer(c_int), value :: id + end function cslib_unpack_double + + function cslib_unpack_string(ptr,id) bind(c) + use iso_c_binding + type(c_ptr) :: cslib_unpack_string + type(c_ptr), value :: ptr + integer(c_int), value :: id + end function cslib_unpack_string + + function cslib_unpack(ptr,id) bind(c) + use iso_c_binding + type(c_ptr) :: cslib_unpack + type(c_ptr), value :: ptr + integer(c_int), value :: id + end function cslib_unpack + + subroutine cslib_unpack_parallel(ptr,id,nlocal,ids,nper,data) bind(c) + use iso_c_binding + type(c_ptr), value :: ptr + integer(c_int), value :: id,nlocal,nper + type(c_ptr), value :: ids,data + end subroutine cslib_unpack_parallel + + function cslib_extract(ptr,flag) bind(c) + use iso_c_binding + integer(c_int) :: cslib_extract + type(c_ptr), value :: ptr + integer(c_int), value :: flag + end function cslib_extract +end interface + +end module cslib_wrap diff --git a/lib/message/cslib/src/cslib_wrap.h b/lib/message/cslib/src/cslib_wrap.h new file mode 100644 index 0000000000..bf7df029c3 --- /dev/null +++ b/lib/message/cslib/src/cslib_wrap.h @@ -0,0 +1,54 @@ +/* ---------------------------------------------------------------------- + CSlib - Client/server library for code coupling + http://cslib.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright 2018 National Technology & Engineering Solutions of + Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with + NTESS, the U.S. Government retains certain rights in this software. + This software is distributed under the modified Berkeley Software + Distribution (BSD) License. + + See the README file in the top-level CSlib directory. +------------------------------------------------------------------------- */ + +/* C style library interface to CSlib class + ifdefs allow this file to be included in a C program +*/ + +#ifdef __cplusplus +extern "C" { +#endif + +void cslib_open(int, const char *, const void *, const void *, void **); +void cslib_open_fortran(int, const char *, const char *, const void *, void **); +void cslib_open_fortran_mpi_one(int, const char *, const void *, + const void *, void **); +void cslib_close(void *); + +void cslib_send(void *, int, int); + +void cslib_pack_int(void *, int, int); +void cslib_pack_int64(void *, int, int64_t); +void cslib_pack_float(void *, int, float); +void cslib_pack_double(void *, int, double); +void cslib_pack_string(void *, int, char *); +void cslib_pack(void *, int, int, int, void *); +void cslib_pack_parallel(void *, int, int, int, int *, int, void *); + +int cslib_recv(void *, int *, int **, int **, int **); + +int cslib_unpack_int(void *, int); +int64_t cslib_unpack_int64(void *, int); +float cslib_unpack_float(void *, int); +double cslib_unpack_double(void *, int); +char *cslib_unpack_string(void *, int); +void *cslib_unpack(void *, int); +void cslib_unpack_data(void *, int, void *); +void cslib_unpack_parallel(void *, int, int, int *, int, void *); + +int cslib_extract(void *, int); + +#ifdef __cplusplus +} +#endif diff --git a/lib/message/cslib/src/msg.cpp b/lib/message/cslib/src/msg.cpp new file mode 100644 index 0000000000..c67e4a5c8c --- /dev/null +++ b/lib/message/cslib/src/msg.cpp @@ -0,0 +1,110 @@ +/* ---------------------------------------------------------------------- + CSlib - Client/server library for code coupling + http://cslib.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright 2018 National Technology & Engineering Solutions of + Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with + NTESS, the U.S. Government retains certain rights in this software. + This software is distributed under the modified Berkeley Software + Distribution (BSD) License. + + See the README file in the top-level CSlib directory. +------------------------------------------------------------------------- */ + +#include +#include +#include +#include + +#include "msg.h" + +using namespace CSLIB_NS; + +/* ---------------------------------------------------------------------- */ + +Msg::Msg(int csflag, const void *ptr, MPI_Comm cworld) +{ + world = cworld; + MPI_Comm_rank(world,&me); + MPI_Comm_size(world,&nprocs); + + init(csflag); +} + +/* ---------------------------------------------------------------------- */ + +Msg::Msg(int csflag, const void *ptr) +{ + world = 0; + me = 0; + nprocs = 1; + + init(csflag); +} + +/* ---------------------------------------------------------------------- */ + +void Msg::init(int csflag) +{ + client = server = 0; + if (csflag == 0) client = 1; + else if (csflag == 1) server = 1; + + nsend = nrecv = 0; +} + +/* ---------------------------------------------------------------------- */ + +void Msg::allocate(int nheader, int &maxheader, int *&header, + int nbuf, int &maxbuf, char *&buf) +{ + if (nheader > maxheader) { + sfree(header); + maxheader = nheader; + header = (int *) smalloc(maxheader*sizeof(int)); + } + + if (nbuf > maxbuf) { + sfree(buf); + maxbuf = nbuf; + buf = (char *) smalloc(maxbuf*sizeof(char)); + } +} + +/* ---------------------------------------------------------------------- */ + +void *Msg::smalloc(int nbytes) +{ + if (nbytes == 0) return NULL; + void *ptr = (void *) malloc(nbytes); + if (ptr == NULL) { + char str[128]; + sprintf(str,"Failed to allocate %d bytes",nbytes); + } + return ptr; +} + +/* ---------------------------------------------------------------------- */ + +void Msg::sfree(void *ptr) +{ + if (ptr == NULL) return; + free(ptr); +} + +/* ---------------------------------------------------------------------- */ + +void Msg::error_all(const char *str) +{ + if (me == 0) printf("CSlib ERROR: %s\n",str); + MPI_Abort(world,1); +} + +/* ---------------------------------------------------------------------- */ + +void Msg::error_one(const char *str) +{ + printf("CSlib ERROR: %s\n",str); + MPI_Abort(world,1); +} diff --git a/lib/message/cslib/src/msg.h b/lib/message/cslib/src/msg.h new file mode 100644 index 0000000000..f75942b027 --- /dev/null +++ b/lib/message/cslib/src/msg.h @@ -0,0 +1,52 @@ +/* ---------------------------------------------------------------------- + CSlib - Client/server library for code coupling + http://cslib.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright 2018 National Technology & Engineering Solutions of + Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with + NTESS, the U.S. Government retains certain rights in this software. + This software is distributed under the modified Berkeley Software + Distribution (BSD) License. + + See the README file in the top-level CSlib directory. +------------------------------------------------------------------------- */ + +#ifndef MSG_H +#define MSG_H + +#include + +namespace CSLIB_NS { + +class Msg { + public: + int nsend,nrecv; + MPI_Comm world; + + Msg(int, const void *, MPI_Comm); + Msg(int, const void *); + virtual ~Msg() {} + virtual void send(int, int *, int, char *) = 0; + virtual void recv(int &, int *&, int &, char *&) = 0; + + protected: + int me,nprocs; + int client,server; + + int nfield; + int *fieldID,*fieldtype,*fieldlen; + int lengths[2]; + + void init(int); + void allocate(int, int &, int *&, int, int &, char *&); + void *smalloc(int); + void sfree(void *); + void error_all(const char *); + void error_one(const char *); +}; + + +} + +#endif diff --git a/lib/message/cslib/src/msg_file.cpp b/lib/message/cslib/src/msg_file.cpp new file mode 100644 index 0000000000..d97e249fad --- /dev/null +++ b/lib/message/cslib/src/msg_file.cpp @@ -0,0 +1,143 @@ +/* ---------------------------------------------------------------------- + CSlib - Client/server library for code coupling + http://cslib.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright 2018 National Technology & Engineering Solutions of + Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with + NTESS, the U.S. Government retains certain rights in this software. + This software is distributed under the modified Berkeley Software + Distribution (BSD) License. + + See the README file in the top-level CSlib directory. +------------------------------------------------------------------------- */ + +#include +#include +#include +#include +#include +#include + +#include "msg_file.h" + +using namespace CSLIB_NS; + +#define MAXLINE 256 +#define SLEEP 0.1 // delay in CPU secs to check for message file + +/* ---------------------------------------------------------------------- */ + +MsgFile::MsgFile(int csflag, const void *ptr, MPI_Comm cworld) : + Msg(csflag, ptr, cworld) +{ + char *filename = (char *) ptr; + init(filename); +} + +/* ---------------------------------------------------------------------- */ + +MsgFile::MsgFile(int csflag, const void *ptr) : Msg(csflag, ptr) +{ + char *filename = (char *) ptr; + init(filename); +} + +/* ---------------------------------------------------------------------- */ + +MsgFile::~MsgFile() +{ + delete [] fileroot; +} + +/* ---------------------------------------------------------------------- */ + +void MsgFile::init(char *filename) +{ + int n = strlen(filename) + 1; + fileroot = new char[n]; + strcpy(fileroot,filename); +} + +/* ---------------------------------------------------------------------- */ + +void MsgFile::send(int nheader, int *header, int nbuf, char *buf) +{ + char filename[MAXLINE]; + + lengths[0] = nheader; + lengths[1] = nbuf; + + if (me == 0) { + if (client) sprintf(filename,"%s.%s",fileroot,"client"); + else if (server) sprintf(filename,"%s.%s",fileroot,"server"); + + fp = fopen(filename,"wb"); + if (!fp) error_one("send(): Could not open send message file"); + fwrite(lengths,sizeof(int),2,fp); + fwrite(header,sizeof(int),nheader,fp); + fwrite(buf,1,nbuf,fp); + fclose(fp); + } + + // create empty signal file + + if (me == 0) { + if (client) sprintf(filename,"%s.%s",fileroot,"client.signal"); + else if (server) sprintf(filename,"%s.%s",fileroot,"server.signal"); + fp = fopen(filename,"w"); + fclose(fp); + } +} + +/* ---------------------------------------------------------------------- */ + +void MsgFile::recv(int &maxheader, int *&header, int &maxbuf, char *&buf) +{ + char filename[MAXLINE]; + + // wait until signal file exists to open message file + + if (me == 0) { + if (client) sprintf(filename,"%s.%s",fileroot,"server.signal"); + else if (server) sprintf(filename,"%s.%s",fileroot,"client.signal"); + + int delay = (int) (1000000 * SLEEP); + while (1) { + fp = fopen(filename,"r"); + if (fp) break; + usleep(delay); + } + fclose(fp); + + if (client) sprintf(filename,"%s.%s",fileroot,"server"); + else if (server) sprintf(filename,"%s.%s",fileroot,"client"); + fp = fopen(filename,"rb"); + if (!fp) error_one("recv(): Could not open recv message file"); + } + + // read and broadcast data + + if (me == 0) fread(lengths,sizeof(int),2,fp); + if (nprocs > 1) MPI_Bcast(lengths,2,MPI_INT,0,world); + + int nheader = lengths[0]; + int nbuf = lengths[1]; + allocate(nheader,maxheader,header,nbuf,maxbuf,buf); + + if (me == 0) fread(header,sizeof(int),nheader,fp); + if (nprocs > 1) MPI_Bcast(header,nheader,MPI_INT,0,world); + + if (me == 0) fread(buf,1,nbuf,fp); + if (nprocs > 1) MPI_Bcast(buf,nbuf,MPI_CHAR,0,world); + + // delete both message and signal file + + if (me == 0) { + fclose(fp); + unlink(filename); + if (client) sprintf(filename,"%s.%s",fileroot,"server.signal"); + else if (server) sprintf(filename,"%s.%s",fileroot,"client.signal"); + unlink(filename); + } +} diff --git a/lib/message/cslib/src/msg_file.h b/lib/message/cslib/src/msg_file.h new file mode 100644 index 0000000000..d6bd802607 --- /dev/null +++ b/lib/message/cslib/src/msg_file.h @@ -0,0 +1,40 @@ +/* ---------------------------------------------------------------------- + CSlib - Client/server library for code coupling + http://cslib.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright 2018 National Technology & Engineering Solutions of + Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with + NTESS, the U.S. Government retains certain rights in this software. + This software is distributed under the modified Berkeley Software + Distribution (BSD) License. + + See the README file in the top-level CSlib directory. +------------------------------------------------------------------------- */ + +#ifndef MSG_FILE_H +#define MSG_FILE_H + +#include +#include "msg.h" + +namespace CSLIB_NS { + +class MsgFile : public Msg { + public: + MsgFile(int, const void *, MPI_Comm); + MsgFile(int, const void *); + ~MsgFile(); + void send(int, int *, int, char *); + void recv(int &, int *&, int &, char *&); + + private: + char *fileroot; + FILE *fp; + + void init(char *); +}; + +} + +#endif diff --git a/lib/message/cslib/src/msg_mpi_one.cpp b/lib/message/cslib/src/msg_mpi_one.cpp new file mode 100644 index 0000000000..db11735b27 --- /dev/null +++ b/lib/message/cslib/src/msg_mpi_one.cpp @@ -0,0 +1,82 @@ +/* ---------------------------------------------------------------------- + CSlib - Client/server library for code coupling + http://cslib.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright 2018 National Technology & Engineering Solutions of + Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with + NTESS, the U.S. Government retains certain rights in this software. + This software is distributed under the modified Berkeley Software + Distribution (BSD) License. + + See the README file in the top-level CSlib directory. +------------------------------------------------------------------------- */ + +#include +#include +#include +#include +#include +#include + +#include "msg_mpi_one.h" + +using namespace CSLIB_NS; + +/* ---------------------------------------------------------------------- */ + +MsgMPIOne::MsgMPIOne(int csflag, const void *ptr, MPI_Comm cworld) : + Msg(csflag, ptr, cworld) +{ + // NOTE: ideally would skip this call if mpi/two + init(ptr); +} + +/* ---------------------------------------------------------------------- */ + +void MsgMPIOne::init(const void *ptr) +{ + MPI_Comm *pbothcomm = (MPI_Comm *) ptr; + bothcomm = *pbothcomm; + + if (client) { + MPI_Comm_size(world,&nprocs); + otherroot = nprocs; + } else if (server) { + otherroot = 0; + } +} + +/* ---------------------------------------------------------------------- */ + +void MsgMPIOne::send(int nheader, int *header, int nbuf, char *buf) +{ + lengths[0] = nheader; + lengths[1] = nbuf; + + if (me == 0) { + MPI_Send(lengths,2,MPI_INT,otherroot,0,bothcomm); + MPI_Send(header,nheader,MPI_INT,otherroot,0,bothcomm); + MPI_Send(buf,nbuf,MPI_CHAR,otherroot,0,bothcomm); + } +} + +/* ---------------------------------------------------------------------- */ + +void MsgMPIOne::recv(int &maxheader, int *&header, int &maxbuf, char *&buf) +{ + MPI_Status status; + + if (me == 0) MPI_Recv(lengths,2,MPI_INT,otherroot,0,bothcomm,&status); + if (nprocs > 1) MPI_Bcast(lengths,2,MPI_INT,0,world); + + int nheader = lengths[0]; + int nbuf = lengths[1]; + allocate(nheader,maxheader,header,nbuf,maxbuf,buf); + + if (me == 0) MPI_Recv(header,nheader,MPI_INT,otherroot,0,bothcomm,&status); + if (nprocs > 1) MPI_Bcast(header,nheader,MPI_INT,0,world); + + if (me == 0) MPI_Recv(buf,nbuf,MPI_CHAR,otherroot,0,bothcomm,&status); + if (nprocs > 1) MPI_Bcast(buf,nbuf,MPI_CHAR,0,world); +} diff --git a/lib/message/cslib/src/msg_mpi_one.h b/lib/message/cslib/src/msg_mpi_one.h new file mode 100644 index 0000000000..4b4140a3f7 --- /dev/null +++ b/lib/message/cslib/src/msg_mpi_one.h @@ -0,0 +1,38 @@ +/* ---------------------------------------------------------------------- + CSlib - Client/server library for code coupling + http://cslib.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright 2018 National Technology & Engineering Solutions of + Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with + NTESS, the U.S. Government retains certain rights in this software. + This software is distributed under the modified Berkeley Software + Distribution (BSD) License. + + See the README file in the top-level CSlib directory. +------------------------------------------------------------------------- */ + +#ifndef MSG_MPI_ONE_H +#define MSG_MPI_ONE_H + +#include "msg.h" + +namespace CSLIB_NS { + +class MsgMPIOne : public Msg { + public: + MsgMPIOne(int, const void *, MPI_Comm); + virtual ~MsgMPIOne() {} + void send(int, int *, int, char *); + void recv(int &, int *&, int &, char *&); + + protected: + MPI_Comm bothcomm; + int otherroot; + + void init(const void *); +}; + +} + +#endif diff --git a/lib/message/cslib/src/msg_mpi_two.cpp b/lib/message/cslib/src/msg_mpi_two.cpp new file mode 100644 index 0000000000..e9a9e87eeb --- /dev/null +++ b/lib/message/cslib/src/msg_mpi_two.cpp @@ -0,0 +1,81 @@ +/* ---------------------------------------------------------------------- + CSlib - Client/server library for code coupling + http://cslib.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright 2018 National Technology & Engineering Solutions of + Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with + NTESS, the U.S. Government retains certain rights in this software. + This software is distributed under the modified Berkeley Software + Distribution (BSD) License. + + See the README file in the top-level CSlib directory. +------------------------------------------------------------------------- */ + +#include +#include +#include +#include +#include +#include + +#include "msg_mpi_two.h" + +using namespace CSLIB_NS; + +/* ---------------------------------------------------------------------- */ + +MsgMPITwo::MsgMPITwo(int csflag, const void *ptr, MPI_Comm cworld) : + MsgMPIOne(csflag, ptr, cworld) +{ + char *filename = (char *) ptr; + init(filename); +} + +/* ---------------------------------------------------------------------- */ + +MsgMPITwo::~MsgMPITwo() +{ + // free the inter comm that spans both client and server + + MPI_Comm_free(&bothcomm); + MPI_Close_port(port); +} + +/* ---------------------------------------------------------------------- */ + +void MsgMPITwo::init(char *filename) +{ + if (client) { + if (me == 0) { + FILE *fp = NULL; + while (!fp) { + fp = fopen(filename,"r"); + if (!fp) sleep(1); + } + fgets(port,MPI_MAX_PORT_NAME,fp); + //printf("Client port: %s\n",port); + fclose(fp); + } + + MPI_Bcast(port,MPI_MAX_PORT_NAME,MPI_CHAR,0,world); + MPI_Comm_connect(port,MPI_INFO_NULL,0,world,&bothcomm); + //if (me == 0) printf("CLIENT comm connect\n"); + if (me == 0) unlink(filename); + + } else if (server) { + MPI_Open_port(MPI_INFO_NULL,port); + + if (me == 0) { + //printf("Server name: %s\n",port); + FILE *fp = fopen(filename,"w"); + fprintf(fp,"%s",port); + fclose(fp); + } + + MPI_Comm_accept(port,MPI_INFO_NULL,0,world,&bothcomm); + //if (me == 0) printf("SERVER comm accept\n"); + } + + otherroot = 0; +} diff --git a/lib/message/cslib/src/msg_mpi_two.h b/lib/message/cslib/src/msg_mpi_two.h new file mode 100644 index 0000000000..7b31db5a63 --- /dev/null +++ b/lib/message/cslib/src/msg_mpi_two.h @@ -0,0 +1,35 @@ +/* ---------------------------------------------------------------------- + CSlib - Client/server library for code coupling + http://cslib.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright 2018 National Technology & Engineering Solutions of + Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with + NTESS, the U.S. Government retains certain rights in this software. + This software is distributed under the modified Berkeley Software + Distribution (BSD) License. + + See the README file in the top-level CSlib directory. +------------------------------------------------------------------------- */ + +#ifndef MSG_MPI_TWO_H +#define MSG_MPI_TWO_H + +#include "msg_mpi_one.h" + +namespace CSLIB_NS { + +class MsgMPITwo : public MsgMPIOne { + public: + MsgMPITwo(int, const void *, MPI_Comm); + ~MsgMPITwo(); + + private: + char port[MPI_MAX_PORT_NAME]; + + void init(char *); +}; + +} + +#endif diff --git a/lib/message/cslib/src/msg_zmq.cpp b/lib/message/cslib/src/msg_zmq.cpp new file mode 100644 index 0000000000..c2d408f3a5 --- /dev/null +++ b/lib/message/cslib/src/msg_zmq.cpp @@ -0,0 +1,140 @@ +/* ---------------------------------------------------------------------- + CSlib - Client/server library for code coupling + http://cslib.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright 2018 National Technology & Engineering Solutions of + Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with + NTESS, the U.S. Government retains certain rights in this software. + This software is distributed under the modified Berkeley Software + Distribution (BSD) License. + + See the README file in the top-level CSlib directory. +------------------------------------------------------------------------- */ + +#include +#include +#include +#include +#include +#include + +#include "msg_zmq.h" + +using namespace CSLIB_NS; + +/* ---------------------------------------------------------------------- */ + +MsgZMQ::MsgZMQ(int csflag, const void *ptr, MPI_Comm cworld) : + Msg(csflag, ptr, cworld) +{ + char *port = (char *) ptr; + init(port); +} + +MsgZMQ::MsgZMQ(int csflag, const void *ptr) : Msg(csflag, ptr) +{ + char *port = (char *) ptr; + init(port); +} + +/* ---------------------------------------------------------------------- */ + +MsgZMQ::~MsgZMQ() +{ + if (me == 0) { + zmq_close(socket); + zmq_ctx_destroy(context); + } +} + +/* ---------------------------------------------------------------------- */ + +void MsgZMQ::init(char *port) +{ +#ifdef ZMQ_NO + error_all("constructor(): Library not built with ZMQ support"); +#endif + + if (me == 0) { + int n = strlen(port) + 8; + char *socket_name = new char[n]; + strcpy(socket_name,"tcp://"); + strcat(socket_name,port); + + if (client) { + context = zmq_ctx_new(); + socket = zmq_socket(context,ZMQ_REQ); + zmq_connect(socket,socket_name); + } else if (server) { + context = zmq_ctx_new(); + socket = zmq_socket(context,ZMQ_REP); + int rc = zmq_bind(socket,socket_name); + if (rc) error_one("constructor(): Server could not make socket connection"); + } + + delete [] socket_name; + } +} + +/* ---------------------------------------------------------------------- + client/server sockets (REQ/REP) must follow this protocol: + client sends request (REQ) which server receives + server sends response (REP) which client receives + every exchange is of this form, server cannot initiate a send + thus each ZMQ send below has a following ZMQ recv, except last one + if client calls send(), it will next call recv() + if server calls send(), it will next call recv() from its wait loop + in either case, recv() issues a ZMQ recv to match last ZMQ send here +------------------------------------------------------------------------- */ + +void MsgZMQ::send(int nheader, int *header, int nbuf, char *buf) +{ + lengths[0] = nheader; + lengths[1] = nbuf; + + if (me == 0) { + zmq_send(socket,lengths,2*sizeof(int),0); + zmq_recv(socket,NULL,0,0); + } + + if (me == 0) { + zmq_send(socket,header,nheader*sizeof(int),0); + zmq_recv(socket,NULL,0,0); + } + + if (me == 0) zmq_send(socket,buf,nbuf,0); +} + +/* ---------------------------------------------------------------------- + client/server sockets (REQ/REP) must follow this protocol: + client sends request (REQ) which server receives + server sends response (REP) which client receives + every exchange is of this form, server cannot initiate a send + thus each ZMQ recv below has a following ZMQ send, except last one + if client calls recv(), it will next call send() to ping server again, + if server calls recv(), it will next call send() to respond to client + in either case, send() issues a ZMQ send to match last ZMQ recv here +------------------------------------------------------------------------- */ + +void MsgZMQ::recv(int &maxheader, int *&header, int &maxbuf, char *&buf) +{ + if (me == 0) { + zmq_recv(socket,lengths,2*sizeof(int),0); + zmq_send(socket,NULL,0,0); + } + if (nprocs > 1) MPI_Bcast(lengths,2,MPI_INT,0,world); + + int nheader = lengths[0]; + int nbuf = lengths[1]; + allocate(nheader,maxheader,header,nbuf,maxbuf,buf); + + if (me == 0) { + zmq_recv(socket,header,nheader*sizeof(int),0); + zmq_send(socket,NULL,0,0); + } + if (nprocs > 1) MPI_Bcast(header,nheader,MPI_INT,0,world); + + if (me == 0) zmq_recv(socket,buf,nbuf,0); + if (nprocs > 1) MPI_Bcast(buf,nbuf,MPI_CHAR,0,world); +} diff --git a/lib/message/cslib/src/msg_zmq.h b/lib/message/cslib/src/msg_zmq.h new file mode 100644 index 0000000000..c0621a26ff --- /dev/null +++ b/lib/message/cslib/src/msg_zmq.h @@ -0,0 +1,38 @@ +/* ---------------------------------------------------------------------- + CSlib - Client/server library for code coupling + http://cslib.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright 2018 National Technology & Engineering Solutions of + Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with + NTESS, the U.S. Government retains certain rights in this software. + This software is distributed under the modified Berkeley Software + Distribution (BSD) License. + + See the README file in the top-level CSlib directory. +------------------------------------------------------------------------- */ + +#ifndef MSG_ZMQ_H +#define MSG_ZMQ_H + +#include "msg.h" + +namespace CSLIB_NS { + +class MsgZMQ : public Msg { + public: + MsgZMQ(int, const void *, MPI_Comm); + MsgZMQ(int, const void *); + ~MsgZMQ(); + void send(int, int *, int, char *); + void recv(int &, int *&, int &, char *&); + + private: + void *context,*socket; + + void init(char *); +}; + +} + +#endif diff --git a/lib/scafacos/Install.py b/lib/scafacos/Install.py new file mode 100644 index 0000000000..d23e8a3686 --- /dev/null +++ b/lib/scafacos/Install.py @@ -0,0 +1,165 @@ +#!/usr/bin/env python + +# Install.py tool to download, unpack, build, and link to the Scafacos library +# used to automate the steps described in the README file in this dir + +from __future__ import print_function +import sys,os,re,subprocess + +# help message + +help = """ +Syntax from src dir: make lib-scafacos args="-b" + or: make lib-scafacos args="-p /usr/local/scafacos" +Syntax from lib dir: python Install.py -b + or: python Install.py -p /usr/local/scafacos + +specify zero or more options, order does not matter + + -b = download and build the Scafacos library + -p = specify folder of existing Scafacos installation + + always creates includelink, liblink to Scafacos dirs + +Example: + +make lib-scafacos args="-b" # download/build in lib/scafacos/scafacos +make lib-scafacos args="-p $HOME/scafacos" # use existing Scafacos installation in $HOME +""" + +# settings + +version = "scafacos-1.0.1" +url = "https://github.com/scafacos/scafacos/releases/download/v1.0.1/scafacos-1.0.1.tar.gz" +#url = "https://gigamove.rz.rwth-aachen.de/d/id/CTzyApN76MXMJ6/dd/100" % version + +# print error message or help + +def error(str=None): + if not str: print(help) + else: print("ERROR",str) + sys.exit() + +# expand to full path name +# process leading '~' or relative path + +def fullpath(path): + return os.path.abspath(os.path.expanduser(path)) + +def which(program): + def is_exe(fpath): + return os.path.isfile(fpath) and os.access(fpath, os.X_OK) + + fpath, fname = os.path.split(program) + if fpath: + if is_exe(program): + return program + else: + for path in os.environ["PATH"].split(os.pathsep): + path = path.strip('"') + exe_file = os.path.join(path, program) + if is_exe(exe_file): + return exe_file + + return None + +def geturl(url,fname): + success = False + + if which('curl') != None: + cmd = 'curl -L -o "%s" %s' % (fname,url) + try: + subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) + success = True + except subprocess.CalledProcessError as e: + print("Calling curl failed with: %s" % e.output.decode('UTF-8')) + + if not success and which('wget') != None: + cmd = 'wget -O "%s" %s' % (fname,url) + print("Wget command: %s" % cmd) + try: + subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) + success = True + except subprocess.CalledProcessError as e: + print("Calling wget failed with: %s" % e.output.decode('UTF-8')) + + if not success: + error("Failed to download source code with 'curl' or 'wget'") + return + +# parse args + +args = sys.argv[1:] +nargs = len(args) + +homepath = "." + +buildflag = True +pathflag = False +linkflag = True + +iarg = 0 +while iarg < nargs: + if args[iarg] == "-v": + if iarg+2 > nargs: error() + version = args[iarg+1] + iarg += 2 + elif args[iarg] == "-p": + if iarg+2 > nargs: error() + scafacospath = fullpath(args[iarg+1]) + pathflag = True + iarg += 2 + elif args[iarg] == "-b": + buildflag = True + iarg += 1 + else: error() + +homepath = fullpath(homepath) +homedir = "%s/%s" % (homepath,version) + +if (pathflag): + if not os.path.isdir(scafacospath): error("Scafacos path does not exist") + homedir =scafacospath + +if (buildflag and pathflag): + error("Cannot use -b and -p flag at the same time") + +# download and unpack Scafacos tarball + +if buildflag: + print("Downloading Scafacos ...") + geturl(url,"%s/%s.tar.gz" % (homepath,version)) + + print("Unpacking Scafacos tarball ...") + if os.path.exists("%s/%s" % (homepath,version)): + cmd = 'rm -rf "%s/%s"' % (homepath,version) + subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) + cmd = 'cd "%s"; tar -xzvf %s.tar.gz' % (homepath,version) + subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) + os.remove("%s/%s.tar.gz" % (homepath,version)) + if os.path.basename(homedir) != version: + if os.path.exists(homedir): + cmd = 'rm -rf "%s"' % homedir + subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) + os.rename("%s/%s" % (homepath,version),homedir) + +# build Scafacos + +if buildflag: + print("Building Scafacos ...") + cmd = 'cd "%s"; ./configure --prefix="`pwd`/build" --disable-doc --enable-fcs-solvers=fmm,p2nfft,direct,ewald,p3m --with-internal-fftw --with-internal-pfft --with-internal-pnfft CC=mpicc FC=mpif90 CXX=mpicxx F77= > log.txt; make -j; make install' % homedir + txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) + print(txt.decode('UTF-8')) + +# create 2 links in lib/scafacos to Scafacos include/lib dirs + +if linkflag: + print("Creating links to Scafacos include and lib files") + if os.path.isfile("includelink") or os.path.islink("includelink"): + os.remove("includelink") + if os.path.isfile("liblink") or os.path.islink("liblink"): + os.remove("liblink") + cmd = 'ln -s "%s/build/include" includelink' % homedir + subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) + cmd = 'ln -s "%s/build/lib" liblink' % homedir + subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) diff --git a/lib/scafacos/README b/lib/scafacos/README new file mode 100644 index 0000000000..e5f1ecd92c --- /dev/null +++ b/lib/scafacos/README @@ -0,0 +1,76 @@ +This directory contains links to the ScaFaCoS library which +is required to use the KSPACE scafacos and its kspace_style +scafacos command in a LAMMPS input script. + +The ScaFaCoS library is available at http://scafacos.de or +on github at https://github.com/scafacos, the libary was +developed by a consortium of different universities in +Germany (Bonn, Chemnitz, Stuttgart, Wuppertal) and +the Research Centre Juelich (Juelich Supercomputing Centre). + +----------------- + +Instructions: + +1.) Download ScaFaCoS at http://scafacos.de or directly from github + https://github.com/scafacos where you can either clone the + repository or download the latest stable release. + NOTE: For the P2NFFT solver, you require an installation of the + GNU Scientific Library (GSL). Also to ensure the correct + linker-flags are used, ScaFaCoS employs the pkg-config + tool, which is also required. + If you cloned the repository, please refer to 2.), else continue + with 3.) + +2.) If you cloned the git repository, you require autotools to setup + the library. For that the following packages are required: + m4 + autotools + automake + libtools + In the build_aux folder of the scafacos folder, you can find the + get_autotools.sh script, that downloads and installs the tools + to ${HOME}/local. To change the target folder, please change the + value of 'myprefix' in that script. + To start the auto-configuration process, please run the './bootstrap' + command in the scafacos base-folder. + +3.) If you downloaded the library as a tarball, please extract the file + to somewhere in your file system, or if you finished running + './bootstrap', please run './configure' in the base folder. + Important flags for './configure' are: + --prefix=: sets the directory the compiled files will + be installed to [default: /usr/local] + --fcs-enable-solvers=: sets the list of solvers that are going to + be built. By default all solvers will be + built. Currently supported by the kspace in LAMMPS + are: direct, ewald, fmm, p2nfft + The other solvers might work, but support + is purely experimental at the moment. To + give a list of solvers, use a comma seperated + list. + --fcs-disable-doc: disables the compilation of the documentation, + e.g. if no Latex is available on the system. + +4.) To build the library after configuration, run 'make' from the base folder. + +5.) To install the libray in the designated installation folder, run 'make install'. + Installation is required, as ScaFaCoS does not support an in-source build! + +6.) Create two soft links to this directory (lib/scafacos) to where the libary + is installed. E.g. if you built ScaFaCoS in the default install directory: + % ln -s /usr/local/include includelink + % ln -s /usr/local/lib liblink + for any custom directory : + % ln -s /include includelink + % ln -s /lib liblink + +7.) ScaFaCoS uses the pkg-config tool to supply the correct, so you need to setup your + PKG_CONFIG_PATH environment variable to include the lib/pkgconfig folder in the + installation directory. + Depending on the shell you use, this can be done either by: + % export PKG_CONFIG_PATH=/lib/pkgconfig:${PKG_CONFIG_PATH} + or + % setenv PKG_CONFIG_PATH=/lib/pkgconfig:${PKG_CONFIG_PATH} + +----------------- diff --git a/potentials/CH.KC b/potentials/CH.KC index 1b4f7503ea..029f682f34 100644 --- a/potentials/CH.KC +++ b/potentials/CH.KC @@ -6,3 +6,4 @@ C C 3.328819 21.847167 12.060173 4.711099 6.678908e-4 0.7718101 3.143921 12.660270 1.0 2.0 C H 3.156492 37.400478 8.3910462e-3 55.06177 5.176215e-5 0.4437309 2.508847 11.479055 1.0 1.5 H H 2.218816 4.5283006e-5 4.8685736e-5 2.027741 1.193945 0.8968523 0.238105 9.2194017e-5 1.0 1.2 +H C 3.156492 37.400478 8.3910462e-3 55.06177 5.176215e-5 0.4437309 2.508847 11.479055 1.0 2.2 diff --git a/python/lammps.py b/python/lammps.py index 417427eb4b..598e4c506f 100644 --- a/python/lammps.py +++ b/python/lammps.py @@ -173,6 +173,9 @@ class lammps(object): self.lib.lammps_open(narg,cargs,comm_val,byref(self.lmp)) else: + if lammps.has_mpi4py: + from mpi4py import MPI + self.comm = MPI.COMM_WORLD self.opened = 1 if cmdargs: cmdargs.insert(0,"lammps.py") @@ -209,6 +212,7 @@ class lammps(object): self.c_bigint = get_ctypes_int(self.extract_setting("bigint")) self.c_tagint = get_ctypes_int(self.extract_setting("tagint")) self.c_imageint = get_ctypes_int(self.extract_setting("imageint")) + self._installed_packages = None # shut-down LAMMPS instance @@ -235,7 +239,7 @@ class lammps(object): if cmd: cmd = cmd.encode() self.lib.lammps_command(self.lmp,cmd) - if self.uses_exceptions and self.lib.lammps_has_error(self.lmp): + if self.has_exceptions and self.lib.lammps_has_error(self.lmp): sb = create_string_buffer(100) error_type = self.lib.lammps_get_last_error_message(self.lmp, sb, 100) error_msg = sb.value.decode().strip() @@ -562,13 +566,36 @@ class lammps(object): shrinkexceed) @property - def uses_exceptions(self): + def has_exceptions(self): """ Return whether the LAMMPS shared library was compiled with C++ exceptions handling enabled """ - try: - if self.lib.lammps_has_error: - return True - except(AttributeError): - return False + return self.lib.lammps_config_has_exceptions() != 0 + + @property + def has_gzip_support(self): + return self.lib.lammps_config_has_gzip_support() != 0 + + @property + def has_png_support(self): + return self.lib.lammps_config_has_png_support() != 0 + + @property + def has_jpeg_support(self): + return self.lib.lammps_config_has_jpeg_support() != 0 + + @property + def has_ffmpeg_support(self): + return self.lib.lammps_config_has_ffmpeg_support() != 0 + + @property + def installed_packages(self): + if self._installed_packages is None: + self._installed_packages = [] + npackages = self.lib.lammps_config_package_count() + sb = create_string_buffer(100) + for idx in range(npackages): + self.lib.lammps_config_package_name(idx, sb, 100) + self._installed_packages.append(sb.value.decode()) + return self._installed_packages # ------------------------------------------------------------------------- # ------------------------------------------------------------------------- @@ -684,6 +711,12 @@ class Atom(object): self.lmp.eval("vy[%d]" % self.index), self.lmp.eval("vz[%d]" % self.index)) + @velocity.setter + def velocity(self, value): + self.lmp.set("atom", self.index, "vx", value[0]) + self.lmp.set("atom", self.index, "vy", value[1]) + self.lmp.set("atom", self.index, "vz", value[2]) + @property def force(self): return (self.lmp.eval("fx[%d]" % self.index), @@ -714,6 +747,11 @@ class Atom2D(Atom): return (self.lmp.eval("vx[%d]" % self.index), self.lmp.eval("vy[%d]" % self.index)) + @velocity.setter + def velocity(self, value): + self.lmp.set("atom", self.index, "vx", value[0]) + self.lmp.set("atom", self.index, "vy", value[1]) + @property def force(self): return (self.lmp.eval("fx[%d]" % self.index), @@ -827,6 +865,10 @@ class PyLammps(object): def run(self, *args, **kwargs): output = self.__getattr__('run')(*args, **kwargs) + + if(lammps.has_mpi4py): + output = self.lmp.comm.bcast(output, root=0) + self.runs += get_thermo_data(output) return output diff --git a/src/.gitignore b/src/.gitignore index 3ae05079d2..df3a22a5cd 100644 --- a/src/.gitignore +++ b/src/.gitignore @@ -5,6 +5,7 @@ /lmp_* /style_*.h +/lmpinstalledpkgs.h /*_gpu.h /*_gpu.cpp @@ -130,6 +131,27 @@ /pair_lj_charmmfsw_coul_long.cpp /pair_lj_charmmfsw_coul_long.h +/atom_vec_spin.cpp +/atom_vec_spin.h +/compute_spin.cpp +/compute_spin.h +/fix_langevin_spin.cpp +/fix_langevin_spin.h +/fix_nve_spin.cpp +/fix_nve_spin.h +/fix_precession_spin.cpp +/fix_precession_spin.h +/pair_spin.cpp +/pair_spin.h +/pair_spin_dmi.cpp +/pair_spin_dmi.h +/pair_spin_exchange.cpp +/pair_spin_exchange.h +/pair_spin_magelec.cpp +/pair_spin_magelec.h +/pair_spin_neel.cpp +/pair_spin_neel.h + /angle_cg_cmm.cpp /angle_cg_cmm.h /angle_charmm.cpp @@ -707,6 +729,8 @@ /pair_eam.h /pair_eam_alloy.cpp /pair_eam_alloy.h +/pair_eam_cd.cpp +/pair_eam_cd.h /pair_eam_fs.cpp /pair_eam_fs.h /pair_edip.cpp diff --git a/src/ASPHERE/fix_nve_asphere.cpp b/src/ASPHERE/fix_nve_asphere.cpp index a33848f1a1..61e3c35293 100644 --- a/src/ASPHERE/fix_nve_asphere.cpp +++ b/src/ASPHERE/fix_nve_asphere.cpp @@ -62,7 +62,7 @@ void FixNVEAsphere::init() /* ---------------------------------------------------------------------- */ -void FixNVEAsphere::initial_integrate(int vflag) +void FixNVEAsphere::initial_integrate(int /*vflag*/) { double dtfm; double inertia[3],omega[3]; diff --git a/src/ASPHERE/fix_nve_asphere_noforce.cpp b/src/ASPHERE/fix_nve_asphere_noforce.cpp index d944b68f35..9cc430592a 100644 --- a/src/ASPHERE/fix_nve_asphere_noforce.cpp +++ b/src/ASPHERE/fix_nve_asphere_noforce.cpp @@ -64,7 +64,7 @@ void FixNVEAsphereNoforce::init() /* ---------------------------------------------------------------------- */ -void FixNVEAsphereNoforce::initial_integrate(int vflag) +void FixNVEAsphereNoforce::initial_integrate(int /*vflag*/) { AtomVecEllipsoid::Bonus *bonus; if (avec) bonus = avec->bonus; diff --git a/src/ASPHERE/fix_nve_line.cpp b/src/ASPHERE/fix_nve_line.cpp index c145e99fcb..51a502df89 100644 --- a/src/ASPHERE/fix_nve_line.cpp +++ b/src/ASPHERE/fix_nve_line.cpp @@ -81,7 +81,7 @@ void FixNVELine::init() /* ---------------------------------------------------------------------- */ -void FixNVELine::initial_integrate(int vflag) +void FixNVELine::initial_integrate(int /*vflag*/) { double dtfm,dtirotate,length,theta; diff --git a/src/ASPHERE/fix_nve_tri.cpp b/src/ASPHERE/fix_nve_tri.cpp index d06063d905..fb9bf64c58 100644 --- a/src/ASPHERE/fix_nve_tri.cpp +++ b/src/ASPHERE/fix_nve_tri.cpp @@ -75,7 +75,7 @@ void FixNVETri::init() /* ---------------------------------------------------------------------- */ -void FixNVETri::initial_integrate(int vflag) +void FixNVETri::initial_integrate(int /*vflag*/) { double dtfm; double omega[3]; diff --git a/src/BODY/body_nparticle.cpp b/src/BODY/body_nparticle.cpp index 684e5768da..10529ad3af 100644 --- a/src/BODY/body_nparticle.cpp +++ b/src/BODY/body_nparticle.cpp @@ -195,7 +195,7 @@ void BodyNparticle::data_body(int ibonus, int ninteger, int ndouble, called by Molecule class which needs single body size ------------------------------------------------------------------------- */ -double BodyNparticle::radius_body(int ninteger, int ndouble, +double BodyNparticle::radius_body(int /*ninteger*/, int ndouble, int *ifile, double *dfile) { int nsub = ifile[0]; @@ -258,7 +258,7 @@ void BodyNparticle::output(int ibonus, int m, double *values) /* ---------------------------------------------------------------------- */ -int BodyNparticle::image(int ibonus, double flag1, double flag2, +int BodyNparticle::image(int ibonus, double flag1, double /*flag2*/, int *&ivec, double **&darray) { double p[3][3]; diff --git a/src/BODY/body_rounded_polygon.cpp b/src/BODY/body_rounded_polygon.cpp new file mode 100644 index 0000000000..00a09c912d --- /dev/null +++ b/src/BODY/body_rounded_polygon.cpp @@ -0,0 +1,452 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Trung Dac Nguyen (ndactrung@gmail.com) +------------------------------------------------------------------------- */ + +#include +#include "body_rounded_polygon.h" +#include "atom_vec_body.h" +#include "atom.h" +#include "force.h" +#include "domain.h" +#include "math_extra.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; + +#define EPSILON 1.0e-7 +enum{SPHERE,LINE}; // also in DumpImage + +/* ---------------------------------------------------------------------- */ + +BodyRoundedPolygon::BodyRoundedPolygon(LAMMPS *lmp, int narg, char **arg) : + Body(lmp, narg, arg) +{ + if (narg != 3) error->all(FLERR,"Invalid body rounded/polygon command"); + + if (domain->dimension != 2) + error->all(FLERR,"Atom_style body rounded/polygon " + "can only be used in 2d simulations"); + + // nmin and nmax are minimum and maximum number of vertices + + int nmin = force->inumeric(FLERR,arg[1]); + int nmax = force->inumeric(FLERR,arg[2]); + if (nmin <= 0 || nmin > nmax) + error->all(FLERR,"Invalid body rounded/polygon command"); + + size_forward = 0; + + // 1 integer for number of vertices, + // 3*nmax doubles for vertex coordinates + 2*nmax doubles for edge ends + // 1 double for the enclosing radius + // 1 double for the rounded radius + + size_border = 1 + 3*nmax + 2*nmax + 1 + 1; + + // NOTE: need to set appropriate nnbin param for dcp + + icp = new MyPoolChunk(1,1); + dcp = new MyPoolChunk(3*nmin+2*nmin+1+1,3*nmax+2*nmax+1+1); + + memory->create(imflag,nmax,"body/rounded/polygon:imflag"); + memory->create(imdata,nmax,7,"body/nparticle:imdata"); +} + +/* ---------------------------------------------------------------------- */ + +BodyRoundedPolygon::~BodyRoundedPolygon() +{ + delete icp; + delete dcp; + memory->destroy(imflag); + memory->destroy(imdata); +} + +/* ---------------------------------------------------------------------- */ + +int BodyRoundedPolygon::nsub(AtomVecBody::Bonus *bonus) +{ + return bonus->ivalue[0]; +} + +/* ---------------------------------------------------------------------- */ + +double *BodyRoundedPolygon::coords(AtomVecBody::Bonus *bonus) +{ + return bonus->dvalue; +} + +/* ---------------------------------------------------------------------- */ + +int BodyRoundedPolygon::nedges(AtomVecBody::Bonus *bonus) +{ + int nvertices = bonus->ivalue[0]; + if (nvertices == 1) return 0; + else if (nvertices == 2) return 1; + return nvertices; +} + +/* ---------------------------------------------------------------------- */ + +double *BodyRoundedPolygon::edges(AtomVecBody::Bonus *bonus) +{ + return bonus->dvalue+3*nsub(bonus); +} + +/* ---------------------------------------------------------------------- */ + +double BodyRoundedPolygon::enclosing_radius(struct AtomVecBody::Bonus *bonus) +{ + int nvertices = bonus->ivalue[0]; + if (nvertices == 1 || nvertices == 2) + return *(bonus->dvalue+3*nsub(bonus)+2); + return *(bonus->dvalue + 3*nsub(bonus) + 2*nsub(bonus)); +} + +/* ---------------------------------------------------------------------- */ + +double BodyRoundedPolygon::rounded_radius(struct AtomVecBody::Bonus *bonus) +{ + int nvertices = bonus->ivalue[0]; + if (nvertices == 1 || nvertices == 2) + return *(bonus->dvalue+3*nsub(bonus)+2+1); + return *(bonus->dvalue + 3*nsub(bonus) + 2*nsub(bonus)+1); +} + +/* ---------------------------------------------------------------------- */ + +int BodyRoundedPolygon::pack_border_body(AtomVecBody::Bonus *bonus, double *buf) +{ + int nsub = bonus->ivalue[0]; + buf[0] = nsub; + memcpy(&buf[1],bonus->dvalue,(3*nsub+2*nsub+1+1)*sizeof(double)); + return 1+(3*nsub+2*nsub+1+1); +} + +/* ---------------------------------------------------------------------- */ + +int BodyRoundedPolygon::unpack_border_body(AtomVecBody::Bonus *bonus, + double *buf) +{ + int nsub = static_cast (buf[0]); + bonus->ivalue[0] = nsub; + memcpy(bonus->dvalue,&buf[1],(3*nsub+2*nsub+1+1)*sizeof(double)); + return 1+(3*nsub+2*nsub+1+1); +} + +/* ---------------------------------------------------------------------- + populate bonus data structure with data file values +------------------------------------------------------------------------- */ + +void BodyRoundedPolygon::data_body(int ibonus, int ninteger, int ndouble, + int *ifile, double *dfile) +{ + AtomVecBody::Bonus *bonus = &avec->bonus[ibonus]; + + // set ninteger, ndouble in bonus and allocate 2 vectors of ints, doubles + + if (ninteger != 1) + error->one(FLERR,"Incorrect # of integer values in " + "Bodies section of data file"); + int nsub = ifile[0]; + if (nsub < 1) + error->one(FLERR,"Incorrect integer value in " + "Bodies section of data file"); + + // nentries = number of double entries to be read from Body section: + // 6 for inertia + 3*nsub for vertex coords + 1 for rounded radius + + int nentries = 6 + 3*nsub + 1; + if (ndouble != nentries) + error->one(FLERR,"Incorrect # of floating-point values in " + "Bodies section of data file"); + + bonus->ninteger = 1; + bonus->ivalue = icp->get(bonus->iindex); + bonus->ivalue[0] = nsub; + bonus->ndouble = 3*nsub + 2*nsub + 1 + 1; + bonus->dvalue = dcp->get(bonus->ndouble,bonus->dindex); + + // diagonalize inertia tensor + + double tensor[3][3]; + tensor[0][0] = dfile[0]; + tensor[1][1] = dfile[1]; + tensor[2][2] = dfile[2]; + tensor[0][1] = tensor[1][0] = dfile[3]; + tensor[0][2] = tensor[2][0] = dfile[4]; + tensor[1][2] = tensor[2][1] = dfile[5]; + + double *inertia = bonus->inertia; + double evectors[3][3]; + int ierror = MathExtra::jacobi(tensor,inertia,evectors); + if (ierror) error->one(FLERR, + "Insufficient Jacobi rotations for body nparticle"); + + // if any principal moment < scaled EPSILON, set to 0.0 + + double max; + max = MAX(inertia[0],inertia[1]); + max = MAX(max,inertia[2]); + + if (inertia[0] < EPSILON*max) inertia[0] = 0.0; + if (inertia[1] < EPSILON*max) inertia[1] = 0.0; + if (inertia[2] < EPSILON*max) inertia[2] = 0.0; + + // exyz_space = principal axes in space frame + + double ex_space[3],ey_space[3],ez_space[3]; + + ex_space[0] = evectors[0][0]; + ex_space[1] = evectors[1][0]; + ex_space[2] = evectors[2][0]; + ey_space[0] = evectors[0][1]; + ey_space[1] = evectors[1][1]; + ey_space[2] = evectors[2][1]; + ez_space[0] = evectors[0][2]; + ez_space[1] = evectors[1][2]; + ez_space[2] = evectors[2][2]; + + // enforce 3 evectors as a right-handed coordinate system + // flip 3rd vector if needed + + double cross[3]; + MathExtra::cross3(ex_space,ey_space,cross); + if (MathExtra::dot3(cross,ez_space) < 0.0) MathExtra::negate3(ez_space); + + // create initial quaternion + + MathExtra::exyz_to_q(ex_space,ey_space,ez_space,bonus->quat); + + // bonus->dvalue = the first 3*nsub elements are sub-particle displacements + // find the enclosing radius of the body from the maximum displacement + + int i,m; + double delta[3], rsq, erad, rrad; + double erad2 = 0; + int j = 6; + int k = 0; + for (i = 0; i < nsub; i++) { + delta[0] = dfile[j]; + delta[1] = dfile[j+1]; + delta[2] = dfile[j+2]; + MathExtra::transpose_matvec(ex_space,ey_space,ez_space, + delta,&bonus->dvalue[k]); + rsq = delta[0] * delta[0] + delta[1] * delta[1] + + delta[2] * delta[2]; + if (rsq > erad2) erad2 = rsq; + j += 3; + k += 3; + } + + // .. the next 2*nsub elements are edge ends + + int nedges; + if (nsub == 1) { // spheres + nedges = 0; + bonus->dvalue[k] = 0; + *(&bonus->dvalue[k]+1) = 0; + k += 2; + + // the last element of bonus->dvalue is the rounded & enclosing radius + + rrad = 0.5 * dfile[j]; + bonus->dvalue[k] = rrad; + erad = rrad; + + k++; + bonus->dvalue[k] = rrad; + + atom->radius[bonus->ilocal] = erad; + + } else if (nsub == 2) { // rods + nedges = 1; + for (i = 0; i < nedges; i++) { + bonus->dvalue[k] = 0; + *(&bonus->dvalue[k]+1) = 1; + k += 2; + } + + erad = sqrt(erad2); + bonus->dvalue[k] = erad; + + // the last element of bonus->dvalue is the rounded radius + + rrad = 0.5 * dfile[j]; + k++; + bonus->dvalue[k] = rrad; + + atom->radius[bonus->ilocal] = erad + rrad; + + } else { // polygons + nedges = nsub; + for (i = 0; i < nedges; i++) { + bonus->dvalue[k] = i; + m = i+1; + if (m == nedges) m = 0; + *(&bonus->dvalue[k]+1) = m; + k += 2; + } + + // the next to last element is the enclosing radius + + erad = sqrt(erad2); + bonus->dvalue[k] = erad; + + // the last element of bonus->dvalue is the rounded radius + + rrad = 0.5 * dfile[j]; + k++; + bonus->dvalue[k] = rrad; + + atom->radius[bonus->ilocal] = erad + rrad; + } +} + +/* ---------------------------------------------------------------------- + return radius of body particle defined by ifile/dfile params + params are ordered as in data file + called by Molecule class which needs single body size +------------------------------------------------------------------------- */ + +double BodyRoundedPolygon::radius_body(int /*ninteger*/, int ndouble, + int *ifile, double *dfile) +{ + int nsub = ifile[0]; + if (nsub < 1) + error->one(FLERR,"Incorrect integer value in " + "Bodies section of data file"); + if (ndouble != 6 + 3*nsub + 1) + error->one(FLERR,"Incorrect # of floating-point values in " + "Bodies section of data file"); + + // sub-particle coords are relative to body center at (0,0,0) + // offset = 6 for sub-particle coords + + double onerad; + double maxrad = 0.0; + double delta[3]; + + int offset = 6; + for (int i = 0; i < nsub; i++) { + delta[0] = dfile[offset]; + delta[1] = dfile[offset+1]; + delta[2] = dfile[offset+2]; + offset += 3; + onerad = MathExtra::len3(delta); + maxrad = MAX(maxrad,onerad); + } + + // add in radius of rounded corners + + return maxrad + 0.5*dfile[offset]; +} + +/* ---------------------------------------------------------------------- */ + +int BodyRoundedPolygon::noutcol() +{ + // the number of columns for the vertex coordinates + + return 3; +} + +/* ---------------------------------------------------------------------- */ + +int BodyRoundedPolygon::noutrow(int ibonus) +{ + // only return the first nsub rows for the vertex coordinates + + return avec->bonus[ibonus].ivalue[0]; +} + +/* ---------------------------------------------------------------------- */ + +void BodyRoundedPolygon::output(int ibonus, int m, double *values) +{ + AtomVecBody::Bonus *bonus = &avec->bonus[ibonus]; + + double p[3][3]; + MathExtra::quat_to_mat(bonus->quat,p); + MathExtra::matvec(p,&bonus->dvalue[3*m],values); + + double *x = atom->x[bonus->ilocal]; + values[0] += x[0]; + values[1] += x[1]; + values[2] += x[2]; +} + +/* ---------------------------------------------------------------------- */ + +int BodyRoundedPolygon::image(int ibonus, double flag1, double /*flag2*/, + int *&ivec, double **&darray) +{ + int j; + double p[3][3]; + double *x, rrad; + + AtomVecBody::Bonus *bonus = &avec->bonus[ibonus]; + int n = bonus->ivalue[0]; + + if (n == 1) { + for (int i = 0; i < n; i++) { + imflag[i] = SPHERE; + MathExtra::quat_to_mat(bonus->quat,p); + MathExtra::matvec(p,&bonus->dvalue[3*i],imdata[i]); + + rrad = enclosing_radius(bonus); + x = atom->x[bonus->ilocal]; + imdata[i][0] += x[0]; + imdata[i][1] += x[1]; + imdata[i][2] += x[2]; + if (flag1 <= 0) imdata[i][3] = 2*rrad; + else imdata[i][3] = flag1; + } + + } else { + + // first end pt of each line + + for (int i = 0; i < n; i++) { + imflag[i] = LINE; + MathExtra::quat_to_mat(bonus->quat,p); + MathExtra::matvec(p,&bonus->dvalue[3*i],imdata[i]); + + rrad = rounded_radius(bonus); + x = atom->x[bonus->ilocal]; + imdata[i][0] += x[0]; + imdata[i][1] += x[1]; + imdata[i][2] += x[2]; + if (flag1 <= 0) imdata[i][6] = 2*rrad; + else imdata[i][6] = flag1; + } + + // second end pt of each line + + for (int i = 0; i < n; i++) { + j = i+1; + if (j == n) j = 0; + imdata[i][3] = imdata[j][0]; + imdata[i][4] = imdata[j][1]; + imdata[i][5] = imdata[j][2]; + } + } + + ivec = imflag; + darray = imdata; + return n; +} diff --git a/src/BODY/body_rounded_polygon.h b/src/BODY/body_rounded_polygon.h new file mode 100644 index 0000000000..b6f45c5cf5 --- /dev/null +++ b/src/BODY/body_rounded_polygon.h @@ -0,0 +1,86 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef BODY_CLASS + +BodyStyle(rounded/polygon,BodyRoundedPolygon) + +#else + +#ifndef LMP_BODY_ROUNDED_POLYGON_H +#define LMP_BODY_ROUNDED_POLYGON_H + +#include "body.h" +#include "atom_vec_body.h" + +namespace LAMMPS_NS { + +class BodyRoundedPolygon : public Body { + public: + BodyRoundedPolygon(class LAMMPS *, int, char **); + ~BodyRoundedPolygon(); + int nsub(struct AtomVecBody::Bonus *); + double *coords(struct AtomVecBody::Bonus *); + int nedges(struct AtomVecBody::Bonus *); + double *edges(struct AtomVecBody::Bonus *); + double enclosing_radius(struct AtomVecBody::Bonus *); + double rounded_radius(struct AtomVecBody::Bonus *); + + int pack_border_body(struct AtomVecBody::Bonus *, double *); + int unpack_border_body(struct AtomVecBody::Bonus *, double *); + void data_body(int, int, int, int *, double *); + double radius_body(int, int, int *, double *); + + int noutrow(int); + int noutcol(); + void output(int, int, double *); + int image(int, double, double, int *&, double **&); + + private: + int *imflag; + double **imdata; +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Invalid body rounded/polygon command + +Arguments in atom-style command are not correct. + +E: Invalid format in Bodies section of data file + +The specified number of integer or floating point values does not +appear. + +E: Incorrect # of integer values in Bodies section of data file + +See doc page for body style. + +E: Incorrect integer value in Bodies section of data file + +See doc page for body style. + +E: Incorrect # of floating-point values in Bodies section of data file + +See doc page for body style. + +E: Insufficient Jacobi rotations for body nparticle + +Eigensolve for rigid body was not sufficiently accurate. + +*/ diff --git a/src/BODY/body_rounded_polyhedron.cpp b/src/BODY/body_rounded_polyhedron.cpp new file mode 100644 index 0000000000..0e2ebbed83 --- /dev/null +++ b/src/BODY/body_rounded_polyhedron.cpp @@ -0,0 +1,526 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Trung Dac Nguyen (ndactrung@gmail.com) +------------------------------------------------------------------------- */ + +#include +#include "body_rounded_polyhedron.h" +#include "atom_vec_body.h" +#include "atom.h" +#include "force.h" +#include "domain.h" +#include "math_extra.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; + +#define EPSILON 1.0e-7 +#define MAX_FACE_SIZE 4 // maximum number of vertices per face (for now) + +enum{SPHERE,LINE}; // also in DumpImage + +/* ---------------------------------------------------------------------- */ + +BodyRoundedPolyhedron::BodyRoundedPolyhedron(LAMMPS *lmp, int narg, char **arg) : + Body(lmp, narg, arg) +{ + if (narg != 3) error->all(FLERR,"Invalid body rounded/polygon command"); + + // nmin and nmax are minimum and maximum number of vertices + + int nmin = force->inumeric(FLERR,arg[1]); + int nmax = force->inumeric(FLERR,arg[2]); + if (nmin <= 0 || nmin > nmax) + error->all(FLERR,"Invalid body rounded/polyhedron command"); + + size_forward = 0; + + // 3 integers: 1 for no. of vertices, 1 for no. of edges, 1 for no. of faces + // 3*nmax doubles for vertex coordinates + 2*nmax doubles for edge ends + + // (MAX_FACE_SIZE+1)*nmax for faces + // 1 double for the enclosing radius + // 1 double for the rounded radius + + size_border = 3 + 3*nmax + 2*nmax + MAX_FACE_SIZE*nmax + 1 + 1; + + // NOTE: need to set appropriate nnbin param for dcp + + icp = new MyPoolChunk(1,3); + dcp = new MyPoolChunk(3*nmin+2+1+1, + 3*nmax+2*nmax+MAX_FACE_SIZE*nmax+1+1); + + memory->create(imflag,2*nmax,"body/rounded/polyhedron:imflag"); + memory->create(imdata,2*nmax,7,"body/polyhedron:imdata"); +} + +/* ---------------------------------------------------------------------- */ + +BodyRoundedPolyhedron::~BodyRoundedPolyhedron() +{ + delete icp; + delete dcp; + memory->destroy(imflag); + memory->destroy(imdata); +} + +/* ---------------------------------------------------------------------- */ + +int BodyRoundedPolyhedron::nsub(AtomVecBody::Bonus *bonus) +{ + return bonus->ivalue[0]; +} + +/* ---------------------------------------------------------------------- */ + +double *BodyRoundedPolyhedron::coords(AtomVecBody::Bonus *bonus) +{ + return bonus->dvalue; +} + +/* ---------------------------------------------------------------------- */ + +int BodyRoundedPolyhedron::nedges(AtomVecBody::Bonus *bonus) +{ + int nvertices = bonus->ivalue[0]; + int nedges = bonus->ivalue[1]; + //int nfaces = bonus->ivalue[2]; + if (nvertices == 1) return 0; + else if (nvertices == 2) return 1; + return nedges; //(nvertices+nfaces-2); // Euler's polyon formula: V-E+F=2 +} + +/* ---------------------------------------------------------------------- */ + +double *BodyRoundedPolyhedron::edges(AtomVecBody::Bonus *bonus) +{ + return bonus->dvalue+3*nsub(bonus); +} + +/* ---------------------------------------------------------------------- */ + +int BodyRoundedPolyhedron::nfaces(AtomVecBody::Bonus *bonus) +{ + return bonus->ivalue[2]; +} + +/* ---------------------------------------------------------------------- */ + +double *BodyRoundedPolyhedron::faces(AtomVecBody::Bonus *bonus) +{ + int nvertices = bonus->ivalue[0]; + if (nvertices == 1 || nvertices == 2) return NULL; + return bonus->dvalue+3*nsub(bonus)+2*nedges(bonus); +} + +/* ---------------------------------------------------------------------- */ + +double BodyRoundedPolyhedron::enclosing_radius(struct AtomVecBody::Bonus *bonus) +{ + int nvertices = bonus->ivalue[0]; + if (nvertices == 1 || nvertices == 2) + return *(bonus->dvalue+3*nsub(bonus)+2); + return *(bonus->dvalue+3*nsub(bonus) + 2*nedges(bonus) + + MAX_FACE_SIZE*nfaces(bonus)); +} + +/* ---------------------------------------------------------------------- */ + +double BodyRoundedPolyhedron::rounded_radius(struct AtomVecBody::Bonus *bonus) +{ + int nvertices = bonus->ivalue[0]; + if (nvertices == 1 || nvertices == 2) + return *(bonus->dvalue+3*nsub(bonus)+2+1); + return *(bonus->dvalue+3*nsub(bonus) + 2*nedges(bonus) + + MAX_FACE_SIZE*nfaces(bonus)+1); +} + +/* ---------------------------------------------------------------------- */ + +int BodyRoundedPolyhedron::pack_border_body(AtomVecBody::Bonus *bonus, double *buf) +{ + int nsub = bonus->ivalue[0]; + int ned = bonus->ivalue[1]; + int nfac = bonus->ivalue[2]; + buf[0] = nsub; + buf[1] = ned; + buf[2] = nfac; + int ndouble; + if (nsub == 1 || nsub == 2) ndouble = 3*nsub+2+MAX_FACE_SIZE*nfac+1+1; + else ndouble = 3*nsub+2*ned+MAX_FACE_SIZE*nfac+1+1; + memcpy(&buf[3],bonus->dvalue,ndouble*sizeof(double)); + return 3+ndouble; +} + +/* ---------------------------------------------------------------------- */ + +int BodyRoundedPolyhedron::unpack_border_body(AtomVecBody::Bonus *bonus, + double *buf) +{ + int nsub = static_cast (buf[0]); + int ned = static_cast (buf[1]); + int nfac = static_cast (buf[2]); + bonus->ivalue[0] = nsub; + bonus->ivalue[1] = ned; + bonus->ivalue[2] = nfac; + int ndouble; + if (nsub == 1 || nsub == 2) ndouble = 3*nsub+2+MAX_FACE_SIZE*nfac+1+1; + else ndouble = 3*nsub+2*ned+MAX_FACE_SIZE*nfac+1+1; + memcpy(bonus->dvalue,&buf[3],ndouble*sizeof(double)); + return 3+ndouble; +} + +/* ---------------------------------------------------------------------- + populate bonus data structure with data file values +------------------------------------------------------------------------- */ + +void BodyRoundedPolyhedron::data_body(int ibonus, int ninteger, int ndouble, + int *ifile, double *dfile) +{ + AtomVecBody::Bonus *bonus = &avec->bonus[ibonus]; + + // set ninteger, ndouble in bonus and allocate 2 vectors of ints, doubles + + if (ninteger != 3) + error->one(FLERR,"Incorrect # of integer values in " + "Bodies section of data file"); + int nsub = ifile[0]; + int ned = ifile[1]; + int nfac = ifile[2]; + if (nsub < 1) + error->one(FLERR,"Incorrect integer value in " + "Bodies section of data file"); + + // nentries = number of double entries to be read from Body section: + // nsub == 1 || nsub == 2 || nsub == 3: + // 6 for inertia + 3*nsub for vertex coords + 1 for rounded radius + // nsub > 3: + // 6 for inertia + 3*nsub for vertex coords + 2*nsub for edges + + // 3*nfaces + 1 for rounded radius + + int nedges,nentries; + if (nsub == 1 || nsub == 2) { + nentries = 6 + 3*nsub + 1; + } else { + nedges = ned; //nsub + nfac - 2; + nentries = 6 + 3*nsub + 2*nedges + MAX_FACE_SIZE*nfac + 1; + } + if (ndouble != nentries) + error->one(FLERR,"Incorrect # of floating-point values in " + "Bodies section of data file"); + + bonus->ninteger = 3; + bonus->ivalue = icp->get(bonus->iindex); + bonus->ivalue[0] = nsub; + bonus->ivalue[1] = ned; + bonus->ivalue[2] = nfac; + if (nsub == 1 || nsub == 2) bonus->ndouble = 3*nsub + 2*nsub + 1 + 1; + else bonus->ndouble = 3*nsub + 2*nedges + MAX_FACE_SIZE*nfac + 1 + 1; + bonus->dvalue = dcp->get(bonus->ndouble,bonus->dindex); + + // diagonalize inertia tensor + + double tensor[3][3]; + tensor[0][0] = dfile[0]; + tensor[1][1] = dfile[1]; + tensor[2][2] = dfile[2]; + tensor[0][1] = tensor[1][0] = dfile[3]; + tensor[0][2] = tensor[2][0] = dfile[4]; + tensor[1][2] = tensor[2][1] = dfile[5]; + + double *inertia = bonus->inertia; + double evectors[3][3]; + int ierror = MathExtra::jacobi(tensor,inertia,evectors); + if (ierror) error->one(FLERR, + "Insufficient Jacobi rotations for body nparticle"); + + // if any principal moment < scaled EPSILON, set to 0.0 + + double max; + max = MAX(inertia[0],inertia[1]); + max = MAX(max,inertia[2]); + + if (inertia[0] < EPSILON*max) inertia[0] = 0.0; + if (inertia[1] < EPSILON*max) inertia[1] = 0.0; + if (inertia[2] < EPSILON*max) inertia[2] = 0.0; + + // exyz_space = principal axes in space frame + + double ex_space[3],ey_space[3],ez_space[3]; + + ex_space[0] = evectors[0][0]; + ex_space[1] = evectors[1][0]; + ex_space[2] = evectors[2][0]; + ey_space[0] = evectors[0][1]; + ey_space[1] = evectors[1][1]; + ey_space[2] = evectors[2][1]; + ez_space[0] = evectors[0][2]; + ez_space[1] = evectors[1][2]; + ez_space[2] = evectors[2][2]; + + // enforce 3 evectors as a right-handed coordinate system + // flip 3rd vector if needed + + double cross[3]; + MathExtra::cross3(ex_space,ey_space,cross); + if (MathExtra::dot3(cross,ez_space) < 0.0) MathExtra::negate3(ez_space); + + // create initial quaternion + + MathExtra::exyz_to_q(ex_space,ey_space,ez_space,bonus->quat); + + // bonus->dvalue = the first 3*nsub elements are sub-particle displacements + // find the enclosing radius of the body from the maximum displacement + + int i,m; + double delta[3], rsq, erad, rrad; + double erad2 = 0; + int j = 6; + int k = 0; + for (i = 0; i < nsub; i++) { + delta[0] = dfile[j]; + delta[1] = dfile[j+1]; + delta[2] = dfile[j+2]; + MathExtra::transpose_matvec(ex_space,ey_space,ez_space, + delta,&bonus->dvalue[k]); + rsq = delta[0] * delta[0] + delta[1] * delta[1] + + delta[2] * delta[2]; + if (rsq > erad2) erad2 = rsq; + j += 3; + k += 3; + } + + // .. the next 2*nsub elements are edge ends + + if (nsub == 1) { // spheres + nedges = 0; + bonus->dvalue[k] = 0; + *(&bonus->dvalue[k]+1) = 0; + k += 2; + + rrad = 0.5 * dfile[j]; + bonus->dvalue[k] = rrad; + erad = rrad; // enclosing radius = rounded_radius + + // the last element of bonus->dvalue is the rounded radius + + k++; + bonus->dvalue[k] = rrad; + + atom->radius[bonus->ilocal] = erad; + + } else if (nsub == 2) { // rods + nedges = 1; + for (i = 0; i < nedges; i++) { + bonus->dvalue[k] = 0; + *(&bonus->dvalue[k]+1) = 1; + k += 2; + } + + erad = sqrt(erad2); + bonus->dvalue[k] = erad; + + // the last element of bonus->dvalue is the rounded radius + + rrad = 0.5 * dfile[j]; + k++; + bonus->dvalue[k] = rrad; + + atom->radius[bonus->ilocal] = erad + rrad; + + } else { // polyhedra + + // edges + + for (i = 0; i < nedges; i++) { + bonus->dvalue[k] = dfile[j]; + *(&bonus->dvalue[k]+1) = dfile[j+1]; + k += 2; + j += 2; + } + + // faces + + for (i = 0; i < nfac; i++) { + for (m = 0; m < MAX_FACE_SIZE; m++) + *(&bonus->dvalue[k]+m) = dfile[j+m]; + k += MAX_FACE_SIZE; + j += MAX_FACE_SIZE; + } + + // the next to last element is the enclosing radius + + erad = sqrt(erad2); + bonus->dvalue[k] = erad; + + // the last element bonus-> dvalue is the rounded radius + + rrad = 0.5 * dfile[j]; + k++; + bonus->dvalue[k] = rrad; + + atom->radius[bonus->ilocal] = erad + rrad; + } +} + +/* ---------------------------------------------------------------------- + return radius of body particle defined by ifile/dfile params + params are ordered as in data file + called by Molecule class which needs single body size +------------------------------------------------------------------------- */ + +double BodyRoundedPolyhedron::radius_body(int /*ninteger*/, int ndouble, + int *ifile, double *dfile) +{ + int nsub = ifile[0]; + int ned = ifile[1]; + int nfac = ifile[2]; + int nedges = ned; //nsub + nfac - 2; + + int nentries; + if (nsub == 1 || nsub == 2) nentries = 6 + 3*nsub + 1; + else nentries = 6 + 3*nsub + 2*nedges + MAX_FACE_SIZE*nfac + 1; + + if (nsub < 1) + error->one(FLERR,"Incorrect integer value in " + "Bodies section of data file"); + if (ndouble != nentries) + error->one(FLERR,"Incorrect # of floating-point values in " + "Bodies section of data file"); + + // sub-particle coords are relative to body center at (0,0,0) + // offset = 6 for sub-particle coords + + double onerad; + double maxrad = 0.0; + double delta[3]; + + int offset = 6; + for (int i = 0; i < nsub; i++) { + delta[0] = dfile[offset]; + delta[1] = dfile[offset+1]; + delta[2] = dfile[offset+2]; + offset += 3; + onerad = MathExtra::len3(delta); + maxrad = MAX(maxrad,onerad); + } + + if (nsub > 2) offset += (2*nedges+MAX_FACE_SIZE*nfac); + + // add in radius of rounded corners + + return maxrad + 0.5*dfile[offset]; +} + +/* ---------------------------------------------------------------------- */ + +int BodyRoundedPolyhedron::noutcol() +{ + // the number of columns for the vertex coordinates + + return 3; +} + +/* ---------------------------------------------------------------------- */ + +int BodyRoundedPolyhedron::noutrow(int ibonus) +{ + // only return the first nsub rows for the vertex coordinates + + return avec->bonus[ibonus].ivalue[0]; +} + +/* ---------------------------------------------------------------------- */ + +void BodyRoundedPolyhedron::output(int ibonus, int m, double *values) +{ + AtomVecBody::Bonus *bonus = &avec->bonus[ibonus]; + + double p[3][3]; + MathExtra::quat_to_mat(bonus->quat,p); + MathExtra::matvec(p,&bonus->dvalue[3*m],values); + + double *x = atom->x[bonus->ilocal]; + values[0] += x[0]; + values[1] += x[1]; + values[2] += x[2]; +} + +/* ---------------------------------------------------------------------- */ + +int BodyRoundedPolyhedron::image(int ibonus, double flag1, double /*flag2*/, + int *&ivec, double **&darray) +{ + int nelements; + double p[3][3]; + double *x, rrad; + + AtomVecBody::Bonus *bonus = &avec->bonus[ibonus]; + int nvertices = bonus->ivalue[0]; + + if (nvertices == 1) { // spheres + + for (int i = 0; i < nvertices; i++) { + imflag[i] = SPHERE; + MathExtra::quat_to_mat(bonus->quat,p); + MathExtra::matvec(p,&bonus->dvalue[3*i],imdata[i]); + + rrad = enclosing_radius(bonus); + x = atom->x[bonus->ilocal]; + imdata[i][0] += x[0]; + imdata[i][1] += x[1]; + imdata[i][2] += x[2]; + if (flag1 <= 0) imdata[i][3] = 2*rrad; + else imdata[i][3] = flag1; + } + + nelements = nvertices; + } else { + //int nfaces = bonus->ivalue[2]; + int nedges = bonus->ivalue[1]; //nvertices + nfaces - 2; + if (nvertices == 2) nedges = 1; // special case: rods + double* edge_ends = &bonus->dvalue[3*nvertices]; + int pt1, pt2; + + for (int i = 0; i < nedges; i++) { + imflag[i] = LINE; + + pt1 = static_cast(edge_ends[2*i]); + pt2 = static_cast(edge_ends[2*i+1]); + + MathExtra::quat_to_mat(bonus->quat,p); + MathExtra::matvec(p,&bonus->dvalue[3*pt1],imdata[i]); + MathExtra::matvec(p,&bonus->dvalue[3*pt2],&imdata[i][3]); + + rrad = rounded_radius(bonus); + x = atom->x[bonus->ilocal]; + imdata[i][0] += x[0]; + imdata[i][1] += x[1]; + imdata[i][2] += x[2]; + imdata[i][3] += x[0]; + imdata[i][4] += x[1]; + imdata[i][5] += x[2]; + + if (flag1 <= 0) imdata[i][6] = 2*rrad; + else imdata[i][6] = flag1; + } + + nelements = nedges; + } + + ivec = imflag; + darray = imdata; + return nelements; +} diff --git a/src/BODY/body_rounded_polyhedron.h b/src/BODY/body_rounded_polyhedron.h new file mode 100644 index 0000000000..e5b15fd8f9 --- /dev/null +++ b/src/BODY/body_rounded_polyhedron.h @@ -0,0 +1,88 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef BODY_CLASS + +BodyStyle(rounded/polyhedron,BodyRoundedPolyhedron) + +#else + +#ifndef LMP_BODY_ROUNDED_POLYHEDRON_H +#define LMP_BODY_ROUNDED_POLYHEDRON_H + +#include "body.h" +#include "atom_vec_body.h" + +namespace LAMMPS_NS { + +class BodyRoundedPolyhedron : public Body { + public: + BodyRoundedPolyhedron(class LAMMPS *, int, char **); + ~BodyRoundedPolyhedron(); + int nsub(struct AtomVecBody::Bonus *); + double *coords(struct AtomVecBody::Bonus *); + int nedges(struct AtomVecBody::Bonus *); + double *edges(struct AtomVecBody::Bonus *); + int nfaces(struct AtomVecBody::Bonus *); + double *faces(struct AtomVecBody::Bonus *); + double enclosing_radius(struct AtomVecBody::Bonus *); + double rounded_radius(struct AtomVecBody::Bonus *); + + int pack_border_body(struct AtomVecBody::Bonus *, double *); + int unpack_border_body(struct AtomVecBody::Bonus *, double *); + void data_body(int, int, int, int *, double *); + double radius_body(int, int, int *, double *); + + int noutrow(int); + int noutcol(); + void output(int, int, double *); + int image(int, double, double, int *&, double **&); + + private: + int *imflag; + double **imdata; +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Invalid body rounded/polyhedron command + +Arguments in atom-style command are not correct. + +E: Invalid format in Bodies section of data file + +The specified number of integer or floating point values does not +appear. + +E: Incorrect # of integer values in Bodies section of data file + +See doc page for body style. + +E: Incorrect integer value in Bodies section of data file + +See doc page for body style. + +E: Incorrect # of floating-point values in Bodies section of data file + +See doc page for body style. + +E: Insufficient Jacobi rotations for body rounded/polyhedron + +Eigensolve for rigid body was not sufficiently accurate. + +*/ diff --git a/src/BODY/fix_nve_body.cpp b/src/BODY/fix_nve_body.cpp index 0606723cb7..0c74facf34 100644 --- a/src/BODY/fix_nve_body.cpp +++ b/src/BODY/fix_nve_body.cpp @@ -54,7 +54,7 @@ void FixNVEBody::init() /* ---------------------------------------------------------------------- */ -void FixNVEBody::initial_integrate(int vflag) +void FixNVEBody::initial_integrate(int /*vflag*/) { double dtfm; double omega[3]; diff --git a/src/BODY/fix_wall_body_polygon.cpp b/src/BODY/fix_wall_body_polygon.cpp new file mode 100644 index 0000000000..3f8c08b6bd --- /dev/null +++ b/src/BODY/fix_wall_body_polygon.cpp @@ -0,0 +1,825 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Trung Dac Nguyen (ndactrung@gmail.com) +------------------------------------------------------------------------- */ + +#include +#include +#include +#include "fix_wall_body_polygon.h" +#include "atom.h" +#include "atom_vec_body.h" +#include "body_rounded_polygon.h" +#include "domain.h" +#include "update.h" +#include "force.h" +#include "pair.h" +#include "modify.h" +#include "respa.h" +#include "math_const.h" +#include "math_extra.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; +using namespace FixConst; +using namespace MathConst; + +enum{XPLANE=0,YPLANE=1,ZCYLINDER}; // XYZ PLANE need to be 0,1,2 +enum{HOOKE,HOOKE_HISTORY}; + +enum {INVALID=0,NONE=1,VERTEX=2}; +enum {FAR=0,XLO,XHI,YLO,YHI}; + +//#define _POLYGON_DEBUG +#define DELTA 10000 +#define EPSILON 1e-2 +#define BIG 1.0e20 +#define MAX_CONTACTS 4 // maximum number of contacts for 2D models +#define EFF_CONTACTS 2 // effective contacts for 2D models + +/* ---------------------------------------------------------------------- */ + +FixWallBodyPolygon::FixWallBodyPolygon(LAMMPS *lmp, int narg, char **arg) : + Fix(lmp, narg, arg) +{ + if (narg < 7) error->all(FLERR,"Illegal fix wall/body/polygon command"); + + if (!atom->body_flag) + error->all(FLERR,"Fix wall/body/polygon requires " + "atom style body/rounded/polygon"); + + restart_peratom = 1; + create_attribute = 1; + + // wall/particle coefficients + + kn = force->numeric(FLERR,arg[3]); + + c_n = force->numeric(FLERR,arg[4]); + if (strcmp(arg[5],"NULL") == 0) c_t = 0.5 * c_n; + else c_t = force->numeric(FLERR,arg[5]); + + if (kn < 0.0 || c_n < 0.0 || c_t < 0.0) + error->all(FLERR,"Illegal fix wall/body/polygon command"); + + // wallstyle args + + int iarg = 6; + if (strcmp(arg[iarg],"xplane") == 0) { + if (narg < iarg+3) error->all(FLERR,"Illegal fix wall/body/polygon command"); + wallstyle = XPLANE; + if (strcmp(arg[iarg+1],"NULL") == 0) lo = -BIG; + else lo = force->numeric(FLERR,arg[iarg+1]); + if (strcmp(arg[iarg+2],"NULL") == 0) hi = BIG; + else hi = force->numeric(FLERR,arg[iarg+2]); + iarg += 3; + } else if (strcmp(arg[iarg],"yplane") == 0) { + if (narg < iarg+3) error->all(FLERR,"Illegal fix wall/body/polygon command"); + wallstyle = YPLANE; + if (strcmp(arg[iarg+1],"NULL") == 0) lo = -BIG; + else lo = force->numeric(FLERR,arg[iarg+1]); + if (strcmp(arg[iarg+2],"NULL") == 0) hi = BIG; + else hi = force->numeric(FLERR,arg[iarg+2]); + iarg += 3; + } else if (strcmp(arg[iarg],"zcylinder") == 0) { + if (narg < iarg+2) error->all(FLERR,"Illegal fix wall/body/polygon command"); + wallstyle = ZCYLINDER; + lo = hi = 0.0; + cylradius = force->numeric(FLERR,arg[iarg+1]); + iarg += 2; + } + + // check for trailing keyword/values + + wiggle = 0; + + while (iarg < narg) { + if (strcmp(arg[iarg],"wiggle") == 0) { + if (iarg+4 > narg) error->all(FLERR,"Illegal fix wall/body/polygon command"); + if (strcmp(arg[iarg+1],"x") == 0) axis = 0; + else if (strcmp(arg[iarg+1],"y") == 0) axis = 1; + else if (strcmp(arg[iarg+1],"z") == 0) axis = 2; + else error->all(FLERR,"Illegal fix wall/body/polygon command"); + amplitude = force->numeric(FLERR,arg[iarg+2]); + period = force->numeric(FLERR,arg[iarg+3]); + wiggle = 1; + iarg += 4; + } else error->all(FLERR,"Illegal fix wall/body/polygon command"); + } + + if (wallstyle == XPLANE && domain->xperiodic) + error->all(FLERR,"Cannot use wall in periodic dimension"); + if (wallstyle == YPLANE && domain->yperiodic) + error->all(FLERR,"Cannot use wall in periodic dimension"); + if (wallstyle == ZCYLINDER && (domain->xperiodic || domain->yperiodic)) + error->all(FLERR,"Cannot use wall in periodic dimension"); + + if (wiggle && wallstyle == ZCYLINDER && axis != 2) + error->all(FLERR,"Invalid wiggle direction for fix wall/body/polygon"); + + // setup oscillations + + if (wiggle) omega = 2.0*MY_PI / period; + + time_origin = update->ntimestep; + + dmax = nmax = 0; + discrete = NULL; + dnum = dfirst = NULL; + + edmax = ednummax = 0; + edge = NULL; + ednum = edfirst = NULL; + + enclosing_radius = NULL; + rounded_radius = NULL; +} + +/* ---------------------------------------------------------------------- */ + +FixWallBodyPolygon::~FixWallBodyPolygon() +{ + memory->destroy(discrete); + memory->destroy(dnum); + memory->destroy(dfirst); + + memory->destroy(edge); + memory->destroy(ednum); + memory->destroy(edfirst); + + memory->destroy(enclosing_radius); + memory->destroy(rounded_radius); +} + +/* ---------------------------------------------------------------------- */ + +int FixWallBodyPolygon::setmask() +{ + int mask = 0; + mask |= POST_FORCE; + return mask; +} + +/* ---------------------------------------------------------------------- */ + +void FixWallBodyPolygon::init() +{ + dt = update->dt; + + avec = (AtomVecBody *) atom->style_match("body"); + if (!avec) + error->all(FLERR,"Pair body/rounded/polygon requires atom style body"); + if (strcmp(avec->bptr->style,"rounded/polygon") != 0) + error->all(FLERR,"Pair body/rounded/polygon requires " + "body style rounded/polygon"); + bptr = (BodyRoundedPolygon *) avec->bptr; + + // set pairstyle from body/polygonular pair style + + if (force->pair_match("body/rounded/polygon",1)) + pairstyle = HOOKE; + else error->all(FLERR,"Fix wall/body/polygon is incompatible with Pair style"); +} + +/* ---------------------------------------------------------------------- */ + +void FixWallBodyPolygon::setup(int vflag) +{ + if (strstr(update->integrate_style,"verlet")) + post_force(vflag); +} + +/* ---------------------------------------------------------------------- */ + +void FixWallBodyPolygon::post_force(int /*vflag*/) +{ + double vwall[3],dx,dy,dz,del1,del2,delxy,delr,rsq,eradi,rradi,wall_pos; + int i,ni,npi,ifirst,nei,iefirst,side; + double facc[3]; + + // set position of wall to initial settings and velocity to 0.0 + // if wiggle, set wall position and velocity accordingly + + double wlo = lo; + double whi = hi; + vwall[0] = vwall[1] = vwall[2] = 0.0; + if (wiggle) { + double arg = omega * (update->ntimestep - time_origin) * dt; + if (wallstyle == axis) { + wlo = lo + amplitude - amplitude*cos(arg); + whi = hi + amplitude - amplitude*cos(arg); + } + vwall[axis] = amplitude*omega*sin(arg); + } + + // loop over all my atoms + // rsq = distance from wall + // dx,dy,dz = signed distance from wall + // for rotating cylinder, reset vwall based on particle position + // skip atom if not close enough to wall + // if wall was set to NULL, it's skipped since lo/hi are infinity + // compute force and torque on atom if close enough to wall + // via wall potential matched to pair potential + + double **x = atom->x; + double **v = atom->v; + double **f = atom->f; + int *body = atom->body; + double *radius = atom->radius; + double **torque = atom->torque; + double **angmom = atom->angmom; + int *mask = atom->mask; + int nlocal = atom->nlocal; + + // grow the per-atom lists if necessary and initialize + + if (atom->nmax > nmax) { + memory->destroy(dnum); + memory->destroy(dfirst); + memory->destroy(ednum); + memory->destroy(edfirst); + memory->destroy(enclosing_radius); + memory->destroy(rounded_radius); + nmax = atom->nmax; + memory->create(dnum,nmax,"fix:dnum"); + memory->create(dfirst,nmax,"fix:dfirst"); + memory->create(ednum,nmax,"fix:ednum"); + memory->create(edfirst,nmax,"fix:edfirst"); + memory->create(enclosing_radius,nmax,"fix:enclosing_radius"); + memory->create(rounded_radius,nmax,"fix:rounded_radius"); + } + + ndiscrete = nedge = 0; + for (i = 0; i < nlocal; i++) + dnum[i] = ednum[i] = 0; + + for (i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + + if (body[i] < 0) continue; + + dx = dy = dz = 0.0; + side = FAR; + if (wallstyle == XPLANE) { + del1 = x[i][0] - wlo; + del2 = whi - x[i][0]; + if (del1 < del2) { + dx = del1; + wall_pos = wlo; + side = XLO; + } else { + dx = -del2; + wall_pos = whi; + side = XHI; + } + } else if (wallstyle == YPLANE) { + del1 = x[i][1] - wlo; + del2 = whi - x[i][1]; + if (del1 < del2) { + dy = del1; + wall_pos = wlo; + side = YLO; + } else { + dy = -del2; + wall_pos = whi; + side = YHI; + } + } else if (wallstyle == ZCYLINDER) { + delxy = sqrt(x[i][0]*x[i][0] + x[i][1]*x[i][1]); + delr = cylradius - delxy; + if (delr > eradi) dz = cylradius; + else { + dx = -delr/delxy * x[i][0]; + dy = -delr/delxy * x[i][1]; + } + } + + rsq = dx*dx + dy*dy + dz*dz; + if (rsq > radius[i]*radius[i]) continue; + + if (dnum[i] == 0) body2space(i); + npi = dnum[i]; + ifirst = dfirst[i]; + nei = ednum[i]; + iefirst = edfirst[i]; + eradi = enclosing_radius[i]; + rradi = rounded_radius[i]; + + // reset vertex and edge forces + + for (ni = 0; ni < npi; ni++) { + discrete[ifirst+ni][3] = 0; + discrete[ifirst+ni][4] = 0; + discrete[ifirst+ni][5] = 0; + } + + for (ni = 0; ni < nei; ni++) { + edge[iefirst+ni][2] = 0; + edge[iefirst+ni][3] = 0; + edge[iefirst+ni][4] = 0; + } + + int interact, num_contacts, done; + double delta_a, delta_ua, j_a; + Contact contact_list[MAX_CONTACTS]; + + num_contacts = 0; + facc[0] = facc[1] = facc[2] = 0; + interact = vertex_against_wall(i, wall_pos, x, f, torque, side, + contact_list, num_contacts, facc); + + if (num_contacts >= 2) { + + // find the first two distinct contacts + + done = 0; + for (int m = 0; m < num_contacts-1; m++) { + for (int n = m+1; n < num_contacts; n++) { + delta_a = contact_separation(contact_list[m], contact_list[n]); + if (delta_a > 0) { + delta_ua = 1.0; + j_a = delta_a / (EFF_CONTACTS * delta_ua); + if (j_a < 1.0) j_a = 1.0; + + // scale the force at both contacts + + contact_forces(contact_list[m], j_a, x, v, angmom, f, torque, + vwall, facc); + contact_forces(contact_list[n], j_a, x, v, angmom, f, torque, + vwall, facc); + done = 1; + break; + } + } + if (done == 1) break; + } + + } else if (num_contacts == 1) { + + // if there's only one contact, it should be handled here + // since forces/torques have not been accumulated from vertex2wall() + + contact_forces(contact_list[0], 1.0, x, v, angmom, f, torque, + vwall, facc); + } + } // group bit + } +} + +/* ---------------------------------------------------------------------- */ + +void FixWallBodyPolygon::reset_dt() +{ + dt = update->dt; +} + +/* ---------------------------------------------------------------------- + convert N sub-particles in body I to space frame using current quaternion + store sub-particle space-frame displacements from COM in discrete list +------------------------------------------------------------------------- */ + +void FixWallBodyPolygon::body2space(int i) +{ + int ibonus = atom->body[i]; + AtomVecBody::Bonus *bonus = &avec->bonus[ibonus]; + int nsub = bptr->nsub(bonus); + double *coords = bptr->coords(bonus); + int body_num_edges = bptr->nedges(bonus); + double* vertices = bptr->edges(bonus); + double eradius = bptr->enclosing_radius(bonus); + double rradius = bptr->rounded_radius(bonus); + + // get the number of sub-particles (vertices) + // and the index of the first vertex of my body in the list + + dnum[i] = nsub; + dfirst[i] = ndiscrete; + + // grow the vertex list if necessary + // the first 3 columns are for coords, the last 3 for forces + + if (ndiscrete + nsub > dmax) { + dmax += DELTA; + memory->grow(discrete,dmax,6,"fix:discrete"); + } + + double p[3][3]; + MathExtra::quat_to_mat(bonus->quat,p); + + for (int m = 0; m < nsub; m++) { + MathExtra::matvec(p,&coords[3*m],discrete[ndiscrete]); + discrete[ndiscrete][3] = 0; + discrete[ndiscrete][4] = 0; + discrete[ndiscrete][5] = 0; + ndiscrete++; + } + + // get the number of edges (vertices) + // and the index of the first edge of my body in the list + + ednum[i] = body_num_edges; + edfirst[i] = nedge; + + // grow the edge list if necessary + // the first 2 columns are for vertex indices within body, + // the last 3 for forces + + if (nedge + body_num_edges > edmax) { + edmax += DELTA; + memory->grow(edge,edmax,5,"fix:edge"); + } + + for (int m = 0; m < body_num_edges; m++) { + edge[nedge][0] = static_cast(vertices[2*m+0]); + edge[nedge][1] = static_cast(vertices[2*m+1]); + edge[nedge][2] = 0; + edge[nedge][3] = 0; + edge[nedge][4] = 0; + nedge++; + } + + enclosing_radius[i] = eradius; + rounded_radius[i] = rradius; +} + +/* ---------------------------------------------------------------------- + Determine the interaction mode between i's vertices against the wall + + i = atom i (body i) + x = atoms' coordinates + f = atoms' forces + torque = atoms' torques + Return: + contact_list = list of contacts between i and the wall + num_contacts = number of contacts between i's vertices and the wall + interact = 0 no interaction with the wall + 1 there's at least one vertex of i interacts + with the wall +---------------------------------------------------------------------- */ + +int FixWallBodyPolygon::vertex_against_wall(int i, double wall_pos, + double** x, double** f, double** torque, int side, + Contact* contact_list, int &num_contacts, double* /*facc*/) +{ + int ni, npi, ifirst, interact; + double xpi[3], eradi, rradi; + double fx, fy, fz; + + npi = dnum[i]; + ifirst = dfirst[i]; + eradi = enclosing_radius[i]; + rradi = rounded_radius[i]; + + interact = 0; + + // loop through body i's vertices + + for (ni = 0; ni < npi; ni++) { + + // convert body-fixed coordinates to space-fixed, xi + + xpi[0] = x[i][0] + discrete[ifirst+ni][0]; + xpi[1] = x[i][1] + discrete[ifirst+ni][1]; + xpi[2] = x[i][2] + discrete[ifirst+ni][2]; + + int mode, contact; + double d, R, hi[3], delx, dely, delz, fpair; + double rij; + + // compute the distance from the vertex xpi to the wall + + mode = compute_distance_to_wall(xpi, rradi, wall_pos, side, + d, hi, contact); + + if (mode == INVALID || mode == NONE) continue; + + if (mode == VERTEX) { + + interact = 1; + + // vertex i interacts with the wall + + delx = xpi[0] - hi[0]; + dely = xpi[1] - hi[1]; + delz = xpi[2] - hi[2]; + + // R = surface separation = d shifted by the rounded radius + // R = d - p1.rounded_radius; + // note: the force is defined for R, not for d + // R > 0: no interaction + // R <= 0: deformation between vertex i and the wall + + rij = sqrt(delx*delx + dely*dely + delz*delz); + R = rij - rradi; + + // the normal frictional term -c_n * vn will be added later + + if (R <= 0) { // deformation occurs + fpair = -kn * R; + } else fpair = 0.0; + + fx = delx*fpair/rij; + fy = dely*fpair/rij; + fz = delz*fpair/rij; + + #ifdef _POLYGON_DEBUG + printf(" Interaction between vertex %d of %d and wall:", ni); + printf(" mode = %d; contact = %d; d = %f; rij = %f\n", + mode, contact, d, rij); + printf(" R = %f\n", R); + printf(" fpair = %f\n", fpair); + #endif + + if (contact == 1) { + + // vertex ni of body i contacts with edge nj of body j + + contact_list[num_contacts].ibody = i; + contact_list[num_contacts].jbody = -1; + contact_list[num_contacts].vertex = ni; + contact_list[num_contacts].edge = -1; + contact_list[num_contacts].xv[0] = xpi[0]; + contact_list[num_contacts].xv[1] = xpi[1]; + contact_list[num_contacts].xv[2] = xpi[2]; + contact_list[num_contacts].xe[0] = hi[0]; + contact_list[num_contacts].xe[1] = hi[1]; + contact_list[num_contacts].xe[2] = hi[2]; + contact_list[num_contacts].separation = R; + num_contacts++; + + // store forces to vertex ni to be rescaled later, + // if there are 2 contacts + + discrete[ifirst+ni][3] = fx; + discrete[ifirst+ni][4] = fy; + discrete[ifirst+ni][5] = fz; + + #ifdef _POLYGON_DEBUG + printf(" Stored forces at vertex and edge for accumulating later.\n"); + #endif + + } else { // no contact + + // accumulate force and torque to the body directly + + f[i][0] += fx; + f[i][1] += fy; + f[i][2] += fz; + sum_torque(x[i], xpi, fx, fy, fz, torque[i]); + + } // end if contact + + } // end if mode + + } // end for looping through the vertices of body i + + return interact; +} + +/* ------------------------------------------------------------------------- + Compute the distance between a vertex to the wall + another body + Input: + x0 = coordinate of the tested vertex + rradi = rounded radius of the vertex + wall_pos = position of the wall + Output: + d = Distance from a point x0 to an wall + hi = coordinates of the projection of x0 on the wall + contact = 0 no contact between the queried vertex and the wall + 1 contact detected + return NONE if there is no interaction + EDGE if the tested vertex interacts with the wall +------------------------------------------------------------------------- */ + +int FixWallBodyPolygon::compute_distance_to_wall(double* x0, double rradi, + double wall_pos, int side, double &d, double hi[3], int &contact) +{ + int mode; + double delxy; + + // h0 = position of the projection of x0 on the wall + if (wallstyle == XPLANE) { + hi[0] = wall_pos; + hi[1] = x0[1]; + hi[2] = x0[2]; + } else if (wallstyle == YPLANE) { + hi[0] = x0[0]; + hi[1] = wall_pos; + hi[2] = x0[2]; + } else if (wallstyle == ZCYLINDER) { + delxy = sqrt(x0[0]*x0[0] + x0[1]*x0[1]); + hi[0] = x0[0]*cylradius/delxy; + hi[1] = x0[1]*cylradius/delxy; + hi[2] = x0[2]; + } + + // distance from x0 to the wall = distance from x0 to hi + + distance(hi, x0, d); + + // determine the interaction mode + + if (d < rradi) { + mode = VERTEX; + contact = 1; + } else { + mode = NONE; + if (side == XLO) { + if (x0[0] < wall_pos) mode = VERTEX; + } else if (side == XHI) { + if (x0[0] > wall_pos) mode = VERTEX; + } else if (side == YLO) { + if (x0[1] < wall_pos) mode = VERTEX; + } else if (side == YHI) { + if (x0[1] > wall_pos) mode = VERTEX; + } + } + + if (mode == NONE) contact = 0; + else contact = 1; + + return mode; +} + +/* ---------------------------------------------------------------------- + Compute the contact forces between two bodies + modify the force stored at the vertex and edge in contact by j_a + sum forces and torque to the corresponding bodies + fn = normal friction component + ft = tangential friction component (-c_t * vrt) +------------------------------------------------------------------------- */ + +void FixWallBodyPolygon::contact_forces(Contact& contact, double j_a, + double** x, double** v, double** angmom, double** f, + double** torque, double* vwall, double* facc) +{ + int ibody,ibonus,ifirst, ni; + double fx,fy,fz,delx,dely,delz,rsq,rsqinv; + double vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3; + double fn[3],ft[3],vi[3]; + double *quat, *inertia; + AtomVecBody::Bonus *bonus; + + ibody = contact.ibody; + + // compute the velocity of the vertex in the space-fixed frame + + ibonus = atom->body[ibody]; + bonus = &avec->bonus[ibonus]; + quat = bonus->quat; + inertia = bonus->inertia; + total_velocity(contact.xv, x[ibody], v[ibody], angmom[ibody], + inertia, quat, vi); + + // vector pointing from the vertex to the point on the wall + + delx = contact.xv[0] - contact.xe[0]; + dely = contact.xv[1] - contact.xe[1]; + delz = contact.xv[2] - contact.xe[2]; + rsq = delx*delx + dely*dely + delz*delz; + rsqinv = 1.0/rsq; + + // relative translational velocity + + vr1 = vi[0] - vwall[0]; + vr2 = vi[1] - vwall[1]; + vr3 = vi[2] - vwall[2]; + + // normal component + + vnnr = vr1*delx + vr2*dely + vr3*delz; + vn1 = delx*vnnr * rsqinv; + vn2 = dely*vnnr * rsqinv; + vn3 = delz*vnnr * rsqinv; + + // tangential component + + vt1 = vr1 - vn1; + vt2 = vr2 - vn2; + vt3 = vr3 - vn3; + + // normal friction term at contact + + fn[0] = -c_n * vn1; + fn[1] = -c_n * vn2; + fn[2] = -c_n * vn3; + + // tangential friction term at contact + // excluding the tangential deformation term for now + + ft[0] = -c_t * vt1; + ft[1] = -c_t * vt2; + ft[2] = -c_t * vt3; + + // only the cohesive force is scaled by j_a + + ifirst = dfirst[ibody]; + ni = contact.vertex; + + fx = discrete[ifirst+ni][3] * j_a + fn[0] + ft[0]; + fy = discrete[ifirst+ni][4] * j_a + fn[1] + ft[1]; + fz = discrete[ifirst+ni][5] * j_a + fn[2] + ft[2]; + f[ibody][0] += fx; + f[ibody][1] += fy; + f[ibody][2] += fz; + sum_torque(x[ibody], contact.xv, fx, fy, fz, torque[ibody]); + + // accumulate forces to the vertex only + + facc[0] += fx; facc[1] += fy; facc[2] += fz; + + #ifdef _POLYGON_DEBUG + printf("From contact forces: vertex fx %f fy %f fz %f\n" + " torque body %d: %f %f %f\n", + discrete[ifirst+ni][3], discrete[ifirst+ni][4], discrete[ifirst+ni][5], + atom->tag[ibody],torque[ibody][0],torque[ibody][1],torque[ibody][2]); + #endif +} + +/* ---------------------------------------------------------------------- + Determine the length of the contact segment, i.e. the separation between + 2 contacts +------------------------------------------------------------------------- */ + +double FixWallBodyPolygon::contact_separation(const Contact& c1, + const Contact& c2) +{ + double x1 = c1.xv[0]; + double y1 = c1.xv[1]; + double x2 = c1.xe[0]; + double y2 = c1.xe[1]; + double x3 = c2.xv[0]; + double y3 = c2.xv[1]; + + double delta_a = 0.0; + if (fabs(x2 - x1) > EPSILON) { + double A = (y2 - y1) / (x2 - x1); + delta_a = fabs(y1 - A * x1 - y3 + A * x3) / sqrt(1 + A * A); + } else { + delta_a = fabs(x1 - x3); + } + + return delta_a; +} + +/* ---------------------------------------------------------------------- + Accumulate torque to body from the force f=(fx,fy,fz) acting at point x +------------------------------------------------------------------------- */ + +void FixWallBodyPolygon::sum_torque(double* xm, double *x, double fx, + double fy, double fz, double* torque) +{ + double rx = x[0] - xm[0]; + double ry = x[1] - xm[1]; + double rz = x[2] - xm[2]; + double tx = ry * fz - rz * fy; + double ty = rz * fx - rx * fz; + double tz = rx * fy - ry * fx; + torque[0] += tx; + torque[1] += ty; + torque[2] += tz; +} + +/* ---------------------------------------------------------------------- + Calculate the total velocity of a point (vertex, a point on an edge): + vi = vcm + omega ^ (p - xcm) +------------------------------------------------------------------------- */ + +void FixWallBodyPolygon::total_velocity(double* p, double *xcm, + double* vcm, double *angmom, double *inertia, + double *quat, double* vi) +{ + double r[3],omega[3],ex_space[3],ey_space[3],ez_space[3]; + r[0] = p[0] - xcm[0]; + r[1] = p[1] - xcm[1]; + r[2] = p[2] - xcm[2]; + MathExtra::q_to_exyz(quat,ex_space,ey_space,ez_space); + MathExtra::angmom_to_omega(angmom,ex_space,ey_space,ez_space, + inertia,omega); + vi[0] = omega[1]*r[2] - omega[2]*r[1] + vcm[0]; + vi[1] = omega[2]*r[0] - omega[0]*r[2] + vcm[1]; + vi[2] = omega[0]*r[1] - omega[1]*r[0] + vcm[2]; +} + +/* ---------------------------------------------------------------------- */ + +void FixWallBodyPolygon::distance(const double* x2, const double* x1, + double& r) { + r = sqrt((x2[0] - x1[0]) * (x2[0] - x1[0]) + + (x2[1] - x1[1]) * (x2[1] - x1[1]) + + (x2[2] - x1[2]) * (x2[2] - x1[2])); +} diff --git a/src/BODY/fix_wall_body_polygon.h b/src/BODY/fix_wall_body_polygon.h new file mode 100644 index 0000000000..b71dcb0683 --- /dev/null +++ b/src/BODY/fix_wall_body_polygon.h @@ -0,0 +1,131 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef FIX_CLASS + +FixStyle(wall/body/polygon,FixWallBodyPolygon) + +#else + +#ifndef LMP_FIX_WALL_BODY_POLYGON_H +#define LMP_FIX_WALL_BODY_POLYGON_H + +#include "fix.h" + +namespace LAMMPS_NS { + +class FixWallBodyPolygon : public Fix { + public: + FixWallBodyPolygon(class LAMMPS *, int, char **); + virtual ~FixWallBodyPolygon(); + int setmask(); + void init(); + void setup(int); + virtual void post_force(int); + void reset_dt(); + + struct Contact { + int ibody, jbody; // body (i.e. atom) indices (not tags) + int vertex; // vertex of the first polygon + int edge; // edge of the second polygon + double xv[3]; // coordinates of the vertex + double xe[3]; // coordinates of the projection of the vertex on the edge + double separation;// separation at contact + }; + + protected: + int wallstyle,pairstyle,wiggle,axis; + double kn; // normal repulsion strength + double c_n; // normal damping coefficient + double c_t; // tangential damping coefficient + double lo,hi,cylradius; + double amplitude,period,omega; + double dt; + int time_origin; + + class AtomVecBody *avec; + class BodyRoundedPolygon *bptr; + + double **discrete; // list of all sub-particles for all bodies + int ndiscrete; // number of discretes in list + int dmax; // allocated size of discrete list + int *dnum; // number of discretes per line, 0 if uninit + int *dfirst; // index of first discrete per each line + int nmax; // allocated size of dnum,dfirst vectors + + double **edge; // list of all edge for all bodies + int nedge; // number of edge in list + int edmax; // allocated size of edge list + int *ednum; // number of edges per line, 0 if uninit + int *edfirst; // index of first edge per each line + int ednummax; // allocated size of ednum,edfirst vectors + + double *enclosing_radius; // enclosing radii for all bodies + double *rounded_radius; // rounded radii for all bodies + + void body2space(int); + + int vertex_against_wall(int ibody, double wall_pos, double** x, + double** f, double** torque, int side, + Contact* contact_list, int &num_contacts, + double* facc); + + int compute_distance_to_wall(double* x0, double rradi, double wall_pos, + int side, double &d, double hi[3], int &contact); + double contact_separation(const Contact& c1, const Contact& c2); + void contact_forces(Contact& contact, double j_a, double** x, + double** v, double** angmom, double** f, double** torque, + double* vwall, double* facc); + void sum_torque(double* xm, double *x, double fx, + double fy, double fz, double* torque); + void total_velocity(double* p, double *xcm, double* vcm, double *angmom, + double *inertia, double *quat, double* vi); + void distance(const double* x2, const double* x1, double& r); + +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Fix wall/body/polygon requires atom style body rounded/polygon + +Self-explanatory. + +E: Cannot use wall in periodic dimension + +Self-explanatory. + +E: Cannot wiggle and shear fix wall/body/polygon + +Cannot specify both options at the same time. + +E: Invalid wiggle direction for fix wall/body/polygon + +Self-explanatory. + +E: Fix wall/body/polygon is incompatible with Pair style + +Must use a body pair style to define the parameters needed for +this fix. + +*/ diff --git a/src/BODY/fix_wall_body_polyhedron.cpp b/src/BODY/fix_wall_body_polyhedron.cpp new file mode 100644 index 0000000000..9504e256b4 --- /dev/null +++ b/src/BODY/fix_wall_body_polyhedron.cpp @@ -0,0 +1,940 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Trung Dac Nguyen (ndactrung@gmail.com) +------------------------------------------------------------------------- */ + +#include +#include +#include +#include "fix_wall_body_polyhedron.h" +#include "atom.h" +#include "atom_vec_body.h" +#include "body_rounded_polyhedron.h" +#include "domain.h" +#include "update.h" +#include "force.h" +#include "pair.h" +#include "modify.h" +#include "respa.h" +#include "math_const.h" +#include "math_extra.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; +using namespace FixConst; +using namespace MathConst; + +enum{XPLANE=0,YPLANE=1,ZPLANE}; // XYZ PLANE need to be 0,1,2 +enum{HOOKE,HOOKE_HISTORY}; + +enum {INVALID=0,NONE=1,VERTEX=2}; +enum {FAR=0,XLO,XHI,YLO,YHI,ZLO,ZHI}; + +//#define _POLYHEDRON_DEBUG +#define DELTA 10000 +#define EPSILON 1e-2 +#define BIG 1.0e20 +#define MAX_CONTACTS 4 // maximum number of contacts for 2D models +#define EFF_CONTACTS 2 // effective contacts for 2D models + +/* ---------------------------------------------------------------------- */ + +FixWallBodyPolyhedron::FixWallBodyPolyhedron(LAMMPS *lmp, int narg, char **arg) : + Fix(lmp, narg, arg) +{ + if (narg < 7) error->all(FLERR,"Illegal fix wall/body/polyhedron command"); + + if (!atom->body_flag) + error->all(FLERR,"Fix wall/body/polyhedron requires " + "atom style body/rounded/polyhedron"); + + restart_peratom = 1; + create_attribute = 1; + + // wall/particle coefficients + + kn = force->numeric(FLERR,arg[3]); + + c_n = force->numeric(FLERR,arg[4]); + if (strcmp(arg[5],"NULL") == 0) c_t = 0.5 * c_n; + else c_t = force->numeric(FLERR,arg[5]); + + if (kn < 0.0 || c_n < 0.0 || c_t < 0.0) + error->all(FLERR,"Illegal fix wall/body/polyhedron command"); + + // wallstyle args + + int iarg = 6; + if (strcmp(arg[iarg],"xplane") == 0) { + if (narg < iarg+3) error->all(FLERR,"Illegal fix wall/body/polyhedron command"); + wallstyle = XPLANE; + if (strcmp(arg[iarg+1],"NULL") == 0) lo = -BIG; + else lo = force->numeric(FLERR,arg[iarg+1]); + if (strcmp(arg[iarg+2],"NULL") == 0) hi = BIG; + else hi = force->numeric(FLERR,arg[iarg+2]); + iarg += 3; + } else if (strcmp(arg[iarg],"yplane") == 0) { + if (narg < iarg+3) error->all(FLERR,"Illegal fix wall/body/polyhedron command"); + wallstyle = YPLANE; + if (strcmp(arg[iarg+1],"NULL") == 0) lo = -BIG; + else lo = force->numeric(FLERR,arg[iarg+1]); + if (strcmp(arg[iarg+2],"NULL") == 0) hi = BIG; + else hi = force->numeric(FLERR,arg[iarg+2]); + iarg += 3; + } else if (strcmp(arg[iarg],"zplane") == 0) { + if (narg < iarg+3) error->all(FLERR,"Illegal fix wall/body/polyhedron command"); + wallstyle = ZPLANE; + if (strcmp(arg[iarg+1],"NULL") == 0) lo = -BIG; + else lo = force->numeric(FLERR,arg[iarg+1]); + if (strcmp(arg[iarg+2],"NULL") == 0) hi = BIG; + else hi = force->numeric(FLERR,arg[iarg+2]); + iarg += 3; + } + + // check for trailing keyword/values + + wiggle = 0; + + while (iarg < narg) { + if (strcmp(arg[iarg],"wiggle") == 0) { + if (iarg+4 > narg) error->all(FLERR,"Illegal fix wall/body/polyhedron command"); + if (strcmp(arg[iarg+1],"x") == 0) axis = 0; + else if (strcmp(arg[iarg+1],"y") == 0) axis = 1; + else if (strcmp(arg[iarg+1],"z") == 0) axis = 2; + else error->all(FLERR,"Illegal fix wall/body/polyhedron command"); + amplitude = force->numeric(FLERR,arg[iarg+2]); + period = force->numeric(FLERR,arg[iarg+3]); + wiggle = 1; + iarg += 4; + } else error->all(FLERR,"Illegal fix wall/body/polyhedron command"); + } + + if (wallstyle == XPLANE && domain->xperiodic) + error->all(FLERR,"Cannot use wall in periodic dimension"); + if (wallstyle == YPLANE && domain->yperiodic) + error->all(FLERR,"Cannot use wall in periodic dimension"); + if (wallstyle == ZPLANE && domain->zperiodic) + error->all(FLERR,"Cannot use wall in periodic dimension"); + + // setup oscillations + + if (wiggle) omega = 2.0*MY_PI / period; + + time_origin = update->ntimestep; + + dmax = nmax = 0; + discrete = NULL; + dnum = dfirst = NULL; + + edmax = ednummax = 0; + edge = NULL; + ednum = edfirst = NULL; + + facmax = facnummax = 0; + face = NULL; + facnum = facfirst = NULL; + + enclosing_radius = NULL; + rounded_radius = NULL; +} + +/* ---------------------------------------------------------------------- */ + +FixWallBodyPolyhedron::~FixWallBodyPolyhedron() +{ + memory->destroy(discrete); + memory->destroy(dnum); + memory->destroy(dfirst); + + memory->destroy(edge); + memory->destroy(ednum); + memory->destroy(edfirst); + + memory->destroy(face); + memory->destroy(facnum); + memory->destroy(facfirst); + + memory->destroy(enclosing_radius); + memory->destroy(rounded_radius); +} + +/* ---------------------------------------------------------------------- */ + +int FixWallBodyPolyhedron::setmask() +{ + int mask = 0; + mask |= POST_FORCE; + return mask; +} + +/* ---------------------------------------------------------------------- */ + +void FixWallBodyPolyhedron::init() +{ + dt = update->dt; + + avec = (AtomVecBody *) atom->style_match("body"); + if (!avec) + error->all(FLERR,"Pair body/rounded/polyhedron requires atom style body"); + if (strcmp(avec->bptr->style,"rounded/polyhedron") != 0) + error->all(FLERR,"Pair body/rounded/polyhedron requires " + "body style rounded/polyhedron"); + bptr = (BodyRoundedPolyhedron *) avec->bptr; + + // set pairstyle from body/polyhedronular pair style + + if (force->pair_match("body/rounded/polyhedron",1)) + pairstyle = HOOKE; + else error->all(FLERR,"Fix wall/body/polyhedron is incompatible with Pair style"); +} + +/* ---------------------------------------------------------------------- */ + +void FixWallBodyPolyhedron::setup(int vflag) +{ + if (strstr(update->integrate_style,"verlet")) + post_force(vflag); +} + +/* ---------------------------------------------------------------------- */ + +void FixWallBodyPolyhedron::post_force(int /*vflag*/) +{ + double vwall[3],dx,dy,dz,del1,del2,rsq,eradi,rradi,wall_pos; + int i,ni,npi,ifirst,nei,iefirst,nfi,iffirst,side; + double facc[3]; + + // set position of wall to initial settings and velocity to 0.0 + // if wiggle, set wall position and velocity accordingly + + double wlo = lo; + double whi = hi; + vwall[0] = vwall[1] = vwall[2] = 0.0; + if (wiggle) { + double arg = omega * (update->ntimestep - time_origin) * dt; + if (wallstyle == axis) { + wlo = lo + amplitude - amplitude*cos(arg); + whi = hi + amplitude - amplitude*cos(arg); + } + vwall[axis] = amplitude*omega*sin(arg); + } + + // loop over all my atoms + // rsq = distance from wall + // dx,dy,dz = signed distance from wall + // for rotating cylinder, reset vwall based on particle position + // skip atom if not close enough to wall + // if wall was set to NULL, it's skipped since lo/hi are infinity + // compute force and torque on atom if close enough to wall + // via wall potential matched to pair potential + + double **x = atom->x; + double **v = atom->v; + double **f = atom->f; + int *body = atom->body; + double *radius = atom->radius; + double **torque = atom->torque; + double **angmom = atom->angmom; + int *mask = atom->mask; + int nlocal = atom->nlocal; + + // grow the per-atom lists if necessary and initialize + + if (atom->nmax > nmax) { + memory->destroy(dnum); + memory->destroy(dfirst); + memory->destroy(ednum); + memory->destroy(edfirst); + memory->destroy(facnum); + memory->destroy(facfirst); + memory->destroy(enclosing_radius); + memory->destroy(rounded_radius); + nmax = atom->nmax; + memory->create(dnum,nmax,"fix:dnum"); + memory->create(dfirst,nmax,"fix:dfirst"); + memory->create(ednum,nmax,"fix:ednum"); + memory->create(edfirst,nmax,"fix:edfirst"); + memory->create(facnum,nmax,"fix:facnum"); + memory->create(facfirst,nmax,"fix:facfirst"); + memory->create(enclosing_radius,nmax,"fix:enclosing_radius"); + memory->create(rounded_radius,nmax,"fix:rounded_radius"); + } + + ndiscrete = nedge = nface = 0; + for (i = 0; i < nlocal; i++) + dnum[i] = ednum[i] = facnum[i] = 0; + + for (i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + + if (body[i] < 0) continue; + + dx = dy = dz = 0.0; + side = FAR; + if (wallstyle == XPLANE) { + del1 = x[i][0] - wlo; + del2 = whi - x[i][0]; + if (del1 < del2) { + dx = del1; + wall_pos = wlo; + side = XLO; + } else { + dx = -del2; + wall_pos = whi; + side = XHI; + } + } else if (wallstyle == YPLANE) { + del1 = x[i][1] - wlo; + del2 = whi - x[i][1]; + if (del1 < del2) { + dy = del1; + wall_pos = wlo; + side = YLO; + } else { + dy = -del2; + wall_pos = whi; + side = YHI; + } + } else if (wallstyle == ZPLANE) { + del1 = x[i][2] - wlo; + del2 = whi - x[i][2]; + if (del1 < del2) { + dy = del1; + wall_pos = wlo; + side = ZLO; + } else { + dy = -del2; + wall_pos = whi; + side = ZHI; + } + } + + rsq = dx*dx + dy*dy + dz*dz; + if (rsq > radius[i]*radius[i]) continue; + + if (dnum[i] == 0) body2space(i); + npi = dnum[i]; + ifirst = dfirst[i]; + nei = ednum[i]; + iefirst = edfirst[i]; + nfi = facnum[i]; + iffirst = facfirst[i]; + eradi = enclosing_radius[i]; + rradi = rounded_radius[i]; + + if (npi == 1) { + sphere_against_wall(i, wall_pos, side, vwall, x, v, f, angmom, torque); + continue; + } + + // reset vertex and edge forces + + for (ni = 0; ni < npi; ni++) { + discrete[ifirst+ni][3] = 0; + discrete[ifirst+ni][4] = 0; + discrete[ifirst+ni][5] = 0; + discrete[ifirst+ni][6] = 0; + } + + for (ni = 0; ni < nei; ni++) { + edge[iefirst+ni][2] = 0; + edge[iefirst+ni][3] = 0; + edge[iefirst+ni][4] = 0; + edge[iefirst+ni][5] = 0; + } + + int interact, num_contacts; + Contact contact_list[MAX_CONTACTS]; + + num_contacts = 0; + facc[0] = facc[1] = facc[2] = 0; + interact = edge_against_wall(i, wall_pos, side, vwall, x, f, torque, + contact_list, num_contacts, facc); + + } // group bit + } +} + +/* ---------------------------------------------------------------------- */ + +void FixWallBodyPolyhedron::reset_dt() +{ + dt = update->dt; +} + +/* ---------------------------------------------------------------------- + convert N sub-particles in body I to space frame using current quaternion + store sub-particle space-frame displacements from COM in discrete list +------------------------------------------------------------------------- */ + +void FixWallBodyPolyhedron::body2space(int i) +{ + int ibonus = atom->body[i]; + AtomVecBody::Bonus *bonus = &avec->bonus[ibonus]; + int nsub = bptr->nsub(bonus); + double *coords = bptr->coords(bonus); + int body_num_edges = bptr->nedges(bonus); + double* edge_ends = bptr->edges(bonus); + int body_num_faces = bptr->nfaces(bonus); + double* face_pts = bptr->faces(bonus); + double eradius = bptr->enclosing_radius(bonus); + double rradius = bptr->rounded_radius(bonus); + + // get the number of sub-particles (vertices) + // and the index of the first vertex of my body in the list + + dnum[i] = nsub; + dfirst[i] = ndiscrete; + + // grow the vertex list if necessary + // the first 3 columns are for coords, the last 3 for forces + + if (ndiscrete + nsub > dmax) { + dmax += DELTA; + memory->grow(discrete,dmax,7,"fix:discrete"); + } + + double p[3][3]; + MathExtra::quat_to_mat(bonus->quat,p); + + for (int m = 0; m < nsub; m++) { + MathExtra::matvec(p,&coords[3*m],discrete[ndiscrete]); + discrete[ndiscrete][3] = 0; + discrete[ndiscrete][4] = 0; + discrete[ndiscrete][5] = 0; + discrete[ndiscrete][6] = 0; + ndiscrete++; + } + + // get the number of edges (vertices) + // and the index of the first edge of my body in the list + + ednum[i] = body_num_edges; + edfirst[i] = nedge; + + // grow the edge list if necessary + // the first 2 columns are for vertex indices within body, + // the last 3 for forces + + if (nedge + body_num_edges > edmax) { + edmax += DELTA; + memory->grow(edge,edmax,6,"fix:edge"); + } + + for (int m = 0; m < body_num_edges; m++) { + edge[nedge][0] = static_cast(edge_ends[2*m+0]); + edge[nedge][1] = static_cast(edge_ends[2*m+1]); + edge[nedge][2] = 0; + edge[nedge][3] = 0; + edge[nedge][4] = 0; + edge[nedge][5] = 0; + nedge++; + } + + // get the number of faces and the index of the first face + + facnum[i] = body_num_faces; + facfirst[i] = nface; + + // grow the face list if necessary + // the first 3 columns are for vertex indices within body, the last 3 for forces + + if (nface + body_num_faces > facmax) { + facmax += DELTA; + memory->grow(face,facmax,6,"pair:face"); + } + + for (int m = 0; m < body_num_faces; m++) { + face[nface][0] = static_cast(face_pts[3*m+0]); + face[nface][1] = static_cast(face_pts[3*m+1]); + face[nface][2] = static_cast(face_pts[3*m+2]); + face[nface][3] = 0; + face[nface][4] = 0; + face[nface][5] = 0; + nface++; + } + + enclosing_radius[i] = eradius; + rounded_radius[i] = rradius; +} + +/* ---------------------------------------------------------------------- + Determine the interaction mode between a sphere against the wall + + i = atom i (body i) + x = atoms' coordinates + f = atoms' forces + torque = atoms' torques +---------------------------------------------------------------------- */ + +int FixWallBodyPolyhedron::sphere_against_wall(int i, double wall_pos, + int /*side*/, double* vwall, double** x, double** v, double** f, + double** angmom, double** torque) +{ + int mode; + double rradi,hi[3],d,delx,dely,delz,R,fpair,fx,fy,fz; + + rradi = rounded_radius[i]; + mode = NONE; + + if (wallstyle == XPLANE) { + hi[0] = wall_pos; + hi[1] = x[i][1]; + hi[2] = x[i][2]; + } else if (wallstyle == YPLANE) { + hi[0] = x[i][0]; + hi[1] = wall_pos; + hi[2] = x[i][2]; + } else if (wallstyle == ZPLANE) { + hi[0] = x[i][0]; + hi[1] = x[i][1]; + hi[2] = wall_pos; + } + + distance(hi, x[i], d); + + if (d <= rradi) { + delx = x[i][0] - hi[0]; + dely = x[i][1] - hi[1]; + delz = x[i][2] - hi[2]; + R = d - rradi; + + fpair = -kn * R; + + fx = delx*fpair/d; + fy = dely*fpair/d; + fz = delz*fpair/d; + + contact_forces(i, 1.0, x[i], hi, delx, dely, delz, + fx, fy, fz, x, v, angmom, f, torque, vwall); + mode = VERTEX; + } + + return mode; +} + +/* ---------------------------------------------------------------------- + Determine the interaction mode between i's vertices against the wall + + i = atom i (body i) + x = atoms' coordinates + f = atoms' forces + torque = atoms' torques + Output: + contact_list = list of contacts between i and the wall + num_contacts = number of contacts between i's vertices and the wall + Return: + number of contacts of the edge to the wall (0, 1 or 2) +---------------------------------------------------------------------- */ + +int FixWallBodyPolyhedron::edge_against_wall(int i, double wall_pos, + int side, double* vwall, double** x, double** /*f*/, double** /*torque*/, + Contact* /*contact_list*/, int &/*num_contacts*/, double* /*facc*/) +{ + int ni, nei, mode, contact; + double rradi; + + nei = ednum[i]; + rradi = rounded_radius[i]; + + contact = 0; + + // loop through body i's edges + + for (ni = 0; ni < nei; ni++) + mode = compute_distance_to_wall(i, ni, x[i], rradi, wall_pos, side, vwall, + contact); + + return contact; +} + +/* ------------------------------------------------------------------------- + Compute the distance between a vertex to the wall + another body + Input: + x0 = coordinate of the tested vertex + rradi = rounded radius of the vertex + wall_pos = position of the wall + Output: + d = Distance from a point x0 to an wall + hi = coordinates of the projection of x0 on the wall + contact = 0 no contact between the queried vertex and the wall + 1 contact detected + return NONE if there is no interaction + VERTEX if the tested vertex interacts with the wall +------------------------------------------------------------------------- */ + +int FixWallBodyPolyhedron::compute_distance_to_wall(int ibody, int edge_index, + double *xmi, double rounded_radius_i, double wall_pos, + int /*side*/, double* vwall, int &contact) +{ + int mode,ifirst,iefirst,npi1,npi2; + double d1,d2,xpi1[3],xpi2[3],hi[3]; + double fx,fy,fz,fpair,delx,dely,delz,R; + + double** x = atom->x; + double** v = atom->v; + double** f = atom->f; + double** torque = atom->torque; + double** angmom = atom->angmom; + + // two ends of the edge from body i + + ifirst = dfirst[ibody]; + iefirst = edfirst[ibody]; + npi1 = static_cast(edge[iefirst+edge_index][0]); + npi2 = static_cast(edge[iefirst+edge_index][1]); + + xpi1[0] = xmi[0] + discrete[ifirst+npi1][0]; + xpi1[1] = xmi[1] + discrete[ifirst+npi1][1]; + xpi1[2] = xmi[2] + discrete[ifirst+npi1][2]; + + xpi2[0] = xmi[0] + discrete[ifirst+npi2][0]; + xpi2[1] = xmi[1] + discrete[ifirst+npi2][1]; + xpi2[2] = xmi[2] + discrete[ifirst+npi2][2]; + + // determine the intersection of the edge to the wall + + mode = NONE; + double j_a = 1.0; + + if (wallstyle == XPLANE) { + hi[0] = wall_pos; + hi[1] = xpi1[1]; + hi[2] = xpi1[2]; + } else if (wallstyle == YPLANE) { + hi[0] = xpi1[0]; + hi[1] = wall_pos; + hi[2] = xpi1[2]; + } else if (wallstyle == ZPLANE) { + hi[0] = xpi1[0]; + hi[1] = xpi1[1]; + hi[2] = wall_pos; + } + + distance(hi, xpi1, d1); + + if (d1 <= rounded_radius_i && static_cast(discrete[ifirst+npi1][6]) == 0) { + delx = xpi1[0] - hi[0]; + dely = xpi1[1] - hi[1]; + delz = xpi1[2] - hi[2]; + R = d1 - rounded_radius_i; + + fpair = -kn * R; + + fx = delx*fpair/d1; + fy = dely*fpair/d1; + fz = delz*fpair/d1; + + contact_forces(ibody, j_a, xpi1, hi, delx, dely, delz, + fx, fy, fz, x, v, angmom, f, torque, vwall); + discrete[ifirst+npi1][6] = 1; + contact++; + mode = VERTEX; + } + + if (wallstyle == XPLANE) { + hi[0] = wall_pos; + hi[1] = xpi2[1]; + hi[2] = xpi2[2]; + } else if (wallstyle == YPLANE) { + hi[0] = xpi2[0]; + hi[1] = wall_pos; + hi[2] = xpi2[2]; + } else if (wallstyle == ZPLANE) { + hi[0] = xpi2[0]; + hi[1] = xpi2[1]; + hi[2] = wall_pos; + } + + distance(hi, xpi2, d2); + + if (d2 <= rounded_radius_i && static_cast(discrete[ifirst+npi2][6]) == 0) { + delx = xpi2[0] - hi[0]; + dely = xpi2[1] - hi[1]; + delz = xpi2[2] - hi[2]; + R = d2 - rounded_radius_i; + + fpair = -kn * R; + + fx = delx*fpair/d2; + fy = dely*fpair/d2; + fz = delz*fpair/d2; + + contact_forces(ibody, j_a, xpi2, hi, delx, dely, delz, + fx, fy, fz, x, v, angmom, f, torque, vwall); + discrete[ifirst+npi2][6] = 1; + contact++; + mode = VERTEX; + } + + return mode; +} + +/* ---------------------------------------------------------------------- + Compute contact forces between two bodies + modify the force stored at the vertex and edge in contact by j_a + sum forces and torque to the corresponding bodies + fn = normal friction component + ft = tangential friction component (-c_t * v_t) +------------------------------------------------------------------------- */ + +void FixWallBodyPolyhedron::contact_forces(int ibody, + double j_a, double *xi, double * /*xj*/, double delx, double dely, double delz, + double fx, double fy, double fz, double** x, double** v, double** angmom, + double** f, double** torque, double* vwall) +{ + int ibonus; + double fxt,fyt,fzt,rsq,rsqinv; + double vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3; + double fn[3],ft[3],vi[3]; + double *quat, *inertia; + AtomVecBody::Bonus *bonus; + + // compute the velocity of the vertex in the space-fixed frame + + ibonus = atom->body[ibody]; + bonus = &avec->bonus[ibonus]; + quat = bonus->quat; + inertia = bonus->inertia; + total_velocity(xi, x[ibody], v[ibody], angmom[ibody], + inertia, quat, vi); + + // vector pointing from the contact point on ibody to the wall + + rsq = delx*delx + dely*dely + delz*delz; + rsqinv = 1.0/rsq; + + // relative translational velocity + + vr1 = vi[0] - vwall[0]; + vr2 = vi[1] - vwall[1]; + vr3 = vi[2] - vwall[2]; + + // normal component + + vnnr = vr1*delx + vr2*dely + vr3*delz; + vn1 = delx*vnnr * rsqinv; + vn2 = dely*vnnr * rsqinv; + vn3 = delz*vnnr * rsqinv; + + // tangential component + + vt1 = vr1 - vn1; + vt2 = vr2 - vn2; + vt3 = vr3 - vn3; + + // normal friction term at contact + + fn[0] = -c_n * vn1; + fn[1] = -c_n * vn2; + fn[2] = -c_n * vn3; + + // tangential friction term at contact + // excluding the tangential deformation term for now + + ft[0] = -c_t * vt1; + ft[1] = -c_t * vt2; + ft[2] = -c_t * vt3; + + fxt = fx; fyt = fy; fzt = fz; + fx = fxt * j_a + fn[0] + ft[0]; + fy = fyt * j_a + fn[1] + ft[1]; + fz = fzt * j_a + fn[2] + ft[2]; + + f[ibody][0] += fx; + f[ibody][1] += fy; + f[ibody][2] += fz; + sum_torque(x[ibody], xi, fx, fy, fz, torque[ibody]); + + #ifdef _POLYHEDRON_DEBUG + printf("From contact forces: vertex fx %f fy %f fz %f\n" + " torque body %d: %f %f %f\n" + " torque body %d: %f %f %f\n", + fxt, fyt, fzt, + atom->tag[ibody],torque[ibody][0],torque[ibody][1],torque[ibody][2], + atom->tag[jbody],torque[jbody][0],torque[jbody][1],torque[jbody][2]); + #endif +} + +/* ---------------------------------------------------------------------- + Compute the contact forces between two bodies + modify the force stored at the vertex and edge in contact by j_a + sum forces and torque to the corresponding bodies + fn = normal friction component + ft = tangential friction component (-c_t * vrt) +------------------------------------------------------------------------- */ + +void FixWallBodyPolyhedron::contact_forces(Contact& contact, double j_a, + double** x, double** v, double** angmom, double** f, + double** torque, double* vwall, double* facc) +{ + int ibody,ibonus,ifirst,ni; + double fx,fy,fz,delx,dely,delz,rsq,rsqinv; + double vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3; + double fn[3],ft[3],vi[3]; + double *quat, *inertia; + AtomVecBody::Bonus *bonus; + + ibody = contact.ibody; + + // compute the velocity of the vertex in the space-fixed frame + + ibonus = atom->body[ibody]; + bonus = &avec->bonus[ibonus]; + quat = bonus->quat; + inertia = bonus->inertia; + total_velocity(contact.xv, x[ibody], v[ibody], angmom[ibody], + inertia, quat, vi); + + // vector pointing from the vertex to the point on the wall + + delx = contact.xv[0] - contact.xe[0]; + dely = contact.xv[1] - contact.xe[1]; + delz = contact.xv[2] - contact.xe[2]; + rsq = delx*delx + dely*dely + delz*delz; + rsqinv = 1.0/rsq; + + // relative translational velocity + + vr1 = vi[0] - vwall[0]; + vr2 = vi[1] - vwall[1]; + vr3 = vi[2] - vwall[2]; + + // normal component + + vnnr = vr1*delx + vr2*dely + vr3*delz; + vn1 = delx*vnnr * rsqinv; + vn2 = dely*vnnr * rsqinv; + vn3 = delz*vnnr * rsqinv; + + // tangential component + + vt1 = vr1 - vn1; + vt2 = vr2 - vn2; + vt3 = vr3 - vn3; + + // normal friction term at contact + + fn[0] = -c_n * vn1; + fn[1] = -c_n * vn2; + fn[2] = -c_n * vn3; + + // tangential friction term at contact + // excluding the tangential deformation term for now + + ft[0] = -c_t * vt1; + ft[1] = -c_t * vt2; + ft[2] = -c_t * vt3; + + // only the cohesive force is scaled by j_a + + ifirst = dfirst[ibody]; + ni = contact.vertex; + + fx = discrete[ifirst+ni][3] * j_a + fn[0] + ft[0]; + fy = discrete[ifirst+ni][4] * j_a + fn[1] + ft[1]; + fz = discrete[ifirst+ni][5] * j_a + fn[2] + ft[2]; + f[ibody][0] += fx; + f[ibody][1] += fy; + f[ibody][2] += fz; + sum_torque(x[ibody], contact.xv, fx, fy, fz, torque[ibody]); + + // accumulate forces to the vertex only + + facc[0] += fx; facc[1] += fy; facc[2] += fz; + + #ifdef _POLYHEDRON_DEBUG + printf("From contact forces: vertex fx %f fy %f fz %f\n" + " torque body %d: %f %f %f\n", + discrete[ifirst+ni][3], discrete[ifirst+ni][4], discrete[ifirst+ni][5], + atom->tag[ibody],torque[ibody][0],torque[ibody][1],torque[ibody][2]); + #endif +} + +/* ---------------------------------------------------------------------- + Determine the length of the contact segment, i.e. the separation between + 2 contacts +------------------------------------------------------------------------- */ + +double FixWallBodyPolyhedron::contact_separation(const Contact& c1, + const Contact& c2) +{ + double x1 = c1.xv[0]; + double y1 = c1.xv[1]; + double x2 = c1.xe[0]; + double y2 = c1.xe[1]; + double x3 = c2.xv[0]; + double y3 = c2.xv[1]; + + double delta_a = 0.0; + if (fabs(x2 - x1) > EPSILON) { + double A = (y2 - y1) / (x2 - x1); + delta_a = fabs(y1 - A * x1 - y3 + A * x3) / sqrt(1 + A * A); + } else { + delta_a = fabs(x1 - x3); + } + + return delta_a; +} + +/* ---------------------------------------------------------------------- + Accumulate torque to body from the force f=(fx,fy,fz) acting at point x +------------------------------------------------------------------------- */ + +void FixWallBodyPolyhedron::sum_torque(double* xm, double *x, double fx, + double fy, double fz, double* torque) +{ + double rx = x[0] - xm[0]; + double ry = x[1] - xm[1]; + double rz = x[2] - xm[2]; + double tx = ry * fz - rz * fy; + double ty = rz * fx - rx * fz; + double tz = rx * fy - ry * fx; + torque[0] += tx; + torque[1] += ty; + torque[2] += tz; +} + +/* ---------------------------------------------------------------------- + Calculate the total velocity of a point (vertex, a point on an edge): + vi = vcm + omega ^ (p - xcm) +------------------------------------------------------------------------- */ + +void FixWallBodyPolyhedron::total_velocity(double* p, double *xcm, + double* vcm, double *angmom, double *inertia, + double *quat, double* vi) +{ + double r[3],omega[3],ex_space[3],ey_space[3],ez_space[3]; + r[0] = p[0] - xcm[0]; + r[1] = p[1] - xcm[1]; + r[2] = p[2] - xcm[2]; + MathExtra::q_to_exyz(quat,ex_space,ey_space,ez_space); + MathExtra::angmom_to_omega(angmom,ex_space,ey_space,ez_space, + inertia,omega); + vi[0] = omega[1]*r[2] - omega[2]*r[1] + vcm[0]; + vi[1] = omega[2]*r[0] - omega[0]*r[2] + vcm[1]; + vi[2] = omega[0]*r[1] - omega[1]*r[0] + vcm[2]; +} + +/* ---------------------------------------------------------------------- */ + +void FixWallBodyPolyhedron::distance(const double* x2, const double* x1, + double& r) { + r = sqrt((x2[0] - x1[0]) * (x2[0] - x1[0]) + + (x2[1] - x1[1]) * (x2[1] - x1[1]) + + (x2[2] - x1[2]) * (x2[2] - x1[2])); +} diff --git a/src/BODY/fix_wall_body_polyhedron.h b/src/BODY/fix_wall_body_polyhedron.h new file mode 100644 index 0000000000..ff7b7ca7cf --- /dev/null +++ b/src/BODY/fix_wall_body_polyhedron.h @@ -0,0 +1,143 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef FIX_CLASS + +FixStyle(wall/body/polyhedron,FixWallBodyPolyhedron) + +#else + +#ifndef LMP_FIX_WALL_BODY_POLYHERON_H +#define LMP_FIX_WALL_BODY_POLYHERON_H + +#include "fix.h" + +namespace LAMMPS_NS { + +class FixWallBodyPolyhedron : public Fix { + public: + FixWallBodyPolyhedron(class LAMMPS *, int, char **); + virtual ~FixWallBodyPolyhedron(); + int setmask(); + void init(); + void setup(int); + virtual void post_force(int); + void reset_dt(); + + struct Contact { + int ibody, jbody; // body (i.e. atom) indices (not tags) + int vertex; // vertex of the first polygon + int edge; // edge of the second polygon + double xv[3]; // coordinates of the vertex + double xe[3]; // coordinates of the projection of the vertex on the edge + double separation;// separation at contact + }; + + protected: + int wallstyle,pairstyle,wiggle,axis; + double kn,c_n,c_t; + double lo,hi,cylradius; + double amplitude,period,omega; + double dt; + int time_origin; + + class AtomVecBody *avec; + class BodyRoundedPolyhedron *bptr; + + double **discrete; // list of all sub-particles for all bodies + int ndiscrete; // number of discretes in list + int dmax; // allocated size of discrete list + int *dnum; // number of discretes per line, 0 if uninit + int *dfirst; // index of first discrete per each line + int nmax; // allocated size of dnum,dfirst vectors + + double **edge; // list of all edge for all bodies + int nedge; // number of edge in list + int edmax; // allocated size of edge list + int *ednum; // number of edges per line, 0 if uninit + int *edfirst; // index of first edge per each line + int ednummax; // allocated size of ednum,edfirst vectors + + double **face; // list of all edge for all bodies + int nface; // number of faces in list + int facmax; // allocated size of face list + int *facnum; // number of faces per line, 0 if uninit + int *facfirst; // index of first face per each line + int facnummax; // allocated size of facnum,facfirst vectors + + double *enclosing_radius; // enclosing radii for all bodies + double *rounded_radius; // rounded radii for all bodies + + void body2space(int); + + int edge_against_wall(int ibody, double wall_pos, int side, double* vwall, + double** x, double** f, double** torque, Contact* contact_list, + int &num_contacts, double* facc); + int sphere_against_wall(int i, double wall_pos, int side, double* vwall, + double** x, double** v, double** f, double** angmom, double** torque); + + int compute_distance_to_wall(int ibody, int edge_index, double *xmi, + double rounded_radius_i, double wall_pos, int side, + double* vwall, int &contact); + double contact_separation(const Contact& c1, const Contact& c2); + void contact_forces(int ibody, double j_a, double *xi, double *xj, + double delx, double dely, double delz, + double fx, double fy, double fz, double** x, double** v, + double** angmom, double** f, double** torque, double* vwall); + + void contact_forces(Contact& contact, double j_a, double** x, + double** v, double** angmom, double** f, double** torque, + double* vwall, double* facc); + void sum_torque(double* xm, double *x, double fx, + double fy, double fz, double* torque); + void total_velocity(double* p, double *xcm, double* vcm, double *angmom, + double *inertia, double *quat, double* vi); + void distance(const double* x2, const double* x1, double& r); + +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Fix wall/body/polyhedron requires atom style body rounded/polyhedron + +Self-explanatory. + +E: Cannot use wall in periodic dimension + +Self-explanatory. + +E: Cannot wiggle and shear fix wall/body/polygon + +Cannot specify both options at the same time. + +E: Invalid wiggle direction for fix wall/body/polygon + +Self-explanatory. + +E: Fix wall/body/polygon is incompatible with Pair style + +Must use a body pair style to define the parameters needed for +this fix. + +*/ diff --git a/src/BODY/pair_body.cpp b/src/BODY/pair_body_nparticle.cpp similarity index 95% rename from src/BODY/pair_body.cpp rename to src/BODY/pair_body_nparticle.cpp index 8c12c0cf36..80b45beb4e 100644 --- a/src/BODY/pair_body.cpp +++ b/src/BODY/pair_body_nparticle.cpp @@ -15,7 +15,7 @@ #include #include #include -#include "pair_body.h" +#include "pair_body_nparticle.h" #include "math_extra.h" #include "atom.h" #include "atom_vec_body.h" @@ -32,7 +32,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -PairBody::PairBody(LAMMPS *lmp) : Pair(lmp) +PairBodyNparticle::PairBodyNparticle(LAMMPS *lmp) : Pair(lmp) { dmax = nmax = 0; discrete = NULL; @@ -44,7 +44,7 @@ PairBody::PairBody(LAMMPS *lmp) : Pair(lmp) /* ---------------------------------------------------------------------- */ -PairBody::~PairBody() +PairBodyNparticle::~PairBodyNparticle() { memory->destroy(discrete); memory->destroy(dnum); @@ -66,7 +66,7 @@ PairBody::~PairBody() /* ---------------------------------------------------------------------- */ -void PairBody::compute(int eflag, int vflag) +void PairBodyNparticle::compute(int eflag, int vflag) { int i,j,ii,jj,inum,jnum,itype,jtype; int ni,nj,npi,npj,ifirst,jfirst; @@ -336,7 +336,7 @@ void PairBody::compute(int eflag, int vflag) allocate all arrays ------------------------------------------------------------------------- */ -void PairBody::allocate() +void PairBodyNparticle::allocate() { allocated = 1; int n = atom->ntypes; @@ -361,7 +361,7 @@ void PairBody::allocate() global settings ------------------------------------------------------------------------- */ -void PairBody::settings(int narg, char **arg) +void PairBodyNparticle::settings(int narg, char **arg) { if (narg != 1) error->all(FLERR,"Illegal pair_style command"); @@ -381,7 +381,7 @@ void PairBody::settings(int narg, char **arg) set coeffs for one or more type pairs ------------------------------------------------------------------------- */ -void PairBody::coeff(int narg, char **arg) +void PairBodyNparticle::coeff(int narg, char **arg) { if (narg < 4 || narg > 5) error->all(FLERR,"Incorrect args for pair coefficients"); @@ -415,12 +415,12 @@ void PairBody::coeff(int narg, char **arg) init specific to this pair style ------------------------------------------------------------------------- */ -void PairBody::init_style() +void PairBodyNparticle::init_style() { avec = (AtomVecBody *) atom->style_match("body"); - if (!avec) error->all(FLERR,"Pair body requires atom style body"); + if (!avec) error->all(FLERR,"Pair body/nparticle requires atom style body"); if (strcmp(avec->bptr->style,"nparticle") != 0) - error->all(FLERR,"Pair body requires body style nparticle"); + error->all(FLERR,"Pair body/nparticle requires body style nparticle"); bptr = (BodyNparticle *) avec->bptr; neighbor->request(this,instance_me); @@ -430,7 +430,7 @@ void PairBody::init_style() init for one type pair i,j and corresponding j,i ------------------------------------------------------------------------- */ -double PairBody::init_one(int i, int j) +double PairBodyNparticle::init_one(int i, int j) { if (setflag[i][j] == 0) { epsilon[i][j] = mix_energy(epsilon[i][i],epsilon[j][j], @@ -459,7 +459,7 @@ double PairBody::init_one(int i, int j) store sub-particle space-frame displacements from COM in discrete list ------------------------------------------------------------------------- */ -void PairBody::body2space(int i) +void PairBodyNparticle::body2space(int i) { int ibonus = atom->body[i]; AtomVecBody::Bonus *bonus = &avec->bonus[ibonus]; diff --git a/src/BODY/pair_body.h b/src/BODY/pair_body_nparticle.h similarity index 90% rename from src/BODY/pair_body.h rename to src/BODY/pair_body_nparticle.h index 94fbdf34df..9c7d832b64 100644 --- a/src/BODY/pair_body.h +++ b/src/BODY/pair_body_nparticle.h @@ -13,21 +13,21 @@ #ifdef PAIR_CLASS -PairStyle(body,PairBody) +PairStyle(body/nparticle,PairBodyNparticle) #else -#ifndef LMP_PAIR_BODY_H -#define LMP_PAIR_BODY_H +#ifndef LMP_PAIR_BODY_NPARTICLE_H +#define LMP_PAIR_BODY_NPARTICLE_H #include "pair.h" namespace LAMMPS_NS { -class PairBody : public Pair { +class PairBodyNparticle : public Pair { public: - PairBody(class LAMMPS *); - ~PairBody(); + PairBodyNparticle(class LAMMPS *); + ~PairBodyNparticle(); void compute(int, int); void settings(int, char **); void coeff(int, char **); diff --git a/src/BODY/pair_body_rounded_polygon.cpp b/src/BODY/pair_body_rounded_polygon.cpp new file mode 100644 index 0000000000..6a176f1083 --- /dev/null +++ b/src/BODY/pair_body_rounded_polygon.cpp @@ -0,0 +1,1379 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Trung Dac Nguyen (ndactrung@gmail.com) + Ref: Fraige, Langston, Matchett and Dodds, Particuology 2008, 6:455-466 + Note: The current implementation has not taken into account + the contact history for friction forces. +------------------------------------------------------------------------- */ + +#include +#include +#include +#include +#include "pair_body_rounded_polygon.h" +#include "math_extra.h" +#include "atom.h" +#include "atom_vec_body.h" +#include "body_rounded_polygon.h" +#include "comm.h" +#include "force.h" +#include "fix.h" +#include "modify.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; + +#define DELTA 10000 +#define EPSILON 1e-3 +#define MAX_CONTACTS 4 // maximum number of contacts for 2D models +#define EFF_CONTACTS 2 // effective contacts for 2D models + +//#define _CONVEX_POLYGON +//#define _POLYGON_DEBUG + +enum {INVALID=0,NONE=1,VERTEXI=2,VERTEXJ=3,EDGE=4}; + +/* ---------------------------------------------------------------------- */ + +PairBodyRoundedPolygon::PairBodyRoundedPolygon(LAMMPS *lmp) : Pair(lmp) +{ + dmax = nmax = 0; + discrete = NULL; + dnum = dfirst = NULL; + + edmax = ednummax = 0; + edge = NULL; + ednum = edfirst = NULL; + + enclosing_radius = NULL; + rounded_radius = NULL; + maxerad = NULL; + + single_enable = 0; + restartinfo = 0; + + c_n = 0.1; + c_t = 0.2; + mu = 0.0; + delta_ua = 1.0; +} + +/* ---------------------------------------------------------------------- */ + +PairBodyRoundedPolygon::~PairBodyRoundedPolygon() +{ + memory->destroy(discrete); + memory->destroy(dnum); + memory->destroy(dfirst); + + memory->destroy(edge); + memory->destroy(ednum); + memory->destroy(edfirst); + + memory->destroy(enclosing_radius); + memory->destroy(rounded_radius); + + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + + memory->destroy(k_n); + memory->destroy(k_na); + memory->destroy(maxerad); + } +} + +/* ---------------------------------------------------------------------- */ + +void PairBodyRoundedPolygon::compute(int eflag, int vflag) +{ + int i,j,ii,jj,inum,jnum,itype,jtype; + int ni,nj,npi,npj,ifirst,jfirst; + int nei,nej,iefirst,jefirst; + double xtmp,ytmp,ztmp,delx,dely,delz,evdwl; + double rsq,rsqinv,r,radi,radj,eradi,eradj,rradi,rradj,k_nij,k_naij; + double xi[3],xj[3],facc[3]; + int *ilist,*jlist,*numneigh,**firstneigh; + + evdwl = 0.0; + if (eflag || vflag) ev_setup(eflag,vflag); + else evflag = vflag_fdotr = 0; + + double **x = atom->x; + double **v = atom->v; + double **f = atom->f; + double **torque = atom->torque; + double **angmom = atom->angmom; + double *radius = atom->radius; + tagint* tag = atom->tag; + int *body = atom->body; + int *type = atom->type; + int nlocal = atom->nlocal; + int nall = nlocal + atom->nghost; + int newton_pair = force->newton_pair; + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // grow the per-atom lists if necessary and initialize + + if (atom->nmax > nmax) { + memory->destroy(dnum); + memory->destroy(dfirst); + memory->destroy(ednum); + memory->destroy(edfirst); + memory->destroy(enclosing_radius); + memory->destroy(rounded_radius); + nmax = atom->nmax; + memory->create(dnum,nmax,"pair:dnum"); + memory->create(dfirst,nmax,"pair:dfirst"); + memory->create(ednum,nmax,"pair:ednum"); + memory->create(edfirst,nmax,"pair:edfirst"); + memory->create(enclosing_radius,nmax,"pair:enclosing_radius"); + memory->create(rounded_radius,nmax,"pair:rounded_radius"); + } + + ndiscrete = nedge = 0; + for (i = 0; i < nall; i++) + dnum[i] = ednum[i] = 0; + + // loop over neighbors of my atoms + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + itype = type[i]; + radi = radius[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + if (body[i] >= 0) { + if (dnum[i] == 0) body2space(i); + npi = dnum[i]; + ifirst = dfirst[i]; + nei = ednum[i]; + iefirst = edfirst[i]; + eradi = enclosing_radius[i]; + rradi = rounded_radius[i]; + } + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + j &= NEIGHMASK; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + jtype = type[j]; + radj = radius[j]; + + // body/body interactions + + evdwl = 0.0; + facc[0] = facc[1] = facc[2] = 0; + + if (body[i] < 0 || body[j] < 0) continue; + + if (dnum[j] == 0) body2space(j); + npj = dnum[j]; + jfirst = dfirst[j]; + nej = ednum[j]; + jefirst = edfirst[j]; + eradj = enclosing_radius[j]; + rradj = rounded_radius[j]; + + k_nij = k_n[itype][jtype]; + k_naij = k_na[itype][jtype]; + + // no interaction + + r = sqrt(rsq); + if (r > radi + radj + cut_inner) continue; + rsqinv = 1.0 / rsq; + + if (npi == 1 && npj == 1) { + sphere_against_sphere(i, j, delx, dely, delz, rsq, + k_nij, k_naij, x, v, f, evflag); + continue; + } + + // reset vertex and edge forces + + for (ni = 0; ni < npi; ni++) { + discrete[ifirst+ni][3] = 0; + discrete[ifirst+ni][4] = 0; + discrete[ifirst+ni][5] = 0; + } + + for (nj = 0; nj < npj; nj++) { + discrete[jfirst+nj][3] = 0; + discrete[jfirst+nj][4] = 0; + discrete[jfirst+nj][5] = 0; + } + + for (ni = 0; ni < nei; ni++) { + edge[iefirst+ni][2] = 0; + edge[iefirst+ni][3] = 0; + edge[iefirst+ni][4] = 0; + } + + for (nj = 0; nj < nej; nj++) { + edge[jefirst+nj][2] = 0; + edge[jefirst+nj][3] = 0; + edge[jefirst+nj][4] = 0; + } + + int interact, num_contacts, done; + double delta_a, j_a; + Contact contact_list[MAX_CONTACTS]; + + num_contacts = 0; + + // check interaction between i's vertices and j' edges + + interact = vertex_against_edge(i, j, k_nij, k_naij, + x, f, torque, tag, contact_list, + num_contacts, evdwl, facc); + + // check interaction between j's vertices and i' edges + + interact = vertex_against_edge(j, i, k_nij, k_naij, + x, f, torque, tag, contact_list, + num_contacts, evdwl, facc); + + if (num_contacts >= 2) { + + // find the first two distinct contacts + + done = 0; + for (int m = 0; m < num_contacts-1; m++) { + for (int n = m+1; n < num_contacts; n++) { + delta_a = contact_separation(contact_list[m], contact_list[n]); + if (delta_a > 0) { + j_a = delta_a / (EFF_CONTACTS * delta_ua); + if (j_a < 1.0) j_a = 1.0; + + // scale the force at both contacts + + contact_forces(contact_list[m], j_a, x, v, angmom, f, torque, + evdwl, facc); + contact_forces(contact_list[n], j_a, x, v, angmom, f, torque, + evdwl, facc); + done = 1; + + #ifdef _POLYGON_DEBUG + printf(" Two separate contacts %d and %d: delta_a = %f; j_a = %f\n", + m, n, delta_a, j_a); + printf(" %d: vertex %d of body %d and edge %d of body %d; " + "xv = %f %f %f; xe = %f %f %f\n", + m, contact_list[m].vertex, contact_list[m].ibody, + contact_list[m].edge, contact_list[m].jbody, + contact_list[m].xv[0], contact_list[m].xv[1], + contact_list[m].xv[2], contact_list[m].xe[0], + contact_list[m].xe[1], contact_list[m].xe[2]); + printf(" %d: vertex %d of body %d and edge %d of body %d; " + "xv = %f %f %f; xe = %f %f %f\n", + n, contact_list[n].vertex, contact_list[n].ibody, + contact_list[n].edge, contact_list[n].jbody, + contact_list[n].xv[0], contact_list[n].xv[1], + contact_list[n].xv[2], contact_list[n].xe[0], + contact_list[n].xe[1], contact_list[n].xe[2]); + #endif + + break; + } + } + if (done == 1) break; + } + + + } else if (num_contacts == 1) { + + // if there's only one contact, it should be handled here + // since forces/torques have not been accumulated from vertex2edge() + + contact_forces(contact_list[0], 1.0, x, v, angmom, f, torque, evdwl, facc); + + #ifdef _POLYGON_DEBUG + printf("One contact between vertex %d of body %d and edge %d of body %d:\n", + contact_list[0].vertex, tag[contact_list[0].ibody], + contact_list[0].edge, tag[contact_list[0].jbody]); + printf("xv = %f %f %f; xe = %f %f %f\n", + contact_list[0].xv[0], contact_list[0].xv[1], contact_list[0].xv[2], + contact_list[0].xe[0], contact_list[0].xe[1], contact_list[0].xe[2]); + #endif + } + + #ifdef _POLYGON_DEBUG + int num_overlapping_contacts = 0; + for (int m = 0; m < num_contacts-1; m++) { + for (int n = m+1; n < num_contacts; n++) { + double l = contact_separation(contact_list[m], contact_list[n]); + if (l < EPSILON) num_overlapping_contacts++; + } + } + printf("There are %d contacts detected, %d of which overlap.\n", + num_contacts, num_overlapping_contacts); + #endif + + if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,evdwl,0.0, + facc[0],facc[1],facc[2],delx,dely,delz); + + } // end for jj + } + + if (vflag_fdotr) virial_fdotr_compute(); +} + +/* ---------------------------------------------------------------------- + allocate all arrays +------------------------------------------------------------------------- */ + +void PairBodyRoundedPolygon::allocate() +{ + allocated = 1; + int n = atom->ntypes; + + memory->create(setflag,n+1,n+1,"pair:setflag"); + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + setflag[i][j] = 0; + + memory->create(cutsq,n+1,n+1,"pair:cutsq"); + + memory->create(k_n,n+1,n+1,"pair:k_n"); + memory->create(k_na,n+1,n+1,"pair:k_na"); + memory->create(maxerad,n+1,"pair:maxerad"); +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairBodyRoundedPolygon::settings(int narg, char **arg) +{ + if (narg < 5) error->all(FLERR,"Illegal pair_style command"); + + c_n = force->numeric(FLERR,arg[0]); + c_t = force->numeric(FLERR,arg[1]); + mu = force->numeric(FLERR,arg[2]); + delta_ua = force->numeric(FLERR,arg[3]); + cut_inner = force->numeric(FLERR,arg[4]); + + if (delta_ua < 0) delta_ua = 1; +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairBodyRoundedPolygon::coeff(int narg, char **arg) +{ + if (narg < 4 || narg > 5) + error->all(FLERR,"Incorrect args for pair coefficients"); + if (!allocated) allocate(); + + int ilo,ihi,jlo,jhi; + force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi); + force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi); + + double k_n_one = force->numeric(FLERR,arg[2]); + double k_na_one = force->numeric(FLERR,arg[3]); + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + for (int j = MAX(jlo,i); j <= jhi; j++) { + k_n[i][j] = k_n_one; + k_na[i][j] = k_na_one; + setflag[i][j] = 1; + count++; + } + } + + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); +} + +/* ---------------------------------------------------------------------- + init specific to this pair style +------------------------------------------------------------------------- */ + +void PairBodyRoundedPolygon::init_style() +{ + avec = (AtomVecBody *) atom->style_match("body"); + if (!avec) + error->all(FLERR,"Pair body/rounded/polygon requires atom style body"); + if (strcmp(avec->bptr->style,"rounded/polygon") != 0) + error->all(FLERR,"Pair body/rounded/polygon requires " + "body style rounded/polygon"); + bptr = (BodyRoundedPolygon *) avec->bptr; + + if (force->newton_pair == 0) + error->all(FLERR,"Pair style body/rounded/polygon requires " + "newton pair on"); + + if (comm->ghost_velocity == 0) + error->all(FLERR,"Pair body/rounded/polygon requires " + "ghost atoms store velocity"); + + neighbor->request(this); + + // find the maximum enclosing radius for each atom type + + int i, itype; + double eradi; + int* body = atom->body; + int* type = atom->type; + int ntypes = atom->ntypes; + int nlocal = atom->nlocal; + + if (atom->nmax > nmax) { + memory->destroy(dnum); + memory->destroy(dfirst); + memory->destroy(ednum); + memory->destroy(edfirst); + memory->destroy(enclosing_radius); + memory->destroy(rounded_radius); + nmax = atom->nmax; + memory->create(dnum,nmax,"pair:dnum"); + memory->create(dfirst,nmax,"pair:dfirst"); + memory->create(ednum,nmax,"pair:ednum"); + memory->create(edfirst,nmax,"pair:edfirst"); + memory->create(enclosing_radius,nmax,"pair:enclosing_radius"); + memory->create(rounded_radius,nmax,"pair:rounded_radius"); + } + + ndiscrete = nedge = 0; + for (i = 0; i < nlocal; i++) + dnum[i] = ednum[i] = 0; + + double *merad = NULL; + memory->create(merad,ntypes+1,"pair:merad"); + for (i = 1; i <= ntypes; i++) + maxerad[i] = merad[i] = 0; + + int ipour; + for (ipour = 0; ipour < modify->nfix; ipour++) + if (strcmp(modify->fix[ipour]->style,"pour") == 0) break; + if (ipour == modify->nfix) ipour = -1; + + int idep; + for (idep = 0; idep < modify->nfix; idep++) + if (strcmp(modify->fix[idep]->style,"deposit") == 0) break; + if (idep == modify->nfix) idep = -1; + + for (i = 1; i <= ntypes; i++) { + merad[i] = 0.0; + if (ipour >= 0) { + itype = i; + merad[i] = + *((double *) modify->fix[ipour]->extract("radius",itype)); + } + if (idep >= 0) { + itype = i; + merad[i] = + *((double *) modify->fix[idep]->extract("radius",itype)); + } + } + + for (i = 0; i < nlocal; i++) { + itype = type[i]; + if (body[i] >= 0) { + if (dnum[i] == 0) body2space(i); + eradi = enclosing_radius[i]; + if (eradi > merad[itype]) merad[itype] = eradi; + } else + merad[itype] = 0; + } + + MPI_Allreduce(&merad[1],&maxerad[1],ntypes,MPI_DOUBLE,MPI_MAX,world); + + memory->destroy(merad); +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairBodyRoundedPolygon::init_one(int i, int j) +{ + k_n[j][i] = k_n[i][j]; + k_na[j][i] = k_na[i][j]; + + return (maxerad[i]+maxerad[j]); +} + +/* ---------------------------------------------------------------------- + convert N sub-particles in body I to space frame using current quaternion + store sub-particle space-frame displacements from COM in discrete list +------------------------------------------------------------------------- */ + +void PairBodyRoundedPolygon::body2space(int i) +{ + int ibonus = atom->body[i]; + AtomVecBody::Bonus *bonus = &avec->bonus[ibonus]; + int nsub = bptr->nsub(bonus); + double *coords = bptr->coords(bonus); + int body_num_edges = bptr->nedges(bonus); + double* edge_ends = bptr->edges(bonus); + double eradius = bptr->enclosing_radius(bonus); + double rradius = bptr->rounded_radius(bonus); + + // get the number of sub-particles (vertices) + // and the index of the first vertex of my body in the list + + dnum[i] = nsub; + dfirst[i] = ndiscrete; + + // grow the vertex list if necessary + // the first 3 columns are for coords, the last 3 for forces + + if (ndiscrete + nsub > dmax) { + dmax += DELTA; + memory->grow(discrete,dmax,6,"pair:discrete"); + } + + double p[3][3]; + MathExtra::quat_to_mat(bonus->quat,p); + + for (int m = 0; m < nsub; m++) { + MathExtra::matvec(p,&coords[3*m],discrete[ndiscrete]); + discrete[ndiscrete][3] = 0; + discrete[ndiscrete][4] = 0; + discrete[ndiscrete][5] = 0; + ndiscrete++; + } + + // get the number of edges (vertices) + // and the index of the first edge of my body in the list + + ednum[i] = body_num_edges; + edfirst[i] = nedge; + + // grow the edge list if necessary + // the first 2 columns are for vertex indices within body, the last 3 for forces + + if (nedge + body_num_edges > edmax) { + edmax += DELTA; + memory->grow(edge,edmax,5,"pair:edge"); + } + + for (int m = 0; m < body_num_edges; m++) { + edge[nedge][0] = static_cast(edge_ends[2*m+0]); + edge[nedge][1] = static_cast(edge_ends[2*m+1]); + edge[nedge][2] = 0; + edge[nedge][3] = 0; + edge[nedge][4] = 0; + nedge++; + } + + enclosing_radius[i] = eradius; + rounded_radius[i] = rradius; +} + +/* ---------------------------------------------------------------------- + Interaction between two spheres with different radii + according to the 2D model from Fraige et al. +---------------------------------------------------------------------- */ + +void PairBodyRoundedPolygon::sphere_against_sphere(int i, int j, + double delx, double dely, double delz, double rsq, + double k_n, double k_na, double** /*x*/, double** v, + double** f, int evflag) +{ + double eradi,eradj,rradi,rradj; + double vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3; + double rij,rsqinv,R,fx,fy,fz,fn[3],ft[3],fpair,shift,energy; + int nlocal = atom->nlocal; + int newton_pair = force->newton_pair; + + eradi = enclosing_radius[i]; + rradi = rounded_radius[i]; + + eradj = enclosing_radius[j]; + rradj = rounded_radius[j]; + + rsqinv = 1.0/rsq; + rij = sqrt(rsq); + R = rij - (rradi + rradj); + shift = k_na * cut_inner; + + energy = 0; + + if (R <= 0) { // deformation occurs + fpair = -k_n * R - shift; + energy = (0.5 * k_n * R + shift) * R; + } else if (R <= cut_inner) { // not deforming but cohesive ranges overlap + fpair = k_na * R - shift; + energy = (-0.5 * k_na * R + shift) * R; + } else fpair = 0.0; + + fx = delx*fpair/rij; + fy = dely*fpair/rij; + fz = delz*fpair/rij; + + if (R <= EPSILON) { // in contact + + // relative translational velocity + + vr1 = v[i][0] - v[j][0]; + vr2 = v[i][1] - v[j][1]; + vr3 = v[i][2] - v[j][2]; + + // normal component + + vnnr = vr1*delx + vr2*dely + vr3*delz; + vn1 = delx*vnnr * rsqinv; + vn2 = dely*vnnr * rsqinv; + vn3 = delz*vnnr * rsqinv; + + // tangential component + + vt1 = vr1 - vn1; + vt2 = vr2 - vn2; + vt3 = vr3 - vn3; + + // normal friction term at contact + + fn[0] = -c_n * vn1; + fn[1] = -c_n * vn2; + fn[2] = -c_n * vn3; + + // tangential friction term at contact + // excluding the tangential deformation term + + ft[0] = -c_t * vt1; + ft[1] = -c_t * vt2; + ft[2] = -c_t * vt3; + } + + f[i][0] += fx; + f[i][1] += fy; + f[i][2] += fz; + + if (newton_pair || j < nlocal) { + f[j][0] -= fx; + f[j][1] -= fy; + f[j][2] -= fz; + } + + if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair, + energy,0.0,fx,fy,fz,delx,dely,delz); +} + +/* ---------------------------------------------------------------------- + Determine the interaction mode between i's vertices against j's edges + + i = atom i (body i) + j = atom j (body j) + x = atoms' coordinates + f = atoms' forces + torque = atoms' torques + tag = atoms' tags + contact_list = list of contacts + num_contacts = number of contacts between i's vertices and j's edges + Return: + interact = 0 no interaction at all + 1 there's at least one case where i's vertices interacts + with j's edges +---------------------------------------------------------------------- */ + +int PairBodyRoundedPolygon::vertex_against_edge(int i, int j, + double k_n, double k_na, + double** x, double** f, + double** torque, tagint* tag, + Contact* contact_list, + int &num_contacts, + double &evdwl, double* facc) +{ + int ni, npi, ifirst, nei, iefirst; + int nj, npj, jfirst, nej, jefirst; + double xpi[3], xpj[3], dist, eradi, eradj, rradi, rradj; + double fx, fy, fz, energy; + int interact; + + npi = dnum[i]; + ifirst = dfirst[i]; + nei = ednum[i]; + iefirst = edfirst[i]; + eradi = enclosing_radius[i]; + rradi = rounded_radius[i]; + + npj = dnum[j]; + jfirst = dfirst[j]; + nej = ednum[j]; + jefirst = edfirst[j]; + eradj = enclosing_radius[j]; + rradj = rounded_radius[j]; + + energy = 0; + interact = 0; + + // loop through body i's vertices + + for (ni = 0; ni < npi; ni++) { + + // convert body-fixed coordinates to space-fixed, xi + + xpi[0] = x[i][0] + discrete[ifirst+ni][0]; + xpi[1] = x[i][1] + discrete[ifirst+ni][1]; + xpi[2] = x[i][2] + discrete[ifirst+ni][2]; + + // compute the distance from the vertex to the COM of body j + + distance(xpi, x[j], dist); + + #ifdef _POLYGON_DEBUG + printf("Distance between vertex %d of body %d (%0.1f %0.1f %0.1f) " + "to body %d's COM: %f (cut = %0.1f)\n", + ni, xpi[0], xpi[1], xpi[2], atom->tag[i], atom->tag[j], dist, + eradj + rradi + rradj + cut_inner); + #endif + + // the vertex is within the enclosing circle (sphere) of body j, + // possibly interacting + + if (dist > eradj + rradj + rradi + cut_inner) continue; + + int mode, contact, p2vertex; + double d, R, hi[3], t, delx, dely, delz, fpair, shift; + double rij; + + // loop through body j's edges + + for (nj = 0; nj < nej; nj++) { + + // compute the distance between the edge nj to the vertex xpi + + mode = compute_distance_to_vertex(j, nj, x[j], rradj, + xpi, rradi, cut_inner, + d, hi, t, contact); + + if (mode == INVALID || mode == NONE) continue; + + if (mode == VERTEXI || mode == VERTEXJ) { + + interact = 1; + + // vertex i interacts with a vertex of the edge, but does not contact + + if (mode == VERTEXI) p2vertex = edge[jefirst+nj][0]; + else if (mode == VERTEXJ) p2vertex = edge[jefirst+nj][1]; + + // double xj[3]; + // p2.body2space(p2vertex, xj); + xpj[0] = x[j][0] + discrete[jfirst+p2vertex][0]; + xpj[1] = x[j][1] + discrete[jfirst+p2vertex][1]; + xpj[2] = x[j][2] + discrete[jfirst+p2vertex][2]; + + delx = xpi[0] - xpj[0]; + dely = xpi[1] - xpj[1]; + delz = xpi[2] - xpj[2]; + + // R = surface separation = rij shifted by the rounded radii + // R = rij - (p1.rounded_radius + p2.rounded_radius); + // note: the force is defined for R, not for rij + // R > rc: no interaction between vertex ni and p2vertex + // 0 < R < rc: cohesion between vertex ni and p2vertex + // R < 0: deformation between vertex ni and p2vertex + + rij = sqrt(delx*delx + dely*dely + delz*delz); + R = rij - (rradi + rradj); + shift = k_na * cut_inner; + + // the normal frictional term -c_n * vn will be added later + + if (R <= 0) { // deformation occurs + fpair = -k_n * R - shift; + energy += (0.5 * k_n * R + shift) * R; + } else if (R <= cut_inner) { // not deforming but cohesive ranges overlap + fpair = k_na * R - shift; + energy += (-0.5 * k_na * R + shift) * R; + } else fpair = 0.0; + + fx = delx*fpair/rij; + fy = dely*fpair/rij; + fz = delz*fpair/rij; + + #ifdef _POLYGON_DEBUG + printf(" Interaction between vertex %d of %d and vertex %d of %d:", + ni, tag[i], p2vertex, tag[j]); + printf(" mode = %d; contact = %d; d = %f; rij = %f, t = %f\n", + mode, contact, d, rij, t); + printf(" R = %f; cut_inner = %f\n", R, cut_inner); + printf(" fpair = %f\n", fpair); + #endif + + // add forces to body i and body j directly + // avoid double counts this pair of vertices + // i and j can be either local or ghost atoms (bodies) + // probably need more work here when the vertices' interaction + // are not symmetric, e.g. j interacts with the edge + // consisting of i but in mode = EDGE instead of VERTEX*. + // OR, for the time being assume that the edge length is + // sufficiently greater than the rounded radius to distinguish + // vertex-vertex from vertex-edge contact modes. + // Special case: when i is a sphere, also accumulate + + if (tag[i] < tag[j] || npi == 1) { + + f[i][0] += fx; + f[i][1] += fy; + f[i][2] += fz; + sum_torque(x[i], xpi, fx, fy, fz, torque[i]); + + f[j][0] -= fx; + f[j][1] -= fy; + f[j][2] -= fz; + sum_torque(x[j], xpj, -fx, -fy, -fz, torque[j]); + + facc[0] += fx; facc[1] += fy; facc[2] += fz; + + #ifdef _POLYGON_DEBUG + printf(" from vertex-vertex: " + "force on vertex %d of body %d: fx %f fy %f fz %f\n" + " torque body %d: %f %f %f\n" + " torque body %d: %f %f %f\n", ni, tag[i], fx, fy, fz, + tag[i],torque[i][0],torque[i][1],torque[i][2], + tag[j],torque[j][0],torque[j][1],torque[j][2]); + #endif + } + + #ifdef _CONVEX_POLYGON + // done with the edges from body j, + // given that vertex ni interacts with only one vertex + // from one edge of body j + break; + #endif + + } else if (mode == EDGE) { + + interact = 1; + + // vertex i interacts with the edge + + delx = xpi[0] - hi[0]; + dely = xpi[1] - hi[1]; + delz = xpi[2] - hi[2]; + + // R = surface separation = d shifted by the rounded radii + // R = d - (p1.rounded_radius + p2.rounded_radius); + // Note: the force is defined for R, not for d + // R > rc: no interaction between vertex i and edge j + // 0 < R < rc: cohesion between vertex i and edge j + // R < 0: deformation between vertex i and edge j + // rij = sqrt(delx*delx + dely*dely + delz*delz); + + R = d - (rradi + rradj); + shift = k_na * cut_inner; + + // the normal frictional term -c_n * vn will be added later + + if (R <= 0) { // deformation occurs + fpair = -k_n * R - shift; + energy += (0.5 * k_n * R + shift) * R; + } else if (R <= cut_inner) { // not deforming but cohesive ranges overlap + fpair = k_na * R - shift; + energy += (-0.5 * k_na * R + shift) * R; + } else fpair = 0.0; + + fx = delx*fpair/d; + fy = dely*fpair/d; + fz = delz*fpair/d; + + #ifdef _POLYGON_DEBUG + printf(" Interaction between vertex %d of %d and edge %d of %d:", + ni, tag[i], nj, tag[j]); + printf(" mode = %d; contact = %d; d = %f; t = %f\n", + mode, contact, d, t); + printf(" R = %f; cut_inner = %f\n", R, cut_inner); + printf(" fpair = %f\n", fpair); + #endif + + if (contact == 1) { + + // vertex ni of body i contacts with edge nj of body j + + contact_list[num_contacts].ibody = i; + contact_list[num_contacts].jbody = j; + contact_list[num_contacts].vertex = ni; + contact_list[num_contacts].edge = nj; + contact_list[num_contacts].xv[0] = xpi[0]; + contact_list[num_contacts].xv[1] = xpi[1]; + contact_list[num_contacts].xv[2] = xpi[2]; + contact_list[num_contacts].xe[0] = hi[0]; + contact_list[num_contacts].xe[1] = hi[1]; + contact_list[num_contacts].xe[2] = hi[2]; + contact_list[num_contacts].separation = R; + num_contacts++; + + // store forces to vertex ni and the edge nj + // to be rescaled later + + discrete[ifirst+ni][3] = fx; + discrete[ifirst+ni][4] = fy; + discrete[ifirst+ni][5] = fz; + + edge[jefirst+nj][2] = -fx; + edge[jefirst+nj][3] = -fy; + edge[jefirst+nj][4] = -fz; + + #ifdef _POLYGON_DEBUG + printf(" Stored forces at vertex and edge for accumulating later.\n"); + #endif + + } else { // no contact + + // accumulate force and torque to both bodies directly + + f[i][0] += fx; + f[i][1] += fy; + f[i][2] += fz; + sum_torque(x[i], xpi, fx, fy, fz, torque[i]); + + f[j][0] -= fx; + f[j][1] -= fy; + f[j][2] -= fz; + sum_torque(x[j], hi, -fx, -fy, -fz, torque[j]); + + facc[0] += fx; facc[1] += fy; facc[2] += fz; + + #ifdef _POLYGON_DEBUG + printf(" from vertex-edge, no contact: " + "force on vertex %d of body %d: fx %f fy %f fz %f\n" + " torque body %d: %f %f %f\n" + " torque body %d: %f %f %f\n", ni, tag[i], fx, fy, fz, + tag[i],torque[i][0],torque[i][1],torque[i][2], + tag[j],torque[j][0],torque[j][1],torque[j][2]); + #endif + } // end if contact + + #ifdef _CONVEX_POLYGON + // done with the edges from body j, + // given that vertex ni interacts with only one edge from body j + break; + #endif + } // end if mode + + } // end for looping through the edges of body j + + } // end for looping through the vertices of body i + + evdwl += energy; + + return interact; +} + +/* ------------------------------------------------------------------------- + Compute the distance between an edge of body i and a vertex from + another body + Input: + ibody = body i (i.e. atom i) + edge_index = edge index of body i + xmi = atom i's coordinates (body i's center of mass) + x0 = coordinate of the tested vertex from another body + x0_rounded_radius = rounded radius of the tested vertex + cut_inner = cutoff for vertex-vertex and vertex-edge interaction + Output: + d = Distance from a point x0 to an edge + hi = coordinates of the projection of x0 on the edge + t = ratio to determine the relative position of hi + wrt xi and xj on the segment + contact = 0 no contact between the queried vertex and the edge + 1 contact detected + return + INVALID if the edge index is invalid + NONE if there is no interaction + VERTEXI if the tested vertex interacts with the first vertex of the edge + VERTEXJ if the tested vertex interacts with the second vertex of the edge + EDGE if the tested vertex interacts with the edge +------------------------------------------------------------------------- */ + +int PairBodyRoundedPolygon::compute_distance_to_vertex(int ibody, + int edge_index, + double *xmi, + double rounded_radius, + double* x0, + double x0_rounded_radius, + double cut_inner, + double &d, + double hi[3], + double &t, + int &contact) +{ + if (edge_index >= ednum[ibody]) return INVALID; + + int mode,ifirst,iefirst,npi1,npi2; + double xi1[3],xi2[3],u[3],v[3],uij[3]; + double udotv, magv, magucostheta; + double delx,dely,delz; + + ifirst = dfirst[ibody]; + iefirst = edfirst[ibody]; + npi1 = static_cast(edge[iefirst+edge_index][0]); + npi2 = static_cast(edge[iefirst+edge_index][1]); + + // compute the space-fixed coordinates for the vertices of the edge + + xi1[0] = xmi[0] + discrete[ifirst+npi1][0]; + xi1[1] = xmi[1] + discrete[ifirst+npi1][1]; + xi1[2] = xmi[2] + discrete[ifirst+npi1][2]; + + xi2[0] = xmi[0] + discrete[ifirst+npi2][0]; + xi2[1] = xmi[1] + discrete[ifirst+npi2][1]; + xi2[2] = xmi[2] + discrete[ifirst+npi2][2]; + + // u = x0 - xi1 + + u[0] = x0[0] - xi1[0]; + u[1] = x0[1] - xi1[1]; + u[2] = x0[2] - xi1[2]; + + // v = xi2 - xi1 + + v[0] = xi2[0] - xi1[0]; + v[1] = xi2[1] - xi1[1]; + v[2] = xi2[2] - xi1[2]; + + // dot product between u and v = magu * magv * costheta + + udotv = u[0] * v[0] + u[1] * v[1] + u[2] * v[2]; + magv = sqrt(v[0] * v[0] + v[1] * v[1] + v[2] * v[2]); + magucostheta = udotv / magv; + + // uij is the unit vector pointing from xi to xj + + uij[0] = v[0] / magv; + uij[1] = v[1] / magv; + uij[2] = v[2] / magv; + + // position of the projection of x0 on the line (xi, xj) + + hi[0] = xi1[0] + magucostheta * uij[0]; + hi[1] = xi1[1] + magucostheta * uij[1]; + hi[2] = xi1[2] + magucostheta * uij[2]; + + // distance from x0 to the line (xi, xj) = distance from x0 to hi + + distance(hi, x0, d); + + // determine the interaction mode + // for 2D: a vertex can interact with one edge at most + // for 3D: a vertex can interact with one face at most + + mode = NONE; + contact = 0; + + if (d > rounded_radius + x0_rounded_radius + cut_inner) { + + // if the vertex is far away from the edge + + mode = NONE; + + } else { + + // check if x0 (the queried vertex) and xmi (the body's center of mass) + // are on the different sides of the edge + + #ifdef _CONVEX_POLYGON + int m = opposite_sides(xi1, xi2, x0, xmi); + #else + int m = 1; + #endif + + if (m == 0) { + + // x0 and xmi are on not the opposite sides of the edge + // leave xpi for another edge to detect + + mode = NONE; + + } else { + + // x0 and xmi are on the different sides + // t is the ratio to detect if x0 is closer to the vertices xi or xj + + if (fabs(xi2[0] - xi1[0]) > EPSILON) + t = (hi[0] - xi1[0]) / (xi2[0] - xi1[0]); + else if (fabs(xi2[1] - xi1[1]) > EPSILON) + t = (hi[1] - xi1[1]) / (xi2[1] - xi1[1]); + else if (fabs(xi2[2] - xi1[2]) > EPSILON) + t = (hi[2] - xi1[2]) / (xi2[2] - xi1[2]); + + double contact_dist = rounded_radius + x0_rounded_radius; + if (t >= 0 && t <= 1) { + mode = EDGE; + if (d < contact_dist + EPSILON) + contact = 1; + + } else { // t < 0 || t > 1: closer to either vertices of the edge + + if (t < 0) { + // measure the distance from x0 to xi1 + delx = x0[0] - xi1[0]; + dely = x0[1] - xi1[1]; + delz = x0[2] - xi1[2]; + double dx0xi1 = sqrt(delx*delx + dely*dely + delz*delz); + if (dx0xi1 > contact_dist + cut_inner) + mode = NONE; + else + mode = VERTEXI; + } else { + // measure the distance from x0 to xi2 + delx = x0[0] - xi2[0]; + dely = x0[1] - xi2[1]; + delz = x0[2] - xi2[2]; + double dx0xi2 = sqrt(delx*delx + dely*dely + delz*delz); + if (dx0xi2 > contact_dist + cut_inner) + mode = NONE; + else + mode = VERTEXJ; + } + } // end if t >= 0 && t <= 1 + } // end if x0 and xmi are on the same side of the edge + } + + return mode; +} + +/* ---------------------------------------------------------------------- + Compute contact forces between two bodies + modify the force stored at the vertex and edge in contact by j_a + sum forces and torque to the corresponding bodies + fn = normal friction component + ft = tangential friction component (-c_t * v_t) +------------------------------------------------------------------------- */ + +void PairBodyRoundedPolygon::contact_forces(Contact& contact, double j_a, + double** x, double** v, double** angmom, double** f, + double** torque, double &/*evdwl*/, double* facc) +{ + int ibody,jbody,ibonus,jbonus,ifirst,jefirst,ni,nj; + double fx,fy,fz,delx,dely,delz,rsq,rsqinv; + double vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3; + double fn[3],ft[3],vi[3],vj[3]; + double *quat, *inertia; + AtomVecBody::Bonus *bonus; + + ibody = contact.ibody; + jbody = contact.jbody; + + // compute the velocity of the vertex in the space-fixed frame + + ibonus = atom->body[ibody]; + bonus = &avec->bonus[ibonus]; + quat = bonus->quat; + inertia = bonus->inertia; + total_velocity(contact.xv, x[ibody], v[ibody], angmom[ibody], + inertia, quat, vi); + + // compute the velocity of the point on the edge in the space-fixed frame + + jbonus = atom->body[jbody]; + bonus = &avec->bonus[jbonus]; + quat = bonus->quat; + inertia = bonus->inertia; + total_velocity(contact.xe, x[jbody], v[jbody], angmom[jbody], + inertia, quat, vj); + + // vector pointing from the vertex to the point on the edge + + delx = contact.xv[0] - contact.xe[0]; + dely = contact.xv[1] - contact.xe[1]; + delz = contact.xv[2] - contact.xe[2]; + rsq = delx*delx + dely*dely + delz*delz; + rsqinv = 1.0/rsq; + + // relative translational velocity + + vr1 = vi[0] - vj[0]; + vr2 = vi[1] - vj[1]; + vr3 = vi[2] - vj[2]; + + // normal component + + vnnr = vr1*delx + vr2*dely + vr3*delz; + vn1 = delx*vnnr * rsqinv; + vn2 = dely*vnnr * rsqinv; + vn3 = delz*vnnr * rsqinv; + + // tangential component + + vt1 = vr1 - vn1; + vt2 = vr2 - vn2; + vt3 = vr3 - vn3; + + // normal friction term at contact + + fn[0] = -c_n * vn1; + fn[1] = -c_n * vn2; + fn[2] = -c_n * vn3; + + // tangential friction term at contact + // excluding the tangential deformation term for now + + ft[0] = -c_t * vt1; + ft[1] = -c_t * vt2; + ft[2] = -c_t * vt3; + + // only the cohesive force is scaled by j_a + // mu * fne = tangential friction deformation during gross sliding + // see Eq. 4, Fraige et al. + + ifirst = dfirst[ibody]; + ni = contact.vertex; + + fx = discrete[ifirst+ni][3] * j_a + fn[0] + ft[0] + + mu * discrete[ifirst+ni][3]; + fy = discrete[ifirst+ni][4] * j_a + fn[1] + ft[1] + + mu * discrete[ifirst+ni][4]; + fz = discrete[ifirst+ni][5] * j_a + fn[2] + ft[2] + + mu * discrete[ifirst+ni][5]; + f[ibody][0] += fx; + f[ibody][1] += fy; + f[ibody][2] += fz; + sum_torque(x[ibody], contact.xv, fx, fy, fz, torque[ibody]); + + // accumulate forces to the vertex only + + facc[0] += fx; facc[1] += fy; facc[2] += fz; + + // only the cohesive force is scaled by j_a + // mu * fne = tangential friction deformation during gross sliding + // Eq. 4, Fraige et al. + + jefirst = edfirst[jbody]; + nj = contact.edge; + + fx = edge[jefirst+nj][2] * j_a - fn[0] - ft[0] + + mu * edge[jefirst+nj][2]; + fy = edge[jefirst+nj][3] * j_a - fn[1] - ft[1] + + mu * edge[jefirst+nj][3]; + fz = edge[jefirst+nj][4] * j_a - fn[2] - ft[2] + + mu * edge[jefirst+nj][4]; + f[jbody][0] += fx; + f[jbody][1] += fy; + f[jbody][2] += fz; + sum_torque(x[jbody], contact.xe, fx, fy, fz, torque[jbody]); + + #ifdef _POLYGON_DEBUG + printf("From contact forces: vertex fx %f fy %f fz %f\n" + " torque body %d: %f %f %f\n" + " torque body %d: %f %f %f\n", + discrete[ifirst+ni][3], discrete[ifirst+ni][4], discrete[ifirst+ni][5], + atom->tag[ibody],torque[ibody][0],torque[ibody][1],torque[ibody][2], + atom->tag[jbody],torque[jbody][0],torque[jbody][1],torque[jbody][2]); + #endif +} + +/* ---------------------------------------------------------------------- + Determine the length of the contact segment, i.e. the separation between + 2 contacts, should be extended for 3D models. +------------------------------------------------------------------------- */ + +double PairBodyRoundedPolygon::contact_separation(const Contact& c1, + const Contact& c2) +{ + double x1 = c1.xv[0]; + double y1 = c1.xv[1]; + double x2 = c1.xe[0]; + double y2 = c1.xe[1]; + double x3 = c2.xv[0]; + double y3 = c2.xv[1]; + + double delta_a = 0.0; + if (fabs(x2 - x1) > EPSILON) { + double A = (y2 - y1) / (x2 - x1); + delta_a = fabs(y1 - A * x1 - y3 + A * x3) / sqrt(1 + A * A); + } else { + delta_a = fabs(x1 - x3); + } + + return delta_a; +} + +/* ---------------------------------------------------------------------- + Accumulate torque to body from the force f=(fx,fy,fz) acting at point x +------------------------------------------------------------------------- */ + +void PairBodyRoundedPolygon::sum_torque(double* xm, double *x, double fx, + double fy, double fz, double* torque) +{ + double rx = x[0] - xm[0]; + double ry = x[1] - xm[1]; + double rz = x[2] - xm[2]; + double tx = ry * fz - rz * fy; + double ty = rz * fx - rx * fz; + double tz = rx * fy - ry * fx; + torque[0] += tx; + torque[1] += ty; + torque[2] += tz; +} + +/* ---------------------------------------------------------------------- + Test if two points a and b are in opposite sides of the line that + connects two points x1 and x2 +------------------------------------------------------------------------- */ + +int PairBodyRoundedPolygon::opposite_sides(double* x1, double* x2, + double* a, double* b) +{ + double m_a = (x1[1] - x2[1])*(a[0] - x1[0]) + (x2[0] - x1[0])*(a[1] - x1[1]); + double m_b = (x1[1] - x2[1])*(b[0] - x1[0]) + (x2[0] - x1[0])*(b[1] - x1[1]); + // equal to zero when either a or b is inline with the line x1-x2 + if (m_a * m_b <= 0) + return 1; + else + return 0; +} + +/* ---------------------------------------------------------------------- + Calculate the total velocity of a point (vertex, a point on an edge): + vi = vcm + omega ^ (p - xcm) +------------------------------------------------------------------------- */ + +void PairBodyRoundedPolygon::total_velocity(double* p, double *xcm, + double* vcm, double *angmom, double *inertia, + double *quat, double* vi) +{ + double r[3],omega[3],ex_space[3],ey_space[3],ez_space[3]; + r[0] = p[0] - xcm[0]; + r[1] = p[1] - xcm[1]; + r[2] = p[2] - xcm[2]; + MathExtra::q_to_exyz(quat,ex_space,ey_space,ez_space); + MathExtra::angmom_to_omega(angmom,ex_space,ey_space,ez_space, + inertia,omega); + vi[0] = omega[1]*r[2] - omega[2]*r[1] + vcm[0]; + vi[1] = omega[2]*r[0] - omega[0]*r[2] + vcm[1]; + vi[2] = omega[0]*r[1] - omega[1]*r[0] + vcm[2]; +} + +/* ---------------------------------------------------------------------- */ + +void PairBodyRoundedPolygon::distance(const double* x2, const double* x1, + double& r) +{ + r = sqrt((x2[0] - x1[0]) * (x2[0] - x1[0]) + + (x2[1] - x1[1]) * (x2[1] - x1[1]) + + (x2[2] - x1[2]) * (x2[2] - x1[2])); +} + diff --git a/src/BODY/pair_body_rounded_polygon.h b/src/BODY/pair_body_rounded_polygon.h new file mode 100644 index 0000000000..aabe86270c --- /dev/null +++ b/src/BODY/pair_body_rounded_polygon.h @@ -0,0 +1,137 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS + +PairStyle(body/rounded/polygon,PairBodyRoundedPolygon) + +#else + +#ifndef LMP_PAIR_BODY_ROUNDED_POLYGON_H +#define LMP_PAIR_BODY_ROUNDED_POLYGON_H + +#include "pair.h" + +namespace LAMMPS_NS { + +class PairBodyRoundedPolygon : public Pair { + public: + PairBodyRoundedPolygon(class LAMMPS *); + ~PairBodyRoundedPolygon(); + void compute(int, int); + void settings(int, char **); + void coeff(int, char **); + void init_style(); + double init_one(int, int); + + struct Contact { + int ibody, jbody; // body (i.e. atom) indices (not tags) + int vertex; // vertex of the first polygon + int edge; // edge of the second polygon + double xv[3]; // coordinates of the vertex + double xe[3]; // coordinates of the projection of the vertex on the edge + double separation;// separation at contact + }; + + protected: + double **k_n; // normal repulsion strength + double **k_na; // normal attraction strength + double c_n; // normal damping coefficient + double c_t; // tangential damping coefficient + double mu; // normal friction coefficient during gross sliding + double delta_ua; // contact line (area for 3D models) modification factor + double cut_inner; // cutoff for interaction between vertex-edge surfaces + + class AtomVecBody *avec; + class BodyRoundedPolygon *bptr; + + double **discrete; // list of all sub-particles for all bodies + int ndiscrete; // number of discretes in list + int dmax; // allocated size of discrete list + int *dnum; // number of discretes per line, 0 if uninit + int *dfirst; // index of first discrete per each line + int nmax; // allocated size of dnum,dfirst vectors + + double **edge; // list of all edge for all bodies + int nedge; // number of edge in list + int edmax; // allocated size of edge list + int *ednum; // number of edges per line, 0 if uninit + int *edfirst; // index of first edge per each line + int ednummax; // allocated size of ednum,edfirst vectors + + double *enclosing_radius; // enclosing radii for all bodies + double *rounded_radius; // rounded radii for all bodies + double *maxerad; // per-type maximum enclosing radius + + void allocate(); + void body2space(int); + + // sphere-sphere interaction + void sphere_against_sphere(int i, int j, double delx, double dely, double delz, + double rsq, double k_n, double k_na, + double** x, double** v, double** f, int evflag); + // vertex-edge interaction + int vertex_against_edge(int i, int j, double k_n, double k_na, + double** x, double** f, double** torque, + tagint* tag, Contact* contact_list, + int &num_contacts, double &evdwl, double* facc); + // compute distance between a point and an edge from another body + int compute_distance_to_vertex(int ibody, int edge_index, double* xmi, + double rounded_radius, double* x0, + double x0_rounded_radius, double cut_inner, + double &d, double hi[3], double &t, + int &contact); + // compute contact forces if contact points are detected + void contact_forces(Contact& contact, double j_a, + double** x, double** v, double** angmom, double** f, + double** torque, double &evdwl, double* facc); + + // compute the separation between two contacts + double contact_separation(const Contact& c1, const Contact& c2); + + // accumulate torque to a body given a force at a given point + void sum_torque(double* xm, double *x, double fx, + double fy, double fz, double* torque); + // helper functions + int opposite_sides(double* x1, double* x2, double* a, double* b); + void total_velocity(double* p, double *xcm, double* vcm, double *angmom, + double *inertia, double *quat, double* vi); + inline void distance(const double* x2, const double* x1, double& r); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Incorrect args for pair coefficients + +Self-explanatory. Check the input script or data file. + +E: Pair body/rounded/polygon requires atom style body rounded/polygon + +Self-explanatory. + +E: Pair body requires body style rounded/polygon + +This pair style is specific to the rounded/polygon body style. + +*/ diff --git a/src/BODY/pair_body_rounded_polyhedron.cpp b/src/BODY/pair_body_rounded_polyhedron.cpp new file mode 100644 index 0000000000..eea2aa3724 --- /dev/null +++ b/src/BODY/pair_body_rounded_polyhedron.cpp @@ -0,0 +1,2390 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Trung Dac Nguyen (ndactrung@gmail.com) + Ref: Wang, Yu, Langston, Fraige, Particle shape effects in discrete + element modelling of cohesive angular particles, Granular Matter 2011, + 13:1-12. + Note: The current implementation has not taken into account + the contact history for friction forces. +------------------------------------------------------------------------- */ + +#include +#include +#include +#include +#include "pair_body_rounded_polyhedron.h" +#include "math_extra.h" +#include "atom.h" +#include "atom_vec_body.h" +#include "body_rounded_polyhedron.h" +#include "comm.h" +#include "force.h" +#include "fix.h" +#include "modify.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "memory.h" +#include "error.h" +#include "math_extra.h" +#include "math_const.h" + +using namespace LAMMPS_NS; +using namespace MathExtra; +using namespace MathConst; + +#define DELTA 10000 +#define EPSILON 1e-3 +#define MAX_FACE_SIZE 4 // maximum number of vertices per face (same as BodyRoundedPolyhedron) +#define MAX_CONTACTS 32 // for 3D models (including duplicated counts) + +//#define _POLYHEDRON_DEBUG + +enum {EE_INVALID=0,EE_NONE,EE_INTERACT}; +enum {EF_INVALID=0,EF_NONE,EF_PARALLEL,EF_SAME_SIDE_OF_FACE, + EF_INTERSECT_INSIDE,EF_INTERSECT_OUTSIDE}; + +/* ---------------------------------------------------------------------- */ + +PairBodyRoundedPolyhedron::PairBodyRoundedPolyhedron(LAMMPS *lmp) : Pair(lmp) +{ + dmax = nmax = 0; + discrete = NULL; + dnum = dfirst = NULL; + + edmax = ednummax = 0; + edge = NULL; + ednum = edfirst = NULL; + + facmax = facnummax = 0; + face = NULL; + facnum = facfirst = NULL; + + enclosing_radius = NULL; + rounded_radius = NULL; + maxerad = NULL; + + single_enable = 0; + restartinfo = 0; + + c_n = 0.1; + c_t = 0.2; + mu = 0.0; + A_ua = 1.0; + + k_n = NULL; + k_na = NULL; +} + +/* ---------------------------------------------------------------------- */ + +PairBodyRoundedPolyhedron::~PairBodyRoundedPolyhedron() +{ + memory->destroy(discrete); + memory->destroy(dnum); + memory->destroy(dfirst); + + memory->destroy(edge); + memory->destroy(ednum); + memory->destroy(edfirst); + + memory->destroy(face); + memory->destroy(facnum); + memory->destroy(facfirst); + + memory->destroy(enclosing_radius); + memory->destroy(rounded_radius); + memory->destroy(maxerad); + + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + + memory->destroy(k_n); + memory->destroy(k_na); + } +} + +/* ---------------------------------------------------------------------- */ + +void PairBodyRoundedPolyhedron::compute(int eflag, int vflag) +{ + int i,j,ii,jj,inum,jnum,itype,jtype; + int ni,nj,npi,npj,ifirst,jfirst,nei,nej,iefirst,jefirst; + double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,facc[3]; + double rsq,eradi,eradj; + int *ilist,*jlist,*numneigh,**firstneigh; + + evdwl = 0.0; + if (eflag || vflag) ev_setup(eflag,vflag); + else evflag = vflag_fdotr = 0; + + double **x = atom->x; + double **v = atom->v; + double **f = atom->f; + double **torque = atom->torque; + double **angmom = atom->angmom; + int *body = atom->body; + int *type = atom->type; + int nlocal = atom->nlocal; + int nall = nlocal + atom->nghost; + int newton_pair = force->newton_pair; + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // grow the per-atom lists if necessary and initialize + + if (atom->nmax > nmax) { + memory->destroy(dnum); + memory->destroy(dfirst); + memory->destroy(ednum); + memory->destroy(edfirst); + memory->destroy(facnum); + memory->destroy(facfirst); + memory->destroy(enclosing_radius); + memory->destroy(rounded_radius); + nmax = atom->nmax; + memory->create(dnum,nmax,"pair:dnum"); + memory->create(dfirst,nmax,"pair:dfirst"); + memory->create(ednum,nmax,"pair:ednum"); + memory->create(edfirst,nmax,"pair:edfirst"); + memory->create(facnum,nmax,"pair:facnum"); + memory->create(facfirst,nmax,"pair:facfirst"); + memory->create(enclosing_radius,nmax,"pair:enclosing_radius"); + memory->create(rounded_radius,nmax,"pair:rounded_radius"); + } + + ndiscrete = nedge = nface = 0; + for (i = 0; i < nall; i++) + dnum[i] = ednum[i] = facnum[i] = 0; + + // loop over neighbors of my atoms + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + if (body[i] >= 0) { + if (dnum[i] == 0) body2space(i); + npi = dnum[i]; + ifirst = dfirst[i]; + nei = ednum[i]; + iefirst = edfirst[i]; + eradi = enclosing_radius[i]; + } + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + j &= NEIGHMASK; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + jtype = type[j]; + + // body/body interactions + + evdwl = 0.0; + facc[0] = facc[1] = facc[2] = 0; + + if (body[i] < 0 || body[j] < 0) continue; + + if (dnum[j] == 0) body2space(j); + npj = dnum[j]; + jfirst = dfirst[j]; + nej = ednum[j]; + jefirst = edfirst[j]; + eradj = enclosing_radius[j]; + + // no interaction + + double r = sqrt(rsq); + if (r > eradi + eradj + cut_inner) continue; + + // sphere-sphere interaction + + if (npi == 1 && npj == 1) { + sphere_against_sphere(i, j, itype, jtype, delx, dely, delz, + rsq, v, f, evflag); + continue; + } + + // reset vertex and edge forces + + for (ni = 0; ni < npi; ni++) { + discrete[ifirst+ni][3] = 0; + discrete[ifirst+ni][4] = 0; + discrete[ifirst+ni][5] = 0; + discrete[ifirst+ni][6] = 0; + } + + for (nj = 0; nj < npj; nj++) { + discrete[jfirst+nj][3] = 0; + discrete[jfirst+nj][4] = 0; + discrete[jfirst+nj][5] = 0; + discrete[jfirst+nj][6] = 0; + } + + for (ni = 0; ni < nei; ni++) { + edge[iefirst+ni][2] = 0; + edge[iefirst+ni][3] = 0; + edge[iefirst+ni][4] = 0; + edge[iefirst+ni][5] = 0; + } + + for (nj = 0; nj < nej; nj++) { + edge[jefirst+nj][2] = 0; + edge[jefirst+nj][3] = 0; + edge[jefirst+nj][4] = 0; + edge[jefirst+nj][5] = 0; + } + + // one of the two bodies is a sphere + + if (npj == 1) { + sphere_against_face(i, j, itype, jtype, x, v, f, torque, + angmom, evflag); + sphere_against_edge(i, j, itype, jtype, x, v, f, torque, + angmom, evflag); + continue; + } else if (npi == 1) { + sphere_against_face(j, i, jtype, itype, x, v, f, torque, + angmom, evflag); + sphere_against_edge(j, i, jtype, itype, x, v, f, torque, + angmom, evflag); + continue; + } + + int interact, num_contacts; + Contact contact_list[MAX_CONTACTS]; + + num_contacts = 0; + + // check interaction between i's edges and j' faces + #ifdef _POLYHEDRON_DEBUG + printf("INTERACTION between edges of %d vs. faces of %d:\n", i, j); + #endif + interact = edge_against_face(i, j, itype, jtype, x, contact_list, + num_contacts, evdwl, facc); + + // check interaction between j's edges and i' faces + #ifdef _POLYHEDRON_DEBUG + printf("\nINTERACTION between edges of %d vs. faces of %d:\n", j, i); + #endif + interact = edge_against_face(j, i, jtype, itype, x, contact_list, + num_contacts, evdwl, facc); + + // check interaction between i's edges and j' edges + #ifdef _POLYHEDRON_DEBUG + printf("INTERACTION between edges of %d vs. edges of %d:\n", i, j); + #endif + interact = edge_against_edge(i, j, itype, jtype, x, contact_list, + num_contacts, evdwl, facc); + + // estimate the contact area + // also consider point contacts and line contacts + + if (num_contacts > 0) { + rescale_cohesive_forces(x, f, torque, contact_list, num_contacts, + itype, jtype, facc); + } + + if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,evdwl,0.0, + facc[0],facc[1],facc[2],delx,dely,delz); + + } // end for jj + } + + if (vflag_fdotr) virial_fdotr_compute(); +} + +/* ---------------------------------------------------------------------- + allocate all arrays +------------------------------------------------------------------------- */ + +void PairBodyRoundedPolyhedron::allocate() +{ + allocated = 1; + int n = atom->ntypes; + + memory->create(setflag,n+1,n+1,"pair:setflag"); + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + setflag[i][j] = 0; + + memory->create(cutsq,n+1,n+1,"pair:cutsq"); + + memory->create(k_n,n+1,n+1,"pair:k_n"); + memory->create(k_na,n+1,n+1,"pair:k_na"); + memory->create(maxerad,n+1,"pair:maxerad"); +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairBodyRoundedPolyhedron::settings(int narg, char **arg) +{ + if (narg < 5) error->all(FLERR,"Illegal pair_style command"); + + c_n = force->numeric(FLERR,arg[0]); + c_t = force->numeric(FLERR,arg[1]); + mu = force->numeric(FLERR,arg[2]); + A_ua = force->numeric(FLERR,arg[3]); + cut_inner = force->numeric(FLERR,arg[4]); + + if (A_ua < 0) A_ua = 1; +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairBodyRoundedPolyhedron::coeff(int narg, char **arg) +{ + if (narg < 4 || narg > 5) + error->all(FLERR,"Incorrect args for pair coefficients"); + if (!allocated) allocate(); + + int ilo,ihi,jlo,jhi; + force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi); + force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi); + + double k_n_one = force->numeric(FLERR,arg[2]); + double k_na_one = force->numeric(FLERR,arg[3]); + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + for (int j = MAX(jlo,i); j <= jhi; j++) { + k_n[i][j] = k_n_one; + k_na[i][j] = k_na_one; + setflag[i][j] = 1; + count++; + } + } + + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); +} + +/* ---------------------------------------------------------------------- + init specific to this pair style +------------------------------------------------------------------------- */ + +void PairBodyRoundedPolyhedron::init_style() +{ + avec = (AtomVecBody *) atom->style_match("body"); + if (!avec) error->all(FLERR,"Pair body/rounded/polyhedron requires " + "atom style body"); + if (strcmp(avec->bptr->style,"rounded/polyhedron") != 0) + error->all(FLERR,"Pair body/rounded/polyhedron requires " + "body style rounded/polyhedron"); + bptr = (BodyRoundedPolyhedron *) avec->bptr; + + if (force->newton_pair == 0) + error->all(FLERR,"Pair style body/rounded/polyhedron requires " + "newton pair on"); + + if (comm->ghost_velocity == 0) + error->all(FLERR,"Pair body/rounded/polyhedron requires " + "ghost atoms store velocity"); + + neighbor->request(this); + + // find the maximum enclosing radius for each atom type + + int i, itype; + double eradi; + int* body = atom->body; + int* type = atom->type; + int ntypes = atom->ntypes; + int nlocal = atom->nlocal; + + if (atom->nmax > nmax) { + memory->destroy(dnum); + memory->destroy(dfirst); + memory->destroy(ednum); + memory->destroy(edfirst); + memory->destroy(facnum); + memory->destroy(facfirst); + memory->destroy(enclosing_radius); + memory->destroy(rounded_radius); + nmax = atom->nmax; + memory->create(dnum,nmax,"pair:dnum"); + memory->create(dfirst,nmax,"pair:dfirst"); + memory->create(ednum,nmax,"pair:ednum"); + memory->create(edfirst,nmax,"pair:edfirst"); + memory->create(facnum,nmax,"pair:facnum"); + memory->create(facfirst,nmax,"pair:facfirst"); + memory->create(enclosing_radius,nmax,"pair:enclosing_radius"); + memory->create(rounded_radius,nmax,"pair:rounded_radius"); + } + + ndiscrete = nedge = nface = 0; + for (i = 0; i < nlocal; i++) + dnum[i] = ednum[i] = facnum[i] = 0; + + double *merad = NULL; + memory->create(merad,ntypes+1,"pair:merad"); + for (i = 1; i <= ntypes; i++) + maxerad[i] = merad[i] = 0; + + int ipour; + for (ipour = 0; ipour < modify->nfix; ipour++) + if (strcmp(modify->fix[ipour]->style,"pour") == 0) break; + if (ipour == modify->nfix) ipour = -1; + + int idep; + for (idep = 0; idep < modify->nfix; idep++) + if (strcmp(modify->fix[idep]->style,"deposit") == 0) break; + if (idep == modify->nfix) idep = -1; + + for (i = 1; i <= ntypes; i++) { + merad[i] = 0.0; + if (ipour >= 0) { + itype = i; + merad[i] = + *((double *) modify->fix[ipour]->extract("radius",itype)); + } + if (idep >= 0) { + itype = i; + merad[i] = + *((double *) modify->fix[idep]->extract("radius",itype)); + } + } + + for (i = 0; i < nlocal; i++) { + itype = type[i]; + if (body[i] >= 0) { + if (dnum[i] == 0) body2space(i); + eradi = enclosing_radius[i]; + if (eradi > merad[itype]) merad[itype] = eradi; + } else + merad[itype] = 0; + } + + MPI_Allreduce(&merad[1],&maxerad[1],ntypes,MPI_DOUBLE,MPI_MAX,world); + + memory->destroy(merad); + + sanity_check(); +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairBodyRoundedPolyhedron::init_one(int i, int j) +{ + k_n[j][i] = k_n[i][j]; + k_na[j][i] = k_na[i][j]; + + return (maxerad[i]+maxerad[j]); +} + +/* ---------------------------------------------------------------------- + convert N sub-particles in body I to space frame using current quaternion + store sub-particle space-frame displacements from COM in discrete list +------------------------------------------------------------------------- */ + +void PairBodyRoundedPolyhedron::body2space(int i) +{ + int ibonus = atom->body[i]; + AtomVecBody::Bonus *bonus = &avec->bonus[ibonus]; + int nsub = bptr->nsub(bonus); + double *coords = bptr->coords(bonus); + int body_num_edges = bptr->nedges(bonus); + double* edge_ends = bptr->edges(bonus); + int body_num_faces = bptr->nfaces(bonus); + double* face_pts = bptr->faces(bonus); + double eradius = bptr->enclosing_radius(bonus); + double rradius = bptr->rounded_radius(bonus); + + // get the number of sub-particles (vertices) + // and the index of the first vertex of my body in the list + + dnum[i] = nsub; + dfirst[i] = ndiscrete; + + // grow the vertex list if necessary + // the first 3 columns are for coords, the last 3 for forces + + if (ndiscrete + nsub > dmax) { + dmax += DELTA; + memory->grow(discrete,dmax,7,"pair:discrete"); + } + + double p[3][3]; + MathExtra::quat_to_mat(bonus->quat,p); + + for (int m = 0; m < nsub; m++) { + MathExtra::matvec(p,&coords[3*m],discrete[ndiscrete]); + discrete[ndiscrete][3] = 0; + discrete[ndiscrete][4] = 0; + discrete[ndiscrete][5] = 0; + discrete[ndiscrete][6] = 0; + ndiscrete++; + } + + // get the number of edges (vertices) + // and the index of the first edge of my body in the list + + ednum[i] = body_num_edges; + edfirst[i] = nedge; + + // grow the edge list if necessary + // the first 2 columns are for vertex indices within body, the last 3 for forces + + if (nedge + body_num_edges > edmax) { + edmax += DELTA; + memory->grow(edge,edmax,6,"pair:edge"); + } + + for (int m = 0; m < body_num_edges; m++) { + edge[nedge][0] = static_cast(edge_ends[2*m+0]); + edge[nedge][1] = static_cast(edge_ends[2*m+1]); + edge[nedge][2] = 0; + edge[nedge][3] = 0; + edge[nedge][4] = 0; + edge[nedge][5] = 0; + nedge++; + } + + // get the number of faces and the index of the first face + + facnum[i] = body_num_faces; + facfirst[i] = nface; + + // grow the face list if necessary + // the first 3 columns are for vertex indices within body, the last 3 for forces + + if (nface + body_num_faces > facmax) { + facmax += DELTA; + memory->grow(face,facmax,MAX_FACE_SIZE,"pair:face"); + } + + for (int m = 0; m < body_num_faces; m++) { + for (int k = 0; k < MAX_FACE_SIZE; k++) + face[nface][k] = static_cast(face_pts[MAX_FACE_SIZE*m+k]); + nface++; + } + + enclosing_radius[i] = eradius; + rounded_radius[i] = rradius; +} + +/* ---------------------------------------------------------------------- + Interaction between two spheres with different radii + according to the 2D model from Fraige et al. +---------------------------------------------------------------------- */ + +void PairBodyRoundedPolyhedron::sphere_against_sphere(int ibody, int jbody, + int itype, int jtype, double delx, double dely, double delz, double rsq, + double** v, double** f, int evflag) +{ + double rradi,rradj,contact_dist; + double vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3; + double rij,rsqinv,R,fx,fy,fz,fn[3],ft[3],fpair,energy; + int nlocal = atom->nlocal; + int newton_pair = force->newton_pair; + + rradi = rounded_radius[ibody]; + rradj = rounded_radius[jbody]; + contact_dist = rradi + rradj; + + rij = sqrt(rsq); + R = rij - contact_dist; + + energy = 0; + kernel_force(R, itype, jtype, energy, fpair); + + fx = delx*fpair/rij; + fy = dely*fpair/rij; + fz = delz*fpair/rij; + + if (R <= 0) { // in contact + + // relative translational velocity + + vr1 = v[ibody][0] - v[jbody][0]; + vr2 = v[ibody][1] - v[jbody][1]; + vr3 = v[ibody][2] - v[jbody][2]; + + // normal component + + rsqinv = 1.0/rsq; + vnnr = vr1*delx + vr2*dely + vr3*delz; + vn1 = delx*vnnr * rsqinv; + vn2 = dely*vnnr * rsqinv; + vn3 = delz*vnnr * rsqinv; + + // tangential component + + vt1 = vr1 - vn1; + vt2 = vr2 - vn2; + vt3 = vr3 - vn3; + + // normal friction term at contact + + fn[0] = -c_n * vn1; + fn[1] = -c_n * vn2; + fn[2] = -c_n * vn3; + + // tangential friction term at contact, + // excluding the tangential deformation term for now + + ft[0] = -c_t * vt1; + ft[1] = -c_t * vt2; + ft[2] = -c_t * vt3; + + fx += fn[0] + ft[0]; + fy += fn[1] + ft[1]; + fz += fn[2] + ft[2]; + } + + f[ibody][0] += fx; + f[ibody][1] += fy; + f[ibody][2] += fz; + + if (newton_pair || jbody < nlocal) { + f[jbody][0] -= fx; + f[jbody][1] -= fy; + f[jbody][2] -= fz; + } + + if (evflag) ev_tally_xyz(ibody,jbody,nlocal,newton_pair, + energy,0.0,fx,fy,fz,delx,dely,delz); +} + +/* ---------------------------------------------------------------------- + Interaction bt the edges of a polyhedron (ibody) and a sphere (jbody) +---------------------------------------------------------------------- */ + +void PairBodyRoundedPolyhedron::sphere_against_edge(int ibody, int jbody, + int itype, int jtype, double** x, double** v, double** f, double** torque, + double** angmom, int evflag) +{ + int ni,nei,ifirst,iefirst,npi1,npi2,ibonus; + double xi1[3],xi2[3],vti[3],h[3],fn[3],ft[3],d,t; + double delx,dely,delz,rsq,rij,rsqinv,R,fx,fy,fz,fpair,energy; + double rradi,rradj,contact_dist; + double vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3; + double *quat, *inertia; + AtomVecBody::Bonus *bonus; + + int nlocal = atom->nlocal; + int newton_pair = force->newton_pair; + + ifirst = dfirst[ibody]; + iefirst = edfirst[ibody]; + nei = ednum[ibody]; + + rradi = rounded_radius[ibody]; + rradj = rounded_radius[jbody]; + contact_dist = rradi + rradj; + + for (ni = 0; ni < nei; ni++) { + + npi1 = static_cast(edge[iefirst+ni][0]); + npi2 = static_cast(edge[iefirst+ni][1]); + + // compute the space-fixed coordinates for the vertices of the face + + xi1[0] = x[ibody][0] + discrete[ifirst+npi1][0]; + xi1[1] = x[ibody][1] + discrete[ifirst+npi1][1]; + xi1[2] = x[ibody][2] + discrete[ifirst+npi1][2]; + + xi2[0] = x[ibody][0] + discrete[ifirst+npi2][0]; + xi2[1] = x[ibody][1] + discrete[ifirst+npi2][1]; + xi2[2] = x[ibody][2] + discrete[ifirst+npi2][2]; + + // find the projection of the jbody's COM on the edge + + project_pt_line(x[jbody], xi1, xi2, h, d, t); + + if (d > contact_dist + cut_inner) continue; + if (t < 0 || t > 1) continue; + + if (fabs(t) < EPSILON) { + if (static_cast(discrete[ifirst+npi1][6]) == 1) + continue; + else { + h[0] = xi1[0]; + h[1] = xi1[1]; + h[2] = xi1[2]; + discrete[ifirst+npi1][6] = 1; + } + } + + if (fabs(t-1) < EPSILON) { + if (static_cast(discrete[ifirst+npi2][6]) == 1) + continue; + else { + h[0] = xi2[0]; + h[1] = xi2[1]; + h[2] = xi2[2]; + discrete[ifirst+npi2][6] = 1; + } + } + + delx = h[0] - x[jbody][0]; + dely = h[1] - x[jbody][1]; + delz = h[2] - x[jbody][2]; + rsq = delx*delx + dely*dely + delz*delz; + rsqinv = (rsq == 0.0) ? 0.0 : 1.0/rsq; + rij = sqrt(rsq); + R = rij - contact_dist; + + energy = 0; + kernel_force(R, itype, jtype, energy, fpair); + + fx = delx*fpair/rij; + fy = dely*fpair/rij; + fz = delz*fpair/rij; + + if (R <= 0) { // in contact + + // compute the velocity of the vertex in the space-fixed frame + + ibonus = atom->body[ibody]; + bonus = &avec->bonus[ibonus]; + quat = bonus->quat; + inertia = bonus->inertia; + total_velocity(h, x[ibody], v[ibody], angmom[ibody], + inertia, quat, vti); + + // relative translational velocity + + vr1 = vti[0] - v[jbody][0]; + vr2 = vti[1] - v[jbody][1]; + vr3 = vti[2] - v[jbody][2]; + + // normal component + + vnnr = vr1*delx + vr2*dely + vr3*delz; + vn1 = delx*vnnr * rsqinv; + vn2 = dely*vnnr * rsqinv; + vn3 = delz*vnnr * rsqinv; + + // tangential component + + vt1 = vr1 - vn1; + vt2 = vr2 - vn2; + vt3 = vr3 - vn3; + + // normal friction term at contact + + fn[0] = -c_n * vn1; + fn[1] = -c_n * vn2; + fn[2] = -c_n * vn3; + + // tangential friction term at contact, + // excluding the tangential deformation term + + ft[0] = -c_t * vt1; + ft[1] = -c_t * vt2; + ft[2] = -c_t * vt3; + + fx += fn[0] + ft[0]; + fy += fn[1] + ft[1]; + fz += fn[2] + ft[2]; + } + + f[ibody][0] += fx; + f[ibody][1] += fy; + f[ibody][2] += fz; + sum_torque(x[ibody], h, fx, fy, fz, torque[ibody]); + + if (newton_pair || jbody < nlocal) { + f[jbody][0] -= fx; + f[jbody][1] -= fy; + f[jbody][2] -= fz; + } + + if (evflag) ev_tally_xyz(ibody,jbody,nlocal,newton_pair, + energy,0.0,fx,fy,fz,delx,dely,delz); + } +} + +/* ---------------------------------------------------------------------- + Interaction bt the faces of a polyhedron (ibody) and a sphere (jbody) +---------------------------------------------------------------------- */ + +void PairBodyRoundedPolyhedron::sphere_against_face(int ibody, int jbody, + int itype, int jtype, double** x, double** v, double** f, double** torque, + double** angmom, int evflag) +{ + int ni,nfi,inside,ifirst,iffirst,npi1,npi2,npi3,ibonus,tmp; + double xi1[3],xi2[3],xi3[3],ui[3],vi[3],vti[3],n[3],h[3],fn[3],ft[3],d; + double delx,dely,delz,rsq,rij,rsqinv,R,fx,fy,fz,fpair,energy; + double rradi,rradj,contact_dist; + double vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3; + double *quat, *inertia; + AtomVecBody::Bonus *bonus; + + int nlocal = atom->nlocal; + int newton_pair = force->newton_pair; + + ifirst = dfirst[ibody]; + iffirst = facfirst[ibody]; + nfi = facnum[ibody]; + + rradi = rounded_radius[ibody]; + rradj = rounded_radius[jbody]; + contact_dist = rradi + rradj; + + for (ni = 0; ni < nfi; ni++) { + + npi1 = static_cast(face[iffirst+ni][0]); + npi2 = static_cast(face[iffirst+ni][1]); + npi3 = static_cast(face[iffirst+ni][2]); + + // compute the space-fixed coordinates for the vertices of the face + + xi1[0] = x[ibody][0] + discrete[ifirst+npi1][0]; + xi1[1] = x[ibody][1] + discrete[ifirst+npi1][1]; + xi1[2] = x[ibody][2] + discrete[ifirst+npi1][2]; + + xi2[0] = x[ibody][0] + discrete[ifirst+npi2][0]; + xi2[1] = x[ibody][1] + discrete[ifirst+npi2][1]; + xi2[2] = x[ibody][2] + discrete[ifirst+npi2][2]; + + xi3[0] = x[ibody][0] + discrete[ifirst+npi3][0]; + xi3[1] = x[ibody][1] + discrete[ifirst+npi3][1]; + xi3[2] = x[ibody][2] + discrete[ifirst+npi3][2]; + + // find the normal unit vector of the face + + MathExtra::sub3(xi2, xi1, ui); + MathExtra::sub3(xi3, xi1, vi); + MathExtra::cross3(ui, vi, n); + MathExtra::norm3(n); + + // skip if the COM of the two bodies are in the same side of the face + + if (opposite_sides(n, xi1, x[ibody], x[jbody]) == 0) continue; + + // find the projection of the sphere on the face + + project_pt_plane(x[jbody], xi1, xi2, xi3, h, d, inside); + + inside_polygon(ibody, ni, x[ibody], h, NULL, inside, tmp); + if (inside == 0) continue; + + delx = h[0] - x[jbody][0]; + dely = h[1] - x[jbody][1]; + delz = h[2] - x[jbody][2]; + rsq = delx*delx + dely*dely + delz*delz; + rij = sqrt(rsq); + R = rij - contact_dist; + + energy = 0; + kernel_force(R, itype, jtype, energy, fpair); + + fx = delx*fpair/rij; + fy = dely*fpair/rij; + fz = delz*fpair/rij; + + if (R <= 0) { // in contact + + // compute the velocity of the vertex in the space-fixed frame + + ibonus = atom->body[ibody]; + bonus = &avec->bonus[ibonus]; + quat = bonus->quat; + inertia = bonus->inertia; + total_velocity(h, x[ibody], v[ibody], angmom[ibody], + inertia, quat, vti); + + // relative translational velocity + + vr1 = vti[0] - v[jbody][0]; + vr2 = vti[1] - v[jbody][1]; + vr3 = vti[2] - v[jbody][2]; + + // normal component + + rsqinv = 1.0/rsq; + vnnr = vr1*delx + vr2*dely + vr3*delz; + vn1 = delx*vnnr * rsqinv; + vn2 = dely*vnnr * rsqinv; + vn3 = delz*vnnr * rsqinv; + + // tangential component + + vt1 = vr1 - vn1; + vt2 = vr2 - vn2; + vt3 = vr3 - vn3; + + // normal friction term at contact + + fn[0] = -c_n * vn1; + fn[1] = -c_n * vn2; + fn[2] = -c_n * vn3; + + // tangential friction term at contact, + // excluding the tangential deformation term for now + + ft[0] = -c_t * vt1; + ft[1] = -c_t * vt2; + ft[2] = -c_t * vt3; + + fx += fn[0] + ft[0]; + fy += fn[1] + ft[1]; + fz += fn[2] + ft[2]; + } + + f[ibody][0] += fx; + f[ibody][1] += fy; + f[ibody][2] += fz; + sum_torque(x[ibody], h, fx, fy, fz, torque[ibody]); + + if (newton_pair || jbody < nlocal) { + f[jbody][0] -= fx; + f[jbody][1] -= fy; + f[jbody][2] -= fz; + } + + if (evflag) ev_tally_xyz(ibody,jbody,nlocal,newton_pair, + energy,0.0,fx,fy,fz,delx,dely,delz); + } +} + +/* ---------------------------------------------------------------------- + Determine the interaction mode between i's edges against j's edges + + i = atom i (body i) + j = atom j (body j) + x = atoms' coordinates + f = atoms' forces + torque = atoms' torques + tag = atoms' tags + contact_list = list of contacts + num_contacts = number of contacts between i's edges and j's edges + Return: + +---------------------------------------------------------------------- */ + +int PairBodyRoundedPolyhedron::edge_against_edge(int ibody, int jbody, + int itype, int jtype, double** x, Contact* contact_list, int &num_contacts, + double &evdwl, double* facc) +{ + int ni,nei,nj,nej,interact; + double rradi,rradj,energy; + + nei = ednum[ibody]; + rradi = rounded_radius[ibody]; + nej = ednum[jbody]; + rradj = rounded_radius[jbody]; + + energy = 0; + interact = EE_NONE; + + // loop through body i's edges + + for (ni = 0; ni < nei; ni++) { + + for (nj = 0; nj < nej; nj++) { + + // compute the distance between the edge nj to the edge ni + #ifdef _POLYHEDRON_DEBUG + printf("Compute interaction between edge %d of body %d " + "with edge %d of body %d:\n", + nj, jbody, ni, ibody); + #endif + + interact = interaction_edge_to_edge(ibody, ni, x[ibody], rradi, + jbody, nj, x[jbody], rradj, + itype, jtype, cut_inner, + contact_list, num_contacts, + energy, facc); + } + + } // end for looping through the edges of body i + + evdwl += energy; + + return interact; +} + +/* ---------------------------------------------------------------------- + Determine the interaction mode between i's edges against j's faces + + i = atom i (body i) + j = atom j (body j) + x = atoms' coordinates + f = atoms' forces + torque = atoms' torques + tag = atoms' tags + contact_list = list of contacts + num_contacts = number of contacts between i's edges and j's faces + Return: + +---------------------------------------------------------------------- */ + +int PairBodyRoundedPolyhedron::edge_against_face(int ibody, int jbody, + int itype, int jtype, double** x, Contact* contact_list, int &num_contacts, + double &evdwl, double* facc) +{ + int ni,nei,nj,nfj,interact; + double rradi,rradj,energy; + + nei = ednum[ibody]; + rradi = rounded_radius[ibody]; + nfj = facnum[jbody]; + rradj = rounded_radius[jbody]; + + energy = 0; + interact = EF_NONE; + + // loop through body i's edges + + for (ni = 0; ni < nei; ni++) { + + // loop through body j's faces + + for (nj = 0; nj < nfj; nj++) { + + // compute the distance between the face nj to the edge ni + #ifdef _POLYHEDRON_DEBUG + printf("Compute interaction between face %d of body %d with " + "edge %d of body %d:\n", + nj, jbody, ni, ibody); + #endif + + interact = interaction_face_to_edge(jbody, nj, x[jbody], rradj, + ibody, ni, x[ibody], rradi, + itype, jtype, cut_inner, + contact_list, num_contacts, + energy, facc); + } + + } // end for looping through the edges of body i + + evdwl += energy; + + return interact; +} + +/* ------------------------------------------------------------------------- + Compute the distance between an edge of body i and an edge from + another body + Input: + ibody = body i (i.e. atom i) + face_index = face index of body i + xmi = atom i's coordinates (body i's center of mass) + rounded_radius_i = rounded radius of the body i + jbody = body i (i.e. atom j) + edge_index = coordinate of the tested edge from another body + xmj = atom j's coordinates (body j's center of mass) + rounded_radius_j = rounded radius of the body j + cut_inner = cutoff for vertex-vertex and vertex-edge interaction + Output: + d = Distance from a point x0 to an edge + hi = coordinates of the projection of x0 on the edge + + contact = 0 no contact between the queried edge and the face + 1 contact detected + return + INVALID if the face index is invalid + NONE if there is no interaction +------------------------------------------------------------------------- */ + +int PairBodyRoundedPolyhedron::interaction_edge_to_edge(int ibody, + int edge_index_i, double *xmi, double rounded_radius_i, + int jbody, int edge_index_j, double *xmj, double rounded_radius_j, + int itype, int jtype, double cut_inner, + Contact* contact_list, int &num_contacts, double &energy, double* facc) +{ + int ifirst,iefirst,jfirst,jefirst,npi1,npi2,npj1,npj2,interact; + double xi1[3],xi2[3],xpj1[3],xpj2[3]; + double r,t1,t2,h1[3],h2[3]; + double contact_dist; + + double** x = atom->x; + double** v = atom->v; + double** f = atom->f; + double** torque = atom->torque; + double** angmom = atom->angmom; + + ifirst = dfirst[ibody]; + iefirst = edfirst[ibody]; + npi1 = static_cast(edge[iefirst+edge_index_i][0]); + npi2 = static_cast(edge[iefirst+edge_index_i][1]); + + // compute the space-fixed coordinates for the edge ends + + xi1[0] = xmi[0] + discrete[ifirst+npi1][0]; + xi1[1] = xmi[1] + discrete[ifirst+npi1][1]; + xi1[2] = xmi[2] + discrete[ifirst+npi1][2]; + + xi2[0] = xmi[0] + discrete[ifirst+npi2][0]; + xi2[1] = xmi[1] + discrete[ifirst+npi2][1]; + xi2[2] = xmi[2] + discrete[ifirst+npi2][2]; + + // two ends of the edge from body j + + jfirst = dfirst[jbody]; + jefirst = edfirst[jbody]; + npj1 = static_cast(edge[jefirst+edge_index_j][0]); + npj2 = static_cast(edge[jefirst+edge_index_j][1]); + + xpj1[0] = xmj[0] + discrete[jfirst+npj1][0]; + xpj1[1] = xmj[1] + discrete[jfirst+npj1][1]; + xpj1[2] = xmj[2] + discrete[jfirst+npj1][2]; + + xpj2[0] = xmj[0] + discrete[jfirst+npj2][0]; + xpj2[1] = xmj[1] + discrete[jfirst+npj2][1]; + xpj2[2] = xmj[2] + discrete[jfirst+npj2][2]; + + contact_dist = rounded_radius_i + rounded_radius_j; + + int jflag = 1; + distance_bt_edges(xpj1, xpj2, xi1, xi2, h1, h2, t1, t2, r); + + #ifdef _POLYHEDRON_DEBUG + double ui[3],uj[3]; + MathExtra::sub3(xi1,xi2,ui); + MathExtra::norm3(ui); + MathExtra::sub3(xpj1,xpj2,uj); + MathExtra::norm3(uj); + double dot = MathExtra::dot3(ui, uj); + printf(" edge npi1 = %d (%f %f %f); npi2 = %d (%f %f %f) vs." + " edge npj1 = %d (%f %f %f); npj2 = %d (%f %f %f): " + "t1 = %f; t2 = %f; r = %f; dot = %f\n", + npi1, xi1[0], xi1[1], xi1[2], npi2, xi2[0], xi2[1], xi2[2], + npj1, xpj1[0], xpj1[1], xpj1[2], npj2, xpj2[0], xpj2[1], xpj2[2], + t1, t2, r, dot); + #endif + + interact = EE_NONE; + + // singularity case, ignore interactions + + if (r < EPSILON) return interact; + + // include the vertices for interactions + + if (t1 >= 0 && t1 <= 1 && t2 >= 0 && t2 <= 1 && + r < contact_dist + cut_inner) { + pair_force_and_torque(jbody, ibody, h1, h2, r, contact_dist, + jtype, itype, x, v, f, torque, angmom, + jflag, energy, facc); + + interact = EE_INTERACT; + if (r <= contact_dist) { + // store the contact info + contact_list[num_contacts].ibody = ibody; + contact_list[num_contacts].jbody = jbody; + contact_list[num_contacts].xi[0] = h2[0]; + contact_list[num_contacts].xi[1] = h2[1]; + contact_list[num_contacts].xi[2] = h2[2]; + contact_list[num_contacts].xj[0] = h1[0]; + contact_list[num_contacts].xj[1] = h1[1]; + contact_list[num_contacts].xj[2] = h1[2]; + contact_list[num_contacts].type = 1; + contact_list[num_contacts].separation = r - contact_dist; + contact_list[num_contacts].unique = 1; + num_contacts++; + } + } else { + + } + + return interact; +} + +/* ------------------------------------------------------------------------- + Compute the interaction between a face of body i and an edge from + another body + Input: + ibody = body i (i.e. atom i) + face_index = face index of body i + xmi = atom i's coordinates (body i's center of mass) + rounded_radius_i = rounded radius of the body i + jbody = body i (i.e. atom j) + edge_index = coordinate of the tested edge from another body + xmj = atom j's coordinates (body j's center of mass) + rounded_radius_j = rounded radius of the body j + cut_inner = cutoff for vertex-vertex and vertex-edge interaction + Output: + d = Distance from a point x0 to an edge + hi = coordinates of the projection of x0 on the edge + + contact = 0 no contact between the queried edge and the face + 1 contact detected + return + INVALID if the face index is invalid + NONE if there is no interaction +------------------------------------------------------------------------- */ + +int PairBodyRoundedPolyhedron::interaction_face_to_edge(int ibody, + int face_index, double *xmi, double rounded_radius_i, + int jbody, int edge_index, double *xmj, double rounded_radius_j, + int itype, int jtype, double cut_inner, + Contact* contact_list, int &num_contacts, double &energy, double* facc) +{ + if (face_index >= facnum[ibody]) return EF_INVALID; + + int ifirst,iffirst,jfirst,npi1,npi2,npi3; + int jefirst,npj1,npj2; + double xi1[3],xi2[3],xi3[3],xpj1[3],xpj2[3],ui[3],vi[3],n[3]; + + double** x = atom->x; + double** v = atom->v; + double** f = atom->f; + double** torque = atom->torque; + double** angmom = atom->angmom; + + ifirst = dfirst[ibody]; + iffirst = facfirst[ibody]; + npi1 = static_cast(face[iffirst+face_index][0]); + npi2 = static_cast(face[iffirst+face_index][1]); + npi3 = static_cast(face[iffirst+face_index][2]); + + // compute the space-fixed coordinates for the vertices of the face + + xi1[0] = xmi[0] + discrete[ifirst+npi1][0]; + xi1[1] = xmi[1] + discrete[ifirst+npi1][1]; + xi1[2] = xmi[2] + discrete[ifirst+npi1][2]; + + xi2[0] = xmi[0] + discrete[ifirst+npi2][0]; + xi2[1] = xmi[1] + discrete[ifirst+npi2][1]; + xi2[2] = xmi[2] + discrete[ifirst+npi2][2]; + + xi3[0] = xmi[0] + discrete[ifirst+npi3][0]; + xi3[1] = xmi[1] + discrete[ifirst+npi3][1]; + xi3[2] = xmi[2] + discrete[ifirst+npi3][2]; + + // find the normal unit vector of the face, ensure it point outward of the body + + MathExtra::sub3(xi2, xi1, ui); + MathExtra::sub3(xi3, xi1, vi); + MathExtra::cross3(ui, vi, n); + MathExtra::norm3(n); + + double xc[3], dot, ans[3]; + xc[0] = (xi1[0] + xi2[0] + xi3[0])/3.0; + xc[1] = (xi1[1] + xi2[1] + xi3[1])/3.0; + xc[2] = (xi1[2] + xi2[2] + xi3[2])/3.0; + MathExtra::sub3(xc, xmi, ans); + dot = MathExtra::dot3(ans, n); + if (dot < 0) MathExtra::negate3(n); + + // two ends of the edge from body j + + jfirst = dfirst[jbody]; + jefirst = edfirst[jbody]; + npj1 = static_cast(edge[jefirst+edge_index][0]); + npj2 = static_cast(edge[jefirst+edge_index][1]); + + xpj1[0] = xmj[0] + discrete[jfirst+npj1][0]; + xpj1[1] = xmj[1] + discrete[jfirst+npj1][1]; + xpj1[2] = xmj[2] + discrete[jfirst+npj1][2]; + + xpj2[0] = xmj[0] + discrete[jfirst+npj2][0]; + xpj2[1] = xmj[1] + discrete[jfirst+npj2][1]; + xpj2[2] = xmj[2] + discrete[jfirst+npj2][2]; + + // no interaction if two ends of the edge + // are on the same side with the COM wrt the face + + if (opposite_sides(n, xi1, xmi, xpj1) == 0 && + opposite_sides(n, xi1, xmi, xpj2) == 0) + return EF_NONE; + + // determine the intersection of the edge to the face + + double hi1[3], hi2[3], d1, d2, contact_dist; + int inside1 = 0; + int inside2 = 0; + + // enum {EF_PARALLEL=0,EF_SAME_SIDE_OF_FACE, + // EF_INTERSECT_INSIDE,EF_INTERSECT_OUTSIDE}; + + int interact = edge_face_intersect(xi1, xi2, xi3, xpj1, xpj2, + hi1, hi2, d1, d2, inside1, inside2); + + inside_polygon(ibody, face_index, xmi, hi1, hi2, inside1, inside2); + + contact_dist = rounded_radius_i + rounded_radius_j; + + // both endpoints are on the same side of, or parallel to, the face + // and both are out of the interaction zone + + if (interact == EF_SAME_SIDE_OF_FACE || interact == EF_PARALLEL) { + + if (d1 > contact_dist + cut_inner && d2 > contact_dist + cut_inner) + return EF_NONE; + + int num_outside = 0; + int jflag = 1; + + #ifdef _POLYHEDRON_DEBUG + if (interact == EF_SAME_SIDE_OF_FACE) + printf(" - same side of face\n"); + else if (interact == EF_PARALLEL) + printf(" - parallel\n"); + printf(" face: xi1 (%f %f %f) xi2 (%f %f %f) xi3 (%f %f %f)\n", + xi1[0], xi1[1], xi1[2], xi2[0], xi2[1], xi2[2], xi3[0], xi3[1], xi3[2]); + printf(" edge: xpj1 (%f %f %f) xpj2 (%f %f %f)\n", + xpj1[0], xpj1[1], xpj1[2], xpj2[0], xpj2[1], xpj2[2]); + #endif + + // xpj1 is in the interaction zone + // and its projection on the face is inside the triangle + // compute vertex-face interaction and accumulate force/torque to both bodies + + if (d1 <= contact_dist + cut_inner) { + if (inside1) { + if (static_cast(discrete[jfirst+npj1][6]) == 0) { + pair_force_and_torque(jbody, ibody, xpj1, hi1, d1, contact_dist, + jtype, itype, x, v, f, torque, angmom, + jflag, energy, facc); + #ifdef _POLYHEDRON_DEBUG + printf(" - compute pair force between vertex %d from edge %d of body %d " + "with face %d of body %d: d1 = %f\n", + npj1, edge_index, jbody, face_index, ibody, d1); + #endif + + if (d1 <= contact_dist) { + // store the contact info + contact_list[num_contacts].ibody = ibody; + contact_list[num_contacts].jbody = jbody; + contact_list[num_contacts].xi[0] = hi1[0]; + contact_list[num_contacts].xi[1] = hi1[1]; + contact_list[num_contacts].xi[2] = hi1[2]; + contact_list[num_contacts].xj[0] = xpj1[0]; + contact_list[num_contacts].xj[1] = xpj1[1]; + contact_list[num_contacts].xj[2] = xpj1[2]; + contact_list[num_contacts].type = 0; + contact_list[num_contacts].separation = d1 - contact_dist; + contact_list[num_contacts].unique = 1; + num_contacts++; + } + + discrete[jfirst+npj1][6] = 1; + } + } else { + num_outside++; + } + } + + // xpj2 is in the interaction zone + // and its projection on the face is inside the triangle + // compute vertex-face interaction and accumulate force/torque to both bodies + + if (d2 <= contact_dist + cut_inner) { + if (inside2) { + if (static_cast(discrete[jfirst+npj2][6]) == 0) { + pair_force_and_torque(jbody, ibody, xpj2, hi2, d2, contact_dist, + jtype, itype, x, v, f, torque, angmom, + jflag, energy, facc); + #ifdef _POLYHEDRON_DEBUG + printf(" - compute pair force between vertex %d from edge %d of body %d " + "with face %d of body %d: d2 = %f\n", + npj2, edge_index, jbody, face_index, ibody, d2); + #endif + + if (d2 <= contact_dist) { + // store the contact info + contact_list[num_contacts].ibody = ibody; + contact_list[num_contacts].jbody = jbody; + contact_list[num_contacts].xi[0] = hi2[0]; + contact_list[num_contacts].xi[1] = hi2[1]; + contact_list[num_contacts].xi[2] = hi2[2]; + contact_list[num_contacts].xj[0] = xpj2[0]; + contact_list[num_contacts].xj[1] = xpj2[1]; + contact_list[num_contacts].xj[2] = xpj2[2]; + contact_list[num_contacts].type = 0; + contact_list[num_contacts].separation = d2 - contact_dist; + contact_list[num_contacts].unique = 1; + num_contacts++; + } + discrete[jfirst+npj2][6] = 1; + } + } else { + num_outside++; + } + } + + // both ends have projection outside of the face + // compute interaction between the edge with the three edges of the face + + if (num_outside == 2) { + + #ifdef _POLYHEDRON_DEBUG + printf(" - outside = 2\n"); + printf(" - compute pair force between edge %d of body %d " + "with 3 edges of face %d of body %d\n", + edge_index, jbody, face_index, ibody); + #endif + + interact = EF_INTERSECT_OUTSIDE; + + } + + } else if (interact == EF_INTERSECT_OUTSIDE) { + + // compute interaction between the edge with the three edges of the face + + #ifdef _POLYHEDRON_DEBUG + printf(" - intersect outside triangle\n"); + printf(" - compute pair force between edge %d of body %d " + "with face %d of body %d\n", edge_index, jbody, face_index, ibody); + printf(" face: xi1 (%f %f %f) xi2 (%f %f %f) xi3 (%f %f %f)\n", + xi1[0], xi1[1], xi1[2], xi2[0], xi2[1], xi2[2], xi3[0], xi3[1], xi3[2]); + printf(" edge: xpj1 (%f %f %f) xpj2 (%f %f %f)\n", + xpj1[0], xpj1[1], xpj1[2], xpj2[0], xpj2[1], xpj2[2]); + + #endif + } else if (interact == EF_INTERSECT_INSIDE) { + // need to do something here to resolve overlap!! + // p is the intersection between the edge and the face + int jflag = 1; + if (d1 < d2) + pair_force_and_torque(jbody, ibody, xpj1, hi1, d1, contact_dist, + jtype, itype, x, v, f, torque, angmom, + jflag, energy, facc); + else + pair_force_and_torque(jbody, ibody, xpj2, hi2, d2, contact_dist, + jtype, itype, x, v, f, torque, angmom, + jflag, energy, facc); + } + + return interact; +} + +/* ---------------------------------------------------------------------- + Compute forces and torques between two bodies caused by the interaction + between a pair of points on either bodies (similar to sphere-sphere) +------------------------------------------------------------------------- */ + +void PairBodyRoundedPolyhedron::pair_force_and_torque(int ibody, int jbody, + double* pi, double* pj, double r, double contact_dist, + int itype, int jtype, double** x, + double** v, double** f, double** torque, double** angmom, + int jflag, double& energy, double* facc) +{ + double delx,dely,delz,R,fx,fy,fz,fpair; + + delx = pi[0] - pj[0]; + dely = pi[1] - pj[1]; + delz = pi[2] - pj[2]; + R = r - contact_dist; + + kernel_force(R, itype, jtype, energy, fpair); + + fx = delx*fpair/r; + fy = dely*fpair/r; + fz = delz*fpair/r; + + #ifdef _POLYHEDRON_DEBUG + printf(" - R = %f; r = %f; k_na = %f; shift = %f; fpair = %f;" + " energy = %f; jflag = %d\n", R, r, k_na, shift, fpair, + energy, jflag); + #endif + + if (R <= 0) { + + // contact: accumulate normal and tangential contact force components + + contact_forces(ibody, jbody, pi, pj, delx, dely, delz, fx, fy, fz, + x, v, angmom, f, torque, facc); + } else { + + // accumulate force and torque to both bodies directly + + f[ibody][0] += fx; + f[ibody][1] += fy; + f[ibody][2] += fz; + sum_torque(x[ibody], pi, fx, fy, fz, torque[ibody]); + + facc[0] += fx; facc[1] += fy; facc[2] += fz; + + if (jflag) { + f[jbody][0] -= fx; + f[jbody][1] -= fy; + f[jbody][2] -= fz; + sum_torque(x[jbody], pj, -fx, -fy, -fz, torque[jbody]); + } + } +} + +/* ---------------------------------------------------------------------- + Kernel force is model-dependent and can be derived for other styles + here is the harmonic potential (linear piece-wise forces) in Wang et al. +------------------------------------------------------------------------- */ + +void PairBodyRoundedPolyhedron::kernel_force(double R, int itype, int jtype, + double& energy, double& fpair) +{ + double kn = k_n[itype][jtype]; + double kna = k_na[itype][jtype]; + double shift = kna * cut_inner; + double e = 0; + if (R <= 0) { // deformation occurs + fpair = -kn * R - shift; + e = (0.5 * kn * R + shift) * R; + } else if (R <= cut_inner) { // not deforming but cohesive ranges overlap + fpair = kna * R - shift; + e = (-0.5 * kna * R + shift) * R; + } else fpair = 0.0; + energy += e; +} + +/* ---------------------------------------------------------------------- + Compute contact forces between two bodies + modify the force stored at the vertex and edge in contact by j_a + sum forces and torque to the corresponding bodies + fx,fy,fz = unscaled cohesive forces + fn = normal friction component + ft = tangential friction component (-c_t * v_t) +------------------------------------------------------------------------- */ + +void PairBodyRoundedPolyhedron::contact_forces(int ibody, int jbody, + double *xi, double *xj, double delx, double dely, double delz, + double fx, double fy, double fz, double** x, double** v, double** angmom, + double** f, double** torque, double* facc) +{ + int ibonus,jbonus; + double rsq,rsqinv,vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3; + double fn[3],ft[3],vi[3],vj[3]; + double *quat, *inertia; + AtomVecBody::Bonus *bonus; + + // compute the velocity of the vertex in the space-fixed frame + + ibonus = atom->body[ibody]; + bonus = &avec->bonus[ibonus]; + quat = bonus->quat; + inertia = bonus->inertia; + total_velocity(xi, x[ibody], v[ibody], angmom[ibody], + inertia, quat, vi); + + // compute the velocity of the point on the edge in the space-fixed frame + + jbonus = atom->body[jbody]; + bonus = &avec->bonus[jbonus]; + quat = bonus->quat; + inertia = bonus->inertia; + total_velocity(xj, x[jbody], v[jbody], angmom[jbody], + inertia, quat, vj); + + // vector pointing from the contact point on ibody to that on jbody + + rsq = delx*delx + dely*dely + delz*delz; + rsqinv = 1.0/rsq; + + // relative translational velocity + + vr1 = vi[0] - vj[0]; + vr2 = vi[1] - vj[1]; + vr3 = vi[2] - vj[2]; + + // normal component + + vnnr = vr1*delx + vr2*dely + vr3*delz; + vn1 = delx*vnnr * rsqinv; + vn2 = dely*vnnr * rsqinv; + vn3 = delz*vnnr * rsqinv; + + // tangential component + + vt1 = vr1 - vn1; + vt2 = vr2 - vn2; + vt3 = vr3 - vn3; + + // normal friction term at contact + + fn[0] = -c_n * vn1; + fn[1] = -c_n * vn2; + fn[2] = -c_n * vn3; + + // tangential friction term at contact + // excluding the tangential deformation term for now + + ft[0] = -c_t * vt1; + ft[1] = -c_t * vt2; + ft[2] = -c_t * vt3; + + // these are contact forces (F_n, F_t and F_ne) only + // cohesive forces will be scaled by j_a after contact area is computed + // mu * fne = tangential friction deformation during gross sliding + // see Eq. 4, Fraige et al. + + fx = fn[0] + ft[0] + mu * fx; + fy = fn[1] + ft[1] + mu * fy; + fz = fn[2] + ft[2] + mu * fz; + + f[ibody][0] += fx; + f[ibody][1] += fy; + f[ibody][2] += fz; + sum_torque(x[ibody], xi, fx, fy, fz, torque[ibody]); + + f[jbody][0] -= fx; + f[jbody][1] -= fy; + f[jbody][2] -= fz; + sum_torque(x[jbody], xj, -fx, -fy, -fz, torque[jbody]); + + facc[0] += fx; facc[1] += fy; facc[2] += fz; + + #ifdef _POLYHEDRON_DEBUG + printf("contact ibody = %d: f = %f %f %f; torque = %f %f %f\n", ibody, + f[ibody][0], f[ibody][1], f[ibody][2], + torque[ibody][0], torque[ibody][1], torque[ibody][2]); + printf("contact jbody = %d: f = %f %f %f; torque = %f %f %f\n", jbody, + f[jbody][0], f[jbody][1], f[jbody][2], + torque[jbody][0], torque[jbody][1], torque[jbody][2]); + #endif +} + +/* ---------------------------------------------------------------------- + Rescale the forces and torques for all the contacts +------------------------------------------------------------------------- */ + +void PairBodyRoundedPolyhedron::rescale_cohesive_forces(double** x, + double** f, double** torque, Contact* contact_list, int &num_contacts, + int itype, int jtype, double* facc) +{ + int m,ibody,jbody; + double delx,dely,delz,fx,fy,fz,R,fpair,r,contact_area; + + int num_unique_contacts = 0; + if (num_contacts == 1) { + num_unique_contacts = 1; + contact_area = 0; + } else if (num_contacts == 2) { + num_unique_contacts = 2; + contact_area = num_contacts * A_ua; + } else { + find_unique_contacts(contact_list, num_contacts); + + double xc[3],dx,dy,dz; + xc[0] = xc[1] = xc[2] = 0; + num_unique_contacts = 0; + for (int m = 0; m < num_contacts; m++) { + if (contact_list[m].unique == 0) continue; + xc[0] += contact_list[m].xi[0]; + xc[1] += contact_list[m].xi[1]; + xc[2] += contact_list[m].xi[2]; + num_unique_contacts++; + } + + xc[0] /= (double)num_unique_contacts; + xc[1] /= (double)num_unique_contacts; + xc[2] /= (double)num_unique_contacts; + + contact_area = 0.0; + for (int m = 0; m < num_contacts; m++) { + if (contact_list[m].unique == 0) continue; + dx = contact_list[m].xi[0] - xc[0]; + dy = contact_list[m].xi[1] - xc[1]; + dz = contact_list[m].xi[2] - xc[2]; + contact_area += (dx*dx + dy*dy + dz*dz); + } + contact_area *= (MY_PI/(double)num_unique_contacts); + } + + double j_a = contact_area / (num_unique_contacts * A_ua); + if (j_a < 1.0) j_a = 1.0; + for (m = 0; m < num_contacts; m++) { + if (contact_list[m].unique == 0) continue; + + ibody = contact_list[m].ibody; + jbody = contact_list[m].jbody; + + delx = contact_list[m].xi[0] - contact_list[m].xj[0]; + dely = contact_list[m].xi[1] - contact_list[m].xj[1]; + delz = contact_list[m].xi[2] - contact_list[m].xj[2]; + r = sqrt(delx*delx + dely*dely + delz*delz); + R = contact_list[m].separation; + + double energy = 0; + kernel_force(R, itype, jtype, energy, fpair); + + fpair *= j_a; + fx = delx*fpair/r; + fy = dely*fpair/r; + fz = delz*fpair/r; + + f[ibody][0] += fx; + f[ibody][1] += fy; + f[ibody][2] += fz; + sum_torque(x[ibody], contact_list[m].xi, fx, fy, fz, torque[ibody]); + + f[jbody][0] -= fx; + f[jbody][1] -= fy; + f[jbody][2] -= fz; + sum_torque(x[jbody], contact_list[m].xj, -fx, -fy, -fz, torque[jbody]); + + facc[0] += fx; facc[1] += fy; facc[2] += fz; + } +} + +/* ---------------------------------------------------------------------- + Accumulate torque to body from the force f=(fx,fy,fz) acting at point x +------------------------------------------------------------------------- */ + +void PairBodyRoundedPolyhedron::sum_torque(double* xm, double *x, double fx, + double fy, double fz, double* torque) +{ + double rx = x[0] - xm[0]; + double ry = x[1] - xm[1]; + double rz = x[2] - xm[2]; + double tx = ry * fz - rz * fy; + double ty = rz * fx - rx * fz; + double tz = rx * fy - ry * fx; + torque[0] += tx; + torque[1] += ty; + torque[2] += tz; +} + +/* ---------------------------------------------------------------------- + Test if two points a and b are in opposite sides of a plane defined by + a normal vector n and a point x0 +------------------------------------------------------------------------- */ + +int PairBodyRoundedPolyhedron::opposite_sides(double* n, double* x0, + double* a, double* b) +{ + double m_a = n[0]*(a[0] - x0[0])+n[1]*(a[1] - x0[1])+n[2]*(a[2] - x0[2]); + double m_b = n[0]*(b[0] - x0[0])+n[1]*(b[1] - x0[1])+n[2]*(b[2] - x0[2]); + // equal to zero when either a or b is on the plane + if (m_a * m_b <= 0) + return 1; + else + return 0; +} + +/* ---------------------------------------------------------------------- + Test if a line segment defined by two points a and b intersects with + a triangle defined by three points x1, x2 and x3 +------------------------------------------------------------------------- */ + +int PairBodyRoundedPolyhedron::edge_face_intersect(double* x1, double* x2, + double* x3, double* a, double* b, double* h_a, double* h_b, + double& d_a, double& d_b, int& inside_a, int& inside_b) +{ + double s[3], u[3], v[3], n[3]; + + // line director + + MathExtra::sub3(b, a, s); + + // plane normal vector + + MathExtra::sub3(x2, x1, u); + MathExtra::sub3(x3, x1, v); + MathExtra::cross3(u, v, n); + MathExtra::norm3(n); + + // find the projection of a and b to the plane and the corresponding distances + + project_pt_plane(a, x1, x2, x3, h_a, d_a, inside_a); + + project_pt_plane(b, x1, x2, x3, h_b, d_b, inside_b); + + // check if the line segment is parallel to the plane + + double dot = MathExtra::dot3(s, n); + if (fabs(dot) < EPSILON) return EF_PARALLEL; + + // solve for the intersection between the line and the plane + + double m[3][3], invm[3][3], p[3], ans[3]; + m[0][0] = -s[0]; + m[0][1] = u[0]; + m[0][2] = v[0]; + + m[1][0] = -s[1]; + m[1][1] = u[1]; + m[1][2] = v[1]; + + m[2][0] = -s[2]; + m[2][1] = u[2]; + m[2][2] = v[2]; + + MathExtra::sub3(a, x1, p); + MathExtra::invert3(m, invm); + MathExtra::matvec(invm, p, ans); + + // p is reused for the intersection point + // s = b - a + + double t = ans[0]; + p[0] = a[0] + s[0] * t; + p[1] = a[1] + s[1] * t; + p[2] = a[2] + s[2] * t; + + // check if p is inside the triangle, excluding the edges and vertices + // the edge-edge and edge-vertices are handled separately + + int inside = 0; + if (ans[1] > 0 && ans[2] > 0 && ans[1] + ans[2] < 1) + inside = 1; + + int interact; + if (t < 0 || t > 1) { + interact = EF_SAME_SIDE_OF_FACE; + } else { + if (inside == 1) + interact = EF_INTERSECT_INSIDE; + else + interact = EF_INTERSECT_OUTSIDE; + } + + return interact; +} + +/* ---------------------------------------------------------------------- + Find the projection of q on the plane defined by point p and the normal + unit vector n: q_proj = q - dot(q - p, n) * n + and the distance d from q to the plane +------------------------------------------------------------------------- */ + +void PairBodyRoundedPolyhedron::project_pt_plane(const double* q, + const double* p, const double* n, + double* q_proj, double &d) +{ + double dot, ans[3], n_p[3]; + n_p[0] = n[0]; n_p[1] = n[1]; n_p[2] = n[2]; + MathExtra::sub3(q, p, ans); + dot = MathExtra::dot3(ans, n_p); + MathExtra::scale3(dot, n_p); + MathExtra::sub3(q, n_p, q_proj); + MathExtra::sub3(q, q_proj, ans); + d = MathExtra::len3(ans); +} + +/* ---------------------------------------------------------------------- + Check if points q1 and q2 are inside a convex polygon, i.e. a face of + a polyhedron + ibody = atom i's index + face_index = face index of the body + xmi = atom i's coordinates + q1 = tested point on the face (e.g. the projection of a point) + q2 = another point (can be NULL) for face-edge intersection + Output: + inside1 = 1 if q1 is inside the polygon, 0 otherwise + inside2 = 1 if q2 is inside the polygon, 0 otherwise +------------------------------------------------------------------------- */ + +void PairBodyRoundedPolyhedron::inside_polygon(int ibody, int face_index, + double* xmi, const double* q1, const double* q2, + int& inside1, int& inside2) + +{ + int i,n,ifirst,iffirst,npi1,npi2; + double xi1[3],xi2[3],u[3],v[3],costheta,anglesum1,anglesum2,magu,magv; + + ifirst = dfirst[ibody]; + iffirst = facfirst[ibody]; + anglesum1 = anglesum2 = 0;; + for (i = 0; i < MAX_FACE_SIZE; i++) { + npi1 = static_cast(face[iffirst+face_index][i]); + if (npi1 < 0) break; + n = i + 1; + if (n <= MAX_FACE_SIZE - 1) { + npi2 = static_cast(face[iffirst+face_index][n]); + if (npi2 < 0) npi2 = static_cast(face[iffirst+face_index][0]); + } else { + npi2 = static_cast(face[iffirst+face_index][0]); + } + + xi1[0] = xmi[0] + discrete[ifirst+npi1][0]; + xi1[1] = xmi[1] + discrete[ifirst+npi1][1]; + xi1[2] = xmi[2] + discrete[ifirst+npi1][2]; + + xi2[0] = xmi[0] + discrete[ifirst+npi2][0]; + xi2[1] = xmi[1] + discrete[ifirst+npi2][1]; + xi2[2] = xmi[2] + discrete[ifirst+npi2][2]; + + MathExtra::sub3(xi1,q1,u); + MathExtra::sub3(xi2,q1,v); + magu = MathExtra::len3(u); + magv = MathExtra::len3(v); + + // the point is at either vertices + + if (magu * magv < EPSILON) inside1 = 1; + else { + costheta = MathExtra::dot3(u,v)/(magu*magv); + anglesum1 += acos(costheta); + } + + if (q2 != NULL) { + MathExtra::sub3(xi1,q2,u); + MathExtra::sub3(xi2,q2,v); + magu = MathExtra::len3(u); + magv = MathExtra::len3(v); + if (magu * magv < EPSILON) inside2 = 1; + else { + costheta = MathExtra::dot3(u,v)/(magu*magv); + anglesum2 += acos(costheta); + } + } + } + + if (fabs(anglesum1 - MY_2PI) < EPSILON) inside1 = 1; + else inside1 = 0; + + if (q2 != NULL) { + if (fabs(anglesum2 - MY_2PI) < EPSILON) inside2 = 1; + else inside2 = 0; + } +} + +/* ---------------------------------------------------------------------- + Find the projection of q on the plane defined by 3 points x1, x2 and x3 + returns the distance d from q to the plane and whether the projected + point is inside the triangle defined by (x1, x2, x3) +------------------------------------------------------------------------- */ + +void PairBodyRoundedPolyhedron::project_pt_plane(const double* q, + const double* x1, const double* x2, const double* x3, double* q_proj, + double &d, int& inside) +{ + double u[3],v[3],n[3]; + + // plane normal vector + + MathExtra::sub3(x2, x1, u); + MathExtra::sub3(x3, x1, v); + MathExtra::cross3(u, v, n); + MathExtra::norm3(n); + + // solve for the intersection between the line and the plane + + double m[3][3], invm[3][3], p[3], ans[3]; + m[0][0] = -n[0]; + m[0][1] = u[0]; + m[0][2] = v[0]; + + m[1][0] = -n[1]; + m[1][1] = u[1]; + m[1][2] = v[1]; + + m[2][0] = -n[2]; + m[2][1] = u[2]; + m[2][2] = v[2]; + + MathExtra::sub3(q, x1, p); + MathExtra::invert3(m, invm); + MathExtra::matvec(invm, p, ans); + + double t = ans[0]; + q_proj[0] = q[0] + n[0] * t; + q_proj[1] = q[1] + n[1] * t; + q_proj[2] = q[2] + n[2] * t; + + // check if the projection point is inside the triangle + // exclude the edges and vertices + // edge-sphere and sphere-sphere interactions are handled separately + + inside = 0; + if (ans[1] > 0 && ans[2] > 0 && ans[1] + ans[2] < 1) { + inside = 1; + } + + // distance from q to q_proj + + MathExtra::sub3(q, q_proj, ans); + d = MathExtra::len3(ans); +} + +/* ---------------------------------------------------------------------- */ + +void PairBodyRoundedPolyhedron::project_pt_line(const double* q, + const double* xi1, const double* xi2, double* h, double& d, double& t) +{ + double u[3],v[3],r[3],s; + + MathExtra::sub3(xi2, xi1, u); + MathExtra::norm3(u); + MathExtra::sub3(q, xi1, v); + + s = MathExtra::dot3(u, v); + h[0] = xi1[0] + s * u[0]; + h[1] = xi1[1] + s * u[1]; + h[2] = xi1[2] + s * u[2]; + + MathExtra::sub3(q, h, r); + d = MathExtra::len3(r); + + if (fabs(xi2[0] - xi1[0]) > 0) + t = (h[0] - xi1[0])/(xi2[0] - xi1[0]); + else if (fabs(xi2[1] - xi1[1]) > 0) + t = (h[1] - xi1[1])/(xi2[1] - xi1[1]); + else if (fabs(xi2[2] - xi1[2]) > 0) + t = (h[2] - xi1[2])/(xi2[2] - xi1[2]); +} + +/* ---------------------------------------------------------------------- + compute the shortest distance between two edges (line segments) + x1, x2: two endpoints of the first edge + x3, x4: two endpoints of the second edge + h1: the end point of the shortest segment perpendicular to both edges + on the line (x1;x2) + h2: the end point of the shortest segment perpendicular to both edges + on the line (x3;x4) + t1: fraction of h1 in the segment (x1,x2) + t2: fraction of h2 in the segment (x3,x4) +------------------------------------------------------------------------- */ + +void PairBodyRoundedPolyhedron::distance_bt_edges(const double* x1, + const double* x2, const double* x3, const double* x4, + double* h1, double* h2, double& t1, double& t2, double& r) +{ + double u[3],v[3],n[3],dot; + + // set the default returned values + + t1 = -2; + t2 = 2; + r = 0; + + // find the edge unit directors and their dot product + + MathExtra::sub3(x2, x1, u); + MathExtra::norm3(u); + MathExtra::sub3(x4, x3, v); + MathExtra::norm3(v); + dot = MathExtra::dot3(u,v); + dot = fabs(dot); + + // check if two edges are parallel + // find the two ends of the overlapping segment, if any + + if (fabs(dot - 1.0) < EPSILON) { + + double s1,s2,x13[3],x23[3],x13h[3]; + double t13,t23,t31,t41,x31[3],x41[3]; + t13=t23=t31=t41=0.0; + + MathExtra::sub3(x1,x3,x13); // x13 = x1 - x3 + MathExtra::sub3(x2,x3,x23); // x23 = x2 - x3 + + s1 = MathExtra::dot3(x13,v); + x13h[0] = x13[0] - s1*v[0]; + x13h[1] = x13[1] - s1*v[1]; + x13h[2] = x13[2] - s1*v[2]; + r = MathExtra::len3(x13h); + + // x13 is the projection of x1 on x3-x4 + + x13[0] = x3[0] + s1*v[0]; + x13[1] = x3[1] + s1*v[1]; + x13[2] = x3[2] + s1*v[2]; + + // x23 is the projection of x2 on x3-x4 + + s2 = MathExtra::dot3(x23,v); + x23[0] = x3[0] + s2*v[0]; + x23[1] = x3[1] + s2*v[1]; + x23[2] = x3[2] + s2*v[2]; + + // find the fraction of the projection points on the edges + + if (fabs(x4[0] - x3[0]) > 0) + t13 = (x13[0] - x3[0])/(x4[0] - x3[0]); + else if (fabs(x4[1] - x3[1]) > 0) + t13 = (x13[1] - x3[1])/(x4[1] - x3[1]); + else if (fabs(x4[2] - x3[2]) > 0) + t13 = (x13[2] - x3[2])/(x4[2] - x3[2]); + + if (fabs(x4[0] - x3[0]) > 0) + t23 = (x23[0] - x3[0])/(x4[0] - x3[0]); + else if (fabs(x4[1] - x3[1]) > 0) + t23 = (x23[1] - x3[1])/(x4[1] - x3[1]); + else if (fabs(x4[2] - x3[2]) > 0) + t23 = (x23[2] - x3[2])/(x4[2] - x3[2]); + + if (fabs(x23[0] - x13[0]) > 0) + t31 = (x3[0] - x13[0])/(x23[0] - x13[0]); + else if (fabs(x23[1] - x13[1]) > 0) + t31 = (x3[1] - x13[1])/(x23[1] - x13[1]); + else if (fabs(x23[2] - x13[2]) > 0) + t31 = (x3[2] - x13[2])/(x23[2] - x13[2]); + + // x31 is the projection of x3 on x1-x2 + + x31[0] = x1[0] + t31*(x2[0] - x1[0]); + x31[1] = x1[1] + t31*(x2[1] - x1[1]); + x31[2] = x1[2] + t31*(x2[2] - x1[2]); + + if (fabs(x23[0] - x13[0]) > 0) + t41 = (x4[0] - x13[0])/(x23[0] - x13[0]); + else if (fabs(x23[1] - x13[1]) > 0) + t41 = (x4[1] - x13[1])/(x23[1] - x13[1]); + else if (fabs(x23[2] - x13[2]) > 0) + t41 = (x4[2] - x13[2])/(x23[2] - x13[2]); + + // x41 is the projection of x4 on x1-x2 + + x41[0] = x1[0] + t41*(x2[0] - x1[0]); + x41[1] = x1[1] + t41*(x2[1] - x1[1]); + x41[2] = x1[2] + t41*(x2[2] - x1[2]); + + // determine two ends from the overlapping segments + + int n1 = 0; + int n2 = 0; + if (t13 >= 0 && t13 <= 1) { + h1[0] = x1[0]; + h1[1] = x1[1]; + h1[2] = x1[2]; + h2[0] = x13[0]; + h2[1] = x13[1]; + h2[2] = x13[2]; + t1 = 0; + t2 = t13; + n1++; + n2++; + } + if (t23 >= 0 && t23 <= 1) { + if (n1 == 0) { + h1[0] = x2[0]; + h1[1] = x2[1]; + h1[2] = x2[2]; + h2[0] = x23[0]; + h2[1] = x23[1]; + h2[2] = x23[2]; + t1 = 1; + t2 = t23; + n1++; + n2++; + } else { + h1[0] = (x1[0]+x2[0])/2; + h1[1] = (x1[1]+x2[1])/2; + h1[2] = (x1[2]+x2[2])/2; + h2[0] = (x13[0]+x23[0])/2; + h2[1] = (x13[1]+x23[1])/2; + h2[2] = (x13[2]+x23[2])/2; + t1 = 0.5; + t2 = (t13+t23)/2; + n1++; + n2++; + } + } + + if (n1 == 0 && n2 == 0) { + if (t31 >= 0 && t31 <= 1) { + h1[0] = x31[0]; + h1[1] = x31[1]; + h1[2] = x31[2]; + h2[0] = x3[0]; + h2[1] = x3[1]; + h2[2] = x3[2]; + t1 = t31; + t2 = 0; + n1++; + n2++; + } + if (t41 >= 0 && t41 <= 1) { + if (n1 == 0) { + h1[0] = x41[0]; + h1[1] = x41[1]; + h1[2] = x41[2]; + h2[0] = x4[0]; + h2[1] = x4[1]; + h2[2] = x4[2]; + t1 = t41; + t2 = 1; + n1++; + n2++; + } else { + h1[0] = (x31[0]+x41[0])/2; + h1[1] = (x31[1]+x41[1])/2; + h1[2] = (x31[2]+x41[2])/2; + h2[0] = (x3[0]+x4[0])/2; + h2[1] = (x3[1]+x4[1])/2; + h2[2] = (x3[2]+x4[2])/2; + t1 = (t31+t41)/2; + t2 = 0.5; + n1++; + n2++; + } + } + } + + // if n1 == 0 and n2 == 0 at this point, + // which means no overlapping segments bt two parallel edges, + // return the default values of t1 and t2 + + return; + + } + + // find the vector n perpendicular to both edges + + MathExtra::cross3(u, v, n); + MathExtra::norm3(n); + + // find the intersection of the line (x3,x4) and the plane (x1,x2,n) + // s = director of the line (x3,x4) + // n_p = plane normal vector of the plane (x1,x2,n) + + double s[3], n_p[3]; + MathExtra::sub3(x4, x3, s); + MathExtra::sub3(x2, x1, u); + MathExtra::cross3(u, n, n_p); + MathExtra::norm3(n_p); + + // solve for the intersection between the line and the plane + + double m[3][3], invm[3][3], p[3], ans[3]; + m[0][0] = -s[0]; + m[0][1] = u[0]; + m[0][2] = n[0]; + + m[1][0] = -s[1]; + m[1][1] = u[1]; + m[1][2] = n[1]; + + m[2][0] = -s[2]; + m[2][1] = u[2]; + m[2][2] = n[2]; + + MathExtra::sub3(x3, x1, p); + MathExtra::invert3(m, invm); + MathExtra::matvec(invm, p, ans); + + t2 = ans[0]; + h2[0] = x3[0] + s[0] * t2; + h2[1] = x3[1] + s[1] * t2; + h2[2] = x3[2] + s[2] * t2; + + project_pt_plane(h2, x1, n, h1, r); + + if (fabs(x2[0] - x1[0]) > 0) + t1 = (h1[0] - x1[0])/(x2[0] - x1[0]); + else if (fabs(x2[1] - x1[1]) > 0) + t1 = (h1[1] - x1[1])/(x2[1] - x1[1]); + else if (fabs(x2[2] - x1[2]) > 0) + t1 = (h1[2] - x1[2])/(x2[2] - x1[2]); +} + +/* ---------------------------------------------------------------------- + Calculate the total velocity of a point (vertex, a point on an edge): + vi = vcm + omega ^ (p - xcm) +------------------------------------------------------------------------- */ + +void PairBodyRoundedPolyhedron::total_velocity(double* p, double *xcm, + double* vcm, double *angmom, double *inertia, double *quat, double* vi) +{ + double r[3],omega[3],ex_space[3],ey_space[3],ez_space[3]; + r[0] = p[0] - xcm[0]; + r[1] = p[1] - xcm[1]; + r[2] = p[2] - xcm[2]; + MathExtra::q_to_exyz(quat,ex_space,ey_space,ez_space); + MathExtra::angmom_to_omega(angmom,ex_space,ey_space,ez_space, + inertia,omega); + vi[0] = omega[1]*r[2] - omega[2]*r[1] + vcm[0]; + vi[1] = omega[2]*r[0] - omega[0]*r[2] + vcm[1]; + vi[2] = omega[0]*r[1] - omega[1]*r[0] + vcm[2]; +} + +/* ---------------------------------------------------------------------- + Determine the length of the contact segment, i.e. the separation between + 2 contacts, should be extended for 3D models. +------------------------------------------------------------------------- */ + +double PairBodyRoundedPolyhedron::contact_separation(const Contact& c1, + const Contact& c2) +{ + double x1 = 0.5*(c1.xi[0] + c1.xj[0]); + double y1 = 0.5*(c1.xi[1] + c1.xj[1]); + double z1 = 0.5*(c1.xi[2] + c1.xj[2]); + double x2 = 0.5*(c2.xi[0] + c2.xj[0]); + double y2 = 0.5*(c2.xi[1] + c2.xj[1]); + double z2 = 0.5*(c2.xi[2] + c2.xj[2]); + double rsq = (x2 - x1)*(x2 - x1) + (y2 - y1)*(y2 - y1) + (z2 - z1)*(z2 - z1); + return rsq; +} + +/* ---------------------------------------------------------------------- + find the number of unique contacts +------------------------------------------------------------------------- */ + +void PairBodyRoundedPolyhedron::find_unique_contacts(Contact* contact_list, + int& num_contacts) +{ + int n = num_contacts; + for (int i = 0; i < n - 1; i++) { + + for (int j = i + 1; j < n; j++) { + if (contact_list[i].unique == 0) continue; + double d = contact_separation(contact_list[i], contact_list[j]); + if (d < EPSILON) contact_list[j].unique = 0; + } + } +} + +/* ---------------------------------------------------------------------- */ + +void PairBodyRoundedPolyhedron::sanity_check() +{ + + double x1[3],x2[3],x3[3],x4[3],h_a[3],h_b[3],d_a,d_b; + double a[3],b[3],t_a,t_b; + + x1[0] = 0; x1[1] = 3; x1[2] = 0; + x2[0] = 3; x2[1] = 0; x2[2] = 0; + x3[0] = 4; x3[1] = 3; x3[2] = 0; + x4[0] = 5; x4[1] = 3; x4[2] = 0; + + a[0] = 0; a[1] = 0; a[2] = 0; + b[0] = 4; b[1] = 0; b[2] = 0; + + project_pt_line(a, x1, x2, h_a, d_a, t_a); + project_pt_line(b, x1, x2, h_b, d_b, t_b); +/* + printf("h_a: %f %f %f; h_b: %f %f %f; t_a = %f; t_b = %f; d = %f; d_b = %f\n", + h_a[0], h_a[1], h_a[2], h_b[0], h_b[1], h_b[2], t_a, t_b, d_a, d_b); +*/ +/* + int inside_a, inside_b; + int mode = edge_face_intersect(x1, x2, x3, a, b, h_a, h_b, d_a, d_b, + inside_a, inside_b); + + double u[3],v[3],n[3]; + MathExtra::sub3(x2, x1, u); + MathExtra::sub3(x3, x1, v); + MathExtra::cross3(u, v, n); + MathExtra::norm3(n); +*/ +/* + project_pt_plane(a, x1, x2, x3, h_a, d_a, inside_a); + printf("h_a: %f %f %f; d = %f: inside %d\n", + h_a[0], h_a[1], h_a[2], d_a, inside_a); + project_pt_plane(b, x1, x2, x3, h_b, d_b, inside_b); + printf("h_b: %f %f %f; d = %f: inside %d\n", + h_b[0], h_b[1], h_b[2], d_b, inside_b); +*/ +/* + distance_bt_edges(x1, x2, x3, x4, h_a, h_b, t_a, t_b, d_a); + printf("h_a: %f %f %f; h_b: %f %f %f; t_a = %f; t_b = %f; d = %f\n", + h_a[0], h_a[1], h_a[2], h_b[0], h_b[1], h_b[2], t_a, t_b, d_a); +*/ +} + diff --git a/src/BODY/pair_body_rounded_polyhedron.h b/src/BODY/pair_body_rounded_polyhedron.h new file mode 100644 index 0000000000..71c04ff966 --- /dev/null +++ b/src/BODY/pair_body_rounded_polyhedron.h @@ -0,0 +1,200 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS + +PairStyle(body/rounded/polyhedron,PairBodyRoundedPolyhedron) + +#else + +#ifndef LMP_PAIR_BODY_ROUNDED_POLYHEDRON_H +#define LMP_PAIR_BODY_ROUNDED_POLYHEDRON_H + +#include "pair.h" + +namespace LAMMPS_NS { + +class PairBodyRoundedPolyhedron : public Pair { + public: + PairBodyRoundedPolyhedron(class LAMMPS *); + ~PairBodyRoundedPolyhedron(); + void compute(int, int); + void settings(int, char **); + void coeff(int, char **); + void init_style(); + double init_one(int, int); + + virtual void kernel_force(double R, int itype, int jtype, + double& energy, double& fpair); + + struct Contact { + int ibody, jbody; // body (i.e. atom) indices (not tags) + int type; // 0 = VERTEX-FACE; 1 = EDGE-EDGE + double fx,fy,fz; // unscaled cohesive forces at contact + double xi[3]; // coordinates of the contact point on ibody + double xj[3]; // coordinates of the contact point on jbody + double separation; // contact surface separation + int unique; + }; + + protected: + double **k_n; // normal repulsion strength + double **k_na; // normal attraction strength + double c_n; // normal damping coefficient + double c_t; // tangential damping coefficient + double mu; // normal friction coefficient during gross sliding + double A_ua; // characteristic contact area + double cut_inner; // cutoff for interaction between vertex-edge surfaces + + class AtomVecBody *avec; + class BodyRoundedPolyhedron *bptr; + + double **discrete; // list of all sub-particles for all bodies + int ndiscrete; // number of discretes in list + int dmax; // allocated size of discrete list + int *dnum; // number of discretes per line, 0 if uninit + int *dfirst; // index of first discrete per each line + int nmax; // allocated size of dnum,dfirst vectors + + double **edge; // list of all edge for all bodies + int nedge; // number of edge in list + int edmax; // allocated size of edge list + int *ednum; // number of edges per line, 0 if uninit + int *edfirst; // index of first edge per each line + int ednummax; // allocated size of ednum,edfirst vectors + + double **face; // list of all edge for all bodies + int nface; // number of faces in list + int facmax; // allocated size of face list + int *facnum; // number of faces per line, 0 if uninit + int *facfirst; // index of first face per each line + int facnummax; // allocated size of facnum,facfirst vectors + + double *enclosing_radius; // enclosing radii for all bodies + double *rounded_radius; // rounded radii for all bodies + double *maxerad; // per-type maximum enclosing radius + + void allocate(); + void body2space(int); + + // sphere-sphere interaction + void sphere_against_sphere(int ibody, int jbody, int itype, int jtype, + double delx, double dely, double delz, double rsq, + double** v, double** f, int evflag); + // sphere-edge interaction + void sphere_against_edge(int ibody, int jbody, int itype, int jtype, + double** x, double** v, double** f, double** torque, + double** angmom, int evflag); + // sphere-face interaction + void sphere_against_face(int ibody, int jbody, int itype, int jtype, + double** x, double** v, double** f, double** torque, + double** angmom, int evflag); + // edge-edge interactions + int edge_against_edge(int ibody, int jbody, int itype, int jtype, + double** x,Contact* contact_list, int &num_contacts, + double &evdwl, double* facc); + // edge-face interactions + int edge_against_face(int ibody, int jbody, int itype, int jtype, + double** x, Contact* contact_list, int &num_contacts, + double &evdwl, double* facc); + + // a face vs. a single edge + int interaction_face_to_edge(int ibody, int face_index, double* xmi, + double rounded_radius_i, int jbody, int edge_index, + double* xmj, double rounded_radius_j, + int itype, int jtype, double cut_inner, + Contact* contact_list, int &num_contacts, + double& energy, double* facc); + // an edge vs. an edge from another body + int interaction_edge_to_edge(int ibody, int edge_index_i, double* xmi, + double rounded_radius_i, int jbody, int edge_index_j, + double* xmj, double rounded_radius_j, + int itype, int jtype, double cut_inner, + Contact* contact_list, int &num_contacts, + double& energy, double* facc); + + // compute contact forces if contact points are detected + void contact_forces(int ibody, int jbody, double *xi, double *xj, + double delx, double dely, double delz, double fx, double fy, double fz, + double** x, double** v, double** angmom, double** f, double** torque, + double* facc); + + // compute force and torque between two bodies given a pair of interacting points + void pair_force_and_torque(int ibody, int jbody, double* pi, double* pj, + double r, double contact_dist, int itype, int jtype, + double** x, double** v, double** f, double** torque, + double** angmom, int jflag, double& energy, double* facc); + + // rescale the cohesive forces if a contact area is detected + void rescale_cohesive_forces(double** x, double** f, double** torque, + Contact* contact_list, int &num_contacts, + int itype, int jtype, double* facc); + + // compute the separation between two contacts + double contact_separation(const Contact& c1, const Contact& c2); + + // detect the unique contact points (as there may be double counts) + void find_unique_contacts(Contact* contact_list, int& num_contacts); + + // accumulate torque to a body given a force at a given point + void sum_torque(double* xm, double *x, double fx, double fy, double fz, double* torque); + + // find the intersection point (if any) between an edge and a face + int edge_face_intersect(double* x1, double* x2, double* x3, double* a, double* b, + double* hi1, double* hi2, double& d1, double& d2, + int& inside_a, int& inside_b); + // helper functions + int opposite_sides(double* n, double* x0, double* a, double* b); + void project_pt_plane(const double* q, const double* p, + const double* n, double* q_proj, double &d); + void project_pt_plane(const double* q, const double* x1, const double* x2, + const double* x3, double* q_proj, double &d, int& inside); + void project_pt_line(const double* q, const double* xi1, const double* xi2, + double* h, double& d, double& t); + void inside_polygon(int ibody, int face_index, double* xmi, + const double* q1, const double* q2, int& inside1, int& inside2); + + void distance_bt_edges(const double* x1, const double* x2, + const double* x3, const double* x4, + double* h1, double* h2, double& t1, double& t2, double& r); + void total_velocity(double* p, double *xcm, double* vcm, double *angmom, + double *inertia, double *quat, double* vi); + void sanity_check(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Incorrect args for pair coefficients + +Self-explanatory. Check the input script or data file. + +E: Pair body/rounded/polyhedron requires atom style body rounded/polyhedron + +Self-explanatory. + +E: Pair body requires body style rounded/polyhedron + +This pair style is specific to the rounded/polyhedron body style. + +*/ diff --git a/src/CLASS2/bond_class2.cpp b/src/CLASS2/bond_class2.cpp index c3dc09715c..af20313e0a 100644 --- a/src/CLASS2/bond_class2.cpp +++ b/src/CLASS2/bond_class2.cpp @@ -209,7 +209,7 @@ void BondClass2::write_data(FILE *fp) /* ---------------------------------------------------------------------- */ -double BondClass2::single(int type, double rsq, int i, int j, double &fforce) +double BondClass2::single(int type, double rsq, int /*i*/, int /*j*/, double &fforce) { double r = sqrt(rsq); double dr = r - r0[type]; diff --git a/src/CLASS2/improper_class2.cpp b/src/CLASS2/improper_class2.cpp index 3b3811584d..77f594af9d 100644 --- a/src/CLASS2/improper_class2.cpp +++ b/src/CLASS2/improper_class2.cpp @@ -633,7 +633,7 @@ void ImproperClass2::read_restart(FILE *fp) angle-angle interactions within improper ------------------------------------------------------------------------- */ -void ImproperClass2::angleangle(int eflag, int vflag) +void ImproperClass2::angleangle(int eflag, int /*vflag*/) { int i1,i2,i3,i4,i,j,k,n,type; double eimproper; diff --git a/src/CLASS2/pair_lj_class2.cpp b/src/CLASS2/pair_lj_class2.cpp index e255807ab6..6451921dc5 100644 --- a/src/CLASS2/pair_lj_class2.cpp +++ b/src/CLASS2/pair_lj_class2.cpp @@ -377,8 +377,8 @@ void PairLJClass2::write_data_all(FILE *fp) /* ---------------------------------------------------------------------- */ -double PairLJClass2::single(int i, int j, int itype, int jtype, double rsq, - double factor_coul, double factor_lj, +double PairLJClass2::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq, + double /*factor_coul*/, double factor_lj, double &fforce) { double r2inv,rinv,r3inv,r6inv,forcelj,philj; diff --git a/src/COLLOID/pair_colloid.cpp b/src/COLLOID/pair_colloid.cpp index 4448d6e110..c16dbf41af 100644 --- a/src/COLLOID/pair_colloid.cpp +++ b/src/COLLOID/pair_colloid.cpp @@ -469,8 +469,8 @@ void PairColloid::write_data_all(FILE *fp) /* ---------------------------------------------------------------------- */ -double PairColloid::single(int i, int j, int itype, int jtype, double rsq, - double factor_coul, double factor_lj, +double PairColloid::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq, + double /*factor_coul*/, double factor_lj, double &fforce) { double K[9],h[4],g[4]; diff --git a/src/COLLOID/pair_lubricate.cpp b/src/COLLOID/pair_lubricate.cpp index f0f7ce8c14..de53d91818 100644 --- a/src/COLLOID/pair_lubricate.cpp +++ b/src/COLLOID/pair_lubricate.cpp @@ -749,7 +749,7 @@ void PairLubricate::read_restart_settings(FILE *fp) /* ---------------------------------------------------------------------- */ int PairLubricate::pack_forward_comm(int n, int *list, double *buf, - int pbc_flag, int *pbc) + int /*pbc_flag*/, int * /*pbc*/) { int i,j,m; @@ -797,7 +797,7 @@ void PairLubricate::unpack_forward_comm(int n, int first, double *buf) if type pair setting, return -2 if no type pairs are set ------------------------------------------------------------------------- */ -int PairLubricate::pre_adapt(char *name, int ilo, int ihi, int jlo, int jhi) +int PairLubricate::pre_adapt(char *name, int /*ilo*/, int /*ihi*/, int /*jlo*/, int /*jhi*/) { if (strcmp(name,"mu") == 0) return 0; return -1; @@ -809,7 +809,7 @@ int PairLubricate::pre_adapt(char *name, int ilo, int ihi, int jlo, int jhi) if type pair setting, set I-J and J-I coeffs ------------------------------------------------------------------------- */ -void PairLubricate::adapt(int which, int ilo, int ihi, int jlo, int jhi, +void PairLubricate::adapt(int /*which*/, int /*ilo*/, int /*ihi*/, int /*jlo*/, int /*jhi*/, double value) { mu = value; diff --git a/src/COLLOID/pair_lubricateU.cpp b/src/COLLOID/pair_lubricateU.cpp index 11fb213157..35fe33c84e 100644 --- a/src/COLLOID/pair_lubricateU.cpp +++ b/src/COLLOID/pair_lubricateU.cpp @@ -2010,7 +2010,7 @@ void PairLubricateU::copy_uo_vec(int inum, double **f, double **torque, /* ---------------------------------------------------------------------- */ int PairLubricateU::pack_forward_comm(int n, int *list, double *buf, - int pbc_flag, int *pbc) + int /*pbc_flag*/, int * /*pbc*/) { int i,j,m; diff --git a/src/COLLOID/pair_yukawa_colloid.cpp b/src/COLLOID/pair_yukawa_colloid.cpp index 5965fd3aa8..d21bc43524 100644 --- a/src/COLLOID/pair_yukawa_colloid.cpp +++ b/src/COLLOID/pair_yukawa_colloid.cpp @@ -160,9 +160,9 @@ double PairYukawaColloid::init_one(int i, int j) /* ---------------------------------------------------------------------- */ -double PairYukawaColloid::single(int i, int j, int itype, int jtype, +double PairYukawaColloid::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq, - double factor_coul, double factor_lj, + double /*factor_coul*/, double factor_lj, double &fforce) { double r,rinv,screening,forceyukawa,phi; diff --git a/src/GPU/gpu_extra.h b/src/GPU/gpu_extra.h index 56a4f15f1b..111d13c563 100644 --- a/src/GPU/gpu_extra.h +++ b/src/GPU/gpu_extra.h @@ -58,6 +58,9 @@ namespace GPU_EXTRA { else if (all_success == -11) error->all(FLERR, "Invalid custom OpenCL parameter string."); + else if (all_success == -12) + error->all(FLERR, + "Invalid OpenCL platform ID."); else error->all(FLERR,"Unknown error in GPU library"); } diff --git a/src/GRANULAR/fix_freeze.cpp b/src/GRANULAR/fix_freeze.cpp index 0f581be01c..73c1c9fc11 100644 --- a/src/GRANULAR/fix_freeze.cpp +++ b/src/GRANULAR/fix_freeze.cpp @@ -83,7 +83,7 @@ void FixFreeze::setup(int vflag) /* ---------------------------------------------------------------------- */ -void FixFreeze::post_force(int vflag) +void FixFreeze::post_force(int /*vflag*/) { double **f = atom->f; double **torque = atom->torque; @@ -110,7 +110,7 @@ void FixFreeze::post_force(int vflag) /* ---------------------------------------------------------------------- */ -void FixFreeze::post_force_respa(int vflag, int ilevel, int iloop) +void FixFreeze::post_force_respa(int vflag, int /*ilevel*/, int /*iloop*/) { post_force(vflag); } diff --git a/src/GRANULAR/fix_wall_gran.cpp b/src/GRANULAR/fix_wall_gran.cpp index 368ff99fb7..f0957423f9 100644 --- a/src/GRANULAR/fix_wall_gran.cpp +++ b/src/GRANULAR/fix_wall_gran.cpp @@ -302,7 +302,7 @@ void FixWallGran::setup(int vflag) /* ---------------------------------------------------------------------- */ -void FixWallGran::post_force(int vflag) +void FixWallGran::post_force(int /*vflag*/) { int i,j; double dx,dy,dz,del1,del2,delxy,delr,rsq,rwall,meff; @@ -446,7 +446,7 @@ void FixWallGran::post_force(int vflag) /* ---------------------------------------------------------------------- */ -void FixWallGran::post_force_respa(int vflag, int ilevel, int iloop) +void FixWallGran::post_force_respa(int vflag, int ilevel, int /*iloop*/) { if (ilevel == nlevels_respa-1) post_force(vflag); } @@ -1041,7 +1041,7 @@ void FixWallGran::grow_arrays(int nmax) copy values within local atom-based arrays ------------------------------------------------------------------------- */ -void FixWallGran::copy_arrays(int i, int j, int delflag) +void FixWallGran::copy_arrays(int i, int j, int /*delflag*/) { if (history) for (int m = 0; m < sheardim; m++) @@ -1136,7 +1136,7 @@ int FixWallGran::maxsize_restart() size of atom nlocal's restart data ------------------------------------------------------------------------- */ -int FixWallGran::size_restart(int nlocal) +int FixWallGran::size_restart(int /*nlocal*/) { if (!history) return 0; return 1 + sheardim; diff --git a/src/GRANULAR/fix_wall_gran_region.cpp b/src/GRANULAR/fix_wall_gran_region.cpp index 12fa25714c..4a6be5f3c9 100644 --- a/src/GRANULAR/fix_wall_gran_region.cpp +++ b/src/GRANULAR/fix_wall_gran_region.cpp @@ -130,7 +130,7 @@ void FixWallGranRegion::init() /* ---------------------------------------------------------------------- */ -void FixWallGranRegion::post_force(int vflag) +void FixWallGranRegion::post_force(int /*vflag*/) { int i,m,nc,iwall; double dx,dy,dz,rsq,meff; @@ -347,7 +347,7 @@ void FixWallGranRegion::grow_arrays(int nmax) copy values within local atom-based arrays ------------------------------------------------------------------------- */ -void FixWallGranRegion::copy_arrays(int i, int j, int delflag) +void FixWallGranRegion::copy_arrays(int i, int j, int /*delflag*/) { int m,n,iwall; diff --git a/src/GRANULAR/pair_gran_hertz_history.cpp b/src/GRANULAR/pair_gran_hertz_history.cpp index 9d4f5c1a9b..d1f3c7bbe1 100644 --- a/src/GRANULAR/pair_gran_hertz_history.cpp +++ b/src/GRANULAR/pair_gran_hertz_history.cpp @@ -306,9 +306,9 @@ void PairGranHertzHistory::settings(int narg, char **arg) /* ---------------------------------------------------------------------- */ -double PairGranHertzHistory::single(int i, int j, int itype, int jtype, +double PairGranHertzHistory::single(int i, int j, int /*itype*/, int /*jtype*/, double rsq, - double factor_coul, double factor_lj, + double /*factor_coul*/, double /*factor_lj*/, double &fforce) { double radi,radj,radsum; diff --git a/src/GRANULAR/pair_gran_hooke.cpp b/src/GRANULAR/pair_gran_hooke.cpp index 4937c2fe8b..5244396ead 100644 --- a/src/GRANULAR/pair_gran_hooke.cpp +++ b/src/GRANULAR/pair_gran_hooke.cpp @@ -219,8 +219,8 @@ void PairGranHooke::compute(int eflag, int vflag) /* ---------------------------------------------------------------------- */ -double PairGranHooke::single(int i, int j, int itype, int jtype, double rsq, - double factor_coul, double factor_lj, +double PairGranHooke::single(int i, int j, int /*itype*/, int /*jtype*/, double rsq, + double /*factor_coul*/, double /*factor_lj*/, double &fforce) { double radi,radj,radsum,r,rinv,rsqinv; diff --git a/src/GRANULAR/pair_gran_hooke_history.cpp b/src/GRANULAR/pair_gran_hooke_history.cpp index d70c7391e2..c014510fca 100644 --- a/src/GRANULAR/pair_gran_hooke_history.cpp +++ b/src/GRANULAR/pair_gran_hooke_history.cpp @@ -587,9 +587,9 @@ void PairGranHookeHistory::reset_dt() /* ---------------------------------------------------------------------- */ -double PairGranHookeHistory::single(int i, int j, int itype, int jtype, +double PairGranHookeHistory::single(int i, int j, int /*itype*/, int /*jtype*/, double rsq, - double factor_coul, double factor_lj, + double /*factor_coul*/, double /*factor_lj*/, double &fforce) { double radi,radj,radsum; @@ -746,7 +746,7 @@ double PairGranHookeHistory::single(int i, int j, int itype, int jtype, /* ---------------------------------------------------------------------- */ int PairGranHookeHistory::pack_forward_comm(int n, int *list, double *buf, - int pbc_flag, int *pbc) + int /*pbc_flag*/, int * /*pbc*/) { int i,j,m; diff --git a/src/KOKKOS/Install.sh b/src/KOKKOS/Install.sh index c6fab2a1b1..08c7468a49 100755 --- a/src/KOKKOS/Install.sh +++ b/src/KOKKOS/Install.sh @@ -93,6 +93,8 @@ action domain_kokkos.cpp action domain_kokkos.h action fix_deform_kokkos.cpp action fix_deform_kokkos.h +action fix_enforce2d_kokkos.cpp +action fix_enforce2d_kokkos.h action fix_eos_table_rx_kokkos.cpp fix_eos_table_rx.cpp action fix_eos_table_rx_kokkos.h fix_eos_table_rx.h action fix_langevin_kokkos.cpp diff --git a/src/KOKKOS/comm_kokkos.cpp b/src/KOKKOS/comm_kokkos.cpp index 96d1c64d0d..21840b7c3e 100644 --- a/src/KOKKOS/comm_kokkos.cpp +++ b/src/KOKKOS/comm_kokkos.cpp @@ -404,12 +404,30 @@ void CommKokkos::forward_comm_pair_device(Pair *pair) // if self, set recv buffer to send buffer if (sendproc[iswap] != me) { - if (recvnum[iswap]) - MPI_Irecv(k_buf_recv_pair.view().data(),nsize*recvnum[iswap],MPI_DOUBLE, + double* buf_send_pair; + double* buf_recv_pair; + if (lmp->kokkos->gpu_direct_flag) { + buf_send_pair = k_buf_send_pair.view().data(); + buf_recv_pair = k_buf_recv_pair.view().data(); + } else { + k_buf_send_pair.modify(); + k_buf_send_pair.sync(); + buf_send_pair = k_buf_send_pair.h_view.data(); + buf_recv_pair = k_buf_recv_pair.h_view.data(); + } + + if (recvnum[iswap]) { + MPI_Irecv(buf_recv_pair,nsize*recvnum[iswap],MPI_DOUBLE, recvproc[iswap],0,world,&request); + } if (sendnum[iswap]) - MPI_Send(k_buf_send_pair.view().data(),n,MPI_DOUBLE,sendproc[iswap],0,world); + MPI_Send(buf_send_pair,n,MPI_DOUBLE,sendproc[iswap],0,world); if (recvnum[iswap]) MPI_Wait(&request,MPI_STATUS_IGNORE); + + if (!lmp->kokkos->gpu_direct_flag) { + k_buf_recv_pair.modify(); + k_buf_recv_pair.sync(); + } } else k_buf_recv_pair = k_buf_send_pair; // unpack buffer diff --git a/src/KOKKOS/fix_enforce2d_kokkos.cpp b/src/KOKKOS/fix_enforce2d_kokkos.cpp new file mode 100644 index 0000000000..26075b269c --- /dev/null +++ b/src/KOKKOS/fix_enforce2d_kokkos.cpp @@ -0,0 +1,168 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing authors: Stefan Paquay & Matthew Peterson (Brandeis University) +------------------------------------------------------------------------- */ + +#include "atom_masks.h" +#include "atom_kokkos.h" +#include "comm.h" +#include "error.h" +#include "fix_enforce2d_kokkos.h" + + +using namespace LAMMPS_NS; + + +template +FixEnforce2DKokkos::FixEnforce2DKokkos(LAMMPS *lmp, int narg, char **arg) : + FixEnforce2D(lmp, narg, arg) +{ + kokkosable = 1; + atomKK = (AtomKokkos *) atom; + execution_space = ExecutionSpaceFromDevice::space; + + datamask_read = V_MASK | F_MASK | OMEGA_MASK | MASK_MASK + | TORQUE_MASK | ANGMOM_MASK; + + datamask_modify = V_MASK | F_MASK | OMEGA_MASK + | TORQUE_MASK | ANGMOM_MASK; +} + + +template +void FixEnforce2DKokkos::setup(int vflag) +{ + post_force(vflag); +} + + +template +void FixEnforce2DKokkos::post_force(int vflag) +{ + atomKK->sync(execution_space,datamask_read); + + v = atomKK->k_v.view(); + f = atomKK->k_f.view(); + + if( atomKK->omega_flag ) + omega = atomKK->k_omega.view(); + + if( atomKK->angmom_flag ) + angmom = atomKK->k_angmom.view(); + + if( atomKK->torque_flag ) + torque = atomKK->k_torque.view(); + + + mask = atomKK->k_mask.view(); + + int nlocal = atomKK->nlocal; + if (igroup == atomKK->firstgroup) nlocal = atomKK->nfirst; + + int flag_mask = 0; + if( atomKK->omega_flag ) flag_mask |= 1; + if( atomKK->angmom_flag ) flag_mask |= 2; + if( atomKK->torque_flag ) flag_mask |= 4; + + copymode = 1; + switch( flag_mask ){ + case 0:{ + FixEnforce2DKokkosPostForceFunctor functor(this); + Kokkos::parallel_for(nlocal,functor); + break; + } + case 1:{ + FixEnforce2DKokkosPostForceFunctor functor(this); + Kokkos::parallel_for(nlocal,functor); + break; + } + case 2:{ + FixEnforce2DKokkosPostForceFunctor functor(this); + Kokkos::parallel_for(nlocal,functor); + break; + } + case 3:{ + FixEnforce2DKokkosPostForceFunctor functor(this); + Kokkos::parallel_for(nlocal,functor); + break; + } + case 4:{ + FixEnforce2DKokkosPostForceFunctor functor(this); + Kokkos::parallel_for(nlocal,functor); + break; + } + case 5:{ + FixEnforce2DKokkosPostForceFunctor functor(this); + Kokkos::parallel_for(nlocal,functor); + break; + } + case 6:{ + FixEnforce2DKokkosPostForceFunctor functor(this); + Kokkos::parallel_for(nlocal,functor); + break; + } + case 7:{ + FixEnforce2DKokkosPostForceFunctor functor(this); + Kokkos::parallel_for(nlocal,functor); + break; + } + default: + error->all(FLERR, "Flag in fix_enforce2d_kokkos outside of what it should be"); + } + copymode = 0; + + atomKK->modified(execution_space,datamask_modify); + + for (int m = 0; m < nfixlist; m++) { + atomKK->sync(flist[m]->execution_space,flist[m]->datamask_read); + flist[m]->enforce2d(); + atomKK->modified(flist[m]->execution_space,flist[m]->datamask_modify); + } + +} + + +template +template +void FixEnforce2DKokkos::post_force_item( int i ) const +{ + if (mask[i] & groupbit){ + v(i,2) = 0.0; + f(i,2) = 0.0; + + if(omega_flag){ + omega(i,0) = 0.0; + omega(i,1) = 0.0; + } + + if(angmom_flag){ + angmom(i,0) = 0.0; + angmom(i,1) = 0.0; + } + + if(torque_flag){ + torque(i,0) = 0.0; + torque(i,1) = 0.0; + } + } +} + + +namespace LAMMPS_NS { +template class FixEnforce2DKokkos; +#ifdef KOKKOS_HAVE_CUDA +template class FixEnforce2DKokkos; +#endif +} diff --git a/src/KOKKOS/fix_enforce2d_kokkos.h b/src/KOKKOS/fix_enforce2d_kokkos.h new file mode 100644 index 0000000000..520a58de04 --- /dev/null +++ b/src/KOKKOS/fix_enforce2d_kokkos.h @@ -0,0 +1,84 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef FIX_CLASS + +FixStyle(enforce2d/kk,FixEnforce2DKokkos) +FixStyle(enforce2d/kk/device,FixEnforce2DKokkos) +FixStyle(enforce2d/kk/host,FixEnforce2DKokkos) + +#else + +#ifndef LMP_FIX_ENFORCE2D_KOKKOS_H +#define LMP_FIX_ENFORCE2D_KOKKOS_H + +#include "fix_enforce2d.h" +#include "kokkos_type.h" + +namespace LAMMPS_NS { + +template +class FixEnforce2DKokkos : public FixEnforce2D { + public: + FixEnforce2DKokkos(class LAMMPS *, int, char **); + // ~FixEnforce2DKokkos() {} + void setup(int); + void post_force(int); + + template + KOKKOS_INLINE_FUNCTION + void post_force_item(const int i) const; + + // void min_setup(int); Kokkos does not support minimization (yet) + // void min_post_force(int); Kokkos does not support minimization (yet) + // void post_force_respa(int, int, int); No RRESPA support yet. + + private: + typename ArrayTypes::t_v_array v; + typename ArrayTypes::t_f_array f; + + typename ArrayTypes::t_v_array omega; + typename ArrayTypes::t_v_array angmom; + typename ArrayTypes::t_f_array torque; + + typename ArrayTypes::t_int_1d mask; +}; + + +template +struct FixEnforce2DKokkosPostForceFunctor { + typedef DeviceType device_type; + FixEnforce2DKokkos c; + + FixEnforce2DKokkosPostForceFunctor(FixEnforce2DKokkos* c_ptr): + c(*c_ptr) {}; + + KOKKOS_INLINE_FUNCTION + void operator()(const int i) const { + c.template post_force_item (i); + } +}; + + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Flag in fix_enforce2d_kokkos outside of what it should be + +LAMMPS developer-only error. + +*/ diff --git a/src/KOKKOS/fix_nh_kokkos.cpp b/src/KOKKOS/fix_nh_kokkos.cpp index 679690ea82..347177b7f4 100644 --- a/src/KOKKOS/fix_nh_kokkos.cpp +++ b/src/KOKKOS/fix_nh_kokkos.cpp @@ -148,7 +148,7 @@ void FixNHKokkos::setup(int vflag) if (pstat_flag) { double kt = boltz * t_target; - double nkt = atom->natoms * kt; + double nkt = (atom->natoms + 1) * kt; for (int i = 0; i < 3; i++) if (p_flag[i]) diff --git a/src/KOKKOS/fix_qeq_reax_kokkos.cpp b/src/KOKKOS/fix_qeq_reax_kokkos.cpp index 52822856ee..578afd2077 100644 --- a/src/KOKKOS/fix_qeq_reax_kokkos.cpp +++ b/src/KOKKOS/fix_qeq_reax_kokkos.cpp @@ -247,6 +247,13 @@ void FixQEqReaxKokkos::pre_force(int vflag) k_t.template modify(); k_t.template sync(); + need_dup = lmp->kokkos->need_dup(); + + if (need_dup) + dup_o = Kokkos::Experimental::create_scatter_view (d_o); // allocate duplicated memory + else + ndup_o = Kokkos::Experimental::create_scatter_view (d_o); + // 1st cg solve over b_s, s cg_solve1(); @@ -262,6 +269,10 @@ void FixQEqReaxKokkos::pre_force(int vflag) if (!allocated_flag) allocated_flag = 1; + + // free duplicated memory + if (need_dup) + dup_o = decltype(dup_o)(); } /* ---------------------------------------------------------------------- */ @@ -480,10 +491,12 @@ void FixQEqReaxKokkos::cg_solve1() if (neighflag == HALF) { FixQEqReaxKokkosSparse13Functor sparse13_functor(this); Kokkos::parallel_for(inum,sparse13_functor); - } else { + } else if (neighflag == HALFTHREAD) { FixQEqReaxKokkosSparse13Functor sparse13_functor(this); Kokkos::parallel_for(inum,sparse13_functor); } + if (need_dup) + Kokkos::Experimental::contribute(d_o, dup_o); } else { Kokkos::parallel_for(Kokkos::TeamPolicy (inum, teamsize), *this); } @@ -531,18 +544,21 @@ void FixQEqReaxKokkos::cg_solve1() Kokkos::parallel_for(inum,sparse22_functor); if (neighflag != FULL) { Kokkos::parallel_for(Kokkos::RangePolicy(nlocal,nlocal+atom->nghost),*this); + if (need_dup) + dup_o.reset_except(d_o); if (neighflag == HALF) { FixQEqReaxKokkosSparse23Functor sparse23_functor(this); Kokkos::parallel_for(inum,sparse23_functor); - } else { + } else if (neighflag == HALFTHREAD) { FixQEqReaxKokkosSparse23Functor sparse23_functor(this); Kokkos::parallel_for(inum,sparse23_functor); } + if (need_dup) + Kokkos::Experimental::contribute(d_o, dup_o); } else { Kokkos::parallel_for(Kokkos::TeamPolicy (inum, teamsize), *this); } - if (neighflag != FULL) { k_o.template modify(); k_o.template sync(); @@ -607,13 +623,17 @@ void FixQEqReaxKokkos::cg_solve2() Kokkos::parallel_for(inum,sparse32_functor); if (neighflag != FULL) { Kokkos::parallel_for(Kokkos::RangePolicy(nlocal,nlocal+atom->nghost),*this); + if (need_dup) + dup_o.reset_except(d_o); if (neighflag == HALF) { FixQEqReaxKokkosSparse33Functor sparse33_functor(this); Kokkos::parallel_for(inum,sparse33_functor); - } else { + } else if (neighflag == HALFTHREAD) { FixQEqReaxKokkosSparse33Functor sparse33_functor(this); Kokkos::parallel_for(inum,sparse33_functor); } + if (need_dup) + Kokkos::Experimental::contribute(d_o, dup_o); } else { Kokkos::parallel_for(Kokkos::TeamPolicy (inum, teamsize), *this); } @@ -661,13 +681,17 @@ void FixQEqReaxKokkos::cg_solve2() Kokkos::parallel_for(inum,sparse22_functor); if (neighflag != FULL) { Kokkos::parallel_for(Kokkos::RangePolicy(nlocal,nlocal+atom->nghost),*this); + if (need_dup) + dup_o.reset_except(d_o); if (neighflag == HALF) { FixQEqReaxKokkosSparse23Functor sparse23_functor(this); Kokkos::parallel_for(inum,sparse23_functor); - } else { + } else if (neighflag == HALFTHREAD) { FixQEqReaxKokkosSparse23Functor sparse23_functor(this); Kokkos::parallel_for(inum,sparse23_functor); } + if (need_dup) + Kokkos::Experimental::contribute(d_o, dup_o); } else { Kokkos::parallel_for(Kokkos::TeamPolicy (inum, teamsize), *this); } @@ -779,8 +803,9 @@ template KOKKOS_INLINE_FUNCTION void FixQEqReaxKokkos::sparse13_item(int ii) const { - // The q array is atomic for Half/Thread neighbor style - Kokkos::View::value> > a_o = d_o; + // The q array is duplicated for OpenMP, atomic for CUDA, and neither for Serial + auto v_o = ScatterViewHelper::value,decltype(dup_o),decltype(ndup_o)>::get(dup_o,ndup_o); + auto a_o = v_o.template access::value>(); const int i = d_ilist[ii]; if (mask[i] & groupbit) { @@ -831,8 +856,9 @@ template KOKKOS_INLINE_FUNCTION void FixQEqReaxKokkos::sparse23_item(int ii) const { - // The q array is atomic for Half/Thread neighbor style - Kokkos::View::value> > a_o = d_o; + // The q array is duplicated for OpenMP, atomic for CUDA, and neither for Serial + auto v_o = ScatterViewHelper::value,decltype(dup_o),decltype(ndup_o)>::get(dup_o,ndup_o); + auto a_o = v_o.template access::value>(); const int i = d_ilist[ii]; if (mask[i] & groupbit) { @@ -890,8 +916,9 @@ template KOKKOS_INLINE_FUNCTION void FixQEqReaxKokkos::sparse33_item(int ii) const { - // The q array is atomic for Half/Thread neighbor style - Kokkos::View::value> > a_o = d_o; + // The q array is duplicated for OpenMP, atomic for CUDA, and neither for Serial + auto v_o = ScatterViewHelper::value,decltype(dup_o),decltype(ndup_o)>::get(dup_o,ndup_o); + auto a_o = v_o.template access::value>(); const int i = d_ilist[ii]; if (mask[i] & groupbit) { diff --git a/src/KOKKOS/fix_qeq_reax_kokkos.h b/src/KOKKOS/fix_qeq_reax_kokkos.h index 517b541f6f..23bb4f32ee 100644 --- a/src/KOKKOS/fix_qeq_reax_kokkos.h +++ b/src/KOKKOS/fix_qeq_reax_kokkos.h @@ -148,6 +148,7 @@ class FixQEqReaxKokkos : public FixQEqReax { private: int inum; int allocated_flag; + int need_dup; typedef Kokkos::DualView tdual_int_1d; Kokkos::DualView k_params; @@ -192,6 +193,9 @@ class FixQEqReaxKokkos : public FixQEqReax { HAT::t_ffloat_2d h_s_hist, h_t_hist; typename AT::t_ffloat_2d_randomread r_s_hist, r_t_hist; + Kokkos::Experimental::ScatterView dup_o; + Kokkos::Experimental::ScatterView ndup_o; + void init_shielding_k(); void init_hist(); void allocate_matrix(); diff --git a/src/KOKKOS/fix_shardlow_kokkos.cpp b/src/KOKKOS/fix_shardlow_kokkos.cpp index 70055bf8c9..99e51ebe38 100644 --- a/src/KOKKOS/fix_shardlow_kokkos.cpp +++ b/src/KOKKOS/fix_shardlow_kokkos.cpp @@ -157,7 +157,6 @@ void FixShardlowKokkos::init() k_pairDPDE->k_cutsq.template sync(); d_cutsq = k_pairDPDE->k_cutsq.template view(); - const double boltz2 = 2.0*force->boltz; for (int i = 1; i <= ntypes; i++) { for (int j = i; j <= ntypes; j++) { F_FLOAT cutone = k_pairDPDE->cut[i][j]; @@ -165,7 +164,7 @@ void FixShardlowKokkos::init() else k_params.h_view(i,j).cutinv = FLT_MAX; k_params.h_view(i,j).halfsigma = 0.5*k_pairDPDE->sigma[i][j]; k_params.h_view(i,j).kappa = k_pairDPDE->kappa[i][j]; - k_params.h_view(i,j).alpha = sqrt(boltz2*k_pairDPDE->kappa[i][j]); + k_params.h_view(i,j).alpha = k_pairDPDE->alpha[i][j]; k_params.h_view(j,i) = k_params.h_view(i,j); diff --git a/src/KOKKOS/gridcomm_kokkos.cpp b/src/KOKKOS/gridcomm_kokkos.cpp index 847fa5907a..64a9d6992f 100644 --- a/src/KOKKOS/gridcomm_kokkos.cpp +++ b/src/KOKKOS/gridcomm_kokkos.cpp @@ -18,6 +18,7 @@ #include "memory_kokkos.h" #include "error.h" #include "kokkos_base.h" +#include "kokkos.h" using namespace LAMMPS_NS; @@ -526,11 +527,28 @@ void GridCommKokkos::forward_comm(KSpace *kspace, int which) DeviceType::fence(); if (swap[m].sendproc != me) { - MPI_Irecv(k_buf2.view().data(),nforward*swap[m].nunpack,MPI_FFT_SCALAR, + FFT_SCALAR* buf1; + FFT_SCALAR* buf2; + if (lmp->kokkos->gpu_direct_flag) { + buf1 = k_buf1.view().data(); + buf2 = k_buf2.view().data(); + } else { + k_buf1.modify(); + k_buf1.sync(); + buf1 = k_buf1.h_view.data(); + buf2 = k_buf2.h_view.data(); + } + + MPI_Irecv(buf2,nforward*swap[m].nunpack,MPI_FFT_SCALAR, swap[m].recvproc,0,gridcomm,&request); - MPI_Send(k_buf1.view().data(),nforward*swap[m].npack,MPI_FFT_SCALAR, + MPI_Send(buf1,nforward*swap[m].npack,MPI_FFT_SCALAR, swap[m].sendproc,0,gridcomm); MPI_Wait(&request,MPI_STATUS_IGNORE); + + if (!lmp->kokkos->gpu_direct_flag) { + k_buf2.modify(); + k_buf2.sync(); + } } kspaceKKBase->unpack_forward_kspace_kokkos(which,k_buf2,swap[m].nunpack,k_unpacklist,m); @@ -559,11 +577,28 @@ void GridCommKokkos::reverse_comm(KSpace *kspace, int which) DeviceType::fence(); if (swap[m].recvproc != me) { - MPI_Irecv(k_buf2.view().data(),nreverse*swap[m].npack,MPI_FFT_SCALAR, + FFT_SCALAR* buf1; + FFT_SCALAR* buf2; + if (lmp->kokkos->gpu_direct_flag) { + buf1 = k_buf1.view().data(); + buf2 = k_buf2.view().data(); + } else { + k_buf1.modify(); + k_buf1.sync(); + buf1 = k_buf1.h_view.data(); + buf2 = k_buf2.h_view.data(); + } + + MPI_Irecv(buf2,nreverse*swap[m].npack,MPI_FFT_SCALAR, swap[m].sendproc,0,gridcomm,&request); - MPI_Send(k_buf1.view().data(),nreverse*swap[m].nunpack,MPI_FFT_SCALAR, + MPI_Send(buf1,nreverse*swap[m].nunpack,MPI_FFT_SCALAR, swap[m].recvproc,0,gridcomm); MPI_Wait(&request,MPI_STATUS_IGNORE); + + if (!lmp->kokkos->gpu_direct_flag) { + k_buf2.modify(); + k_buf2.sync(); + } } kspaceKKBase->unpack_reverse_kspace_kokkos(which,k_buf2,swap[m].npack,k_packlist,m); diff --git a/src/KOKKOS/kokkos.cpp b/src/KOKKOS/kokkos.cpp index 3bbff6be7e..9973b5a688 100644 --- a/src/KOKKOS/kokkos.cpp +++ b/src/KOKKOS/kokkos.cpp @@ -11,6 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include #include #include #include @@ -25,6 +26,37 @@ #include "error.h" #include "memory_kokkos.h" +#ifdef KOKKOS_HAVE_CUDA + +// for detecting GPU-direct support: +// the function int have_gpu_direct() +// - returns -1 if GPU-direct support is unknown +// - returns 0 if no GPU-direct support available +// - returns 1 if GPU-direct support is available + +#define GPU_DIRECT_UNKNOWN static int have_gpu_direct() {return -1;} + +// OpenMPI supports detecting GPU-direct as of version 2.0.0 +#if OPEN_MPI + +#if (OMPI_MAJOR_VERSION >= 2) +#include +#if defined(MPIX_CUDA_AWARE_SUPPORT) +static int have_gpu_direct() { return MPIX_Query_cuda_support(); } +#else +GPU_DIRECT_UNKNOWN +#endif + +#else // old OpenMPI +GPU_DIRECT_UNKNOWN +#endif + +#else // unknown MPI library +GPU_DIRECT_UNKNOWN +#endif + +#endif // KOKKOS_HAVE_CUDA + using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ @@ -106,13 +138,39 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) // initialize Kokkos if (me == 0) { - if (screen) fprintf(screen," using %d GPU(s)\n",ngpu); - if (logfile) fprintf(logfile," using %d GPU(s)\n",ngpu); + if (screen) fprintf(screen," will use up to %d GPU(s) per node\n",ngpu); + if (logfile) fprintf(logfile," will use up to %d GPU(s) per node\n",ngpu); } #ifdef KOKKOS_HAVE_CUDA if (ngpu <= 0) error->all(FLERR,"Kokkos has been compiled for CUDA but no GPUs are requested"); + + // check and warn about GPU-direct availability when using multiple MPI tasks + + int nmpi = 0; + MPI_Comm_size(world,&nmpi); + if ((nmpi > 1) && (me == 0)) { + if ( 1 == have_gpu_direct() ) { + ; // all good, nothing to warn about + } else if (-1 == have_gpu_direct() ) { + error->warning(FLERR,"Kokkos with CUDA assumes GPU-direct is available," + " but cannot determine if this is the case\n try" + " '-pk kokkos gpu/direct off' when getting segmentation faults"); + } else if ( 0 == have_gpu_direct() ) { + error->warning(FLERR,"GPU-direct is NOT available, " + "using '-pk kokkos gpu/direct off' by default"); + } else { + ; // should never get here + } + } +#endif + +#ifndef KOKKOS_HAVE_SERIAL + if (num_threads == 1) + error->warning(FLERR,"When using a single thread, the Kokkos Serial backend " + "(i.e. Makefile.kokkos_mpi_only) gives better performance " + "than the OpenMP backend"); #endif Kokkos::InitArguments args; @@ -133,6 +191,12 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) exchange_comm_on_host = 0; forward_comm_on_host = 0; reverse_comm_on_host = 0; + gpu_direct_flag = 1; + +#if KOKKOS_USE_CUDA + // only if we can safely detect, that GPU-direct is not available, change default + if (0 == have_gpu_direct()) gpu_direct_flag = 0; +#endif #ifdef KILL_KOKKOS_ON_SIGSEGV signal(SIGSEGV, my_signal_handler); @@ -163,6 +227,7 @@ void KokkosLMP::accelerator(int narg, char **arg) double binsize = 0.0; exchange_comm_classic = forward_comm_classic = reverse_comm_classic = 0; exchange_comm_on_host = forward_comm_on_host = reverse_comm_on_host = 0; + gpu_direct_flag = 1; int iarg = 0; while (iarg < narg) { @@ -204,6 +269,7 @@ void KokkosLMP::accelerator(int narg, char **arg) if (iarg+2 > narg) error->all(FLERR,"Illegal package kokkos command"); if (strcmp(arg[iarg+1],"no") == 0) { exchange_comm_classic = forward_comm_classic = reverse_comm_classic = 1; + exchange_comm_on_host = forward_comm_on_host = reverse_comm_on_host = 0; } else if (strcmp(arg[iarg+1],"host") == 0) { exchange_comm_classic = forward_comm_classic = reverse_comm_classic = 0; exchange_comm_on_host = forward_comm_on_host = reverse_comm_on_host = 1; @@ -245,9 +311,26 @@ void KokkosLMP::accelerator(int narg, char **arg) reverse_comm_on_host = 0; } else error->all(FLERR,"Illegal package kokkos command"); iarg += 2; + } else if (strcmp(arg[iarg],"gpu/direct") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal package kokkos command"); + if (strcmp(arg[iarg+1],"off") == 0) gpu_direct_flag = 0; + else if (strcmp(arg[iarg+1],"on") == 0) gpu_direct_flag = 1; + else error->all(FLERR,"Illegal package kokkos command"); + iarg += 2; } else error->all(FLERR,"Illegal package kokkos command"); } + // if "gpu/direct off" and "comm device", change to "comm host" + + if (!gpu_direct_flag) { + if (exchange_comm_classic == 0 && exchange_comm_on_host == 0) + exchange_comm_on_host = 1; + if (forward_comm_classic == 0 && forward_comm_on_host == 0) + forward_comm_on_host = 1; + if (reverse_comm_classic == 0 && reverse_comm_on_host == 0) + reverse_comm_on_host = 1; + } + // set newton flags // set neighbor binsize, same as neigh_modify command diff --git a/src/KOKKOS/kokkos.h b/src/KOKKOS/kokkos.h index 846b7254af..e1e17a425a 100644 --- a/src/KOKKOS/kokkos.h +++ b/src/KOKKOS/kokkos.h @@ -16,6 +16,7 @@ #include "pointers.h" #include "kokkos_type.h" +#include "pair_kokkos.h" namespace LAMMPS_NS { @@ -34,11 +35,24 @@ class KokkosLMP : protected Pointers { int num_threads,ngpu; int numa; int auto_sync; + int gpu_direct_flag; KokkosLMP(class LAMMPS *, int, char **); ~KokkosLMP(); void accelerator(int, char **); int neigh_count(int); + + template + int need_dup() + { + int value = 0; + + if (neighflag == HALFTHREAD) + value = NeedDup::value; + + return value; + } + private: static void my_signal_handler(int); }; diff --git a/src/KOKKOS/kokkos_type.h b/src/KOKKOS/kokkos_type.h index ddea35ca88..b88c92ff73 100644 --- a/src/KOKKOS/kokkos_type.h +++ b/src/KOKKOS/kokkos_type.h @@ -20,6 +20,9 @@ #include #include #include +#include + +enum{FULL=1u,HALFTHREAD=2u,HALF=4u,N2=8u}; #if defined(KOKKOS_HAVE_CXX11) #undef ISFINITE @@ -205,6 +208,100 @@ struct ExecutionSpaceFromDevice { }; #endif + +// Determine memory traits for force array +// Do atomic trait when running HALFTHREAD neighbor list style +template +struct AtomicF { + enum {value = Kokkos::Unmanaged}; +}; + +template<> +struct AtomicF { + enum {value = Kokkos::Atomic|Kokkos::Unmanaged}; +}; + + +// Determine memory traits for force array +// Do atomic trait when running HALFTHREAD neighbor list style with CUDA +template +struct AtomicDup { + enum {value = Kokkos::Experimental::ScatterNonAtomic}; +}; + +#ifdef KOKKOS_ENABLE_CUDA +template<> +struct AtomicDup { + enum {value = Kokkos::Experimental::ScatterAtomic}; +}; +#endif + +#ifdef LMP_KOKKOS_USE_ATOMICS + +#ifdef KOKKOS_ENABLE_OPENMP +template<> +struct AtomicDup { + enum {value = Kokkos::Experimental::ScatterAtomic}; +}; +#endif + +#ifdef KOKKOS_ENABLE_THREADS +template<> +struct AtomicDup { + enum {value = Kokkos::Experimental::ScatterAtomic}; +}; +#endif + +#endif + + +// Determine duplication traits for force array +// Use duplication when running threaded and not using atomics +template +struct NeedDup { + enum {value = Kokkos::Experimental::ScatterNonDuplicated}; +}; + +#ifndef LMP_KOKKOS_USE_ATOMICS + +#ifdef KOKKOS_ENABLE_OPENMP +template<> +struct NeedDup { + enum {value = Kokkos::Experimental::ScatterDuplicated}; +}; +#endif + +#ifdef KOKKOS_ENABLE_THREADS +template<> +struct NeedDup { + enum {value = Kokkos::Experimental::ScatterDuplicated}; +}; +#endif + +#endif + +template +class ScatterViewHelper {}; + +template +class ScatterViewHelper { +public: + KOKKOS_INLINE_FUNCTION + static T1 get(const T1 &dup, const T2 &nondup) { + return dup; + } +}; + +template +class ScatterViewHelper { +public: + KOKKOS_INLINE_FUNCTION + static T2 get(const T1 &dup, const T2 &nondup) { + return nondup; + } +}; + + // define precision // handle global precision, force, energy, positions, kspace separately diff --git a/src/KOKKOS/neigh_list_kokkos.h b/src/KOKKOS/neigh_list_kokkos.h index 1c433f321c..585422c54f 100644 --- a/src/KOKKOS/neigh_list_kokkos.h +++ b/src/KOKKOS/neigh_list_kokkos.h @@ -20,8 +20,6 @@ namespace LAMMPS_NS { -enum{FULL=1u,HALFTHREAD=2u,HALF=4u,N2=8u}; - class AtomNeighbors { public: diff --git a/src/KOKKOS/pair_dpd_fdt_energy_kokkos.cpp b/src/KOKKOS/pair_dpd_fdt_energy_kokkos.cpp index 7ff536f8dd..038d95394a 100644 --- a/src/KOKKOS/pair_dpd_fdt_energy_kokkos.cpp +++ b/src/KOKKOS/pair_dpd_fdt_energy_kokkos.cpp @@ -591,7 +591,7 @@ void PairDPDfdtEnergyKokkos::operator()(TagPairDPDfdtEnergyComputeNo // Compute uCond randnum = rand_gen.normal(); kappa_ij = STACKPARAMS?m_params[itype][jtype].kappa:params(itype,jtype).kappa; - alpha_ij = sqrt(2.0*boltz*kappa_ij); + alpha_ij = STACKPARAMS?m_params[itype][jtype].alpha:params(itype,jtype).alpha; randPair = alpha_ij*wr*randnum*dtinvsqrt; uTmp = kappa_ij*(1.0/dpdTheta[i] - 1.0/dpdTheta[j])*wd; @@ -676,6 +676,7 @@ double PairDPDfdtEnergyKokkos::init_one(int i, int j) k_params.h_view(i,j).a0 = a0[i][j]; k_params.h_view(i,j).sigma = sigma[i][j]; k_params.h_view(i,j).kappa = kappa[i][j]; + k_params.h_view(i,j).alpha = alpha[i][j]; k_params.h_view(j,i) = k_params.h_view(i,j); if(i::compute(int eflag_in, int vflag_in) x = atomKK->k_x.view(); f = atomKK->k_f.view(); - v_rho = k_rho.view(); type = atomKK->k_type.view(); tag = atomKK->k_tag.view(); nlocal = atom->nlocal; @@ -122,6 +121,19 @@ void PairEAMAlloyKokkos::compute(int eflag_in, int vflag_in) d_ilist = k_list->d_ilist; int inum = list->inum; + need_dup = lmp->kokkos->need_dup(); + if (need_dup) { + dup_rho = Kokkos::Experimental::create_scatter_view(d_rho); + dup_f = Kokkos::Experimental::create_scatter_view(f); + dup_eatom = Kokkos::Experimental::create_scatter_view(d_eatom); + dup_vatom = Kokkos::Experimental::create_scatter_view(d_vatom); + } else { + ndup_rho = Kokkos::Experimental::create_scatter_view(d_rho); + ndup_f = Kokkos::Experimental::create_scatter_view(f); + ndup_eatom = Kokkos::Experimental::create_scatter_view(d_eatom); + ndup_vatom = Kokkos::Experimental::create_scatter_view(d_vatom); + } + copymode = 1; // zero out density @@ -233,6 +245,9 @@ void PairEAMAlloyKokkos::compute(int eflag_in, int vflag_in) } } + if (need_dup) + Kokkos::Experimental::contribute(f, dup_f); + if (eflag_global) eng_vdwl += ev.evdwl; if (vflag_global) { virial[0] += ev.v[0]; @@ -244,11 +259,15 @@ void PairEAMAlloyKokkos::compute(int eflag_in, int vflag_in) } if (eflag_atom) { + if (need_dup) + Kokkos::Experimental::contribute(d_eatom, dup_eatom); k_eatom.template modify(); k_eatom.template sync(); } if (vflag_atom) { + if (need_dup) + Kokkos::Experimental::contribute(d_vatom, dup_vatom); k_vatom.template modify(); k_vatom.template sync(); } @@ -256,6 +275,14 @@ void PairEAMAlloyKokkos::compute(int eflag_in, int vflag_in) if (vflag_fdotr) pair_virial_fdotr_compute(this); copymode = 0; + + // free duplicated memory + if (need_dup) { + dup_rho = decltype(dup_rho)(); + dup_f = decltype(dup_f)(); + dup_eatom = decltype(dup_eatom)(); + dup_vatom = decltype(dup_vatom)(); + } } /* ---------------------------------------------------------------------- @@ -503,8 +530,10 @@ void PairEAMAlloyKokkos::operator()(TagPairEAMAlloyKernelA::value> > rho = v_rho; + // The rho array is duplicated for OpenMP, atomic for CUDA, and neither for Serial + + auto v_rho = ScatterViewHelper::value,decltype(dup_rho),decltype(ndup_rho)>::get(dup_rho,ndup_rho); + auto a_rho = v_rho.template access::value>(); const int i = d_ilist[ii]; const X_FLOAT xtmp = x(i,0); @@ -672,8 +701,10 @@ template KOKKOS_INLINE_FUNCTION void PairEAMAlloyKokkos::operator()(TagPairEAMAlloyKernelC, const int &ii, EV_FLOAT& ev) const { - // The f array is atomic for Half/Thread neighbor style - Kokkos::View::value> > a_f = f; + // The f array is duplicated for OpenMP, atomic for CUDA, and neither for Serial + + auto v_f = ScatterViewHelper::value,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f); + auto a_f = v_f.template access::value>(); const int i = d_ilist[ii]; const X_FLOAT xtmp = x(i,0); @@ -780,18 +811,22 @@ void PairEAMAlloyKokkos::ev_tally(EV_FLOAT &ev, const int &i, const const int EFLAG = eflag; const int VFLAG = vflag_either; - // The eatom and vatom arrays are atomic for Half/Thread neighbor style - Kokkos::View::value> > v_eatom = k_eatom.view(); - Kokkos::View::value> > v_vatom = k_vatom.view(); + // The eatom and vatom arrays are duplicated for OpenMP, atomic for CUDA, and neither for Serial + + auto v_eatom = ScatterViewHelper::value,decltype(dup_eatom),decltype(ndup_eatom)>::get(dup_eatom,ndup_eatom); + auto a_eatom = v_eatom.template access::value>(); + + auto v_vatom = ScatterViewHelper::value,decltype(dup_vatom),decltype(ndup_vatom)>::get(dup_vatom,ndup_vatom); + auto a_vatom = v_vatom.template access::value>(); if (EFLAG) { if (eflag_atom) { const E_FLOAT epairhalf = 0.5 * epair; if (NEIGHFLAG!=FULL) { - if (NEWTON_PAIR || i < nlocal) v_eatom[i] += epairhalf; - if (NEWTON_PAIR || j < nlocal) v_eatom[j] += epairhalf; + if (NEWTON_PAIR || i < nlocal) a_eatom[i] += epairhalf; + if (NEWTON_PAIR || j < nlocal) a_eatom[j] += epairhalf; } else { - v_eatom[i] += epairhalf; + a_eatom[i] += epairhalf; } } } @@ -835,28 +870,28 @@ void PairEAMAlloyKokkos::ev_tally(EV_FLOAT &ev, const int &i, const if (vflag_atom) { if (NEIGHFLAG!=FULL) { if (NEWTON_PAIR || i < nlocal) { - v_vatom(i,0) += 0.5*v0; - v_vatom(i,1) += 0.5*v1; - v_vatom(i,2) += 0.5*v2; - v_vatom(i,3) += 0.5*v3; - v_vatom(i,4) += 0.5*v4; - v_vatom(i,5) += 0.5*v5; + a_vatom(i,0) += 0.5*v0; + a_vatom(i,1) += 0.5*v1; + a_vatom(i,2) += 0.5*v2; + a_vatom(i,3) += 0.5*v3; + a_vatom(i,4) += 0.5*v4; + a_vatom(i,5) += 0.5*v5; } if (NEWTON_PAIR || j < nlocal) { - v_vatom(j,0) += 0.5*v0; - v_vatom(j,1) += 0.5*v1; - v_vatom(j,2) += 0.5*v2; - v_vatom(j,3) += 0.5*v3; - v_vatom(j,4) += 0.5*v4; - v_vatom(j,5) += 0.5*v5; + a_vatom(j,0) += 0.5*v0; + a_vatom(j,1) += 0.5*v1; + a_vatom(j,2) += 0.5*v2; + a_vatom(j,3) += 0.5*v3; + a_vatom(j,4) += 0.5*v4; + a_vatom(j,5) += 0.5*v5; } } else { - v_vatom(i,0) += 0.5*v0; - v_vatom(i,1) += 0.5*v1; - v_vatom(i,2) += 0.5*v2; - v_vatom(i,3) += 0.5*v3; - v_vatom(i,4) += 0.5*v4; - v_vatom(i,5) += 0.5*v5; + a_vatom(i,0) += 0.5*v0; + a_vatom(i,1) += 0.5*v1; + a_vatom(i,2) += 0.5*v2; + a_vatom(i,3) += 0.5*v3; + a_vatom(i,4) += 0.5*v4; + a_vatom(i,5) += 0.5*v5; } } } @@ -1165,4 +1200,3 @@ template class PairEAMAlloyKokkos; template class PairEAMAlloyKokkos; #endif } - diff --git a/src/KOKKOS/pair_eam_alloy_kokkos.h b/src/KOKKOS/pair_eam_alloy_kokkos.h index 5848399672..6593ccae73 100644 --- a/src/KOKKOS/pair_eam_alloy_kokkos.h +++ b/src/KOKKOS/pair_eam_alloy_kokkos.h @@ -129,10 +129,19 @@ class PairEAMAlloyKokkos : public PairEAM, public KokkosBase { typename ArrayTypes::t_efloat_1d d_eatom; typename ArrayTypes::t_virial_array d_vatom; + int need_dup; + Kokkos::Experimental::ScatterView dup_rho; + Kokkos::Experimental::ScatterView dup_f; + Kokkos::Experimental::ScatterView dup_eatom; + Kokkos::Experimental::ScatterView dup_vatom; + Kokkos::Experimental::ScatterView ndup_rho; + Kokkos::Experimental::ScatterView ndup_f; + Kokkos::Experimental::ScatterView ndup_eatom; + Kokkos::Experimental::ScatterView ndup_vatom; + DAT::tdual_ffloat_1d k_rho; DAT::tdual_ffloat_1d k_fp; typename AT::t_ffloat_1d d_rho; - typename AT::t_ffloat_1d v_rho; typename AT::t_ffloat_1d d_fp; HAT::t_ffloat_1d h_rho; HAT::t_ffloat_1d h_fp; diff --git a/src/KOKKOS/pair_eam_fs_kokkos.cpp b/src/KOKKOS/pair_eam_fs_kokkos.cpp index 627b56b84a..8f5571bf29 100644 --- a/src/KOKKOS/pair_eam_fs_kokkos.cpp +++ b/src/KOKKOS/pair_eam_fs_kokkos.cpp @@ -109,7 +109,6 @@ void PairEAMFSKokkos::compute(int eflag_in, int vflag_in) x = atomKK->k_x.view(); f = atomKK->k_f.view(); - v_rho = k_rho.view(); type = atomKK->k_type.view(); tag = atomKK->k_tag.view(); nlocal = atom->nlocal; @@ -122,6 +121,19 @@ void PairEAMFSKokkos::compute(int eflag_in, int vflag_in) d_ilist = k_list->d_ilist; int inum = list->inum; + need_dup = lmp->kokkos->need_dup(); + if (need_dup) { + dup_rho = Kokkos::Experimental::create_scatter_view(d_rho); + dup_f = Kokkos::Experimental::create_scatter_view(f); + dup_eatom = Kokkos::Experimental::create_scatter_view(d_eatom); + dup_vatom = Kokkos::Experimental::create_scatter_view(d_vatom); + } else { + ndup_rho = Kokkos::Experimental::create_scatter_view(d_rho); + ndup_f = Kokkos::Experimental::create_scatter_view(f); + ndup_eatom = Kokkos::Experimental::create_scatter_view(d_eatom); + ndup_vatom = Kokkos::Experimental::create_scatter_view(d_vatom); + } + copymode = 1; // zero out density @@ -233,6 +245,9 @@ void PairEAMFSKokkos::compute(int eflag_in, int vflag_in) } } + if (need_dup) + Kokkos::Experimental::contribute(f, dup_f); + if (eflag_global) eng_vdwl += ev.evdwl; if (vflag_global) { virial[0] += ev.v[0]; @@ -246,16 +261,28 @@ void PairEAMFSKokkos::compute(int eflag_in, int vflag_in) if (vflag_fdotr) pair_virial_fdotr_compute(this); if (eflag_atom) { + if (need_dup) + Kokkos::Experimental::contribute(d_eatom, dup_eatom); k_eatom.template modify(); k_eatom.template sync(); } if (vflag_atom) { + if (need_dup) + Kokkos::Experimental::contribute(d_vatom, dup_vatom); k_vatom.template modify(); k_vatom.template sync(); } copymode = 0; + + // free duplicated memory + if (need_dup) { + dup_rho = decltype(dup_rho)(); + dup_f = decltype(dup_f)(); + dup_eatom = decltype(dup_eatom)(); + dup_vatom = decltype(dup_vatom)(); + } } /* ---------------------------------------------------------------------- @@ -503,8 +530,10 @@ void PairEAMFSKokkos::operator()(TagPairEAMFSKernelA::value> > rho = v_rho; + // The rho array is duplicated for OpenMP, atomic for CUDA, and neither for Serial + + auto v_rho = ScatterViewHelper::value,decltype(dup_rho),decltype(ndup_rho)>::get(dup_rho,ndup_rho); + auto a_rho = v_rho.template access::value>(); const int i = d_ilist[ii]; const X_FLOAT xtmp = x(i,0); @@ -672,8 +701,10 @@ template KOKKOS_INLINE_FUNCTION void PairEAMFSKokkos::operator()(TagPairEAMFSKernelC, const int &ii, EV_FLOAT& ev) const { - // The f array is atomic for Half/Thread neighbor style - Kokkos::View::value> > a_f = f; + // The f array is duplicated for OpenMP, atomic for CUDA, and neither for Serial + + auto v_f = ScatterViewHelper::value,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f); + auto a_f = v_f.template access::value>(); const int i = d_ilist[ii]; const X_FLOAT xtmp = x(i,0); @@ -780,18 +811,22 @@ void PairEAMFSKokkos::ev_tally(EV_FLOAT &ev, const int &i, const int const int EFLAG = eflag; const int VFLAG = vflag_either; - // The eatom and vatom arrays are atomic for Half/Thread neighbor style - Kokkos::View::value> > v_eatom = k_eatom.view(); - Kokkos::View::value> > v_vatom = k_vatom.view(); + // The eatom and vatom arrays are duplicated for OpenMP, atomic for CUDA, and neither for Serial + + auto v_eatom = ScatterViewHelper::value,decltype(dup_eatom),decltype(ndup_eatom)>::get(dup_eatom,ndup_eatom); + auto a_eatom = v_eatom.template access::value>(); + + auto v_vatom = ScatterViewHelper::value,decltype(dup_vatom),decltype(ndup_vatom)>::get(dup_vatom,ndup_vatom); + auto a_vatom = v_vatom.template access::value>(); if (EFLAG) { if (eflag_atom) { const E_FLOAT epairhalf = 0.5 * epair; if (NEIGHFLAG!=FULL) { - if (NEWTON_PAIR || i < nlocal) v_eatom[i] += epairhalf; - if (NEWTON_PAIR || j < nlocal) v_eatom[j] += epairhalf; + if (NEWTON_PAIR || i < nlocal) a_eatom[i] += epairhalf; + if (NEWTON_PAIR || j < nlocal) a_eatom[j] += epairhalf; } else { - v_eatom[i] += epairhalf; + a_eatom[i] += epairhalf; } } } @@ -835,28 +870,28 @@ void PairEAMFSKokkos::ev_tally(EV_FLOAT &ev, const int &i, const int if (vflag_atom) { if (NEIGHFLAG!=FULL) { if (NEWTON_PAIR || i < nlocal) { - v_vatom(i,0) += 0.5*v0; - v_vatom(i,1) += 0.5*v1; - v_vatom(i,2) += 0.5*v2; - v_vatom(i,3) += 0.5*v3; - v_vatom(i,4) += 0.5*v4; - v_vatom(i,5) += 0.5*v5; + a_vatom(i,0) += 0.5*v0; + a_vatom(i,1) += 0.5*v1; + a_vatom(i,2) += 0.5*v2; + a_vatom(i,3) += 0.5*v3; + a_vatom(i,4) += 0.5*v4; + a_vatom(i,5) += 0.5*v5; } if (NEWTON_PAIR || j < nlocal) { - v_vatom(j,0) += 0.5*v0; - v_vatom(j,1) += 0.5*v1; - v_vatom(j,2) += 0.5*v2; - v_vatom(j,3) += 0.5*v3; - v_vatom(j,4) += 0.5*v4; - v_vatom(j,5) += 0.5*v5; + a_vatom(j,0) += 0.5*v0; + a_vatom(j,1) += 0.5*v1; + a_vatom(j,2) += 0.5*v2; + a_vatom(j,3) += 0.5*v3; + a_vatom(j,4) += 0.5*v4; + a_vatom(j,5) += 0.5*v5; } } else { - v_vatom(i,0) += 0.5*v0; - v_vatom(i,1) += 0.5*v1; - v_vatom(i,2) += 0.5*v2; - v_vatom(i,3) += 0.5*v3; - v_vatom(i,4) += 0.5*v4; - v_vatom(i,5) += 0.5*v5; + a_vatom(i,0) += 0.5*v0; + a_vatom(i,1) += 0.5*v1; + a_vatom(i,2) += 0.5*v2; + a_vatom(i,3) += 0.5*v3; + a_vatom(i,4) += 0.5*v4; + a_vatom(i,5) += 0.5*v5; } } } @@ -1174,4 +1209,3 @@ template class PairEAMFSKokkos; template class PairEAMFSKokkos; #endif } - diff --git a/src/KOKKOS/pair_eam_fs_kokkos.h b/src/KOKKOS/pair_eam_fs_kokkos.h index ce0b572ea2..f75605ff6d 100644 --- a/src/KOKKOS/pair_eam_fs_kokkos.h +++ b/src/KOKKOS/pair_eam_fs_kokkos.h @@ -129,10 +129,19 @@ class PairEAMFSKokkos : public PairEAM, public KokkosBase { typename ArrayTypes::t_efloat_1d d_eatom; typename ArrayTypes::t_virial_array d_vatom; + int need_dup; + Kokkos::Experimental::ScatterView dup_rho; + Kokkos::Experimental::ScatterView dup_f; + Kokkos::Experimental::ScatterView dup_eatom; + Kokkos::Experimental::ScatterView dup_vatom; + Kokkos::Experimental::ScatterView ndup_rho; + Kokkos::Experimental::ScatterView ndup_f; + Kokkos::Experimental::ScatterView ndup_eatom; + Kokkos::Experimental::ScatterView ndup_vatom; + DAT::tdual_ffloat_1d k_rho; DAT::tdual_ffloat_1d k_fp; typename AT::t_ffloat_1d d_rho; - typename AT::t_ffloat_1d v_rho; typename AT::t_ffloat_1d d_fp; HAT::t_ffloat_1d h_rho; HAT::t_ffloat_1d h_fp; diff --git a/src/KOKKOS/pair_eam_kokkos.cpp b/src/KOKKOS/pair_eam_kokkos.cpp index 1bfb8255dc..a1431334b4 100644 --- a/src/KOKKOS/pair_eam_kokkos.cpp +++ b/src/KOKKOS/pair_eam_kokkos.cpp @@ -34,7 +34,6 @@ using namespace LAMMPS_NS; - /* ---------------------------------------------------------------------- */ template @@ -104,7 +103,6 @@ void PairEAMKokkos::compute(int eflag_in, int vflag_in) x = atomKK->k_x.view(); f = atomKK->k_f.view(); - v_rho = k_rho.view(); type = atomKK->k_type.view(); tag = atomKK->k_tag.view(); nlocal = atom->nlocal; @@ -117,6 +115,19 @@ void PairEAMKokkos::compute(int eflag_in, int vflag_in) d_ilist = k_list->d_ilist; int inum = list->inum; + need_dup = lmp->kokkos->need_dup(); + if (need_dup) { + dup_rho = Kokkos::Experimental::create_scatter_view(d_rho); + dup_f = Kokkos::Experimental::create_scatter_view(f); + dup_eatom = Kokkos::Experimental::create_scatter_view(d_eatom); + dup_vatom = Kokkos::Experimental::create_scatter_view(d_vatom); + } else { + ndup_rho = Kokkos::Experimental::create_scatter_view(d_rho); + ndup_f = Kokkos::Experimental::create_scatter_view(f); + ndup_eatom = Kokkos::Experimental::create_scatter_view(d_eatom); + ndup_vatom = Kokkos::Experimental::create_scatter_view(d_vatom); + } + copymode = 1; // zero out density @@ -228,6 +239,9 @@ void PairEAMKokkos::compute(int eflag_in, int vflag_in) } } + if (need_dup) + Kokkos::Experimental::contribute(f, dup_f); + if (eflag_global) eng_vdwl += ev.evdwl; if (vflag_global) { virial[0] += ev.v[0]; @@ -241,16 +255,28 @@ void PairEAMKokkos::compute(int eflag_in, int vflag_in) if (vflag_fdotr) pair_virial_fdotr_compute(this); if (eflag_atom) { + if (need_dup) + Kokkos::Experimental::contribute(d_eatom, dup_eatom); k_eatom.template modify(); k_eatom.template sync(); } if (vflag_atom) { + if (need_dup) + Kokkos::Experimental::contribute(d_vatom, dup_vatom); k_vatom.template modify(); k_vatom.template sync(); } copymode = 0; + + // free duplicated memory + if (need_dup) { + dup_rho = decltype(dup_rho)(); + dup_f = decltype(dup_f)(); + dup_eatom = decltype(dup_eatom)(); + dup_vatom = decltype(dup_vatom)(); + } } /* ---------------------------------------------------------------------- @@ -503,8 +529,10 @@ void PairEAMKokkos::operator()(TagPairEAMKernelA::value> > rho = v_rho; + // The rho array is duplicated for OpenMP, atomic for CUDA, and neither for Serial + + auto v_rho = ScatterViewHelper::value,decltype(dup_rho),decltype(ndup_rho)>::get(dup_rho,ndup_rho); + auto a_rho = v_rho.template access::value>(); const int i = d_ilist[ii]; const X_FLOAT xtmp = x(i,0); @@ -538,13 +566,13 @@ void PairEAMKokkos::operator()(TagPairEAMKernelA KOKKOS_INLINE_FUNCTION void PairEAMKokkos::operator()(TagPairEAMKernelC, const int &ii, EV_FLOAT& ev) const { - // The f array is atomic for Half/Thread neighbor style - Kokkos::View::value> > a_f = f; + // The f array is duplicated for OpenMP, atomic for CUDA, and neither for Serial + + auto v_f = ScatterViewHelper::value,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f); + auto a_f = v_f.template access::value>(); const int i = d_ilist[ii]; const X_FLOAT xtmp = x(i,0); @@ -778,18 +808,22 @@ void PairEAMKokkos::ev_tally(EV_FLOAT &ev, const int &i, const int & const int EFLAG = eflag; const int VFLAG = vflag_either; - // The eatom and vatom arrays are atomic for Half/Thread neighbor style - Kokkos::View::value> > v_eatom = k_eatom.view(); - Kokkos::View::value> > v_vatom = k_vatom.view(); + // The eatom and vatom arrays are duplicated for OpenMP, atomic for CUDA, and neither for Serial + + auto v_eatom = ScatterViewHelper::value,decltype(dup_eatom),decltype(ndup_eatom)>::get(dup_eatom,ndup_eatom); + auto a_eatom = v_eatom.template access::value>(); + + auto v_vatom = ScatterViewHelper::value,decltype(dup_vatom),decltype(ndup_vatom)>::get(dup_vatom,ndup_vatom); + auto a_vatom = v_vatom.template access::value>(); if (EFLAG) { if (eflag_atom) { const E_FLOAT epairhalf = 0.5 * epair; if (NEIGHFLAG!=FULL) { - if (NEWTON_PAIR || i < nlocal) v_eatom[i] += epairhalf; - if (NEWTON_PAIR || j < nlocal) v_eatom[j] += epairhalf; + if (NEWTON_PAIR || i < nlocal) a_eatom[i] += epairhalf; + if (NEWTON_PAIR || j < nlocal) a_eatom[j] += epairhalf; } else { - v_eatom[i] += epairhalf; + a_eatom[i] += epairhalf; } } } @@ -833,28 +867,28 @@ void PairEAMKokkos::ev_tally(EV_FLOAT &ev, const int &i, const int & if (vflag_atom) { if (NEIGHFLAG!=FULL) { if (NEWTON_PAIR || i < nlocal) { - v_vatom(i,0) += 0.5*v0; - v_vatom(i,1) += 0.5*v1; - v_vatom(i,2) += 0.5*v2; - v_vatom(i,3) += 0.5*v3; - v_vatom(i,4) += 0.5*v4; - v_vatom(i,5) += 0.5*v5; + a_vatom(i,0) += 0.5*v0; + a_vatom(i,1) += 0.5*v1; + a_vatom(i,2) += 0.5*v2; + a_vatom(i,3) += 0.5*v3; + a_vatom(i,4) += 0.5*v4; + a_vatom(i,5) += 0.5*v5; } if (NEWTON_PAIR || j < nlocal) { - v_vatom(j,0) += 0.5*v0; - v_vatom(j,1) += 0.5*v1; - v_vatom(j,2) += 0.5*v2; - v_vatom(j,3) += 0.5*v3; - v_vatom(j,4) += 0.5*v4; - v_vatom(j,5) += 0.5*v5; + a_vatom(j,0) += 0.5*v0; + a_vatom(j,1) += 0.5*v1; + a_vatom(j,2) += 0.5*v2; + a_vatom(j,3) += 0.5*v3; + a_vatom(j,4) += 0.5*v4; + a_vatom(j,5) += 0.5*v5; } } else { - v_vatom(i,0) += 0.5*v0; - v_vatom(i,1) += 0.5*v1; - v_vatom(i,2) += 0.5*v2; - v_vatom(i,3) += 0.5*v3; - v_vatom(i,4) += 0.5*v4; - v_vatom(i,5) += 0.5*v5; + a_vatom(i,0) += 0.5*v0; + a_vatom(i,1) += 0.5*v1; + a_vatom(i,2) += 0.5*v2; + a_vatom(i,3) += 0.5*v3; + a_vatom(i,4) += 0.5*v4; + a_vatom(i,5) += 0.5*v5; } } } diff --git a/src/KOKKOS/pair_eam_kokkos.h b/src/KOKKOS/pair_eam_kokkos.h index c821750da5..4040eba858 100644 --- a/src/KOKKOS/pair_eam_kokkos.h +++ b/src/KOKKOS/pair_eam_kokkos.h @@ -126,10 +126,19 @@ class PairEAMKokkos : public PairEAM, public KokkosBase { typename ArrayTypes::t_efloat_1d d_eatom; typename ArrayTypes::t_virial_array d_vatom; + int need_dup; + Kokkos::Experimental::ScatterView dup_rho; + Kokkos::Experimental::ScatterView dup_f; + Kokkos::Experimental::ScatterView dup_eatom; + Kokkos::Experimental::ScatterView dup_vatom; + Kokkos::Experimental::ScatterView ndup_rho; + Kokkos::Experimental::ScatterView ndup_f; + Kokkos::Experimental::ScatterView ndup_eatom; + Kokkos::Experimental::ScatterView ndup_vatom; + DAT::tdual_ffloat_1d k_rho; DAT::tdual_ffloat_1d k_fp; typename AT::t_ffloat_1d d_rho; - typename AT::t_ffloat_1d v_rho; typename AT::t_ffloat_1d d_fp; HAT::t_ffloat_1d h_rho; HAT::t_ffloat_1d h_fp; diff --git a/src/KOKKOS/pair_kokkos.h b/src/KOKKOS/pair_kokkos.h index 6257566ba7..ab616d2c07 100644 --- a/src/KOKKOS/pair_kokkos.h +++ b/src/KOKKOS/pair_kokkos.h @@ -23,6 +23,7 @@ #include "neighbor_kokkos.h" #include "neigh_list_kokkos.h" #include "Kokkos_Vectorization.hpp" +#include "Kokkos_ScatterView.hpp" namespace LAMMPS_NS { @@ -47,45 +48,48 @@ struct DoCoul<1> { typedef CoulTag type; }; -// Determine memory traits for force array -// Do atomic trait when running HALFTHREAD neighbor list style -template -struct AtomicF { - enum {value = Kokkos::Unmanaged}; -}; - -template<> -struct AtomicF { - enum {value = Kokkos::Atomic|Kokkos::Unmanaged}; -}; //Specialisation for Neighborlist types Half, HalfThread, Full template struct PairComputeFunctor { typedef typename PairStyle::device_type device_type ; + typedef ArrayTypes AT; // Reduction type, contains evdwl, ecoul and virial[6] typedef EV_FLOAT value_type; // The copy of the pair style PairStyle c; + typename AT::t_f_array f; + typename AT::t_efloat_1d d_eatom; + typename AT::t_virial_array d_vatom; // The force array is atomic for Half/Thread neighbor style - Kokkos::View::value> > f; + //Kokkos::View::value> > f; + Kokkos::Experimental::ScatterView::value > dup_f; // The eatom and vatom arrays are atomic for Half/Thread neighbor style - Kokkos::View::value> > eatom; - Kokkos::View::value> > vatom; + //Kokkos::View::value> > eatom; + Kokkos::Experimental::ScatterView::value > dup_eatom; + + //Kokkos::View::value> > vatom; + Kokkos::Experimental::ScatterView::value > dup_vatom; + + NeighListKokkos list; PairComputeFunctor(PairStyle* c_ptr, NeighListKokkos* list_ptr): - c(*c_ptr),f(c.f),eatom(c.d_eatom), - vatom(c.d_vatom),list(*list_ptr) {}; + c(*c_ptr),list(*list_ptr) { + // allocate duplicated memory + dup_f = Kokkos::Experimental::create_scatter_view::value >(c.f); + dup_eatom = Kokkos::Experimental::create_scatter_view::value >(c.d_eatom); + dup_vatom = Kokkos::Experimental::create_scatter_view::value >(c.d_vatom); + }; // Call cleanup_copy which sets allocations NULL which are destructed by the PairStyle ~PairComputeFunctor() {c.cleanup_copy();list.copymode = 1;}; @@ -94,12 +98,25 @@ struct PairComputeFunctor { return j >> SBBITS & 3; } + void contribute() { + Kokkos::Experimental::contribute(c.f, dup_f); + + if (c.eflag_atom) + Kokkos::Experimental::contribute(c.d_eatom, dup_eatom); + + if (c.vflag_atom) + Kokkos::Experimental::contribute(c.d_vatom, dup_vatom); + } + // Loop over neighbors of one atom without coulomb interaction // This function is called in parallel template KOKKOS_FUNCTION EV_FLOAT compute_item(const int& ii, const NeighListKokkos &list, const NoCoulTag&) const { + + auto a_f = dup_f.template access::value>(); + EV_FLOAT ev; const int i = list.d_ilist[ii]; const X_FLOAT xtmp = c.x(i,0); @@ -133,9 +150,9 @@ struct PairComputeFunctor { fztmp += delz*fpair; if ((NEIGHFLAG==HALF || NEIGHFLAG==HALFTHREAD) && (NEWTON_PAIR || j < c.nlocal)) { - f(j,0) -= delx*fpair; - f(j,1) -= dely*fpair; - f(j,2) -= delz*fpair; + a_f(j,0) -= delx*fpair; + a_f(j,1) -= dely*fpair; + a_f(j,2) -= delz*fpair; } if (EVFLAG) { @@ -151,9 +168,9 @@ struct PairComputeFunctor { } - f(i,0) += fxtmp; - f(i,1) += fytmp; - f(i,2) += fztmp; + a_f(i,0) += fxtmp; + a_f(i,1) += fytmp; + a_f(i,2) += fztmp; return ev; } @@ -164,6 +181,9 @@ struct PairComputeFunctor { KOKKOS_FUNCTION EV_FLOAT compute_item(const int& ii, const NeighListKokkos &list, const CoulTag& ) const { + + auto a_f = dup_f.template access::value>(); + EV_FLOAT ev; const int i = list.d_ilist[ii]; const X_FLOAT xtmp = c.x(i,0); @@ -204,9 +224,9 @@ struct PairComputeFunctor { fztmp += delz*fpair; if ((NEIGHFLAG==HALF || NEIGHFLAG==HALFTHREAD) && (NEWTON_PAIR || j < c.nlocal)) { - f(j,0) -= delx*fpair; - f(j,1) -= dely*fpair; - f(j,2) -= delz*fpair; + a_f(j,0) -= delx*fpair; + a_f(j,1) -= dely*fpair; + a_f(j,2) -= delz*fpair; } if (EVFLAG) { @@ -228,9 +248,9 @@ struct PairComputeFunctor { } } - f(i,0) += fxtmp; - f(i,1) += fytmp; - f(i,2) += fztmp; + a_f(i,0) += fxtmp; + a_f(i,1) += fytmp; + a_f(i,2) += fztmp; return ev; } @@ -240,6 +260,9 @@ struct PairComputeFunctor { const F_FLOAT &epair, const F_FLOAT &fpair, const F_FLOAT &delx, const F_FLOAT &dely, const F_FLOAT &delz) const { + auto a_eatom = dup_eatom.template access::value>(); + auto a_vatom = dup_vatom.template access::value>(); + const int EFLAG = c.eflag; const int NEWTON_PAIR = c.newton_pair; const int VFLAG = c.vflag_either; @@ -247,8 +270,8 @@ struct PairComputeFunctor { if (EFLAG) { if (c.eflag_atom) { const E_FLOAT epairhalf = 0.5 * epair; - if (NEWTON_PAIR || i < c.nlocal) eatom[i] += epairhalf; - if ((NEWTON_PAIR || j < c.nlocal) && NEIGHFLAG != FULL) eatom[j] += epairhalf; + if (NEWTON_PAIR || i < c.nlocal) a_eatom[i] += epairhalf; + if ((NEWTON_PAIR || j < c.nlocal) && NEIGHFLAG != FULL) a_eatom[j] += epairhalf; } } @@ -299,20 +322,20 @@ struct PairComputeFunctor { if (c.vflag_atom) { if (NEWTON_PAIR || i < c.nlocal) { - vatom(i,0) += 0.5*v0; - vatom(i,1) += 0.5*v1; - vatom(i,2) += 0.5*v2; - vatom(i,3) += 0.5*v3; - vatom(i,4) += 0.5*v4; - vatom(i,5) += 0.5*v5; + a_vatom(i,0) += 0.5*v0; + a_vatom(i,1) += 0.5*v1; + a_vatom(i,2) += 0.5*v2; + a_vatom(i,3) += 0.5*v3; + a_vatom(i,4) += 0.5*v4; + a_vatom(i,5) += 0.5*v5; } if ((NEWTON_PAIR || j < c.nlocal) && NEIGHFLAG != FULL) { - vatom(j,0) += 0.5*v0; - vatom(j,1) += 0.5*v1; - vatom(j,2) += 0.5*v2; - vatom(j,3) += 0.5*v3; - vatom(j,4) += 0.5*v4; - vatom(j,5) += 0.5*v5; + a_vatom(j,0) += 0.5*v0; + a_vatom(j,1) += 0.5*v1; + a_vatom(j,2) += 0.5*v2; + a_vatom(j,3) += 0.5*v3; + a_vatom(j,4) += 0.5*v4; + a_vatom(j,5) += 0.5*v5; } } } @@ -351,6 +374,9 @@ struct PairComputeFunctor { return j >> SBBITS & 3; } + + void contribute() {} + template KOKKOS_FUNCTION EV_FLOAT compute_item(const int& ii, @@ -489,10 +515,12 @@ EV_FLOAT pair_compute_neighlist (PairStyle* fpair, typename Kokkos::Impl::enable PairComputeFunctor ff(fpair,list); if (fpair->eflag || fpair->vflag) Kokkos::parallel_reduce(list->inum,ff,ev); else Kokkos::parallel_for(list->inum,ff); + ff.contribute(); } else { PairComputeFunctor ff(fpair,list); if (fpair->eflag || fpair->vflag) Kokkos::parallel_reduce(list->inum,ff,ev); else Kokkos::parallel_for(list->inum,ff); + ff.contribute(); } return ev; } diff --git a/src/KOKKOS/pair_reaxc_kokkos.cpp b/src/KOKKOS/pair_reaxc_kokkos.cpp index bb9f8ab417..46ecddfd83 100644 --- a/src/KOKKOS/pair_reaxc_kokkos.cpp +++ b/src/KOKKOS/pair_reaxc_kokkos.cpp @@ -343,6 +343,7 @@ void PairReaxCKokkos::init_md() swa = control->nonb_low; swb = control->nonb_cut; + enobondsflag = control->enobondsflag; if (fabs(swa) > 0.01 ) error->warning(FLERR,"Warning: non-zero lower Taper-radius cutoff"); @@ -707,6 +708,19 @@ void PairReaxCKokkos::compute(int eflag_in, int vflag_in) d_neighbors = k_list->d_neighbors; d_ilist = k_list->d_ilist; + need_dup = lmp->kokkos->need_dup(); + + // allocate duplicated memory + if (need_dup) { + dup_f = Kokkos::Experimental::create_scatter_view(f); + dup_eatom = Kokkos::Experimental::create_scatter_view(d_eatom); + dup_vatom = Kokkos::Experimental::create_scatter_view(d_vatom); + } else { + ndup_f = Kokkos::Experimental::create_scatter_view(f); + ndup_eatom = Kokkos::Experimental::create_scatter_view(d_eatom); + ndup_vatom = Kokkos::Experimental::create_scatter_view(d_vatom); + } + if (eflag_global) { for (int i = 0; i < 14; i++) pvector[i] = 0.0; @@ -776,6 +790,15 @@ void PairReaxCKokkos::compute(int eflag_in, int vflag_in) allocate_array(); } + // allocate duplicated memory + if (need_dup) { + dup_dDeltap_self = Kokkos::Experimental::create_scatter_view(d_dDeltap_self); + dup_total_bo = Kokkos::Experimental::create_scatter_view(d_total_bo); + } else { + ndup_dDeltap_self = Kokkos::Experimental::create_scatter_view(d_dDeltap_self); + ndup_total_bo = Kokkos::Experimental::create_scatter_view(d_total_bo); + } + // Neighbor lists for bond and hbond // try, resize if necessary @@ -798,7 +821,7 @@ void PairReaxCKokkos::compute(int eflag_in, int vflag_in) if (neighflag == HALF) Kokkos::parallel_for(Kokkos::RangePolicy >(0,ignum),*this); else if (neighflag == HALFTHREAD) - Kokkos::parallel_for(Kokkos::RangePolicy >(0,ignum),*this); + Kokkos::parallel_for(Kokkos::RangePolicy >(0,ignum),*this); else //(neighflag == FULL) Kokkos::parallel_for(Kokkos::RangePolicy(0,ignum),*this); @@ -813,14 +836,40 @@ void PairReaxCKokkos::compute(int eflag_in, int vflag_in) if (resize_hb) maxhb++; resize = resize_bo || resize_hb; - if (resize) allocate_array(); + if (resize) { + allocate_array(); + if (need_dup) { + dup_dDeltap_self = Kokkos::Experimental::create_scatter_view(d_dDeltap_self); + dup_total_bo = Kokkos::Experimental::create_scatter_view(d_total_bo); + } else { + ndup_dDeltap_self = Kokkos::Experimental::create_scatter_view(d_dDeltap_self); + ndup_total_bo = Kokkos::Experimental::create_scatter_view(d_total_bo); + } + } } + // allocate duplicated memory + if (need_dup) { + dup_CdDelta = Kokkos::Experimental::create_scatter_view(d_CdDelta); + //dup_Cdbo = Kokkos::Experimental::create_scatter_view(d_Cdbo); + //dup_Cdbopi = Kokkos::Experimental::create_scatter_view(d_Cdbopi); + //dup_Cdbopi2 = Kokkos::Experimental::create_scatter_view(d_Cdbopi2); + } else { + ndup_CdDelta = Kokkos::Experimental::create_scatter_view(d_CdDelta); + //ndup_Cdbo = Kokkos::Experimental::create_scatter_view(d_Cdbo); + //ndup_Cdbopi = Kokkos::Experimental::create_scatter_view(d_Cdbopi); + //ndup_Cdbopi2 = Kokkos::Experimental::create_scatter_view(d_Cdbopi2); + } + + // reduction over duplicated memory + if (need_dup) + Kokkos::Experimental::contribute(d_total_bo, dup_total_bo); // needed in BondOrder1 + // Bond order if (neighflag == HALF) { Kokkos::parallel_for(Kokkos::RangePolicy(0,ignum),*this); } else if (neighflag == HALFTHREAD) { - Kokkos::parallel_for(Kokkos::RangePolicy(0,ignum),*this); + Kokkos::parallel_for(Kokkos::RangePolicy(0,ignum),*this); } Kokkos::parallel_for(Kokkos::RangePolicy(0,ignum),*this); Kokkos::parallel_for(Kokkos::RangePolicy(0,ignum),*this); @@ -919,9 +968,30 @@ void PairReaxCKokkos::compute(int eflag_in, int vflag_in) pvector[7] = ev.ereax[8]; ev_all.evdwl += ev.ereax[8]; + // reduction over duplicated memory + if (need_dup) { + Kokkos::Experimental::contribute(d_dDeltap_self, dup_dDeltap_self); // needed in ComputeBond2 + Kokkos::Experimental::contribute(d_CdDelta, dup_CdDelta); // needed in ComputeBond2 + + //Kokkos::Experimental::contribute(d_Cdbo, dup_Cdbo); // needed in UpdateBond, but also used in UpdateBond + //Kokkos::Experimental::contribute(d_Cdbopi, dup_Cdbopi); // needed in UpdateBond, but also used in UpdateBond + //Kokkos::Experimental::contribute(d_Cdbopi2, dup_Cdbopi2); // needed in UpdateBond, but also used in UpdateBond + //dup_Cdbo.reset_except(d_Cdbo); + //dup_Cdbopi.reset_except(d_Cdbopi); + //dup_Cdbopi2.reset_except(d_Cdbopi2); + } + // Bond force if (neighflag == HALF) { Kokkos::parallel_for(Kokkos::RangePolicy >(0,ignum),*this); + + // reduction over duplicated memory + //if (need_dup) { + // Kokkos::Experimental::contribute(d_Cdbo, dup_Cdbo); // needed in ComputeBond2 + // Kokkos::Experimental::contribute(d_Cdbopi, dup_Cdbopi); // needed in ComputeBond2 + // Kokkos::Experimental::contribute(d_Cdbopi2, dup_Cdbopi2); // needed in ComputeBond2 + //} + if (evflag) Kokkos::parallel_reduce(Kokkos::RangePolicy >(0,ignum),*this,ev); else @@ -930,6 +1000,14 @@ void PairReaxCKokkos::compute(int eflag_in, int vflag_in) pvector[0] += ev.evdwl; } else { //if (neighflag == HALFTHREAD) { Kokkos::parallel_for(Kokkos::RangePolicy >(0,ignum),*this); + + // reduction over duplicated memory + //if (need_dup) { + // Kokkos::Experimental::contribute(d_Cdbo, dup_Cdbo); // needed in ComputeBond2 + // Kokkos::Experimental::contribute(d_Cdbopi, dup_Cdbopi); // needed in ComputeBond2 + // Kokkos::Experimental::contribute(d_Cdbopi2, dup_Cdbopi2); // needed in ComputeBond2 + //} + if (evflag) Kokkos::parallel_reduce(Kokkos::RangePolicy >(0,ignum),*this,ev); else @@ -938,6 +1016,10 @@ void PairReaxCKokkos::compute(int eflag_in, int vflag_in) pvector[0] += ev.evdwl; } + // reduction over duplicated memory + if (need_dup) + Kokkos::Experimental::contribute(f, dup_f); + if (eflag_global) { eng_vdwl += ev_all.evdwl; eng_coul += ev_all.ecoul; @@ -954,11 +1036,15 @@ void PairReaxCKokkos::compute(int eflag_in, int vflag_in) if (vflag_fdotr) pair_virial_fdotr_compute(this); if (eflag_atom) { + if (need_dup) + Kokkos::Experimental::contribute(d_eatom, dup_eatom); k_eatom.template modify(); k_eatom.template sync(); } if (vflag_atom) { + if (need_dup) + Kokkos::Experimental::contribute(d_vatom, dup_vatom); k_vatom.template modify(); k_vatom.template sync(); } @@ -967,6 +1053,19 @@ void PairReaxCKokkos::compute(int eflag_in, int vflag_in) FindBondSpecies(); copymode = 0; + + // free duplicated memory + if (need_dup) { + dup_f = decltype(dup_f)(); + dup_dDeltap_self = decltype(dup_dDeltap_self)(); + dup_total_bo = decltype(dup_total_bo)(); + dup_CdDelta = decltype(dup_CdDelta)(); + //dup_Cdbo = decltype(dup_Cdbo)(); + //dup_Cdbopi = decltype(dup_Cdbopi)(); + //dup_Cdbopi2 = decltype(dup_Cdbopi2)(); + dup_eatom = decltype(dup_eatom)(); + dup_vatom = decltype(dup_vatom)(); + } } /* ---------------------------------------------------------------------- */ @@ -1005,8 +1104,10 @@ template KOKKOS_INLINE_FUNCTION void PairReaxCKokkos::operator()(PairReaxComputeLJCoulomb, const int &ii, EV_FLOAT_REAX& ev) const { - // The f array is atomic for Half/Thread neighbor style - Kokkos::View::value> > a_f = f; + // The f array is duplicated for OpenMP, atomic for CUDA, and neither for Serial + + auto v_f = ScatterViewHelper::value,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f); + auto a_f = v_f.template access::value>(); F_FLOAT powr_vdw, powgi_vdw, fn13, dfn13, exp1, exp2, etmp; F_FLOAT evdwl, fvdwl; @@ -1164,8 +1265,10 @@ template KOKKOS_INLINE_FUNCTION void PairReaxCKokkos::operator()(PairReaxComputeTabulatedLJCoulomb, const int &ii, EV_FLOAT_REAX& ev) const { - // The f array is atomic for Half/Thread neighbor style - Kokkos::View::value> > a_f = f; + // The f array is duplicated for OpenMP, atomic for CUDA, and neither for Serial + + auto v_f = ScatterViewHelper::value,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f); + auto a_f = v_f.template access::value>(); const int i = d_ilist[ii]; const X_FLOAT xtmp = x(i,0); @@ -1365,18 +1468,18 @@ void PairReaxCKokkos::operator()(PairReaxZero, const int &n) const { template KOKKOS_INLINE_FUNCTION void PairReaxCKokkos::operator()(PairReaxZeroEAtom, const int &i) const { - v_eatom(i) = 0.0; + d_eatom(i) = 0.0; } template KOKKOS_INLINE_FUNCTION void PairReaxCKokkos::operator()(PairReaxZeroVAtom, const int &i) const { - v_vatom(i,0) = 0.0; - v_vatom(i,1) = 0.0; - v_vatom(i,2) = 0.0; - v_vatom(i,3) = 0.0; - v_vatom(i,4) = 0.0; - v_vatom(i,5) = 0.0; + d_vatom(i,0) = 0.0; + d_vatom(i,1) = 0.0; + d_vatom(i,2) = 0.0; + d_vatom(i,3) = 0.0; + d_vatom(i,4) = 0.0; + d_vatom(i,5) = 0.0; } /* ---------------------------------------------------------------------- */ @@ -1546,8 +1649,11 @@ void PairReaxCKokkos::operator()(PairReaxBuildListsHalf, if (d_resize_bo() || d_resize_hb()) return; - Kokkos::View::value> > a_dDeltap_self = d_dDeltap_self; - Kokkos::View::value> > a_total_bo = d_total_bo; + auto v_dDeltap_self = ScatterViewHelper::value,decltype(dup_dDeltap_self),decltype(ndup_dDeltap_self)>::get(dup_dDeltap_self,ndup_dDeltap_self); + auto a_dDeltap_self = v_dDeltap_self.template access::value>(); + + auto v_total_bo = ScatterViewHelper::value,decltype(dup_total_bo),decltype(ndup_total_bo)>::get(dup_total_bo,ndup_total_bo); + auto a_total_bo = v_total_bo.template access::value>(); const int i = d_ilist[ii]; const X_FLOAT xtmp = x(i,0); @@ -2238,10 +2344,8 @@ template KOKKOS_INLINE_FUNCTION void PairReaxCKokkos::operator()(PairReaxComputeMulti2, const int &ii, EV_FLOAT_REAX& ev) const { - Kokkos::View::value> > a_CdDelta = d_CdDelta; - Kokkos::View::value> > a_Cdbo = d_Cdbo; - Kokkos::View::value> > a_Cdbopi = d_Cdbopi; - Kokkos::View::value> > a_Cdbopi2 = d_Cdbopi2; + auto v_CdDelta = ScatterViewHelper::value,decltype(dup_CdDelta),decltype(ndup_CdDelta)>::get(dup_CdDelta,ndup_CdDelta); + auto a_CdDelta = v_CdDelta.template access::value>(); const int i = d_ilist[ii]; const int itype = type(i); @@ -2272,12 +2376,12 @@ void PairReaxCKokkos::operator()(PairReaxComputeMulti2 0 || control->enobondsflag) + if (numbonds > 0 || enobondsflag) e_lp = p_lp2 * d_Delta_lp[i] * inv_expvd2; const F_FLOAT dElp = p_lp2 * inv_expvd2 + 75.0 * p_lp2 * d_Delta_lp[i] * expvd2 * inv_expvd2*inv_expvd2; const F_FLOAT CElp = dElp * d_dDelta_lp[i]; - if (numbonds > 0 || control->enobondsflag) + if (numbonds > 0 || enobondsflag) a_CdDelta[i] += CElp; if (eflag) ev.ereax[0] += e_lp; @@ -2314,7 +2418,7 @@ void PairReaxCKokkos::operator()(PairReaxComputeMulti2 0 || control->enobondsflag) + if (numbonds > 0 || enobondsflag) e_un = -p_ovun5 * (1.0 - exp_ovun6) * inv_exp_ovun2n * inv_exp_ovun8; if (eflag) ev.ereax[2] += e_un; @@ -2334,7 +2438,7 @@ void PairReaxCKokkos::operator()(PairReaxComputeMulti2 0 || control->enobondsflag) + if (numbonds > 0 || enobondsflag) a_CdDelta[i] += CEunder3; const int j_start = d_bo_first[i]; @@ -2392,9 +2496,12 @@ template KOKKOS_INLINE_FUNCTION void PairReaxCKokkos::operator()(PairReaxComputeAngular, const int &ii, EV_FLOAT_REAX& ev) const { - Kokkos::View::value> > a_f = f; + auto v_f = ScatterViewHelper::value,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f); + auto a_f = v_f.template access::value>(); Kokkos::View::value> > a_Cdbo = d_Cdbo; - Kokkos::View::value> > a_CdDelta = d_CdDelta; + + auto v_CdDelta = ScatterViewHelper::value,decltype(dup_CdDelta),decltype(ndup_CdDelta)>::get(dup_CdDelta,ndup_CdDelta); + auto a_CdDelta = v_CdDelta.template access::value>(); const int i = d_ilist[ii]; const int itype = type(i); @@ -2701,9 +2808,13 @@ template KOKKOS_INLINE_FUNCTION void PairReaxCKokkos::operator()(PairReaxComputeTorsion, const int &ii, EV_FLOAT_REAX& ev) const { - Kokkos::View::value> > a_f = f; - Kokkos::View::value> > a_CdDelta = d_CdDelta; + auto v_f = ScatterViewHelper::value,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f); + auto a_f = v_f.template access::value>(); + + auto v_CdDelta = ScatterViewHelper::value,decltype(dup_CdDelta),decltype(ndup_CdDelta)>::get(dup_CdDelta,ndup_CdDelta); + auto a_CdDelta = v_CdDelta.template access::value>(); Kokkos::View::value> > a_Cdbo = d_Cdbo; + //auto a_Cdbo = dup_Cdbo.template access::value>(); // in reaxc_torsion_angles: j = i, k = j, i = k; @@ -3073,7 +3184,8 @@ template KOKKOS_INLINE_FUNCTION void PairReaxCKokkos::operator()(PairReaxComputeHydrogen, const int &ii, EV_FLOAT_REAX& ev) const { - Kokkos::View::value> > a_f = f; + auto v_f = ScatterViewHelper::value,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f); + auto a_f = v_f.template access::value>(); int hblist[MAX_BONDS]; F_FLOAT theta, cos_theta, sin_xhz4, cos_xhz1, sin_theta2; @@ -3223,6 +3335,9 @@ void PairReaxCKokkos::operator()(PairReaxUpdateBond, cons Kokkos::View::value> > a_Cdbo = d_Cdbo; Kokkos::View::value> > a_Cdbopi = d_Cdbopi; Kokkos::View::value> > a_Cdbopi2 = d_Cdbopi2; + //auto a_Cdbo = dup_Cdbo.template access::value>(); + //auto a_Cdbopi = dup_Cdbopi.template access::value>(); + //auto a_Cdbopi2 = dup_Cdbopi2.template access::value>(); const int i = d_ilist[ii]; const tagint itag = tag(i); @@ -3269,8 +3384,11 @@ template KOKKOS_INLINE_FUNCTION void PairReaxCKokkos::operator()(PairReaxComputeBond1, const int &ii, EV_FLOAT_REAX& ev) const { - Kokkos::View::value> > a_f = f; - Kokkos::View::value> > a_CdDelta = d_CdDelta; + auto v_f = ScatterViewHelper::value,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f); + auto a_f = v_f.template access::value>(); + + auto v_CdDelta = ScatterViewHelper::value,decltype(dup_CdDelta),decltype(ndup_CdDelta)>::get(dup_CdDelta,ndup_CdDelta); + auto a_CdDelta = v_CdDelta.template access::value>(); F_FLOAT delij[3]; F_FLOAT p_be1, p_be2, De_s, De_p, De_pp, pow_BOs_be2, exp_be12, CEbo, ebond; @@ -3407,7 +3525,8 @@ template KOKKOS_INLINE_FUNCTION void PairReaxCKokkos::operator()(PairReaxComputeBond2, const int &ii, EV_FLOAT_REAX& ev) const { - Kokkos::View::value> > a_f = f; + auto v_f = ScatterViewHelper::value,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f); + auto a_f = v_f.template access::value>(); F_FLOAT delij[3], delik[3], deljk[3], tmpvec[3]; F_FLOAT dBOp_i[3], dBOp_k[3], dln_BOp_pi[3], dln_BOp_pi2[3]; @@ -3619,9 +3738,13 @@ void PairReaxCKokkos::ev_tally(EV_FLOAT_REAX &ev, const int &i, cons { const int VFLAG = vflag_either; - // The eatom and vatom arrays are atomic for Half/Thread neighbor style - Kokkos::View::value> > a_eatom = v_eatom; - Kokkos::View::value> > a_vatom = v_vatom; + // The eatom and vatom arrays are duplicated for OpenMP, atomic for CUDA, and neither for Serial + + auto v_eatom = ScatterViewHelper::value,decltype(dup_eatom),decltype(ndup_eatom)>::get(dup_eatom,ndup_eatom); + auto a_eatom = v_eatom.template access::value>(); + + auto v_vatom = ScatterViewHelper::value,decltype(dup_vatom),decltype(ndup_vatom)>::get(dup_vatom,ndup_vatom); + auto a_vatom = v_vatom.template access::value>(); if (eflag_atom) { const E_FLOAT epairhalf = 0.5 * epair; @@ -3684,10 +3807,13 @@ void PairReaxCKokkos::e_tally(EV_FLOAT_REAX &ev, const int &i, const const F_FLOAT &epair) const { - // The eatom array is atomic for Half/Thread neighbor style + // The eatom array is duplicated for OpenMP, atomic for CUDA, and neither for Serial + if (eflag_atom) { - Kokkos::View::value> > a_eatom = v_eatom; + auto v_eatom = ScatterViewHelper::value,decltype(dup_eatom),decltype(ndup_eatom)>::get(dup_eatom,ndup_eatom); + auto a_eatom = v_eatom.template access::value>(); + const E_FLOAT epairhalf = 0.5 * epair; a_eatom[i] += epairhalf; a_eatom[j] += epairhalf; @@ -3702,8 +3828,9 @@ KOKKOS_INLINE_FUNCTION void PairReaxCKokkos::e_tally_single(EV_FLOAT_REAX &ev, const int &i, const F_FLOAT &epair) const { - // The eatom array is atomic for Half/Thread neighbor style - Kokkos::View::value> > a_eatom = v_eatom; + // The eatom array is duplicated for OpenMP, atomic for CUDA, and neither for Serial + auto v_eatom = ScatterViewHelper::value,decltype(dup_eatom),decltype(ndup_eatom)>::get(dup_eatom,ndup_eatom); + auto a_eatom = v_eatom.template access::value>(); a_eatom[i] += epair; } @@ -3736,7 +3863,9 @@ void PairReaxCKokkos::v_tally(EV_FLOAT_REAX &ev, const int &i, } if (vflag_atom) { - Kokkos::View::value> > a_vatom = v_vatom; + auto v_vatom = ScatterViewHelper::value,decltype(dup_vatom),decltype(ndup_vatom)>::get(dup_vatom,ndup_vatom); + auto a_vatom = v_vatom.template access::value>(); + a_vatom(i,0) += v[0]; a_vatom(i,1) += v[1]; a_vatom(i,2) += v[2]; a_vatom(i,3) += v[3]; a_vatom(i,4) += v[4]; a_vatom(i,5) += v[5]; } @@ -3751,8 +3880,9 @@ void PairReaxCKokkos::v_tally3(EV_FLOAT_REAX &ev, const int &i, cons F_FLOAT *fj, F_FLOAT *fk, F_FLOAT *drij, F_FLOAT *drik) const { - // The eatom and vatom arrays are atomic for Half/Thread neighbor style - Kokkos::View::value> > a_vatom = v_vatom; + // The eatom and vatom arrays are duplicated for OpenMP, atomic for CUDA, and neither for Serial + auto v_vatom = ScatterViewHelper::value,decltype(dup_vatom),decltype(ndup_vatom)>::get(dup_vatom,ndup_vatom); + auto a_vatom = v_vatom.template access::value>(); F_FLOAT v[6]; @@ -3792,7 +3922,8 @@ void PairReaxCKokkos::v_tally4(EV_FLOAT_REAX &ev, const int &i, cons const int &l, F_FLOAT *fi, F_FLOAT *fj, F_FLOAT *fk, F_FLOAT *dril, F_FLOAT *drjl, F_FLOAT *drkl) const { - // The vatom array is atomic for Half/Thread neighbor style + // The vatom array is duplicated for OpenMP, atomic for CUDA, and neither for Serial + F_FLOAT v[6]; v[0] = dril[0]*fi[0] + drjl[0]*fj[0] + drkl[0]*fk[0]; @@ -3812,7 +3943,9 @@ void PairReaxCKokkos::v_tally4(EV_FLOAT_REAX &ev, const int &i, cons } if (vflag_atom) { - Kokkos::View::value> > a_vatom = v_vatom; + auto v_vatom = ScatterViewHelper::value,decltype(dup_vatom),decltype(ndup_vatom)>::get(dup_vatom,ndup_vatom); + auto a_vatom = v_vatom.template access::value>(); + a_vatom(i,0) += 0.25 * v[0]; a_vatom(i,1) += 0.25 * v[1]; a_vatom(i,2) += 0.25 * v[2]; a_vatom(i,3) += 0.25 * v[3]; a_vatom(i,4) += 0.25 * v[4]; a_vatom(i,5) += 0.25 * v[5]; a_vatom(j,0) += 0.25 * v[0]; a_vatom(j,1) += 0.25 * v[1]; a_vatom(j,2) += 0.25 * v[2]; @@ -3909,13 +4042,13 @@ void PairReaxCKokkos::ev_setup(int eflag, int vflag, int) maxeatom = atom->nmax; memoryKK->destroy_kokkos(k_eatom,eatom); memoryKK->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom"); - v_eatom = k_eatom.view(); + d_eatom = k_eatom.view(); } if (vflag_atom && atom->nmax > maxvatom) { maxvatom = atom->nmax; memoryKK->destroy_kokkos(k_vatom,vatom); memoryKK->create_kokkos(k_vatom,vatom,maxvatom,6,"pair:vatom"); - v_vatom = k_vatom.view(); + d_vatom = k_vatom.view(); } // zero accumulators diff --git a/src/KOKKOS/pair_reaxc_kokkos.h b/src/KOKKOS/pair_reaxc_kokkos.h index 5175e274a8..89dfc4d884 100644 --- a/src/KOKKOS/pair_reaxc_kokkos.h +++ b/src/KOKKOS/pair_reaxc_kokkos.h @@ -380,11 +380,10 @@ class PairReaxCKokkos : public PairReaxC { typename AT::t_tagint_1d_randomread molecule; DAT::tdual_efloat_1d k_eatom; - typename AT::t_efloat_1d v_eatom; + typename AT::t_efloat_1d d_eatom; DAT::tdual_virial_array k_vatom; - typename ArrayTypes::t_virial_array d_vatom; - typename AT::t_virial_array v_vatom; + typename AT::t_virial_array d_vatom; HAT::t_virial_array h_vatom; DAT::tdual_float_1d k_tap; @@ -401,6 +400,28 @@ class PairReaxCKokkos : public PairReaxC { typename AT::t_ffloat_2d_dl d_C1dbopi2, d_C2dbopi2, d_C3dbopi2, d_C4dbopi2; typename AT::t_ffloat_2d_dl d_Cdbo, d_Cdbopi, d_Cdbopi2, d_dDeltap_self; + Kokkos::Experimental::ScatterView dup_total_bo; + Kokkos::Experimental::ScatterView dup_CdDelta; + Kokkos::Experimental::ScatterView dup_eatom; + Kokkos::Experimental::ScatterView dup_f; + Kokkos::Experimental::ScatterView dup_vatom; + Kokkos::Experimental::ScatterView dup_dDeltap_self; + Kokkos::Experimental::ScatterView dup_Cdbo; + Kokkos::Experimental::ScatterView dup_Cdbopi; + Kokkos::Experimental::ScatterView dup_Cdbopi2; + + Kokkos::Experimental::ScatterView ndup_total_bo; + Kokkos::Experimental::ScatterView ndup_CdDelta; + Kokkos::Experimental::ScatterView ndup_eatom; + Kokkos::Experimental::ScatterView ndup_f; + Kokkos::Experimental::ScatterView ndup_vatom; + Kokkos::Experimental::ScatterView ndup_dDeltap_self; + Kokkos::Experimental::ScatterView ndup_Cdbo; + Kokkos::Experimental::ScatterView ndup_Cdbopi; + Kokkos::Experimental::ScatterView ndup_Cdbopi2; + + int need_dup; + typedef Kokkos::DualView tdual_ffloat_2d_n7; typedef typename tdual_ffloat_2d_n7::t_dev_const_randomread t_ffloat_2d_n7_randomread; typedef typename tdual_ffloat_2d_n7::t_host t_host_ffloat_2d_n7; @@ -427,7 +448,7 @@ class PairReaxCKokkos : public PairReaxC { friend void pair_virial_fdotr_compute(PairReaxCKokkos*); - int bocnt,hbcnt; + int bocnt,hbcnt,enobondsflag; typedef LR_lookup_table_kk LR_lookup_table_kk_DT; diff --git a/src/KOKKOS/pair_snap_kokkos.h b/src/KOKKOS/pair_snap_kokkos.h index 5c68284219..b2019879ed 100644 --- a/src/KOKKOS/pair_snap_kokkos.h +++ b/src/KOKKOS/pair_snap_kokkos.h @@ -129,6 +129,12 @@ inline double dist2(double* x,double* y); typename AT::t_f_array f; typename AT::t_int_1d_randomread type; + int need_dup; + Kokkos::Experimental::ScatterView dup_f; + Kokkos::Experimental::ScatterView dup_vatom; + Kokkos::Experimental::ScatterView ndup_f; + Kokkos::Experimental::ScatterView ndup_vatom; + friend void pair_virial_fdotr_compute(PairSNAPKokkos*); }; diff --git a/src/KOKKOS/pair_snap_kokkos_impl.h b/src/KOKKOS/pair_snap_kokkos_impl.h index a024e5cbd1..c452042cfe 100644 --- a/src/KOKKOS/pair_snap_kokkos_impl.h +++ b/src/KOKKOS/pair_snap_kokkos_impl.h @@ -170,6 +170,15 @@ void PairSNAPKokkos::compute(int eflag_in, int vflag_in) d_ilist = k_list->d_ilist; int inum = list->inum; + need_dup = lmp->kokkos->need_dup(); + if (need_dup) { + dup_f = Kokkos::Experimental::create_scatter_view(f); + dup_vatom = Kokkos::Experimental::create_scatter_view(d_vatom); + } else { + ndup_f = Kokkos::Experimental::create_scatter_view(f); + ndup_vatom = Kokkos::Experimental::create_scatter_view(d_vatom); + } + /* for (int i = 0; i < nlocal; i++) { typename t_neigh_list::t_neighs neighs_i = neigh_list.get_neighs(i); @@ -232,6 +241,9 @@ void PairSNAPKokkos::compute(int eflag_in, int vflag_in) //if (step%10==0) // printf(" %e %e %e %e %e (%e %e): %e\n",t1,t2,t3,t4,t5,t6,t7,t1+t2+t3+t4+t5); + if (need_dup) + Kokkos::Experimental::contribute(f, dup_f); + if (eflag_global) eng_vdwl += ev.evdwl; if (vflag_global) { virial[0] += ev.v[0]; @@ -244,18 +256,28 @@ void PairSNAPKokkos::compute(int eflag_in, int vflag_in) if (vflag_fdotr) pair_virial_fdotr_compute(this); + if (eflag_atom) { k_eatom.template modify(); k_eatom.template sync(); } if (vflag_atom) { + if (need_dup) + Kokkos::Experimental::contribute(d_vatom, dup_vatom); k_vatom.template modify(); k_vatom.template sync(); } atomKK->modified(execution_space,F_MASK); + copymode = 0; + + // free duplicated memory + if (need_dup) { + dup_f = decltype(dup_f)(); + dup_vatom = decltype(dup_vatom)(); + } } /* ---------------------------------------------------------------------- @@ -349,8 +371,11 @@ template template KOKKOS_INLINE_FUNCTION void PairSNAPKokkos::operator() (TagPairSNAP,const typename Kokkos::TeamPolicy >::member_type& team, EV_FLOAT& ev) const { - // The f array is atomic for Half/Thread neighbor style - Kokkos::View::value> > a_f = f; + + // The f array is duplicated for OpenMP, atomic for CUDA, and neither for Serial + + auto v_f = ScatterViewHelper::value,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f); + auto a_f = v_f.template access::value>(); const int ii = team.league_rank(); const int i = d_ilist[ii]; @@ -591,8 +616,10 @@ void PairSNAPKokkos::v_tally_xyz(EV_FLOAT &ev, const int &i, const i const F_FLOAT &fx, const F_FLOAT &fy, const F_FLOAT &fz, const F_FLOAT &delx, const F_FLOAT &dely, const F_FLOAT &delz) const { - // The vatom array is atomic for Half/Thread neighbor style - Kokkos::View::value> > v_vatom = k_vatom.view(); + // The vatom array is duplicated for OpenMP, atomic for CUDA, and neither for Serial + + auto v_vatom = ScatterViewHelper::value,decltype(dup_vatom),decltype(ndup_vatom)>::get(dup_vatom,ndup_vatom); + auto a_vatom = v_vatom.template access::value>(); const E_FLOAT v0 = delx*fx; const E_FLOAT v1 = dely*fy; @@ -611,18 +638,18 @@ void PairSNAPKokkos::v_tally_xyz(EV_FLOAT &ev, const int &i, const i } if (vflag_atom) { - v_vatom(i,0) += 0.5*v0; - v_vatom(i,1) += 0.5*v1; - v_vatom(i,2) += 0.5*v2; - v_vatom(i,3) += 0.5*v3; - v_vatom(i,4) += 0.5*v4; - v_vatom(i,5) += 0.5*v5; - v_vatom(j,0) += 0.5*v0; - v_vatom(j,1) += 0.5*v1; - v_vatom(j,2) += 0.5*v2; - v_vatom(j,3) += 0.5*v3; - v_vatom(j,4) += 0.5*v4; - v_vatom(j,5) += 0.5*v5; + a_vatom(i,0) += 0.5*v0; + a_vatom(i,1) += 0.5*v1; + a_vatom(i,2) += 0.5*v2; + a_vatom(i,3) += 0.5*v3; + a_vatom(i,4) += 0.5*v4; + a_vatom(i,5) += 0.5*v5; + a_vatom(j,0) += 0.5*v0; + a_vatom(j,1) += 0.5*v1; + a_vatom(j,2) += 0.5*v2; + a_vatom(j,3) += 0.5*v3; + a_vatom(j,4) += 0.5*v4; + a_vatom(j,5) += 0.5*v5; } } diff --git a/src/KOKKOS/pair_sw_kokkos.cpp b/src/KOKKOS/pair_sw_kokkos.cpp index 8f4903c767..5452d2293f 100644 --- a/src/KOKKOS/pair_sw_kokkos.cpp +++ b/src/KOKKOS/pair_sw_kokkos.cpp @@ -115,6 +115,17 @@ void PairSWKokkos::compute(int eflag_in, int vflag_in) d_numneigh = k_list->d_numneigh; d_neighbors = k_list->d_neighbors; + need_dup = lmp->kokkos->need_dup(); + if (need_dup) { + dup_f = Kokkos::Experimental::create_scatter_view(f); + dup_eatom = Kokkos::Experimental::create_scatter_view(d_eatom); + dup_vatom = Kokkos::Experimental::create_scatter_view(d_vatom); + } else { + ndup_f = Kokkos::Experimental::create_scatter_view(f); + ndup_eatom = Kokkos::Experimental::create_scatter_view(d_eatom); + ndup_vatom = Kokkos::Experimental::create_scatter_view(d_vatom); + } + copymode = 1; EV_FLOAT ev; @@ -160,6 +171,9 @@ void PairSWKokkos::compute(int eflag_in, int vflag_in) ev_all += ev; } + if (need_dup) + Kokkos::Experimental::contribute(f, dup_f); + if (eflag_global) eng_vdwl += ev_all.evdwl; if (vflag_global) { virial[0] += ev_all.v[0]; @@ -171,11 +185,15 @@ void PairSWKokkos::compute(int eflag_in, int vflag_in) } if (eflag_atom) { + if (need_dup) + Kokkos::Experimental::contribute(d_eatom, dup_eatom); k_eatom.template modify(); k_eatom.template sync(); } if (vflag_atom) { + if (need_dup) + Kokkos::Experimental::contribute(d_vatom, dup_vatom); k_vatom.template modify(); k_vatom.template sync(); } @@ -183,6 +201,13 @@ void PairSWKokkos::compute(int eflag_in, int vflag_in) if (vflag_fdotr) pair_virial_fdotr_compute(this); copymode = 0; + + // free duplicated memory + if (need_dup) { + dup_f = decltype(dup_f)(); + dup_eatom = decltype(dup_eatom)(); + dup_vatom = decltype(dup_vatom)(); + } } @@ -222,9 +247,10 @@ template KOKKOS_INLINE_FUNCTION void PairSWKokkos::operator()(TagPairSWComputeHalf, const int &ii, EV_FLOAT& ev) const { - // The f array is atomic + // The f array is duplicated for OpenMP, atomic for CUDA, and neither for Serial - Kokkos::View::value> > a_f = f; + auto v_f = ScatterViewHelper::value,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f); + auto a_f = v_f.template access::value>(); F_FLOAT delr1[3],delr2[3],fj[3],fk[3]; F_FLOAT evdwl = 0.0; @@ -777,17 +803,19 @@ void PairSWKokkos::ev_tally(EV_FLOAT &ev, const int &i, const int &j { const int VFLAG = vflag_either; - // The eatom and vatom arrays are atomic for half/thread neighbor list + // The eatom and vatom arrays are duplicated for OpenMP, atomic for CUDA, and neither for Serial - Kokkos::View::value> > v_eatom = k_eatom.view(); - Kokkos::View::value> > v_vatom = k_vatom.view(); + auto v_eatom = ScatterViewHelper::value,decltype(dup_eatom),decltype(ndup_eatom)>::get(dup_eatom,ndup_eatom); + auto a_eatom = v_eatom.template access::value>(); + auto v_vatom = ScatterViewHelper::value,decltype(dup_vatom),decltype(ndup_vatom)>::get(dup_vatom,ndup_vatom); + auto a_vatom = v_vatom.template access::value>(); if (eflag_atom) { const E_FLOAT epairhalf = 0.5 * epair; - v_eatom[i] += epairhalf; + a_eatom[i] += epairhalf; if (NEIGHFLAG != FULL) - v_eatom[j] += epairhalf; + a_eatom[j] += epairhalf; } if (VFLAG) { @@ -817,20 +845,20 @@ void PairSWKokkos::ev_tally(EV_FLOAT &ev, const int &i, const int &j } if (vflag_atom) { - v_vatom(i,0) += 0.5*v0; - v_vatom(i,1) += 0.5*v1; - v_vatom(i,2) += 0.5*v2; - v_vatom(i,3) += 0.5*v3; - v_vatom(i,4) += 0.5*v4; - v_vatom(i,5) += 0.5*v5; + a_vatom(i,0) += 0.5*v0; + a_vatom(i,1) += 0.5*v1; + a_vatom(i,2) += 0.5*v2; + a_vatom(i,3) += 0.5*v3; + a_vatom(i,4) += 0.5*v4; + a_vatom(i,5) += 0.5*v5; if (NEIGHFLAG != FULL) { - v_vatom(j,0) += 0.5*v0; - v_vatom(j,1) += 0.5*v1; - v_vatom(j,2) += 0.5*v2; - v_vatom(j,3) += 0.5*v3; - v_vatom(j,4) += 0.5*v4; - v_vatom(j,5) += 0.5*v5; + a_vatom(j,0) += 0.5*v0; + a_vatom(j,1) += 0.5*v1; + a_vatom(j,2) += 0.5*v2; + a_vatom(j,3) += 0.5*v3; + a_vatom(j,4) += 0.5*v4; + a_vatom(j,5) += 0.5*v5; } } } @@ -853,17 +881,20 @@ void PairSWKokkos::ev_tally3(EV_FLOAT &ev, const int &i, const int & const int VFLAG = vflag_either; -// The eatom and vatom arrays are atomic for half/thread neighbor list + // The eatom and vatom arrays are duplicated for OpenMP, atomic for CUDA, and neither for Serial - Kokkos::View::value> > v_eatom = k_eatom.view(); - Kokkos::View::value> > v_vatom = k_vatom.view(); + auto v_eatom = ScatterViewHelper::value,decltype(dup_eatom),decltype(ndup_eatom)>::get(dup_eatom,ndup_eatom); + auto a_eatom = v_eatom.template access::value>(); + + auto v_vatom = ScatterViewHelper::value,decltype(dup_vatom),decltype(ndup_vatom)>::get(dup_vatom,ndup_vatom); + auto a_vatom = v_vatom.template access::value>(); if (eflag_atom) { epairthird = THIRD * (evdwl + ecoul); - v_eatom[i] += epairthird; + a_eatom[i] += epairthird; if (NEIGHFLAG != FULL) { - v_eatom[j] += epairthird; - v_eatom[k] += epairthird; + a_eatom[j] += epairthird; + a_eatom[k] += epairthird; } } @@ -885,18 +916,18 @@ void PairSWKokkos::ev_tally3(EV_FLOAT &ev, const int &i, const int & } if (vflag_atom) { - v_vatom(i,0) += THIRD*v[0]; v_vatom(i,1) += THIRD*v[1]; - v_vatom(i,2) += THIRD*v[2]; v_vatom(i,3) += THIRD*v[3]; - v_vatom(i,4) += THIRD*v[4]; v_vatom(i,5) += THIRD*v[5]; + a_vatom(i,0) += THIRD*v[0]; a_vatom(i,1) += THIRD*v[1]; + a_vatom(i,2) += THIRD*v[2]; a_vatom(i,3) += THIRD*v[3]; + a_vatom(i,4) += THIRD*v[4]; a_vatom(i,5) += THIRD*v[5]; if (NEIGHFLAG != FULL) { - v_vatom(j,0) += THIRD*v[0]; v_vatom(j,1) += THIRD*v[1]; - v_vatom(j,2) += THIRD*v[2]; v_vatom(j,3) += THIRD*v[3]; - v_vatom(j,4) += THIRD*v[4]; v_vatom(j,5) += THIRD*v[5]; + a_vatom(j,0) += THIRD*v[0]; a_vatom(j,1) += THIRD*v[1]; + a_vatom(j,2) += THIRD*v[2]; a_vatom(j,3) += THIRD*v[3]; + a_vatom(j,4) += THIRD*v[4]; a_vatom(j,5) += THIRD*v[5]; - v_vatom(k,0) += THIRD*v[0]; v_vatom(k,1) += THIRD*v[1]; - v_vatom(k,2) += THIRD*v[2]; v_vatom(k,3) += THIRD*v[3]; - v_vatom(k,4) += THIRD*v[4]; v_vatom(k,5) += THIRD*v[5]; + a_vatom(k,0) += THIRD*v[0]; a_vatom(k,1) += THIRD*v[1]; + a_vatom(k,2) += THIRD*v[2]; a_vatom(k,3) += THIRD*v[3]; + a_vatom(k,4) += THIRD*v[4]; a_vatom(k,5) += THIRD*v[5]; } } } diff --git a/src/KOKKOS/pair_sw_kokkos.h b/src/KOKKOS/pair_sw_kokkos.h index eb59d5bc3c..1a3f0b862f 100644 --- a/src/KOKKOS/pair_sw_kokkos.h +++ b/src/KOKKOS/pair_sw_kokkos.h @@ -134,6 +134,14 @@ class PairSWKokkos : public PairSW { typename AT::t_efloat_1d d_eatom; typename AT::t_virial_array d_vatom; + int need_dup; + Kokkos::Experimental::ScatterView dup_f; + Kokkos::Experimental::ScatterView dup_eatom; + Kokkos::Experimental::ScatterView dup_vatom; + Kokkos::Experimental::ScatterView ndup_f; + Kokkos::Experimental::ScatterView ndup_eatom; + Kokkos::Experimental::ScatterView ndup_vatom; + typename AT::t_int_1d_randomread d_type2frho; typename AT::t_int_2d_randomread d_type2rhor; typename AT::t_int_2d_randomread d_type2z2r; diff --git a/src/KOKKOS/pair_table_kokkos.cpp b/src/KOKKOS/pair_table_kokkos.cpp index 7b06f814bb..b72df04c5f 100644 --- a/src/KOKKOS/pair_table_kokkos.cpp +++ b/src/KOKKOS/pair_table_kokkos.cpp @@ -128,21 +128,25 @@ void PairTableKokkos::compute_style(int eflag_in, int vflag_in) ff(this,(NeighListKokkos*) list); if (eflag || vflag) Kokkos::parallel_reduce(list->inum,ff,ev); else Kokkos::parallel_for(list->inum,ff); + ff.contribute(); } else if (neighflag == HALFTHREAD) { PairComputeFunctor,HALFTHREAD,false,S_TableCompute > ff(this,(NeighListKokkos*) list); if (eflag || vflag) Kokkos::parallel_reduce(list->inum,ff,ev); else Kokkos::parallel_for(list->inum,ff); + ff.contribute(); } else if (neighflag == HALF) { PairComputeFunctor,HALF,false,S_TableCompute > f(this,(NeighListKokkos*) list); if (eflag || vflag) Kokkos::parallel_reduce(list->inum,f,ev); else Kokkos::parallel_for(list->inum,f); + f.contribute(); } else if (neighflag == N2) { PairComputeFunctor,N2,false,S_TableCompute > f(this,(NeighListKokkos*) list); if (eflag || vflag) Kokkos::parallel_reduce(list->inum,f,ev); else Kokkos::parallel_for(list->inum,f); + f.contribute(); } } else { if (neighflag == FULL) { @@ -150,21 +154,25 @@ void PairTableKokkos::compute_style(int eflag_in, int vflag_in) f(this,(NeighListKokkos*) list); if (eflag || vflag) Kokkos::parallel_reduce(list->inum,f,ev); else Kokkos::parallel_for(list->inum,f); + f.contribute(); } else if (neighflag == HALFTHREAD) { PairComputeFunctor,HALFTHREAD,true,S_TableCompute > f(this,(NeighListKokkos*) list); if (eflag || vflag) Kokkos::parallel_reduce(list->inum,f,ev); else Kokkos::parallel_for(list->inum,f); + f.contribute(); } else if (neighflag == HALF) { PairComputeFunctor,HALF,true,S_TableCompute > f(this,(NeighListKokkos*) list); if (eflag || vflag) Kokkos::parallel_reduce(list->inum,f,ev); else Kokkos::parallel_for(list->inum,f); + f.contribute(); } else if (neighflag == N2) { PairComputeFunctor,N2,true,S_TableCompute > f(this,(NeighListKokkos*) list); if (eflag || vflag) Kokkos::parallel_reduce(list->inum,f,ev); else Kokkos::parallel_for(list->inum,f); + f.contribute(); } } diff --git a/src/KOKKOS/pair_tersoff_kokkos.cpp b/src/KOKKOS/pair_tersoff_kokkos.cpp index cb4def2d37..c3e1494d0b 100644 --- a/src/KOKKOS/pair_tersoff_kokkos.cpp +++ b/src/KOKKOS/pair_tersoff_kokkos.cpp @@ -200,6 +200,17 @@ void PairTersoffKokkos::compute(int eflag_in, int vflag_in) d_neighbors = k_list->d_neighbors; d_ilist = k_list->d_ilist; + need_dup = lmp->kokkos->need_dup(); + if (need_dup) { + dup_f = Kokkos::Experimental::create_scatter_view(f); + dup_eatom = Kokkos::Experimental::create_scatter_view(d_eatom); + dup_vatom = Kokkos::Experimental::create_scatter_view(d_vatom); + } else { + ndup_f = Kokkos::Experimental::create_scatter_view(f); + ndup_eatom = Kokkos::Experimental::create_scatter_view(d_eatom); + ndup_vatom = Kokkos::Experimental::create_scatter_view(d_vatom); + } + copymode = 1; EV_FLOAT ev; @@ -243,6 +254,9 @@ void PairTersoffKokkos::compute(int eflag_in, int vflag_in) ev_all += ev; } + if (need_dup) + Kokkos::Experimental::contribute(f, dup_f); + if (eflag_global) eng_vdwl += ev_all.evdwl; if (vflag_global) { virial[0] += ev_all.v[0]; @@ -254,11 +268,15 @@ void PairTersoffKokkos::compute(int eflag_in, int vflag_in) } if (eflag_atom) { + if (need_dup) + Kokkos::Experimental::contribute(d_eatom, dup_eatom); k_eatom.template modify(); k_eatom.template sync(); } if (vflag_atom) { + if (need_dup) + Kokkos::Experimental::contribute(d_vatom, dup_vatom); k_vatom.template modify(); k_vatom.template sync(); } @@ -266,6 +284,13 @@ void PairTersoffKokkos::compute(int eflag_in, int vflag_in) if (vflag_fdotr) pair_virial_fdotr_compute(this); copymode = 0; + + // free duplicated memory + if (need_dup) { + dup_f = decltype(dup_f)(); + dup_eatom = decltype(dup_eatom)(); + dup_vatom = decltype(dup_vatom)(); + } } /* ---------------------------------------------------------------------- */ @@ -304,8 +329,10 @@ template KOKKOS_INLINE_FUNCTION void PairTersoffKokkos::operator()(TagPairTersoffComputeHalf, const int &ii, EV_FLOAT& ev) const { - // The f array is atomic for Half/Thread neighbor style - Kokkos::View::value> > a_f = f; + // The f array is duplicated for OpenMP, atomic for CUDA, and neither for Serial + + auto v_f = ScatterViewHelper::value,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f); + auto a_f = v_f.template access::value>(); const int i = d_ilist[ii]; if (i >= nlocal) return; @@ -1117,14 +1144,18 @@ void PairTersoffKokkos::ev_tally(EV_FLOAT &ev, const int &i, const i { const int VFLAG = vflag_either; - // The eatom and vatom arrays are atomic for Half/Thread neighbor style - Kokkos::View::value> > v_eatom = k_eatom.view(); - Kokkos::View::value> > v_vatom = k_vatom.view(); + // The eatom and vatom arrays are duplicated for OpenMP, atomic for CUDA, and neither for Serial + + auto v_eatom = ScatterViewHelper::value,decltype(dup_eatom),decltype(ndup_eatom)>::get(dup_eatom,ndup_eatom); + auto a_eatom = v_eatom.template access::value>(); + + auto v_vatom = ScatterViewHelper::value,decltype(dup_vatom),decltype(ndup_vatom)>::get(dup_vatom,ndup_vatom); + auto a_vatom = v_vatom.template access::value>(); if (eflag_atom) { const E_FLOAT epairhalf = 0.5 * epair; - v_eatom[i] += epairhalf; - if (NEIGHFLAG != FULL) v_eatom[j] += epairhalf; + a_eatom[i] += epairhalf; + if (NEIGHFLAG != FULL) a_eatom[j] += epairhalf; } if (VFLAG) { @@ -1154,20 +1185,20 @@ void PairTersoffKokkos::ev_tally(EV_FLOAT &ev, const int &i, const i } if (vflag_atom) { - v_vatom(i,0) += 0.5*v0; - v_vatom(i,1) += 0.5*v1; - v_vatom(i,2) += 0.5*v2; - v_vatom(i,3) += 0.5*v3; - v_vatom(i,4) += 0.5*v4; - v_vatom(i,5) += 0.5*v5; + a_vatom(i,0) += 0.5*v0; + a_vatom(i,1) += 0.5*v1; + a_vatom(i,2) += 0.5*v2; + a_vatom(i,3) += 0.5*v3; + a_vatom(i,4) += 0.5*v4; + a_vatom(i,5) += 0.5*v5; if (NEIGHFLAG != FULL) { - v_vatom(j,0) += 0.5*v0; - v_vatom(j,1) += 0.5*v1; - v_vatom(j,2) += 0.5*v2; - v_vatom(j,3) += 0.5*v3; - v_vatom(j,4) += 0.5*v4; - v_vatom(j,5) += 0.5*v5; + a_vatom(j,0) += 0.5*v0; + a_vatom(j,1) += 0.5*v1; + a_vatom(j,2) += 0.5*v2; + a_vatom(j,3) += 0.5*v3; + a_vatom(j,4) += 0.5*v4; + a_vatom(j,5) += 0.5*v5; } } } @@ -1181,9 +1212,10 @@ KOKKOS_INLINE_FUNCTION void PairTersoffKokkos::v_tally3(EV_FLOAT &ev, const int &i, const int &j, const int &k, F_FLOAT *fj, F_FLOAT *fk, F_FLOAT *drij, F_FLOAT *drik) const { + // The vatom array is duplicated for OpenMP, atomic for CUDA, and neither for Serial - // The eatom and vatom arrays are atomic for Half/Thread neighbor style - Kokkos::View::value> > v_vatom = k_vatom.view(); + auto v_vatom = ScatterViewHelper::value,decltype(dup_vatom),decltype(ndup_vatom)>::get(dup_vatom,ndup_vatom); + auto a_vatom = v_vatom.template access::value>(); F_FLOAT v[6]; @@ -1204,13 +1236,13 @@ void PairTersoffKokkos::v_tally3(EV_FLOAT &ev, const int &i, const i } if (vflag_atom) { - v_vatom(i,0) += v[0]; v_vatom(i,1) += v[1]; v_vatom(i,2) += v[2]; - v_vatom(i,3) += v[3]; v_vatom(i,4) += v[4]; v_vatom(i,5) += v[5]; + a_vatom(i,0) += v[0]; a_vatom(i,1) += v[1]; a_vatom(i,2) += v[2]; + a_vatom(i,3) += v[3]; a_vatom(i,4) += v[4]; a_vatom(i,5) += v[5]; if (NEIGHFLAG != FULL) { - v_vatom(j,0) += v[0]; v_vatom(j,1) += v[1]; v_vatom(j,2) += v[2]; - v_vatom(j,3) += v[3]; v_vatom(j,4) += v[4]; v_vatom(j,5) += v[5]; - v_vatom(k,0) += v[0]; v_vatom(k,1) += v[1]; v_vatom(k,2) += v[2]; - v_vatom(k,3) += v[3]; v_vatom(k,4) += v[4]; v_vatom(k,5) += v[5]; + a_vatom(j,0) += v[0]; a_vatom(j,1) += v[1]; a_vatom(j,2) += v[2]; + a_vatom(j,3) += v[3]; a_vatom(j,4) += v[4]; a_vatom(j,5) += v[5]; + a_vatom(k,0) += v[0]; a_vatom(k,1) += v[1]; a_vatom(k,2) += v[2]; + a_vatom(k,3) += v[3]; a_vatom(k,4) += v[4]; a_vatom(k,5) += v[5]; } } diff --git a/src/KOKKOS/pair_tersoff_kokkos.h b/src/KOKKOS/pair_tersoff_kokkos.h index 2dac2c5991..f73d4fe2d8 100644 --- a/src/KOKKOS/pair_tersoff_kokkos.h +++ b/src/KOKKOS/pair_tersoff_kokkos.h @@ -202,6 +202,14 @@ class PairTersoffKokkos : public PairTersoff { typename ArrayTypes::t_efloat_1d d_eatom; typename ArrayTypes::t_virial_array d_vatom; + int need_dup; + Kokkos::Experimental::ScatterView dup_f; + Kokkos::Experimental::ScatterView dup_eatom; + Kokkos::Experimental::ScatterView dup_vatom; + Kokkos::Experimental::ScatterView ndup_f; + Kokkos::Experimental::ScatterView ndup_eatom; + Kokkos::Experimental::ScatterView ndup_vatom; + typedef Kokkos::DualView tdual_ffloat_2d_n7; typedef typename tdual_ffloat_2d_n7::t_dev_const_randomread t_ffloat_2d_n7_randomread; typedef typename tdual_ffloat_2d_n7::t_host t_host_ffloat_2d_n7; diff --git a/src/KOKKOS/pair_tersoff_mod_kokkos.cpp b/src/KOKKOS/pair_tersoff_mod_kokkos.cpp index 0d150f83e4..61493794ba 100644 --- a/src/KOKKOS/pair_tersoff_mod_kokkos.cpp +++ b/src/KOKKOS/pair_tersoff_mod_kokkos.cpp @@ -200,6 +200,17 @@ void PairTersoffMODKokkos::compute(int eflag_in, int vflag_in) d_neighbors = k_list->d_neighbors; d_ilist = k_list->d_ilist; + need_dup = lmp->kokkos->need_dup(); + if (need_dup) { + dup_f = Kokkos::Experimental::create_scatter_view(f); + dup_eatom = Kokkos::Experimental::create_scatter_view(d_eatom); + dup_vatom = Kokkos::Experimental::create_scatter_view(d_vatom); + } else { + ndup_f = Kokkos::Experimental::create_scatter_view(f); + ndup_eatom = Kokkos::Experimental::create_scatter_view(d_eatom); + ndup_vatom = Kokkos::Experimental::create_scatter_view(d_vatom); + } + copymode = 1; EV_FLOAT ev; @@ -243,6 +254,9 @@ void PairTersoffMODKokkos::compute(int eflag_in, int vflag_in) ev_all += ev; } + if (need_dup) + Kokkos::Experimental::contribute(f, dup_f); + if (eflag_global) eng_vdwl += ev_all.evdwl; if (vflag_global) { virial[0] += ev_all.v[0]; @@ -254,11 +268,15 @@ void PairTersoffMODKokkos::compute(int eflag_in, int vflag_in) } if (eflag_atom) { + if (need_dup) + Kokkos::Experimental::contribute(d_eatom, dup_eatom); k_eatom.template modify(); k_eatom.template sync(); } if (vflag_atom) { + if (need_dup) + Kokkos::Experimental::contribute(d_vatom, dup_vatom); k_vatom.template modify(); k_vatom.template sync(); } @@ -266,6 +284,13 @@ void PairTersoffMODKokkos::compute(int eflag_in, int vflag_in) if (vflag_fdotr) pair_virial_fdotr_compute(this); copymode = 0; + + // free duplicated memory + if (need_dup) { + dup_f = decltype(dup_f)(); + dup_eatom = decltype(dup_eatom)(); + dup_vatom = decltype(dup_vatom)(); + } } /* ---------------------------------------------------------------------- */ @@ -304,8 +329,10 @@ template KOKKOS_INLINE_FUNCTION void PairTersoffMODKokkos::operator()(TagPairTersoffMODComputeHalf, const int &ii, EV_FLOAT& ev) const { - // The f array is atomic for Half/Thread neighbor style - Kokkos::View::value> > a_f = f; + // The f array is duplicated for OpenMP, atomic for CUDA, and neither for Serial + + auto v_f = ScatterViewHelper::value,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f); + auto a_f = v_f.template access::value>(); const int i = d_ilist[ii]; if (i >= nlocal) return; @@ -1120,14 +1147,18 @@ void PairTersoffMODKokkos::ev_tally(EV_FLOAT &ev, const int &i, cons { const int VFLAG = vflag_either; - // The eatom and vatom arrays are atomic for Half/Thread neighbor style - Kokkos::View::value> > v_eatom = k_eatom.view(); - Kokkos::View::value> > v_vatom = k_vatom.view(); + // The eatom and vatom arrays are duplicated for OpenMP, atomic for CUDA, and neither for Serial + + auto v_eatom = ScatterViewHelper::value,decltype(dup_eatom),decltype(ndup_eatom)>::get(dup_eatom,ndup_eatom); + auto a_eatom = v_eatom.template access::value>(); + + auto v_vatom = ScatterViewHelper::value,decltype(dup_vatom),decltype(ndup_vatom)>::get(dup_vatom,ndup_vatom); + auto a_vatom = v_vatom.template access::value>(); if (eflag_atom) { const E_FLOAT epairhalf = 0.5 * epair; - v_eatom[i] += epairhalf; - if (NEIGHFLAG != FULL) v_eatom[j] += epairhalf; + a_eatom[i] += epairhalf; + if (NEIGHFLAG != FULL) a_eatom[j] += epairhalf; } if (VFLAG) { @@ -1157,20 +1188,20 @@ void PairTersoffMODKokkos::ev_tally(EV_FLOAT &ev, const int &i, cons } if (vflag_atom) { - v_vatom(i,0) += 0.5*v0; - v_vatom(i,1) += 0.5*v1; - v_vatom(i,2) += 0.5*v2; - v_vatom(i,3) += 0.5*v3; - v_vatom(i,4) += 0.5*v4; - v_vatom(i,5) += 0.5*v5; + a_vatom(i,0) += 0.5*v0; + a_vatom(i,1) += 0.5*v1; + a_vatom(i,2) += 0.5*v2; + a_vatom(i,3) += 0.5*v3; + a_vatom(i,4) += 0.5*v4; + a_vatom(i,5) += 0.5*v5; if (NEIGHFLAG != FULL) { - v_vatom(j,0) += 0.5*v0; - v_vatom(j,1) += 0.5*v1; - v_vatom(j,2) += 0.5*v2; - v_vatom(j,3) += 0.5*v3; - v_vatom(j,4) += 0.5*v4; - v_vatom(j,5) += 0.5*v5; + a_vatom(j,0) += 0.5*v0; + a_vatom(j,1) += 0.5*v1; + a_vatom(j,2) += 0.5*v2; + a_vatom(j,3) += 0.5*v3; + a_vatom(j,4) += 0.5*v4; + a_vatom(j,5) += 0.5*v5; } } } @@ -1184,9 +1215,10 @@ KOKKOS_INLINE_FUNCTION void PairTersoffMODKokkos::v_tally3(EV_FLOAT &ev, const int &i, const int &j, const int &k, F_FLOAT *fj, F_FLOAT *fk, F_FLOAT *drij, F_FLOAT *drik) const { + // The vatom array is duplicated for OpenMP, atomic for CUDA, and neither for Serial - // The eatom and vatom arrays are atomic for Half/Thread neighbor style - Kokkos::View::value> > v_vatom = k_vatom.view(); + auto v_vatom = ScatterViewHelper::value,decltype(dup_vatom),decltype(ndup_vatom)>::get(dup_vatom,ndup_vatom); + auto a_vatom = v_vatom.template access::value>(); F_FLOAT v[6]; @@ -1207,13 +1239,13 @@ void PairTersoffMODKokkos::v_tally3(EV_FLOAT &ev, const int &i, cons } if (vflag_atom) { - v_vatom(i,0) += v[0]; v_vatom(i,1) += v[1]; v_vatom(i,2) += v[2]; - v_vatom(i,3) += v[3]; v_vatom(i,4) += v[4]; v_vatom(i,5) += v[5]; + a_vatom(i,0) += v[0]; a_vatom(i,1) += v[1]; a_vatom(i,2) += v[2]; + a_vatom(i,3) += v[3]; a_vatom(i,4) += v[4]; a_vatom(i,5) += v[5]; if (NEIGHFLAG != FULL) { - v_vatom(j,0) += v[0]; v_vatom(j,1) += v[1]; v_vatom(j,2) += v[2]; - v_vatom(j,3) += v[3]; v_vatom(j,4) += v[4]; v_vatom(j,5) += v[5]; - v_vatom(k,0) += v[0]; v_vatom(k,1) += v[1]; v_vatom(k,2) += v[2]; - v_vatom(k,3) += v[3]; v_vatom(k,4) += v[4]; v_vatom(k,5) += v[5]; + a_vatom(j,0) += v[0]; a_vatom(j,1) += v[1]; a_vatom(j,2) += v[2]; + a_vatom(j,3) += v[3]; a_vatom(j,4) += v[4]; a_vatom(j,5) += v[5]; + a_vatom(k,0) += v[0]; a_vatom(k,1) += v[1]; a_vatom(k,2) += v[2]; + a_vatom(k,3) += v[3]; a_vatom(k,4) += v[4]; a_vatom(k,5) += v[5]; } } diff --git a/src/KOKKOS/pair_tersoff_mod_kokkos.h b/src/KOKKOS/pair_tersoff_mod_kokkos.h index dd5efb50f1..d7c94ffc93 100644 --- a/src/KOKKOS/pair_tersoff_mod_kokkos.h +++ b/src/KOKKOS/pair_tersoff_mod_kokkos.h @@ -202,6 +202,14 @@ class PairTersoffMODKokkos : public PairTersoffMOD { typename ArrayTypes::t_efloat_1d d_eatom; typename ArrayTypes::t_virial_array d_vatom; + int need_dup; + Kokkos::Experimental::ScatterView dup_f; + Kokkos::Experimental::ScatterView dup_eatom; + Kokkos::Experimental::ScatterView dup_vatom; + Kokkos::Experimental::ScatterView ndup_f; + Kokkos::Experimental::ScatterView ndup_eatom; + Kokkos::Experimental::ScatterView ndup_vatom; + typedef Kokkos::DualView tdual_ffloat_2d_n7; typedef typename tdual_ffloat_2d_n7::t_dev_const_randomread t_ffloat_2d_n7_randomread; typedef typename tdual_ffloat_2d_n7::t_host t_host_ffloat_2d_n7; diff --git a/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp b/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp index 2fb9675db6..f51da2afde 100644 --- a/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp +++ b/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp @@ -214,6 +214,17 @@ void PairTersoffZBLKokkos::compute(int eflag_in, int vflag_in) d_neighbors = k_list->d_neighbors; d_ilist = k_list->d_ilist; + need_dup = lmp->kokkos->need_dup(); + if (need_dup) { + dup_f = Kokkos::Experimental::create_scatter_view(f); + dup_eatom = Kokkos::Experimental::create_scatter_view(d_eatom); + dup_vatom = Kokkos::Experimental::create_scatter_view(d_vatom); + } else { + ndup_f = Kokkos::Experimental::create_scatter_view(f); + ndup_eatom = Kokkos::Experimental::create_scatter_view(d_eatom); + ndup_vatom = Kokkos::Experimental::create_scatter_view(d_vatom); + } + copymode = 1; EV_FLOAT ev; @@ -257,6 +268,9 @@ void PairTersoffZBLKokkos::compute(int eflag_in, int vflag_in) ev_all += ev; } + if (need_dup) + Kokkos::Experimental::contribute(f, dup_f); + if (eflag_global) eng_vdwl += ev_all.evdwl; if (vflag_global) { virial[0] += ev_all.v[0]; @@ -268,11 +282,15 @@ void PairTersoffZBLKokkos::compute(int eflag_in, int vflag_in) } if (eflag_atom) { + if (need_dup) + Kokkos::Experimental::contribute(d_eatom, dup_eatom); k_eatom.template modify(); k_eatom.template sync(); } if (vflag_atom) { + if (need_dup) + Kokkos::Experimental::contribute(d_vatom, dup_vatom); k_vatom.template modify(); k_vatom.template sync(); } @@ -280,6 +298,13 @@ void PairTersoffZBLKokkos::compute(int eflag_in, int vflag_in) if (vflag_fdotr) pair_virial_fdotr_compute(this); copymode = 0; + + // free duplicated memory + if (need_dup) { + dup_f = decltype(dup_f)(); + dup_eatom = decltype(dup_eatom)(); + dup_vatom = decltype(dup_vatom)(); + } } /* ---------------------------------------------------------------------- */ @@ -318,8 +343,10 @@ template KOKKOS_INLINE_FUNCTION void PairTersoffZBLKokkos::operator()(TagPairTersoffZBLComputeHalf, const int &ii, EV_FLOAT& ev) const { - // The f array is atomic for Half/Thread neighbor style - Kokkos::View::value> > a_f = f; + // The f array is duplicated for OpenMP, atomic for CUDA, and neither for Serial + + auto v_f = ScatterViewHelper::value,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f); + auto a_f = v_f.template access::value>(); const int i = d_ilist[ii]; if (i >= nlocal) return; @@ -1214,14 +1241,18 @@ void PairTersoffZBLKokkos::ev_tally(EV_FLOAT &ev, const int &i, cons { const int VFLAG = vflag_either; - // The eatom and vatom arrays are atomic for Half/Thread neighbor style - Kokkos::View::value> > v_eatom = k_eatom.view(); - Kokkos::View::value> > v_vatom = k_vatom.view(); + // The eatom and vatom arrays are duplicated for OpenMP, atomic for CUDA, and neither for Serial + + auto v_eatom = ScatterViewHelper::value,decltype(dup_eatom),decltype(ndup_eatom)>::get(dup_eatom,ndup_eatom); + auto a_eatom = v_eatom.template access::value>(); + + auto v_vatom = ScatterViewHelper::value,decltype(dup_vatom),decltype(ndup_vatom)>::get(dup_vatom,ndup_vatom); + auto a_vatom = v_vatom.template access::value>(); if (eflag_atom) { const E_FLOAT epairhalf = 0.5 * epair; - v_eatom[i] += epairhalf; - if (NEIGHFLAG != FULL) v_eatom[j] += epairhalf; + a_eatom[i] += epairhalf; + if (NEIGHFLAG != FULL) a_eatom[j] += epairhalf; } if (VFLAG) { @@ -1251,20 +1282,20 @@ void PairTersoffZBLKokkos::ev_tally(EV_FLOAT &ev, const int &i, cons } if (vflag_atom) { - v_vatom(i,0) += 0.5*v0; - v_vatom(i,1) += 0.5*v1; - v_vatom(i,2) += 0.5*v2; - v_vatom(i,3) += 0.5*v3; - v_vatom(i,4) += 0.5*v4; - v_vatom(i,5) += 0.5*v5; + a_vatom(i,0) += 0.5*v0; + a_vatom(i,1) += 0.5*v1; + a_vatom(i,2) += 0.5*v2; + a_vatom(i,3) += 0.5*v3; + a_vatom(i,4) += 0.5*v4; + a_vatom(i,5) += 0.5*v5; if (NEIGHFLAG != FULL) { - v_vatom(j,0) += 0.5*v0; - v_vatom(j,1) += 0.5*v1; - v_vatom(j,2) += 0.5*v2; - v_vatom(j,3) += 0.5*v3; - v_vatom(j,4) += 0.5*v4; - v_vatom(j,5) += 0.5*v5; + a_vatom(j,0) += 0.5*v0; + a_vatom(j,1) += 0.5*v1; + a_vatom(j,2) += 0.5*v2; + a_vatom(j,3) += 0.5*v3; + a_vatom(j,4) += 0.5*v4; + a_vatom(j,5) += 0.5*v5; } } } @@ -1278,9 +1309,10 @@ KOKKOS_INLINE_FUNCTION void PairTersoffZBLKokkos::v_tally3(EV_FLOAT &ev, const int &i, const int &j, const int &k, F_FLOAT *fj, F_FLOAT *fk, F_FLOAT *drij, F_FLOAT *drik) const { + // The vatom array is duplicated for OpenMP, atomic for CUDA, and neither for Serial - // The eatom and vatom arrays are atomic for Half/Thread neighbor style - Kokkos::View::value> > v_vatom = k_vatom.view(); + auto v_vatom = ScatterViewHelper::value,decltype(dup_vatom),decltype(ndup_vatom)>::get(dup_vatom,ndup_vatom); + auto a_vatom = v_vatom.template access::value>(); F_FLOAT v[6]; @@ -1301,13 +1333,13 @@ void PairTersoffZBLKokkos::v_tally3(EV_FLOAT &ev, const int &i, cons } if (vflag_atom) { - v_vatom(i,0) += v[0]; v_vatom(i,1) += v[1]; v_vatom(i,2) += v[2]; - v_vatom(i,3) += v[3]; v_vatom(i,4) += v[4]; v_vatom(i,5) += v[5]; + a_vatom(i,0) += v[0]; a_vatom(i,1) += v[1]; a_vatom(i,2) += v[2]; + a_vatom(i,3) += v[3]; a_vatom(i,4) += v[4]; a_vatom(i,5) += v[5]; if (NEIGHFLAG != FULL) { - v_vatom(j,0) += v[0]; v_vatom(j,1) += v[1]; v_vatom(j,2) += v[2]; - v_vatom(j,3) += v[3]; v_vatom(j,4) += v[4]; v_vatom(j,5) += v[5]; - v_vatom(k,0) += v[0]; v_vatom(k,1) += v[1]; v_vatom(k,2) += v[2]; - v_vatom(k,3) += v[3]; v_vatom(k,4) += v[4]; v_vatom(k,5) += v[5]; + a_vatom(j,0) += v[0]; a_vatom(j,1) += v[1]; a_vatom(j,2) += v[2]; + a_vatom(j,3) += v[3]; a_vatom(j,4) += v[4]; a_vatom(j,5) += v[5]; + a_vatom(k,0) += v[0]; a_vatom(k,1) += v[1]; a_vatom(k,2) += v[2]; + a_vatom(k,3) += v[3]; a_vatom(k,4) += v[4]; a_vatom(k,5) += v[5]; } } diff --git a/src/KOKKOS/pair_tersoff_zbl_kokkos.h b/src/KOKKOS/pair_tersoff_zbl_kokkos.h index 45982bd420..3af4e0d8eb 100644 --- a/src/KOKKOS/pair_tersoff_zbl_kokkos.h +++ b/src/KOKKOS/pair_tersoff_zbl_kokkos.h @@ -207,6 +207,14 @@ class PairTersoffZBLKokkos : public PairTersoffZBL { typename ArrayTypes::t_efloat_1d d_eatom; typename ArrayTypes::t_virial_array d_vatom; + int need_dup; + Kokkos::Experimental::ScatterView dup_f; + Kokkos::Experimental::ScatterView dup_eatom; + Kokkos::Experimental::ScatterView dup_vatom; + Kokkos::Experimental::ScatterView ndup_f; + Kokkos::Experimental::ScatterView ndup_eatom; + Kokkos::Experimental::ScatterView ndup_vatom; + typedef Kokkos::DualView tdual_ffloat_2d_n7; typedef typename tdual_ffloat_2d_n7::t_dev_const_randomread t_ffloat_2d_n7_randomread; typedef typename tdual_ffloat_2d_n7::t_host t_host_ffloat_2d_n7; diff --git a/src/KSPACE/fft3d.cpp b/src/KSPACE/fft3d.cpp index 6da7f197ee..7d3c8c83f2 100644 --- a/src/KSPACE/fft3d.cpp +++ b/src/KSPACE/fft3d.cpp @@ -14,7 +14,7 @@ /* ---------------------------------------------------------------------- Contributing authors: Jim Shepherd (GA Tech) added SGI SCSL support Axel Kohlmeyer (Temple U) added support for - FFTW3, KISSFFT, Dfti/MKL, and ACML. + FFTW3, KISS FFT, Dfti/MKL, and ACML. Phil Blood (PSC) added single precision FFT. Paul Coffman (IBM) added MPI collectives remap ------------------------------------------------------------------------- */ @@ -26,7 +26,7 @@ #include "fft3d.h" #include "remap.h" -#ifdef FFT_KISSFFT +#ifdef FFT_KISS /* include kissfft implementation */ #include "kissfft.h" #endif @@ -104,11 +104,13 @@ void fft_3d(FFT_DATA *in, FFT_DATA *out, int flag, struct fft_plan_3d *plan) DftiComputeForward(plan->handle_fast,data); else DftiComputeBackward(plan->handle_fast,data); + /* #elif defined(FFT_FFTW2) if (flag == -1) fftw(plan->plan_fast_forward,total/length,data,1,length,NULL,0,0); else - fftw(plan->plan_fast_backward,total/length,data,1,length,NULL,0,0); + fftw(plan->plan_fast_backward,total/length,data,1,length,NULL,0,0); + */ #elif defined(FFT_FFTW3) if (flag == -1) theplan=plan->plan_fast_forward; @@ -143,11 +145,13 @@ void fft_3d(FFT_DATA *in, FFT_DATA *out, int flag, struct fft_plan_3d *plan) DftiComputeForward(plan->handle_mid,data); else DftiComputeBackward(plan->handle_mid,data); + /* #elif defined(FFT_FFTW2) if (flag == -1) fftw(plan->plan_mid_forward,total/length,data,1,length,NULL,0,0); else fftw(plan->plan_mid_backward,total/length,data,1,length,NULL,0,0); + */ #elif defined(FFT_FFTW3) if (flag == -1) theplan=plan->plan_mid_forward; @@ -182,11 +186,13 @@ void fft_3d(FFT_DATA *in, FFT_DATA *out, int flag, struct fft_plan_3d *plan) DftiComputeForward(plan->handle_slow,data); else DftiComputeBackward(plan->handle_slow,data); + /* #elif defined(FFT_FFTW2) if (flag == -1) fftw(plan->plan_slow_forward,total/length,data,1,length,NULL,0,0); else fftw(plan->plan_slow_backward,total/length,data,1,length,NULL,0,0); + */ #elif defined(FFT_FFTW3) if (flag == -1) theplan=plan->plan_slow_forward; @@ -520,6 +526,7 @@ struct fft_plan_3d *fft_3d_create_plan( (out_khi-out_klo+1); } + /* #elif defined(FFT_FFTW2) plan->plan_fast_forward = @@ -561,6 +568,7 @@ struct fft_plan_3d *fft_3d_create_plan( plan->normnum = (out_ihi-out_ilo+1) * (out_jhi-out_jlo+1) * (out_khi-out_klo+1); } + */ #elif defined(FFT_FFTW3) plan->plan_fast_forward = @@ -660,6 +668,7 @@ void fft_3d_destroy_plan(struct fft_plan_3d *plan) DftiFreeDescriptor(&(plan->handle_fast)); DftiFreeDescriptor(&(plan->handle_mid)); DftiFreeDescriptor(&(plan->handle_slow)); + /* #elif defined(FFT_FFTW2) if (plan->plan_slow_forward != plan->plan_fast_forward && plan->plan_slow_forward != plan->plan_mid_forward) { @@ -672,6 +681,7 @@ void fft_3d_destroy_plan(struct fft_plan_3d *plan) } fftw_destroy_plan(plan->plan_fast_forward); fftw_destroy_plan(plan->plan_fast_backward); + */ #elif defined(FFT_FFTW3) FFTW_API(destroy_plan)(plan->plan_slow_forward); FFTW_API(destroy_plan)(plan->plan_slow_backward); @@ -809,6 +819,7 @@ void fft_1d_only(FFT_DATA *data, int nsize, int flag, struct fft_plan_3d *plan) DftiComputeBackward(plan->handle_mid,data); DftiComputeBackward(plan->handle_slow,data); } + /* #elif defined(FFT_FFTW2) if (flag == -1) { fftw(plan->plan_fast_forward,total1/length1,data,1,0,NULL,0,0); @@ -819,6 +830,7 @@ void fft_1d_only(FFT_DATA *data, int nsize, int flag, struct fft_plan_3d *plan) fftw(plan->plan_mid_backward,total2/length2,data,1,0,NULL,0,0); fftw(plan->plan_slow_backward,total3/length3,data,1,0,NULL,0,0); } + */ #elif defined(FFT_FFTW3) FFTW_API(plan) theplan; if (flag == -1) diff --git a/src/KSPACE/fft3d.h b/src/KSPACE/fft3d.h index 9a9caaef26..a51818d986 100644 --- a/src/KSPACE/fft3d.h +++ b/src/KSPACE/fft3d.h @@ -24,8 +24,8 @@ typedef float FFT_SCALAR; typedef double FFT_SCALAR; #endif +// if user set FFTW, it means FFTW3 -// set default fftw library. switch to FFT_FFTW3 when convenient. #ifdef FFT_FFTW #define FFT_FFTW3 #endif @@ -41,13 +41,13 @@ typedef double FFT_SCALAR; typedef float _Complex FFT_DATA; #define FFT_MKL_PREC DFTI_SINGLE -#elif defined(FFT_FFTW2) -#if defined(FFTW_SIZE) -#include "sfftw.h" -#else -#include "fftw.h" -#endif -typedef FFTW_COMPLEX FFT_DATA; +//#elif defined(FFT_FFTW2) +//#if defined(FFTW_SIZE) +//#include "sfftw.h" +//#else +//#include "fftw.h" +//#endif +//typedef FFTW_COMPLEX FFT_DATA; #elif defined(FFT_FFTW3) #include "fftw3.h" @@ -57,8 +57,9 @@ typedef fftwf_complex FFT_DATA; #else /* use a stripped down version of kiss fft as default fft */ -#ifndef FFT_KISSFFT -#define FFT_KISSFFT + +#ifndef FFT_KISS +#define FFT_KISS #endif #define kiss_fft_scalar float typedef struct { @@ -81,13 +82,13 @@ typedef struct kiss_fft_state* kiss_fft_cfg; typedef double _Complex FFT_DATA; #define FFT_MKL_PREC DFTI_DOUBLE -#elif defined(FFT_FFTW2) -#if defined(FFTW_SIZE) -#include "dfftw.h" -#else -#include "fftw.h" -#endif -typedef FFTW_COMPLEX FFT_DATA; +//#elif defined(FFT_FFTW2) +//#if defined(FFTW_SIZE) +//#include "dfftw.h" +//#else +//#include "fftw.h" +//#endif +//typedef FFTW_COMPLEX FFT_DATA; #elif defined(FFT_FFTW3) #include "fftw3.h" @@ -97,8 +98,8 @@ typedef fftw_complex FFT_DATA; #else /* use a stripped down version of kiss fft as default fft */ -#ifndef FFT_KISSFFT -#define FFT_KISSFFT +#ifndef FFT_KISS +#define FFT_KISS #endif #define kiss_fft_scalar double typedef struct { @@ -138,13 +139,13 @@ struct fft_plan_3d { DFTI_DESCRIPTOR *handle_fast; DFTI_DESCRIPTOR *handle_mid; DFTI_DESCRIPTOR *handle_slow; -#elif defined(FFT_FFTW2) - fftw_plan plan_fast_forward; - fftw_plan plan_fast_backward; - fftw_plan plan_mid_forward; - fftw_plan plan_mid_backward; - fftw_plan plan_slow_forward; - fftw_plan plan_slow_backward; +//#elif defined(FFT_FFTW2) +// fftw_plan plan_fast_forward; +// fftw_plan plan_fast_backward; +// fftw_plan plan_mid_forward; +// fftw_plan plan_mid_backward; +//fftw_plan plan_slow_forward; +//fftw_plan plan_slow_backward; #elif defined(FFT_FFTW3) FFTW_API(plan) plan_fast_forward; FFTW_API(plan) plan_fast_backward; @@ -152,7 +153,7 @@ struct fft_plan_3d { FFTW_API(plan) plan_mid_backward; FFTW_API(plan) plan_slow_forward; FFTW_API(plan) plan_slow_backward; -#elif defined(FFT_KISSFFT) +#elif defined(FFT_KISS) kiss_fft_cfg cfg_fast_forward; kiss_fft_cfg cfg_fast_backward; kiss_fft_cfg cfg_mid_forward; diff --git a/src/KSPACE/kissfft.h b/src/KSPACE/kissfft.h index 4e15f494a9..c95b648dcb 100644 --- a/src/KSPACE/kissfft.h +++ b/src/KSPACE/kissfft.h @@ -13,6 +13,7 @@ changes 2008-2011 by Axel Kohlmeyer */ + #ifndef LMP_FFT_KISSFFT #define LMP_FFT_KISSFFT diff --git a/src/KSPACE/msm.cpp b/src/KSPACE/msm.cpp index 9f3221449b..efa2c87296 100644 --- a/src/KSPACE/msm.cpp +++ b/src/KSPACE/msm.cpp @@ -177,7 +177,7 @@ void MSM::init() if (sizeof(FFT_SCALAR) != 8) error->all(FLERR,"Cannot (yet) use single precision with MSM " - "(remove -DFFT_SINGLE from Makefile and recompile)"); + "(remove -DFFT_SINGLE from Makefile and re-compile)"); // extract short-range Coulombic cutoff from pair style @@ -419,7 +419,7 @@ void MSM::setup() boxlo = domain->boxlo_lamda; // ghost grid points depend on direct sum interaction limits, - // so need to recompute local grid + // so need to re-compute local grid set_grid_local(); diff --git a/src/KSPACE/pair_coul_long.cpp b/src/KSPACE/pair_coul_long.cpp index 4b10782ee6..8db5979b39 100644 --- a/src/KSPACE/pair_coul_long.cpp +++ b/src/KSPACE/pair_coul_long.cpp @@ -338,9 +338,9 @@ void PairCoulLong::read_restart_settings(FILE *fp) /* ---------------------------------------------------------------------- */ -double PairCoulLong::single(int i, int j, int itype, int jtype, +double PairCoulLong::single(int i, int j, int /*itype*/, int /*jtype*/, double rsq, - double factor_coul, double factor_lj, + double factor_coul, double /*factor_lj*/, double &fforce) { double r2inv,r,grij,expm2,t,erfc,prefactor; diff --git a/src/KSPACE/pair_coul_msm.cpp b/src/KSPACE/pair_coul_msm.cpp index f5cd9a0445..ab59dfa4c1 100644 --- a/src/KSPACE/pair_coul_msm.cpp +++ b/src/KSPACE/pair_coul_msm.cpp @@ -169,9 +169,9 @@ void PairCoulMSM::compute(int eflag, int vflag) /* ---------------------------------------------------------------------- */ -double PairCoulMSM::single(int i, int j, int itype, int jtype, +double PairCoulMSM::single(int i, int j, int /*itype*/, int /*jtype*/, double rsq, - double factor_coul, double factor_lj, + double factor_coul, double /*factor_lj*/, double &fforce) { double r2inv,r,egamma,fgamma,prefactor; diff --git a/src/KSPACE/pppm_disp.cpp b/src/KSPACE/pppm_disp.cpp index aea57da326..b8cd52c5fe 100644 --- a/src/KSPACE/pppm_disp.cpp +++ b/src/KSPACE/pppm_disp.cpp @@ -8052,7 +8052,7 @@ void PPPMDisp::compute_rho_coeff(FFT_SCALAR **coeff , FFT_SCALAR **dcoeff, extended to non-neutral systems (J. Chem. Phys. 131, 094107). ------------------------------------------------------------------------- */ -void PPPMDisp::slabcorr(int eflag) +void PPPMDisp::slabcorr(int /*eflag*/) { // compute local contribution to global dipole moment diff --git a/src/KSPACE/remap.cpp b/src/KSPACE/remap.cpp index 81dd692f4f..26541f121e 100644 --- a/src/KSPACE/remap.cpp +++ b/src/KSPACE/remap.cpp @@ -234,7 +234,7 @@ struct remap_plan_3d *remap_3d_create_plan( int in_klo, int in_khi, int out_ilo, int out_ihi, int out_jlo, int out_jhi, int out_klo, int out_khi, - int nqty, int permute, int memory, int precision, int usecollective) + int nqty, int permute, int memory, int /*precision*/, int usecollective) { diff --git a/src/LATTE/fix_latte.cpp b/src/LATTE/fix_latte.cpp index 4a3fc81f51..a89be57bed 100644 --- a/src/LATTE/fix_latte.cpp +++ b/src/LATTE/fix_latte.cpp @@ -42,6 +42,13 @@ extern "C" { int latte_abiversion(); } +// the ABIVERSION number here must be kept consistent +// with its counterpart in the LATTE library and the +// prototype above. We want to catch mismatches with +// a meaningful error messages, as they can cause +// difficult to debug crashes or memory corruption. + +#define LATTE_ABIVERSION 20180622 #define INVOKED_PERATOM 8 /* ---------------------------------------------------------------------- */ @@ -55,7 +62,7 @@ FixLatte::FixLatte(LAMMPS *lmp, int narg, char **arg) : if (comm->nprocs != 1) error->all(FLERR,"Fix latte currently runs only in serial"); - if (20180622 != latte_abiversion()) + if (LATTE_ABIVERSION != latte_abiversion()) error->all(FLERR,"LAMMPS is linked against incompatible LATTE library"); if (narg != 4) error->all(FLERR,"Illegal fix latte command"); @@ -182,7 +189,7 @@ void FixLatte::init() /* ---------------------------------------------------------------------- */ -void FixLatte::init_list(int id, NeighList *ptr) +void FixLatte::init_list(int /*id*/, NeighList * /*ptr*/) { // list = ptr; } @@ -216,13 +223,13 @@ void FixLatte::setup_pre_reverse(int eflag, int vflag) integrate electronic degrees of freedom ------------------------------------------------------------------------- */ -void FixLatte::initial_integrate(int vflag) {} +void FixLatte::initial_integrate(int /*vflag*/) {} /* ---------------------------------------------------------------------- store eflag, so can use it in post_force to tally per-atom energies ------------------------------------------------------------------------- */ -void FixLatte::pre_reverse(int eflag, int vflag) +void FixLatte::pre_reverse(int eflag, int /*vflag*/) { eflag_caller = eflag; } diff --git a/src/MAKE/MACHINES/Makefile.aarch64_arm_openmpi_armpl b/src/MAKE/MACHINES/Makefile.aarch64_arm_openmpi_armpl new file mode 100644 index 0000000000..0f5087618b --- /dev/null +++ b/src/MAKE/MACHINES/Makefile.aarch64_arm_openmpi_armpl @@ -0,0 +1,121 @@ +# g++_openmpi = OpenMPI with compiler set to GNU g++ + +SHELL = /bin/sh + +# --------------------------------------------------------------------- +# compiler/linker settings +# specify flags and libraries needed for your compiler + +#export OMPI_CXX = armclang++ +CC = mpicxx +CCFLAGS = -O3 -mcpu=native +SHFLAGS = -fPIC +DEPFLAGS = -M + +LINK = mpicxx +LINKFLAGS = -g -O +LIB = +SIZE = size + +ARCHIVE = ar +ARFLAGS = -rc +SHLIBFLAGS = -shared + +# --------------------------------------------------------------------- +# LAMMPS-specific settings, all OPTIONAL +# specify settings for LAMMPS features you will use +# if you change any -D setting, do full re-compile after "make clean" + +# LAMMPS ifdef settings +# see possible settings in Section 2.2 (step 4) of manual + +LMP_INC = -DLAMMPS_GZIP + +# MPI library +# see discussion in Section 2.2 (step 5) of manual +# MPI wrapper compiler/linker can provide this info +# can point to dummy MPI library in src/STUBS as in Makefile.serial +# use -D MPICH and OMPI settings in INC to avoid C++ lib conflicts +# INC = path for mpi.h, MPI compiler settings +# PATH = path for MPI library +# LIB = name of MPI library + +MPI_INC = -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 +MPI_PATH = +MPI_LIB = + +# FFT library +# see discussion in Section 2.2 (step 6) of manaul +# can be left blank to use provided KISS FFT library +# INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings +# PATH = path for FFT library +# LIB = name of FFT library + +FFT_INC = -DFFT_FFTW +FFT_PATH = -L$(ARMPL_LIBRARIES) +FFT_LIB = -larmpl_lp64 + +# JPEG and/or PNG library +# see discussion in Section 2.2 (step 7) of manual +# only needed if -DLAMMPS_JPEG or -DLAMMPS_PNG listed with LMP_INC +# INC = path(s) for jpeglib.h and/or png.h +# PATH = path(s) for JPEG library and/or PNG library +# LIB = name(s) of JPEG library and/or PNG library + +JPG_INC = +JPG_PATH = +JPG_LIB = + +# --------------------------------------------------------------------- +# build rules and dependencies +# do not edit this section + +include Makefile.package.settings +include Makefile.package + +EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC) +EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH) +EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) +EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS) +EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS) + +# Path to src files + +vpath %.cpp .. +vpath %.h .. + +# Link target + +$(EXE): $(OBJ) $(EXTRA_LINK_DEPENDS) + $(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE) + $(SIZE) $(EXE) + +# Library targets + +lib: $(OBJ) $(EXTRA_LINK_DEPENDS) + $(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ) + +shlib: $(OBJ) $(EXTRA_LINK_DEPENDS) + $(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \ + $(OBJ) $(EXTRA_LIB) $(LIB) + +# Compilation rules + +%.o:%.cpp $(EXTRA_CPP_DEPENDS) + $(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $< + +%.d:%.cpp $(EXTRA_CPP_DEPENDS) + $(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@ + +%.o:%.cu $(EXTRA_CPP_DEPENDS) + $(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $< + +# Individual dependencies + +depend : fastdep.exe $(SRC) + @./fastdep.exe $(EXTRA_INC) -- $^ > .depend || exit 1 + +fastdep.exe: ../DEPEND/fastdep.c + cc -O -o $@ $< + +sinclude .depend diff --git a/src/MAKE/MACHINES/Makefile.aarch64_arm_serial_armpl b/src/MAKE/MACHINES/Makefile.aarch64_arm_serial_armpl new file mode 100644 index 0000000000..c303a97e17 --- /dev/null +++ b/src/MAKE/MACHINES/Makefile.aarch64_arm_serial_armpl @@ -0,0 +1,120 @@ +# arm_serial = Arm armclang compiler, no MPI + +SHELL = /bin/sh + +# --------------------------------------------------------------------- +# compiler/linker settings +# specify flags and libraries needed for your compiler + +CC = armclang++ +CCFLAGS = -O3 -mcpu=native +SHFLAGS = -fPIC +DEPFLAGS = -M + +LINK = armclang++ +LINKFLAGS = -g -O +LIB = +SIZE = size + +ARCHIVE = ar +ARFLAGS = -rc +SHLIBFLAGS = -shared + +# --------------------------------------------------------------------- +# LAMMPS-specific settings, all OPTIONAL +# specify settings for LAMMPS features you will use +# if you change any -D setting, do full re-compile after "make clean" + +# LAMMPS ifdef settings +# see possible settings in Section 2.2 (step 4) of manual + +LMP_INC = -DLAMMPS_GZIP + +# MPI library +# see discussion in Section 2.2 (step 5) of manual +# MPI wrapper compiler/linker can provide this info +# can point to dummy MPI library in src/STUBS as in Makefile.serial +# use -D MPICH and OMPI settings in INC to avoid C++ lib conflicts +# INC = path for mpi.h, MPI compiler settings +# PATH = path for MPI library +# LIB = name of MPI library + +MPI_INC = -I../STUBS +MPI_PATH = -L../STUBS +MPI_LIB = -lmpi_stubs + +# FFT library +# see discussion in Section 2.2 (step 6) of manaul +# can be left blank to use provided KISS FFT library +# INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings +# PATH = path for FFT library +# LIB = name of FFT library + +FFT_INC = -DFFT_FFTW +FFT_PATH = -L$(ARMPL_LIBRARIES) +FFT_LIB = -larmpl_lp64 + +# JPEG and/or PNG library +# see discussion in Section 2.2 (step 7) of manual +# only needed if -DLAMMPS_JPEG or -DLAMMPS_PNG listed with LMP_INC +# INC = path(s) for jpeglib.h and/or png.h +# PATH = path(s) for JPEG library and/or PNG library +# LIB = name(s) of JPEG library and/or PNG library + +JPG_INC = +JPG_PATH = +JPG_LIB = + +# --------------------------------------------------------------------- +# build rules and dependencies +# do not edit this section + +include Makefile.package.settings +include Makefile.package + +EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC) +EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH) +EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) +EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS) +EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS) + +# Path to src files + +vpath %.cpp .. +vpath %.h .. + +# Link target + +$(EXE): $(OBJ) $(EXTRA_LINK_DEPENDS) + $(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE) + $(SIZE) $(EXE) + +# Library targets + +lib: $(OBJ) $(EXTRA_LINK_DEPENDS) + $(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ) + +shlib: $(OBJ) $(EXTRA_LINK_DEPENDS) + $(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \ + $(OBJ) $(EXTRA_LIB) $(LIB) + +# Compilation rules + +%.o:%.cpp $(EXTRA_CPP_DEPENDS) + $(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $< + +%.d:%.cpp $(EXTRA_CPP_DEPENDS) + $(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@ + +%.o:%.cu $(EXTRA_CPP_DEPENDS) + $(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $< + +# Individual dependencies + +depend : fastdep.exe $(SRC) + @./fastdep.exe $(EXTRA_INC) -- $^ > .depend || exit 1 + +fastdep.exe: ../DEPEND/fastdep.c + cc -O -o $@ $< + +sinclude .depend diff --git a/src/MAKE/MACHINES/Makefile.aarch64_g++_openmpi_armpl b/src/MAKE/MACHINES/Makefile.aarch64_g++_openmpi_armpl new file mode 100644 index 0000000000..b3cc1f48a3 --- /dev/null +++ b/src/MAKE/MACHINES/Makefile.aarch64_g++_openmpi_armpl @@ -0,0 +1,121 @@ +# g++_openmpi = OpenMPI with compiler set to GNU g++ + +SHELL = /bin/sh + +# --------------------------------------------------------------------- +# compiler/linker settings +# specify flags and libraries needed for your compiler + +export OMPI_CXX = g++ +CC = mpicxx +CCFLAGS = -O3 -march=native -mcpu=native +SHFLAGS = -fPIC +DEPFLAGS = -M + +LINK = mpicxx +LINKFLAGS = -O +LIB = +SIZE = size + +ARCHIVE = ar +ARFLAGS = -rc +SHLIBFLAGS = -shared + +# --------------------------------------------------------------------- +# LAMMPS-specific settings, all OPTIONAL +# specify settings for LAMMPS features you will use +# if you change any -D setting, do full re-compile after "make clean" + +# LAMMPS ifdef settings +# see possible settings in Section 2.2 (step 4) of manual + +LMP_INC = -DLAMMPS_GZIP + +# MPI library +# see discussion in Section 2.2 (step 5) of manual +# MPI wrapper compiler/linker can provide this info +# can point to dummy MPI library in src/STUBS as in Makefile.serial +# use -D MPICH and OMPI settings in INC to avoid C++ lib conflicts +# INC = path for mpi.h, MPI compiler settings +# PATH = path for MPI library +# LIB = name of MPI library + +MPI_INC = -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 +MPI_PATH = +MPI_LIB = + +# FFT library +# see discussion in Section 2.2 (step 6) of manaul +# can be left blank to use provided KISS FFT library +# INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings +# PATH = path for FFT library +# LIB = name of FFT library + +FFT_INC = -DFFT_FFTW +FFT_PATH = -L$(ARMPL_LIBRARIES) +FFT_LIB = -larmpl_lp64 + +# JPEG and/or PNG library +# see discussion in Section 2.2 (step 7) of manual +# only needed if -DLAMMPS_JPEG or -DLAMMPS_PNG listed with LMP_INC +# INC = path(s) for jpeglib.h and/or png.h +# PATH = path(s) for JPEG library and/or PNG library +# LIB = name(s) of JPEG library and/or PNG library + +JPG_INC = +JPG_PATH = +JPG_LIB = + +# --------------------------------------------------------------------- +# build rules and dependencies +# do not edit this section + +include Makefile.package.settings +include Makefile.package + +EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC) +EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH) +EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) +EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS) +EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS) + +# Path to src files + +vpath %.cpp .. +vpath %.h .. + +# Link target + +$(EXE): $(OBJ) $(EXTRA_LINK_DEPENDS) + $(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE) + $(SIZE) $(EXE) + +# Library targets + +lib: $(OBJ) $(EXTRA_LINK_DEPENDS) + $(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ) + +shlib: $(OBJ) $(EXTRA_LINK_DEPENDS) + $(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \ + $(OBJ) $(EXTRA_LIB) $(LIB) + +# Compilation rules + +%.o:%.cpp $(EXTRA_CPP_DEPENDS) + $(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $< + +%.d:%.cpp $(EXTRA_CPP_DEPENDS) + $(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@ + +%.o:%.cu $(EXTRA_CPP_DEPENDS) + $(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $< + +# Individual dependencies + +depend : fastdep.exe $(SRC) + @./fastdep.exe $(EXTRA_INC) -- $^ > .depend || exit 1 + +fastdep.exe: ../DEPEND/fastdep.c + cc -O -o $@ $< + +sinclude .depend diff --git a/src/MAKE/MACHINES/Makefile.aarch64_g++_serial_armpl b/src/MAKE/MACHINES/Makefile.aarch64_g++_serial_armpl new file mode 100644 index 0000000000..45c0bb162b --- /dev/null +++ b/src/MAKE/MACHINES/Makefile.aarch64_g++_serial_armpl @@ -0,0 +1,120 @@ +# g++_serial = GNU g++ compiler, no MPI + +SHELL = /bin/sh + +# --------------------------------------------------------------------- +# compiler/linker settings +# specify flags and libraries needed for your compiler + +CC = g++ +CCFLAGS = -O3 -march=native -mcpu=native +SHFLAGS = -fPIC +DEPFLAGS = -M + +LINK = g++ +LINKFLAGS = -O +LIB = +SIZE = size + +ARCHIVE = ar +ARFLAGS = -rc +SHLIBFLAGS = -shared + +# --------------------------------------------------------------------- +# LAMMPS-specific settings, all OPTIONAL +# specify settings for LAMMPS features you will use +# if you change any -D setting, do full re-compile after "make clean" + +# LAMMPS ifdef settings +# see possible settings in Section 2.2 (step 4) of manual + +LMP_INC = -DLAMMPS_GZIP + +# MPI library +# see discussion in Section 2.2 (step 5) of manual +# MPI wrapper compiler/linker can provide this info +# can point to dummy MPI library in src/STUBS as in Makefile.serial +# use -D MPICH and OMPI settings in INC to avoid C++ lib conflicts +# INC = path for mpi.h, MPI compiler settings +# PATH = path for MPI library +# LIB = name of MPI library + +MPI_INC = -I../STUBS +MPI_PATH = -L../STUBS +MPI_LIB = -lmpi_stubs + +# FFT library +# see discussion in Section 2.2 (step 6) of manaul +# can be left blank to use provided KISS FFT library +# INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings +# PATH = path for FFT library +# LIB = name of FFT library + +FFT_INC = -DFFT_FFTW +FFT_PATH = -L$(ARMPL_LIBRARIES) +FFT_LIB = -larmpl_lp64 + +# JPEG and/or PNG library +# see discussion in Section 2.2 (step 7) of manual +# only needed if -DLAMMPS_JPEG or -DLAMMPS_PNG listed with LMP_INC +# INC = path(s) for jpeglib.h and/or png.h +# PATH = path(s) for JPEG library and/or PNG library +# LIB = name(s) of JPEG library and/or PNG library + +JPG_INC = +JPG_PATH = +JPG_LIB = + +# --------------------------------------------------------------------- +# build rules and dependencies +# do not edit this section + +include Makefile.package.settings +include Makefile.package + +EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC) +EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH) +EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) +EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS) +EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS) + +# Path to src files + +vpath %.cpp .. +vpath %.h .. + +# Link target + +$(EXE): $(OBJ) $(EXTRA_LINK_DEPENDS) + $(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE) + $(SIZE) $(EXE) + +# Library targets + +lib: $(OBJ) $(EXTRA_LINK_DEPENDS) + $(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ) + +shlib: $(OBJ) $(EXTRA_LINK_DEPENDS) + $(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \ + $(OBJ) $(EXTRA_LIB) $(LIB) + +# Compilation rules + +%.o:%.cpp $(EXTRA_CPP_DEPENDS) + $(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $< + +%.d:%.cpp $(EXTRA_CPP_DEPENDS) + $(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@ + +%.o:%.cu $(EXTRA_CPP_DEPENDS) + $(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $< + +# Individual dependencies + +depend : fastdep.exe $(SRC) + @./fastdep.exe $(EXTRA_INC) -- $^ > .depend || exit 1 + +fastdep.exe: ../DEPEND/fastdep.c + cc -O -o $@ $< + +sinclude .depend diff --git a/src/MAKE/MACHINES/Makefile.theta b/src/MAKE/MACHINES/Makefile.theta new file mode 100644 index 0000000000..cad5a03b42 --- /dev/null +++ b/src/MAKE/MACHINES/Makefile.theta @@ -0,0 +1,133 @@ +# knl = Flags for Knights Landing Xeon Phi Processor,Intel Compiler/MPI,MKL FFT +# module load perftools-base perftools +# make theta -j 8 +# pat_build -g mpi -u ./lmp_theta + +SHELL = /bin/sh + +# --------------------------------------------------------------------- +# compiler/linker settings +# specify flags and libraries needed for your compiler + +CC = CC -mkl +#OPTFLAGS = -O0 +OPTFLAGS = -xMIC-AVX512 -O3 -fp-model fast=2 -no-prec-div -qoverride-limits +CCFLAGS = -g -qopenmp -DLAMMPS_MEMALIGN=64 -qno-offload \ + -fno-alias -ansi-alias -restrict $(OPTFLAGS) +#CCFLAGS += -DLMP_INTEL_NO_TBB +#CCFLAGS += -DLAMMPS_BIGBIG +#CCFLAGS += -D_USE_PAPI +#CCFLAGS += -D_USE_CRAYPAT_API +SHFLAGS = -fPIC +DEPFLAGS = -M + +LINK = $(CC) +LINKFLAGS = -g -qopenmp $(OPTFLAGS) +LINKFLAGS += -dynamic +LIB = +#LIB += -L${TBBROOT}/lib/intel64/gcc4.7 -ltbbmalloc +LIB += -ltbbmalloc +#LIB += /soft/debuggers/forge-7.0-2017-02-16/lib/64/libdmallocthcxx.a -zmuldefs +SIZE = size + +ARCHIVE = ar +ARFLAGS = -rc +SHLIBFLAGS = -shared + +# --------------------------------------------------------------------- +# LAMMPS-specific settings, all OPTIONAL +# specify settings for LAMMPS features you will use +# if you change any -D setting, do full re-compile after "make clean" + +# LAMMPS ifdef settings +# see possible settings in Section 2.2 (step 4) of manual + +LMP_INC = -DLAMMPS_GZIP #-DLAMMPS_JPEG + +# MPI library +# see discussion in Section 2.2 (step 5) of manual +# MPI wrapper compiler/linker can provide this info +# can point to dummy MPI library in src/STUBS as in Makefile.serial +# use -D MPICH and OMPI settings in INC to avoid C++ lib conflicts +# INC = path for mpi.h, MPI compiler settings +# PATH = path for MPI library +# LIB = name of MPI library + +MPI_INC = -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 +MPI_PATH = +MPI_LIB = + +# FFT library +# see discussion in Section 2.2 (step 6) of manaul +# can be left blank to use provided KISS FFT library +# INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings +# PATH = path for FFT library +# LIB = name of FFT library + +FFT_INC = -DFFT_MKL -DFFT_SINGLE +FFT_PATH = +FFT_LIB = -L$(MKLROOT)/lib/intel64/ -Wl,--start-group -lmkl_intel_ilp64 \ + -lmkl_intel_thread -lmkl_core -Wl,--end-group + +# JPEG and/or PNG library +# see discussion in Section 2.2 (step 7) of manual +# only needed if -DLAMMPS_JPEG or -DLAMMPS_PNG listed with LMP_INC +# INC = path(s) for jpeglib.h and/or png.h +# PATH = path(s) for JPEG library and/or PNG library +# LIB = name(s) of JPEG library and/or PNG library + +JPG_INC = +JPG_PATH = +JPG_LIB = + +# --------------------------------------------------------------------- +# build rules and dependencies +# do not edit this section + +include Makefile.package.settings +include Makefile.package + +EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC) +EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH) +EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) + +# Path to src files + +vpath %.cpp .. +vpath %.h .. + +# Link target + +$(EXE): $(OBJ) + $(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE) + $(SIZE) $(EXE) + +# Library targets + +lib: $(OBJ) + $(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ) + +shlib: $(OBJ) + $(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \ + $(OBJ) $(EXTRA_LIB) $(LIB) + +# Compilation rules + +%.o:%.cpp + $(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $< + +%.d:%.cpp + $(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@ + +%.o:%.cu + $(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $< + +# Individual dependencies + +depend : fastdep.exe $(SRC) + @./fastdep.exe $(EXTRA_INC) -- $^ > .depend || exit 1 + +fastdep.exe: ../DEPEND/fastdep.c + icc -O -o $@ $< + +sinclude .depend diff --git a/src/MANYBODY/fix_qeq_comb.cpp b/src/MANYBODY/fix_qeq_comb.cpp index b8d9c7e6df..e46da9bfe7 100644 --- a/src/MANYBODY/fix_qeq_comb.cpp +++ b/src/MANYBODY/fix_qeq_comb.cpp @@ -159,7 +159,7 @@ void FixQEQComb::min_post_force(int vflag) /* ---------------------------------------------------------------------- */ -void FixQEQComb::post_force(int vflag) +void FixQEQComb::post_force(int /*vflag*/) { int i,ii,iloop,loopmax,inum,*ilist; double heatpq,qmass,dtq,dtq2; @@ -276,7 +276,7 @@ void FixQEQComb::post_force(int vflag) /* ---------------------------------------------------------------------- */ -void FixQEQComb::post_force_respa(int vflag, int ilevel, int iloop) +void FixQEQComb::post_force_respa(int vflag, int ilevel, int /*iloop*/) { if (ilevel == ilevel_respa) post_force(vflag); } @@ -293,7 +293,7 @@ double FixQEQComb::memory_usage() /* ---------------------------------------------------------------------- */ int FixQEQComb::pack_forward_comm(int n, int *list, double *buf, - int pbc_flag, int *pbc) + int /*pbc_flag*/, int * /*pbc*/) { int i,j,m; diff --git a/src/MANYBODY/pair_adp.cpp b/src/MANYBODY/pair_adp.cpp index d0b4d19758..831f1d0efa 100644 --- a/src/MANYBODY/pair_adp.cpp +++ b/src/MANYBODY/pair_adp.cpp @@ -424,7 +424,7 @@ void PairADP::allocate() global settings ------------------------------------------------------------------------- */ -void PairADP::settings(int narg, char **arg) +void PairADP::settings(int narg, char **/*arg*/) { if (narg > 0) error->all(FLERR,"Illegal pair_style command"); } @@ -521,7 +521,7 @@ void PairADP::init_style() init for one type pair i,j and corresponding j,i ------------------------------------------------------------------------- */ -double PairADP::init_one(int i, int j) +double PairADP::init_one(int /*i*/, int /*j*/) { // single global cutoff = max of cut from all files read in // for funcfl could be multiple files @@ -935,7 +935,7 @@ void PairADP::grab(FILE *fp, int n, double *list) /* ---------------------------------------------------------------------- */ int PairADP::pack_forward_comm(int n, int *list, double *buf, - int pbc_flag, int *pbc) + int /*pbc_flag*/, int * /*pbc*/) { int i,j,m; diff --git a/src/MANYBODY/pair_airebo.cpp b/src/MANYBODY/pair_airebo.cpp index 3be27354c1..ac3ed36a83 100644 --- a/src/MANYBODY/pair_airebo.cpp +++ b/src/MANYBODY/pair_airebo.cpp @@ -425,7 +425,7 @@ void PairAIREBO::REBO_neigh() REBO forces and energy ------------------------------------------------------------------------- */ -void PairAIREBO::FREBO(int eflag, int vflag) +void PairAIREBO::FREBO(int eflag, int /*vflag*/) { int i,j,k,m,ii,inum,itype,jtype; tagint itag,jtag; @@ -524,7 +524,7 @@ void PairAIREBO::FREBO(int eflag, int vflag) find 3- and 4-step paths between atoms I,J via REBO neighbor lists ------------------------------------------------------------------------- */ -void PairAIREBO::FLJ(int eflag, int vflag) +void PairAIREBO::FLJ(int eflag, int /*vflag*/) { int i,j,k,m,ii,jj,kk,mm,inum,jnum,itype,jtype,ktype,mtype; int atomi,atomj,atomk,atomm; @@ -893,7 +893,7 @@ void PairAIREBO::FLJ(int eflag, int vflag) torsional forces and energy ------------------------------------------------------------------------- */ -void PairAIREBO::TORSION(int eflag, int vflag) +void PairAIREBO::TORSION(int eflag, int /*vflag*/) { int i,j,k,l,ii,inum; tagint itag,jtag; @@ -2116,7 +2116,7 @@ but of the vector r_ij. */ -double PairAIREBO::bondorderLJ(int i, int j, double rij_mod[3], double rijmag_mod, +double PairAIREBO::bondorderLJ(int i, int j, double /*rij_mod*/[3], double rijmag_mod, double VA, double rij[3], double rijmag, double **f, int vflag_atom) { diff --git a/src/MANYBODY/pair_atm.cpp b/src/MANYBODY/pair_atm.cpp new file mode 100644 index 0000000000..a6e52faeba --- /dev/null +++ b/src/MANYBODY/pair_atm.cpp @@ -0,0 +1,374 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Sergey Lishchuk +------------------------------------------------------------------------- */ + +#include +#include "pair_atm.h" +#include "atom.h" +#include "citeme.h" +#include "comm.h" +#include "error.h" +#include "force.h" +#include "memory.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" + +using namespace LAMMPS_NS; + +static const char cite_atm_package[] = + "ATM package:\n\n" + "@Article{Lishchuk:2012:164501,\n" + " author = {S. V. Lishchuk},\n" + " title = {Role of three-body interactions in formation of bulk viscosity in liquid argon},\n" + " journal = {J.~Chem.~Phys.},\n" + " year = 2012,\n" + " volume = 136,\n" + " pages = {164501}\n" + "}\n\n"; + +/* ---------------------------------------------------------------------- */ + +PairATM::PairATM(LAMMPS *lmp) : Pair(lmp) +{ + if (lmp->citeme) lmp->citeme->add(cite_atm_package); + + single_enable = 0; + restartinfo = 1; + one_coeff = 0; + manybody_flag = 1; +} + +/* ---------------------------------------------------------------------- + check if allocated, since class can be destructed when incomplete +------------------------------------------------------------------------- */ + +PairATM::~PairATM() +{ + if (copymode) return; + + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + + memory->destroy(nu); + } +} + +/* ---------------------------------------------------------------------- + workhorse routine that computes pairwise interactions +------------------------------------------------------------------------- */ + +void PairATM::compute(int eflag, int vflag) +{ + int i,j,k,ii,jj,kk,inum,jnum,jnumm1; + double xi,yi,zi,evdwl; + double rij2,rik2,rjk2; + double rij[3],rik[3],rjk[3],fj[3],fk[3]; + double nu_local; + int *ilist,*jlist,*numneigh,**firstneigh; + + evdwl = 0.0; + if (eflag || vflag) ev_setup(eflag,vflag); + else evflag = vflag_fdotr = 0; + + double **x = atom->x; + double **f = atom->f; + int *type = atom->type; + + double cutoff_squared = cut_global*cut_global; + double triple = cut_triple*cut_triple*cut_triple; + double cutoff_triple_sixth = triple*triple; + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // triple loop over local atoms and neighbors twice + // must compute each IJK triplet interaction exactly once + // by proc that owns the triplet atom with smallest x coord + // special logic to break ties if multiple atoms have same x or y coords + // inner two loops for jj=1,Jnum and kk=jj+1,Jnum insure + // the pair of other 2 non-minimum-x atoms is only considered once + // triplet geometry criteria for calculation: + // each pair distance <= cutoff + // produce of 3 pair distances <= cutoff_triple^3 + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + xi = x[i][0]; + yi = x[i][1]; + zi = x[i][2]; + + jlist = firstneigh[i]; + jnum = numneigh[i]; + jnumm1 = jnum - 1; + + for (jj = 0; jj < jnumm1; jj++) { + j = jlist[jj]; + j &= NEIGHMASK; + + rij[0] = x[j][0] - xi; + if (rij[0] < 0.0) continue; + rij[1] = x[j][1] - yi; + if (rij[0] == 0.0 and rij[1] < 0.0) continue; + rij[2] = x[j][2] - zi; + if (rij[0] == 0.0 and rij[1] == 0.0 and rij[2] < 0.0) continue; + rij2 = rij[0]*rij[0] + rij[1]*rij[1] + rij[2]*rij[2]; + if (rij2 > cutoff_squared) continue; + + for (kk = jj+1; kk < jnum; kk++) { + k = jlist[kk]; + k &= NEIGHMASK; + + rik[0] = x[k][0] - xi; + if (rik[0] < 0.0) continue; + rik[1] = x[k][1] - yi; + if (rik[0] == 0.0 and rik[1] < 0.0) continue; + rik[2] = x[k][2] - zi; + if (rik[0] == 0.0 and rik[1] == 0.0 and rik[2] < 0.0) continue; + rik2 = rik[0]*rik[0] + rik[1]*rik[1] + rik[2]*rik[2]; + if (rik2 > cutoff_squared) continue; + + rjk[0] = x[k][0] - x[j][0]; + rjk[1] = x[k][1] - x[j][1]; + rjk[2] = x[k][2] - x[j][2]; + rjk2 = rjk[0]*rjk[0] + rjk[1]*rjk[1] + rjk[2]*rjk[2]; + if (rjk2 > cutoff_squared) continue; + + double r6 = rij2*rjk2*rik2; + if (r6 > cutoff_triple_sixth) continue; + + nu_local = nu[type[i]][type[j]][type[k]]; + if (nu_local == 0.0) continue; + + interaction_ddd(nu_local, + r6,rij2,rik2,rjk2,rij,rik,rjk,fj,fk,eflag,evdwl); + + f[i][0] -= fj[0] + fk[0]; + f[i][1] -= fj[1] + fk[1]; + f[i][2] -= fj[2] + fk[2]; + f[j][0] += fj[0]; + f[j][1] += fj[1]; + f[j][2] += fj[2]; + f[k][0] += fk[0]; + f[k][1] += fk[1]; + f[k][2] += fk[2]; + + if (evflag) ev_tally3(i,j,k,evdwl,0.0,fj,fk,rij,rik); + } + } + } + + if (vflag_fdotr) virial_fdotr_compute(); +} + +/* ---------------------------------------------------------------------- */ + +void PairATM::allocate() +{ + allocated = 1; + int n = atom->ntypes; + + memory->create(setflag,n+1,n+1,"pair:setflag"); + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + setflag[i][j] = 0; + + memory->create(cutsq,n+1,n+1,"pair:cutsq"); + + memory->create(nu,n+1,n+1,n+1,"pair:nu"); + + // initialize all nu values to 0.0 + + for (int i = 1; i <= n; i++) + for (int j = 1; j <= n; j++) + for (int k = 1; k <= n; k++) + nu[i][j][k] = 0.0; +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairATM::settings(int narg, char **arg) +{ + if (narg != 2) error->all(FLERR,"Illegal pair_style command"); + + cut_global = force->numeric(FLERR,arg[0]); + cut_triple = force->numeric(FLERR,arg[1]); +} + +/* ---------------------------------------------------------------------- + set coefficients for one I,J,K type triplet +------------------------------------------------------------------------- */ + +void PairATM::coeff(int narg, char **arg) +{ + if (narg != 4) error->all(FLERR,"Incorrect args for pair coefficients"); + if (!allocated) allocate(); + + int ilo,ihi,jlo,jhi,klo,khi; + force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi); + force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi); + force->bounds(FLERR,arg[2],atom->ntypes,klo,khi); + + double nu_one = force->numeric(FLERR,arg[3]); + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + for (int j = MAX(jlo,i); j<=jhi; j++) { + for (int k = MAX(klo,j); k<=khi; k++) { + nu[i][j][k] = nu_one; + count++; + } + setflag[i][j] = 1; + } + } + + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); +} + +/* ---------------------------------------------------------------------- + init specific to this pair style +------------------------------------------------------------------------- */ + +void PairATM::init_style() +{ + if (force->newton_pair == 0) + error->all(FLERR,"Pair style ATM requires newton pair on"); + + // need a full neighbor list + + int irequest = neighbor->request(this,instance_me); + neighbor->requests[irequest]->half = 0; + neighbor->requests[irequest]->full = 1; +} + +/* ---------------------------------------------------------------------- + init for one i,j type pair and corresponding j,i + also for all k type permutations +------------------------------------------------------------------------- */ + +double PairATM::init_one(int i, int j) +{ + if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); + + // set all 6 symmetric permutations of I,J,K types to same nu value + + int ntypes = atom->ntypes; + for (int k = j; k <= ntypes; k++) + nu[i][k][j] = nu[j][i][k] = nu[j][k][i] = nu[k][i][j] = nu[k][j][i] = + nu[i][j][k]; + + return cut_global; +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairATM::write_restart(FILE *fp) +{ + write_restart_settings(fp); + + int i,j,k; + for (i = 1; i <= atom->ntypes; i++) { + for (j = i; j <= atom->ntypes; j++) { + fwrite(&setflag[i][j],sizeof(int),1,fp); + if (setflag[i][j]) + for (k = j; k <= atom->ntypes; k++) + fwrite(&nu[i][j][k],sizeof(double),1,fp); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairATM::read_restart(FILE *fp) +{ + read_restart_settings(fp); + allocate(); + + int i,j,k; + int me = comm->me; + for (i = 1; i <= atom->ntypes; i++) { + for (j = i; j <= atom->ntypes; j++) { + if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); + if (setflag[i][j]) for (k = j; k <= atom->ntypes; k++) { + if (me == 0) fread(&nu[i][j][k],sizeof(double),1,fp); + MPI_Bcast(&nu[i][j][k],1,MPI_DOUBLE,0,world); + } + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairATM::write_restart_settings(FILE *fp) +{ + fwrite(&cut_global,sizeof(double),1,fp); + fwrite(&cut_triple,sizeof(double),1,fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairATM::read_restart_settings(FILE *fp) +{ + int me = comm->me; + if (me == 0) { + fread(&cut_global,sizeof(double),1,fp); + fread(&cut_triple,sizeof(double),1,fp); + } + MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut_triple,1,MPI_DOUBLE,0,world); +} + +/* ---------------------------------------------------------------------- + Axilrod-Teller-Muto (dipole-dipole-dipole) potential +------------------------------------------------------------------------- */ + +void PairATM::interaction_ddd(double nu, double r6, + double rij2, double rik2, double rjk2, + double *rij, double *rik, double *rjk, + double *fj, double *fk, int eflag, double &eng) +{ + double r5inv,rri,rrj,rrk,rrr; + r5inv = nu / (r6*r6*sqrt(r6)); + rri = rik[0]*rij[0] + rik[1]*rij[1] + rik[2]*rij[2]; + rrj = rij[0]*rjk[0] + rij[1]*rjk[1] + rij[2]*rjk[2]; + rrk = rjk[0]*rik[0] + rjk[1]*rik[1] + rjk[2]*rik[2]; + rrr = 5.0*rri*rrj*rrk; + for (int i = 0; i < 3; i++) { + fj[i] = rrj*(rrk - rri)*rik[i] - + (rrk*rri - rjk2*rik2 + rrr/rij2) * rij[i] + + (rrk*rri - rik2*rij2 + rrr/rjk2) * rjk[i]; + fj[i] *= 3.0*r5inv; + fk[i] = rrk*(rri + rrj)*rij[i] + + (rri*rrj + rik2*rij2 - rrr/rjk2) * rjk[i] + + (rri*rrj + rij2*rjk2 - rrr/rik2) * rik[i]; + fk[i] *= 3.0*r5inv; + } + if (eflag) eng = (r6 - 0.6*rrr)*r5inv; +} diff --git a/src/MANYBODY/pair_atm.h b/src/MANYBODY/pair_atm.h new file mode 100644 index 0000000000..70883a81c7 --- /dev/null +++ b/src/MANYBODY/pair_atm.h @@ -0,0 +1,77 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS + +PairStyle(atm,PairATM) + +#else + +#ifndef LMP_PAIR_ATM_H +#define LMP_PAIR_ATM_H + +#include "pair.h" + +namespace LAMMPS_NS { + +class PairATM : public Pair { + public: + PairATM(class LAMMPS *); + virtual ~PairATM(); + virtual void compute(int, int); + void settings(int, char **); + virtual void coeff(int, char **); + virtual void init_style(); + virtual double init_one(int, int); + void write_restart(FILE *); + void read_restart(FILE *); + void write_restart_settings(FILE *); + void read_restart_settings(FILE *); + + protected: + double cut_global,cut_triple; + double ***nu; + + void allocate(); + void interaction_ddd(double, double, double, double, double, double *, + double *, double *, double *, double *, int, double &); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal pair_style command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Incorrect args for pair coefficients + +Self-explanatory. Check the input script or data file. + +E: Pair style ATM requires newton pair on + +See the newton command. This is a restriction to use the ATM +potential. + +E: All pair coeffs are not set + +All pair coefficients must be set in the data file or by the +pair_coeff command before running a simulation. + +*/ diff --git a/src/MANYBODY/pair_comb.cpp b/src/MANYBODY/pair_comb.cpp index de686d4bcf..e7b0d27b6e 100644 --- a/src/MANYBODY/pair_comb.cpp +++ b/src/MANYBODY/pair_comb.cpp @@ -432,7 +432,7 @@ void PairComb::allocate() global settings ------------------------------------------------------------------------- */ -void PairComb::settings(int narg, char **arg) +void PairComb::settings(int narg, char **/*arg*/) { if (narg > 0) error->all(FLERR,"Illegal pair_style command"); } @@ -1542,7 +1542,7 @@ void PairComb::potal_calc(double &calc1, double &calc2, double &calc3) void PairComb::tri_point(double rsq, int &mr1, int &mr2, int &mr3, double &sr1, double &sr2, - double &sr3, int &itype) + double &sr3, int &/*itype*/) { double r, rin, dr, dd, rr1, rridr, rridr2; @@ -1572,7 +1572,7 @@ void PairComb::tri_point(double rsq, int &mr1, int &mr2, void PairComb::direct(int inty, int mr1, int mr2, int mr3, double rsq, double sr1, double sr2, double sr3, double iq, double jq, - double potal, double fac11, double fac11e, + double /*potal*/, double fac11, double fac11e, double &pot_tmp, double &pot_d) { double r,erfcc,fafbn1,potij,sme2,esucon; @@ -2002,7 +2002,7 @@ void PairComb::Over_cor(Param *param, double rsq1, int NCoi, /* ---------------------------------------------------------------------- */ int PairComb::pack_forward_comm(int n, int *list, double *buf, - int pbc_flag, int *pbc) + int /*pbc_flag*/, int * /*pbc*/) { int i,j,m; diff --git a/src/MANYBODY/pair_comb3.cpp b/src/MANYBODY/pair_comb3.cpp index b4f9c02206..72360be5f0 100644 --- a/src/MANYBODY/pair_comb3.cpp +++ b/src/MANYBODY/pair_comb3.cpp @@ -1569,7 +1569,7 @@ void PairComb3::compute(int eflag, int vflag) /* ---------------------------------------------------------------------- */ void PairComb3::repulsive(Param *parami, Param *paramj, double rsq, - double &fforce,int eflag, double &eng, double iq, double jq) + double &fforce,int /*eflag*/, double &eng, double iq, double jq) { double r,tmp_fc,tmp_fc_d,Di,Dj; double caj,vrcs,fvrcs; @@ -1614,7 +1614,7 @@ void PairComb3::repulsive(Param *parami, Param *paramj, double rsq, /* ---------------------------------------------------------------------- */ double PairComb3::zeta(Param *parami, Param *paramj, double rsqij, - double rsqik, double *delrij, double *delrik, int i, double xcn) + double rsqik, double *delrij, double *delrik, int /*i*/, double xcn) { double rij,rik,costheta,arg,ex_delr,rlm3; @@ -1661,7 +1661,7 @@ void PairComb3::selfp6p(Param *parami, Param *paramj, double rsq, /* ---------------------------------------------------------------------- */ double PairComb3::ep6p(Param *paramj, Param *paramk, double rsqij, double rsqik, - double *delrij, double *delrik , double &zet_add) + double *delrij, double *delrik , double &/*zet_add*/) { double comtt; double pplp0 = paramj->p6p0; @@ -2109,7 +2109,7 @@ void PairComb3::coord(Param *param, double r, int i, void PairComb3::cntri_int(int tri_flag, double xval, double yval, double zval, int ixmin, int iymin, int izmin, double &vval, - double &dvalx, double &dvaly, double &dvalz, Param *param) + double &dvalx, double &dvaly, double &dvalz, Param * /*param*/) { double x; vval = 0.0; dvalx = 0.0; dvaly = 0.0; dvalz = 0.0; @@ -2254,7 +2254,7 @@ void PairComb3::comb_gijk_d(double costheta, Param *param, double nco_tmp, void PairComb3::attractive(Param *parami, Param *paramj , Param *paramk, double prefac_ij1, double prefac_ij2, double prefac_ij3, double prefac_ij4, double prefac_ij5, double rsqij, double rsqik, double *delrij, - double *delrik, double *fi, double *fj,double *fk, int i, double xcn) + double *delrik, double *fi, double *fj,double *fk, int /*i*/, double xcn) { double rij_hat[3],rik_hat[3]; double rij,rijinv,rik,rikinv; @@ -2867,7 +2867,7 @@ void PairComb3::field(Param *parami, Param *paramj, double rsq, double iq, /* ---------------------------------------------------------------------- */ -double PairComb3::rad_init(double rsq2,Param *param,int i, +double PairComb3::rad_init(double rsq2,Param *param,int /*i*/, double &radtot, double cnconj) { double r, fc1k, radcut; @@ -2882,7 +2882,7 @@ double PairComb3::rad_init(double rsq2,Param *param,int i, /* ---------------------------------------------------------------------- */ void PairComb3::rad_calc(double r, Param *parami, Param *paramj, - double kconjug, double lconjug, int i, int j, double xcn, double ycn) + double kconjug, double lconjug, int /*i*/, int /*j*/, double xcn, double ycn) { int ixmin, iymin, izmin; int radindx; @@ -3061,7 +3061,7 @@ double PairComb3::bbtor1(int torindx, Param *paramk, Param *paraml, /* ---------------------------------------------------------------------- */ void PairComb3::tor_calc(double r, Param *parami, Param *paramj, - double kconjug, double lconjug, int i, int j, double xcn, double ycn) + double kconjug, double lconjug, int /*i*/, int /*j*/, double xcn, double ycn) { int ixmin, iymin, izmin; double vtor, dtorx, dtory, dtorz; @@ -3589,7 +3589,7 @@ void PairComb3::qfo_dipole(double fac11, int mr1, int mr2, int mr3, void PairComb3::qfo_short(Param *parami, Param *paramj, double rsq, double iq, double jq, double &fqij, double &fqji, - int i, int j, int nj) + int i, int /*j*/, int nj) { double r, tmp_fc; double Di, Dj, dDi, dDj, Bsi, Bsj, dBsi, dBsj; @@ -3863,7 +3863,7 @@ double PairComb3::switching_d(double rr) /* ---------------------------------------------------------------------- */ int PairComb3::pack_forward_comm(int n, int *list, double *buf, - int pbc_flag, int *pbc) + int /*pbc_flag*/, int * /*pbc*/) { int i,j,m; diff --git a/src/MANYBODY/pair_eam.cpp b/src/MANYBODY/pair_eam.cpp index 9e70b19eea..87bcebb111 100644 --- a/src/MANYBODY/pair_eam.cpp +++ b/src/MANYBODY/pair_eam.cpp @@ -347,7 +347,7 @@ void PairEAM::allocate() global settings ------------------------------------------------------------------------- */ -void PairEAM::settings(int narg, char **arg) +void PairEAM::settings(int narg, char **/*arg*/) { if (narg > 0) error->all(FLERR,"Illegal pair_style command"); } @@ -795,7 +795,7 @@ void PairEAM::grab(FILE *fptr, int n, double *list) /* ---------------------------------------------------------------------- */ double PairEAM::single(int i, int j, int itype, int jtype, - double rsq, double factor_coul, double factor_lj, + double rsq, double /*factor_coul*/, double /*factor_lj*/, double &fforce) { int m; @@ -829,7 +829,7 @@ double PairEAM::single(int i, int j, int itype, int jtype, /* ---------------------------------------------------------------------- */ int PairEAM::pack_forward_comm(int n, int *list, double *buf, - int pbc_flag, int *pbc) + int /*pbc_flag*/, int * /*pbc*/) { int i,j,m; diff --git a/src/MANYBODY/pair_eam_cd.cpp b/src/MANYBODY/pair_eam_cd.cpp new file mode 100644 index 0000000000..5b8b241b45 --- /dev/null +++ b/src/MANYBODY/pair_eam_cd.cpp @@ -0,0 +1,677 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Alexander Stukowski + Technical University of Darmstadt, + Germany Department of Materials Science +------------------------------------------------------------------------- */ + +#include +#include +#include +#include +#include "pair_eam_cd.h" +#include "atom.h" +#include "force.h" +#include "comm.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; + +#define ASSERT(cond) +#define MAXLINE 1024 // This sets the maximum line length in EAM input files. + +PairEAMCD::PairEAMCD(LAMMPS *lmp, int _cdeamVersion) + : PairEAM(lmp), PairEAMAlloy(lmp), cdeamVersion(_cdeamVersion) +{ + single_enable = 0; + restartinfo = 0; + + rhoB = NULL; + D_values = NULL; + hcoeff = NULL; + + // Set communication buffer sizes needed by this pair style. + + if (cdeamVersion == 1) { + comm_forward = 4; + comm_reverse = 3; + } else if (cdeamVersion == 2) { + comm_forward = 3; + comm_reverse = 2; + } else { + error->all(FLERR,"Invalid eam/cd potential version."); + } +} + +PairEAMCD::~PairEAMCD() +{ + memory->destroy(rhoB); + memory->destroy(D_values); + if (hcoeff) delete[] hcoeff; +} + +void PairEAMCD::compute(int eflag, int vflag) +{ + int i,j,ii,jj,inum,jnum,itype,jtype; + double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair; + double rsq,rhoip,rhojp,recip,phi; + int *ilist,*jlist,*numneigh,**firstneigh; + + evdwl = 0.0; + if (eflag || vflag) ev_setup(eflag,vflag); + else evflag = vflag_fdotr = eflag_global = eflag_atom = 0; + + // Grow per-atom arrays if necessary + + if (atom->nmax > nmax) { + memory->destroy(rho); + memory->destroy(fp); + memory->destroy(rhoB); + memory->destroy(D_values); + nmax = atom->nmax; + memory->create(rho,nmax,"pair:rho"); + memory->create(rhoB,nmax,"pair:rhoB"); + memory->create(fp,nmax,"pair:fp"); + memory->create(D_values,nmax,"pair:D_values"); + } + + double **x = atom->x; + double **f = atom->f; + int *type = atom->type; + int nlocal = atom->nlocal; + int newton_pair = force->newton_pair; + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // Zero out per-atom arrays. + + int m = nlocal + atom->nghost; + for (i = 0; i < m; i++) { + rho[i] = 0.0; + rhoB[i] = 0.0; + D_values[i] = 0.0; + } + + // Stage I + + // Compute rho and rhoB at each local atom site. + + // Additionally calculate the D_i values here if we are using the + // one-site formulation. For the two-site formulation we have to + // calculate the D values in an extra loop (Stage II). + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + j &= NEIGHMASK; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + if (rsq < cutforcesq) { + jtype = type[j]; + double r = sqrt(rsq); + const EAMTableIndex index = radiusToTableIndex(r); + double localrho = RhoOfR(index, jtype, itype); + rho[i] += localrho; + if (jtype == speciesB) rhoB[i] += localrho; + if (newton_pair || j < nlocal) { + localrho = RhoOfR(index, itype, jtype); + rho[j] += localrho; + if (itype == speciesB) rhoB[j] += localrho; + } + + if (cdeamVersion == 1 && itype != jtype) { + + // Note: if the i-j interaction is not concentration dependent (because either + // i or j are not species A or B) then its contribution to D_i and D_j should + // be ignored. + // This if-clause is only required for a ternary. + + if ((itype == speciesA && jtype == speciesB) + || (jtype == speciesA && itype == speciesB)) { + double Phi_AB = PhiOfR(index, itype, jtype, 1.0 / r); + D_values[i] += Phi_AB; + if (newton_pair || j < nlocal) + D_values[j] += Phi_AB; + } + } + } + } + } + + // Communicate and sum densities. + + if (newton_pair) { + communicationStage = 1; + comm->reverse_comm_pair(this); + } + + // fp = derivative of embedding energy at each atom + // phi = embedding energy at each atom + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + EAMTableIndex index = rhoToTableIndex(rho[i]); + fp[i] = FPrimeOfRho(index, type[i]); + if (eflag) { + phi = FofRho(index, type[i]); + if (eflag_global) eng_vdwl += phi; + if (eflag_atom) eatom[i] += phi; + } + } + + // Communicate derivative of embedding function and densities + // and D_values (this for one-site formulation only). + + communicationStage = 2; + comm->forward_comm_pair(this); + + // The electron densities may not drop to zero because then the + // concentration would no longer be defined. But the concentration + // is not needed anyway if there is no interaction with another atom, + // which is the case if the electron density is exactly zero. + // That's why the following lines have been commented out. + // + //for (i = 0; i < nlocal + atom->nghost; i++) { + // if (rho[i] == 0 && (type[i] == speciesA || type[i] == speciesB)) + // error->one(FLERR,"CD-EAM potential routine: Detected atom with zero electron density."); + //} + + // Stage II + // This is only required for the original two-site formulation of the CD-EAM potential. + + if (cdeamVersion == 2) { + + // Compute intermediate value D_i for each atom. + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + // This code line is required for ternary alloys. + + if (itype != speciesA && itype != speciesB) continue; + + double x_i = rhoB[i] / rho[i]; // Concentration at atom i. + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + j &= NEIGHMASK; + jtype = type[j]; + if (itype == jtype) continue; + + // This code line is required for ternary alloys. + + if (jtype != speciesA && jtype != speciesB) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + if (rsq < cutforcesq) { + double r = sqrt(rsq); + const EAMTableIndex index = radiusToTableIndex(r); + + // The concentration independent part of the cross pair potential. + + double Phi_AB = PhiOfR(index, itype, jtype, 1.0 / r); + + // Average concentration of two sites + + double x_ij = 0.5 * (x_i + rhoB[j]/rho[j]); + + // Calculate derivative of h(x_ij) polynomial function. + + double h_prime = evalHprime(x_ij); + + D_values[i] += h_prime * Phi_AB / (2.0 * rho[i] * rho[i]); + if (newton_pair || j < nlocal) + D_values[j] += h_prime * Phi_AB / (2.0 * rho[j] * rho[j]); + } + } + } + + // Communicate and sum D values. + + if (newton_pair) { + communicationStage = 3; + comm->reverse_comm_pair(this); + } + communicationStage = 4; + comm->forward_comm_pair(this); + } + + // Stage III + + // Compute force acting on each atom. + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + itype = type[i]; + + jlist = firstneigh[i]; + jnum = numneigh[i]; + + // Concentration at site i + // The value -1 indicates: no concentration dependence for all interactions of atom i. + // It will be replaced by the concentration at site i if atom i is either A or B. + + double x_i = -1.0; + double D_i, h_prime_i; + + // This if-clause is only required for ternary alloys. + + if ((itype == speciesA || itype == speciesB) && rho[i] != 0.0) { + + // Compute local concentration at site i. + + x_i = rhoB[i]/rho[i]; + ASSERT(x_i >= 0 && x_i<=1.0); + + if (cdeamVersion == 1) { + + // Calculate derivative of h(x_i) polynomial function. + + h_prime_i = evalHprime(x_i); + D_i = D_values[i] * h_prime_i / (2.0 * rho[i] * rho[i]); + } else if (cdeamVersion == 2) { + D_i = D_values[i]; + } else { + ASSERT(false); + } + } + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + j &= NEIGHMASK; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + if (rsq < cutforcesq) { + jtype = type[j]; + double r = sqrt(rsq); + const EAMTableIndex index = radiusToTableIndex(r); + + // rhoip = derivative of (density at atom j due to atom i) + // rhojp = derivative of (density at atom i due to atom j) + // psip needs both fp[i] and fp[j] terms since r_ij appears in two + // terms of embed eng: Fi(sum rho_ij) and Fj(sum rho_ji) + // hence embed' = Fi(sum rho_ij) rhojp + Fj(sum rho_ji) rhoip + + rhoip = RhoPrimeOfR(index, itype, jtype); + rhojp = RhoPrimeOfR(index, jtype, itype); + fpair = fp[i]*rhojp + fp[j]*rhoip; + recip = 1.0/r; + + // The value -1 indicates: no concentration dependence for this + // i-j pair because atom j is not of species A nor B. + + double x_j = -1; + + // This code line is required for ternary alloy. + + if (jtype == speciesA || jtype == speciesB) { + ASSERT(rho[i] != 0.0); + ASSERT(rho[j] != 0.0); + + // Compute local concentration at site j. + + x_j = rhoB[j]/rho[j]; + ASSERT(x_j >= 0 && x_j<=1.0); + + double D_j=0.0; + if (cdeamVersion == 1) { + + // Calculate derivative of h(x_j) polynomial function. + + double h_prime_j = evalHprime(x_j); + D_j = D_values[j] * h_prime_j / (2.0 * rho[j] * rho[j]); + } else if (cdeamVersion == 2) { + D_j = D_values[j]; + } else { + ASSERT(false); + } + double t2 = -rhoB[j]; + if (itype == speciesB) t2 += rho[j]; + fpair += D_j * rhoip * t2; + } + + // This if-clause is only required for a ternary alloy. + // Actually we don't need it at all because D_i should be zero + // anyway if atom i has no concentration dependent interactions + // (because it is not species A or B). + + if (x_i != -1.0) { + double t1 = -rhoB[i]; + if (jtype == speciesB) t1 += rho[i]; + fpair += D_i * rhojp * t1; + } + + double phip; + double phi = PhiOfR(index, itype, jtype, recip, phip); + if (itype == jtype || x_i == -1.0 || x_j == -1.0) { + + // Case of no concentration dependence. + + fpair += phip; + } else { + + // We have a concentration dependence for the i-j interaction. + + double h=0.0; + if (cdeamVersion == 1) { + + // Calculate h(x_i) polynomial function. + + double h_i = evalH(x_i); + + // Calculate h(x_j) polynomial function. + + double h_j = evalH(x_j); + h = 0.5 * (h_i + h_j); + } else if (cdeamVersion == 2) { + + // Average concentration. + + double x_ij = 0.5 * (x_i + x_j); + + // Calculate h(x_ij) polynomial function. + + h = evalH(x_ij); + } else { + ASSERT(false); + } + fpair += h * phip; + phi *= h; + } + + // Divide by r_ij and negate to get forces from gradient. + + fpair /= -r; + + f[i][0] += delx*fpair; + f[i][1] += dely*fpair; + f[i][2] += delz*fpair; + if (newton_pair || j < nlocal) { + f[j][0] -= delx*fpair; + f[j][1] -= dely*fpair; + f[j][2] -= delz*fpair; + } + + if (eflag) evdwl = phi; + if (evflag) ev_tally(i,j,nlocal,newton_pair,evdwl,0.0,fpair,delx,dely,delz); + } + } + } + + if (vflag_fdotr) virial_fdotr_compute(); +} + +/* ---------------------------------------------------------------------- */ + +void PairEAMCD::coeff(int narg, char **arg) +{ + PairEAMAlloy::coeff(narg, arg); + + // Make sure the EAM file is a CD-EAM binary alloy. + + if (setfl->nelements < 2) + error->all(FLERR,"The EAM file must contain at least 2 elements to be used with the eam/cd pair style."); + + // Read in the coefficients of the h polynomial from the end of the EAM file. + + read_h_coeff(arg[2]); + + // Determine which atom type is the A species and which is the B + // species in the alloy. By default take the first element (index 0) + // in the EAM file as the A species and the second element (index 1) + // in the EAM file as the B species. + + speciesA = -1; + speciesB = -1; + for (int i = 1; i <= atom->ntypes; i++) { + if (map[i] == 0) { + if (speciesA >= 0) + error->all(FLERR,"The first element from the EAM file may only be mapped to a single atom type."); + speciesA = i; + } + if (map[i] == 1) { + if (speciesB >= 0) + error->all(FLERR,"The second element from the EAM file may only be mapped to a single atom type."); + speciesB = i; + } + } + if (speciesA < 0) + error->all(FLERR,"The first element from the EAM file must be mapped to exactly one atom type."); + if (speciesB < 0) + error->all(FLERR,"The second element from the EAM file must be mapped to exactly one atom type."); +} + +/* ---------------------------------------------------------------------- + Reads in the h(x) polynomial coefficients +------------------------------------------------------------------------- */ + +void PairEAMCD::read_h_coeff(char *filename) +{ + if (comm->me == 0) { + + // Open potential file + + FILE *fptr; + char line[MAXLINE]; + char nextline[MAXLINE]; + fptr = force->open_potential(filename); + if (fptr == NULL) { + char str[128]; + sprintf(str,"Cannot open EAM potential file %s", filename); + error->one(FLERR,str); + } + + // h coefficients are stored at the end of the file. + // Skip to last line of file. + + while(fgets(nextline, MAXLINE, fptr) != NULL) { + strcpy(line, nextline); + } + char* ptr = strtok(line, " \t\n\r\f"); + int degree = atoi(ptr); + nhcoeff = degree+1; + hcoeff = new double[nhcoeff]; + int i = 0; + while((ptr = strtok(NULL," \t\n\r\f")) != NULL && i < nhcoeff) { + hcoeff[i++] = atof(ptr); + } + if (i != nhcoeff || nhcoeff < 1) + error->one(FLERR,"Failed to read h(x) function coefficients from EAM file."); + + // Close the potential file. + + fclose(fptr); + } + + MPI_Bcast(&nhcoeff, 1, MPI_INT, 0, world); + if (comm->me != 0) hcoeff = new double[nhcoeff]; + MPI_Bcast(hcoeff, nhcoeff, MPI_DOUBLE, 0, world); +} + + +/* ---------------------------------------------------------------------- */ + +int PairEAMCD::pack_forward_comm(int n, int *list, double *buf, + int /*pbc_flag*/, int * /*pbc*/) +{ + int i,j,m; + + m = 0; + if (communicationStage == 2) { + if (cdeamVersion == 1) { + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = fp[j]; + buf[m++] = rho[j]; + buf[m++] = rhoB[j]; + buf[m++] = D_values[j]; + } + return m; + } else if (cdeamVersion == 2) { + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = fp[j]; + buf[m++] = rho[j]; + buf[m++] = rhoB[j]; + } + return m; + } else { ASSERT(false); return 0; } + } else if (communicationStage == 4) { + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = D_values[j]; + } + return m; + } else return 0; +} + +/* ---------------------------------------------------------------------- */ + +void PairEAMCD::unpack_forward_comm(int n, int first, double *buf) +{ + int i,m,last; + + m = 0; + last = first + n; + if (communicationStage == 2) { + if (cdeamVersion == 1) { + for (i = first; i < last; i++) { + fp[i] = buf[m++]; + rho[i] = buf[m++]; + rhoB[i] = buf[m++]; + D_values[i] = buf[m++]; + } + } else if (cdeamVersion == 2) { + for (i = first; i < last; i++) { + fp[i] = buf[m++]; + rho[i] = buf[m++]; + rhoB[i] = buf[m++]; + } + } else { + ASSERT(false); + } + } else if (communicationStage == 4) { + for (i = first; i < last; i++) { + D_values[i] = buf[m++]; + } + } +} + +/* ---------------------------------------------------------------------- */ +int PairEAMCD::pack_reverse_comm(int n, int first, double *buf) +{ + int i,m,last; + + m = 0; + last = first + n; + + if (communicationStage == 1) { + if (cdeamVersion == 1) { + for (i = first; i < last; i++) { + buf[m++] = rho[i]; + buf[m++] = rhoB[i]; + buf[m++] = D_values[i]; + } + return m; + } else if (cdeamVersion == 2) { + for (i = first; i < last; i++) { + buf[m++] = rho[i]; + buf[m++] = rhoB[i]; + } + return m; + } else { ASSERT(false); return 0; } + } else if (communicationStage == 3) { + for (i = first; i < last; i++) { + buf[m++] = D_values[i]; + } + return m; + } else return 0; +} + +/* ---------------------------------------------------------------------- */ + +void PairEAMCD::unpack_reverse_comm(int n, int *list, double *buf) +{ + int i,j,m; + + m = 0; + if (communicationStage == 1) { + if (cdeamVersion == 1) { + for (i = 0; i < n; i++) { + j = list[i]; + rho[j] += buf[m++]; + rhoB[j] += buf[m++]; + D_values[j] += buf[m++]; + } + } else if (cdeamVersion == 2) { + for (i = 0; i < n; i++) { + j = list[i]; + rho[j] += buf[m++]; + rhoB[j] += buf[m++]; + } + } else { + ASSERT(false); + } + } else if (communicationStage == 3) { + for (i = 0; i < n; i++) { + j = list[i]; + D_values[j] += buf[m++]; + } + } +} + +/* ---------------------------------------------------------------------- + memory usage of local atom-based arrays +------------------------------------------------------------------------- */ +double PairEAMCD::memory_usage() +{ + double bytes = 2 * nmax * sizeof(double); + return PairEAMAlloy::memory_usage() + bytes; +} diff --git a/src/USER-MISC/pair_cdeam.h b/src/MANYBODY/pair_eam_cd.h similarity index 93% rename from src/USER-MISC/pair_cdeam.h rename to src/MANYBODY/pair_eam_cd.h index 934b7601a4..ee84fb09c5 100644 --- a/src/USER-MISC/pair_cdeam.h +++ b/src/MANYBODY/pair_eam_cd.h @@ -13,26 +13,26 @@ #ifdef PAIR_CLASS -PairStyle(eam/cd,PairCDEAM_OneSite) -PairStyle(eam/cd/old,PairCDEAM_TwoSite) +PairStyle(eam/cd,PairEAMCD_OneSite) +PairStyle(eam/cd/old,PairEAMCD_TwoSite) #else -#ifndef LMP_PAIR_CDEAM_H -#define LMP_PAIR_CDEAM_H +#ifndef LMP_PAIR_EAM_CD_H +#define LMP_PAIR_EAM_CD_H #include "pair_eam_alloy.h" namespace LAMMPS_NS { -class PairCDEAM : public PairEAMAlloy +class PairEAMCD : public PairEAMAlloy { public: /// Constructor. - PairCDEAM(class LAMMPS*, int cdeamVersion); + PairEAMCD(class LAMMPS*, int cdeamVersion); /// Destructor. - virtual ~PairCDEAM(); + virtual ~PairEAMCD(); /// Calculates the energies and forces for all atoms in the system. virtual void compute(int, int); @@ -211,19 +211,19 @@ public: }; /// The one-site concentration formulation of CD-EAM. - class PairCDEAM_OneSite : public PairCDEAM + class PairEAMCD_OneSite : public PairEAMCD { public: /// Constructor. - PairCDEAM_OneSite(class LAMMPS* lmp) : PairEAM(lmp), PairCDEAM(lmp, 1) {} + PairEAMCD_OneSite(class LAMMPS* lmp) : PairEAM(lmp), PairEAMCD(lmp, 1) {} }; /// The two-site concentration formulation of CD-EAM. - class PairCDEAM_TwoSite : public PairCDEAM + class PairEAMCD_TwoSite : public PairEAMCD { public: /// Constructor. - PairCDEAM_TwoSite(class LAMMPS* lmp) : PairEAM(lmp), PairCDEAM(lmp, 2) {} + PairEAMCD_TwoSite(class LAMMPS* lmp) : PairEAM(lmp), PairEAMCD(lmp, 2) {} }; } diff --git a/src/MANYBODY/pair_eim.cpp b/src/MANYBODY/pair_eim.cpp index b810d444fc..6703e159e6 100644 --- a/src/MANYBODY/pair_eim.cpp +++ b/src/MANYBODY/pair_eim.cpp @@ -342,7 +342,7 @@ void PairEIM::allocate() global settings ------------------------------------------------------------------------- */ -void PairEIM::settings(int narg, char **arg) +void PairEIM::settings(int narg, char **/*arg*/) { if (narg > 0) error->all(FLERR,"Illegal pair_style command"); } @@ -850,7 +850,7 @@ void PairEIM::array2spline() /* ---------------------------------------------------------------------- */ void PairEIM::interpolate(int n, double delta, double *f, - double **spline, double origin) + double **spline, double /*origin*/) { for (int m = 1; m <= n; m++) spline[m][6] = f[m]; @@ -1087,7 +1087,7 @@ double PairEIM::funccoul(int i, int j, double r) /* ---------------------------------------------------------------------- */ int PairEIM::pack_forward_comm(int n, int *list, double *buf, - int pbc_flag, int *pbc) + int /*pbc_flag*/, int * /*pbc*/) { int i,j,m; diff --git a/src/MANYBODY/pair_gw.cpp b/src/MANYBODY/pair_gw.cpp index 35f092b580..0aff4970bb 100644 --- a/src/MANYBODY/pair_gw.cpp +++ b/src/MANYBODY/pair_gw.cpp @@ -257,7 +257,7 @@ void PairGW::allocate() global settings ------------------------------------------------------------------------- */ -void PairGW::settings(int narg, char **arg) +void PairGW::settings(int narg, char **/*arg*/) { if (narg != 0) error->all(FLERR,"Illegal pair_style command"); } diff --git a/src/MANYBODY/pair_lcbop.cpp b/src/MANYBODY/pair_lcbop.cpp index d334defcc6..57373c4f85 100644 --- a/src/MANYBODY/pair_lcbop.cpp +++ b/src/MANYBODY/pair_lcbop.cpp @@ -121,7 +121,7 @@ void PairLCBOP::allocate() global settings ------------------------------------------------------------------------- */ -void PairLCBOP::settings(int narg, char **arg) { +void PairLCBOP::settings(int narg, char **/*arg*/) { if( narg != 0 ) error->all(FLERR,"Illegal pair_style command"); } @@ -353,7 +353,7 @@ void PairLCBOP::SR_neigh() Short range forces and energy ------------------------------------------------------------------------- */ -void PairLCBOP::FSR(int eflag, int vflag) +void PairLCBOP::FSR(int eflag, int /*vflag*/) { int i,j,jj,ii,inum; tagint itag,jtag; @@ -449,7 +449,7 @@ void PairLCBOP::FSR(int eflag, int vflag) compute long range forces and energy ------------------------------------------------------------------------- */ -void PairLCBOP::FLR(int eflag, int vflag) +void PairLCBOP::FLR(int eflag, int /*vflag*/) { int i,j,jj,ii; tagint itag,jtag; diff --git a/src/MANYBODY/pair_nb3b_harmonic.cpp b/src/MANYBODY/pair_nb3b_harmonic.cpp index 36be9c2b90..01718d14cd 100644 --- a/src/MANYBODY/pair_nb3b_harmonic.cpp +++ b/src/MANYBODY/pair_nb3b_harmonic.cpp @@ -174,7 +174,7 @@ void PairNb3bHarmonic::allocate() global settings ------------------------------------------------------------------------- */ -void PairNb3bHarmonic::settings(int narg, char **arg) +void PairNb3bHarmonic::settings(int narg, char **/*arg*/) { if (narg != 0) error->all(FLERR,"Illegal pair_style command"); } @@ -454,7 +454,7 @@ void PairNb3bHarmonic::setup_params() /* ---------------------------------------------------------------------- */ -void PairNb3bHarmonic::threebody(Param *paramij, Param *paramik, +void PairNb3bHarmonic::threebody(Param * /*paramij*/, Param * /*paramik*/, Param *paramijk, double rsq1, double rsq2, double *delr1, double *delr2, diff --git a/src/MANYBODY/pair_polymorphic.cpp b/src/MANYBODY/pair_polymorphic.cpp index 2afb08b7a1..ce9af66d30 100644 --- a/src/MANYBODY/pair_polymorphic.cpp +++ b/src/MANYBODY/pair_polymorphic.cpp @@ -450,7 +450,7 @@ void PairPolymorphic::allocate() global settings ------------------------------------------------------------------------- */ -void PairPolymorphic::settings(int narg, char **arg) +void PairPolymorphic::settings(int narg, char **/*arg*/) { if (narg != 0) error->all(FLERR,"Illegal pair_style command"); } diff --git a/src/MANYBODY/pair_rebo.cpp b/src/MANYBODY/pair_rebo.cpp index 37948f3038..1f31c0b0cd 100644 --- a/src/MANYBODY/pair_rebo.cpp +++ b/src/MANYBODY/pair_rebo.cpp @@ -24,7 +24,7 @@ PairREBO::PairREBO(LAMMPS *lmp) : PairAIREBO(lmp) {} global settings ------------------------------------------------------------------------- */ -void PairREBO::settings(int narg, char **arg) +void PairREBO::settings(int narg, char **/*arg*/) { if (narg != 0) error->all(FLERR,"Illegal pair_style command"); diff --git a/src/MANYBODY/pair_sw.cpp b/src/MANYBODY/pair_sw.cpp index 6fbc00204c..da470d568a 100644 --- a/src/MANYBODY/pair_sw.cpp +++ b/src/MANYBODY/pair_sw.cpp @@ -239,7 +239,7 @@ void PairSW::allocate() global settings ------------------------------------------------------------------------- */ -void PairSW::settings(int narg, char **arg) +void PairSW::settings(int narg, char **/*arg*/) { if (narg != 0) error->all(FLERR,"Illegal pair_style command"); } diff --git a/src/MANYBODY/pair_tersoff.cpp b/src/MANYBODY/pair_tersoff.cpp index 507b07e29a..45068e5c2e 100644 --- a/src/MANYBODY/pair_tersoff.cpp +++ b/src/MANYBODY/pair_tersoff.cpp @@ -280,7 +280,7 @@ void PairTersoff::allocate() global settings ------------------------------------------------------------------------- */ -void PairTersoff::settings(int narg, char **arg) +void PairTersoff::settings(int narg, char **/*arg*/) { if (narg != 0) error->all(FLERR,"Illegal pair_style command"); } diff --git a/src/MANYBODY/pair_vashishta.cpp b/src/MANYBODY/pair_vashishta.cpp index 8506c9a69f..54b184ea39 100644 --- a/src/MANYBODY/pair_vashishta.cpp +++ b/src/MANYBODY/pair_vashishta.cpp @@ -245,7 +245,7 @@ void PairVashishta::allocate() global settings ------------------------------------------------------------------------- */ -void PairVashishta::settings(int narg, char **arg) +void PairVashishta::settings(int narg, char **/*arg*/) { if (narg != 0) error->all(FLERR,"Illegal pair_style command"); } diff --git a/src/MC/fix_atom_swap.cpp b/src/MC/fix_atom_swap.cpp index 4d9377022b..3e981c5609 100644 --- a/src/MC/fix_atom_swap.cpp +++ b/src/MC/fix_atom_swap.cpp @@ -695,7 +695,7 @@ void FixAtomSwap::update_swap_atoms_list() /* ---------------------------------------------------------------------- */ -int FixAtomSwap::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc) +int FixAtomSwap::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int * /*pbc*/) { int i,j,m; diff --git a/src/MC/fix_bond_break.cpp b/src/MC/fix_bond_break.cpp index 9a5b59b601..a1c9bb3ab0 100644 --- a/src/MC/fix_bond_break.cpp +++ b/src/MC/fix_bond_break.cpp @@ -693,7 +693,7 @@ int FixBondBreak::dedup(int nstart, int nstop, tagint *copy) /* ---------------------------------------------------------------------- */ -void FixBondBreak::post_integrate_respa(int ilevel, int iloop) +void FixBondBreak::post_integrate_respa(int ilevel, int /*iloop*/) { if (ilevel == nlevels_respa-1) post_integrate(); } @@ -701,7 +701,7 @@ void FixBondBreak::post_integrate_respa(int ilevel, int iloop) /* ---------------------------------------------------------------------- */ int FixBondBreak::pack_forward_comm(int n, int *list, double *buf, - int pbc_flag, int *pbc) + int /*pbc_flag*/, int * /*pbc*/) { int i,j,k,m,ns; diff --git a/src/MC/fix_bond_create.cpp b/src/MC/fix_bond_create.cpp index 8e9db6a18b..e1dd18cb5b 100644 --- a/src/MC/fix_bond_create.cpp +++ b/src/MC/fix_bond_create.cpp @@ -258,14 +258,14 @@ void FixBondCreate::init() /* ---------------------------------------------------------------------- */ -void FixBondCreate::init_list(int id, NeighList *ptr) +void FixBondCreate::init_list(int /*id*/, NeighList *ptr) { list = ptr; } /* ---------------------------------------------------------------------- */ -void FixBondCreate::setup(int vflag) +void FixBondCreate::setup(int /*vflag*/) { int i,j,m; @@ -1206,7 +1206,7 @@ int FixBondCreate::dedup(int nstart, int nstop, tagint *copy) /* ---------------------------------------------------------------------- */ -void FixBondCreate::post_integrate_respa(int ilevel, int iloop) +void FixBondCreate::post_integrate_respa(int ilevel, int /*iloop*/) { if (ilevel == nlevels_respa-1) post_integrate(); } @@ -1214,7 +1214,7 @@ void FixBondCreate::post_integrate_respa(int ilevel, int iloop) /* ---------------------------------------------------------------------- */ int FixBondCreate::pack_forward_comm(int n, int *list, double *buf, - int pbc_flag, int *pbc) + int /*pbc_flag*/, int * /*pbc*/) { int i,j,k,m,ns; @@ -1347,7 +1347,7 @@ void FixBondCreate::grow_arrays(int nmax) copy values within local atom-based arrays ------------------------------------------------------------------------- */ -void FixBondCreate::copy_arrays(int i, int j, int delflag) +void FixBondCreate::copy_arrays(int i, int j, int /*delflag*/) { bondcount[j] = bondcount[i]; } diff --git a/src/MC/fix_bond_swap.cpp b/src/MC/fix_bond_swap.cpp index d6df4d9a96..9a72667907 100644 --- a/src/MC/fix_bond_swap.cpp +++ b/src/MC/fix_bond_swap.cpp @@ -182,7 +182,7 @@ void FixBondSwap::init() /* ---------------------------------------------------------------------- */ -void FixBondSwap::init_list(int id, NeighList *ptr) +void FixBondSwap::init_list(int /*id*/, NeighList *ptr) { list = ptr; } diff --git a/src/MC/fix_gcmc.cpp b/src/MC/fix_gcmc.cpp index 6221e6d52c..b40ce6a1b3 100644 --- a/src/MC/fix_gcmc.cpp +++ b/src/MC/fix_gcmc.cpp @@ -1589,6 +1589,7 @@ void FixGCMC::attempt_atomic_deletion_full() } } if (force->kspace) force->kspace->qsum_qsq(); + if (force->pair->tail_flag) force->pair->reinit(); double energy_after = energy_full(); if (random_equal->uniform() < @@ -1607,6 +1608,7 @@ void FixGCMC::attempt_atomic_deletion_full() if (q_flag) atom->q[i] = q_tmp; } if (force->kspace) force->kspace->qsum_qsq(); + if (force->pair->tail_flag) force->pair->reinit(); energy_stored = energy_before; } update_gas_atoms_list(); @@ -1700,6 +1702,7 @@ void FixGCMC::attempt_atomic_insertion_full() comm->borders(); if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost); if (force->kspace) force->kspace->qsum_qsq(); + if (force->pair->tail_flag) force->pair->reinit(); double energy_after = energy_full(); if (energy_after < MAXENERGYTEST && @@ -1712,6 +1715,7 @@ void FixGCMC::attempt_atomic_insertion_full() atom->natoms--; if (proc_flag) atom->nlocal--; if (force->kspace) force->kspace->qsum_qsq(); + if (force->pair->tail_flag) force->pair->reinit(); energy_stored = energy_before; } update_gas_atoms_list(); @@ -1949,6 +1953,7 @@ void FixGCMC::attempt_molecule_deletion_full() } } if (force->kspace) force->kspace->qsum_qsq(); + if (force->pair->tail_flag) force->pair->reinit(); double energy_after = energy_full(); // energy_before corrected by energy_intra @@ -1981,6 +1986,7 @@ void FixGCMC::attempt_molecule_deletion_full() } } if (force->kspace) force->kspace->qsum_qsq(); + if (force->pair->tail_flag) force->pair->reinit(); } update_gas_atoms_list(); delete[] tmpmask; @@ -2151,6 +2157,7 @@ void FixGCMC::attempt_molecule_insertion_full() comm->borders(); if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost); if (force->kspace) force->kspace->qsum_qsq(); + if (force->pair->tail_flag) force->pair->reinit(); double energy_after = energy_full(); // energy_after corrected by energy_intra @@ -2181,6 +2188,7 @@ void FixGCMC::attempt_molecule_insertion_full() } else i++; } if (force->kspace) force->kspace->qsum_qsq(); + if (force->pair->tail_flag) force->pair->reinit(); } update_gas_atoms_list(); } diff --git a/src/MC/fix_tfmc.cpp b/src/MC/fix_tfmc.cpp index b821710353..46c5e592ae 100644 --- a/src/MC/fix_tfmc.cpp +++ b/src/MC/fix_tfmc.cpp @@ -158,7 +158,7 @@ void FixTFMC::init() /* ---------------------------------------------------------------------- */ -void FixTFMC::initial_integrate(int vflag) +void FixTFMC::initial_integrate(int /*vflag*/) { double boltz = force->boltz; double **x = atom->x; diff --git a/src/MC/pair_dsmc.cpp b/src/MC/pair_dsmc.cpp index 02f9754c2a..c71eaa2295 100644 --- a/src/MC/pair_dsmc.cpp +++ b/src/MC/pair_dsmc.cpp @@ -65,7 +65,7 @@ PairDSMC::~PairDSMC() /* ---------------------------------------------------------------------- */ -void PairDSMC::compute(int eflag, int vflag) +void PairDSMC::compute(int /*eflag*/, int /*vflag*/) { double **x = atom->x; double *mass = atom->mass; @@ -405,7 +405,7 @@ void PairDSMC::read_restart_settings(FILE *fp) the next nrezero timesteps -------------------------------------------------------------------------*/ -void PairDSMC::recompute_V_sigma_max(int icell) +void PairDSMC::recompute_V_sigma_max(int /*icell*/) { int i,j,k; double Vsigma_max = 0; @@ -459,7 +459,7 @@ double PairDSMC::V_sigma(int i, int j) generate new velocities for collided particles -------------------------------------------------------------------------*/ -void PairDSMC::scatter_random(int i, int j, int icell) +void PairDSMC::scatter_random(int i, int j, int /*icell*/) { double mag_delv,cos_phi,cos_squared,r,theta; double delv[3],vcm[3]; diff --git a/src/MEAM/pair_meam.cpp b/src/MEAM/pair_meam.cpp index 687055aa6a..5aa13ab02e 100644 --- a/src/MEAM/pair_meam.cpp +++ b/src/MEAM/pair_meam.cpp @@ -325,7 +325,7 @@ void PairMEAM::allocate() global settings ------------------------------------------------------------------------- */ -void PairMEAM::settings(int narg, char **arg) +void PairMEAM::settings(int narg, char **/*arg*/) { if (narg != 0) error->all(FLERR,"Illegal pair_style command"); } @@ -448,7 +448,7 @@ void PairMEAM::init_list(int id, NeighList *ptr) init for one type pair i,j and corresponding j,i ------------------------------------------------------------------------- */ -double PairMEAM::init_one(int i, int j) +double PairMEAM::init_one(int /*i*/, int /*j*/) { return cutmax; } @@ -734,7 +734,7 @@ void PairMEAM::read_files(char *globalfile, char *userfile) /* ---------------------------------------------------------------------- */ int PairMEAM::pack_forward_comm(int n, int *list, double *buf, - int pbc_flag, int *pbc) + int /*pbc_flag*/, int * /*pbc*/) { int i,j,k,m; diff --git a/src/MESSAGE/Install.sh b/src/MESSAGE/Install.sh new file mode 100644 index 0000000000..853dbddcdd --- /dev/null +++ b/src/MESSAGE/Install.sh @@ -0,0 +1,67 @@ +# Install/unInstall package files in LAMMPS +# mode = 0/1/2 for uninstall/install/update + +mode=$1 + +# arg1 = file, arg2 = file it depends on + +# enforce using portable C locale +LC_ALL=C +export LC_ALL + +action () { + if (test $mode = 0) then + rm -f ../$1 + elif (! cmp -s $1 ../$1) then + if (test -z "$2" || test -e ../$2) then + cp $1 .. + if (test $mode = 2) then + echo " updating src/$1" + fi + fi + elif (test -n "$2") then + if (test ! -e ../$2) then + rm -f ../$1 + fi + fi +} + +# all package files with no dependencies + +for file in *.cpp *.h; do + test -f ${file} && action $file +done + +# edit 2 Makefile.package files to include/exclude package info + +if (test $1 = 1) then + + if (test -e ../Makefile.package) then + sed -i -e 's/[^ \t]*message[^ \t]* //' ../Makefile.package + sed -i -e 's|^PKG_INC =[ \t]*|&-I../../lib/message/cslib/src |' ../Makefile.package + sed -i -e 's|^PKG_PATH =[ \t]*|&-L../../lib/message/cslib/src |' ../Makefile.package + sed -i -e 's|^PKG_LIB =[ \t]*|&-lmessage |' ../Makefile.package + sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(message_SYSINC) |' ../Makefile.package + sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(message_SYSLIB) |' ../Makefile.package + sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(message_SYSPATH) |' ../Makefile.package + fi + + if (test -e ../Makefile.package.settings) then + sed -i -e '/^include.*message.*$/d' ../Makefile.package.settings + # multiline form needed for BSD sed on Macs + sed -i -e '4 i \ +include ..\/..\/lib\/message\/Makefile.lammps +' ../Makefile.package.settings + fi + +elif (test $1 = 0) then + + if (test -e ../Makefile.package) then + sed -i -e 's/[^ \t]*message[^ \t]* //' ../Makefile.package + fi + + if (test -e ../Makefile.package.settings) then + sed -i -e '/^include.*message.*$/d' ../Makefile.package.settings + fi + +fi diff --git a/src/MESSAGE/fix_client_md.cpp b/src/MESSAGE/fix_client_md.cpp new file mode 100644 index 0000000000..aca5cd41f9 --- /dev/null +++ b/src/MESSAGE/fix_client_md.cpp @@ -0,0 +1,325 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include +#include +#include "fix_client_md.h" +#include "update.h" +#include "atom.h" +#include "comm.h" +#include "domain.h" +#include "force.h" +#include "memory.h" +#include "error.h" + +// CSlib interface + +#include "cslib.h" + +using namespace LAMMPS_NS; +using namespace CSLIB_NS; +using namespace FixConst; + +enum{OTHER,REAL,METAL}; +enum{SETUP=1,STEP}; +enum{DIM=1,PERIODICITY,ORIGIN,BOX,NATOMS,NTYPES,TYPES,COORDS,UNITS,CHARGE}; +enum{FORCES=1,ENERGY,PRESSURE,ERROR}; + +/* ---------------------------------------------------------------------- */ + +FixClientMD::FixClientMD(LAMMPS *lmp, int narg, char **arg) : + Fix(lmp, narg, arg) +{ + if (lmp->clientserver != 1) + error->all(FLERR,"Fix client/md requires LAMMPS be running as a client"); + if (!atom->map_style) error->all(FLERR,"Fix client/md requires atom map"); + + if (sizeof(tagint) != 4) + error->all(FLERR,"Fix client/md requires 4-byte atom IDs"); + + if (strcmp(update->unit_style,"real") == 0) units = REAL; + else if (strcmp(update->unit_style,"metal") == 0) units = METAL; + else units = OTHER; + + scalar_flag = 1; + global_freq = 1; + extscalar = 1; + virial_flag = 1; + thermo_virial = 1; + + inv_nprocs = 1.0 / comm->nprocs; + if (domain->dimension == 2) + box[0][2] = box[1][2] = box[2][0] = box[2][1] = box[2][2] = 0.0; + + maxatom = 0; + xpbc = NULL; + + // unit conversion factors for REAL + // otherwise not needed + // message received in METAL units, convert to local REAL units + + fconvert = econvert = pconvert = 1.0; + if (units == REAL) { + fconvert = econvert = 23.06035; // eV -> Kcal/mole + pconvert = 0.986923; // bars -> atmospheres + } +} + +/* ---------------------------------------------------------------------- */ + +FixClientMD::~FixClientMD() +{ + memory->destroy(xpbc); + + CSlib *cs = (CSlib *) lmp->cslib; + + // all-done message to server + + cs->send(-1,0); + + int nfield; + int *fieldID,*fieldtype,*fieldlen; + int msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen); + + // clean-up + + delete cs; + lmp->cslib = NULL; +} + +/* ---------------------------------------------------------------------- */ + +int FixClientMD::setmask() +{ + int mask = 0; + mask |= POST_FORCE; + mask |= MIN_POST_FORCE; + mask |= THERMO_ENERGY; + return mask; +} + +/* ---------------------------------------------------------------------- */ + +void FixClientMD::init() +{ + if (3*atom->natoms > INT_MAX) + error->all(FLERR,"Fix client/md max atoms is 1/3 of 2^31"); +} + +/* ---------------------------------------------------------------------- */ + +void FixClientMD::setup(int vflag) +{ + CSlib *cs = (CSlib *) lmp->cslib; + + // SETUP send at beginning of each run + // required fields: DIM, PERIODICTY, ORIGIN, BOX, NATOMS, NTYPES, TYPES, COORDS + // optional fields: others in enum above + + int nfields = 8; + if (units == OTHER) nfields++; + if (atom->q_flag) nfields++; + + cs->send(SETUP,nfields); + + cs->pack_int(DIM,domain->dimension); + cs->pack(PERIODICITY,1,3,domain->periodicity); + + pack_box(); + cs->pack(ORIGIN,4,3,domain->boxlo); + cs->pack(BOX,4,9,&box[0][0]); + + cs->pack_int(NATOMS,atom->natoms); + cs->pack_int(NTYPES,atom->ntypes); + + cs->pack_parallel(TYPES,1,atom->nlocal,atom->tag,1,atom->type); + pack_coords(); + cs->pack_parallel(COORDS,4,atom->nlocal,atom->tag,3,xpbc); + + if (units == OTHER) cs->pack_string(UNITS,update->unit_style); + + if (atom->q_flag) + cs->pack_parallel(CHARGE,4,atom->nlocal,atom->tag,1,atom->q); + + // receive initial forces, energy, virial + + receive_fev(vflag); + + if (server_error) { + char str[64]; + sprintf(str,"Fix client/md received server error %d\n",server_error); + error->all(FLERR,str); + } +} + +/* ---------------------------------------------------------------------- */ + +void FixClientMD::min_setup(int vflag) +{ + setup(vflag); +} + +/* ---------------------------------------------------------------------- */ + +void FixClientMD::post_force(int vflag) +{ + int i,j,m; + + // energy and virial setup + + if (vflag) v_setup(vflag); + else evflag = 0; + + // STEP send every step + // required fields: COORDS + // optional fields: ORIGIN, BOX + + // send coords + + CSlib *cs = (CSlib *) lmp->cslib; + + int nfields = 1; + if (domain->box_change) nfields += 2; + + cs->send(STEP,nfields); + + pack_coords(); + cs->pack_parallel(COORDS,4,atom->nlocal,atom->tag,3,xpbc); + + if (domain->box_change) { + pack_box(); + cs->pack(ORIGIN,4,3,domain->boxlo); + cs->pack(BOX,4,9,&box[0][0]); + } + + // receive forces, energy, virial + + receive_fev(vflag); + + if (server_error) { + char str[64]; + sprintf(str,"Fix client/md received server error %d\n",server_error); + error->all(FLERR,str); + } +} + +/* ---------------------------------------------------------------------- */ + +void FixClientMD::min_post_force(int vflag) +{ + post_force(vflag); +} + +/* ---------------------------------------------------------------------- + potential energy from server +------------------------------------------------------------------------- */ + +double FixClientMD::compute_scalar() +{ + return eng; +} + +/* ---------------------------------------------------------------------- + pack local coords into xpbc, enforcing PBC +------------------------------------------------------------------------- */ + +void FixClientMD::pack_coords() +{ + double **x = atom->x; + int nlocal = atom->nlocal; + + if (nlocal > maxatom) { + memory->destroy(xpbc); + maxatom = atom->nmax; + memory->create(xpbc,3*maxatom,"message:xpbc"); + } + + memcpy(xpbc,&x[0][0],3*nlocal*sizeof(double)); + + int j = 0; + for (int i = 0; i < nlocal; i++) { + domain->remap(&xpbc[j]); + j += 3; + } +} + +/* ---------------------------------------------------------------------- + pack box info into box = 3 edge vectors of simulation box +------------------------------------------------------------------------- */ + +void FixClientMD::pack_box() +{ + double *boxlo = domain->boxlo; + double *boxhi = domain->boxhi; + + box[0][0] = boxhi[0] - boxlo[0]; + box[0][1] = 0.0; + box[0][2] = 0.0; + box[1][0] = domain->xy; + box[1][1] = boxhi[1] - boxlo[1]; + box[1][2] = 0.0; + box[2][0] = domain->xz; + box[2][1] = domain->yz; + box[2][2] = boxhi[2] - boxlo[2]; +} + +/* ---------------------------------------------------------------------- + receive message from server + required fields: FORCES, ENERGY, PRESSURE + optional field: ERROR +------------------------------------------------------------------------- */ + +void FixClientMD::receive_fev(int vflag) +{ + CSlib *cs = (CSlib *) lmp->cslib; + + int nfield; + int *fieldID,*fieldtype,*fieldlen; + + int msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen); + + double *forces = (double *) cs->unpack(FORCES); + double **f = atom->f; + int nlocal = atom->nlocal; + bigint natoms = atom->natoms; + int m; + + int j = 0; + for (tagint id = 1; id <= natoms; id++) { + m = atom->map(id); + if (m < 0 || m >= nlocal) j += 3; + else { + f[m][0] += fconvert * forces[j++]; + f[m][1] += fconvert * forces[j++]; + f[m][2] += fconvert * forces[j++]; + } + } + + eng = econvert * cs->unpack_double(ENERGY); + + if (vflag) { + double *v = (double *) cs->unpack(PRESSURE); + + double nktv2p = force->nktv2p; + double volume = domain->xprd * domain->yprd * domain->zprd; + double factor = inv_nprocs * pconvert * volume / nktv2p; + + for (int i = 0; i < 6; i++) + virial[i] = factor * v[i]; + } + + // error return + + server_error = 0; + if (nfield == 4) server_error = cs->unpack_int(ERROR); +} diff --git a/src/MESSAGE/fix_client_md.h b/src/MESSAGE/fix_client_md.h new file mode 100644 index 0000000000..1c874c7278 --- /dev/null +++ b/src/MESSAGE/fix_client_md.h @@ -0,0 +1,65 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef FIX_CLASS + +FixStyle(client/md,FixClientMD) + +#else + +#ifndef LMP_FIX_CLIENT_MD_H +#define LMP_FIX_CLIENT_MD_H + +#include "fix.h" + +namespace LAMMPS_NS { + +class FixClientMD : public Fix { + public: + FixClientMD(class LAMMPS *, int, char **); + ~FixClientMD(); + int setmask(); + void init(); + void setup(int); + void min_setup(int); + void post_force(int); + void min_post_force(int); + double compute_scalar(); + + private: + int maxatom,units,server_error; + double eng; + double inv_nprocs; + double fconvert,econvert,pconvert; + double box[3][3]; + double *xpbc; + + void pack_coords(); + void pack_box(); + void receive_fev(int); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +*/ diff --git a/src/MESSAGE/message.cpp b/src/MESSAGE/message.cpp new file mode 100644 index 0000000000..329ce1fbd9 --- /dev/null +++ b/src/MESSAGE/message.cpp @@ -0,0 +1,90 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include +#include "message.h" +#include "error.h" + +// CSlib interface + +#include "cslib.h" + +using namespace LAMMPS_NS; +using namespace CSLIB_NS; + +// customize by adding a new server protocol enum + +enum{MD,MC}; + +/* ---------------------------------------------------------------------- */ + +void Message::command(int narg, char **arg) +{ + if (narg < 3) error->all(FLERR,"Illegal message command"); + + int clientserver; + if (strcmp(arg[0],"client") == 0) clientserver = 1; + else if (strcmp(arg[0],"server") == 0) clientserver = 2; + else error->all(FLERR,"Illegal message command"); + lmp->clientserver = clientserver; + + // customize by adding a new server protocol + + int protocol; + if (strcmp(arg[1],"md") == 0) protocol = MD; + else if (strcmp(arg[1],"mc") == 0) protocol = MC; + else error->all(FLERR,"Unknown message protocol"); + + // instantiate CSlib with chosen communication mode + + if (strcmp(arg[2],"file") == 0 || strcmp(arg[2],"zmq") == 0 || + strcmp(arg[2],"mpi/two") == 0) { + if (narg != 4) error->all(FLERR,"Illegal message command"); + lmp->cslib = new CSlib(clientserver-1,arg[2],arg[3],&world); + + } else if (strcmp(arg[2],"mpi/one") == 0) { + if (narg != 3) error->all(FLERR,"Illegal message command"); + if (!lmp->cscomm) + error->all(FLERR,"Message mpi/one mode, but -mpi cmdline arg not used"); + lmp->cslib = new CSlib(clientserver-1,arg[2],&lmp->cscomm,&world); + + } else error->all(FLERR,"Illegal message command"); + + // perform initial handshake between client and server + // other code being coupled to must perform similar operation + // client sends protocol with msgID = 0 + // server matches it and replies + + CSlib *cs = (CSlib *) lmp->cslib; + + if (clientserver == 1) { + cs->send(0,1); + cs->pack_string(1,arg[1]); + + int nfield; + int *fieldID,*fieldtype,*fieldlen; + int msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen); + if (msgID != 0) error->one(FLERR,"Bad initial client/server handshake"); + + } else { + int nfield; + int *fieldID,*fieldtype,*fieldlen; + int msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen); + if (msgID != 0) error->one(FLERR,"Bad initial client/server handshake"); + char *pstr = cs->unpack_string(1); + if (strcmp(pstr,arg[1]) != 0) + error->one(FLERR,"Mismatch in client/server protocol"); + + cs->send(0,0); + } +} diff --git a/src/MESSAGE/message.h b/src/MESSAGE/message.h new file mode 100644 index 0000000000..c384a5a7b7 --- /dev/null +++ b/src/MESSAGE/message.h @@ -0,0 +1,40 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef COMMAND_CLASS + +CommandStyle(message,Message) + +#else + +#ifndef LMP_MESSAGE_H +#define LMP_MESSAGE_H + +#include "pointers.h" + +namespace LAMMPS_NS { + +class Message : protected Pointers { + public: + Message(class LAMMPS *lmp) : Pointers(lmp) {}; + void command(int, char **); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/MESSAGE/server.cpp b/src/MESSAGE/server.cpp new file mode 100644 index 0000000000..f587fb76df --- /dev/null +++ b/src/MESSAGE/server.cpp @@ -0,0 +1,50 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include +#include "server.h" +#include "error.h" + +// customize by adding a new server protocol include and enum + +#include "server_md.h" +#include "server_mc.h" + +using namespace LAMMPS_NS; + +enum{MD,MC}; + +/* ---------------------------------------------------------------------- */ + +void Server::command(int narg, char **arg) +{ + if (narg != 1) error->all(FLERR,"Illegal server command"); + + if (lmp->clientserver != 2) + error->all(FLERR,"Message command not used to setup LAMMPS as a server"); + + // customize by adding a new server protocol + + int protocol; + if (strcmp(arg[0],"md") == 0) protocol = MD; + else if (strcmp(arg[0],"mc") == 0) protocol = MC; + else error->all(FLERR,"Unknown message protocol"); + + if (protocol == MD) { + ServerMD *server = new ServerMD(lmp); + server->loop(); + } else if (protocol == MC) { + ServerMC *server = new ServerMC(lmp); + server->loop(); + } +} diff --git a/src/MESSAGE/server.h b/src/MESSAGE/server.h new file mode 100644 index 0000000000..579f6ab6f1 --- /dev/null +++ b/src/MESSAGE/server.h @@ -0,0 +1,40 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef COMMAND_CLASS + +CommandStyle(server,Server) + +#else + +#ifndef LMP_SERVER_H +#define LMP_SERVER_H + +#include "pointers.h" + +namespace LAMMPS_NS { + +class Server : protected Pointers { + public: + Server(class LAMMPS *lmp) : Pointers(lmp) {}; + void command(int, char **); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/MESSAGE/server_mc.cpp b/src/MESSAGE/server_mc.cpp new file mode 100644 index 0000000000..8a7344e86b --- /dev/null +++ b/src/MESSAGE/server_mc.cpp @@ -0,0 +1,148 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "server_mc.h" +#include "atom.h" +#include "update.h" +#include "integrate.h" +#include "input.h" +#include "output.h" +#include "thermo.h" +#include "error.h" + +// CSlib interface + +#include "cslib.h" + +using namespace LAMMPS_NS; +using namespace CSLIB_NS; + +enum{NATOMS=1,EINIT,DISPLACE,ACCEPT,RUN}; + +/* ---------------------------------------------------------------------- */ + +ServerMC::ServerMC(LAMMPS *lmp) : Pointers(lmp) {} + +/* ---------------------------------------------------------------------- */ + +void ServerMC::loop() +{ + int i,j,m; + double xold[3],xnew[3]; + tagint atomid; + + CSlib *cs = (CSlib *) lmp->cslib; + + // require atom map + + if (!atom->map_style) error->all(FLERR,"Server mode requires atom map"); + + // initialize LAMMPS for dynamics + + input->one("run 0"); + + //update->whichflag = 1; + //lmp->init(); + + // loop on messages + // receive a message, process it, send return message if necessary + + int msgID,nfield; + int *fieldID,*fieldtype,*fieldlen; + + while (1) { + msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen); + if (msgID < 0) break; + + if (msgID == NATOMS) { + + cs->send(msgID,1); + cs->pack_int(1,atom->natoms); + + } else if (msgID == EINIT) { + + double dval; + output->thermo->evaluate_keyword((char *) "pe",&dval); + + cs->send(msgID,2); + cs->pack_double(1,dval); + double *coords = NULL; + if (atom->nlocal) coords = &atom->x[0][0]; + cs->pack_parallel(2,4,atom->nlocal,atom->tag,3,coords); + + } else if (msgID == DISPLACE) { + + atomid = cs->unpack_int(1); + double *xnew = (double *) cs->unpack(2); + double **x = atom->x; + + m = atom->map(atomid); + if (m >= 0 && m < atom->nlocal) { + xold[0] = x[m][0]; + xold[1] = x[m][1]; + xold[2] = x[m][2]; + x[m][0] = xnew[0]; + x[m][1] = xnew[1]; + x[m][2] = xnew[2]; + } + + input->one("run 0"); + double dval; + output->thermo->evaluate_keyword((char *) "pe",&dval); + + cs->send(msgID,1); + cs->pack_double(1,dval); + + } else if (msgID == ACCEPT) { + + int accept = cs->unpack_int(1); + double **x = atom->x; + + if (!accept) { + m = atom->map(atomid); + if (m >= 0 && m < atom->nlocal) { + x[m][0] = xold[0]; + x[m][1] = xold[1]; + x[m][2] = xold[2]; + } + } + + cs->send(msgID,0); + + } else if (msgID == RUN) { + + int nsteps = cs->unpack_int(1); + + //input->one("run 100"); + + update->nsteps = nsteps; + update->firststep = update->ntimestep; + update->laststep = update->ntimestep + nsteps; + + update->integrate->setup(1); + update->integrate->run(nsteps); + + cs->send(msgID,0); + + } else error->all(FLERR,"Server received unrecognized message"); + } + + // final reply to client + + cs->send(0,0); + + // clean up + + delete cs; + lmp->cslib = NULL; +} diff --git a/src/MESSAGE/server_mc.h b/src/MESSAGE/server_mc.h new file mode 100644 index 0000000000..d0fb489429 --- /dev/null +++ b/src/MESSAGE/server_mc.h @@ -0,0 +1,29 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifndef LMP_SERVER_MC_H +#define LMP_SERVER_MC_H + +#include "pointers.h" + +namespace LAMMPS_NS { + +class ServerMC : protected Pointers { + public: + ServerMC(class LAMMPS *); + void loop(); +}; + +} + +#endif diff --git a/src/MESSAGE/server_md.cpp b/src/MESSAGE/server_md.cpp new file mode 100644 index 0000000000..aa771b7d46 --- /dev/null +++ b/src/MESSAGE/server_md.cpp @@ -0,0 +1,389 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include +#include +#include "server_md.h" +#include "atom.h" +#include "atom_vec.h" +#include "update.h" +#include "integrate.h" +#include "kspace.h" +#include "force.h" +#include "pair.h" +#include "neighbor.h" +#include "comm.h" +#include "domain.h" +#include "memory.h" +#include "error.h" + +// CSlib interface + +#include "cslib.h" + +using namespace LAMMPS_NS; +using namespace CSLIB_NS; + +enum{OTHER,REAL,METAL}; +enum{SETUP=1,STEP}; +enum{DIM=1,PERIODICITY,ORIGIN,BOX,NATOMS,NTYPES,TYPES,COORDS,UNITS,CHARGE}; +enum{FORCES=1,ENERGY,PRESSURE,ERROR}; + +/* ---------------------------------------------------------------------- */ + +ServerMD::ServerMD(LAMMPS *lmp) : Pointers(lmp) +{ + if (domain->box_exist == 0) + error->all(FLERR,"Server command before simulation box is defined"); + + if (!atom->map_style) error->all(FLERR,"Server md requires atom map"); + if (atom->tag_enable == 0) error->all(FLERR,"Server md requires atom IDs"); + if (sizeof(tagint) != 4) error->all(FLERR,"Server md requires 4-byte atom IDs"); + + if (strcmp(update->unit_style,"real") == 0) units = REAL; + else if (strcmp(update->unit_style,"metal") == 0) units = METAL; + else units = OTHER; + + // unit conversion factors for REAL + // otherwise not needed + // local computation in REAL units, send message in METAL units + + fconvert = econvert = pconvert = 1.0; + if (units == REAL) { + fconvert = econvert = 1.0 / 23.06035; // Kcal/mole -> eV + pconvert = 1.0 / 0.986923; // atmospheres -> bars + } + + fcopy = NULL; +} + +/* ---------------------------------------------------------------------- */ + +ServerMD::~ServerMD() +{ + memory->destroy(fcopy); +} + +/* ---------------------------------------------------------------------- */ + +void ServerMD::loop() +{ + int i,j,m; + + // cs = instance of CSlib + + CSlib *cs = (CSlib *) lmp->cslib; + + // counters + + int forcecalls = 0; + int neighcalls = 0; + + // loop on messages + // receive a message, process it, send return message + + int msgID,nfield; + int *fieldID,*fieldtype,*fieldlen; + + while (1) { + msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen); + if (msgID < 0) break; + + // SETUP receive at beginning of each run + // required fields: DIM, PERIODICTY, ORIGIN, BOX, + // NATOMS, NTYPES, TYPES, COORDS + // optional fields: others in enum above + + if (msgID == SETUP) { + + int dim = 0; + int *periodicity = NULL; + int natoms = -1; + int ntypes = -1; + double *origin = NULL; + double *box = NULL; + int *types = NULL; + double *coords = NULL; + char *unit_style = NULL; + double *charge = NULL; + + for (int ifield = 0; ifield < nfield; ifield++) { + if (fieldID[ifield] == DIM) { + dim = cs->unpack_int(DIM); + if (dim != domain->dimension) + error->all(FLERR,"Server md dimension mis-match with client"); + } else if (fieldID[ifield] == PERIODICITY) { + periodicity = (int *) cs->unpack(PERIODICITY); + if (periodicity[0] != domain->periodicity[0] || + periodicity[1] != domain->periodicity[1] || + periodicity[2] != domain->periodicity[2]) + error->all(FLERR,"Server md periodicity mis-match with client"); + } else if (fieldID[ifield] == ORIGIN) { + origin = (double *) cs->unpack(ORIGIN); + } else if (fieldID[ifield] == BOX) { + box = (double *) cs->unpack(BOX); + } else if (fieldID[ifield] == NATOMS) { + natoms = cs->unpack_int(NATOMS); + if (3*natoms > INT_MAX) + error->all(FLERR,"Server md max atoms is 1/3 of 2^31"); + } else if (fieldID[ifield] == NTYPES) { + ntypes = cs->unpack_int(NTYPES); + if (ntypes != atom->ntypes) + error->all(FLERR,"Server md ntypes mis-match with client"); + } else if (fieldID[ifield] == TYPES) { + types = (int *) cs->unpack(TYPES); + } else if (fieldID[ifield] == COORDS) { + coords = (double *) cs->unpack(COORDS); + + } else if (fieldID[ifield] == UNITS) { + unit_style = (char *) cs->unpack(UNITS); + } else if (fieldID[ifield] == CHARGE) { + charge = (double *) cs->unpack(CHARGE); + } else error->all(FLERR,"Server md setup field unknown"); + } + + if (dim == 0 || !periodicity || !origin || !box || + natoms < 0 || ntypes < 0 || !types || !coords) + error->all(FLERR,"Required server md setup field not received"); + + if (unit_style && strcmp(unit_style,update->unit_style) != 0) + error->all(FLERR,"Server md does not match client units"); + + if (charge && atom->q_flag == 0) + error->all(FLERR,"Server md does not define atom attribute q"); + + // reset box, global and local + // reset proc decomposition + + if ((box[3] != 0.0 || box[6] != 0.0 || box[7] != 0.0) && + domain->triclinic == 0) + error->all(FLERR,"Server md is not initialized for a triclinic box"); + + box_change(origin,box); + + domain->set_initial_box(); + domain->set_global_box(); + comm->set_proc_grid(); + domain->set_local_box(); + + // clear all atoms + + atom->nlocal = 0; + atom->nghost = 0; + + // add atoms that are in my sub-box + + int nlocal = 0; + for (int i = 0; i < natoms; i++) { + if (!domain->ownatom(i+1,&coords[3*i],NULL,0)) continue; + atom->avec->create_atom(types[i],&coords[3*i]); + atom->tag[nlocal] = i+1; + if (charge) atom->q[nlocal] = charge[i]; + nlocal++; + } + + int ntotal; + MPI_Allreduce(&atom->nlocal,&ntotal,1,MPI_INT,MPI_SUM,world); + if (ntotal != natoms) + error->all(FLERR,"Server md atom count does not match client"); + + atom->map_init(); + atom->map_set(); + atom->natoms = natoms; + + // allocate fcopy if needed + + if (units == REAL) { + memory->destroy(fcopy); + memory->create(fcopy,atom->nlocal,3,"server/md:fcopy"); + } + + // perform system setup() for dynamics + // also OK for minimization, since client runs minimizer + // return forces, energy, virial to client + + update->whichflag = 1; + lmp->init(); + update->integrate->setup_minimal(1); + neighcalls++; + forcecalls++; + + send_fev(msgID); + + // STEP receive at each timestep of run or minimization + // required fields: COORDS + // optional fields: ORIGIN, BOX + + } else if (msgID == STEP) { + + double *coords = NULL; + double *origin = NULL; + double *box = NULL; + + for (int ifield = 0; ifield < nfield; ifield++) { + if (fieldID[ifield] == COORDS) { + coords = (double *) cs->unpack(COORDS); + } else if (fieldID[ifield] == ORIGIN) { + origin = (double *) cs->unpack(ORIGIN); + } else if (fieldID[ifield] == BOX) { + box = (double *) cs->unpack(BOX); + } else error->all(FLERR,"Server md step field unknown"); + } + + if (!coords) + error->all(FLERR,"Required server md step field not received"); + + // change box size/shape, only if origin and box received + // reset global/local box like FixDeform at end_of_step() + + if (origin && box) { + if ((box[3] != 0.0 || box[6] != 0.0 || box[7] != 0.0) && + domain->triclinic == 0) + error->all(FLERR,"Server md is not initialized for a triclinic box"); + box_change(origin,box); + domain->set_global_box(); + domain->set_local_box(); + } + + // assign received coords to owned atoms + // closest_image() insures xyz matches current server PBC + + double **x = atom->x; + int nlocal = atom->nlocal; + int nall = atom->natoms; + + j = 0; + for (tagint id = 1; id <= nall; id++) { + m = atom->map(id); + if (m < 0 || m >= nlocal) j += 3; + else { + domain->closest_image(x[m],&coords[j],x[m]); + j += 3; + } + } + + // if no need to reneighbor: + // ghost comm + // setup_minimal(0) which just computes forces + // else: + // setup_minimal(1) for pbc, reset_box, reneigh, forces + + int nflag = neighbor->decide(); + if (nflag == 0) { + comm->forward_comm(); + update->integrate->setup_minimal(0); + } else { + update->integrate->setup_minimal(1); + neighcalls++; + } + + forcecalls++; + + send_fev(msgID); + + } else error->all(FLERR,"Server MD received unrecognized message"); + } + + // final reply to client + + cs->send(0,0); + + // stats + + if (comm->me == 0) { + if (screen) { + fprintf(screen,"Server MD calls = %d\n",forcecalls); + fprintf(screen,"Server MD reneighborings = %d\n",neighcalls); + } + if (logfile) { + fprintf(logfile,"Server MD calls = %d\n",forcecalls); + fprintf(logfile,"Server MD reneighborings %d\n",neighcalls); + } + } + + // clean up + + delete cs; + lmp->cslib = NULL; +} + +/* ---------------------------------------------------------------------- + box change due to received message +------------------------------------------------------------------------- */ + +void ServerMD::box_change(double *origin, double *box) +{ + domain->boxlo[0] = origin[0]; + domain->boxlo[1] = origin[1]; + domain->boxlo[2] = origin[2]; + + domain->boxhi[0] = origin[0] + box[0]; + domain->boxhi[1] = origin[1] + box[4]; + domain->boxhi[2] = origin[2] + box[8]; + + domain->xy = box[3]; + domain->xz = box[6]; + domain->yz = box[7]; +} + +/* ---------------------------------------------------------------------- + return message with forces, energy, pressure tensor + pressure tensor should be just pair and KSpace contributions + required fields: FORCES, ENERGY, PRESSURE + optional field: ERROR (not ever sending) +------------------------------------------------------------------------- */ + +void ServerMD::send_fev(int msgID) +{ + CSlib *cs = (CSlib *) lmp->cslib; + + cs->send(msgID,3); + + double *forces = NULL; + if (atom->nlocal) { + if (units != REAL) forces = &atom->f[0][0]; + else { + double **f = atom->f; + int nlocal = atom->nlocal; + for (int i = 0; i < nlocal; i++) { + fcopy[i][0] = fconvert*f[i][0]; + fcopy[i][1] = fconvert*f[i][1]; + fcopy[i][2] = fconvert*f[i][2]; + } + forces = &fcopy[0][0]; + } + } + cs->pack_parallel(FORCES,4,atom->nlocal,atom->tag,3,forces); + + double eng = force->pair->eng_vdwl + force->pair->eng_coul; + double engall; + MPI_Allreduce(&eng,&engall,1,MPI_DOUBLE,MPI_SUM,world); + engall *= econvert; + cs->pack_double(ENERGY,engall); + + double v[6],vall[6]; + for (int i = 0; i < 6; i++) + v[i] = force->pair->virial[i]; + MPI_Allreduce(&v,&vall,6,MPI_DOUBLE,MPI_SUM,world); + + if (force->kspace) + for (int i = 0; i < 6; i++) + vall[i] += force->kspace->virial[i]; + + double nktv2p = force->nktv2p; + double volume = domain->xprd * domain->yprd * domain->zprd; + double factor = pconvert / volume * nktv2p; + for (int i = 0; i < 6; i++) vall[i] *= factor; + + cs->pack(PRESSURE,4,6,vall); +} diff --git a/src/MESSAGE/server_md.h b/src/MESSAGE/server_md.h new file mode 100644 index 0000000000..289d70bdd8 --- /dev/null +++ b/src/MESSAGE/server_md.h @@ -0,0 +1,38 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifndef LMP_SERVER_MD_H +#define LMP_SERVER_MD_H + +#include "pointers.h" + +namespace LAMMPS_NS { + +class ServerMD : protected Pointers { + public: + ServerMD(class LAMMPS *); + ~ServerMD(); + void loop(); + + private: + int units; + double fconvert,econvert,pconvert; + double **fcopy; + + void box_change(double *, double *); + void send_fev(int); +}; + +} + +#endif diff --git a/src/MISC/fix_efield.cpp b/src/MISC/fix_efield.cpp index 1fa141e2bf..004c8ad7bc 100644 --- a/src/MISC/fix_efield.cpp +++ b/src/MISC/fix_efield.cpp @@ -412,7 +412,7 @@ void FixEfield::post_force(int vflag) /* ---------------------------------------------------------------------- */ -void FixEfield::post_force_respa(int vflag, int ilevel, int iloop) +void FixEfield::post_force_respa(int vflag, int ilevel, int /*iloop*/) { if (ilevel == ilevel_respa) post_force(vflag); } diff --git a/src/MISC/fix_gld.cpp b/src/MISC/fix_gld.cpp index 370730133e..2bf02889a5 100644 --- a/src/MISC/fix_gld.cpp +++ b/src/MISC/fix_gld.cpp @@ -217,7 +217,7 @@ void FixGLD::init() First half of a timestep (V^{n} -> V^{n+1/2}; X^{n} -> X^{n+1}) ------------------------------------------------------------------------- */ -void FixGLD::initial_integrate(int vflag) +void FixGLD::initial_integrate(int /*vflag*/) { double dtfm; double ftm2v = force->ftm2v; @@ -444,7 +444,7 @@ void FixGLD::final_integrate() /* ---------------------------------------------------------------------- */ -void FixGLD::initial_integrate_respa(int vflag, int ilevel, int iloop) +void FixGLD::initial_integrate_respa(int vflag, int ilevel, int /*iloop*/) { dtv = step_respa[ilevel]; dtf = 0.5 * step_respa[ilevel] * (force->ftm2v); @@ -458,7 +458,7 @@ void FixGLD::initial_integrate_respa(int vflag, int ilevel, int iloop) /* ---------------------------------------------------------------------- */ -void FixGLD::final_integrate_respa(int ilevel, int iloop) +void FixGLD::final_integrate_respa(int ilevel, int /*iloop*/) { dtf = 0.5 * step_respa[ilevel] * (force->ftm2v); final_integrate(); @@ -507,7 +507,7 @@ void FixGLD::grow_arrays(int nmax) copy values within local atom-based arrays ------------------------------------------------------------------------- */ -void FixGLD::copy_arrays(int i, int j, int delflag) +void FixGLD::copy_arrays(int i, int j, int /*delflag*/) { for (int k = 0; k < 3*prony_terms; k++) { s_gld[j][k] = s_gld[i][k]; @@ -588,7 +588,7 @@ void FixGLD::unpack_restart(int nlocal, int nth) fixes on a given processor. ------------------------------------------------------------------------- */ -int FixGLD::size_restart(int nlocal) +int FixGLD::size_restart(int /*nlocal*/) { return 3*prony_terms+1; } diff --git a/src/MISC/fix_orient_bcc.cpp b/src/MISC/fix_orient_bcc.cpp index c5ba6514a9..c614577933 100644 --- a/src/MISC/fix_orient_bcc.cpp +++ b/src/MISC/fix_orient_bcc.cpp @@ -230,7 +230,7 @@ void FixOrientBCC::init() /* ---------------------------------------------------------------------- */ -void FixOrientBCC::init_list(int id, NeighList *ptr) +void FixOrientBCC::init_list(int /*id*/, NeighList *ptr) { list = ptr; } @@ -250,7 +250,7 @@ void FixOrientBCC::setup(int vflag) /* ---------------------------------------------------------------------- */ -void FixOrientBCC::post_force(int vflag) +void FixOrientBCC::post_force(int /*vflag*/) { int i,j,k,ii,jj,inum,jnum,m,n,nn,nsort; tagint id_self; @@ -471,7 +471,7 @@ void FixOrientBCC::post_force(int vflag) /* ---------------------------------------------------------------------- */ -void FixOrientBCC::post_force_respa(int vflag, int ilevel, int iloop) +void FixOrientBCC::post_force_respa(int vflag, int ilevel, int /*iloop*/) { if (ilevel == ilevel_respa) post_force(vflag); } @@ -488,7 +488,7 @@ double FixOrientBCC::compute_scalar() /* ---------------------------------------------------------------------- */ int FixOrientBCC::pack_forward_comm(int n, int *list, double *buf, - int pbc_flag, int *pbc) + int /*pbc_flag*/, int * /*pbc*/) { int i,j,k,num; tagint id; diff --git a/src/MISC/fix_orient_fcc.cpp b/src/MISC/fix_orient_fcc.cpp index 5786571a89..5b394adde7 100644 --- a/src/MISC/fix_orient_fcc.cpp +++ b/src/MISC/fix_orient_fcc.cpp @@ -228,7 +228,7 @@ void FixOrientFCC::init() /* ---------------------------------------------------------------------- */ -void FixOrientFCC::init_list(int id, NeighList *ptr) +void FixOrientFCC::init_list(int /*id*/, NeighList *ptr) { list = ptr; } @@ -248,7 +248,7 @@ void FixOrientFCC::setup(int vflag) /* ---------------------------------------------------------------------- */ -void FixOrientFCC::post_force(int vflag) +void FixOrientFCC::post_force(int /*vflag*/) { int i,j,k,ii,jj,inum,jnum,m,n,nn,nsort; tagint id_self; @@ -469,7 +469,7 @@ void FixOrientFCC::post_force(int vflag) /* ---------------------------------------------------------------------- */ -void FixOrientFCC::post_force_respa(int vflag, int ilevel, int iloop) +void FixOrientFCC::post_force_respa(int vflag, int ilevel, int /*iloop*/) { if (ilevel == ilevel_respa) post_force(vflag); } @@ -486,7 +486,7 @@ double FixOrientFCC::compute_scalar() /* ---------------------------------------------------------------------- */ int FixOrientFCC::pack_forward_comm(int n, int *list, double *buf, - int pbc_flag, int *pbc) + int /*pbc_flag*/, int * /*pbc*/) { int i,j,k,num; tagint id; diff --git a/src/MISC/fix_ttm.cpp b/src/MISC/fix_ttm.cpp index 7ffd979e50..c8f33c73b7 100644 --- a/src/MISC/fix_ttm.cpp +++ b/src/MISC/fix_ttm.cpp @@ -235,7 +235,7 @@ void FixTTM::setup(int vflag) /* ---------------------------------------------------------------------- */ -void FixTTM::post_force(int vflag) +void FixTTM::post_force(int /*vflag*/) { double **x = atom->x; double **v = atom->v; @@ -287,7 +287,7 @@ void FixTTM::post_force(int vflag) /* ---------------------------------------------------------------------- */ -void FixTTM::post_force_setup(int vflag) +void FixTTM::post_force_setup(int /*vflag*/) { double **f = atom->f; int *mask = atom->mask; @@ -306,14 +306,14 @@ void FixTTM::post_force_setup(int vflag) /* ---------------------------------------------------------------------- */ -void FixTTM::post_force_respa(int vflag, int ilevel, int iloop) +void FixTTM::post_force_respa(int vflag, int ilevel, int /*iloop*/) { if (ilevel == nlevels_respa-1) post_force(vflag); } /* ---------------------------------------------------------------------- */ -void FixTTM::post_force_respa_setup(int vflag, int ilevel, int iloop) +void FixTTM::post_force_respa_setup(int vflag, int ilevel, int /*iloop*/) { if (ilevel == nlevels_respa-1) post_force_setup(vflag); } @@ -685,7 +685,7 @@ int FixTTM::maxsize_restart() size of atom nlocal's restart data ------------------------------------------------------------------------- */ -int FixTTM::size_restart(int nlocal) +int FixTTM::size_restart(int /*nlocal*/) { return 4; } diff --git a/src/MISC/pair_nm_cut.cpp b/src/MISC/pair_nm_cut.cpp index a778d7a5b6..ce077a7a04 100644 --- a/src/MISC/pair_nm_cut.cpp +++ b/src/MISC/pair_nm_cut.cpp @@ -401,8 +401,8 @@ void PairNMCut::write_data_all(FILE *fp) /* ---------------------------------------------------------------------- */ -double PairNMCut::single(int i, int j, int itype, int jtype, - double rsq, double factor_coul, double factor_lj, +double PairNMCut::single(int /*i*/, int /*j*/, int itype, int jtype, + double rsq, double /*factor_coul*/, double factor_lj, double &fforce) { double r2inv,r,forcenm,phinm; diff --git a/src/MISC/xdr_compat.cpp b/src/MISC/xdr_compat.cpp index 3987aa02fc..0f4d73cdd9 100644 --- a/src/MISC/xdr_compat.cpp +++ b/src/MISC/xdr_compat.cpp @@ -650,7 +650,7 @@ xdrstdio_setpos (XDR *xdrs, unsigned int pos) } static xdr_int32_t * -xdrstdio_inline (XDR *xdrs, int len) +xdrstdio_inline (XDR * /*xdrs*/, int /*len*/) { /* * Must do some work to implement this: must insure diff --git a/src/MOLECULE/angle_cosine.cpp b/src/MOLECULE/angle_cosine.cpp index e3472dfd7a..7fb7ce4c27 100644 --- a/src/MOLECULE/angle_cosine.cpp +++ b/src/MOLECULE/angle_cosine.cpp @@ -172,7 +172,7 @@ void AngleCosine::coeff(int narg, char **arg) /* ---------------------------------------------------------------------- */ -double AngleCosine::equilibrium_angle(int i) +double AngleCosine::equilibrium_angle(int /*i*/) { return MY_PI; } diff --git a/src/MOLECULE/angle_cosine_periodic.cpp b/src/MOLECULE/angle_cosine_periodic.cpp index 4e620b436e..e8dd970b3b 100644 --- a/src/MOLECULE/angle_cosine_periodic.cpp +++ b/src/MOLECULE/angle_cosine_periodic.cpp @@ -222,7 +222,7 @@ void AngleCosinePeriodic::coeff(int narg, char **arg) /* ---------------------------------------------------------------------- */ -double AngleCosinePeriodic::equilibrium_angle(int i) +double AngleCosinePeriodic::equilibrium_angle(int /*i*/) { return MY_PI; } diff --git a/src/MOLECULE/bond_fene.cpp b/src/MOLECULE/bond_fene.cpp index b6da72bfaf..671290b0ad 100644 --- a/src/MOLECULE/bond_fene.cpp +++ b/src/MOLECULE/bond_fene.cpp @@ -242,7 +242,7 @@ void BondFENE::write_data(FILE *fp) /* ---------------------------------------------------------------------- */ -double BondFENE::single(int type, double rsq, int i, int j, +double BondFENE::single(int type, double rsq, int /*i*/, int /*j*/, double &fforce) { double r0sq = r0[type] * r0[type]; diff --git a/src/MOLECULE/bond_fene_expand.cpp b/src/MOLECULE/bond_fene_expand.cpp index 26b699d7bf..3e191683fb 100644 --- a/src/MOLECULE/bond_fene_expand.cpp +++ b/src/MOLECULE/bond_fene_expand.cpp @@ -253,7 +253,7 @@ void BondFENEExpand::write_data(FILE *fp) /* ---------------------------------------------------------------------- */ -double BondFENEExpand::single(int type, double rsq, int i, int j, +double BondFENEExpand::single(int type, double rsq, int /*i*/, int /*j*/, double &fforce) { double r = sqrt(rsq); diff --git a/src/MOLECULE/bond_gromos.cpp b/src/MOLECULE/bond_gromos.cpp index 8e989259af..279f4fb2d4 100644 --- a/src/MOLECULE/bond_gromos.cpp +++ b/src/MOLECULE/bond_gromos.cpp @@ -190,7 +190,7 @@ void BondGromos::write_data(FILE *fp) /* ---------------------------------------------------------------------- */ -double BondGromos::single(int type, double rsq, int i, int j, +double BondGromos::single(int type, double rsq, int /*i*/, int /*j*/, double &fforce) { double dr = rsq - r0[type]*r0[type]; diff --git a/src/MOLECULE/bond_harmonic.cpp b/src/MOLECULE/bond_harmonic.cpp index e7f510d2de..f795610b37 100644 --- a/src/MOLECULE/bond_harmonic.cpp +++ b/src/MOLECULE/bond_harmonic.cpp @@ -190,7 +190,7 @@ void BondHarmonic::write_data(FILE *fp) /* ---------------------------------------------------------------------- */ -double BondHarmonic::single(int type, double rsq, int i, int j, +double BondHarmonic::single(int type, double rsq, int /*i*/, int /*j*/, double &fforce) { double r = sqrt(rsq); diff --git a/src/MOLECULE/bond_morse.cpp b/src/MOLECULE/bond_morse.cpp index 35be50e8df..06af28f2b0 100644 --- a/src/MOLECULE/bond_morse.cpp +++ b/src/MOLECULE/bond_morse.cpp @@ -196,7 +196,7 @@ void BondMorse::write_data(FILE *fp) /* ---------------------------------------------------------------------- */ -double BondMorse::single(int type, double rsq, int i, int j, +double BondMorse::single(int type, double rsq, int /*i*/, int /*j*/, double &fforce) { double r = sqrt(rsq); diff --git a/src/MOLECULE/bond_nonlinear.cpp b/src/MOLECULE/bond_nonlinear.cpp index 3926c3494b..645b081779 100644 --- a/src/MOLECULE/bond_nonlinear.cpp +++ b/src/MOLECULE/bond_nonlinear.cpp @@ -191,7 +191,7 @@ void BondNonlinear::write_data(FILE *fp) /* ---------------------------------------------------------------------- */ -double BondNonlinear::single(int type, double rsq, int i, int j, +double BondNonlinear::single(int type, double rsq, int /*i*/, int /*j*/, double &fforce) { double r = sqrt(rsq); diff --git a/src/MOLECULE/bond_quartic.cpp b/src/MOLECULE/bond_quartic.cpp index f581c7f331..f200030d6c 100644 --- a/src/MOLECULE/bond_quartic.cpp +++ b/src/MOLECULE/bond_quartic.cpp @@ -251,7 +251,7 @@ void BondQuartic::init_style() return an equilbrium bond length ------------------------------------------------------------------------- */ -double BondQuartic::equilibrium_distance(int i) +double BondQuartic::equilibrium_distance(int /*i*/) { return 0.97; } diff --git a/src/MOLECULE/bond_table.cpp b/src/MOLECULE/bond_table.cpp index 7515f713df..a5c579042b 100644 --- a/src/MOLECULE/bond_table.cpp +++ b/src/MOLECULE/bond_table.cpp @@ -244,7 +244,7 @@ void BondTable::read_restart(FILE *fp) /* ---------------------------------------------------------------------- */ -double BondTable::single(int type, double rsq, int i, int j, +double BondTable::single(int type, double rsq, int /*i*/, int /*j*/, double &fforce) { double r = sqrt(rsq); diff --git a/src/MOLECULE/fix_cmap.cpp b/src/MOLECULE/fix_cmap.cpp index 5ef2e662ab..b527eef020 100644 --- a/src/MOLECULE/fix_cmap.cpp +++ b/src/MOLECULE/fix_cmap.cpp @@ -295,7 +295,7 @@ void FixCMAP::pre_neighbor() store eflag, so can use it in post_force to tally per-atom energies ------------------------------------------------------------------------- */ -void FixCMAP::pre_reverse(int eflag, int vflag) +void FixCMAP::pre_reverse(int eflag, int /*vflag*/) { eflag_caller = eflag; } @@ -604,7 +604,7 @@ void FixCMAP::post_force(int vflag) /* ---------------------------------------------------------------------- */ -void FixCMAP::post_force_respa(int vflag, int ilevel, int iloop) +void FixCMAP::post_force_respa(int vflag, int ilevel, int /*iloop*/) { if (ilevel == nlevels_respa-1) post_force(vflag); } @@ -1163,7 +1163,7 @@ void FixCMAP::read_data_section(char *keyword, int n, char *buf, /* ---------------------------------------------------------------------- */ -bigint FixCMAP::read_data_skip_lines(char *keyword) +bigint FixCMAP::read_data_skip_lines(char * /*keyword*/) { return ncmap; } @@ -1173,7 +1173,7 @@ bigint FixCMAP::read_data_skip_lines(char *keyword) only called by proc 0 ------------------------------------------------------------------------- */ -void FixCMAP::write_data_header(FILE *fp, int mth) +void FixCMAP::write_data_header(FILE *fp, int /*mth*/) { fprintf(fp,BIGINT_FORMAT " cmap crossterms\n",ncmap); } @@ -1186,7 +1186,7 @@ void FixCMAP::write_data_header(FILE *fp, int mth) ny = columns = type + 5 atom IDs ------------------------------------------------------------------------- */ -void FixCMAP::write_data_section_size(int mth, int &nx, int &ny) +void FixCMAP::write_data_section_size(int /*mth*/, int &nx, int &ny) { int i,m; @@ -1206,7 +1206,7 @@ void FixCMAP::write_data_section_size(int mth, int &nx, int &ny) buf allocated by caller as owned crossterms by 6 ------------------------------------------------------------------------- */ -void FixCMAP::write_data_section_pack(int mth, double **buf) +void FixCMAP::write_data_section_pack(int /*mth*/, double **buf) { int i,m; @@ -1237,7 +1237,7 @@ void FixCMAP::write_data_section_pack(int mth, double **buf) only called by proc 0 ------------------------------------------------------------------------- */ -void FixCMAP::write_data_section_keyword(int mth, FILE *fp) +void FixCMAP::write_data_section_keyword(int /*mth*/, FILE *fp) { fprintf(fp,"\nCMAP\n\n"); } @@ -1249,7 +1249,7 @@ void FixCMAP::write_data_section_keyword(int mth, FILE *fp) only called by proc 0 ------------------------------------------------------------------------- */ -void FixCMAP::write_data_section(int mth, FILE *fp, +void FixCMAP::write_data_section(int /*mth*/, FILE *fp, int n, double **buf, int index) { for (int i = 0; i < n; i++) @@ -1383,7 +1383,7 @@ void FixCMAP::grow_arrays(int nmax) copy values within local atom-based array ------------------------------------------------------------------------- */ -void FixCMAP::copy_arrays(int i, int j, int delflag) +void FixCMAP::copy_arrays(int i, int j, int /*delflag*/) { num_crossterm[j] = num_crossterm[i]; diff --git a/src/MOLECULE/pair_hbond_dreiding_lj.cpp b/src/MOLECULE/pair_hbond_dreiding_lj.cpp index 26ff499dec..c0c885d4d4 100644 --- a/src/MOLECULE/pair_hbond_dreiding_lj.cpp +++ b/src/MOLECULE/pair_hbond_dreiding_lj.cpp @@ -468,7 +468,7 @@ double PairHbondDreidingLJ::init_one(int i, int j) double PairHbondDreidingLJ::single(int i, int j, int itype, int jtype, double rsq, - double factor_coul, double factor_lj, + double /*factor_coul*/, double /*factor_lj*/, double &fforce) { int k,kk,ktype,knum,m; diff --git a/src/MOLECULE/pair_hbond_dreiding_morse.cpp b/src/MOLECULE/pair_hbond_dreiding_morse.cpp index 749053164c..f464d2c621 100644 --- a/src/MOLECULE/pair_hbond_dreiding_morse.cpp +++ b/src/MOLECULE/pair_hbond_dreiding_morse.cpp @@ -371,7 +371,7 @@ void PairHbondDreidingMorse::init_style() double PairHbondDreidingMorse::single(int i, int j, int itype, int jtype, double rsq, - double factor_coul, double factor_lj, + double /*factor_coul*/, double /*factor_lj*/, double &fforce) { int k,kk,ktype,knum,m; diff --git a/src/MOLECULE/pair_tip4p_cut.cpp b/src/MOLECULE/pair_tip4p_cut.cpp index e9f52b8724..79dd79b180 100644 --- a/src/MOLECULE/pair_tip4p_cut.cpp +++ b/src/MOLECULE/pair_tip4p_cut.cpp @@ -443,7 +443,7 @@ void PairTIP4PCut::init_style() init for one type pair i,j and corresponding j,i ------------------------------------------------------------------------- */ -double PairTIP4PCut::init_one(int i, int j) +double PairTIP4PCut::init_one(int /*i*/, int /*j*/) { // include TIP4P qdist in full cutoff, qdist = 0.0 if not TIP4P diff --git a/src/Makefile b/src/Makefile index d17a2ccbd9..2ee7885562 100644 --- a/src/Makefile +++ b/src/Makefile @@ -18,7 +18,7 @@ OBJDIR = Obj_$@ OBJSHDIR = Obj_shared_$@ SRC = $(wildcard *.cpp) -INC = $(wildcard *.h) +INC = $(filter-out lmpinstalledpkgs.h,$(wildcard *.h)) OBJ = $(SRC:.cpp=.o) SRCLIB = $(filter-out main.cpp,$(SRC)) @@ -53,26 +53,26 @@ endif # PACKEXT = subset that require an external (downloaded) library PACKAGE = asphere body class2 colloid compress coreshell dipole gpu \ - granular kim kokkos kspace latte manybody mc meam misc \ + granular kim kokkos kspace latte manybody mc meam message misc \ molecule mpiio mscg opt peri poems \ - python qeq reax replica rigid shock snap srd voronoi + python qeq reax replica rigid shock snap spin srd voronoi PACKUSER = user-atc user-awpmd user-bocs user-cgdna user-cgsdk user-colvars \ user-diffraction user-dpd user-drude user-eff user-fep user-h5md \ user-intel user-lb user-manifold user-meamc user-meso \ user-mgpt user-misc user-mofff user-molfile \ user-netcdf user-omp user-phonon user-qmmm user-qtb \ - user-quip user-reaxc user-smd user-smtbq user-sph user-tally \ - user-uef user-vtk + user-quip user-reaxc user-scafacos user-smd user-smtbq \ + user-sph user-tally user-uef user-vtk -PACKLIB = compress gpu kim kokkos latte meam mpiio mscg poems \ +PACKLIB = compress gpu kim kokkos latte meam message mpiio mscg poems \ python reax voronoi \ user-atc user-awpmd user-colvars user-h5md user-lb user-molfile \ - user-netcdf user-qmmm user-quip user-smd user-vtk + user-netcdf user-qmmm user-quip user-scafacos user-smd user-vtk PACKSYS = compress mpiio python user-lb -PACKINT = gpu kokkos meam poems reax user-atc user-awpmd user-colvars +PACKINT = gpu kokkos meam message poems reax user-atc user-awpmd user-colvars PACKEXT = kim mscg voronoi \ user-h5md user-molfile user-netcdf user-qmmm user-quip \ @@ -150,6 +150,21 @@ help: for file in $$files; do head -1 $$file; done @echo '' + +lmpinstalledpkgs.h: $(SRC) $(INC) + @echo 'Gathering installed package information (may take a little while)' + @echo '#ifndef LMP_INSTALLED_PKGS_H' > lmpinstalledpkgs.tmp + @echo '#define LMP_INSTALLED_PKGS_H' >> lmpinstalledpkgs.tmp + @echo 'const char * LAMMPS_NS::LAMMPS::installed_packages[] = {' >> lmpinstalledpkgs.tmp + @for p in $(PACKAGEUC) $(PACKUSERUC); do info=$$($(SHELL) Package.sh $$p installed); \ + [ -n "$$info" ] && echo "\"$$info\"" | sed -e 's/".*package \(.*\)"/"\1",/' >> lmpinstalledpkgs.tmp || :; done + @echo ' NULL };' >> lmpinstalledpkgs.tmp + @echo '#endif' >> lmpinstalledpkgs.tmp + @if [ -f lmpinstalledpkgs.h ]; \ + then test "`diff --brief lmpinstalledpkgs.tmp lmpinstalledpkgs.h`" != "" && \ + mv lmpinstalledpkgs.tmp lmpinstalledpkgs.h || rm lmpinstalledpkgs.tmp ; \ + else mv lmpinstalledpkgs.tmp lmpinstalledpkgs.h ; fi + # Build LAMMPS in one of 4 modes # exe = exe with static compile in Obj_machine (default) # shexe = exe with shared compile in Obj_shared_machine @@ -163,6 +178,8 @@ help: -f MAKE/MACHINES/Makefile.$@ -o -f MAKE/MINE/Makefile.$@ @if [ ! -d $(objdir) ]; then mkdir $(objdir); fi @$(SHELL) Make.sh style + @$(MAKE) $(MFLAGS) lmpinstalledpkgs.h + @echo 'Compiling LAMMPS for machine $@' @if [ -f MAKE/MACHINES/Makefile.$@ ]; \ then cp MAKE/MACHINES/Makefile.$@ $(objdir)/Makefile; fi @if [ -f MAKE/OPTIONS/Makefile.$@ ]; \ diff --git a/src/PERI/fix_peri_neigh.cpp b/src/PERI/fix_peri_neigh.cpp index 42d86e14b2..66137e6a01 100644 --- a/src/PERI/fix_peri_neigh.cpp +++ b/src/PERI/fix_peri_neigh.cpp @@ -140,7 +140,7 @@ void FixPeriNeigh::init() /* ---------------------------------------------------------------------- */ -void FixPeriNeigh::init_list(int id, NeighList *ptr) +void FixPeriNeigh::init_list(int /*id*/, NeighList *ptr) { list = ptr; } @@ -159,7 +159,7 @@ void FixPeriNeigh::min_setup(int vflag) must be done in setup (not init) since fix init comes before neigh init ------------------------------------------------------------------------- */ -void FixPeriNeigh::setup(int vflag) +void FixPeriNeigh::setup(int /*vflag*/) { int i,j,ii,jj,itype,jtype,inum,jnum; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; @@ -441,7 +441,7 @@ void FixPeriNeigh::grow_arrays(int nmax) copy values within local atom-based arrays ------------------------------------------------------------------------- */ -void FixPeriNeigh::copy_arrays(int i, int j, int delflag) +void FixPeriNeigh::copy_arrays(int i, int j, int /*delflag*/) { npartner[j] = npartner[i]; for (int m = 0; m < npartner[j]; m++) { @@ -514,7 +514,7 @@ int FixPeriNeigh::unpack_exchange(int nlocal, double *buf) /* ---------------------------------------------------------------------- */ int FixPeriNeigh::pack_forward_comm(int n, int *list, double *buf, - int pbc_flag, int *pbc) + int /*pbc_flag*/, int * /*pbc*/) { int i,j,m; diff --git a/src/PERI/pair_peri_eps.cpp b/src/PERI/pair_peri_eps.cpp index 9950c36f41..76267426c6 100644 --- a/src/PERI/pair_peri_eps.cpp +++ b/src/PERI/pair_peri_eps.cpp @@ -434,7 +434,7 @@ void PairPeriEPS::allocate() global settings ------------------------------------------------------------------------- */ -void PairPeriEPS::settings(int narg, char **arg) +void PairPeriEPS::settings(int narg, char **/*arg*/) { if (narg) error->all(FLERR,"Illegal pair_style command"); } @@ -799,7 +799,7 @@ double PairPeriEPS::compute_DeviatoricForceStateNorm(int i) ---------------------------------------------------------------------- */ int PairPeriEPS::pack_forward_comm(int n, int *list, double *buf, - int pbc_flag, int *pbc) + int /*pbc_flag*/, int * /*pbc*/) { int i,j,m; diff --git a/src/PERI/pair_peri_lps.cpp b/src/PERI/pair_peri_lps.cpp index 4c48223b07..383b91c6f5 100644 --- a/src/PERI/pair_peri_lps.cpp +++ b/src/PERI/pair_peri_lps.cpp @@ -364,7 +364,7 @@ void PairPeriLPS::allocate() global settings ------------------------------------------------------------------------- */ -void PairPeriLPS::settings(int narg, char **arg) +void PairPeriLPS::settings(int narg, char **/*arg*/) { if (narg) error->all(FLERR,"Illegal pair_style command"); } @@ -631,7 +631,7 @@ void PairPeriLPS::compute_dilatation() ---------------------------------------------------------------------- */ int PairPeriLPS::pack_forward_comm(int n, int *list, double *buf, - int pbc_flag, int *pbc) + int /*pbc_flag*/, int * /*pbc*/) { int i,j,m; diff --git a/src/PERI/pair_peri_pmb.cpp b/src/PERI/pair_peri_pmb.cpp index 81461f0b83..772e47f2d6 100644 --- a/src/PERI/pair_peri_pmb.cpp +++ b/src/PERI/pair_peri_pmb.cpp @@ -297,7 +297,7 @@ void PairPeriPMB::allocate() global settings ------------------------------------------------------------------------- */ -void PairPeriPMB::settings(int narg, char **arg) +void PairPeriPMB::settings(int narg, char **/*arg*/) { if (narg) error->all(FLERR,"Illegal pair_style command"); } @@ -441,7 +441,7 @@ void PairPeriPMB::read_restart(FILE *fp) /* ---------------------------------------------------------------------- */ double PairPeriPMB::single(int i, int j, int itype, int jtype, double rsq, - double factor_coul, double factor_lj, + double /*factor_coul*/, double /*factor_lj*/, double &fforce) { double delx0,dely0,delz0,rsq0; diff --git a/src/PERI/pair_peri_ves.cpp b/src/PERI/pair_peri_ves.cpp index a9f620ef4b..7590077f0e 100644 --- a/src/PERI/pair_peri_ves.cpp +++ b/src/PERI/pair_peri_ves.cpp @@ -411,7 +411,7 @@ void PairPeriVES::allocate() global settings ------------------------------------------------------------------------- */ -void PairPeriVES::settings(int narg, char **arg) +void PairPeriVES::settings(int narg, char **/*arg*/) { if (narg) error->all(FLERR,"Illegal pair_style command"); } @@ -697,7 +697,7 @@ void PairPeriVES::compute_dilatation() ---------------------------------------------------------------------- */ int PairPeriVES::pack_forward_comm(int n, int *list, double *buf, - int pbc_flag, int *pbc) + int /*pbc_flag*/, int * /*pbc*/) { int i,j,m; diff --git a/src/PYTHON/python_impl.cpp b/src/PYTHON/python_impl.cpp index 9f018ad602..cc5edaf3f5 100644 --- a/src/PYTHON/python_impl.cpp +++ b/src/PYTHON/python_impl.cpp @@ -344,7 +344,7 @@ void PythonImpl::invoke_function(int ifunc, char *result) } else if (otype == DOUBLE) { sprintf(result,"%.15g",PyFloat_AsDouble(pValue)); } else if (otype == STRING) { - char *pystr = PY_STRING_AS_STRING(pValue); + const char *pystr = PY_STRING_AS_STRING(pValue); if (pfuncs[ifunc].longstr) strncpy(pfuncs[ifunc].longstr,pystr,pfuncs[ifunc].length_longstr); else strncpy(result,pystr,VALUELENGTH-1); diff --git a/src/Purge.list b/src/Purge.list index 2e854ead3d..c70392c935 100644 --- a/src/Purge.list +++ b/src/Purge.list @@ -1,6 +1,7 @@ # auto-generated style files style_angle.h style_atom.h +style_body.h style_bond.h style_command.h style_compute.h @@ -12,10 +13,26 @@ style_integrate.h style_kspace.h style_minimize.h style_pair.h +style_reader.h style_region.h style_neigh_bin.h style_neigh_pair.h style_neigh_stencil.h +style_nbin.h +style_npair.h +style_nstencil.h +style_ntopo.h +# other auto-generated files +lmpinstalledpkgs.h +# renamed on 6 September 2018 +pair_cdeam_omp.h +pair_cdeam_omp.cpp +# renamed on 31 July 2018 +pair_cdeam.h +pair_cdeam.cpp +# renamed on 20 July 2018 +pair_body.h +pair_body.cpp # deleted on 4 April 2018 pair_kim_version.h # deleted on 15 December 2017 diff --git a/src/QEQ/fix_qeq.cpp b/src/QEQ/fix_qeq.cpp index 8acf4498f5..0fe041209f 100644 --- a/src/QEQ/fix_qeq.cpp +++ b/src/QEQ/fix_qeq.cpp @@ -274,7 +274,7 @@ void FixQEq::reallocate_matrix() /* ---------------------------------------------------------------------- */ -void FixQEq::init_list(int id, NeighList *ptr) +void FixQEq::init_list(int /*id*/, NeighList *ptr) { list = ptr; } @@ -329,7 +329,7 @@ void FixQEq::init_storage() /* ---------------------------------------------------------------------- */ -void FixQEq::pre_force_respa(int vflag, int ilevel, int iloop) +void FixQEq::pre_force_respa(int vflag, int ilevel, int /*iloop*/) { if (ilevel == nlevels_respa-1) pre_force(vflag); } @@ -471,7 +471,7 @@ void FixQEq::calculate_Q() /* ---------------------------------------------------------------------- */ int FixQEq::pack_forward_comm(int n, int *list, double *buf, - int pbc_flag, int *pbc) + int /*pbc_flag*/, int * /*pbc*/) { int m; @@ -552,7 +552,7 @@ void FixQEq::grow_arrays(int nmax) copy values within fictitious charge arrays ------------------------------------------------------------------------- */ -void FixQEq::copy_arrays(int i, int j, int delflag) +void FixQEq::copy_arrays(int i, int j, int /*delflag*/) { for (int m = 0; m < nprev; m++) { s_hist[j][m] = s_hist[i][m]; diff --git a/src/QEQ/fix_qeq_dynamic.cpp b/src/QEQ/fix_qeq_dynamic.cpp index aeb8dd2c59..f496c7e6c0 100644 --- a/src/QEQ/fix_qeq_dynamic.cpp +++ b/src/QEQ/fix_qeq_dynamic.cpp @@ -88,7 +88,7 @@ void FixQEqDynamic::init() /* ---------------------------------------------------------------------- */ -void FixQEqDynamic::pre_force(int vflag) +void FixQEqDynamic::pre_force(int /*vflag*/) { int i,ii,iloop,inum,*ilist; double qmass,dtq2; @@ -247,7 +247,7 @@ double FixQEqDynamic::compute_eneg() /* ---------------------------------------------------------------------- */ int FixQEqDynamic::pack_forward_comm(int n, int *list, double *buf, - int pbc_flag, int *pbc) + int /*pbc_flag*/, int * /*pbc*/) { int m=0; diff --git a/src/QEQ/fix_qeq_fire.cpp b/src/QEQ/fix_qeq_fire.cpp index db63bec206..83c9907f1b 100644 --- a/src/QEQ/fix_qeq_fire.cpp +++ b/src/QEQ/fix_qeq_fire.cpp @@ -104,7 +104,7 @@ void FixQEqFire::init() /* ---------------------------------------------------------------------- */ -void FixQEqFire::pre_force(int vflag) +void FixQEqFire::pre_force(int /*vflag*/) { int inum, *ilist; int i,ii,iloop; @@ -311,7 +311,7 @@ double FixQEqFire::compute_eneg() /* ---------------------------------------------------------------------- */ int FixQEqFire::pack_forward_comm(int n, int *list, double *buf, - int pbc_flag, int *pbc) + int /*pbc_flag*/, int * /*pbc*/) { int m = 0; diff --git a/src/QEQ/fix_qeq_point.cpp b/src/QEQ/fix_qeq_point.cpp index bf7130c1d6..db2d800c06 100644 --- a/src/QEQ/fix_qeq_point.cpp +++ b/src/QEQ/fix_qeq_point.cpp @@ -67,7 +67,7 @@ void FixQEqPoint::init() /* ---------------------------------------------------------------------- */ -void FixQEqPoint::pre_force(int vflag) +void FixQEqPoint::pre_force(int /*vflag*/) { if (update->ntimestep % nevery) return; diff --git a/src/QEQ/fix_qeq_shielded.cpp b/src/QEQ/fix_qeq_shielded.cpp index 70898fd96c..88cd1ab3ad 100644 --- a/src/QEQ/fix_qeq_shielded.cpp +++ b/src/QEQ/fix_qeq_shielded.cpp @@ -111,7 +111,7 @@ void FixQEqShielded::init_shielding() /* ---------------------------------------------------------------------- */ -void FixQEqShielded::pre_force(int vflag) +void FixQEqShielded::pre_force(int /*vflag*/) { if (update->ntimestep % nevery) return; diff --git a/src/QEQ/fix_qeq_slater.cpp b/src/QEQ/fix_qeq_slater.cpp index 4ddcf06357..81fdc73241 100644 --- a/src/QEQ/fix_qeq_slater.cpp +++ b/src/QEQ/fix_qeq_slater.cpp @@ -107,7 +107,7 @@ void FixQEqSlater::extract_streitz() /* ---------------------------------------------------------------------- */ -void FixQEqSlater::pre_force(int vflag) +void FixQEqSlater::pre_force(int /*vflag*/) { if (update->ntimestep % nevery) return; diff --git a/src/REPLICA/fix_event.cpp b/src/REPLICA/fix_event.cpp index 3b9b49ac57..8fc5de6b16 100644 --- a/src/REPLICA/fix_event.cpp +++ b/src/REPLICA/fix_event.cpp @@ -241,7 +241,7 @@ void FixEvent::grow_arrays(int nmax) copy values within local atom-based array ------------------------------------------------------------------------- */ -void FixEvent::copy_arrays(int i, int j, int delflag) +void FixEvent::copy_arrays(int i, int j, int /*delflag*/) { xevent[j][0] = xevent[i][0]; xevent[j][1] = xevent[i][1]; diff --git a/src/REPLICA/fix_neb.cpp b/src/REPLICA/fix_neb.cpp index e5d24da392..dc86c70956 100644 --- a/src/REPLICA/fix_neb.cpp +++ b/src/REPLICA/fix_neb.cpp @@ -270,7 +270,7 @@ void FixNEB::min_setup(int vflag) /* ---------------------------------------------------------------------- */ -void FixNEB::min_post_force(int vflag) +void FixNEB::min_post_force(int /*vflag*/) { double vprev,vnext; double delxp,delyp,delzp,delxn,delyn,delzn; diff --git a/src/RIGID/fix_rattle.cpp b/src/RIGID/fix_rattle.cpp index 7ade8d6848..403f3091c6 100644 --- a/src/RIGID/fix_rattle.cpp +++ b/src/RIGID/fix_rattle.cpp @@ -185,7 +185,7 @@ void FixRattle::post_force(int vflag) /* ---------------------------------------------------------------------- */ -void FixRattle::post_force_respa(int vflag, int ilevel, int iloop) +void FixRattle::post_force_respa(int vflag, int ilevel, int /*iloop*/) { // remember vflag for the coordinate correction in this->final_integrate @@ -625,7 +625,7 @@ void FixRattle::update_v_half_nocons() /* ---------------------------------------------------------------------- */ -void FixRattle::update_v_half_nocons_respa(int ilevel) +void FixRattle::update_v_half_nocons_respa(int /*ilevel*/) { // carry out unconstrained velocity update diff --git a/src/RIGID/fix_rigid.cpp b/src/RIGID/fix_rigid.cpp index 7104d30849..c15a909ada 100644 --- a/src/RIGID/fix_rigid.cpp +++ b/src/RIGID/fix_rigid.cpp @@ -1030,7 +1030,6 @@ void FixRigid::enforce2d() void FixRigid::compute_forces_and_torques() { int i,ibody; - double dtfm; // sum over atoms to get force and torque on rigid body @@ -1096,7 +1095,7 @@ void FixRigid::compute_forces_and_torques() /* ---------------------------------------------------------------------- */ -void FixRigid::post_force(int vflag) +void FixRigid::post_force(int /*vflag*/) { if (langflag) apply_langevin_thermostat(); if (earlyflag) compute_forces_and_torques(); @@ -1141,7 +1140,7 @@ void FixRigid::final_integrate() /* ---------------------------------------------------------------------- */ -void FixRigid::initial_integrate_respa(int vflag, int ilevel, int iloop) +void FixRigid::initial_integrate_respa(int vflag, int ilevel, int /*iloop*/) { dtv = step_respa[ilevel]; dtf = 0.5 * step_respa[ilevel] * force->ftm2v; @@ -1153,7 +1152,7 @@ void FixRigid::initial_integrate_respa(int vflag, int ilevel, int iloop) /* ---------------------------------------------------------------------- */ -void FixRigid::final_integrate_respa(int ilevel, int iloop) +void FixRigid::final_integrate_respa(int ilevel, int /*iloop*/) { dtf = 0.5 * step_respa[ilevel] * force->ftm2v; final_integrate(); @@ -2478,7 +2477,7 @@ void FixRigid::grow_arrays(int nmax) copy values within local atom-based arrays ------------------------------------------------------------------------- */ -void FixRigid::copy_arrays(int i, int j, int delflag) +void FixRigid::copy_arrays(int i, int j, int /*delflag*/) { body[j] = body[i]; xcmimage[j] = xcmimage[i]; diff --git a/src/RIGID/fix_rigid_nh.cpp b/src/RIGID/fix_rigid_nh.cpp index 96c44d15b5..4dceb1b8b4 100644 --- a/src/RIGID/fix_rigid_nh.cpp +++ b/src/RIGID/fix_rigid_nh.cpp @@ -591,9 +591,9 @@ void FixRigidNH::initial_integrate(int vflag) void FixRigidNH::final_integrate() { - int i,ibody; + int ibody; double tmp,scale_t[3],scale_r; - double dtfm,xy,xz,yz; + double dtfm; double mbody[3],tbody[3],fquat[4]; double dtf2 = dtf * 2.0; diff --git a/src/RIGID/fix_rigid_nh_small.cpp b/src/RIGID/fix_rigid_nh_small.cpp index 135a1fb4bd..5016d3f168 100644 --- a/src/RIGID/fix_rigid_nh_small.cpp +++ b/src/RIGID/fix_rigid_nh_small.cpp @@ -618,7 +618,7 @@ void FixRigidNHSmall::initial_integrate(int vflag) void FixRigidNHSmall::final_integrate() { - int i,ibody; + int ibody; double tmp,scale_t[3],scale_r; double dtfm; double mbody[3],tbody[3],fquat[4]; diff --git a/src/RIGID/fix_rigid_small.cpp b/src/RIGID/fix_rigid_small.cpp index c1de89efc7..d5d3d36083 100644 --- a/src/RIGID/fix_rigid_small.cpp +++ b/src/RIGID/fix_rigid_small.cpp @@ -867,7 +867,7 @@ void FixRigidSmall::enforce2d() /* ---------------------------------------------------------------------- */ -void FixRigidSmall::post_force(int vflag) +void FixRigidSmall::post_force(int /*vflag*/) { if (langflag) apply_langevin_thermostat(); if (earlyflag) compute_forces_and_torques(); @@ -1004,7 +1004,7 @@ void FixRigidSmall::final_integrate() /* ---------------------------------------------------------------------- */ -void FixRigidSmall::initial_integrate_respa(int vflag, int ilevel, int iloop) +void FixRigidSmall::initial_integrate_respa(int vflag, int ilevel, int /*iloop*/) { dtv = step_respa[ilevel]; dtf = 0.5 * step_respa[ilevel] * force->ftm2v; @@ -1016,7 +1016,7 @@ void FixRigidSmall::initial_integrate_respa(int vflag, int ilevel, int iloop) /* ---------------------------------------------------------------------- */ -void FixRigidSmall::final_integrate_respa(int ilevel, int iloop) +void FixRigidSmall::final_integrate_respa(int ilevel, int /*iloop*/) { dtf = 0.5 * step_respa[ilevel] * force->ftm2v; final_integrate(); @@ -2999,7 +2999,7 @@ int FixRigidSmall::unpack_exchange(int nlocal, double *buf) ------------------------------------------------------------------------- */ int FixRigidSmall::pack_forward_comm(int n, int *list, double *buf, - int pbc_flag, int *pbc) + int /*pbc_flag*/, int * /*pbc*/) { int i,j; double *xcm,*vcm,*quat,*omega,*ex_space,*ey_space,*ez_space,*conjqm; diff --git a/src/RIGID/fix_shake.cpp b/src/RIGID/fix_shake.cpp index 0beef3bfa2..e0d1bf132b 100644 --- a/src/RIGID/fix_shake.cpp +++ b/src/RIGID/fix_shake.cpp @@ -2451,7 +2451,7 @@ void FixShake::grow_arrays(int nmax) copy values within local atom-based arrays ------------------------------------------------------------------------- */ -void FixShake::copy_arrays(int i, int j, int delflag) +void FixShake::copy_arrays(int i, int j, int /*delflag*/) { int flag = shake_flag[j] = shake_flag[i]; if (flag == 1) { @@ -2528,7 +2528,7 @@ void FixShake::update_arrays(int i, int atom_offset) ------------------------------------------------------------------------- */ void FixShake::set_molecule(int nlocalprev, tagint tagprev, int imol, - double *xgeom, double *vcm, double *quat) + double * /*xgeom*/, double * /*vcm*/, double * /*quat*/) { int m,flag; diff --git a/src/SHOCK/fix_append_atoms.cpp b/src/SHOCK/fix_append_atoms.cpp index d898d2a790..2e515839c5 100644 --- a/src/SHOCK/fix_append_atoms.cpp +++ b/src/SHOCK/fix_append_atoms.cpp @@ -231,7 +231,7 @@ int FixAppendAtoms::setmask() /* ---------------------------------------------------------------------- */ -void FixAppendAtoms::initial_integrate(int vflag) +void FixAppendAtoms::initial_integrate(int /*vflag*/) { if (update->ntimestep % freq == 0) next_reneighbor = update->ntimestep; } @@ -331,7 +331,7 @@ int FixAppendAtoms::get_spatial() /* ---------------------------------------------------------------------- */ -void FixAppendAtoms::post_force(int vflag) +void FixAppendAtoms::post_force(int /*vflag*/) { double **f = atom->f; double **v = atom->v; diff --git a/src/SHOCK/fix_msst.cpp b/src/SHOCK/fix_msst.cpp index a7890c3afa..c800e8a85d 100644 --- a/src/SHOCK/fix_msst.cpp +++ b/src/SHOCK/fix_msst.cpp @@ -357,7 +357,7 @@ void FixMSST::init() compute T,P before integrator starts ------------------------------------------------------------------------- */ -void FixMSST::setup(int vflag) +void FixMSST::setup(int /*vflag*/) { lagrangian_position = 0.0; @@ -442,7 +442,7 @@ void FixMSST::setup(int vflag) 1st half of Verlet update ------------------------------------------------------------------------- */ -void FixMSST::initial_integrate(int vflag) +void FixMSST::initial_integrate(int /*vflag*/) { int i,k; double p_msst; // MSST driving pressure diff --git a/src/SHOCK/fix_wall_piston.cpp b/src/SHOCK/fix_wall_piston.cpp index 7146b46c1e..eb89e19517 100644 --- a/src/SHOCK/fix_wall_piston.cpp +++ b/src/SHOCK/fix_wall_piston.cpp @@ -171,7 +171,7 @@ int FixWallPiston::setmask() /* ---------------------------------------------------------------------- */ -void FixWallPiston::initial_integrate(int vflag) +void FixWallPiston::initial_integrate(int /*vflag*/) { next_reneighbor = update->ntimestep; } diff --git a/src/SNAP/compute_sna_atom.cpp b/src/SNAP/compute_sna_atom.cpp index 0d8b0bae14..a2c1f55788 100644 --- a/src/SNAP/compute_sna_atom.cpp +++ b/src/SNAP/compute_sna_atom.cpp @@ -184,7 +184,7 @@ void ComputeSNAAtom::init() /* ---------------------------------------------------------------------- */ -void ComputeSNAAtom::init_list(int id, NeighList *ptr) +void ComputeSNAAtom::init_list(int /*id*/, NeighList *ptr) { list = ptr; } diff --git a/src/SNAP/compute_snad_atom.cpp b/src/SNAP/compute_snad_atom.cpp index b0fef8e1e3..800d1942e3 100644 --- a/src/SNAP/compute_snad_atom.cpp +++ b/src/SNAP/compute_snad_atom.cpp @@ -186,7 +186,7 @@ void ComputeSNADAtom::init() /* ---------------------------------------------------------------------- */ -void ComputeSNADAtom::init_list(int id, NeighList *ptr) +void ComputeSNADAtom::init_list(int /*id*/, NeighList *ptr) { list = ptr; } diff --git a/src/SNAP/compute_snav_atom.cpp b/src/SNAP/compute_snav_atom.cpp index cf66b1c136..2b823f7b8b 100644 --- a/src/SNAP/compute_snav_atom.cpp +++ b/src/SNAP/compute_snav_atom.cpp @@ -181,7 +181,7 @@ void ComputeSNAVAtom::init() /* ---------------------------------------------------------------------- */ -void ComputeSNAVAtom::init_list(int id, NeighList *ptr) +void ComputeSNAVAtom::init_list(int /*id*/, NeighList *ptr) { list = ptr; } diff --git a/src/SNAP/compute_snav_atom.h b/src/SNAP/compute_snav_atom.h index 2eb9fb804f..7d39786ef9 100644 --- a/src/SNAP/compute_snav_atom.h +++ b/src/SNAP/compute_snav_atom.h @@ -45,7 +45,6 @@ class ComputeSNAVAtom : public Compute { double *radelem; double *wjelem; class SNA** snaptr; - double cutmax; int quadraticflag; }; diff --git a/src/SNAP/sna.cpp b/src/SNAP/sna.cpp index 3150573043..7ed1bc1e23 100644 --- a/src/SNAP/sna.cpp +++ b/src/SNAP/sna.cpp @@ -1231,7 +1231,7 @@ void SNA::compute_uarray(double x, double y, double z, } void SNA::compute_uarray_omp(double x, double y, double z, - double z0, double r, int sub_threads) + double z0, double r, int /*sub_threads*/) { double r0inv; double a_r, b_r, a_i, b_i; diff --git a/src/SPIN/README b/src/SPIN/README new file mode 100644 index 0000000000..e371e39767 --- /dev/null +++ b/src/SPIN/README @@ -0,0 +1,25 @@ +The SPIN package enables coupled spin dynamics and molecular +dynamics simulations. + +The package provides the following features: + +* defining a classical magnetic atomic spin associated to each magnetic +atom in the system +* integrating the equations of motion for the coupled spin-lattice system +* implementing magnetic pair interactions and magnetic forces +* thermostating and applying a transverse damping to the magnetic spins +* computing and outputing magnetic quantities + +The different options provided by this package are explained in the +LAMMPS documentation. + +Once you have successfully built LAMMPS with this package, you can test +it using one of the input files provided from the examples/SPIN dir: + +./lmp_serial < lammps/examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp + + +== Credits and license == + +The person who created this package is Julien Tranchida (jtranch at +sandia.gov). You can contact him if you have questions. diff --git a/src/SPIN/atom_vec_spin.cpp b/src/SPIN/atom_vec_spin.cpp new file mode 100644 index 0000000000..24c4480e04 --- /dev/null +++ b/src/SPIN/atom_vec_spin.cpp @@ -0,0 +1,952 @@ +/* ---------------------------------------------------------------------- + + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. + +------------------------------------------------------------------------- */ + +/* ------------------------------------------------------------------------ + Contributing authors: Julien Tranchida (SNL) + Aidan Thompson (SNL) + + Please cite the related publication: + Tranchida, J., Plimpton, S. J., Thibaudeau, P., & Thompson, A. P. (2018). + Massively parallel symplectic algorithm for coupled magnetic spin dynamics + and molecular dynamics. Journal of Computational Physics. +------------------------------------------------------------------------- */ + +#include +#include +#include +#include "atom.h" +#include "atom_vec_spin.h" +#include "comm.h" +#include "domain.h" +#include "error.h" +#include "fix.h" +#include "memory.h" +#include "modify.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +AtomVecSpin::AtomVecSpin(LAMMPS *lmp) : AtomVec(lmp) +{ + molecular = 0; + mass_type = 1; + forceclearflag = 1; + + comm_x_only = 0; + comm_f_only = 0; + size_forward = 7; + size_reverse = 6; + size_border = 10; + size_velocity = 3; + size_data_atom = 9; + size_data_vel = 4; + xcol_data = 4; + + atom->sp_flag = 1; +} + + +/* ---------------------------------------------------------------------- + grow atom arrays + n = 0 grows arrays by a chunk + n > 0 allocates arrays to size n +------------------------------------------------------------------------- */ + +void AtomVecSpin::grow(int n) +{ + if (n == 0) grow_nmax(); + else nmax = n; + atom->nmax = nmax; + if (nmax < 0 || nmax > MAXSMALLINT) + error->one(FLERR,"Per-processor system is too big"); + + tag = memory->grow(atom->tag,nmax,"atom:tag"); + type = memory->grow(atom->type,nmax,"atom:type"); + mask = memory->grow(atom->mask,nmax,"atom:mask"); + image = memory->grow(atom->image,nmax,"atom:image"); + + // allocating mech. quantities + + x = memory->grow(atom->x,nmax,3,"atom:x"); + v = memory->grow(atom->v,nmax,3,"atom:v"); + f = memory->grow(atom->f,nmax*comm->nthreads,3,"atom:f"); + + // allocating mag. quantities + + sp = memory->grow(atom->sp,nmax,4,"atom:sp"); + fm = memory->grow(atom->fm,nmax*comm->nthreads,3,"atom:fm"); + + if (atom->nextra_grow) + for (int iextra = 0; iextra < atom->nextra_grow; iextra++) + modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax); +} + +/* ---------------------------------------------------------------------- + reset local array ptrs +------------------------------------------------------------------------- */ + +void AtomVecSpin::grow_reset() +{ + tag = atom->tag; type = atom->type; + mask = atom->mask; image = atom->image; + x = atom->x; v = atom->v; f = atom->f; + sp = atom->sp; fm = atom->fm; +} + + +/* ---------------------------------------------------------------------- + copy atom I info to atom J +------------------------------------------------------------------------- */ + +void AtomVecSpin::copy(int i, int j, int delflag) +{ + tag[j] = tag[i]; + type[j] = type[i]; + mask[j] = mask[i]; + image[j] = image[i]; + x[j][0] = x[i][0]; + x[j][1] = x[i][1]; + x[j][2] = x[i][2]; + v[j][0] = v[i][0]; + v[j][1] = v[i][1]; + v[j][2] = v[i][2]; + + sp[j][0] = sp[i][0]; + sp[j][1] = sp[i][1]; + sp[j][2] = sp[i][2]; + sp[j][3] = sp[i][3]; + + if (atom->nextra_grow) + for (int iextra = 0; iextra < atom->nextra_grow; iextra++) + modify->fix[atom->extra_grow[iextra]]->copy_arrays(i,j,delflag); +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecSpin::pack_comm(int n, int *list, double *buf, + int pbc_flag, int *pbc) +{ + int i,j,m; + double dx,dy,dz; + + m = 0; + if (pbc_flag == 0) { + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = x[j][0]; + buf[m++] = x[j][1]; + buf[m++] = x[j][2]; + buf[m++] = sp[j][0]; + buf[m++] = sp[j][1]; + buf[m++] = sp[j][2]; + buf[m++] = sp[j][3]; + } + } else { + if (domain->triclinic == 0) { + dx = pbc[0]*domain->xprd; + dy = pbc[1]*domain->yprd; + dz = pbc[2]*domain->zprd; + } else { + dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz; + dy = pbc[1]*domain->yprd + pbc[3]*domain->yz; + dz = pbc[2]*domain->zprd; + } + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = x[j][0] + dx; + buf[m++] = x[j][1] + dy; + buf[m++] = x[j][2] + dz; + buf[m++] = sp[j][0]; + buf[m++] = sp[j][1]; + buf[m++] = sp[j][2]; + buf[m++] = sp[j][3]; + } + } + return m; +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecSpin::pack_comm_vel(int n, int *list, double *buf, + int pbc_flag, int *pbc) +{ + int i,j,m; + double dx,dy,dz,dvx,dvy,dvz; + + m = 0; + if (pbc_flag == 0) { + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = x[j][0]; + buf[m++] = x[j][1]; + buf[m++] = x[j][2]; + buf[m++] = sp[j][0]; + buf[m++] = sp[j][1]; + buf[m++] = sp[j][2]; + buf[m++] = sp[j][3]; + buf[m++] = v[j][0]; + buf[m++] = v[j][1]; + buf[m++] = v[j][2]; + } + } else { + if (domain->triclinic == 0) { + dx = pbc[0]*domain->xprd; + dy = pbc[1]*domain->yprd; + dz = pbc[2]*domain->zprd; + } else { + dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz; + dy = pbc[1]*domain->yprd + pbc[3]*domain->yz; + dz = pbc[2]*domain->zprd; + } + if (!deform_vremap) { + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = x[j][0] + dx; + buf[m++] = x[j][1] + dy; + buf[m++] = x[j][2] + dz; + buf[m++] = sp[j][0]; + buf[m++] = sp[j][1]; + buf[m++] = sp[j][2]; + buf[m++] = sp[j][3]; + buf[m++] = v[j][0]; + buf[m++] = v[j][1]; + buf[m++] = v[j][2]; + } + } else { + dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4]; + dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3]; + dvz = pbc[2]*h_rate[2]; + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = x[j][0] + dx; + buf[m++] = x[j][1] + dy; + buf[m++] = x[j][2] + dz; + buf[m++] = sp[j][0]; + buf[m++] = sp[j][1]; + buf[m++] = sp[j][2]; + buf[m++] = sp[j][3]; + if (mask[i] & deform_groupbit) { + buf[m++] = v[j][0] + dvx; + buf[m++] = v[j][1] + dvy; + buf[m++] = v[j][2] + dvz; + } else { + buf[m++] = v[j][0]; + buf[m++] = v[j][1]; + buf[m++] = v[j][2]; + } + } + } + } + return m; +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecSpin::pack_comm_hybrid(int n, int *list, double *buf) +{ + int i,j,m; + + m = 0; + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = sp[j][0]; + buf[m++] = sp[j][1]; + buf[m++] = sp[j][2]; + buf[m++] = sp[j][3]; + } + return m; +} + +/* ---------------------------------------------------------------------- */ + +void AtomVecSpin::unpack_comm(int n, int first, double *buf) +{ + int i,m,last; + + m = 0; + last = first + n; + for (i = first; i < last; i++) { + x[i][0] = buf[m++]; + x[i][1] = buf[m++]; + x[i][2] = buf[m++]; + sp[i][0] = buf[m++]; + sp[i][1] = buf[m++]; + sp[i][2] = buf[m++]; + sp[i][3] = buf[m++]; + } +} + +/* ---------------------------------------------------------------------- */ + +void AtomVecSpin::unpack_comm_vel(int n, int first, double *buf) +{ + int i,m,last; + + m = 0; + last = first + n; + for (i = first; i < last; i++) { + x[i][0] = buf[m++]; + x[i][1] = buf[m++]; + x[i][2] = buf[m++]; + sp[i][0] = buf[m++]; + sp[i][1] = buf[m++]; + sp[i][2] = buf[m++]; + sp[i][3] = buf[m++]; + v[i][0] = buf[m++]; + v[i][1] = buf[m++]; + v[i][2] = buf[m++]; + } +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecSpin::unpack_comm_hybrid(int n, int first, double *buf) +{ + int i,m,last; + + m = 0; + last = first + n; + for (i = first; i < last; i++) { + sp[i][0] = buf[m++]; + sp[i][1] = buf[m++]; + sp[i][2] = buf[m++]; + sp[i][3] = buf[m++]; + } + return m; +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecSpin::pack_reverse(int n, int first, double *buf) +{ + int i,m,last; + m = 0; + last = first + n; + for (i = first; i < last; i++) { + buf[m++] = f[i][0]; + buf[m++] = f[i][1]; + buf[m++] = f[i][2]; + buf[m++] = fm[i][0]; + buf[m++] = fm[i][1]; + buf[m++] = fm[i][2]; + } + + return m; +} + +/* ---------------------------------------------------------------------- */ + +void AtomVecSpin::unpack_reverse(int n, int *list, double *buf) +{ + int i,j,m; + m = 0; + for (i = 0; i < n; i++) { + j = list[i]; + f[j][0] += buf[m++]; + f[j][1] += buf[m++]; + f[j][2] += buf[m++]; + fm[j][0] += buf[m++]; + fm[j][1] += buf[m++]; + fm[j][2] += buf[m++]; + } +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecSpin::pack_border(int n, int *list, double *buf, + int pbc_flag, int *pbc) +{ + int i,j,m; + double dx,dy,dz; + + m = 0; + if (pbc_flag == 0) { + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = x[j][0]; + buf[m++] = x[j][1]; + buf[m++] = x[j][2]; + buf[m++] = ubuf(tag[j]).d; + buf[m++] = ubuf(type[j]).d; + buf[m++] = ubuf(mask[j]).d; + buf[m++] = sp[j][0]; + buf[m++] = sp[j][1]; + buf[m++] = sp[j][2]; + buf[m++] = sp[j][3]; + } + } else { + if (domain->triclinic == 0) { + dx = pbc[0]*domain->xprd; + dy = pbc[1]*domain->yprd; + dz = pbc[2]*domain->zprd; + } else { + dx = pbc[0]; + dy = pbc[1]; + dz = pbc[2]; + } + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = x[j][0] + dx; + buf[m++] = x[j][1] + dy; + buf[m++] = x[j][2] + dz; + buf[m++] = ubuf(tag[j]).d; + buf[m++] = ubuf(type[j]).d; + buf[m++] = ubuf(mask[j]).d; + buf[m++] = sp[j][0]; + buf[m++] = sp[j][1]; + buf[m++] = sp[j][2]; + buf[m++] = sp[j][3]; + } + } + + if (atom->nextra_border) + for (int iextra = 0; iextra < atom->nextra_border; iextra++) + m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]); + + return m; +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecSpin::pack_border_vel(int n, int *list, double *buf, + int pbc_flag, int *pbc) +{ + int i,j,m; + double dx,dy,dz,dvx,dvy,dvz; + + m = 0; + if (pbc_flag == 0) { + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = x[j][0]; + buf[m++] = x[j][1]; + buf[m++] = x[j][2]; + buf[m++] = ubuf(tag[j]).d; + buf[m++] = ubuf(type[j]).d; + buf[m++] = ubuf(mask[j]).d; + buf[m++] = sp[j][0]; + buf[m++] = sp[j][1]; + buf[m++] = sp[j][2]; + buf[m++] = sp[j][3]; + buf[m++] = v[j][0]; + buf[m++] = v[j][1]; + buf[m++] = v[j][2]; + } + } else { + if (domain->triclinic == 0) { + dx = pbc[0]*domain->xprd; + dy = pbc[1]*domain->yprd; + dz = pbc[2]*domain->zprd; + } else { + dx = pbc[0]; + dy = pbc[1]; + dz = pbc[2]; + } + if (!deform_vremap) { + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = x[j][0] + dx; + buf[m++] = x[j][1] + dy; + buf[m++] = x[j][2] + dz; + buf[m++] = ubuf(tag[j]).d; + buf[m++] = ubuf(type[j]).d; + buf[m++] = ubuf(mask[j]).d; + buf[m++] = sp[j][0]; + buf[m++] = sp[j][1]; + buf[m++] = sp[j][2]; + buf[m++] = sp[j][3]; + buf[m++] = v[j][0]; + buf[m++] = v[j][1]; + buf[m++] = v[j][2]; + } + } else { + dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4]; + dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3]; + dvz = pbc[2]*h_rate[2]; + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = x[j][0] + dx; + buf[m++] = x[j][1] + dy; + buf[m++] = x[j][2] + dz; + buf[m++] = ubuf(tag[j]).d; + buf[m++] = ubuf(type[j]).d; + buf[m++] = ubuf(mask[j]).d; + buf[m++] = sp[j][0]; + buf[m++] = sp[j][1]; + buf[m++] = sp[j][2]; + buf[m++] = sp[j][3]; + if (mask[i] & deform_groupbit) { + buf[m++] = v[j][0] + dvx; + buf[m++] = v[j][1] + dvy; + buf[m++] = v[j][2] + dvz; + } else { + buf[m++] = v[j][0]; + buf[m++] = v[j][1]; + buf[m++] = v[j][2]; + } + } + } + } + + if (atom->nextra_border) + for (int iextra = 0; iextra < atom->nextra_border; iextra++) + m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]); + + return m; +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecSpin::pack_border_hybrid(int n, int *list, double *buf) +{ + int i,j,m; + + m = 0; + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = sp[j][0]; + buf[m++] = sp[j][1]; + buf[m++] = sp[j][2]; + buf[m++] = sp[j][3]; + } + + return m; +} + +/* ---------------------------------------------------------------------- */ + +void AtomVecSpin::unpack_border(int n, int first, double *buf) +{ + int i,m,last; + + m = 0; + last = first + n; + for (i = first; i < last; i++) { + if (i == nmax) grow(0); + x[i][0] = buf[m++]; + x[i][1] = buf[m++]; + x[i][2] = buf[m++]; + tag[i] = (tagint) ubuf(buf[m++]).i; + type[i] = (int) ubuf(buf[m++]).i; + mask[i] = (int) ubuf(buf[m++]).i; + sp[i][0] = buf[m++]; + sp[i][1] = buf[m++]; + sp[i][2] = buf[m++]; + sp[i][3] = buf[m++]; + } + + if (atom->nextra_border) + for (int iextra = 0; iextra < atom->nextra_border; iextra++) + m += modify->fix[atom->extra_border[iextra]]-> + unpack_border(n,first,&buf[m]); + +} + +/* ---------------------------------------------------------------------- */ + +void AtomVecSpin::unpack_border_vel(int n, int first, double *buf) +{ + int i,m,last; + + m = 0; + last = first + n; + for (i = first; i < last; i++) { + if (i == nmax) grow(0); + x[i][0] = buf[m++]; + x[i][1] = buf[m++]; + x[i][2] = buf[m++]; + tag[i] = (tagint) ubuf(buf[m++]).i; + type[i] = (int) ubuf(buf[m++]).i; + mask[i] = (int) ubuf(buf[m++]).i; + sp[i][0] = buf[m++]; + sp[i][1] = buf[m++]; + sp[i][2] = buf[m++]; + sp[i][3] = buf[m++]; + v[i][0] = buf[m++]; + v[i][1] = buf[m++]; + v[i][2] = buf[m++]; + } + + if (atom->nextra_border) + for (int iextra = 0; iextra < atom->nextra_border; iextra++) + m += modify->fix[atom->extra_border[iextra]]-> + unpack_border(n,first,&buf[m]); + +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecSpin::unpack_border_hybrid(int n, int first, double *buf) +{ + int i,m,last; + + m = 0; + last = first + n; + for (i = first; i < last; i++) { + sp[i][0] = buf[m++]; + sp[i][1] = buf[m++]; + sp[i][2] = buf[m++]; + sp[i][3] = buf[m++]; + } + + return m; +} + +/* ---------------------------------------------------------------------- + pack all atom quantities for shipping to another proc + xyz must be 1st 3 values, so that comm::exchange can test on them +------------------------------------------------------------------------- */ + +int AtomVecSpin::pack_exchange(int i, double *buf) +{ + int m = 1; + buf[m++] = x[i][0]; + buf[m++] = x[i][1]; + buf[m++] = x[i][2]; + buf[m++] = v[i][0]; + buf[m++] = v[i][1]; + buf[m++] = v[i][2]; + buf[m++] = ubuf(tag[i]).d; + buf[m++] = ubuf(type[i]).d; + buf[m++] = ubuf(mask[i]).d; + buf[m++] = ubuf(image[i]).d; + + buf[m++] = sp[i][0]; + buf[m++] = sp[i][1]; + buf[m++] = sp[i][2]; + buf[m++] = sp[i][3]; + + if (atom->nextra_grow) + for (int iextra = 0; iextra < atom->nextra_grow; iextra++) + m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf[m]); + + buf[0] = m; + return m; +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecSpin::unpack_exchange(double *buf) +{ + int nlocal = atom->nlocal; + if (nlocal == nmax) grow(0); + + int m = 1; + x[nlocal][0] = buf[m++]; + x[nlocal][1] = buf[m++]; + x[nlocal][2] = buf[m++]; + v[nlocal][0] = buf[m++]; + v[nlocal][1] = buf[m++]; + v[nlocal][2] = buf[m++]; + tag[nlocal] = (tagint) ubuf(buf[m++]).i; + type[nlocal] = (int) ubuf(buf[m++]).i; + mask[nlocal] = (int) ubuf(buf[m++]).i; + image[nlocal] = (imageint) ubuf(buf[m++]).i; + + sp[nlocal][0] = buf[m++]; + sp[nlocal][1] = buf[m++]; + sp[nlocal][2] = buf[m++]; + sp[nlocal][3] = buf[m++]; + + if (atom->nextra_grow) + for (int iextra = 0; iextra < atom->nextra_grow; iextra++) + m += modify->fix[atom->extra_grow[iextra]]-> + unpack_exchange(nlocal,&buf[m]); + + atom->nlocal++; + + return m; +} + +/* ---------------------------------------------------------------------- + size of restart data for all atoms owned by this proc + include extra data stored by fixes +------------------------------------------------------------------------- */ + +int AtomVecSpin::size_restart() +{ + int i; + + int nlocal = atom->nlocal; + int n = 15 * nlocal; + + if (atom->nextra_restart) + for (int iextra = 0; iextra < atom->nextra_restart; iextra++) + for (i = 0; i < nlocal; i++) + n += modify->fix[atom->extra_restart[iextra]]->size_restart(i); + + return n; +} + +/* ---------------------------------------------------------------------- + pack atom I's data for restart file including extra quantities + xyz must be 1st 3 values, so that read_restart can test on them + molecular types may be negative, but write as positive +------------------------------------------------------------------------- */ + +int AtomVecSpin::pack_restart(int i, double *buf) +{ + int m = 1; + + buf[m++] = x[i][0]; + buf[m++] = x[i][1]; + buf[m++] = x[i][2]; + buf[m++] = ubuf(tag[i]).d; + buf[m++] = ubuf(type[i]).d; + buf[m++] = ubuf(mask[i]).d; + buf[m++] = ubuf(image[i]).d; + buf[m++] = v[i][0]; + buf[m++] = v[i][1]; + buf[m++] = v[i][2]; + + buf[m++] = sp[i][0]; + buf[m++] = sp[i][1]; + buf[m++] = sp[i][2]; + buf[m++] = sp[i][3]; + + if (atom->nextra_restart) + for (int iextra = 0; iextra < atom->nextra_restart; iextra++) + m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i,&buf[m]); + + buf[0] = m; + return m; +} + +/* ---------------------------------------------------------------------- + unpack data for one atom from restart file including extra quantities +------------------------------------------------------------------------- */ + +int AtomVecSpin::unpack_restart(double *buf) +{ + int nlocal = atom->nlocal; + if (nlocal == nmax) { + grow(0); + if (atom->nextra_store) + memory->grow(atom->extra,nmax,atom->nextra_store,"atom:extra"); + } + + int m = 1; + x[nlocal][0] = buf[m++]; + x[nlocal][1] = buf[m++]; + x[nlocal][2] = buf[m++]; + tag[nlocal] = (tagint) ubuf(buf[m++]).i; + type[nlocal] = (int) ubuf(buf[m++]).i; + mask[nlocal] = (int) ubuf(buf[m++]).i; + image[nlocal] = (imageint) ubuf(buf[m++]).i; + v[nlocal][0] = buf[m++]; + v[nlocal][1] = buf[m++]; + v[nlocal][2] = buf[m++]; + + sp[nlocal][0] = buf[m++]; + sp[nlocal][1] = buf[m++]; + sp[nlocal][2] = buf[m++]; + sp[nlocal][3] = buf[m++]; + + double **extra = atom->extra; + if (atom->nextra_store) { + int size = static_cast (buf[0]) - m; + for (int i = 0; i < size; i++) extra[nlocal][i] = buf[m++]; + } + + atom->nlocal++; + return m; +} + +/* ---------------------------------------------------------------------- + create one atom of itype at coord + set other values to defaults +------------------------------------------------------------------------- */ + +void AtomVecSpin::create_atom(int itype, double *coord) +{ + + int nlocal = atom->nlocal; + if (nlocal == nmax) grow(0); + + tag[nlocal] = 0; + type[nlocal] = itype; + x[nlocal][0] = coord[0]; + x[nlocal][1] = coord[1]; + x[nlocal][2] = coord[2]; + mask[nlocal] = 1; + image[nlocal] = ((imageint) IMGMAX << IMG2BITS) | + ((imageint) IMGMAX << IMGBITS) | IMGMAX; + v[nlocal][0] = 0.0; + v[nlocal][1] = 0.0; + v[nlocal][2] = 0.0; + + sp[nlocal][0] = 0.0; + sp[nlocal][1] = 0.0; + sp[nlocal][2] = 0.0; + sp[nlocal][3] = 0.0; + + atom->nlocal++; +} + +/* ---------------------------------------------------------------------- + unpack one line from Atoms section of data file + initialize other atom quantities +------------------------------------------------------------------------- */ + +void AtomVecSpin::data_atom(double *coord, imageint imagetmp, char **values) +{ + int nlocal = atom->nlocal; + if (nlocal == nmax) grow(0); + + tag[nlocal] = ATOTAGINT(values[0]); + type[nlocal] = atoi(values[1]); + if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) + error->one(FLERR,"Invalid atom type in Atoms section of data file"); + + x[nlocal][0] = coord[0]; + x[nlocal][1] = coord[1]; + x[nlocal][2] = coord[2]; + + sp[nlocal][3] = atof(values[2]); + sp[nlocal][0] = atof(values[6]); + sp[nlocal][1] = atof(values[7]); + sp[nlocal][2] = atof(values[8]); + double inorm = 1.0/sqrt(sp[nlocal][0]*sp[nlocal][0] + + sp[nlocal][1]*sp[nlocal][1] + + sp[nlocal][2]*sp[nlocal][2]); + sp[nlocal][0] *= inorm; + sp[nlocal][1] *= inorm; + sp[nlocal][2] *= inorm; + + image[nlocal] = imagetmp; + + mask[nlocal] = 1; + v[nlocal][0] = 0.0; + v[nlocal][1] = 0.0; + v[nlocal][2] = 0.0; + + atom->nlocal++; +} + +/* ---------------------------------------------------------------------- + unpack hybrid quantities from one line in Atoms section of data file + initialize other atom quantities for this sub-style +------------------------------------------------------------------------- */ + +int AtomVecSpin::data_atom_hybrid(int nlocal, char **values) +{ + + sp[nlocal][0] = atof(values[0]); + sp[nlocal][1] = atof(values[1]); + sp[nlocal][2] = atof(values[2]); + double inorm = 1.0/sqrt(sp[nlocal][0]*sp[nlocal][0] + + sp[nlocal][1]*sp[nlocal][1] + + sp[nlocal][2]*sp[nlocal][2]); + sp[nlocal][0] *= inorm; + sp[nlocal][1] *= inorm; + sp[nlocal][2] *= inorm; + sp[nlocal][3] = atof(values[3]); + + return 4; +} + +/* ---------------------------------------------------------------------- + pack atom info for data file including 3 image flags +------------------------------------------------------------------------- */ + +void AtomVecSpin::pack_data(double **buf) +{ + int nlocal = atom->nlocal; + for (int i = 0; i < nlocal; i++) { + buf[i][0] = ubuf(tag[i]).d; + buf[i][1] = ubuf(type[i]).d; + buf[i][2] = sp[i][3]; + buf[i][3] = x[i][0]; + buf[i][4] = x[i][1]; + buf[i][5] = x[i][2]; + buf[i][6] = sp[i][0]; + buf[i][7] = sp[i][1]; + buf[i][8] = sp[i][2]; + buf[i][9] = ubuf((image[i] & IMGMASK) - IMGMAX).d; + buf[i][10] = ubuf((image[i] >> IMGBITS & IMGMASK) - IMGMAX).d; + buf[i][11] = ubuf((image[i] >> IMG2BITS) - IMGMAX).d; + } +} + +/* ---------------------------------------------------------------------- + pack hybrid atom info for data file +------------------------------------------------------------------------- */ + +int AtomVecSpin::pack_data_hybrid(int i, double *buf) +{ + buf[0] = sp[i][0]; + buf[1] = sp[i][1]; + buf[2] = sp[i][2]; + buf[3] = sp[i][3]; + return 4; +} + +/* ---------------------------------------------------------------------- + write atom info to data file including 3 image flags +------------------------------------------------------------------------- */ + +void AtomVecSpin::write_data(FILE *fp, int n, double **buf) +{ + for (int i = 0; i < n; i++) + fprintf(fp,TAGINT_FORMAT \ + " %d %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e " + "%-1.16e %d %d %d\n", + (tagint) ubuf(buf[i][0]).i,(int) ubuf(buf[i][1]).i, + buf[i][2],buf[i][3],buf[i][4], + buf[i][5],buf[i][6],buf[i][7],buf[i][8], + (int) ubuf(buf[i][9]).i,(int) ubuf(buf[i][10]).i, + (int) ubuf(buf[i][11]).i); +} + +/* ---------------------------------------------------------------------- + write hybrid atom info to data file +------------------------------------------------------------------------- */ + +int AtomVecSpin::write_data_hybrid(FILE *fp, double *buf) +{ + fprintf(fp," %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e",buf[0],buf[1],buf[2],buf[3],buf[4]); + return 4; +} + +/* ---------------------------------------------------------------------- + return # of bytes of allocated memory +------------------------------------------------------------------------- */ + +bigint AtomVecSpin::memory_usage() +{ + bigint bytes = 0; + + if (atom->memcheck("tag")) bytes += memory->usage(tag,nmax); + if (atom->memcheck("type")) bytes += memory->usage(type,nmax); + if (atom->memcheck("mask")) bytes += memory->usage(mask,nmax); + if (atom->memcheck("image")) bytes += memory->usage(image,nmax); + if (atom->memcheck("x")) bytes += memory->usage(x,nmax,3); + if (atom->memcheck("v")) bytes += memory->usage(v,nmax,3); + if (atom->memcheck("f")) bytes += memory->usage(f,nmax*comm->nthreads,3); + + if (atom->memcheck("sp")) bytes += memory->usage(sp,nmax,4); + if (atom->memcheck("fm")) bytes += memory->usage(fm,nmax*comm->nthreads,3); + + return bytes; +} + +void AtomVecSpin::force_clear(int /*n*/, size_t nbytes) +{ + memset(&atom->f[0][0],0,3*nbytes); + memset(&atom->fm[0][0],0,3*nbytes); +} + + diff --git a/src/SPIN/atom_vec_spin.h b/src/SPIN/atom_vec_spin.h new file mode 100644 index 0000000000..34bc55b99f --- /dev/null +++ b/src/SPIN/atom_vec_spin.h @@ -0,0 +1,93 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef ATOM_CLASS + +AtomStyle(spin,AtomVecSpin) + +#else + +#ifndef LMP_ATOM_VEC_SPIN_H +#define LMP_ATOM_VEC_SPIN_H + +#include "atom_vec.h" + +namespace LAMMPS_NS { + +class AtomVecSpin : public AtomVec { + public: + AtomVecSpin(class LAMMPS *); + void grow(int); + void grow_reset(); + void copy(int, int, int); + int pack_comm(int, int *, double *, int, int *); + int pack_comm_vel(int, int *, double *, int, int *); + int pack_comm_hybrid(int, int *, double *); + void unpack_comm(int, int, double *); + void unpack_comm_vel(int, int, double *); + int unpack_comm_hybrid(int, int, double *); + int pack_reverse(int, int, double *); + void unpack_reverse(int, int *, double *); + int pack_border(int, int *, double *, int, int *); + int pack_border_vel(int, int *, double *, int, int *); + int pack_border_hybrid(int, int *, double *); + void unpack_border(int, int, double *); + void unpack_border_vel(int, int, double *); + int unpack_border_hybrid(int, int, double *); + int pack_exchange(int, double *); + int unpack_exchange(double *); + int size_restart(); + int pack_restart(int, double *); + int unpack_restart(double *); + void create_atom(int, double *); + void data_atom(double *, imageint, char **); + int data_atom_hybrid(int, char **); + void pack_data(double **); + int pack_data_hybrid(int, double *); + void write_data(FILE *, int, double **); + int write_data_hybrid(FILE *, double *); + bigint memory_usage(); + + // clear magnetic and mechanic forces + + void force_clear(int, size_t); + + + private: + tagint *tag; + int *type,*mask; + imageint *image; + double **x,**v,**f; // lattice quantities + double **sp,**fm; // spin quantities + // sp[i][0-2] direction of the spin i + // sp[i][3] atomic magnetic moment of the spin i + +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Per-processor system is too big + +The number of owned atoms plus ghost atoms on a single +processor must fit in 32-bit integer. + +E: Invalid atom type in Atoms section of data file + +Atom types must range from 1 to specified # of types. + +*/ diff --git a/src/SPIN/compute_spin.cpp b/src/SPIN/compute_spin.cpp new file mode 100644 index 0000000000..dc16190c98 --- /dev/null +++ b/src/SPIN/compute_spin.cpp @@ -0,0 +1,154 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ------------------------------------------------------------------------ + Contributing authors: Julien Tranchida (SNL) + Aidan Thompson (SNL) + + Please cite the related publication: + Tranchida, J., Plimpton, S. J., Thibaudeau, P., & Thompson, A. P. (2018). + Massively parallel symplectic algorithm for coupled magnetic spin dynamics + and molecular dynamics. Journal of Computational Physics. +------------------------------------------------------------------------- */ + +#include +#include +#include "atom.h" +#include "compute_spin.h" +#include "domain.h" +#include "error.h" +#include "force.h" +#include "math_special.h" +#include "math_const.h" +#include "memory.h" +#include "modify.h" +#include "update.h" + +using namespace LAMMPS_NS; +using namespace MathSpecial; +using namespace MathConst; + +/* ---------------------------------------------------------------------- */ + +ComputeSpin::ComputeSpin(LAMMPS *lmp, int narg, char **arg) : + Compute(lmp, narg, arg) +{ + if ((narg != 3) && (narg != 4)) error->all(FLERR,"Illegal compute compute/spin command"); + + vector_flag = 1; + size_vector = 6; + extvector = 0; + + init(); + + allocate(); + +} + +/* ---------------------------------------------------------------------- */ + +ComputeSpin::~ComputeSpin() +{ + memory->destroy(vector); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeSpin::init() +{ + hbar = force->hplanck/MY_2PI; + kb = force->boltz; +} + +/* ---------------------------------------------------------------------- */ + +void ComputeSpin::compute_vector() +{ + int i; + int countsp, countsptot; + double mag[4], magtot[4]; + double magenergy, magenergytot; + double tempnum, tempnumtot; + double tempdenom, tempdenomtot; + double spintemperature; + + invoked_vector = update->ntimestep; + + countsp = countsptot = 0.0; + mag[0] = mag[1] = mag[2] = mag[3] = 0.0; + magtot[0] = magtot[1] = magtot[2] = magtot[3] = 0.0; + magenergy = magenergytot = 0.0; + tempnum = tempnumtot = 0.0; + tempdenom = tempdenomtot = 0.0; + spintemperature = 0.0; + + int *mask = atom->mask; + double **sp = atom->sp; + double **fm = atom->fm; + double tx,ty,tz; + + int nlocal = atom->nlocal; + + // compute total magnetization and magnetic energy + // compute spin temperature (Nurdin et al., Phys. Rev. E 61, 2000) + + for (i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + if (atom->sp_flag) { + mag[0] += sp[i][0]; + mag[1] += sp[i][1]; + mag[2] += sp[i][2]; + magenergy -= (sp[i][0]*fm[i][0] + sp[i][1]*fm[i][1] + sp[i][2]*fm[i][2]); + tx = sp[i][1]*fm[i][2]-sp[i][2]*fm[i][1]; + ty = sp[i][2]*fm[i][0]-sp[i][0]*fm[i][2]; + tz = sp[i][0]*fm[i][1]-sp[i][1]*fm[i][0]; + tempnum += tx*tx+ty*ty+tz*tz; + tempdenom += sp[i][0]*fm[i][0]+fm[i][1]*sp[i][1]+sp[i][2]*fm[i][2]; + countsp++; + } + } + else error->all(FLERR,"Compute compute/spin requires atom/spin style"); + } + + MPI_Allreduce(mag,magtot,4,MPI_DOUBLE,MPI_SUM,world); + MPI_Allreduce(&magenergy,&magenergytot,1,MPI_DOUBLE,MPI_SUM,world); + MPI_Allreduce(&tempnum,&tempnumtot,1,MPI_DOUBLE,MPI_SUM,world); + MPI_Allreduce(&tempdenom,&tempdenomtot,1,MPI_DOUBLE,MPI_SUM,world); + MPI_Allreduce(&countsp,&countsptot,1,MPI_INT,MPI_SUM,world); + + double scale = 1.0/countsptot; + magtot[0] *= scale; + magtot[1] *= scale; + magtot[2] *= scale; + magtot[3] = sqrt((magtot[0]*magtot[0])+(magtot[1]*magtot[1])+(magtot[2]*magtot[2])); + spintemperature = hbar*tempnumtot; + spintemperature /= (kb*tempdenomtot); + + vector[0] = magtot[0]; + vector[1] = magtot[1]; + vector[2] = magtot[2]; + vector[3] = magtot[3]; + vector[4] = magenergytot*hbar; + vector[5] = spintemperature; + +} + +/* ---------------------------------------------------------------------- + free and reallocate arrays +------------------------------------------------------------------------- */ + +void ComputeSpin::allocate() +{ + memory->create(vector,6,"compute/spin:vector"); +} + diff --git a/src/SPIN/compute_spin.h b/src/SPIN/compute_spin.h new file mode 100644 index 0000000000..b57876b7a0 --- /dev/null +++ b/src/SPIN/compute_spin.h @@ -0,0 +1,61 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef COMPUTE_CLASS + +ComputeStyle(compute/spin,ComputeSpin) + +#else + +#ifndef LMP_COMPUTE_SPIN_H +#define LMP_COMPUTE_SPIN_H + +#include "compute.h" + +namespace LAMMPS_NS { + +class ComputeSpin : public Compute { + public: + ComputeSpin(class LAMMPS *, int, char **); + ~ComputeSpin(); + void init(); + void compute_vector(); + + private: + double kb,hbar; + + void allocate(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Chunk/atom compute does not exist for compute compute/spin + +Self-explanatory. + +E: Compute compute/spin does not use chunk/atom compute + +The style of the specified compute is not chunk/atom. + +*/ diff --git a/src/SPIN/fix_langevin_spin.cpp b/src/SPIN/fix_langevin_spin.cpp new file mode 100644 index 0000000000..55b4d8dfec --- /dev/null +++ b/src/SPIN/fix_langevin_spin.cpp @@ -0,0 +1,199 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ------------------------------------------------------------------------ + Contributing authors: Julien Tranchida (SNL) + Aidan Thompson (SNL) + + Please cite the related publication: + Tranchida, J., Plimpton, S. J., Thibaudeau, P., & Thompson, A. P. (2018). + Massively parallel symplectic algorithm for coupled magnetic spin dynamics + and molecular dynamics. Journal of Computational Physics. +------------------------------------------------------------------------- */ + +#include +#include +#include +#include + +#include "atom.h" +#include "atom_vec_ellipsoid.h" +#include "comm.h" +#include "compute.h" +#include "domain.h" +#include "error.h" +#include "fix_langevin_spin.h" +#include "force.h" +#include "group.h" +#include "input.h" +#include "math_const.h" +#include "math_extra.h" +#include "memory.h" +#include "modify.h" +#include "random_mars.h" +#include "random_park.h" +#include "region.h" +#include "respa.h" +#include "update.h" +#include "variable.h" + +using namespace LAMMPS_NS; +using namespace FixConst; +using namespace MathConst; + +/* ---------------------------------------------------------------------- */ + +FixLangevinSpin::FixLangevinSpin(LAMMPS *lmp, int narg, char **arg) : + Fix(lmp, narg, arg), id_temp(NULL), random(NULL) +{ + if (narg != 6) error->all(FLERR,"Illegal langevin/spin command"); + + dynamic_group_allow = 1; + scalar_flag = 1; + global_freq = 1; + extscalar = 1; + nevery = 1; + + temp = force->numeric(FLERR,arg[3]); + alpha_t = force->numeric(FLERR,arg[4]); + seed = force->inumeric(FLERR,arg[5]); + + if (alpha_t < 0.0) { + error->all(FLERR,"Illegal langevin/spin command"); + } else if (alpha_t == 0.0) { + tdamp_flag = 0; + } else { + tdamp_flag = 1; + } + + if (temp < 0.0) { + error->all(FLERR,"Illegal langevin/spin command"); + } else if (temp == 0.0) { + temp_flag = 0; + } else { + temp_flag = 1; + } + + // initialize Marsaglia RNG with processor-unique seed + + random = new RanPark(lmp,seed + comm->me); + +} + +/* ---------------------------------------------------------------------- */ + +FixLangevinSpin::~FixLangevinSpin() +{ + memory->destroy(spi); + memory->destroy(fmi); + delete random; +} + +/* ---------------------------------------------------------------------- */ + +int FixLangevinSpin::setmask() +{ + int mask = 0; + mask |= POST_FORCE; + mask |= POST_FORCE_RESPA; + mask |= END_OF_STEP; + mask |= THERMO_ENERGY; + return mask; +} + +/* ---------------------------------------------------------------------- */ + +void FixLangevinSpin::init() +{ + // fix_langevin_spin has to be the last defined fix + + int flag_force = 0; + int flag_lang = 0; + for (int i = 0; i < modify->nfix; i++) { + if (strcmp("precession/spin",modify->fix[i]->style)==0) flag_force = MAX(flag_force,i); + if (strcmp("langevin/spin",modify->fix[i]->style)==0) flag_lang = i; + } + if (flag_force >= flag_lang) error->all(FLERR,"Fix langevin/spin has to come after all other spin fixes"); + + memory->create(spi,3,"langevin:spi"); + memory->create(fmi,3,"langevin:fmi"); + + gil_factor = 1.0/(1.0+(alpha_t)*(alpha_t)); + dts = update->dt; + + double hbar = force->hplanck/MY_2PI; // eV/(rad.THz) + double kb = force->boltz; // eV/K + D = (MY_2PI*alpha_t*gil_factor*kb*temp); + D /= (hbar*dts); + sigma = sqrt(2.0*D); +} + +/* ---------------------------------------------------------------------- */ + +void FixLangevinSpin::setup(int vflag) +{ + if (strstr(update->integrate_style,"verlet")) + post_force(vflag); + else { + ((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1); + post_force_respa(vflag,nlevels_respa-1,0); + ((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1); + } +} + +/* ---------------------------------------------------------------------- */ + +void FixLangevinSpin::add_tdamping(double spi[3], double fmi[3]) +{ + double cpx = fmi[1]*spi[2] - fmi[2]*spi[1]; + double cpy = fmi[2]*spi[0] - fmi[0]*spi[2]; + double cpz = fmi[0]*spi[1] - fmi[1]*spi[0]; + + // adding the transverse damping + + fmi[0] -= alpha_t*cpx; + fmi[1] -= alpha_t*cpy; + fmi[2] -= alpha_t*cpz; +} + +/* ---------------------------------------------------------------------- */ + +void FixLangevinSpin::add_temperature(double fmi[3]) +{ + + double rx = sigma*(2.0*random->uniform() - 1.0); + double ry = sigma*(2.0*random->uniform() - 1.0); + double rz = sigma*(2.0*random->uniform() - 1.0); + + // adding the random field + + fmi[0] += rx; + fmi[1] += ry; + fmi[2] += rz; + + // adding gilbert's prefactor + + fmi[0] *= gil_factor; + fmi[1] *= gil_factor; + fmi[2] *= gil_factor; + +} + + +/* ---------------------------------------------------------------------- */ + +void FixLangevinSpin::post_force_respa(int vflag, int ilevel, int /*iloop*/) +{ + if (ilevel == nlevels_respa-1) post_force(vflag); +} + diff --git a/src/SPIN/fix_langevin_spin.h b/src/SPIN/fix_langevin_spin.h new file mode 100644 index 0000000000..5358438396 --- /dev/null +++ b/src/SPIN/fix_langevin_spin.h @@ -0,0 +1,108 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef FIX_CLASS + +FixStyle(langevin/spin,FixLangevinSpin) + +#else + +#ifndef LMP_FIX_LANGEVIN_SPIN_H +#define LMP_FIX_LANGEVIN_SPIN_H + +#include "fix.h" + +namespace LAMMPS_NS { + +class FixLangevinSpin : public Fix { + public: + FixLangevinSpin(class LAMMPS *, int, char **); + virtual ~FixLangevinSpin(); + int setmask(); + void init(); + void setup(int); + void post_force_respa(int, int, int); + void add_tdamping(double spi[3], double fmi[3]); // add transverse damping + void add_temperature(double fmi[3]); // add temperature + int tdamp_flag, ldamp_flag, temp_flag; // damping and temperature flags + + protected: + double *spi, *fmi; + double alpha_t; // transverse mag. damping + double dts; // magnetic timestep + double temp; // spin bath temperature + double D,sigma; // bath intensity var. + double gil_factor; // gilbert's prefactor + + char *id_temp; + class Compute *temperature; + + int nlevels_respa; + class RanPark *random; + int seed; + +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal langevin/spin command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Fix langevin period must be > 0.0 + +The time window for temperature relaxation must be > 0 + +W: Energy tally does not account for 'zero yes' + +The energy removed by using the 'zero yes' flag is not accounted +for in the energy tally and thus energy conservation cannot be +monitored in this case. + + +E: Variable for fix langevin is invalid style + +It must be an equal-style variable. + + +E: Cannot zero Langevin force of 0 atoms + +The group has zero atoms, so you cannot request its force +be zeroed. + +E: Fix langevin variable returned negative temperature + +Self-explanatory. + +E: Could not find fix_modify temperature ID + +The compute ID for computing temperature does not exist. + +E: Fix_modify temperature ID does not compute temperature + +The compute ID assigned to the fix must compute temperature. + +W: Group for fix_modify temp != fix group + +The fix_modify command is specifying a temperature computation that +computes a temperature on a different group of atoms than the fix +itself operates on. This is probably not what you want to do. + +*/ diff --git a/src/SPIN/fix_nve_spin.cpp b/src/SPIN/fix_nve_spin.cpp new file mode 100644 index 0000000000..898eb95396 --- /dev/null +++ b/src/SPIN/fix_nve_spin.cpp @@ -0,0 +1,642 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ------------------------------------------------------------------------ + Contributing authors: Julien Tranchida (SNL) + Aidan Thompson (SNL) + + Please cite the related publication: + Tranchida, J., Plimpton, S. J., Thibaudeau, P., & Thompson, A. P. (2018). + Massively parallel symplectic algorithm for coupled magnetic spin dynamics + and molecular dynamics. Journal of Computational Physics. +------------------------------------------------------------------------- */ + +#include +#include +#include + +#include "atom.h" +#include "atom_vec.h" +#include "citeme.h" +#include "comm.h" +#include "domain.h" +#include "error.h" +#include "fix_precession_spin.h" +#include "fix_nve_spin.h" +#include "fix_langevin_spin.h" +#include "force.h" +#include "math_vector.h" +#include "math_extra.h" +#include "math_const.h" +#include "memory.h" +#include "modify.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "pair.h" +#include "pair_hybrid.h" +#include "pair_spin.h" +#include "respa.h" +#include "update.h" + +using namespace LAMMPS_NS; +using namespace FixConst; +using namespace MathConst; +using namespace MathExtra; + +static const char cite_fix_nve_spin[] = + "fix nve/spin command:\n\n" + "@article{tranchida2018massively,\n" + "title={Massively parallel symplectic algorithm for coupled magnetic spin " + "dynamics and molecular dynamics},\n" + "author={Tranchida, J and Plimpton, SJ and Thibaudeau, P and Thompson, AP},\n" + "journal={Journal of Computational Physics},\n" + "year={2018},\n" + "publisher={Elsevier}\n" + "}\n\n"; + +enum{NONE}; + +/* ---------------------------------------------------------------------- */ + +FixNVESpin::FixNVESpin(LAMMPS *lmp, int narg, char **arg) : + Fix(lmp, narg, arg), + pair(NULL), spin_pairs(NULL), + rsec(NULL), stack_head(NULL), stack_foot(NULL), + backward_stacks(NULL), forward_stacks(NULL) +{ + if (lmp->citeme) lmp->citeme->add(cite_fix_nve_spin); + + if (narg < 4) error->all(FLERR,"Illegal fix/NVE/spin command"); + + time_integrate = 1; + sector_flag = NONE; + lattice_flag = 1; + nlocal_max = 0; + npairs = 0; + npairspin = 0; + + + // checking if map array or hash is defined + + if (atom->map_style == 0) + error->all(FLERR,"Fix NVE/spin requires an atom map, see atom_modify"); + + // defining sector_flag + + int nprocs_tmp = comm->nprocs; + if (nprocs_tmp == 1) { + sector_flag = 0; + } else if (nprocs_tmp >= 1) { + sector_flag = 1; + } else error->all(FLERR,"Illegal fix/NVE/spin command"); + + // defining lattice_flag + + int iarg = 3; + while (iarg < narg) { + if (strcmp(arg[iarg],"lattice") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal fix/NVE/spin command"); + if (strcmp(arg[iarg+1],"no") == 0) lattice_flag = 0; + else if (strcmp(arg[iarg+1],"yes") == 0) lattice_flag = 1; + else error->all(FLERR,"Illegal fix/NVE/spin command"); + iarg += 2; + } else error->all(FLERR,"Illegal fix/NVE/spin command"); + } + + // check if the atom/spin style is defined + + if (!atom->sp_flag) + error->all(FLERR,"Fix NVE/spin requires atom/spin style"); + + // check if sector_flag is correctly defined + + if (sector_flag == 0 && nprocs_tmp > 1) + error->all(FLERR,"Illegal fix/NVE/spin command"); + + // initialize the magnetic interaction flags + + pair_spin_flag = 0; + precession_spin_flag = 0; + maglangevin_flag = 0; + tdamp_flag = temp_flag = 0; + +} + +/* ---------------------------------------------------------------------- */ + +FixNVESpin::~FixNVESpin() +{ + memory->destroy(rsec); + memory->destroy(stack_head); + memory->destroy(stack_foot); + memory->destroy(forward_stacks); + memory->destroy(backward_stacks); + delete [] spin_pairs; +} + +/* ---------------------------------------------------------------------- */ + +int FixNVESpin::setmask() +{ + int mask = 0; + mask |= INITIAL_INTEGRATE; + mask |= PRE_NEIGHBOR; + mask |= FINAL_INTEGRATE; + return mask; +} + +/* ---------------------------------------------------------------------- */ + +void FixNVESpin::init() +{ + + // set timesteps + + dtv = update->dt; + dtf = 0.5 * update->dt * force->ftm2v; + dts = 0.25 * update->dt; + npairs = npairspin = 0; + + // set ptrs on Pair/Spin styles + + // loop 1: obtain # of Pairs, and # of Pair/Spin styles + + if (force->pair_match("spin",0,0)) { // only one Pair/Spin style + pair = force->pair_match("spin",0,0); + npairs = pair->instance_total; + npairspin = 1; + } else if (force->pair_match("spin",0,1)) { // more than one Pair/Spin style + pair = force->pair_match("spin",0,1); + npairs = pair->instance_total; + for (int i = 0; ipair_match("spin",0,i)) { + npairspin ++; + } + } + } + + // init length of vector of ptrs to Pair/Spin styles + + if (npairspin > 0) { + spin_pairs = new PairSpin*[npairspin]; + } + + // loop 2: fill vector with ptrs to Pair/Spin styles + + int count = 0; + if (npairspin == 1) { + count = 1; + spin_pairs[0] = (PairSpin *) force->pair_match("spin",0,0); + } else if (npairspin > 1) { + for (int i = 0; ipair_match("spin",0,i)) { + spin_pairs[count] = (PairSpin *) force->pair_match("spin",0,i); + count++; + } + } + } + + if (count != npairspin) + error->all(FLERR,"Incorrect number of spin pairs"); + + if (npairspin >= 1) pair_spin_flag = 1; + + // ptrs FixPrecessionSpin classes + + int iforce; + for (iforce = 0; iforce < modify->nfix; iforce++) { + if (strstr(modify->fix[iforce]->style,"precession/spin")) { + precession_spin_flag = 1; + lockprecessionspin = (FixPrecessionSpin *) modify->fix[iforce]; + } + } + + // ptrs on the FixLangevinSpin class + + for (iforce = 0; iforce < modify->nfix; iforce++) { + if (strstr(modify->fix[iforce]->style,"langevin/spin")) { + maglangevin_flag = 1; + locklangevinspin = (FixLangevinSpin *) modify->fix[iforce]; + } + } + + if (maglangevin_flag) { + if (locklangevinspin->tdamp_flag == 1) tdamp_flag = 1; + if (locklangevinspin->temp_flag == 1) temp_flag = 1; + } + + // setting the sector variables/lists + + nsectors = 0; + memory->create(rsec,3,"NVE/spin:rsec"); + + // perform the sectoring operation + + if (sector_flag) sectoring(); + + // init. size of stacking lists (sectoring) + + nlocal_max = atom->nlocal; + stack_head = memory->grow(stack_head,nsectors,"NVE/spin:stack_head"); + stack_foot = memory->grow(stack_foot,nsectors,"NVE/spin:stack_foot"); + backward_stacks = memory->grow(backward_stacks,nlocal_max,"NVE/spin:backward_stacks"); + forward_stacks = memory->grow(forward_stacks,nlocal_max,"NVE/spin:forward_stacks"); + if (nlocal_max == 0) + error->all(FLERR,"Incorrect value of nlocal_max"); + +} + +/* ---------------------------------------------------------------------- */ + +void FixNVESpin::initial_integrate(int /*vflag*/) +{ + double dtfm; + + double **x = atom->x; + double **v = atom->v; + double **f = atom->f; + double *rmass = atom->rmass; + double *mass = atom->mass; + int nlocal = atom->nlocal; + if (igroup == atom->firstgroup) nlocal = atom->nfirst; + int *type = atom->type; + int *mask = atom->mask; + + // update half v for all atoms + + if (lattice_flag) { + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + if (rmass) dtfm = dtf / rmass[i]; + else dtfm = dtf / mass[type[i]]; + v[i][0] += dtfm * f[i][0]; + v[i][1] += dtfm * f[i][1]; + v[i][2] += dtfm * f[i][2]; + } + } + } + + // update half s for all atoms + + if (sector_flag) { // sectoring seq. update + for (int j = 0; j < nsectors; j++) { // advance quarter s for nlocal + comm->forward_comm(); + int i = stack_foot[j]; + while (i >= 0) { + ComputeInteractionsSpin(i); + AdvanceSingleSpin(i); + i = forward_stacks[i]; + } + } + for (int j = nsectors-1; j >= 0; j--) { // advance quarter s for nlocal + comm->forward_comm(); + int i = stack_head[j]; + while (i >= 0) { + ComputeInteractionsSpin(i); + AdvanceSingleSpin(i); + i = backward_stacks[i]; + } + } + } else if (sector_flag == 0) { // serial seq. update + comm->forward_comm(); // comm. positions of ghost atoms + for (int i = 0; i < nlocal; i++){ // advance quarter s for nlocal + ComputeInteractionsSpin(i); + AdvanceSingleSpin(i); + } + for (int i = nlocal-1; i >= 0; i--){ // advance quarter s for nlocal + ComputeInteractionsSpin(i); + AdvanceSingleSpin(i); + } + } else error->all(FLERR,"Illegal fix NVE/spin command"); + + // update x for all particles + + if (lattice_flag) { + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + x[i][0] += dtv * v[i][0]; + x[i][1] += dtv * v[i][1]; + x[i][2] += dtv * v[i][2]; + } + } + } + + // update half s for all particles + + if (sector_flag) { // sectoring seq. update + for (int j = 0; j < nsectors; j++) { // advance quarter s for nlocal + comm->forward_comm(); + int i = stack_foot[j]; + while (i >= 0) { + ComputeInteractionsSpin(i); + AdvanceSingleSpin(i); + i = forward_stacks[i]; + } + } + for (int j = nsectors-1; j >= 0; j--) { // advance quarter s for nlocal + comm->forward_comm(); + int i = stack_head[j]; + while (i >= 0) { + ComputeInteractionsSpin(i); + AdvanceSingleSpin(i); + i = backward_stacks[i]; + } + } + } else if (sector_flag == 0) { // serial seq. update + comm->forward_comm(); // comm. positions of ghost atoms + for (int i = 0; i < nlocal; i++){ // advance quarter s for nlocal-1 + ComputeInteractionsSpin(i); + AdvanceSingleSpin(i); + } + for (int i = nlocal-1; i >= 0; i--){ // advance quarter s for nlocal-1 + ComputeInteractionsSpin(i); + AdvanceSingleSpin(i); + } + } else error->all(FLERR,"Illegal fix NVE/spin command"); + +} + +/* ---------------------------------------------------------------------- + setup pre_neighbor() +---------------------------------------------------------------------- */ + +void FixNVESpin::setup_pre_neighbor() +{ + pre_neighbor(); +} + +/* ---------------------------------------------------------------------- + store in two linked lists the advance order of the spins (sectoring) +---------------------------------------------------------------------- */ + +void FixNVESpin::pre_neighbor() +{ + double **x = atom->x; + int nlocal = atom->nlocal; + + if (nlocal_max < nlocal) { // grow linked lists if necessary + nlocal_max = nlocal; + backward_stacks = memory->grow(backward_stacks,nlocal_max,"NVE/spin:backward_stacks"); + forward_stacks = memory->grow(forward_stacks,nlocal_max,"NVE/spin:forward_stacks"); + } + + for (int j = 0; j < nsectors; j++) { + stack_head[j] = -1; + stack_foot[j] = -1; + } + + int nseci; + for (int j = 0; j < nsectors; j++) { // stacking backward order + for (int i = 0; i < nlocal; i++) { + nseci = coords2sector(x[i]); + if (j != nseci) continue; + backward_stacks[i] = stack_head[j]; + stack_head[j] = i; + } + } + for (int j = nsectors-1; j >= 0; j--) { // stacking forward order + for (int i = nlocal-1; i >= 0; i--) { + nseci = coords2sector(x[i]); + if (j != nseci) continue; + forward_stacks[i] = stack_foot[j]; + stack_foot[j] = i; + } + } + +} + +/* ---------------------------------------------------------------------- + compute the magnetic torque for the spin ii +---------------------------------------------------------------------- */ + +void FixNVESpin::ComputeInteractionsSpin(int i) +{ + double spi[3], fmi[3]; + + double **sp = atom->sp; + double **fm = atom->fm; + + // force computation for spin i + + spi[0] = sp[i][0]; + spi[1] = sp[i][1]; + spi[2] = sp[i][2]; + + fmi[0] = fmi[1] = fmi[2] = 0.0; + + // update magnetic pair interactions + + if (pair_spin_flag) { + for (int k = 0; k < npairspin; k++) { + spin_pairs[k]->compute_single_pair(i,fmi); + } + } + + // update magnetic precession interactions + + if (precession_spin_flag) { + lockprecessionspin->compute_single_precession(i,spi,fmi); + } + + // update langevin damping and random force + + if (maglangevin_flag) { // mag. langevin + if (tdamp_flag) { // transverse damping + locklangevinspin->add_tdamping(spi,fmi); + } + if (temp_flag) { // spin temperature + locklangevinspin->add_temperature(fmi); + } + } + + // replace the magnetic force fm[i] by its new value fmi + + fm[i][0] = fmi[0]; + fm[i][1] = fmi[1]; + fm[i][2] = fmi[2]; + +} + +/* ---------------------------------------------------------------------- + divide each domain into 8 sectors +---------------------------------------------------------------------- */ + +void FixNVESpin::sectoring() +{ + int sec[3]; + double sublo[3],subhi[3]; + double* sublotmp = domain->sublo; + double* subhitmp = domain->subhi; + for (int dim = 0 ; dim < 3 ; dim++) { + sublo[dim]=sublotmp[dim]; + subhi[dim]=subhitmp[dim]; + } + + const double rsx = subhi[0] - sublo[0]; + const double rsy = subhi[1] - sublo[1]; + const double rsz = subhi[2] - sublo[2]; + + // extract larger cutoff from PairSpin styles + + double rv, cutoff; + rv = cutoff = 0.0; + int dim = 0; + for (int i = 0; i < npairspin ; i++) { + cutoff = *((double *) spin_pairs[i]->extract("cut",dim)); + rv = MAX(rv,cutoff); + } + + if (rv == 0.0) + error->all(FLERR,"Illegal sectoring operation"); + + double rax = rsx/rv; + double ray = rsy/rv; + double raz = rsz/rv; + + sec[0] = 1; + sec[1] = 1; + sec[2] = 1; + if (rax >= 2.0) sec[0] = 2; + if (ray >= 2.0) sec[1] = 2; + if (raz >= 2.0) sec[2] = 2; + + nsectors = sec[0]*sec[1]*sec[2]; + + if (sector_flag == 1 && nsectors != 8) + error->all(FLERR,"Illegal sectoring operation"); + + rsec[0] = rsx; + rsec[1] = rsy; + rsec[2] = rsz; + if (sec[0] == 2) rsec[0] = rsx/2.0; + if (sec[1] == 2) rsec[1] = rsy/2.0; + if (sec[2] == 2) rsec[2] = rsz/2.0; + +} + +/* ---------------------------------------------------------------------- + define sector for an atom at a position x[i] +---------------------------------------------------------------------- */ + +int FixNVESpin::coords2sector(double *x) +{ + int nseci; + int seci[3]; + double sublo[3]; + double* sublotmp = domain->sublo; + for (int dim = 0 ; dim<3 ; dim++) { + sublo[dim]=sublotmp[dim]; + } + + seci[0] = x[0] > (sublo[0] + rsec[0]); + seci[1] = x[1] > (sublo[1] + rsec[1]); + seci[2] = x[2] > (sublo[2] + rsec[2]); + + nseci = (seci[0] + 2*seci[1] + 4*seci[2]); + + return nseci; +} + +/* ---------------------------------------------------------------------- + advance the spin i of a timestep dts +---------------------------------------------------------------------- */ + +void FixNVESpin::AdvanceSingleSpin(int i) +{ + int j=0; + int *sametag = atom->sametag; + double **sp = atom->sp; + double **fm = atom->fm; + double msq,scale,fm2,energy,dts2; + double cp[3],g[3]; + + cp[0] = cp[1] = cp[2] = 0.0; + g[0] = g[1] = g[2] = 0.0; + fm2 = (fm[i][0]*fm[i][0])+(fm[i][1]*fm[i][1])+(fm[i][2]*fm[i][2]); + energy = (sp[i][0]*fm[i][0])+(sp[i][1]*fm[i][1])+(sp[i][2]*fm[i][2]); + dts2 = dts*dts; + + cp[0] = fm[i][1]*sp[i][2]-fm[i][2]*sp[i][1]; + cp[1] = fm[i][2]*sp[i][0]-fm[i][0]*sp[i][2]; + cp[2] = fm[i][0]*sp[i][1]-fm[i][1]*sp[i][0]; + + g[0] = sp[i][0]+cp[0]*dts; + g[1] = sp[i][1]+cp[1]*dts; + g[2] = sp[i][2]+cp[2]*dts; + + g[0] += (fm[i][0]*energy-0.5*sp[i][0]*fm2)*0.5*dts2; + g[1] += (fm[i][1]*energy-0.5*sp[i][1]*fm2)*0.5*dts2; + g[2] += (fm[i][2]*energy-0.5*sp[i][2]*fm2)*0.5*dts2; + + g[0] /= (1+0.25*fm2*dts2); + g[1] /= (1+0.25*fm2*dts2); + g[2] /= (1+0.25*fm2*dts2); + + sp[i][0] = g[0]; + sp[i][1] = g[1]; + sp[i][2] = g[2]; + + // renormalization (check if necessary) + + msq = g[0]*g[0] + g[1]*g[1] + g[2]*g[2]; + scale = 1.0/sqrt(msq); + sp[i][0] *= scale; + sp[i][1] *= scale; + sp[i][2] *= scale; + + // comm. sp[i] to atoms with same tag (for serial algo) + + if (sector_flag == 0) { + if (sametag[i] >= 0) { + j = sametag[i]; + while (j >= 0) { + sp[j][0] = sp[i][0]; + sp[j][1] = sp[i][1]; + sp[j][2] = sp[i][2]; + j = sametag[j]; + } + } + } + +} + +/* ---------------------------------------------------------------------- */ + +void FixNVESpin::final_integrate() +{ + double dtfm; + + double **v = atom->v; + double **f = atom->f; + double *rmass = atom->rmass; + double *mass = atom->mass; + int nlocal = atom->nlocal; + if (igroup == atom->firstgroup) nlocal = atom->nfirst; + int *type = atom->type; + int *mask = atom->mask; + + // update half v for all particles + + if (lattice_flag) { + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + if (rmass) dtfm = dtf / rmass[i]; + else dtfm = dtf / mass[type[i]]; + v[i][0] += dtfm * f[i][0]; + v[i][1] += dtfm * f[i][1]; + v[i][2] += dtfm * f[i][2]; + } + } + } + +} diff --git a/src/SPIN/fix_nve_spin.h b/src/SPIN/fix_nve_spin.h new file mode 100644 index 0000000000..afc1db14d6 --- /dev/null +++ b/src/SPIN/fix_nve_spin.h @@ -0,0 +1,112 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef FIX_CLASS + +FixStyle(nve/spin,FixNVESpin) + +#else + +#ifndef LMP_FIX_NVE_SPIN_H +#define LMP_FIX_NVE_SPIN_H + +#include "fix.h" +#include "pair.h" +#include "pair_spin.h" + +namespace LAMMPS_NS { + +class FixNVESpin : public Fix { +friend class PairSpin; + public: + FixNVESpin(class LAMMPS *, int, char **); + virtual ~FixNVESpin(); + int setmask(); + void init(); + virtual void initial_integrate(int); + virtual void final_integrate(); + + void ComputeInteractionsSpin(int); // compute and advance single spin functions + void AdvanceSingleSpin(int); + + void sectoring(); // sectoring operation functions + int coords2sector(double *); + + void setup_pre_neighbor(); + void pre_neighbor(); + + int lattice_flag; // lattice_flag = 0 if spins only + // lattice_flag = 1 if spin-lattice calc. + + + protected: + int sector_flag; // sector_flag = 0 if serial algorithm + // sector_flag = 1 if parallel algorithm + + double dtv, dtf, dts; // velocity, force, and spin timesteps + + int nlocal_max; // max value of nlocal (for lists size) + + int pair_spin_flag; // magnetic pair flags + int precession_spin_flag; // magnetic precession flags + int maglangevin_flag; // magnetic langevin flags + int tdamp_flag, temp_flag; + + // pointers to magnetic fixes + + class FixPrecessionSpin *lockprecessionspin; + class FixLangevinSpin *locklangevinspin; + + // pointers to magnetic pair styles + + int npairs, npairspin; // # of pairs, and # of spin pairs + class Pair *pair; + class PairSpin **spin_pairs; // vector of spin pairs + + // sectoring variables + + int nsectors; + double *rsec; + + // stacking variables for sectoring algorithm + + int *stack_head; // index of first atom in backward_stacks + int *stack_foot; // index of first atom in forward_stacks + int *backward_stacks; // index of next atom in backward stack + int *forward_stacks; // index of next atom in forward stack + +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal fix NVE/spin command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Pair spin requires atom attribute spin + +An atom/spin style with this attribute is needed. + +E: Illegal sectoring operation + +The number of processes does not match the size of the system. +See the documentation of the sectoring method. + +*/ diff --git a/src/SPIN/fix_precession_spin.cpp b/src/SPIN/fix_precession_spin.cpp new file mode 100644 index 0000000000..d3edb3ae8a --- /dev/null +++ b/src/SPIN/fix_precession_spin.cpp @@ -0,0 +1,282 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ------------------------------------------------------------------------ + Contributing authors: Julien Tranchida (SNL) + Aidan Thompson (SNL) + + Please cite the related publication: + Tranchida, J., Plimpton, S. J., Thibaudeau, P., & Thompson, A. P. (2018). + Massively parallel symplectic algorithm for coupled magnetic spin dynamics + and molecular dynamics. Journal of Computational Physics. +------------------------------------------------------------------------- */ + +#include +#include +#include +#include + +#include "atom.h" +#include "domain.h" +#include "error.h" +#include "fix_precession_spin.h" +#include "force.h" +#include "input.h" +#include "math_const.h" +#include "memory.h" +#include "modify.h" +#include "respa.h" +#include "update.h" +#include "variable.h" + +using namespace LAMMPS_NS; +using namespace FixConst; +using namespace MathConst; + +enum{CONSTANT,EQUAL}; + +/* ---------------------------------------------------------------------- */ + +FixPrecessionSpin::FixPrecessionSpin(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg) +{ + if (narg < 7) error->all(FLERR,"Illegal precession/spin command"); + + // magnetic interactions coded for cartesian coordinates + + hbar = force->hplanck/MY_2PI; + + dynamic_group_allow = 1; + scalar_flag = 1; + global_freq = 1; + extscalar = 1; + respa_level_support = 1; + ilevel_respa = 0; + + magstr = NULL; + magfieldstyle = CONSTANT; + + H_field = 0.0; + nhx = nhy = nhz = 0.0; + hx = hy = hz = 0.0; + Ka = 0.0; + nax = nay = naz = 0.0; + Kax = Kay = Kaz = 0.0; + + zeeman_flag = aniso_flag = 0; + + int iarg = 3; + while (iarg < narg) { + if (strcmp(arg[iarg],"zeeman") == 0) { + if (iarg+4 > narg) error->all(FLERR,"Illegal fix precession/spin command"); + zeeman_flag = 1; + H_field = force->numeric(FLERR,arg[iarg+1]); + nhx = force->numeric(FLERR,arg[iarg+2]); + nhy = force->numeric(FLERR,arg[iarg+3]); + nhz = force->numeric(FLERR,arg[iarg+4]); + iarg += 5; + } else if (strcmp(arg[iarg],"anisotropy") == 0) { + if (iarg+4 > narg) error->all(FLERR,"Illegal fix precession/spin command"); + aniso_flag = 1; + Ka = force->numeric(FLERR,arg[iarg+1]); + nax = force->numeric(FLERR,arg[iarg+2]); + nay = force->numeric(FLERR,arg[iarg+3]); + naz = force->numeric(FLERR,arg[iarg+4]); + iarg += 5; + } else error->all(FLERR,"Illegal precession/spin command"); + } + + degree2rad = MY_PI/180.0; + time_origin = update->ntimestep; + + eflag = 0; + emag = 0.0; +} + +/* ---------------------------------------------------------------------- */ + +FixPrecessionSpin::~FixPrecessionSpin() +{ + delete [] magstr; +} + +/* ---------------------------------------------------------------------- */ + +int FixPrecessionSpin::setmask() +{ + int mask = 0; + mask |= POST_FORCE; + mask |= THERMO_ENERGY; + mask |= POST_FORCE_RESPA; + return mask; +} + + +/* ---------------------------------------------------------------------- */ + +void FixPrecessionSpin::init() +{ + const double hbar = force->hplanck/MY_2PI; // eV/(rad.THz) + const double mub = 5.78901e-5; // in eV/T + const double gyro = mub/hbar; // in rad.THz/T + + H_field *= gyro; // in rad.THz + Ka /= hbar; // in rad.THz + + if (strstr(update->integrate_style,"respa")) { + ilevel_respa = ((Respa *) update->integrate)->nlevels-1; + if (respa_level >= 0) ilevel_respa = MIN(respa_level,ilevel_respa); + } + + if (magstr) { + magvar = input->variable->find(magstr); + if (magvar < 0) + error->all(FLERR,"Illegal precession/spin command"); + if (!input->variable->equalstyle(magvar)) + error->all(FLERR,"Illegal precession/spin command"); + } + + varflag = CONSTANT; + if (magfieldstyle != CONSTANT) varflag = EQUAL; + + // set magnetic field components + + if (varflag == CONSTANT) set_magneticprecession(); + +} + +/* ---------------------------------------------------------------------- */ + +void FixPrecessionSpin::setup(int vflag) +{ + if (strstr(update->integrate_style,"verlet")) + post_force(vflag); + else { + ((Respa *) update->integrate)->copy_flevel_f(ilevel_respa); + post_force_respa(vflag,ilevel_respa,0); + ((Respa *) update->integrate)->copy_f_flevel(ilevel_respa); + } +} + +/* ---------------------------------------------------------------------- */ + +void FixPrecessionSpin::post_force(int /*vflag*/) +{ + // update mag field with time (potential improvement) + + if (varflag != CONSTANT) { + modify->clearstep_compute(); + modify->addstep_compute(update->ntimestep + 1); + set_magneticprecession(); // update mag. field if time-dep. + } + + double **sp = atom->sp; + double **fm = atom->fm; + double spi[3], fmi[3]; + const int nlocal = atom->nlocal; + + eflag = 0; + emag = 0.0; + + for (int i = 0; i < nlocal; i++) { + spi[0] = sp[i][0]; + spi[1] = sp[i][1]; + spi[2] = sp[i][2]; + fmi[0] = fmi[1] = fmi[2] = 0.0; + + if (zeeman_flag) { // compute Zeeman interaction + compute_zeeman(i,fmi); + emag -= (spi[0]*fmi[0] + spi[1]*fmi[1] + spi[2]*fmi[2]); + } + + if (aniso_flag) { // compute magnetic anisotropy + compute_anisotropy(spi,fmi); + emag -= (spi[0]*fmi[0] + spi[1]*fmi[1] + spi[2]*fmi[2]); + } + + fm[i][0] += fmi[0]; + fm[i][1] += fmi[1]; + fm[i][2] += fmi[2]; + } + emag *= hbar; +} + +/* ---------------------------------------------------------------------- */ + +void FixPrecessionSpin::compute_single_precession(int i, double spi[3], double fmi[3]) +{ + if (zeeman_flag) { + compute_zeeman(i,fmi); + } + if (aniso_flag) { + compute_anisotropy(spi,fmi); + } +} + + +/* ---------------------------------------------------------------------- */ + +void FixPrecessionSpin::compute_zeeman(int i, double fmi[3]) +{ + double **sp = atom->sp; + fmi[0] -= sp[i][3]*hx; + fmi[1] -= sp[i][3]*hy; + fmi[2] -= sp[i][3]*hz; +} + +/* ---------------------------------------------------------------------- */ + +void FixPrecessionSpin::compute_anisotropy(double spi[3], double fmi[3]) +{ + double scalar = nax*spi[0] + nay*spi[1] + naz*spi[2]; + fmi[0] += scalar*Kax; + fmi[1] += scalar*Kay; + fmi[2] += scalar*Kaz; +} + +/* ---------------------------------------------------------------------- */ + +void FixPrecessionSpin::post_force_respa(int vflag, int ilevel, int /*iloop*/) +{ + if (ilevel == ilevel_respa) post_force(vflag); +} + +/* ---------------------------------------------------------------------- */ + +void FixPrecessionSpin::set_magneticprecession() +{ + if (zeeman_flag) { + hx = H_field*nhx; + hy = H_field*nhy; + hz = H_field*nhz; + } + if (aniso_flag) { + Kax = 2.0*Ka*nax; + Kay = 2.0*Ka*nay; + Kaz = 2.0*Ka*naz; + } +} + +/* ---------------------------------------------------------------------- + potential energy in magnetic field +------------------------------------------------------------------------- */ + +double FixPrecessionSpin::compute_scalar() +{ + // only sum across procs one time + + if (eflag == 0) { + MPI_Allreduce(&emag,&emag_all,1,MPI_DOUBLE,MPI_SUM,world); + eflag = 1; + } + return emag_all; +} diff --git a/src/SPIN/fix_precession_spin.h b/src/SPIN/fix_precession_spin.h new file mode 100644 index 0000000000..53ae4ba124 --- /dev/null +++ b/src/SPIN/fix_precession_spin.h @@ -0,0 +1,92 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef FIX_CLASS + +FixStyle(precession/spin,FixPrecessionSpin) + +#else + +#ifndef LMP_FIX_PRECESSION_SPIN_H +#define LMP_FIX_PRECESSION_SPIN_H + +#include "fix.h" + +namespace LAMMPS_NS { + +class FixPrecessionSpin : public Fix { + friend class FixPour; + + public: + FixPrecessionSpin(class LAMMPS *, int, char **); + ~FixPrecessionSpin(); + int setmask(); + void init(); + void setup(int); + virtual void post_force(int); + virtual void post_force_respa(int, int, int); + double compute_scalar(); + + int zeeman_flag, aniso_flag; + void compute_single_precession(int, double *, double *); + void compute_zeeman(int, double *); + void compute_anisotropy(double *, double *); + + protected: + int style; // style of the magnetic precession + + double degree2rad; + double hbar; + int ilevel_respa; + int time_origin; + int eflag; + double emag, emag_all; + + int varflag; + int magfieldstyle; + int magvar; + char *magstr; + + // zeeman field intensity and direction + + double H_field; + double nhx, nhy, nhz; + double hx, hy, hz; // temp. force variables + + // magnetic anisotropy intensity and direction + + double Ka; + double nax, nay, naz; + double Kax, Kay, Kaz; // temp. force variables + + void set_magneticprecession(); + +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal precession/spin command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +precession/spin fix command has 7 arguments: +fix ID group precession/spin magnitude (T or eV) style (zeeman or anisotropy) +direction (3 cartesian coordinates) +*/ diff --git a/src/SPIN/pair_spin.cpp b/src/SPIN/pair_spin.cpp new file mode 100644 index 0000000000..929b79bef3 --- /dev/null +++ b/src/SPIN/pair_spin.cpp @@ -0,0 +1,96 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ------------------------------------------------------------------------ + Contributing authors: Julien Tranchida (SNL) + Aidan Thompson (SNL) + + Please cite the related publication: + Tranchida, J., Plimpton, S. J., Thibaudeau, P., & Thompson, A. P. (2018). + Massively parallel symplectic algorithm for coupled magnetic spin dynamics + and molecular dynamics. Journal of Computational Physics. +------------------------------------------------------------------------- */ + +#include +#include +#include + +#include "atom.h" +#include "comm.h" +#include "error.h" +#include "fix.h" +#include "fix_nve_spin.h" +#include "force.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "math_const.h" +#include "memory.h" +#include "modify.h" +#include "pair.h" +#include "pair_hybrid.h" +#include "pair_hybrid_overlay.h" +#include "pair_spin.h" +#include "update.h" + +using namespace LAMMPS_NS; +using namespace MathConst; + +/* ---------------------------------------------------------------------- */ + +PairSpin::PairSpin(LAMMPS *lmp) : Pair(lmp) +{ + hbar = force->hplanck/MY_2PI; + single_enable = 0; + no_virial_fdotr_compute = 1; +} + +/* ---------------------------------------------------------------------- */ + +PairSpin::~PairSpin() {} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairSpin::settings(int narg, char **/*arg*/) +{ + if (narg < 1 || narg > 2) + error->all(FLERR,"Incorrect number of args in pair_style pair/spin command"); + + // pair/spin need the metal unit style + + if (strcmp(update->unit_style,"metal") != 0) + error->all(FLERR,"pair/spin style requires metal units"); + +} + +/* ---------------------------------------------------------------------- + init specific to this pair style +------------------------------------------------------------------------- */ + +void PairSpin::init_style() +{ + if (!atom->sp_flag) + error->all(FLERR,"Pair spin requires atom/spin style"); + + // checking if nve/spin is a listed fix + + int ifix = 0; + while (ifix < modify->nfix) { + if (strcmp(modify->fix[ifix]->style,"nve/spin") == 0) break; + ifix++; + } + if (ifix == modify->nfix) + error->all(FLERR,"pair/spin style requires nve/spin"); +} diff --git a/src/SPIN/pair_spin.h b/src/SPIN/pair_spin.h new file mode 100644 index 0000000000..100eec1732 --- /dev/null +++ b/src/SPIN/pair_spin.h @@ -0,0 +1,70 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS + +PairStyle(pair/spin,PairSpin) + +#else + +#ifndef LMP_PAIR_SPIN_H +#define LMP_PAIR_SPIN_H + +#include "pair.h" + +namespace LAMMPS_NS { + +class PairSpin : public Pair { +friend class FixNVESpin; + public: + PairSpin(class LAMMPS *); + virtual ~PairSpin(); + virtual void settings(int, char **); + virtual void coeff(int, char **) {} + virtual void init_style(); + virtual double init_one(int, int) {return 0.0;} + virtual void *extract(const char *, int &) {return NULL;} + + virtual void compute(int, int) {} + virtual void compute_single_pair(int, double *) {} + + protected: + double hbar; // Planck constant (eV.ps.rad-1) + + virtual void allocate() {} +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Incorrect args in pair_spin command + +Self-explanatory. + +E: Spin simulations require metal unit style + +Self-explanatory. + +E: Incorrect args for pair coefficients + +Self-explanatory. Check the input script or data file. + +E: Pair spin requires atom attribute spin + +The atom style defined does not have these attributes. + +*/ diff --git a/src/SPIN/pair_spin_dmi.cpp b/src/SPIN/pair_spin_dmi.cpp new file mode 100644 index 0000000000..6f8114042e --- /dev/null +++ b/src/SPIN/pair_spin_dmi.cpp @@ -0,0 +1,565 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ------------------------------------------------------------------------ + Contributing authors: Julien Tranchida (SNL) + Aidan Thompson (SNL) + + Please cite the related publication: + Tranchida, J., Plimpton, S. J., Thibaudeau, P., & Thompson, A. P. (2018). + Massively parallel symplectic algorithm for coupled magnetic spin dynamics + and molecular dynamics. Journal of Computational Physics. +------------------------------------------------------------------------- */ + +#include +#include +#include + +#include "atom.h" +#include "comm.h" +#include "error.h" +#include "force.h" +#include "fix.h" +#include "fix_nve_spin.h" +#include "pair_hybrid.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "math_const.h" +#include "memory.h" +#include "modify.h" +#include "pair_spin_dmi.h" +#include "update.h" + +using namespace LAMMPS_NS; +using namespace MathConst; + +/* ---------------------------------------------------------------------- */ + +PairSpinDmi::PairSpinDmi(LAMMPS *lmp) : PairSpin(lmp), +lockfixnvespin(NULL) +{ + single_enable = 0; + no_virial_fdotr_compute = 1; + lattice_flag = 0; +} + +/* ---------------------------------------------------------------------- */ + +PairSpinDmi::~PairSpinDmi() +{ + if (allocated) { + memory->destroy(setflag); + memory->destroy(cut_spin_dmi); + memory->destroy(DM); + memory->destroy(v_dmx); + memory->destroy(v_dmy); + memory->destroy(v_dmz); + memory->destroy(vmech_dmx); + memory->destroy(vmech_dmy); + memory->destroy(vmech_dmz); + memory->destroy(cutsq); + } +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairSpinDmi::settings(int narg, char **arg) +{ + if (narg < 1 || narg > 2) + error->all(FLERR,"Incorrect number of args in pair/spin/dmi command"); + + if (strcmp(update->unit_style,"metal") != 0) + error->all(FLERR,"Spin simulations require metal unit style"); + + cut_spin_dmi_global = force->numeric(FLERR,arg[0]); + + // reset cutoffs that have been explicitly set + + if (allocated) { + int i,j; + for (i = 1; i <= atom->ntypes; i++) { + for (j = i+1; j <= atom->ntypes; j++) { + if (setflag[i][j]) { + cut_spin_dmi[i][j] = cut_spin_dmi_global; + } + } + } + } + +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type spin pairs (only one for now) +------------------------------------------------------------------------- */ + +void PairSpinDmi::coeff(int narg, char **arg) +{ + if (!allocated) allocate(); + + // check if args correct + + if (strcmp(arg[2],"dmi") != 0) + error->all(FLERR,"Incorrect args in pair_style command"); + if (narg != 8) + error->all(FLERR,"Incorrect args in pair_style command"); + + int ilo,ihi,jlo,jhi; + force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi); + force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi); + + const double rij = force->numeric(FLERR,arg[3]); + const double dm = (force->numeric(FLERR,arg[4])); + double dmx = force->numeric(FLERR,arg[5]); + double dmy = force->numeric(FLERR,arg[6]); + double dmz = force->numeric(FLERR,arg[7]); + + double inorm = 1.0/(dmx*dmx+dmy*dmy+dmz*dmz); + dmx *= inorm; + dmy *= inorm; + dmz *= inorm; + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + for (int j = MAX(jlo,i); j <= jhi; j++) { + cut_spin_dmi[i][j] = rij; + DM[i][j] = dm; + v_dmx[i][j] = dmx * dm / hbar; + v_dmy[i][j] = dmy * dm / hbar; + v_dmz[i][j] = dmz * dm / hbar; + vmech_dmx[i][j] = dmx * dm; + vmech_dmy[i][j] = dmy * dm; + vmech_dmz[i][j] = dmz * dm; + setflag[i][j] = 1; + count++; + } + } + if (count == 0) + error->all(FLERR,"Incorrect args in pair_style command"); + +} + +/* ---------------------------------------------------------------------- + init specific to this pair style +------------------------------------------------------------------------- */ + +void PairSpinDmi::init_style() +{ + if (!atom->sp_flag) + error->all(FLERR,"Pair spin requires atom/spin style"); + + // need a full neighbor list + + int irequest = neighbor->request(this,instance_me); + neighbor->requests[irequest]->half = 0; + neighbor->requests[irequest]->full = 1; + + // checking if nve/spin is a listed fix + + int ifix = 0; + while (ifix < modify->nfix) { + if (strcmp(modify->fix[ifix]->style,"nve/spin") == 0) break; + ifix++; + } + if (ifix == modify->nfix) + error->all(FLERR,"pair/spin style requires nve/spin"); + + // get the lattice_flag from nve/spin + + for (int i = 0; i < modify->nfix; i++) { + if (strcmp(modify->fix[i]->style,"nve/spin") == 0) { + lockfixnvespin = (FixNVESpin *) modify->fix[i]; + lattice_flag = lockfixnvespin->lattice_flag; + } + } + +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairSpinDmi::init_one(int i, int j) +{ + if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); + + DM[j][i] = DM[i][j]; + v_dmx[j][i] = v_dmx[i][j]; + v_dmy[j][i] = v_dmy[i][j]; + v_dmz[j][i] = v_dmz[i][j]; + vmech_dmx[j][i] = vmech_dmx[i][j]; + vmech_dmy[j][i] = vmech_dmy[i][j]; + vmech_dmz[j][i] = vmech_dmz[i][j]; + cut_spin_dmi[j][i] = cut_spin_dmi[i][j]; + + return cut_spin_dmi_global; +} + +/* ---------------------------------------------------------------------- + extract the larger cutoff +------------------------------------------------------------------------- */ + +void *PairSpinDmi::extract(const char *str, int &dim) +{ + dim = 0; + if (strcmp(str,"cut") == 0) return (void *) &cut_spin_dmi_global; + return NULL; +} + +/* ---------------------------------------------------------------------- */ + +void PairSpinDmi::compute(int eflag, int vflag) +{ + int i,j,ii,jj,inum,jnum,itype,jtype; + double evdwl, ecoul; + double xi[3], eij[3]; + double delx,dely,delz; + double spi[3], spj[3]; + double fi[3], fmi[3]; + double local_cut2; + double rsq, inorm; + int *ilist,*jlist,*numneigh,**firstneigh; + + evdwl = ecoul = 0.0; + if (eflag || vflag) ev_setup(eflag,vflag); + else evflag = vflag_fdotr = 0; + + double **x = atom->x; + double **f = atom->f; + double **fm = atom->fm; + double **sp = atom->sp; + int *type = atom->type; + int nlocal = atom->nlocal; + int newton_pair = force->newton_pair; + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // dmi computation + // loop over all atoms + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + itype = type[i]; + + jlist = firstneigh[i]; + jnum = numneigh[i]; + xi[0] = x[i][0]; + xi[1] = x[i][1]; + xi[2] = x[i][2]; + spi[0] = sp[i][0]; + spi[1] = sp[i][1]; + spi[2] = sp[i][2]; + + + // loop on neighbors + + for (jj = 0; jj < jnum; jj++) { + + j = jlist[jj]; + j &= NEIGHMASK; + jtype = type[j]; + + spj[0] = sp[j][0]; + spj[1] = sp[j][1]; + spj[2] = sp[j][2]; + + evdwl = 0.0; + fi[0] = fi[1] = fi[2] = 0.0; + fmi[0] = fmi[1] = fmi[2] = 0.0; + + delx = xi[0] - x[j][0]; + dely = xi[1] - x[j][1]; + delz = xi[2] - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + inorm = 1.0/sqrt(rsq); + eij[0] = -inorm*delx; + eij[1] = -inorm*dely; + eij[2] = -inorm*delz; + + local_cut2 = cut_spin_dmi[itype][jtype]*cut_spin_dmi[itype][jtype]; + + // compute dmi interaction + + if (rsq <= local_cut2) { + compute_dmi(i,j,eij,fmi,spj); + if (lattice_flag) { + compute_dmi_mech(i,j,rsq,eij,fi,spi,spj); + } + } + + f[i][0] += fi[0]; + f[i][1] += fi[1]; + f[i][2] += fi[2]; + fm[i][0] += fmi[0]; + fm[i][1] += fmi[1]; + fm[i][2] += fmi[2]; + + if (newton_pair || j < nlocal) { + f[j][0] -= fi[0]; + f[j][1] -= fi[1]; + f[j][2] -= fi[2]; + } + + if (eflag) { + evdwl -= (spi[0]*fmi[0] + spi[1]*fmi[1] + spi[2]*fmi[2]); + evdwl *= hbar; + } else evdwl = 0.0; + + if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair, + evdwl,ecoul,fi[0],fi[1],fi[2],delx,dely,delz); + } + } + + if (vflag_fdotr) virial_fdotr_compute(); + +} + +/* ---------------------------------------------------------------------- */ + +void PairSpinDmi::compute_single_pair(int ii, double fmi[3]) +{ + int *type = atom->type; + double **x = atom->x; + double **sp = atom->sp; + double local_cut2; + double xi[3], eij[3]; + double delx,dely,delz; + double spj[3]; + + int i,j,jnum,itype,jtype; + int *ilist,*jlist,*numneigh,**firstneigh; + + double rsq, inorm; + + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + i = ilist[ii]; + itype = type[i]; + + xi[0] = x[i][0]; + xi[1] = x[i][1]; + xi[2] = x[i][2]; + + jlist = firstneigh[i]; + jnum = numneigh[i]; + + for (int jj = 0; jj < jnum; jj++) { + + j = jlist[jj]; + j &= NEIGHMASK; + jtype = type[j]; + + spj[0] = sp[j][0]; + spj[1] = sp[j][1]; + spj[2] = sp[j][2]; + + delx = xi[0] - x[j][0]; + dely = xi[1] - x[j][1]; + delz = xi[2] - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + inorm = 1.0/sqrt(rsq); + eij[0] = -inorm*delx; + eij[1] = -inorm*dely; + eij[2] = -inorm*delz; + + local_cut2 = cut_spin_dmi[itype][jtype]*cut_spin_dmi[itype][jtype]; + + if (rsq <= local_cut2) { + compute_dmi(i,j,eij,fmi,spj); + } + + } + +} + +/* ---------------------------------------------------------------------- + compute the dmi interaction between spin i and spin j +------------------------------------------------------------------------- */ + +void PairSpinDmi::compute_dmi(int i, int j, double eij[3], double fmi[3], double spj[3]) +{ + int *type = atom->type; + int itype, jtype; + double dmix, dmiy, dmiz; + itype = type[i]; + jtype = type[j]; + + dmix = eij[1]*v_dmz[itype][jtype] - eij[2]*v_dmy[itype][jtype]; + dmiy = eij[2]*v_dmx[itype][jtype] - eij[0]*v_dmz[itype][jtype]; + dmiz = eij[0]*v_dmy[itype][jtype] - eij[1]*v_dmx[itype][jtype]; + + fmi[0] -= (spj[1]*dmiz - spj[2]*dmiy); + fmi[1] -= (spj[2]*dmix - spj[0]*dmiz); + fmi[2] -= (spj[0]*dmiy - spj[1]*dmix); +} + +/* ---------------------------------------------------------------------- + compute the mechanical force due to the dmi interaction between atom i and atom j +------------------------------------------------------------------------- */ + +void PairSpinDmi::compute_dmi_mech(int i, int j, double rsq, double /*eij*/[3], + double fi[3], double spi[3], double spj[3]) +{ + int *type = atom->type; + int itype, jtype; + double dmix,dmiy,dmiz; + itype = type[i]; + jtype = type[j]; + double csx,csy,csz,cdmx,cdmy,cdmz,irij; + + irij = 1.0/sqrt(rsq); + + dmix = vmech_dmx[itype][jtype]; + dmiy = vmech_dmy[itype][jtype]; + dmiz = vmech_dmz[itype][jtype]; + + csx = (spi[1]*spj[2] - spi[2]*spj[1]); + csy = (spi[2]*spj[0] - spi[0]*spj[2]); + csz = (spi[0]*spj[1] - spi[1]*spj[0]); + + cdmx = (dmiy*csz - dmiz*csy); + cdmy = (dmiz*csx - dmix*csz); + cdmz = (dmix*csy - dmiy*csz); + + fi[0] += irij*cdmx; + fi[1] += irij*cdmy; + fi[2] += irij*cdmz; +} + +/* ---------------------------------------------------------------------- + allocate all arrays +------------------------------------------------------------------------- */ + +void PairSpinDmi::allocate() +{ + allocated = 1; + int n = atom->ntypes; + + memory->create(setflag,n+1,n+1,"pair:setflag"); + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + setflag[i][j] = 0; + + memory->create(cut_spin_dmi,n+1,n+1,"pair:cut_spin_dmi"); + memory->create(DM,n+1,n+1,"pair:DM"); + memory->create(v_dmx,n+1,n+1,"pair:DM_vector_x"); + memory->create(v_dmy,n+1,n+1,"pair:DM_vector_y"); + memory->create(v_dmz,n+1,n+1,"pair:DM_vector_z"); + memory->create(vmech_dmx,n+1,n+1,"pair:DMmech_vector_x"); + memory->create(vmech_dmy,n+1,n+1,"pair:DMmech_vector_y"); + memory->create(vmech_dmz,n+1,n+1,"pair:DMmech_vector_z"); + + memory->create(cutsq,n+1,n+1,"pair:cutsq"); + +} + + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairSpinDmi::write_restart(FILE *fp) +{ + write_restart_settings(fp); + + int i,j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) { + fwrite(&setflag[i][j],sizeof(int),1,fp); + if (setflag[i][j]) { + fwrite(&DM[i][j],sizeof(double),1,fp); + fwrite(&v_dmx[i][j],sizeof(double),1,fp); + fwrite(&v_dmy[i][j],sizeof(double),1,fp); + fwrite(&v_dmz[i][j],sizeof(double),1,fp); + fwrite(&vmech_dmx[i][j],sizeof(double),1,fp); + fwrite(&vmech_dmy[i][j],sizeof(double),1,fp); + fwrite(&vmech_dmz[i][j],sizeof(double),1,fp); + fwrite(&cut_spin_dmi[i][j],sizeof(double),1,fp); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairSpinDmi::read_restart(FILE *fp) +{ + read_restart_settings(fp); + + allocate(); + + int i,j; + int me = comm->me; + for (i = 1; i <= atom->ntypes; i++) { + for (j = i; j <= atom->ntypes; j++) { + if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); + if (setflag[i][j]) { + if (me == 0) { + fread(&DM[i][j],sizeof(double),1,fp); + fread(&v_dmx[i][j],sizeof(double),1,fp); + fread(&v_dmy[i][j],sizeof(double),1,fp); + fread(&v_dmz[i][j],sizeof(double),1,fp); + fread(&vmech_dmx[i][j],sizeof(double),1,fp); + fread(&vmech_dmy[i][j],sizeof(double),1,fp); + fread(&vmech_dmz[i][j],sizeof(double),1,fp); + fread(&cut_spin_dmi[i][j],sizeof(double),1,fp); + } + MPI_Bcast(&DM[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&v_dmx[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&v_dmy[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&v_dmz[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&vmech_dmx[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&vmech_dmy[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&vmech_dmz[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut_spin_dmi[i][j],1,MPI_DOUBLE,0,world); + } + } + } +} + + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairSpinDmi::write_restart_settings(FILE *fp) +{ + fwrite(&cut_spin_dmi_global,sizeof(double),1,fp); + fwrite(&offset_flag,sizeof(int),1,fp); + fwrite(&mix_flag,sizeof(int),1,fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairSpinDmi::read_restart_settings(FILE *fp) +{ + if (comm->me == 0) { + fread(&cut_spin_dmi_global,sizeof(double),1,fp); + fread(&offset_flag,sizeof(int),1,fp); + fread(&mix_flag,sizeof(int),1,fp); + } + MPI_Bcast(&cut_spin_dmi_global,1,MPI_DOUBLE,0,world); + MPI_Bcast(&offset_flag,1,MPI_INT,0,world); + MPI_Bcast(&mix_flag,1,MPI_INT,0,world); +} diff --git a/src/SPIN/pair_spin_dmi.h b/src/SPIN/pair_spin_dmi.h new file mode 100644 index 0000000000..68e42e879d --- /dev/null +++ b/src/SPIN/pair_spin_dmi.h @@ -0,0 +1,85 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS + +PairStyle(spin/dmi,PairSpinDmi) + +#else + +#ifndef LMP_PAIR_SPIN_DMI_H +#define LMP_PAIR_SPIN_DMI_H + +#include "pair_spin.h" + +namespace LAMMPS_NS { + +class PairSpinDmi : public PairSpin { + public: + PairSpinDmi(class LAMMPS *); + virtual ~PairSpinDmi(); + void settings(int, char **); + void coeff(int, char **); + void init_style(); + double init_one(int, int); + void *extract(const char *, int &); + + void compute(int, int); + void compute_single_pair(int, double *); + + void compute_dmi(int, int, double *, double *, double *); + void compute_dmi_mech(int, int, double, double *, double *, double *, double *); + + void write_restart(FILE *); + void read_restart(FILE *); + void write_restart_settings(FILE *); + void read_restart_settings(FILE *); + + double cut_spin_dmi_global; // short range pair cutoff + + protected: + double **DM; // dmi coeff in eV + double **v_dmx, **v_dmy, **v_dmz; // dmi direction + double **vmech_dmx, **vmech_dmy, **vmech_dmz; // dmi mech direction + double **cut_spin_dmi; // cutoff distance dmi + + int lattice_flag; // flag for mech force computation + class FixNVESpin *lockfixnvespin; // ptr to FixNVESpin for setups + + void allocate(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Incorrect args in pair_spin command + +Self-explanatory. + +E: Spin simulations require metal unit style + +Self-explanatory. + +E: Incorrect args for pair coefficients + +Self-explanatory. Check the input script or data file. + +E: Pair spin requires atom attribute spin + +The atom style defined does not have these attributes. + +*/ diff --git a/src/SPIN/pair_spin_exchange.cpp b/src/SPIN/pair_spin_exchange.cpp new file mode 100644 index 0000000000..cc074bb97d --- /dev/null +++ b/src/SPIN/pair_spin_exchange.cpp @@ -0,0 +1,530 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ------------------------------------------------------------------------ + Contributing authors: Julien Tranchida (SNL) + Aidan Thompson (SNL) + + Please cite the related publication: + Tranchida, J., Plimpton, S. J., Thibaudeau, P., & Thompson, A. P. (2018). + Massively parallel symplectic algorithm for coupled magnetic spin dynamics + and molecular dynamics. Journal of Computational Physics. +------------------------------------------------------------------------- */ + +#include +#include +#include + +#include "atom.h" +#include "comm.h" +#include "error.h" +#include "fix.h" +#include "fix_nve_spin.h" +#include "force.h" +#include "pair_hybrid.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "math_const.h" +#include "memory.h" +#include "modify.h" +#include "pair_spin_exchange.h" +#include "update.h" + +using namespace LAMMPS_NS; +using namespace MathConst; + +/* ---------------------------------------------------------------------- */ + +PairSpinExchange::PairSpinExchange(LAMMPS *lmp) : PairSpin(lmp), +lockfixnvespin(NULL) +{ + single_enable = 0; + no_virial_fdotr_compute = 1; + lattice_flag = 0; +} + +/* ---------------------------------------------------------------------- */ + +PairSpinExchange::~PairSpinExchange() +{ + if (allocated) { + memory->destroy(setflag); + memory->destroy(cut_spin_exchange); + memory->destroy(J1_mag); + memory->destroy(J1_mech); + memory->destroy(J2); + memory->destroy(J3); + memory->destroy(cutsq); // to be implemented + } +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairSpinExchange::settings(int narg, char **arg) +{ + if (narg < 1 || narg > 2) + error->all(FLERR,"Incorrect number of args in pair_style pair/spin command"); + + if (strcmp(update->unit_style,"metal") != 0) + error->all(FLERR,"Spin simulations require metal unit style"); + + cut_spin_exchange_global = force->numeric(FLERR,arg[0]); + + // reset cutoffs that have been explicitly set + + if (allocated) { + int i,j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i+1; j <= atom->ntypes; j++) + if (setflag[i][j]) { + cut_spin_exchange[i][j] = cut_spin_exchange_global; + } + } + +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type spin pairs (only one for now) +------------------------------------------------------------------------- */ + +void PairSpinExchange::coeff(int narg, char **arg) +{ + if (!allocated) allocate(); + + // check if args correct + + if (strcmp(arg[2],"exchange") != 0) + error->all(FLERR,"Incorrect args in pair_style command"); + if (narg != 7) + error->all(FLERR,"Incorrect args in pair_style command"); + + int ilo,ihi,jlo,jhi; + force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi); + force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi); + + // get exchange arguments from input command + + const double rc = force->numeric(FLERR,arg[3]); + const double j1 = force->numeric(FLERR,arg[4]); + const double j2 = force->numeric(FLERR,arg[5]); + const double j3 = force->numeric(FLERR,arg[6]); + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + for (int j = MAX(jlo,i); j <= jhi; j++) { + cut_spin_exchange[i][j] = rc; + J1_mag[i][j] = j1/hbar; + J1_mech[i][j] = j1; + J2[i][j] = j2; + J3[i][j] = j3; + setflag[i][j] = 1; + count++; + } + } + + if (count == 0) error->all(FLERR,"Incorrect args in pair_style command"); +} + +/* ---------------------------------------------------------------------- + init specific to this pair style +------------------------------------------------------------------------- */ + +void PairSpinExchange::init_style() +{ + if (!atom->sp_flag) + error->all(FLERR,"Pair spin requires atom/spin style"); + + // need a full neighbor list + + int irequest = neighbor->request(this,instance_me); + neighbor->requests[irequest]->half = 0; + neighbor->requests[irequest]->full = 1; + + // checking if nve/spin is a listed fix + + int ifix = 0; + while (ifix < modify->nfix) { + if (strcmp(modify->fix[ifix]->style,"nve/spin") == 0) break; + ifix++; + } + if (ifix == modify->nfix) + error->all(FLERR,"pair/spin style requires nve/spin"); + + // get the lattice_flag from nve/spin + + for (int i = 0; i < modify->nfix; i++) { + if (strcmp(modify->fix[i]->style,"nve/spin") == 0) { + lockfixnvespin = (FixNVESpin *) modify->fix[i]; + lattice_flag = lockfixnvespin->lattice_flag; + } + } + +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairSpinExchange::init_one(int i, int j) +{ + + if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); + + J1_mag[j][i] = J1_mag[i][j]; + J1_mech[j][i] = J1_mech[i][j]; + J2[j][i] = J2[i][j]; + J3[j][i] = J3[i][j]; + cut_spin_exchange[j][i] = cut_spin_exchange[i][j]; + + return cut_spin_exchange_global; +} + +/* ---------------------------------------------------------------------- + extract the larger cutoff +------------------------------------------------------------------------- */ + +void *PairSpinExchange::extract(const char *str, int &dim) +{ + dim = 0; + if (strcmp(str,"cut") == 0) return (void *) &cut_spin_exchange_global; + return NULL; +} + +/* ---------------------------------------------------------------------- */ + +void PairSpinExchange::compute(int eflag, int vflag) +{ + int i,j,ii,jj,inum,jnum,itype,jtype; + double evdwl, ecoul; + double xi[3], eij[3]; + double delx,dely,delz; + double spi[3], spj[3]; + double fi[3], fmi[3]; + double local_cut2; + double rsq, inorm; + int *ilist,*jlist,*numneigh,**firstneigh; + + evdwl = ecoul = 0.0; + if (eflag || vflag) ev_setup(eflag,vflag); + else evflag = vflag_fdotr = 0; + + double **x = atom->x; + double **f = atom->f; + double **fm = atom->fm; + double **sp = atom->sp; + int *type = atom->type; + int nlocal = atom->nlocal; + int newton_pair = force->newton_pair; + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // computation of the exchange interaction + // loop over atoms and their neighbors + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + itype = type[i]; + + jlist = firstneigh[i]; + jnum = numneigh[i]; + xi[0] = x[i][0]; + xi[1] = x[i][1]; + xi[2] = x[i][2]; + spi[0] = sp[i][0]; + spi[1] = sp[i][1]; + spi[2] = sp[i][2]; + + // loop on neighbors + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + j &= NEIGHMASK; + jtype = type[j]; + + spj[0] = sp[j][0]; + spj[1] = sp[j][1]; + spj[2] = sp[j][2]; + + evdwl = 0.0; + fi[0] = fi[1] = fi[2] = 0.0; + fmi[0] = fmi[1] = fmi[2] = 0.0; + + delx = xi[0] - x[j][0]; + dely = xi[1] - x[j][1]; + delz = xi[2] - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + inorm = 1.0/sqrt(rsq); + eij[0] = -inorm*delx; + eij[1] = -inorm*dely; + eij[2] = -inorm*delz; + + local_cut2 = cut_spin_exchange[itype][jtype]*cut_spin_exchange[itype][jtype]; + + // compute exchange interaction + + if (rsq <= local_cut2) { + compute_exchange(i,j,rsq,fmi,spj); + if (lattice_flag) { + compute_exchange_mech(i,j,rsq,eij,fi,spi,spj); + } + } + + f[i][0] += fi[0]; + f[i][1] += fi[1]; + f[i][2] += fi[2]; + fm[i][0] += fmi[0]; + fm[i][1] += fmi[1]; + fm[i][2] += fmi[2]; + + if (newton_pair || j < nlocal) { + f[j][0] -= fi[0]; + f[j][1] -= fi[1]; + f[j][2] -= fi[2]; + } + + if (eflag) { + evdwl -= (spi[0]*fmi[0] + spi[1]*fmi[1] + spi[2]*fmi[2]); + evdwl *= hbar; + } else evdwl = 0.0; + + if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair, + evdwl,ecoul,fi[0],fi[1],fi[2],delx,dely,delz); + } + } + + if (vflag_fdotr) virial_fdotr_compute(); + +} + +/* ---------------------------------------------------------------------- + update the pair interactions fmi acting on the spin ii +------------------------------------------------------------------------- */ + +void PairSpinExchange::compute_single_pair(int ii, double fmi[3]) +{ + + int *type = atom->type; + double **x = atom->x; + double **sp = atom->sp; + double local_cut2; + double xi[3], rij[3]; + double delx,dely,delz; + double spj[3]; + + int i,j,jnum,itype,jtype; + int *ilist,*jlist,*numneigh,**firstneigh; + + double rsq; + + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + i = ilist[ii]; + itype = type[i]; + + xi[0] = x[i][0]; + xi[1] = x[i][1]; + xi[2] = x[i][2]; + + jlist = firstneigh[i]; + jnum = numneigh[i]; + + for (int jj = 0; jj < jnum; jj++) { + + j = jlist[jj]; + j &= NEIGHMASK; + jtype = type[j]; + local_cut2 = cut_spin_exchange[itype][jtype]*cut_spin_exchange[itype][jtype]; + + spj[0] = sp[j][0]; + spj[1] = sp[j][1]; + spj[2] = sp[j][2]; + + delx = xi[0] - x[j][0]; + dely = xi[1] - x[j][1]; + delz = xi[2] - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + if (rsq <= local_cut2) { + compute_exchange(i,j,rsq,fmi,spj); + } + } + +} + +/* ---------------------------------------------------------------------- + compute exchange interaction between spins i and j +------------------------------------------------------------------------- */ + +void PairSpinExchange::compute_exchange(int i, int j, double rsq, double fmi[3], double spj[3]) +{ + int *type = atom->type; + int itype, jtype; + double Jex, ra; + itype = type[i]; + jtype = type[j]; + + ra = rsq/J3[itype][jtype]/J3[itype][jtype]; + Jex = 4.0*J1_mag[itype][jtype]*ra; + Jex *= (1.0-J2[itype][jtype]*ra); + Jex *= exp(-ra); + + fmi[0] += Jex*spj[0]; + fmi[1] += Jex*spj[1]; + fmi[2] += Jex*spj[2]; +} + +/* ---------------------------------------------------------------------- + compute the mechanical force due to the exchange interaction between atom i and atom j +------------------------------------------------------------------------- */ + +void PairSpinExchange::compute_exchange_mech(int i, int j, double rsq, double eij[3], + double fi[3], double spi[3], double spj[3]) +{ + int *type = atom->type; + int itype, jtype; + double Jex, Jex_mech, ra, rr, iJ3; + itype = type[i]; + jtype = type[j]; + + Jex = J1_mech[itype][jtype]; + iJ3 = 1.0/(J3[itype][jtype]*J3[itype][jtype]); + + ra = rsq*iJ3; + rr = sqrt(rsq)*iJ3; + + Jex_mech = 1.0-ra-J2[itype][jtype]*ra*(2.0-ra); + Jex_mech *= 8.0*Jex*rr*exp(-ra); + Jex_mech *= (spi[0]*spj[0]+spi[1]*spj[1]+spi[2]*spj[2]); + + fi[0] -= Jex_mech*eij[0]; + fi[1] -= Jex_mech*eij[1]; + fi[2] -= Jex_mech*eij[2]; +} + +/* ---------------------------------------------------------------------- + allocate all arrays +------------------------------------------------------------------------- */ + +void PairSpinExchange::allocate() +{ + allocated = 1; + int n = atom->ntypes; + + memory->create(setflag,n+1,n+1,"pair:setflag"); + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + setflag[i][j] = 0; + + memory->create(cut_spin_exchange,n+1,n+1,"pair/spin/exchange:cut_spin_exchange"); + memory->create(J1_mag,n+1,n+1,"pair/spin/exchange:J1_mag"); + memory->create(J1_mech,n+1,n+1,"pair/spin/exchange:J1_mech"); + memory->create(J2,n+1,n+1,"pair/spin/exchange:J2"); + memory->create(J3,n+1,n+1,"pair/spin/exchange:J3"); + memory->create(cutsq,n+1,n+1,"pair:cutsq"); +} + + + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairSpinExchange::write_restart(FILE *fp) +{ + write_restart_settings(fp); + + int i,j; + for (i = 1; i <= atom->ntypes; i++) { + for (j = i; j <= atom->ntypes; j++) { + fwrite(&setflag[i][j],sizeof(int),1,fp); + if (setflag[i][j]) { + fwrite(&J1_mag[i][j],sizeof(double),1,fp); + fwrite(&J1_mech[i][j],sizeof(double),1,fp); + fwrite(&J2[i][j],sizeof(double),1,fp); + fwrite(&J3[i][j],sizeof(double),1,fp); + fwrite(&cut_spin_exchange[i][j],sizeof(double),1,fp); + } + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairSpinExchange::read_restart(FILE *fp) +{ + read_restart_settings(fp); + + allocate(); + + int i,j; + int me = comm->me; + for (i = 1; i <= atom->ntypes; i++) { + for (j = i; j <= atom->ntypes; j++) { + if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); + if (setflag[i][j]) { + if (me == 0) { + fread(&J1_mag[i][j],sizeof(double),1,fp); + fread(&J1_mech[i][j],sizeof(double),1,fp); + fread(&J2[i][j],sizeof(double),1,fp); + fread(&J2[i][j],sizeof(double),1,fp); + fread(&cut_spin_exchange[i][j],sizeof(double),1,fp); + } + MPI_Bcast(&J1_mag[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&J1_mech[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&J2[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&J3[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut_spin_exchange[i][j],1,MPI_DOUBLE,0,world); + } + } + } +} + + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairSpinExchange::write_restart_settings(FILE *fp) +{ + fwrite(&cut_spin_exchange_global,sizeof(double),1,fp); + fwrite(&offset_flag,sizeof(int),1,fp); + fwrite(&mix_flag,sizeof(int),1,fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairSpinExchange::read_restart_settings(FILE *fp) +{ + if (comm->me == 0) { + fread(&cut_spin_exchange_global,sizeof(double),1,fp); + fread(&offset_flag,sizeof(int),1,fp); + fread(&mix_flag,sizeof(int),1,fp); + } + MPI_Bcast(&cut_spin_exchange_global,1,MPI_DOUBLE,0,world); + MPI_Bcast(&offset_flag,1,MPI_INT,0,world); + MPI_Bcast(&mix_flag,1,MPI_INT,0,world); +} + diff --git a/src/SPIN/pair_spin_exchange.h b/src/SPIN/pair_spin_exchange.h new file mode 100644 index 0000000000..b524a513eb --- /dev/null +++ b/src/SPIN/pair_spin_exchange.h @@ -0,0 +1,85 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS + +PairStyle(spin/exchange,PairSpinExchange) + +#else + +#ifndef LMP_PAIR_SPIN_EXCHANGE_H +#define LMP_PAIR_SPIN_EXCHANGE_H + +#include "pair_spin.h" + +namespace LAMMPS_NS { + +class PairSpinExchange : public PairSpin { + public: + PairSpinExchange(class LAMMPS *); + virtual ~PairSpinExchange(); + void settings(int, char **); + void coeff(int, char **); + void init_style(); + double init_one(int, int); + void *extract(const char *, int &); + + void compute(int, int); + void compute_single_pair(int, double *); + + void compute_exchange(int, int, double, double *, double *); + void compute_exchange_mech(int, int, double, double *, double *, double *, double *); + + void write_restart(FILE *); + void read_restart(FILE *); + void write_restart_settings(FILE *); + void read_restart_settings(FILE *); + + double cut_spin_exchange_global; // global exchange cutoff distance + + protected: + double **J1_mag; // exchange coeffs in eV + double **J1_mech; // mech exchange coeffs in + double **J2, **J3; // J1 in eV, J2 adim, J3 in Ang + double **cut_spin_exchange; // cutoff distance exchange + + int lattice_flag; // flag for mech force computation + class FixNVESpin *lockfixnvespin; // ptr to FixNVESpin for setups + + void allocate(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Incorrect args in pair_spin command + +Self-explanatory. + +E: Spin simulations require metal unit style + +Self-explanatory. + +E: Incorrect args for pair coefficients + +Self-explanatory. Check the input script or data file. + +E: Pair spin requires atom attribute spin + +The atom style defined does not have these attributes. + +*/ diff --git a/src/SPIN/pair_spin_magelec.cpp b/src/SPIN/pair_spin_magelec.cpp new file mode 100644 index 0000000000..570c995754 --- /dev/null +++ b/src/SPIN/pair_spin_magelec.cpp @@ -0,0 +1,543 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ------------------------------------------------------------------------ + Contributing authors: Julien Tranchida (SNL) + Aidan Thompson (SNL) + + Please cite the related publication: + Tranchida, J., Plimpton, S. J., Thibaudeau, P., & Thompson, A. P. (2018). + Massively parallel symplectic algorithm for coupled magnetic spin dynamics + and molecular dynamics. Journal of Computational Physics. +------------------------------------------------------------------------- */ + +#include +#include +#include + +#include "atom.h" +#include "comm.h" +#include "error.h" +#include "fix.h" +#include "fix_nve_spin.h" +#include "force.h" +#include "pair_hybrid.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "math_const.h" +#include "memory.h" +#include "modify.h" +#include "pair_spin_magelec.h" +#include "update.h" + +using namespace LAMMPS_NS; +using namespace MathConst; + +/* ---------------------------------------------------------------------- */ + +PairSpinMagelec::PairSpinMagelec(LAMMPS *lmp) : PairSpin(lmp), +lockfixnvespin(NULL) +{ + single_enable = 0; + no_virial_fdotr_compute = 1; + lattice_flag = 0; +} + +/* ---------------------------------------------------------------------- */ + +PairSpinMagelec::~PairSpinMagelec() +{ + if (allocated) { + memory->destroy(setflag); + memory->destroy(cut_spin_magelec); + memory->destroy(ME); + memory->destroy(ME_mech); + memory->destroy(v_mex); + memory->destroy(v_mey); + memory->destroy(v_mez); + memory->destroy(cutsq); // to be deteled + } +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairSpinMagelec::settings(int narg, char **arg) +{ + if (narg < 1 || narg > 2) + error->all(FLERR,"Incorrect number of args in pair_style pair/spin command"); + + if (strcmp(update->unit_style,"metal") != 0) + error->all(FLERR,"Spin simulations require metal unit style"); + + cut_spin_magelec_global = force->numeric(FLERR,arg[0]); + + // reset cutoffs that have been explicitly set + + if (allocated) { + int i,j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i+1; j <= atom->ntypes; j++) + if (setflag[i][j]) { + cut_spin_magelec[i][j] = cut_spin_magelec_global; + } + } + +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type spin pairs (only one for now) +------------------------------------------------------------------------- */ + +void PairSpinMagelec::coeff(int narg, char **arg) +{ + if (!allocated) allocate(); + + // check if args correct + + if (strcmp(arg[2],"magelec") != 0) + error->all(FLERR,"Incorrect args in pair_style command"); + if (narg != 8) + error->all(FLERR,"Incorrect args in pair_style command"); + + int ilo,ihi,jlo,jhi; + force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi); + force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi); + + const double rij = force->numeric(FLERR,arg[3]); + const double magelec = (force->numeric(FLERR,arg[4])); + double mex = force->numeric(FLERR,arg[5]); + double mey = force->numeric(FLERR,arg[6]); + double mez = force->numeric(FLERR,arg[7]); + + double inorm = 1.0/(mex*mex+mey*mey+mez*mez); + mex *= inorm; + mey *= inorm; + mez *= inorm; + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + for (int j = MAX(jlo,i); j <= jhi; j++) { + cut_spin_magelec[i][j] = rij; + ME[i][j] = magelec/hbar; + ME_mech[i][j] = magelec; + v_mex[i][j] = mex; + v_mey[i][j] = mey; + v_mez[i][j] = mez; + setflag[i][j] = 1; + count++; + } + } + if (count == 0) + error->all(FLERR,"Incorrect args in pair_style command"); + +} + +/* ---------------------------------------------------------------------- + init specific to this pair style +------------------------------------------------------------------------- */ + +void PairSpinMagelec::init_style() +{ + if (!atom->sp_flag) + error->all(FLERR,"Pair spin requires atom/spin style"); + + // need a full neighbor list + + int irequest = neighbor->request(this,instance_me); + neighbor->requests[irequest]->half = 0; + neighbor->requests[irequest]->full = 1; + + // checking if nve/spin is a listed fix + + int ifix = 0; + while (ifix < modify->nfix) { + if (strcmp(modify->fix[ifix]->style,"nve/spin") == 0) break; + ifix++; + } + if (ifix == modify->nfix) + error->all(FLERR,"pair/spin style requires nve/spin"); + + // get the lattice_flag from nve/spin + + for (int i = 0; i < modify->nfix; i++) { + if (strcmp(modify->fix[i]->style,"nve/spin") == 0) { + lockfixnvespin = (FixNVESpin *) modify->fix[i]; + lattice_flag = lockfixnvespin->lattice_flag; + } + } + +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairSpinMagelec::init_one(int i, int j) +{ + if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); + + ME[j][i] = ME[i][j]; + ME_mech[j][i] = ME_mech[i][j]; + v_mex[j][i] = v_mex[i][j]; + v_mey[j][i] = v_mey[i][j]; + v_mez[j][i] = v_mez[i][j]; + cut_spin_magelec[j][i] = cut_spin_magelec[i][j]; + + return cut_spin_magelec_global; +} + +/* ---------------------------------------------------------------------- + extract the larger cutoff +------------------------------------------------------------------------- */ + +void *PairSpinMagelec::extract(const char *str, int &dim) +{ + dim = 0; + if (strcmp(str,"cut") == 0) return (void *) &cut_spin_magelec_global; + return NULL; +} + + +/* ---------------------------------------------------------------------- */ + +void PairSpinMagelec::compute(int eflag, int vflag) +{ + int i,j,ii,jj,inum,jnum,itype,jtype; + double evdwl, ecoul; + double xi[3], eij[3]; + double delx,dely,delz; + double spi[3], spj[3]; + double fi[3], fmi[3]; + double local_cut2; + double rsq, inorm; + int *ilist,*jlist,*numneigh,**firstneigh; + + evdwl = ecoul = 0.0; + if (eflag || vflag) ev_setup(eflag,vflag); + else evflag = vflag_fdotr = 0; + + double **x = atom->x; + double **f = atom->f; + double **fm = atom->fm; + double **sp = atom->sp; + int *type = atom->type; + int nlocal = atom->nlocal; + int newton_pair = force->newton_pair; + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // magneto-electric computation + // loop over atoms and their neighbors + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + itype = type[i]; + + jlist = firstneigh[i]; + jnum = numneigh[i]; + xi[0] = x[i][0]; + xi[1] = x[i][1]; + xi[2] = x[i][2]; + spi[0] = sp[i][0]; + spi[1] = sp[i][1]; + spi[2] = sp[i][2]; + + // loop on neighbors + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + j &= NEIGHMASK; + jtype = type[j]; + + spj[0] = sp[j][0]; + spj[1] = sp[j][1]; + spj[2] = sp[j][2]; + + evdwl = 0.0; + fi[0] = fi[1] = fi[2] = 0.0; + fmi[0] = fmi[1] = fmi[2] = 0.0; + + delx = xi[0] - x[j][0]; + dely = xi[1] - x[j][1]; + delz = xi[2] - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + inorm = 1.0/sqrt(rsq); + eij[0] = -inorm*delx; + eij[1] = -inorm*dely; + eij[2] = -inorm*delz; + + local_cut2 = cut_spin_magelec[itype][jtype]*cut_spin_magelec[itype][jtype]; + + // compute me interaction + + if (rsq <= local_cut2) { + compute_magelec(i,j,rsq,eij,fmi,spj); + if (lattice_flag) { + compute_magelec_mech(i,j,fi,spi,spj); + } + } + + f[i][0] += fi[0]; + f[i][1] += fi[1]; + f[i][2] += fi[2]; + fm[i][0] += fmi[0]; + fm[i][1] += fmi[1]; + fm[i][2] += fmi[2]; + + if (newton_pair || j < nlocal) { + f[j][0] -= fi[0]; + f[j][1] -= fi[1]; + f[j][2] -= fi[2]; + } + + if (eflag) { + evdwl -= (spi[0]*fmi[0] + spi[1]*fmi[1] + spi[2]*fmi[2]); + evdwl *= hbar; + } else evdwl = 0.0; + + if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair, + evdwl,ecoul,fi[0],fi[1],fi[2],delx,dely,delz); + } + } + + if (vflag_fdotr) virial_fdotr_compute(); + +} + +/* ---------------------------------------------------------------------- */ + +void PairSpinMagelec::compute_single_pair(int ii, double fmi[3]) +{ + int *type = atom->type; + double **x = atom->x; + double **sp = atom->sp; + double local_cut2; + double xi[3], eij[3]; + double delx,dely,delz; + double spj[3]; + + int i,j,jnum,itype,jtype; + int *ilist,*jlist,*numneigh,**firstneigh; + + double rsq, inorm; + + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + i = ilist[ii]; + itype = type[i]; + + xi[0] = x[i][0]; + xi[1] = x[i][1]; + xi[2] = x[i][2]; + + jlist = firstneigh[i]; + jnum = numneigh[i]; + + for (int jj = 0; jj < jnum; jj++) { + + j = jlist[jj]; + j &= NEIGHMASK; + jtype = type[j]; + local_cut2 = cut_spin_magelec[itype][jtype]*cut_spin_magelec[itype][jtype]; + + spj[0] = sp[j][0]; + spj[1] = sp[j][1]; + spj[2] = sp[j][2]; + + delx = xi[0] - x[j][0]; + dely = xi[1] - x[j][1]; + delz = xi[2] - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + inorm = 1.0/sqrt(rsq); + eij[0] = -inorm*delx; + eij[1] = -inorm*dely; + eij[2] = -inorm*delz; + + if (rsq <= local_cut2) { + compute_magelec(i,j,rsq,eij,fmi,spj); + } + } + +} + +/* ---------------------------------------------------------------------- */ + +void PairSpinMagelec::compute_magelec(int i, int j, double /*rsq*/, double eij[3], double fmi[3], double spj[3]) +{ + int *type = atom->type; + int itype, jtype; + double meix,meiy,meiz; + double vx,vy,vz; + itype = type[i]; + jtype = type[j]; + + vx = v_mex[itype][jtype]; + vy = v_mey[itype][jtype]; + vz = v_mez[itype][jtype]; + + meix = vy*eij[2] - vz*eij[1]; + meiy = vz*eij[0] - vx*eij[2]; + meiz = vx*eij[1] - vy*eij[0]; + + meix *= ME[itype][jtype]; + meiy *= ME[itype][jtype]; + meiz *= ME[itype][jtype]; + + fmi[0] += spj[1]*meiz - spj[2]*meiy; + fmi[1] += spj[2]*meix - spj[0]*meiz; + fmi[2] += spj[0]*meiy - spj[1]*meix; +} + +/* ---------------------------------------------------------------------- */ + +void PairSpinMagelec::compute_magelec_mech(int i, int j, double fi[3], double spi[3], double spj[3]) +{ + int *type = atom->type; + int itype, jtype; + itype = type[i]; + jtype = type[j]; + + double meix,meiy,meiz; + double vx, vy, vz; + + vx = v_mex[itype][jtype]; + vy = v_mey[itype][jtype]; + vz = v_mez[itype][jtype]; + + meix = spi[1]*spi[2] - spi[2]*spj[1]; + meiy = spi[2]*spi[0] - spi[0]*spj[2]; + meiz = spi[0]*spi[1] - spi[1]*spj[0]; + + meix *= ME_mech[itype][jtype]; + meiy *= ME_mech[itype][jtype]; + meiz *= ME_mech[itype][jtype]; + + fi[0] += meiy*vz - meiz*vy; + fi[1] += meiz*vx - meix*vz; + fi[2] += meix*vy - meiy*vx; + +} + +/* ---------------------------------------------------------------------- + allocate all arrays +------------------------------------------------------------------------- */ + +void PairSpinMagelec::allocate() +{ + allocated = 1; + int n = atom->ntypes; + + memory->create(setflag,n+1,n+1,"pair:setflag"); + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + setflag[i][j] = 0; + + memory->create(cut_spin_magelec,n+1,n+1,"pair/spin/me:cut_spin_magelec"); + memory->create(ME,n+1,n+1,"pair/spin/me:ME"); + memory->create(ME_mech,n+1,n+1,"pair/spin/me:ME_mech"); + memory->create(v_mex,n+1,n+1,"pair/spin/me:ME_vector_x"); + memory->create(v_mey,n+1,n+1,"pair/spin/me:ME_vector_y"); + memory->create(v_mez,n+1,n+1,"pair/spin/me:ME_vector_z"); + memory->create(cutsq,n+1,n+1,"pair:cutsq"); +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairSpinMagelec::write_restart(FILE *fp) +{ + write_restart_settings(fp); + + int i,j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) { + fwrite(&setflag[i][j],sizeof(int),1,fp); + if (setflag[i][j]) { + fwrite(&ME[i][j],sizeof(double),1,fp); + fwrite(&v_mex[i][j],sizeof(double),1,fp); + fwrite(&v_mey[i][j],sizeof(double),1,fp); + fwrite(&v_mez[i][j],sizeof(double),1,fp); + fwrite(&cut_spin_magelec[i][j],sizeof(double),1,fp); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairSpinMagelec::read_restart(FILE *fp) +{ + read_restart_settings(fp); + + allocate(); + + int i,j; + int me = comm->me; + for (i = 1; i <= atom->ntypes; i++) { + for (j = i; j <= atom->ntypes; j++) { + if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); + if (setflag[i][j]) { + if (me == 0) { + fread(&ME[i][j],sizeof(double),1,fp); + fread(&v_mex[i][j],sizeof(double),1,fp); + fread(&v_mey[i][j],sizeof(double),1,fp); + fread(&v_mez[i][j],sizeof(double),1,fp); + fread(&cut_spin_magelec[i][j],sizeof(double),1,fp); + } + MPI_Bcast(&ME[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&v_mex[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&v_mey[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&v_mez[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut_spin_magelec[i][j],1,MPI_DOUBLE,0,world); + } + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairSpinMagelec::write_restart_settings(FILE *fp) +{ + fwrite(&cut_spin_magelec_global,sizeof(double),1,fp); + fwrite(&offset_flag,sizeof(int),1,fp); + fwrite(&mix_flag,sizeof(int),1,fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairSpinMagelec::read_restart_settings(FILE *fp) +{ + if (comm->me == 0) { + fread(&cut_spin_magelec_global,sizeof(double),1,fp); + fread(&offset_flag,sizeof(int),1,fp); + fread(&mix_flag,sizeof(int),1,fp); + } + MPI_Bcast(&cut_spin_magelec_global,1,MPI_DOUBLE,0,world); + MPI_Bcast(&offset_flag,1,MPI_INT,0,world); + MPI_Bcast(&mix_flag,1,MPI_INT,0,world); +} diff --git a/src/SPIN/pair_spin_magelec.h b/src/SPIN/pair_spin_magelec.h new file mode 100644 index 0000000000..ce13476271 --- /dev/null +++ b/src/SPIN/pair_spin_magelec.h @@ -0,0 +1,84 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS + +PairStyle(spin/magelec,PairSpinMagelec) + +#else + +#ifndef LMP_PAIR_SPIN_MAGELEC_H +#define LMP_PAIR_SPIN_MAGELEC_H + +#include "pair_spin.h" + +namespace LAMMPS_NS { + +class PairSpinMagelec : public PairSpin { + public: + PairSpinMagelec(class LAMMPS *); + virtual ~PairSpinMagelec(); + void settings(int, char **); + void coeff(int, char **); + void init_style(); + double init_one(int, int); + void *extract(const char *, int &); + + void compute(int, int); + void compute_single_pair(int, double *); + + void compute_magelec(int, int, double, double *, double *, double *); + void compute_magelec_mech(int, int, double *, double *, double *); + + void write_restart(FILE *); + void read_restart(FILE *); + void write_restart_settings(FILE *); + void read_restart_settings(FILE *); + + double cut_spin_magelec_global; // global me cutoff + + protected: + double **ME, **ME_mech; // magelec coeff in eV + double **v_mex, **v_mey, **v_mez; // magelec direction + double **cut_spin_magelec; // magelec cutoff distance + + int lattice_flag; // flag for mech force computation + class FixNVESpin *lockfixnvespin; // ptr to FixNVESpin for setups + + void allocate(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Incorrect args in pair_spin command + +Self-explanatory. + +E: Spin simulations require metal unit style + +Self-explanatory. + +E: Incorrect args for pair coefficients + +Self-explanatory. Check the input script or data file. + +E: Pair spin requires atom attribute spin + +The atom style defined does not have these attributes. + +*/ diff --git a/src/SPIN/pair_spin_neel.cpp b/src/SPIN/pair_spin_neel.cpp new file mode 100644 index 0000000000..55f537cf4f --- /dev/null +++ b/src/SPIN/pair_spin_neel.cpp @@ -0,0 +1,722 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ------------------------------------------------------------------------ + Contributing authors: Julien Tranchida (SNL) + Aidan Thompson (SNL) + + Please cite the related publication: + Tranchida, J., Plimpton, S. J., Thibaudeau, P., & Thompson, A. P. (2018). + Massively parallel symplectic algorithm for coupled magnetic spin dynamics + and molecular dynamics. Journal of Computational Physics. +------------------------------------------------------------------------- */ + +#include +#include +#include + +#include "atom.h" +#include "comm.h" +#include "error.h" +#include "force.h" +#include "fix.h" +#include "fix_nve_spin.h" +#include "force.h" +#include "pair_hybrid.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "math_const.h" +#include "memory.h" +#include "modify.h" +#include "pair_spin_neel.h" +#include "update.h" + +using namespace LAMMPS_NS; +using namespace MathConst; + +/* ---------------------------------------------------------------------- */ + +PairSpinNeel::PairSpinNeel(LAMMPS *lmp) : PairSpin(lmp), +lockfixnvespin(NULL) +{ + single_enable = 0; + no_virial_fdotr_compute = 1; + lattice_flag = 0; +} + +/* ---------------------------------------------------------------------- */ + +PairSpinNeel::~PairSpinNeel() +{ + if (allocated) { + memory->destroy(setflag); + memory->destroy(cut_spin_neel); + memory->destroy(g1); + memory->destroy(g1_mech); + memory->destroy(g2); + memory->destroy(g3); + memory->destroy(q1); + memory->destroy(q1_mech); + memory->destroy(q2); + memory->destroy(q3); + memory->destroy(cutsq); // to be deleted + } +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairSpinNeel::settings(int narg, char **arg) +{ + if (narg < 1 || narg > 2) + error->all(FLERR,"Incorrect number of args in pair_style pair/spin command"); + + if (strcmp(update->unit_style,"metal") != 0) + error->all(FLERR,"Spin simulations require metal unit style"); + + cut_spin_neel_global = force->numeric(FLERR,arg[0]); + + // reset cutoffs that have been explicitly set + + if (allocated) { + int i,j; + for (i = 1; i <= atom->ntypes; i++) { + for (j = i+1; j <= atom->ntypes; j++) { + if (setflag[i][j]) { + cut_spin_neel[i][j] = cut_spin_neel_global; + } + } + } + } + +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type spin pairs (only one for now) +------------------------------------------------------------------------- */ + +void PairSpinNeel::coeff(int narg, char **arg) +{ + if (!allocated) allocate(); + + // check if args correct + + if (strcmp(arg[2],"neel") != 0) + error->all(FLERR,"Incorrect args in pair_style command"); + if (narg != 10) + error->all(FLERR,"Incorrect args in pair_style command"); + + int ilo,ihi,jlo,jhi; + force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi); + force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi); + + const double rij = force->numeric(FLERR,arg[3]); + const double k1 = force->numeric(FLERR,arg[4]); + const double k2 = force->numeric(FLERR,arg[5]); + const double k3 = force->numeric(FLERR,arg[6]); + const double l1 = force->numeric(FLERR,arg[7]); + const double l2 = force->numeric(FLERR,arg[8]); + const double l3 = force->numeric(FLERR,arg[9]); + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + for (int j = MAX(jlo,i); j <= jhi; j++) { + cut_spin_neel[i][j] = rij; + g1[i][j] = k1/hbar; + q1[i][j] = l1/hbar; + g1_mech[i][j] = k1; + q1_mech[i][j] = l1; + g2[i][j] = k2; + g3[i][j] = k3; + q2[i][j] = l2; + q3[i][j] = l3; + setflag[i][j] = 1; + count++; + } + } + if (count == 0) + error->all(FLERR,"Incorrect args in pair_style command"); + +} + +/* ---------------------------------------------------------------------- + init specific to this pair style +------------------------------------------------------------------------- */ + +void PairSpinNeel::init_style() +{ + if (!atom->sp_flag) + error->all(FLERR,"Pair spin requires atom/spin style"); + + // need a full neighbor list + + int irequest = neighbor->request(this,instance_me); + neighbor->requests[irequest]->half = 0; + neighbor->requests[irequest]->full = 1; + + // checking if nve/spin is a listed fix + + int ifix = 0; + while (ifix < modify->nfix) { + if (strcmp(modify->fix[ifix]->style,"nve/spin") == 0) break; + ifix++; + } + if (ifix == modify->nfix) + error->all(FLERR,"pair/spin style requires nve/spin"); + + // get the lattice_flag from nve/spin + + for (int i = 0; i < modify->nfix; i++) { + if (strcmp(modify->fix[i]->style,"nve/spin") == 0) { + lockfixnvespin = (FixNVESpin *) modify->fix[i]; + lattice_flag = lockfixnvespin->lattice_flag; + } + } + +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairSpinNeel::init_one(int i, int j) +{ + if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); + + g1[j][i] = g1[i][j]; + g1_mech[j][i] = g1_mech[i][j]; + g2[j][i] = g2[i][j]; + g3[j][i] = g3[i][j]; + q1[j][i] = q1[i][j]; + q1_mech[j][i] = q1_mech[i][j]; + q2[j][i] = q2[i][j]; + q3[j][i] = q3[i][j]; + + return cut_spin_neel_global; +} + +/* ---------------------------------------------------------------------- + extract the larger cutoff +------------------------------------------------------------------------- */ + +void *PairSpinNeel::extract(const char *str, int &dim) +{ + dim = 0; + if (strcmp(str,"cut") == 0) return (void *) &cut_spin_neel_global; + return NULL; +} + +/* ---------------------------------------------------------------------- */ + +void PairSpinNeel::compute(int eflag, int vflag) +{ + int i,j,ii,jj,inum,jnum,itype,jtype; + double evdwl,ecoul; + double xi[3], rij[3], eij[3]; + double spi[3], spj[3]; + double fi[3], fmi[3]; + double local_cut2; + double rsq, inorm; + int *ilist,*jlist,*numneigh,**firstneigh; + + evdwl = ecoul = 0.0; + if (eflag || vflag) ev_setup(eflag,vflag); + else evflag = vflag_fdotr = 0; + + double **x = atom->x; + double **f = atom->f; + double **fm = atom->fm; + double **sp = atom->sp; + int *type = atom->type; + int nlocal = atom->nlocal; + int newton_pair = force->newton_pair; + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // computation of the neel interaction + // loop over atoms and their neighbors + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + itype = type[i]; + + jlist = firstneigh[i]; + jnum = numneigh[i]; + xi[0] = x[i][0]; + xi[1] = x[i][1]; + xi[2] = x[i][2]; + spi[0] = sp[i][0]; + spi[1] = sp[i][1]; + spi[2] = sp[i][2]; + + // loop on neighbors + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + j &= NEIGHMASK; + + spj[0] = sp[j][0]; + spj[1] = sp[j][1]; + spj[2] = sp[j][2]; + + evdwl = 0.0; + + fi[0] = fi[1] = fi[2] = 0.0; + fmi[0] = fmi[1] = fmi[2] = 0.0; + rij[0] = rij[1] = rij[2] = 0.0; + + rij[0] = x[j][0] - xi[0]; + rij[1] = x[j][1] - xi[1]; + rij[2] = x[j][2] - xi[2]; + rsq = rij[0]*rij[0] + rij[1]*rij[1] + rij[2]*rij[2]; + inorm = 1.0/sqrt(rsq); + eij[0] = rij[0]*inorm; + eij[1] = rij[1]*inorm; + eij[2] = rij[2]*inorm; + + itype = type[i]; + jtype = type[j]; + + local_cut2 = cut_spin_neel[itype][jtype]*cut_spin_neel[itype][jtype]; + + // compute neel interaction + + if (rsq <= local_cut2) { + compute_neel(i,j,rsq,eij,fmi,spi,spj); + if (lattice_flag) { + compute_neel_mech(i,j,rsq,eij,fi,spi,spj); + } + } + + f[i][0] += fi[0]; + f[i][1] += fi[1]; + f[i][2] += fi[2]; + fm[i][0] += fmi[0]; + fm[i][1] += fmi[1]; + fm[i][2] += fmi[2]; + + if (newton_pair || j < nlocal) { + f[j][0] -= fi[0]; + f[j][1] -= fi[1]; + f[j][2] -= fi[2]; + } + + if (eflag) { + evdwl = (spi[0]*fmi[0] + spi[1]*fmi[1] + spi[2]*fmi[2]); + evdwl *= hbar; + } else evdwl = 0.0; + + if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair, + evdwl,ecoul,fi[0],fi[1],fi[2],rij[0],rij[1],rij[2]); + } + } + + if (vflag_fdotr) virial_fdotr_compute(); + +} + +/* ---------------------------------------------------------------------- */ + +void PairSpinNeel::compute_single_pair(int ii, double fmi[3]) +{ + int *type = atom->type; + double **x = atom->x; + double **sp = atom->sp; + double local_cut2; + + double xi[3], rij[3], eij[3]; + double spi[3], spj[3]; + + int i,j,jnum,itype,jtype; + int *ilist,*jlist,*numneigh,**firstneigh; + + double rsq, inorm; + + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + i = ilist[ii]; + itype = type[i]; + + spi[0] = sp[i][0]; + spi[1] = sp[i][1]; + spi[2] = sp[i][2]; + + xi[0] = x[i][0]; + xi[1] = x[i][1]; + xi[2] = x[i][2]; + + eij[0] = eij[1] = eij[2] = 0.0; + + jlist = firstneigh[i]; + jnum = numneigh[i]; + + for (int jj = 0; jj < jnum; jj++) { + + j = jlist[jj]; + j &= NEIGHMASK; + jtype = type[j]; + + local_cut2 = cut_spin_neel[itype][jtype]*cut_spin_neel[itype][jtype]; + + spj[0] = sp[j][0]; + spj[1] = sp[j][1]; + spj[2] = sp[j][2]; + + rij[0] = x[j][0] - xi[0]; + rij[1] = x[j][1] - xi[1]; + rij[2] = x[j][2] - xi[2]; + rsq = rij[0]*rij[0] + rij[1]*rij[1] + rij[2]*rij[2]; + inorm = 1.0/sqrt(rsq); + eij[0] = inorm*rij[0]; + eij[1] = inorm*rij[1]; + eij[2] = inorm*rij[2]; + + if (rsq <= local_cut2) { + compute_neel(i,j,rsq,eij,fmi,spi,spj); + } + } + +} + +/* ---------------------------------------------------------------------- */ + +void PairSpinNeel::compute_neel(int i, int j, double rsq, double eij[3], double fmi[3], double spi[3], double spj[3]) +{ + int *type = atom->type; + int itype, jtype; + itype = type[i]; + jtype = type[j]; + + double gij, q1ij, q2ij, ra; + double pdx, pdy, pdz; + double pq1x, pq1y, pq1z; + double pq2x, pq2y, pq2z; + + // pseudo-dipolar component + + ra = rsq/g3[itype][jtype]/g3[itype][jtype]; + gij = 4.0*g1[itype][jtype]*ra; + gij *= (1.0-g2[itype][jtype]*ra); + gij *= exp(-ra); + + double scalar_eij_si = eij[0]*spi[0] + eij[1]*spi[1] + eij[2]*spi[2]; + double scalar_eij_sj = eij[0]*spj[0] + eij[1]*spj[1] + eij[2]*spj[2]; + double scalar_si_sj = spi[0]*spj[0] + spi[1]*spj[1] + spi[2]*spj[2]; + + double gij_eij_sj = gij*scalar_eij_sj; + double gij_3 = gij/3.0; + pdx = gij_eij_sj*eij[0] - gij_3*spj[0]; + pdy = gij_eij_sj*eij[1] - gij_3*spj[1]; + pdz = gij_eij_sj*eij[2] - gij_3*spj[2]; + + // pseudo-quadrupolar component + + ra = rsq/q3[itype][jtype]/q3[itype][jtype]; + q1ij = 4.0*q1[itype][jtype]*ra; + q1ij *= (1.0-q2[itype][jtype]*ra); + q1ij *= exp(-ra); + q2ij = (-2.0*q1ij/9.0); + + double scalar_eij_si_2 = scalar_eij_si*scalar_eij_si; + pq1x = -(scalar_eij_si_2*scalar_eij_si_2 - scalar_si_sj/3.0)*spj[0]/3.0; + pq1y = -(scalar_eij_si_2*scalar_eij_si_2 - scalar_si_sj/3.0)*spj[1]/3.0; + pq1z = -(scalar_eij_si_2*scalar_eij_si_2 - scalar_si_sj/3.0)*spj[2]/3.0; + + double pqt1 = (scalar_eij_sj*scalar_eij_sj-scalar_si_sj/3.0); + pq1x += pqt1*(2.0*scalar_eij_si*eij[0] - spj[0]/3.0); + pq1y += pqt1*(2.0*scalar_eij_si*eij[1] - spj[1]/3.0); + pq1z += pqt1*(2.0*scalar_eij_si*eij[2] - spj[2]/3.0); + + pq1x *= q1ij; + pq1y *= q1ij; + pq1z *= q1ij; + + double scalar_eij_sj_3 = scalar_eij_sj*scalar_eij_sj*scalar_eij_sj; + pq2x = 3.0*scalar_eij_si_2*scalar_eij_sj*eij[0] + scalar_eij_sj_3*eij[0]; + pq2y = 3.0*scalar_eij_si_2*scalar_eij_sj*eij[1] + scalar_eij_sj_3*eij[1]; + pq2z = 3.0*scalar_eij_si_2*scalar_eij_sj*eij[2] + scalar_eij_sj_3*eij[2]; + + pq2x *= q2ij; + pq2y *= q2ij; + pq2z *= q2ij; + + // adding three contributions + + fmi[0] += (pdx + pq1x + pq2x); + fmi[1] += (pdy + pq1y + pq2y); + fmi[2] += (pdz + pq1z + pq2z); +} + +/* ---------------------------------------------------------------------- */ + +void PairSpinNeel::compute_neel_mech(int i, int j, double rsq, double eij[3], double fi[3], double spi[3], double spj[3]) +{ + int *type = atom->type; + int itype, jtype; + itype = type[i]; + jtype = type[j]; + + double g_mech, gij, dgij; + double q_mech, q1ij, dq1ij; + double q2ij, dq2ij; + double pdx, pdy, pdz; + double pq1x, pq1y, pq1z; + double pq2x, pq2y, pq2z; + double ra, rr, drij, ig3, iq3; + + drij = sqrt(rsq); + + double scalar_si_sj = spi[0]*spj[0]+spi[1]*spj[1]+spi[2]*spj[2]; + double scalar_eij_si = eij[0]*spi[0]+eij[1]*spi[1]+eij[2]*spi[2]; + double scalar_eij_sj = eij[0]*spj[0]+eij[1]*spj[1]+eij[2]*spj[2]; + + // pseudo-dipolar component + + g_mech = g1_mech[itype][jtype]; + ig3 = 1.0/(g3[itype][jtype]*g3[itype][jtype]); + + ra = rsq*ig3; + rr = drij*ig3; + + gij = 4.0*g_mech*ra; + gij *= (1.0-g2[itype][jtype]*ra); + gij *= exp(-ra); + + dgij = 1.0-ra-g2[itype][jtype]*ra*(2.0-ra); + dgij *= 8.0*g_mech*rr*exp(-ra); + + double pdt1 = (dgij-2.0*gij/drij)*scalar_eij_si*scalar_eij_sj; + pdt1 -= scalar_si_sj*dgij/3.0; + double pdt2 = scalar_eij_sj*gij/drij; + double pdt3 = scalar_eij_si*gij/drij; + pdx = -(pdt1*eij[0] + pdt2*spi[0] + pdt3*spj[0]); + pdy = -(pdt1*eij[1] + pdt2*spi[1] + pdt3*spj[1]); + pdz = -(pdt1*eij[2] + pdt2*spi[2] + pdt3*spj[2]); + + // pseudo-quadrupolar component + + q_mech = q1_mech[itype][jtype]; + iq3 = 1.0/(q3[itype][jtype]*q3[itype][jtype]); + + ra = rsq*iq3; + rr = drij*iq3; + + q1ij = 4.0*q_mech*ra; + q1ij *= (1.0-q2[itype][jtype]*ra); + q1ij *= exp(-ra); + q2ij = -2.0*q1ij/9.0; + + dq1ij = 1.0-ra-q2[itype][jtype]*ra*(2.0-ra); + dq1ij *= 8.0*q_mech*rr*exp(-ra); + dq2ij = -2.0*dq1ij/9.0; + + double scalar_eij_si_2 = scalar_eij_si*scalar_eij_si; + double scalar_eij_sj_2 = scalar_eij_sj*scalar_eij_sj; + double pqt1 = scalar_eij_si_2 - scalar_si_sj/3.0; + double pqt2 = scalar_eij_sj_2 - scalar_si_sj/3.0; + pq1x = dq1ij * pqt1 * pqt2 * eij[0]; + pq1y = dq1ij * pqt1 * pqt2 * eij[1]; + pq1z = dq1ij * pqt1 * pqt2 * eij[2]; + + double scalar_eij_si_3 = scalar_eij_si*scalar_eij_si*scalar_eij_si; + double scalar_eij_sj_3 = scalar_eij_sj*scalar_eij_sj*scalar_eij_sj; + double scalar_si_sj_2 = scalar_si_sj*scalar_si_sj; +/* double pqt3 = 2.0*scalar_eij_si*scalar_eij_sj_3/drij; + double pqt4 = 2.0*scalar_eij_sj*scalar_eij_si_3/drij; + double pqt5 = -2.0*scalar_si_sj*scalar_eij_si/(3.0*drij); + double pqt6 = -2.0*scalar_si_sj*scalar_eij_sj/(3.0*drij); +// pq1x += q1ij*(spi[0]*(pqt3+pqt6) + spj[0]*(pqt4+)); + pq1x += q1ij*(pqt3*spi[0]+pqt4*spj[0]+pqt5*spi[0]+pqt6*spi[0]); + pq1y += q1ij*(pqt3*spi[1]+pqt4*spj[1]+pqt5*spi[1]+pqt6*spj[1]); + pq1z += q1ij*(pqt3*spi[2]+pqt4*spj[2]+pqt5*spi[2]+pqt6*spj[2]); +*/ + double pqt3 = 2.0*scalar_eij_si*(scalar_eij_sj_2-scalar_si_sj/3.0)/drij; + double pqt4 = 2.0*scalar_eij_sj*(scalar_eij_si_2-scalar_si_sj/3.0)/drij; + pq1x += q1ij*(pqt3*spi[0] + pqt4*spj[0]); + pq1y += q1ij*(pqt3*spi[1] + pqt4*spj[1]); + pq1z += q1ij*(pqt3*spi[2] + pqt4*spj[2]); + double pqt7 = 4.0*scalar_eij_si_2*scalar_eij_sj_2/drij; + double pqt8 = 2.0*scalar_si_sj_2*scalar_eij_sj/(3.0*drij); + double pqt9 = 2.0*scalar_si_sj_2*scalar_eij_si/(3.0*drij); + pq1x -= q1ij*(pqt7 + pqt8 + pqt9)*eij[0]; + pq1y -= q1ij*(pqt7 + pqt8 + pqt9)*eij[1]; + pq1z -= q1ij*(pqt7 + pqt8 + pqt9)*eij[2]; + +/* + double pqt3 = 2.0*scalar_eij_si*(scalar_eij_sj_2-scalar_si_sj/3.0)/drij; + double pqt4 = 2.0*scalar_eij_sj*(scalar_eij_si_2-scalar_si_sj/3.0)/drij; + pq1x += q1ij*(pqt3*spi[0] + pqt4*spj[0]); + pq1y += q1ij*(pqt3*spi[1] + pqt4*spj[1]); + pq1z += q1ij*(pqt3*spi[2] + pqt4*spj[2]); +*/ + + //double scalar_eij_si_3 = scalar_eij_si*scalar_eij_si*scalar_eij_si; + //double scalar_eij_sj_3 = scalar_eij_sj*scalar_eij_sj*scalar_eij_sj; + double pqt10 = scalar_eij_sj*scalar_eij_si_3; + double pqt11 = scalar_eij_si*scalar_eij_sj_3; + pq2x = dq2ij*(pqt10 + pqt11)*eij[0]; + pq2y = dq2ij*(pqt10 + pqt11)*eij[1]; + pq2z = dq2ij*(pqt10 + pqt11)*eij[2]; + + double pqt12 = scalar_eij_si_3/drij; + double pqt13 = scalar_eij_sj_3/drij; + double pqt14 = 3.0*scalar_eij_sj*scalar_eij_si_2/drij; + double pqt15 = 3.0*scalar_eij_si*scalar_eij_sj_2/drij; + pq2x += q2ij*((pqt12+pqt15)*spj[0]+(pqt13+pqt14)*spi[0]); + pq2y += q2ij*((pqt12+pqt15)*spj[1]+(pqt13+pqt14)*spi[1]); + pq2z += q2ij*((pqt12+pqt15)*spj[2]+(pqt13+pqt14)*spi[2]); + double pqt16 = 4.0*scalar_eij_sj*scalar_eij_si_3/drij; + double pqt17 = 4.0*scalar_eij_si*scalar_eij_sj_3/drij; + pq2x -= q2ij*(pqt16 + pqt17)*eij[0]; + pq2y -= q2ij*(pqt16 + pqt17)*eij[1]; + pq2z -= q2ij*(pqt16 + pqt17)*eij[2]; + + // adding three contributions + + fi[0] = pdx + pq1x + pq2x; + fi[1] = pdy + pq1y + pq2y; + fi[2] = pdz + pq1z + pq2z; +} + +/* ---------------------------------------------------------------------- + allocate all arrays +------------------------------------------------------------------------- */ + +void PairSpinNeel::allocate() +{ + allocated = 1; + int n = atom->ntypes; + + memory->create(setflag,n+1,n+1,"pair:setflag"); + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + setflag[i][j] = 0; + + memory->create(cut_spin_neel,n+1,n+1,"pair/spin/soc/neel:cut_spin_neel"); + + memory->create(g1,n+1,n+1,"pair/spin/soc/neel:g1"); + memory->create(g1_mech,n+1,n+1,"pair/spin/soc/neel:g1_mech"); + memory->create(g2,n+1,n+1,"pair/spin/soc/neel:g2"); + memory->create(g3,n+1,n+1,"pair/spin/soc/neel:g3"); + + memory->create(q1,n+1,n+1,"pair/spin/soc/neel:q1"); + memory->create(q1_mech,n+1,n+1,"pair/spin/soc/neel:q1_mech"); + memory->create(q2,n+1,n+1,"pair/spin/soc/neel:q2"); + memory->create(q3,n+1,n+1,"pair/spin/soc/neel:q3"); + + memory->create(cutsq,n+1,n+1,"pair/spin/soc/neel:cutsq"); + +} + + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairSpinNeel::write_restart(FILE *fp) +{ + write_restart_settings(fp); + + int i,j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) { + fwrite(&setflag[i][j],sizeof(int),1,fp); + if (setflag[i][j]) { + fwrite(&g1[i][j],sizeof(double),1,fp); + fwrite(&g1_mech[i][j],sizeof(double),1,fp); + fwrite(&g2[i][j],sizeof(double),1,fp); + fwrite(&g3[i][j],sizeof(double),1,fp); + fwrite(&q1[i][j],sizeof(double),1,fp); + fwrite(&q1_mech[i][j],sizeof(double),1,fp); + fwrite(&q2[i][j],sizeof(double),1,fp); + fwrite(&q3[i][j],sizeof(double),1,fp); + fwrite(&cut_spin_neel[i][j],sizeof(double),1,fp); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairSpinNeel::read_restart(FILE *fp) +{ + read_restart_settings(fp); + + allocate(); + + int i,j; + int me = comm->me; + for (i = 1; i <= atom->ntypes; i++) { + for (j = i; j <= atom->ntypes; j++) { + if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); + if (setflag[i][j]) { + if (me == 0) { + fread(&g1[i][j],sizeof(double),1,fp); + fread(&g1_mech[i][j],sizeof(double),1,fp); + fread(&g2[i][j],sizeof(double),1,fp); + fread(&g2[i][j],sizeof(double),1,fp); + fread(&q1[i][j],sizeof(double),1,fp); + fread(&q1_mech[i][j],sizeof(double),1,fp); + fread(&q2[i][j],sizeof(double),1,fp); + fread(&q2[i][j],sizeof(double),1,fp); + fread(&cut_spin_neel[i][j],sizeof(double),1,fp); + } + MPI_Bcast(&g1[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&g1_mech[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&g2[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&g3[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&q1[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&q1_mech[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&q2[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&q3[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut_spin_neel[i][j],1,MPI_DOUBLE,0,world); + } + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairSpinNeel::write_restart_settings(FILE *fp) +{ + fwrite(&cut_spin_neel_global,sizeof(double),1,fp); + fwrite(&offset_flag,sizeof(int),1,fp); + fwrite(&mix_flag,sizeof(int),1,fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairSpinNeel::read_restart_settings(FILE *fp) +{ + if (comm->me == 0) { + fread(&cut_spin_neel_global,sizeof(double),1,fp); + fread(&offset_flag,sizeof(int),1,fp); + fread(&mix_flag,sizeof(int),1,fp); + } + MPI_Bcast(&cut_spin_neel_global,1,MPI_DOUBLE,0,world); + MPI_Bcast(&offset_flag,1,MPI_INT,0,world); + MPI_Bcast(&mix_flag,1,MPI_INT,0,world); +} diff --git a/src/SPIN/pair_spin_neel.h b/src/SPIN/pair_spin_neel.h new file mode 100644 index 0000000000..f60d7d2dca --- /dev/null +++ b/src/SPIN/pair_spin_neel.h @@ -0,0 +1,90 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS + +PairStyle(spin/neel,PairSpinNeel) + +#else + +#ifndef LMP_PAIR_SPIN_NEEL_H +#define LMP_PAIR_SPIN_NEEL_H + +#include "pair_spin.h" + +namespace LAMMPS_NS { + +class PairSpinNeel : public PairSpin { + public: + PairSpinNeel(class LAMMPS *); + virtual ~PairSpinNeel(); + void settings(int, char **); + void coeff(int, char **); + void init_style(); + double init_one(int, int); + void *extract(const char *, int &); + + void compute(int, int); + void compute_single_pair(int, double *); + + void compute_neel(int, int, double, double *, double *, double *, double *); + void compute_neel_mech(int, int, double, double *, double *, double *, double *); + + void write_restart(FILE *); + void read_restart(FILE *); + void write_restart_settings(FILE *); + void read_restart_settings(FILE *); + + double cut_spin_neel_global; // global neel cutoff distance + + protected: + + // pseudo-dipolar and pseudo-quadrupolar coeff. + + double **g1, **g1_mech; // neel coeffs gij + double **g2, **g3; // g1 in eV, g2 adim, g3 in Ang + double **q1, **q1_mech; // neel coeffs qij + double **q2, **q3; // q1 in eV, q2 adim, q3 in Ang + double **cut_spin_neel; // cutoff distance exchange + + int lattice_flag; // flag for mech force computation + class FixNVESpin *lockfixnvespin; // ptr to FixNVESpin for setups + + + void allocate(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Incorrect args in pair_spin command + +Self-explanatory. + +E: Spin simulations require metal unit style + +Self-explanatory. + +E: Incorrect args for pair coefficients + +Self-explanatory. Check the input script or data file. + +E: Pair spin requires atom attribute spin + +The atom style defined does not have these attributes. + +*/ diff --git a/src/SRD/fix_srd.cpp b/src/SRD/fix_srd.cpp index 564c1e98d7..186f51e06a 100644 --- a/src/SRD/fix_srd.cpp +++ b/src/SRD/fix_srd.cpp @@ -440,7 +440,7 @@ void FixSRD::init() /* ---------------------------------------------------------------------- */ -void FixSRD::setup(int vflag) +void FixSRD::setup(int /*vflag*/) { setup_bounds(); @@ -703,7 +703,7 @@ void FixSRD::pre_neighbor() when collision occurs, change x,v of SRD, force,torque of BIG particle ------------------------------------------------------------------------- */ -void FixSRD::post_force(int vflag) +void FixSRD::post_force(int /*vflag*/) { int i,m,ix,iy,iz; @@ -2168,8 +2168,8 @@ void FixSRD::collision_ellipsoid_inexact(double *xs, double *xb, norm = surface normal of collision pt at time of collision ------------------------------------------------------------------------- */ -double FixSRD::collision_line_exact(double *xs, double *xb, - double *vs, double *vb, Big *big, +double FixSRD::collision_line_exact(double * /*xs*/, double * /*xb*/, + double * /*vs*/, double * /*vb*/, Big * /*big*/, double dt_step, double *xscoll, double *xbcoll, double *norm) @@ -2197,8 +2197,8 @@ double FixSRD::collision_line_exact(double *xs, double *xb, norm = surface normal of collision pt at time of collision ------------------------------------------------------------------------- */ -double FixSRD::collision_tri_exact(double *xs, double *xb, - double *vs, double *vb, Big *big, +double FixSRD::collision_tri_exact(double * /*xs*/, double * /*xb*/, + double * /*vs*/, double * /*vb*/, Big * /*big*/, double dt_step, double *xscoll, double *xbcoll, double *norm) diff --git a/src/USER-BOCS/fix_bocs.cpp b/src/USER-BOCS/fix_bocs.cpp index 37e128f556..03fc94ae58 100644 --- a/src/USER-BOCS/fix_bocs.cpp +++ b/src/USER-BOCS/fix_bocs.cpp @@ -625,11 +625,9 @@ void FixBocs::init() // NJD MRD 2 functions int FixBocs::read_F_table( char *filename, int p_basis_type ) { - char separator = ','; FILE *fpi; int N_columns = 2, n_entries = 0, i; float f1, f2; - double n1, n2; int test_sscanf; double **data = (double **) calloc(N_columns,sizeof(double *)); char * line = (char *) calloc(200,sizeof(char)); @@ -790,7 +788,7 @@ void FixBocs::build_cubic_splines( double **data ) compute T,P before integrator starts ------------------------------------------------------------------------- */ -void FixBocs::setup(int vflag) +void FixBocs::setup(int /*vflag*/) { // tdof needed by compute_temp_target() @@ -846,7 +844,7 @@ void FixBocs::setup(int vflag) if (pstat_flag) { double kt = boltz * t_target; - double nkt = atom->natoms * kt; + double nkt = (atom->natoms + 1) * kt; for (int i = 0; i < 3; i++) if (p_flag[i]) @@ -875,7 +873,7 @@ void FixBocs::setup(int vflag) 1st half of Verlet update ------------------------------------------------------------------------- */ -void FixBocs::initial_integrate(int vflag) +void FixBocs::initial_integrate(int /*vflag*/) { // update eta_press_dot @@ -970,7 +968,7 @@ void FixBocs::final_integrate() /* ---------------------------------------------------------------------- */ -void FixBocs::initial_integrate_respa(int vflag, int ilevel, int iloop) +void FixBocs::initial_integrate_respa(int /*vflag*/, int ilevel, int /*iloop*/) { // set timesteps by level @@ -1039,7 +1037,7 @@ void FixBocs::initial_integrate_respa(int vflag, int ilevel, int iloop) /* ---------------------------------------------------------------------- */ -void FixBocs::final_integrate_respa(int ilevel, int iloop) +void FixBocs::final_integrate_respa(int ilevel, int /*iloop*/) { // set timesteps by level @@ -1508,7 +1506,7 @@ double FixBocs::compute_scalar() double volume; double energy; double kt = boltz * t_target; - double lkt_press = kt; + double lkt_press = 0.0; int ich; if (dimension == 3) volume = domain->xprd * domain->yprd * domain->zprd; else volume = domain->xprd * domain->yprd; @@ -1539,15 +1537,21 @@ double FixBocs::compute_scalar() // sum is over barostatted dimensions if (pstat_flag) { - for (i = 0; i < 3; i++) - if (p_flag[i]) + for (i = 0; i < 3; i++) { + if (p_flag[i]) { energy += 0.5*omega_dot[i]*omega_dot[i]*omega_mass[i] + p_hydro*(volume-vol0) / (pdim*nktv2p); + lkt_press += kt; + } + } if (pstyle == TRICLINIC) { - for (i = 3; i < 6; i++) - if (p_flag[i]) + for (i = 3; i < 6; i++) { + if (p_flag[i]) { energy += 0.5*omega_dot[i]*omega_dot[i]*omega_mass[i]; + lkt_press += kt; + } + } } // extra contributions from thermostat chain for barostat @@ -1880,15 +1884,14 @@ void FixBocs::nhc_temp_integrate() void FixBocs::nhc_press_integrate() { - int ich,i; + int ich,i,pdof; double expfac,factor_etap,kecurrent; double kt = boltz * t_target; - double lkt_press = kt; // Update masses, to preserve initial freq, if flag set if (omega_mass_flag) { - double nkt = atom->natoms * kt; + double nkt = (atom->natoms + 1) * kt; for (int i = 0; i < 3; i++) if (p_flag[i]) omega_mass[i] = nkt/(p_freq[i]*p_freq[i]); @@ -1912,14 +1915,24 @@ void FixBocs::nhc_press_integrate() } kecurrent = 0.0; - for (i = 0; i < 3; i++) - if (p_flag[i]) kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i]; - - if (pstyle == TRICLINIC) { - for (i = 3; i < 6; i++) - if (p_flag[i]) kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i]; + pdof = 0; + for (i = 0; i < 3; i++) { + if (p_flag[i]) { + kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i]; + pdof++; + } } + if (pstyle == TRICLINIC) { + for (i = 3; i < 6; i++) { + if (p_flag[i]) { + kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i]; + pdof++; + } + } + } + + double lkt_press = pdof * kt; etap_dotdot[0] = (kecurrent - lkt_press)/etap_mass[0]; double ncfac = 1.0/nc_pchain; diff --git a/src/USER-CGDNA/bond_oxdna_fene.cpp b/src/USER-CGDNA/bond_oxdna_fene.cpp index 47d8d8f60b..34a25a9b5a 100644 --- a/src/USER-CGDNA/bond_oxdna_fene.cpp +++ b/src/USER-CGDNA/bond_oxdna_fene.cpp @@ -56,7 +56,7 @@ BondOxdnaFene::~BondOxdnaFene() compute vector COM-sugar-phosphate backbone interaction site in oxDNA ------------------------------------------------------------------------- */ void BondOxdnaFene::compute_interaction_sites(double e1[3], - double e2[3], double r[3]) + double /*e2*/[3], double r[3]) { double d_cs=-0.4; @@ -316,7 +316,7 @@ void BondOxdnaFene::write_data(FILE *fp) /* ---------------------------------------------------------------------- */ -double BondOxdnaFene::single(int type, double rsq, int i, int j, +double BondOxdnaFene::single(int type, double rsq, int /*i*/, int /*j*/, double &fforce) { double r = sqrt(rsq); diff --git a/src/USER-CGDNA/fix_nve_dot.cpp b/src/USER-CGDNA/fix_nve_dot.cpp index 63f38a4e12..72b3388793 100644 --- a/src/USER-CGDNA/fix_nve_dot.cpp +++ b/src/USER-CGDNA/fix_nve_dot.cpp @@ -62,7 +62,7 @@ void FixNVEDot::init() /* ---------------------------------------------------------------------- */ -void FixNVEDot::initial_integrate(int vflag) +void FixNVEDot::initial_integrate(int /*vflag*/) { double *shape,*quat; double fquat[4],conjqm[4],inertia[3]; diff --git a/src/USER-CGDNA/fix_nve_dotc_langevin.cpp b/src/USER-CGDNA/fix_nve_dotc_langevin.cpp index 90f7b1caeb..c73801c97a 100644 --- a/src/USER-CGDNA/fix_nve_dotc_langevin.cpp +++ b/src/USER-CGDNA/fix_nve_dotc_langevin.cpp @@ -127,7 +127,7 @@ void FixNVEDotcLangevin::compute_target() /* ---------------------------------------------------------------------- */ -void FixNVEDotcLangevin::initial_integrate(int vflag) +void FixNVEDotcLangevin::initial_integrate(int /*vflag*/) { double *shape,*quat; double fquat[4],conjqm[4],inertia[3]; diff --git a/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp b/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp index 151e752692..d31890ea52 100644 --- a/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp +++ b/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp @@ -542,7 +542,7 @@ void PairOxdna2Coaxstk::allocate() global settings ------------------------------------------------------------------------- */ -void PairOxdna2Coaxstk::settings(int narg, char **arg) +void PairOxdna2Coaxstk::settings(int narg, char **/*arg*/) { if (narg != 0) error->all(FLERR,"Illegal pair_style command"); diff --git a/src/USER-CGDNA/pair_oxdna2_dh.cpp b/src/USER-CGDNA/pair_oxdna2_dh.cpp index 974ade89c1..da6e1f8bbd 100644 --- a/src/USER-CGDNA/pair_oxdna2_dh.cpp +++ b/src/USER-CGDNA/pair_oxdna2_dh.cpp @@ -264,7 +264,7 @@ void PairOxdna2Dh::allocate() global settings ------------------------------------------------------------------------- */ -void PairOxdna2Dh::settings(int narg, char **arg) +void PairOxdna2Dh::settings(int narg, char **/*arg*/) { if (narg != 0) error->all(FLERR,"Illegal pair_style command"); } diff --git a/src/USER-CGDNA/pair_oxdna_coaxstk.cpp b/src/USER-CGDNA/pair_oxdna_coaxstk.cpp index 0eb75fbb43..ca03bcb35c 100644 --- a/src/USER-CGDNA/pair_oxdna_coaxstk.cpp +++ b/src/USER-CGDNA/pair_oxdna_coaxstk.cpp @@ -666,7 +666,7 @@ void PairOxdnaCoaxstk::allocate() global settings ------------------------------------------------------------------------- */ -void PairOxdnaCoaxstk::settings(int narg, char **arg) +void PairOxdnaCoaxstk::settings(int narg, char **/*arg*/) { if (narg != 0) error->all(FLERR,"Illegal pair_style command"); diff --git a/src/USER-CGDNA/pair_oxdna_excv.cpp b/src/USER-CGDNA/pair_oxdna_excv.cpp index e2b8334078..719a63b5f4 100644 --- a/src/USER-CGDNA/pair_oxdna_excv.cpp +++ b/src/USER-CGDNA/pair_oxdna_excv.cpp @@ -92,7 +92,7 @@ PairOxdnaExcv::~PairOxdnaExcv() compute vector COM-excluded volume interaction sites in oxDNA ------------------------------------------------------------------------- */ void PairOxdnaExcv::compute_interaction_sites(double e1[3], - double e2[3], double rs[3], double rb[3]) + double /*e2*/[3], double rs[3], double rb[3]) { double d_cs=-0.4, d_cb=+0.4; @@ -441,7 +441,7 @@ void PairOxdnaExcv::allocate() global settings ------------------------------------------------------------------------- */ -void PairOxdnaExcv::settings(int narg, char **arg) +void PairOxdnaExcv::settings(int narg, char **/*arg*/) { if (narg != 0) error->all(FLERR,"Illegal pair_style command"); diff --git a/src/USER-CGDNA/pair_oxdna_hbond.cpp b/src/USER-CGDNA/pair_oxdna_hbond.cpp index ce1bfe036a..cb9f61bd7e 100644 --- a/src/USER-CGDNA/pair_oxdna_hbond.cpp +++ b/src/USER-CGDNA/pair_oxdna_hbond.cpp @@ -601,7 +601,7 @@ void PairOxdnaHbond::allocate() global settings ------------------------------------------------------------------------- */ -void PairOxdnaHbond::settings(int narg, char **arg) +void PairOxdnaHbond::settings(int narg, char **/*arg*/) { if (narg != 0) error->all(FLERR,"Illegal pair_style command"); diff --git a/src/USER-CGDNA/pair_oxdna_stk.cpp b/src/USER-CGDNA/pair_oxdna_stk.cpp index 8c4498e627..f713e4d27c 100644 --- a/src/USER-CGDNA/pair_oxdna_stk.cpp +++ b/src/USER-CGDNA/pair_oxdna_stk.cpp @@ -647,7 +647,7 @@ void PairOxdnaStk::allocate() global settings ------------------------------------------------------------------------- */ -void PairOxdnaStk::settings(int narg, char **arg) +void PairOxdnaStk::settings(int narg, char **/*arg*/) { if (narg != 0) error->all(FLERR,"Illegal pair_style command"); diff --git a/src/USER-CGDNA/pair_oxdna_xstk.cpp b/src/USER-CGDNA/pair_oxdna_xstk.cpp index e5b9de81c0..c4c23bf2c9 100644 --- a/src/USER-CGDNA/pair_oxdna_xstk.cpp +++ b/src/USER-CGDNA/pair_oxdna_xstk.cpp @@ -611,7 +611,7 @@ void PairOxdnaXstk::allocate() global settings ------------------------------------------------------------------------- */ -void PairOxdnaXstk::settings(int narg, char **arg) +void PairOxdnaXstk::settings(int narg, char **/*arg*/) { if (narg != 0) error->all(FLERR,"Illegal pair_style command"); diff --git a/src/USER-CGSDK/lj_sdk_common.h b/src/USER-CGSDK/lj_sdk_common.h index c1f2cf215a..51dcb4c2b7 100644 --- a/src/USER-CGSDK/lj_sdk_common.h +++ b/src/USER-CGSDK/lj_sdk_common.h @@ -27,6 +27,7 @@ namespace LJSDKParms { // LJ type flags. list of supported LJ exponent combinations enum {LJ_NOT_SET=0, LJ9_6, LJ12_4, LJ12_6, NUM_LJ_TYPES}; +#if defined(LMP_NEED_SDK_FIND_LJ_TYPE) static int find_lj_type(const char *label, const char * const * const list) { for (int i=0; i < NUM_LJ_TYPES; ++i) @@ -34,6 +35,7 @@ namespace LJSDKParms { return LJ_NOT_SET; } +#endif static const char * const lj_type_list[] = {"none", "lj9_6", "lj12_4", "lj12_6"}; static const double lj_prefact[] = {0.0, 6.75, 2.59807621135332, 4.0}; diff --git a/src/USER-CGSDK/pair_lj_sdk.cpp b/src/USER-CGSDK/pair_lj_sdk.cpp index cbcba7f6b2..3404beb58a 100644 --- a/src/USER-CGSDK/pair_lj_sdk.cpp +++ b/src/USER-CGSDK/pair_lj_sdk.cpp @@ -33,6 +33,7 @@ #include "memory.h" #include "error.h" +#define LMP_NEED_SDK_FIND_LJ_TYPE 1 #include "lj_sdk_common.h" using namespace LAMMPS_NS; diff --git a/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp b/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp index 1d93363e20..c51235518b 100644 --- a/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp +++ b/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp @@ -34,6 +34,7 @@ #include "memory.h" #include "error.h" +#define LMP_NEED_SDK_FIND_LJ_TYPE 1 #include "lj_sdk_common.h" using namespace LAMMPS_NS; diff --git a/src/USER-COLVARS/fix_colvars.h b/src/USER-COLVARS/fix_colvars.h index 509eca5de3..3029ba9db5 100644 --- a/src/USER-COLVARS/fix_colvars.h +++ b/src/USER-COLVARS/fix_colvars.h @@ -34,7 +34,6 @@ FixStyle(colvars,FixColvars) #define LMP_FIX_COLVARS_H #include "fix.h" -#include // forward declaration class colvarproxy_lammps; @@ -77,13 +76,6 @@ class FixColvars : public Fix { int num_coords; // total number of atoms controlled by this fix tagint *taglist; // list of all atom IDs referenced by colvars. - // TODO get rid of these - // std::vector *coords; // coordinates of colvar atoms - // std::vector *forces; // received forces of colvar atoms - // std::vector *oforce; // old total forces of colvar atoms - // std::vector *masses; - // std::vector *charges; - int nmax; // size of atom communication buffer. int size_one; // bytes per atom in communication buffer. struct commdata *comm_buf; // communication buffer diff --git a/src/USER-DIFFRACTION/fix_saed_vtk.cpp b/src/USER-DIFFRACTION/fix_saed_vtk.cpp index 45bfeca48b..ad9c76ac6b 100644 --- a/src/USER-DIFFRACTION/fix_saed_vtk.cpp +++ b/src/USER-DIFFRACTION/fix_saed_vtk.cpp @@ -325,7 +325,7 @@ void FixSAEDVTK::init() only does something if nvalid = current timestep ------------------------------------------------------------------------- */ -void FixSAEDVTK::setup(int vflag) +void FixSAEDVTK::setup(int /*vflag*/) { end_of_step(); } diff --git a/src/USER-DPD/fix_dpd_energy.cpp b/src/USER-DPD/fix_dpd_energy.cpp index d89ea7759a..5759a164f5 100644 --- a/src/USER-DPD/fix_dpd_energy.cpp +++ b/src/USER-DPD/fix_dpd_energy.cpp @@ -57,7 +57,7 @@ int FixDPDenergy::setmask() allow for both per-type and per-atom mass ------------------------------------------------------------------------- */ -void FixDPDenergy::initial_integrate(int vflag) +void FixDPDenergy::initial_integrate(int /*vflag*/) { int nlocal = atom->nlocal; if (igroup == atom->firstgroup) nlocal = atom->nfirst; diff --git a/src/USER-DPD/fix_eos_table_rx.cpp b/src/USER-DPD/fix_eos_table_rx.cpp index 73144c0a0f..181c7dccfa 100644 --- a/src/USER-DPD/fix_eos_table_rx.cpp +++ b/src/USER-DPD/fix_eos_table_rx.cpp @@ -178,7 +178,7 @@ int FixEOStableRX::setmask() /* ---------------------------------------------------------------------- */ -void FixEOStableRX::setup(int vflag) +void FixEOStableRX::setup(int /*vflag*/) { int nlocal = atom->nlocal; int *mask = atom->mask; @@ -803,7 +803,7 @@ void FixEOStableRX::temperature_lookup(int id, double ui, double &thetai) /* ---------------------------------------------------------------------- */ -int FixEOStableRX::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc) +int FixEOStableRX::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int * /*pbc*/) { int ii,jj,m; double *uChem = atom->uChem; diff --git a/src/USER-DPD/fix_rx.cpp b/src/USER-DPD/fix_rx.cpp index be78989bb5..1a9c43704d 100644 --- a/src/USER-DPD/fix_rx.cpp +++ b/src/USER-DPD/fix_rx.cpp @@ -668,7 +668,7 @@ void FixRX::init_list(int, class NeighList* ptr) /* ---------------------------------------------------------------------- */ -void FixRX::setup_pre_force(int vflag) +void FixRX::setup_pre_force(int /*vflag*/) { int nlocal = atom->nlocal; int nghost = atom->nghost; @@ -727,9 +727,9 @@ void FixRX::setup_pre_force(int vflag) /* ---------------------------------------------------------------------- */ -void FixRX::pre_force(int vflag) +void FixRX::pre_force(int /*vflag*/) { - TimerType timer_start = getTimeStamp(); + //TimerType timer_start = getTimeStamp(); int nlocal = atom->nlocal; int nghost = atom->nghost; @@ -808,7 +808,7 @@ void FixRX::pre_force(int vflag) comm->forward_comm_fix(this); if(localTempFlag) delete [] dpdThetaLocal; - TimerType timer_stop = getTimeStamp(); + //TimerType timer_stop = getTimeStamp(); double time_ODE = getElapsedTime(timer_localTemperature, timer_ODE); @@ -1191,7 +1191,7 @@ void FixRX::rkf45_step (const int neq, const double h, double y[], double y_out[ return; } -int FixRX::rkf45_h0 (const int neq, const double t, const double t_stop, +int FixRX::rkf45_h0 (const int neq, const double t, const double /*t_stop*/, const double hmin, const double hmax, double& h0, double y[], double rwk[], void* v_params) { @@ -1668,7 +1668,7 @@ int FixRX::rhs(double t, const double *y, double *dydt, void *params) /* ---------------------------------------------------------------------- */ -int FixRX::rhs_dense(double t, const double *y, double *dydt, void *params) +int FixRX::rhs_dense(double /*t*/, const double *y, double *dydt, void *params) { UserRHSData *userData = (UserRHSData *) params; @@ -1702,7 +1702,7 @@ int FixRX::rhs_dense(double t, const double *y, double *dydt, void *params) /* ---------------------------------------------------------------------- */ -int FixRX::rhs_sparse(double t, const double *y, double *dydt, void *v_params) const +int FixRX::rhs_sparse(double /*t*/, const double *y, double *dydt, void *v_params) const { UserRHSData *userData = (UserRHSData *) v_params; @@ -1885,7 +1885,7 @@ void FixRX::computeLocalTemperature() /* ---------------------------------------------------------------------- */ -int FixRX::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc) +int FixRX::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int * /*pbc*/) { int ii,jj,m; double tmp; diff --git a/src/USER-DPD/fix_shardlow.cpp b/src/USER-DPD/fix_shardlow.cpp index 06185dee7e..4e133480ad 100644 --- a/src/USER-DPD/fix_shardlow.cpp +++ b/src/USER-DPD/fix_shardlow.cpp @@ -145,14 +145,14 @@ void FixShardlow::init() /* ---------------------------------------------------------------------- */ -void FixShardlow::init_list(int id, NeighList *ptr) +void FixShardlow::init_list(int /*id*/, NeighList *ptr) { list = ptr; } /* ---------------------------------------------------------------------- */ -void FixShardlow::setup(int vflag) +void FixShardlow::setup(int /*vflag*/) { bool fixShardlow = false; @@ -354,9 +354,8 @@ void FixShardlow::ssa_update_dpde( double *uMech = atom->uMech; double *dpdTheta = atom->dpdTheta; - double *cut_i, *cut2_i, *sigma_i, *kappa_i; + double *cut_i, *cut2_i, *sigma_i, *kappa_i, *alpha_i; double theta_ij_inv, theta_i_inv; - const double boltz2 = 2.0*force->boltz; const double boltz_inv = 1.0/force->boltz; const double ftm2v = force->ftm2v; @@ -389,6 +388,7 @@ while (ct-- > 0) { cut_i = pairDPDE->cut[itype]; sigma_i = pairDPDE->sigma[itype]; kappa_i = pairDPDE->kappa[itype]; + alpha_i = pairDPDE->alpha[itype]; theta_i_inv = 1.0/dpdTheta[i]; const double mass_i = (rmass) ? rmass[i] : mass[itype]; const double massinv_i = 1.0 / mass_i; @@ -448,7 +448,7 @@ while (ct-- > 0) { // Compute uCond double kappa_ij = kappa_i[jtype]; - double alpha_ij = sqrt(boltz2*kappa_ij); + double alpha_ij = alpha_i[jtype]; double del_uCond = alpha_ij*wr*dtsqrt * es_normal(RNGstate); del_uCond += kappa_ij*(theta_i_inv - theta_j_inv)*wdt; @@ -527,7 +527,7 @@ while (ct-- > 0) { rand_state[id] = RNGstate; } -void FixShardlow::initial_integrate(int vflag) +void FixShardlow::initial_integrate(int /*vflag*/) { int ii; @@ -646,7 +646,7 @@ fprintf(stdout, "\n%6d %6d,%6d %6d: " /* ---------------------------------------------------------------------- */ -int FixShardlow::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc) +int FixShardlow::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int * /*pbc*/) { int ii,jj,m; double **v = atom->v; diff --git a/src/USER-DPD/pair_dpd_fdt.cpp b/src/USER-DPD/pair_dpd_fdt.cpp index aeade16e7c..12e6d9f257 100644 --- a/src/USER-DPD/pair_dpd_fdt.cpp +++ b/src/USER-DPD/pair_dpd_fdt.cpp @@ -433,8 +433,8 @@ void PairDPDfdt::read_restart_settings(FILE *fp) /* ---------------------------------------------------------------------- */ -double PairDPDfdt::single(int i, int j, int itype, int jtype, double rsq, - double factor_coul, double factor_dpd, double &fforce) +double PairDPDfdt::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq, + double /*factor_coul*/, double factor_dpd, double &fforce) { double r,rinv,wr,wd,phi; diff --git a/src/USER-DPD/pair_dpd_fdt_energy.cpp b/src/USER-DPD/pair_dpd_fdt_energy.cpp index d1f3cceed4..42c23e3ad2 100644 --- a/src/USER-DPD/pair_dpd_fdt_energy.cpp +++ b/src/USER-DPD/pair_dpd_fdt_energy.cpp @@ -65,6 +65,7 @@ PairDPDfdtEnergy::~PairDPDfdtEnergy() memory->destroy(a0); memory->destroy(sigma); memory->destroy(kappa); + memory->destroy(alpha); memory->destroy(duCond); memory->destroy(duMech); } @@ -269,7 +270,7 @@ void PairDPDfdtEnergy::compute(int eflag, int vflag) // Compute uCond randnum = random->gaussian(); kappa_ij = kappa[itype][jtype]; - alpha_ij = sqrt(2.0*force->boltz*kappa_ij); + alpha_ij = alpha[itype][jtype]; randPair = alpha_ij*wr*randnum*dtinvsqrt; uTmp = kappa_ij*(1.0/dpdTheta[i] - 1.0/dpdTheta[j])*wd; @@ -322,6 +323,7 @@ void PairDPDfdtEnergy::allocate() memory->create(a0,n+1,n+1,"pair:a0"); memory->create(sigma,n+1,n+1,"pair:sigma"); memory->create(kappa,n+1,n+1,"pair:kappa"); + memory->create(alpha,n+1,n+1,"pair:alpha"); if (!splitFDT_flag) { memory->create(duCond,nlocal+nghost+1,"pair:duCond"); memory->create(duMech,nlocal+nghost+1,"pair:duMech"); @@ -374,11 +376,12 @@ void PairDPDfdtEnergy::coeff(int narg, char **arg) double a0_one = force->numeric(FLERR,arg[2]); double sigma_one = force->numeric(FLERR,arg[3]); double cut_one = cut_global; - double kappa_one; + double kappa_one, alpha_one; a0_is_zero = (a0_one == 0.0); // Typical use with SSA is to set a0 to zero kappa_one = force->numeric(FLERR,arg[4]); + alpha_one = sqrt(2.0*force->boltz*kappa_one); if (narg == 6) cut_one = force->numeric(FLERR,arg[5]); int count = 0; @@ -387,6 +390,7 @@ void PairDPDfdtEnergy::coeff(int narg, char **arg) a0[i][j] = a0_one; sigma[i][j] = sigma_one; kappa[i][j] = kappa_one; + alpha[i][j] = alpha_one; cut[i][j] = cut_one; setflag[i][j] = 1; count++; @@ -435,6 +439,7 @@ double PairDPDfdtEnergy::init_one(int i, int j) a0[j][i] = a0[i][j]; sigma[j][i] = sigma[i][j]; kappa[j][i] = kappa[i][j]; + alpha[j][i] = alpha[i][j]; return cut[i][j]; } @@ -488,6 +493,7 @@ void PairDPDfdtEnergy::read_restart(FILE *fp) MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&kappa[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world); + alpha[i][j] = sqrt(2.0*force->boltz*kappa[i][j]); a0_is_zero = a0_is_zero && (a0[i][j] == 0.0); // verify the zero assumption } } @@ -528,8 +534,8 @@ void PairDPDfdtEnergy::read_restart_settings(FILE *fp) /* ---------------------------------------------------------------------- */ -double PairDPDfdtEnergy::single(int i, int j, int itype, int jtype, double rsq, - double factor_coul, double factor_dpd, double &fforce) +double PairDPDfdtEnergy::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq, + double /*factor_coul*/, double factor_dpd, double &fforce) { double r,rinv,wr,wd,phi; diff --git a/src/USER-DPD/pair_dpd_fdt_energy.h b/src/USER-DPD/pair_dpd_fdt_energy.h index dce39f83f0..e21b48f7bd 100644 --- a/src/USER-DPD/pair_dpd_fdt_energy.h +++ b/src/USER-DPD/pair_dpd_fdt_energy.h @@ -43,7 +43,7 @@ class PairDPDfdtEnergy : public Pair { double **cut; double **a0; - double **sigma,**kappa; + double **sigma,**kappa,**alpha; double *duCond,*duMech; int seed; diff --git a/src/USER-DPD/pair_multi_lucy.cpp b/src/USER-DPD/pair_multi_lucy.cpp index 3d204a849e..f911d8299e 100644 --- a/src/USER-DPD/pair_multi_lucy.cpp +++ b/src/USER-DPD/pair_multi_lucy.cpp @@ -781,7 +781,7 @@ void PairMultiLucy::computeLocalDensity() } /* ---------------------------------------------------------------------- */ -int PairMultiLucy::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc) +int PairMultiLucy::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int * /*pbc*/) { int i,j,m; double *rho = atom->rho; diff --git a/src/USER-DPD/pair_multi_lucy_rx.cpp b/src/USER-DPD/pair_multi_lucy_rx.cpp index 0070ca82d9..13c838fe01 100644 --- a/src/USER-DPD/pair_multi_lucy_rx.cpp +++ b/src/USER-DPD/pair_multi_lucy_rx.cpp @@ -1019,7 +1019,7 @@ void PairMultiLucyRX::getMixingWeights(int id, double &mixWtSite1old, double &mi /* ---------------------------------------------------------------------- */ -int PairMultiLucyRX::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc) +int PairMultiLucyRX::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int * /*pbc*/) { int i,j,m; double *rho = atom->rho; diff --git a/src/USER-DPD/pair_table_rx.cpp b/src/USER-DPD/pair_table_rx.cpp index 221944edc5..1e7bc440d1 100644 --- a/src/USER-DPD/pair_table_rx.cpp +++ b/src/USER-DPD/pair_table_rx.cpp @@ -439,7 +439,7 @@ void PairTableRX::coeff(int narg, char **arg) /* ---------------------------------------------------------------------- */ double PairTableRX::single(int i, int j, int itype, int jtype, double rsq, - double factor_coul, double factor_lj, + double /*factor_coul*/, double factor_lj, double &fforce) { int itable; diff --git a/src/USER-DRUDE/fix_drude.cpp b/src/USER-DRUDE/fix_drude.cpp index 19fd775715..7800efe7ff 100644 --- a/src/USER-DRUDE/fix_drude.cpp +++ b/src/USER-DRUDE/fix_drude.cpp @@ -235,7 +235,7 @@ void FixDrude::grow_arrays(int nmax) copy values within local atom-based array ------------------------------------------------------------------------- */ -void FixDrude::copy_arrays(int i, int j, int delflag) +void FixDrude::copy_arrays(int i, int j, int /*delflag*/) { drudeid[j] = drudeid[i]; } diff --git a/src/USER-DRUDE/fix_langevin_drude.cpp b/src/USER-DRUDE/fix_langevin_drude.cpp index 235c5d224b..b9d1139f83 100644 --- a/src/USER-DRUDE/fix_langevin_drude.cpp +++ b/src/USER-DRUDE/fix_langevin_drude.cpp @@ -157,7 +157,7 @@ void FixLangevinDrude::init() /* ---------------------------------------------------------------------- */ -void FixLangevinDrude::setup(int vflag) +void FixLangevinDrude::setup(int /*vflag*/) { if (!strstr(update->integrate_style,"verlet")) error->all(FLERR,"RESPA style not compatible with fix langevin/drude"); diff --git a/src/USER-DRUDE/pair_thole.cpp b/src/USER-DRUDE/pair_thole.cpp index 8c20ee8c42..6901ad1f2d 100644 --- a/src/USER-DRUDE/pair_thole.cpp +++ b/src/USER-DRUDE/pair_thole.cpp @@ -363,7 +363,7 @@ void PairThole::read_restart_settings(FILE *fp) /* ---------------------------------------------------------------------- */ double PairThole::single(int i, int j, int itype, int jtype, - double rsq, double factor_coul, double factor_lj, + double rsq, double factor_coul, double /*factor_lj*/, double &fforce) { double r2inv,rinv,r,phicoul; diff --git a/src/USER-EFF/compute_temp_deform_eff.cpp b/src/USER-EFF/compute_temp_deform_eff.cpp index d3856e431d..23abb4f99d 100644 --- a/src/USER-EFF/compute_temp_deform_eff.cpp +++ b/src/USER-EFF/compute_temp_deform_eff.cpp @@ -290,7 +290,7 @@ void ComputeTempDeformEff::remove_bias_all() assume remove_bias() was previously called ------------------------------------------------------------------------- */ -void ComputeTempDeformEff::restore_bias(int i, double *v) +void ComputeTempDeformEff::restore_bias(int /*i*/, double *v) { v[0] += vbias[0]; v[1] += vbias[1]; diff --git a/src/USER-EFF/compute_temp_region_eff.cpp b/src/USER-EFF/compute_temp_region_eff.cpp index 4548914ce1..659bdfca5e 100644 --- a/src/USER-EFF/compute_temp_region_eff.cpp +++ b/src/USER-EFF/compute_temp_region_eff.cpp @@ -263,7 +263,7 @@ void ComputeTempRegionEff::remove_bias_all() assume remove_bias() was previously called ------------------------------------------------------------------------- */ -void ComputeTempRegionEff::restore_bias(int i, double *v) +void ComputeTempRegionEff::restore_bias(int /*i*/, double *v) { v[0] += vbias[0]; v[1] += vbias[1]; diff --git a/src/USER-EFF/fix_langevin_eff.cpp b/src/USER-EFF/fix_langevin_eff.cpp index 2d0eef8e85..d362113997 100644 --- a/src/USER-EFF/fix_langevin_eff.cpp +++ b/src/USER-EFF/fix_langevin_eff.cpp @@ -63,7 +63,7 @@ FixLangevinEff::~FixLangevinEff() /* ---------------------------------------------------------------------- */ -void FixLangevinEff::post_force(int vflag) +void FixLangevinEff::post_force(int /*vflag*/) { if (tallyflag) post_force_tally(); else post_force_no_tally(); diff --git a/src/USER-EFF/fix_nve_eff.cpp b/src/USER-EFF/fix_nve_eff.cpp index 584714a44e..699dd9f949 100644 --- a/src/USER-EFF/fix_nve_eff.cpp +++ b/src/USER-EFF/fix_nve_eff.cpp @@ -68,7 +68,7 @@ void FixNVEEff::init() allow for both per-type and per-atom mass ------------------------------------------------------------------------- */ -void FixNVEEff::initial_integrate(int vflag) +void FixNVEEff::initial_integrate(int /*vflag*/) { double dtfm; @@ -145,7 +145,7 @@ void FixNVEEff::final_integrate() /* ---------------------------------------------------------------------- */ -void FixNVEEff::initial_integrate_respa(int vflag, int ilevel, int iloop) +void FixNVEEff::initial_integrate_respa(int vflag, int ilevel, int /*iloop*/) { dtv = step_respa[ilevel]; dtf = 0.5 * step_respa[ilevel] * force->ftm2v; @@ -159,7 +159,7 @@ void FixNVEEff::initial_integrate_respa(int vflag, int ilevel, int iloop) /* ---------------------------------------------------------------------- */ -void FixNVEEff::final_integrate_respa(int ilevel, int iloop) +void FixNVEEff::final_integrate_respa(int ilevel, int /*iloop*/) { dtf = 0.5 * step_respa[ilevel] * force->ftm2v; final_integrate(); diff --git a/src/USER-EFF/pair_eff_cut.cpp b/src/USER-EFF/pair_eff_cut.cpp index 0379c0264b..b4e9011e33 100644 --- a/src/USER-EFF/pair_eff_cut.cpp +++ b/src/USER-EFF/pair_eff_cut.cpp @@ -1009,7 +1009,7 @@ void PairEffCut::read_restart_settings(FILE *fp) these arrays are stored locally by pair style ------------------------------------------------------------------------- */ -void PairEffCut::min_xf_pointers(int ignore, double **xextra, double **fextra) +void PairEffCut::min_xf_pointers(int /*ignore*/, double **xextra, double **fextra) { // grow arrays if necessary // need to be atom->nmax in length @@ -1031,7 +1031,7 @@ void PairEffCut::min_xf_pointers(int ignore, double **xextra, double **fextra) calculate and store in min_eradius and min_erforce ------------------------------------------------------------------------- */ -void PairEffCut::min_xf_get(int ignore) +void PairEffCut::min_xf_get(int /*ignore*/) { double *eradius = atom->eradius; double *erforce = atom->erforce; @@ -1050,7 +1050,7 @@ void PairEffCut::min_xf_get(int ignore) propagate the change back to eradius ------------------------------------------------------------------------- */ -void PairEffCut::min_x_set(int ignore) +void PairEffCut::min_x_set(int /*ignore*/) { double *eradius = atom->eradius; int *spin = atom->spin; diff --git a/src/USER-FEP/fix_adapt_fep.cpp b/src/USER-FEP/fix_adapt_fep.cpp index 3b8c9d4201..7304bc4ef6 100644 --- a/src/USER-FEP/fix_adapt_fep.cpp +++ b/src/USER-FEP/fix_adapt_fep.cpp @@ -387,7 +387,7 @@ void FixAdaptFEP::init() /* ---------------------------------------------------------------------- */ -void FixAdaptFEP::setup_pre_force(int vflag) +void FixAdaptFEP::setup_pre_force(int /*vflag*/) { change_settings(); } @@ -402,7 +402,7 @@ void FixAdaptFEP::setup_pre_force_respa(int vflag, int ilevel) /* ---------------------------------------------------------------------- */ -void FixAdaptFEP::pre_force(int vflag) +void FixAdaptFEP::pre_force(int /*vflag*/) { if (nevery == 0) return; diff --git a/src/USER-FEP/pair_coul_cut_soft.cpp b/src/USER-FEP/pair_coul_cut_soft.cpp index 5bcb5a7522..529ffe6b09 100644 --- a/src/USER-FEP/pair_coul_cut_soft.cpp +++ b/src/USER-FEP/pair_coul_cut_soft.cpp @@ -347,7 +347,7 @@ void PairCoulCutSoft::write_data_all(FILE *fp) /* ---------------------------------------------------------------------- */ double PairCoulCutSoft::single(int i, int j, int itype, int jtype, - double rsq, double factor_coul, double factor_lj, + double rsq, double factor_coul, double /*factor_lj*/, double &fforce) { double forcecoul,phicoul; diff --git a/src/USER-FEP/pair_coul_long_soft.cpp b/src/USER-FEP/pair_coul_long_soft.cpp index 94bb3659fa..e45dbe72d6 100644 --- a/src/USER-FEP/pair_coul_long_soft.cpp +++ b/src/USER-FEP/pair_coul_long_soft.cpp @@ -348,7 +348,7 @@ void PairCoulLongSoft::read_restart_settings(FILE *fp) double PairCoulLongSoft::single(int i, int j, int itype, int jtype, double rsq, - double factor_coul, double factor_lj, + double factor_coul, double /*factor_lj*/, double &fforce) { double r,grij,expm2,t,erfc,prefactor; diff --git a/src/USER-FEP/pair_lj_cut_soft.cpp b/src/USER-FEP/pair_lj_cut_soft.cpp index 4aaa5c2925..a33445f6f8 100644 --- a/src/USER-FEP/pair_lj_cut_soft.cpp +++ b/src/USER-FEP/pair_lj_cut_soft.cpp @@ -735,8 +735,8 @@ void PairLJCutSoft::write_data_all(FILE *fp) /* ---------------------------------------------------------------------- */ -double PairLJCutSoft::single(int i, int j, int itype, int jtype, double rsq, - double factor_coul, double factor_lj, +double PairLJCutSoft::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq, + double /*factor_coul*/, double factor_lj, double &fforce) { double forcelj,philj; diff --git a/src/USER-FEP/pair_morse_soft.cpp b/src/USER-FEP/pair_morse_soft.cpp index 7a897e1870..965d570863 100644 --- a/src/USER-FEP/pair_morse_soft.cpp +++ b/src/USER-FEP/pair_morse_soft.cpp @@ -360,8 +360,8 @@ void PairMorseSoft::write_data_all(FILE *fp) /* ---------------------------------------------------------------------- */ -double PairMorseSoft::single(int i, int j, int itype, int jtype, double rsq, - double factor_coul, double factor_lj, +double PairMorseSoft::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq, + double /*factor_coul*/, double factor_lj, double &fforce) { double r, dr, dexp, dexp2, dexp3, phi; diff --git a/src/USER-INTEL/angle_charmm_intel.cpp b/src/USER-INTEL/angle_charmm_intel.cpp index 672b70b6f6..f2542fc0c7 100644 --- a/src/USER-INTEL/angle_charmm_intel.cpp +++ b/src/USER-INTEL/angle_charmm_intel.cpp @@ -332,7 +332,7 @@ void AngleCharmmIntel::init_style() template void AngleCharmmIntel::pack_force_const(ForceConst &fc, - IntelBuffers *buffers) + IntelBuffers * /*buffers*/) { const int bp1 = atom->nangletypes + 1; fc.set_ntypes(bp1,memory); diff --git a/src/USER-INTEL/angle_harmonic_intel.cpp b/src/USER-INTEL/angle_harmonic_intel.cpp index 74639f3aeb..5777dad947 100644 --- a/src/USER-INTEL/angle_harmonic_intel.cpp +++ b/src/USER-INTEL/angle_harmonic_intel.cpp @@ -314,7 +314,7 @@ void AngleHarmonicIntel::init_style() template void AngleHarmonicIntel::pack_force_const(ForceConst &fc, - IntelBuffers *buffers) + IntelBuffers * /*buffers*/) { const int bp1 = atom->nangletypes + 1; fc.set_ntypes(bp1,memory); diff --git a/src/USER-INTEL/bond_fene_intel.cpp b/src/USER-INTEL/bond_fene_intel.cpp index 2d70049a89..9d54269c05 100644 --- a/src/USER-INTEL/bond_fene_intel.cpp +++ b/src/USER-INTEL/bond_fene_intel.cpp @@ -291,7 +291,7 @@ void BondFENEIntel::init_style() template void BondFENEIntel::pack_force_const(ForceConst &fc, - IntelBuffers *buffers) + IntelBuffers * /*buffers*/) { const int bp1 = atom->nbondtypes + 1; fc.set_ntypes(bp1,memory); diff --git a/src/USER-INTEL/bond_harmonic_intel.cpp b/src/USER-INTEL/bond_harmonic_intel.cpp index ed9cab082e..65894efa05 100644 --- a/src/USER-INTEL/bond_harmonic_intel.cpp +++ b/src/USER-INTEL/bond_harmonic_intel.cpp @@ -262,7 +262,7 @@ void BondHarmonicIntel::init_style() template void BondHarmonicIntel::pack_force_const(ForceConst &fc, - IntelBuffers *buffers) + IntelBuffers * /*buffers*/) { const int bp1 = atom->nbondtypes + 1; fc.set_ntypes(bp1,memory); diff --git a/src/USER-INTEL/dihedral_fourier_intel.cpp b/src/USER-INTEL/dihedral_fourier_intel.cpp index 6ad25f1ce4..6ccc165c61 100644 --- a/src/USER-INTEL/dihedral_fourier_intel.cpp +++ b/src/USER-INTEL/dihedral_fourier_intel.cpp @@ -401,7 +401,7 @@ void DihedralFourierIntel::init_style() template void DihedralFourierIntel::pack_force_const(ForceConst &fc, - IntelBuffers *buffers) + IntelBuffers * /*buffers*/) { const int bp1 = atom->ndihedraltypes + 1; fc.set_ntypes(bp1, setflag, nterms, memory); diff --git a/src/USER-INTEL/dihedral_harmonic_intel.cpp b/src/USER-INTEL/dihedral_harmonic_intel.cpp index b2bf54102c..ae5eb914e7 100644 --- a/src/USER-INTEL/dihedral_harmonic_intel.cpp +++ b/src/USER-INTEL/dihedral_harmonic_intel.cpp @@ -396,7 +396,7 @@ void DihedralHarmonicIntel::init_style() template void DihedralHarmonicIntel::pack_force_const(ForceConst &fc, - IntelBuffers *buffers) + IntelBuffers * /*buffers*/) { const int bp1 = atom->ndihedraltypes + 1; fc.set_ntypes(bp1,memory); diff --git a/src/USER-INTEL/dihedral_opls_intel.cpp b/src/USER-INTEL/dihedral_opls_intel.cpp index 832ce7ed50..ef95cc75bb 100644 --- a/src/USER-INTEL/dihedral_opls_intel.cpp +++ b/src/USER-INTEL/dihedral_opls_intel.cpp @@ -416,7 +416,7 @@ void DihedralOPLSIntel::init_style() template void DihedralOPLSIntel::pack_force_const(ForceConst &fc, - IntelBuffers *buffers) + IntelBuffers * /*buffers*/) { const int bp1 = atom->ndihedraltypes + 1; fc.set_ntypes(bp1,memory); diff --git a/src/USER-INTEL/fix_intel.cpp b/src/USER-INTEL/fix_intel.cpp index 7a206f472a..3a67b60632 100644 --- a/src/USER-INTEL/fix_intel.cpp +++ b/src/USER-INTEL/fix_intel.cpp @@ -349,7 +349,7 @@ void FixIntel::init() /* ---------------------------------------------------------------------- */ -void FixIntel::setup(int vflag) +void FixIntel::setup(int /*vflag*/) { if (neighbor->style != Neighbor::BIN) error->all(FLERR, @@ -539,7 +539,7 @@ void FixIntel::check_neighbor_intel() /* ---------------------------------------------------------------------- */ -void FixIntel::pre_reverse(int eflag, int vflag) +void FixIntel::pre_reverse(int /*eflag*/, int /*vflag*/) { if (_force_array_m != 0) { if (_need_reduce) { @@ -652,7 +652,7 @@ template void FixIntel::add_results(const ft * _noalias const f_in, const acc_t * _noalias const ev_global, const int eatom, const int vatom, - const int offload) { + const int /*offload*/) { start_watch(TIME_PACK); int f_length; #ifdef _LMP_INTEL_OFFLOAD @@ -719,16 +719,18 @@ void FixIntel::add_results(const ft * _noalias const f_in, template void FixIntel::add_oresults(const ft * _noalias const f_in, const acc_t * _noalias const ev_global, - const int eatom, const int vatom, + const int eatom, const int /*vatom*/, const int out_offset, const int nall) { lmp_ft * _noalias const f = (lmp_ft *) lmp->atom->f[0] + out_offset; if (atom->torque) { if (f_in[1].w) + { if (f_in[1].w == 1) error->all(FLERR,"Bad matrix inversion in mldivide3"); else error->all(FLERR, "Sphere particles not yet supported for gayberne/intel"); + } } int packthreads; diff --git a/src/USER-INTEL/fix_intel.h b/src/USER-INTEL/fix_intel.h index d7093e79bb..e6e09be503 100644 --- a/src/USER-INTEL/fix_intel.h +++ b/src/USER-INTEL/fix_intel.h @@ -74,7 +74,7 @@ class FixIntel : public Fix { inline int nbor_pack_width() const { return _nbor_pack_width; } inline void nbor_pack_width(const int w) { _nbor_pack_width = w; } inline int three_body_neighbor() { return _three_body_neighbor; } - inline void three_body_neighbor(const int i) { _three_body_neighbor = 1; } + inline void three_body_neighbor(const int /*i*/) { _three_body_neighbor = 1; } inline int need_zero(const int tid) { if (_need_reduce == 0 && tid > 0) return 1; @@ -82,7 +82,8 @@ class FixIntel : public Fix { } inline void set_reduce_flag() { if (_nthreads > 1) _need_reduce = 1; } inline int lrt() { - if (force->kspace_match("pppm/intel", 0)) return _lrt; + if (force->kspace_match("pppm/intel", 0) && update->whichflag == 1) + return _lrt; else return 0; } inline int pppm_table() { @@ -158,8 +159,8 @@ class FixIntel : public Fix { inline int host_start_neighbor() { return 0; } inline int host_start_pair() { return 0; } inline void zero_timers() {} - inline void start_watch(const int which) {} - inline double stop_watch(const int which) { return 0.0; } + inline void start_watch(const int /*which*/) {} + inline double stop_watch(const int /*which*/) { return 0.0; } double * off_watch_pair() { return NULL; } double * off_watch_neighbor() { return NULL; } inline void balance_stamp() {} @@ -237,7 +238,7 @@ class FixIntel : public Fix { /* ---------------------------------------------------------------------- */ -void FixIntel::get_buffern(const int offload, int &nlocal, int &nall, +void FixIntel::get_buffern(const int /*offload*/, int &nlocal, int &nall, int &minlocal) { #ifdef _LMP_INTEL_OFFLOAD if (_separate_buffers) { @@ -272,7 +273,7 @@ void FixIntel::get_buffern(const int offload, int &nlocal, int &nall, /* ---------------------------------------------------------------------- */ void FixIntel::add_result_array(IntelBuffers::vec3_acc_t *f_in, - double *ev_in, const int offload, + double *ev_in, const int /*offload*/, const int eatom, const int vatom, const int rflag) { #ifdef _LMP_INTEL_OFFLOAD @@ -300,7 +301,7 @@ void FixIntel::add_result_array(IntelBuffers::vec3_acc_t *f_in, /* ---------------------------------------------------------------------- */ void FixIntel::add_result_array(IntelBuffers::vec3_acc_t *f_in, - double *ev_in, const int offload, + double *ev_in, const int /*offload*/, const int eatom, const int vatom, const int rflag) { #ifdef _LMP_INTEL_OFFLOAD @@ -328,7 +329,7 @@ void FixIntel::add_result_array(IntelBuffers::vec3_acc_t *f_in, /* ---------------------------------------------------------------------- */ void FixIntel::add_result_array(IntelBuffers::vec3_acc_t *f_in, - float *ev_in, const int offload, + float *ev_in, const int /*offload*/, const int eatom, const int vatom, const int rflag) { #ifdef _LMP_INTEL_OFFLOAD diff --git a/src/USER-INTEL/fix_nh_intel.cpp b/src/USER-INTEL/fix_nh_intel.cpp index 44253e8bb0..bf4764f104 100644 --- a/src/USER-INTEL/fix_nh_intel.cpp +++ b/src/USER-INTEL/fix_nh_intel.cpp @@ -464,7 +464,6 @@ void FixNHIntel::nve_x() { double * _noalias const x = atom->x[0]; double * _noalias const v = atom->v[0]; - const double * _noalias const f = atom->f[0]; // x update by full step only for atoms in group diff --git a/src/USER-INTEL/fix_nve_asphere_intel.cpp b/src/USER-INTEL/fix_nve_asphere_intel.cpp index 17bbcff771..7eeb8a1635 100644 --- a/src/USER-INTEL/fix_nve_asphere_intel.cpp +++ b/src/USER-INTEL/fix_nve_asphere_intel.cpp @@ -79,12 +79,8 @@ void FixNVEAsphereIntel::setup(int vflag) /* ---------------------------------------------------------------------- */ -void FixNVEAsphereIntel::initial_integrate(int vflag) +void FixNVEAsphereIntel::initial_integrate(int /*vflag*/) { - double dtfm; - double inertia[3],omega[3]; - double *shape,*quat; - AtomVecEllipsoid::Bonus *bonus = avec->bonus; int *ellipsoid = atom->ellipsoid; double * _noalias const x = atom->x[0]; @@ -94,7 +90,6 @@ void FixNVEAsphereIntel::initial_integrate(int vflag) double **angmom = atom->angmom; double **torque = atom->torque; - double *rmass = atom->rmass; int nlocal = atom->nlocal; if (igroup == atom->firstgroup) nlocal = atom->nfirst; @@ -143,8 +138,6 @@ void FixNVEAsphereIntel::final_integrate() { if (neighbor->ago == 0) reset_dt(); - double dtfm; - double * _noalias const v = atom->v[0]; const double * _noalias const f = atom->f[0]; double * _noalias const angmom = atom->angmom[0]; diff --git a/src/USER-INTEL/fix_nve_intel.cpp b/src/USER-INTEL/fix_nve_intel.cpp index c0f6da06ae..7dee31d2f4 100644 --- a/src/USER-INTEL/fix_nve_intel.cpp +++ b/src/USER-INTEL/fix_nve_intel.cpp @@ -56,7 +56,7 @@ void FixNVEIntel::setup(int vflag) allow for both per-type and per-atom mass ------------------------------------------------------------------------- */ -void FixNVEIntel::initial_integrate(int vflag) +void FixNVEIntel::initial_integrate(int /*vflag*/) { // update v and x of atoms in group diff --git a/src/USER-INTEL/improper_cvff_intel.cpp b/src/USER-INTEL/improper_cvff_intel.cpp index e0ef2162d1..c20c004657 100644 --- a/src/USER-INTEL/improper_cvff_intel.cpp +++ b/src/USER-INTEL/improper_cvff_intel.cpp @@ -428,7 +428,7 @@ void ImproperCvffIntel::init_style() template void ImproperCvffIntel::pack_force_const(ForceConst &fc, - IntelBuffers *buffers) + IntelBuffers * /*buffers*/) { const int bp1 = atom->nimpropertypes + 1; fc.set_ntypes(bp1,memory); diff --git a/src/USER-INTEL/improper_harmonic_intel.cpp b/src/USER-INTEL/improper_harmonic_intel.cpp index 60cbe16358..167095150e 100644 --- a/src/USER-INTEL/improper_harmonic_intel.cpp +++ b/src/USER-INTEL/improper_harmonic_intel.cpp @@ -384,7 +384,7 @@ void ImproperHarmonicIntel::init_style() template void ImproperHarmonicIntel::pack_force_const(ForceConst &fc, - IntelBuffers *buffers) + IntelBuffers * /*buffers*/) { const int bp1 = atom->nimpropertypes + 1; fc.set_ntypes(bp1,memory); diff --git a/src/USER-INTEL/intel_buffers.cpp b/src/USER-INTEL/intel_buffers.cpp index 0f32cb48b2..05176e1fd1 100644 --- a/src/USER-INTEL/intel_buffers.cpp +++ b/src/USER-INTEL/intel_buffers.cpp @@ -109,7 +109,7 @@ void IntelBuffers::free_buffers() template void IntelBuffers::_grow(const int nall, const int nlocal, const int nthreads, - const int offload_end) + const int /*offload_end*/) { free_buffers(); _buf_size = static_cast(nall) * 1.1 + 1; @@ -200,7 +200,7 @@ void IntelBuffers::free_nmax() /* ---------------------------------------------------------------------- */ template -void IntelBuffers::_grow_nmax(const int offload_end) +void IntelBuffers::_grow_nmax(const int /*offload_end*/) { #ifdef _LMP_INTEL_OFFLOAD free_nmax(); @@ -264,7 +264,7 @@ void IntelBuffers::free_list_local() template void IntelBuffers::_grow_list_local(NeighList *list, - const int offload_end) + const int /*offload_end*/) { free_list_local(); int size = list->get_maxlocal(); @@ -310,10 +310,10 @@ void IntelBuffers::free_nbor_list() /* ---------------------------------------------------------------------- */ template -void IntelBuffers::_grow_nbor_list(NeighList *list, +void IntelBuffers::_grow_nbor_list(NeighList * /*list*/, const int nlocal, const int nthreads, - const int offload_end, + const int /*offload_end*/, const int pack_width) { free_nbor_list(); @@ -382,7 +382,7 @@ void IntelBuffers::free_ccache() /* ---------------------------------------------------------------------- */ template -void IntelBuffers::grow_ccache(const int off_flag, +void IntelBuffers::grow_ccache(const int /*off_flag*/, const int nthreads, const int width) { @@ -481,7 +481,7 @@ void IntelBuffers::free_ncache() /* ---------------------------------------------------------------------- */ template -void IntelBuffers::grow_ncache(const int off_flag, +void IntelBuffers::grow_ncache(const int /*off_flag*/, const int nthreads) { const int nsize = get_max_nbors() * 3; diff --git a/src/USER-INTEL/intel_buffers.h b/src/USER-INTEL/intel_buffers.h index 8040715b2e..e8225a4a30 100644 --- a/src/USER-INTEL/intel_buffers.h +++ b/src/USER-INTEL/intel_buffers.h @@ -135,24 +135,24 @@ class IntelBuffers { void set_ntypes(const int ntypes, const int use_ghost_cut = 0); - inline int * firstneigh(const NeighList *list) { return _list_alloc; } - inline int * cnumneigh(const NeighList *list) { return _cnumneigh; } + inline int * firstneigh(const NeighList * /*list*/) { return _list_alloc; } + inline int * cnumneigh(const NeighList * /*list*/) { return _cnumneigh; } inline int * get_atombin() { return _atombin; } inline int * get_binpacked() { return _binpacked; } - inline atom_t * get_x(const int offload = 1) { + inline atom_t * get_x(const int /*offload*/ = 1) { #ifdef _LMP_INTEL_OFFLOAD if (_separate_buffers && offload == 0) return _host_x; #endif return _x; } - inline flt_t * get_q(const int offload = 1) { + inline flt_t * get_q(const int /*offload*/ = 1) { #ifdef _LMP_INTEL_OFFLOAD if (_separate_buffers && offload == 0) return _host_q; #endif return _q; } - inline quat_t * get_quat(const int offload = 1) { + inline quat_t * get_quat(const int /*offload*/ = 1) { #ifdef _LMP_INTEL_OFFLOAD if (_separate_buffers && offload == 0) return _host_quat; #endif diff --git a/src/USER-INTEL/intel_intrinsics_airebo.h b/src/USER-INTEL/intel_intrinsics_airebo.h index 4a86d8db29..b20f9c8ad1 100644 --- a/src/USER-INTEL/intel_intrinsics_airebo.h +++ b/src/USER-INTEL/intel_intrinsics_airebo.h @@ -2057,8 +2057,8 @@ public: } VEC_INLINE static ivec set( - int i15, int i14, int i13, int i12, int i11, int i10, int i9, int i8, - int i7, int i6, int i5, int i4, int i3, int i2, int i1, int i0 + int /*i15*/, int /*i14*/, int /*i13*/, int /*i12*/, int /*i11*/, int /*i10*/, int /*i9*/, int /*i8*/, + int /*i7*/, int /*i6*/, int /*i5*/, int /*i4*/, int /*i3*/, int /*i2*/, int /*i1*/, int i0 ) { return i0; } @@ -2243,7 +2243,7 @@ public: FVEC_BINOP(*, mul) FVEC_BINOP(/, div) - VEC_INLINE static void gather_prefetch0(const ivec &idx, const void * mem) {} + VEC_INLINE static void gather_prefetch0(const ivec & /*idx*/, const void * /*mem*/) {} }; class avec { diff --git a/src/USER-INTEL/intel_preprocess.h b/src/USER-INTEL/intel_preprocess.h index 29cc45f755..2f1b02a49f 100644 --- a/src/USER-INTEL/intel_preprocess.h +++ b/src/USER-INTEL/intel_preprocess.h @@ -134,7 +134,21 @@ enum {TIME_PACK, TIME_HOST_NEIGHBOR, TIME_HOST_PAIR, TIME_OFFLOAD_NEIGHBOR, #define INTEL_HTHREADS 2 #endif -#define IP_PRE_get_stride(stride, n, datasize, torque) \ +#if INTEL_DATA_ALIGN > 1 + +#define IP_PRE_edge_align(n, esize) \ + { \ + const int pad_mask = ~static_cast(INTEL_DATA_ALIGN/esize-1); \ + n = (n + INTEL_DATA_ALIGN / esize - 1) & pad_mask; \ + } + +#else + +#define IP_PRE_edge_align(n, esize) \ + +#endif + +#define IP_PRE_get_stride(stride, n, datasize, torque) \ { \ int blength = n; \ if (torque) blength *= 2; \ @@ -303,7 +317,7 @@ enum {TIME_PACK, TIME_HOST_NEIGHBOR, TIME_HOST_PAIR, TIME_OFFLOAD_NEIGHBOR, { \ tid = 0; \ ifrom = 0; \ - ip = 1; \ + ip = vecsize; \ ito = inum; \ } @@ -316,7 +330,7 @@ enum {TIME_PACK, TIME_HOST_NEIGHBOR, TIME_HOST_PAIR, TIME_OFFLOAD_NEIGHBOR, acc_t *f_scalar = &f_start[0].x; \ flt_t *x_scalar = &pos[minlocal].x; \ int f_stride4 = f_stride * 4; \ - _alignvar(acc_t ovv[INTEL_COMPILE_WIDTH],64); \ + _alignvar(acc_t ovv[16],64); \ int vwidth; \ if (sizeof(acc_t) == sizeof(double)) \ vwidth = INTEL_COMPILE_WIDTH/2; \ @@ -516,6 +530,22 @@ inline double MIC_Wtime() { return time; } +#define IP_PRE_neighbor_pad(jnum, offload) \ +{ \ + const int opad_mask = ~static_cast(INTEL_MIC_NBOR_PAD * \ + sizeof(float) / \ + sizeof(flt_t) - 1); \ + const int pad_mask = ~static_cast(INTEL_NBOR_PAD * \ + sizeof(float) / \ + sizeof(flt_t) - 1); \ + if (offload && INTEL_MIC_NBOR_PAD > 1) \ + jnum = (jnum + INTEL_MIC_NBOR_PAD * sizeof(float) / \ + sizeof(flt_t) - 1) & opad_mask; \ + else if (INTEL_NBOR_PAD > 1) \ + jnum = (jnum + INTEL_NBOR_PAD * sizeof(float) / \ + sizeof(flt_t) - 1) & pad_mask; \ +} + #define IP_PRE_pack_separate_buffers(fix, buffers, ago, offload, \ nlocal, nall) \ { \ @@ -644,6 +674,23 @@ inline double MIC_Wtime() { #else +#if INTEL_NBOR_PAD > 1 + +#define IP_PRE_neighbor_pad(jnum, offload) \ +{ \ + const int pad_mask = ~static_cast(INTEL_NBOR_PAD * \ + sizeof(float) / \ + sizeof(flt_t) - 1); \ + jnum = (jnum + INTEL_NBOR_PAD * sizeof(float) / \ + sizeof(flt_t) - 1) & pad_mask; \ +} + +#else + +#define IP_PRE_neighbor_pad(jnum, offload) + +#endif + #define MIC_Wtime MPI_Wtime #define IP_PRE_pack_separate_buffers(fix, buffers, ago, offload, \ nlocal, nall) diff --git a/src/USER-INTEL/nbin_intel.cpp b/src/USER-INTEL/nbin_intel.cpp index e071b141fe..789fa35b42 100644 --- a/src/USER-INTEL/nbin_intel.cpp +++ b/src/USER-INTEL/nbin_intel.cpp @@ -192,15 +192,10 @@ void NBinIntel::bin_atoms(IntelBuffers * buffers) { // ---------- Bin Atoms ------------- _fix->start_watch(TIME_HOST_NEIGHBOR); - const ATOM_T * _noalias const x = buffers->get_x(); + //const ATOM_T * _noalias const x = buffers->get_x(); int * _noalias const atombin = this->_atombin; int * _noalias const binpacked = this->_binpacked; - - const double sboxlo0 = bboxlo[0] + mbinxlo/bininvx; - const double sboxlo1 = bboxlo[1] + mbinylo/bininvy; - const double sboxlo2 = bboxlo[2] + mbinzlo/bininvz; - int i, ibin; for (i = 0; i < mbins; i++) binhead[i] = -1; diff --git a/src/USER-INTEL/npair_full_bin_ghost_intel.cpp b/src/USER-INTEL/npair_full_bin_ghost_intel.cpp index 24d5076c34..74a04f0e7d 100644 --- a/src/USER-INTEL/npair_full_bin_ghost_intel.cpp +++ b/src/USER-INTEL/npair_full_bin_ghost_intel.cpp @@ -106,17 +106,15 @@ void NPairFullBinGhostIntel::fbi(NeighList * list, /* ---------------------------------------------------------------------- */ template -void NPairFullBinGhostIntel::fbi(const int offload, NeighList * list, +void NPairFullBinGhostIntel::fbi(const int /*offload*/, NeighList * list, IntelBuffers * buffers, const int pstart, const int pend) { if (pend-pstart == 0) return; const int nall = atom->nlocal + atom->nghost; - int pad = 1; int nall_t = nall; const int aend = nall; - const int pack_width = _fix->nbor_pack_width(); const ATOM_T * _noalias const x = buffers->get_x(); int * _noalias const firstneigh = buffers->firstneigh(list); const int e_nall = nall_t; @@ -156,9 +154,6 @@ void NPairFullBinGhostIntel::fbi(const int offload, NeighList * list, tagint * const molecule = atom->molecule; #endif - int *molindex = atom->molindex; - int *molatom = atom->molatom; - Molecule **onemols = atom->avec->onemols; int moltemplate; if (molecular == 2) moltemplate = 1; else moltemplate = 0; @@ -168,8 +163,8 @@ void NPairFullBinGhostIntel::fbi(const int offload, NeighList * list, int tnum; int *overflow; - double *timer_compute; #ifdef _LMP_INTEL_OFFLOAD + double *timer_compute; if (offload) { timer_compute = _fix->off_watch_neighbor(); tnum = buffers->get_off_threads(); @@ -207,6 +202,17 @@ void NPairFullBinGhostIntel::fbi(const int offload, NeighList * list, const int mbinz = this->mbinz; const int * const stencilxyz = &this->stencilxyz[0][0]; + int sb = 1; + if (special_flag[1] == 0) { + sb = 2; + if (special_flag[2] == 0) { + sb = 3; + if (special_flag[3] == 0) + sb = 4; + } + } + const int special_bound = sb; + #ifdef _LMP_INTEL_OFFLOAD const int * _noalias const binhead = this->binhead; const int * _noalias const bins = this->bins; @@ -230,7 +236,7 @@ void NPairFullBinGhostIntel::fbi(const int offload, NeighList * list, in(ncachex,ncachey,ncachez,ncachej:length(0) alloc_if(0) free_if(0)) \ in(ncachejtype,ncachetag:length(0) alloc_if(0) free_if(0)) \ in(ncache_stride,maxnbors,nthreads,maxspecial,nstencil,e_nall,offload) \ - in(separate_buffers,aend,nlocal,molecular,ntypes,mbinx,mbiny) \ + in(separate_buffers,aend,nlocal,molecular,ntypes,mbinx,mbiny,special_bound)\ in(mbinz,xperiodic,yperiodic,zperiodic,xprd_half,yprd_half,zprd_half) \ in(stencilxyz:length(3*nstencil)) \ out(overflow:length(5) alloc_if(0) free_if(0)) \ @@ -287,8 +293,6 @@ void NPairFullBinGhostIntel::fbi(const int offload, NeighList * list, int e_ito = ito; const int list_size = (e_ito + tid * 2 + 2) * maxnbors; - int which; - int pack_offset = maxnbors; int ct = (ifrom + tid * 2) * maxnbors; int *neighptr = firstneigh + ct; @@ -303,7 +307,7 @@ void NPairFullBinGhostIntel::fbi(const int offload, NeighList * list, int * _noalias const ttag = ncachetag + toffs; // loop over all atoms in other bins in stencil, store every pair - int istart, icount, ncount, oldbin = -9999999, lane, max_chunk; + int ncount, oldbin = -9999999; for (int i = ifrom; i < ito; i++) { const flt_t xtmp = x[i].x; const flt_t ytmp = x[i].y; @@ -418,41 +422,109 @@ void NPairFullBinGhostIntel::fbi(const int offload, NeighList * list, } } // for u + if (molecular && i < nlocal) { + int alln = n; + n = 0; + #if defined(LMP_SIMD_COMPILER) + #pragma vector aligned + #ifdef LMP_INTEL_NBOR_COMPAT + #pragma ivdep + #else + #pragma simd + #endif + #endif + for (int u = 0; u < alln; u++) { + int which; + int addme = 1; + int j = neighptr[u]; + if (need_ic && j < 0) { + which = 0; + j = -j - 1; + } else + ofind_special(which, special, nspecial, i, tag[j]); + if (which) { + j = j ^ (which << SBBITS); + if (which < special_bound) addme = 0; + } + #ifdef LMP_INTEL_NBOR_COMPAT + if (addme) neighptr2[n++] = j; + #else + neighptr2[n++] = j; + #endif + } + alln = n2; + n2 = maxnbors * 2; + #if defined(LMP_SIMD_COMPILER) + #pragma vector aligned + #ifdef LMP_INTEL_NBOR_COMPAT + #pragma ivdep + #else + #pragma simd + #endif + #endif + for (int u = n2; u < alln; u++) { + int which; + int addme = 1; + int j = neighptr[u]; + if (need_ic && j < 0) { + which = 0; + j = -j - 1; + } else + ofind_special(which, special, nspecial, i, tag[j]); + if (which) { + j = j ^ (which << SBBITS); + if (which < special_bound) addme = 0; + } + #ifdef LMP_INTEL_NBOR_COMPAT + if (addme) neighptr2[n2++] = j; + #else + neighptr2[n2++] = j; + #endif + } + } + #ifndef _LMP_INTEL_OFFLOAD if (exclude) { int alln = n; n = maxnbors; - for (int u = pack_offset; u < alln; u++) { - const int j = neighptr[u]; - int pj = j; - if (need_ic) - if (pj < 0) pj = -j - 1; - const int jtype = x[pj].w; - if (exclusion(i,pj,itype,jtype,mask,molecule)) continue; - neighptr[n++] = j; + #if defined(LMP_SIMD_COMPILER) + #pragma vector aligned + #pragma ivdep + #endif + for (int u = n; u < alln; u++) { + int addme = 1; + const int js = neighptr[u]; + const int j = js & NEIGHMASK; + const int jtype = x[j].w; + if (exclusion(i,j,itype,jtype,mask,molecule)) addme = 0; + if (addme) neighptr2[n++] = js; } alln = n2; n2 = maxnbors * 2; + #if defined(LMP_SIMD_COMPILER) + #pragma vector aligned + #pragma ivdep + #endif for (int u = n2; u < alln; u++) { - const int j = neighptr[u]; - int pj = j; - if (need_ic) - if (pj < 0) pj = -j - 1; - const int jtype = x[pj].w; - if (exclusion(i,pj,itype,jtype,mask,molecule)) continue; - neighptr[n2++] = j; + int addme = 1; + const int js = neighptr[u]; + const int j = js & NEIGHMASK; + const int jtype = x[j].w; + if (exclusion(i,j,itype,jtype,mask,molecule)) addme = 0; + if (addme) neighptr2[n2++] = js; } } #endif + int ns = n - maxnbors; int alln = n; atombin[i] = ns; n = 0; for (int u = maxnbors; u < alln; u++) - neighptr[n++] = neighptr[u]; + neighptr[n++] = neighptr2[u]; ns += n2 - maxnbors * 2; for (int u = maxnbors * 2; u < n2; u++) - neighptr[n++] = neighptr[u]; + neighptr[n++] = neighptr2[u]; if (ns > maxnbors) *overflow = 1; ilist[i] = i; @@ -460,9 +532,7 @@ void NPairFullBinGhostIntel::fbi(const int offload, NeighList * list, numneigh[i] = ns; ct += ns; - const int alignb = (INTEL_DATA_ALIGN / sizeof(int)); - const int edge = ct & (alignb - 1); - if (edge) ct += alignb - edge; + IP_PRE_edge_align(ct, sizeof(int)); neighptr = firstneigh + ct; if (ct + obound > list_size) { if (i < ito - 1) { @@ -477,84 +547,11 @@ void NPairFullBinGhostIntel::fbi(const int offload, NeighList * list, numneigh[i] = 0; #ifdef _LMP_INTEL_OFFLOAD - int ghost_offset = 0, nall_offset = e_nall; if (separate_buffers) { - for (int i = ifrom; i < ito; ++i) { - int * _noalias jlist = firstneigh + cnumneigh[i]; - const int jnum = numneigh[i]; - #if __INTEL_COMPILER+0 > 1499 - #pragma vector aligned - #pragma simd - #endif - for (int jj = 0; jj < jnum; jj++) { - int j = jlist[jj]; - if (need_ic && j < 0) j = -j - 1; - } - } - overflow[LMP_LOCAL_MIN] = 0; overflow[LMP_LOCAL_MAX] = nlocal - 1; overflow[LMP_GHOST_MIN] = nlocal; overflow[LMP_GHOST_MAX] = e_nall - 1; - - int nghost = overflow[LMP_GHOST_MAX] + 1 - overflow[LMP_GHOST_MIN]; - if (nghost < 0) nghost = 0; - if (offload) { - ghost_offset = overflow[LMP_GHOST_MIN] - overflow[LMP_LOCAL_MAX] - 1; - nall_offset = overflow[LMP_LOCAL_MAX] + 1 + nghost; - } else { - ghost_offset = overflow[LMP_GHOST_MIN] - nlocal; - nall_offset = nlocal + nghost; - } - } // if separate_buffers - #endif - - if (molecular) { - int ito_m = ito; - if (ito >= nlocal) ito_m = nlocal; - for (int i = ifrom; i < ito_m; ++i) { - int * _noalias jlist = firstneigh + cnumneigh[i]; - const int jnum = numneigh[i]; - - #if defined(LMP_SIMD_COMPILER) - #pragma vector aligned - #pragma simd - #endif - for (int jj = 0; jj < jnum; jj++) { - const int j = jlist[jj]; - if (need_ic && j < 0) { - which = 0; - jlist[jj] = -j - 1; - } else - ofind_special(which, special, nspecial, i, tag[j]); - #ifdef _LMP_INTEL_OFFLOAD - if (j >= nlocal) { - if (j == e_nall) - jlist[jj] = nall_offset; - else if (which) - jlist[jj] = (j-ghost_offset) ^ (which << SBBITS); - else jlist[jj]-=ghost_offset; - } else - #endif - if (which) jlist[jj] = j ^ (which << SBBITS); - } - } // for i - } // if molecular - #ifdef _LMP_INTEL_OFFLOAD - else if (separate_buffers) { - for (int i = ifrom; i < ito; ++i) { - int * _noalias jlist = firstneigh + cnumneigh[i]; - const int jnum = numneigh[i]; - int jj = 0; - #pragma vector aligned - #pragma simd - for (jj = 0; jj < jnum; jj++) { - if (jlist[jj] >= nlocal) { - if (jlist[jj] == e_nall) jlist[jj] = nall_offset; - else jlist[jj] -= ghost_offset; - } - } - } } #endif } // end omp diff --git a/src/USER-INTEL/npair_intel.cpp b/src/USER-INTEL/npair_intel.cpp index d3d2745aee..6d4529752a 100644 --- a/src/USER-INTEL/npair_intel.cpp +++ b/src/USER-INTEL/npair_intel.cpp @@ -54,27 +54,20 @@ NPairIntel::~NPairIntel() { template -void NPairIntel::bin_newton(const int offload, NeighList *list, +void NPairIntel::bin_newton(const int /*offload*/, NeighList *list, IntelBuffers *buffers, const int astart, const int aend, - const int offload_end) { + const int /*offload_end*/) { if (aend-astart == 0) return; const int nall = atom->nlocal + atom->nghost; - int pad = 1; int nall_t = nall; #ifdef _LMP_INTEL_OFFLOAD if (offload_noghost && offload) nall_t = atom->nlocal; - if (THREE == 0 && offload) { - if (INTEL_MIC_NBOR_PAD > 1) - pad = INTEL_MIC_NBOR_PAD * sizeof(float) / sizeof(flt_t); - } else #endif - if (THREE == 0 && INTEL_NBOR_PAD > 1) - pad = INTEL_NBOR_PAD * sizeof(float) / sizeof(flt_t); - const int pad_width = pad; + const int pack_width = _fix->nbor_pack_width(); const ATOM_T * _noalias const x = buffers->get_x(); @@ -116,8 +109,8 @@ void NPairIntel::bin_newton(const int offload, NeighList *list, int tnum; int *overflow; - double *timer_compute; #ifdef _LMP_INTEL_OFFLOAD + double *timer_compute; if (offload) { timer_compute = _fix->off_watch_neighbor(); tnum = buffers->get_off_threads(); @@ -150,6 +143,17 @@ void NPairIntel::bin_newton(const int offload, NeighList *list, int * _noalias const ncachetag = buffers->get_ncachetag(); const int ncache_stride = buffers->ncache_stride(); + int sb = 1; + if (special_flag[1] == 0) { + sb = 2; + if (special_flag[2] == 0) { + sb = 3; + if (special_flag[3] == 0) + sb = 4; + } + } + const int special_bound = sb; + #ifdef _LMP_INTEL_OFFLOAD const int * _noalias const binhead = this->binhead; const int * _noalias const bins = this->bins; @@ -172,9 +176,9 @@ void NPairIntel::bin_newton(const int offload, NeighList *list, in(ncachex,ncachey,ncachez,ncachej:length(0) alloc_if(0) free_if(0)) \ in(ncachejtype,ncachetag:length(0) alloc_if(0) free_if(0)) \ in(ncache_stride,maxnbors,nthreads,maxspecial,nstencil,e_nall,offload) \ - in(pad_width,offload_end,separate_buffers,astart,aend,nlocal,molecular) \ + in(offload_end,separate_buffers,astart,aend,nlocal,molecular) \ in(ntypes,xperiodic,yperiodic,zperiodic,xprd_half,yprd_half,zprd_half) \ - in(pack_width) \ + in(pack_width,special_bound) \ out(overflow:length(5) alloc_if(0) free_if(0)) \ out(timer_compute:length(1) alloc_if(0) free_if(0)) \ signal(tag) @@ -226,19 +230,25 @@ void NPairIntel::bin_newton(const int offload, NeighList *list, ifrom += astart; ito += astart; int e_ito = ito; + #ifdef LMP_INTEL_3BODY_FAST if (THREE && ito == num) { int imod = ito & (pack_width - 1); if (imod) e_ito += pack_width - imod; } + #endif const int list_size = (e_ito + tid * 2 + 2) * maxnbors; - int which; - - int pack_offset = maxnbors; - if (THREE) pack_offset *= pack_width; + #ifdef LMP_INTEL_3BODY_FAST + const int pack_offset = maxnbors * pack_width; + const int obound = pack_offset + maxnbors * 2; + #else + const int pack_offset = 0; + const int obound = maxnbors * 3; + #endif int ct = (ifrom + tid * 2) * maxnbors; int *neighptr = firstneigh + ct; - const int obound = pack_offset + maxnbors * 2; + int *neighptr2; + if (THREE) neighptr2 = neighptr; const int toffs = tid * ncache_stride; flt_t * _noalias const tx = ncachex + toffs; @@ -255,11 +265,14 @@ void NPairIntel::bin_newton(const int offload, NeighList *list, int * _noalias itjtype; // loop over all atoms in other bins in stencil, store every pair - int istart, icount, ncount, oldbin = -9999999, lane, max_chunk; + int istart, icount, ncount, oldbin = -9999999; + #ifdef LMP_INTEL_3BODY_FAST + int lane, max_chunk; if (THREE) { lane = 0; max_chunk = 0; } + #endif for (int i = ifrom; i < ito; i++) { const flt_t xtmp = x[i].x; const flt_t ytmp = x[i].y; @@ -298,9 +311,7 @@ void NPairIntel::bin_newton(const int offload, NeighList *list, if (FULL == 0 || TRI == 1) { icount = 0; istart = ncount; - const int alignb = INTEL_DATA_ALIGN / sizeof(int); - int nedge = istart & (alignb - 1); - if (nedge) istart + (alignb - nedge); + IP_PRE_edge_align(istart, sizeof(int)); itx = tx + istart; ity = ty + istart; itz = tz + istart; @@ -383,11 +394,12 @@ void NPairIntel::bin_newton(const int offload, NeighList *list, // ---------------------- Loop over other bins - int n2, *neighptr2; + int n2; if (THREE) { + #ifdef LMP_INTEL_3BODY_FAST n = pack_offset; + #endif n2 = pack_offset + maxnbors; - neighptr2 = neighptr; } #if defined(LMP_SIMD_COMPILER) #pragma vector aligned @@ -461,49 +473,132 @@ void NPairIntel::bin_newton(const int offload, NeighList *list, } } // for u + if (molecular) { + if (!THREE) neighptr2 = neighptr; + int alln = n; + + n = pack_offset; + #if defined(LMP_SIMD_COMPILER) + #pragma vector aligned + #ifdef LMP_INTEL_NBOR_COMPAT + #pragma ivdep + #else + #pragma simd + #endif + #endif + for (int u = n; u < alln; u++) { + int which; + int addme = 1; + int j = neighptr[u]; + if (need_ic && j < 0) { + which = 0; + j = -j - 1; + } else + ofind_special(which, special, nspecial, i, tag[j]); + + if (which) { + j = j ^ (which << SBBITS); + if (which < special_bound) addme = 0; + } + #ifdef LMP_INTEL_NBOR_COMPAT + if (addme) neighptr2[n++] = j; + #else + neighptr2[n++]=j; + #endif + } + + if (THREE) { + alln = n2; + n2 = pack_offset + maxnbors; + + #if defined(LMP_SIMD_COMPILER) + #pragma vector aligned + #ifdef LMP_INTEL_NBOR_COMPAT + #pragma ivdep + #else + #pragma simd + #endif + #endif + for (int u = n2; u < alln; u++) { + int which; + int addme = 1; + int j = neighptr[u]; + if (need_ic && j < 0) { + which = 0; + j = -j - 1; + } else + ofind_special(which, special, nspecial, i, tag[j]); + if (which) { + j = j ^ (which << SBBITS); + if (which < special_bound) addme = 0; + } + #ifdef LMP_INTEL_NBOR_COMPAT + if (addme) neighptr2[n2++] = j; + #else + neighptr2[n2++]=j; + #endif + } + } + } + #ifndef _LMP_INTEL_OFFLOAD if (exclude) { + neighptr2 = neighptr; int alln = n; - if (THREE) n = pack_offset; - else n = 0; - for (int u = pack_offset; u < alln; u++) { - const int j = neighptr[u]; - int pj = j; - if (need_ic) - if (pj < 0) pj = -j - 1; - const int jtype = x[pj].w; - if (exclusion(i,pj,itype,jtype,mask,molecule)) continue; - neighptr[n++] = j; + n = pack_offset; + + #if defined(LMP_SIMD_COMPILER) + #pragma vector aligned + #pragma ivdep + #endif + for (int u = n; u < alln; u++) { + int addme = 1; + const int js = neighptr[u]; + const int j = js & NEIGHMASK; + const int jtype = x[j].w; + if (exclusion(i,j,itype,jtype,mask,molecule)) addme = 0; + if (addme) neighptr2[n++] = js; } if (THREE) { alln = n2; n2 = pack_offset + maxnbors; - for (int u = pack_offset + maxnbors; u < alln; u++) { - const int j = neighptr[u]; - int pj = j; - if (need_ic) - if (pj < 0) pj = -j - 1; - const int jtype = x[pj].w; - if (exclusion(i,pj,itype,jtype,mask,molecule)) continue; - neighptr[n2++] = j; + #if defined(LMP_SIMD_COMPILER) + #pragma vector aligned + #pragma ivdep + #endif + for (int u = n2; u < alln; u++) { + int addme = 1; + const int js = neighptr[u]; + const int j = js & NEIGHMASK; + const int jtype = x[j].w; + if (exclusion(i,j,itype,jtype,mask,molecule)) addme = 0; + if (addme) neighptr2[n2++] = js; } } } #endif + int ns; if (THREE) { - int alln = n; ns = n - pack_offset; atombin[i] = ns; + ns += n2 - pack_offset - maxnbors; + + #ifdef LMP_INTEL_3BODY_FAST n = lane; for (int u = pack_offset; u < alln; u++) { - neighptr[n] = neighptr[u]; + neighptr[n] = neighptr2[u]; n += pack_width; } - ns += n2 - pack_offset - maxnbors; + #endif + for (int u = pack_offset + maxnbors; u < n2; u++) { - neighptr[n] = neighptr[u]; + #ifdef LMP_INTEL_3BODY_FAST + neighptr[n] = neighptr2[u]; n += pack_width; + #else + neighptr[n++] = neighptr2[u]; + #endif } if (ns > maxnbors) *overflow = 1; } else @@ -512,34 +607,33 @@ void NPairIntel::bin_newton(const int offload, NeighList *list, ilist[i] = i; cnumneigh[i] = ct; if (THREE) { + #ifdef LMP_INTEL_3BODY_FAST cnumneigh[i] += lane; + #endif numneigh[i] = ns; } else { - int edge = n & (pad_width - 1); - if (edge) { - const int pad_end = n + (pad_width - edge); - #if defined(LMP_SIMD_COMPILER) - #pragma vector aligned - #pragma loop_count min=1, max=INTEL_COMPILE_WIDTH-1, \ - avg=INTEL_COMPILE_WIDTH/2 - #endif - for ( ; n < pad_end; n++) - neighptr[n] = e_nall; - } numneigh[i] = n; + int pad_end = n; + IP_PRE_neighbor_pad(pad_end, offload); + #if defined(LMP_SIMD_COMPILER) + #pragma vector aligned + #pragma loop_count min=1, max=INTEL_COMPILE_WIDTH-1, \ + avg=INTEL_COMPILE_WIDTH/2 + #endif + for ( ; n < pad_end; n++) + neighptr[n] = e_nall; } + #ifdef LMP_INTEL_3BODY_FAST if (THREE) { if (ns > max_chunk) max_chunk = ns; lane++; if (lane == pack_width) { ct += max_chunk * pack_width; - const int alignb = (INTEL_DATA_ALIGN / sizeof(int)); - const int edge = ct & (alignb - 1); - if (edge) ct += alignb - edge; + IP_PRE_edge_align(ct, sizeof(int)); neighptr = firstneigh + ct; + neighptr2 = neighptr; max_chunk = 0; - pack_offset = maxnbors * pack_width; lane = 0; if (ct + obound > list_size) { if (i < ito - 1) { @@ -548,12 +642,13 @@ void NPairIntel::bin_newton(const int offload, NeighList *list, } } } - } else { + } else + #endif + { ct += n; - const int alignb = (INTEL_DATA_ALIGN / sizeof(int)); - const int edge = ct & (alignb - 1); - if (edge) ct += alignb - edge; + //IP_PRE_edge_align(ct, sizeof(int)); neighptr = firstneigh + ct; + if (THREE) neighptr2 = neighptr; if (ct + obound > list_size) { if (i < ito - 1) { *overflow = 1; @@ -573,14 +668,14 @@ void NPairIntel::bin_newton(const int offload, NeighList *list, if (separate_buffers) { for (int i = ifrom; i < ito; ++i) { int * _noalias jlist = firstneigh + cnumneigh[i]; - const int jnum = numneigh[i]; + int jnum = numneigh[i]; + if (!THREE) IP_PRE_neighbor_pad(jnum, offload); #if __INTEL_COMPILER+0 > 1499 #pragma vector aligned #pragma simd reduction(max:vlmax,vgmax) reduction(min:vlmin, vgmin) #endif for (int jj = 0; jj < jnum; jj++) { - int j = jlist[jj]; - if (need_ic && j < 0) j = -j - 1; + const int j = jlist[jj] & NEIGHMASK; if (j < nlocal) { if (j < vlmin) vlmin = j; if (j > vlmax) vlmax = j; @@ -615,72 +710,20 @@ void NPairIntel::bin_newton(const int offload, NeighList *list, ghost_offset = overflow[LMP_GHOST_MIN] - nlocal; nall_offset = nlocal + nghost; } - } // if separate_buffers - #endif - if (molecular) { for (int i = ifrom; i < ito; ++i) { int * _noalias jlist = firstneigh + cnumneigh[i]; - const int jnum = numneigh[i]; - - if (THREE) { - const int trip = jnum * pack_width; - for (int jj = 0; jj < trip; jj+=pack_width) { - const int j = jlist[jj]; - if (need_ic && j < 0) { - which = 0; - jlist[jj] = -j - 1; - } else - ofind_special(which, special, nspecial, i, tag[j]); - #ifdef _LMP_INTEL_OFFLOAD - if (j >= nlocal) { - if (j == e_nall) - jlist[jj] = nall_offset; - else if (which) - jlist[jj] = (j-ghost_offset) ^ (which << SBBITS); - else jlist[jj]-=ghost_offset; - } else - #endif - if (which) jlist[jj] = j ^ (which << SBBITS); - } - } else { - #if defined(LMP_SIMD_COMPILER) - #pragma vector aligned - #pragma simd - #endif - for (int jj = 0; jj < jnum; jj++) { - const int j = jlist[jj]; - if (need_ic && j < 0) { - which = 0; - jlist[jj] = -j - 1; - } else - ofind_special(which, special, nspecial, i, tag[j]); - #ifdef _LMP_INTEL_OFFLOAD - if (j >= nlocal) { - if (j == e_nall) - jlist[jj] = nall_offset; - else if (which) - jlist[jj] = (j-ghost_offset) ^ (which << SBBITS); - else jlist[jj]-=ghost_offset; - } else - #endif - if (which) jlist[jj] = j ^ (which << SBBITS); - } - } - } // for i - } // if molecular - #ifdef _LMP_INTEL_OFFLOAD - else if (separate_buffers) { - for (int i = ifrom; i < ito; ++i) { - int * _noalias jlist = firstneigh + cnumneigh[i]; - const int jnum = numneigh[i]; + int jnum = numneigh[i]; + if (!THREE) IP_PRE_neighbor_pad(jnum, offload); int jj = 0; #pragma vector aligned #pragma simd for (jj = 0; jj < jnum; jj++) { - if (jlist[jj] >= nlocal) { - if (jlist[jj] == e_nall) jlist[jj] = nall_offset; - else jlist[jj] -= ghost_offset; + const int which = jlist[jj] >> SBBITS & 3; + const int j = jlist[jj] & NEIGHMASK; + if (j >= nlocal) { + if (j == e_nall) jlist[jj] = nall_offset; + else jlist[jj] = (j - ghost_offset) ^ (which << SBBITS); } } } diff --git a/src/USER-INTEL/pair_airebo_intel.cpp b/src/USER-INTEL/pair_airebo_intel.cpp index 07f33f7ebe..601144a3c0 100644 --- a/src/USER-INTEL/pair_airebo_intel.cpp +++ b/src/USER-INTEL/pair_airebo_intel.cpp @@ -2200,7 +2200,7 @@ typedef typename intr_types::bvec bvec; VEC_INLINE inline static void aut_loadatoms_vec( AtomAIREBOT * atoms, ivec j_vec, - fvec *x, fvec * y, fvec * z, bvec * type_mask, int * map, ivec map_i, + fvec *x, fvec * y, fvec * z, bvec * type_mask, int * /*map*/, ivec map_i, ivec c_1 ) { const ivec c_4 = ivec::set1(4); @@ -2413,7 +2413,7 @@ static fvec aut_eval_poly_lin_pd_2(int n, flt_t * vals, ivec idx, fvec x, } static fvec aut_mask_gSpline_pd_2(KernelArgsAIREBOT * ka, - bvec active_mask, int itype, fvec cosjik, + bvec /*active_mask*/, int itype, fvec cosjik, fvec Nij, fvec *dgdc, fvec *dgdN) { int i; flt_t * gDom = NULL; @@ -2835,7 +2835,7 @@ static void aut_frebo_data_writeback( static void aut_frebo_N_spline_force( KernelArgsAIREBOT * _noalias ka, struct aut_frebo_data * _noalias data, int itype, int jtype, ivec vi, - ivec vj, fvec VA, fvec dN, fvec dNconj, fvec Nconj) { + ivec /*vj*/, fvec VA, fvec dN, fvec dNconj, fvec Nconj) { ivec c_i1 = ivec::set1(1); fvec c_2 = fvec::set1(2); fvec c_TOL = fvec::set1(TOL); @@ -2999,8 +2999,8 @@ static fvec aut_frebo_sum_omega( KernelArgsAIREBOT * _noalias ka, struct aut_frebo_data * _noalias i_data, struct aut_frebo_data * _noalias j_data, - int itype, int jtype, - ivec vi, ivec vj, + int /*itype*/, int /*jtype*/, + ivec /*vi*/, ivec /*vj*/, fvec r23x, fvec r23y, fvec r23z, fvec r23mag, fvec VA, fvec fij[3] ) { @@ -3284,7 +3284,7 @@ static void aut_torsion_vec( KernelArgsAIREBOT * ka, struct aut_frebo_data * i_data, struct aut_frebo_data * j_data, - ivec i, ivec j, fvec wij, fvec dwij + ivec /*i*/, ivec /*j*/, fvec wij, fvec dwij ) { AtomAIREBOT * x = ka->x; int * map = ka->map; @@ -4134,7 +4134,7 @@ exceed_limits: /* * Attempt to look up an element in the hash-map. */ -static fvec aut_airebo_lj_tap_test_path(KernelArgsAIREBOT * ka, +static fvec aut_airebo_lj_tap_test_path(KernelArgsAIREBOT * /*ka*/, struct aut_airebo_lj_test_path_result_data * test_path_result, bvec need_search, ivec i_bc, ivec j, LennardJonesPathAIREBOT path[fvec::VL] diff --git a/src/USER-INTEL/pair_buck_coul_cut_intel.cpp b/src/USER-INTEL/pair_buck_coul_cut_intel.cpp index 71aad95bc5..39fa9014db 100644 --- a/src/USER-INTEL/pair_buck_coul_cut_intel.cpp +++ b/src/USER-INTEL/pair_buck_coul_cut_intel.cpp @@ -142,6 +142,7 @@ void PairBuckCoulCutIntel::eval(const int offload, const int vflag, ATOM_T * _noalias const x = buffers->get_x(offload); flt_t * _noalias const q = buffers->get_q(offload); + const int * _noalias const ilist = list->ilist; const int * _noalias const numneigh = list->numneigh; const int * _noalias const cnumneigh = buffers->cnumneigh(list); const int * _noalias const firstneigh = buffers->firstneigh(list); @@ -185,6 +186,7 @@ void PairBuckCoulCutIntel::eval(const int offload, const int vflag, in(numneigh:length(0) alloc_if(0) free_if(0)) \ in(x:length(x_size) alloc_if(0) free_if(0)) \ in(q:length(q_size) alloc_if(0) free_if(0)) \ + in(ilist:length(0) alloc_if(0) free_if(0)) \ in(overflow:length(0) alloc_if(0) free_if(0)) \ in(astart,nthreads,qqrd2e,inum,nall,ntypes,vflag,eatom) \ in(f_stride,nlocal,minlocal,separate_flag,offload) \ @@ -221,15 +223,17 @@ void PairBuckCoulCutIntel::eval(const int offload, const int vflag, FORCE_T * _noalias const f = f_start + foff; if (NEWTON_PAIR) memset(f + minlocal, 0, f_stride * sizeof(FORCE_T)); - for (int i = iifrom; i < iito; i += iip) { + for (int ii = iifrom; ii < iito; ii += iip) { + const int i = ilist[ii]; const int itype = x[i].w; const int ptr_off = itype * ntypes; const C_FORCE_T * _noalias const c_forcei = c_force + ptr_off; const C_ENERGY_T * _noalias const c_energyi = c_energy + ptr_off; const C_CUT_T * _noalias const c_cuti = c_cut + ptr_off; - const int * _noalias const jlist = firstneigh + cnumneigh[i]; - const int jnum = numneigh[i]; + const int * _noalias const jlist = firstneigh + cnumneigh[ii]; + int jnum = numneigh[ii]; + IP_PRE_neighbor_pad(jnum, offload); acc_t fxtmp,fytmp,fztmp,fwtmp; acc_t sevdwl, secoul, sv0, sv1, sv2, sv3, sv4, sv5; diff --git a/src/USER-INTEL/pair_buck_coul_long_intel.cpp b/src/USER-INTEL/pair_buck_coul_long_intel.cpp index bba8a7b5e7..fe4d408a13 100644 --- a/src/USER-INTEL/pair_buck_coul_long_intel.cpp +++ b/src/USER-INTEL/pair_buck_coul_long_intel.cpp @@ -142,6 +142,7 @@ void PairBuckCoulLongIntel::eval(const int offload, const int vflag, ATOM_T * _noalias const x = buffers->get_x(offload); flt_t * _noalias const q = buffers->get_q(offload); + const int * _noalias const ilist = list->ilist; const int * _noalias const numneigh = list->numneigh; const int * _noalias const cnumneigh = buffers->cnumneigh(list); const int * _noalias const firstneigh = buffers->firstneigh(list); @@ -209,6 +210,7 @@ void PairBuckCoulLongIntel::eval(const int offload, const int vflag, in(numneigh:length(0) alloc_if(0) free_if(0)) \ in(x:length(x_size) alloc_if(0) free_if(0)) \ in(q:length(q_size) alloc_if(0) free_if(0)) \ + in(ilist:length(0) alloc_if(0) free_if(0)) \ in(overflow:length(0) alloc_if(0) free_if(0)) \ in(ccachex,ccachey,ccachez,ccachew:length(0) alloc_if(0) free_if(0)) \ in(ccachei,ccachej:length(0) alloc_if(0) free_if(0)) \ @@ -255,15 +257,17 @@ void PairBuckCoulLongIntel::eval(const int offload, const int vflag, int * _noalias const tj = ccachei + toffs; int * _noalias const tjtype = ccachej + toffs; - for (int i = iifrom; i < iito; i += iip) { + for (int ii = iifrom; ii < iito; ii += iip) { + const int i = ilist[ii]; const int itype = x[i].w; const int ptr_off = itype * ntypes; const C_FORCE_T * _noalias const c_forcei = c_force + ptr_off; const C_ENERGY_T * _noalias const c_energyi = c_energy + ptr_off; const flt_t * _noalias const rho_invi = rho_inv + ptr_off; - const int * _noalias const jlist = firstneigh + cnumneigh[i]; - const int jnum = numneigh[i]; + const int * _noalias const jlist = firstneigh + cnumneigh[ii]; + int jnum = numneigh[ii]; + IP_PRE_neighbor_pad(jnum, offload); acc_t fxtmp,fytmp,fztmp,fwtmp; acc_t sevdwl, secoul, sv0, sv1, sv2, sv3, sv4, sv5; diff --git a/src/USER-INTEL/pair_buck_intel.cpp b/src/USER-INTEL/pair_buck_intel.cpp index f5dde26393..8ce3d121e0 100644 --- a/src/USER-INTEL/pair_buck_intel.cpp +++ b/src/USER-INTEL/pair_buck_intel.cpp @@ -133,6 +133,7 @@ void PairBuckIntel::eval(const int offload, const int vflag, ATOM_T * _noalias const x = buffers->get_x(offload); + const int * _noalias const ilist = list->ilist; const int * _noalias const numneigh = list->numneigh; const int * _noalias const cnumneigh = buffers->cnumneigh(list); const int * _noalias const firstneigh = buffers->firstneigh(list); @@ -169,6 +170,7 @@ void PairBuckIntel::eval(const int offload, const int vflag, in(cnumneigh:length(0) alloc_if(0) free_if(0)) \ in(numneigh:length(0) alloc_if(0) free_if(0)) \ in(x:length(x_size) alloc_if(0) free_if(0)) \ + in(ilist:length(0) alloc_if(0) free_if(0)) \ in(overflow:length(0) alloc_if(0) free_if(0)) \ in(astart,nthreads,inum,nall,ntypes,vflag,eatom) \ in(f_stride,nlocal,minlocal,separate_flag,offload) \ @@ -205,14 +207,16 @@ void PairBuckIntel::eval(const int offload, const int vflag, FORCE_T * _noalias const f = f_start + foff; if (NEWTON_PAIR) memset(f + minlocal, 0, f_stride * sizeof(FORCE_T)); - for (int i = iifrom; i < iito; i += iip) { + for (int ii = iifrom; ii < iito; ii += iip) { + const int i = ilist[ii]; const int itype = x[i].w; const int ptr_off = itype * ntypes; const C_FORCE_T * _noalias const c_forcei = c_force + ptr_off; const C_ENERGY_T * _noalias const c_energyi = c_energy + ptr_off; - const int * _noalias const jlist = firstneigh + cnumneigh[i]; - const int jnum = numneigh[i]; + const int * _noalias const jlist = firstneigh + cnumneigh[ii]; + int jnum = numneigh[ii]; + IP_PRE_neighbor_pad(jnum, offload); acc_t fxtmp,fytmp,fztmp,fwtmp; acc_t sevdwl, sv0, sv1, sv2, sv3, sv4, sv5; diff --git a/src/USER-INTEL/pair_dpd_intel.cpp b/src/USER-INTEL/pair_dpd_intel.cpp index cb8c06cacc..7c33ed21d3 100644 --- a/src/USER-INTEL/pair_dpd_intel.cpp +++ b/src/USER-INTEL/pair_dpd_intel.cpp @@ -171,6 +171,7 @@ void PairDPDIntel::eval(const int offload, const int vflag, lmp_vt *v = (lmp_vt *)atom->v[0]; const flt_t dtinvsqrt = 1.0/sqrt(update->dt); + const int * _noalias const ilist = list->ilist; const int * _noalias const numneigh = list->numneigh; const int * _noalias const cnumneigh = buffers->cnumneigh(list); const int * _noalias const firstneigh = buffers->firstneigh(list); @@ -237,7 +238,8 @@ void PairDPDIntel::eval(const int offload, const int vflag, gamma = param[3].gamma; sigma = param[3].sigma; } - for (int i = iifrom; i < iito; i += iip) { + for (int ii = iifrom; ii < iito; ii += iip) { + const int i = ilist[ii]; int itype, ptr_off; const FC_PACKED1_T * _noalias parami; if (!ONETYPE) { @@ -246,8 +248,9 @@ void PairDPDIntel::eval(const int offload, const int vflag, parami = param + ptr_off; } - const int * _noalias const jlist = firstneigh + cnumneigh[i]; - const int jnum = numneigh[i]; + const int * _noalias const jlist = firstneigh + cnumneigh[ii]; + int jnum = numneigh[ii]; + IP_PRE_neighbor_pad(jnum, offload); acc_t fxtmp, fytmp, fztmp, fwtmp; acc_t sevdwl, sv0, sv1, sv2, sv3, sv4, sv5; diff --git a/src/USER-INTEL/pair_eam_intel.cpp b/src/USER-INTEL/pair_eam_intel.cpp index 94799cdba2..ce9ede69d6 100644 --- a/src/USER-INTEL/pair_eam_intel.cpp +++ b/src/USER-INTEL/pair_eam_intel.cpp @@ -164,8 +164,7 @@ void PairEAMIntel::eval(const int offload, const int vflag, memory->destroy(rho); memory->destroy(fp); nmax = atom->nmax; - int edge = (nmax * sizeof(acc_t)) % INTEL_DATA_ALIGN; - if (edge) nmax += (INTEL_DATA_ALIGN - edge) / sizeof(acc_t); + IP_PRE_edge_align(nmax, sizeof(acc_t)); if (NEWTON_PAIR) memory->create(rho,nmax*comm->nthreads,"pair:rho"); else @@ -192,6 +191,7 @@ void PairEAMIntel::eval(const int offload, const int vflag, ATOM_T * _noalias const x = buffers->get_x(offload); + const int * _noalias const ilist = list->ilist; const int * _noalias const numneigh = list->numneigh; const int * _noalias const cnumneigh = buffers->cnumneigh(list); const int * _noalias const firstneigh = buffers->firstneigh(list); @@ -286,14 +286,16 @@ void PairEAMIntel::eval(const int offload, const int vflag, rhor_joff = rhor_ioff + _onetype * jstride; frho_ioff = fstride * _onetype; } - for (int i = iifrom; i < iito; ++i) { + for (int ii = iifrom; ii < iito; ++ii) { + const int i = ilist[ii]; int itype, rhor_ioff; if (!ONETYPE) { itype = x[i].w; rhor_ioff = istride * itype; } - const int * _noalias const jlist = firstneigh + cnumneigh[i]; - const int jnum = numneigh[i]; + const int * _noalias const jlist = firstneigh + cnumneigh[ii]; + int jnum = numneigh[ii]; + IP_PRE_neighbor_pad(jnum, offload); const flt_t xtmp = x[i].x; const flt_t ytmp = x[i].y; @@ -411,7 +413,8 @@ void PairEAMIntel::eval(const int offload, const int vflag, #pragma vector aligned #pragma simd reduction(+:tevdwl) #endif - for (int i = iifrom; i < iito; ++i) { + for (int ii = iifrom; ii < iito; ++ii) { + const int i = ilist[ii]; int itype; if (!ONETYPE) itype = x[i].w; flt_t p = rho[i]*frdrho + (flt_t)1.0; @@ -457,7 +460,8 @@ void PairEAMIntel::eval(const int offload, const int vflag, // compute forces on each atom // loop over neighbors of my atoms - for (int i = iifrom; i < iito; ++i) { + for (int ii = iifrom; ii < iito; ++ii) { + const int i = ilist[ii]; int itype, rhor_ioff; const flt_t * _noalias scale_fi; if (!ONETYPE) { @@ -465,8 +469,9 @@ void PairEAMIntel::eval(const int offload, const int vflag, rhor_ioff = istride * itype; scale_fi = scale_f + itype*ntypes; } - const int * _noalias const jlist = firstneigh + cnumneigh[i]; - const int jnum = numneigh[i]; + const int * _noalias const jlist = firstneigh + cnumneigh[ii]; + int jnum = numneigh[ii]; + IP_PRE_neighbor_pad(jnum, offload); acc_t fxtmp, fytmp, fztmp, fwtmp; acc_t sevdwl, sv0, sv1, sv2, sv3, sv4, sv5; @@ -761,14 +766,12 @@ void PairEAMIntel::ForceConst::set_ntypes(const int ntypes, if (ntypes > 0) { _cop = cop; _nr = nr + 1; - int edge = (_nr * sizeof(flt_t)) % INTEL_DATA_ALIGN; - if (edge) _nr += (INTEL_DATA_ALIGN - edge) / sizeof(flt_t); + IP_PRE_edge_align(_nr, sizeof(flt_t)); memory->create(rhor_spline_f,ntypes*ntypes*_nr,"fc.rhor_spline_f"); memory->create(rhor_spline_e,ntypes*ntypes*_nr,"fc.rhor_spline_e"); memory->create(z2r_spline_t,ntypes*ntypes*_nr,"fc.z2r_spline_t"); _nrho = nrho + 1; - edge = (_nrho * sizeof(flt_t)) % INTEL_DATA_ALIGN; - if (edge) _nrho += (INTEL_DATA_ALIGN - edge) / sizeof(flt_t); + IP_PRE_edge_align(_nrho, sizeof(flt_t)); memory->create(frho_spline_f,ntypes*_nrho,"fc.frho_spline_f"); memory->create(frho_spline_e,ntypes*_nrho,"fc.frho_spline_e"); memory->create(scale_f,ntypes,ntypes,"fc.scale_f"); @@ -781,7 +784,7 @@ void PairEAMIntel::ForceConst::set_ntypes(const int ntypes, /* ---------------------------------------------------------------------- */ int PairEAMIntel::pack_forward_comm(int n, int *list, double *buf, - int pbc_flag, int *pbc) + int /*pbc_flag*/, int * /*pbc*/) { if (fix->precision() == FixIntel::PREC_MODE_DOUBLE) return pack_forward_comm(n, list, buf, fp); diff --git a/src/USER-INTEL/pair_gayberne_intel.cpp b/src/USER-INTEL/pair_gayberne_intel.cpp index 1f05ad0efc..30941a7594 100644 --- a/src/USER-INTEL/pair_gayberne_intel.cpp +++ b/src/USER-INTEL/pair_gayberne_intel.cpp @@ -226,7 +226,7 @@ void PairGayBerneIntel::eval(const int offload, const int vflag, } #endif - // const int * _noalias const ilist = list->ilist; + const int * _noalias const ilist = list->ilist; const int * _noalias const numneigh = list->numneigh; const int * _noalias const cnumneigh = buffers->cnumneigh(list); const int * _noalias const firstneigh = buffers->firstneigh(list); @@ -287,6 +287,7 @@ void PairGayBerneIntel::eval(const int offload, const int vflag, in(numneigh:length(0) alloc_if(0) free_if(0)) \ in(x:length(x_size) alloc_if(0) free_if(0)) \ in(quat:length(nall+1) alloc_if(0) free_if(0)) \ + in(ilist:length(0) alloc_if(0) free_if(0)) \ in(overflow:length(0) alloc_if(0) free_if(0)) \ in(nthreads,inum,nall,ntypes,vflag,eatom,minlocal,separate_flag) \ in(astart,nlocal,f_stride,max_nbors,mu,gamma,upsilon,offload,pad_width) \ @@ -364,15 +365,16 @@ void PairGayBerneIntel::eval(const int offload, const int vflag, int * _noalias const jlist_form = jlist_formi + tid * max_nbors; int ierror = 0; - for (int i = iifrom; i < iito; i += iip) { - // const int i = ilist[ii]; + for (int ii = iifrom; ii < iito; ii += iip) { + const int i = ilist[ii]; const int itype = x[i].w; const int ptr_off = itype * ntypes; const FC_PACKED1_T * _noalias const ijci = ijc + ptr_off; const FC_PACKED2_T * _noalias const lj34i = lj34 + ptr_off; - const int * _noalias const jlist = firstneigh + cnumneigh[i]; - const int jnum = numneigh[i]; + const int * _noalias const jlist = firstneigh + cnumneigh[ii]; + int jnum = numneigh[ii]; + IP_PRE_neighbor_pad(jnum, offload); const flt_t xtmp = x[i].x; const flt_t ytmp = x[i].y; @@ -428,15 +430,13 @@ void PairGayBerneIntel::eval(const int offload, const int vflag, } else multiple_forms = true; } - const int edge = packed_j & (pad_width - 1); - if (edge) { - const int packed_end = packed_j + (pad_width - edge); - #if defined(LMP_SIMD_COMPILER) - #pragma loop_count min=1, max=15, avg=8 - #endif - for ( ; packed_j < packed_end; packed_j++) - jlist_form[packed_j] = nall; - } + int packed_end = packed_j; + IP_PRE_neighbor_pad(packed_end, offload); + #if defined(LMP_SIMD_COMPILER) + #pragma loop_count min=1, max=15, avg=8 + #endif + for ( ; packed_j < packed_end; packed_j++) + jlist_form[packed_j] = nall; // ------------------------------------------------------------- diff --git a/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.cpp b/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.cpp index 7485395bef..8e6395c388 100644 --- a/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.cpp +++ b/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.cpp @@ -136,6 +136,7 @@ void PairLJCharmmCoulCharmmIntel::eval(const int offload, const int vflag, ATOM_T * _noalias const x = buffers->get_x(offload); flt_t * _noalias const q = buffers->get_q(offload); + const int * _noalias const ilist = list->ilist; const int * _noalias const numneigh = list->numneigh; const int * _noalias const cnumneigh = buffers->cnumneigh(list); const int * _noalias const firstneigh = buffers->firstneigh(list); @@ -189,6 +190,7 @@ void PairLJCharmmCoulCharmmIntel::eval(const int offload, const int vflag, in(numneigh:length(0) alloc_if(0) free_if(0)) \ in(x:length(x_size) alloc_if(0) free_if(0)) \ in(q:length(q_size) alloc_if(0) free_if(0)) \ + in(ilist:length(0) alloc_if(0) free_if(0)) \ in(overflow:length(0) alloc_if(0) free_if(0)) \ in(ccachex,ccachey,ccachez,ccachew:length(0) alloc_if(0) free_if(0)) \ in(ccachei,ccachej:length(0) alloc_if(0) free_if(0)) \ @@ -238,16 +240,17 @@ void PairLJCharmmCoulCharmmIntel::eval(const int offload, const int vflag, int * _noalias const tj = ccachei + toffs; int * _noalias const tjtype = ccachej + toffs; - for (int i = iifrom; i < iito; i += iip) { - // const int i = ilist[ii]; + for (int ii = iifrom; ii < iito; ii += iip) { + const int i = ilist[ii]; const int itype = x[i].w; const int ptr_off = itype * ntypes; const flt_t * _noalias const cutsqi = cutsq + ptr_off; const LJ_T * _noalias const lji = lj + ptr_off; - const int * _noalias const jlist = firstneigh + cnumneigh[i]; - const int jnum = numneigh[i]; + const int * _noalias const jlist = firstneigh + cnumneigh[ii]; + int jnum = numneigh[ii]; + IP_PRE_neighbor_pad(jnum, offload); acc_t fxtmp,fytmp,fztmp,fwtmp; acc_t sevdwl, secoul, sv0, sv1, sv2, sv3, sv4, sv5; diff --git a/src/USER-INTEL/pair_lj_charmm_coul_long_intel.cpp b/src/USER-INTEL/pair_lj_charmm_coul_long_intel.cpp index 25cca59714..a01a4688a5 100644 --- a/src/USER-INTEL/pair_lj_charmm_coul_long_intel.cpp +++ b/src/USER-INTEL/pair_lj_charmm_coul_long_intel.cpp @@ -140,6 +140,7 @@ void PairLJCharmmCoulLongIntel::eval(const int offload, const int vflag, ATOM_T * _noalias const x = buffers->get_x(offload); flt_t * _noalias const q = buffers->get_q(offload); + const int * _noalias const ilist = list->ilist; const int * _noalias const numneigh = list->numneigh; const int * _noalias const cnumneigh = buffers->cnumneigh(list); const int * _noalias const firstneigh = buffers->firstneigh(list); @@ -210,6 +211,7 @@ void PairLJCharmmCoulLongIntel::eval(const int offload, const int vflag, in(numneigh:length(0) alloc_if(0) free_if(0)) \ in(x:length(x_size) alloc_if(0) free_if(0)) \ in(q:length(q_size) alloc_if(0) free_if(0)) \ + in(ilist:length(0) alloc_if(0) free_if(0)) \ in(overflow:length(0) alloc_if(0) free_if(0)) \ in(ccachex,ccachey,ccachez,ccachew:length(0) alloc_if(0) free_if(0)) \ in(ccachei,ccachej:length(0) alloc_if(0) free_if(0)) \ @@ -258,16 +260,17 @@ void PairLJCharmmCoulLongIntel::eval(const int offload, const int vflag, int * _noalias const tj = ccachei + toffs; int * _noalias const tjtype = ccachej + toffs; - for (int i = iifrom; i < iito; i += iip) { - // const int i = ilist[ii]; + for (int ii = iifrom; ii < iito; ii += iip) { + const int i = ilist[ii]; const int itype = x[i].w; const int ptr_off = itype * ntypes; const flt_t * _noalias const cutsqi = cutsq + ptr_off; const LJ_T * _noalias const lji = lj + ptr_off; - const int * _noalias const jlist = firstneigh + cnumneigh[i]; - const int jnum = numneigh[i]; + const int * _noalias const jlist = firstneigh + cnumneigh[ii]; + int jnum = numneigh[ii]; + IP_PRE_neighbor_pad(jnum, offload); acc_t fxtmp,fytmp,fztmp,fwtmp; acc_t sevdwl, secoul, sv0, sv1, sv2, sv3, sv4, sv5; diff --git a/src/USER-INTEL/pair_lj_cut_coul_long_intel.cpp b/src/USER-INTEL/pair_lj_cut_coul_long_intel.cpp index cb7381270d..ab0b5b3d55 100644 --- a/src/USER-INTEL/pair_lj_cut_coul_long_intel.cpp +++ b/src/USER-INTEL/pair_lj_cut_coul_long_intel.cpp @@ -139,6 +139,7 @@ void PairLJCutCoulLongIntel::eval(const int offload, const int vflag, ATOM_T * _noalias const x = buffers->get_x(offload); flt_t * _noalias const q = buffers->get_q(offload); + const int * _noalias const ilist = list->ilist; const int * _noalias const numneigh = list->numneigh; const int * _noalias const cnumneigh = buffers->cnumneigh(list); const int * _noalias const firstneigh = buffers->firstneigh(list); @@ -204,6 +205,7 @@ void PairLJCutCoulLongIntel::eval(const int offload, const int vflag, in(numneigh:length(0) alloc_if(0) free_if(0)) \ in(x:length(x_size) alloc_if(0) free_if(0)) \ in(q:length(q_size) alloc_if(0) free_if(0)) \ + in(ilist:length(0) alloc_if(0) free_if(0)) \ in(overflow:length(0) alloc_if(0) free_if(0)) \ in(ccachex,ccachey,ccachez,ccachew:length(0) alloc_if(0) free_if(0)) \ in(ccachei,ccachej:length(0) alloc_if(0) free_if(0)) \ @@ -250,15 +252,17 @@ void PairLJCutCoulLongIntel::eval(const int offload, const int vflag, int * _noalias const tj = ccachei + toffs; int * _noalias const tjtype = ccachej + toffs; - for (int i = iifrom; i < iito; i += iip) { + for (int ii = iifrom; ii < iito; ii += iip) { + const int i = ilist[ii]; const int itype = x[i].w; const int ptr_off = itype * ntypes; const C_FORCE_T * _noalias const c_forcei = c_force + ptr_off; const C_ENERGY_T * _noalias const c_energyi = c_energy + ptr_off; - const int * _noalias const jlist = firstneigh + cnumneigh[i]; - const int jnum = numneigh[i]; + const int * _noalias const jlist = firstneigh + cnumneigh[ii]; + int jnum = numneigh[ii]; + IP_PRE_neighbor_pad(jnum, offload); acc_t fxtmp,fytmp,fztmp,fwtmp; acc_t sevdwl, secoul, sv0, sv1, sv2, sv3, sv4, sv5; diff --git a/src/USER-INTEL/pair_lj_cut_intel.cpp b/src/USER-INTEL/pair_lj_cut_intel.cpp index b16f6230cc..c973639709 100644 --- a/src/USER-INTEL/pair_lj_cut_intel.cpp +++ b/src/USER-INTEL/pair_lj_cut_intel.cpp @@ -148,6 +148,7 @@ void PairLJCutIntel::eval(const int offload, const int vflag, ATOM_T * _noalias const x = buffers->get_x(offload); + const int * _noalias const ilist = list->ilist; const int * _noalias const numneigh = list->numneigh; const int * _noalias const cnumneigh = buffers->cnumneigh(list); const int * _noalias const firstneigh = buffers->firstneigh(list); @@ -207,7 +208,8 @@ void PairLJCutIntel::eval(const int offload, const int vflag, lj4 = lj34[3].lj4; offset = ljc12o[3].offset; } - for (int i = iifrom; i < iito; i += iip) { + for (int ii = iifrom; ii < iito; ii += iip) { + const int i = ilist[ii]; int itype, ptr_off; const FC_PACKED1_T * _noalias ljc12oi; const FC_PACKED2_T * _noalias lj34i; @@ -217,9 +219,9 @@ void PairLJCutIntel::eval(const int offload, const int vflag, ljc12oi = ljc12o + ptr_off; lj34i = lj34 + ptr_off; } - - const int * _noalias const jlist = firstneigh + cnumneigh[i]; - const int jnum = numneigh[i]; + const int * _noalias const jlist = firstneigh + cnumneigh[ii]; + int jnum = numneigh[ii]; + IP_PRE_neighbor_pad(jnum, offload); acc_t fxtmp, fytmp, fztmp, fwtmp; acc_t sevdwl, sv0, sv1, sv2, sv3, sv4, sv5; diff --git a/src/USER-INTEL/pair_rebo_intel.cpp b/src/USER-INTEL/pair_rebo_intel.cpp index bc7197000b..3decc0154b 100644 --- a/src/USER-INTEL/pair_rebo_intel.cpp +++ b/src/USER-INTEL/pair_rebo_intel.cpp @@ -28,7 +28,7 @@ PairREBOIntel::PairREBOIntel(LAMMPS *lmp) : PairAIREBOIntel(lmp) {} global settings ------------------------------------------------------------------------- */ -void PairREBOIntel::settings(int narg, char **arg) +void PairREBOIntel::settings(int narg, char **/*arg*/) { if (narg != 0) error->all(FLERR,"Illegal pair_style command"); diff --git a/src/USER-INTEL/pair_sw_intel.cpp b/src/USER-INTEL/pair_sw_intel.cpp index 421de91ee9..aff8ba88a7 100644 --- a/src/USER-INTEL/pair_sw_intel.cpp +++ b/src/USER-INTEL/pair_sw_intel.cpp @@ -42,7 +42,6 @@ #include "suffix.h" #ifdef LMP_USE_AVXCD -#define OUTER_CHUNK 1 #include "intel_simd.h" using namespace ip_simd; #endif @@ -174,7 +173,7 @@ template void PairSWIntel::eval(const int offload, const int vflag, IntelBuffers *buffers, const ForceConst &fc, const int astart, - const int aend, const int pad_width) + const int aend, const int /*pad_width*/) { const int inum = aend - astart; if (inum == 0) return; @@ -185,6 +184,7 @@ void PairSWIntel::eval(const int offload, const int vflag, IP_PRE_pack_separate_buffers(fix, buffers, ago, offload, nlocal, nall); ATOM_T * _noalias const x = buffers->get_x(offload); + const int * _noalias const ilist = list->ilist; const int * _noalias const numneighhalf = buffers->get_atombin(); const int * _noalias const numneigh = list->numneigh; const int * _noalias const cnumneigh = buffers->cnumneigh(list); @@ -230,6 +230,7 @@ void PairSWIntel::eval(const int offload, const int vflag, in(cnumneigh:length(0) alloc_if(0) free_if(0)) \ in(numneigh:length(0) alloc_if(0) free_if(0)) \ in(x:length(x_size) alloc_if(0) free_if(0)) \ + in(ilist:length(0) alloc_if(0) free_if(0)) \ in(numneighhalf:length(0) alloc_if(0) free_if(0)) \ in(overflow:length(0) alloc_if(0) free_if(0)) \ in(ccachex,ccachey,ccachez,ccachew:length(0) alloc_if(0) free_if(0)) \ @@ -298,7 +299,8 @@ void PairSWIntel::eval(const int offload, const int vflag, } } - for (int i = iifrom; i < iito; i += iip) { + for (int ii = iifrom; ii < iito; ii += iip) { + const int i = ilist[ii]; int itype, itype_offset; const flt_t xtmp = x[i].x; const flt_t ytmp = x[i].y; @@ -309,9 +311,9 @@ void PairSWIntel::eval(const int offload, const int vflag, itype_offset = itype * ntypes; } - const int * _noalias const jlist = firstneigh + cnumneigh[i]; - const int jnum = numneigh[i]; - const int jnumhalf = numneighhalf[i]; + const int * _noalias const jlist = firstneigh + cnumneigh[ii]; + const int jnum = numneigh[ii]; + const int jnumhalf = numneighhalf[ii]; acc_t fxtmp, fytmp, fztmp, fwtmp; acc_t sevdwl; @@ -346,9 +348,13 @@ void PairSWIntel::eval(const int offload, const int vflag, } } - int ejrem = ejnum & (pad_width - 1); - if (ejrem) ejrem = pad_width - ejrem; - const int ejnum_pad = ejnum + ejrem; + int ejnum_pad = ejnum; + IP_PRE_neighbor_pad(ejnum_pad, offload); + #if defined(LMP_SIMD_COMPILER) + #pragma vector aligned + #pragma loop_count min=1, max=INTEL_COMPILE_WIDTH-1, \ + avg=INTEL_COMPILE_WIDTH/2 + #endif for (int jj = ejnum; jj < ejnum_pad; jj++) { tdelx[jj] = (flt_t)0.0; tdely[jj] = (flt_t)0.0; @@ -594,6 +600,7 @@ void PairSWIntel::eval(const int offload, const int vflag, IP_PRE_pack_separate_buffers(fix, buffers, ago, offload, nlocal, nall); ATOM_T * _noalias const x = buffers->get_x(offload); + const int * _noalias const ilist = list->ilist; const int * _noalias const numneighhalf = buffers->get_atombin(); const int * _noalias const numneigh = list->numneigh; const int * _noalias const cnumneigh = buffers->cnumneigh(list); @@ -641,6 +648,7 @@ void PairSWIntel::eval(const int offload, const int vflag, in(cnumneigh:length(0) alloc_if(0) free_if(0)) \ in(numneigh:length(0) alloc_if(0) free_if(0)) \ in(x:length(x_size) alloc_if(0) free_if(0)) \ + in(ilist:length(0) alloc_if(0) free_if(0)) \ in(numneighhalf:length(0) alloc_if(0) free_if(0)) \ in(overflow:length(0) alloc_if(0) free_if(0)) \ in(ccachex,ccachey,ccachez,ccachew:length(0) alloc_if(0) free_if(0)) \ @@ -714,24 +722,24 @@ void PairSWIntel::eval(const int offload, const int vflag, } } - SIMD_int ilist = SIMD_set(0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15); const SIMD_int goffset = SIMD_set(0,16,32,48,64,80,96,112,128, 144,160,176,192,208,224,240); - ilist = ilist + iifrom; acc_t * const dforce = &(f[0].x); for (int i = iifrom; i < iito; i += iip) { - SIMD_mask imask = ilist < iito; + SIMD_int ilistv = SIMD_load(ilist + i); + SIMD_int goffset = ilistv * 16; + SIMD_mask imask = ilistv < iito; SIMD_flt_t xtmp, ytmp, ztmp; SIMD_int itype, itype_offset; if (ONETYPE) - SIMD_atom_gather(imask, &(x[i].x), goffset, xtmp, ytmp, ztmp); + SIMD_atom_gather(imask, &(x[0].x), goffset, xtmp, ytmp, ztmp); else { - SIMD_atom_gather(imask, &(x[i].x), goffset, xtmp, ytmp, ztmp, itype); + SIMD_atom_gather(imask, &(x[0].x), goffset, xtmp, ytmp, ztmp, itype); itype_offset = itype * ntypes; } - #ifdef OUTER_CHUNK + #ifdef LMP_INTEL_3BODY_FAST const int* ng = firstneigh + cnumneigh[i] - swidth; #else SIMD_int ng = SIMD_load(cnumneigh + i); @@ -765,7 +773,7 @@ void PairSWIntel::eval(const int offload, const int vflag, for (int jj = 0; jj < jnum_max; jj++) { SIMD_mask jmask = jj < jnum; - #ifdef OUTER_CHUNK + #ifdef LMP_INTEL_3BODY_FAST ng += swidth; SIMD_int j = SIMD_load(ng); #else @@ -1025,15 +1033,15 @@ void PairSWIntel::eval(const int offload, const int vflag, } } // for jj second loop - SIMD_iforce_update(imask, &(f[i].x), goffset, fxtmp, fytmp, fztmp, + SIMD_iforce_update(imask, &(f[0].x), goffset, fxtmp, fytmp, fztmp, EFLAG, eatom, fwtmp); if (is_same::value == 0) { imask = imask >> 8; - SIMD_iforce_update(imask, &(f[i+8].x), goffset, fxtmp2, fytmp2, + SIMD_int goffset2 = _mm512_shuffle_i32x4(goffset, goffset, 238); + SIMD_iforce_update(imask, &(f[0].x), goffset2, fxtmp2, fytmp2, fztmp2, EFLAG, eatom, fwtmp2); } if (EFLAG) oevdwl += SIMD_sum(sevdwl); - ilist = ilist + iip; } // for ii IP_PRE_fdotr_reduce_omp(1, nall, minlocal, nthreads, f_start, f_stride, diff --git a/src/USER-INTEL/pair_tersoff_intel.cpp b/src/USER-INTEL/pair_tersoff_intel.cpp index c772546928..584b371784 100644 --- a/src/USER-INTEL/pair_tersoff_intel.cpp +++ b/src/USER-INTEL/pair_tersoff_intel.cpp @@ -208,6 +208,7 @@ struct IntelKernelTersoff : public lmp_intel::vector_routines const int * _noalias const cnumneigh, const int * _noalias const firstneigh, int ntypes, typename IntelBuffers::atom_t * _noalias const x, + const int * _noalias const ilist, const c_inner_t * _noalias const c_inner, const c_outer_t * _noalias const c_outer, typename IntelBuffers::vec3_acc_t * _noalias const f, @@ -271,6 +272,7 @@ void PairTersoffIntel::eval(const int offload, const int vflag, tagint * _noalias tag = this->atom->tag; flt_t * _noalias const q = buffers->get_q(offload); + const int * _noalias const ilist = list->ilist; const int * _noalias const numneigh = list->numneigh; const int * _noalias const cnumneigh = buffers->cnumneigh(list); const int * _noalias const numneighhalf = buffers->get_atombin(); @@ -311,6 +313,7 @@ void PairTersoffIntel::eval(const int offload, const int vflag, in(numneigh:length(0) alloc_if(0) free_if(0)) \ in(numneighhalf:length(0) alloc_if(0) free_if(0)) \ in(x:length(x_size) alloc_if(0) free_if(0)) \ + in(ilist:length(0) alloc_if(0) free_if(0)) \ in(overflow:length(0) alloc_if(0) free_if(0)) \ in(astart,nthreads,inum,nall,ntypes,vflag,eatom) \ in(f_stride,nlocal,minlocal,separate_flag,offload) \ @@ -349,8 +352,9 @@ void PairTersoffIntel::eval(const int offload, const int vflag, { acc_t sevdwl; sevdwl = 0.; - #define ARGS iito, iifrom, eatom, vflag, numneigh, numneighhalf, cnumneigh, \ - firstneigh, ntypes, x, c_inner, c_outer, f, &sevdwl + #define ARGS iito, iifrom, eatom, vflag, numneigh, numneighhalf, \ + cnumneigh, firstneigh, ntypes, x, ilist, c_inner, \ + c_outer, f, &sevdwl // Pick the variable i algorithm under specific conditions // do use scalar algorithm with very short vectors int VL = lmp_intel::vector_routines::VL; @@ -1135,6 +1139,7 @@ void IntelKernelTersoff::kernel( const int * _noalias const cnumneigh, const int * _noalias const firstneigh, int ntypes, typename IntelBuffers::atom_t * _noalias const x, + const int * _noalias const ilist, const c_inner_t * _noalias const c_inner, const c_outer_t * _noalias const c_outer, typename IntelBuffers::vec3_acc_t * _noalias const f, @@ -1155,12 +1160,12 @@ void IntelKernelTersoff::kernel( for (ii = iifrom; ii < iito; ii++) { // Right now this loop is scalar, to allow for the compiler to do // its prefetching magic. - int i = ii; + int i = ilist[ii]; int w_i = x[i].w; flt_t x_i = x[i].x; flt_t y_i = x[i].y; flt_t z_i = x[i].z; - int jlist_off_i = cnumneigh[i]; + int jlist_off_i = cnumneigh[ii]; int jnum = numneigh[ii]; for (jj = 0; jj < jnum; jj++) { int j = firstneigh[jlist_off_i + jj] & NEIGHMASK; @@ -1173,7 +1178,7 @@ void IntelKernelTersoff::kernel( if (rsq < cutsq) { is[compress_idx] = ii; js[compress_idx] = j; - if (jj < numneighhalf[i]) + if (jj < numneighhalf[ii]) repulsive_flag[compress_idx] = 1; compress_idx += 1; } diff --git a/src/USER-INTEL/pppm_disp_intel.cpp b/src/USER-INTEL/pppm_disp_intel.cpp index 0a41e5d8a5..3b05658278 100644 --- a/src/USER-INTEL/pppm_disp_intel.cpp +++ b/src/USER-INTEL/pppm_disp_intel.cpp @@ -723,7 +723,7 @@ void PPPMDispIntel::particle_map(double delx, double dely, double delz, double sft, int** p2g, int nup, int nlow, int nxlo, int nylo, int nzlo, int nxhi, int nyhi, int nzhi, - IntelBuffers *buffers) + IntelBuffers * /*buffers*/) { int nlocal = atom->nlocal; int nthr = comm->nthreads; @@ -790,7 +790,7 @@ void PPPMDispIntel::particle_map(double delx, double dely, double delz, ------------------------------------------------------------------------- */ template -void PPPMDispIntel::make_rho_c(IntelBuffers *buffers) +void PPPMDispIntel::make_rho_c(IntelBuffers * /*buffers*/) { // clear 3d density array @@ -940,7 +940,7 @@ void PPPMDispIntel::make_rho_c(IntelBuffers *buffers) ------------------------------------------------------------------------- */ template -void PPPMDispIntel::make_rho_g(IntelBuffers *buffers) +void PPPMDispIntel::make_rho_g(IntelBuffers * /*buffers*/) { // clear 3d density array @@ -1091,7 +1091,7 @@ void PPPMDispIntel::make_rho_g(IntelBuffers *buffers) ------------------------------------------------------------------------- */ template -void PPPMDispIntel::make_rho_a(IntelBuffers *buffers) +void PPPMDispIntel::make_rho_a(IntelBuffers * /*buffers*/) { // clear 3d density array @@ -1225,7 +1225,7 @@ void PPPMDispIntel::make_rho_a(IntelBuffers *buffers) ------------------------------------------------------------------------- */ template -void PPPMDispIntel::make_rho_none(IntelBuffers *buffers) +void PPPMDispIntel::make_rho_none(IntelBuffers * /*buffers*/) { FFT_SCALAR * _noalias global_density = &(density_brick_none[0][nzlo_out_6][nylo_out_6][nxlo_out_6]); @@ -1373,7 +1373,7 @@ void PPPMDispIntel::make_rho_none(IntelBuffers *buffers) ------------------------------------------------------------------------- */ template -void PPPMDispIntel::fieldforce_c_ik(IntelBuffers *buffers) +void PPPMDispIntel::fieldforce_c_ik(IntelBuffers * /*buffers*/) { // loop over my charges, interpolate electric field from nearby grid points @@ -1520,7 +1520,7 @@ void PPPMDispIntel::fieldforce_c_ik(IntelBuffers *buffers) ------------------------------------------------------------------------- */ template -void PPPMDispIntel::fieldforce_c_ad(IntelBuffers *buffers) +void PPPMDispIntel::fieldforce_c_ad(IntelBuffers * /*buffers*/) { // loop over my charges, interpolate electric field from nearby grid points @@ -1725,7 +1725,7 @@ void PPPMDispIntel::fieldforce_c_ad(IntelBuffers *buffers) ------------------------------------------------------------------------- */ template -void PPPMDispIntel::fieldforce_g_ik(IntelBuffers *buffers) +void PPPMDispIntel::fieldforce_g_ik(IntelBuffers * /*buffers*/) { // loop over my charges, interpolate electric field from nearby grid points @@ -1869,7 +1869,7 @@ void PPPMDispIntel::fieldforce_g_ik(IntelBuffers *buffers) ------------------------------------------------------------------------- */ template -void PPPMDispIntel::fieldforce_g_ad(IntelBuffers *buffers) +void PPPMDispIntel::fieldforce_g_ad(IntelBuffers * /*buffers*/) { // loop over my charges, interpolate electric field from nearby grid points @@ -2069,7 +2069,7 @@ void PPPMDispIntel::fieldforce_g_ad(IntelBuffers *buffers) ------------------------------------------------------------------------- */ template -void PPPMDispIntel::fieldforce_a_ik(IntelBuffers *buffers) +void PPPMDispIntel::fieldforce_a_ik(IntelBuffers * /*buffers*/) { // loop over my charges, interpolate electric field from nearby grid points @@ -2282,7 +2282,7 @@ void PPPMDispIntel::fieldforce_a_ik(IntelBuffers *buffers) ------------------------------------------------------------------------- */ template -void PPPMDispIntel::fieldforce_a_ad(IntelBuffers *buffers) +void PPPMDispIntel::fieldforce_a_ad(IntelBuffers * /*buffers*/) { // loop over my charges, interpolate electric field from nearby grid points @@ -2594,7 +2594,7 @@ void PPPMDispIntel::fieldforce_a_ad(IntelBuffers *buffers) ------------------------------------------------------------------------- */ template -void PPPMDispIntel::fieldforce_none_ik(IntelBuffers *buffers) +void PPPMDispIntel::fieldforce_none_ik(IntelBuffers * /*buffers*/) { // loop over my charges, interpolate electric field from nearby grid points @@ -2755,7 +2755,7 @@ void PPPMDispIntel::fieldforce_none_ik(IntelBuffers *buffers) ------------------------------------------------------------------------- */ template -void PPPMDispIntel::fieldforce_none_ad(IntelBuffers *buffers) +void PPPMDispIntel::fieldforce_none_ad(IntelBuffers * /*buffers*/) { // loop over my charges, interpolate electric field from nearby grid points // (nx,ny,nz) = global coords of grid pt to "lower left" of charge diff --git a/src/USER-INTEL/pppm_intel.cpp b/src/USER-INTEL/pppm_intel.cpp index 46a55e558a..e5540e6377 100644 --- a/src/USER-INTEL/pppm_intel.cpp +++ b/src/USER-INTEL/pppm_intel.cpp @@ -255,7 +255,7 @@ void PPPMIntel::compute_first(int eflag, int vflag) /* ---------------------------------------------------------------------- */ -void PPPMIntel::compute_second(int eflag, int vflag) +void PPPMIntel::compute_second(int /*eflag*/, int /*vflag*/) { int i,j; diff --git a/src/USER-INTEL/verlet_lrt_intel.cpp b/src/USER-INTEL/verlet_lrt_intel.cpp index 962202e228..5dd0da1939 100644 --- a/src/USER-INTEL/verlet_lrt_intel.cpp +++ b/src/USER-INTEL/verlet_lrt_intel.cpp @@ -157,7 +157,7 @@ void VerletLRTIntel::setup(int flag) pthread_create(&_kspace_thread, &_kspace_attr, &VerletLRTIntel::k_launch_loop, this); #elif defined(_LMP_INTEL_LRT_11) - std::thread kspace_thread; + std::thread _kspace_thread; if (kspace_compute_flag) _kspace_thread=std::thread([=]{ _intel_kspace->compute_first(eflag, vflag); }); diff --git a/src/USER-INTEL/verlet_lrt_intel.h b/src/USER-INTEL/verlet_lrt_intel.h index 7380cc6376..6c44ba7e57 100644 --- a/src/USER-INTEL/verlet_lrt_intel.h +++ b/src/USER-INTEL/verlet_lrt_intel.h @@ -24,14 +24,20 @@ IntegrateStyle(verlet/lrt/intel,VerletLRTIntel) #include "pppm_intel.h" #ifdef LMP_INTEL_USELRT -#ifdef LMP_INTEL_LRT11 -#define _LMP_INTEL_LRT_11 -#include -#else -#define _LMP_INTEL_LRT_PTHREAD -#include -#endif - + #if defined(LMP_INTEL_LRT11) || defined(__APPLE__) + #if __cplusplus > 199711L + #define _LMP_INTEL_LRT_11 + #include + #else + #undef LMP_INTEL_USELRT + #ifdef LMP_INTEL_LRT11 + #error C++11 support required for LMP_INTEL_LRT11 define + #endif + #endif + #else + #define _LMP_INTEL_LRT_PTHREAD + #include + #endif #endif namespace LAMMPS_NS { diff --git a/src/USER-LB/fix_lb_fluid.cpp b/src/USER-LB/fix_lb_fluid.cpp index 7a0bd0572e..fecd6f2b25 100644 --- a/src/USER-LB/fix_lb_fluid.cpp +++ b/src/USER-LB/fix_lb_fluid.cpp @@ -646,7 +646,7 @@ void FixLbFluid::init(void) } -void FixLbFluid::setup(int vflag) +void FixLbFluid::setup(int /*vflag*/) { //-------------------------------------------------------------------------- // Need to calculate the force on the fluid for a restart run. @@ -655,7 +655,7 @@ void FixLbFluid::setup(int vflag) calc_fluidforce(); } -void FixLbFluid::initial_integrate(int vflag) +void FixLbFluid::initial_integrate(int /*vflag*/) { //-------------------------------------------------------------------------- // Print a header labelling any output printed to the screen. @@ -711,7 +711,7 @@ void FixLbFluid::initial_integrate(int vflag) streamout(); } -void FixLbFluid::post_force(int vflag) +void FixLbFluid::post_force(int /*vflag*/) { if(fixviscouslb==1) calc_fluidforce(); @@ -741,7 +741,7 @@ void FixLbFluid::grow_arrays(int nmax) //========================================================================== // copy values within local atom-based array //========================================================================== -void FixLbFluid::copy_arrays(int i, int j, int delflag) +void FixLbFluid::copy_arrays(int i, int j, int /*delflag*/) { hydroF[j][0] = hydroF[i][0]; hydroF[j][1] = hydroF[i][1]; diff --git a/src/USER-LB/fix_lb_pc.cpp b/src/USER-LB/fix_lb_pc.cpp index 9fd0dab51d..c5c12d6c11 100644 --- a/src/USER-LB/fix_lb_pc.cpp +++ b/src/USER-LB/fix_lb_pc.cpp @@ -118,7 +118,7 @@ void FixLbPC::init() } /* ---------------------------------------------------------------------- */ -void FixLbPC::initial_integrate(int vflag) { +void FixLbPC::initial_integrate(int /*vflag*/) { double dtfm; @@ -285,7 +285,7 @@ void FixLbPC::grow_arrays(int nmax) copy values within local atom-based array ------------------------------------------------------------------------- */ -void FixLbPC::copy_arrays(int i, int j, int delflag) +void FixLbPC::copy_arrays(int i, int j, int /*delflag*/) { force_old[j][0] = force_old[i][0]; diff --git a/src/USER-LB/fix_lb_rigid_pc_sphere.cpp b/src/USER-LB/fix_lb_rigid_pc_sphere.cpp index dddd060fa4..2601539727 100644 --- a/src/USER-LB/fix_lb_rigid_pc_sphere.cpp +++ b/src/USER-LB/fix_lb_rigid_pc_sphere.cpp @@ -1454,7 +1454,7 @@ void FixLbRigidPCSphere::grow_arrays(int nmax) copy values within local atom-based arrays ------------------------------------------------------------------------- */ -void FixLbRigidPCSphere::copy_arrays(int i, int j, int delflag) +void FixLbRigidPCSphere::copy_arrays(int i, int j, int /*delflag*/) { body[j] = body[i]; up[j][0] = up[i][0]; diff --git a/src/USER-LB/fix_lb_viscous.cpp b/src/USER-LB/fix_lb_viscous.cpp index 8ee4d8419e..afe23477be 100644 --- a/src/USER-LB/fix_lb_viscous.cpp +++ b/src/USER-LB/fix_lb_viscous.cpp @@ -109,7 +109,7 @@ void FixLbViscous::min_setup(int vflag) /* ---------------------------------------------------------------------- */ -void FixLbViscous::post_force(int vflag) +void FixLbViscous::post_force(int /*vflag*/) { // apply drag force to atoms in group // direction is opposed to velocity vector @@ -132,7 +132,7 @@ void FixLbViscous::post_force(int vflag) /* ---------------------------------------------------------------------- */ -void FixLbViscous::post_force_respa(int vflag, int ilevel, int iloop) +void FixLbViscous::post_force_respa(int vflag, int ilevel, int /*iloop*/) { if (ilevel == nlevels_respa-1) post_force(vflag); } diff --git a/src/USER-MANIFOLD/fix_manifoldforce.cpp b/src/USER-MANIFOLD/fix_manifoldforce.cpp index 04172d5c92..4e717ce556 100644 --- a/src/USER-MANIFOLD/fix_manifoldforce.cpp +++ b/src/USER-MANIFOLD/fix_manifoldforce.cpp @@ -149,7 +149,7 @@ void FixManifoldForce::min_setup(int vflag) /* ---------------------------------------------------------------------- */ -void FixManifoldForce::post_force(int vflag) +void FixManifoldForce::post_force(int /*vflag*/) { double **x = atom->x; double **f = atom->f; @@ -177,7 +177,7 @@ void FixManifoldForce::post_force(int vflag) /* ---------------------------------------------------------------------- */ -void FixManifoldForce::post_force_respa(int vflag, int ilevel, int iloop) +void FixManifoldForce::post_force_respa(int vflag, int /*ilevel*/, int /*iloop*/) { post_force(vflag); } diff --git a/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp b/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp index 4dcc3f9704..3c6c70f6df 100644 --- a/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp +++ b/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp @@ -307,7 +307,7 @@ void FixNVEManifoldRattle::update_var_params() /* ----------------------------------------------------------------------------- ---------------------------------------------------------------------------*/ -int FixNVEManifoldRattle::dof(int igroup) +int FixNVEManifoldRattle::dof(int /*igroup*/) { int *mask = atom->mask; int nlocal = atom->nlocal; @@ -348,7 +348,7 @@ double FixNVEManifoldRattle::memory_usage() /* ----------------------------------------------------------------------------- ---------------------------------------------------------------------------*/ -void FixNVEManifoldRattle::initial_integrate(int vflag) +void FixNVEManifoldRattle::initial_integrate(int /*vflag*/) { update_var_params(); nve_x_rattle(igroup, groupbit); diff --git a/src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp b/src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp index 973a5bcf43..2a204d2048 100644 --- a/src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp +++ b/src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp @@ -229,7 +229,7 @@ void FixNVTManifoldRattle::init() -void FixNVTManifoldRattle::setup(int vflag) +void FixNVTManifoldRattle::setup(int /*vflag*/) { compute_temp_target(); @@ -371,7 +371,7 @@ void FixNVTManifoldRattle::nh_v_temp() // Most of this logic is based on fix_nh: -void FixNVTManifoldRattle::initial_integrate(int vflag) +void FixNVTManifoldRattle::initial_integrate(int /*vflag*/) { update_var_params(); diff --git a/src/USER-MANIFOLD/manifold.h b/src/USER-MANIFOLD/manifold.h index 6eb09010ef..b0727c346d 100644 --- a/src/USER-MANIFOLD/manifold.h +++ b/src/USER-MANIFOLD/manifold.h @@ -61,7 +61,7 @@ namespace user_manifold { virtual const char *id() = 0; - virtual void set_atom_id( tagint a_id ){} + virtual void set_atom_id( tagint /*a_id*/ ){} virtual int nparams() = 0; // double *get_params(){ return params; }; diff --git a/src/USER-MANIFOLD/manifold_cylinder.cpp b/src/USER-MANIFOLD/manifold_cylinder.cpp index c13581c640..28062d7a27 100644 --- a/src/USER-MANIFOLD/manifold_cylinder.cpp +++ b/src/USER-MANIFOLD/manifold_cylinder.cpp @@ -5,8 +5,8 @@ using namespace LAMMPS_NS; using namespace user_manifold; -manifold_cylinder::manifold_cylinder( LAMMPS *lmp, int argc, - char **argv ) : manifold(lmp) +manifold_cylinder::manifold_cylinder( LAMMPS *lmp, int /*argc*/, + char **/*argv*/ ) : manifold(lmp) {} diff --git a/src/USER-MANIFOLD/manifold_cylinder_dent.cpp b/src/USER-MANIFOLD/manifold_cylinder_dent.cpp index 21d4087d7c..4df4c833d3 100644 --- a/src/USER-MANIFOLD/manifold_cylinder_dent.cpp +++ b/src/USER-MANIFOLD/manifold_cylinder_dent.cpp @@ -8,8 +8,8 @@ using namespace LAMMPS_NS; using namespace user_manifold; -manifold_cylinder_dent::manifold_cylinder_dent( LAMMPS *lmp, int argc, - char **argv ) : manifold(lmp) +manifold_cylinder_dent::manifold_cylinder_dent( LAMMPS *lmp, int /*argc*/, + char **/*argv*/ ) : manifold(lmp) {} diff --git a/src/USER-MANIFOLD/manifold_dumbbell.cpp b/src/USER-MANIFOLD/manifold_dumbbell.cpp index fa7edc6e4a..c40a5fff9f 100644 --- a/src/USER-MANIFOLD/manifold_dumbbell.cpp +++ b/src/USER-MANIFOLD/manifold_dumbbell.cpp @@ -6,7 +6,7 @@ using namespace LAMMPS_NS; using namespace user_manifold; -manifold_dumbbell::manifold_dumbbell( LAMMPS *lmp, int argc, char **argv ) : manifold(lmp) +manifold_dumbbell::manifold_dumbbell( LAMMPS *lmp, int /*argc*/, char **/*argv*/ ) : manifold(lmp) {} diff --git a/src/USER-MANIFOLD/manifold_ellipsoid.cpp b/src/USER-MANIFOLD/manifold_ellipsoid.cpp index f590123dc3..d5e7bb146e 100644 --- a/src/USER-MANIFOLD/manifold_ellipsoid.cpp +++ b/src/USER-MANIFOLD/manifold_ellipsoid.cpp @@ -4,7 +4,7 @@ using namespace LAMMPS_NS; using namespace user_manifold; -manifold_ellipsoid::manifold_ellipsoid( LAMMPS *lmp, int narg, char **argv ) : manifold(lmp) +manifold_ellipsoid::manifold_ellipsoid( LAMMPS *lmp, int /*narg*/, char **/*argv*/ ) : manifold(lmp) {} diff --git a/src/USER-MANIFOLD/manifold_gaussian_bump.cpp b/src/USER-MANIFOLD/manifold_gaussian_bump.cpp index a9ee35bbfc..b95162740b 100644 --- a/src/USER-MANIFOLD/manifold_gaussian_bump.cpp +++ b/src/USER-MANIFOLD/manifold_gaussian_bump.cpp @@ -25,7 +25,6 @@ public: cubic_hermite( double x0, double x1, double y0, double y1, double yp0, double yp1, LAMMPS_NS::Error *err ) : - x0(x0), x1(x1), y0(y0), y1(y1), yp0(yp0), yp1(yp1), a( 2*x0 + 2 - 2*x1 ), b( -3*x0 - 3 + 3*x1 ), c( 1.0 ), @@ -34,6 +33,7 @@ public: u( -3*y0 + 3*y1 - 2*yp0 - yp1 ), v( yp0 ), w( y0 ), + x0(x0), x1(x1), y0(y0), y1(y1), yp0(yp0), yp1(yp1), err(err) { test(); @@ -133,7 +133,7 @@ public: // Manifold itself: manifold_gaussian_bump::manifold_gaussian_bump(class LAMMPS* lmp, - int narg, char **arg) + int /*narg*/, char **/*arg*/) : manifold(lmp), lut_z(NULL), lut_zp(NULL) {} diff --git a/src/USER-MANIFOLD/manifold_plane.cpp b/src/USER-MANIFOLD/manifold_plane.cpp index d33617fbfb..6c3f17393a 100644 --- a/src/USER-MANIFOLD/manifold_plane.cpp +++ b/src/USER-MANIFOLD/manifold_plane.cpp @@ -4,7 +4,7 @@ using namespace LAMMPS_NS; using namespace user_manifold; -manifold_plane::manifold_plane( LAMMPS *lmp, int argc, char **argv ) : +manifold_plane::manifold_plane( LAMMPS *lmp, int /*argc*/, char **/*argv*/ ) : manifold(lmp) {} @@ -16,7 +16,7 @@ double manifold_plane::g( const double *x ) } -void manifold_plane::n( const double *x, double *n ) +void manifold_plane::n( const double * /*x*/, double *n ) { n[0] = params[0]; n[1] = params[1]; diff --git a/src/USER-MANIFOLD/manifold_plane_wiggle.cpp b/src/USER-MANIFOLD/manifold_plane_wiggle.cpp index ccf0a794da..983702b6f3 100644 --- a/src/USER-MANIFOLD/manifold_plane_wiggle.cpp +++ b/src/USER-MANIFOLD/manifold_plane_wiggle.cpp @@ -5,7 +5,7 @@ using namespace LAMMPS_NS; using namespace user_manifold; -manifold_plane_wiggle::manifold_plane_wiggle( LAMMPS *lmp, int argc, char **argv ) : +manifold_plane_wiggle::manifold_plane_wiggle( LAMMPS *lmp, int /*argc*/, char **/*argv*/ ) : manifold(lmp) {} diff --git a/src/USER-MANIFOLD/manifold_sphere.h b/src/USER-MANIFOLD/manifold_sphere.h index 5d4ae55fda..d9cd46c9c3 100644 --- a/src/USER-MANIFOLD/manifold_sphere.h +++ b/src/USER-MANIFOLD/manifold_sphere.h @@ -40,7 +40,7 @@ namespace user_manifold { nn[2] = 2*x[2]; } - virtual void H( double *x, double h[3][3] ) + virtual void H( double * /*x*/, double h[3][3] ) { h[0][1] = h[0][2] = h[1][0] = h[1][2] = h[2][0] = h[2][1] = 0.0; h[0][0] = h[1][1] = h[2][2] = 2.0; diff --git a/src/USER-MANIFOLD/manifold_spine.cpp b/src/USER-MANIFOLD/manifold_spine.cpp index 308190c528..0ca4c67002 100644 --- a/src/USER-MANIFOLD/manifold_spine.cpp +++ b/src/USER-MANIFOLD/manifold_spine.cpp @@ -8,7 +8,7 @@ using namespace user_manifold; -manifold_spine::manifold_spine( LAMMPS *lmp, int argc, char **argv ) +manifold_spine::manifold_spine( LAMMPS *lmp, int /*argc*/, char **/*argv*/ ) : manifold(lmp) { power = 4; diff --git a/src/USER-MANIFOLD/manifold_thylakoid.cpp b/src/USER-MANIFOLD/manifold_thylakoid.cpp index b7eb155ba2..93cf60ad03 100644 --- a/src/USER-MANIFOLD/manifold_thylakoid.cpp +++ b/src/USER-MANIFOLD/manifold_thylakoid.cpp @@ -12,7 +12,7 @@ using namespace LAMMPS_NS; using namespace user_manifold; -manifold_thylakoid::manifold_thylakoid( LAMMPS *lmp, int narg, char ** arg) +manifold_thylakoid::manifold_thylakoid( LAMMPS *lmp, int /*narg*/, char ** /*arg*/) : manifold(lmp) { // You can NOT depend on proper construction of the domains in @@ -117,7 +117,7 @@ void manifold_thylakoid::n( const double *x, double *n ) } } -thyla_part *manifold_thylakoid::get_thyla_part( const double *x, int *err_flag, std::size_t *idx ) +thyla_part *manifold_thylakoid::get_thyla_part( const double *x, int * /*err_flag*/, std::size_t *idx ) { for( std::size_t i = 0; i < parts.size(); ++i ){ diff --git a/src/USER-MANIFOLD/manifold_torus.cpp b/src/USER-MANIFOLD/manifold_torus.cpp index 44a17725b5..0b4ca24370 100644 --- a/src/USER-MANIFOLD/manifold_torus.cpp +++ b/src/USER-MANIFOLD/manifold_torus.cpp @@ -6,7 +6,7 @@ using namespace LAMMPS_NS; using namespace user_manifold; -manifold_torus::manifold_torus( LAMMPS *lmp, int argc, char **argv ) : manifold(lmp) +manifold_torus::manifold_torus( LAMMPS *lmp, int /*argc*/, char **/*argv*/ ) : manifold(lmp) {} diff --git a/src/USER-MEAMC/meam_dens_final.cpp b/src/USER-MEAMC/meam_dens_final.cpp index de188e497d..2be215c282 100644 --- a/src/USER-MEAMC/meam_dens_final.cpp +++ b/src/USER-MEAMC/meam_dens_final.cpp @@ -5,7 +5,7 @@ using namespace LAMMPS_NS; void MEAM::meam_dens_final(int nlocal, int eflag_either, int eflag_global, int eflag_atom, double* eng_vdwl, - double* eatom, int ntype, int* type, int* fmap, int& errorflag) + double* eatom, int /*ntype*/, int* type, int* fmap, int& errorflag) { int i, elti; int m; diff --git a/src/USER-MEAMC/meam_dens_init.cpp b/src/USER-MEAMC/meam_dens_init.cpp index e1a7509ab3..4bbaa42596 100644 --- a/src/USER-MEAMC/meam_dens_init.cpp +++ b/src/USER-MEAMC/meam_dens_init.cpp @@ -93,7 +93,7 @@ MEAM::meam_dens_init(int i, int ntype, int* type, int* fmap, double** x, void MEAM::getscreen(int i, double* scrfcn, double* dscrfcn, double* fcpair, double** x, int numneigh, - int* firstneigh, int numneigh_full, int* firstneigh_full, int ntype, int* type, int* fmap) + int* firstneigh, int numneigh_full, int* firstneigh_full, int /*ntype*/, int* type, int* fmap) { int jn, j, kn, k; int elti, eltj, eltk; @@ -256,7 +256,7 @@ MEAM::getscreen(int i, double* scrfcn, double* dscrfcn, double* fcpair, double** // ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc void -MEAM::calc_rho1(int i, int ntype, int* type, int* fmap, double** x, int numneigh, int* firstneigh, +MEAM::calc_rho1(int i, int /*ntype*/, int* type, int* fmap, double** x, int numneigh, int* firstneigh, double* scrfcn, double* fcpair) { int jn, j, m, n, p, elti, eltj; diff --git a/src/USER-MEAMC/meam_force.cpp b/src/USER-MEAMC/meam_force.cpp index 85314dd8a2..06fbb57adb 100644 --- a/src/USER-MEAMC/meam_force.cpp +++ b/src/USER-MEAMC/meam_force.cpp @@ -7,7 +7,7 @@ using namespace LAMMPS_NS; void MEAM::meam_force(int i, int eflag_either, int eflag_global, int eflag_atom, int vflag_atom, double* eng_vdwl, - double* eatom, int ntype, int* type, int* fmap, double** x, int numneigh, int* firstneigh, + double* eatom, int /*ntype*/, int* type, int* fmap, double** x, int numneigh, int* firstneigh, int numneigh_full, int* firstneigh_full, int fnoffset, double** f, double** vatom) { int j, jn, k, kn, kk, m, n, p, q; diff --git a/src/USER-MEAMC/meam_setup_global.cpp b/src/USER-MEAMC/meam_setup_global.cpp index 7f8ad3d81f..503ee65496 100644 --- a/src/USER-MEAMC/meam_setup_global.cpp +++ b/src/USER-MEAMC/meam_setup_global.cpp @@ -3,7 +3,7 @@ using namespace LAMMPS_NS; void -MEAM::meam_setup_global(int nelt, lattice_t* lat, double* z, int* ielement, double* atwt, double* alpha, +MEAM::meam_setup_global(int nelt, lattice_t* lat, double* z, int* ielement, double* /*atwt*/, double* alpha, double* b0, double* b1, double* b2, double* b3, double* alat, double* esub, double* asub, double* t0, double* t1, double* t2, double* t3, double* rozero, int* ibar) diff --git a/src/USER-MEAMC/pair_meamc.cpp b/src/USER-MEAMC/pair_meamc.cpp index 027e4c27a7..eca1040c9c 100644 --- a/src/USER-MEAMC/pair_meamc.cpp +++ b/src/USER-MEAMC/pair_meamc.cpp @@ -195,7 +195,7 @@ void PairMEAMC::allocate() global settings ------------------------------------------------------------------------- */ -void PairMEAMC::settings(int narg, char **arg) +void PairMEAMC::settings(int narg, char **/*arg*/) { if (narg != 0) error->all(FLERR,"Illegal pair_style command"); } @@ -312,7 +312,7 @@ void PairMEAMC::init_list(int id, NeighList *ptr) init for one type pair i,j and corresponding j,i ------------------------------------------------------------------------- */ -double PairMEAMC::init_one(int i, int j) +double PairMEAMC::init_one(int /*i*/, int /*j*/) { return cutmax; } @@ -598,7 +598,7 @@ void PairMEAMC::read_files(char *globalfile, char *userfile) /* ---------------------------------------------------------------------- */ int PairMEAMC::pack_forward_comm(int n, int *list, double *buf, - int pbc_flag, int *pbc) + int /*pbc_flag*/, int * /*pbc*/) { int i,j,k,m; diff --git a/src/USER-MESO/fix_edpd_source.cpp b/src/USER-MESO/fix_edpd_source.cpp index 8b03e05181..24bef2b1f7 100644 --- a/src/USER-MESO/fix_edpd_source.cpp +++ b/src/USER-MESO/fix_edpd_source.cpp @@ -87,7 +87,7 @@ void FixEDPDSource::init() /* ---------------------------------------------------------------------- */ -void FixEDPDSource::post_force(int vflag) +void FixEDPDSource::post_force(int /*vflag*/) { double **x = atom->x; double *edpd_flux = atom->edpd_flux; diff --git a/src/USER-MESO/fix_mvv_dpd.cpp b/src/USER-MESO/fix_mvv_dpd.cpp index c97a2d779c..f663165f78 100644 --- a/src/USER-MESO/fix_mvv_dpd.cpp +++ b/src/USER-MESO/fix_mvv_dpd.cpp @@ -72,7 +72,7 @@ void FixMvvDPD::init() allow for both per-type and per-atom mass ------------------------------------------------------------------------- */ -void FixMvvDPD::initial_integrate(int vflag) +void FixMvvDPD::initial_integrate(int /*vflag*/) { double dtfm; double **x = atom->x; diff --git a/src/USER-MESO/fix_mvv_edpd.cpp b/src/USER-MESO/fix_mvv_edpd.cpp index 89a831e121..8719d0d262 100644 --- a/src/USER-MESO/fix_mvv_edpd.cpp +++ b/src/USER-MESO/fix_mvv_edpd.cpp @@ -78,7 +78,7 @@ void FixMvvEDPD::init() allow for both per-type and per-atom mass ------------------------------------------------------------------------- */ -void FixMvvEDPD::initial_integrate(int vflag) +void FixMvvEDPD::initial_integrate(int /*vflag*/) { double dtfm,dtT; // update v and x and cc of atoms in group diff --git a/src/USER-MESO/fix_mvv_tdpd.cpp b/src/USER-MESO/fix_mvv_tdpd.cpp index e16171800b..24b1bbcf48 100644 --- a/src/USER-MESO/fix_mvv_tdpd.cpp +++ b/src/USER-MESO/fix_mvv_tdpd.cpp @@ -76,7 +76,7 @@ void FixMvvTDPD::init() allow for both per-type and per-atom mass ------------------------------------------------------------------------- */ -void FixMvvTDPD::initial_integrate(int vflag) +void FixMvvTDPD::initial_integrate(int /*vflag*/) { double dtfm; // update v and x and cc of atoms in group diff --git a/src/USER-MESO/fix_tdpd_source.cpp b/src/USER-MESO/fix_tdpd_source.cpp index 64964a4c98..89e8005b43 100644 --- a/src/USER-MESO/fix_tdpd_source.cpp +++ b/src/USER-MESO/fix_tdpd_source.cpp @@ -88,7 +88,7 @@ void FixTDPDSource::init() /* ---------------------------------------------------------------------- */ -void FixTDPDSource::post_force(int vflag) +void FixTDPDSource::post_force(int /*vflag*/) { double **x = atom->x; double **cc_flux = atom->cc_flux; diff --git a/src/USER-MESO/pair_edpd.cpp b/src/USER-MESO/pair_edpd.cpp index 351637a842..5ed63a2a8b 100644 --- a/src/USER-MESO/pair_edpd.cpp +++ b/src/USER-MESO/pair_edpd.cpp @@ -530,7 +530,7 @@ void PairEDPD::read_restart_settings(FILE *fp) /* ---------------------------------------------------------------------- */ double PairEDPD::single(int i, int j, int itype, int jtype, double rsq, - double factor_coul, double factor_dpd, double &fforce) + double /*factor_coul*/, double factor_dpd, double &fforce) { double r,rinv,wc,phi; double *T = atom->edpd_temp; diff --git a/src/USER-MESO/pair_mdpd_rhosum.cpp b/src/USER-MESO/pair_mdpd_rhosum.cpp index 1264d03ed3..806a63f898 100644 --- a/src/USER-MESO/pair_mdpd_rhosum.cpp +++ b/src/USER-MESO/pair_mdpd_rhosum.cpp @@ -186,7 +186,7 @@ void PairMDPDRhoSum::allocate() { global settings ------------------------------------------------------------------------- */ -void PairMDPDRhoSum::settings(int narg, char **arg) { +void PairMDPDRhoSum::settings(int narg, char **/*arg*/) { if (narg != 0) error->all(FLERR,"Illegal number of setting arguments for pair_style mdpd/rhosum"); } @@ -236,8 +236,8 @@ double PairMDPDRhoSum::init_one(int i, int j) { /* ---------------------------------------------------------------------- */ -double PairMDPDRhoSum::single(int i, int j, int itype, int jtype, double rsq, - double factor_coul, double factor_lj, double &fforce) { +double PairMDPDRhoSum::single(int /*i*/, int /*j*/, int /*itype*/, int /*jtype*/, double /*rsq*/, + double /*factor_coul*/, double /*factor_lj*/, double &fforce) { fforce = 0.0; return 0.0; @@ -246,7 +246,7 @@ double PairMDPDRhoSum::single(int i, int j, int itype, int jtype, double rsq, /* ---------------------------------------------------------------------- */ int PairMDPDRhoSum::pack_forward_comm(int n, int *list, double *buf, - int pbc_flag, int *pbc) { + int /*pbc_flag*/, int * /*pbc*/) { int i, j, m; double *rho = atom->rho; diff --git a/src/USER-MESO/pair_tdpd.cpp b/src/USER-MESO/pair_tdpd.cpp index b8bbf6d622..821d8c0486 100644 --- a/src/USER-MESO/pair_tdpd.cpp +++ b/src/USER-MESO/pair_tdpd.cpp @@ -465,8 +465,8 @@ void PairTDPD::read_restart_settings(FILE *fp) /* ---------------------------------------------------------------------- */ -double PairTDPD::single(int i, int j, int itype, int jtype, double rsq, - double factor_coul, double factor_dpd, double &fforce) +double PairTDPD::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq, + double /*factor_coul*/, double factor_dpd, double &fforce) { double r,rinv,wc,phi; diff --git a/src/USER-MGPT/mgpt_linalg.cpp b/src/USER-MGPT/mgpt_linalg.cpp index 94a4e21ea6..68701037f4 100644 --- a/src/USER-MGPT/mgpt_linalg.cpp +++ b/src/USER-MGPT/mgpt_linalg.cpp @@ -81,8 +81,8 @@ #define const #endif static void transprod_generic(const double * restrict A, - const double * restrict B, - double * restrict C) { + const double * restrict B, + double * restrict C) { const int lda = 8,n = mgpt_linalg::matrix_size; int i,j,k; double s; @@ -90,15 +90,15 @@ static void transprod_generic(const double * restrict A, for(j = 0; jall(__FILE__,__LINE__,"Illegal pair_style command"); } @@ -2025,7 +2025,7 @@ void PairMGPT::init_list(int id, NeighList *ptr) /* ---------------------------------------------------------------------- init for one type pair i,j and corresponding j,i ------------------------------------------------------------------------- */ -double PairMGPT::init_one(int i, int j) +double PairMGPT::init_one(int /*i*/, int /*j*/) { return cutoff; } diff --git a/src/USER-MISC/Install.sh b/src/USER-MISC/Install.sh deleted file mode 100755 index 2d42125ec3..0000000000 --- a/src/USER-MISC/Install.sh +++ /dev/null @@ -1,40 +0,0 @@ -# Install/unInstall package files in LAMMPS -# mode = 0/1/2 for uninstall/install/update - -mode=$1 - -# enforce using portable C locale -LC_ALL=C -export LC_ALL - -# arg1 = file, arg2 = file it depends on - -action () { - if (test $mode = 0) then - rm -f ../$1 - elif (! cmp -s $1 ../$1) then - if (test -z "$2" || test -e ../$2) then - cp $1 .. - if (test $mode = 2) then - echo " updating src/$1" - fi - fi - elif (test ! -n "$2") then - if (test ! -e ../$2) then - rm -f ../$1 - fi - fi -} - -# all package files -# only a few files have dependencies - -for file in *.cpp *.h; do - if (test $file = "pair_cdeam.cpp") then - action pair_cdeam.cpp pair_eam_alloy.cpp - elif (test $file = "pair_cdeam.h") then - action pair_cdeam.h pair_eam_alloy.cpp - else - test -f ${file} && action $file - fi -done diff --git a/src/USER-MISC/README b/src/USER-MISC/README index 222c06b4c4..0f9e7bf383 100644 --- a/src/USER-MISC/README +++ b/src/USER-MISC/README @@ -29,6 +29,7 @@ bond_style harmonic/shift/cut, Carsten Svaneborg, science at zqex.dk, 8 Aug 11 compute ackland/atom, Gerolf Ziegenhain, gerolf at ziegenhain.com, 4 Oct 2007 compute basal/atom, Christopher Barrett, cdb333 at cavs.msstate.edu, 3 Mar 2013 compute cnp/atom, Paulo Branicio (USC), branicio at usc.edu, 31 May 2017 +compute entropy/atom, Pablo Piaggi (EPFL), pablo.piaggi at epfl.ch, 15 June 2018 compute temp/rotate, Laurent Joly (U Lyon), ljoly.ulyon at gmail.com, 8 Aug 11 compute PRESSURE/GREM, David Stelter, dstelter@bu.edu, 22 Nov 16 dihedral_style cosine/shift/exp, Carsten Svaneborg, science at zqex.dk, 8 Aug 11 @@ -64,7 +65,6 @@ pair_style buck/mdf, Paolo Raiteri, p.raiteri at curtin.edu.au, 2 Dec 15 pair_style coul/diel, Axel Kohlmeyer, akohlmey at gmail.com, 1 Dec 11 pair_style dipole/sf, Mario Orsi, orsimario at gmail.com, 8 Aug 11 pair_style edip, Luca Ferraro, luca.ferraro at caspur.it, 15 Sep 11 -pair_style eam/cd, Alexander Stukowski, stukowski at mm.tu-darmstadt.de, 7 Nov 09 pair_style extep, Jaap Kroes (Radboud U), jaapkroes at gmail dot com, 28 Nov 17 pair_style gauss/cut, Axel Kohlmeyer, akohlmey at gmail.com, 1 Dec 11 pair_style lennard/mdf, Paolo Raiteri, p.raiteri at curtin.edu.au, 2 Dec 15 diff --git a/src/USER-MISC/angle_dipole.cpp b/src/USER-MISC/angle_dipole.cpp index bcb631c61f..c4186da472 100644 --- a/src/USER-MISC/angle_dipole.cpp +++ b/src/USER-MISC/angle_dipole.cpp @@ -229,7 +229,7 @@ void AngleDipole::write_data(FILE *fp) used by ComputeAngleLocal ------------------------------------------------------------------------- */ -double AngleDipole::single(int type, int iRef, int iDip, int iDummy) +double AngleDipole::single(int type, int iRef, int iDip, int /*iDummy*/) { double **x = atom->x; // position vector double **mu = atom->mu; // point-dipole components and moment magnitude diff --git a/src/USER-MISC/bond_harmonic_shift.cpp b/src/USER-MISC/bond_harmonic_shift.cpp index 7148c5438d..b34f71e888 100644 --- a/src/USER-MISC/bond_harmonic_shift.cpp +++ b/src/USER-MISC/bond_harmonic_shift.cpp @@ -203,7 +203,7 @@ void BondHarmonicShift::write_data(FILE *fp) /* ---------------------------------------------------------------------- */ -double BondHarmonicShift::single(int type, double rsq, int i, int j, +double BondHarmonicShift::single(int type, double rsq, int /*i*/, int /*j*/, double &fforce) { double r = sqrt(rsq); diff --git a/src/USER-MISC/bond_harmonic_shift_cut.cpp b/src/USER-MISC/bond_harmonic_shift_cut.cpp index 20c8a1a300..a58df70878 100644 --- a/src/USER-MISC/bond_harmonic_shift_cut.cpp +++ b/src/USER-MISC/bond_harmonic_shift_cut.cpp @@ -205,7 +205,7 @@ void BondHarmonicShiftCut::write_data(FILE *fp) /* ---------------------------------------------------------------------- */ -double BondHarmonicShiftCut::single(int type, double rsq, int i, int j, +double BondHarmonicShiftCut::single(int type, double rsq, int /*i*/, int /*j*/, double &fforce) { fforce = 0.0; diff --git a/src/USER-MISC/compute_ackland_atom.cpp b/src/USER-MISC/compute_ackland_atom.cpp index a17aefe71b..bcf41591eb 100644 --- a/src/USER-MISC/compute_ackland_atom.cpp +++ b/src/USER-MISC/compute_ackland_atom.cpp @@ -105,7 +105,7 @@ void ComputeAcklandAtom::init() /* ---------------------------------------------------------------------- */ -void ComputeAcklandAtom::init_list(int id, NeighList *ptr) +void ComputeAcklandAtom::init_list(int /*id*/, NeighList *ptr) { list = ptr; } diff --git a/src/USER-MISC/compute_basal_atom.cpp b/src/USER-MISC/compute_basal_atom.cpp index 4d8627a11f..3b9b38343d 100644 --- a/src/USER-MISC/compute_basal_atom.cpp +++ b/src/USER-MISC/compute_basal_atom.cpp @@ -85,7 +85,7 @@ void ComputeBasalAtom::init() /* ---------------------------------------------------------------------- */ -void ComputeBasalAtom::init_list(int id, NeighList *ptr) +void ComputeBasalAtom::init_list(int /*id*/, NeighList *ptr) { list = ptr; } diff --git a/src/USER-MISC/compute_cnp_atom.cpp b/src/USER-MISC/compute_cnp_atom.cpp index 51cf3ab07a..6fa16f1a9a 100644 --- a/src/USER-MISC/compute_cnp_atom.cpp +++ b/src/USER-MISC/compute_cnp_atom.cpp @@ -121,7 +121,7 @@ void ComputeCNPAtom::init() /* ---------------------------------------------------------------------- */ -void ComputeCNPAtom::init_list(int id, NeighList *ptr) +void ComputeCNPAtom::init_list(int /*id*/, NeighList *ptr) { list = ptr; } diff --git a/src/USER-MISC/compute_entropy_atom.cpp b/src/USER-MISC/compute_entropy_atom.cpp new file mode 100644 index 0000000000..4946bc437e --- /dev/null +++ b/src/USER-MISC/compute_entropy_atom.cpp @@ -0,0 +1,342 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Pablo Piaggi (EPFL Lausanne) +------------------------------------------------------------------------- */ + +#include +#include +#include +#include "compute_entropy_atom.h" +#include "atom.h" +#include "update.h" +#include "modify.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "force.h" +#include "pair.h" +#include "comm.h" +#include "math_extra.h" +#include "math_const.h" +#include "memory.h" +#include "error.h" +#include "domain.h" + + +using namespace LAMMPS_NS; +using namespace MathConst; + +/* ---------------------------------------------------------------------- */ + +ComputeEntropyAtom:: +ComputeEntropyAtom(LAMMPS *lmp, int narg, char **arg) : + Compute(lmp, narg, arg), + pair_entropy(NULL), pair_entropy_avg(NULL) +{ + if (narg < 5 || narg > 10) + error->all(FLERR,"Illegal compute entropy/atom command; wrong number" + " of arguments"); + + // Arguments are: sigma cutoff avg yes/no cutoff2 local yes/no + // sigma is the gaussian width + // cutoff is the cutoff for the calculation of g(r) + // avg is optional and allows averaging the pair entropy over neighbors + // the next argument should be yes or no + // cutoff2 is the cutoff for the averaging + // local is optional and allows using the local density to normalize + // the g(r) + + sigma = force->numeric(FLERR,arg[3]); + if (sigma <= 0.0) error->all(FLERR,"Illegal compute entropy/atom" + " command; sigma must be positive"); + cutoff = force->numeric(FLERR,arg[4]); + if (cutoff <= 0.0) error->all(FLERR,"Illegal compute entropy/atom" + " command; cutoff must be positive"); + + avg_flag = 0; + local_flag = 0; + + // optional keywords + int iarg = 5; + while (iarg < narg) { + if (strcmp(arg[iarg],"avg") == 0) { + if (iarg+2 > narg) + error->all(FLERR,"Illegal compute entropy/atom;" + " missing arguments after avg"); + if (strcmp(arg[iarg+1],"yes") == 0) avg_flag = 1; + else if (strcmp(arg[iarg+1],"no") == 0) avg_flag = 0; + else error->all(FLERR,"Illegal compute entropy/atom;" + " argument after avg should be yes or no"); + cutoff2 = force->numeric(FLERR,arg[iarg+2]); + if (cutoff2 < 0.0) error->all(FLERR,"Illegal compute entropy/atom" + " command; negative cutoff2"); + cutsq2 = cutoff2*cutoff2; + iarg += 3; + } else if (strcmp(arg[iarg],"local") == 0) { + if (strcmp(arg[iarg+1],"yes") == 0) local_flag = 1; + else if (strcmp(arg[iarg+1],"no") == 0) local_flag = 0; + else error->all(FLERR,"Illegal compute entropy/atom;" + " argument after local should be yes or no"); + iarg += 2; + } else error->all(FLERR,"Illegal compute entropy/atom; argument after" + " sigma and cutoff should be avg or local"); + } + + + cutsq = cutoff*cutoff; + nbin = static_cast(cutoff / sigma) + 1; + nmax = 0; + maxneigh = 0; + // Number of bins above and below the central one that will be + // considered as affected by the gaussian kernel + // 3 seems a good compromise between speed and good mollification + deltabin = 3; + deltar = sigma; + peratom_flag = 1; + size_peratom_cols = 0; +} + +/* ---------------------------------------------------------------------- */ + +ComputeEntropyAtom::~ComputeEntropyAtom() +{ + memory->destroy(pair_entropy); + if (avg_flag) memory->destroy(pair_entropy_avg); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeEntropyAtom::init() +{ + if (force->pair == NULL) + error->all(FLERR,"Compute entropy/atom requires a pair style be" + " defined"); + + if ( (cutoff+cutoff2) > (force->pair->cutforce + neighbor->skin) ) + { + error->all(FLERR,"Compute entropy/atom cutoff is longer than the" + " pairwise cutoff. Increase the neighbor list skin" + " distance."); + } + + int count = 0; + for (int i = 0; i < modify->ncompute; i++) + if (strcmp(modify->compute[i]->style,"entropy/atom") == 0) count++; + if (count > 1 && comm->me == 0) + error->warning(FLERR,"More than one compute entropy/atom"); + + // need a full neighbor list with neighbors of the ghost atoms + + int irequest = neighbor->request(this,instance_me); + neighbor->requests[irequest]->pair = 0; + neighbor->requests[irequest]->compute = 1; + neighbor->requests[irequest]->half = 0; + neighbor->requests[irequest]->full = 1; + neighbor->requests[irequest]->occasional = 0; + neighbor->requests[irequest]->ghost = 1; + +} + +/* ---------------------------------------------------------------------- */ + +void ComputeEntropyAtom::init_list(int /*id*/, NeighList *ptr) +{ + list = ptr; +} + +/* ---------------------------------------------------------------------- */ + +void ComputeEntropyAtom::compute_peratom() +{ + int i,j,ii,jj,inum,jnum; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + int *ilist,*jlist,*numneigh,**firstneigh; + double *rbin = new double[nbin]; + double *rbinsq = new double[nbin]; + + invoked_peratom = update->ntimestep; + + // Initialize distance vectors + for (int i = 0; i < nbin; i++) { + rbin[i] = i*deltar; + rbinsq[i] = rbin[i]*rbin[i]; + } + + // grow pair_entropy and pair_entropy_avg array if necessary + + if (atom->nmax > nmax) { + if (!avg_flag) { + memory->destroy(pair_entropy); + nmax = atom->nmax; + memory->create(pair_entropy,nmax,"entropy/atom:pair_entropy"); + vector_atom = pair_entropy; + } else { + memory->destroy(pair_entropy); + memory->destroy(pair_entropy_avg); + nmax = atom->nmax; + memory->create(pair_entropy,nmax,"entropy/atom:pair_entropy"); + memory->create(pair_entropy_avg,nmax, + "entropy/atom:pair_entropy_avg"); + vector_atom = pair_entropy_avg; + } + } + + inum = list->inum + list->gnum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // Compute some constants + double sigmasq2=2*sigma*sigma; + double volume = domain->xprd * domain->yprd * domain->zprd; + double density = atom->natoms / volume; + + // compute pair entropy for each atom in group + // use full neighbor list + + double **x = atom->x; + int *mask = atom->mask; + double *gofr = new double[nbin]; + double *integrand = new double[nbin]; + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + if (mask[i] & groupbit) { + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + // If local density is used, calculate it + if (local_flag) { + double neigh_cutoff = force->pair->cutforce + neighbor->skin; + double volume = + (4./3.)*MY_PI*neigh_cutoff*neigh_cutoff*neigh_cutoff; + density = jnum / volume; + } + + // calculate kernel normalization + // Normalization of g(r) + double normConstantBase = 4*MY_PI*density; + // Normalization of gaussian + normConstantBase *= sqrt(2.*MY_PI)*sigma; + double invNormConstantBase = 1./normConstantBase; + + // loop over list of all neighbors within force cutoff + + // initialize gofr + for(int k=0;k (nbin-1)) minbin=nbin-1; + maxbin=bin + deltabin; + if (maxbin > (nbin-1)) maxbin=nbin-1; + for(int k=minbin;kx; double **f = atom->f; @@ -252,7 +252,7 @@ void FixAddTorque::post_force(int vflag) /* ---------------------------------------------------------------------- */ -void FixAddTorque::post_force_respa(int vflag, int ilevel, int iloop) +void FixAddTorque::post_force_respa(int vflag, int ilevel, int /*iloop*/) { if (ilevel == ilevel_respa) post_force(vflag); } diff --git a/src/USER-MISC/fix_ave_correlate_long.cpp b/src/USER-MISC/fix_ave_correlate_long.cpp index da6d041287..0ce6121bf9 100644 --- a/src/USER-MISC/fix_ave_correlate_long.cpp +++ b/src/USER-MISC/fix_ave_correlate_long.cpp @@ -412,7 +412,7 @@ void FixAveCorrelateLong::init() only does something if nvalid = current timestep ------------------------------------------------------------------------- */ -void FixAveCorrelateLong::setup(int vflag) +void FixAveCorrelateLong::setup(int /*vflag*/) { end_of_step(); } diff --git a/src/USER-MISC/fix_bond_react.cpp b/src/USER-MISC/fix_bond_react.cpp index fb56945fd3..a6f08a7376 100644 --- a/src/USER-MISC/fix_bond_react.cpp +++ b/src/USER-MISC/fix_bond_react.cpp @@ -264,6 +264,9 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : memory->create(edge,max_natoms,nreacts,"bond/react:edge"); memory->create(landlocked_atoms,max_natoms,nreacts,"bond/react:landlocked_atoms"); + for (int j = 0; j < nreacts; j++) + for (int i = 0; i < max_natoms; i++) edge[i][j] = 0; + // read all superimpose files afterward for (int i = 0; i < nreacts; i++) { open(files[i]); @@ -585,7 +588,7 @@ void FixBondReact::init() /* ---------------------------------------------------------------------- */ -void FixBondReact::init_list(int id, NeighList *ptr) +void FixBondReact::init_list(int /*id*/, NeighList *ptr) { list = ptr; } @@ -958,6 +961,10 @@ void FixBondReact::superimpose_algorithm() local_num_mega = 0; ghostly_num_mega = 0; + // indicates local ghosts of other procs + int tmp; + localsendlist = (int *) comm->extract("localsendlist",tmp); + // quick description of important global indices you'll see floating about: // 'pion' is the pioneer loop index // 'neigh' in the first neighbor index @@ -1060,8 +1067,8 @@ void FixBondReact::superimpose_algorithm() hang_catch++; // let's go ahead and catch the simplest of hangs //if (hang_catch > onemol->natoms*4) - if (hang_catch > atom->nlocal*3) { - error->all(FLERR,"Excessive iteration of superimpose algorithm"); + if (hang_catch > atom->nlocal*30) { + error->one(FLERR,"Excessive iteration of superimpose algorithm"); } } } @@ -1551,6 +1558,39 @@ void FixBondReact::find_landlocked_atoms(int myrxn) error->one(FLERR,"Atom affected by reaction too close to template edge"); } + // additionally, if a bond changes type, but neither involved atom is landlocked, bad + // would someone want to change an angle type but not bond or atom types? (etc.) ...hopefully not yet + for (int i = 0; i < twomol->natoms; i++) { + if (landlocked_atoms[i][myrxn] == 0) { + for (int j = 0; j < twomol->num_bond[i]; j++) { + int twomol_atomj = twomol->bond_atom[i][j]; + if (landlocked_atoms[twomol_atomj-1][myrxn] == 0) { + int onemol_atomi = equivalences[i][1][myrxn]; + int onemol_batom; + for (int m = 0; m < onemol->num_bond[onemol_atomi-1]; m++) { + onemol_batom = onemol->bond_atom[onemol_atomi-1][m]; + if (onemol_batom == equivalences[twomol_atomj-1][1][myrxn]) { + if (twomol->bond_type[i][j] != onemol->bond_type[onemol_atomi-1][m]) { + error->one(FLERR,"Bond type affected by reaction too close to template edge"); + } + } + } + if (newton_bond) { + int onemol_atomj = equivalences[twomol_atomj-1][1][myrxn]; + for (int m = 0; m < onemol->num_bond[onemol_atomj-1]; m++) { + onemol_batom = onemol->bond_atom[onemol_atomj-1][m]; + if (onemol_batom == equivalences[i][1][myrxn]) { + if (twomol->bond_type[i][j] != onemol->bond_type[onemol_atomj-1][m]) { + error->one(FLERR,"Bond type affected by reaction too close to template edge"); + } + } + } + } + } + } + } + } + // also, if atoms change number of bonds, but aren't landlocked, that could be bad if (me == 0) for (int i = 0; i < twomol->natoms; i++) { @@ -1821,16 +1861,23 @@ if so, flag for broadcasting for perusal by all processors void FixBondReact::glove_ghostcheck() { - // it appears this little loop was deemed important enough for its own function! - // noteworthy: it's only relevant for parallel - // here we add glove to either local_mega_glove or ghostly_mega_glove + // ghostly_mega_glove includes atoms that are ghosts, either of this proc or another + // 'ghosts of another' indication taken from comm->sendlist + int ghostly = 0; - for (int i = 0; i < onemol->natoms; i++) { - if (atom->map(glove[i][1]) >= atom->nlocal) { - ghostly = 1; - break; + if (comm->style == 0) { + for (int i = 0; i < onemol->natoms; i++) { + int ilocal = atom->map(glove[i][1]); + if (ilocal >= atom->nlocal || localsendlist[ilocal] == 1) { + ghostly = 1; + break; + } } + } else { + #if !defined(MPI_STUBS) + ghostly = 1; + #endif } if (ghostly == 1) { @@ -2064,7 +2111,7 @@ void FixBondReact::update_everything() nspecial[atom->map(update_mega_glove[jj+1][i])][1]++; nspecial[atom->map(update_mega_glove[jj+1][i])][2]++; } - for (int n = nspecial[atom->map(update_mega_glove[jj+1][i])][2]; n > insert_num; n--) { + for (int n = nspecial[atom->map(update_mega_glove[jj+1][i])][2]-1; n > insert_num; n--) { special[atom->map(update_mega_glove[jj+1][i])][n] = special[atom->map(update_mega_glove[jj+1][i])][n-1]; } special[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->special[j][k]-1][1][rxnID]][i]; @@ -2445,7 +2492,6 @@ void FixBondReact::read(int myrxn) sscanf(line,"%d",&jbonding[myrxn]); } else if (strcmp(keyword,"EdgeIDs") == 0) { edgeflag = 1; - for (int i = 0; i < onemol->natoms; i++) edge[i][myrxn] = 0; EdgeIDs(line, myrxn); } else if (strcmp(keyword,"Equivalences") == 0) { equivflag = 1; @@ -2457,8 +2503,8 @@ void FixBondReact::read(int myrxn) } // error check - if (bondflag == 0 || equivflag == 0 || edgeflag == 0) - error->all(FLERR,"Superimpose file missing BondingIDs, EdgeIDs, or Equivalences section\n"); + if (bondflag == 0 || equivflag == 0) + error->all(FLERR,"Superimpose file missing BondingIDs or Equivalences section\n"); } void FixBondReact::EdgeIDs(char *line, int myrxn) @@ -2585,7 +2631,7 @@ double FixBondReact::compute_vector(int n) /* ---------------------------------------------------------------------- */ -void FixBondReact::post_integrate_respa(int ilevel, int iloop) +void FixBondReact::post_integrate_respa(int ilevel, int /*iloop*/) { if (ilevel == nlevels_respa-1) post_integrate(); } @@ -2593,7 +2639,7 @@ void FixBondReact::post_integrate_respa(int ilevel, int iloop) /* ---------------------------------------------------------------------- */ int FixBondReact::pack_forward_comm(int n, int *list, double *buf, - int pbc_flag, int *pbc) + int /*pbc_flag*/, int * /*pbc*/) { int i,j,k,m,ns; diff --git a/src/USER-MISC/fix_bond_react.h b/src/USER-MISC/fix_bond_react.h index 8ff71141f8..08756f8131 100644 --- a/src/USER-MISC/fix_bond_react.h +++ b/src/USER-MISC/fix_bond_react.h @@ -122,6 +122,7 @@ class FixBondReact : public Fix { tagint **local_mega_glove; // consolidation local of reaction instances tagint **ghostly_mega_glove; // consolidation nonlocal of reaction instances tagint **global_mega_glove; // consolidation (inter-processor) of gloves containing nonlocal atoms + int *localsendlist; // indicates ghosts of other procs int local_num_mega; // num of local reaction instances int ghostly_num_mega; // num of ghostly reaction instances int global_megasize; // num of reaction instances in global_mega_glove diff --git a/src/USER-MISC/fix_filter_corotate.cpp b/src/USER-MISC/fix_filter_corotate.cpp index 91c7033513..56ab2b3df9 100644 --- a/src/USER-MISC/fix_filter_corotate.cpp +++ b/src/USER-MISC/fix_filter_corotate.cpp @@ -705,7 +705,7 @@ double FixFilterCorotate::compute_array(int,int) return 1; } -void FixFilterCorotate::pre_force_respa(int vflag, int ilevel, int iloop) +void FixFilterCorotate::pre_force_respa(int /*vflag*/, int ilevel, int /*iloop*/) { if (ilevel == nlevels_respa-1) { @@ -717,7 +717,7 @@ void FixFilterCorotate::pre_force_respa(int vflag, int ilevel, int iloop) } } -void FixFilterCorotate::post_force_respa(int vflag, int ilevel, int iloop) +void FixFilterCorotate::post_force_respa(int /*vflag*/, int ilevel, int /*iloop*/) { if (ilevel == nlevels_respa-1) { @@ -1699,7 +1699,7 @@ void FixFilterCorotate::general_cluster(int index, int index_in_list) } int FixFilterCorotate::pack_forward_comm(int n, int *list, double *buf, - int pbc_flag, int *pbc) + int /*pbc_flag*/, int * /*pbc*/) { int i,j,m; double**f = atom->f; @@ -1839,7 +1839,7 @@ double FixFilterCorotate::memory_usage() * copy values within local atom-based arrays * ------------------------------------------------------------------------- */ -void FixFilterCorotate::copy_arrays(int i, int j, int delflag) +void FixFilterCorotate::copy_arrays(int i, int j, int /*delflag*/) { int flag = shake_flag[j] = shake_flag[i]; if (flag == 1) { diff --git a/src/USER-MISC/fix_flow_gauss.cpp b/src/USER-MISC/fix_flow_gauss.cpp index 6a1e508030..b6366ec509 100644 --- a/src/USER-MISC/fix_flow_gauss.cpp +++ b/src/USER-MISC/fix_flow_gauss.cpp @@ -155,7 +155,7 @@ void FixFlowGauss::setup(int vflag) /* ---------------------------------------------------------------------- this is where Gaussian dynamics constraint is applied ------------------------------------------------------------------------- */ -void FixFlowGauss::post_force(int vflag) +void FixFlowGauss::post_force(int /*vflag*/) { double **f = atom->f; double **v = atom->v; @@ -222,7 +222,7 @@ void FixFlowGauss::post_force(int vflag) } -void FixFlowGauss::post_force_respa(int vflag, int ilevel, int iloop) +void FixFlowGauss::post_force_respa(int vflag, int ilevel, int /*iloop*/) { if (ilevel == ilevel_respa) post_force(vflag); } diff --git a/src/USER-MISC/fix_gle.cpp b/src/USER-MISC/fix_gle.cpp index 584b33bfe7..0b08fab4ca 100644 --- a/src/USER-MISC/fix_gle.cpp +++ b/src/USER-MISC/fix_gle.cpp @@ -582,7 +582,7 @@ void FixGLE::gle_integrate() energy += deltae*0.5*force->mvv2e; } -void FixGLE::initial_integrate(int vflag) +void FixGLE::initial_integrate(int /*vflag*/) { double dtfm; @@ -685,7 +685,7 @@ void FixGLE::final_integrate() } /* ---------------------------------------------------------------------- */ -void FixGLE::initial_integrate_respa(int vflag, int ilevel, int iloop) +void FixGLE::initial_integrate_respa(int vflag, int ilevel, int /*iloop*/) { dtv = step_respa[ilevel]; dtf = 0.5 * step_respa[ilevel] * force->ftm2v; @@ -699,7 +699,7 @@ void FixGLE::initial_integrate_respa(int vflag, int ilevel, int iloop) else { final_integrate();} } -void FixGLE::final_integrate_respa(int ilevel, int iloop) +void FixGLE::final_integrate_respa(int ilevel, int /*iloop*/) { dtv = step_respa[ilevel]; dtf = 0.5 * step_respa[ilevel] * force->ftm2v; @@ -793,7 +793,7 @@ void FixGLE::grow_arrays(int nmax) copy values within local atom-based arrays ------------------------------------------------------------------------- */ -void FixGLE::copy_arrays(int i, int j, int delflag) +void FixGLE::copy_arrays(int i, int j, int /*delflag*/) { for (int k = 0; k < 3*ns; k++) gle_s[j][k] = gle_s[i][k]; } @@ -868,7 +868,7 @@ void FixGLE::unpack_restart(int nlocal, int nth) fixes on a given processor. ------------------------------------------------------------------------- */ -int FixGLE::size_restart(int nlocal) +int FixGLE::size_restart(int /*nlocal*/) { return 3*ns+1; } diff --git a/src/USER-MISC/fix_grem.cpp b/src/USER-MISC/fix_grem.cpp index a5f8c34448..635acf705c 100644 --- a/src/USER-MISC/fix_grem.cpp +++ b/src/USER-MISC/fix_grem.cpp @@ -256,7 +256,7 @@ void FixGrem::min_setup(int vflag) /* ---------------------------------------------------------------------- */ -void FixGrem::post_force(int vflag) +void FixGrem::post_force(int /*vflag*/) { double **f = atom->f; int *mask = atom->mask; diff --git a/src/USER-MISC/fix_imd.cpp b/src/USER-MISC/fix_imd.cpp index abf9e7cb0b..1c3eafdc46 100644 --- a/src/USER-MISC/fix_imd.cpp +++ b/src/USER-MISC/fix_imd.cpp @@ -811,7 +811,7 @@ void FixIMD::ioworker() /* ---------------------------------------------------------------------- */ /* Main IMD protocol handler: * Send coodinates, energies, and add IMD forces to atoms. */ -void FixIMD::post_force(int vflag) +void FixIMD::post_force(int /*vflag*/) { /* check for reconnect */ if (imd_inactive) { @@ -1153,7 +1153,7 @@ void FixIMD::post_force(int vflag) } /* ---------------------------------------------------------------------- */ -void FixIMD::post_force_respa(int vflag, int ilevel, int iloop) +void FixIMD::post_force_respa(int vflag, int ilevel, int /*iloop*/) { /* only process IMD on the outmost RESPA level. */ if (ilevel == nlevels_respa-1) post_force(vflag); diff --git a/src/USER-MISC/fix_ipi.cpp b/src/USER-MISC/fix_ipi.cpp index c4750ce49e..32892d87a8 100644 --- a/src/USER-MISC/fix_ipi.cpp +++ b/src/USER-MISC/fix_ipi.cpp @@ -269,7 +269,7 @@ void FixIPI::init() neighbor->every = 1; } -void FixIPI::initial_integrate(int vflag) +void FixIPI::initial_integrate(int /*vflag*/) { /* This is called at the beginning of the integration loop, * and will be used to read positions from the socket. Then, diff --git a/src/USER-MISC/fix_nvk.cpp b/src/USER-MISC/fix_nvk.cpp index dbf7b56fe2..2ac2a7c9fc 100644 --- a/src/USER-MISC/fix_nvk.cpp +++ b/src/USER-MISC/fix_nvk.cpp @@ -94,7 +94,7 @@ void FixNVK::init() allow for both per-type and per-atom mass ------------------------------------------------------------------------- */ -void FixNVK::initial_integrate(int vflag) +void FixNVK::initial_integrate(int /*vflag*/) { double sm; double a,b,sqtb,s,sdot; @@ -190,7 +190,7 @@ void FixNVK::final_integrate() /* ---------------------------------------------------------------------- */ -void FixNVK::initial_integrate_respa(int vflag, int ilevel, int iloop) +void FixNVK::initial_integrate_respa(int vflag, int ilevel, int /*iloop*/) { dtv = step_respa[ilevel]; dtf = 0.5 * step_respa[ilevel]; @@ -204,7 +204,7 @@ void FixNVK::initial_integrate_respa(int vflag, int ilevel, int iloop) /* ---------------------------------------------------------------------- */ -void FixNVK::final_integrate_respa(int ilevel, int iloop) +void FixNVK::final_integrate_respa(int ilevel, int /*iloop*/) { dtf = 0.5 * step_respa[ilevel]; final_integrate(); diff --git a/src/USER-MISC/fix_pimd.cpp b/src/USER-MISC/fix_pimd.cpp index e65ae6ae28..eba8ed5d0c 100644 --- a/src/USER-MISC/fix_pimd.cpp +++ b/src/USER-MISC/fix_pimd.cpp @@ -214,7 +214,7 @@ void FixPIMD::setup(int vflag) /* ---------------------------------------------------------------------- */ -void FixPIMD::initial_integrate(int vflag) +void FixPIMD::initial_integrate(int /*vflag*/) { nhc_update_v(); nhc_update_x(); @@ -229,7 +229,7 @@ void FixPIMD::final_integrate() /* ---------------------------------------------------------------------- */ -void FixPIMD::post_force(int flag) +void FixPIMD::post_force(int /*flag*/) { for(int i=0; inlocal; i++) for(int j=0; j<3; j++) atom->f[i][j] /= np; @@ -686,7 +686,7 @@ void FixPIMD::comm_exec(double **ptr) /* ---------------------------------------------------------------------- */ int FixPIMD::pack_forward_comm(int n, int *list, double *buf, - int pbc_flag, int *pbc) + int /*pbc_flag*/, int * /*pbc*/) { int i,j,m; @@ -744,7 +744,7 @@ void FixPIMD::grow_arrays(int nmax) /* ---------------------------------------------------------------------- */ -void FixPIMD::copy_arrays(int i, int j, int delflag) +void FixPIMD::copy_arrays(int i, int j, int /*delflag*/) { int i_pos = i*3; int j_pos = j*3; @@ -832,7 +832,7 @@ int FixPIMD::maxsize_restart() /* ---------------------------------------------------------------------- */ -int FixPIMD::size_restart(int nlocal) +int FixPIMD::size_restart(int /*nlocal*/) { return size_peratom_cols+1; } diff --git a/src/USER-MISC/fix_rhok.cpp b/src/USER-MISC/fix_rhok.cpp index bbc4ce417a..78d63b79a8 100644 --- a/src/USER-MISC/fix_rhok.cpp +++ b/src/USER-MISC/fix_rhok.cpp @@ -144,7 +144,7 @@ FixRhok::min_setup( int inVFlag ) // Modify the forces calculated in the main force loop of ordinary MD void -FixRhok::post_force( int inVFlag ) +FixRhok::post_force( int /*inVFlag*/ ) { double **x = atom->x; double **f = atom->f; @@ -206,7 +206,7 @@ FixRhok::post_force( int inVFlag ) // Forces in RESPA loop void -FixRhok::post_force_respa( int inVFlag, int inILevel, int inILoop ) +FixRhok::post_force_respa( int inVFlag, int inILevel, int /*inILoop*/ ) { if( inILevel == mNLevelsRESPA - 1 ) post_force( inVFlag ); diff --git a/src/USER-MISC/fix_smd.cpp b/src/USER-MISC/fix_smd.cpp index a42690c280..cbebdebdbf 100644 --- a/src/USER-MISC/fix_smd.cpp +++ b/src/USER-MISC/fix_smd.cpp @@ -461,7 +461,7 @@ void FixSMD::restart(char *buf) /* ---------------------------------------------------------------------- */ -void FixSMD::post_force_respa(int vflag, int ilevel, int iloop) +void FixSMD::post_force_respa(int vflag, int ilevel, int /*iloop*/) { if (ilevel == ilevel_respa) post_force(vflag); } diff --git a/src/USER-MISC/fix_srp.cpp b/src/USER-MISC/fix_srp.cpp index e4d85e8674..ebc161ff99 100644 --- a/src/USER-MISC/fix_srp.cpp +++ b/src/USER-MISC/fix_srp.cpp @@ -145,7 +145,7 @@ void FixSRP::init() insert bond particles ------------------------------------------------------------------------- */ -void FixSRP::setup_pre_force(int zz) +void FixSRP::setup_pre_force(int /*zz*/) { double **x = atom->x; double **xold; @@ -394,7 +394,7 @@ void FixSRP::grow_arrays(int nmax) called when move to new proc ------------------------------------------------------------------------- */ -void FixSRP::copy_arrays(int i, int j, int delflag) +void FixSRP::copy_arrays(int i, int j, int /*delflag*/) { for (int m = 0; m < 2; m++) array[j][m] = array[i][m]; @@ -589,7 +589,7 @@ int FixSRP::maxsize_restart() size of atom nlocal's restart data ------------------------------------------------------------------------- */ -int FixSRP::size_restart(int nlocal) +int FixSRP::size_restart(int /*nlocal*/) { return 3; } @@ -632,7 +632,7 @@ void FixSRP::restart(char *buf) pair srp sets the bond type in this fix ------------------------------------------------------------------------- */ -int FixSRP::modify_param(int narg, char **arg) +int FixSRP::modify_param(int /*narg*/, char **arg) { if (strcmp(arg[0],"btype") == 0) { btype = atoi(arg[1]); diff --git a/src/USER-MISC/fix_ti_spring.cpp b/src/USER-MISC/fix_ti_spring.cpp index 5812142763..305e29e033 100644 --- a/src/USER-MISC/fix_ti_spring.cpp +++ b/src/USER-MISC/fix_ti_spring.cpp @@ -167,7 +167,7 @@ void FixTISpring::min_setup(int vflag) /* ---------------------------------------------------------------------- */ -void FixTISpring::post_force(int vflag) +void FixTISpring::post_force(int /*vflag*/) { // do not calculate forces during equilibration if ((update->ntimestep - t0) < t_equil) return; @@ -200,7 +200,7 @@ void FixTISpring::post_force(int vflag) /* ---------------------------------------------------------------------- */ -void FixTISpring::post_force_respa(int vflag, int ilevel, int iloop) +void FixTISpring::post_force_respa(int vflag, int ilevel, int /*iloop*/) { if (ilevel == nlevels_respa-1) post_force(vflag); } @@ -214,7 +214,7 @@ void FixTISpring::min_post_force(int vflag) /* ---------------------------------------------------------------------- */ -void FixTISpring::initial_integrate(int vflag) +void FixTISpring::initial_integrate(int /*vflag*/) { // Update the coupling parameter value if needed if ((update->ntimestep - t0) < t_equil) return; @@ -278,7 +278,7 @@ void FixTISpring::grow_arrays(int nmax) copy values within local atom-based array ------------------------------------------------------------------------- */ -void FixTISpring::copy_arrays(int i, int j, int delflag) +void FixTISpring::copy_arrays(int i, int j, int /*delflag*/) { xoriginal[j][0] = xoriginal[i][0]; xoriginal[j][1] = xoriginal[i][1]; @@ -354,7 +354,7 @@ int FixTISpring::maxsize_restart() size of atom nlocal's restart data ------------------------------------------------------------------------- */ -int FixTISpring::size_restart(int nlocal) +int FixTISpring::size_restart(int /*nlocal*/) { return 4; } diff --git a/src/USER-MISC/fix_ttm_mod.cpp b/src/USER-MISC/fix_ttm_mod.cpp index 1e1e62b638..65f8e90ec3 100644 --- a/src/USER-MISC/fix_ttm_mod.cpp +++ b/src/USER-MISC/fix_ttm_mod.cpp @@ -357,7 +357,7 @@ void FixTTMMod::setup(int vflag) /* ---------------------------------------------------------------------- */ -void FixTTMMod::post_force(int vflag) +void FixTTMMod::post_force(int /*vflag*/) { double **x = atom->x; double **v = atom->v; @@ -451,7 +451,7 @@ void FixTTMMod::post_force(int vflag) /* ---------------------------------------------------------------------- */ -void FixTTMMod::post_force_setup(int vflag) +void FixTTMMod::post_force_setup(int /*vflag*/) { double **f = atom->f; int *mask = atom->mask; @@ -468,14 +468,14 @@ void FixTTMMod::post_force_setup(int vflag) /* ---------------------------------------------------------------------- */ -void FixTTMMod::post_force_respa(int vflag, int ilevel, int iloop) +void FixTTMMod::post_force_respa(int vflag, int ilevel, int /*iloop*/) { if (ilevel == nlevels_respa-1) post_force(vflag); } /* ---------------------------------------------------------------------- */ -void FixTTMMod::post_force_respa_setup(int vflag, int ilevel, int iloop) +void FixTTMMod::post_force_respa_setup(int vflag, int ilevel, int /*iloop*/) { if (ilevel == nlevels_respa-1) post_force_setup(vflag); } @@ -916,7 +916,7 @@ int FixTTMMod::maxsize_restart() size of atom nlocal's restart data ------------------------------------------------------------------------- */ -int FixTTMMod::size_restart(int nlocal) +int FixTTMMod::size_restart(int /*nlocal*/) { return 4; } diff --git a/src/USER-MISC/fix_wall_region_ees.cpp b/src/USER-MISC/fix_wall_region_ees.cpp index 82a78d3e73..33bf636e64 100644 --- a/src/USER-MISC/fix_wall_region_ees.cpp +++ b/src/USER-MISC/fix_wall_region_ees.cpp @@ -149,7 +149,7 @@ void FixWallRegionEES::min_setup(int vflag) /* ---------------------------------------------------------------------- */ -void FixWallRegionEES::post_force(int vflag) +void FixWallRegionEES::post_force(int /*vflag*/) { //sth is needed here, but I dont know what //that is calculation of sn @@ -246,7 +246,7 @@ void FixWallRegionEES::post_force(int vflag) /* ---------------------------------------------------------------------- */ -void FixWallRegionEES::post_force_respa(int vflag, int ilevel, int iloop) +void FixWallRegionEES::post_force_respa(int vflag, int ilevel, int /*iloop*/) { if (ilevel == nlevels_respa-1) post_force(vflag); } diff --git a/src/USER-MISC/pair_agni.cpp b/src/USER-MISC/pair_agni.cpp index 11bf2ae01e..998582f619 100644 --- a/src/USER-MISC/pair_agni.cpp +++ b/src/USER-MISC/pair_agni.cpp @@ -246,7 +246,7 @@ void PairAGNI::allocate() global settings ------------------------------------------------------------------------- */ -void PairAGNI::settings(int narg, char **arg) +void PairAGNI::settings(int narg, char **/*arg*/) { if (narg != 0) error->all(FLERR,"Illegal pair_style command"); } @@ -394,7 +394,7 @@ void PairAGNI::read_file(char *file) if (nwords == 0) continue; if (nwords > MAXWORD) - error->all(FLERR,"Increase MAXWORD and recompile"); + error->all(FLERR,"Increase MAXWORD and re-compile"); // words = ptrs to all words in line diff --git a/src/USER-MISC/pair_buck_mdf.cpp b/src/USER-MISC/pair_buck_mdf.cpp index 457d75bc77..61d32892fc 100644 --- a/src/USER-MISC/pair_buck_mdf.cpp +++ b/src/USER-MISC/pair_buck_mdf.cpp @@ -391,8 +391,8 @@ void PairBuckMDF::read_restart_settings(FILE *fp) /* ---------------------------------------------------------------------- */ -double PairBuckMDF::single(int i, int j, int itype, int jtype, - double rsq, double factor_coul, double factor_lj, +double PairBuckMDF::single(int /*i*/, int /*j*/, int itype, int jtype, + double rsq, double /*factor_coul*/, double factor_lj, double &fforce) { double r2inv,r6inv,r,rexp,forcebuck,phibuck; diff --git a/src/USER-MISC/pair_cdeam.cpp b/src/USER-MISC/pair_cdeam.cpp deleted file mode 100644 index 53d9036a61..0000000000 --- a/src/USER-MISC/pair_cdeam.cpp +++ /dev/null @@ -1,644 +0,0 @@ -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -/* ---------------------------------------------------------------------- - Contributing author: Alexander Stukowski - Technical University of Darmstadt, - Germany Department of Materials Science -------------------------------------------------------------------------- */ - -#include -#include -#include -#include -#include "pair_cdeam.h" -#include "atom.h" -#include "force.h" -#include "comm.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "memory.h" -#include "error.h" - -using namespace LAMMPS_NS; - -// This is for debugging purposes. The ASSERT() macro is used in the code to check -// if everything runs as expected. Change this to #if 0 if you don't need the checking. -#if 0 - #define ASSERT(cond) ((!(cond)) ? my_failure(error,__FILE__,__LINE__) : my_noop()) - - inline void my_noop() {} - inline void my_failure(Error* error, const char* file, int line) { - char str[1024]; - sprintf(str,"Assertion failure: File %s, line %i", file, line); - error->one(FLERR,str); - } -#else - #define ASSERT(cond) -#endif - -#define MAXLINE 1024 // This sets the maximum line length in EAM input files. - -PairCDEAM::PairCDEAM(LAMMPS *lmp, int _cdeamVersion) : PairEAM(lmp), PairEAMAlloy(lmp), cdeamVersion(_cdeamVersion) -{ - single_enable = 0; - restartinfo = 0; - - rhoB = NULL; - D_values = NULL; - hcoeff = NULL; - - // Set communication buffer sizes needed by this pair style. - if(cdeamVersion == 1) { - comm_forward = 4; - comm_reverse = 3; - } - else if(cdeamVersion == 2) { - comm_forward = 3; - comm_reverse = 2; - } - else { - error->all(FLERR,"Invalid CD-EAM potential version."); - } -} - -PairCDEAM::~PairCDEAM() -{ - memory->destroy(rhoB); - memory->destroy(D_values); - if(hcoeff) delete[] hcoeff; -} - -void PairCDEAM::compute(int eflag, int vflag) -{ - int i,j,ii,jj,inum,jnum,itype,jtype; - double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair; - double rsq,rhoip,rhojp,recip,phi; - int *ilist,*jlist,*numneigh,**firstneigh; - - evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = eflag_global = eflag_atom = 0; - - // Grow per-atom arrays if necessary - if(atom->nmax > nmax) { - memory->destroy(rho); - memory->destroy(fp); - memory->destroy(rhoB); - memory->destroy(D_values); - nmax = atom->nmax; - memory->create(rho,nmax,"pair:rho"); - memory->create(rhoB,nmax,"pair:rhoB"); - memory->create(fp,nmax,"pair:fp"); - memory->create(D_values,nmax,"pair:D_values"); - } - - double **x = atom->x; - double **f = atom->f; - int *type = atom->type; - int nlocal = atom->nlocal; - int newton_pair = force->newton_pair; - - inum = list->inum; - ilist = list->ilist; - numneigh = list->numneigh; - firstneigh = list->firstneigh; - - // Zero out per-atom arrays. - int m = nlocal + atom->nghost; - for(i = 0; i < m; i++) { - rho[i] = 0.0; - rhoB[i] = 0.0; - D_values[i] = 0.0; - } - - // Stage I - - // Compute rho and rhoB at each local atom site. - // Additionally calculate the D_i values here if we are using the one-site formulation. - // For the two-site formulation we have to calculate the D values in an extra loop (Stage II). - for(ii = 0; ii < inum; ii++) { - i = ilist[ii]; - xtmp = x[i][0]; - ytmp = x[i][1]; - ztmp = x[i][2]; - itype = type[i]; - jlist = firstneigh[i]; - jnum = numneigh[i]; - - for(jj = 0; jj < jnum; jj++) { - j = jlist[jj]; - j &= NEIGHMASK; - - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; - - if(rsq < cutforcesq) { - jtype = type[j]; - double r = sqrt(rsq); - const EAMTableIndex index = radiusToTableIndex(r); - double localrho = RhoOfR(index, jtype, itype); - rho[i] += localrho; - if(jtype == speciesB) rhoB[i] += localrho; - if(newton_pair || j < nlocal) { - localrho = RhoOfR(index, itype, jtype); - rho[j] += localrho; - if(itype == speciesB) rhoB[j] += localrho; - } - - if(cdeamVersion == 1 && itype != jtype) { - // Note: if the i-j interaction is not concentration dependent (because either - // i or j are not species A or B) then its contribution to D_i and D_j should - // be ignored. - // This if-clause is only required for a ternary. - if((itype == speciesA && jtype == speciesB) || (jtype == speciesA && itype == speciesB)) { - double Phi_AB = PhiOfR(index, itype, jtype, 1.0 / r); - D_values[i] += Phi_AB; - if(newton_pair || j < nlocal) - D_values[j] += Phi_AB; - } - } - } - } - } - - // Communicate and sum densities. - if(newton_pair) { - communicationStage = 1; - comm->reverse_comm_pair(this); - } - - // fp = derivative of embedding energy at each atom - // phi = embedding energy at each atom - for(ii = 0; ii < inum; ii++) { - i = ilist[ii]; - EAMTableIndex index = rhoToTableIndex(rho[i]); - fp[i] = FPrimeOfRho(index, type[i]); - if(eflag) { - phi = FofRho(index, type[i]); - if (eflag_global) eng_vdwl += phi; - if (eflag_atom) eatom[i] += phi; - } - } - - // Communicate derivative of embedding function and densities - // and D_values (this for one-site formulation only). - communicationStage = 2; - comm->forward_comm_pair(this); - - // The electron densities may not drop to zero because then the concentration would no longer be defined. - // But the concentration is not needed anyway if there is no interaction with another atom, which is the case - // if the electron density is exactly zero. That's why the following lines have been commented out. - // - //for(i = 0; i < nlocal + atom->nghost; i++) { - // if(rho[i] == 0 && (type[i] == speciesA || type[i] == speciesB)) - // error->one(FLERR,"CD-EAM potential routine: Detected atom with zero electron density."); - //} - - // Stage II - // This is only required for the original two-site formulation of the CD-EAM potential. - - if(cdeamVersion == 2) { - // Compute intermediate value D_i for each atom. - for(ii = 0; ii < inum; ii++) { - i = ilist[ii]; - xtmp = x[i][0]; - ytmp = x[i][1]; - ztmp = x[i][2]; - itype = type[i]; - jlist = firstneigh[i]; - jnum = numneigh[i]; - - // This code line is required for ternary alloys. - if(itype != speciesA && itype != speciesB) continue; - - double x_i = rhoB[i] / rho[i]; // Concentration at atom i. - - for(jj = 0; jj < jnum; jj++) { - j = jlist[jj]; - j &= NEIGHMASK; - jtype = type[j]; - if(itype == jtype) continue; - - // This code line is required for ternary alloys. - if(jtype != speciesA && jtype != speciesB) continue; - - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; - - if(rsq < cutforcesq) { - double r = sqrt(rsq); - const EAMTableIndex index = radiusToTableIndex(r); - - // The concentration independent part of the cross pair potential. - double Phi_AB = PhiOfR(index, itype, jtype, 1.0 / r); - - // Average concentration of two sites - double x_ij = 0.5 * (x_i + rhoB[j]/rho[j]); - - // Calculate derivative of h(x_ij) polynomial function. - double h_prime = evalHprime(x_ij); - - D_values[i] += h_prime * Phi_AB / (2.0 * rho[i] * rho[i]); - if(newton_pair || j < nlocal) - D_values[j] += h_prime * Phi_AB / (2.0 * rho[j] * rho[j]); - } - } - } - - // Communicate and sum D values. - if(newton_pair) { - communicationStage = 3; - comm->reverse_comm_pair(this); - } - communicationStage = 4; - comm->forward_comm_pair(this); - } - - // Stage III - - // Compute force acting on each atom. - for(ii = 0; ii < inum; ii++) { - i = ilist[ii]; - xtmp = x[i][0]; - ytmp = x[i][1]; - ztmp = x[i][2]; - itype = type[i]; - - jlist = firstneigh[i]; - jnum = numneigh[i]; - - // Concentration at site i - double x_i = -1.0; // The value -1 indicates: no concentration dependence for all interactions of atom i. - // It will be replaced by the concentration at site i if atom i is either A or B. - - double D_i, h_prime_i; - - // This if-clause is only required for ternary alloys. - if((itype == speciesA || itype == speciesB) && rho[i] != 0.0) { - - // Compute local concentration at site i. - x_i = rhoB[i]/rho[i]; - ASSERT(x_i >= 0 && x_i<=1.0); - - if(cdeamVersion == 1) { - // Calculate derivative of h(x_i) polynomial function. - h_prime_i = evalHprime(x_i); - D_i = D_values[i] * h_prime_i / (2.0 * rho[i] * rho[i]); - } else if(cdeamVersion == 2) { - D_i = D_values[i]; - } else { - ASSERT(false); - } - } - - for(jj = 0; jj < jnum; jj++) { - j = jlist[jj]; - j &= NEIGHMASK; - - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; - - if(rsq < cutforcesq) { - jtype = type[j]; - double r = sqrt(rsq); - const EAMTableIndex index = radiusToTableIndex(r); - - // rhoip = derivative of (density at atom j due to atom i) - // rhojp = derivative of (density at atom i due to atom j) - // psip needs both fp[i] and fp[j] terms since r_ij appears in two - // terms of embed eng: Fi(sum rho_ij) and Fj(sum rho_ji) - // hence embed' = Fi(sum rho_ij) rhojp + Fj(sum rho_ji) rhoip - rhoip = RhoPrimeOfR(index, itype, jtype); - rhojp = RhoPrimeOfR(index, jtype, itype); - fpair = fp[i]*rhojp + fp[j]*rhoip; - recip = 1.0/r; - - double x_j = -1; // The value -1 indicates: no concentration dependence for this i-j pair - // because atom j is not of species A nor B. - - // This code line is required for ternary alloy. - if(jtype == speciesA || jtype == speciesB) { - ASSERT(rho[i] != 0.0); - ASSERT(rho[j] != 0.0); - - // Compute local concentration at site j. - x_j = rhoB[j]/rho[j]; - ASSERT(x_j >= 0 && x_j<=1.0); - - double D_j=0.0; - if(cdeamVersion == 1) { - // Calculate derivative of h(x_j) polynomial function. - double h_prime_j = evalHprime(x_j); - D_j = D_values[j] * h_prime_j / (2.0 * rho[j] * rho[j]); - } else if(cdeamVersion == 2) { - D_j = D_values[j]; - } else { - ASSERT(false); - } - double t2 = -rhoB[j]; - if(itype == speciesB) t2 += rho[j]; - fpair += D_j * rhoip * t2; - } - - // This if-clause is only required for a ternary alloy. - // Actually we don't need it at all because D_i should be zero anyway if - // atom i has no concentration dependent interactions (because it is not species A or B). - if(x_i != -1.0) { - double t1 = -rhoB[i]; - if(jtype == speciesB) t1 += rho[i]; - fpair += D_i * rhojp * t1; - } - - double phip; - double phi = PhiOfR(index, itype, jtype, recip, phip); - if(itype == jtype || x_i == -1.0 || x_j == -1.0) { - // Case of no concentration dependence. - fpair += phip; - } else { - // We have a concentration dependence for the i-j interaction. - double h=0.0; - if(cdeamVersion == 1) { - // Calculate h(x_i) polynomial function. - double h_i = evalH(x_i); - // Calculate h(x_j) polynomial function. - double h_j = evalH(x_j); - h = 0.5 * (h_i + h_j); - } else if(cdeamVersion == 2) { - // Average concentration. - double x_ij = 0.5 * (x_i + x_j); - // Calculate h(x_ij) polynomial function. - h = evalH(x_ij); - } else { - ASSERT(false); - } - fpair += h * phip; - phi *= h; - } - - // Divide by r_ij and negate to get forces from gradient. - fpair /= -r; - - f[i][0] += delx*fpair; - f[i][1] += dely*fpair; - f[i][2] += delz*fpair; - if(newton_pair || j < nlocal) { - f[j][0] -= delx*fpair; - f[j][1] -= dely*fpair; - f[j][2] -= delz*fpair; - } - - if(eflag) evdwl = phi; - if(evflag) ev_tally(i,j,nlocal,newton_pair,evdwl,0.0,fpair,delx,dely,delz); - } - } - } - - if(vflag_fdotr) virial_fdotr_compute(); -} - -/* ---------------------------------------------------------------------- */ - -void PairCDEAM::coeff(int narg, char **arg) -{ - PairEAMAlloy::coeff(narg, arg); - - // Make sure the EAM file is a CD-EAM binary alloy. - if(setfl->nelements < 2) - error->all(FLERR,"The EAM file must contain at least 2 elements to be used with the eam/cd pair style."); - - // Read in the coefficients of the h polynomial from the end of the EAM file. - read_h_coeff(arg[2]); - - // Determine which atom type is the A species and which is the B species in the alloy. - // By default take the first element (index 0) in the EAM file as the A species - // and the second element (index 1) in the EAM file as the B species. - speciesA = -1; - speciesB = -1; - for(int i = 1; i <= atom->ntypes; i++) { - if(map[i] == 0) { - if(speciesA >= 0) - error->all(FLERR,"The first element from the EAM file may only be mapped to a single atom type."); - speciesA = i; - } - if(map[i] == 1) { - if(speciesB >= 0) - error->all(FLERR,"The second element from the EAM file may only be mapped to a single atom type."); - speciesB = i; - } - } - if(speciesA < 0) - error->all(FLERR,"The first element from the EAM file must be mapped to exactly one atom type."); - if(speciesB < 0) - error->all(FLERR,"The second element from the EAM file must be mapped to exactly one atom type."); -} - -/* ---------------------------------------------------------------------- - Reads in the h(x) polynomial coefficients -------------------------------------------------------------------------- */ -void PairCDEAM::read_h_coeff(char *filename) -{ - if(comm->me == 0) { - // Open potential file - FILE *fptr; - char line[MAXLINE]; - char nextline[MAXLINE]; - fptr = force->open_potential(filename); - if (fptr == NULL) { - char str[128]; - sprintf(str,"Cannot open EAM potential file %s", filename); - error->one(FLERR,str); - } - - // h coefficients are stored at the end of the file. - // Skip to last line of file. - while(fgets(nextline, MAXLINE, fptr) != NULL) { - strcpy(line, nextline); - } - char* ptr = strtok(line, " \t\n\r\f"); - int degree = atoi(ptr); - nhcoeff = degree+1; - hcoeff = new double[nhcoeff]; - int i = 0; - while((ptr = strtok(NULL," \t\n\r\f")) != NULL && i < nhcoeff) { - hcoeff[i++] = atof(ptr); - } - if(i != nhcoeff || nhcoeff < 1) - error->one(FLERR,"Failed to read h(x) function coefficients from EAM file."); - - // Close the potential file. - fclose(fptr); - } - - MPI_Bcast(&nhcoeff, 1, MPI_INT, 0, world); - if(comm->me != 0) hcoeff = new double[nhcoeff]; - MPI_Bcast(hcoeff, nhcoeff, MPI_DOUBLE, 0, world); -} - - -/* ---------------------------------------------------------------------- */ - -int PairCDEAM::pack_forward_comm(int n, int *list, double *buf, - int pbc_flag, int *pbc) -{ - int i,j,m; - - m = 0; - if(communicationStage == 2) { - if(cdeamVersion == 1) { - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = fp[j]; - buf[m++] = rho[j]; - buf[m++] = rhoB[j]; - buf[m++] = D_values[j]; - } - return m; - } - else if(cdeamVersion == 2) { - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = fp[j]; - buf[m++] = rho[j]; - buf[m++] = rhoB[j]; - } - return m; - } - else { ASSERT(false); return 0; } - } - else if(communicationStage == 4) { - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = D_values[j]; - } - return m; - } - else return 0; -} - -/* ---------------------------------------------------------------------- */ - -void PairCDEAM::unpack_forward_comm(int n, int first, double *buf) -{ - int i,m,last; - - m = 0; - last = first + n; - if(communicationStage == 2) { - if(cdeamVersion == 1) { - for(i = first; i < last; i++) { - fp[i] = buf[m++]; - rho[i] = buf[m++]; - rhoB[i] = buf[m++]; - D_values[i] = buf[m++]; - } - } - else if(cdeamVersion == 2) { - for(i = first; i < last; i++) { - fp[i] = buf[m++]; - rho[i] = buf[m++]; - rhoB[i] = buf[m++]; - } - } else { - ASSERT(false); - } - } - else if(communicationStage == 4) { - for(i = first; i < last; i++) { - D_values[i] = buf[m++]; - } - } -} - -/* ---------------------------------------------------------------------- */ -int PairCDEAM::pack_reverse_comm(int n, int first, double *buf) -{ - int i,m,last; - - m = 0; - last = first + n; - - if(communicationStage == 1) { - if(cdeamVersion == 1) { - for(i = first; i < last; i++) { - buf[m++] = rho[i]; - buf[m++] = rhoB[i]; - buf[m++] = D_values[i]; - } - return m; - } - else if(cdeamVersion == 2) { - for(i = first; i < last; i++) { - buf[m++] = rho[i]; - buf[m++] = rhoB[i]; - } - return m; - } - else { ASSERT(false); return 0; } - } - else if(communicationStage == 3) { - for(i = first; i < last; i++) { - buf[m++] = D_values[i]; - } - return m; - } - else return 0; -} - -/* ---------------------------------------------------------------------- */ - -void PairCDEAM::unpack_reverse_comm(int n, int *list, double *buf) -{ - int i,j,m; - - m = 0; - if(communicationStage == 1) { - if(cdeamVersion == 1) { - for(i = 0; i < n; i++) { - j = list[i]; - rho[j] += buf[m++]; - rhoB[j] += buf[m++]; - D_values[j] += buf[m++]; - } - } else if(cdeamVersion == 2) { - for(i = 0; i < n; i++) { - j = list[i]; - rho[j] += buf[m++]; - rhoB[j] += buf[m++]; - } - } else { - ASSERT(false); - } - } - else if(communicationStage == 3) { - for(i = 0; i < n; i++) { - j = list[i]; - D_values[j] += buf[m++]; - } - } -} - -/* ---------------------------------------------------------------------- - memory usage of local atom-based arrays -------------------------------------------------------------------------- */ -double PairCDEAM::memory_usage() -{ - double bytes = 2 * nmax * sizeof(double); - return PairEAMAlloy::memory_usage() + bytes; -} diff --git a/src/USER-MISC/pair_coul_diel.cpp b/src/USER-MISC/pair_coul_diel.cpp index 3f07df3d98..0154e89731 100644 --- a/src/USER-MISC/pair_coul_diel.cpp +++ b/src/USER-MISC/pair_coul_diel.cpp @@ -326,7 +326,7 @@ void PairCoulDiel::read_restart_settings(FILE *fp) /* ---------------------------------------------------------------------- */ double PairCoulDiel::single(int i, int j, int itype, int jtype, - double rsq, double factor_coul, double factor_lj, + double rsq, double factor_coul, double /*factor_lj*/, double &fforce) { double r, rarg,forcedielec,phidielec; diff --git a/src/USER-MISC/pair_coul_shield.cpp b/src/USER-MISC/pair_coul_shield.cpp index deec7da81f..11df975c19 100644 --- a/src/USER-MISC/pair_coul_shield.cpp +++ b/src/USER-MISC/pair_coul_shield.cpp @@ -341,7 +341,7 @@ void PairCoulShield::read_restart_settings(FILE *fp) /* ---------------------------------------------------------------------- */ double PairCoulShield::single(int i, int j, int itype, int jtype, - double rsq, double factor_coul, double factor_lj, + double rsq, double factor_coul, double /*factor_lj*/, double &fforce) { double r, rarg,Vc,fvc,forcecoul,phishieldec; diff --git a/src/USER-MISC/pair_edip.cpp b/src/USER-MISC/pair_edip.cpp index 2976d7ad73..4716e271d7 100644 --- a/src/USER-MISC/pair_edip.cpp +++ b/src/USER-MISC/pair_edip.cpp @@ -621,7 +621,7 @@ void PairEDIP::allocate() global settings ------------------------------------------------------------------------- */ -void PairEDIP::settings(int narg, char **arg) +void PairEDIP::settings(int narg, char **/*arg*/) { if (narg != 0) error->all(FLERR,"Illegal pair_style command"); } diff --git a/src/USER-MISC/pair_edip_multi.cpp b/src/USER-MISC/pair_edip_multi.cpp index 6be57eee74..fc76aadb0b 100644 --- a/src/USER-MISC/pair_edip_multi.cpp +++ b/src/USER-MISC/pair_edip_multi.cpp @@ -516,7 +516,7 @@ void PairEDIPMulti::allocate() global settings ------------------------------------------------------------------------- */ -void PairEDIPMulti::settings(int narg, char **arg) +void PairEDIPMulti::settings(int narg, char **/*arg*/) { if (narg != 0) error->all(FLERR,"Illegal pair_style command"); } diff --git a/src/USER-MISC/pair_extep.cpp b/src/USER-MISC/pair_extep.cpp index 5a8cdf2884..49c562471f 100644 --- a/src/USER-MISC/pair_extep.cpp +++ b/src/USER-MISC/pair_extep.cpp @@ -442,7 +442,7 @@ void PairExTeP::allocate() global settings ------------------------------------------------------------------------- */ -void PairExTeP::settings(int narg, char **arg) +void PairExTeP::settings(int narg, char **/*arg*/) { if (narg != 0) error->all(FLERR,"Illegal pair_style command"); } diff --git a/src/USER-MISC/pair_gauss_cut.cpp b/src/USER-MISC/pair_gauss_cut.cpp index 85f7c02887..a000eff028 100644 --- a/src/USER-MISC/pair_gauss_cut.cpp +++ b/src/USER-MISC/pair_gauss_cut.cpp @@ -374,8 +374,8 @@ void PairGaussCut::write_data_all(FILE *fp) /* ---------------------------------------------------------------------- */ -double PairGaussCut::single(int i, int j, int itype, int jtype, double rsq, - double factor_coul, double factor_lj, +double PairGaussCut::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq, + double /*factor_coul*/, double factor_lj, double &fforce) { double r, rexp,ugauss,phigauss; diff --git a/src/USER-MISC/pair_ilp_graphene_hbn.cpp b/src/USER-MISC/pair_ilp_graphene_hbn.cpp index 7c637e4faf..07ba50ab9f 100644 --- a/src/USER-MISC/pair_ilp_graphene_hbn.cpp +++ b/src/USER-MISC/pair_ilp_graphene_hbn.cpp @@ -1007,8 +1007,8 @@ void PairILPGrapheneHBN::read_file(char *filename) /* ---------------------------------------------------------------------- */ -double PairILPGrapheneHBN::single(int i, int j, int itype, int jtype, double rsq, - double factor_coul, double factor_lj, +double PairILPGrapheneHBN::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq, + double /*factor_coul*/, double factor_lj, double &fforce) { double r,r2inv,r6inv,r8inv,forcelj,philj,fpair; @@ -1044,7 +1044,7 @@ double PairILPGrapheneHBN::single(int i, int j, int itype, int jtype, double rsq /* ---------------------------------------------------------------------- */ int PairILPGrapheneHBN::pack_forward_comm(int n, int *list, double *buf, - int pbc_flag, int *pbc) + int /*pbc_flag*/, int * /*pbc*/) { int i,j,m,id,ip,l; diff --git a/src/USER-MISC/pair_kolmogorov_crespi_full.cpp b/src/USER-MISC/pair_kolmogorov_crespi_full.cpp index 93a2376c33..e952342b74 100644 --- a/src/USER-MISC/pair_kolmogorov_crespi_full.cpp +++ b/src/USER-MISC/pair_kolmogorov_crespi_full.cpp @@ -1012,8 +1012,8 @@ void PairKolmogorovCrespiFull::read_file(char *filename) /* ---------------------------------------------------------------------- */ -double PairKolmogorovCrespiFull::single(int i, int j, int itype, int jtype, double rsq, - double factor_coul, double factor_lj, +double PairKolmogorovCrespiFull::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq, + double /*factor_coul*/, double factor_lj, double &fforce) { double r,r2inv,r6inv,r8inv,forcelj,philj; @@ -1047,7 +1047,7 @@ double PairKolmogorovCrespiFull::single(int i, int j, int itype, int jtype, doub /* ---------------------------------------------------------------------- */ int PairKolmogorovCrespiFull::pack_forward_comm(int n, int *list, double *buf, - int pbc_flag, int *pbc) + int /*pbc_flag*/, int * /*pbc*/) { int i,j,m,l,ip,id; diff --git a/src/USER-MISC/pair_lennard_mdf.cpp b/src/USER-MISC/pair_lennard_mdf.cpp index f6e7f7f56b..45d0da4d83 100644 --- a/src/USER-MISC/pair_lennard_mdf.cpp +++ b/src/USER-MISC/pair_lennard_mdf.cpp @@ -352,9 +352,9 @@ void PairLJ_AB_MDF::read_restart_settings(FILE *fp) /* ---------------------------------------------------------------------- */ -double PairLJ_AB_MDF::single(int i, int j, int itype, int jtype, +double PairLJ_AB_MDF::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq, - double factor_coul, double factor_lj, + double /*factor_coul*/, double factor_lj, double &fforce) { double r2inv,r6inv,forcelj,philj; diff --git a/src/USER-MISC/pair_lj_mdf.cpp b/src/USER-MISC/pair_lj_mdf.cpp index d43a6c3086..891239016b 100644 --- a/src/USER-MISC/pair_lj_mdf.cpp +++ b/src/USER-MISC/pair_lj_mdf.cpp @@ -352,9 +352,9 @@ void PairLJMDF::read_restart_settings(FILE *fp) /* ---------------------------------------------------------------------- */ -double PairLJMDF::single(int i, int j, int itype, int jtype, +double PairLJMDF::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq, - double factor_coul, double factor_lj, + double /*factor_coul*/, double factor_lj, double &fforce) { double r2inv,r6inv,forcelj,philj; diff --git a/src/USER-MISC/pair_meam_spline.cpp b/src/USER-MISC/pair_meam_spline.cpp index 750f6ac5bb..e6ea6c2ae4 100644 --- a/src/USER-MISC/pair_meam_spline.cpp +++ b/src/USER-MISC/pair_meam_spline.cpp @@ -360,7 +360,7 @@ void PairMEAMSpline::allocate() global settings ------------------------------------------------------------------------- */ -void PairMEAMSpline::settings(int narg, char **arg) +void PairMEAMSpline::settings(int narg, char **/*arg*/) { if(narg != 0) error->all(FLERR,"Illegal pair_style command"); } @@ -592,7 +592,7 @@ void PairMEAMSpline::init_list(int id, NeighList *ptr) /* ---------------------------------------------------------------------- init for one type pair i,j and corresponding j,i ------------------------------------------------------------------------- */ -double PairMEAMSpline::init_one(int i, int j) +double PairMEAMSpline::init_one(int /*i*/, int /*j*/) { return cutoff; } @@ -600,7 +600,7 @@ double PairMEAMSpline::init_one(int i, int j) /* ---------------------------------------------------------------------- */ int PairMEAMSpline::pack_forward_comm(int n, int *list, double *buf, - int pbc_flag, int *pbc) + int /*pbc_flag*/, int * /*pbc*/) { int* list_iter = list; int* list_iter_end = list + n; @@ -618,14 +618,14 @@ void PairMEAMSpline::unpack_forward_comm(int n, int first, double *buf) /* ---------------------------------------------------------------------- */ -int PairMEAMSpline::pack_reverse_comm(int n, int first, double *buf) +int PairMEAMSpline::pack_reverse_comm(int /*n*/, int /*first*/, double * /*buf*/) { return 0; } /* ---------------------------------------------------------------------- */ -void PairMEAMSpline::unpack_reverse_comm(int n, int *list, double *buf) +void PairMEAMSpline::unpack_reverse_comm(int /*n*/, int * /*list*/, double * /*buf*/) { } diff --git a/src/USER-MISC/pair_meam_sw_spline.cpp b/src/USER-MISC/pair_meam_sw_spline.cpp index f6b7212f9c..891913ccfc 100644 --- a/src/USER-MISC/pair_meam_sw_spline.cpp +++ b/src/USER-MISC/pair_meam_sw_spline.cpp @@ -372,7 +372,7 @@ void PairMEAMSWSpline::allocate() global settings ------------------------------------------------------------------------- */ -void PairMEAMSWSpline::settings(int narg, char **arg) +void PairMEAMSWSpline::settings(int narg, char **/*arg*/) { if(narg != 0) error->all(FLERR,"Illegal pair_style command"); } @@ -552,7 +552,7 @@ void PairMEAMSWSpline::init_list(int id, NeighList *ptr) /* ---------------------------------------------------------------------- init for one type pair i,j and corresponding j,i ------------------------------------------------------------------------- */ -double PairMEAMSWSpline::init_one(int i, int j) +double PairMEAMSWSpline::init_one(int /*i*/, int /*j*/) { return cutoff; } @@ -560,7 +560,7 @@ double PairMEAMSWSpline::init_one(int i, int j) /* ---------------------------------------------------------------------- */ int PairMEAMSWSpline::pack_forward_comm(int n, int *list, double *buf, - int pbc_flag, int *pbc) + int /*pbc_flag*/, int * /*pbc*/) { int* list_iter = list; int* list_iter_end = list + n; @@ -578,14 +578,14 @@ void PairMEAMSWSpline::unpack_forward_comm(int n, int first, double *buf) /* ---------------------------------------------------------------------- */ -int PairMEAMSWSpline::pack_reverse_comm(int n, int first, double *buf) +int PairMEAMSWSpline::pack_reverse_comm(int /*n*/, int /*first*/, double * /*buf*/) { return 0; } /* ---------------------------------------------------------------------- */ -void PairMEAMSWSpline::unpack_reverse_comm(int n, int *list, double *buf) +void PairMEAMSWSpline::unpack_reverse_comm(int /*n*/, int * /*list*/, double * /*buf*/) { } diff --git a/src/USER-MISC/pair_momb.cpp b/src/USER-MISC/pair_momb.cpp index 12a40bb08b..927181ebf6 100644 --- a/src/USER-MISC/pair_momb.cpp +++ b/src/USER-MISC/pair_momb.cpp @@ -365,8 +365,8 @@ void PairMomb::read_restart_settings(FILE *fp) /* ---------------------------------------------------------------------- */ -double PairMomb::single(int i, int j, int itype, int jtype, double rsq, - double factor_coul, double factor_lj, +double PairMomb::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq, + double /*factor_coul*/, double factor_lj, double &fforce) { double r,dr,dexp,phi,r2inv,r6inv,ddexp,invexp; diff --git a/src/USER-MISC/pair_morse_smooth_linear.cpp b/src/USER-MISC/pair_morse_smooth_linear.cpp index 8a9c89cf69..a88e7a1a27 100644 --- a/src/USER-MISC/pair_morse_smooth_linear.cpp +++ b/src/USER-MISC/pair_morse_smooth_linear.cpp @@ -30,7 +30,6 @@ using namespace LAMMPS_NS; PairMorseSmoothLinear::PairMorseSmoothLinear(LAMMPS *lmp) : Pair(lmp) { writedata = 1; - } /* ---------------------------------------------------------------------- */ @@ -117,7 +116,7 @@ void PairMorseSmoothLinear::compute(int eflag, int vflag) if (eflag) { evdwl = d0[itype][jtype] * (dexp*dexp - 2.0*dexp) - - offset[itype][jtype]; + offset[itype][jtype]; evdwl -= ( r - cut[itype][jtype] ) * der_at_cutoff[itype][jtype]; evdwl *= factor_lj; } @@ -203,6 +202,14 @@ void PairMorseSmoothLinear::coeff(int narg, char **arg) alpha[i][j] = alpha_one; r0[i][j] = r0_one; cut[i][j] = cut_one; + + morse1[i][j] = 2.0*d0[i][j]*alpha[i][j]; + + double alpha_dr = -alpha[i][j] * (cut[i][j] - r0[i][j]); + + offset[i][j] = d0[i][j] * (exp(2.0*alpha_dr) - 2.0*exp(alpha_dr)); + der_at_cutoff[i][j] = -2.0*alpha[i][j]*d0[i][j] * (exp(2.0*alpha_dr) - exp(alpha_dr)); + setflag[i][j] = 1; count++; } @@ -222,17 +229,13 @@ double PairMorseSmoothLinear::init_one(int i, int j) morse1[i][j] = 2.0*d0[i][j]*alpha[i][j]; - double alpha_dr = -alpha[i][j] * (cut[i][j] - r0[i][j]); - - offset[i][j] = d0[i][j] * (exp(2.0*alpha_dr) - 2.0*exp(alpha_dr)); - der_at_cutoff[i][j] = -2.0*alpha[i][j]*d0[i][j] * (exp(2.0*alpha_dr) - exp(alpha_dr)); - d0[j][i] = d0[i][j]; alpha[j][i] = alpha[i][j]; r0[j][i] = r0[i][j]; morse1[j][i] = morse1[i][j]; der_at_cutoff[j][i] = der_at_cutoff[i][j]; offset[j][i] = offset[i][j]; + cut[j][i] = cut[i][j]; return cut[i][j]; } @@ -337,8 +340,8 @@ void PairMorseSmoothLinear::write_data_all(FILE *fp) /* ---------------------------------------------------------------------- */ -double PairMorseSmoothLinear::single(int i, int j, int itype, int jtype, double rsq, - double factor_coul, double factor_lj, +double PairMorseSmoothLinear::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq, + double /*factor_coul*/, double factor_lj, double &fforce) { double r,dr,dexp,phi; diff --git a/src/USER-MISC/pair_tersoff_table.cpp b/src/USER-MISC/pair_tersoff_table.cpp index c2362b8de9..d7e28a1e40 100644 --- a/src/USER-MISC/pair_tersoff_table.cpp +++ b/src/USER-MISC/pair_tersoff_table.cpp @@ -719,7 +719,7 @@ void PairTersoffTable::allocate() global settings ------------------------------------------------------------------------- */ -void PairTersoffTable::settings(int narg, char **arg) +void PairTersoffTable::settings(int narg, char **/*arg*/) { if (narg != 0) error->all(FLERR,"Illegal pair_style command"); } diff --git a/src/USER-MOFFF/angle_cosine_buck6d.cpp b/src/USER-MOFFF/angle_cosine_buck6d.cpp index b5800db2be..3f87aeb757 100644 --- a/src/USER-MOFFF/angle_cosine_buck6d.cpp +++ b/src/USER-MOFFF/angle_cosine_buck6d.cpp @@ -56,7 +56,7 @@ AngleCosineBuck6d::~AngleCosineBuck6d() void AngleCosineBuck6d::compute(int eflag, int vflag) { - int i,i1,i2,i3,n,type,itype,jtype; + int i1,i2,i3,n,type,itype,jtype; double delx1,dely1,delz1,delx2,dely2,delz2; double eangle,f1[3],f3[3]; double rsq1,rsq2,r1,r2,c,s,a,a11,a12,a22; @@ -309,7 +309,7 @@ void AngleCosineBuck6d::init_style() /* ---------------------------------------------------------------------- */ -double AngleCosineBuck6d::equilibrium_angle(int i) +double AngleCosineBuck6d::equilibrium_angle(int /*i*/) { return MY_PI; } diff --git a/src/USER-MOFFF/improper_inversion_harmonic.cpp b/src/USER-MOFFF/improper_inversion_harmonic.cpp index 53a7b4729a..9608d58054 100644 --- a/src/USER-MOFFF/improper_inversion_harmonic.cpp +++ b/src/USER-MOFFF/improper_inversion_harmonic.cpp @@ -139,7 +139,6 @@ void ImproperInversionHarmonic::invang(const int &i1,const int &i2, double upx,upy,upz,upn,rup,umx,umy,umz,umn,rum,wwr; double rucb,rudb,rvcb,rvdb,rupupn,rumumn; - double **x = atom->x; double **f = atom->f; int nlocal = atom->nlocal; int newton_bond = force->newton_bond; @@ -242,7 +241,7 @@ void ImproperInversionHarmonic::invang(const int &i1,const int &i2, f[i4][2] += f4[2]; } - double rb1x, rb1y, rb1z, rb2x, rb2y, rb2z, rb3x, rb3y, rb3z; + double rb3x, rb3y, rb3z; if (evflag) rb3x = vb1x - vb2x; @@ -253,7 +252,7 @@ void ImproperInversionHarmonic::invang(const int &i1,const int &i2, vb3x,vb3y,vb3z, vb2x,vb2y,vb2z, rb3x,rb3y,rb3z); - } +} /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_cdeam_omp.cpp b/src/USER-OMP/pair_eam_cd_omp.cpp similarity index 97% rename from src/USER-OMP/pair_cdeam_omp.cpp rename to src/USER-OMP/pair_eam_cd_omp.cpp index c3a9454567..68c01c83d2 100644 --- a/src/USER-OMP/pair_cdeam_omp.cpp +++ b/src/USER-OMP/pair_eam_cd_omp.cpp @@ -15,7 +15,7 @@ #include #include -#include "pair_cdeam_omp.h" +#include "pair_eam_cd_omp.h" #include "atom.h" #include "comm.h" #include "error.h" @@ -44,8 +44,8 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -PairCDEAMOMP::PairCDEAMOMP(LAMMPS *lmp, int _cdeamVersion) : - PairEAM(lmp), PairCDEAM(lmp,_cdeamVersion), ThrOMP(lmp, THR_PAIR) +PairEAMCDOMP::PairEAMCDOMP(LAMMPS *lmp, int _cdeamVersion) : + PairEAM(lmp), PairEAMCD(lmp,_cdeamVersion), ThrOMP(lmp, THR_PAIR) { suffix_flag |= Suffix::OMP; respa_enable = 0; @@ -53,7 +53,7 @@ PairCDEAMOMP::PairCDEAMOMP(LAMMPS *lmp, int _cdeamVersion) : /* ---------------------------------------------------------------------- */ -void PairCDEAMOMP::compute(int eflag, int vflag) +void PairEAMCDOMP::compute(int eflag, int vflag) { if (eflag || vflag) { ev_setup(eflag,vflag); @@ -143,7 +143,7 @@ void PairCDEAMOMP::compute(int eflag, int vflag) } template -void PairCDEAMOMP::eval(int iifrom, int iito, ThrData * const thr) +void PairEAMCDOMP::eval(int iifrom, int iito, ThrData * const thr) { int i,j,ii,jj,jnum,itype,jtype; double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair; @@ -534,10 +534,10 @@ void PairCDEAMOMP::eval(int iifrom, int iito, ThrData * const thr) /* ---------------------------------------------------------------------- */ -double PairCDEAMOMP::memory_usage() +double PairEAMCDOMP::memory_usage() { double bytes = memory_usage_thr(); - bytes += PairCDEAM::memory_usage(); + bytes += PairEAMCD::memory_usage(); return bytes; } diff --git a/src/USER-OMP/pair_cdeam_omp.h b/src/USER-OMP/pair_eam_cd_omp.h similarity index 71% rename from src/USER-OMP/pair_cdeam_omp.h rename to src/USER-OMP/pair_eam_cd_omp.h index 2839ab0ed0..d46a5383f5 100644 --- a/src/USER-OMP/pair_cdeam_omp.h +++ b/src/USER-OMP/pair_eam_cd_omp.h @@ -17,23 +17,23 @@ #ifdef PAIR_CLASS -PairStyle(eam/cd/omp,PairCDEAM_OneSiteOMP) -PairStyle(eam/cd/old/omp,PairCDEAM_TwoSiteOMP) +PairStyle(eam/cd/omp,PairEAMCD_OneSiteOMP) +PairStyle(eam/cd/old/omp,PairEAMCD_TwoSiteOMP) #else -#ifndef LMP_PAIR_CDEAM_OMP_H -#define LMP_PAIR_CDEAM_OMP_H +#ifndef LMP_PAIR_EAM_CD_OMP_H +#define LMP_PAIR_EAM_CD_OMP_H -#include "pair_cdeam.h" +#include "pair_eam_cd.h" #include "thr_omp.h" namespace LAMMPS_NS { -class PairCDEAMOMP : public PairCDEAM, public ThrOMP { +class PairEAMCDOMP : public PairEAMCD, public ThrOMP { public: - PairCDEAMOMP(class LAMMPS *, int); + PairEAMCDOMP(class LAMMPS *, int); virtual void compute(int, int); virtual double memory_usage(); @@ -44,19 +44,19 @@ class PairCDEAMOMP : public PairCDEAM, public ThrOMP { }; /// The one-site concentration formulation of CD-EAM. - class PairCDEAM_OneSiteOMP : public PairCDEAMOMP + class PairEAMCD_OneSiteOMP : public PairEAMCDOMP { public: /// Constructor. - PairCDEAM_OneSiteOMP(class LAMMPS* lmp) : PairEAM(lmp), PairCDEAMOMP(lmp, 1) {} + PairEAMCD_OneSiteOMP(class LAMMPS* lmp) : PairEAM(lmp), PairEAMCDOMP(lmp, 1) {} }; /// The two-site concentration formulation of CD-EAM. - class PairCDEAM_TwoSiteOMP : public PairCDEAMOMP + class PairEAMCD_TwoSiteOMP : public PairEAMCDOMP { public: /// Constructor. - PairCDEAM_TwoSiteOMP(class LAMMPS* lmp) : PairEAM(lmp), PairCDEAMOMP(lmp, 2) {} + PairEAMCD_TwoSiteOMP(class LAMMPS* lmp) : PairEAM(lmp), PairEAMCDOMP(lmp, 2) {} }; } diff --git a/src/USER-PHONON/fix_phonon.cpp b/src/USER-PHONON/fix_phonon.cpp index 3a37c67a38..cdbe4068bc 100644 --- a/src/USER-PHONON/fix_phonon.cpp +++ b/src/USER-PHONON/fix_phonon.cpp @@ -299,7 +299,7 @@ void FixPhonon::init() /* ---------------------------------------------------------------------- */ -void FixPhonon::setup(int flag) +void FixPhonon::setup(int /*flag*/) { // initialize accumulating variables for (int i = 0; i < sysdim; ++i) TempSum[i] = 0.; diff --git a/src/USER-QTB/fix_qbmsst.cpp b/src/USER-QTB/fix_qbmsst.cpp index fa5ee75bcb..e8a4f85eaa 100644 --- a/src/USER-QTB/fix_qbmsst.cpp +++ b/src/USER-QTB/fix_qbmsst.cpp @@ -424,7 +424,7 @@ void FixQBMSST::init() /* ---------------------------------------------------------------------- compute T,P before integrator starts ------------------------------------------------------------------------- */ -void FixQBMSST::setup(int vflag) +void FixQBMSST::setup(int /*vflag*/) { lagrangian_position = 0.0; @@ -507,7 +507,7 @@ void FixQBMSST::setup(int vflag) /* ---------------------------------------------------------------------- 1st half of Verlet update ------------------------------------------------------------------------- */ -void FixQBMSST::initial_integrate(int vflag) +void FixQBMSST::initial_integrate(int /*vflag*/) { int sd; sd = direction; @@ -1157,7 +1157,7 @@ void FixQBMSST::grow_arrays(int nmax) /* ---------------------------------------------------------------------- copy values within local atom-based array ------------------------------------------------------------------------- */ -void FixQBMSST::copy_arrays(int i, int j, int delflag) +void FixQBMSST::copy_arrays(int i, int j, int /*delflag*/) { for (int m = 0; m < 2*N_f; m++) { random_array_0[j][m] = random_array_0[i][m]; diff --git a/src/USER-QTB/fix_qtb.cpp b/src/USER-QTB/fix_qtb.cpp index 7f9a6510be..015f953b8e 100644 --- a/src/USER-QTB/fix_qtb.cpp +++ b/src/USER-QTB/fix_qtb.cpp @@ -239,7 +239,7 @@ void FixQTB::setup(int vflag) /* ---------------------------------------------------------------------- post_force ------------------------------------------------------------------------- */ -void FixQTB::post_force(int vflag) +void FixQTB::post_force(int /*vflag*/) { double gamma1,gamma3; @@ -334,7 +334,7 @@ void FixQTB::post_force(int vflag) /* ---------------------------------------------------------------------- post_force_respa ------------------------------------------------------------------------- */ -void FixQTB::post_force_respa(int vflag, int ilevel, int iloop) +void FixQTB::post_force_respa(int vflag, int ilevel, int /*iloop*/) { if (ilevel == nlevels_respa-1) post_force(vflag); } @@ -392,7 +392,7 @@ void FixQTB::grow_arrays(int nmax) /* ---------------------------------------------------------------------- copy values within local atom-based array ------------------------------------------------------------------------- */ -void FixQTB::copy_arrays(int i, int j, int delflag) +void FixQTB::copy_arrays(int i, int j, int /*delflag*/) { for (int m = 0; m < 2*N_f; m++) { random_array_0[j][m] = random_array_0[i][m]; diff --git a/src/USER-QUIP/pair_quip.cpp b/src/USER-QUIP/pair_quip.cpp index 0c00a5ef59..6f5040d037 100644 --- a/src/USER-QUIP/pair_quip.cpp +++ b/src/USER-QUIP/pair_quip.cpp @@ -212,7 +212,7 @@ void PairQUIP::compute(int eflag, int vflag) global settings ------------------------------------------------------------------------- */ -void PairQUIP::settings(int narg, char **arg) +void PairQUIP::settings(int narg, char **/*arg*/) { if (narg != 0) error->all(FLERR,"Illegal pair_style command"); if (strcmp(force->pair_style,"hybrid") == 0) @@ -315,7 +315,7 @@ void PairQUIP::init_style() init for one type pair i,j and corresponding j,i ------------------------------------------------------------------------- */ -double PairQUIP::init_one(int i, int j) +double PairQUIP::init_one(int /*i*/, int /*j*/) { return cutoff; } diff --git a/src/USER-REAXC/fix_qeq_reax.cpp b/src/USER-REAXC/fix_qeq_reax.cpp index a2f4d3d0e9..6f0b93235f 100644 --- a/src/USER-REAXC/fix_qeq_reax.cpp +++ b/src/USER-REAXC/fix_qeq_reax.cpp @@ -381,7 +381,7 @@ void FixQEqReax::init() /* ---------------------------------------------------------------------- */ -void FixQEqReax::init_list(int id, NeighList *ptr) +void FixQEqReax::init_list(int /*id*/, NeighList *ptr) { list = ptr; } @@ -485,7 +485,7 @@ void FixQEqReax::init_storage() /* ---------------------------------------------------------------------- */ -void FixQEqReax::pre_force(int vflag) +void FixQEqReax::pre_force(int /*vflag*/) { double t_start, t_end; @@ -518,7 +518,7 @@ void FixQEqReax::pre_force(int vflag) /* ---------------------------------------------------------------------- */ -void FixQEqReax::pre_force_respa(int vflag, int ilevel, int iloop) +void FixQEqReax::pre_force_respa(int vflag, int ilevel, int /*iloop*/) { if (ilevel == nlevels_respa-1) pre_force(vflag); } @@ -833,7 +833,7 @@ void FixQEqReax::calculate_Q() /* ---------------------------------------------------------------------- */ int FixQEqReax::pack_forward_comm(int n, int *list, double *buf, - int pbc_flag, int *pbc) + int /*pbc_flag*/, int * /*pbc*/) { int m; @@ -952,7 +952,7 @@ void FixQEqReax::grow_arrays(int nmax) copy values within fictitious charge arrays ------------------------------------------------------------------------- */ -void FixQEqReax::copy_arrays(int i, int j, int delflag) +void FixQEqReax::copy_arrays(int i, int j, int /*delflag*/) { for (int m = 0; m < nprev; m++) { s_hist[j][m] = s_hist[i][m]; diff --git a/src/USER-REAXC/fix_reaxc.cpp b/src/USER-REAXC/fix_reaxc.cpp index df06217993..c470173663 100644 --- a/src/USER-REAXC/fix_reaxc.cpp +++ b/src/USER-REAXC/fix_reaxc.cpp @@ -105,7 +105,7 @@ void FixReaxC::grow_arrays(int nmax) copy values within local atom-based arrays ------------------------------------------------------------------------- */ -void FixReaxC::copy_arrays(int i, int j, int delflag) +void FixReaxC::copy_arrays(int i, int j, int /*delflag*/) { num_bonds[j] = num_bonds[i]; num_hbonds[j] = num_hbonds[i]; @@ -136,7 +136,7 @@ int FixReaxC::unpack_exchange(int nlocal, double *buf) /* ---------------------------------------------------------------------- */ int FixReaxC::pack_forward_comm(int n, int *list, double *buf, - int pbc_flag, int *pbc) + int /*pbc_flag*/, int * /*pbc*/) { int i,j,m; diff --git a/src/USER-REAXC/fix_reaxc_bonds.cpp b/src/USER-REAXC/fix_reaxc_bonds.cpp index b38d137412..fb40b2042e 100644 --- a/src/USER-REAXC/fix_reaxc_bonds.cpp +++ b/src/USER-REAXC/fix_reaxc_bonds.cpp @@ -112,7 +112,7 @@ int FixReaxCBonds::setmask() /* ---------------------------------------------------------------------- */ -void FixReaxCBonds::setup(int vflag) +void FixReaxCBonds::setup(int /*vflag*/) { end_of_step(); } @@ -137,7 +137,7 @@ void FixReaxCBonds::end_of_step() /* ---------------------------------------------------------------------- */ -void FixReaxCBonds::Output_ReaxC_Bonds(bigint ntimestep, FILE *fp) +void FixReaxCBonds::Output_ReaxC_Bonds(bigint /*ntimestep*/, FILE * /*fp*/) { int i, j; @@ -185,7 +185,7 @@ void FixReaxCBonds::Output_ReaxC_Bonds(bigint ntimestep, FILE *fp) /* ---------------------------------------------------------------------- */ -void FixReaxCBonds::FindBond(struct _reax_list *lists, int &numbonds) +void FixReaxCBonds::FindBond(struct _reax_list * /*lists*/, int &numbonds) { int *ilist, i, ii, inum; int j, pj, nj; diff --git a/src/USER-REAXC/fix_reaxc_species.cpp b/src/USER-REAXC/fix_reaxc_species.cpp index 61b4cebf96..8ec7f4174f 100644 --- a/src/USER-REAXC/fix_reaxc_species.cpp +++ b/src/USER-REAXC/fix_reaxc_species.cpp @@ -281,7 +281,7 @@ int FixReaxCSpecies::setmask() /* ---------------------------------------------------------------------- */ -void FixReaxCSpecies::setup(int vflag) +void FixReaxCSpecies::setup(int /*vflag*/) { ntotal = static_cast (atom->natoms); if (Name == NULL) @@ -427,7 +427,7 @@ void FixReaxCSpecies::create_fix() /* ---------------------------------------------------------------------- */ -void FixReaxCSpecies::init_list(int id, NeighList *ptr) +void FixReaxCSpecies::init_list(int /*id*/, NeighList *ptr) { list = ptr; } @@ -442,7 +442,7 @@ void FixReaxCSpecies::post_integrate() /* ---------------------------------------------------------------------- */ -void FixReaxCSpecies::Output_ReaxC_Bonds(bigint ntimestep, FILE *fp) +void FixReaxCSpecies::Output_ReaxC_Bonds(bigint ntimestep, FILE * /*fp*/) { int Nmole, Nspec; @@ -946,7 +946,7 @@ int FixReaxCSpecies::nint(const double &r) /* ---------------------------------------------------------------------- */ int FixReaxCSpecies::pack_forward_comm(int n, int *list, double *buf, - int pbc_flag, int *pbc) + int /*pbc_flag*/, int * /*pbc*/) { int i,j,m; diff --git a/src/USER-REAXC/pair_reaxc.cpp b/src/USER-REAXC/pair_reaxc.cpp index 7f77d875bc..378d20952c 100644 --- a/src/USER-REAXC/pair_reaxc.cpp +++ b/src/USER-REAXC/pair_reaxc.cpp @@ -751,7 +751,7 @@ int PairReaxC::write_reax_lists() /* ---------------------------------------------------------------------- */ -void PairReaxC::read_reax_forces(int vflag) +void PairReaxC::read_reax_forces(int /*vflag*/) { for( int i = 0; i < system->N; ++i ) { system->my_atoms[i].f[0] = workspace->f[i][0]; diff --git a/src/USER-REAXC/reaxc_allocate.cpp b/src/USER-REAXC/reaxc_allocate.cpp index a07f090f92..c6c103b6f4 100644 --- a/src/USER-REAXC/reaxc_allocate.cpp +++ b/src/USER-REAXC/reaxc_allocate.cpp @@ -39,8 +39,8 @@ important: we cannot know the exact number of atoms that will fall into a process's box throughout the whole simulation. therefore we need to make upper bound estimates for various data structures */ -int PreAllocate_Space( reax_system *system, control_params *control, - storage *workspace, MPI_Comm comm ) +int PreAllocate_Space( reax_system *system, control_params * /*control*/, + storage * workspace, MPI_Comm comm ) { int mincap = system->mincap; double safezone = system->safezone; @@ -60,6 +60,8 @@ int PreAllocate_Space( reax_system *system, control_params *control, workspace->forceReduction = NULL; workspace->valence_angle_atom_myoffset = NULL; workspace->my_ext_pressReduction = NULL; +#else + LMP_UNUSED_PARAM(workspace); #endif return SUCCESS; @@ -68,8 +70,8 @@ int PreAllocate_Space( reax_system *system, control_params *control, /************* system *************/ -int Allocate_System( reax_system *system, int local_cap, int total_cap, - char *msg ) +int Allocate_System( reax_system *system, int /*local_cap*/, int total_cap, + char * /*msg*/ ) { system->my_atoms = (reax_atom*) realloc( system->my_atoms, total_cap*sizeof(reax_atom) ); @@ -116,7 +118,7 @@ void DeAllocate_System( reax_system *system ) /************* workspace *************/ -void DeAllocate_Workspace( control_params *control, storage *workspace ) +void DeAllocate_Workspace( control_params * /*control*/, storage *workspace ) { int i; @@ -204,9 +206,9 @@ void DeAllocate_Workspace( control_params *control, storage *workspace ) } -int Allocate_Workspace( reax_system *system, control_params *control, +int Allocate_Workspace( reax_system * /*system*/, control_params * control, storage *workspace, int local_cap, int total_cap, - MPI_Comm comm, char *msg ) + MPI_Comm comm, char * /*msg*/ ) { int i, total_real, total_rvec, local_rvec; @@ -307,6 +309,8 @@ int Allocate_Workspace( reax_system *system, control_params *control, workspace->valence_angle_atom_myoffset = (int *) scalloc(sizeof(int), total_cap, "valence_angle_atom_myoffset", comm); workspace->my_ext_pressReduction = (rvec *) calloc(sizeof(rvec), control->nthreads); +#else + LMP_UNUSED_PARAM(control); #endif return SUCCESS; diff --git a/src/USER-REAXC/reaxc_bond_orders.cpp b/src/USER-REAXC/reaxc_bond_orders.cpp index 468164a2c0..572d27526c 100644 --- a/src/USER-REAXC/reaxc_bond_orders.cpp +++ b/src/USER-REAXC/reaxc_bond_orders.cpp @@ -359,8 +359,8 @@ int BOp( storage *workspace, reax_list *bonds, double bo_cut, } -void BO( reax_system *system, control_params *control, simulation_data *data, - storage *workspace, reax_list **lists, output_controls *out_control ) +void BO( reax_system *system, control_params * /*control*/, simulation_data * /*data*/, + storage *workspace, reax_list **lists, output_controls * /*out_control*/ ) { int i, j, pj, type_i, type_j; int start_i, end_i, sym_index; diff --git a/src/USER-REAXC/reaxc_bonds.cpp b/src/USER-REAXC/reaxc_bonds.cpp index 9678addd6b..6fde18e5c2 100644 --- a/src/USER-REAXC/reaxc_bonds.cpp +++ b/src/USER-REAXC/reaxc_bonds.cpp @@ -31,9 +31,9 @@ #include "reaxc_tool_box.h" #include "reaxc_vector.h" -void Bonds( reax_system *system, control_params *control, +void Bonds( reax_system *system, control_params * /*control*/, simulation_data *data, storage *workspace, reax_list **lists, - output_controls *out_control ) + output_controls * /*out_control*/ ) { int i, j, pj, natoms; int start_i, end_i; diff --git a/src/USER-REAXC/reaxc_forces.cpp b/src/USER-REAXC/reaxc_forces.cpp index 00b29824ea..dfcc9fd4ae 100644 --- a/src/USER-REAXC/reaxc_forces.cpp +++ b/src/USER-REAXC/reaxc_forces.cpp @@ -41,9 +41,9 @@ interaction_function Interaction_Functions[NUM_INTRS]; -void Dummy_Interaction( reax_system *system, control_params *control, - simulation_data *data, storage *workspace, - reax_list **lists, output_controls *out_control ) +void Dummy_Interaction( reax_system * /*system*/, control_params * /*control*/, + simulation_data * /*data*/, storage * /*workspace*/, + reax_list **/*lists*/, output_controls * /*out_control*/ ) { } @@ -68,7 +68,7 @@ void Init_Force_Functions( control_params *control ) void Compute_Bonded_Forces( reax_system *system, control_params *control, simulation_data *data, storage *workspace, reax_list **lists, output_controls *out_control, - MPI_Comm comm ) + MPI_Comm /*comm*/ ) { int i; @@ -83,7 +83,7 @@ void Compute_Bonded_Forces( reax_system *system, control_params *control, void Compute_NonBonded_Forces( reax_system *system, control_params *control, simulation_data *data, storage *workspace, reax_list **lists, output_controls *out_control, - MPI_Comm comm ) + MPI_Comm /*comm*/ ) { /* van der Waals and Coulomb interactions */ @@ -98,7 +98,7 @@ void Compute_NonBonded_Forces( reax_system *system, control_params *control, void Compute_Total_Force( reax_system *system, control_params *control, simulation_data *data, storage *workspace, - reax_list **lists, mpi_datatypes *mpi_data ) + reax_list **lists, mpi_datatypes * /*mpi_data*/ ) { int i, pj; reax_list *bonds = (*lists) + BONDS; @@ -114,8 +114,8 @@ void Compute_Total_Force( reax_system *system, control_params *control, } -void Validate_Lists( reax_system *system, storage *workspace, reax_list **lists, - int step, int n, int N, int numH, MPI_Comm comm ) +void Validate_Lists( reax_system *system, storage * /*workspace*/, reax_list **lists, + int step, int /*n*/, int N, int numH, MPI_Comm comm ) { int i, comp, Hindex; reax_list *bonds, *hbonds; @@ -173,7 +173,7 @@ void Validate_Lists( reax_system *system, storage *workspace, reax_list **lists, void Init_Forces_noQEq( reax_system *system, control_params *control, simulation_data *data, storage *workspace, - reax_list **lists, output_controls *out_control, + reax_list **lists, output_controls * /*out_control*/, MPI_Comm comm ) { int i, j, pj; int start_i, end_i; @@ -317,7 +317,7 @@ void Init_Forces_noQEq( reax_system *system, control_params *control, void Estimate_Storages( reax_system *system, control_params *control, reax_list **lists, int *Htop, int *hb_top, - int *bond_top, int *num_3body, MPI_Comm comm ) + int *bond_top, int *num_3body, MPI_Comm /*comm*/ ) { int i, j, pj; int start_i, end_i; diff --git a/src/USER-REAXC/reaxc_hydrogen_bonds.cpp b/src/USER-REAXC/reaxc_hydrogen_bonds.cpp index cb516b24f7..6442dd47e9 100644 --- a/src/USER-REAXC/reaxc_hydrogen_bonds.cpp +++ b/src/USER-REAXC/reaxc_hydrogen_bonds.cpp @@ -33,7 +33,7 @@ void Hydrogen_Bonds( reax_system *system, control_params *control, simulation_data *data, storage *workspace, - reax_list **lists, output_controls *out_control ) + reax_list **lists, output_controls * /*out_control*/ ) { int i, j, k, pi, pk; int type_i, type_j, type_k; diff --git a/src/USER-REAXC/reaxc_init_md.cpp b/src/USER-REAXC/reaxc_init_md.cpp index 4af21284f2..88fb9cf17f 100644 --- a/src/USER-REAXC/reaxc_init_md.cpp +++ b/src/USER-REAXC/reaxc_init_md.cpp @@ -36,7 +36,7 @@ #include "reaxc_tool_box.h" #include "reaxc_vector.h" -int Init_System( reax_system *system, control_params *control, char *msg ) +int Init_System( reax_system *system, control_params *control, char * /*msg*/ ) { int i; reax_atom *atom; @@ -66,7 +66,7 @@ int Init_System( reax_system *system, control_params *control, char *msg ) int Init_Simulation_Data( reax_system *system, control_params *control, - simulation_data *data, char *msg ) + simulation_data *data, char * /*msg*/ ) { Reset_Simulation_Data( data, control->virial ); @@ -139,8 +139,8 @@ int Init_Workspace( reax_system *system, control_params *control, /************** setup communication data structures **************/ -int Init_MPI_Datatypes( reax_system *system, storage *workspace, - mpi_datatypes *mpi_data, MPI_Comm comm, char *msg ) +int Init_MPI_Datatypes( reax_system *system, storage * /*workspace*/, + mpi_datatypes *mpi_data, MPI_Comm comm, char * /*msg*/ ) { /* setup the world */ @@ -151,8 +151,8 @@ int Init_MPI_Datatypes( reax_system *system, storage *workspace, } int Init_Lists( reax_system *system, control_params *control, - simulation_data *data, storage *workspace, reax_list **lists, - mpi_datatypes *mpi_data, char *msg ) + simulation_data * /*data*/, storage * /*workspace*/, reax_list **lists, + mpi_datatypes *mpi_data, char * /*msg*/ ) { int i, total_hbonds, total_bonds, bond_cap, num_3body, cap_3body, Htop; int *hb_top, *bond_top; diff --git a/src/USER-REAXC/reaxc_io_tools.cpp b/src/USER-REAXC/reaxc_io_tools.cpp index 4d58f7514d..b63fee2309 100644 --- a/src/USER-REAXC/reaxc_io_tools.cpp +++ b/src/USER-REAXC/reaxc_io_tools.cpp @@ -88,7 +88,7 @@ int Init_Output_Files( reax_system *system, control_params *control, /************************ close output files ************************/ int Close_Output_Files( reax_system *system, control_params *control, - output_controls *out_control, mpi_datatypes *mpi_data ) + output_controls *out_control, mpi_datatypes * /*mpi_data*/ ) { if( out_control->write_steps > 0 ) End_Traj( system->my_rank, out_control ); diff --git a/src/USER-REAXC/reaxc_lookup.cpp b/src/USER-REAXC/reaxc_lookup.cpp index 9db8b7b9f6..918099a631 100644 --- a/src/USER-REAXC/reaxc_lookup.cpp +++ b/src/USER-REAXC/reaxc_lookup.cpp @@ -151,7 +151,7 @@ void Complete_Cubic_Spline( const double *h, const double *f, double v0, double int Init_Lookup_Tables( reax_system *system, control_params *control, - storage *workspace, mpi_datatypes *mpi_data, char *msg ) + storage *workspace, mpi_datatypes *mpi_data, char * /*msg*/ ) { int i, j, r; int num_atom_types; diff --git a/src/USER-REAXC/reaxc_multi_body.cpp b/src/USER-REAXC/reaxc_multi_body.cpp index ce5b966529..360a9431cf 100644 --- a/src/USER-REAXC/reaxc_multi_body.cpp +++ b/src/USER-REAXC/reaxc_multi_body.cpp @@ -32,7 +32,7 @@ void Atom_Energy( reax_system *system, control_params *control, simulation_data *data, storage *workspace, reax_list **lists, - output_controls *out_control ) + output_controls * /*out_control*/ ) { int i, j, pj, type_i, type_j; double Delta_lpcorr, dfvl; diff --git a/src/USER-REAXC/reaxc_nonbonded.cpp b/src/USER-REAXC/reaxc_nonbonded.cpp index 9c223428a6..b44632ec29 100644 --- a/src/USER-REAXC/reaxc_nonbonded.cpp +++ b/src/USER-REAXC/reaxc_nonbonded.cpp @@ -33,7 +33,7 @@ void vdW_Coulomb_Energy( reax_system *system, control_params *control, simulation_data *data, storage *workspace, - reax_list **lists, output_controls *out_control ) + reax_list **lists, output_controls * /*out_control*/ ) { int i, j, pj, natoms; int start_i, end_i, flag; @@ -206,7 +206,7 @@ void vdW_Coulomb_Energy( reax_system *system, control_params *control, void Tabulated_vdW_Coulomb_Energy( reax_system *system,control_params *control, simulation_data *data, storage *workspace, reax_list **lists, - output_controls *out_control ) + output_controls * /*out_control*/ ) { int i, j, pj, r, natoms; int type_i, type_j, tmin, tmax; diff --git a/src/USER-REAXC/reaxc_reset_tools.cpp b/src/USER-REAXC/reaxc_reset_tools.cpp index 4ec744e7b1..1b16f10aee 100644 --- a/src/USER-REAXC/reaxc_reset_tools.cpp +++ b/src/USER-REAXC/reaxc_reset_tools.cpp @@ -87,7 +87,7 @@ void Reset_Pressures( simulation_data *data ) } -void Reset_Simulation_Data( simulation_data* data, int virial ) +void Reset_Simulation_Data( simulation_data* data, int /*virial*/ ) { Reset_Energies( &data->my_en ); Reset_Energies( &data->sys_en ); diff --git a/src/USER-REAXC/reaxc_torsion_angles.cpp b/src/USER-REAXC/reaxc_torsion_angles.cpp index c5a7f23b30..2abfbde61d 100644 --- a/src/USER-REAXC/reaxc_torsion_angles.cpp +++ b/src/USER-REAXC/reaxc_torsion_angles.cpp @@ -41,7 +41,7 @@ double Calculate_Omega( rvec dvec_ij, double r_ij, three_body_interaction_data *p_jkl, rvec dcos_omega_di, rvec dcos_omega_dj, rvec dcos_omega_dk, rvec dcos_omega_dl, - output_controls *out_control ) + output_controls * /*out_control*/ ) { double unnorm_cos_omega, unnorm_sin_omega, omega; double sin_ijk, cos_ijk, sin_jkl, cos_jkl; diff --git a/src/USER-REAXC/reaxc_traj.cpp b/src/USER-REAXC/reaxc_traj.cpp index ae2bba2150..c1f3e8ae8f 100644 --- a/src/USER-REAXC/reaxc_traj.cpp +++ b/src/USER-REAXC/reaxc_traj.cpp @@ -48,7 +48,7 @@ int Reallocate_Output_Buffer( output_controls *out_control, int req_space, } -void Write_Skip_Line( output_controls *out_control, mpi_datatypes *mpi_data, +void Write_Skip_Line( output_controls *out_control, mpi_datatypes * /*mpi_data*/, int my_rank, int skip, int num_section ) { if( my_rank == MASTER_NODE ) @@ -259,7 +259,7 @@ int Write_Header( reax_system *system, control_params *control, } -int Write_Init_Desc( reax_system *system, control_params *control, +int Write_Init_Desc( reax_system *system, control_params * /*control*/, output_controls *out_control, mpi_datatypes *mpi_data ) { int i, me, np, cnt, buffer_len, buffer_req; @@ -482,7 +482,7 @@ int Write_Frame_Header( reax_system *system, control_params *control, -int Write_Atoms( reax_system *system, control_params *control, +int Write_Atoms( reax_system *system, control_params * /*control*/, output_controls *out_control, mpi_datatypes *mpi_data ) { int i, me, np, line_len, buffer_len, buffer_req, cnt; diff --git a/src/USER-REAXC/reaxc_valence_angles.cpp b/src/USER-REAXC/reaxc_valence_angles.cpp index c92996e56b..118735fbbd 100644 --- a/src/USER-REAXC/reaxc_valence_angles.cpp +++ b/src/USER-REAXC/reaxc_valence_angles.cpp @@ -76,7 +76,7 @@ void Calculate_dCos_Theta( rvec dvec_ji, double d_ji, rvec dvec_jk, double d_jk, void Valence_Angles( reax_system *system, control_params *control, simulation_data *data, storage *workspace, - reax_list **lists, output_controls *out_control ) + reax_list **lists, output_controls * /*out_control*/ ) { int i, j, pi, k, pk, t; int type_i, type_j, type_k; diff --git a/src/USER-SCAFACOS/Install.sh b/src/USER-SCAFACOS/Install.sh new file mode 100755 index 0000000000..964212fc51 --- /dev/null +++ b/src/USER-SCAFACOS/Install.sh @@ -0,0 +1,54 @@ +# Install/unInstall package files in LAMMPS +# mode = 0/1/2 for uninstall/install/update + +mode=$1 + +# enforce using portable C locale +LC_ALL=C +export LC_ALL + +# arg1 = file, arg2 = file it depends on + +action () { + if (test $mode = 0) then + rm -f ../$1 + elif (! cmp -s $1 ../$1) then + if (test -z "$2" || test -e ../$2) then + cp $1 .. + if (test $mode = 2) then + echo " updating src/$1" + fi + fi + elif (test -n "$2") then + if (test ! -e ../$2) then + rm -f ../$1 + fi + fi +} + +# all package files with no dependencies + +for file in *.cpp *.h; do + test -f ${file} && action $file +done + +# edit 2 Makefile.package files to include/exclude package info + +if (test $1 = 1) then + + if (test -e ../Makefile.package) then + sed -i -e 's/`.*scafacos.*` //' ../Makefile.package + sed -i -e 's/[^ \t]*scafacos[^ \t]* //' ../Makefile.package + sed -i -e 's|^PKG_INC =[ \t]*|&-I../../lib/scafacos/includelink |' ../Makefile.package + sed -i -e 's|^PKG_PATH =[ \t]*|&-L../../lib/scafacos/liblink |' ../Makefile.package + sed -i -e 's%^PKG_LIB =[ \t]*%&`grep Libs: ../../lib/scafacos/liblink/pkgconfig/scafacos.pc | cut -d " " -f 2-` %' ../Makefile.package + fi + +elif (test $1 = 0) then + + if (test -e ../Makefile.package) then + sed -i -e 's/`.*scafacos.*` //' ../Makefile.package + sed -i -e 's/[^ \t]*scafacos[^ \t]* //' ../Makefile.package + fi + +fi diff --git a/src/USER-SCAFACOS/README b/src/USER-SCAFACOS/README new file mode 100644 index 0000000000..42d2e2c0f7 --- /dev/null +++ b/src/USER-SCAFACOS/README @@ -0,0 +1,25 @@ +This package provides a kspace style which is a wrapper for the +ScaFaCoS long-range Coulomb solver library. The library provides +a selection of different long-range Coulomb solvers, which can be +used to calculate the Coloumic forces between charged particles. +More information about the ScaFaCoS library can be found on this +web site: http://scafacos.de. ScaFaCoS was designed and implemented +by a consortium of German universities (Bonn, Chemnitz, Stuttgart, +Wuppertal and others) and the Juelich Supercomputing Centre +(Forschungszentrum Juelich). + +The use of the scafacos kspace requires the download and installation +of the library on the system. This can be done in lib/scafacos or +elsewhere in your system. Details of the download and build process +for ScaFaCoS are given in the lib/scafacos/README file and it can also +be done via the make lib-user-scafacos command from the LAMMPS +source directory. + +Once you have successfully built LAMMPS with this package and the +ScaFaCoS library, you can test it using an input file from the +examples scafacos dir, e.g.: + +lmp_serial -in lammps/examples/USER/scafacos/in.scafacos.fmm + +For questions about ScaFaCoS, please contact: +r.halver@fz-juelich.de or g.sutmann@fz-juelich.de diff --git a/src/USER-SCAFACOS/scafacos.cpp b/src/USER-SCAFACOS/scafacos.cpp new file mode 100644 index 0000000000..52bb0e46c4 --- /dev/null +++ b/src/USER-SCAFACOS/scafacos.cpp @@ -0,0 +1,483 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Rene Halver (JSC) +------------------------------------------------------------------------- */ + +#include +#include +#include +#include "scafacos.h" +#include "atom.h" +#include "comm.h" +#include "domain.h" +#include "force.h" +#include "memory.h" +#include "error.h" + +// ScaFaCoS library + +#include +#include +#include "fcs.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +Scafacos::Scafacos(LAMMPS *lmp, int narg, char **arg) : KSpace(lmp, narg, arg) +{ + if (narg != 2) error->all(FLERR,"Illegal scafacos command"); + + int n = strlen(arg[0]) + 1; + method = new char[n]; + strcpy(method,arg[0]); + tolerance = force->numeric(FLERR,arg[1]); + + // optional ScaFaCoS library setting defaults + // choose the correct default tolerance type for chosen method + // throw an error if a not yet supported solver is chosen + if (strcmp(method,"fmm") == 0) + { + tolerance_type = FCS_TOLERANCE_TYPE_ENERGY; + fmm_tuning_flag = 0; + } + else if (strcmp(method,"p3m") == 0 || + strcmp(method,"p2nfft") == 0 || + strcmp(method,"ewald") == 0) + { + tolerance_type = FCS_TOLERANCE_TYPE_FIELD; + } + else if (strcmp(method,"direct") == 0) + { + // direct summation has no tolerance type + } + else + { + error->all(FLERR,"Unsupported ScaFaCoS method"); + } + + // initializations + + me = comm->me; + initialized = 0; + + maxatom = 0; + xpbc = NULL; + epot = NULL; + efield = NULL; +} + +/* ---------------------------------------------------------------------- */ + +Scafacos::~Scafacos() +{ + delete [] method; + + memory->destroy(xpbc); + memory->destroy(epot); + memory->destroy(efield); + + // clean up of the ScaFaCoS handle and internal arrays + fcs_destroy((FCS)fcs); +} + +/* ---------------------------------------------------------------------- */ + +void Scafacos::init() +{ + // error checks + if (screen && me == 0) fprintf(screen, + "Setting up ScaFaCoS with solver %s ...\n",method); + if (logfile && me == 0) fprintf(logfile, + "Setting up ScaFaCoS with solver %s ...\n",method); + + if (!atom->q_flag) + error->all(FLERR,"Kspace style requires atom attribute q"); + + if (domain->dimension == 2) + error->all(FLERR,"Cannot use ScaFaCoS with 2d simulation"); + + if (domain->triclinic) + error->all(FLERR,"Cannot use ScaFaCoS with triclinic domain yet"); + + if (atom->natoms > INT_MAX && sizeof(int) != 8) + error->all(FLERR,"Scafacos atom count exceeds 2B"); + + if (atom->molecular > 0) + error->all(FLERR, + "Cannot use Scafacos with molecular charged systems yet"); + + FCSResult result; + + // one-time initialization of ScaFaCoS + + qqrd2e = force->qqrd2e; + + if (!initialized) { + result = fcs_init((FCS*)&fcs,method,world); + check_result((void*)&result); + + setup_handle(); + + // using other methods lead to termination of the program, + // since they have no tolerance tuning methods + if ( strcmp(method,"fmm") == 0 || + strcmp(method,"p3m") == 0 || + strcmp(method,"p2nfft") == 0 || + strcmp(method,"ewald") == 0) + { + result = fcs_set_tolerance((FCS)fcs,tolerance_type,tolerance); + check_result((void*)&result); + } + + double **x = atom->x; + double *q = atom->q; + int nlocal = atom->nlocal; + + if (strcmp(method,"fmm") == 0) + { + if (fmm_tuning_flag == 1) + fcs_fmm_set_internal_tuning((FCS)fcs,FCS_FMM_INHOMOGENOUS_SYSTEM); + else + fcs_fmm_set_internal_tuning((FCS)fcs,FCS_FMM_HOMOGENOUS_SYSTEM); + } + + // for the FMM at least one particle is required per process + if (strcmp(method,"fmm") == 0) + { + int empty = (nlocal==0)?1:0; + MPI_Allreduce(MPI_IN_PLACE,&empty,1,MPI_INT,MPI_SUM,world); + if (empty > 0) + fcs_set_redistribute((FCS)fcs,1); + else + fcs_set_redistribute((FCS)fcs,0); + } + + result = fcs_tune((FCS)fcs,nlocal,&x[0][0],q); + check_result((void*)&result); + // more useful here, since the parameters should be tuned now + if (me == 0) fcs_print_parameters((FCS)fcs); + } + + initialized = 1; +} + +/* ---------------------------------------------------------------------- */ + +void Scafacos::compute(int eflag, int vflag) +{ + double **x = atom->x; + double *q = atom->q; + int nlocal = atom->nlocal; + + const double qscale = qqrd2e; + FCSResult result; + + // for the FMM at least one particle is required per process + if (strcmp(method,"fmm")) + { + int empty = (nlocal==0)?1:0; + MPI_Allreduce(MPI_IN_PLACE,&empty,1,MPI_INT,MPI_SUM,world); + if (empty > 0) + fcs_set_redistribute((FCS)fcs,1); + else + fcs_set_redistribute((FCS)fcs,0); + } + + if (eflag || vflag) ev_setup(eflag,vflag); + else + { + eflag_atom = 0; + vflag_global = 0; + } + + // grow xpbc, epot, efield if necessary + + if (nlocal > maxatom || maxatom == 0) { + memory->destroy(xpbc); + memory->destroy(epot); + memory->destroy(efield); + maxatom = atom->nmax; + memory->create(xpbc,3*maxatom,"scafacos:xpbc"); + memory->create(epot,maxatom,"scafacos:epot"); + memory->create(efield,maxatom,3,"scafacos:efield"); + } + + if (vflag_global) + { + fcs_set_compute_virial((FCS)fcs,1); + //if (strcmp(method,"p3m") == 0) + // error->all(FLERR,"ScaFaCoS p3m does not support computation of virial"); + } + + // pack coords into xpbc and apply PBC + memcpy(xpbc,&x[0][0],3*nlocal*sizeof(double)); + + + if (domain->xperiodic || domain -> yperiodic || domain -> zperiodic){ + int j = 0; + for (int i = 0; i < nlocal; i++) { + domain->remap(&xpbc[j]); + j += 3; + } + } + // if simulation box has changed, call fcs_tune() + + if (box_has_changed()) { + setup_handle(); + result = fcs_tune((FCS)fcs,nlocal,xpbc,q); + check_result((void*)&result); + } + + // invoke ScaFaCoS solver + + result = fcs_run((FCS)fcs,nlocal,xpbc,q,&efield[0][0],epot); + check_result((void*)&result); + + // extract virial + + if (vflag_global) + { + fcs_get_virial((FCS)fcs,virial_int); + virial[0] = virial_int[0]; + virial[1] = virial_int[1]; + virial[2] = virial_int[2]; + virial[3] = virial_int[4]; + virial[4] = virial_int[5]; + virial[5] = virial_int[8]; + } + + // apply Efield to each particle + // accumulate total energy + + double **f = atom->f; + + double qone; + double myeng = 0.0; + + for (int i = 0; i < nlocal; i++) { + qone = q[i] * qscale; + f[i][0] += qone * efield[i][0]; + f[i][1] += qone * efield[i][1]; + f[i][2] += qone * efield[i][2]; + myeng += 0.5 * qone * epot[i]; + } + + if (eflag_atom) { + for (int i = 0; i < nlocal; i++) + eatom[i] = 0.5 * qscale * q[i] * epot[i]; + } + + MPI_Allreduce(&myeng,&energy,1,MPI_DOUBLE,MPI_SUM,world); +} + +/* ---------------------------------------------------------------------- */ + +int Scafacos::modify_param(int narg, char **arg) +{ + // add any Scafacos options here you want to expose to LAMMPS + // syntax: kspace_modify scafacos keyword value1 value2 ... + // keyword = tolerance + // value1 = energy, energy_rel, etc + // everyone of these should have a default, so user doesn't need to set + + if (strcmp(arg[0],"scafacos") != 0) return 0; + + if (strcmp(arg[1],"tolerance") == 0) { + if (narg < 3) error->all(FLERR, + "Illegal kspace_modify command (tolerance)"); + if (strcmp(arg[2],"energy") == 0) + tolerance_type = FCS_TOLERANCE_TYPE_ENERGY; + else if (strcmp(arg[2],"energy_rel") == 0) + tolerance_type = FCS_TOLERANCE_TYPE_ENERGY_REL; + else if (strcmp(arg[2],"field") == 0) + tolerance_type = FCS_TOLERANCE_TYPE_FIELD; + else if (strcmp(arg[2],"field_rel") == 0) + tolerance_type = FCS_TOLERANCE_TYPE_FIELD_REL; + else if (strcmp(arg[2],"potential") == 0) + tolerance_type = FCS_TOLERANCE_TYPE_POTENTIAL; + else if (strcmp(arg[2],"potential_rel") == 0) + tolerance_type = FCS_TOLERANCE_TYPE_POTENTIAL_REL; + else error->all(FLERR, + "Illegal kspace_modify command (tolerance argument)"); + // check if method is compatatible to chosen tolerance type + if( + ( + strcmp(method,"fmm") == 0 && + ( + tolerance_type != FCS_TOLERANCE_TYPE_ENERGY && + tolerance_type != FCS_TOLERANCE_TYPE_ENERGY_REL + ) + ) || + ( + strcmp(method,"p2nfft") == 0 && + ( + tolerance_type != FCS_TOLERANCE_TYPE_FIELD && + tolerance_type != FCS_TOLERANCE_TYPE_POTENTIAL + ) + ) || + ( + strcmp(method,"p3m") == 0 && + ( + tolerance_type != FCS_TOLERANCE_TYPE_FIELD + ) + ) || + ( + strcmp(method,"ewald") == 0 && + ( + tolerance_type != FCS_TOLERANCE_TYPE_FIELD + ) + ) + ) + error->all(FLERR,"Illegal kspace_modify command \ + (invalid tolerance / method combination)"); + return 3; + } + + // keyword = fmm_inhomogen_tuning + // value1 = 0, 1 + // 0 -> homogenous system (default) + // 1 -> inhomogenous system (more internal tuning is provided (sequential!)) + if (strcmp(arg[1],"fmm_tuning") == 0) + { + if (screen && me == 0) fprintf(screen, + "ScaFaCoS setting fmm inhomogen tuning ...\n"); + if (logfile && me == 0) fprintf(logfile, + "ScaFaCoS setting fmm inhomogen tuning ...\n"); + if (narg < 3) error->all(FLERR, + "Illegal kspace_modify command (fmm_tuning)"); + fmm_tuning_flag = atoi(arg[2]); + return 3; + } + + return 0; +} + +/* ---------------------------------------------------------------------- + memory usage of local arrays +------------------------------------------------------------------------- */ + +double Scafacos::memory_usage() +{ + double bytes = 0.0; + bytes += maxatom * sizeof(double); + bytes += 3*maxatom * sizeof(double); + return bytes; +} + +/* ---------------------------------------------------------------------- + setup of ScaFaCoS handle with common parameters +------------------------------------------------------------------------- */ + +void Scafacos::setup_handle() +{ + FCSResult result; + + // store simulation box params + + // setup periodicity + old_periodicity[0] = domain->xperiodic; + old_periodicity[1] = domain->yperiodic; + old_periodicity[2] = domain->zperiodic; + + // setup box origin (lower left front corner of the system) + old_origin[0] = domain->boxlo[0]; + old_origin[1] = domain->boxlo[1]; + old_origin[2] = domain->boxlo[2]; + + // setup box vectors (base vectors of the system box) + old_box_x[0] = domain->prd[0]; + old_box_x[1] = old_box_x[2] = 0.0; + old_box_y[1] = domain->prd[1]; + old_box_y[0] = old_box_y[2] = 0.0; + old_box_z[2] = domain->prd[2]; + old_box_z[1] = old_box_z[0] = 0.0; + + // setup number of atoms in the system + old_natoms = atom->natoms; + + // store parameters to ScaFaCoS handle + result = fcs_set_box_a((FCS)fcs,old_box_x); + check_result((void*)&result); + + result = fcs_set_box_b((FCS)fcs,old_box_y); + check_result((void*)&result); + + result = fcs_set_box_c((FCS)fcs,old_box_z); + check_result((void*)&result); + + result = fcs_set_box_origin((FCS)fcs,old_origin); + check_result((void*)&result); + + result = fcs_set_periodicity((FCS)fcs,old_periodicity); + check_result((void*)&result); + + result = fcs_set_total_particles((FCS)fcs,old_natoms); + check_result((void*)&result); + + // allow ScaFaCoS to calculate the near field computations for now + // TODO: allow the delegation of the near field computations + // within LAMMPS + // (near_field_flag = 1 -> enables the internal near field calcs + // 0 -> disables the internal near field calcs + int near_field_flag = 1; + result = fcs_set_near_field_flag((FCS)fcs,near_field_flag); + check_result((void*)&result); +} + +/* ---------------------------------------------------------------------- + check if box parameters changed, requiring a new call to fcs_tune +------------------------------------------------------------------------- */ + +bool Scafacos::box_has_changed() +{ + int *periodicity = domain->periodicity; + double *prd = domain->prd; + + bool changed = + (periodicity[0] != old_periodicity[0]) || + (periodicity[1] != old_periodicity[1]) || + (periodicity[2] != old_periodicity[2]) || + (domain->boundary[0][0] != old_origin[0]) || + (domain->boundary[1][0] != old_origin[1]) || + (domain->boundary[2][0] != old_origin[2]) || + (prd[0] != old_box_x[0]) || + (prd[1] != old_box_y[1]) || + (prd[2] != old_box_z[2]) || + (atom->natoms != old_natoms); + + return changed; +} + +/* ---------------------------------------------------------------------- + check ScaFaCoS result for error condition +------------------------------------------------------------------------- */ + +void Scafacos::check_result(void* result_p) +{ + FCSResult result = *(FCSResult*)result_p; + + if (!result) return; + + std::stringstream ss; + ss << "ScaFaCoS: " << fcs_result_get_function(result) << "\n" + << fcs_result_get_message(result) << "\n"; + fcs_result_destroy(result); + std::string err_msg = ss.str(); + const char *str = err_msg.c_str(); + + error->one(FLERR,str); +} + diff --git a/src/USER-SCAFACOS/scafacos.h b/src/USER-SCAFACOS/scafacos.h new file mode 100644 index 0000000000..fdf15739a6 --- /dev/null +++ b/src/USER-SCAFACOS/scafacos.h @@ -0,0 +1,73 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef KSPACE_CLASS + +KSpaceStyle(scafacos,Scafacos) + +#else + +#ifndef LMP_SCAFACOS_H +#define LMP_SCAFACOS_H + +#include "kspace.h" +//#include "fcs.h" + +namespace LAMMPS_NS { + +class Scafacos : public KSpace { + public: + Scafacos(class LAMMPS *, int, char **); + ~Scafacos(); + void init(); + void setup() {} + void compute(int, int); + int modify_param(int, char **); + double memory_usage(); + + private: + int me; + + char *method; + double tolerance; + double *xpbc,*epot,**efield; + int tolerance_type; + int initialized,maxatom; + + int fmm_tuning_flag; + + void* fcs; // ScaFaCoS handle + + // simulation state: box, natoms + // so ScaFaCoS can detect if changes, e.g. for NPT + + double old_box_x[3],old_box_y[3],old_box_z[3]; + double old_origin[3]; + int old_periodicity[3]; + int old_natoms; + + double virial_int[9]; + + void check_result(void*); + void setup_handle(); + bool box_has_changed(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/USER-SMD/atom_vec_smd.cpp b/src/USER-SMD/atom_vec_smd.cpp index e99f3c5169..020284312b 100644 --- a/src/USER-SMD/atom_vec_smd.cpp +++ b/src/USER-SMD/atom_vec_smd.cpp @@ -208,7 +208,7 @@ void AtomVecSMD::copy(int i, int j, int delflag) { /* ---------------------------------------------------------------------- */ -int AtomVecSMD::pack_comm(int n, int *list, double *buf, int pbc_flag, int *pbc) { +int AtomVecSMD::pack_comm(int /*n*/, int * /*list*/, double * /*buf*/, int /*pbc_flag*/, int * /*pbc*/) { error->one(FLERR, "atom vec tlsph can only be used with ghost velocities turned on"); return -1; } @@ -333,7 +333,7 @@ int AtomVecSMD::pack_comm_hybrid(int n, int *list, double *buf) { /* ---------------------------------------------------------------------- */ -void AtomVecSMD::unpack_comm(int n, int first, double *buf) { +void AtomVecSMD::unpack_comm(int /*n*/, int /*first*/, double * /*buf*/) { error->one(FLERR, "atom vec tlsph can only be used with ghost velocities turned on"); } @@ -441,7 +441,7 @@ int AtomVecSMD::unpack_reverse_hybrid(int n, int *list, double *buf) { /* ---------------------------------------------------------------------- */ -int AtomVecSMD::pack_border(int n, int *list, double *buf, int pbc_flag, int *pbc) { +int AtomVecSMD::pack_border(int /*n*/, int * /*list*/, double * /*buf*/, int /*pbc_flag*/, int * /*pbc*/) { error->one(FLERR, "atom vec tlsph can only be used with ghost velocities turned on"); return -1; } @@ -633,7 +633,7 @@ int AtomVecSMD::pack_border_hybrid(int n, int *list, double *buf) { /* ---------------------------------------------------------------------- */ -void AtomVecSMD::unpack_border(int n, int first, double *buf) { +void AtomVecSMD::unpack_border(int /*n*/, int /*first*/, double * /*buf*/) { error->one(FLERR, "atom vec tlsph can only be used with ghost velocities turned on"); } @@ -1098,7 +1098,7 @@ void AtomVecSMD::data_atom(double *coord, imageint imagetmp, char **values) { initialize other atom quantities for this sub-style ------------------------------------------------------------------------- */ -int AtomVecSMD::data_atom_hybrid(int nlocal, char **values) { +int AtomVecSMD::data_atom_hybrid(int /*nlocal*/, char **/*values*/) { error->one(FLERR, "hybrid atom style functionality not yet implemented for atom style smd"); return -1; } @@ -1120,7 +1120,7 @@ void AtomVecSMD::data_vel(int m, char **values) { unpack hybrid quantities from one line in Velocities section of data file ------------------------------------------------------------------------- */ -int AtomVecSMD::data_vel_hybrid(int m, char **values) { +int AtomVecSMD::data_vel_hybrid(int /*m*/, char **/*values*/) { error->one(FLERR, "hybrid atom style functionality not yet implemented for atom style smd"); return 0; } @@ -1158,7 +1158,7 @@ void AtomVecSMD::pack_data(double **buf) { pack hybrid atom info for data file ------------------------------------------------------------------------- */ -int AtomVecSMD::pack_data_hybrid(int i, double *buf) { +int AtomVecSMD::pack_data_hybrid(int /*i*/, double * /*buf*/) { error->one(FLERR, "hybrid atom style functionality not yet implemented for atom style smd"); return -1; } @@ -1180,7 +1180,7 @@ void AtomVecSMD::write_data(FILE *fp, int n, double **buf) { write hybrid atom info to data file ------------------------------------------------------------------------- */ -int AtomVecSMD::write_data_hybrid(FILE *fp, double *buf) { +int AtomVecSMD::write_data_hybrid(FILE * /*fp*/, double * /*buf*/) { error->one(FLERR, "hybrid atom style functionality not yet implemented for atom style smd"); return -1; } @@ -1203,7 +1203,7 @@ void AtomVecSMD::pack_vel(double **buf) { pack hybrid velocity info for data file ------------------------------------------------------------------------- */ -int AtomVecSMD::pack_vel_hybrid(int i, double *buf) { +int AtomVecSMD::pack_vel_hybrid(int /*i*/, double * /*buf*/) { error->one(FLERR, "hybrid atom style functionality not yet implemented for atom style smd"); return 0; } @@ -1222,7 +1222,7 @@ void AtomVecSMD::write_vel(FILE *fp, int n, double **buf) { write hybrid velocity info to data file ------------------------------------------------------------------------- */ -int AtomVecSMD::write_vel_hybrid(FILE *fp, double *buf) { +int AtomVecSMD::write_vel_hybrid(FILE * /*fp*/, double * /*buf*/) { error->one(FLERR, "hybrid atom style functionality not yet implemented for atom style smd"); return 3; } diff --git a/src/USER-SMD/fix_smd_adjust_dt.cpp b/src/USER-SMD/fix_smd_adjust_dt.cpp index 3685248d5e..f015c6c4df 100644 --- a/src/USER-SMD/fix_smd_adjust_dt.cpp +++ b/src/USER-SMD/fix_smd_adjust_dt.cpp @@ -86,13 +86,13 @@ void FixSMDTlsphDtReset::init() { /* ---------------------------------------------------------------------- */ -void FixSMDTlsphDtReset::setup(int vflag) { +void FixSMDTlsphDtReset::setup(int /*vflag*/) { end_of_step(); } /* ---------------------------------------------------------------------- */ -void FixSMDTlsphDtReset::initial_integrate(int vflag) { +void FixSMDTlsphDtReset::initial_integrate(int /*vflag*/) { //printf("in adjust_dt: dt = %20.10f\n", update->dt); diff --git a/src/USER-SMD/fix_smd_integrate_tlsph.cpp b/src/USER-SMD/fix_smd_integrate_tlsph.cpp index 4668e673fc..1eae45161f 100644 --- a/src/USER-SMD/fix_smd_integrate_tlsph.cpp +++ b/src/USER-SMD/fix_smd_integrate_tlsph.cpp @@ -125,7 +125,7 @@ void FixSMDIntegrateTlsph::init() { /* ---------------------------------------------------------------------- ------------------------------------------------------------------------- */ -void FixSMDIntegrateTlsph::initial_integrate(int vflag) { +void FixSMDIntegrateTlsph::initial_integrate(int /*vflag*/) { double dtfm, vsq, scale; // update v and x of atoms in group diff --git a/src/USER-SMD/fix_smd_integrate_ulsph.cpp b/src/USER-SMD/fix_smd_integrate_ulsph.cpp index a145deeb61..685d6af5a8 100644 --- a/src/USER-SMD/fix_smd_integrate_ulsph.cpp +++ b/src/USER-SMD/fix_smd_integrate_ulsph.cpp @@ -158,7 +158,7 @@ void FixSMDIntegrateUlsph::init() { allow for both per-type and per-atom mass ------------------------------------------------------------------------- */ -void FixSMDIntegrateUlsph::initial_integrate(int vflag) { +void FixSMDIntegrateUlsph::initial_integrate(int /*vflag*/) { double **x = atom->x; double **v = atom->v; double **f = atom->f; diff --git a/src/USER-SMD/fix_smd_move_triangulated_surface.cpp b/src/USER-SMD/fix_smd_move_triangulated_surface.cpp index d4afbe0535..b0944f1186 100644 --- a/src/USER-SMD/fix_smd_move_triangulated_surface.cpp +++ b/src/USER-SMD/fix_smd_move_triangulated_surface.cpp @@ -248,7 +248,7 @@ void FixSMDMoveTriSurf::init() { /* ---------------------------------------------------------------------- ------------------------------------------------------------------------- */ -void FixSMDMoveTriSurf::initial_integrate(int vflag) { +void FixSMDMoveTriSurf::initial_integrate(int /*vflag*/) { double **x = atom->x; double **x0 = atom->x0; double **v = atom->v; @@ -461,7 +461,7 @@ void FixSMDMoveTriSurf::reset_dt() { /* ---------------------------------------------------------------------- */ -int FixSMDMoveTriSurf::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc) { +int FixSMDMoveTriSurf::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int * /*pbc*/) { int i, j, m; double **x0 = atom->x0; double **smd_data_9 = atom->smd_data_9; diff --git a/src/USER-SMD/fix_smd_setvel.cpp b/src/USER-SMD/fix_smd_setvel.cpp index 5e7cdbad38..4bc8b5127b 100644 --- a/src/USER-SMD/fix_smd_setvel.cpp +++ b/src/USER-SMD/fix_smd_setvel.cpp @@ -231,7 +231,7 @@ void FixSMDSetVel::min_setup(int vflag) { /* ---------------------------------------------------------------------- */ //void FixSMDSetVel::initial_integrate(int vflag) { -void FixSMDSetVel::post_force(int vflag) { +void FixSMDSetVel::post_force(int /*vflag*/) { double **x = atom->x; double **f = atom->f; double **v = atom->v; diff --git a/src/USER-SMD/fix_smd_setvel.h b/src/USER-SMD/fix_smd_setvel.h index b987a56f6c..a3e650e682 100644 --- a/src/USER-SMD/fix_smd_setvel.h +++ b/src/USER-SMD/fix_smd_setvel.h @@ -56,7 +56,6 @@ class FixSMDSetVel : public Fix { int xvar,yvar,zvar,xstyle,ystyle,zstyle; double foriginal[3],foriginal_all[3]; int force_flag; - int nlevels_respa; int maxatom; double **sforce; diff --git a/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp b/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp index 3e2812aa12..a2813cc3ca 100644 --- a/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp +++ b/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp @@ -149,7 +149,7 @@ void FixSMD_TLSPH_ReferenceConfiguration::pre_exchange() { if (updateFlag > 0) { if (comm->me == 0) { - printf("**** updating ref config at step: %ld\n", update->ntimestep); + printf("**** updating ref config at step: " BIGINT_FORMAT "\n", update->ntimestep); } for (i = 0; i < nlocal; i++) { @@ -199,7 +199,7 @@ void FixSMD_TLSPH_ReferenceConfiguration::pre_exchange() { so can be migrated or stored with atoms ------------------------------------------------------------------------- */ -void FixSMD_TLSPH_ReferenceConfiguration::setup(int vflag) { +void FixSMD_TLSPH_ReferenceConfiguration::setup(int /*vflag*/) { int i, j, ii, jj, n, inum, jnum; int *ilist, *jlist, *numneigh, **firstneigh; double r, h, wf, wfd; @@ -386,7 +386,7 @@ void FixSMD_TLSPH_ReferenceConfiguration::grow_arrays(int nmax) { copy values within local atom-based arrays ------------------------------------------------------------------------- */ -void FixSMD_TLSPH_ReferenceConfiguration::copy_arrays(int i, int j, int delflag) { +void FixSMD_TLSPH_ReferenceConfiguration::copy_arrays(int i, int j, int /*delflag*/) { npartner[j] = npartner[i]; for (int m = 0; m < npartner[j]; m++) { partner[j][m] = partner[i][m]; @@ -470,7 +470,7 @@ int FixSMD_TLSPH_ReferenceConfiguration::pack_restart(int i, double *buf) { unpack values from atom->extra array to restart the fix ------------------------------------------------------------------------- */ -void FixSMD_TLSPH_ReferenceConfiguration::unpack_restart(int nlocal, int nth) { +void FixSMD_TLSPH_ReferenceConfiguration::unpack_restart(int /*nlocal*/, int /*nth*/) { // ipage = NULL if being called from granular pair style init() // skip to Nth set of extra values @@ -512,7 +512,7 @@ int FixSMD_TLSPH_ReferenceConfiguration::size_restart(int nlocal) { /* ---------------------------------------------------------------------- */ -int FixSMD_TLSPH_ReferenceConfiguration::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc) { +int FixSMD_TLSPH_ReferenceConfiguration::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int * /*pbc*/) { int i, j, m; double *radius = atom->radius; double *vfrac = atom->vfrac; diff --git a/src/USER-SMD/fix_smd_wall_surface.cpp b/src/USER-SMD/fix_smd_wall_surface.cpp index 97c2ead5fc..4dd415f53e 100644 --- a/src/USER-SMD/fix_smd_wall_surface.cpp +++ b/src/USER-SMD/fix_smd_wall_surface.cpp @@ -110,7 +110,7 @@ void FixSMDWallSurface::min_setup(int vflag) { must be done in setup (not init) since fix init comes before neigh init ------------------------------------------------------------------------- */ -void FixSMDWallSurface::setup(int vflag) { +void FixSMDWallSurface::setup(int /*vflag*/) { if (!first) return; diff --git a/src/USER-SMD/pair_smd_hertz.cpp b/src/USER-SMD/pair_smd_hertz.cpp index 815db4a450..13f48e995e 100644 --- a/src/USER-SMD/pair_smd_hertz.cpp +++ b/src/USER-SMD/pair_smd_hertz.cpp @@ -373,7 +373,7 @@ double PairHertz::memory_usage() { return 0.0; } -void *PairHertz::extract(const char *str, int &i) { +void *PairHertz::extract(const char *str, int &/*i*/) { //printf("in PairTriSurf::extract\n"); if (strcmp(str, "smd/hertz/stable_time_increment_ptr") == 0) { return (void *) &stable_time_increment; diff --git a/src/USER-SMD/pair_smd_tlsph.cpp b/src/USER-SMD/pair_smd_tlsph.cpp index 4dd16c4d83..09fe3b1180 100644 --- a/src/USER-SMD/pair_smd_tlsph.cpp +++ b/src/USER-SMD/pair_smd_tlsph.cpp @@ -1802,7 +1802,7 @@ double PairTlsph::memory_usage() { extract method to provide access to this class' data structures ------------------------------------------------------------------------- */ -void *PairTlsph::extract(const char *str, int &i) { +void *PairTlsph::extract(const char *str, int &/*i*/) { //printf("in PairTlsph::extract\n"); if (strcmp(str, "smd/tlsph/Fincr_ptr") == 0) { return (void *) Fincr; @@ -1839,7 +1839,7 @@ void *PairTlsph::extract(const char *str, int &i) { /* ---------------------------------------------------------------------- */ -int PairTlsph::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc) { +int PairTlsph::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int * /*pbc*/) { int i, j, m; tagint *mol = atom->molecule; double *damage = atom->damage; @@ -1928,7 +1928,7 @@ void PairTlsph::unpack_forward_comm(int n, int first, double *buf) { ------------------------------------------------------------------------- */ void PairTlsph::effective_longitudinal_modulus(const int itype, const double dt, const double d_iso, const double p_rate, - const Matrix3d d_dev, const Matrix3d sigma_dev_rate, const double damage, double &K_eff, double &mu_eff, double &M_eff) { + const Matrix3d d_dev, const Matrix3d sigma_dev_rate, const double /*damage*/, double &K_eff, double &mu_eff, double &M_eff) { double M0; // initial longitudinal modulus double shear_rate_sq; @@ -2094,7 +2094,7 @@ void PairTlsph::ComputeStressDeviator(const int i, const Matrix3d sigmaInitial_d /* ---------------------------------------------------------------------- Compute damage. Called from AssembleStress(). ------------------------------------------------------------------------- */ -void PairTlsph::ComputeDamage(const int i, const Matrix3d strain, const Matrix3d stress, Matrix3d &stress_damaged) { +void PairTlsph::ComputeDamage(const int i, const Matrix3d strain, const Matrix3d stress, Matrix3d &/*stress_damaged*/) { double *eff_plastic_strain = atom->eff_plastic_strain; double *eff_plastic_strain_rate = atom->eff_plastic_strain_rate; double *radius = atom->radius; diff --git a/src/USER-SMD/pair_smd_triangulated_surface.cpp b/src/USER-SMD/pair_smd_triangulated_surface.cpp index b8bff7e799..e40c876ec3 100644 --- a/src/USER-SMD/pair_smd_triangulated_surface.cpp +++ b/src/USER-SMD/pair_smd_triangulated_surface.cpp @@ -834,7 +834,7 @@ double PairTriSurf::clamp(const double a, const double min, const double max) { } } -void *PairTriSurf::extract(const char *str, int &i) { +void *PairTriSurf::extract(const char *str, int &/*i*/) { //printf("in PairTriSurf::extract\n"); if (strcmp(str, "smd/tri_surface/stable_time_increment_ptr") == 0) { return (void *) &stable_time_increment; diff --git a/src/USER-SMD/pair_smd_ulsph.cpp b/src/USER-SMD/pair_smd_ulsph.cpp index 96eb912fae..ff3720b2ff 100644 --- a/src/USER-SMD/pair_smd_ulsph.cpp +++ b/src/USER-SMD/pair_smd_ulsph.cpp @@ -1487,7 +1487,7 @@ double PairULSPH::memory_usage() { /* ---------------------------------------------------------------------- */ -int PairULSPH::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc) { +int PairULSPH::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int * /*pbc*/) { double *vfrac = atom->vfrac; double *eff_plastic_strain = atom->eff_plastic_strain; int i, j, m; @@ -1562,7 +1562,7 @@ void PairULSPH::unpack_forward_comm(int n, int first, double *buf) { * EXTRACT */ -void *PairULSPH::extract(const char *str, int &i) { +void *PairULSPH::extract(const char *str, int &/*i*/) { //printf("in extract\n"); if (strcmp(str, "smd/ulsph/smoothVel_ptr") == 0) { return (void *) smoothVel; diff --git a/src/USER-SMD/smd_material_models.cpp b/src/USER-SMD/smd_material_models.cpp index e3deb199b6..4213428872 100644 --- a/src/USER-SMD/smd_material_models.cpp +++ b/src/USER-SMD/smd_material_models.cpp @@ -97,7 +97,7 @@ void ShockEOS(double rho, double rho0, double e, double e0, double c0, double S, final pressure pFinal ------------------------------------------------------------------------- */ -void polynomialEOS(double rho, double rho0, double e, double C0, double C1, double C2, double C3, double C4, double C5, double C6, +void polynomialEOS(double rho, double rho0, double /*e*/, double C0, double C1, double C2, double C3, double /*C4*/, double /*C5*/, double /*C6*/, double pInitial, double dt, double &pFinal, double &p_rate) { double mu = rho / rho0 - 1.0; @@ -307,7 +307,7 @@ void LinearPlasticStrength(const double G, const double yieldStress, const Matri output: sigmaFinal_dev, sigmaFinal_dev_rate__: final stress deviator and its rate. ------------------------------------------------------------------------- */ void JohnsonCookStrength(const double G, const double cp, const double espec, const double A, const double B, const double a, - const double C, const double epdot0, const double T0, const double Tmelt, const double M, const double dt, const double ep, + const double C, const double epdot0, const double T0, const double Tmelt, const double /*M*/, const double dt, const double ep, const double epdot, const Matrix3d sigmaInitial_dev, const Matrix3d d_dev, Matrix3d &sigmaFinal_dev__, Matrix3d &sigma_dev_rate__, double &plastic_strain_increment) { diff --git a/src/USER-SMTBQ/pair_smtbq.cpp b/src/USER-SMTBQ/pair_smtbq.cpp index 1028d8a897..a8cce49749 100644 --- a/src/USER-SMTBQ/pair_smtbq.cpp +++ b/src/USER-SMTBQ/pair_smtbq.cpp @@ -242,7 +242,7 @@ void PairSMTBQ::allocate() global settings ------------------------------------------------------------------------- */ -void PairSMTBQ::settings(int narg, char **arg) +void PairSMTBQ::settings(int narg, char **/*arg*/) { if (narg > 0) error->all(FLERR,"Illegal pair_style command"); } @@ -1592,7 +1592,7 @@ void PairSMTBQ::tabqeq() /* ---------------------------------------------------------------------*/ void PairSMTBQ::potqeq(int i, int j, double qi, double qj, double rsq, - double &fforce, int eflag, double &eng) + double &fforce, int /*eflag*/, double &eng) { /* =================================================================== @@ -1840,7 +1840,7 @@ void PairSMTBQ::pot_ES2 (int i, int j, double rsq, double &pot) -------------------------------------------------------------------- */ void PairSMTBQ::rep_OO(Intparam *intparam, double rsq, double &fforce, - int eflag, double &eng) + int /*eflag*/, double &eng) { double r,tmp_exp,tmp; double A = intparam->abuck ; @@ -1858,7 +1858,7 @@ void PairSMTBQ::rep_OO(Intparam *intparam, double rsq, double &fforce, void PairSMTBQ::Attr_OO(Intparam *intparam, double rsq, double &fforce, - int eflag, double &eng) + int /*eflag*/, double &eng) { double r,tmp_exp; double aOO = intparam->aOO ; @@ -1980,8 +1980,8 @@ void PairSMTBQ::tabsm() /* -------------------------------------------------------------- */ -void PairSMTBQ::repulsive(Intparam *intparam, double rsq, int i, int j, - double &fforce, int eflag, double &eng) +void PairSMTBQ::repulsive(Intparam *intparam, double rsq, int /*i*/, int /*j*/, + double &fforce, int /*eflag*/, double &eng) { /* ================================================ @@ -2031,7 +2031,7 @@ void PairSMTBQ::repulsive(Intparam *intparam, double rsq, int i, int j, void PairSMTBQ::attractive(Intparam *intparam, double rsq, - int eflag, int i, double iq, int j, double jq) + int /*eflag*/, int i, double /*iq*/, int /*j*/, double /*jq*/) { int itype,l; double r,t1,t2,xi,sds; @@ -3334,7 +3334,7 @@ void PairSMTBQ::groupQEqAllParallel_QEq() /* ---------------------------------------------------------------------- */ -void PairSMTBQ::Init_charge(int *nQEq, int *nQEqa, int *nQEqc) +void PairSMTBQ::Init_charge(int * /*nQEq*/, int * /*nQEqa*/, int * /*nQEqc*/) { int ii,i,gp,itype; int *ilist,test[nteam],init[nteam]; @@ -3391,7 +3391,7 @@ void PairSMTBQ::Init_charge(int *nQEq, int *nQEqa, int *nQEqc) * COMMUNICATION * ---------------------------------------------------------------------- */ -int PairSMTBQ::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc) +int PairSMTBQ::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int * /*pbc*/) { int i,j,m; diff --git a/src/USER-SPH/fix_meso.cpp b/src/USER-SPH/fix_meso.cpp index d7a5d81517..b688eccfea 100644 --- a/src/USER-SPH/fix_meso.cpp +++ b/src/USER-SPH/fix_meso.cpp @@ -64,7 +64,7 @@ void FixMeso::init() { dtf = 0.5 * update->dt * force->ftm2v; } -void FixMeso::setup_pre_force(int vflag) +void FixMeso::setup_pre_force(int /*vflag*/) { // set vest equal to v double **v = atom->v; @@ -87,7 +87,7 @@ void FixMeso::setup_pre_force(int vflag) allow for both per-type and per-atom mass ------------------------------------------------------------------------- */ -void FixMeso::initial_integrate(int vflag) { +void FixMeso::initial_integrate(int /*vflag*/) { // update v and x and rho and e of atoms in group double **x = atom->x; diff --git a/src/USER-SPH/fix_meso_stationary.cpp b/src/USER-SPH/fix_meso_stationary.cpp index f5fc306320..29e8a1554c 100644 --- a/src/USER-SPH/fix_meso_stationary.cpp +++ b/src/USER-SPH/fix_meso_stationary.cpp @@ -67,7 +67,7 @@ void FixMesoStationary::init() { allow for both per-type and per-atom mass ------------------------------------------------------------------------- */ -void FixMesoStationary::initial_integrate(int vflag) { +void FixMesoStationary::initial_integrate(int /*vflag*/) { double *rho = atom->rho; double *drho = atom->drho; diff --git a/src/USER-SPH/pair_sph_heatconduction.cpp b/src/USER-SPH/pair_sph_heatconduction.cpp index 6f0cf7eca2..4a8990d6fd 100644 --- a/src/USER-SPH/pair_sph_heatconduction.cpp +++ b/src/USER-SPH/pair_sph_heatconduction.cpp @@ -155,7 +155,7 @@ void PairSPHHeatConduction::allocate() { global settings ------------------------------------------------------------------------- */ -void PairSPHHeatConduction::settings(int narg, char **arg) { +void PairSPHHeatConduction::settings(int narg, char **/*arg*/) { if (narg != 0) error->all(FLERR, "Illegal number of setting arguments for pair_style sph/heatconduction"); @@ -211,8 +211,8 @@ double PairSPHHeatConduction::init_one(int i, int j) { /* ---------------------------------------------------------------------- */ -double PairSPHHeatConduction::single(int i, int j, int itype, int jtype, - double rsq, double factor_coul, double factor_lj, double &fforce) { +double PairSPHHeatConduction::single(int /*i*/, int /*j*/, int /*itype*/, int /*jtype*/, + double /*rsq*/, double /*factor_coul*/, double /*factor_lj*/, double &fforce) { fforce = 0.0; return 0.0; diff --git a/src/USER-SPH/pair_sph_idealgas.cpp b/src/USER-SPH/pair_sph_idealgas.cpp index 99fba05917..32b3e61233 100644 --- a/src/USER-SPH/pair_sph_idealgas.cpp +++ b/src/USER-SPH/pair_sph_idealgas.cpp @@ -197,7 +197,7 @@ void PairSPHIdealGas::allocate() { global settings ------------------------------------------------------------------------- */ -void PairSPHIdealGas::settings(int narg, char **arg) { +void PairSPHIdealGas::settings(int narg, char **/*arg*/) { if (narg != 0) error->all(FLERR, "Illegal number of setting arguments for pair_style sph/idealgas"); @@ -252,8 +252,8 @@ double PairSPHIdealGas::init_one(int i, int j) { /* ---------------------------------------------------------------------- */ -double PairSPHIdealGas::single(int i, int j, int itype, int jtype, - double rsq, double factor_coul, double factor_lj, double &fforce) { +double PairSPHIdealGas::single(int /*i*/, int /*j*/, int /*itype*/, int /*jtype*/, + double /*rsq*/, double /*factor_coul*/, double /*factor_lj*/, double &fforce) { fforce = 0.0; return 0.0; diff --git a/src/USER-SPH/pair_sph_lj.cpp b/src/USER-SPH/pair_sph_lj.cpp index 5cefdf87c4..c382833baf 100644 --- a/src/USER-SPH/pair_sph_lj.cpp +++ b/src/USER-SPH/pair_sph_lj.cpp @@ -204,7 +204,7 @@ void PairSPHLJ::allocate() { global settings ------------------------------------------------------------------------- */ -void PairSPHLJ::settings(int narg, char **arg) { +void PairSPHLJ::settings(int narg, char **/*arg*/) { if (narg != 0) error->all(FLERR, "Illegal number of setting arguments for pair_style sph/lj"); @@ -261,8 +261,8 @@ double PairSPHLJ::init_one(int i, int j) { /* ---------------------------------------------------------------------- */ -double PairSPHLJ::single(int i, int j, int itype, int jtype, - double rsq, double factor_coul, double factor_lj, double &fforce) { +double PairSPHLJ::single(int /*i*/, int /*j*/, int /*itype*/, int /*jtype*/, + double /*rsq*/, double /*factor_coul*/, double /*factor_lj*/, double &fforce) { fforce = 0.0; return 0.0; diff --git a/src/USER-SPH/pair_sph_rhosum.cpp b/src/USER-SPH/pair_sph_rhosum.cpp index 605187d3a7..7a3c78efd0 100644 --- a/src/USER-SPH/pair_sph_rhosum.cpp +++ b/src/USER-SPH/pair_sph_rhosum.cpp @@ -278,8 +278,8 @@ double PairSPHRhoSum::init_one(int i, int j) { /* ---------------------------------------------------------------------- */ -double PairSPHRhoSum::single(int i, int j, int itype, int jtype, double rsq, - double factor_coul, double factor_lj, double &fforce) { +double PairSPHRhoSum::single(int /*i*/, int /*j*/, int /*itype*/, int /*jtype*/, double /*rsq*/, + double /*factor_coul*/, double /*factor_lj*/, double &fforce) { fforce = 0.0; return 0.0; @@ -288,7 +288,7 @@ double PairSPHRhoSum::single(int i, int j, int itype, int jtype, double rsq, /* ---------------------------------------------------------------------- */ int PairSPHRhoSum::pack_forward_comm(int n, int *list, double *buf, - int pbc_flag, int *pbc) { + int /*pbc_flag*/, int * /*pbc*/) { int i, j, m; double *rho = atom->rho; diff --git a/src/USER-SPH/pair_sph_taitwater.cpp b/src/USER-SPH/pair_sph_taitwater.cpp index 00500b940d..42b318f2c9 100644 --- a/src/USER-SPH/pair_sph_taitwater.cpp +++ b/src/USER-SPH/pair_sph_taitwater.cpp @@ -225,7 +225,7 @@ void PairSPHTaitwater::allocate() { global settings ------------------------------------------------------------------------- */ -void PairSPHTaitwater::settings(int narg, char **arg) { +void PairSPHTaitwater::settings(int narg, char **/*arg*/) { if (narg != 0) error->all(FLERR, "Illegal number of setting arguments for pair_style sph/taitwater"); @@ -293,8 +293,8 @@ double PairSPHTaitwater::init_one(int i, int j) { /* ---------------------------------------------------------------------- */ -double PairSPHTaitwater::single(int i, int j, int itype, int jtype, - double rsq, double factor_coul, double factor_lj, double &fforce) { +double PairSPHTaitwater::single(int /*i*/, int /*j*/, int /*itype*/, int /*jtype*/, + double /*rsq*/, double /*factor_coul*/, double /*factor_lj*/, double &fforce) { fforce = 0.0; return 0.0; diff --git a/src/USER-SPH/pair_sph_taitwater_morris.cpp b/src/USER-SPH/pair_sph_taitwater_morris.cpp index 80607cb333..8012895af8 100644 --- a/src/USER-SPH/pair_sph_taitwater_morris.cpp +++ b/src/USER-SPH/pair_sph_taitwater_morris.cpp @@ -225,7 +225,7 @@ void PairSPHTaitwaterMorris::allocate() { global settings ------------------------------------------------------------------------- */ -void PairSPHTaitwaterMorris::settings(int narg, char **arg) { +void PairSPHTaitwaterMorris::settings(int narg, char **/*arg*/) { if (narg != 0) error->all(FLERR, "Illegal number of setting arguments for pair_style sph/taitwater/morris"); @@ -289,8 +289,8 @@ double PairSPHTaitwaterMorris::init_one(int i, int j) { /* ---------------------------------------------------------------------- */ -double PairSPHTaitwaterMorris::single(int i, int j, int itype, int jtype, - double rsq, double factor_coul, double factor_lj, double &fforce) { +double PairSPHTaitwaterMorris::single(int /*i*/, int /*j*/, int /*itype*/, int /*jtype*/, + double /*rsq*/, double /*factor_coul*/, double /*factor_lj*/, double &fforce) { fforce = 0.0; return 0.0; diff --git a/src/USER-UEF/fix_nh_uef.cpp b/src/USER-UEF/fix_nh_uef.cpp index cd0b2ba268..bffcd7849f 100644 --- a/src/USER-UEF/fix_nh_uef.cpp +++ b/src/USER-UEF/fix_nh_uef.cpp @@ -348,7 +348,7 @@ void FixNHUef::final_integrate() * at outer level: call this->final_integrate() * at other levels: rotate -> 2nd verlet step -> rotate back * ---------------------------------------------------------------------- */ -void FixNHUef::final_integrate_respa(int ilevel, int iloop) +void FixNHUef::final_integrate_respa(int ilevel, int /*iloop*/) { // set timesteps by level dtf = 0.5 * step_respa[ilevel] * force->ftm2v; @@ -536,10 +536,26 @@ void FixNHUef::pre_exchange() rotate_x(rot); rotate_f(rot); - // put all atoms in the new box - double **x = atom->x; + // this is a generalization of what is done in domain->image_flip(...) + int ri[3][3]; + uefbox->get_inverse_cob(ri); imageint *image = atom->image; int nlocal = atom->nlocal; + for (int i=0; i> IMGBITS & IMGMASK) - IMGMAX; + iold[2] = (image[i] >> IMG2BITS) - IMGMAX; + inew[0] = ri[0][0]*iold[0] + ri[0][1]*iold[1] + ri[0][2]*iold[2]; + inew[1] = ri[1][0]*iold[0] + ri[1][1]*iold[1] + ri[1][2]*iold[2]; + inew[2] = ri[2][0]*iold[0] + ri[2][1]*iold[1] + ri[2][2]*iold[2]; + image[i] = ((imageint) (inew[0] + IMGMAX) & IMGMASK) | + (((imageint) (inew[1] + IMGMAX) & IMGMASK) << IMGBITS) | + (((imageint) (inew[2] + IMGMAX) & IMGMASK) << IMG2BITS); + } + + // put all atoms in the new box + double **x = atom->x; for (int i=0; iremap(x[i],image[i]); // move atoms to the right processors diff --git a/src/USER-UEF/uef_utils.cpp b/src/USER-UEF/uef_utils.cpp index a5498d605f..a2e6cb291e 100644 --- a/src/USER-UEF/uef_utils.cpp +++ b/src/USER-UEF/uef_utils.cpp @@ -30,47 +30,54 @@ namespace LAMMPS_NS { UEFBox::UEFBox() { + // initial box (also an inverse eigenvector matrix of automorphisms) + double x = 0.327985277605681; double y = 0.591009048506103; double z = 0.736976229099578; l0[0][0]= z; l0[0][1]= y; l0[0][2]= x; l0[1][0]=-x; l0[1][1]= z; l0[1][2]=-y; l0[2][0]=-y; l0[2][1]= x; l0[2][2]= z; + // spectra of the two automorpisms (log of eigenvalues) + w1[0]=-1.177725211523360; w1[1]=-0.441448620566067; w1[2]= 1.619173832089425; w2[0]= w1[1]; w2[1]= w1[2]; w2[2]= w1[0]; + // initialize theta // strain = w1 * theta1 + w2 * theta2 + theta[0]=theta[1]=0; - //set up the initial box l and change of basis matrix r + for (int k=0;k<3;k++) - for (int j=0;j<3;j++) - { + for (int j=0;j<3;j++) { l[k][j] = l0[k][j]; r[j][k]=(j==k); + ri[j][k]=(j==k); } // get the initial rotation and upper triangular matrix + rotation_matrix(rot, lrot ,l); // this is just a way to calculate the automorphisms // themselves, which play a minor role in the calculations // it's overkill, but only called once + double t1[3][3]; double t1i[3][3]; double t2[3][3]; double t2i[3][3]; double l0t[3][3]; for (int k=0; k<3; ++k) - for (int j=0; j<3; ++j) - { + for (int j=0; j<3; ++j) { t1[k][j] = exp(w1[k])*l0[k][j]; t1i[k][j] = exp(-w1[k])*l0[k][j]; t2[k][j] = exp(w2[k])*l0[k][j]; @@ -82,8 +89,7 @@ UEFBox::UEFBox() mul_m2(l0t,t2); mul_m2(l0t,t2i); for (int k=0; k<3; ++k) - for (int j=0; j<3; ++j) - { + for (int j=0; j<3; ++j) { a1[k][j] = round(t1[k][j]); a1i[k][j] = round(t1i[k][j]); a2[k][j] = round(t2[k][j]); @@ -92,6 +98,7 @@ UEFBox::UEFBox() // winv used to transform between // strain increments and theta increments + winv[0][0] = w2[1]; winv[0][1] = -w2[0]; winv[1][0] = -w1[1]; @@ -102,7 +109,9 @@ UEFBox::UEFBox() winv[k][j] /= d; } -// get volume-correct r basis in: basis*cbrt(vol) = q*r +/* ---------------------------------------------------------------------- + get volume-correct r basis in: basis*cbrt(vol) = q*r +------------------------------------------------------------------------- */ void UEFBox::get_box(double x[3][3], double v) { v = cbrtf(v); @@ -111,7 +120,9 @@ void UEFBox::get_box(double x[3][3], double v) x[k][j] = lrot[k][j]*v; } -// get rotation matrix q in: basis = q*r +/* ---------------------------------------------------------------------- + get rotation matrix q in: basis = q*r +------------------------------------------------------------------------- */ void UEFBox::get_rot(double x[3][3]) { for (int k=0;k<3;k++) @@ -119,20 +130,32 @@ void UEFBox::get_rot(double x[3][3]) x[k][j]=rot[k][j]; } -// diagonal, incompressible deformation +/* ---------------------------------------------------------------------- + get inverse change of basis matrix +------------------------------------------------------------------------- */ +void UEFBox::get_inverse_cob(int x[3][3]) +{ + for (int k=0;k<3;k++) + for (int j=0;j<3;j++) + x[k][j]=ri[k][j]; +} + +/* ---------------------------------------------------------------------- + apply diagonal, incompressible deformation +------------------------------------------------------------------------- */ void UEFBox::step_deform(const double ex, const double ey) { // increment theta values used in the reduction + theta[0] +=winv[0][0]*ex + winv[0][1]*ey; theta[1] +=winv[1][0]*ex + winv[1][1]*ey; - // deformation of the box. reduce() needs to - // be called regularly or calculation will become - // unstable + // deformation of the box. reduce() needs to be called regularly or + // calculation will become unstable + double eps[3]; eps[0]=ex; eps[1] = ey; eps[2] = -ex-ey; - for (int k=0;k<3;k++) - { + for (int k=0;k<3;k++) { eps[k] = exp(eps[k]); l[k][0] = eps[k]*l[k][0]; l[k][1] = eps[k]*l[k][1]; @@ -140,68 +163,84 @@ void UEFBox::step_deform(const double ex, const double ey) } rotation_matrix(rot,lrot, l); } -// reuduce the current basis + +/* ---------------------------------------------------------------------- + reduce the current basis +------------------------------------------------------------------------- */ bool UEFBox::reduce() { - // determine how many times to apply the automorphisms - // and find new theta values + // determine how many times to apply the automorphisms and find new theta + // values + int f1 = round(theta[0]); int f2 = round(theta[1]); theta[0] -= f1; theta[1] -= f2; - // store old change or basis matrix to determine if it - // changes + // store old change or basis matrix to determine if it changes + int r0[3][3]; for (int k=0;k<3;k++) for (int j=0;j<3;j++) r0[k][j]=r[k][j]; - // this modifies the old change basis matrix to - // handle the case where the automorphism transforms - // the box but the reduced basis doesn't change + // this modifies the old change basis matrix to handle the case where the + // automorphism transforms the box but the reduced basis doesn't change // (r0 should still equal r at the end) + if (f1 > 0) for (int k=0;k 0) for (int k=0;k (-q)*m = (-r) will hold row-wise + if (r[0][0] < 0){ neg_row(q,0); neg_row(r,0); } if (r[1][1] < 0){ neg_row(q,1); neg_row(r,1); } if (r[2][2] < 0){ neg_row(q,2); neg_row(r,2); } } - - -//sort columns in order of increasing length -void col_sort(double b[3][3],int r[3][3]) +/* ---------------------------------------------------------------------- + sort columns of b in order of increasing length + mimic column operations on ri and r +------------------------------------------------------------------------- */ +void col_sort(double b[3][3],int r[3][3],int ri[3][3]) { - if (col_prod(b,0,0)>col_prod(b,1,1)) - { + if (col_prod(b,0,0)>col_prod(b,1,1)) { col_swap(b,0,1); col_swap(r,0,1); + col_swap(ri,0,1); } - if (col_prod(b,0,0)>col_prod(b,2,2)) - { + if (col_prod(b,0,0)>col_prod(b,2,2)) { col_swap(b,0,2); col_swap(r,0,2); + col_swap(ri,0,2); } - if (col_prod(b,1,1)>col_prod(b,2,2)) - { + if (col_prod(b,1,1)>col_prod(b,2,2)) { col_swap(b,1,2); col_swap(r,1,2); + col_swap(ri,1,2); } } - -// 1-2 reduction (Graham-Schmidt) -void red12(double b[3][3],int r[3][3]) +/* ---------------------------------------------------------------------- + 1-2 reduction (Graham-Schmidt) +------------------------------------------------------------------------- */ +void red12(double b[3][3],int r[3][3],int ri[3][3]) { int y = round(col_prod(b,0,1)/col_prod(b,0,0)); b[0][1] -= y*b[0][0]; @@ -276,16 +318,23 @@ void red12(double b[3][3],int r[3][3]) r[0][1] -= y*r[0][0]; r[1][1] -= y*r[1][0]; r[2][1] -= y*r[2][0]; - if (col_prod(b,1,1) < col_prod(b,0,0)) - { + + ri[0][0] += y*ri[0][1]; + ri[1][0] += y*ri[1][1]; + ri[2][0] += y*ri[2][1]; + + if (col_prod(b,1,1) < col_prod(b,0,0)) { col_swap(b,0,1); col_swap(r,0,1); - red12(b,r); + col_swap(ri,0,1); + red12(b,r,ri); } } -// The Semaev condition for a 3-reduced basis -void red3(double b[3][3], int r[3][3]) +/* ---------------------------------------------------------------------- + Apply the Semaev condition for a 3-reduced basis +------------------------------------------------------------------------- */ +void red3(double b[3][3], int r[3][3], int ri[3][3]) { double b11 = col_prod(b,0,0); double b22 = col_prod(b,1,1); @@ -304,63 +353,97 @@ void red3(double b[3][3], int r[3][3]) x1v[0] = floor(y1); x1v[1] = x1v[0]+1; x2v[0] = floor(y2); x2v[1] = x2v[0]+1; for (int k=0;k<2;k++) - for (int j=0;j<2;j++) - { + for (int j=0;j<2;j++) { double a[3]; a[0] = b[0][2] + x1v[k]*b[0][0] + x2v[j]*b[0][1]; a[1] = b[1][2] + x1v[k]*b[1][0] + x2v[j]*b[1][1]; a[2] = b[2][2] + x1v[k]*b[2][0] + x2v[j]*b[2][1]; double val=a[0]*a[0]+a[1]*a[1]+a[2]*a[2]; - if (val T col_prod(T x[3][3], int c1, int c2) { @@ -56,8 +57,7 @@ T col_prod(T x[3][3], int c1, int c2) template void col_swap(T x[3][3], int c1, int c2) { - for (int k=0;k<3;k++) - { + for (int k=0;k<3;k++) { T t = x[k][c2]; x[k][c2]=x[k][c1]; x[k][c1]=t; @@ -101,9 +101,21 @@ bool mat_same(T x1[3][3], T x2[3][3]) } template -void mul_m1(T m1[3][3], const T m2[3][3]) +void transpose(T m[3][3]) { T t[3][3]; + for (int k=0;k<3;k++) + for (int j=k+1;j<3;j++) { + T x = m[k][j]; + m[k][j] = m[j][k]; + m[j][k] = x; + } +} + +template +void mul_m1(T1 m1[3][3], const T2 m2[3][3]) +{ + T1 t[3][3]; for (int k=0;k<3;k++) for (int j=0;j<3;j++) t[k][j]=m1[k][j]; @@ -113,10 +125,10 @@ void mul_m1(T m1[3][3], const T m2[3][3]) m1[k][j] = t[k][0]*m2[0][j] + t[k][1]*m2[1][j] + t[k][2]*m2[2][j]; } -template -void mul_m2(const T m1[3][3], T m2[3][3]) +template +void mul_m2(const T1 m1[3][3], T2 m2[3][3]) { - T t[3][3]; + T2 t[3][3]; for (int k=0;k<3;k++) for (int j=0;j<3;j++) t[k][j]=m2[k][j]; diff --git a/src/accelerator_kokkos.h b/src/accelerator_kokkos.h index 8bbb6c4788..e64bde24be 100644 --- a/src/accelerator_kokkos.h +++ b/src/accelerator_kokkos.h @@ -66,8 +66,8 @@ class AtomKokkos : public Atom { tagint **k_special; AtomKokkos(class LAMMPS *lmp) : Atom(lmp) {} ~AtomKokkos() {} - void sync(const ExecutionSpace space, unsigned int mask) {} - void modified(const ExecutionSpace space, unsigned int mask) {} + void sync(const ExecutionSpace /*space*/, unsigned int /*mask*/) {} + void modified(const ExecutionSpace /*space*/, unsigned int /*mask*/) {} }; class CommKokkos : public CommBrick { diff --git a/src/accelerator_omp.h b/src/accelerator_omp.h index 6caa0826fe..25910ae800 100644 --- a/src/accelerator_omp.h +++ b/src/accelerator_omp.h @@ -17,47 +17,6 @@ // true interface to USER-OMP -// this part is used inside the neighbor.h header file to -// add functions to the Neighbor class definition - -#ifdef LMP_INSIDE_NEIGHBOR_H - - void half_nsq_no_newton_omp(class NeighList *); - void half_nsq_no_newton_ghost_omp(class NeighList *); - void half_nsq_newton_omp(class NeighList *); - - void half_bin_no_newton_omp(class NeighList *); - void half_bin_no_newton_ghost_omp(class NeighList *); - void half_bin_newton_omp(class NeighList *); - void half_bin_newton_tri_omp(class NeighList *); - - void half_multi_no_newton_omp(class NeighList *); - void half_multi_newton_omp(class NeighList *); - void half_multi_newton_tri_omp(class NeighList *); - - void full_nsq_omp(class NeighList *); - void full_nsq_ghost_omp(class NeighList *); - void full_bin_omp(class NeighList *); - void full_bin_ghost_omp(class NeighList *); - void full_multi_omp(class NeighList *); - - void half_from_full_no_newton_omp(class NeighList *); - void half_from_full_newton_omp(class NeighList *); - - void granular_nsq_no_newton_omp(class NeighList *); - void granular_nsq_newton_omp(class NeighList *); - void granular_bin_no_newton_omp(class NeighList *); - void granular_bin_newton_omp(class NeighList *); - void granular_bin_newton_tri_omp(class NeighList *); - - void respa_nsq_no_newton_omp(class NeighList *); - void respa_nsq_newton_omp(class NeighList *); - void respa_bin_no_newton_omp(class NeighList *); - void respa_bin_newton_omp(class NeighList *); - void respa_bin_newton_tri_omp(class NeighList *); - -#else /* !LMP_INSIDE_NEIGHBOR_H */ - // provide a DomainOMP class with some overrides for Domain #include "domain.h" @@ -68,8 +27,8 @@ namespace LAMMPS_NS { class DomainOMP : public Domain { public: - DomainOMP(class LAMMPS *lmp) : Domain(lmp) {}; - virtual ~DomainOMP() {}; + DomainOMP(class LAMMPS *lmp) : Domain(lmp) {} + virtual ~DomainOMP() {} // multi-threaded versions virtual void pbc(); @@ -81,48 +40,5 @@ class DomainOMP : public Domain { } #endif /* LMP_DOMAIN_OMP_H */ -#endif /* !LMP_INSIDE_NEIGHBOR_H */ - -#else /* !LMP_USER_OMP */ - -// dummy interface to USER-OMP -// needed for compiling when USER-OMP is not installed - -#ifdef LMP_INSIDE_NEIGHBOR_H - - void half_nsq_no_newton_omp(class NeighList *) {} - void half_nsq_no_newton_ghost_omp(class NeighList *) {} - void half_nsq_newton_omp(class NeighList *) {} - - void half_bin_no_newton_omp(class NeighList *) {} - void half_bin_no_newton_ghost_omp(class NeighList *) {} - void half_bin_newton_omp(class NeighList *) {} - void half_bin_newton_tri_omp(class NeighList *) {} - - void half_multi_no_newton_omp(class NeighList *) {} - void half_multi_newton_omp(class NeighList *) {} - void half_multi_newton_tri_omp(class NeighList *) {} - - void full_nsq_omp(class NeighList *) {} - void full_nsq_ghost_omp(class NeighList *) {} - void full_bin_omp(class NeighList *) {} - void full_bin_ghost_omp(class NeighList *) {} - void full_multi_omp(class NeighList *) {} - - void half_from_full_no_newton_omp(class NeighList *) {} - void half_from_full_newton_omp(class NeighList *) {} - - void granular_nsq_no_newton_omp(class NeighList *) {} - void granular_nsq_newton_omp(class NeighList *) {} - void granular_bin_no_newton_omp(class NeighList *) {} - void granular_bin_newton_omp(class NeighList *) {} - void granular_bin_newton_tri_omp(class NeighList *) {} - - void respa_nsq_no_newton_omp(class NeighList *) {} - void respa_nsq_newton_omp(class NeighList *) {} - void respa_bin_no_newton_omp(class NeighList *) {} - void respa_bin_newton_omp(class NeighList *) {} - void respa_bin_newton_tri_omp(class NeighList *) {} -#endif #endif /* !LMP_USER_OMP */ diff --git a/src/angle_zero.cpp b/src/angle_zero.cpp index e5191c4fb2..d7b7c9cdb5 100644 --- a/src/angle_zero.cpp +++ b/src/angle_zero.cpp @@ -148,7 +148,7 @@ void AngleZero::write_data(FILE *fp) /* ---------------------------------------------------------------------- */ -double AngleZero::single(int type, int i1, int i2, int i3) +double AngleZero::single(int /*type*/, int /*i1*/, int /*i2*/, int /*i3*/) { return 0.0; } diff --git a/src/atom.cpp b/src/atom.cpp index 56bfd04de7..95f5406d95 100644 --- a/src/atom.cpp +++ b/src/atom.cpp @@ -96,6 +96,10 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp) rho = drho = e = de = cv = NULL; vest = NULL; + // SPIN package + + sp = fm = NULL; + // USER-DPD uCond = uMech = uChem = uCG = uCGnew = NULL; @@ -166,6 +170,10 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp) radius_flag = rmass_flag = 0; ellipsoid_flag = line_flag = tri_flag = body_flag = 0; + // magnetic flags + + sp_flag = 0; + vfrac_flag = 0; spin_flag = eradius_flag = ervel_flag = erforce_flag = ervelforce_flag = 0; cs_flag = csforce_flag = vforce_flag = etag_flag = 0; @@ -267,6 +275,9 @@ Atom::~Atom() memory->destroy(tri); memory->destroy(body); + memory->destroy(sp); + memory->destroy(fm); + memory->destroy(vfrac); memory->destroy(s0); memory->destroy(x0); @@ -419,6 +430,10 @@ void Atom::create_avec(const char *style, int narg, char **arg, int trysuffix) radius_flag = rmass_flag = 0; ellipsoid_flag = line_flag = tri_flag = body_flag = 0; + // magnetic flags + + sp_flag = 0; + vfrac_flag = 0; spin_flag = eradius_flag = ervel_flag = erforce_flag = ervelforce_flag = 0; cs_flag = csforce_flag = vforce_flag = etag_flag = 0; @@ -1501,7 +1516,7 @@ void Atom::set_mass(const char *file, int line, int itype, double value) called from reading of input script ------------------------------------------------------------------------- */ -void Atom::set_mass(const char *file, int line, int narg, char **arg) +void Atom::set_mass(const char *file, int line, int /*narg*/, char **arg) { if (mass == NULL) error->all(file,line,"Cannot set mass for this atom style"); @@ -1518,7 +1533,8 @@ void Atom::set_mass(const char *file, int line, int narg, char **arg) } /* ---------------------------------------------------------------------- - set all masses as read in from restart file + set all masses + called from reading of restart file, also from ServerMD ------------------------------------------------------------------------- */ void Atom::set_mass(double *values) diff --git a/src/atom.h b/src/atom.h index abfa6e5eb5..7e003dff5e 100644 --- a/src/atom.h +++ b/src/atom.h @@ -61,6 +61,11 @@ class Atom : protected Pointers { double *radius,*rmass; int *ellipsoid,*line,*tri,*body; + // SPIN package + + double **sp; + double **fm; + // PERI package double *vfrac,*s0; @@ -146,6 +151,10 @@ class Atom : protected Pointers { int rho_flag,e_flag,cv_flag,vest_flag; int dpd_flag,edpd_flag,tdpd_flag; + //USER-SPIN package + + int sp_flag; + // USER-SMD package int smd_flag; diff --git a/src/atom_vec.cpp b/src/atom_vec.cpp index b04bfba34c..a7ca6fcb19 100644 --- a/src/atom_vec.cpp +++ b/src/atom_vec.cpp @@ -66,7 +66,7 @@ void AtomVec::store_args(int narg, char **arg) no additional args by default ------------------------------------------------------------------------- */ -void AtomVec::process_args(int narg, char **arg) +void AtomVec::process_args(int narg, char ** /*arg*/) { if (narg) error->all(FLERR,"Invalid atom_style command"); } diff --git a/src/atom_vec_body.cpp b/src/atom_vec_body.cpp index 4d3b5643ae..5a277627ee 100644 --- a/src/atom_vec_body.cpp +++ b/src/atom_vec_body.cpp @@ -82,6 +82,9 @@ AtomVecBody::~AtomVecBody() void AtomVecBody::process_args(int narg, char **arg) { + // suppress unused parameter warning dependent on style_body.h + (void)(arg); + if (narg < 1) error->all(FLERR,"Invalid atom_style body command"); if (0) bptr = NULL; diff --git a/src/balance.cpp b/src/balance.cpp index 86deb55b47..2a953caf47 100644 --- a/src/balance.cpp +++ b/src/balance.cpp @@ -350,13 +350,13 @@ void Balance::command(int narg, char **arg) domain->set_local_box(); // move particles to new processors via irregular() + // set disable = 0, so weights migrate with atoms for imbfinal calculation if (domain->triclinic) domain->x2lamda(atom->nlocal); Irregular *irregular = new Irregular(lmp); if (wtflag) fixstore->disable = 0; if (style == BISECTION) irregular->migrate_atoms(1,1,rcb->sendproc); else irregular->migrate_atoms(1); - if (wtflag) fixstore->disable = 1; delete irregular; if (domain->triclinic) domain->lamda2x(atom->nlocal); @@ -377,9 +377,11 @@ void Balance::command(int narg, char **arg) } // imbfinal = final imbalance + // set disable = 1, so weights no longer migrate with atoms double maxfinal; double imbfinal = imbalance_factor(maxfinal); + if (wtflag) fixstore->disable = 1; // stats output @@ -540,6 +542,8 @@ void Balance::weight_storage(char *prefix) fixstore = (FixStore *) modify->fix[modify->nfix-1]; } else fixstore = (FixStore *) modify->fix[ifix]; + // do not carry weights with atoms during normal atom migration + fixstore->disable = 1; if (prefix) delete [] fixargs[0]; @@ -643,6 +647,21 @@ int *Balance::bisection(int sortflag) double *shrinklo = &shrinkall[0]; double *shrinkhi = &shrinkall[3]; + // if shrink size in any dim is zero, use box size in that dim + + if (shrinklo[0] == shrinkhi[0]) { + shrinklo[0] = boxlo[0]; + shrinkhi[0] = boxhi[0]; + } + if (shrinklo[1] == shrinkhi[1]) { + shrinklo[1] = boxlo[1]; + shrinkhi[1] = boxhi[1]; + } + if (shrinklo[2] == shrinkhi[2]) { + shrinklo[2] = boxlo[2]; + shrinkhi[2] = boxhi[2]; + } + // invoke RCB // then invert() to create list of proc assignments for my atoms // NOTE: (3/2017) can remove undocumented "old" option at some point diff --git a/src/body.cpp b/src/body.cpp index 42f4ccbdd3..78e2f5d71b 100644 --- a/src/body.cpp +++ b/src/body.cpp @@ -21,7 +21,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -Body::Body(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) +Body::Body(LAMMPS *lmp, int /*narg*/, char **arg) : Pointers(lmp) { int n = strlen(arg[0]) + 1; style = new char[n]; diff --git a/src/bond_zero.cpp b/src/bond_zero.cpp index 9fd9d4a580..9fcf300b21 100644 --- a/src/bond_zero.cpp +++ b/src/bond_zero.cpp @@ -149,8 +149,8 @@ void BondZero::write_data(FILE *fp) /* ---------------------------------------------------------------------- */ -double BondZero::single(int type, double rsq, int i, int j, - double &fforce) +double BondZero::single(int /*type*/, double /*rsq*/, int /*i*/, int /*j*/, + double & /*fforce*/) { return 0.0; } diff --git a/src/comm.h b/src/comm.h index 298f435c3d..2579f9b283 100644 --- a/src/comm.h +++ b/src/comm.h @@ -112,6 +112,9 @@ class Comm : protected Pointers { int read_lines_from_file(FILE *, int, int, char *); int read_lines_from_file_universe(FILE *, int, int, char *); + // extract data useful to other classes + virtual void *extract(const char *, int &) {return NULL;} + protected: int bordergroup; // only communicate this group in borders diff --git a/src/comm_brick.cpp b/src/comm_brick.cpp index 3aa6d7748c..4015240af8 100644 --- a/src/comm_brick.cpp +++ b/src/comm_brick.cpp @@ -55,7 +55,8 @@ CommBrick::CommBrick(LAMMPS *lmp) : size_reverse_send(NULL), size_reverse_recv(NULL), slablo(NULL), slabhi(NULL), multilo(NULL), multihi(NULL), cutghostmulti(NULL), pbc_flag(NULL), pbc(NULL), firstrecv(NULL), - sendlist(NULL), maxsendlist(NULL), buf_send(NULL), buf_recv(NULL) + sendlist(NULL), localsendlist(NULL), maxsendlist(NULL), + buf_send(NULL), buf_recv(NULL) { style = 0; layout = Comm::LAYOUT_UNIFORM; @@ -74,6 +75,7 @@ CommBrick::~CommBrick() } if (sendlist) for (int i = 0; i < maxswap; i++) memory->destroy(sendlist[i]); + if (localsendlist) memory->destroy(localsendlist); memory->sfree(sendlist); memory->destroy(maxsendlist); @@ -88,7 +90,7 @@ CommBrick::~CommBrick() // The call to Comm::copy_arrays() then converts the shallow copy // into a deep copy of the class with the new layout. -CommBrick::CommBrick(LAMMPS *lmp, Comm *oldcomm) : Comm(*oldcomm) +CommBrick::CommBrick(LAMMPS * /*lmp*/, Comm *oldcomm) : Comm(*oldcomm) { if (oldcomm->layout == Comm::LAYOUT_TILED) error->all(FLERR,"Cannot change to comm_style brick from tiled layout"); @@ -457,7 +459,7 @@ int CommBrick::updown(int dim, int dir, int loc, other per-atom attributes may also be sent via pack/unpack routines ------------------------------------------------------------------------- */ -void CommBrick::forward_comm(int dummy) +void CommBrick::forward_comm(int /*dummy*/) { int n; MPI_Request request; @@ -1469,6 +1471,33 @@ void CommBrick::free_multi() multilo = multihi = NULL; } +/* ---------------------------------------------------------------------- + extract data potentially useful to other classes +------------------------------------------------------------------------- */ + +void *CommBrick::extract(const char *str, int &dim) +{ + if (strcmp(str,"localsendlist") == 0) { + int i, iswap, isend; + if (!localsendlist) + memory->create(localsendlist,atom->nlocal,"comm:localsendlist"); + else + memory->grow(localsendlist,atom->nlocal,"comm:localsendlist"); + + for (i = 0; i < atom->nlocal; i++) + localsendlist[i] = 0; + + for (iswap = 0; iswap < nswap; iswap++) + for (isend = 0; isend < sendnum[iswap]; isend++) + if (sendlist[iswap][isend] < atom->nlocal) + localsendlist[sendlist[iswap][isend]] = 1; + + return (void *) localsendlist; + } + + return NULL; +} + /* ---------------------------------------------------------------------- return # of bytes of allocated memory ------------------------------------------------------------------------- */ diff --git a/src/comm_brick.h b/src/comm_brick.h index 461ee84b40..b3a3a7e094 100644 --- a/src/comm_brick.h +++ b/src/comm_brick.h @@ -46,6 +46,7 @@ class CommBrick : public Comm { void forward_comm_array(int, double **); // forward comm of array int exchange_variable(int, double *, double *&); // exchange on neigh stencil + void *extract(const char *,int &); virtual bigint memory_usage(); protected: @@ -67,6 +68,7 @@ class CommBrick : public Comm { int *firstrecv; // where to put 1st recv atom in each swap int **sendlist; // list of atoms to send in each swap + int *localsendlist; // indexed list of local sendlist atoms int *maxsendlist; // max size of send list for each swap double *buf_send; // send buffer for all comm diff --git a/src/comm_tiled.cpp b/src/comm_tiled.cpp index 584be94bf3..d7d2e4725d 100644 --- a/src/comm_tiled.cpp +++ b/src/comm_tiled.cpp @@ -55,7 +55,7 @@ CommTiled::CommTiled(LAMMPS *lmp) : Comm(lmp) // The call to Comm::copy_arrays() then converts the shallow copy // into a deep copy of the class with the new layout. -CommTiled::CommTiled(LAMMPS *lmp, Comm *oldcomm) : Comm(*oldcomm) +CommTiled::CommTiled(LAMMPS * /*lmp*/, Comm *oldcomm) : Comm(*oldcomm) { style = 1; layout = oldcomm->layout; @@ -438,7 +438,7 @@ void CommTiled::setup() other per-atom attributes may also be sent via pack/unpack routines ------------------------------------------------------------------------- */ -void CommTiled::forward_comm(int dummy) +void CommTiled::forward_comm(int /*dummy*/) { int i,irecv,n,nsend,nrecv; AtomVec *avec = atom->avec; @@ -1164,7 +1164,7 @@ void CommTiled::reverse_comm_fix(Fix *fix, int size) NOTE: how to setup one big buf recv with correct offsets ?? ------------------------------------------------------------------------- */ -void CommTiled::reverse_comm_fix_variable(Fix *fix) +void CommTiled::reverse_comm_fix_variable(Fix * /*fix*/) { error->all(FLERR,"Reverse comm fix variable not yet supported by CommTiled"); } @@ -1428,7 +1428,7 @@ void CommTiled::forward_comm_array(int nsize, double **array) NOTE: this method is currently not used ------------------------------------------------------------------------- */ -int CommTiled::exchange_variable(int n, double *inbuf, double *&outbuf) +int CommTiled::exchange_variable(int n, double * /*inbuf*/, double *& /*outbuf*/) { int nrecv = n; return nrecv; @@ -1509,7 +1509,7 @@ void CommTiled::box_drop_brick(int idim, double *lo, double *hi, int &indexme) no need to split lo/hi box as recurse b/c OK if box extends outside RCB box ------------------------------------------------------------------------- */ -void CommTiled::box_drop_tiled(int idim, double *lo, double *hi, int &indexme) +void CommTiled::box_drop_tiled(int /*idim*/, double *lo, double *hi, int &indexme) { box_drop_tiled_recurse(lo,hi,0,nprocs-1,indexme); } @@ -1601,7 +1601,7 @@ void CommTiled::box_other_brick(int idim, int idir, return other box owned by proc as lo/hi corner pts ------------------------------------------------------------------------- */ -void CommTiled::box_other_tiled(int idim, int idir, +void CommTiled::box_other_tiled(int /*idim*/, int /*idir*/, int proc, double *lo, double *hi) { double (*split)[2] = rcbinfo[proc].mysplit; diff --git a/src/compute_aggregate_atom.cpp b/src/compute_aggregate_atom.cpp index 56855fcc29..6c8c8e5d9a 100644 --- a/src/compute_aggregate_atom.cpp +++ b/src/compute_aggregate_atom.cpp @@ -98,7 +98,7 @@ void ComputeAggregateAtom::init() /* ---------------------------------------------------------------------- */ -void ComputeAggregateAtom::init_list(int id, NeighList *ptr) +void ComputeAggregateAtom::init_list(int /*id*/, NeighList *ptr) { list = ptr; } @@ -231,7 +231,7 @@ void ComputeAggregateAtom::compute_peratom() /* ---------------------------------------------------------------------- */ int ComputeAggregateAtom::pack_forward_comm(int n, int *list, double *buf, - int pbc_flag, int *pbc) + int /*pbc_flag*/, int * /*pbc*/) { int i,j,m; diff --git a/src/compute_angle_local.cpp b/src/compute_angle_local.cpp index 7137077158..95faad54ad 100644 --- a/src/compute_angle_local.cpp +++ b/src/compute_angle_local.cpp @@ -21,6 +21,8 @@ #include "domain.h" #include "force.h" #include "angle.h" +#include "input.h" +#include "variable.h" #include "math_const.h" #include "memory.h" #include "error.h" @@ -30,11 +32,13 @@ using namespace MathConst; #define DELTA 10000 +enum{THETA,ENG,VARIABLE}; + /* ---------------------------------------------------------------------- */ ComputeAngleLocal::ComputeAngleLocal(LAMMPS *lmp, int narg, char **arg) : Compute(lmp, narg, arg), - vlocal(NULL), alocal(NULL) + bstyle(NULL), vstr(NULL), vvar(NULL), tstr(NULL), vlocal(NULL), alocal(NULL) { if (narg < 4) error->all(FLERR,"Illegal compute angle/local command"); @@ -42,19 +46,82 @@ ComputeAngleLocal::ComputeAngleLocal(LAMMPS *lmp, int narg, char **arg) : error->all(FLERR,"Compute angle/local used when angles are not allowed"); local_flag = 1; + + // style args + nvalues = narg - 3; + bstyle = new int[nvalues]; + vstr = new char*[nvalues]; + vvar = new int[nvalues]; + + nvalues = 0; + tflag = 0; + nvar = 0; + + int iarg; + for (iarg = 3; iarg < narg; iarg++) { + if (strcmp(arg[iarg],"theta") == 0) { + bstyle[nvalues++] = THETA; + tflag = 1; + } else if (strcmp(arg[iarg],"eng") == 0) { + bstyle[nvalues++] = ENG; + } else if (strncmp(arg[iarg],"v_",2) == 0) { + bstyle[nvalues++] = VARIABLE; + int n = strlen(arg[iarg]); + vstr[nvar] = new char[n]; + strcpy(vstr[nvar],&arg[iarg][2]); + nvar++; + } else break; + } + + // optional args + + setflag = 0; + tstr = NULL; + + while (iarg < narg) { + if (strcmp(arg[iarg],"set") == 0) { + setflag = 1; + if (iarg+3 > narg) error->all(FLERR,"Illegal compute angle/local command"); + if (strcmp(arg[iarg+1],"theta") == 0) { + delete [] tstr; + int n = strlen(arg[iarg+2]) + 1; + tstr = new char[n]; + strcpy(tstr,arg[iarg+2]); + tflag = 1; + } else error->all(FLERR,"Illegal compute angle/local command"); + iarg += 3; + } else error->all(FLERR,"Illegal compute angle/local command"); + } + + // error check + + if (nvar) { + if (!setflag) + error->all(FLERR,"Compute angle/local variable requires a set variable"); + for (int i = 0; i < nvar; i++) { + vvar[i] = input->variable->find(vstr[i]); + if (vvar[i] < 0) + error->all(FLERR,"Variable name for copute angle/local does not exist"); + if (!input->variable->equalstyle(vvar[i])) + error->all(FLERR,"Variable for compute angle/local is invalid style"); + } + + if (tstr) { + tvar = input->variable->find(tstr); + if (tvar < 0) + error->all(FLERR,"Variable name for compute angle/local does not exist"); + if (!input->variable->internalstyle(tvar)) + error->all(FLERR,"Variable for compute angle/local is invalid style"); + } + } else if (setflag) + error->all(FLERR,"Compute angle/local set with no variable"); + + // initialize output + if (nvalues == 1) size_local_cols = 0; else size_local_cols = nvalues; - tflag = eflag = -1; - nvalues = 0; - - for (int iarg = 3; iarg < narg; iarg++) { - if (strcmp(arg[iarg],"theta") == 0) tflag = nvalues++; - else if (strcmp(arg[iarg],"eng") == 0) eflag = nvalues++; - else error->all(FLERR,"Invalid keyword in compute angle/local command"); - } - nmax = 0; vlocal = NULL; alocal = NULL; @@ -64,6 +131,13 @@ ComputeAngleLocal::ComputeAngleLocal(LAMMPS *lmp, int narg, char **arg) : ComputeAngleLocal::~ComputeAngleLocal() { + delete [] bstyle; + for (int i = 0; i < nvar; i++) delete [] vstr[i]; + delete [] vstr; + delete [] vvar; + + delete [] tstr; + memory->destroy(vlocal); memory->destroy(alocal); } @@ -75,6 +149,20 @@ void ComputeAngleLocal::init() if (force->angle == NULL) error->all(FLERR,"No angle style is defined for compute angle/local"); + if (nvar) { + for (int i = 0; i < nvar; i++) { + vvar[i] = input->variable->find(vstr[i]); + if (vvar[i] < 0) + error->all(FLERR,"Variable name for compute angle/local does not exist"); + } + + if (tstr) { + tvar = input->variable->find(tstr); + if (tvar < 0) + error->all(FLERR,"Variable name for compute angle/local does not exist"); + } + } + // do initial memory allocation so that memory_usage() is correct ncount = compute_angles(0); @@ -109,11 +197,11 @@ void ComputeAngleLocal::compute_local() int ComputeAngleLocal::compute_angles(int flag) { - int i,m,n,na,atom1,atom2,atom3,imol,iatom,atype; + int i,m,n,na,atom1,atom2,atom3,imol,iatom,atype,ivar; tagint tagprev; double delx1,dely1,delz1,delx2,dely2,delz2; - double rsq1,rsq2,r1,r2,c; - double *tbuf,*ebuf; + double rsq1,rsq2,r1,r2,c,theta; + double *ptr; double **x = atom->x; tagint *tag = atom->tag; @@ -131,17 +219,7 @@ int ComputeAngleLocal::compute_angles(int flag) int nlocal = atom->nlocal; int molecular = atom->molecular; - if (flag) { - if (nvalues == 1) { - if (tflag >= 0) tbuf = vlocal; - if (eflag >= 0) ebuf = vlocal; - } else { - if (tflag >= 0 && alocal) tbuf = &alocal[0][tflag]; - else tbuf = NULL; - if (eflag >= 0 && alocal) ebuf = &alocal[0][eflag]; - else ebuf = NULL; - } - } + // loop over all atoms and their angles Angle *angle = force->angle; @@ -175,39 +253,62 @@ int ComputeAngleLocal::compute_angles(int flag) if (atom3 < 0 || !(mask[atom3] & groupbit)) continue; if (atype == 0) continue; - if (flag) { - if (tflag >= 0) { - delx1 = x[atom1][0] - x[atom2][0]; - dely1 = x[atom1][1] - x[atom2][1]; - delz1 = x[atom1][2] - x[atom2][2]; - domain->minimum_image(delx1,dely1,delz1); + if (!flag) { + m++; + continue; + } - rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1; - r1 = sqrt(rsq1); + // theta needed by one or more outputs - delx2 = x[atom3][0] - x[atom2][0]; - dely2 = x[atom3][1] - x[atom2][1]; - delz2 = x[atom3][2] - x[atom2][2]; - domain->minimum_image(delx2,dely2,delz2); + if (tflag) { + delx1 = x[atom1][0] - x[atom2][0]; + dely1 = x[atom1][1] - x[atom2][1]; + delz1 = x[atom1][2] - x[atom2][2]; + domain->minimum_image(delx1,dely1,delz1); - rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2; - r2 = sqrt(rsq2); + rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1; + r1 = sqrt(rsq1); + + delx2 = x[atom3][0] - x[atom2][0]; + dely2 = x[atom3][1] - x[atom2][1]; + delz2 = x[atom3][2] - x[atom2][2]; + domain->minimum_image(delx2,dely2,delz2); - // c = cosine of angle + rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2; + r2 = sqrt(rsq2); - c = delx1*delx2 + dely1*dely2 + delz1*delz2; - c /= r1*r2; - if (c > 1.0) c = 1.0; - if (c < -1.0) c = -1.0; - tbuf[n] = 180.0*acos(c)/MY_PI; + // c = cosine of angle + // theta = angle in radians + + c = delx1*delx2 + dely1*dely2 + delz1*delz2; + c /= r1*r2; + if (c > 1.0) c = 1.0; + if (c < -1.0) c = -1.0; + theta = acos(c); + } + + if (nvalues == 1) ptr = &vlocal[m]; + else ptr = alocal[m]; + + if (nvar) { + ivar = 0; + if (tstr) input->variable->internal_set(tvar,theta); + } + + for (n = 0; n < nvalues; n++) { + switch (bstyle[n]) { + case THETA: + ptr[n] = 180.0*theta/MY_PI; + break; + case ENG: + if (atype > 0) ptr[n] = angle->single(atype,atom1,atom2,atom3); + else ptr[n] = 0.0; + break; + case VARIABLE: + ptr[n] = input->variable->compute_equal(vvar[ivar]); + ivar++; + break; } - - if (eflag >= 0) { - if (atype > 0) - ebuf[n] = angle->single(atype,atom1,atom2,atom3); - else ebuf[n] = 0.0; - } - n += nvalues; } m++; diff --git a/src/compute_angle_local.h b/src/compute_angle_local.h index 6f59d7f097..a95e23206d 100644 --- a/src/compute_angle_local.h +++ b/src/compute_angle_local.h @@ -33,8 +33,12 @@ class ComputeAngleLocal : public Compute { double memory_usage(); private: - int nvalues,tflag,eflag; - int ncount; + int nvalues,nvar,ncount,setflag,tflag; + + int tvar; + int *bstyle,*vvar; + char *tstr; + char **vstr; int nmax; double *vlocal; diff --git a/src/compute_bond_local.cpp b/src/compute_bond_local.cpp index 985e3ef075..6a179cf1b4 100644 --- a/src/compute_bond_local.cpp +++ b/src/compute_bond_local.cpp @@ -21,8 +21,10 @@ #include "domain.h" #include "force.h" #include "bond.h" -#include "math_extra.h" #include "comm.h" +#include "input.h" +#include "variable.h" +#include "math_extra.h" #include "memory.h" #include "error.h" @@ -31,13 +33,13 @@ using namespace LAMMPS_NS; #define DELTA 10000 #define EPSILON 1.0e-12 -enum{DIST,VELVIB,OMEGA,ENGTRANS,ENGVIB,ENGROT,ENGPOT,FORCE}; +enum{DIST,VELVIB,OMEGA,ENGTRANS,ENGVIB,ENGROT,ENGPOT,FORCE,VARIABLE}; /* ---------------------------------------------------------------------- */ ComputeBondLocal::ComputeBondLocal(LAMMPS *lmp, int narg, char **arg) : Compute(lmp, narg, arg), - bstyle(NULL), vlocal(NULL), alocal(NULL) + bstyle(NULL), vstr(NULL), vvar(NULL), dstr(NULL), vlocal(NULL), alocal(NULL) { if (narg < 4) error->all(FLERR,"Illegal compute bond/local command"); @@ -47,14 +49,18 @@ ComputeBondLocal::ComputeBondLocal(LAMMPS *lmp, int narg, char **arg) : local_flag = 1; comm_forward = 3; + // style args + nvalues = narg - 3; - if (nvalues == 1) size_local_cols = 0; - else size_local_cols = nvalues; - bstyle = new int[nvalues]; - + vstr = new char*[nvalues]; + vvar = new int[nvalues]; + nvalues = 0; - for (int iarg = 3; iarg < narg; iarg++) { + nvar = 0; + + int iarg; + for (iarg = 3; iarg < narg; iarg++) { if (strcmp(arg[iarg],"dist") == 0) bstyle[nvalues++] = DIST; else if (strcmp(arg[iarg],"engpot") == 0) bstyle[nvalues++] = ENGPOT; else if (strcmp(arg[iarg],"force") == 0) bstyle[nvalues++] = FORCE; @@ -63,9 +69,58 @@ ComputeBondLocal::ComputeBondLocal(LAMMPS *lmp, int narg, char **arg) : else if (strcmp(arg[iarg],"engtrans") == 0) bstyle[nvalues++] = ENGTRANS; else if (strcmp(arg[iarg],"omega") == 0) bstyle[nvalues++] = OMEGA; else if (strcmp(arg[iarg],"velvib") == 0) bstyle[nvalues++] = VELVIB; - else error->all(FLERR,"Invalid keyword in compute bond/local command"); + else if (strncmp(arg[iarg],"v_",2) == 0) { + bstyle[nvalues++] = VARIABLE; + int n = strlen(arg[iarg]); + vstr[nvar] = new char[n]; + strcpy(vstr[nvar],&arg[iarg][2]); + nvar++; + } else break; } + // optional args + + setflag = 0; + dstr = NULL; + + while (iarg < narg) { + if (strcmp(arg[iarg],"set") == 0) { + setflag = 1; + if (iarg+3 > narg) error->all(FLERR,"Illegal compute bond/local command"); + if (strcmp(arg[iarg+1],"dist") == 0) { + delete [] dstr; + int n = strlen(arg[iarg+2]) + 1; + dstr = new char[n]; + strcpy(dstr,arg[iarg+2]); + } else error->all(FLERR,"Illegal compute bond/local command"); + iarg += 3; + } else error->all(FLERR,"Illegal compute bond/local command"); + } + + // error check + + if (nvar) { + if (!setflag) + error->all(FLERR,"Compute bond/local variable requires a set variable"); + for (int i = 0; i < nvar; i++) { + vvar[i] = input->variable->find(vstr[i]); + if (vvar[i] < 0) + error->all(FLERR,"Variable name for copute bond/local does not exist"); + if (!input->variable->equalstyle(vvar[i])) + error->all(FLERR,"Variable for compute bond/local is invalid style"); + } + + if (dstr) { + dvar = input->variable->find(dstr); + if (dvar < 0) + error->all(FLERR,"Variable name for compute bond/local does not exist"); + if (!input->variable->internalstyle(dvar)) + error->all(FLERR,"Variable for compute bond/local is invalid style"); + } + } else if (setflag) + error->all(FLERR,"Compute bond/local set with no variable"); + + // set singleflag if need to call bond->single() // set velflag if compute any quantities based on velocities @@ -77,6 +132,11 @@ ComputeBondLocal::ComputeBondLocal(LAMMPS *lmp, int narg, char **arg) : bstyle[i] == ENGVIB || bstyle[i] == ENGROT) velflag = 1; } + // initialize output + + if (nvalues == 1) size_local_cols = 0; + else size_local_cols = nvalues; + nmax = 0; vlocal = NULL; alocal = NULL; @@ -86,9 +146,15 @@ ComputeBondLocal::ComputeBondLocal(LAMMPS *lmp, int narg, char **arg) : ComputeBondLocal::~ComputeBondLocal() { + delete [] bstyle; + for (int i = 0; i < nvar; i++) delete [] vstr[i]; + delete [] vstr; + delete [] vvar; + + delete [] dstr; + memory->destroy(vlocal); memory->destroy(alocal); - delete [] bstyle; } /* ---------------------------------------------------------------------- */ @@ -98,6 +164,20 @@ void ComputeBondLocal::init() if (force->bond == NULL) error->all(FLERR,"No bond style is defined for compute bond/local"); + if (nvar) { + for (int i = 0; i < nvar; i++) { + vvar[i] = input->variable->find(vstr[i]); + if (vvar[i] < 0) + error->all(FLERR,"Variable name for compute bond/local does not exist"); + } + + if (dstr) { + dvar = input->variable->find(dstr); + if (dvar < 0) + error->all(FLERR,"Variable name for compute bond/local does not exist"); + } + } + // set ghostvelflag if need to acquire ghost atom velocities if (velflag && !comm->ghost_velocity) ghostvelflag = 1; @@ -140,7 +220,7 @@ void ComputeBondLocal::compute_local() int ComputeBondLocal::compute_bonds(int flag) { - int i,m,n,nb,atom1,atom2,imol,iatom,btype; + int i,m,n,nb,atom1,atom2,imol,iatom,btype,ivar; tagint tagprev; double dx,dy,dz,rsq; double mass1,mass2,masstotal,invmasstotal; @@ -297,6 +377,11 @@ int ComputeBondLocal::compute_bonds(int flag) if (nvalues == 1) ptr = &vlocal[m]; else ptr = alocal[m]; + if (nvar) { + ivar = 0; + if (dstr) input->variable->internal_set(dvar,sqrt(rsq)); + } + for (n = 0; n < nvalues; n++) { switch (bstyle[n]) { case DIST: @@ -323,6 +408,10 @@ int ComputeBondLocal::compute_bonds(int flag) case VELVIB: ptr[n] = vvib; break; + case VARIABLE: + ptr[n] = input->variable->compute_equal(vvar[ivar]); + ivar++; + break; } } } @@ -337,7 +426,7 @@ int ComputeBondLocal::compute_bonds(int flag) /* ---------------------------------------------------------------------- */ int ComputeBondLocal::pack_forward_comm(int n, int *list, double *buf, - int pbc_flag, int *pbc) + int /*pbc_flag*/, int * /*pbc*/) { int i,j,m; diff --git a/src/compute_bond_local.h b/src/compute_bond_local.h index b3e99fc61b..17111a941c 100644 --- a/src/compute_bond_local.h +++ b/src/compute_bond_local.h @@ -35,10 +35,13 @@ class ComputeBondLocal : public Compute { double memory_usage(); private: - int nvalues; - int ncount; - int *bstyle; + int nvalues,nvar,ncount,setflag; + int singleflag,velflag,ghostvelflag,initflag; + int dvar; + int *bstyle,*vvar; + char *dstr; + char **vstr; int nmax; double *vlocal; diff --git a/src/compute_centro_atom.cpp b/src/compute_centro_atom.cpp index 48af453635..5096879b32 100644 --- a/src/compute_centro_atom.cpp +++ b/src/compute_centro_atom.cpp @@ -110,7 +110,7 @@ void ComputeCentroAtom::init() /* ---------------------------------------------------------------------- */ -void ComputeCentroAtom::init_list(int id, NeighList *ptr) +void ComputeCentroAtom::init_list(int /*id*/, NeighList *ptr) { list = ptr; } diff --git a/src/compute_chunk_spread_atom.cpp b/src/compute_chunk_spread_atom.cpp new file mode 100644 index 0000000000..c5fd27b0c1 --- /dev/null +++ b/src/compute_chunk_spread_atom.cpp @@ -0,0 +1,352 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include +#include +#include "compute_chunk_spread_atom.h" +#include "atom.h" +#include "update.h" +#include "modify.h" +#include "fix.h" +#include "compute.h" +#include "compute_chunk_atom.h" +#include "input.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; + +enum{COMPUTE,FIX}; + +#define INVOKED_VECTOR 2 +#define INVOKED_ARRAY 4 +#define INVOKED_PERATOM 8 + +/* ---------------------------------------------------------------------- */ + +ComputeChunkSpreadAtom:: +ComputeChunkSpreadAtom(LAMMPS *lmp, int narg, char **arg) : + Compute(lmp, narg, arg), + idchunk(NULL), ids(NULL), which(NULL), argindex(NULL), value2index(NULL) +{ + if (narg < 5) error->all(FLERR,"Illegal compute chunk/spread/atom command"); + + // ID of compute chunk/atom + + int n = strlen(arg[3]) + 1; + idchunk = new char[n]; + strcpy(idchunk,arg[3]); + init_chunk(); + + // expand args if any have wildcard character "*" + + int iarg = 4; + int expand = 0; + char **earg; + int nargnew = input->expand_args(narg-iarg,&arg[iarg],1,earg); + + if (earg != &arg[iarg]) expand = 1; + arg = earg; + + // parse values + + which = new int[nargnew]; + argindex = new int[nargnew]; + ids = new char*[nargnew]; + value2index = new int[nargnew]; + nvalues = 0; + + iarg = 0; + while (iarg < nargnew) { + ids[nvalues] = NULL; + + if (strncmp(arg[iarg],"c_",2) == 0 || + strncmp(arg[iarg],"f_",2) == 0) { + if (arg[iarg][0] == 'c') which[nvalues] = COMPUTE; + else if (arg[iarg][0] == 'f') which[nvalues] = FIX; + + int n = strlen(arg[iarg]); + char *suffix = new char[n]; + strcpy(suffix,&arg[iarg][2]); + + char *ptr = strchr(suffix,'['); + if (ptr) { + if (suffix[strlen(suffix)-1] != ']') + error->all(FLERR,"Illegal compute chunk/spread/atom command"); + argindex[nvalues] = atoi(ptr+1); + *ptr = '\0'; + } else argindex[nvalues] = 0; + + n = strlen(suffix) + 1; + ids[nvalues] = new char[n]; + strcpy(ids[nvalues],suffix); + nvalues++; + delete [] suffix; + + } else error->all(FLERR,"Illegal compute chunk/spread/atom command"); + + iarg++; + } + + // if wildcard expansion occurred, free earg memory from expand_args() + + if (expand) { + for (int i = 0; i < nargnew; i++) delete [] earg[i]; + memory->sfree(earg); + } + + // setup and error check + // for compute, must calculate per-chunk values, i.e. style ends in "/chunk" + // for fix, assume a global vector or array is per-chunk data + + for (int i = 0; i < nvalues; i++) { + if (which[i] == COMPUTE) { + int icompute = modify->find_compute(ids[i]); + if (icompute < 0) + error->all(FLERR,"Compute ID for compute chunk/spread/atom " + "does not exist"); + + char *ptr = strstr(modify->compute[icompute]->style,"/chunk"); + if (!ptr || (ptr != modify->compute[icompute]->style + + strlen(modify->compute[icompute]->style) - strlen("/chunk"))) + error->all(FLERR,"Compute for compute chunk/spread/atom " + "does not calculate per-chunk values"); + + if (argindex[i] == 0) { + if (!modify->compute[icompute]->vector_flag) + error->all(FLERR,"Compute chunk/spread/atom compute " + "does not calculate global vector"); + } else { + if (!modify->compute[icompute]->array_flag) + error->all(FLERR,"Compute chunk/spread/atom compute " + "does not calculate global array"); + if (argindex[i] > modify->compute[icompute]->size_array_cols) + error->all(FLERR,"Compute chunk/spread/atom compute array " + "is accessed out-of-range"); + } + + } else if (which[i] == FIX) { + int ifix = modify->find_fix(ids[i]); + if (ifix < 0) + error->all(FLERR,"Fix ID for compute chunk/spread/atom does not exist"); + if (argindex[i] == 0) { + if (!modify->fix[ifix]->vector_flag) + error->all(FLERR,"Compute chunk/spread/atom fix " + "does not calculate global vector"); + } else { + if (!modify->fix[ifix]->array_flag) + error->all(FLERR,"Compute chunk/spread/atom fix " + "does not calculate global array"); + if (argindex[i] > modify->fix[ifix]->size_array_cols) + error->all(FLERR,"Compute chunk/spread/atom fix array " + "is accessed out-of-range"); + } + } + } + + // this compute produces a peratom vector or array + + peratom_flag = 1; + if (nvalues == 1) size_peratom_cols = 0; + else size_peratom_cols = nvalues; + + // per-atom vector or array + + nmax = 0; + vector_atom = NULL; + array_atom = NULL; +} + +/* ---------------------------------------------------------------------- */ + +ComputeChunkSpreadAtom::~ComputeChunkSpreadAtom() +{ + delete [] idchunk; + + delete [] which; + delete [] argindex; + for (int i = 0; i < nvalues; i++) delete [] ids[i]; + delete [] ids; + delete [] value2index; + + memory->destroy(vector_atom); + memory->destroy(array_atom); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeChunkSpreadAtom::init() +{ + init_chunk(); + + // set indices of all computes,fixes,variables + + for (int m = 0; m < nvalues; m++) { + if (which[m] == COMPUTE) { + int icompute = modify->find_compute(ids[m]); + if (icompute < 0) + error->all(FLERR,"Compute ID for compute chunk/spread/atom " + "does not exist"); + value2index[m] = icompute; + + } else if (which[m] == FIX) { + int ifix = modify->find_fix(ids[m]); + if (ifix < 0) + error->all(FLERR,"Fix ID for compute chunk/spread/atom does not exist"); + value2index[m] = ifix; + } + } +} + +/* ---------------------------------------------------------------------- */ + +void ComputeChunkSpreadAtom::init_chunk() +{ + int icompute = modify->find_compute(idchunk); + if (icompute < 0) + error->all(FLERR,"Chunk/atom compute does not exist for compute chunk/spread/atom"); + cchunk = (ComputeChunkAtom *) modify->compute[icompute]; + if (strcmp(cchunk->style,"chunk/atom") != 0) + error->all(FLERR,"Compute chunk/spread/atom does not use chunk/atom compute"); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeChunkSpreadAtom::compute_peratom() +{ + invoked_peratom = update->ntimestep; + + // grow local vector_atom or array_atom if necessary + + if (atom->nmax > nmax) { + if (nvalues == 1) { + memory->destroy(vector_atom); + nmax = atom->nmax; + memory->create(vector_atom,nmax,"chunk/spread/atom:vector_atom"); + } else { + memory->destroy(array_atom); + nmax = atom->nmax; + memory->create(array_atom,nmax,nvalues,"chunk/spread/atom:array_atom"); + } + } + + // compute chunk/atom assigns atoms to chunk IDs + // extract ichunk index vector from compute + // ichunk = 1 to Nchunk for included atoms, 0 for excluded atoms + + int nchunk = cchunk->setup_chunks(); + cchunk->compute_ichunk(); + int *ichunk = cchunk->ichunk; + + // loop over values, access compute or fix + // loop over atoms, use chunk ID of each atom to store value from compute/fix + + int *mask = atom->mask; + int nlocal = atom->nlocal; + + int i,m,n,index,nstride; + double *ptr; + + for (m = 0; m < nvalues; m++) { + n = value2index[m]; + + // copy compute/fix values into vector_atom or array_atom + // nstride between values for each atom + + if (nvalues == 1) { + ptr = vector_atom; + nstride = 1; + } else { + ptr = &array_atom[0][m]; + nstride = nvalues; + } + + // invoke compute if not previously invoked + + if (which[m] == COMPUTE) { + Compute *compute = modify->compute[n]; + + if (argindex[m] == 0) { + if (!(compute->invoked_flag & INVOKED_VECTOR)) { + compute->compute_vector(); + compute->invoked_flag |= INVOKED_VECTOR; + } + double *cvector = compute->vector; + for (i = 0; i < nlocal; i++, ptr += nstride) { + *ptr = 0.0; + if (!(mask[i] & groupbit)) continue; + index = ichunk[i]-1; + if (index < 0 || index >= nchunk) continue; + *ptr = cvector[index]; + } + + } else { + if (!(compute->invoked_flag & INVOKED_ARRAY)) { + compute->compute_array(); + compute->invoked_flag |= INVOKED_ARRAY; + } + int icol = argindex[m]-1; + double **carray = compute->array; + for (i = 0; i < nlocal; i++, ptr += nstride) { + *ptr = 0.0; + if (!(mask[i] & groupbit)) continue; + index = ichunk[i]-1; + if (index < 0 || index >= nchunk) continue; + *ptr = carray[index][icol]; + } + } + + // access fix data, check if fix frequency is a match + // are assuming the fix global vector/array is per-chunk data + // check if index exceeds fix output length/rows + + } else if (which[m] == FIX) { + Fix *fix = modify->fix[n]; + if (update->ntimestep % fix->global_freq) + error->all(FLERR,"Fix used in compute chunk/spread/atom not " + "computed at compatible time"); + + if (argindex[m] == 0) { + int nfix = fix->size_vector; + for (i = 0; i < nlocal; i++, ptr += nstride) { + *ptr = 0.0; + if (!(mask[i] & groupbit)) continue; + index = ichunk[i]-1; + if (index < 0 || index >= nchunk || index >= nfix) continue; + *ptr = fix->compute_vector(index); + } + + } else { + int icol = argindex[m]-1; + int nfix = fix->size_array_rows; + for (i = 0; i < nlocal; i++, ptr += nstride) { + *ptr = 0.0; + if (!(mask[i] & groupbit)) continue; + index = ichunk[i]-1; + if (index < 0 || index >= nchunk || index >= nfix) continue; + *ptr = fix->compute_array(index,icol); + } + } + } + } +} + +/* ---------------------------------------------------------------------- + memory usage of local atom-based array +------------------------------------------------------------------------- */ + +double ComputeChunkSpreadAtom::memory_usage() +{ + double bytes = nmax*nvalues * sizeof(double); + return bytes; +} diff --git a/src/compute_chunk_spread_atom.h b/src/compute_chunk_spread_atom.h new file mode 100644 index 0000000000..80ee186450 --- /dev/null +++ b/src/compute_chunk_spread_atom.h @@ -0,0 +1,60 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef COMPUTE_CLASS + +ComputeStyle(chunk/spread/atom,ComputeChunkSpreadAtom) + +#else + +#ifndef LMP_COMPUTE_CHUNK_SPREAD_ATOM_H +#define LMP_COMPUTE_CHUNK_SPREAD_ATOM_H + +#include "compute.h" + +namespace LAMMPS_NS { + +class ComputeChunkSpreadAtom : public Compute { + public: + ComputeChunkSpreadAtom(class LAMMPS *, int, char **); + ~ComputeChunkSpreadAtom(); + void init(); + void compute_peratom(); + double memory_usage(); + + protected: + int mode,nvalues; + char *idchunk; + char **ids; + int *which,*argindex,*value2index; + + int nmax; + class ComputeChunkAtom *cchunk; + + void init_chunk(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +*/ diff --git a/src/compute_cluster_atom.cpp b/src/compute_cluster_atom.cpp index 146f8fd1b3..0c34b42671 100644 --- a/src/compute_cluster_atom.cpp +++ b/src/compute_cluster_atom.cpp @@ -31,6 +31,8 @@ using namespace LAMMPS_NS; +enum{CLUSTER,MASK,COORDS}; + /* ---------------------------------------------------------------------- */ ComputeClusterAtom::ComputeClusterAtom(LAMMPS *lmp, int narg, char **arg) : @@ -44,7 +46,7 @@ ComputeClusterAtom::ComputeClusterAtom(LAMMPS *lmp, int narg, char **arg) : peratom_flag = 1; size_peratom_cols = 0; - comm_forward = 1; + comm_forward = 3; nmax = 0; } @@ -87,7 +89,7 @@ void ComputeClusterAtom::init() /* ---------------------------------------------------------------------- */ -void ComputeClusterAtom::init_list(int id, NeighList *ptr) +void ComputeClusterAtom::init_list(int /*id*/, NeighList *ptr) { list = ptr; } @@ -122,10 +124,19 @@ void ComputeClusterAtom::compute_peratom() numneigh = list->numneigh; firstneigh = list->firstneigh; + // if update->post_integrate set: + // a dynamic group in FixGroup is invoking a variable with this compute + // thus ghost atom coords need to be up-to-date after initial_integrate() + + if (update->post_integrate) { + commflag = COORDS; + comm->forward_comm_compute(this); + } + // if group is dynamic, insure ghost atom masks are current if (group->dynamic[igroup]) { - commflag = 0; + commflag = MASK; comm->forward_comm_compute(this); } @@ -147,7 +158,7 @@ void ComputeClusterAtom::compute_peratom() // iterate until no changes in my atoms // then check if any proc made changes - commflag = 1; + commflag = CLUSTER; double **x = atom->x; int change,done,anychange; @@ -198,22 +209,30 @@ void ComputeClusterAtom::compute_peratom() /* ---------------------------------------------------------------------- */ int ComputeClusterAtom::pack_forward_comm(int n, int *list, double *buf, - int pbc_flag, int *pbc) + int /*pbc_flag*/, int * /*pbc*/) { int i,j,m; m = 0; - if (commflag) { + if (commflag == CLUSTER) { for (i = 0; i < n; i++) { j = list[i]; buf[m++] = clusterID[j]; } - } else { + } else if (commflag == MASK) { int *mask = atom->mask; for (i = 0; i < n; i++) { j = list[i]; buf[m++] = ubuf(mask[j]).d; } + } else if (commflag == COORDS) { + double **x = atom->x; + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = x[j][0]; + buf[m++] = x[j][1]; + buf[m++] = x[j][2]; + } } return m; @@ -227,11 +246,18 @@ void ComputeClusterAtom::unpack_forward_comm(int n, int first, double *buf) m = 0; last = first + n; - if (commflag) + if (commflag == CLUSTER) { for (i = first; i < last; i++) clusterID[i] = buf[m++]; - else { + } else if (commflag == MASK) { int *mask = atom->mask; for (i = first; i < last; i++) mask[i] = (int) ubuf(buf[m++]).i; + } else if (commflag == COORDS) { + double **x = atom->x; + for (i = first; i < last; i++) { + x[i][0] = buf[m++]; + x[i][1] = buf[m++]; + x[i][2] = buf[m++]; + } } } diff --git a/src/compute_cna_atom.cpp b/src/compute_cna_atom.cpp index a1b97d9404..b8ad3f0f64 100644 --- a/src/compute_cna_atom.cpp +++ b/src/compute_cna_atom.cpp @@ -100,7 +100,7 @@ void ComputeCNAAtom::init() /* ---------------------------------------------------------------------- */ -void ComputeCNAAtom::init_list(int id, NeighList *ptr) +void ComputeCNAAtom::init_list(int /*id*/, NeighList *ptr) { list = ptr; } diff --git a/src/compute_contact_atom.cpp b/src/compute_contact_atom.cpp index f3c4513b01..e60a51832a 100644 --- a/src/compute_contact_atom.cpp +++ b/src/compute_contact_atom.cpp @@ -80,7 +80,7 @@ void ComputeContactAtom::init() /* ---------------------------------------------------------------------- */ -void ComputeContactAtom::init_list(int id, NeighList *ptr) +void ComputeContactAtom::init_list(int /*id*/, NeighList *ptr) { list = ptr; } diff --git a/src/compute_coord_atom.cpp b/src/compute_coord_atom.cpp index b86d818d06..33b318ea17 100644 --- a/src/compute_coord_atom.cpp +++ b/src/compute_coord_atom.cpp @@ -153,7 +153,7 @@ void ComputeCoordAtom::init() /* ---------------------------------------------------------------------- */ -void ComputeCoordAtom::init_list(int id, NeighList *ptr) +void ComputeCoordAtom::init_list(int /*id*/, NeighList *ptr) { list = ptr; } @@ -311,7 +311,7 @@ void ComputeCoordAtom::compute_peratom() /* ---------------------------------------------------------------------- */ int ComputeCoordAtom::pack_forward_comm(int n, int *list, double *buf, - int pbc_flag, int *pbc) + int /*pbc_flag*/, int * /*pbc*/) { int i,m=0,j; for (i = 0; i < n; ++i) { diff --git a/src/compute_dihedral_local.cpp b/src/compute_dihedral_local.cpp index 42d1476ad2..7444630090 100644 --- a/src/compute_dihedral_local.cpp +++ b/src/compute_dihedral_local.cpp @@ -21,6 +21,9 @@ #include "domain.h" #include "force.h" #include "dihedral.h" +#include "input.h" +#include "variable.h" + #include "math_const.h" #include "memory.h" #include "error.h" @@ -31,11 +34,13 @@ using namespace MathConst; #define DELTA 10000 #define SMALL 0.001 +enum{PHI,VARIABLE}; + /* ---------------------------------------------------------------------- */ ComputeDihedralLocal::ComputeDihedralLocal(LAMMPS *lmp, int narg, char **arg) : Compute(lmp, narg, arg), - vlocal(NULL), alocal(NULL) + bstyle(NULL), vstr(NULL), vvar(NULL), pstr(NULL), vlocal(NULL), alocal(NULL) { if (narg < 4) error->all(FLERR,"Illegal compute dihedral/local command"); @@ -44,18 +49,80 @@ ComputeDihedralLocal::ComputeDihedralLocal(LAMMPS *lmp, int narg, char **arg) : "Compute dihedral/local used when dihedrals are not allowed"); local_flag = 1; + + // style args + nvalues = narg - 3; + bstyle = new int[nvalues]; + vstr = new char*[nvalues]; + vvar = new int[nvalues]; + + nvalues = 0; + nvar = 0; + + int iarg; + for (iarg = 3; iarg < narg; iarg++) { + if (strcmp(arg[iarg],"phi") == 0) { + bstyle[nvalues++] = PHI; + } else if (strncmp(arg[iarg],"v_",2) == 0) { + bstyle[nvalues++] = VARIABLE; + int n = strlen(arg[iarg]); + vstr[nvar] = new char[n]; + strcpy(vstr[nvar],&arg[iarg][2]); + nvar++; + } else break; + } + + // optional args + + setflag = 0; + pstr = NULL; + + while (iarg < narg) { + if (strcmp(arg[iarg],"set") == 0) { + setflag = 1; + if (iarg+3 > narg) + error->all(FLERR,"Illegal compute dihedral/local command"); + if (strcmp(arg[iarg+1],"phi") == 0) { + delete [] pstr; + int n = strlen(arg[iarg+2]) + 1; + pstr = new char[n]; + strcpy(pstr,arg[iarg+2]); + } else error->all(FLERR,"Illegal compute dihedral/local command"); + iarg += 3; + } else error->all(FLERR,"Illegal compute dihedral/local command"); + } + + // error check + + if (nvar) { + if (!setflag) + error->all(FLERR,"Compute dihedral/local variable requires a set variable"); + for (int i = 0; i < nvar; i++) { + vvar[i] = input->variable->find(vstr[i]); + if (vvar[i] < 0) + error->all(FLERR, + "Variable name for copute dihedral/local does not exist"); + if (!input->variable->equalstyle(vvar[i])) + error->all(FLERR,"Variable for compute dihedral/local is invalid style"); + } + + if (pstr) { + pvar = input->variable->find(pstr); + if (pvar < 0) + error->all(FLERR, + "Variable name for compute dihedral/local does not exist"); + if (!input->variable->internalstyle(pvar)) + error->all(FLERR,"Variable for compute dihedral/local is invalid style"); + } + } else if (setflag) + error->all(FLERR,"Compute dihedral/local set with no variable"); + + // initialize output + if (nvalues == 1) size_local_cols = 0; else size_local_cols = nvalues; - pflag = -1; - nvalues = 0; - - for (int iarg = 3; iarg < narg; iarg++) { - if (strcmp(arg[iarg],"phi") == 0) pflag = nvalues++; - else error->all(FLERR,"Invalid keyword in compute dihedral/local command"); - } - nmax = 0; vlocal = NULL; alocal = NULL; @@ -65,6 +132,13 @@ ComputeDihedralLocal::ComputeDihedralLocal(LAMMPS *lmp, int narg, char **arg) : ComputeDihedralLocal::~ComputeDihedralLocal() { + delete [] bstyle; + for (int i = 0; i < nvar; i++) delete [] vstr[i]; + delete [] vstr; + delete [] vvar; + + delete [] pstr; + memory->destroy(vlocal); memory->destroy(alocal); } @@ -76,6 +150,22 @@ void ComputeDihedralLocal::init() if (force->dihedral == NULL) error->all(FLERR,"No dihedral style is defined for compute dihedral/local"); + if (nvar) { + for (int i = 0; i < nvar; i++) { + vvar[i] = input->variable->find(vstr[i]); + if (vvar[i] < 0) + error->all(FLERR, + "Variable name for compute dihedral/local does not exist"); + } + + if (pstr) { + pvar = input->variable->find(pstr); + if (pvar < 0) + error->all(FLERR, + "Variable name for compute dihedral/local does not exist"); + } + } + // do initial memory allocation so that memory_usage() is correct ncount = compute_dihedrals(0); @@ -107,12 +197,12 @@ void ComputeDihedralLocal::compute_local() int ComputeDihedralLocal::compute_dihedrals(int flag) { - int i,m,n,nd,atom1,atom2,atom3,atom4,imol,iatom; + int i,m,n,nd,atom1,atom2,atom3,atom4,imol,iatom,ivar; tagint tagprev; double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,vb2xm,vb2ym,vb2zm; double ax,ay,az,bx,by,bz,rasq,rbsq,rgsq,rg,ra2inv,rb2inv,rabinv; - double s,c; - double *pbuf; + double s,c,phi; + double *ptr; double **x = atom->x; tagint *tag = atom->tag; @@ -130,14 +220,7 @@ int ComputeDihedralLocal::compute_dihedrals(int flag) int nlocal = atom->nlocal; int molecular = atom->molecular; - if (flag) { - if (nvalues == 1) { - if (pflag >= 0) pbuf = vlocal; - } else { - if (pflag >= 0 && alocal) pbuf = &alocal[0][pflag]; - else pbuf = NULL; - } - } + // loop over all atoms and their dihedrals m = n = 0; for (atom2 = 0; atom2 < nlocal; atom2++) { @@ -169,56 +252,75 @@ int ComputeDihedralLocal::compute_dihedrals(int flag) if (atom3 < 0 || !(mask[atom3] & groupbit)) continue; if (atom4 < 0 || !(mask[atom4] & groupbit)) continue; - if (flag) { + if (!flag) { + m++; + continue; + } - // phi calculation from dihedral style harmonic + // phi calculation from dihedral style harmonic - if (pflag >= 0) { - vb1x = x[atom1][0] - x[atom2][0]; - vb1y = x[atom1][1] - x[atom2][1]; - vb1z = x[atom1][2] - x[atom2][2]; - domain->minimum_image(vb1x,vb1y,vb1z); + vb1x = x[atom1][0] - x[atom2][0]; + vb1y = x[atom1][1] - x[atom2][1]; + vb1z = x[atom1][2] - x[atom2][2]; + domain->minimum_image(vb1x,vb1y,vb1z); - vb2x = x[atom3][0] - x[atom2][0]; - vb2y = x[atom3][1] - x[atom2][1]; - vb2z = x[atom3][2] - x[atom2][2]; - domain->minimum_image(vb2x,vb2y,vb2z); + vb2x = x[atom3][0] - x[atom2][0]; + vb2y = x[atom3][1] - x[atom2][1]; + vb2z = x[atom3][2] - x[atom2][2]; + domain->minimum_image(vb2x,vb2y,vb2z); - vb2xm = -vb2x; - vb2ym = -vb2y; - vb2zm = -vb2z; - domain->minimum_image(vb2xm,vb2ym,vb2zm); + vb2xm = -vb2x; + vb2ym = -vb2y; + vb2zm = -vb2z; + domain->minimum_image(vb2xm,vb2ym,vb2zm); - vb3x = x[atom4][0] - x[atom3][0]; - vb3y = x[atom4][1] - x[atom3][1]; - vb3z = x[atom4][2] - x[atom3][2]; - domain->minimum_image(vb3x,vb3y,vb3z); + vb3x = x[atom4][0] - x[atom3][0]; + vb3y = x[atom4][1] - x[atom3][1]; + vb3z = x[atom4][2] - x[atom3][2]; + domain->minimum_image(vb3x,vb3y,vb3z); - ax = vb1y*vb2zm - vb1z*vb2ym; - ay = vb1z*vb2xm - vb1x*vb2zm; - az = vb1x*vb2ym - vb1y*vb2xm; - bx = vb3y*vb2zm - vb3z*vb2ym; - by = vb3z*vb2xm - vb3x*vb2zm; - bz = vb3x*vb2ym - vb3y*vb2xm; + ax = vb1y*vb2zm - vb1z*vb2ym; + ay = vb1z*vb2xm - vb1x*vb2zm; + az = vb1x*vb2ym - vb1y*vb2xm; + bx = vb3y*vb2zm - vb3z*vb2ym; + by = vb3z*vb2xm - vb3x*vb2zm; + bz = vb3x*vb2ym - vb3y*vb2xm; - rasq = ax*ax + ay*ay + az*az; - rbsq = bx*bx + by*by + bz*bz; - rgsq = vb2xm*vb2xm + vb2ym*vb2ym + vb2zm*vb2zm; - rg = sqrt(rgsq); + rasq = ax*ax + ay*ay + az*az; + rbsq = bx*bx + by*by + bz*bz; + rgsq = vb2xm*vb2xm + vb2ym*vb2ym + vb2zm*vb2zm; + rg = sqrt(rgsq); - ra2inv = rb2inv = 0.0; - if (rasq > 0) ra2inv = 1.0/rasq; - if (rbsq > 0) rb2inv = 1.0/rbsq; - rabinv = sqrt(ra2inv*rb2inv); + ra2inv = rb2inv = 0.0; + if (rasq > 0) ra2inv = 1.0/rasq; + if (rbsq > 0) rb2inv = 1.0/rbsq; + rabinv = sqrt(ra2inv*rb2inv); + + c = (ax*bx + ay*by + az*bz)*rabinv; + s = rg*rabinv*(ax*vb3x + ay*vb3y + az*vb3z); + + if (c > 1.0) c = 1.0; + if (c < -1.0) c = -1.0; + phi = atan2(s,c); - c = (ax*bx + ay*by + az*bz)*rabinv; - s = rg*rabinv*(ax*vb3x + ay*vb3y + az*vb3z); + if (nvalues == 1) ptr = &vlocal[m]; + else ptr = alocal[m]; + + if (nvar) { + ivar = 0; + if (pstr) input->variable->internal_set(pvar,phi); + } - if (c > 1.0) c = 1.0; - if (c < -1.0) c = -1.0; - pbuf[n] = 180.0*atan2(s,c)/MY_PI; + for (n = 0; n < nvalues; n++) { + switch (bstyle[n]) { + case PHI: + ptr[n] = 180.0*phi/MY_PI; + break; + case VARIABLE: + ptr[n] = input->variable->compute_equal(vvar[ivar]); + ivar++; + break; } - n += nvalues; } m++; diff --git a/src/compute_dihedral_local.h b/src/compute_dihedral_local.h index c077e52dbd..d5f6a64183 100644 --- a/src/compute_dihedral_local.h +++ b/src/compute_dihedral_local.h @@ -33,8 +33,12 @@ class ComputeDihedralLocal : public Compute { double memory_usage(); private: - int nvalues,pflag; - int ncount; + int nvalues,nvar,ncount,setflag,tflag; + + int pvar; + int *bstyle,*vvar; + char *pstr; + char **vstr; int nmax; double *vlocal; diff --git a/src/compute_fragment_atom.cpp b/src/compute_fragment_atom.cpp index b9fb2331ec..bb273f3bdb 100644 --- a/src/compute_fragment_atom.cpp +++ b/src/compute_fragment_atom.cpp @@ -159,7 +159,7 @@ void ComputeFragmentAtom::compute_peratom() /* ---------------------------------------------------------------------- */ int ComputeFragmentAtom::pack_forward_comm(int n, int *list, double *buf, - int pbc_flag, int *pbc) + int /*pbc_flag*/, int * /*pbc*/) { int i,j,m; diff --git a/src/compute_group_group.cpp b/src/compute_group_group.cpp index dc94db50f6..51f84b020d 100644 --- a/src/compute_group_group.cpp +++ b/src/compute_group_group.cpp @@ -173,7 +173,7 @@ void ComputeGroupGroup::init() /* ---------------------------------------------------------------------- */ -void ComputeGroupGroup::init_list(int id, NeighList *ptr) +void ComputeGroupGroup::init_list(int /*id*/, NeighList *ptr) { list = ptr; } diff --git a/src/compute_hexorder_atom.cpp b/src/compute_hexorder_atom.cpp index cb2946beba..6d17ae15bd 100644 --- a/src/compute_hexorder_atom.cpp +++ b/src/compute_hexorder_atom.cpp @@ -129,7 +129,7 @@ void ComputeHexOrderAtom::init() /* ---------------------------------------------------------------------- */ -void ComputeHexOrderAtom::init_list(int id, NeighList *ptr) +void ComputeHexOrderAtom::init_list(int /*id*/, NeighList *ptr) { list = ptr; } diff --git a/src/compute_orientorder_atom.cpp b/src/compute_orientorder_atom.cpp index f263fdfaed..8a0a525fdc 100644 --- a/src/compute_orientorder_atom.cpp +++ b/src/compute_orientorder_atom.cpp @@ -187,7 +187,7 @@ void ComputeOrientOrderAtom::init() /* ---------------------------------------------------------------------- */ -void ComputeOrientOrderAtom::init_list(int id, NeighList *ptr) +void ComputeOrientOrderAtom::init_list(int /*id*/, NeighList *ptr) { list = ptr; } @@ -542,4 +542,3 @@ double ComputeOrientOrderAtom::associated_legendre(int l, int m, double x) return p; } - diff --git a/src/compute_pair_local.cpp b/src/compute_pair_local.cpp index 3f1147ed27..e4cbabfd3d 100644 --- a/src/compute_pair_local.cpp +++ b/src/compute_pair_local.cpp @@ -139,7 +139,7 @@ void ComputePairLocal::init() /* ---------------------------------------------------------------------- */ -void ComputePairLocal::init_list(int id, NeighList *ptr) +void ComputePairLocal::init_list(int /*id*/, NeighList *ptr) { list = ptr; } diff --git a/src/compute_property_atom.cpp b/src/compute_property_atom.cpp index 76df5a053d..862a66e3f9 100644 --- a/src/compute_property_atom.cpp +++ b/src/compute_property_atom.cpp @@ -141,7 +141,41 @@ ComputePropertyAtom::ComputePropertyAtom(LAMMPS *lmp, int narg, char **arg) : error->all(FLERR,"Compute property/atom for " "atom property that isn't allocated"); pack_choice[i] = &ComputePropertyAtom::pack_mu; - + } else if (strcmp(arg[iarg],"spx") == 0) { // pack magnetic variables + if (!atom->sp_flag) + error->all(FLERR,"Compute property/atom for " + "atom property that isn't allocated"); + pack_choice[i] = &ComputePropertyAtom::pack_spx; + } else if (strcmp(arg[iarg],"spy") == 0) { + if (!atom->sp_flag) + error->all(FLERR,"Compute property/atom for " + "atom property that isn't allocated"); + pack_choice[i] = &ComputePropertyAtom::pack_spy; + } else if (strcmp(arg[iarg],"spz") == 0) { + if (!atom->sp_flag) + error->all(FLERR,"Compute property/atom for " + "atom property that isn't allocated"); + pack_choice[i] = &ComputePropertyAtom::pack_spz; + } else if (strcmp(arg[iarg],"sp") == 0) { + if (!atom->sp_flag) + error->all(FLERR,"Compute property/atom for " + "atom property that isn't allocated"); + pack_choice[i] = &ComputePropertyAtom::pack_sp; + } else if (strcmp(arg[iarg],"fmx") == 0) { + if (!atom->sp_flag) + error->all(FLERR,"Compute property/atom for " + "atom property that isn't allocated"); + pack_choice[i] = &ComputePropertyAtom::pack_fmx; + } else if (strcmp(arg[iarg],"fmy") == 0) { + if (!atom->sp_flag) + error->all(FLERR,"Compute property/atom for " + "atom property that isn't allocated"); + pack_choice[i] = &ComputePropertyAtom::pack_fmy; + } else if (strcmp(arg[iarg],"fmz") == 0) { + if (!atom->sp_flag) + error->all(FLERR,"Compute property/atom for " + "atom property that isn't allocated"); + pack_choice[i] = &ComputePropertyAtom::pack_fmz; } else if (strcmp(arg[iarg],"radius") == 0) { if (!atom->radius_flag) error->all(FLERR,"Compute property/atom for " @@ -1000,6 +1034,111 @@ void ComputePropertyAtom::pack_mu(int n) /* ---------------------------------------------------------------------- */ +void ComputePropertyAtom::pack_spx(int n) +{ + double **sp = atom->sp; + int *mask = atom->mask; + int nlocal = atom->nlocal; + + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) buf[n] = sp[i][0]; + else buf[n] = 0.0; + n += nvalues; + } +} + +/* ---------------------------------------------------------------------- */ + +void ComputePropertyAtom::pack_spy(int n) +{ + double **sp = atom->sp; + int *mask = atom->mask; + int nlocal = atom->nlocal; + + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) buf[n] = sp[i][1]; + else buf[n] = 0.0; + n += nvalues; + } +} + +/* ---------------------------------------------------------------------- */ + +void ComputePropertyAtom::pack_spz(int n) +{ + double **sp = atom->sp; + int *mask = atom->mask; + int nlocal = atom->nlocal; + + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) buf[n] = sp[i][2]; + else buf[n] = 0.0; + n += nvalues; + } +} + +/* ---------------------------------------------------------------------- */ + +void ComputePropertyAtom::pack_sp(int n) +{ + double **sp = atom->sp; + int *mask = atom->mask; + int nlocal = atom->nlocal; + + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) buf[n] = sp[i][3]; + else buf[n] = 0.0; + n += nvalues; + } +} + +/* ---------------------------------------------------------------------- */ + +void ComputePropertyAtom::pack_fmx(int n) +{ + double **fm = atom->fm; + int *mask = atom->mask; + int nlocal = atom->nlocal; + + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) buf[n] = fm[i][0]; + else buf[n] = 0.0; + n += nvalues; + } +} + +/* ---------------------------------------------------------------------- */ + +void ComputePropertyAtom::pack_fmy(int n) +{ + double **fm = atom->fm; + int *mask = atom->mask; + int nlocal = atom->nlocal; + + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) buf[n] = fm[i][1]; + else buf[n] = 0.0; + n += nvalues; + } +} + +/* ---------------------------------------------------------------------- */ + +void ComputePropertyAtom::pack_fmz(int n) +{ + double **fm = atom->fm; + int *mask = atom->mask; + int nlocal = atom->nlocal; + + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) buf[n] = fm[i][2]; + else buf[n] = 0.0; + n += nvalues; + } +} + +/* ---------------------------------------------------------------------- */ + void ComputePropertyAtom::pack_radius(int n) { double *radius = atom->radius; diff --git a/src/compute_property_atom.h b/src/compute_property_atom.h index a81f39f6a9..0c1ed7e305 100644 --- a/src/compute_property_atom.h +++ b/src/compute_property_atom.h @@ -84,6 +84,14 @@ class ComputePropertyAtom : public Compute { void pack_radius(int); void pack_diameter(int); + void pack_spx(int); // pack magnetic variables + void pack_spy(int); + void pack_spz(int); + void pack_sp(int); + void pack_fmx(int); + void pack_fmy(int); + void pack_fmz(int); + void pack_omegax(int); void pack_omegay(int); void pack_omegaz(int); diff --git a/src/compute_property_local.cpp b/src/compute_property_local.cpp index ad68459650..ddcf5913ca 100644 --- a/src/compute_property_local.cpp +++ b/src/compute_property_local.cpp @@ -308,7 +308,7 @@ void ComputePropertyLocal::init() /* ---------------------------------------------------------------------- */ -void ComputePropertyLocal::init_list(int id, NeighList *ptr) +void ComputePropertyLocal::init_list(int /*id*/, NeighList *ptr) { list = ptr; } diff --git a/src/compute_rdf.cpp b/src/compute_rdf.cpp index f2635c0948..0a0e8fb684 100644 --- a/src/compute_rdf.cpp +++ b/src/compute_rdf.cpp @@ -213,7 +213,7 @@ void ComputeRDF::init() /* ---------------------------------------------------------------------- */ -void ComputeRDF::init_list(int id, NeighList *ptr) +void ComputeRDF::init_list(int /*id*/, NeighList *ptr) { list = ptr; } diff --git a/src/compute_reduce.cpp b/src/compute_reduce.cpp index 7c61d666b2..e3c3c5b70a 100644 --- a/src/compute_reduce.cpp +++ b/src/compute_reduce.cpp @@ -11,6 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include #include #include #include "compute_reduce.h" diff --git a/src/compute_reduce_chunk.cpp b/src/compute_reduce_chunk.cpp new file mode 100644 index 0000000000..beebc5f411 --- /dev/null +++ b/src/compute_reduce_chunk.cpp @@ -0,0 +1,512 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include +#include +#include "compute_reduce_chunk.h" +#include "atom.h" +#include "update.h" +#include "modify.h" +#include "fix.h" +#include "compute.h" +#include "compute_chunk_atom.h" +#include "input.h" +#include "variable.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; + +enum{SUM,MINN,MAXX}; +enum{COMPUTE,FIX,VARIABLE}; + +#define INVOKED_PERATOM 8 + +#define BIG 1.0e20 + +/* ---------------------------------------------------------------------- */ + +ComputeReduceChunk::ComputeReduceChunk(LAMMPS *lmp, int narg, char **arg) : + Compute(lmp, narg, arg), + which(NULL), argindex(NULL), value2index(NULL), idchunk(NULL), ids(NULL), + vlocal(NULL), vglobal(NULL), alocal(NULL), aglobal(NULL), varatom(NULL) +{ + if (narg < 6) error->all(FLERR,"Illegal compute reduce/chunk command"); + + // ID of compute chunk/atom + + int n = strlen(arg[3]) + 1; + idchunk = new char[n]; + strcpy(idchunk,arg[3]); + init_chunk(); + + // mode + + if (strcmp(arg[4],"sum") == 0) mode = SUM; + else if (strcmp(arg[4],"min") == 0) mode = MINN; + else if (strcmp(arg[4],"max") == 0) mode = MAXX; + else error->all(FLERR,"Illegal compute reduce/chunk command"); + + int iarg = 5; + + // expand args if any have wildcard character "*" + + int expand = 0; + char **earg; + int nargnew = input->expand_args(narg-iarg,&arg[iarg],1,earg); + + if (earg != &arg[iarg]) expand = 1; + arg = earg; + + // parse values until one isn't recognized + + which = new int[nargnew]; + argindex = new int[nargnew]; + ids = new char*[nargnew]; + value2index = new int[nargnew]; + nvalues = 0; + + iarg = 0; + while (iarg < nargnew) { + ids[nvalues] = NULL; + + if (strncmp(arg[iarg],"c_",2) == 0 || + strncmp(arg[iarg],"f_",2) == 0 || + strncmp(arg[iarg],"v_",2) == 0) { + if (arg[iarg][0] == 'c') which[nvalues] = COMPUTE; + else if (arg[iarg][0] == 'f') which[nvalues] = FIX; + else if (arg[iarg][0] == 'v') which[nvalues] = VARIABLE; + + int n = strlen(arg[iarg]); + char *suffix = new char[n]; + strcpy(suffix,&arg[iarg][2]); + + char *ptr = strchr(suffix,'['); + if (ptr) { + if (suffix[strlen(suffix)-1] != ']') + error->all(FLERR,"Illegal compute reduce/chunk command"); + argindex[nvalues] = atoi(ptr+1); + *ptr = '\0'; + } else argindex[nvalues] = 0; + + n = strlen(suffix) + 1; + ids[nvalues] = new char[n]; + strcpy(ids[nvalues],suffix); + nvalues++; + delete [] suffix; + + } else error->all(FLERR,"Illegal compute reduce/chunk command"); + + iarg++; + } + + // if wildcard expansion occurred, free earg memory from expand_args() + + if (expand) { + for (int i = 0; i < nargnew; i++) delete [] earg[i]; + memory->sfree(earg); + } + + // error check + + for (int i = 0; i < nvalues; i++) { + if (which[i] == COMPUTE) { + int icompute = modify->find_compute(ids[i]); + if (icompute < 0) + error->all(FLERR,"Compute ID for compute reduce/chunk does not exist"); + if (!modify->compute[icompute]->peratom_flag) + error->all(FLERR,"Compute reduce/chunk compute does not " + "calculate per-atom values"); + if (argindex[i] == 0 && + modify->compute[icompute]->size_peratom_cols != 0) + error->all(FLERR,"Compute reduce/chunk compute does not " + "calculate a per-atom vector"); + if (argindex[i] && modify->compute[icompute]->size_peratom_cols == 0) + error->all(FLERR,"Compute reduce/chunk compute does not " + "calculate a per-atom array"); + if (argindex[i] && + argindex[i] > modify->compute[icompute]->size_peratom_cols) + error->all(FLERR, + "Compute reduce/chunk compute array is accessed out-of-range"); + + } else if (which[i] == FIX) { + int ifix = modify->find_fix(ids[i]); + if (ifix < 0) + error->all(FLERR,"Fix ID for compute reduce/chunk does not exist"); + if (!modify->fix[ifix]->peratom_flag) + error->all(FLERR,"Compute reduce/chunk fix does not " + "calculate per-atom values"); + if (argindex[i] == 0 && + modify->fix[ifix]->size_peratom_cols != 0) + error->all(FLERR,"Compute reduce/chunk fix does not " + "calculate a per-atom vector"); + if (argindex[i] && modify->fix[ifix]->size_peratom_cols == 0) + error->all(FLERR,"Compute reduce/chunk fix does not " + "calculate a per-atom array"); + if (argindex[i] && argindex[i] > modify->fix[ifix]->size_peratom_cols) + error->all(FLERR,"Compute reduce/chunk fix array is " + "accessed out-of-range"); + + } else if (which[i] == VARIABLE) { + int ivariable = input->variable->find(ids[i]); + if (ivariable < 0) + error->all(FLERR,"Variable name for compute reduce/chunk does not exist"); + if (input->variable->atomstyle(ivariable) == 0) + error->all(FLERR,"Compute reduce/chunk variable is " + "not atom-style variable"); + } + } + + // this compute produces either a vector or array + + if (nvalues == 1) { + vector_flag = 1; + size_vector_variable = 1; + extvector = 0; + } else { + array_flag = 1; + size_array_rows_variable = 1; + size_array_cols = nvalues; + extarray = 0; + } + + // setup + + if (mode == SUM) initvalue = 0.0; + else if (mode == MINN) initvalue = BIG; + else if (mode == MAXX) initvalue = -BIG; + + maxchunk = 0; + vlocal = vglobal = NULL; + alocal = aglobal = NULL; + + maxatom = 0; + varatom = NULL; +} + +/* ---------------------------------------------------------------------- */ + +ComputeReduceChunk::~ComputeReduceChunk() +{ + delete [] idchunk; + + delete [] which; + delete [] argindex; + for (int m = 0; m < nvalues; m++) delete [] ids[m]; + delete [] ids; + delete [] value2index; + + memory->destroy(vlocal); + memory->destroy(vglobal); + memory->destroy(alocal); + memory->destroy(aglobal); + + memory->destroy(varatom); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeReduceChunk::init() +{ + init_chunk(); + + // set indices of all computes,fixes,variables + + for (int m = 0; m < nvalues; m++) { + if (which[m] == COMPUTE) { + int icompute = modify->find_compute(ids[m]); + if (icompute < 0) + error->all(FLERR,"Compute ID for compute reduce/chunk does not exist"); + value2index[m] = icompute; + + } else if (which[m] == FIX) { + int ifix = modify->find_fix(ids[m]); + if (ifix < 0) + error->all(FLERR,"Fix ID for compute reduce/chunk does not exist"); + value2index[m] = ifix; + + } else if (which[m] == VARIABLE) { + int ivariable = input->variable->find(ids[m]); + if (ivariable < 0) + error->all(FLERR,"Variable name for compute reduce/chunk does not exist"); + value2index[m] = ivariable; + } + } +} + +/* ---------------------------------------------------------------------- */ + +void ComputeReduceChunk::init_chunk() +{ + int icompute = modify->find_compute(idchunk); + if (icompute < 0) + error->all(FLERR,"Chunk/atom compute does not exist for " + "compute reduce/chunk"); + cchunk = (ComputeChunkAtom *) modify->compute[icompute]; + if (strcmp(cchunk->style,"chunk/atom") != 0) + error->all(FLERR,"Compute reduce/chunk does not use chunk/atom compute"); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeReduceChunk::compute_vector() +{ + invoked_vector = update->ntimestep; + + // compute chunk/atom assigns atoms to chunk IDs + // extract ichunk index vector from compute + // ichunk = 1 to Nchunk for included atoms, 0 for excluded atoms + + nchunk = cchunk->setup_chunks(); + cchunk->compute_ichunk(); + ichunk = cchunk->ichunk; + if (!nchunk) return; + + size_vector = nchunk; + + if (nchunk > maxchunk) { + memory->destroy(vlocal); + memory->destroy(vglobal); + maxchunk = nchunk; + memory->create(vlocal,maxchunk,"reduce/chunk:vlocal"); + memory->create(vglobal,maxchunk,"reduce/chunk:vglobal"); + vector = vglobal; + } + + // perform local reduction of single peratom value + + compute_one(0,vlocal,1); + + // reduce the per-chunk values across all procs + + if (mode == SUM) + MPI_Allreduce(vlocal,vglobal,nchunk,MPI_DOUBLE,MPI_SUM,world); + else if (mode == MINN) + MPI_Allreduce(vlocal,vglobal,nchunk,MPI_DOUBLE,MPI_MIN,world); + else if (mode == MAXX) + MPI_Allreduce(vlocal,vglobal,nchunk,MPI_DOUBLE,MPI_MAX,world); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeReduceChunk::compute_array() +{ + invoked_array = update->ntimestep; + + // compute chunk/atom assigns atoms to chunk IDs + // extract ichunk index vector from compute + // ichunk = 1 to Nchunk for included atoms, 0 for excluded atoms + + nchunk = cchunk->setup_chunks(); + cchunk->compute_ichunk(); + ichunk = cchunk->ichunk; + if (!nchunk) return; + + size_array_rows = nchunk; + + if (nchunk > maxchunk) { + memory->destroy(alocal); + memory->destroy(aglobal); + maxchunk = nchunk; + memory->create(alocal,maxchunk,nvalues,"reduce/chunk:alocal"); + memory->create(aglobal,maxchunk,nvalues,"reduce/chunk:aglobal"); + array = aglobal; + } + + // perform local reduction of all peratom values + + for (int m = 0; m < nvalues; m++) compute_one(m,&alocal[0][m],nvalues); + + // reduce the per-chunk values across all procs + + if (mode == SUM) + MPI_Allreduce(&alocal[0][0],&aglobal[0][0],nchunk*nvalues, + MPI_DOUBLE,MPI_SUM,world); + else if (mode == MINN) + MPI_Allreduce(&alocal[0][0],&aglobal[0][0],nchunk*nvalues, + MPI_DOUBLE,MPI_MIN,world); + else if (mode == MAXX) + MPI_Allreduce(&alocal[0][0],&aglobal[0][0],nchunk*nvalues, + MPI_DOUBLE,MPI_MAX,world); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeReduceChunk::compute_one(int m, double *vchunk, int nstride) +{ + // initialize per-chunk values in accumulation vector + + for (int i = 0; i < nchunk; i += nstride) vchunk[i] = initvalue; + + // loop over my atoms + // use peratom input and chunk ID of each atom to update vector + + int *mask = atom->mask; + int nlocal = atom->nlocal; + + int index; + + if (which[m] == COMPUTE) { + Compute *compute = modify->compute[value2index[m]]; + + if (!(compute->invoked_flag & INVOKED_PERATOM)) { + compute->compute_peratom(); + compute->invoked_flag |= INVOKED_PERATOM; + } + + if (argindex[m] == 0) { + double *vcompute = compute->vector_atom; + for (int i = 0; i < nlocal; i++) { + if (!(mask[i] & groupbit)) continue; + index = ichunk[i]-1; + if (index < 0) continue; + combine(vchunk[index*nstride],vcompute[i]); + } + } else { + double **acompute = compute->array_atom; + int argindexm1 = argindex[m] - 1; + for (int i = 0; i < nlocal; i++) { + if (!(mask[i] & groupbit)) continue; + index = ichunk[i]-1; + if (index < 0) continue; + combine(vchunk[index*nstride],acompute[i][argindexm1]); + } + } + + // access fix fields, check if fix frequency is a match + + } else if (which[m] == FIX) { + Fix *fix = modify->fix[value2index[m]]; + if (update->ntimestep % fix->peratom_freq) + error->all(FLERR,"Fix used in compute reduce/chunk not " + "computed at compatible time"); + + if (argindex[m] == 0) { + double *vfix = fix->vector_atom; + for (int i = 0; i < nlocal; i++) { + if (!(mask[i] & groupbit)) continue; + index = ichunk[i]-1; + if (index < 0) continue; + combine(vchunk[index*nstride],vfix[i]); + } + } else { + double **afix = fix->array_atom; + int argindexm1 = argindex[m] - 1; + for (int i = 0; i < nlocal; i++) { + if (!(mask[i] & groupbit)) continue; + index = ichunk[i]-1; + if (index < 0) continue; + combine(vchunk[index*nstride],afix[i][argindexm1]); + } + } + + // evaluate atom-style variable + + } else if (which[m] == VARIABLE) { + if (atom->nmax > maxatom) { + memory->destroy(varatom); + maxatom = atom->nmax; + memory->create(varatom,maxatom,"reduce/chunk:varatom"); + } + + input->variable->compute_atom(value2index[m],igroup,varatom,1,0); + for (int i = 0; i < nlocal; i++) { + if (!(mask[i] & groupbit)) continue; + index = ichunk[i]-1; + if (index < 0) continue; + combine(vchunk[index*nstride],varatom[i]); + } + } +} + +/* ---------------------------------------------------------------------- + combine two values according to reduction mode +------------------------------------------------------------------------- */ + +void ComputeReduceChunk::combine(double &one, double two) +{ + if (mode == SUM) one += two; + else if (mode == MINN) { + if (two < one) one = two; + } else if (mode == MAXX) { + if (two > one) one = two; + } +} + +/* ---------------------------------------------------------------------- + lock methods: called by fix ave/time + these methods insure vector/array size is locked for Nfreq epoch + by passing lock info along to compute chunk/atom +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + increment lock counter +------------------------------------------------------------------------- */ + +void ComputeReduceChunk::lock_enable() +{ + cchunk->lockcount++; +} + +/* ---------------------------------------------------------------------- + decrement lock counter in compute chunk/atom, if it still exists +------------------------------------------------------------------------- */ + +void ComputeReduceChunk::lock_disable() +{ + int icompute = modify->find_compute(idchunk); + if (icompute >= 0) { + cchunk = (ComputeChunkAtom *) modify->compute[icompute]; + cchunk->lockcount--; + } +} + +/* ---------------------------------------------------------------------- + calculate and return # of chunks = length of vector/array +------------------------------------------------------------------------- */ + +int ComputeReduceChunk::lock_length() +{ + nchunk = cchunk->setup_chunks(); + return nchunk; +} + +/* ---------------------------------------------------------------------- + set the lock from startstep to stopstep +------------------------------------------------------------------------- */ + +void ComputeReduceChunk::lock(Fix *fixptr, bigint startstep, bigint stopstep) +{ + cchunk->lock(fixptr,startstep,stopstep); +} + +/* ---------------------------------------------------------------------- + unset the lock +------------------------------------------------------------------------- */ + +void ComputeReduceChunk::unlock(Fix *fixptr) +{ + cchunk->unlock(fixptr); +} + +/* ---------------------------------------------------------------------- + memory usage of local data +------------------------------------------------------------------------- */ + +double ComputeReduceChunk::memory_usage() +{ + double bytes = (bigint) maxatom * sizeof(double); + if (nvalues == 1) bytes += (bigint) maxchunk * 2 * sizeof(double); + else bytes += (bigint) maxchunk * nvalues * 2 * sizeof(double); + return bytes; +} diff --git a/src/compute_reduce_chunk.h b/src/compute_reduce_chunk.h new file mode 100644 index 0000000000..ac556907b7 --- /dev/null +++ b/src/compute_reduce_chunk.h @@ -0,0 +1,77 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef COMPUTE_CLASS + +ComputeStyle(reduce/chunk,ComputeReduceChunk) + +#else + +#ifndef LMP_COMPUTE_REDUCE_CHUNK_H +#define LMP_COMPUTE_REDUCE_CHUNK_H + +#include "compute.h" + +namespace LAMMPS_NS { + +class ComputeReduceChunk : public Compute { + public: + ComputeReduceChunk(class LAMMPS *, int, char **); + ~ComputeReduceChunk(); + void init(); + void compute_vector(); + void compute_array(); + + void lock_enable(); + void lock_disable(); + int lock_length(); + void lock(class Fix *, bigint, bigint); + void unlock(class Fix *); + + double memory_usage(); + + private: + int mode,nvalues; + int *which,*argindex,*value2index; + char *idchunk; + char **ids; + + int nchunk; + int maxchunk,maxatom; + double initvalue; + double *vlocal,*vglobal; + double **alocal,**aglobal; + double *varatom; + + class ComputeChunkAtom *cchunk; + int *ichunk; + + void init_chunk(); + void compute_one(int, double *, int); + void combine(double &, double); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +*/ diff --git a/src/compute_temp_com.cpp b/src/compute_temp_com.cpp index 35f4512ab2..f2ad40ea43 100644 --- a/src/compute_temp_com.cpp +++ b/src/compute_temp_com.cpp @@ -163,7 +163,7 @@ void ComputeTempCOM::compute_vector() remove velocity bias from atom I to leave thermal velocity ------------------------------------------------------------------------- */ -void ComputeTempCOM::remove_bias(int i, double *v) +void ComputeTempCOM::remove_bias(int /*i*/, double *v) { v[0] -= vbias[0]; v[1] -= vbias[1]; @@ -204,7 +204,7 @@ void ComputeTempCOM::remove_bias_all() assume remove_bias() was previously called ------------------------------------------------------------------------- */ -void ComputeTempCOM::restore_bias(int i, double *v) +void ComputeTempCOM::restore_bias(int /*i*/, double *v) { v[0] += vbias[0]; v[1] += vbias[1]; diff --git a/src/compute_temp_deform.cpp b/src/compute_temp_deform.cpp index 8729204e70..39780b5cf6 100644 --- a/src/compute_temp_deform.cpp +++ b/src/compute_temp_deform.cpp @@ -277,7 +277,7 @@ void ComputeTempDeform::remove_bias_all() assume remove_bias() was previously called ------------------------------------------------------------------------- */ -void ComputeTempDeform::restore_bias(int i, double *v) +void ComputeTempDeform::restore_bias(int /*i*/, double *v) { v[0] += vbias[0]; v[1] += vbias[1]; @@ -289,7 +289,7 @@ void ComputeTempDeform::restore_bias(int i, double *v) assume remove_bias_thr() was previously called with the same buffer b ------------------------------------------------------------------------- */ -void ComputeTempDeform::restore_bias_thr(int i, double *v, double *b) +void ComputeTempDeform::restore_bias_thr(int /*i*/, double *v, double *b) { v[0] += b[0]; v[1] += b[1]; diff --git a/src/compute_temp_partial.cpp b/src/compute_temp_partial.cpp index 4b87a2249e..4425aebdda 100644 --- a/src/compute_temp_partial.cpp +++ b/src/compute_temp_partial.cpp @@ -90,7 +90,7 @@ void ComputeTempPartial::dof_compute() /* ---------------------------------------------------------------------- */ -int ComputeTempPartial::dof_remove(int i) +int ComputeTempPartial::dof_remove(int /*i*/) { int nper = xflag+yflag+zflag; return (domain->dimension - nper); @@ -169,7 +169,7 @@ void ComputeTempPartial::compute_vector() remove velocity bias from atom I to leave thermal velocity ------------------------------------------------------------------------- */ -void ComputeTempPartial::remove_bias(int i, double *v) +void ComputeTempPartial::remove_bias(int /*i*/, double *v) { if (!xflag) { vbias[0] = v[0]; @@ -189,7 +189,7 @@ void ComputeTempPartial::remove_bias(int i, double *v) remove velocity bias from atom I to leave thermal velocity ------------------------------------------------------------------------- */ -void ComputeTempPartial::remove_bias_thr(int i, double *v, double *b) +void ComputeTempPartial::remove_bias_thr(int /*i*/, double *v, double *b) { if (!xflag) { b[0] = v[0]; @@ -275,7 +275,7 @@ void ComputeTempPartial::reapply_bias_all() assume remove_bias() was previously called ------------------------------------------------------------------------- */ -void ComputeTempPartial::restore_bias(int i, double *v) +void ComputeTempPartial::restore_bias(int /*i*/, double *v) { if (!xflag) v[0] += vbias[0]; if (!yflag) v[1] += vbias[1]; @@ -287,7 +287,7 @@ void ComputeTempPartial::restore_bias(int i, double *v) assume remove_bias_thr() was previously called with the same buffer b ------------------------------------------------------------------------- */ -void ComputeTempPartial::restore_bias_thr(int i, double *v, double *b) +void ComputeTempPartial::restore_bias_thr(int /*i*/, double *v, double *b) { if (!xflag) v[0] += b[0]; if (!yflag) v[1] += b[1]; diff --git a/src/compute_temp_ramp.cpp b/src/compute_temp_ramp.cpp index 42d258d8b2..ba572645f3 100644 --- a/src/compute_temp_ramp.cpp +++ b/src/compute_temp_ramp.cpp @@ -279,7 +279,7 @@ void ComputeTempRamp::remove_bias_all() assume remove_bias() was previously called ------------------------------------------------------------------------- */ -void ComputeTempRamp::restore_bias(int i, double *v) +void ComputeTempRamp::restore_bias(int /*i*/, double *v) { v[v_dim] += vbias[v_dim]; } @@ -289,7 +289,7 @@ void ComputeTempRamp::restore_bias(int i, double *v) assume remove_bias_thr() was previously called with the same buffer b ------------------------------------------------------------------------- */ -void ComputeTempRamp::restore_bias_thr(int i, double *v, double *b) +void ComputeTempRamp::restore_bias_thr(int /*i*/, double *v, double *b) { v[v_dim] += b[v_dim]; } diff --git a/src/compute_temp_region.cpp b/src/compute_temp_region.cpp index bde70a20f0..4aa4dac0a1 100644 --- a/src/compute_temp_region.cpp +++ b/src/compute_temp_region.cpp @@ -253,7 +253,7 @@ void ComputeTempRegion::remove_bias_all() assume remove_bias() was previously called ------------------------------------------------------------------------- */ -void ComputeTempRegion::restore_bias(int i, double *v) +void ComputeTempRegion::restore_bias(int /*i*/, double *v) { v[0] += vbias[0]; v[1] += vbias[1]; @@ -265,7 +265,7 @@ void ComputeTempRegion::restore_bias(int i, double *v) assume remove_bias_thr() was previously called with the same buffer b ------------------------------------------------------------------------- */ -void ComputeTempRegion::restore_bias_thr(int i, double *v, double *b) +void ComputeTempRegion::restore_bias_thr(int /*i*/, double *v, double *b) { v[0] += b[0]; v[1] += b[1]; diff --git a/src/dihedral_zero.cpp b/src/dihedral_zero.cpp index bdd2eaadd3..46facdb6db 100644 --- a/src/dihedral_zero.cpp +++ b/src/dihedral_zero.cpp @@ -99,13 +99,13 @@ void DihedralZero::coeff(int narg, char **arg) proc 0 writes out coeffs to restart file ------------------------------------------------------------------------- */ -void DihedralZero::write_restart(FILE *fp) {} +void DihedralZero::write_restart(FILE * /*fp*/) {} /* ---------------------------------------------------------------------- proc 0 reads coeffs from restart file, bcasts them ------------------------------------------------------------------------- */ -void DihedralZero::read_restart(FILE *fp) +void DihedralZero::read_restart(FILE * /*fp*/) { allocate(); for (int i = 1; i <= atom->ndihedraltypes; i++) setflag[i] = 1; @@ -119,4 +119,3 @@ void DihedralZero::write_data(FILE *fp) { for (int i = 1; i <= atom->ndihedraltypes; i++) fprintf(fp,"%d\n",i); } - diff --git a/src/domain.cpp b/src/domain.cpp index 4c1d12018b..8238ab7eea 100644 --- a/src/domain.cpp +++ b/src/domain.cpp @@ -1176,12 +1176,12 @@ int Domain::closest_image(int i, int j) if J is not a valid index like -1, just return it ------------------------------------------------------------------------- */ -int Domain::closest_image(double *pos, int j) +int Domain::closest_image(const double * const pos, int j) { if (j < 0) return j; - int *sametag = atom->sametag; - double **x = atom->x; + const int * const sametag = atom->sametag; + const double * const * const x = atom->x; int closest = j; double delx = pos[0] - x[j][0]; @@ -1208,13 +1208,10 @@ int Domain::closest_image(double *pos, int j) /* ---------------------------------------------------------------------- find and return Xj image = periodic image of Xj that is closest to Xi for triclinic, add/subtract tilt factors in other dims as needed - not currently used (Jan 2017): - used to be called by pair TIP4P styles but no longer, - due to use of other closest_image() method + called by ServerMD class and LammpsInterface in lib/atc. ------------------------------------------------------------------------- */ -void Domain::closest_image(const double * const xi, const double * const xj, - double * const xjimage) +void Domain::closest_image(const double * const xi, const double * const xj, double * const xjimage) { double dx = xj[0] - xi[0]; double dy = xj[1] - xi[1]; @@ -1618,7 +1615,7 @@ void Domain::image_flip(int m, int n, int p) called from create_atoms() in library.cpp ------------------------------------------------------------------------- */ -int Domain::ownatom(int id, double *x, imageint *image, int shrinkexceed) +int Domain::ownatom(int /*id*/, double *x, imageint *image, int shrinkexceed) { double lamda[3]; double *coord,*blo,*bhi,*slo,*shi; diff --git a/src/domain.h b/src/domain.h index 5581f9a45f..9ebdd6ae94 100644 --- a/src/domain.h +++ b/src/domain.h @@ -115,9 +115,8 @@ class Domain : protected Pointers { void minimum_image(double *); void minimum_image_once(double *); int closest_image(int, int); - int closest_image(double *, int); - void closest_image(const double * const, const double * const, - double * const); + int closest_image(const double * const, int); + void closest_image(const double * const, const double * const, double * const); void remap(double *, imageint &); void remap(double *); void remap_near(double *, double *); diff --git a/src/dump.cpp b/src/dump.cpp index 7c171015bb..7cd80dcf71 100644 --- a/src/dump.cpp +++ b/src/dump.cpp @@ -45,7 +45,7 @@ enum{ASCEND,DESCEND}; /* ---------------------------------------------------------------------- */ -Dump::Dump(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) +Dump::Dump(LAMMPS *lmp, int /*narg*/, char **arg) : Pointers(lmp) { MPI_Comm_rank(world,&me); MPI_Comm_size(world,&nprocs); diff --git a/src/dump_custom.cpp b/src/dump_custom.cpp index 40d74a1d74..17ad4b89ef 100644 --- a/src/dump_custom.cpp +++ b/src/dump_custom.cpp @@ -244,15 +244,13 @@ DumpCustom::~DumpCustom() for (int i = 1; i <= ntypes; i++) delete [] typenames[i]; delete [] typenames; - if(vformat) { + if (vformat) { for (int i = 0; i < size_one; i++) delete [] vformat[i]; delete [] vformat; } - if(format_column_user) { - for (int i = 0; i < size_one; i++) delete [] format_column_user[i]; - delete [] format_column_user; - } + for (int i = 0; i < size_one; i++) delete [] format_column_user[i]; + delete [] format_column_user; delete [] columns; } @@ -1025,12 +1023,12 @@ int DumpCustom::count() } else if (thresh_op[ithresh] == XOR) { if (lastflag) { for (i = 0; i < nlocal; i++, ptr += nstride) - if (choose[i] && (*ptr == 0.0 && values[i] == 0.0) || + if ((choose[i] && *ptr == 0.0 && values[i] == 0.0) || (*ptr != 0.0 && values[i] != 0.0)) choose[i] = 0; } else { for (i = 0; i < nlocal; i++, ptr += nstride) - if (choose[i] && (*ptr == 0.0 && value == 0.0) || + if ((choose[i] && *ptr == 0.0 && value == 0.0) || (*ptr != 0.0 && value != 0.0)) choose[i] = 0; } diff --git a/src/dump_image.cpp b/src/dump_image.cpp index 60a1f545c9..a488f65161 100644 --- a/src/dump_image.cpp +++ b/src/dump_image.cpp @@ -1193,7 +1193,7 @@ void DumpImage::create_image() /* ---------------------------------------------------------------------- */ int DumpImage::pack_forward_comm(int n, int *list, double *buf, - int pbc_flag, int *pbc) + int /*pbc_flag*/, int * /*pbc*/) { int i,j,m; diff --git a/src/dump_local.cpp b/src/dump_local.cpp index 0d5172b5c1..8dc0554690 100644 --- a/src/dump_local.cpp +++ b/src/dump_local.cpp @@ -326,7 +326,7 @@ int DumpLocal::count() /* ---------------------------------------------------------------------- */ -void DumpLocal::pack(tagint *dummy) +void DumpLocal::pack(tagint * /*dummy*/) { for (int n = 0; n < size_one; n++) (this->*pack_choice[n])(n); } diff --git a/src/error.cpp b/src/error.cpp index d516050385..913239ac49 100644 --- a/src/error.cpp +++ b/src/error.cpp @@ -16,6 +16,7 @@ #include #include "error.h" #include "universe.h" +#include "update.h" #include "output.h" #include "input.h" @@ -69,8 +70,12 @@ void Error::universe_all(const char *file, int line, const char *str) if (universe->ulogfile) fclose(universe->ulogfile); #ifdef LAMMPS_EXCEPTIONS + + // allow commands if an exception was caught in a run + update->whichflag = 0; + char msg[100]; - sprintf(msg, "ERROR: %s (%s:%d)\n", str, file, line); + snprintf(msg, 100, "ERROR: %s (%s:%d)\n", str, truncpath(file), line); throw LAMMPSException(msg); #else MPI_Finalize(); @@ -90,8 +95,12 @@ void Error::universe_one(const char *file, int line, const char *str) universe->me,str,truncpath(file),line); #ifdef LAMMPS_EXCEPTIONS + + // allow commands if an exception was caught in a run + update->whichflag = 0; + char msg[100]; - sprintf(msg, "ERROR: %s (%s:%d)\n", str, file, line); + snprintf(msg, 100, "ERROR: %s (%s:%d)\n", str, truncpath(file), line); throw LAMMPSAbortException(msg, universe->uworld); #else MPI_Abort(universe->uworld,1); @@ -137,8 +146,12 @@ void Error::all(const char *file, int line, const char *str) } #ifdef LAMMPS_EXCEPTIONS + + // allow commands if an exception was caught in a run + update->whichflag = 0; + char msg[100]; - sprintf(msg, "ERROR: %s (%s:%d)\n", str, file, line); + snprintf(msg, 100, "ERROR: %s (%s:%d)\n", str, truncpath(file), line); if (universe->nworlds > 1) { throw LAMMPSAbortException(msg, universe->uworld); @@ -183,8 +196,12 @@ void Error::one(const char *file, int line, const char *str) universe->me,str,truncpath(file),line); #ifdef LAMMPS_EXCEPTIONS + + // allow commands if an exception was caught in a run + update->whichflag = 0; + char msg[100]; - sprintf(msg, "ERROR on proc %d: %s (%s:%d)\n", me, str, file, line); + snprintf(msg, 100, "ERROR on proc %d: %s (%s:%d)\n", me, str, truncpath(file), line); throw LAMMPSAbortException(msg, world); #else MPI_Abort(world,1); diff --git a/src/fix.cpp b/src/fix.cpp index a54e295798..634bc2393d 100644 --- a/src/fix.cpp +++ b/src/fix.cpp @@ -31,7 +31,7 @@ int Fix::instance_total = 0; /* ---------------------------------------------------------------------- */ -Fix::Fix(LAMMPS *lmp, int narg, char **arg) : +Fix::Fix(LAMMPS *lmp, int /*narg*/, char **arg) : Pointers(lmp), id(NULL), style(NULL), extlist(NULL), vector_atom(NULL), array_atom(NULL), vector_local(NULL), array_local(NULL), eatom(NULL), vatom(NULL) @@ -81,6 +81,7 @@ Fix::Fix(LAMMPS *lmp, int narg, char **arg) : scalar_flag = vector_flag = array_flag = 0; peratom_flag = local_flag = 0; + global_freq = local_freq = peratom_freq = -1; size_vector_variable = size_array_rows_variable = 0; comm_forward = comm_reverse = comm_border = 0; diff --git a/src/fix_adapt.cpp b/src/fix_adapt.cpp index 42cd1bd199..950bc24253 100644 --- a/src/fix_adapt.cpp +++ b/src/fix_adapt.cpp @@ -476,7 +476,7 @@ void FixAdapt::init() /* ---------------------------------------------------------------------- */ -void FixAdapt::setup_pre_force(int vflag) +void FixAdapt::setup_pre_force(int /*vflag*/) { change_settings(); } @@ -491,7 +491,7 @@ void FixAdapt::setup_pre_force_respa(int vflag, int ilevel) /* ---------------------------------------------------------------------- */ -void FixAdapt::pre_force(int vflag) +void FixAdapt::pre_force(int /*vflag*/) { if (nevery == 0) return; if (update->ntimestep % nevery) return; diff --git a/src/fix_addforce.cpp b/src/fix_addforce.cpp index c2eedccd61..d66457a1f1 100644 --- a/src/fix_addforce.cpp +++ b/src/fix_addforce.cpp @@ -361,7 +361,7 @@ void FixAddForce::post_force(int vflag) /* ---------------------------------------------------------------------- */ -void FixAddForce::post_force_respa(int vflag, int ilevel, int iloop) +void FixAddForce::post_force_respa(int vflag, int ilevel, int /*iloop*/) { if (ilevel == ilevel_respa) post_force(vflag); } diff --git a/src/fix_ave_atom.cpp b/src/fix_ave_atom.cpp index a8c3be07af..c8cbad75c9 100644 --- a/src/fix_ave_atom.cpp +++ b/src/fix_ave_atom.cpp @@ -283,7 +283,7 @@ void FixAveAtom::init() only does something if nvalid = current timestep ------------------------------------------------------------------------- */ -void FixAveAtom::setup(int vflag) +void FixAveAtom::setup(int /*vflag*/) { end_of_step(); } @@ -432,7 +432,7 @@ void FixAveAtom::grow_arrays(int nmax) copy values within local atom-based array ------------------------------------------------------------------------- */ -void FixAveAtom::copy_arrays(int i, int j, int delflag) +void FixAveAtom::copy_arrays(int i, int j, int /*delflag*/) { for (int m = 0; m < nvalues; m++) array[j][m] = array[i][m]; diff --git a/src/fix_ave_chunk.cpp b/src/fix_ave_chunk.cpp index 5f727fd3f7..fc3ef6ed6e 100644 --- a/src/fix_ave_chunk.cpp +++ b/src/fix_ave_chunk.cpp @@ -63,7 +63,6 @@ FixAveChunk::FixAveChunk(LAMMPS *lmp, int narg, char **arg) : strcpy(idchunk,arg[6]); global_freq = nfreq; - peratom_freq = nfreq; no_change_box = 1; // expand args if any have wildcard character "*" @@ -557,7 +556,7 @@ void FixAveChunk::init() that nchunk may not track it ------------------------------------------------------------------------- */ -void FixAveChunk::setup(int vflag) +void FixAveChunk::setup(int /*vflag*/) { end_of_step(); } diff --git a/src/fix_ave_correlate.cpp b/src/fix_ave_correlate.cpp index 418464a248..198caf1514 100644 --- a/src/fix_ave_correlate.cpp +++ b/src/fix_ave_correlate.cpp @@ -404,7 +404,7 @@ void FixAveCorrelate::init() only does something if nvalid = current timestep ------------------------------------------------------------------------- */ -void FixAveCorrelate::setup(int vflag) +void FixAveCorrelate::setup(int /*vflag*/) { end_of_step(); } diff --git a/src/fix_ave_histo.cpp b/src/fix_ave_histo.cpp index 7aa5993899..ce32167b74 100644 --- a/src/fix_ave_histo.cpp +++ b/src/fix_ave_histo.cpp @@ -559,7 +559,7 @@ void FixAveHisto::init() only does something if nvalid = current timestep ------------------------------------------------------------------------- */ -void FixAveHisto::setup(int vflag) +void FixAveHisto::setup(int /*vflag*/) { end_of_step(); } diff --git a/src/fix_ave_time.cpp b/src/fix_ave_time.cpp index c3ace29684..53354ee066 100644 --- a/src/fix_ave_time.cpp +++ b/src/fix_ave_time.cpp @@ -529,7 +529,7 @@ void FixAveTime::init() only does something if nvalid = current timestep ------------------------------------------------------------------------- */ -void FixAveTime::setup(int vflag) +void FixAveTime::setup(int /*vflag*/) { end_of_step(); } diff --git a/src/fix_aveforce.cpp b/src/fix_aveforce.cpp index 4432a5dd36..1c87ba5785 100644 --- a/src/fix_aveforce.cpp +++ b/src/fix_aveforce.cpp @@ -194,7 +194,7 @@ void FixAveForce::min_setup(int vflag) /* ---------------------------------------------------------------------- */ -void FixAveForce::post_force(int vflag) +void FixAveForce::post_force(int /*vflag*/) { // update region if necessary @@ -259,7 +259,7 @@ void FixAveForce::post_force(int vflag) /* ---------------------------------------------------------------------- */ -void FixAveForce::post_force_respa(int vflag, int ilevel, int iloop) +void FixAveForce::post_force_respa(int vflag, int ilevel, int /*iloop*/) { // ave + extra force on selected RESPA level // just ave on all other levels diff --git a/src/fix_balance.cpp b/src/fix_balance.cpp index b2f545c73f..8995a57afe 100644 --- a/src/fix_balance.cpp +++ b/src/fix_balance.cpp @@ -114,6 +114,7 @@ FixBalance::FixBalance(LAMMPS *lmp, int narg, char **arg) : if (nevery) force_reneighbor = 1; lastbalance = -1; + next_reneighbor = -1; // compute initial outputs @@ -159,7 +160,7 @@ void FixBalance::init() /* ---------------------------------------------------------------------- */ -void FixBalance::setup(int vflag) +void FixBalance::setup(int /*vflag*/) { // compute final imbalance factor if setup_pre_exchange() invoked balancer // this is called at end of run setup, before output @@ -248,6 +249,10 @@ void FixBalance::pre_neighbor() if (!pending) return; imbfinal = balance->imbalance_factor(maxloadperproc); pending = 0; + + // set disable = 1, so weights no longer migrate with atoms + + if (wtflag) balance->fixstore->disable = 1; } /* ---------------------------------------------------------------------- @@ -275,21 +280,23 @@ void FixBalance::rebalance() // reset proc sub-domains // check and warn if any proc's subbox is smaller than neigh skin - // since may lead to lost atoms in exchange() + // since may lead to lost atoms in comm->exchange() if (domain->triclinic) domain->set_lamda_box(); domain->set_local_box(); domain->subbox_too_small_check(neighbor->skin); // move atoms to new processors via irregular() - // only needed if migrate_check() says an atom moves to far + // for non-RCB only needed if migrate_check() says an atom moves too far // else allow caller's comm->exchange() to do it + // set disable = 0, so weights migrate with atoms + // important to delay disable = 1 until after pre_neighbor imbfinal calc + // b/c atoms may migrate again in comm->exchange() if (domain->triclinic) domain->x2lamda(atom->nlocal); if (wtflag) balance->fixstore->disable = 0; if (lbstyle == BISECTION) irregular->migrate_atoms(0,1,sendproc); else if (irregular->migrate_check()) irregular->migrate_atoms(); - if (wtflag) balance->fixstore->disable = 1; if (domain->triclinic) domain->lamda2x(atom->nlocal); // invoke KSpace setup_grid() to adjust to new proc sub-domains diff --git a/src/fix_drag.cpp b/src/fix_drag.cpp index 6a69dddbf5..e4cf12d1ff 100644 --- a/src/fix_drag.cpp +++ b/src/fix_drag.cpp @@ -90,7 +90,7 @@ void FixDrag::setup(int vflag) /* ---------------------------------------------------------------------- */ -void FixDrag::post_force(int vflag) +void FixDrag::post_force(int /*vflag*/) { // apply drag force to atoms in group of magnitude f_mag // apply in direction (r-r0) if atom is further than delta away @@ -132,7 +132,7 @@ void FixDrag::post_force(int vflag) /* ---------------------------------------------------------------------- */ -void FixDrag::post_force_respa(int vflag, int ilevel, int iloop) +void FixDrag::post_force_respa(int vflag, int ilevel, int /*iloop*/) { if (ilevel == ilevel_respa) post_force(vflag); } diff --git a/src/fix_dt_reset.cpp b/src/fix_dt_reset.cpp index f2a50fd6d1..7566094b48 100644 --- a/src/fix_dt_reset.cpp +++ b/src/fix_dt_reset.cpp @@ -129,7 +129,7 @@ void FixDtReset::init() /* ---------------------------------------------------------------------- */ -void FixDtReset::setup(int vflag) +void FixDtReset::setup(int /*vflag*/) { end_of_step(); } diff --git a/src/fix_enforce2d.cpp b/src/fix_enforce2d.cpp index 4ffd2ca7ac..ef7eb3a0ef 100644 --- a/src/fix_enforce2d.cpp +++ b/src/fix_enforce2d.cpp @@ -38,6 +38,8 @@ FixEnforce2D::FixEnforce2D(LAMMPS *lmp, int narg, char **arg) : FixEnforce2D::~FixEnforce2D() { + if (copymode) return; + delete [] flist; } @@ -110,7 +112,7 @@ void FixEnforce2D::min_setup(int vflag) /* ---------------------------------------------------------------------- */ -void FixEnforce2D::post_force(int vflag) +void FixEnforce2D::post_force(int /*vflag*/) { double **v = atom->v; double **f = atom->f; @@ -162,7 +164,7 @@ void FixEnforce2D::post_force(int vflag) /* ---------------------------------------------------------------------- */ -void FixEnforce2D::post_force_respa(int vflag, int ilevel, int iloop) +void FixEnforce2D::post_force_respa(int vflag, int /*ilevel*/, int /*iloop*/) { post_force(vflag); } diff --git a/src/fix_enforce2d.h b/src/fix_enforce2d.h index cdead78f6a..a3f79309dc 100644 --- a/src/fix_enforce2d.h +++ b/src/fix_enforce2d.h @@ -36,7 +36,7 @@ class FixEnforce2D : public Fix { void post_force_respa(int, int, int); void min_post_force(int); - private: + protected: int nfixlist; class Fix **flist; }; diff --git a/src/fix_external.cpp b/src/fix_external.cpp index 4fcc842f89..5ac9206e7f 100644 --- a/src/fix_external.cpp +++ b/src/fix_external.cpp @@ -129,7 +129,7 @@ void FixExternal::min_setup(int vflag) store eflag, so can use it in post_force to tally per-atom energies ------------------------------------------------------------------------- */ -void FixExternal::pre_reverse(int eflag, int vflag) +void FixExternal::pre_reverse(int eflag, int /*vflag*/) { eflag_caller = eflag; } @@ -305,7 +305,7 @@ void FixExternal::grow_arrays(int nmax) copy values within local atom-based array ------------------------------------------------------------------------- */ -void FixExternal::copy_arrays(int i, int j, int delflag) +void FixExternal::copy_arrays(int i, int j, int /*delflag*/) { fexternal[j][0] = fexternal[i][0]; fexternal[j][1] = fexternal[i][1]; diff --git a/src/fix_gravity.cpp b/src/fix_gravity.cpp index 9ace9d45ff..c3e73d86c9 100644 --- a/src/fix_gravity.cpp +++ b/src/fix_gravity.cpp @@ -247,7 +247,7 @@ void FixGravity::setup(int vflag) /* ---------------------------------------------------------------------- */ -void FixGravity::post_force(int vflag) +void FixGravity::post_force(int /*vflag*/) { // update gravity due to variables @@ -300,7 +300,7 @@ void FixGravity::post_force(int vflag) /* ---------------------------------------------------------------------- */ -void FixGravity::post_force_respa(int vflag, int ilevel, int iloop) +void FixGravity::post_force_respa(int vflag, int ilevel, int /*iloop*/) { if (ilevel == ilevel_respa) post_force(vflag); } diff --git a/src/fix_group.cpp b/src/fix_group.cpp index 2447002bc5..0980ff5456 100644 --- a/src/fix_group.cpp +++ b/src/fix_group.cpp @@ -84,7 +84,7 @@ idregion(NULL), idvar(NULL), idprop(NULL) idprop = new char[n]; strcpy(idprop,arg[iarg+1]); iarg += 2; - } else if (strcmp(arg[iarg],"every") == 0) { + } else if (strcmp(arg[iarg],"every") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal group command"); nevery = force->inumeric(FLERR,arg[iarg+1]); if (nevery <= 0) error->all(FLERR,"Illegal group command"); @@ -176,7 +176,7 @@ void FixGroup::init() assign atoms to group ------------------------------------------------------------------------- */ -void FixGroup::setup(int vflag) +void FixGroup::setup(int /*vflag*/) { set_group(); } @@ -192,7 +192,7 @@ void FixGroup::post_integrate() /* ---------------------------------------------------------------------- */ -void FixGroup::post_integrate_respa(int ilevel, int iloop) +void FixGroup::post_integrate_respa(int ilevel, int /*iloop*/) { if (ilevel == nlevels_respa-1) post_integrate(); } @@ -204,17 +204,22 @@ void FixGroup::set_group() int nlocal = atom->nlocal; // invoke atom-style variable if defined + // set post_integrate flag to 1, then unset after + // this is for any compute to check if it needs to + // operate differently due to invocation this early in timestep + // e.g. perform ghost comm update due to atoms having just moved double *var = NULL; int *ivector = NULL; double *dvector = NULL; - if (varflag) { + update->post_integrate = 1; modify->clearstep_compute(); memory->create(var,nlocal,"fix/group:varvalue"); input->variable->compute_atom(ivar,igroup,var,1,0); modify->addstep_compute(update->ntimestep + nevery); + update->post_integrate = 0; } // invoke per-atom property if defined @@ -254,7 +259,7 @@ void FixGroup::set_group() /* ---------------------------------------------------------------------- */ -void *FixGroup::extract(const char *str, int &unused) +void *FixGroup::extract(const char *str, int &/*unused*/) { if (strcmp(str,"property") == 0 && propflag) return (void *) idprop; if (strcmp(str,"variable") == 0 && varflag) return (void *) idvar; diff --git a/src/fix_halt.cpp b/src/fix_halt.cpp index 7de09a0fa4..983f993ae8 100644 --- a/src/fix_halt.cpp +++ b/src/fix_halt.cpp @@ -184,7 +184,7 @@ void FixHalt::end_of_step() // print message with ID of fix halt in case multiple instances char str[128]; - sprintf(str,"Fix halt %s condition met on step %ld with value %g", + sprintf(str,"Fix halt %s condition met on step " BIGINT_FORMAT " with value %g", id,update->ntimestep,attvalue); if (eflag == HARD) { diff --git a/src/fix_indent.cpp b/src/fix_indent.cpp index ade8cee532..b8e07dfd53 100644 --- a/src/fix_indent.cpp +++ b/src/fix_indent.cpp @@ -182,7 +182,7 @@ void FixIndent::min_setup(int vflag) /* ---------------------------------------------------------------------- */ -void FixIndent::post_force(int vflag) +void FixIndent::post_force(int /*vflag*/) { // indenter values, 0 = energy, 1-3 = force components // wrap variable evaluations with clear/add @@ -357,7 +357,7 @@ void FixIndent::post_force(int vflag) /* ---------------------------------------------------------------------- */ -void FixIndent::post_force_respa(int vflag, int ilevel, int iloop) +void FixIndent::post_force_respa(int vflag, int ilevel, int /*iloop*/) { if (ilevel == ilevel_respa) post_force(vflag); } diff --git a/src/fix_langevin.cpp b/src/fix_langevin.cpp index e4c36cc739..d829982274 100644 --- a/src/fix_langevin.cpp +++ b/src/fix_langevin.cpp @@ -298,7 +298,7 @@ void FixLangevin::setup(int vflag) /* ---------------------------------------------------------------------- */ -void FixLangevin::post_force(int vflag) +void FixLangevin::post_force(int /*vflag*/) { double *rmass = atom->rmass; @@ -441,7 +441,7 @@ void FixLangevin::post_force(int vflag) /* ---------------------------------------------------------------------- */ -void FixLangevin::post_force_respa(int vflag, int ilevel, int iloop) +void FixLangevin::post_force_respa(int vflag, int ilevel, int /*iloop*/) { if (ilevel == nlevels_respa-1) post_force(vflag); } @@ -896,7 +896,7 @@ void FixLangevin::grow_arrays(int nmax) copy values within local atom-based array ------------------------------------------------------------------------- */ -void FixLangevin::copy_arrays(int i, int j, int delflag) +void FixLangevin::copy_arrays(int i, int j, int /*delflag*/) { for (int m = 0; m < nvalues; m++) franprev[j][m] = franprev[i][m]; diff --git a/src/fix_lineforce.cpp b/src/fix_lineforce.cpp index e90152c4e1..aea1a2a25b 100644 --- a/src/fix_lineforce.cpp +++ b/src/fix_lineforce.cpp @@ -80,7 +80,7 @@ void FixLineForce::min_setup(int vflag) /* ---------------------------------------------------------------------- */ -void FixLineForce::post_force(int vflag) +void FixLineForce::post_force(int /*vflag*/) { double **f = atom->f; int *mask = atom->mask; @@ -98,7 +98,7 @@ void FixLineForce::post_force(int vflag) /* ---------------------------------------------------------------------- */ -void FixLineForce::post_force_respa(int vflag, int ilevel, int iloop) +void FixLineForce::post_force_respa(int vflag, int /*ilevel*/, int /*iloop*/) { post_force(vflag); } diff --git a/src/fix_minimize.cpp b/src/fix_minimize.cpp index 06a3ac900d..fa39643a1b 100644 --- a/src/fix_minimize.cpp +++ b/src/fix_minimize.cpp @@ -184,7 +184,7 @@ void FixMinimize::grow_arrays(int nmax) copy values within local atom-based arrays ------------------------------------------------------------------------- */ -void FixMinimize::copy_arrays(int i, int j, int delflag) +void FixMinimize::copy_arrays(int i, int j, int /*delflag*/) { int m,iper,nper,ni,nj; diff --git a/src/fix_move.cpp b/src/fix_move.cpp index 9eadfa5ab4..2f9fb0ebaa 100644 --- a/src/fix_move.cpp +++ b/src/fix_move.cpp @@ -453,7 +453,7 @@ void FixMove::init() set x,v of particles ------------------------------------------------------------------------- */ -void FixMove::initial_integrate(int vflag) +void FixMove::initial_integrate(int /*vflag*/) { int flag; double ddotr,dx,dy,dz; @@ -945,7 +945,7 @@ void FixMove::final_integrate() /* ---------------------------------------------------------------------- */ -void FixMove::initial_integrate_respa(int vflag, int ilevel, int iloop) +void FixMove::initial_integrate_respa(int vflag, int ilevel, int /*iloop*/) { // outermost level - update v and x // all other levels - nothing @@ -955,7 +955,7 @@ void FixMove::initial_integrate_respa(int vflag, int ilevel, int iloop) /* ---------------------------------------------------------------------- */ -void FixMove::final_integrate_respa(int ilevel, int iloop) +void FixMove::final_integrate_respa(int ilevel, int /*iloop*/) { if (ilevel == nlevels_respa-1) final_integrate(); } @@ -1019,7 +1019,7 @@ void FixMove::grow_arrays(int nmax) copy values within local atom-based array ------------------------------------------------------------------------- */ -void FixMove::copy_arrays(int i, int j, int delflag) +void FixMove::copy_arrays(int i, int j, int /*delflag*/) { xoriginal[j][0] = xoriginal[i][0]; xoriginal[j][1] = xoriginal[i][1]; @@ -1238,7 +1238,7 @@ int FixMove::maxsize_restart() size of atom nlocal's restart data ------------------------------------------------------------------------- */ -int FixMove::size_restart(int nlocal) +int FixMove::size_restart(int /*nlocal*/) { return nrestart; } diff --git a/src/fix_neigh_history.cpp b/src/fix_neigh_history.cpp index 3329b604ef..9661409a6a 100644 --- a/src/fix_neigh_history.cpp +++ b/src/fix_neigh_history.cpp @@ -35,7 +35,7 @@ enum{DEFAULT,NPARTNER,PERPARTNER}; // also set in fix neigh/history/omp FixNeighHistory::FixNeighHistory(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg), - npartner(NULL), partner(NULL), valuepartner(NULL), pair(NULL), + pair(NULL), npartner(NULL), partner(NULL), valuepartner(NULL), ipage_atom(NULL), dpage_atom(NULL), ipage_neigh(NULL), dpage_neigh(NULL) { if (narg != 4) error->all(FLERR,"Illegal fix NEIGH_HISTORY command"); @@ -686,7 +686,7 @@ void FixNeighHistory::grow_arrays(int nmax) copy values within local atom-based arrays ------------------------------------------------------------------------- */ -void FixNeighHistory::copy_arrays(int i, int j, int delflag) +void FixNeighHistory::copy_arrays(int i, int j, int /*delflag*/) { // just copy pointers for partner and valuepartner // b/c can't overwrite chunk allocation inside ipage_atom,dpage_atom diff --git a/src/fix_nh.cpp b/src/fix_nh.cpp index 186376d952..a1a562f2bb 100644 --- a/src/fix_nh.cpp +++ b/src/fix_nh.cpp @@ -742,7 +742,7 @@ void FixNH::init() compute T,P before integrator starts ------------------------------------------------------------------------- */ -void FixNH::setup(int vflag) +void FixNH::setup(int /*vflag*/) { // tdof needed by compute_temp_target() @@ -798,7 +798,7 @@ void FixNH::setup(int vflag) if (pstat_flag) { double kt = boltz * t_target; - double nkt = atom->natoms * kt; + double nkt = (atom->natoms + 1) * kt; for (int i = 0; i < 3; i++) if (p_flag[i]) @@ -827,7 +827,7 @@ void FixNH::setup(int vflag) 1st half of Verlet update ------------------------------------------------------------------------- */ -void FixNH::initial_integrate(int vflag) +void FixNH::initial_integrate(int /*vflag*/) { // update eta_press_dot @@ -922,7 +922,7 @@ void FixNH::final_integrate() /* ---------------------------------------------------------------------- */ -void FixNH::initial_integrate_respa(int vflag, int ilevel, int iloop) +void FixNH::initial_integrate_respa(int /*vflag*/, int ilevel, int /*iloop*/) { // set timesteps by level @@ -991,7 +991,7 @@ void FixNH::initial_integrate_respa(int vflag, int ilevel, int iloop) /* ---------------------------------------------------------------------- */ -void FixNH::final_integrate_respa(int ilevel, int iloop) +void FixNH::final_integrate_respa(int ilevel, int /*iloop*/) { // set timesteps by level @@ -1446,7 +1446,7 @@ double FixNH::compute_scalar() double volume; double energy; double kt = boltz * t_target; - double lkt_press = kt; + double lkt_press = 0.0; int ich; if (dimension == 3) volume = domain->xprd * domain->yprd * domain->zprd; else volume = domain->xprd * domain->yprd; @@ -1477,15 +1477,21 @@ double FixNH::compute_scalar() // sum is over barostatted dimensions if (pstat_flag) { - for (i = 0; i < 3; i++) - if (p_flag[i]) + for (i = 0; i < 3; i++) { + if (p_flag[i]) { energy += 0.5*omega_dot[i]*omega_dot[i]*omega_mass[i] + p_hydro*(volume-vol0) / (pdim*nktv2p); + lkt_press += kt; + } + } if (pstyle == TRICLINIC) { - for (i = 3; i < 6; i++) - if (p_flag[i]) + for (i = 3; i < 6; i++) { + if (p_flag[i]) { energy += 0.5*omega_dot[i]*omega_dot[i]*omega_mass[i]; + lkt_press += kt; + } + } } // extra contributions from thermostat chain for barostat @@ -1818,15 +1824,15 @@ void FixNH::nhc_temp_integrate() void FixNH::nhc_press_integrate() { - int ich,i; + int ich,i,pdof; double expfac,factor_etap,kecurrent; double kt = boltz * t_target; - double lkt_press = kt; + double lkt_press; // Update masses, to preserve initial freq, if flag set if (omega_mass_flag) { - double nkt = atom->natoms * kt; + double nkt = (atom->natoms + 1) * kt; for (int i = 0; i < 3; i++) if (p_flag[i]) omega_mass[i] = nkt/(p_freq[i]*p_freq[i]); @@ -1850,14 +1856,22 @@ void FixNH::nhc_press_integrate() } kecurrent = 0.0; + pdof = 0; for (i = 0; i < 3; i++) - if (p_flag[i]) kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i]; + if (p_flag[i]) { + kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i]; + pdof++; + } if (pstyle == TRICLINIC) { for (i = 3; i < 6; i++) - if (p_flag[i]) kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i]; + if (p_flag[i]) { + kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i]; + pdof++; + } } + lkt_press = pdof * kt; etap_dotdot[0] = (kecurrent - lkt_press)/etap_mass[0]; double ncfac = 1.0/nc_pchain; diff --git a/src/fix_nve.cpp b/src/fix_nve.cpp index 58e33b9744..959483230e 100644 --- a/src/fix_nve.cpp +++ b/src/fix_nve.cpp @@ -62,7 +62,7 @@ void FixNVE::init() allow for both per-type and per-atom mass ------------------------------------------------------------------------- */ -void FixNVE::initial_integrate(int vflag) +void FixNVE::initial_integrate(int /*vflag*/) { double dtfm; @@ -143,7 +143,7 @@ void FixNVE::final_integrate() /* ---------------------------------------------------------------------- */ -void FixNVE::initial_integrate_respa(int vflag, int ilevel, int iloop) +void FixNVE::initial_integrate_respa(int vflag, int ilevel, int /*iloop*/) { dtv = step_respa[ilevel]; dtf = 0.5 * step_respa[ilevel] * force->ftm2v; @@ -157,7 +157,7 @@ void FixNVE::initial_integrate_respa(int vflag, int ilevel, int iloop) /* ---------------------------------------------------------------------- */ -void FixNVE::final_integrate_respa(int ilevel, int iloop) +void FixNVE::final_integrate_respa(int ilevel, int /*iloop*/) { dtf = 0.5 * step_respa[ilevel] * force->ftm2v; final_integrate(); diff --git a/src/fix_nve_limit.cpp b/src/fix_nve_limit.cpp index f659597af7..b4fb43e56f 100644 --- a/src/fix_nve_limit.cpp +++ b/src/fix_nve_limit.cpp @@ -83,7 +83,7 @@ void FixNVELimit::init() allow for both per-type and per-atom mass ------------------------------------------------------------------------- */ -void FixNVELimit::initial_integrate(int vflag) +void FixNVELimit::initial_integrate(int /*vflag*/) { double dtfm,vsq,scale; @@ -202,7 +202,7 @@ void FixNVELimit::final_integrate() /* ---------------------------------------------------------------------- */ -void FixNVELimit::initial_integrate_respa(int vflag, int ilevel, int iloop) +void FixNVELimit::initial_integrate_respa(int vflag, int ilevel, int /*iloop*/) { dtv = step_respa[ilevel]; dtf = 0.5 * step_respa[ilevel] * force->ftm2v; @@ -213,7 +213,7 @@ void FixNVELimit::initial_integrate_respa(int vflag, int ilevel, int iloop) /* ---------------------------------------------------------------------- */ -void FixNVELimit::final_integrate_respa(int ilevel, int iloop) +void FixNVELimit::final_integrate_respa(int ilevel, int /*iloop*/) { dtf = 0.5 * step_respa[ilevel] * force->ftm2v; final_integrate(); diff --git a/src/fix_nve_noforce.cpp b/src/fix_nve_noforce.cpp index 3403f4f5ec..d4fca9e676 100644 --- a/src/fix_nve_noforce.cpp +++ b/src/fix_nve_noforce.cpp @@ -54,7 +54,7 @@ void FixNVENoforce::init() /* ---------------------------------------------------------------------- */ -void FixNVENoforce::initial_integrate(int vflag) +void FixNVENoforce::initial_integrate(int /*vflag*/) { double **x = atom->x; double **v = atom->v; diff --git a/src/fix_nve_sphere.cpp b/src/fix_nve_sphere.cpp index fe37324cfb..0bee8b8685 100644 --- a/src/fix_nve_sphere.cpp +++ b/src/fix_nve_sphere.cpp @@ -97,7 +97,7 @@ void FixNVESphere::init() /* ---------------------------------------------------------------------- */ -void FixNVESphere::initial_integrate(int vflag) +void FixNVESphere::initial_integrate(int /*vflag*/) { double dtfm,dtirotate,msq,scale,s2,inv_len_mu; double g[3]; diff --git a/src/fix_planeforce.cpp b/src/fix_planeforce.cpp index f90be6a233..45dc782fcf 100644 --- a/src/fix_planeforce.cpp +++ b/src/fix_planeforce.cpp @@ -80,7 +80,7 @@ void FixPlaneForce::min_setup(int vflag) /* ---------------------------------------------------------------------- */ -void FixPlaneForce::post_force(int vflag) +void FixPlaneForce::post_force(int /*vflag*/) { double **f = atom->f; int *mask = atom->mask; @@ -98,7 +98,7 @@ void FixPlaneForce::post_force(int vflag) /* ---------------------------------------------------------------------- */ -void FixPlaneForce::post_force_respa(int vflag, int ilevel, int iloop) +void FixPlaneForce::post_force_respa(int vflag, int /*ilevel*/, int /*iloop*/) { post_force(vflag); } diff --git a/src/fix_press_berendsen.cpp b/src/fix_press_berendsen.cpp index 792154e93f..95db004436 100644 --- a/src/fix_press_berendsen.cpp +++ b/src/fix_press_berendsen.cpp @@ -334,7 +334,7 @@ void FixPressBerendsen::init() compute T,P before integrator starts ------------------------------------------------------------------------- */ -void FixPressBerendsen::setup(int vflag) +void FixPressBerendsen::setup(int /*vflag*/) { // trigger virial computation on next timestep diff --git a/src/fix_property_atom.cpp b/src/fix_property_atom.cpp index 5ad4dfa4ba..5b12b6def2 100644 --- a/src/fix_property_atom.cpp +++ b/src/fix_property_atom.cpp @@ -292,7 +292,7 @@ void FixPropertyAtom::read_data_section(char *keyword, int n, char *buf, return # of lines in section of data file labeled by keyword ------------------------------------------------------------------------- */ -bigint FixPropertyAtom::read_data_skip_lines(char *keyword) +bigint FixPropertyAtom::read_data_skip_lines(char * /*keyword*/) { return atom->natoms; } @@ -304,7 +304,7 @@ bigint FixPropertyAtom::read_data_skip_lines(char *keyword) ny = columns = tag + nvalues ------------------------------------------------------------------------- */ -void FixPropertyAtom::write_data_section_size(int mth, int &nx, int &ny) +void FixPropertyAtom::write_data_section_size(int /*mth*/, int &nx, int &ny) { nx = atom->nlocal; ny = nvalue + 1; @@ -315,7 +315,7 @@ void FixPropertyAtom::write_data_section_size(int mth, int &nx, int &ny) buf allocated by caller as Nlocal by Nvalues+1 ------------------------------------------------------------------------- */ -void FixPropertyAtom::write_data_section_pack(int mth, double **buf) +void FixPropertyAtom::write_data_section_pack(int /*mth*/, double **buf) { int i; @@ -354,7 +354,7 @@ void FixPropertyAtom::write_data_section_pack(int mth, double **buf) only called by proc 0 ------------------------------------------------------------------------- */ -void FixPropertyAtom::write_data_section_keyword(int mth, FILE *fp) +void FixPropertyAtom::write_data_section_keyword(int /*mth*/, FILE *fp) { if (nvalue == 1 && style[0] == MOLECULE) fprintf(fp,"\nMolecules\n\n"); else if (nvalue == 1 && style[0] == CHARGE) fprintf(fp,"\nCharges\n\n"); @@ -368,8 +368,8 @@ void FixPropertyAtom::write_data_section_keyword(int mth, FILE *fp) only called by proc 0 ------------------------------------------------------------------------- */ -void FixPropertyAtom::write_data_section(int mth, FILE *fp, - int n, double **buf, int index) +void FixPropertyAtom::write_data_section(int /*mth*/, FILE *fp, + int n, double **buf, int /*index*/) { int m; @@ -443,7 +443,7 @@ void FixPropertyAtom::grow_arrays(int nmax) copy values within local atom-based arrays ------------------------------------------------------------------------- */ -void FixPropertyAtom::copy_arrays(int i, int j, int delflag) +void FixPropertyAtom::copy_arrays(int i, int j, int /*delflag*/) { for (int m = 0; m < nvalue; m++) { if (style[m] == MOLECULE) @@ -644,7 +644,7 @@ int FixPropertyAtom::maxsize_restart() size of atom nlocal's restart data ------------------------------------------------------------------------- */ -int FixPropertyAtom::size_restart(int nlocal) +int FixPropertyAtom::size_restart(int /*nlocal*/) { return nvalue+1; } diff --git a/src/fix_read_restart.cpp b/src/fix_read_restart.cpp index b384234b99..3c3178f4af 100644 --- a/src/fix_read_restart.cpp +++ b/src/fix_read_restart.cpp @@ -96,7 +96,7 @@ void FixReadRestart::grow_arrays(int nmax) copy values within local atom-based array ------------------------------------------------------------------------- */ -void FixReadRestart::copy_arrays(int i, int j, int delflag) +void FixReadRestart::copy_arrays(int i, int j, int /*delflag*/) { count[j] = count[i]; for (int m = 0; m < count[i]; m++) extra[j][m] = extra[i][m]; diff --git a/src/fix_recenter.cpp b/src/fix_recenter.cpp index 49e370ac80..75b383d67a 100644 --- a/src/fix_recenter.cpp +++ b/src/fix_recenter.cpp @@ -149,7 +149,7 @@ void FixRecenter::init() /* ---------------------------------------------------------------------- */ -void FixRecenter::initial_integrate(int vflag) +void FixRecenter::initial_integrate(int /*vflag*/) { // target COM // bounding box around domain works for both orthogonal and triclinic @@ -211,7 +211,7 @@ void FixRecenter::initial_integrate(int vflag) /* ---------------------------------------------------------------------- */ -void FixRecenter::initial_integrate_respa(int vflag, int ilevel, int iloop) +void FixRecenter::initial_integrate_respa(int vflag, int ilevel, int /*iloop*/) { // outermost level - operate recenter // all other levels - nothing diff --git a/src/fix_respa.cpp b/src/fix_respa.cpp index 3b9aad1286..64461ba7ca 100644 --- a/src/fix_respa.cpp +++ b/src/fix_respa.cpp @@ -93,7 +93,7 @@ void FixRespa::grow_arrays(int nmax) copy values within local atom-based arrays ------------------------------------------------------------------------- */ -void FixRespa::copy_arrays(int i, int j, int delflag) +void FixRespa::copy_arrays(int i, int j, int /*delflag*/) { for (int k = 0; k < nlevels; k++) { f_level[j][k][0] = f_level[i][k][0]; diff --git a/src/fix_restrain.cpp b/src/fix_restrain.cpp index 6ad229fea7..bb09116374 100644 --- a/src/fix_restrain.cpp +++ b/src/fix_restrain.cpp @@ -188,7 +188,7 @@ void FixRestrain::min_setup(int vflag) /* ---------------------------------------------------------------------- */ -void FixRestrain::post_force(int vflag) +void FixRestrain::post_force(int /*vflag*/) { energy = 0.0; @@ -204,7 +204,7 @@ void FixRestrain::post_force(int vflag) /* ---------------------------------------------------------------------- */ -void FixRestrain::post_force_respa(int vflag, int ilevel, int iloop) +void FixRestrain::post_force_respa(int vflag, int ilevel, int /*iloop*/) { if (ilevel == ilevel_respa) post_force(vflag); } diff --git a/src/fix_setforce.cpp b/src/fix_setforce.cpp index 89b340b0ae..fc8b7aeb59 100644 --- a/src/fix_setforce.cpp +++ b/src/fix_setforce.cpp @@ -219,7 +219,7 @@ void FixSetForce::min_setup(int vflag) /* ---------------------------------------------------------------------- */ -void FixSetForce::post_force(int vflag) +void FixSetForce::post_force(int /*vflag*/) { double **x = atom->x; double **f = atom->f; @@ -293,7 +293,7 @@ void FixSetForce::post_force(int vflag) /* ---------------------------------------------------------------------- */ -void FixSetForce::post_force_respa(int vflag, int ilevel, int iloop) +void FixSetForce::post_force_respa(int vflag, int ilevel, int /*iloop*/) { // set force to desired value on requested level, 0.0 on other levels diff --git a/src/fix_spring.cpp b/src/fix_spring.cpp index ecb84eeb0f..328a0eeafd 100644 --- a/src/fix_spring.cpp +++ b/src/fix_spring.cpp @@ -159,7 +159,7 @@ void FixSpring::min_setup(int vflag) /* ---------------------------------------------------------------------- */ -void FixSpring::post_force(int vflag) +void FixSpring::post_force(int /*vflag*/) { if (styleflag == TETHER) spring_tether(); else spring_couple(); @@ -335,7 +335,7 @@ void FixSpring::spring_couple() /* ---------------------------------------------------------------------- */ -void FixSpring::post_force_respa(int vflag, int ilevel, int iloop) +void FixSpring::post_force_respa(int vflag, int ilevel, int /*iloop*/) { if (ilevel == ilevel_respa) post_force(vflag); } diff --git a/src/fix_spring_chunk.cpp b/src/fix_spring_chunk.cpp index 53e9285a9c..5b5d95b111 100644 --- a/src/fix_spring_chunk.cpp +++ b/src/fix_spring_chunk.cpp @@ -144,7 +144,7 @@ void FixSpringChunk::min_setup(int vflag) /* ---------------------------------------------------------------------- */ -void FixSpringChunk::post_force(int vflag) +void FixSpringChunk::post_force(int /*vflag*/) { int i,m; double dx,dy,dz,r; @@ -231,7 +231,7 @@ void FixSpringChunk::post_force(int vflag) /* ---------------------------------------------------------------------- */ -void FixSpringChunk::post_force_respa(int vflag, int ilevel, int iloop) +void FixSpringChunk::post_force_respa(int vflag, int ilevel, int /*iloop*/) { if (ilevel == ilevel_respa) post_force(vflag); } diff --git a/src/fix_spring_rg.cpp b/src/fix_spring_rg.cpp index c2e226a343..28c8969006 100644 --- a/src/fix_spring_rg.cpp +++ b/src/fix_spring_rg.cpp @@ -95,7 +95,7 @@ void FixSpringRG::setup(int vflag) /* ---------------------------------------------------------------------- */ -void FixSpringRG::post_force(int vflag) +void FixSpringRG::post_force(int /*vflag*/) { // compute current Rg and center-of-mass @@ -142,7 +142,7 @@ void FixSpringRG::post_force(int vflag) /* ---------------------------------------------------------------------- */ -void FixSpringRG::post_force_respa(int vflag, int ilevel, int iloop) +void FixSpringRG::post_force_respa(int vflag, int ilevel, int /*iloop*/) { if (ilevel == ilevel_respa) post_force(vflag); } diff --git a/src/fix_spring_self.cpp b/src/fix_spring_self.cpp index 1a5c89c6a1..670883af41 100644 --- a/src/fix_spring_self.cpp +++ b/src/fix_spring_self.cpp @@ -148,7 +148,7 @@ void FixSpringSelf::min_setup(int vflag) /* ---------------------------------------------------------------------- */ -void FixSpringSelf::post_force(int vflag) +void FixSpringSelf::post_force(int /*vflag*/) { double **x = atom->x; double **f = atom->f; @@ -181,7 +181,7 @@ void FixSpringSelf::post_force(int vflag) /* ---------------------------------------------------------------------- */ -void FixSpringSelf::post_force_respa(int vflag, int ilevel, int iloop) +void FixSpringSelf::post_force_respa(int vflag, int ilevel, int /*iloop*/) { if (ilevel == ilevel_respa) post_force(vflag); } @@ -227,7 +227,7 @@ void FixSpringSelf::grow_arrays(int nmax) copy values within local atom-based array ------------------------------------------------------------------------- */ -void FixSpringSelf::copy_arrays(int i, int j, int delflag) +void FixSpringSelf::copy_arrays(int i, int j, int /*delflag*/) { xoriginal[j][0] = xoriginal[i][0]; xoriginal[j][1] = xoriginal[i][1]; @@ -303,7 +303,7 @@ int FixSpringSelf::maxsize_restart() size of atom nlocal's restart data ------------------------------------------------------------------------- */ -int FixSpringSelf::size_restart(int nlocal) +int FixSpringSelf::size_restart(int /*nlocal*/) { return 4; } diff --git a/src/fix_store.cpp b/src/fix_store.cpp index 3b1f3dca77..9db65d0987 100644 --- a/src/fix_store.cpp +++ b/src/fix_store.cpp @@ -154,8 +154,6 @@ void FixStore::reset_global(int nrow_caller, int ncol_caller) if (vecflag) memory->create(vstore,nrow,"fix/store:vstore"); else memory->create(astore,nrow,ncol,"fix/store:astore"); memory->create(rbuf,nrow*ncol+2,"fix/store:rbuf"); - - // printf("AAA HOW GET HERE\n"); } /* ---------------------------------------------------------------------- @@ -231,7 +229,7 @@ void FixStore::grow_arrays(int nmax) copy values within local atom-based array ------------------------------------------------------------------------- */ -void FixStore::copy_arrays(int i, int j, int delflag) +void FixStore::copy_arrays(int i, int j, int /*delflag*/) { if (disable) return; @@ -326,7 +324,7 @@ int FixStore::maxsize_restart() size of atom nlocal's restart data ------------------------------------------------------------------------- */ -int FixStore::size_restart(int nlocal) +int FixStore::size_restart(int /*nlocal*/) { if (disable) return 1; return nvalues+1; diff --git a/src/fix_store_force.cpp b/src/fix_store_force.cpp index 5e2150f68d..a841714098 100644 --- a/src/fix_store_force.cpp +++ b/src/fix_store_force.cpp @@ -95,7 +95,7 @@ void FixStoreForce::min_setup(int vflag) /* ---------------------------------------------------------------------- */ -void FixStoreForce::post_force(int vflag) +void FixStoreForce::post_force(int /*vflag*/) { if (atom->nmax > nmax) { nmax = atom->nmax; @@ -118,7 +118,7 @@ void FixStoreForce::post_force(int vflag) /* ---------------------------------------------------------------------- */ -void FixStoreForce::post_force_respa(int vflag, int ilevel, int iloop) +void FixStoreForce::post_force_respa(int vflag, int ilevel, int /*iloop*/) { if (ilevel == nlevels_respa-1) post_force(vflag); } diff --git a/src/fix_store_state.cpp b/src/fix_store_state.cpp index 3195e983e3..da899a173c 100644 --- a/src/fix_store_state.cpp +++ b/src/fix_store_state.cpp @@ -446,7 +446,7 @@ void FixStoreState::init() /* ---------------------------------------------------------------------- */ -void FixStoreState::setup(int vflag) +void FixStoreState::setup(int /*vflag*/) { // if first invocation, store current values for compute, fix, variable @@ -580,7 +580,7 @@ void FixStoreState::grow_arrays(int nmax) copy values within local atom-based array ------------------------------------------------------------------------- */ -void FixStoreState::copy_arrays(int i, int j, int delflag) +void FixStoreState::copy_arrays(int i, int j, int /*delflag*/) { for (int m = 0; m < nvalues; m++) values[j][m] = values[i][m]; } @@ -646,7 +646,7 @@ int FixStoreState::maxsize_restart() size of atom nlocal's restart data ------------------------------------------------------------------------- */ -int FixStoreState::size_restart(int nlocal) +int FixStoreState::size_restart(int /*nlocal*/) { return nvalues+1; } diff --git a/src/fix_tmd.cpp b/src/fix_tmd.cpp index 39d4173a63..dd11dfd0c7 100644 --- a/src/fix_tmd.cpp +++ b/src/fix_tmd.cpp @@ -170,7 +170,7 @@ void FixTMD::init() /* ---------------------------------------------------------------------- */ -void FixTMD::initial_integrate(int vflag) +void FixTMD::initial_integrate(int /*vflag*/) { double a,b,c,d,e; double dx,dy,dz,dxkt,dykt,dzkt; @@ -335,7 +335,7 @@ void FixTMD::grow_arrays(int nmax) copy values within local atom-based arrays ------------------------------------------------------------------------- */ -void FixTMD::copy_arrays(int i, int j, int delflag) +void FixTMD::copy_arrays(int i, int j, int /*delflag*/) { xf[j][0] = xf[i][0]; xf[j][1] = xf[i][1]; @@ -412,7 +412,7 @@ void FixTMD::readfile(char *file) m++; } - MPI_Bcast(&eof,sizeof(char *)/sizeof(char),MPI_CHAR,0,world); + MPI_Bcast(&eof,sizeof(char *),MPI_CHAR,0,world); MPI_Bcast(&nlines,1,MPI_INT,0,world); MPI_Bcast(&m,1,MPI_INT,0,world); MPI_Bcast(buffer,m,MPI_CHAR,0,world); diff --git a/src/fix_vector.cpp b/src/fix_vector.cpp index 9b7f016970..6387af7676 100644 --- a/src/fix_vector.cpp +++ b/src/fix_vector.cpp @@ -239,7 +239,7 @@ void FixVector::init() only does something if nvalid = current timestep ------------------------------------------------------------------------- */ -void FixVector::setup(int vflag) +void FixVector::setup(int /*vflag*/) { end_of_step(); } diff --git a/src/fix_viscous.cpp b/src/fix_viscous.cpp index 1d2609c8b6..e845142322 100644 --- a/src/fix_viscous.cpp +++ b/src/fix_viscous.cpp @@ -109,7 +109,7 @@ void FixViscous::min_setup(int vflag) /* ---------------------------------------------------------------------- */ -void FixViscous::post_force(int vflag) +void FixViscous::post_force(int /*vflag*/) { // apply drag force to atoms in group // direction is opposed to velocity vector @@ -134,7 +134,7 @@ void FixViscous::post_force(int vflag) /* ---------------------------------------------------------------------- */ -void FixViscous::post_force_respa(int vflag, int ilevel, int iloop) +void FixViscous::post_force_respa(int vflag, int ilevel, int /*iloop*/) { if (ilevel == ilevel_respa) post_force(vflag); } diff --git a/src/fix_wall.cpp b/src/fix_wall.cpp index 096bbe618a..e84d01191d 100644 --- a/src/fix_wall.cpp +++ b/src/fix_wall.cpp @@ -343,7 +343,7 @@ void FixWall::post_force(int vflag) /* ---------------------------------------------------------------------- */ -void FixWall::post_force_respa(int vflag, int ilevel, int iloop) +void FixWall::post_force_respa(int vflag, int ilevel, int /*iloop*/) { if (ilevel == ilevel_respa) post_force(vflag); } diff --git a/src/fix_wall_region.cpp b/src/fix_wall_region.cpp index ea1b62bfa5..ff147d7446 100644 --- a/src/fix_wall_region.cpp +++ b/src/fix_wall_region.cpp @@ -287,7 +287,7 @@ void FixWallRegion::post_force(int vflag) /* ---------------------------------------------------------------------- */ -void FixWallRegion::post_force_respa(int vflag, int ilevel, int iloop) +void FixWallRegion::post_force_respa(int vflag, int ilevel, int /*iloop*/) { if (ilevel == ilevel_respa) post_force(vflag); } diff --git a/src/group.cpp b/src/group.cpp index 9d33da9acb..3bc3f3d7bf 100644 --- a/src/group.cpp +++ b/src/group.cpp @@ -629,7 +629,7 @@ int Group::find_unused() do not include molID = 0 ------------------------------------------------------------------------- */ -void Group::add_molecules(int igroup, int bit) +void Group::add_molecules(int /*igroup*/, int bit) { // hash = unique molecule IDs of atoms already in group @@ -754,6 +754,18 @@ void Group::read_restart(FILE *fp) // computations on a group of atoms // ---------------------------------------------------------------------- +/* ---------------------------------------------------------------------- + count atoms in group all +------------------------------------------------------------------------- */ + +bigint Group::count_all() +{ + bigint nme = atom->nlocal; + bigint nall; + MPI_Allreduce(&nme,&nall,1,MPI_LMP_BIGINT,MPI_SUM,world); + return nall; +} + /* ---------------------------------------------------------------------- count atoms in group ------------------------------------------------------------------------- */ diff --git a/src/group.h b/src/group.h index 6b6cbb1def..962d37b32a 100644 --- a/src/group.h +++ b/src/group.h @@ -37,6 +37,7 @@ class Group : protected Pointers { void write_restart(FILE *); void read_restart(FILE *); + bigint count_all(); // count atoms in group all bigint count(int); // count atoms in group bigint count(int,int); // count atoms in group & region double mass(int); // total mass of atoms in group diff --git a/src/image.cpp b/src/image.cpp index 301a2af88f..3df167bbf6 100644 --- a/src/image.cpp +++ b/src/image.cpp @@ -1017,6 +1017,8 @@ void Image::write_JPG(FILE *fp) jpeg_finish_compress(&cinfo); jpeg_destroy_compress(&cinfo); +#else + LMP_UNUSED_PARAM(fp); #endif } @@ -1074,6 +1076,8 @@ void Image::write_PNG(FILE *fp) png_destroy_write_struct(&png_ptr, &info_ptr); delete[] row_pointers; +#else + LMP_UNUSED_PARAM(fp); #endif } diff --git a/src/imbalance_var.cpp b/src/imbalance_var.cpp index acb3da8d13..e089b1df0c 100644 --- a/src/imbalance_var.cpp +++ b/src/imbalance_var.cpp @@ -52,7 +52,7 @@ int ImbalanceVar::options(int narg, char **arg) /* -------------------------------------------------------------------- */ -void ImbalanceVar::init(int flag) +void ImbalanceVar::init(int /*flag*/) { id = input->variable->find(name); if (id < 0) { diff --git a/src/improper_zero.cpp b/src/improper_zero.cpp index 25ab3e7bba..8a1fa529c6 100644 --- a/src/improper_zero.cpp +++ b/src/improper_zero.cpp @@ -99,13 +99,13 @@ void ImproperZero::coeff(int narg, char **arg) proc 0 writes out coeffs to restart file ------------------------------------------------------------------------- */ -void ImproperZero::write_restart(FILE *fp) {} +void ImproperZero::write_restart(FILE * /*fp*/) {} /* ---------------------------------------------------------------------- proc 0 reads coeffs from restart file, bcasts them ------------------------------------------------------------------------- */ -void ImproperZero::read_restart(FILE *fp) +void ImproperZero::read_restart(FILE * /*fp*/) { allocate(); for (int i = 1; i <= atom->nimpropertypes; i++) setflag[i] = 1; diff --git a/src/info.cpp b/src/info.cpp index 65c0cd9b53..672ce72b74 100644 --- a/src/info.cpp +++ b/src/info.cpp @@ -44,7 +44,7 @@ #include "error.h" #include -#include +#include #include #include @@ -117,7 +117,8 @@ static const char bstyles[] = "pfsm"; using namespace LAMMPS_NS; using namespace std; -static void print_columns(FILE* fp, vector & styles); +template +static void print_columns(FILE* fp, map * styles); /* ---------------------------------------------------------------------- */ @@ -259,14 +260,35 @@ void Info::command(int narg, char **arg) fprintf(out,"Printed on %s\n",ctime(&now)); if (flags & CONFIG) { - - fprintf(out,"\nLAMMPS version: %s / %s\n", + fprintf(out,"\nLAMMPS version: %s / %s\n\n", universe->version, universe->num_ver); fprintf(out,"sizeof(smallint): %3d-bit\n",(int)sizeof(smallint)*8); fprintf(out,"sizeof(imageint): %3d-bit\n",(int)sizeof(imageint)*8); fprintf(out,"sizeof(tagint): %3d-bit\n",(int)sizeof(tagint)*8); fprintf(out,"sizeof(bigint): %3d-bit\n",(int)sizeof(bigint)*8); + fputs("\nActive compile time flags:\n\n",out); + if (has_gzip_support()) fputs("-DLAMMPS_GZIP\n",out); + if (has_png_support()) fputs("-DLAMMPS_PNG\n",out); + if (has_jpeg_support()) fputs("-DLAMMPS_JPEG\n",out); + if (has_ffmpeg_support()) fputs("-DLAMMPS_FFMPEG\n",out); + if (has_exceptions()) fputs("-DLAMMPS_EXCEPTIONS\n",out); + + const char *pkg; + int ncword, ncline = 0; + + fputs("\nInstalled packages:\n\n",out); + for (int i = 0; NULL != (pkg = lmp->installed_packages[i]); ++i) { + ncword = strlen(pkg); + if (ncline + ncword > 78) { + ncline = 0; + fputs("\n",out); + } + fprintf(out,"%s ",pkg); + ncline += ncword + 1; + } + fputs("\n",out); + #if defined(_WIN32) DWORD fullversion,majorv,minorv,buildv=0; @@ -665,196 +687,98 @@ void Info::available_styles(FILE * out, int flags) void Info::atom_styles(FILE * out) { fprintf(out, "\nAtom styles:\n"); - - vector styles; - - for(Atom::AtomVecCreatorMap::iterator it = atom->avec_map->begin(); it != atom->avec_map->end(); ++it) { - styles.push_back(it->first); - } - - print_columns(out, styles); + print_columns(out, atom->avec_map); fprintf(out, "\n\n\n"); } void Info::integrate_styles(FILE * out) { fprintf(out, "\nIntegrate styles:\n"); - - vector styles; - - for(Update::IntegrateCreatorMap::iterator it = update->integrate_map->begin(); it != update->integrate_map->end(); ++it) { - styles.push_back(it->first); - } - - print_columns(out, styles); + print_columns(out, update->integrate_map); fprintf(out, "\n\n\n"); } void Info::minimize_styles(FILE * out) { fprintf(out, "\nMinimize styles:\n"); - - vector styles; - - for(Update::MinimizeCreatorMap::iterator it = update->minimize_map->begin(); it != update->minimize_map->end(); ++it) { - styles.push_back(it->first); - } - - print_columns(out, styles); + print_columns(out, update->minimize_map); fprintf(out, "\n\n\n"); } void Info::pair_styles(FILE * out) { fprintf(out, "\nPair styles:\n"); - - vector styles; - - for(Force::PairCreatorMap::iterator it = force->pair_map->begin(); it != force->pair_map->end(); ++it) { - styles.push_back(it->first); - } - - print_columns(out, styles); + print_columns(out, force->pair_map); fprintf(out, "\n\n\n"); } void Info::bond_styles(FILE * out) { fprintf(out, "\nBond styles:\n"); - - vector styles; - - for(Force::BondCreatorMap::iterator it = force->bond_map->begin(); it != force->bond_map->end(); ++it) { - styles.push_back(it->first); - } - - print_columns(out, styles); + print_columns(out, force->bond_map); fprintf(out, "\n\n\n"); } void Info::angle_styles(FILE * out) { fprintf(out, "\nAngle styles:\n"); - - vector styles; - - for(Force::AngleCreatorMap::iterator it = force->angle_map->begin(); it != force->angle_map->end(); ++it) { - styles.push_back(it->first); - } - - print_columns(out, styles); + print_columns(out, force->angle_map); fprintf(out, "\n\n\n"); } void Info::dihedral_styles(FILE * out) { fprintf(out, "\nDihedral styles:\n"); - - vector styles; - - for(Force::DihedralCreatorMap::iterator it = force->dihedral_map->begin(); it != force->dihedral_map->end(); ++it) { - styles.push_back(it->first); - } - - print_columns(out, styles); + print_columns(out, force->dihedral_map); fprintf(out, "\n\n\n"); } void Info::improper_styles(FILE * out) { fprintf(out, "\nImproper styles:\n"); - - vector styles; - - for(Force::ImproperCreatorMap::iterator it = force->improper_map->begin(); it != force->improper_map->end(); ++it) { - styles.push_back(it->first); - } - - print_columns(out, styles); + print_columns(out, force->improper_map); fprintf(out, "\n\n\n"); } void Info::kspace_styles(FILE * out) { fprintf(out, "\nKSpace styles:\n"); - - vector styles; - - for(Force::KSpaceCreatorMap::iterator it = force->kspace_map->begin(); it != force->kspace_map->end(); ++it) { - styles.push_back(it->first); - } - - print_columns(out, styles); + print_columns(out, force->kspace_map); fprintf(out, "\n\n\n"); } void Info::fix_styles(FILE * out) { fprintf(out, "\nFix styles:\n"); - - vector styles; - - for(Modify::FixCreatorMap::iterator it = modify->fix_map->begin(); it != modify->fix_map->end(); ++it) { - styles.push_back(it->first); - } - - print_columns(out, styles); + print_columns(out, modify->fix_map); fprintf(out, "\n\n\n"); } void Info::compute_styles(FILE * out) { fprintf(out, "\nCompute styles:\n"); - - vector styles; - - for(Modify::ComputeCreatorMap::iterator it = modify->compute_map->begin(); it != modify->compute_map->end(); ++it) { - styles.push_back(it->first); - } - - print_columns(out, styles); + print_columns(out, modify->compute_map); fprintf(out, "\n\n\n"); } void Info::region_styles(FILE * out) { fprintf(out, "\nRegion styles:\n"); - - vector styles; - - for(Domain::RegionCreatorMap::iterator it = domain->region_map->begin(); it != domain->region_map->end(); ++it) { - styles.push_back(it->first); - } - - print_columns(out, styles); + print_columns(out, domain->region_map); fprintf(out, "\n\n\n"); } void Info::dump_styles(FILE * out) { fprintf(out, "\nDump styles:\n"); - - vector styles; - - for(Output::DumpCreatorMap::iterator it = output->dump_map->begin(); it != output->dump_map->end(); ++it) { - styles.push_back(it->first); - } - - print_columns(out, styles); + print_columns(out, output->dump_map); fprintf(out, "\n\n\n"); } void Info::command_styles(FILE * out) { fprintf(out, "\nCommand styles (add-on input script commands):\n"); - - vector styles; - - for(Input::CommandCreatorMap::iterator it = input->command_map->begin(); it != input->command_map->end(); ++it) { - styles.push_back(it->first); - } - - print_columns(out, styles); + print_columns(out, input->command_map); fprintf(out, "\n\n\n"); } @@ -1089,47 +1013,48 @@ bool Info::is_defined(const char *category, const char *name) return false; } -static void print_columns(FILE* fp, vector & styles) +template +static void print_columns(FILE* fp, map * styles) { - if (styles.size() == 0) { + if (styles->empty()) { fprintf(fp, "\nNone"); return; } - std::sort(styles.begin(), styles.end()); - + // std::map keys are already sorted int pos = 80; - for (int i = 0; i < styles.size(); ++i) { + for(typename map::iterator it = styles->begin(); it != styles->end(); ++it) { + const string & style_name = it->first; // skip "secret" styles - if (isupper(styles[i][0])) continue; + if (isupper(style_name[0])) continue; - int len = styles[i].length(); + int len = style_name.length(); if (pos + len > 80) { fprintf(fp,"\n"); pos = 0; } if (len < 16) { - fprintf(fp,"%-16s",styles[i].c_str()); + fprintf(fp,"%-16s", style_name.c_str()); pos += 16; } else if (len < 32) { - fprintf(fp,"%-32s",styles[i].c_str()); + fprintf(fp,"%-32s", style_name.c_str()); pos += 32; } else if (len < 48) { - fprintf(fp,"%-48s",styles[i].c_str()); + fprintf(fp,"%-48s", style_name.c_str()); pos += 48; } else if (len < 64) { - fprintf(fp,"%-64s",styles[i].c_str()); + fprintf(fp,"%-64s", style_name.c_str()); pos += 64; } else { - fprintf(fp,"%-80s",styles[i].c_str()); + fprintf(fp,"%-80s", style_name.c_str()); pos += 80; } } } -bool Info::has_gzip_support() const { +bool Info::has_gzip_support() { #ifdef LAMMPS_GZIP return true; #else @@ -1137,7 +1062,7 @@ bool Info::has_gzip_support() const { #endif } -bool Info::has_png_support() const { +bool Info::has_png_support() { #ifdef LAMMPS_PNG return true; #else @@ -1145,7 +1070,7 @@ bool Info::has_png_support() const { #endif } -bool Info::has_jpeg_support() const { +bool Info::has_jpeg_support() { #ifdef LAMMPS_JPEG return true; #else @@ -1153,7 +1078,7 @@ bool Info::has_jpeg_support() const { #endif } -bool Info::has_ffmpeg_support() const { +bool Info::has_ffmpeg_support() { #ifdef LAMMPS_FFMPEG return true; #else @@ -1161,7 +1086,7 @@ bool Info::has_ffmpeg_support() const { #endif } -bool Info::has_exceptions() const { +bool Info::has_exceptions() { #ifdef LAMMPS_EXCEPTIONS return true; #else @@ -1169,6 +1094,15 @@ bool Info::has_exceptions() const { #endif } +bool Info::has_package(const char * package_name) { + for(int i = 0; LAMMPS::installed_packages[i] != NULL; ++i) { + if(strcmp(package_name, LAMMPS::installed_packages[i]) == 0) { + return true; + } + } + return false; +} + /* ---------------------------------------------------------------------- */ char **Info::get_variable_names(int &num) { diff --git a/src/info.h b/src/info.h index fb7ca58c47..058400df78 100644 --- a/src/info.h +++ b/src/info.h @@ -33,11 +33,12 @@ class Info : protected Pointers { bool is_defined(const char *, const char *); bool is_available(const char *, const char *); - bool has_gzip_support() const; - bool has_png_support() const; - bool has_jpeg_support() const; - bool has_ffmpeg_support() const; - bool has_exceptions() const; + static bool has_gzip_support(); + static bool has_png_support(); + static bool has_jpeg_support(); + static bool has_ffmpeg_support(); + static bool has_exceptions(); + static bool has_package(const char * package_name); char **get_variable_names(int &num); diff --git a/src/integrate.cpp b/src/integrate.cpp index 97d28d6d7c..d6b27e042d 100644 --- a/src/integrate.cpp +++ b/src/integrate.cpp @@ -24,7 +24,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -Integrate::Integrate(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) +Integrate::Integrate(LAMMPS *lmp, int /*narg*/, char **/*arg*/) : Pointers(lmp) { elist_global = elist_atom = NULL; vlist_global = vlist_atom = NULL; diff --git a/src/kspace.cpp b/src/kspace.cpp index fc8b12288b..b92cd1e9dc 100644 --- a/src/kspace.cpp +++ b/src/kspace.cpp @@ -30,7 +30,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -KSpace::KSpace(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) +KSpace::KSpace(LAMMPS *lmp, int /*narg*/, char **/*arg*/) : Pointers(lmp) { order_allocated = 0; energy = 0.0; @@ -580,7 +580,11 @@ void KSpace::modify_params(int narg, char **arg) else if (strcmp(arg[iarg+1],"no") == 0) auto_disp_flag = 0; else error->all(FLERR,"Illegal kspace_modify command"); iarg += 2; - } else error->all(FLERR,"Illegal kspace_modify command"); + } else { + int n = modify_param(narg-iarg,&arg[iarg]); + if (n == 0) error->all(FLERR,"Illegal kspace_modify command"); + iarg += n; + } } } diff --git a/src/kspace.h b/src/kspace.h index 28c7bcef2a..c25dc93f45 100644 --- a/src/kspace.h +++ b/src/kspace.h @@ -126,6 +126,8 @@ class KSpace : protected Pointers { virtual int timing(int, double &, double &) {return 0;} virtual int timing_1d(int, double &) {return 0;} virtual int timing_3d(int, double &) {return 0;} + + virtual int modify_param(int, char **) {return 0;} virtual double memory_usage() {return 0.0;} /* ---------------------------------------------------------------------- diff --git a/src/lammps.cpp b/src/lammps.cpp index 56af95767b..fcdfecf30a 100644 --- a/src/lammps.cpp +++ b/src/lammps.cpp @@ -31,6 +31,7 @@ #include "style_region.h" #include "universe.h" #include "input.h" +#include "info.h" #include "atom.h" #include "update.h" #include "neighbor.h" @@ -46,10 +47,12 @@ #include "accelerator_omp.h" #include "timer.h" #include "python.h" -#include "memory.h" #include "version.h" +#include "memory.h" #include "error.h" +#include "lmpinstalledpkgs.h" + using namespace LAMMPS_NS; static void print_style(FILE *fp, const char *str, int &pos); @@ -70,12 +73,46 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) output = NULL; python = NULL; + clientserver = 0; + cslib = NULL; + cscomm = 0; + screen = NULL; logfile = NULL; infile = NULL; initclock = MPI_Wtime(); + // check if -mpi is first arg + // if so, then 2 apps were launched with one mpirun command + // this means passed communicator (e.g. MPI_COMM_WORLD) is bigger than LAMMPS + // e.g. for client/server coupling with another code + // in the future LAMMPS might leverage this in other ways + // universe communicator needs to shrink to be just LAMMPS + // syntax: -mpi color + // color = integer for this app, different than other app(s) + // do the following: + // perform an MPI_Comm_split() to create a new LAMMPS-only subcomm + // NOTE: this assumes other app(s) does same thing, else will hang! + // re-create universe with subcomm + // store full multi-app comm in cscomm + // cscomm is used by CSLIB package to exchange messages w/ other app + + int iarg = 1; + if (narg-iarg >= 2 && (strcmp(arg[iarg],"-mpi") == 0 || + strcmp(arg[iarg],"-m") == 0)) { + int me,nprocs; + MPI_Comm_rank(communicator,&me); + MPI_Comm_size(communicator,&nprocs); + int color = atoi(arg[iarg+1]); + MPI_Comm subcomm; + MPI_Comm_split(communicator,color,me,&subcomm); + cscomm = communicator; + communicator = subcomm; + delete universe; + universe = new Universe(this,communicator); + } + // parse input switches int inflag = 0; @@ -104,59 +141,30 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) int *pfirst = NULL; int *plast = NULL; - int iarg = 1; + iarg = 1; while (iarg < narg) { - if (strcmp(arg[iarg],"-partition") == 0 || - strcmp(arg[iarg],"-p") == 0) { - universe->existflag = 1; + + if (strcmp(arg[iarg],"-echo") == 0 || + strcmp(arg[iarg],"-e") == 0) { if (iarg+2 > narg) error->universe_all(FLERR,"Invalid command-line argument"); - iarg++; - while (iarg < narg && arg[iarg][0] != '-') { - universe->add_world(arg[iarg]); - iarg++; - } + iarg += 2; + + } else if (strcmp(arg[iarg],"-help") == 0 || + strcmp(arg[iarg],"-h") == 0) { + if (iarg+1 > narg) + error->universe_all(FLERR,"Invalid command-line argument"); + helpflag = 1; + citeflag = 0; + iarg += 1; + } else if (strcmp(arg[iarg],"-in") == 0 || strcmp(arg[iarg],"-i") == 0) { if (iarg+2 > narg) error->universe_all(FLERR,"Invalid command-line argument"); inflag = iarg + 1; iarg += 2; - } else if (strcmp(arg[iarg],"-screen") == 0 || - strcmp(arg[iarg],"-sc") == 0) { - if (iarg+2 > narg) - error->universe_all(FLERR,"Invalid command-line argument"); - screenflag = iarg + 1; - iarg += 2; - } else if (strcmp(arg[iarg],"-log") == 0 || - strcmp(arg[iarg],"-l") == 0) { - if (iarg+2 > narg) - error->universe_all(FLERR,"Invalid command-line argument"); - logflag = iarg + 1; - iarg += 2; - } else if (strcmp(arg[iarg],"-var") == 0 || - strcmp(arg[iarg],"-v") == 0) { - if (iarg+3 > narg) - error->universe_all(FLERR,"Invalid command-line argument"); - iarg += 3; - while (iarg < narg && arg[iarg][0] != '-') iarg++; - } else if (strcmp(arg[iarg],"-echo") == 0 || - strcmp(arg[iarg],"-e") == 0) { - if (iarg+2 > narg) - error->universe_all(FLERR,"Invalid command-line argument"); - iarg += 2; - } else if (strcmp(arg[iarg],"-pscreen") == 0 || - strcmp(arg[iarg],"-ps") == 0) { - if (iarg+2 > narg) - error->universe_all(FLERR,"Invalid command-line argument"); - partscreenflag = iarg + 1; - iarg += 2; - } else if (strcmp(arg[iarg],"-plog") == 0 || - strcmp(arg[iarg],"-pl") == 0) { - if (iarg+2 > narg) - error->universe_all(FLERR,"Invalid command-line argument"); - partlogflag = iarg + 1; - iarg += 2; + } else if (strcmp(arg[iarg],"-kokkos") == 0 || strcmp(arg[iarg],"-k") == 0) { if (iarg+2 > narg) @@ -169,6 +177,26 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) kkfirst = iarg; while (iarg < narg && arg[iarg][0] != '-') iarg++; kklast = iarg; + + } else if (strcmp(arg[iarg],"-log") == 0 || + strcmp(arg[iarg],"-l") == 0) { + if (iarg+2 > narg) + error->universe_all(FLERR,"Invalid command-line argument"); + logflag = iarg + 1; + iarg += 2; + + } else if (strcmp(arg[iarg],"-mpi") == 0 || + strcmp(arg[iarg],"-m") == 0) { + if (iarg+2 > narg) + error->universe_all(FLERR,"Invalid command-line argument"); + if (iarg != 1) error->universe_all(FLERR,"Invalid command-line argument"); + iarg += 2; + + } else if (strcmp(arg[iarg],"-nocite") == 0 || + strcmp(arg[iarg],"-nc") == 0) { + citeflag = 0; + iarg++; + } else if (strcmp(arg[iarg],"-package") == 0 || strcmp(arg[iarg],"-pk") == 0) { if (iarg+2 > narg) @@ -185,6 +213,69 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) else break; } plast[npack++] = iarg; + + } else if (strcmp(arg[iarg],"-partition") == 0 || + strcmp(arg[iarg],"-p") == 0) { + universe->existflag = 1; + if (iarg+2 > narg) + error->universe_all(FLERR,"Invalid command-line argument"); + iarg++; + while (iarg < narg && arg[iarg][0] != '-') { + universe->add_world(arg[iarg]); + iarg++; + } + + } else if (strcmp(arg[iarg],"-plog") == 0 || + strcmp(arg[iarg],"-pl") == 0) { + if (iarg+2 > narg) + error->universe_all(FLERR,"Invalid command-line argument"); + partlogflag = iarg + 1; + iarg += 2; + + } else if (strcmp(arg[iarg],"-pscreen") == 0 || + strcmp(arg[iarg],"-ps") == 0) { + if (iarg+2 > narg) + error->universe_all(FLERR,"Invalid command-line argument"); + partscreenflag = iarg + 1; + iarg += 2; + + } else if (strcmp(arg[iarg],"-reorder") == 0 || + strcmp(arg[iarg],"-ro") == 0) { + if (iarg+3 > narg) + error->universe_all(FLERR,"Invalid command-line argument"); + if (universe->existflag) + error->universe_all(FLERR,"Cannot use -reorder after -partition"); + universe->reorder(arg[iarg+1],arg[iarg+2]); + iarg += 3; + + } else if (strcmp(arg[iarg],"-restart") == 0 || + strcmp(arg[iarg],"-r") == 0) { + if (iarg+3 > narg) + error->universe_all(FLERR,"Invalid command-line argument"); + restartflag = 1; + rfile = arg[iarg+1]; + dfile = arg[iarg+2]; + // check for restart remap flag + if (strcmp(dfile,"remap") == 0) { + if (iarg+4 > narg) + error->universe_all(FLERR,"Invalid command-line argument"); + restartremapflag = 1; + dfile = arg[iarg+3]; + iarg++; + } + iarg += 3; + // delimit any extra args for the write_data command + wdfirst = iarg; + while (iarg < narg && arg[iarg][0] != '-') iarg++; + wdlast = iarg; + + } else if (strcmp(arg[iarg],"-screen") == 0 || + strcmp(arg[iarg],"-sc") == 0) { + if (iarg+2 > narg) + error->universe_all(FLERR,"Invalid command-line argument"); + screenflag = iarg + 1; + iarg += 2; + } else if (strcmp(arg[iarg],"-suffix") == 0 || strcmp(arg[iarg],"-sf") == 0) { if (iarg+2 > narg) @@ -210,45 +301,14 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) strcpy(suffix,arg[iarg+1]); iarg += 2; } - } else if (strcmp(arg[iarg],"-reorder") == 0 || - strcmp(arg[iarg],"-ro") == 0) { + + } else if (strcmp(arg[iarg],"-var") == 0 || + strcmp(arg[iarg],"-v") == 0) { if (iarg+3 > narg) error->universe_all(FLERR,"Invalid command-line argument"); - if (universe->existflag) - error->universe_all(FLERR,"Cannot use -reorder after -partition"); - universe->reorder(arg[iarg+1],arg[iarg+2]); iarg += 3; - } else if (strcmp(arg[iarg],"-restart") == 0 || - strcmp(arg[iarg],"-r") == 0) { - if (iarg+3 > narg) - error->universe_all(FLERR,"Invalid command-line argument"); - restartflag = 1; - rfile = arg[iarg+1]; - dfile = arg[iarg+2]; - // check for restart remap flag - if (strcmp(dfile,"remap") == 0) { - if (iarg+4 > narg) - error->universe_all(FLERR,"Invalid command-line argument"); - restartremapflag = 1; - dfile = arg[iarg+3]; - iarg++; - } - iarg += 3; - // delimit any extra args for the write_data command - wdfirst = iarg; while (iarg < narg && arg[iarg][0] != '-') iarg++; - wdlast = iarg; - } else if (strcmp(arg[iarg],"-nocite") == 0 || - strcmp(arg[iarg],"-nc") == 0) { - citeflag = 0; - iarg++; - } else if (strcmp(arg[iarg],"-help") == 0 || - strcmp(arg[iarg],"-h") == 0) { - if (iarg+1 > narg) - error->universe_all(FLERR,"Invalid command-line argument"); - helpflag = 1; - citeflag = 0; - iarg += 1; + } else error->universe_all(FLERR,"Invalid command-line argument"); } @@ -592,6 +652,14 @@ LAMMPS::~LAMMPS() delete [] suffix; delete [] suffix2; + // free the MPI comm created by -mpi command-line arg processed in constructor + // it was passed to universe as if original universe world + // may have been split later by partitions, universe will free the splits + // free a copy of uorig here, so check in universe destructor will still work + + MPI_Comm copy = universe->uorig; + if (cscomm) MPI_Comm_free(©); + delete input; delete universe; delete error; @@ -811,6 +879,7 @@ void LAMMPS::help() "-in filename : read input from file, not stdin (-i)\n" "-kokkos on/off ... : turn KOKKOS mode on or off (-k)\n" "-log none/filename : where to send log output (-l)\n" + "-mpicolor color : which exe in a multi-exe mpirun cmd (-m)\n" "-nocite : disable writing log.cite file (-nc)\n" "-package style ... : invoke package command (-pk)\n" "-partition size1 size2 ... : assign partition sizes (-p)\n" @@ -823,7 +892,9 @@ void LAMMPS::help() "-var varname value : set index style variable (-v)\n\n", exename); - fprintf(fp,"List of style options included in this LAMMPS executable\n\n"); + + print_config(fp); + fprintf(fp,"List of individual style options included in this LAMMPS executable\n\n"); int pos = 80; fprintf(fp,"* Atom styles:\n"); @@ -974,3 +1045,28 @@ void print_style(FILE *fp, const char *str, int &pos) pos += 80; } } + +void LAMMPS::print_config(FILE *fp) +{ + const char *pkg; + int ncword, ncline = 0; + + fputs("Active compile time flags:\n\n",fp); + if (Info::has_gzip_support()) fputs("-DLAMMPS_GZIP\n",fp); + if (Info::has_png_support()) fputs("-DLAMMPS_PNG\n",fp); + if (Info::has_jpeg_support()) fputs("-DLAMMPS_JPEG\n",fp); + if (Info::has_ffmpeg_support()) fputs("-DLAMMPS_FFMPEG\n",fp); + if (Info::has_exceptions()) fputs("-DLAMMPS_EXCEPTIONS\n",fp); + + fputs("\nInstalled packages:\n\n",fp); + for (int i = 0; NULL != (pkg = installed_packages[i]); ++i) { + ncword = strlen(pkg); + if (ncline + ncword > 78) { + ncline = 0; + fputs("\n",fp); + } + fprintf(fp,"%s ",pkg); + ncline += ncword + 1; + } + fputs("\n\n",fp); +} diff --git a/src/lammps.h b/src/lammps.h index 1323dcccc8..5ccef3026e 100644 --- a/src/lammps.h +++ b/src/lammps.h @@ -51,6 +51,10 @@ class LAMMPS { int num_package; // number of cmdline package commands int cite_enable; // 1 if generating log.cite, 0 if disabled + int clientserver; // 0 = neither, 1 = client, 2 = server + void *cslib; // client/server messaging via CSlib + MPI_Comm cscomm; // MPI comm for client+server in mpi/one mode + class KokkosLMP *kokkos; // KOKKOS accelerator class class AtomKokkos *atomKK; // KOKKOS version of Atom class class MemoryKokkos *memoryKK; // KOKKOS version of Memory class @@ -59,12 +63,15 @@ class LAMMPS { class CiteMe *citeme; // citation info + static const char * installed_packages[]; + LAMMPS(int, char **, MPI_Comm); ~LAMMPS(); void create(); void post_create(); void init(); void destroy(); + void print_config(FILE *); // print compile time settings private: void help(); diff --git a/src/library.cpp b/src/library.cpp index 0162c560ce..a46689da09 100644 --- a/src/library.cpp +++ b/src/library.cpp @@ -38,6 +38,7 @@ #include "memory.h" #include "error.h" #include "force.h" +#include "info.h" using namespace LAMMPS_NS; @@ -335,7 +336,7 @@ void lammps_free(void *ptr) customize by adding names ------------------------------------------------------------------------- */ -int lammps_extract_setting(void *ptr, char *name) +int lammps_extract_setting(void * /*ptr*/, char *name) { if (strcmp(name,"bigint") == 0) return sizeof(bigint); if (strcmp(name,"tagint") == 0) return sizeof(tagint); @@ -1514,7 +1515,8 @@ void lammps_create_atoms(void *ptr, int n, tagint *id, int *type, if (lmp->atom->natoms != natoms_prev + n) { char str[128]; sprintf(str,"Library warning in lammps_create_atoms, " - "invalid total atoms %ld %ld",lmp->atom->natoms,natoms_prev+n); + "invalid total atoms " BIGINT_FORMAT " " BIGINT_FORMAT, + lmp->atom->natoms,natoms_prev+n); if (lmp->comm->me == 0) lmp->error->warning(FLERR,str); } @@ -1522,6 +1524,56 @@ void lammps_create_atoms(void *ptr, int n, tagint *id, int *type, END_CAPTURE } +// ---------------------------------------------------------------------- +// library API functions for accessing LAMMPS configuration +// ---------------------------------------------------------------------- + +int lammps_config_has_package(char * package_name) { + return Info::has_package(package_name); +} + +int lammps_config_package_count() { + int i = 0; + while(LAMMPS::installed_packages[i] != NULL) { + ++i; + } + return i; +} + +int lammps_config_package_name(int index, char * buffer, int max_size) { + int i = 0; + while(LAMMPS::installed_packages[i] != NULL && i < index) { + ++i; + } + + if(LAMMPS::installed_packages[i] != NULL) { + strncpy(buffer, LAMMPS::installed_packages[i], max_size); + return true; + } + + return false; +} + +int lammps_config_has_gzip_support() { + return Info::has_gzip_support(); +} + +int lammps_config_has_png_support() { + return Info::has_png_support(); +} + +int lammps_config_has_jpeg_support() { + return Info::has_jpeg_support(); +} + +int lammps_config_has_ffmpeg_support() { + return Info::has_ffmpeg_support(); +} + +int lammps_config_has_exceptions() { + return Info::has_exceptions(); +} + // ---------------------------------------------------------------------- // library API functions for error handling // ---------------------------------------------------------------------- diff --git a/src/library.h b/src/library.h index 7c21b98dae..82071f673b 100644 --- a/src/library.h +++ b/src/library.h @@ -55,6 +55,15 @@ void lammps_gather_atoms_subset(void *, char *, int, int, int, int *, void *); void lammps_scatter_atoms(void *, char *, int, int, void *); void lammps_scatter_atoms_subset(void *, char *, int, int, int, int *, void *); +int lammps_config_has_package(char * package_name); +int lammps_config_package_count(); +int lammps_config_package_name(int index, char * buffer, int max_size); +int lammps_config_has_gzip_support(); +int lammps_config_has_png_support(); +int lammps_config_has_jpeg_support(); +int lammps_config_has_ffmpeg_support(); +int lammps_config_has_exceptions(); + // lammps_create_atoms() takes tagint and imageint as args // ifdef insures they are compatible with rest of LAMMPS // caller must match to how LAMMPS library is built diff --git a/src/lmptype.h b/src/lmptype.h index 2be1d2ac38..7c3dbc1c3d 100644 --- a/src/lmptype.h +++ b/src/lmptype.h @@ -46,6 +46,13 @@ #define PRId64 "ld" #endif +// favor qsort over mergesort for stable release +// TODO: to be removed after stable release + +#ifndef LMP_QSORT +#define LMP_QSORT +#endif + namespace LAMMPS_NS { // enum used for KOKKOS host/device flags @@ -206,4 +213,8 @@ typedef int bigint; #include "lmpwindows.h" #endif +// suppress unused parameter warning + +#define LMP_UNUSED_PARAM(x) (void)(x) + #endif diff --git a/src/math_extra.cpp b/src/math_extra.cpp index b70986ce91..0bba2ad401 100644 --- a/src/math_extra.cpp +++ b/src/math_extra.cpp @@ -590,7 +590,7 @@ void inertia_triangle(double *v0, double *v1, double *v2, return symmetric inertia tensor as 6-vector in Voigt notation ------------------------------------------------------------------------- */ -void inertia_triangle(double *idiag, double *quat, double mass, +void inertia_triangle(double *idiag, double *quat, double /*mass*/, double *inertia) { double p[3][3],ptrans[3][3],itemp[3][3],tensor[3][3]; diff --git a/src/memory.h b/src/memory.h index f2faecf6e1..20ea426f90 100644 --- a/src/memory.h +++ b/src/memory.h @@ -50,7 +50,7 @@ class Memory : protected Pointers { } template - TYPE **create(TYPE **&array, int n, const char *name) + TYPE **create(TYPE **& /*array*/, int /*n*/, const char *name) {fail(name); return NULL;} /* ---------------------------------------------------------------------- @@ -68,7 +68,7 @@ class Memory : protected Pointers { } template - TYPE **grow(TYPE **&array, int n, const char *name) + TYPE **grow(TYPE **& /*array*/, int /*n*/, const char *name) {fail(name); return NULL;} /* ---------------------------------------------------------------------- @@ -96,7 +96,7 @@ class Memory : protected Pointers { } template - TYPE **create1d_offset(TYPE **&array, int nlo, int nhi, const char *name) + TYPE **create1d_offset(TYPE **& /*array*/, int /*nlo*/, int /*nhi*/, const char *name) {fail(name); return NULL;} /* ---------------------------------------------------------------------- @@ -131,7 +131,7 @@ class Memory : protected Pointers { } template - TYPE ***create(TYPE ***&array, int n1, int n2, const char *name) + TYPE ***create(TYPE ***& /*array*/, int /*n1*/, int /*n2*/, const char *name) {fail(name); return NULL;} /* ---------------------------------------------------------------------- @@ -158,7 +158,7 @@ class Memory : protected Pointers { } template - TYPE ***grow(TYPE ***&array, int n1, int n2, const char *name) + TYPE ***grow(TYPE ***& /*array*/, int /*n1*/, int /*n2*/, const char *name) {fail(name); return NULL;} /* ---------------------------------------------------------------------- @@ -198,7 +198,7 @@ class Memory : protected Pointers { } template - TYPE ***create_ragged(TYPE ***&array, int n1, int *n2, const char *name) + TYPE ***create_ragged(TYPE ***& /*array*/, int /*n1*/, int * /*n2*/, const char *name) {fail(name); return NULL;} /* ---------------------------------------------------------------------- @@ -217,7 +217,7 @@ class Memory : protected Pointers { } template - TYPE ***create2d_offset(TYPE ***&array, int n1, int n2lo, int n2hi, + TYPE ***create2d_offset(TYPE ***& /*array*/, int /*n1*/, int /*n2lo*/, int /*n2hi*/, const char *name) {fail(name); return NULL;} /* ---------------------------------------------------------------------- @@ -262,7 +262,7 @@ class Memory : protected Pointers { } template - TYPE ****create(TYPE ****&array, int n1, int n2, int n3, const char *name) + TYPE ****create(TYPE ****& /*array*/, int /*n1*/, int /*n2*/, int /*n3*/, const char *name) {fail(name); return NULL;} /* ---------------------------------------------------------------------- @@ -297,7 +297,7 @@ class Memory : protected Pointers { } template - TYPE ****grow(TYPE ****&array, int n1, int n2, int n3, const char *name) + TYPE ****grow(TYPE ****& /*array*/, int /*n1*/, int /*n2*/, int /*n3*/, const char *name) {fail(name); return NULL;} /* ---------------------------------------------------------------------- @@ -330,8 +330,8 @@ class Memory : protected Pointers { } template - TYPE ****create3d_offset(TYPE ****&array, int n1lo, int n1hi, - int n2, int n3, const char *name) + TYPE ****create3d_offset(TYPE ****& /*array*/, int /*n1lo*/, int /*n1hi*/, + int /*n2*/, int /*n3*/, const char *name) {fail(name); return NULL;} /* ---------------------------------------------------------------------- @@ -374,8 +374,8 @@ class Memory : protected Pointers { } template - TYPE ****create3d_offset(TYPE ****&array, int n1lo, int n1hi, - int n2lo, int n2hi, int n3lo, int n3hi, + TYPE ****create3d_offset(TYPE ****& /*array*/, int /*n1lo*/, int /*n1hi*/, + int /*n2lo*/, int /*n2hi*/, int /*n3lo*/, int /*n3hi*/, const char *name) {fail(name); return NULL;} @@ -432,7 +432,7 @@ class Memory : protected Pointers { } template - TYPE *****create(TYPE *****&array, int n1, int n2, int n3, int n4, + TYPE *****create(TYPE *****& /*array*/, int /*n1*/, int /*n2*/, int /*n3*/, int /*n4*/, const char *name) {fail(name); return NULL;} @@ -478,8 +478,8 @@ class Memory : protected Pointers { } template - TYPE ****create4d_offset(TYPE *****&array, int n1, int n2lo, int n2hi, - int n3lo, int n3hi, int n4lo, int n4hi, + TYPE ****create4d_offset(TYPE *****& /*array*/, int /*n1*/, int /*n2lo*/, int /*n2hi*/, + int /*n3lo*/, int /*n3hi*/, int /*n4lo*/, int /*n4hi*/, const char *name) {fail(name); return NULL;} @@ -546,8 +546,8 @@ class Memory : protected Pointers { } template - TYPE ******create(TYPE ******&array, int n1, int n2, int n3, int n4, - int n5, const char *name) + TYPE ******create(TYPE ******& /*array*/, int /*n1*/, int /*n2*/, int /*n3*/, int /*n4*/, + int /*n5*/, const char *name) {fail(name); return NULL;} /* ---------------------------------------------------------------------- diff --git a/src/neighbor.cpp b/src/neighbor.cpp index 912a636227..759f84e29f 100644 --- a/src/neighbor.cpp +++ b/src/neighbor.cpp @@ -2193,7 +2193,7 @@ void Neighbor::set(int narg, char **arg) ditto for lastcall and last_setup_bins ------------------------------------------------------------------------- */ -void Neighbor::reset_timestep(bigint ntimestep) +void Neighbor::reset_timestep(bigint /*ntimestep*/) { for (int i = 0; i < nbin; i++) neigh_bin[i]->last_bin = -1; diff --git a/src/pack.h b/src/pack.h index 066535f5c9..837c33d14b 100644 --- a/src/pack.h +++ b/src/pack.h @@ -22,9 +22,8 @@ struct pack_plan_3d { int nqty; // # of values/element }; - -#if !defined(PACK_POINTER) && !defined(PACK_MEMCPY) -#define PACK_ARRAY +#if !defined(FFT_PACK_POINTER) && !defined(FFT_PACK_MEMCPY) +#define FFT_PACK_ARRAY #endif #ifndef PACK_DATA @@ -47,7 +46,7 @@ struct pack_plan_3d { pack/unpack with array indices ------------------------------------------------------------------------- */ -#ifdef PACK_ARRAY +#ifdef FFT_PACK_ARRAY /* ---------------------------------------------------------------------- pack from data -> buf @@ -274,7 +273,7 @@ static void unpack_3d_permute2_n(PACK_DATA *buf, PACK_DATA *data, struct pack_pl pack/unpack with pointers ------------------------------------------------------------------------- */ -#ifdef PACK_POINTER +#ifdef FFT_PACK_POINTER /* ---------------------------------------------------------------------- pack from data -> buf @@ -523,7 +522,7 @@ static void unpack_3d_permute2_n(PACK_DATA *buf, PACK_DATA *data, struct pack_pl just use PACK_POINTER versions ------------------------------------------------------------------------- */ -#ifdef PACK_MEMCPY +#ifdef FFT_PACK_MEMCPY /* ---------------------------------------------------------------------- pack from data -> buf diff --git a/src/pair.cpp b/src/pair.cpp index 9bb1ad212f..18d561bdb5 100644 --- a/src/pair.cpp +++ b/src/pair.cpp @@ -301,7 +301,7 @@ void Pair::init_style() specific pair style can override this function ------------------------------------------------------------------------- */ -void Pair::init_list(int which, NeighList *ptr) +void Pair::init_list(int /*which*/, NeighList *ptr) { list = ptr; } @@ -693,17 +693,19 @@ void Pair::compute_dummy(int eflag, int vflag) } /* ---------------------------------------------------------------------- */ + void Pair::read_restart(FILE *) { if (comm->me == 0) - error->warning(FLERR,"BUG: restartinfo=1 but no restart support in pair style"); + error->warning(FLERR,"Pair style restartinfo set but has no restart support"); } /* ---------------------------------------------------------------------- */ + void Pair::write_restart(FILE *) { if (comm->me == 0) - error->warning(FLERR,"BUG: restartinfo=1 but no restart support in pair style"); + error->warning(FLERR,"Pair style restartinfo set but has no restart support"); } /* ------------------------------------------------------------------- diff --git a/src/pair_beck.cpp b/src/pair_beck.cpp index cc8e14bf2c..d9c0fb902c 100644 --- a/src/pair_beck.cpp +++ b/src/pair_beck.cpp @@ -327,9 +327,9 @@ void PairBeck::read_restart_settings(FILE *fp) /* ---------------------------------------------------------------------- */ -double PairBeck::single(int i, int j, int itype, int jtype, +double PairBeck::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq, - double factor_coul, double factor_lj, + double /*factor_coul*/, double factor_lj, double &fforce) { double phi_beck,r,rinv; diff --git a/src/pair_born.cpp b/src/pair_born.cpp index ce7a255fd4..1a1db9dd90 100644 --- a/src/pair_born.cpp +++ b/src/pair_born.cpp @@ -407,8 +407,8 @@ void PairBorn::write_data_all(FILE *fp) /* ---------------------------------------------------------------------- */ -double PairBorn::single(int i, int j, int itype, int jtype, - double rsq, double factor_coul, double factor_lj, +double PairBorn::single(int /*i*/, int /*j*/, int itype, int jtype, + double rsq, double /*factor_coul*/, double factor_lj, double &fforce) { double r2inv,r6inv,r,rexp,forceborn,phiborn; diff --git a/src/pair_buck.cpp b/src/pair_buck.cpp index 450ce291cb..8b6d79234b 100644 --- a/src/pair_buck.cpp +++ b/src/pair_buck.cpp @@ -380,8 +380,8 @@ void PairBuck::write_data_all(FILE *fp) /* ---------------------------------------------------------------------- */ -double PairBuck::single(int i, int j, int itype, int jtype, - double rsq, double factor_coul, double factor_lj, +double PairBuck::single(int /*i*/, int /*j*/, int itype, int jtype, + double rsq, double /*factor_coul*/, double factor_lj, double &fforce) { double r2inv,r6inv,r,rexp,forcebuck,phibuck; diff --git a/src/pair_coul_cut.cpp b/src/pair_coul_cut.cpp index edcf26bffe..8741abdb89 100644 --- a/src/pair_coul_cut.cpp +++ b/src/pair_coul_cut.cpp @@ -284,8 +284,8 @@ void PairCoulCut::read_restart_settings(FILE *fp) /* ---------------------------------------------------------------------- */ -double PairCoulCut::single(int i, int j, int itype, int jtype, - double rsq, double factor_coul, double factor_lj, +double PairCoulCut::single(int i, int j, int /*itype*/, int /*jtype*/, + double rsq, double factor_coul, double /*factor_lj*/, double &fforce) { double r2inv,rinv,forcecoul,phicoul; diff --git a/src/pair_coul_debye.cpp b/src/pair_coul_debye.cpp index ee08ab3294..432a015598 100644 --- a/src/pair_coul_debye.cpp +++ b/src/pair_coul_debye.cpp @@ -163,8 +163,8 @@ void PairCoulDebye::read_restart_settings(FILE *fp) /* ---------------------------------------------------------------------- */ -double PairCoulDebye::single(int i, int j, int itype, int jtype, - double rsq, double factor_coul, double factor_lj, +double PairCoulDebye::single(int i, int j, int /*itype*/, int /*jtype*/, + double rsq, double factor_coul, double /*factor_lj*/, double &fforce) { double r2inv,r,rinv,forcecoul,phicoul,screening; diff --git a/src/pair_coul_dsf.cpp b/src/pair_coul_dsf.cpp index f20eae43bd..8cd5f7fece 100644 --- a/src/pair_coul_dsf.cpp +++ b/src/pair_coul_dsf.cpp @@ -221,7 +221,7 @@ void PairCoulDSF::init_style() init for one type pair i,j and corresponding j,i ------------------------------------------------------------------------- */ -double PairCoulDSF::init_one(int i, int j) +double PairCoulDSF::init_one(int /*i*/, int /*j*/) { return cut_coul; } @@ -291,8 +291,8 @@ void PairCoulDSF::read_restart_settings(FILE *fp) /* ---------------------------------------------------------------------- */ -double PairCoulDSF::single(int i, int j, int itype, int jtype, double rsq, - double factor_coul, double factor_lj, +double PairCoulDSF::single(int i, int j, int /*itype*/, int /*jtype*/, double rsq, + double factor_coul, double /*factor_lj*/, double &fforce) { double r2inv,r,erfcc,erfcd,prefactor,t; diff --git a/src/pair_coul_wolf.cpp b/src/pair_coul_wolf.cpp index cd582f0693..762491166e 100644 --- a/src/pair_coul_wolf.cpp +++ b/src/pair_coul_wolf.cpp @@ -219,7 +219,7 @@ void PairCoulWolf::init_style() init for one type pair i,j and corresponding j,i ------------------------------------------------------------------------- */ -double PairCoulWolf::init_one(int i, int j) +double PairCoulWolf::init_one(int /*i*/, int /*j*/) { return cut_coul; } @@ -290,8 +290,8 @@ void PairCoulWolf::read_restart_settings(FILE *fp) only the pair part is calculated here ------------------------------------------------------------------------- */ -double PairCoulWolf::single(int i, int j, int itype, int jtype, double rsq, - double factor_coul, double factor_lj, +double PairCoulWolf::single(int i, int j, int /*itype*/, int /*jtype*/, double rsq, + double factor_coul, double /*factor_lj*/, double &fforce) { double r,prefactor; diff --git a/src/pair_dpd.cpp b/src/pair_dpd.cpp index c209de87ed..5c5fc4254b 100644 --- a/src/pair_dpd.cpp +++ b/src/pair_dpd.cpp @@ -390,8 +390,8 @@ void PairDPD::write_data_all(FILE *fp) /* ---------------------------------------------------------------------- */ -double PairDPD::single(int i, int j, int itype, int jtype, double rsq, - double factor_coul, double factor_dpd, double &fforce) +double PairDPD::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq, + double /*factor_coul*/, double factor_dpd, double &fforce) { double r,rinv,wd,phi; diff --git a/src/pair_gauss.cpp b/src/pair_gauss.cpp index fe53bcc9e1..426389753b 100644 --- a/src/pair_gauss.cpp +++ b/src/pair_gauss.cpp @@ -347,8 +347,8 @@ void PairGauss::write_data_all(FILE *fp) /* ---------------------------------------------------------------------- */ -double PairGauss::single(int i, int j, int itype, int jtype, double rsq, - double factor_coul, double factor_lj, +double PairGauss::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq, + double /*factor_coul*/, double /*factor_lj*/, double &fforce) { double philj = diff --git a/src/pair_hybrid.cpp b/src/pair_hybrid.cpp index dc74dd040d..03747e1de3 100644 --- a/src/pair_hybrid.cpp +++ b/src/pair_hybrid.cpp @@ -844,7 +844,7 @@ void PairHybrid::modify_params(int narg, char **arg) store a local per pair style override for special_lj and special_coul ------------------------------------------------------------------------- */ -void PairHybrid::modify_special(int m, int narg, char **arg) +void PairHybrid::modify_special(int m, int /*narg*/, char **arg) { double special[4]; int i; diff --git a/src/pair_lj96_cut.cpp b/src/pair_lj96_cut.cpp index 28677a393e..457eba0e79 100644 --- a/src/pair_lj96_cut.cpp +++ b/src/pair_lj96_cut.cpp @@ -678,8 +678,8 @@ void PairLJ96Cut::write_data_all(FILE *fp) /* ---------------------------------------------------------------------- */ -double PairLJ96Cut::single(int i, int j, int itype, int jtype, double rsq, - double factor_coul, double factor_lj, +double PairLJ96Cut::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq, + double /*factor_coul*/, double factor_lj, double &fforce) { double r2inv,r3inv,r6inv,forcelj,philj; diff --git a/src/pair_lj_cubic.cpp b/src/pair_lj_cubic.cpp index 4b140e5f05..770caa6359 100644 --- a/src/pair_lj_cubic.cpp +++ b/src/pair_lj_cubic.cpp @@ -175,7 +175,7 @@ void PairLJCubic::allocate() global settings ------------------------------------------------------------------------- */ -void PairLJCubic::settings(int narg, char **arg) +void PairLJCubic::settings(int narg, char **/*arg*/) { if (narg != 0) error->all(FLERR,"Illegal pair_style command"); @@ -321,9 +321,9 @@ void PairLJCubic::read_restart_settings(FILE *fp) /* ---------------------------------------------------------------------- */ -double PairLJCubic::single(int i, int j, int itype, int jtype, +double PairLJCubic::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq, - double factor_coul, double factor_lj, + double /*factor_coul*/, double factor_lj, double &fforce) { double r2inv,r6inv,forcelj,philj; diff --git a/src/pair_lj_cut.cpp b/src/pair_lj_cut.cpp index bb2db6aa2f..13a546f5a5 100644 --- a/src/pair_lj_cut.cpp +++ b/src/pair_lj_cut.cpp @@ -672,8 +672,8 @@ void PairLJCut::write_data_all(FILE *fp) /* ---------------------------------------------------------------------- */ -double PairLJCut::single(int i, int j, int itype, int jtype, double rsq, - double factor_coul, double factor_lj, +double PairLJCut::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq, + double /*factor_coul*/, double factor_lj, double &fforce) { double r2inv,r6inv,forcelj,philj; diff --git a/src/pair_lj_expand.cpp b/src/pair_lj_expand.cpp index ba72d7d45f..9aa58b3b88 100644 --- a/src/pair_lj_expand.cpp +++ b/src/pair_lj_expand.cpp @@ -396,8 +396,8 @@ void PairLJExpand::write_data_all(FILE *fp) /* ---------------------------------------------------------------------- */ -double PairLJExpand::single(int i, int j, int itype, int jtype, double rsq, - double factor_coul, double factor_lj, +double PairLJExpand::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq, + double /*factor_coul*/, double factor_lj, double &fforce) { double r,rshift,rshiftsq,r2inv,r6inv,forcelj,philj; diff --git a/src/pair_lj_gromacs.cpp b/src/pair_lj_gromacs.cpp index 6b2219d2c5..495e96c368 100644 --- a/src/pair_lj_gromacs.cpp +++ b/src/pair_lj_gromacs.cpp @@ -414,9 +414,9 @@ void PairLJGromacs::write_data_all(FILE *fp) /* ---------------------------------------------------------------------- */ -double PairLJGromacs::single(int i, int j, int itype, int jtype, +double PairLJGromacs::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq, - double factor_coul, double factor_lj, + double /*factor_coul*/, double factor_lj, double &fforce) { double r2inv,r6inv,forcelj,philj; diff --git a/src/pair_lj_smooth.cpp b/src/pair_lj_smooth.cpp index 23256d486e..a12046bb3b 100644 --- a/src/pair_lj_smooth.cpp +++ b/src/pair_lj_smooth.cpp @@ -425,8 +425,8 @@ void PairLJSmooth::write_data_all(FILE *fp) /* ---------------------------------------------------------------------- */ -double PairLJSmooth::single(int i, int j, int itype, int jtype, double rsq, - double factor_coul, double factor_lj, +double PairLJSmooth::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq, + double /*factor_coul*/, double factor_lj, double &fforce) { double r2inv,r6inv,forcelj,philj,r,t,tsq,fskin; diff --git a/src/pair_lj_smooth_linear.cpp b/src/pair_lj_smooth_linear.cpp index 592a7f6f41..17c789bcee 100644 --- a/src/pair_lj_smooth_linear.cpp +++ b/src/pair_lj_smooth_linear.cpp @@ -326,9 +326,9 @@ void PairLJSmoothLinear::read_restart_settings(FILE *fp) /* ---------------------------------------------------------------------- */ -double PairLJSmoothLinear::single(int i, int j, int itype, int jtype, +double PairLJSmoothLinear::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq, - double factor_coul, double factor_lj, + double /*factor_coul*/, double factor_lj, double &fforce) { double r2inv,r6inv,forcelj,philj,r,rinv; diff --git a/src/pair_mie_cut.cpp b/src/pair_mie_cut.cpp index 1f9267ca30..c1e1c1ff50 100644 --- a/src/pair_mie_cut.cpp +++ b/src/pair_mie_cut.cpp @@ -682,8 +682,8 @@ void PairMIECut::read_restart_settings(FILE *fp) /* ---------------------------------------------------------------------- */ -double PairMIECut::single(int i, int j, int itype, int jtype, double rsq, - double factor_coul, double factor_mie, +double PairMIECut::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq, + double /*factor_coul*/, double factor_mie, double &fforce) { double r2inv,rgamR,rgamA,forcemie,phimie; diff --git a/src/pair_morse.cpp b/src/pair_morse.cpp index 32ddd723b2..c1031343e1 100644 --- a/src/pair_morse.cpp +++ b/src/pair_morse.cpp @@ -334,8 +334,8 @@ void PairMorse::write_data_all(FILE *fp) /* ---------------------------------------------------------------------- */ -double PairMorse::single(int i, int j, int itype, int jtype, double rsq, - double factor_coul, double factor_lj, +double PairMorse::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq, + double /*factor_coul*/, double factor_lj, double &fforce) { double r,dr,dexp,phi; diff --git a/src/pair_soft.cpp b/src/pair_soft.cpp index f428893fd1..d1c51ac600 100644 --- a/src/pair_soft.cpp +++ b/src/pair_soft.cpp @@ -307,8 +307,8 @@ void PairSoft::write_data_all(FILE *fp) /* ---------------------------------------------------------------------- */ -double PairSoft::single(int i, int j, int itype, int jtype, double rsq, - double factor_coul, double factor_lj, +double PairSoft::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq, + double /*factor_coul*/, double factor_lj, double &fforce) { double r,arg,philj; diff --git a/src/pair_table.cpp b/src/pair_table.cpp index 9e9e41a54c..5c43761cab 100644 --- a/src/pair_table.cpp +++ b/src/pair_table.cpp @@ -993,8 +993,8 @@ void PairTable::read_restart_settings(FILE *fp) /* ---------------------------------------------------------------------- */ -double PairTable::single(int i, int j, int itype, int jtype, double rsq, - double factor_coul, double factor_lj, +double PairTable::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq, + double /*factor_coul*/, double factor_lj, double &fforce) { int itable; diff --git a/src/pair_ufm.cpp b/src/pair_ufm.cpp index 965fe0204e..a9f076f504 100644 --- a/src/pair_ufm.cpp +++ b/src/pair_ufm.cpp @@ -353,8 +353,8 @@ void PairUFM::write_data_all(FILE *fp) /* ---------------------------------------------------------------------- */ -double PairUFM::single(int i, int j, int itype, int jtype, double rsq, - double factor_coul, double factor_lj, +double PairUFM::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq, + double /*factor_coul*/, double factor_lj, double &fforce) { double expuf,phiuf; diff --git a/src/pair_yukawa.cpp b/src/pair_yukawa.cpp index 040664abec..af520fd3da 100644 --- a/src/pair_yukawa.cpp +++ b/src/pair_yukawa.cpp @@ -319,8 +319,8 @@ void PairYukawa::write_data_all(FILE *fp) /* ---------------------------------------------------------------------- */ -double PairYukawa::single(int i, int j, int itype, int jtype, double rsq, - double factor_coul, double factor_lj, +double PairYukawa::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq, + double /*factor_coul*/, double factor_lj, double &fforce) { double r2inv,r,rinv,screening,forceyukawa,phi; diff --git a/src/pair_zbl.cpp b/src/pair_zbl.cpp index 98048f61d0..f23a1e5d56 100644 --- a/src/pair_zbl.cpp +++ b/src/pair_zbl.cpp @@ -267,8 +267,8 @@ double PairZBL::init_one(int i, int j) /* ---------------------------------------------------------------------- */ -double PairZBL::single(int i, int j, int itype, int jtype, double rsq, - double dummy1, double dummy2, +double PairZBL::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq, + double /*dummy1*/, double /*dummy2*/, double &fforce) { double phi,r,t,eswitch,fswitch; diff --git a/src/rcb.cpp b/src/rcb.cpp index 3027920310..630cef309a 100644 --- a/src/rcb.cpp +++ b/src/rcb.cpp @@ -241,9 +241,11 @@ void RCB::compute(int dimension, int n, double **x, double *wt, // dim_select = selected cut dimension // valuehalf_select = valuehalf in that dimension // dotmark_select = dot markings in that dimension + // initialize largest = -1.0 to insure a cut in some dim is accepted + // e.g. if current recursed box is size 0 in all dims int dim_select = -1; - double largest = 0.0; + double largest = -1.0; for (dim = 0; dim < dimension; dim++) { @@ -1106,7 +1108,7 @@ void RCB::compute_old(int dimension, int n, double **x, double *wt, merge of each component of an RCB bounding box ------------------------------------------------------------------------- */ -void box_merge(void *in, void *inout, int *len, MPI_Datatype *dptr) +void box_merge(void *in, void *inout, int * /*len*/, MPI_Datatype * /*dptr*/) { RCB::BBox *box1 = (RCB::BBox *) in; @@ -1136,7 +1138,7 @@ void box_merge(void *in, void *inout, int *len, MPI_Datatype *dptr) all procs must get same proclo,prochi ------------------------------------------------------------------------- */ -void median_merge(void *in, void *inout, int *len, MPI_Datatype *dptr) +void median_merge(void *in, void *inout, int * /*len*/, MPI_Datatype * /*dptr*/) { RCB::Median *med1 = (RCB::Median *) in; diff --git a/src/read_restart.cpp b/src/read_restart.cpp index 1164de6faa..7d8e6ca395 100644 --- a/src/read_restart.cpp +++ b/src/read_restart.cpp @@ -62,7 +62,9 @@ enum{VERSION,SMALLINT,TAGINT,BIGINT, MULTIPROC,MPIIO,PROCSPERFILE,PERPROC, IMAGEINT,BOUNDMIN,TIMESTEP, ATOM_ID,ATOM_MAP_STYLE,ATOM_MAP_USER,ATOM_SORTFREQ,ATOM_SORTBIN, - COMM_MODE,COMM_CUTOFF,COMM_VEL,NO_PAIR}; + COMM_MODE,COMM_CUTOFF,COMM_VEL,NO_PAIR, + EXTRA_BOND_PER_ATOM,EXTRA_ANGLE_PER_ATOM,EXTRA_DIHEDRAL_PER_ATOM, + EXTRA_IMPROPER_PER_ATOM,EXTRA_SPECIAL_PER_ATOM}; #define LB_FACTOR 1.1 @@ -914,6 +916,17 @@ void ReadRestart::header(int incompatible) } else if (flag == COMM_VEL) { comm->ghost_velocity = read_int(); + } else if (flag == EXTRA_BOND_PER_ATOM) { + atom->extra_bond_per_atom = read_int(); + } else if (flag == EXTRA_ANGLE_PER_ATOM) { + atom->extra_angle_per_atom = read_int(); + } else if (flag == EXTRA_DIHEDRAL_PER_ATOM) { + atom->extra_dihedral_per_atom = read_int(); + } else if (flag == EXTRA_IMPROPER_PER_ATOM) { + atom->extra_improper_per_atom = read_int(); + } else if (flag == EXTRA_SPECIAL_PER_ATOM) { + force->special_extra = read_int(); + } else error->all(FLERR,"Invalid flag in header section of restart file"); flag = read_int(); diff --git a/src/reader_xyz.cpp b/src/reader_xyz.cpp index 5cb3476510..37d30bd740 100644 --- a/src/reader_xyz.cpp +++ b/src/reader_xyz.cpp @@ -117,9 +117,9 @@ void ReaderXYZ::skip() only called by proc 0 ------------------------------------------------------------------------- */ -bigint ReaderXYZ::read_header(double box[3][3], int &triclinic, +bigint ReaderXYZ::read_header(double /*box*/[3][3], int &triclinic, int fieldinfo, int nfield, - int *fieldtype, char **fieldlabel, + int *fieldtype, char **/*fieldlabel*/, int scaleflag, int wrapflag, int &fieldflag, int &xflag, int &yflag, int &zflag) { diff --git a/src/region.cpp b/src/region.cpp index 88a414b134..c52c0181aa 100644 --- a/src/region.cpp +++ b/src/region.cpp @@ -28,7 +28,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -Region::Region(LAMMPS *lmp, int narg, char **arg) : +Region::Region(LAMMPS *lmp, int /*narg*/, char **arg) : Pointers(lmp), id(NULL), style(NULL), contact(NULL), list(NULL), xstr(NULL), ystr(NULL), zstr(NULL), tstr(NULL) diff --git a/src/reset_ids.cpp b/src/reset_ids.cpp index 8a33cd535b..b2cf7a9bbc 100644 --- a/src/reset_ids.cpp +++ b/src/reset_ids.cpp @@ -16,6 +16,7 @@ #include "atom_vec.h" #include "domain.h" #include "comm.h" +#include "special.h" #include "memory.h" #include "error.h" @@ -27,7 +28,7 @@ ResetIDs::ResetIDs(LAMMPS *lmp) : Pointers(lmp) {} /* ---------------------------------------------------------------------- */ -void ResetIDs::command(int narg, char **arg) +void ResetIDs::command(int narg, char **/*arg*/) { if (domain->box_exist == 0) error->all(FLERR,"Reset_ids command before simulation box is defined"); @@ -44,7 +45,7 @@ void ResetIDs::command(int narg, char **arg) } // create an atom map if one doesn't exist already - + int mapflag = 0; if (atom->map_style == 0) { mapflag = 1; @@ -93,7 +94,7 @@ void ResetIDs::command(int narg, char **arg) // forward_comm_array acquires new IDs for ghost atoms double **newIDs; - memory->create(newIDs,nall,1,"reset_ids:newIDs"); + memory->create(newIDs,nall,1,"reset_ids:newIDs"); for (int i = 0; i < nlocal; i++) { newIDs[i][0] = tag[i]; @@ -105,7 +106,7 @@ void ResetIDs::command(int narg, char **arg) // loop over bonds, angles, etc and reset IDs in stored topology arrays // only necessary for molecular = 1, not molecular = 2 // badcount = atom IDs that could not be found - + int badcount = 0; if (atom->molecular == 1) { @@ -232,8 +233,15 @@ void ResetIDs::command(int narg, char **arg) atom->map_init(); atom->map_set(); + // need to update exclusions with new atom IDs + + if (atom->molecular == 1) { + Special special(lmp); + special.build(); + } + // delete temporary atom map - + if (mapflag) { atom->map_delete(); atom->map_style = 0; diff --git a/src/respa.cpp b/src/respa.cpp index 73e280b03d..26bae5a1cb 100644 --- a/src/respa.cpp +++ b/src/respa.cpp @@ -774,7 +774,7 @@ void Respa::recurse(int ilevel) clear other arrays as needed ------------------------------------------------------------------------- */ -void Respa::force_clear(int newtonflag) +void Respa::force_clear(int /*newtonflag*/) { if (external_force_clear) return; diff --git a/src/set.cpp b/src/set.cpp index f741760ed5..7eca4e9a9c 100644 --- a/src/set.cpp +++ b/src/set.cpp @@ -44,10 +44,11 @@ using namespace MathConst; enum{ATOM_SELECT,MOL_SELECT,TYPE_SELECT,GROUP_SELECT,REGION_SELECT}; enum{TYPE,TYPE_FRACTION,MOLECULE,X,Y,Z,CHARGE,MASS,SHAPE,LENGTH,TRI, - DIPOLE,DIPOLE_RANDOM,QUAT,QUAT_RANDOM,THETA,THETA_RANDOM,ANGMOM,OMEGA, + DIPOLE,DIPOLE_RANDOM,SPIN,SPIN_RANDOM,QUAT,QUAT_RANDOM, + THETA,THETA_RANDOM,ANGMOM,OMEGA, DIAMETER,DENSITY,VOLUME,IMAGE,BOND,ANGLE,DIHEDRAL,IMPROPER, MESO_E,MESO_CV,MESO_RHO,EDPD_TEMP,EDPD_CV,CC,SMD_MASS_DENSITY, - SMD_CONTACT_RADIUS,DPDTHETA,INAME,DNAME}; + SMD_CONTACT_RADIUS,DPDTHETA,INAME,DNAME,VX,VY,VZ}; #define BIG INT_MAX @@ -140,6 +141,27 @@ void Set::command(int narg, char **arg) set(Z); iarg += 2; + } else if (strcmp(arg[iarg],"vx") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal set command"); + if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) varparse(arg[iarg+1],1); + else dvalue = force->numeric(FLERR,arg[iarg+1]); + set(VX); + iarg += 2; + + } else if (strcmp(arg[iarg],"vy") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal set command"); + if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) varparse(arg[iarg+1],1); + else dvalue = force->numeric(FLERR,arg[iarg+1]); + set(VY); + iarg += 2; + + } else if (strcmp(arg[iarg],"vz") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal set command"); + if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) varparse(arg[iarg+1],1); + else dvalue = force->numeric(FLERR,arg[iarg+1]); + set(VZ); + iarg += 2; + } else if (strcmp(arg[iarg],"charge") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal set command"); if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) varparse(arg[iarg+1],1); @@ -215,6 +237,34 @@ void Set::command(int narg, char **arg) setrandom(DIPOLE_RANDOM); iarg += 3; + } else if (strcmp(arg[iarg],"spin") == 0) { + if (iarg+4 > narg) error->all(FLERR,"Illegal set command"); + if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) varparse(arg[iarg+1],1); + else dvalue = force->numeric(FLERR,arg[iarg+1]); + if (strstr(arg[iarg+2],"v_") == arg[iarg+2]) varparse(arg[iarg+2],2); + else xvalue = force->numeric(FLERR,arg[iarg+2]); + if (strstr(arg[iarg+3],"v_") == arg[iarg+3]) varparse(arg[iarg+3],3); + else yvalue = force->numeric(FLERR,arg[iarg+3]); + if (strstr(arg[iarg+4],"v_") == arg[iarg+4]) varparse(arg[iarg+4],4); + else zvalue = force->numeric(FLERR,arg[iarg+4]); + if (!atom->sp_flag) + error->all(FLERR,"Cannot set this attribute for this atom style"); + set(SPIN); + iarg += 5; + + } else if (strcmp(arg[iarg],"spin/random") == 0) { + if (iarg+3 > narg) error->all(FLERR,"Illegal set command"); + ivalue = force->inumeric(FLERR,arg[iarg+1]); + dvalue = force->numeric(FLERR,arg[iarg+2]); + if (!atom->sp_flag) + error->all(FLERR,"Cannot set this attribute for this atom style"); + if (ivalue <= 0) + error->all(FLERR,"Invalid random number seed in set command"); + if (dvalue <= 0.0) + error->all(FLERR,"Invalid dipole length in set command"); + setrandom(SPIN_RANDOM); + iarg += 3; + } else if (strcmp(arg[iarg],"quat") == 0) { if (iarg+5 > narg) error->all(FLERR,"Illegal set command"); if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) varparse(arg[iarg+1],1); @@ -703,6 +753,9 @@ void Set::set(int keyword) else if (keyword == X) atom->x[i][0] = dvalue; else if (keyword == Y) atom->x[i][1] = dvalue; else if (keyword == Z) atom->x[i][2] = dvalue; + else if (keyword == VX) atom->v[i][0] = dvalue; + else if (keyword == VY) atom->v[i][1] = dvalue; + else if (keyword == VZ) atom->v[i][2] = dvalue; else if (keyword == CHARGE) atom->q[i] = dvalue; else if (keyword == MASS) { if (dvalue <= 0.0) error->one(FLERR,"Invalid mass in set command"); @@ -821,6 +874,18 @@ void Set::set(int keyword) mu[i][2]*mu[i][2]); } + // set magnetic moments + + else if (keyword == SPIN) { + double **sp = atom->sp; + double inorm = 1.0/sqrt(xvalue*xvalue+yvalue*yvalue+zvalue*zvalue); + sp[i][0] = inorm*xvalue; + sp[i][1] = inorm*yvalue; + sp[i][2] = inorm*zvalue; + sp[i][3] = dvalue; + } + + // set quaternion orientation of ellipsoid or tri or body particle // set quaternion orientation of ellipsoid or tri or body particle // enforce quat rotation vector in z dir for 2d systems @@ -981,6 +1046,48 @@ void Set::setrandom(int keyword) } } + + // set spin moments to random orientations in 3d or 2d + // spin length is fixed to unity + + } else if (keyword == SPIN_RANDOM) { + double **sp = atom->sp; + int nlocal = atom->nlocal; + + double sp_sq,scale; + + if (domain->dimension == 3) { + for (i = 0; i < nlocal; i++) + if (select[i]) { + random->reset(seed,x[i]); + sp[i][0] = random->uniform() - 0.5; + sp[i][1] = random->uniform() - 0.5; + sp[i][2] = random->uniform() - 0.5; + sp_sq = sp[i][0]*sp[i][0] + sp[i][1]*sp[i][1] + sp[i][2]*sp[i][2]; + scale = 1.0/sqrt(sp_sq); + sp[i][0] *= scale; + sp[i][1] *= scale; + sp[i][2] *= scale; + sp[i][3] = dvalue; + count++; + } + + } else { + for (i = 0; i < nlocal; i++) + if (select[i]) { + random->reset(seed,x[i]); + sp[i][0] = random->uniform() - 0.5; + sp[i][1] = random->uniform() - 0.5; + sp[i][2] = 0.0; + sp_sq = sp[i][0]*sp[i][0] + sp[i][1]*sp[i][1]; + scale = 1.0/sqrt(sp_sq); + sp[i][0] *= scale; + sp[i][1] *= scale; + sp[i][3] = dvalue; + count++; + } + } + // set quaternions to random orientations in 3d and 2d } else if (keyword == QUAT_RANDOM) { diff --git a/src/thermo.cpp b/src/thermo.cpp index ade7a3c333..ddbbd0f496 100644 --- a/src/thermo.cpp +++ b/src/thermo.cpp @@ -1698,7 +1698,7 @@ void Thermo::compute_timeremain() void Thermo::compute_atoms() { - bivalue = atom->natoms; + bivalue = group->count_all(); } /* ---------------------------------------------------------------------- */ diff --git a/src/update.cpp b/src/update.cpp index aa152a8508..6f9c2c9a07 100644 --- a/src/update.cpp +++ b/src/update.cpp @@ -46,10 +46,10 @@ Update::Update(LAMMPS *lmp) : Pointers(lmp) whichflag = 0; firststep = laststep = 0; beginstep = endstep = 0; - setupflag = 0; - multireplica = 0; - restrict_output = 0; + setupflag = 0; + post_integrate = 0; + multireplica = 0; eflag_global = vflag_global = -1; diff --git a/src/update.h b/src/update.h index 7996440318..d3602ef21e 100644 --- a/src/update.h +++ b/src/update.h @@ -35,6 +35,7 @@ class Update : protected Pointers { int max_eval; // max force evaluations for minimizer int restrict_output; // 1 if output should not write dump/restart int setupflag; // set when setup() is computing forces + int post_integrate; // 1 if now at post_integrate() in timestep int multireplica; // 1 if min across replicas, else 0 bigint eflag_global,eflag_atom; // timestep global/peratom eng is tallied on diff --git a/src/variable.cpp b/src/variable.cpp index 86296b4b40..3c54eac1ef 100644 --- a/src/variable.cpp +++ b/src/variable.cpp @@ -733,7 +733,7 @@ int Variable::find(char *name) called when atom is created ------------------------------------------------------------------------- */ -void Variable::set_arrays(int i) +void Variable::set_arrays(int /*i*/) { for (int i = 0; i < nvar; i++) if (reader[i] && style[i] == ATOMFILE) @@ -1576,7 +1576,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) newtree->nextra = 0; treestack[ntreestack++] = newtree; - } else print_var_error(FLERR,"Mismatched compute in variable formula",ivar); + } else print_var_error(FLERR, + "Mismatched compute in variable formula",ivar); // ---------------- // fix @@ -1584,7 +1585,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) } else if (strncmp(word,"f_",2) == 0 || strncmp(word,"F_",2) == 0) { if (domain->box_exist == 0) - print_var_error(FLERR,"Variable evaluation before simulation box is defined",ivar); + print_var_error(FLERR,"Variable evaluation before " + "simulation box is defined",ivar); // uppercase used to force access of // global vector vs global scalar, and global array vs global vector @@ -1667,11 +1669,14 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) if (index1 > fix->size_array_rows && fix->size_array_rows_variable == 0) - print_var_error(FLERR,"Variable formula fix array is accessed out-of-range",ivar); + print_var_error(FLERR,"Variable formula fix array is " + "accessed out-of-range",ivar); if (index2 > fix->size_array_cols) - print_var_error(FLERR,"Variable formula fix array is accessed out-of-range",ivar); + print_var_error(FLERR,"Variable formula fix array is " + "accessed out-of-range",ivar); if (update->whichflag > 0 && update->ntimestep % fix->global_freq) - print_var_error(FLERR,"Fix in variable not computed at a compatible time",ivar); + print_var_error(FLERR,"Fix in variable not computed at a " + "compatible time",ivar); value1 = fix->compute_array(index1-1,index2-1); if (tree) { @@ -1688,13 +1693,17 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) } else if (nbracket == 0 && fix->vector_flag) { if (update->whichflag > 0 && update->ntimestep % fix->global_freq) - print_var_error(FLERR,"Fix in variable not computed at compatible time",ivar); + print_var_error(FLERR,"Fix in variable not computed at " + "compatible time",ivar); if (tree == NULL) - print_var_error(FLERR,"Fix global vector in ""equal-style variable formula",ivar); + print_var_error(FLERR,"Fix global vector in " + "equal-style variable formula",ivar); if (treetype == ATOM) - print_var_error(FLERR,"Fix global vector in ""atom-style variable formula",ivar); + print_var_error(FLERR,"Fix global vector in " + "atom-style variable formula",ivar); if (fix->size_vector == 0) - print_var_error(FLERR,"Variable formula fix vector is zero length",ivar); + print_var_error(FLERR,"Variable formula " + "fix vector is zero length",ivar); int nvec = fix->size_vector; double *vec; @@ -1726,7 +1735,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) print_var_error(FLERR,"Fix global vector in " "atom-style variable formula",ivar); if (fix->size_array_rows == 0) - print_var_error(FLERR,"Variable formula fix array is zero length",ivar); + print_var_error(FLERR,"Variable formula fix array is " + "zero length",ivar); int nvec = fix->size_array_rows; double *vec; @@ -1785,10 +1795,12 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) fix->size_peratom_cols == 0) { if (tree == NULL) - print_var_error(FLERR,"Per-atom fix in equal-style variable formula",ivar); + print_var_error(FLERR,"Per-atom fix in " + "equal-style variable formula",ivar); if (update->whichflag > 0 && update->ntimestep % fix->peratom_freq) - print_var_error(FLERR,"Fix in variable not computed at compatible time",ivar); + print_var_error(FLERR,"Fix in variable not computed at " + "compatible time",ivar); Tree *newtree = new Tree(); newtree->type = ATOMARRAY; @@ -1805,13 +1817,15 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) fix->size_peratom_cols > 0) { if (tree == NULL) - print_var_error(FLERR,"Per-atom fix in equal-style variable formula",ivar); + print_var_error(FLERR,"Per-atom fix in " + "equal-style variable formula",ivar); if (index1 > fix->size_peratom_cols) print_var_error(FLERR,"Variable formula fix array " "is accessed out-of-range",ivar); if (update->whichflag > 0 && update->ntimestep % fix->peratom_freq) - print_var_error(FLERR,"Fix in variable not computed at compatible time",ivar); + print_var_error(FLERR,"Fix in variable not computed at " + "compatible time",ivar); Tree *newtree = new Tree(); newtree->type = ATOMARRAY; @@ -1878,7 +1892,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) char *var = retrieve(word+2); if (var == NULL) - print_var_error(FLERR,"Invalid variable evaluation in variable formula",ivar); + print_var_error(FLERR,"Invalid variable evaluation in " + "variable formula",ivar); if (tree) { Tree *newtree = new Tree(); newtree->type = VALUE; @@ -1977,7 +1992,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) double *vec; int nvec = compute_vector(ivar,&vec); if (index <= 0 || index > nvec) - print_var_error(FLERR,"Invalid index into vector-style variable",ivar); + print_var_error(FLERR,"Invalid index into " + "vector-style variable",ivar); int m = index; // convert from tagint to int if (tree) { @@ -1989,7 +2005,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) treestack[ntreestack++] = newtree; } else argstack[nargstack++] = vec[m-1]; - } else print_var_error(FLERR,"Mismatched variable in variable formula",ivar); + } else print_var_error(FLERR,"Mismatched variable in " + "variable formula",ivar); // ---------------- // math/group/special function or atom value/vector or @@ -2194,7 +2211,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) if (value2 == 0.0) argstack[nargstack++] = 1.0; else if ((value1 == 0.0) && (value2 < 0.0)) - print_var_error(FLERR,"Invalid power expression in variable formula",ivar); + print_var_error(FLERR,"Invalid power expression in " + "variable formula",ivar); else argstack[nargstack++] = pow(value1,value2); } else if (opprevious == UNARY) { argstack[nargstack++] = -value2; @@ -3368,7 +3386,8 @@ int Variable::math_function(char *word, char *contents, Tree **tree, if (tree) newtree->type = LN; else { if (value1 <= 0.0) - print_var_error(FLERR,"Log of zero/negative value in variable formula",ivar); + print_var_error(FLERR,"Log of zero/negative value in " + "variable formula",ivar); argstack[nargstack++] = log(value1); } } else if (strcmp(word,"log") == 0) { @@ -3377,7 +3396,8 @@ int Variable::math_function(char *word, char *contents, Tree **tree, if (tree) newtree->type = LOG; else { if (value1 <= 0.0) - print_var_error(FLERR,"Log of zero/negative value in variable formula",ivar); + print_var_error(FLERR,"Log of zero/negative value in " + "variable formula",ivar); argstack[nargstack++] = log10(value1); } } else if (strcmp(word,"abs") == 0) { @@ -3482,7 +3502,8 @@ int Variable::math_function(char *word, char *contents, Tree **tree, if (narg != 2) print_var_error(FLERR,"Invalid math function in variable formula",ivar); if (update->whichflag == 0) - print_var_error(FLERR,"Cannot use ramp in variable formula between runs",ivar); + print_var_error(FLERR,"Cannot use ramp in " + "variable formula between runs",ivar); if (tree) newtree->type = RAMP; else { double delta = update->ntimestep - update->beginstep; @@ -3617,7 +3638,8 @@ int Variable::math_function(char *word, char *contents, Tree **tree, if (narg != 2) print_var_error(FLERR,"Invalid math function in variable formula",ivar); if (update->whichflag == 0) - print_var_error(FLERR,"Cannot use vdisplace in variable formula between runs",ivar); + print_var_error(FLERR,"Cannot use vdisplace in " + "variable formula between runs",ivar); if (tree) newtree->type = VDISPLACE; else { double delta = update->ntimestep - update->beginstep; @@ -3629,7 +3651,8 @@ int Variable::math_function(char *word, char *contents, Tree **tree, if (narg != 3) print_var_error(FLERR,"Invalid math function in variable formula",ivar); if (update->whichflag == 0) - print_var_error(FLERR,"Cannot use swiggle in variable formula between runs",ivar); + print_var_error(FLERR,"Cannot use swiggle in " + "variable formula between runs",ivar); if (tree) newtree->type = CWIGGLE; else { if (values[0] == 0.0) @@ -3644,7 +3667,8 @@ int Variable::math_function(char *word, char *contents, Tree **tree, if (narg != 3) print_var_error(FLERR,"Invalid math function in variable formula",ivar); if (update->whichflag == 0) - print_var_error(FLERR,"Cannot use cwiggle in variable formula between runs",ivar); + print_var_error(FLERR,"Cannot use cwiggle in " + "variable formula between runs",ivar); if (tree) newtree->type = CWIGGLE; else { if (values[0] == 0.0) @@ -3709,7 +3733,8 @@ int Variable::group_function(char *word, char *contents, Tree **tree, if (strcmp(word,"count") == 0) { if (narg == 1) value = group->count(igroup); - else if (narg == 2) value = group->count(igroup,region_function(args[1],ivar)); + else if (narg == 2) + value = group->count(igroup,region_function(args[1],ivar)); else print_var_error(FLERR,"Invalid group function in variable formula",ivar); } else if (strcmp(word,"mass") == 0) { @@ -3719,7 +3744,8 @@ int Variable::group_function(char *word, char *contents, Tree **tree, } else if (strcmp(word,"charge") == 0) { if (narg == 1) value = group->charge(igroup); - else if (narg == 2) value = group->charge(igroup,region_function(args[1],ivar)); + else if (narg == 2) + value = group->charge(igroup,region_function(args[1],ivar)); else print_var_error(FLERR,"Invalid group function in variable formula",ivar); } else if (strcmp(word,"xcm") == 0) { @@ -3732,7 +3758,8 @@ int Variable::group_function(char *word, char *contents, Tree **tree, int iregion = region_function(args[2],ivar); double masstotal = group->mass(igroup,iregion); group->xcm(igroup,masstotal,xcm,iregion); - } else print_var_error(FLERR,"Invalid group function in variable formula",ivar); + } else print_var_error(FLERR,"Invalid group function in " + "variable formula",ivar); if (strcmp(args[1],"x") == 0) value = xcm[0]; else if (strcmp(args[1],"y") == 0) value = xcm[1]; else if (strcmp(args[1],"z") == 0) value = xcm[2]; @@ -3748,7 +3775,8 @@ int Variable::group_function(char *word, char *contents, Tree **tree, int iregion = region_function(args[2],ivar); double masstotal = group->mass(igroup,iregion); group->vcm(igroup,masstotal,vcm,iregion); - } else print_var_error(FLERR,"Invalid group function in variable formula",ivar); + } else print_var_error(FLERR,"Invalid group function in " + "variable formula",ivar); if (strcmp(args[1],"x") == 0) value = vcm[0]; else if (strcmp(args[1],"y") == 0) value = vcm[1]; else if (strcmp(args[1],"z") == 0) value = vcm[2]; @@ -3767,7 +3795,8 @@ int Variable::group_function(char *word, char *contents, Tree **tree, } else if (strcmp(word,"bound") == 0) { double minmax[6]; if (narg == 2) group->bounds(igroup,minmax); - else if (narg == 3) group->bounds(igroup,minmax,region_function(args[2],ivar)); + else if (narg == 3) + group->bounds(igroup,minmax,region_function(args[2],ivar)); else print_var_error(FLERR,"Invalid group function in variable formula",ivar); if (strcmp(args[1],"xmin") == 0) value = minmax[0]; else if (strcmp(args[1],"xmax") == 0) value = minmax[1]; @@ -3789,7 +3818,8 @@ int Variable::group_function(char *word, char *contents, Tree **tree, double masstotal = group->mass(igroup,iregion); group->xcm(igroup,masstotal,xcm,iregion); value = group->gyration(igroup,masstotal,xcm,iregion); - } else print_var_error(FLERR,"Invalid group function in variable formula",ivar); + } else print_var_error(FLERR,"Invalid group function in " + "variable formula",ivar); } else if (strcmp(word,"ke") == 0) { if (narg == 1) value = group->ke(igroup); @@ -3808,7 +3838,8 @@ int Variable::group_function(char *word, char *contents, Tree **tree, double masstotal = group->mass(igroup,iregion); group->xcm(igroup,masstotal,xcm,iregion); group->angmom(igroup,xcm,lmom,iregion); - } else print_var_error(FLERR,"Invalid group function in variable formula",ivar); + } else print_var_error(FLERR,"Invalid group function in " + "variable formula",ivar); if (strcmp(args[1],"x") == 0) value = lmom[0]; else if (strcmp(args[1],"y") == 0) value = lmom[1]; else if (strcmp(args[1],"z") == 0) value = lmom[2]; @@ -3826,7 +3857,8 @@ int Variable::group_function(char *word, char *contents, Tree **tree, double masstotal = group->mass(igroup,iregion); group->xcm(igroup,masstotal,xcm,iregion); group->torque(igroup,xcm,tq,iregion); - } else print_var_error(FLERR,"Invalid group function in variable formula",ivar); + } else print_var_error(FLERR,"Invalid group function in " + "variable formula",ivar); if (strcmp(args[1],"x") == 0) value = tq[0]; else if (strcmp(args[1],"y") == 0) value = tq[1]; else if (strcmp(args[1],"z") == 0) value = tq[2]; @@ -3844,7 +3876,8 @@ int Variable::group_function(char *word, char *contents, Tree **tree, double masstotal = group->mass(igroup,iregion); group->xcm(igroup,masstotal,xcm,iregion); group->inertia(igroup,xcm,inertia,iregion); - } else print_var_error(FLERR,"Invalid group function in variable formula",ivar); + } else print_var_error(FLERR,"Invalid group function in " + "variable formula",ivar); if (strcmp(args[1],"xx") == 0) value = inertia[0][0]; else if (strcmp(args[1],"yy") == 0) value = inertia[1][1]; else if (strcmp(args[1],"zz") == 0) value = inertia[2][2]; @@ -3869,7 +3902,8 @@ int Variable::group_function(char *word, char *contents, Tree **tree, group->angmom(igroup,xcm,angmom,iregion); group->inertia(igroup,xcm,inertia,iregion); group->omega(angmom,inertia,omega); - } else print_var_error(FLERR,"Invalid group function in variable formula",ivar); + } else print_var_error(FLERR,"Invalid group function in " + "variable formula",ivar); if (strcmp(args[1],"x") == 0) value = omega[0]; else if (strcmp(args[1],"y") == 0) value = omega[1]; else if (strcmp(args[1],"z") == 0) value = omega[2]; @@ -3924,7 +3958,8 @@ int Variable::special_function(char *word, char *contents, Tree **tree, Tree **treestack, int &ntreestack, double *argstack, int &nargstack, int ivar) { - double value,xvalue,sx,sy,sxx,sxy; + bigint sx,sxx; + double value,sy,sxy; // word not a match to any special function @@ -4020,11 +4055,13 @@ int Variable::special_function(char *word, char *contents, Tree **tree, } else index = 0; int ifix = modify->find_fix(&args[0][2]); - if (ifix < 0) print_var_error(FLERR,"Invalid fix ID in variable formula",ivar); + if (ifix < 0) + print_var_error(FLERR,"Invalid fix ID in variable formula",ivar); fix = modify->fix[ifix]; if (index == 0 && fix->vector_flag) { if (update->whichflag > 0 && update->ntimestep % fix->global_freq) - print_var_error(FLERR,"Fix in variable not computed at compatible time",ivar); + print_var_error(FLERR,"Fix in variable not computed at " + "compatible time",ivar); nvec = fix->size_vector; nstride = 1; } else if (index && fix->array_flag) { @@ -4032,7 +4069,8 @@ int Variable::special_function(char *word, char *contents, Tree **tree, print_var_error(FLERR,"Variable formula fix array " "is accessed out-of-range",ivar); if (update->whichflag > 0 && update->ntimestep % fix->global_freq) - print_var_error(FLERR,"Fix in variable not computed at compatible time",ivar); + print_var_error(FLERR,"Fix in variable not computed at " + "compatible time",ivar); nvec = fix->size_array_rows; nstride = fix->size_array_cols; } else print_var_error(FLERR,"Mismatched fix in variable formula",ivar); @@ -4048,10 +4086,12 @@ int Variable::special_function(char *word, char *contents, Tree **tree, } else index = 0; if (index) - print_var_error(FLERR,"Invalid special function in variable formula",ivar); + print_var_error(FLERR,"Invalid special function in " + "variable formula",ivar); ivar = find(&args[0][2]); if (ivar < 0) - print_var_error(FLERR,"Invalid special function in variable formula",ivar); + print_var_error(FLERR,"Invalid special function in " + "variable formula",ivar); if (style[ivar] != VECTOR) print_var_error(FLERR,"Mis-matched special function variable " "in variable formula",ivar); @@ -4062,12 +4102,16 @@ int Variable::special_function(char *word, char *contents, Tree **tree, nvec = compute_vector(ivar,&vec); nstride = 1; - } else print_var_error(FLERR,"Invalid special function in variable formula",ivar); + } else print_var_error(FLERR,"Invalid special function in " + "variable formula",ivar); value = 0.0; - if (method == SLOPE) sx = sy = sxx = sxy = 0.0; - if (method == XMIN) value = BIG; - if (method == XMAX) value = -BIG; + if (method == SLOPE) { + sx = sxx = 0; + sy = sxy = 0.0; + } + else if (method == XMIN) value = BIG; + else if (method == XMAX) value = -BIG; if (compute) { double *vec; @@ -4084,12 +4128,10 @@ int Variable::special_function(char *word, char *contents, Tree **tree, else if (method == AVE) value += vec[j]; else if (method == TRAP) value += vec[j]; else if (method == SLOPE) { - if (nvec > 1) xvalue = (double) i / (nvec-1); - else xvalue = 0.0; - sx += xvalue; + sx += i; sy += vec[j]; - sxx += xvalue*xvalue; - sxy += xvalue*vec[j]; + sxx += i*i; + sxy += i*vec[j]; } j += nstride; } @@ -4107,12 +4149,10 @@ int Variable::special_function(char *word, char *contents, Tree **tree, else if (method == AVE) value += one; else if (method == TRAP) value += one; else if (method == SLOPE) { - if (nvec > 1) xvalue = (double) i / (nvec-1); - else xvalue = 0.0; - sx += xvalue; + sx += i; sy += one; - sxx += xvalue*xvalue; - sxy += xvalue*one; + sxx += i*i; + sxy += i*one; } } if (method == TRAP) { @@ -4134,12 +4174,10 @@ int Variable::special_function(char *word, char *contents, Tree **tree, else if (method == AVE) value += one; else if (method == TRAP) value += one; else if (method == SLOPE) { - if (nvec > 1) xvalue = (double) i / (nvec-1); - else xvalue = 0.0; - sx += xvalue; + sx += i; sy += one; - sxx += xvalue*xvalue; - sxy += xvalue*one; + sxx += i*i; + sxy += i*one; } } if (method == TRAP) value -= 0.5*vec[0] + 0.5*vec[nvec-1]; @@ -4148,9 +4186,9 @@ int Variable::special_function(char *word, char *contents, Tree **tree, if (method == AVE) value /= nvec; if (method == SLOPE) { - double numerator = sxy - sx*sy; - double denominator = sxx - sx*sx; - if (denominator != 0.0) value = numerator/denominator / nvec; + double numerator = nvec*sxy - sx*sy; + double denominator = nvec*sxx - sx*sx; + if (denominator != 0.0) value = numerator/denominator; else value = BIG; } @@ -4169,7 +4207,8 @@ int Variable::special_function(char *word, char *contents, Tree **tree, } else if (strcmp(word,"gmask") == 0) { if (tree == NULL) - print_var_error(FLERR,"Gmask function in equal-style variable formula",ivar); + print_var_error(FLERR,"Gmask function in equal-style " + "variable formula",ivar); if (narg != 1) print_var_error(FLERR,"Invalid special function in variable formula",ivar); @@ -4186,7 +4225,8 @@ int Variable::special_function(char *word, char *contents, Tree **tree, } else if (strcmp(word,"rmask") == 0) { if (tree == NULL) - print_var_error(FLERR,"Rmask function in equal-style variable formula",ivar); + print_var_error(FLERR,"Rmask function in equal-style " + "variable formula",ivar); if (narg != 1) print_var_error(FLERR,"Invalid special function in variable formula",ivar); @@ -4202,7 +4242,8 @@ int Variable::special_function(char *word, char *contents, Tree **tree, } else if (strcmp(word,"grmask") == 0) { if (tree == NULL) - print_var_error(FLERR,"Grmask function in equal-style variable formula",ivar); + print_var_error(FLERR,"Grmask function in equal-style " + "variable formula",ivar); if (narg != 2) print_var_error(FLERR,"Invalid special function in variable formula",ivar); @@ -4228,7 +4269,8 @@ int Variable::special_function(char *word, char *contents, Tree **tree, int ivar = find(args[0]); if (ivar < 0) - print_var_error(FLERR,"Variable ID in variable formula does not exist",ivar); + print_var_error(FLERR,"Variable ID in " + "variable formula does not exist",ivar); // SCALARFILE has single current value, read next one // save value in tree or on argstack @@ -4253,7 +4295,8 @@ int Variable::special_function(char *word, char *contents, Tree **tree, } else if (style[ivar] == ATOMFILE) { if (tree == NULL) - print_var_error(FLERR,"Atomfile variable in equal-style variable formula",ivar); + print_var_error(FLERR,"Atomfile variable in " + "equal-style variable formula",ivar); double *result; memory->create(result,atom->nlocal,"variable:result"); @@ -4271,11 +4314,13 @@ int Variable::special_function(char *word, char *contents, Tree **tree, newtree->nextra = 0; treestack[ntreestack++] = newtree; - } else print_var_error(FLERR,"Invalid variable style in special function next",ivar); + } else print_var_error(FLERR,"Invalid variable style in " + "special function next",ivar); } else if (strcmp(word,"is_active") == 0) { if (narg != 2) - print_var_error(FLERR,"Invalid is_active() function in variable formula",ivar); + print_var_error(FLERR,"Invalid is_active() function in " + "variable formula",ivar); Info info(lmp); value = (info.is_active(args[0],args[1])) ? 1.0 : 0.0; @@ -4293,7 +4338,8 @@ int Variable::special_function(char *word, char *contents, Tree **tree, } else if (strcmp(word,"is_available") == 0) { if (narg != 2) - print_var_error(FLERR,"Invalid is_available() function in variable formula",ivar); + print_var_error(FLERR,"Invalid is_available() function in " + "variable formula",ivar); Info info(lmp); value = (info.is_available(args[0],args[1])) ? 1.0 : 0.0; @@ -4311,7 +4357,8 @@ int Variable::special_function(char *word, char *contents, Tree **tree, } else if (strcmp(word,"is_defined") == 0) { if (narg != 2) - print_var_error(FLERR,"Invalid is_defined() function in variable formula",ivar); + print_var_error(FLERR,"Invalid is_defined() function in " + "variable formula",ivar); Info info(lmp); value = (info.is_defined(args[0],args[1])) ? 1.0 : 0.0; diff --git a/src/velocity.cpp b/src/velocity.cpp index f83f778f8b..3a0b95fb4d 100644 --- a/src/velocity.cpp +++ b/src/velocity.cpp @@ -410,7 +410,7 @@ void Velocity::create(double t_desired, int seed) /* ---------------------------------------------------------------------- */ -void Velocity::set(int narg, char **arg) +void Velocity::set(int /*narg*/, char **arg) { int xstyle,ystyle,zstyle,varflag; double vx,vy,vz; @@ -579,7 +579,7 @@ void Velocity::set(int narg, char **arg) rescale velocities of a group after computing its temperature ------------------------------------------------------------------------- */ -void Velocity::scale(int narg, char **arg) +void Velocity::scale(int /*narg*/, char **arg) { double t_desired = force->numeric(FLERR,arg[0]); @@ -628,7 +628,7 @@ void Velocity::scale(int narg, char **arg) apply a ramped set of velocities ------------------------------------------------------------------------- */ -void Velocity::ramp(int narg, char **arg) +void Velocity::ramp(int /*narg*/, char **arg) { // set scale factors @@ -705,7 +705,7 @@ void Velocity::ramp(int narg, char **arg) zero linear or angular momentum of a group ------------------------------------------------------------------------- */ -void Velocity::zero(int narg, char **arg) +void Velocity::zero(int /*narg*/, char **arg) { if (strcmp(arg[0],"linear") == 0) { if (rfix < 0) zero_momentum(); diff --git a/src/version.h b/src/version.h index 04baa25f12..0b8c1e8736 100644 --- a/src/version.h +++ b/src/version.h @@ -1 +1 @@ -#define LAMMPS_VERSION "22 Jun 2018" +#define LAMMPS_VERSION "5 Sep 2018" diff --git a/src/write_restart.cpp b/src/write_restart.cpp index 69b731870d..1bfbb382a8 100644 --- a/src/write_restart.cpp +++ b/src/write_restart.cpp @@ -61,7 +61,9 @@ enum{VERSION,SMALLINT,TAGINT,BIGINT, MULTIPROC,MPIIO,PROCSPERFILE,PERPROC, IMAGEINT,BOUNDMIN,TIMESTEP, ATOM_ID,ATOM_MAP_STYLE,ATOM_MAP_USER,ATOM_SORTFREQ,ATOM_SORTBIN, - COMM_MODE,COMM_CUTOFF,COMM_VEL,NO_PAIR}; + COMM_MODE,COMM_CUTOFF,COMM_VEL,NO_PAIR, + EXTRA_BOND_PER_ATOM,EXTRA_ANGLE_PER_ATOM,EXTRA_DIHEDRAL_PER_ATOM, + EXTRA_IMPROPER_PER_ATOM,EXTRA_SPECIAL_PER_ATOM}; /* ---------------------------------------------------------------------- */ @@ -527,6 +529,12 @@ void WriteRestart::header() write_double(COMM_CUTOFF,comm->cutghostuser); write_int(COMM_VEL,comm->ghost_velocity); + write_int(EXTRA_BOND_PER_ATOM,atom->extra_bond_per_atom); + write_int(EXTRA_ANGLE_PER_ATOM,atom->extra_angle_per_atom); + write_int(EXTRA_DIHEDRAL_PER_ATOM,atom->extra_dihedral_per_atom); + write_int(EXTRA_IMPROPER_PER_ATOM,atom->extra_improper_per_atom); + write_int(EXTRA_SPECIAL_PER_ATOM,force->special_extra); + // -1 flag signals end of header int flag = -1; diff --git a/tools/emacs/README.md b/tools/emacs/README.md new file mode 100644 index 0000000000..75504a7000 --- /dev/null +++ b/tools/emacs/README.md @@ -0,0 +1,82 @@ +# GNU Emacs Syntax Highlighting + +> Copyright (C) 2010-2018 Aidan Thompson +> Copyright (C) 2018 Rohit Goswami + +The `lammps-mode.el` file provided in this directory will enable syntax +highlighting for the lammps script syntax in GNU Emacs. The groupings of +commands were originally copied from `tools/vim`. + +## Installation +**Requirements: GNU Emacs 24.\*** + +### Obtaining the Package + +#### MELPA + +The easiest installation method is via MELPA and it is advisable to use one of +the many [MELPA installation methods](https://melpa.org/#/getting-started). + +For example, with [use-package](https://github.com/jwiegley/use-package) one can +simply use the following: + +``` emacs-lisp +(use-package lammps-mode) +``` + +#### Manually + +Assuming for some reason you have downloaded the file to `~/.emacs.d/lisp` you +would do the following (kanged [from here](http://ergoemacs.org/emacs/emacs_installing_packages.html)): + +``` emacs-lisp +;; Tell emacs where is your personal elisp lib dir +(add-to-list 'load-path "~/.emacs.d/lisp/") + +;; load the package. +(load "lammps-mode") +``` + +### Autoloading \& Auto-recognition + +To automatically turn on the LAMMPS mode for editing your input scripts, +use the following line as the **first** line of your script: +``` +# -*- lammps -*- +``` + +For automatically switching on the LAMMPS mode based on filename patterns, +e.g. for `in.*` and `*.lmp` files, add the following code to your `.emacs`: + +``` emacs-lisp +(autoload 'lammps-mode "lammps-mode.el" "LAMMPS mode." t) +(setq auto-mode-alist (append auto-mode-alist + '(("in\\." . lammps-mode)) + '(("\\.lmp\\'" . lammps-mode)) + )) +``` + +## Status + +By far not all commands are included in the syntax file (lammps-mode.el). You +can easily add new ones to the existing classes. + +## Implementation Details + +`lammps-mode` is derived from `shell-script-mode` which provides some basic +syntax highlighting of strings, comments, etc. + +The MELPA recipe used for this package is simply: + +``` emacs-lisp +(lammps-mode :fetcher github :repo "HaoZeke/lammps-mode") +``` + +## Caveats + +* Does not work with Xemacs [See [this comment](https://github.com/lammps/lammps/pull/1022#issuecomment-408871233)] + +## License + +[GNU GPL v2](https://github.com/HaoZeke/lammps-mode/blob/master/LICENSE). +Check the file for more details. diff --git a/tools/emacs/README.txt b/tools/emacs/README.txt deleted file mode 100644 index 8dfc37cb85..0000000000 --- a/tools/emacs/README.txt +++ /dev/null @@ -1,23 +0,0 @@ -=== Emacs Syntax Highlighting === -Created by Aidan Thompson 12/2010 -=============================== - -The lammps.el file provided in this directory will enable syntax -highlighting for the lammps script syntax in emacs. The groupings -of commands were copied from tools/vim. The simulation scripts have to -end on *.lmp or start with in.* (see lammps.el). By far not all -commands are included in the syntax file (lammps.el). -You can easily add new ones to the existing classes. -'lammps-mode' is derived from 'shell-script-mode' which provides -some basic syntax highlighting of strings, comments, etc. - -=To enable the highlighting: -============================ -(0) Create/edit the emacs init file ~/.emacs to contain: - -(load "~/.emacs.d/lammps") - -This file may also be called ~/.emacs.el, or ~/.emacs.d/init.el - -(1) Copy lammps.el to the directory ~/.emacs.d - diff --git a/tools/emacs/lammps.el b/tools/emacs/lammps-mode.el similarity index 73% rename from tools/emacs/lammps.el rename to tools/emacs/lammps-mode.el index d1ebebbbbf..37e8a32116 100644 --- a/tools/emacs/lammps.el +++ b/tools/emacs/lammps-mode.el @@ -1,7 +1,48 @@ -;; LAMMPS auto-mode +;;; lammps-mode.el --- basic syntax highlighting for LAMMPS files + +;; Copyright (C) 2010-18 Aidan Thompson +;; Copyright (C) 2018 Rohit Goswami + +;; Author: Aidan Thompson +;; Maintainer: Rohit Goswami +;; Created: December 4, 2010 +;; Modified: July 30, 2018 +;; Version: 1.5.0 +;; Keywords: languages, faces +;; Homepage: https://github.com/lammps/lammps/tree/master/tools/emacs +;; Package-Requires: ((emacs "24.4")) + +;; This file is not part of GNU Emacs. + +;; This program is free software; you can redistribute it and/or modify +;; it under the terms of the GNU General Public License as published by +;; the Free Software Foundation; either version 2 of the License, or +;; (at your option) any later version. + +;; This program is distributed in the hope that it will be useful, +;; but WITHOUT ANY WARRANTY; without even the implied warranty of +;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +;; GNU General Public License for more details. + +;; You should have received a copy of the GNU General Public License along +;; with this program; if not, write to the Free Software Foundation, Inc., +;; 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. + +;;; Commentary: ;; translation of keyword classes from tools/vim ;; see http://xahlee.org/emacs/elisp_syntax_coloring.html +;; Put this in your .emacs file to enable autoloading of lammps-mode +;; and auto-recognition of "in.*" and "*.lmp" files: +;; +;; (autoload 'lammps-mode "lammps-mode.el" "LAMMPS mode." t) +;; (setq auto-mode-alist (append auto-mode-alist +;; '(("in\\." . lammps-mode)) +;; '(("\\.lmp\\'" . lammps-mode)) +;; )) +;; + +;;; Code: ;; define several keyword classes (defvar lammps-output '("log" @@ -136,6 +177,8 @@ (defvar lammps-variable-regexp "\\$\\({[a-zA-Z0-9_]+}\\)\\|\\$[A-Za-z]") +(defvar lammps-font-lock-keywords) + ;; clear memory (setq lammps-output nil) (setq lammps-read nil) @@ -151,8 +194,7 @@ ;; create the list for font-lock. ;; each class of keyword is given a particular face -(setq - lammps-font-lock-keywords +(setq lammps-font-lock-keywords `((,lammps-output-regexp . font-lock-function-name-face) (,lammps-read-regexp . font-lock-preprocessor-face) (,lammps-lattice-regexp . font-lock-type-face) @@ -199,12 +241,5 @@ (setq lammps-comment-regexp nil) (setq lammps-variable-regexp nil)) -;; apply it to specified filename patterns -(setq - auto-mode-alist - (append - auto-mode-alist - '(("in\\." . lammps-mode)) - '(("\\.lmp\\'" . lammps-mode)) - )) - +(provide 'lammps-mode) +;;; lammps-mode.el ends here diff --git a/tools/moltemplate/.gitignore b/tools/moltemplate/.gitignore new file mode 100644 index 0000000000..d2053ce4dc --- /dev/null +++ b/tools/moltemplate/.gitignore @@ -0,0 +1,180 @@ +# from https://github.com/github/gitignore/blob/master/Python.gitignore + +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] +*$py.class + +# C extensions +*.so + +# Distribution / packaging +.Python +env/ +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +wheels/ +*.egg-info/ +.installed.cfg +*.egg + +# PyInstaller +# Usually these files are written by a python script from a template +# before PyInstaller builds the exe, so as to inject date/other infos into it. +*.manifest +*.spec + +# Installer logs +pip-log.txt +pip-delete-this-directory.txt + +# Unit test / coverage reports +htmlcov/ +.tox/ +.coverage +.coverage.* +.cache +nosetests.xml +coverage.xml +*,cover +.hypothesis/ + +# Translations +*.mo +*.pot + +# Django stuff: +*.log +local_settings.py + +# Flask stuff: +instance/ +.webassets-cache + +# Scrapy stuff: +.scrapy + +# Sphinx documentation +docs/_build/ + +# PyBuilder +target/ + +# Jupyter Notebook +.ipynb_checkpoints + +# pyenv +.python-version + +# celery beat schedule file +celerybeat-schedule + +# dotenv +.env + +# virtualenv +.venv/ +venv/ +ENV/ + +# Spyder project settings +.spyderproject + +# Rope project settings +.ropeproject + +# text-editor temporary files: +*~ + +# misc rubbish +deleteme* +DELETEME* + +######## files specific to moltemplate and lammps ######## + +# latex/bibtex temporary files for the moltemplate manual: +moltemplate_manual*.aux +moltemplate_manual*.bbl +moltemplate_manual*.blg +moltemplate_manual*.log +moltemplate_manual*.out +moltemplate_manual*.toc + +######## files created by running LAMMPS: ######## + +log.lammps +log.cite +traj*.lammpstrj + +######## files generated by running moltemplate: ######## + +system.data +system.in +system.in.init +system.in.settings +system.in.charges +system.psf +ttree_assignments.txt +output_ttree/ + +# Sections from the LAMMPS data file generated by moltemplate.sh +"Data Header"* +"Data Atoms"* +"Data Masses"* +"Data Velocities"* +"Data Bonds"* +"Data Bond List"* +"Data Bonds AtomId AtomId"* +"Data Angles"* +"Data Dihedrals"* +"Data Impropers"* +"Data Bond Coeffs"* +"Data Angle Coeffs"* +"Data Dihedral Coeffs"* +"Data Improper Coeffs"* +"Data Pair Coeffs"* +"Data PairIJ Coeffs"* + +# interactions-by-type (not id. This is not part of the LAMMPS standard.) +"Data Charge By Bond"* +"Data Bonds By Type"* +"Data Angles By Type"* +"Data Dihedrals By Type"* +"Data Impropers By Type"* + +# class2 data sections +"Data BondBond Coeffs"* +"Data BondAngle Coeffs"* +"Data MiddleBondTorsion Coeffs"* +"Data EndBondTorsion Coeffs"* +"Data AngleTorsion Coeffs"* +"Data AngleAngleTorsion Coeffs"* +"Data BondBond13 Coeffs"* +"Data AngleAngle Coeffs"* + +# sections for non-point-like particles: +"Data Ellipsoids"* +"Data Lines"* +"Data Triangles"* + +# periodic boundary conditions +"Data Boundary"* + +# Sections from the LAMMPS input script(s) generated by moltemplate.sh + +"In Init"* +"In Settings"* +"In Coords"* +"In Charges"* +#temporary file created by moltemplate.sh for storing coordinates +tmp_atom_coords.dat + diff --git a/tools/moltemplate/README.md b/tools/moltemplate/README.md index dc63a6bf4a..c0bcb28296 100644 --- a/tools/moltemplate/README.md +++ b/tools/moltemplate/README.md @@ -1,9 +1,11 @@ +[![Build Status](https://travis-ci.org/jewettaij/moltemplate.svg?branch=master)](https://travis-ci.org/jewettaij/moltemplate.svg?branch=master) + Moltemplate =========== ## Description -Moltemplate is a cross-platform text-based molecule builder for LAMMPS. +Moltemplate is a *general* cross-platform text-based molecule builder for **LAMMPS** and **ESPResSo**. Moltemplate was intended for building custom coarse-grained molecular models, but it can be used to prepare realistic all-atom simulations as well. It currently supports the **OPLS**, **COMPASS**, **AMBER**(GAFF,GAFF2), **MARTINI**, **SDK**, **LOPLS**(2015), and **TraPPE**(1998) force fields, and includes approximately 40 examples. (New force fields and examples are added continually by users.) ## Typical usage @@ -45,7 +47,7 @@ Make sure that your default pip install bin directory is in your PATH. (This is pip uninstall moltemplate -If you continue to run into difficulty, try installing moltemplate into a temporary virtual environment by installing "virtualenv", downloading moltemplate (to "~/moltemplate" in the example below), and running these commands: +If you continue to run into difficulty, try installing moltemplate into a temporary virtual environment by installing "*virtualenv*", downloading moltemplate (to "~/moltemplate" in the example below), and running these commands: cd ~/moltemplate virtualenv venv @@ -53,7 +55,9 @@ If you continue to run into difficulty, try installing moltemplate into a tempor pip install . #(now do something useful with moltemplate...) -(You will have to "run source ~/moltemplate/venv/bin/activate" beforehand every time you want to run moltemplate.) If all this fails, then try installing moltemplate by manually updating your \$PATH environment variable. Instructions for doing that are included below. +(You will have to "run source ~/moltemplate/venv/bin/activate" beforehand every time you want to run moltemplate. +The *virtualenv* tool is +[explained in detail here](http://docs.python-guide.org/en/latest/dev/virtualenvs/)) If all this fails, then try installing moltemplate by manually updating your \$PATH environment variable. Instructions for doing that are included below. ## Manual installation: diff --git a/tools/moltemplate/doc/moltemplate_manual.pdf b/tools/moltemplate/doc/moltemplate_manual.pdf index b0122a3fd8..54d8b132bf 100644 Binary files a/tools/moltemplate/doc/moltemplate_manual.pdf and b/tools/moltemplate/doc/moltemplate_manual.pdf differ diff --git a/tools/moltemplate/doc/moltemplate_manual_src/2bead_residue.jpg b/tools/moltemplate/doc/moltemplate_manual_src/2bead_monomer.jpg similarity index 100% rename from tools/moltemplate/doc/moltemplate_manual_src/2bead_residue.jpg rename to tools/moltemplate/doc/moltemplate_manual_src/2bead_monomer.jpg diff --git a/tools/moltemplate/doc/moltemplate_manual_src/2bead_peptide.jpg b/tools/moltemplate/doc/moltemplate_manual_src/2bead_polymer.jpg similarity index 100% rename from tools/moltemplate/doc/moltemplate_manual_src/2bead_peptide.jpg rename to tools/moltemplate/doc/moltemplate_manual_src/2bead_polymer.jpg diff --git a/tools/moltemplate/doc/moltemplate_manual_src/2bead_peptides_nopbc_t=0_LR.jpg b/tools/moltemplate/doc/moltemplate_manual_src/2bead_polymers_nopbc_t=0_LR.jpg similarity index 100% rename from tools/moltemplate/doc/moltemplate_manual_src/2bead_peptides_nopbc_t=0_LR.jpg rename to tools/moltemplate/doc/moltemplate_manual_src/2bead_polymers_nopbc_t=0_LR.jpg diff --git a/tools/moltemplate/doc/moltemplate_manual_src/2bead_peptides_t=100ps_LR.jpg b/tools/moltemplate/doc/moltemplate_manual_src/2bead_polymers_t=100ps_LR.jpg similarity index 100% rename from tools/moltemplate/doc/moltemplate_manual_src/2bead_peptides_t=100ps_LR.jpg rename to tools/moltemplate/doc/moltemplate_manual_src/2bead_polymers_t=100ps_LR.jpg diff --git a/tools/moltemplate/doc/moltemplate_manual_src/dimer+dimer0_transparent_LR.jpg b/tools/moltemplate/doc/moltemplate_manual_src/mol_complex+mol_complex0_transparent_LR.jpg similarity index 100% rename from tools/moltemplate/doc/moltemplate_manual_src/dimer+dimer0_transparent_LR.jpg rename to tools/moltemplate/doc/moltemplate_manual_src/mol_complex+mol_complex0_transparent_LR.jpg diff --git a/tools/moltemplate/doc/moltemplate_manual_src/dimer_LR.jpg b/tools/moltemplate/doc/moltemplate_manual_src/mol_complex_LR.jpg similarity index 100% rename from tools/moltemplate/doc/moltemplate_manual_src/dimer_LR.jpg rename to tools/moltemplate/doc/moltemplate_manual_src/mol_complex_LR.jpg diff --git a/tools/moltemplate/doc/moltemplate_manual_src/moltemplate_manual.tex b/tools/moltemplate/doc/moltemplate_manual_src/moltemplate_manual.tex index 10a3d4fd38..f8ce810fd5 100644 --- a/tools/moltemplate/doc/moltemplate_manual_src/moltemplate_manual.tex +++ b/tools/moltemplate/doc/moltemplate_manual_src/moltemplate_manual.tex @@ -36,7 +36,7 @@ \author{ Andrew Jewett, \\ - Jensen Lab (Caltech), Shea Lab (UCSB) \\ + MGL Lab (Scripps), Jensen Lab (Caltech), Shea Lab (UCSB) \\ \includegraphics[height=0.3cm]{author_email.png} } \date \today @@ -57,8 +57,16 @@ %(which is distributed with moltemplate). %These were created to supplement the moltemplate documentation. +\subsubsection*{Warning: This manual does not explain how to run ``active-matter'' simulations or use all-atom force fields.} +However numerous examples and README files are available to +demonstrate how to run these kinds of simulations. +Downloading these examples is \textit{highly recommended}. +(See section \ref{sec:installation}.) + \section{Introduction} + + Moltemplate is a general molecule builder and force-field database system for LAMMPS. A simple file format has been created to store molecule definitions and force-fields (the LAMMPS-template format, “LTâ€). LT files are templates containing \textit{all} of the text relevant to a particular molecule (including coordinates, bond-topology, angles, force-field parameters, constraints, groups and fixes). Moltemplate can then duplicate the molecule, customize it, and use it as a building-block for constructing larger, more complex molecules. (These molecules can be used to build even larger molecules.) Once built, individual molecules and subunits can be customized (atoms and bonds, and subunits can be inserted, moved, deleted and/or replaced). @@ -320,57 +328,82 @@ under the terms of the open-source 3-clause BSD license. \section{Installation} - -\subsection*{Obtaining Moltemplate} -\textit{If you don't already have moltemplate}, -the most up-to-date version can be downloaded at -\url{http://www.moltemplate.org} -If you obtained moltemplate as a .tar.gz file, -(as opposed to github or pip), you can unpack it using: -\begin{verbatim} -tar -xzvf moltemplate_2017-8-22.tar.gz -\end{verbatim} -(The date will vary from version to version.) -Alternately, if you obtained moltemplate bundled with LAMMPS, -then the \textit{``moltemplate''} directory will probably be located -in the \textit{``tools''} subdirectory of your lammps installation. +\label{sec:installation} There are two ways to install moltemplate: \subsubsection*{Installation Method 1 (pip)} -\textit{If you are familiar with pip}, then run the following command from within outermost directory: +\textit{If you are familiar with pip}, you can install +moltemplate by typing following command in the terminal/shell: + %from within outermost directory: \begin{verbatim} -pip install . +pip install moltemplate \end{verbatim} -\textit{In order for this to work, this directory should contain a file named ``\textbf{setup.py}''.} (If no such file exists, then either proceed to ``Installation Method 2'' below, or download a newer version of moltemplate.) If you receive an error regarding permissions, then run pip this way instead: +%\textit{In order for this to work, this directory should contain a file named ``\textbf{setup.py}''.} (If no such file exists, then either proceed to ``Installation Method 2'' below, or download a newer version of moltemplate.) +If you receive an error regarding permissions, then run pip this way instead: \begin{verbatim} -pip install . --user +pip install moltemplate --user \end{verbatim} Make sure that your default pip install bin directory is in your PATH. (This is usually something like \textapprox/.local/bin/ or \textapprox/anaconda3/bin/. If you have installed anaconda, your PATH should have been updated for you automatically.) Later, you can uninstall moltemplate using: \begin{verbatim} pip uninstall moltemplate \end{verbatim} -\textit{If you continue to run into difficulty}, try installing moltemplate into a temporary virtual environment by installing ``virtualenv'', downloading moltemplate (to ``\textapprox/moltemplate'' in the example below), and running these commands: +\textit{Note: There are is a large variety of detailed moltemplate examples +which will be omitted if you install moltemplate this way. +\textbf{Downloading the examples is strongly recommended.}} +You can do this either by using git: \begin{verbatim} -cd ~/moltemplate +git clone https://github.com/jewettaij/moltemplate ~/moltemplate +\end{verbatim} +or by visiting the \url{http://www.moltemplate.org} web site. +They will be in the ``examples'' subdirectory.) + +\textit{If you run into difficulty with pip}, then try installing +moltemplate into a temporary virtual environment +by installing ``virtualenv'', +%downloading moltemplate (to ``\textapprox/moltemplate'' in the example below), +and running these commands: +\begin{verbatim} +mkdir ~/moltemplate_v +cd ~/moltemplate_v virtualenv venv source venv/bin/activate -pip install . +pip install moltemplate #(now do something useful with moltemplate...) \end{verbatim} -You will have to ``run source \textapprox/moltemplate/venv/bin/activate'' beforehand whenver you want to run moltemplate. If all this fails, then try installing moltemplate by manually updating your \$PATH environment variable. Instructions for doing that are included below. +You will have to ``run source \textapprox/moltemplate\_v/venv/bin/activate'' beforehand whenver you want to run moltemplate again. If all this fails, then try installing moltemplate by manually updating your \$PATH environment variable. Instructions for doing that are included below. \subsubsection*{Installation Method 2} -Alternatively, you can edit your PATH variable manually to include +Alternatively, you can download the moltemplate files and edit your +PATH variable manually to include the subdirectory where the moltemplate.sh script is located (typically ``\textapprox/moltemplate/moltemplate/scripts/''), as well as -the directory containing the most of the python scripts (``\textapprox/moltemplate/moltemplate/''). -Suppose the directory where with the README file is named ``moltemplate'' -and it is located in your home directory: +the directory containing the most of the python scripts +(``\textapprox/moltemplate/moltemplate/''). + +\subsection*{Obtaining Moltemplate} +The most up-to-date version of moltemplate can be downloaded using git. +\begin{verbatim} +git clone https://github.com/jewettaij/moltemplate ~/moltemplate +\end{verbatim} +Later, you can update to the latest version of moltemplate using: +\begin{verbatim} +git pull +\end{verbatim} +Alternatively, you can also download moltemplate as a .tar.gz archive from +\url{http://www.moltemplate.org} +and can unpack it using: +\begin{verbatim} +tar -xzvf moltemplate_2017-8-22.tar.gz +\end{verbatim} +(The date will vary from version to version.) +Somewhat older versions of moltemplate are also bundled with the LAMMPS +source code and are located in the \textit{``tools''} subdirectory. + If you use the \textbf{bash} shell, typically you would edit your \mbox{$\sim$/.bash\_profile}, @@ -409,7 +442,7 @@ If you are using an older version of windows, try following the tutorial written To use LAMMPS and moltemplate, You will also need to install (and learn how to use) a text editor. (Word, Wordpad, and Notepad will not work.) Popular free text editors which you can safely install and run from within the WSL terminal include: nano, ne, emacs, vim, and jove. (Unfortunately, as of 2017-5-17, graphical unix-friendly text editors such as Atom, VSCode, Notepad++, and sublime won't work with WSL, and may cause file system corruption. Avoid these editors for now. (\url{https://www.reddit.com/r/bashonubuntuonwindows/comments/6bu1d1/since_we_shouldnt_edit_files_stored_in_wsl_with/}) -%\pagebreak +\pagebreak \section{Quick reference \textit{(skip on first reading)}} \section*{ @@ -674,7 +707,7 @@ create\_var \{ \textit{variable} \} & Create a variable specific to this molecule object. (Typically this is used to create molecule-ID numbers, for a molecule built from smaller components. -See section \ref{sec:2beadPeptide}.) +See section \ref{sec:2beadPolymer}.) \\ \hline replace \{ \textit{oldvariable} \textit{newvariable} \} & @@ -761,7 +794,7 @@ Note: \mbox{\textit{``\$mol''}} is shorthand for \mbox{\textit{``\$mol:.''}}) \$\textit{mol:}... & The ID number assigned to the molecule to which this object belongs (if applicable). -See sections \ref{sec:2beadPeptide}, +See sections \ref{sec:2beadPolymer}, \ref{sec:ellipsis_mol}, %\ref{sec:paths}, and appendix \ref{sec:adv_variable_syntax}. @@ -897,6 +930,21 @@ you want the scaling to occur. Of omitted, the origin is used.) \\ \hline +\begin{tabular}[t]{l} + \textit{.quat($a,b,c,d$)} \\ + \textit{.quat($a,b,c,d,x_0,y_0,z_0$)} \\ + \textit{.quatT($a,b,c,d$)} \\ + \textit{.quatT($a,b,c,d,x_0,y_0,z_0$)} \\ +\end{tabular} + & + Rotate atom coordinates by the rotation corresponding + to quaternion $a+b\mathbf{i}+c\mathbf{j}+b\mathbf{k}$ + (around \mbox{$(x_0,y_0,z_0)$}, if specified) + The \textit{.quatT(a,b,c,d)} variant performs the inverse rotation. + (Equivalent to \textit{.quat(a,-b,-c,-d)}.) + % Otherwise around $(0,0,0)$) +\\ +\hline \multicolumn{2}{c} { \textbf{ \textit{Note:} @@ -940,7 +988,6 @@ In this example, the first transformation, ``rot()'', is applied to both ``monom - \subsection{moltemplate.sh command line arguments:} \label{sec:args_table} %\begin{table} @@ -1055,7 +1102,7 @@ Do \textit{not} check for common LAMMPS/moltemplate syntax errors. This forces moltemplate.sh to check that there are valid angle and dihedral interactions defined for every 3 or 4 consecutively bonded atoms in the system -(defined in "Data Angles By Type'' and ``Data Dihedrals By Type" sections). +(defined in ``Data Angles By Type'' and ``Data Dihedrals By Type'' sections). \\ \hline -vmd & @@ -1094,10 +1141,16 @@ Invoke VMD after running moltemplate to view the system you have just created. Normally moltemplate.sh reorders the atoms in each bond, angle, dihedral, and improper interaction before writing them to the DATA file in order to help avoid duplicate interactions between the same atoms if listed in different but equivalent orders. Sometimes this is undesirable. \textit{\textbf{To disable this behavior, set ``file.py'' to ``None''.}} You can also manually choose alternate symmetry rules for unusual force fields. (Such as class2 force fields, dihedral\_style spherical, etc... For an example of the file format for ``file.py'', see the ``nbody\_Impropers.py'' file.) \\ \hline +-allow-wildcards & +Allow the use of ``*'' and ``?'' characters within +``pair\_coeff'', ``bond\_coeff'', ``angle\_coeff'', ``dihedral\_coeff'', +and ``improper\_coeff'' commands. (Default) +\\ +\hline \end{tabular} -%\pagebreak +\pagebreak @@ -2061,30 +2114,30 @@ within moltemplate is discouraged. See section \ref{sec:wildcard_bug}.) Objects can be connected together to form larger molecule objects. These objects can be used to form still larger objects. As an example, we define a small 2-atom molecule named ``Monomer'', -and use it to construct a short polymer (``Peptide''). +and use it to construct a short polymer (``Polymer''). \begin{figure}[htbp] \centering \textbf{a)} -\includegraphics[height=3cm]{2bead_residue.jpg} +\includegraphics[height=3cm]{2bead_monomer.jpg} \quad \quad \quad \quad \quad \textbf{b)} -\includegraphics[height=3cm]{2bead_peptide.jpg} +\includegraphics[height=3cm]{2bead_polymer.jpg} \newline \vspace{10 mm} \newline \textbf{c)} -\includegraphics[width=4cm]{2bead_peptides_nopbc_t=0_LR.jpg} +\includegraphics[width=4cm]{2bead_polymers_nopbc_t=0_LR.jpg} \textbf{d)} -\includegraphics[width=4cm]{2bead_peptides_t=100ps_LR.jpg} +\includegraphics[width=4cm]{2bead_polymers_t=100ps_LR.jpg} \caption{ -\label{fig:2bead_peptide} +\label{fig:2bead_polymer} \textbf{a)-b)} \textit{Building a complex system from small pieces:} Construction of a polymer (\textbf{b}) out of smaller (2-atom) subunits (\textbf{a}) using composition and rigid-body transformations. -Bonds connecting different residues together (blue) +Bonds connecting different monomer together (blue) must be declared explicitly, but angle and dihedral interactions will be generated automatically. See section \ref{sec:2bead} for details. @@ -2130,20 +2183,123 @@ Monomer inherits ForceField { \end{verbatim} -Soon will use it to construct a polymer (``Peptide'') +Soon will use it to construct a polymer (``Polymer'') \textit{Note: The ellipsis notation used here ``\$mol:...''. warns moltemplate that the ``Monomer'' molecule may be part of a larger molecule. (This is explained in more detail in section \ref{sec:ellipsis_mol}.) +(Note: The meaning of ``inherits ForceField'' + will be explained below in section \ref{sec:nbody_by_type_intro}) } - + In this example we will define two kinds of molecule objects: -``Monomer'', and ``Peptide'' (\textit{defined later}). -It is often convenient to store atom types, masses, and force-field -parameters in a separate file so that they -can be shared between these different molecules. -We do that in the ``forcefield.lt'' file below: +``Monomer'', and ``Polymer'' (\textit{defined later}). +\subsubsection*{Building a simple polymer} +We construct a short polymer by making 7 copies of ``Monomer'', +rotating and moving each copy: +\label{sec:2beadPolymer} +\begin{verbatim} +# -- file "polymer.lt" -- + +import "monomer.lt" #(defines "Monomer" and "ForceField") + +Polymer inherits ForceField { + + # The next line is optional: + create_var {$mol} #(force all monomers to share the same molecule-ID) + + # Now create some monomers + + mon1 = new Monomer #(no need to move the first monomer) + mon2 = new Monomer.rot(180.0, 1,0,0).move(3.2,0,0) + mon3 = new Monomer.rot(360.0, 1,0,0).move(6.4,0,0) + mon4 = new Monomer.rot(540.0, 1,0,0).move(9.6,0,0) + mon5 = new Monomer.rot(720.0, 1,0,0).move(12.8,0,0) + mon6 = new Monomer.rot(900.0, 1,0,0).move(16.0,0,0) + mon7 = new Monomer.rot(1080.0, 1,0,0).move(19.2,0,0) + + # Now, link the monomers together this way: + write("Data Bonds") { + $bond:backbone1 @bond:Backbone $atom:mon1/ca $atom:mon2/ca + $bond:backbone2 @bond:Backbone $atom:mon2/ca $atom:mon3/ca + $bond:backbone3 @bond:Backbone $atom:mon3/ca $atom:mon4/ca + $bond:backbone4 @bond:Backbone $atom:mon4/ca $atom:mon5/ca + $bond:backbone5 @bond:Backbone $atom:mon5/ca $atom:mon6/ca + $bond:backbone6 @bond:Backbone $atom:mon6/ca $atom:mon7/ca + } +} +\end{verbatim} +The position and orientation of each copy of ``Monomer'' +is specified after the ``new'' statement. +Each ``new'' statement is typically followed by a chain of +move/rotate/scale functions separated by dots, evaluated left-to-right +(optionally followed by square brackets and then more dots). +For example, ``mon2'' is a copy of ``Monomer'' which is first rotated +180 degrees around the X axis (denoted by ``1,0,0''), +and \textbf{then} moved in the (3.2,0,0) direction. +(The last three arguments to the ``rot()'' command + denote the axis of rotation, which does not have to be normalized.) +(A list of available coordinate transformations +is provided in section \ref{sec:xforms_table}.) + +\textit{(Note: Although we did not do this here, +it is sometimes convenient to represent polymers as 1-dimensional arrays. +See sections \ref{sec:arrays} and \ref{sec:random_arrays} for examples.)} + +To bond atoms in different molecules or molecular subunits together, we used +the write(``Data Bonds'') command to append additional bonds to the system. + +%\subsubsection{Sharing atom, bond and angle types} +%Normally you must separately define the parameters for all of the atoms types, +%and bond types, angle types etc... in every type of molecule. +%However different kinds of monomers in a heteropolymer typically will +%share some common backbone atom types and other properties. +%You must be careful to indicate which atom and bond types are shared between +%different monomers by referring them using a ``../'' prefix. +%(See sections \ref{sec:variable_scope}, +%\ref{sec:paths}, and +%\ref{sec:butane} for details and examples.) +%\textit{Note: There is a heteropolymer example in the the +%``2bead\_heteropolymer/'' directory in the online examples. +%This example demonstrates how to share backbone atoms, bonds, and angles. +%You can also define specific angle or dihedral interactions which are +%specific to the atom types in different monomers.} + + +\subsection{Bonded interactions \textit{by type}} +\label{sec:nbody_by_type_intro} + +In this example we did \textit{not} provide a list of all 3-body +and 4-body angle forces between bonded atoms in the polymer. +Moltemplate allows you to manually list all of these interactions +(using the ``write\_once("Data Angles")'' command +from section \ref{sec:spce_example}, +\textit{or} +the ``write\_once("Data Dihedrals")'', +or ``write\_once("Data Impropers")'' commands). +However there are usually many of them. +For this reason, it is often more convenient to provide +moltemplate with instructions to help it automatically figure out +which atoms participate in 3-body and 4-body angle interactions, +and what force field parameters to assign to them. +We will do that below using the following commands: +``write\_once("Data Angles By Type")'', +``write\_once("Data Dihedrals By Type")'', and +``write\_once("Data Impropers By Type")'' + + %Moltemplate can detect consecutively bonded atoms and + %determine the forces between them based on atom type (and bond type). + +Furthermoree, since many different kinds molecules often share +the same rules for creating 3-body and 4-body angle interactions, +it is convenient to organize all of this information +together into one place (eg an object named ``ForceField''). +A ``ForceField'' object will typically include many +``write\_once("Data Angles By Type")'' +commands, as well as force field parameters and related atom type properties. +We also typically store that information in a separate file +(eg ``forcefield.lt'', ``oplsaa.lt'', ``gaff2.lt'', ``compass.lt'', etc...). \begin{verbatim} # -- file "forcefield.lt" -- @@ -2199,14 +2355,14 @@ ForceField { angle_coeff @angle:Sidechain 30.00 132 } + # 4-body interactions in this example are listed by atomType # Rules for determining 4-body (dihedral) interactions by atom & bond type: write_once("Data Dihedrals By Type") { - # dihedralType atmType1 atmType2 atmType3 atmType4 bondType1 bnd2 bnd3 + # dihedralType atmType1 atmType2 atmType3 atmType4 bondType1 bType2 bType3 @dihedral:CCCC @atom:CA @atom:CA @atom:CA @atom:CA @bond:* @bond:* @bond:* @dihedral:RCCR @atom:R @atom:CA @atom:CA @atom:R @bond:* @bond:* @bond:* } - # 4-body interactions in this example are listed by atomType # The forumula used is: # # Udihedral(phi) = K * (1 + cos(n*phi - d)) @@ -2229,111 +2385,22 @@ ForceField { bond_style harmonic angle_style harmonic dihedral_style charmm - pair_style lj/cut/coul/debye 0.1 11.0 - pair_modify mix arithmetic - dielectric 80.0 - special_bonds lj 0.0 0.0 0.0 + pair_style lj/cut 11.0 } } \end{verbatim} - - - -\subsubsection{Building a simple polymer} -We construct a short polymer by making 7 copies of ``Monomer'', -rotating and moving each copy: -\label{sec:2beadPeptide} -\begin{verbatim} -# -- file "peptide.lt" -- - -import "monomer.lt" - -Peptide inherits ForceField { - - create_var {$mol} # optional:force all monomers to share the same molecule-ID - # (The "Data Atoms" in Monomer must use the "$mol:..." notation.) - - res1 = new Monomer - res2 = new Monomer.rot(180.0, 1,0,0).move(3.2,0,0) - res3 = new Monomer.rot(360.0, 1,0,0).move(6.4,0,0) - res4 = new Monomer.rot(540.0, 1,0,0).move(9.6,0,0) - res5 = new Monomer.rot(720.0, 1,0,0).move(12.8,0,0) - res6 = new Monomer.rot(900.0, 1,0,0).move(16.0,0,0) - res7 = new Monomer.rot(1080.0, 1,0,0).move(19.2,0,0) - - # Now, link the residues together this way: - write("Data Bonds") { - $bond:backbone1 @bond:Backbone $atom:res1/ca $atom:res2/ca - $bond:backbone2 @bond:Backbone $atom:res2/ca $atom:res3/ca - $bond:backbone3 @bond:Backbone $atom:res3/ca $atom:res4/ca - $bond:backbone4 @bond:Backbone $atom:res4/ca $atom:res5/ca - $bond:backbone5 @bond:Backbone $atom:res5/ca $atom:res6/ca - $bond:backbone6 @bond:Backbone $atom:res6/ca $atom:res7/ca - } -} -\end{verbatim} -The position and orientation of each copy of ``Monomer'' -is specified after the ``new'' statement. -Each ``new'' statement is typically followed by a chain of -move/rotate/scale functions separated by dots, evaluated left-to-right -(optionally followed by square brackets and then more dots). -For example, ``res2'' is a copy of ``Monomer'' which is first rotated -180 degrees around the X axis (denoted by ``1,0,0''), -and \textbf{then} moved in the (3.2,0,0) direction. -(The last three arguments to the ``rot()'' command - denote the axis of rotation, which does not have to be normalized.) -(A list of available coordinate transformations -is provided in section \ref{sec:xforms_table}.) - -\textit{(Note: Although we did not do this here, -it is sometimes convenient to represent polymers as 1-dimensional arrays. -See sections \ref{sec:arrays} and \ref{sec:random_arrays} for examples.)} - -To bond atoms in different molecules or molecular subunits together, we used -the write(``Data Bonds'') command to append additional bonds to the system. - -%\subsubsection{Sharing atom, bond and angle types} -%Normally you must separately define the parameters for all of the atoms types, -%and bond types, angle types etc... in every type of molecule. -%However different kinds of monomers in a heteropolymer typically will -%share some common backbone atom types and other properties. -%You must be careful to indicate which atom and bond types are shared between -%different monomers by referring them using a ``../'' prefix. -%(See sections \ref{sec:variable_scope}, -%\ref{sec:paths}, and -%\ref{sec:butane} for details and examples.) -%\textit{Note: There is a heteropolymer example in the the -%``2bead\_heteropolymer/'' directory in the online examples. -%This example demonstrates how to share backbone atoms, bonds, and angles. -%You can also define specific angle or dihedral interactions which are -%specific to the atom types in different residues.} - - -\subsection{Bonded interactions \textit{by type}} -\label{sec:nbody_by_type_intro} - -In this example we did \textit{not} provide a list of all 3-body -and 4-body forces between bonded atoms in the polymer. -(for example using the ``write\_once("Data Angles")'' command -from section \ref{sec:spce_example}, -\textit{or} -the ``write\_once("Data Dihedrals")'', -or ``write\_once("Data Impropers")'' commands.) -Instead we provided moltemplate.sh with instructions to help it figure out -which atoms participate in 3-body and 4-body bonded interactions. -Moltemplate can detect consecutively bonded atoms and -determine the forces between them based on atom type. -(Bond type can also be used as a criteria.) -We did this in ``forcefield.lt'' using the -\mbox{``write\_once("Data Angles By Type")''} and -\mbox{``write\_once("Data Dihedrals By Type")''} -commands. -You can also generate improper interactions -between any 4-atoms bonded together in a T-shaped topology -using the ``write\_once("Impropers By Type")'' command. -See appendix \ref{sec:nbody_by_type} for more details. -\textit{(More general interactions are possible. - See appendix \ref{sec:nbody_by_type_custom}.)} +Any molecule that wants to access this information can use the +``inherits ForceField'' keyword. +\textit{(...as we did in the ``monomer.lt'' and ``polymer.lt'' files in theexample above. + Note: the ``import forcefield'' statement was also necessary because the + information is located in a separate file: ``forcefield.lt''.} +%\textit{(Note: You can also generate \textbf{improper} interactions +% %between any 4-atoms bonded together in a T-shaped topology +% the same way, using the ``write\_once("Impropers By Type")'' command. +% See appendix \ref{sec:nbody_by_type} for more details. +\textit{You can customize these ``By Type'' rules further + by altering the bond topology search rules and atom type symmetry. + See appendix \ref{sec:nbody_by_type_custom} for details.)} %\subsubsection*{\textit{(Advanced)} Order matters when sets overlap} %Bonded-interactions are generated in the order they appear in the LT file. @@ -2379,17 +2446,17 @@ with molecules or atoms. (See sections \ref{sec:coords_intro} and \ref{sec:multidimensional_arrays}.) Here we show an easier way to create the short polymer -shown in section \ref{sec:2beadPeptide}. +shown in section \ref{sec:2beadPolymer}. You can make 7 copies of the \textit{Monomer} molecule this way: \begin{verbatim} - res = new Monomer[7] + monomers = new Monomer[7] \end{verbatim} This creates 7 new \textit{Monomer} molecules (named -\mbox{\textit{res[0]}}, -\mbox{\textit{res[1]}}, -\mbox{\textit{res[2]}}, -\mbox{\textit{res[3]}}, ... -\mbox{\textit{res[6]}}). +\mbox{\textit{monomers[0]}}, +\mbox{\textit{monomers[1]}}, +\mbox{\textit{monomers[2]}}, +\mbox{\textit{monomers[3]}}, ... +\mbox{\textit{monomers[6]}}). Unfortunately, by default, the coordinates of each molecule are identical. To prevent the atom coordinates from overlapping, you have several choices: @@ -2398,13 +2465,13 @@ To prevent the atom coordinates from overlapping, you have several choices: After every square-bracket [] in a new command, you can specify a list of transformations to apply. For example, we could have generated atomic coordinates for the -the short polymer in section \ref{sec:2beadPeptide} +the short polymer in section \ref{sec:2beadPolymer} using this command: \begin{verbatim} - res = new Monomer [7].rot(180, 1,0,0).move(3.2,0,0) + monomers = new Monomer [7].rot(180, 1,0,0).move(3.2,0,0) \end{verbatim} This will create 7 molecules. -The coordinates of the first molecule \textit{res[0]} are will be unmodified. +The coordinates of the first molecule \textit{monomers[0]} are will be unmodified. However each successive molecule will have its coordinates cumulatively modified by the commands ``rot(180, 1,0,0)'' followed by ``move(3.2,0,0)''. \subsubsection*{optional: initial customizations (preceding [] brackets)} @@ -2413,7 +2480,7 @@ You can also make adjustments to the initial coordinates of the molecule before it is copied, and before any of the array transformations are applied. For example: \begin{verbatim} - res = new Monomer.scale(1.5) [7].rot(180, 1,0,0).move(3.2,0,0) + monomers = new Monomer.scale(1.5) [7].rot(180, 1,0,0).move(3.2,0,0) \end{verbatim} In this example, the ``scale(1.5)'' transformation is applied once to enlarge every \textit{Monomer} object initially. @@ -2426,17 +2493,17 @@ are applied to build the polymer Alternately you apply transformations to a molecule after they have been created (even if they are part of an array). \begin{verbatim} - res = new Monomer [7] + monomers = new Monomer [7] # Again, the first line creates the molecules named - # "res[0]", "res[1]", "res[2]", "res[3]", ... "res[6]". + # "monomers[0]", "monomers[1]", "monomers[2]", ... "monomers[6]". # The following lines move them into position. - res[1].rot(180.0, 1,0,0).move(3.2,0,0) - res[2].rot(360.0, 1,0,0).move(6.4,0,0) - res[3].rot(540.0, 1,0,0).move(9.6,0,0) - res[4].rot(720.0, 1,0,0).move(12.8,0,0) - res[5].rot(900.0, 1,0,0).move(16.0,0,0) - res[6].rot(1080.0, 1,0,0).move(19.2,0,0) + monomers[1].rot(180.0, 1,0,0).move(3.2,0,0) + monomers[2].rot(360.0, 1,0,0).move(6.4,0,0) + monomers[3].rot(540.0, 1,0,0).move(9.6,0,0) + monomers[4].rot(720.0, 1,0,0).move(12.8,0,0) + monomers[5].rot(900.0, 1,0,0).move(16.0,0,0) + monomers[6].rot(1080.0, 1,0,0).move(19.2,0,0) \end{verbatim} \subsection{Transformation order (general case)} @@ -2454,13 +2521,13 @@ copy of the molecule multiple times. XFORMS2 will be applied $i$ times.) Finally after all the molecules have been created, the list of transformations in XFORMS3 will be applied. -For example, to create a ring of 10 peptides of radius 30.0, +For example, to create a ring of 10 polymers of radius 30.0, centered at position (0,25,0), use this notation: \begin{verbatim} -peptide_ring = new Peptide.move(0,30,0) [10].rot(36,1,0,0) +polymer_ring = new Polymer.move(0,30,0) [10].rot(36,1,0,0) # After creating it, we can move the entire ring # (These commands are applied last.) -peptide_ring[*].move(0,25,0) +polymer_ring[*].move(0,25,0) \end{verbatim} @@ -2618,19 +2685,19 @@ commands appearing later (following ``[50]'') are carried out. \label{sec:array_wildcards_intro} You can move the entire array of molecules using ``[*]'' notation: \begin{verbatim} - res[*].move(0,0,40) + monomers[*].move(0,0,40) \end{verbatim} -(Note that ``res.move(0,0,40)'' does not work. +(Note that ``monomers.move(0,0,40)'' does not work. You must include the ``[*]''.) -You can also use range limits to move only some of the residues: +You can also use range limits to move only some of the monomers: \begin{verbatim} - res[2-4].move(0,0,40) + monomers[2-4].move(0,0,40) \end{verbatim} -This will move only the third, fourth, and fifth residues. +This will move only the third, fourth, and fifth monomers. If you are more familiar with python's slice notation, you can accomplish the same thing using: \begin{verbatim} - res[2:5].move(0,0,40) + monomers[2:5].move(0,0,40) \end{verbatim} (In this case, the second integer (eg ``5'') is interpreted as a strict upper bound.) @@ -2678,10 +2745,10 @@ You can build multidimensional arrays using slice notation as well, for example The same techniques work with multidimensional arrays. Coordinate transformations can be applied to each layer in a multi-dimensional array. -For example, to create a cubic lattice of 3x3x3 peptides: +For example, to create a cubic lattice of 3x3x3 polymers: you would use this syntax: \begin{verbatim} -molecules = new Peptide [3].move(30.0, 0, 0) +molecules = new Polymer [3].move(30.0, 0, 0) [3].move(0, 30.0, 0) [3].move(0, 0, 30.0) \end{verbatim} @@ -2689,14 +2756,14 @@ molecules = new Peptide [3].move(30.0, 0, 0) with cylindrical, helical, conical, or toroidal symmetry.) \subsection{Customizing individual rows, columns, or layers} -Similarly, you can customize the position of individual peptides, +Similarly, you can customize the position of individual polymers, or layers or columns using the methods above: \begin{verbatim} molecules[1][*][*].move(0,20,0) molecules[*][1][*].move(0,0,20) molecules[*][*][1].move(20,0,0) \end{verbatim} -See figure \ref{fig:2bead_peptide}c) +See figure \ref{fig:2bead_polymer}c) \textit{(You can also use slice notation, eg ``molecules[1][0-2][0-1].move(20,0,0)'')} @@ -2858,48 +2925,57 @@ And all of this can be done from anywhere else in the LT file. %\textit{(The notation in section \ref{sec:paths} explains % how to navigate the object hierarchy.)} -For example, suppose we used the ``Peptide'' molecule we defined above -to create a larger, more complex ``Dimer'' molecule. +For example, suppose we used the ``Polymer'' molecule we defined above +to create a larger, more complicated ``MolecularComplex'' molecule. \begin{verbatim} -Dimer { - peptides[0] = new Peptide - peptides[1] = new Peptide.rot(180,1,0,0).move(0, 12.4, 0) +MolecularComplex { + polymers[0] = new Polymer + polymers[1] = new Polymer.rot(180,1,0,0).move(0, 12.4, 0) } -dimer = new Dimer +mol_complex = new MolecularComplex \end{verbatim} -The \textit{Dimer} molecule is shown in figure \ref{fig:dimers}a). -\textit{Optional: If you want all the atoms in a ``Dimer'' to share the same molecule-ID, -then define ``Dimer'' this way:} +The \textit{MolecularComplex} molecule is shown in figure \ref{fig:mol_complex}a). +\textit{Optional: If you want all the atoms in a ``MolecularComplex'' to share the same molecule-ID, +then define ``MolecularComplex'' this way:} \begin{verbatim} -Dimer inherits ForceField { +MolecularComplex inherits ForceField { create_var { $mol } - peptides[0] = new Peptide - peptides[1] = new Peptide.rot(180,1,0,0).move(0, 12.4, 0) + polymers[0] = new Polymer + polymers[1] = new Polymer.rot(180,1,0,0).move(0, 12.4, 0) } \end{verbatim} \textit{For this to work, you must also delete the \mbox{\textit{``create\_var \{\$mol:.\}''}} line from - the definition of the Peptide molecule. See section \ref{sec:2bead}.} + the definition of the Polymer molecule. See section \ref{sec:2bead}.} -We can subsquently customize the position of the 3rd residue -of the second peptide this way: +We can subsquently customize the position of the 3rd monomer (``monomers[2]'') +of the second polymer (``polymers[1]''), this way: \begin{verbatim} -dimer/peptides[1]/res[2].move(0,0.2,0.6) +mol_complex/polymers[1]/monomers[2].move(0,0.2,0.6) \end{verbatim} -This does not effect the position of \textit{res[2]} in \textit{peptides[0]}. -(or in any other \textit{``Peptide''} or \textit{``Dimer''} molecule.) -If you want to move both residues, you could use a wildcard character ``*'' +This does not effect the position of +\textit{monomers[2]} in \textit{polymers[0]}. +(or in any other \textit{``Polymer''} or +\textit{``MolecularComplex''} molecule.) +If you want to do the same thing for both polymers, +you could use a wildcard character ``*'' \begin{verbatim} -dimer/peptides[*]/res[2].move(0,0.2,0.6) +mol_complex/polymers[*]/res[2].move(0,0.2,0.6) \end{verbatim} -(You can also use ranged (slice) notation, such as ``peptides[0-1]'', - as an alternative to ``peptides[*]''. +If you want to move both polymers, you can use: +\begin{verbatim} +mol_complex/polymers[*].move(0,0.2,0.6) +\end{verbatim} +you could use a wildcard character ``*'' +(You can also use ranged (slice) notation, such as ``polymers[0-1]'', + as an alternative to ``polymers[*]''. See section \ref{sec:array_wildcards_intro}. -To make changes that apply to every subsequently created \textit{``Peptide''} or -\textit{``Dimer''} molecule, see section \ref{sec:molecule_customization}.) +To make changes that apply to every subsequently created \textit{``Polymer''} +or \textit{``MolecularComplex''} molecule, +see section \ref{sec:molecule_customization}.) \subsection{Customizing individual atom locations} @@ -2907,10 +2983,10 @@ To make changes that apply to every subsequently created \textit{``Peptide''} or The ``move'' or ``rot'' commands can not be used to control the positions of \textit{individual atoms}. Instead simply overwrite their coordinates this way: -%$atom:dimer/peptides[0]/res[2]/CA $mol:dimer/peptides[1] @atom:R 0 6.4 8.0 0 +%$atom:mol_complex/polymers[0]/res[2]/CA $mol:mol_complex/polymers[1] @atom:R 0 6.4 8.0 0 \begin{verbatim} write("Data Atoms") { - $atom:dimer/peptides[0]/res[2]/ca $mol:... @atom:R 0 6.4 8.2 0.6 + $atom:mol_complex/polymers[0]/res[2]/ca $mol:... @atom:R 0 6.4 8.2 0.6 } \end{verbatim} @@ -2918,8 +2994,8 @@ write("Data Atoms") { \label{sec:adding_atoms_bonds} Adding additional bonds within a molecule can be accomplished by writing additional lines of text to the ``Data Bonds'' section. -(This is what we did when we added bonds between residues to create a polymer - in section \ref{sec:2beadPeptide}.) +(This is what we did when we added bonds between monomers to create a polymer + in section \ref{sec:2beadPolymer}.) Again, bonds and atom names must be referred to by their \textit{full} names. Bonds and bonded interactions can be deleted using the ``delete'' command. (See section \ref{sec:delete}.) @@ -2931,18 +3007,18 @@ Bonds and bonded interactions can be deleted using the ``delete'' command. \subsubsection{Deleting molecules or molecular subunits} Molecules can be further customized by deleting individual atoms, bonds, bonded-interactions, and entire subunits. -We can \textbf{delete} the 3rd residue of the second peptide, +We can \textbf{delete} the 3rd monomer of the second polymer, use the ``delete'' command: \begin{verbatim} -delete dimer/peptides[1]/res[2] +delete mol_complex/polymers[1]/res[2] \end{verbatim} \subsubsection{Deleting atoms, bonds, angles, dihedrals, and impropers} \label{sec:delete_atoms_bonds} Individual atoms or bonds can be deleted in a similar way: \begin{verbatim} -delete dimer/peptides[1]/res[3]/ca #<-- deletes the "ca" atom -delete dimer/peptides[1]/res[4]/cr #<-- deletes the "cr" bond +delete mol_complex/polymers[1]/res[3]/ca #<-- deletes the "ca" atom +delete mol_complex/polymers[1]/res[4]/cr #<-- deletes the "cr" bond \end{verbatim} Whenever an atom or a molecule is deleted, the bonds, angles, dihedrals, and improper interactions involving those atoms are deleted as well. @@ -2961,10 +3037,10 @@ generated by moltemplate are removed as well. are not removed. These need to be deleted manually.) Multiple molecules can moved or deleted in a single command. For example, -the following command deletes the third, fourth, and fifth residues from -both peptides[0] and peptides[1]: +the following command deletes the third, fourth, and fifth monomers from +both polymers[0] and polymers[1]: \begin{verbatim} -delete dimer/peptides[*]/res[2-4] +delete mol_complex/polymers[*]/res[2-4] \end{verbatim} See section \ref{sec:array_wildcards_intro} for an explanation of ranged (``[2-4]'') array notation, @@ -3001,13 +3077,13 @@ to make sure they look reasonable. %By default, this transformations is applied relative %to the coordinate system in which the command was given. %In other words, this command will move the third - %residue of peptides[1] in the +Y direction + %monomer of polymers[1] in the +Y direction %regardless of the direction that the molecule ``res[2]'' is facing. %Alternately, if we want to apply this transformation - %in peptides[1]'s local coordinate system, - %we would use the context(peptides[1]) command: + %in polymers[1]'s local coordinate system, + %we would use the context(polymers[1]) command: %\begin{verbatim} - %dimer2/peptides[1]/res[2].context(peptides[1]).move(0,1,0) + %mol_complex/polymers[1]/res[2].context(polymers[1]).move(0,1,0) %\end{verbatim} @@ -3032,14 +3108,14 @@ to make sure they look reasonable. You can create modified versions of existing molecule \textit{types}, without having to redefine the entire molecule. For example: \begin{verbatim} -Dimer0 = Dimer.move(-9.6,-6.2, 0).scale(0.3125) +MolecularComplex0 = MolecularComplex.move(-9.6,-6.2, 0).scale(0.3125) \end{verbatim} or equivalently: \begin{verbatim} -Dimer0 = Dimer -Dimer0.move(-9.6,-6.2, 0).scale(0.3125) +MolecularComplex0 = MolecularComplex +MolecularComplex0.move(-9.6,-6.2, 0).scale(0.3125) \end{verbatim} -This creates a new type of molecule named ``Dimer0'' whose +This creates a new type of molecule named ``MolecularComplex0'' whose coordinates have been centered and rescaled. (Note that the ``scale()'' command only effects the atomic coordinates. (You will have to override earlier force field settings, @@ -3047,11 +3123,11 @@ such as atomic radii and bond-lengths in order for this to work properly.) If we want to make additional customizations (such as adding atoms, bonds, or molecular subunits), we could use this syntax: \begin{verbatim} -Dimer0 = Dimer +MolecularComplex0 = MolecularComplex -# Add some new atoms connecting the two peptides in the dimer +# Add some new atoms connecting the two polymers in the mol_complex -Dimer0 inherits ForceField { +MolecularComplex0 inherits ForceField { write("Data Atoms") { $atom:t1 $mol:. @atom:CA 0.0 23.0 0.0 0.0 $atom:t2 $mol:. @atom:CA 0.0 24.7 4.0 0.0 @@ -3059,36 +3135,36 @@ Dimer0 inherits ForceField { $atom:t4 $mol:. @atom:CA 0.0 23.0 12.4 0.0 } write("Data Bonds") { - $bond:b1 @bond:Backbone $atom:peptides[0]/res7/CA $atom:t1 + $bond:b1 @bond:Backbone $atom:polymers[0]/res7/CA $atom:t1 $bond:b2 @bond:Backbone $atom:t1 $atom:t2 $bond:b3 @bond:Backbone $atom:t2 $atom:t3 $bond:b4 @bond:Backbone $atom:t3 $atom:t4 - $bond:b5 @bond:Backbone $atom:t4 $atom:peptides[1]/res7/ca + $bond:b5 @bond:Backbone $atom:t4 $atom:polymers[1]/res7/ca } } -# Center and rescale the atoms in all "Dimer0" -Dimer0.move(-9.6,-6.2, 0).scale(0.3125) +# Center and rescale the atoms in all "MolecularComplex0" +MolecularComplex0.move(-9.6,-6.2, 0).scale(0.3125) \end{verbatim} -The result of these modifications is shown in figure \ref{fig:dimers}b). +The result of these modifications is shown in figure \ref{fig:mol_complex}b). \begin{figure}[htbp] \centering \textbf{a)} -\includegraphics[height=3cm]{dimer_LR.jpg} +\includegraphics[height=3cm]{mol_complex_LR.jpg} \hspace{1cm} \textbf{b)} -\includegraphics[height=3cm]{dimer+dimer0_transparent_LR.jpg} +\includegraphics[height=3cm]{mol_complex+mol_complex0_transparent_LR.jpg} %\newline %\vspace{10 mm} %\newline \caption{ -\label{fig:dimers} +\label{fig:mol_complex} \textbf{a)} -The ``Dimer'' molecule. This is a contrived example consisting of -two ``Peptides''. See section \ref{sec:2beadPeptide} +The ``MolecularComplex'' molecule. This is a contrived example consisting of +two ``Polymers''. See section \ref{sec:2beadPolymer} \textbf{b)} -A customized version of the ``Dimer'' molecule. -(The original ``Dimer'' is shown faded in the background for comparison.) +A customized version of the ``MolecularComplex'' molecule. +(The original ``MolecularComplex'' is shown faded in the background for comparison.) } \end{figure} @@ -3109,18 +3185,18 @@ an entire molecule type \textbf{after} all of its internal details \subsubsection*{\textit{(Advanced)} Inheritance} \label{sec:inheritance_intro} -The \textit{Dimer0} molecule is a type of \textit{Dimer} molecule. +The \textit{MolecularComplex0} molecule is a type of \textit{MolecularComplex} molecule. For those who are familiar with programming, relationships like this are analogous to the relationship between parent and child objects in an object-oriented programming language. %What we have done is equivalent to saying that - %\textit{Dimer0} inherits from \textit{Dimer}. + %\textit{MolecularComplex0} inherits from \textit{MolecularComplex}. More general kinds of inheritance are supported by moltemplate and are discussed in section \ref{sec:inheritance}. \subsubsection*{\textit{(Advanced)} Multiple Inheritance} If we wanted, we could have created a new molecule type -(like \textit{``Dimer0''}) +(like \textit{``MolecularComplex0''}) which includes atom types and features from \textit{multiple} different types of molecules. Section \ref{sec:inheritance} mentions one way to do this @@ -3984,10 +4060,8 @@ starting moltemplate and kill the process if it's memory usage exceeds 80\%. \textbf{3)} Limited support for non-point-like atoms: -As of 2014-12-09, only the ``full'', ``angle'', ``atomic'', ``charge'', -and ``molecular'' styles have been tested. -The ``dipole'' atom style \textit{is} fully supported -but it has not been tested. +As of 2017-8-31, only the ``full'', ``angle'', ``atomic'', ``charge'', +``sphere'', ``dipole'', and ``molecular'' styles have been tested. Non-point-like atoms like ``ellipsoid'', ``tri'', ``line'' \textit{should} also work with moltemplate. However these objects @@ -4027,28 +4101,36 @@ Please let me know if it is not working. \textbf{6)} Inconsistent support for wildcard characters (``*'' and ``?'') \label{sec:wildcard_bug} - As of 2014-1-28, - the wildcard character ``*'' + The wildcard character ``*'' is interpreted differently in different parts of an LT file. Wildcard characters work reliably and are used for \textit{string} - pattern matching when inside any of the \textit{``By Type''} sections + pattern matching when inside + ``bond\_coeff'', ``angle\_coeff'', ``dihedral\_coeff'', ``improper\_coeff'', + and most ``pair\_coeff'' commands, + as well as any of the \textit{``By Type''} sections in an LT file (such as \textit{``Data Angles By Type''}, \textit{``Data Dihedrals By Type''}, and \textit{``Data Impropers By Type''}). - However these characters are interpreted differently when they appear - in \textit{pair\_coeff}, \textit{bond\_coeff}, \textit{angle\_coeff} - \textit{dihedral\_coeff}, and \textit{improper\_coeff} commands - (and their corresponding \textit{``Coeff''} sections of a data file). - LAMMPS interprets ``*'' characters appearing in any of the - \textit{coeff} commands as \textit{numeric} wildcard characters. + However these wildcard characters \textit{do not} + within pair\_coeff commands that require \textit{more} + than 2 atom types as arguments. + (such as ``pair\_style hbond/dreiding/lj''. + However manybody pair\_styles which use ``pair\_coeff * *'' + notation work fine.) + As of 2017-8-31, wildcard characters (``*'', ``?'') also fail to work inside + \textit{``bond\_modify''} commands, and other commands used for running + active matter simulations. (Such commands are typically located within the + \textit{``write\_once("In Transitions")''} section of an .LT file.) + LAMMPS interprets ``*'' characters appearing here as + \textit{numeric ranges}, and their behavior depends on the + integers which moltemplate assigns to these variables, + \textit{not} the \textit{names} of the variables. + (See the official documentation for bond\_modify, and bond\_coeff + commands to see how ``*'' characters are interpreted. This can lead to unintended side-effects and is discouraged. - So please avoid ``*'' characters in any of the - \textit{``coeff''} commands - (eg \textit{pair\_coeff, bond\_coeff, angle\_coeff, - dihedral\_coeff, improper\_coeff}). - The ``*'' character can be safely used in array brackets, \textit{[*]}, - or in the \textit{``By Type''} sections. + The ``*'' character can be safely used in array brackets, \textit{[*]}, or in + the varios \textit{``\_coeff''} commands and \textit{``By Type''} sections. (See section \ref{sec:array_wildcards_intro} and appendix \ref{sec:nbody_by_type}.) @@ -4452,7 +4534,7 @@ To specify the atoms in each \textit{representation}, click on the \mbox{\textbf{Selections}} tab. By default ``all'' atoms are selected, however you can select atoms according to atom -\textbf{type}, \textbf{index}, \textbf{resid}, +\textbf{type}, \textbf{index}, \textbf{molid}, \textbf{charge}, \textbf{mass}, \textbf{x}, \textbf{y}, \textbf{z}. This will limit the current display settings to a subset of the atoms/bonds present in your system. @@ -4470,7 +4552,7 @@ and \textit{\textbf{Note:}} In VMD/topotools, -the \textbf{type}, \textbf{index}, and \textbf{resid} +the \textbf{type}, \textbf{index}, and \textbf{molid} properties of each atom correspond to the \textit{@atom}, \textit{\$atom}, and \textit{\$mol} variables for each atom in moltemplate. @@ -4745,7 +4827,7 @@ Keep in mind, that in this example, this could cause other atom-types (for example ``@atom:SPCE/H'') to be assigned to overlapping numbers. %For this reason, the ``-b'' flag is usually used only for %custom user-defined variable categories - %(such as the ``\$resid'' counter example described + %(such as the ``\$monomerid'' counter example described %in section \ref{sec:custom_categories}). @@ -4839,35 +4921,35 @@ By default variables in a given category are always assigned to unique integers. This can be overridden using the ``category'' command. For example, you might have a variable that keeps track of -the position index of each residue in each protein chain. -The first residue in a protein (N-terminus) is assigned ``1'', -the second residue, ``2'', etc, -\textit{regardless} of the number of protein chains in your system. +the monomer in every polymer. +The first monomer in a polymer is assigned ``1'', +the second monomer, ``2'', etc, +\textit{regardless} of the number of polymer in your system. -To do this, we can create a new variable category named ``resid'' which -is defined within the scope of each instance of the ``Protein'' molecule: +To do this, we can create a new variable category named ``monomerid'' which +is defined within the scope of each instance of the ``Polymer'' molecule: \begin{verbatim} -Residue { +Monomer { write("Data Atoms") { - $atom:ca @atom:CA $resid:. 0.0 0.0 0.0 0.0 - $atom:cb @atom:CB $resid:. 0.0 1.53 0.0 0.0 + $atom:ca @atom:CA $monomerid:. 0.0 0.0 0.0 0.0 + $atom:cb @atom:CB $monomerid:. 0.0 1.53 0.0 0.0 } } -Protein { - category $resid(1,1) - residues = Residue[100] +Polymer { + category $monomerid(1,1) + monomers = Monomer[100] } -proteins = Protein[10] +polymers = Polymer[10] \end{verbatim} -In this example, there are 10 proteins containing 100 residues each. -The ``\$resid'' counters will be replaced with integers in the range +In this example, there are 10 polymers containing 100 monomers each. +The ``\$monomerid'' counters will be replaced with integers in the range $1\ldots 100$, (not $1\ldots 1000$, as you might expect). -Because the ``\$resid'' counter is local to the +Because the ``\$monomerid'' counter is local to the protein it is defined within, -``\$resid'' variables in other proteins do not share the same counter, +``\$monomerid'' variables in other proteins do not share the same counter, and can overlap. \subsection{Counting order} @@ -5446,10 +5528,10 @@ However the \textit{\textbf{cpath}} can be specified explicitly, as in this example: ``\$/atom:'' (``/'' denotes explicitly that the counter has global scope). Another example with an explicit \textit{\textbf{cpath}} is -the custom local counter variable named ``\$/proteins[5]/resid:.'' +the custom local counter variable named ``\$/proteins[5]/monomerid:.'' (See section \ref{sec:cpath_simple}.) In this example, the \textit{\textbf{cpath}} is ``\$/proteins[5]'', the -\textit{\textbf{catname}} is ``resid'', +\textit{\textbf{catname}} is ``monomerid'', and the \textit{\textbf{lpath}} is ``.''. (In section \ref{sec:cpath_simple}, @@ -5488,7 +5570,7 @@ then it is equivalent to: \$\textit{\textbf{catname}}:\textit{\textbf{lpath}}. Again, in these cases, \textit{\textbf{lpath}} is a path which is relative to the object in which the variable was referenced. -If \$\textit{\textbf{lpath}} is omitted, then this is equivalent to \$\textit{\textbf{catname}}:. In other words, the the leaf node is the current node, ``.''. (This syntax is often used to count keep track of molecule ID numbers. You can use the counter variable ``\$mol'' to keep track of the current molecule id number, because it counts the molecular objects in which this variable was defined. In this case the name of the category is ``mol''. As in most examples, the category object, \textit{\textbf{cpath}}, is not specified. This means the category object is automatically global. A global category object means that every molecule object is given a unique ID number which is unique for the entire system, not just unique within some local molecule. As a counter-example, consider amino acid residue counters. Each amino acid in a protein can be assigned a residue ID number which identifies it within a single protein chain. However because their category was defined locally at the protein level, these residue ID numbers are not global, and are not uniquely defined if there are multiple protein chains present.) +If \$\textit{\textbf{lpath}} is omitted, then this is equivalent to \$\textit{\textbf{catname}}:. In other words, the the leaf node is the current node, ``.''. (This syntax is often used to count keep track of molecule ID numbers. You can use the counter variable ``\$mol'' to keep track of the current molecule id number, because it counts the molecular objects in which this variable was defined. In this case the name of the category is ``mol''. As in most examples, the category object, \textit{\textbf{cpath}}, is not specified. This means the category object is automatically global. A global category object means that every molecule object is given a unique ID number which is unique for the entire system, not just unique within some local molecule. As a counter-example, consider amino acid residue counters. Each amino acid in a protein can be assigned a residue ID number which identifies it within a single protein chain. However because their category was defined locally at the protein level, these residue ID numbers are not global, and are not uniquely defined if there are multiple protein chains present.) (See section \ref{sec:cpath_simple} for details.) diff --git a/tools/moltemplate/doc/utils/docs_genpoly_lt.txt b/tools/moltemplate/doc/utils/docs_genpoly_lt.txt index dbc751176d..31a0359b6d 100644 --- a/tools/moltemplate/doc/utils/docs_genpoly_lt.txt +++ b/tools/moltemplate/doc/utils/docs_genpoly_lt.txt @@ -13,22 +13,22 @@ Explanation: Usage: - genpoly_lt.py \\ - [-bond btype a1 a2] \\ - [-helix deltaphi] \\ - [-axis x,y,z] \\ - [-circular yes/no/connected] \\ + genpoly_lt.py \ + [-bond btype a1 a2] \ + [-helix deltaphi] \ + [-axis x,y,z] \ + [-circular yes/no/connected] \ [-dir-indices ia ib] \ - [-angle atype a1 a2 a3 i1 i2 i3] \\ - [-dihedral dtype a1 a2 a3 a4 i1 i2 i3 i4] \\ - [-improper itype a1 a2 a3 a4 i1 i2 i3 i4] \\ - [-monomer-name mname] \\ - [-sequence sequence.txt] \\ - [-polymer-name pname] \\ - [-inherits ForceFieldObject] \\ - [-header "import \"monomer.lt\""] \\ - [-cuts cuts.txt] \\ - [-box paddingX,paddingY,paddingZ] \\ + [-angle atype a1 a2 a3 i1 i2 i3] \ + [-dihedral dtype a1 a2 a3 a4 i1 i2 i3 i4] \ + [-improper itype a1 a2 a3 a4 i1 i2 i3 i4] \ + [-monomer-name mname] \ + [-sequence sequence.txt] \ + [-polymer-name pname] \ + [-inherits ForceFieldObject] \ + [-header "import monomer.lt"] \ + [-cuts cuts.txt] \ + [-box paddingX,paddingY,paddingZ] \ < coords.raw > polymer.lt Arguments (optional): diff --git a/tools/moltemplate/examples/all_atom/force_field_AMBER/benzene/moltemplate_files/benzene.lt b/tools/moltemplate/examples/all_atom/force_field_AMBER/benzene/moltemplate_files/benzene.lt index 05c55482d3..8d736e72b3 100644 --- a/tools/moltemplate/examples/all_atom/force_field_AMBER/benzene/moltemplate_files/benzene.lt +++ b/tools/moltemplate/examples/all_atom/force_field_AMBER/benzene/moltemplate_files/benzene.lt @@ -20,18 +20,18 @@ Benzene inherits GAFF { # atomID molID atomType charge X Y Z write('Data Atoms') { - $atom:C1 $mol @atom:ca -0.115 5.274 1.999 -8.568 - $atom:C2 $mol @atom:ca -0.115 6.627 2.018 -8.209 - $atom:C3 $mol @atom:ca -0.115 7.366 0.829 -8.202 - $atom:C4 $mol @atom:ca -0.115 6.752 -0.379 -8.554 - $atom:C5 $mol @atom:ca -0.115 5.399 -0.398 -8.912 - $atom:C6 $mol @atom:ca -0.115 4.660 0.791 -8.919 - $atom:H11 $mol @atom:ha 0.115 4.704 2.916 -8.573 - $atom:H21 $mol @atom:ha 0.115 7.101 2.950 -7.938 - $atom:H31 $mol @atom:ha 0.115 8.410 0.844 -7.926 - $atom:H41 $mol @atom:ha 0.115 7.322 -1.296 -8.548 - $atom:H51 $mol @atom:ha 0.115 4.925 -1.330 -9.183 - $atom:H61 $mol @atom:ha 0.115 3.616 0.776 -9.196 + $atom:C1 $mol @atom:ca -0.115 -0.739 1.189 -0.00733 + $atom:C2 $mol @atom:ca -0.115 0.614 1.208 0.35167 + $atom:C3 $mol @atom:ca -0.115 1.353 0.019 0.35867 + $atom:C4 $mol @atom:ca -0.115 0.739 -1.189 0.00667 + $atom:C5 $mol @atom:ca -0.115 -0.614 -1.208 -0.35133 + $atom:C6 $mol @atom:ca -0.115 -1.353 -0.019 -0.35833 + $atom:H11 $mol @atom:ha 0.115 -1.309 2.106 -0.01233 + $atom:H21 $mol @atom:ha 0.115 1.088 2.14 0.62267 + $atom:H31 $mol @atom:ha 0.115 2.397 0.034 0.63467 + $atom:H41 $mol @atom:ha 0.115 1.309 -2.106 0.01267 + $atom:H51 $mol @atom:ha 0.115 -1.088 -2.14 -0.62233 + $atom:H61 $mol @atom:ha 0.115 -2.397 -0.034 -0.63533 } write('Data Bond List') { diff --git a/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/README_visualize.txt b/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/README_visualize.txt index a3e3ed620e..b39d8901ad 100644 --- a/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/README_visualize.txt +++ b/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/README_visualize.txt @@ -60,8 +60,8 @@ d) Try entering these commands: It can help to shift the location of the periodic boundary box To shift the box in the y direction (for example) do this: - pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} - pbc box -shiftcenterrel {0.0 0.15 0.0} + pbc wrap -compound res -all -shiftcenterrel {-0.05 -0.05 -0.05} + pbc box -shiftcenterrel {-0.05 -0.05 -0.05} Distances are measured in units of box-length fractions, not Angstroms. diff --git a/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/images/ethylene+benzene_50bar_t=100000_LR.jpg b/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/images/ethylene+benzene_50bar_t=100000_LR.jpg new file mode 100644 index 0000000000..b9ff053fcb Binary files /dev/null and b/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/images/ethylene+benzene_50bar_t=100000_LR.jpg differ diff --git a/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/images/ethylene+benzene_box80x80x80_LR.jpg b/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/images/ethylene+benzene_box80x80x80_LR.jpg deleted file mode 100644 index 00c82d3d9f..0000000000 Binary files a/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/images/ethylene+benzene_box80x80x80_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/images/ethylene+benzene_t=0_LR.jpg b/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/images/ethylene+benzene_t=0_LR.jpg new file mode 100644 index 0000000000..65949a4684 Binary files /dev/null and b/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/images/ethylene+benzene_t=0_LR.jpg differ diff --git a/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/moltemplate_files/benzene.lt b/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/moltemplate_files/benzene.lt index 008391688e..25f58dfde8 100644 --- a/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/moltemplate_files/benzene.lt +++ b/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/moltemplate_files/benzene.lt @@ -15,19 +15,20 @@ import "gaff.lt" Benzene inherits GAFF { + # atomID molID atomType charge X Y Z write('Data Atoms') { - $atom:C1 $mol @atom:ca 0.115 5.274 1.999 -8.568 - $atom:C2 $mol @atom:ca 0.115 6.627 2.018 -8.209 - $atom:C3 $mol @atom:ca 0.115 7.366 0.829 -8.202 - $atom:C4 $mol @atom:ca 0.115 6.752 -0.379 -8.554 - $atom:C5 $mol @atom:ca 0.115 5.399 -0.398 -8.912 - $atom:C6 $mol @atom:ca 0.115 4.660 0.791 -8.919 - $atom:H11 $mol @atom:ha -0.115 4.704 2.916 -8.573 - $atom:H21 $mol @atom:ha -0.115 7.101 2.950 -7.938 - $atom:H31 $mol @atom:ha -0.115 8.410 0.844 -7.926 - $atom:H41 $mol @atom:ha -0.115 7.322 -1.296 -8.548 - $atom:H51 $mol @atom:ha -0.115 4.925 -1.330 -9.183 - $atom:H61 $mol @atom:ha -0.115 3.616 0.776 -9.196 + $atom:C1 $mol @atom:ca -0.115 -0.739 1.189 -0.00733 + $atom:C2 $mol @atom:ca -0.115 0.614 1.208 0.35167 + $atom:C3 $mol @atom:ca -0.115 1.353 0.019 0.35867 + $atom:C4 $mol @atom:ca -0.115 0.739 -1.189 0.00667 + $atom:C5 $mol @atom:ca -0.115 -0.614 -1.208 -0.35133 + $atom:C6 $mol @atom:ca -0.115 -1.353 -0.019 -0.35833 + $atom:H11 $mol @atom:ha 0.115 -1.309 2.106 -0.01233 + $atom:H21 $mol @atom:ha 0.115 1.088 2.14 0.62267 + $atom:H31 $mol @atom:ha 0.115 2.397 0.034 0.63467 + $atom:H41 $mol @atom:ha 0.115 1.309 -2.106 0.01267 + $atom:H51 $mol @atom:ha 0.115 -1.088 -2.14 -0.62233 + $atom:H61 $mol @atom:ha 0.115 -2.397 -0.034 -0.63533 } write('Data Bond List') { diff --git a/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/moltemplate_files/system.lt b/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/moltemplate_files/system.lt index f9984a1bb8..994b66b2cd 100644 --- a/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/moltemplate_files/system.lt +++ b/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/moltemplate_files/system.lt @@ -4,26 +4,25 @@ import "benzene.lt" # <- defines the "Benzene" molecule type. # Periodic boundary conditions: write_once("Data Boundary") { - 0.0 80.00 xlo xhi - 0.0 80.00 ylo yhi - 0.0 80.00 zlo zhi + 0.0 48.00 xlo xhi + 0.0 48.00 ylo yhi + 0.0 48.00 zlo zhi } -# Create 1000 ethylenes and 500 benzenes +# Create 216 ethylenes and 108 benzenes -ethylenes = new Ethylene[10].move(8.0, 0, 0) - [10].move(0, 8.0, 0) - [10].move(0, 0, 8.0) +ethylenes = new Ethylene[6].move(8.0, 0, 0) + [6].move(0, 8.0, 0) + [6].move(0, 0, 8.0) -benzenes = new Benzene[10].move(8.0, 0, 0) - [10].move(0, 8.0, 0) - [5].move(0, 0, 16.0) +benzenes = new Benzene[6].move(8.0, 0, 0) + [6].move(0, 8.0, 0) + [3].move(0, 0, 16.0) # Now shift the positions of all of the benzene molecules, # to reduce the chance that they overlap with the ethylene molecules. benzenes[*][*][*].move(4.0, 4.0, 4.0) -# Note: There is also an example in the OPLSAA directory which shows how to -# generate the coordinates using PACKMOL. That allows us to omit all of -# the coordinates and .move() commands. (This works with AMBER/GAFF too.) +# Note: There is also an example which shows how to generate the coordinates +# using PACKMOL. (That allows us to omit the coordinates and .move() commands.) diff --git a/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/run.in.nvt b/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/run.in.nvt index 15283ff82b..e06cd825b3 100644 --- a/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/run.in.nvt +++ b/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/run.in.nvt @@ -35,7 +35,7 @@ include system.in.settings # -- simulation protocol -- -timestep 1.0 +timestep 2.0 dump 1 all custom 5000 traj_nvt.lammpstrj id mol type x y z ix iy iz fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1 thermo 500 diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/WARNING.txt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/WARNING.txt new file mode 100644 index 0000000000..5b2fcfb4b2 --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_COMPASS/WARNING.txt @@ -0,0 +1,38 @@ +# -------- WARNING: -------- + +This directory contains some examples of all-atom simulations using the COMPASS +force field. + +This software is experimental, and the force-fields and equilbration protocols +have not been tested carefully by me. There is no gaurantee that simulations +prepared using moltemplate will reproduce the behavior of other MD codes. + +The moltemplate implementation of COMPASS currently relies on the same +incomplete force-field file that "msi2lmp" uses ("compass_published.frc"). +Unfortunately this means that many force field parameters and some atom types +(such as sp2-carbons) have not (yet) been publicly released and are not +available. + +Currently I recommend that users should run the "cleanup_moltemplate.sh" +script after running "moltemplate.sh system.lt". Then manually check that +the "system.in.settings" and "system.in.charges" files which remain +make sense. Specifically, you must check that the angle_coeff, +dihedral_coeff, bond_coeff commands are not full of zeros (in places +where they should not be zero. This is another consequence of the +fact that the .FRC files I mentioned above are incomplete.) It's a +good idea to also check that the charges in the "system.in.charges" +file seem reasonable (ie. not all zeros). (There is a list of +warnings at the end of the "compass_published.lt" file. You can check +to see if any of the bonds in your system are covered by these +warnings.) Later on hopefully I'll add some automated way to warn +users when these problems arise, but now you should check for them +manually. + +# -------- REQUEST FOR HELP: -------- + +If you notice a problem with these examples, please report it. +Peer-review is the only way to improve this software (or any software). +Other suggestions are also welcome! + +(Contact jewett.aij@gmail.com, 2017-10-03) + diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/README.txt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/README.txt new file mode 100644 index 0000000000..7bf9a484d7 --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/README.txt @@ -0,0 +1,37 @@ +This example is a simple simulation of a long alkane chain, +in a vacuum at room temperature using the COMPASS force field. + +1) Create the "system.data", "system.in.init", and "system.in.settings" +files which LAMMPS will read by running: + +moltemplate.sh system.lt + + +2) Run LAMMPS in this order: + +lmp_mpi -i run.in.min # minimize the energy (to avoid atom overlap) before... +lmp_mpi -i run.in.nvt # running the simulation at constant temperature + +(The name of the LAMMPS executable, eg "lmp_mpi", may vary.) + +---- Details ---- + +The "Alkane50" molecule, as well as the "CH2", and "CH3" monomers it contains +use the COMPASS force-field. This means that when we define these molecules, +we only specify the atom names, bond list, and coordinates. +We do not have to list the atom charges, angles, dihedrals, or impropers. +The rules for creating atomic charge and angle topology are contained in +the "compass_published.lt" file created by step 3) above. The "ch2group.lt", +"ch3group.lt", and "alkane50.lt" files all refer to "compass_published.lt", +(as well as the "COMPASS" force-field object which it defines). Excerpt: + +import "compass_published.lt" +CH2 inherits COMPASS { ... +CH3 inherits COMPASS { ... +Alkane50 inherits COMPASS { ... + +Alternatively, you can manually define a list of angles, dihedrals, and +improper interactions in these files, instead of asking the force-field +to generate them for you. You can also specify some of the angles and +dihedrals explicitly, and let the force-field handle the rest. +(Many of the examples which come with moltemplate do this.) diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/README_remove_irrelevant_info.sh b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/README_remove_irrelevant_info.sh new file mode 100755 index 0000000000..5957289da9 --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/README_remove_irrelevant_info.sh @@ -0,0 +1,8 @@ + +# Note: By default, the system.data and system.in.settings files contain +# extra information for atoms defined in OPLSAA which you are not using +# in this simulation. +# This is harmless, but if you to delete this information from your +# system.in.settings and system.in.data files, run this script: + +cleanup_moltemplate.sh diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/README_run.sh b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/README_run.sh new file mode 100755 index 0000000000..94d6de972c --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/README_run.sh @@ -0,0 +1,34 @@ +# --- Running LAMMPS --- +# +# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS +# input scripts which link to the input scripts and data files +# you hopefully have created earlier with moltemplate.sh: +# system.in.init, system.in.settings, system.data +# If not, carry out the instructions in "README_setup.sh". +# +# -- Instructions: -- +# If "lmp_mpi" is the name of the command you use to invoke lammps, +# then you would run lammps on these files this way: + + +lmp_mpi -i run.in.min # minimization +lmp_mpi -i run.in.nvt # minimization and simulation at constant volume + +#(Note: The constant volume simulation lacks pressure equilibration. These are +# completely separate simulations. The results of the constant pressure +# simulation might be ignored when beginning the simulation at constant +# volume. (This is because restart files in LAMMPS don't always work, +# and I was spending a lot of time trying to convince people it was a +# LAMMPS bug, instead of a moltemplate bug, so I disabled restart files.) +# Read the "run.in.nvt" file to find out how to use the "read_restart" +# command to load the results of the pressure-equilibration simulation, +# before beginning a constant-volume run. + + + + + +# If you have compiled the MPI version of lammps, you can run lammps in parallel +#mpirun -np 4 lmp_mpi -i run.in.npt +#mpirun -np 4 lmp_mpi -i run.in.nvt +# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/README_setup.sh b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/README_setup.sh new file mode 100755 index 0000000000..5cd2142a41 --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/README_setup.sh @@ -0,0 +1,34 @@ + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + + moltemplate.sh system.lt + + # Optional: + # To check for missing angle,dihedral params run moltemplate this way instead: + # moltemplate.sh -checkff system.lt + + + # Moltemplate generates various files with names ending in *.in* and *.data. + # Move them to the directory where you plan to run LAMMPS (in this case "../") + mv -f system.data system.in* ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ + + + + +# Optional: +# Note: The system.data and system.in.settings files contain extra information +# for atoms defined in OPLSAA which you are not using in this simulation. +# This is harmless, but if you to delete this information from your +# system.in.settings and system.in.data files, run this script: +# +# cleanup_moltemplate.sh diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/README_visualize.txt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/README_visualize.txt new file mode 100644 index 0000000000..a3e3ed620e --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/README_visualize.txt @@ -0,0 +1,87 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + Sometimes the solvent or membrane obscures the view of the solute. + It can help to shift the location of the periodic boundary box + To shift the box in the y direction (for example) do this: + + pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} + pbc box -shiftcenterrel {0.0 0.15 0.0} + + Distances are measured in units of box-length fractions, not Angstroms. + + Alternately if you have a solute whose atoms are all of type 1, + then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) + You should check if your periodic boundary conditions are too small. + To do that: + select Graphics->Representations menu option + click on the "Periodic" tab, and + click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. + +5) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/images/ch2_ry90.jpg b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/images/ch2_ry90.jpg new file mode 100644 index 0000000000..39a8879557 Binary files /dev/null and b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/images/ch2_ry90.jpg differ diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/images/ch3_ry60.jpg b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/images/ch3_ry60.jpg new file mode 100644 index 0000000000..ab140a8f9e Binary files /dev/null and b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/images/ch3_ry60.jpg differ diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/images/t=0.jpg b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/images/t=0.jpg new file mode 100644 index 0000000000..39633edd5e Binary files /dev/null and b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/images/t=0.jpg differ diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/images/t=1ns.jpg b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/images/t=1ns.jpg new file mode 100644 index 0000000000..da2fe1185e Binary files /dev/null and b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/images/t=1ns.jpg differ diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/moltemplate_files/alkane50.lt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/moltemplate_files/alkane50.lt new file mode 100644 index 0000000000..da75694c45 --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/moltemplate_files/alkane50.lt @@ -0,0 +1,137 @@ +# This is a simple example showing how to build a long polymer +# (in this case, an alkane chain). I split the +# hexadecane molecule into individual CH2 and CH3 monomers. +# I defined it this way so that you can easily modify +# it to change the length of the alkane chain. + + +import "ch2group.lt" # load the definition of the "CH2" object +import "ch3group.lt" # load the definition of the "CH3" object + + + +Alkane50 inherits COMPASS { + + + create_var {$mol} # optional:force all monomers to share the same molecule-ID + + # This is a long polymer consisting of 48 CH2 groups and 2 CH3 end-caps. + # Rather than create them one-by-one, I decided to create them all + # using a single "new" command. Later, I can modify this array. + + # Create an array of 50 "CH2" objects distributed along the X axis + + monomers = new CH2 [50].rot(180,1,0,0).move(1.2533223,0,0) + + # NOTE: the ".rot(180,1,0,0).move(1.2533223,0,0)" means that each + # successive monomer is rotated 180 degrees (with respect to the previous + # monomer), and then moved 1.2533223 Angstroms down the X axis. + # Alternately, if you are reading the coordinates from a file, you don't have + # to indicate the position & orientation of each monomer. In that case, use: + # monomers = new CH2 [50] + + + # ---- Now, modify the ends: --- + # Delete the CH2 groups at the beginning and end, and replace them with CH3. + + delete monomers[0] + delete monomers[49] + + monomers[0] = new CH3 + monomers[49] = new CH3 + + # Move the CH3 groups to the correct location at either end of the chain: + + #monomers[0].move(0,0,0) # <--(this monomer is already in the correct place) + monomers[49].rot(180.0,0,0,1).move(61.4127927,0,0) #61.4127927=49*1.2533223 + + + ## NOTE: Alternately, you can define the polymer without deleting the ends: + # monomers[0] = new CH3 + # monomers[1-48] = new CH2[48].rot(180,1,0,0).move(1.2533223,0,0) + ## Note: monomers[0] and monomers[1] overlap, so we move 1-48 to make room: + # monomers[1-48].rot(180,1,0,0).move(1.2533223,0,0) # move many monomers + ## Now add the final monomer at the end: + # monomers[49] = new CH3.rot(180.0,0,0,1).move(61.4127927,0,0) + # + ## NOTE: Alternately, you can read the coordinates from a file. + ## In that case, you can use simpler commands: + # monomers[0] = new CH3 + # monomers[1-48] = new CH2[48] + # monomers[49] = new CH3 + + + + # Now add a list of bonds connecting the carbon atoms together: + # (Angles, dihedrals, impropers will be automatically added later.) + + write('Data Bond List') { + $bond:b1 $atom:monomers[0]/C $atom:monomers[1]/C + $bond:b2 $atom:monomers[1]/C $atom:monomers[2]/C + $bond:b3 $atom:monomers[2]/C $atom:monomers[3]/C + $bond:b4 $atom:monomers[3]/C $atom:monomers[4]/C + $bond:b5 $atom:monomers[4]/C $atom:monomers[5]/C + $bond:b6 $atom:monomers[5]/C $atom:monomers[6]/C + $bond:b7 $atom:monomers[6]/C $atom:monomers[7]/C + $bond:b8 $atom:monomers[7]/C $atom:monomers[8]/C + $bond:b9 $atom:monomers[8]/C $atom:monomers[9]/C + $bond:b10 $atom:monomers[9]/C $atom:monomers[10]/C + $bond:b11 $atom:monomers[10]/C $atom:monomers[11]/C + $bond:b12 $atom:monomers[11]/C $atom:monomers[12]/C + $bond:b13 $atom:monomers[12]/C $atom:monomers[13]/C + $bond:b14 $atom:monomers[13]/C $atom:monomers[14]/C + $bond:b15 $atom:monomers[14]/C $atom:monomers[15]/C + $bond:b16 $atom:monomers[15]/C $atom:monomers[16]/C + $bond:b17 $atom:monomers[16]/C $atom:monomers[17]/C + $bond:b18 $atom:monomers[17]/C $atom:monomers[18]/C + $bond:b19 $atom:monomers[18]/C $atom:monomers[19]/C + $bond:b20 $atom:monomers[19]/C $atom:monomers[20]/C + $bond:b21 $atom:monomers[20]/C $atom:monomers[21]/C + $bond:b22 $atom:monomers[21]/C $atom:monomers[22]/C + $bond:b23 $atom:monomers[22]/C $atom:monomers[23]/C + $bond:b24 $atom:monomers[23]/C $atom:monomers[24]/C + $bond:b25 $atom:monomers[24]/C $atom:monomers[25]/C + $bond:b26 $atom:monomers[25]/C $atom:monomers[26]/C + $bond:b27 $atom:monomers[26]/C $atom:monomers[27]/C + $bond:b28 $atom:monomers[27]/C $atom:monomers[28]/C + $bond:b29 $atom:monomers[28]/C $atom:monomers[29]/C + $bond:b30 $atom:monomers[29]/C $atom:monomers[30]/C + $bond:b31 $atom:monomers[30]/C $atom:monomers[31]/C + $bond:b32 $atom:monomers[31]/C $atom:monomers[32]/C + $bond:b33 $atom:monomers[32]/C $atom:monomers[33]/C + $bond:b34 $atom:monomers[33]/C $atom:monomers[34]/C + $bond:b35 $atom:monomers[34]/C $atom:monomers[35]/C + $bond:b36 $atom:monomers[35]/C $atom:monomers[36]/C + $bond:b37 $atom:monomers[36]/C $atom:monomers[37]/C + $bond:b38 $atom:monomers[37]/C $atom:monomers[38]/C + $bond:b39 $atom:monomers[38]/C $atom:monomers[39]/C + $bond:b40 $atom:monomers[39]/C $atom:monomers[40]/C + $bond:b41 $atom:monomers[40]/C $atom:monomers[41]/C + $bond:b42 $atom:monomers[41]/C $atom:monomers[42]/C + $bond:b43 $atom:monomers[42]/C $atom:monomers[43]/C + $bond:b44 $atom:monomers[43]/C $atom:monomers[44]/C + $bond:b45 $atom:monomers[44]/C $atom:monomers[45]/C + $bond:b46 $atom:monomers[45]/C $atom:monomers[46]/C + $bond:b47 $atom:monomers[46]/C $atom:monomers[47]/C + $bond:b48 $atom:monomers[47]/C $atom:monomers[48]/C + $bond:b49 $atom:monomers[48]/C $atom:monomers[49]/C + } + +} # Alkane50 + + + + + + + + +######### (scratchwork calculations for the atomic coordinates) ######### +# Lcc = 1.5350 # length of the C-C bond (Sp3) +# Lch = 1.0930 # length of the C-H bond +# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle) +# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594 +# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754 +# # 0.5*DeltaYc = 0.4431163316030377 +# DeltaZh = Lch*sin(theta/2) # = 0.8924307629540046 +# DeltaYh = Lch*cos(theta/2) # = 0.6310438442242609 diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/moltemplate_files/ch2group.lt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/moltemplate_files/ch2group.lt new file mode 100644 index 0000000000..9bf2c82d7d --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/moltemplate_files/ch2group.lt @@ -0,0 +1,76 @@ +# This file contains a definition for the "CH2" molecular subunit. + +# First, load the COMPASS force field parameters we will need: + +import "compass_published.lt" # <-- defines the "COMPASS" force field + +# (The "compass_published.lt" file is located in the "force_fields" +# subdirectory distributed with moltemplate.) + + +# Then define "CH2": + + +CH2 inherits COMPASS { + + # atom-id mol-id atom-type charge x y z + + write("Data Atoms") { + $atom:C $mol:... @atom:c4 0.0 0.000000 0.000000 0.000000 + $atom:H1 $mol:... @atom:h1 0.0 0.000000 0.631044 0.892431 + $atom:H2 $mol:... @atom:h1 0.0 0.000000 0.631044 -0.892431 + } + + write('Data Bond List') { + $bond:CH1 $atom:C $atom:H1 + $bond:CH2 $atom:C $atom:H2 + } + + # COMMENTS: + # 1) Atom type names are defined in "compass_published.lt". + # 2) In this example, the atomic charge of an atom is calculated by summing + # partial charge contributions from neighboring atoms bonded to this atom. + # (according to the rules in "compass_published.lt"). For this reason, + # we can ignore the "charge" column in the "Data Atoms" section. Just + # leave theses charges as "0.0" for now. Moltemplate will recalculate them. + # 3) The "..." in "$mol:..." tells moltemplate that this molecule may be part + # of a larger molecule, and (if so) to use the larger parent object's + # molecule id number as it's own. + +} # CH2 + + + + + + + + + + + + + + + +# Optional: Shift all the coordinates in the +Y direction by 0.4431163. +# This way, the carbon atom is no longer located at 0,0,0, but the +# axis of an alkane chain containing this monomer is at 0,0,0. +# (This makes it more convenient to construct a polymer later. +# If this is confusing, then simply add 0.4431163 to the Y +# coordinates in the "Data Atoms" section above.) + +CH2.move(0,0.4431163,0) + + + + +######### (scratchwork calculations for the atomic coordinates) ######### +# Lcc = 1.5350 # length of the C-C bond (Sp3) +# Lch = 1.0930 # length of the C-H bond +# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle) +# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594 +# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754 +# # 0.5*DeltaYc = 0.4431163 +# DeltaZh = Lch*sin(theta/2) # = 0.892431 +# DeltaYh = Lch*cos(theta/2) # = 0.631044 diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/moltemplate_files/ch3group.lt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/moltemplate_files/ch3group.lt new file mode 100644 index 0000000000..e66579bf0b --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/moltemplate_files/ch3group.lt @@ -0,0 +1,78 @@ +# This file contains a definition for the "CH3" molecular subunit. + +# First, load the COMPASS force field parameters we will need: + +import "compass_published.lt" # <-- defines the "COMPASS" force field + +# (The "compass_published.lt" file is located in the "force_fields" +# subdirectory distributed with moltemplate.) + + +# Then define "CH3": + + +CH3 inherits COMPASS { + + # atom-id mol-id atom-type charge x y z + + write("Data Atoms") { + $atom:C $mol:... @atom:c4 0.0 0.000000 0.000000 0.000000 + $atom:H1 $mol:... @atom:h1 0.0 0.000000 0.631044 0.892431 + $atom:H2 $mol:... @atom:h1 0.0 0.000000 0.631044 -0.892431 + $atom:H3 $mol:... @atom:h1 0.0 -0.892431 -0.631044 0.000000 + } + + write('Data Bond List') { + $bond:CH1 $atom:C $atom:H1 + $bond:CH2 $atom:C $atom:H2 + $bond:CH3 $atom:C $atom:H3 + } + + # COMMENTS: + # 1) Atom type names are defined in "compass_published.lt". + # 2) In this example, the atomic charge of an atom is calculated by summing + # partial charge contributions from neighboring atoms bonded to this atom. + # (according to the rules in "compass_published.lt"). For this reason, + # we can ignore the "charge" column in the "Data Atoms" section. Just + # leave theses charges as "0.0" for now. Moltemplate will recalculate them. + # 3) The "..." in "$mol:..." tells moltemplate that this molecule may be part + # of a larger molecule, and (if so) to use the larger parent object's + # molecule id number as it's own. + +} # CH3 + + + + + + + + + + + + + + + +# Optional: Shift all the coordinates in the +Y direction by 0.4431163. +# This way, the carbon atom is no longer located at 0,0,0, but the +# axis of an alkane chain containing this monomer is at 0,0,0. +# (This makes it more convenient to construct a polymer later. +# If this is confusing, then simply add 0.4431163 to the Y +# coordinates in the "Data Atoms" section above.) + +CH3.move(0,0.4431163,0) + + + + +######### (scratchwork calculations for the atomic coordinates) ######### +# Lcc = 1.5350 # length of the C-C bond (Sp3) +# Lch = 1.0930 # length of the C-H bond +# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle) +# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594 +# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754 +# # 0.5*DeltaYc = 0.4431163 +# DeltaZh = Lch*sin(theta/2) # = 0.892431 +# DeltaYh = Lch*cos(theta/2) # = 0.631044 diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/moltemplate_files/system.lt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/moltemplate_files/system.lt new file mode 100644 index 0000000000..39c8e4f78d --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/moltemplate_files/system.lt @@ -0,0 +1,30 @@ +import "alkane50.lt" # Defines the "Alkane50" molecule + + +polymer = new Alkane50 + + +# Specify the size of the world the polymer lives in: +write_once("Data Boundary") { + 0.0 72.0 xlo xhi + 0.0 72.0 ylo yhi + 0.0 72.0 zlo zhi +} + + + + + +############################################################################### +# Note: If you want to create multiple polymers, and/or mix them with other +# molecules, just add more "new" commands, for example: +# polymer1 = new Alkane50.move(0,0,10) +# polymer2 = new Alkane50.move(0,0,20) +# : +# ...or use array notation, for example: +# polymers = new Alkane50[20].move(0,0,10) +# +# Note: Multidimensional arrays can be used to fill a planar region or a volume +# polymers = new Alkane50 [4].move(0, 0, 30.0) +# [4].move(0, 30.0, 0) +# [2].move(70.0, 0, 0) diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/run.in.min b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/run.in.min new file mode 100644 index 0000000000..5d0bcffd8e --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/run.in.min @@ -0,0 +1,37 @@ +# PREREQUISITES: +# +# You must use moltemplate.sh to create 3 files: +# system.data system.in.init system.in.settings +# +# ------------------------------- Initialization Section -------------------- + +include "system.in.init" + +# ------------------------------- Atom Definition Section ------------------- + +read_data "system.data" + +# ------------------------------- Settings Section -------------------------- + +include "system.in.settings" +include "system.in.charges" + +# ------------------------------- Run Section ------------------------------- + + +# -- minimization protocol -- + +# Note: The minimization step is not necessary in this example. However +# in general, it's always a good idea to minimize the system beforehand. + +thermo 50 +dump 1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz +minimize 1.0e-4 1.0e-6 100000 400000 + + +# (The "write_restart" and "read_restart" commands were buggy in 2012, +# but they should work also. I prefer "write_data" and "read_data".) + +write_data system_after_min.data + + diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/run.in.nvt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/run.in.nvt new file mode 100644 index 0000000000..d5b77423a2 --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/run.in.nvt @@ -0,0 +1,38 @@ +# PREREQUISITES: +# +# 1) You must use moltemplate.sh to create 3 files: +# system.data system.in.init system.in.settings +# (Follow the instructions in README_setup.sh, +# or run the file as a script using ./README_setup.sh) +# 2) You must minimize the system beforehand by using "run.in.min". +# This will create the file "system_after_min.data" which this file reads. + +# ------------------------------- Initialization Section -------------------- + +include "system.in.init" + +# ------------------------------- Atom Definition Section ------------------- + +# Read the coordinates generated by an earlier simulation + +read_data "system_after_min.data" + +# ------------------------------- Settings Section -------------------------- + +include "system.in.settings" +include "system.in.charges" + +# ------------------------------- Run Section ------------------------------- + +# -- simulation protocol -- + + +timestep 1.0 +dump 1 all custom 1000 traj_nvt.lammpstrj id mol type x y z ix iy iz +fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1 +thermo 500 +#thermo_modify flush yes + +run 1000000 + +write_data system_after_nvt.data diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/README.txt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/README.txt new file mode 100644 index 0000000000..7a16faaed7 --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/README.txt @@ -0,0 +1,37 @@ +This example is a simple simulation of many short alkane chains (butane) in +a box near the boiling point at atmospheric pressure.(Please read "WARNING.TXT") + +1) Create the "system.data", "system.in.init", and "system.in.settings" +files which LAMMPS will read by running: + +moltemplate.sh system.lt + + +2) Run LAMMPS in this order: + +lmp_mpi -i run.in.npt # running the simulation at constant pressure +lmp_mpi -i run.in.nvt # running the simulation at constant temperature + +(The name of the LAMMPS executable, eg "lmp_mpi", may vary.) + +---- Details ---- + +The "Butane" molecule, as well as the "CH2", and "CH3" monomers it contains +use the COMPASS force-field. This means that when we define these molecules, +we only specify the atom names, bond list, and coordinates. +We do not have to list the atom charges, angles, dihedrals, or impropers. +The rules for creating atomic charge and angle topology are contained in +the "compass_published.lt" file created by step 3) above. The "ch2group.lt", +"ch3group.lt", and "butane.lt" files all refer to "compass_published.lt", +(as well as the "COMPASS" force-field object which it defines). Excerpt: + +import "compass_published.lt" +CH2 inherits COMPASS { ... +CH3 inherits COMPASS { ... +Butane inherits COMPASS { ... + +Alternatively, you can manually define a list of angles, dihedrals, and +improper interactions in these files, instead of asking the force-field +to generate them for you. You can also specify some of the angles and +dihedrals explicitly, and let the force-field handle the rest. +(Many of the examples which come with moltemplate do this.) diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/README_remove_irrelevant_info.sh b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/README_remove_irrelevant_info.sh new file mode 100755 index 0000000000..5957289da9 --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/README_remove_irrelevant_info.sh @@ -0,0 +1,8 @@ + +# Note: By default, the system.data and system.in.settings files contain +# extra information for atoms defined in OPLSAA which you are not using +# in this simulation. +# This is harmless, but if you to delete this information from your +# system.in.settings and system.in.data files, run this script: + +cleanup_moltemplate.sh diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/README_run.sh b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/README_run.sh new file mode 100755 index 0000000000..94d6de972c --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/README_run.sh @@ -0,0 +1,34 @@ +# --- Running LAMMPS --- +# +# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS +# input scripts which link to the input scripts and data files +# you hopefully have created earlier with moltemplate.sh: +# system.in.init, system.in.settings, system.data +# If not, carry out the instructions in "README_setup.sh". +# +# -- Instructions: -- +# If "lmp_mpi" is the name of the command you use to invoke lammps, +# then you would run lammps on these files this way: + + +lmp_mpi -i run.in.min # minimization +lmp_mpi -i run.in.nvt # minimization and simulation at constant volume + +#(Note: The constant volume simulation lacks pressure equilibration. These are +# completely separate simulations. The results of the constant pressure +# simulation might be ignored when beginning the simulation at constant +# volume. (This is because restart files in LAMMPS don't always work, +# and I was spending a lot of time trying to convince people it was a +# LAMMPS bug, instead of a moltemplate bug, so I disabled restart files.) +# Read the "run.in.nvt" file to find out how to use the "read_restart" +# command to load the results of the pressure-equilibration simulation, +# before beginning a constant-volume run. + + + + + +# If you have compiled the MPI version of lammps, you can run lammps in parallel +#mpirun -np 4 lmp_mpi -i run.in.npt +#mpirun -np 4 lmp_mpi -i run.in.nvt +# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/README_setup.sh b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/README_setup.sh new file mode 100755 index 0000000000..5cd2142a41 --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/README_setup.sh @@ -0,0 +1,34 @@ + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + + moltemplate.sh system.lt + + # Optional: + # To check for missing angle,dihedral params run moltemplate this way instead: + # moltemplate.sh -checkff system.lt + + + # Moltemplate generates various files with names ending in *.in* and *.data. + # Move them to the directory where you plan to run LAMMPS (in this case "../") + mv -f system.data system.in* ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ + + + + +# Optional: +# Note: The system.data and system.in.settings files contain extra information +# for atoms defined in OPLSAA which you are not using in this simulation. +# This is harmless, but if you to delete this information from your +# system.in.settings and system.in.data files, run this script: +# +# cleanup_moltemplate.sh diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/README_visualize.txt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/README_visualize.txt new file mode 100644 index 0000000000..3ddb8e6065 --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/README_visualize.txt @@ -0,0 +1,87 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + Sometimes the solvent or membrane obscures the view of the solute. + It can help to shift the location of the periodic boundary box + To shift the box in the y direction (for example) do this: + + pbc wrap -compound res -all -shiftcenterrel {-0.05 -0.05 -0.05} + pbc box -shiftcenterrel {-0.05 -0.05 -0.05} -width 0.9 -style tubes + + Distances are measured in units of box-length fractions, not Angstroms. + + Alternately if you have a solute whose atoms are all of type 1, + then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) + You should check if your periodic boundary conditions are too small. + To do that: + select Graphics->Representations menu option + click on the "Periodic" tab, and + click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. + +5) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/images/after_pressure_equilibration_LR.jpg b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/images/after_pressure_equilibration_LR.jpg new file mode 100644 index 0000000000..093f557dd9 Binary files /dev/null and b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/images/after_pressure_equilibration_LR.jpg differ diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/images/butane.jpg b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/images/butane.jpg new file mode 100644 index 0000000000..d1a6e5060b Binary files /dev/null and b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/images/butane.jpg differ diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/images/ch2_ry90.jpg b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/images/ch2_ry90.jpg new file mode 100644 index 0000000000..39a8879557 Binary files /dev/null and b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/images/ch2_ry90.jpg differ diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/images/ch3_ry60.jpg b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/images/ch3_ry60.jpg new file mode 100644 index 0000000000..3fa79ce360 Binary files /dev/null and b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/images/ch3_ry60.jpg differ diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/images/initial_configuration_LR.jpg b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/images/initial_configuration_LR.jpg new file mode 100644 index 0000000000..9fa7d195f3 Binary files /dev/null and b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/images/initial_configuration_LR.jpg differ diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/moltemplate_files/butane.lt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/moltemplate_files/butane.lt new file mode 100644 index 0000000000..ed2c65640e --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/moltemplate_files/butane.lt @@ -0,0 +1,39 @@ +import "ch2group.lt" # load the definition of the "CH2" object +import "ch3group.lt" # load the definition of the "CH3" object + + +Butane inherits COMPASS { + + create_var {$mol} # optional:force all monomers to share the same molecule-ID + + # Create an array of 4 objects distributed along the X axis + + monomer1 = new CH3 + monomer2 = new CH2.rot(180,1,0,0).move(1.2533223,0,0) + monomer3 = new CH2.move(2.5066446,0,0) + monomer4 = new CH3.rot(180,0,0,1).move(3.7599669,0,0) + + # Now add a list of bonds connecting the carbon atoms together: + # (Angles, dihedrals, impropers will be automatically added later.) + + write('Data Bond List') { + $bond:b1 $atom:monomer1/C $atom:monomer2/C + $bond:b2 $atom:monomer2/C $atom:monomer3/C + $bond:b3 $atom:monomer3/C $atom:monomer4/C + } + +} # Butane + + + + + +######### (scratchwork calculations for the atomic coordinates) ######### +# Lcc = 1.5350 # length of the C-C bond (Sp3) +# Lch = 1.0930 # length of the C-H bond +# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle) +# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594 +# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754 +# # 0.5*DeltaYc = 0.4431163316030377 +# DeltaZh = Lch*sin(theta/2) # = 0.8924307629540046 +# DeltaYh = Lch*cos(theta/2) # = 0.6310438442242609 diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/moltemplate_files/ch2group.lt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/moltemplate_files/ch2group.lt new file mode 100644 index 0000000000..c281e4d6ff --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/moltemplate_files/ch2group.lt @@ -0,0 +1,71 @@ +# This file contains a definition for the "CH2" molecular subunit. +# First, load the COMPASS force field parameters we will need: + +import "compass_published.lt" # <-- defines the "COMPASS" force field + +# (The "compass_published.lt" file is located in the "force_fields" +# subdirectory distributed with moltemplate.) +# Then define "CH2": + + + + +CH2 inherits COMPASS { + + # atom-id mol-id atom-type charge x y z + + write("Data Atoms") { + $atom:C $mol:... @atom:c4 0.0 0.000000 0.000000 0.000000 + $atom:H1 $mol:... @atom:h1 0.0 0.000000 0.631044 0.892431 + $atom:H2 $mol:... @atom:h1 0.0 0.000000 0.631044 -0.892431 + } + + write('Data Bond List') { + $bond:CH1 $atom:C $atom:H1 + $bond:CH2 $atom:C $atom:H2 + } + +} # CH2 + + + + +# COMMENTS: +# 1) Atom type names (eg. "c4", "h1") are defined in "compass_published.lt". +# 2) In this example, the atomic charge of an atom is calculated by summing +# partial charge contributions from neighboring atoms bonded to this atom. +# (according to the rules in "compass_published.lt"). For this reason, +# we can ignore the "charge" column in the "Data Atoms" section. Just +# leave theses charges as "0.0" for now. Moltemplate will recalculate them. +# 3) The "..." in "$mol:..." tells moltemplate that this molecule may be part +# of a larger molecule, and (if so) to use the larger parent object's +# molecule id number as it's own. + + + + + + +# Optional: Shift all the coordinates in the +Y direction by 0.4431163. +# This way, the carbon atom is no longer located at 0,0,0, but the +# axis of an alkane chain containing this monomer is at 0,0,0. +# (This makes it more convenient to construct a polymer later. +# If this is confusing, then simply add 0.4431163 to the Y +# coordinates in the "Data Atoms" section above.) + +CH2.move(0,0.4431163,0) + + + + + +######### (scratchwork calculations for the atomic coordinates) ######### +# +# Lcc = 1.5350 # length of the C-C bond (Sp3) +# Lch = 1.0930 # length of the C-H bond +# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle) +# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594 +# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754 +# # 0.5*DeltaYc = 0.4431163 +# DeltaZh = Lch*sin(theta/2) # = 0.892431 +# DeltaYh = Lch*cos(theta/2) # = 0.631044 diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/moltemplate_files/ch3group.lt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/moltemplate_files/ch3group.lt new file mode 100644 index 0000000000..394080230a --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/moltemplate_files/ch3group.lt @@ -0,0 +1,70 @@ +# This file contains a definition for the "CH3" molecular subunit. +# First, load the COMPASS force field parameters we will need: + +import "compass_published.lt" # <-- defines the "COMPASS" force field + +# (The "compass_published.lt" file is located in the "force_fields" +# subdirectory distributed with moltemplate.) +# Then define "CH3": + + + + +CH3 inherits COMPASS { + + # atom-id mol-id atom-type charge x y z + + write("Data Atoms") { + $atom:C $mol:... @atom:c4 0.0 0.000000 0.000000 0.000000 + $atom:H1 $mol:... @atom:h1 0.0 0.000000 0.631044 0.892431 + $atom:H2 $mol:... @atom:h1 0.0 0.000000 0.631044 -0.892431 + $atom:H3 $mol:... @atom:h1 0.0 -0.892431 -0.631044 0.000000 + } + + write('Data Bond List') { + $bond:CH1 $atom:C $atom:H1 + $bond:CH2 $atom:C $atom:H2 + $bond:CH3 $atom:C $atom:H3 + } + +} # CH3 + + + + +# COMMENTS: +# 1) Atom type names (eg. "c4", "h1") are defined in "compass_published.lt". +# 2) In this example, the atomic charge of an atom is calculated by summing +# partial charge contributions from neighboring atoms bonded to this atom. +# (according to the rules in "compass_published.lt"). For this reason, +# we can ignore the "charge" column in the "Data Atoms" section. Just +# leave theses charges as "0.0" for now. Moltemplate will recalculate them. +# 3) The "..." in "$mol:..." tells moltemplate that this molecule may be part +# of a larger molecule, and (if so) to use the larger parent object's +# molecule id number as it's own. + + + + +# Optional: Shift all the coordinates in the +Y direction by 0.4431163. +# This way, the carbon atom is no longer located at 0,0,0, but the +# axis of an alkane chain containing this monomer is at 0,0,0. +# (This makes it more convenient to construct a polymer later. +# If this is confusing, then simply add 0.4431163 to the Y +# coordinates in the "Data Atoms" section above.) + +CH3.move(0,0.4431163,0) + + + + +######### (scratchwork calculations for the atomic coordinates) ######### +# +# Lcc = 1.5350 # length of the C-C bond (Sp3) +# Lch = 1.0930 # length of the C-H bond +# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle) +# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594 +# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754 +# # 0.5*DeltaYc = 0.4431163 +# DeltaZh = Lch*sin(theta/2) # = 0.892431 +# DeltaYh = Lch*cos(theta/2) # = 0.631044 diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/moltemplate_files/system.lt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/moltemplate_files/system.lt new file mode 100644 index 0000000000..1f25ac8e96 --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/moltemplate_files/system.lt @@ -0,0 +1,24 @@ +import "butane.lt" # <- defines the "Butane" molecule type. + +# Periodic boundary conditions: +write_once("Data Boundary") { + 0.0 62.4 xlo xhi + 0.0 62.4 ylo yhi + 0.0 62.4 zlo zhi +} + + + +# Generate an array of 864 = 12 x 12 x 6 Butane molecules +# which (more or less) uniformly fills the simulation box: + +molecules = new Butane [12].move(0, 0, 5.2) + [12].move(0, 5.2, 0) + [6].move(10.4, 0, 0) + + + +# NOTE: The spacing between molecules is large. There should be extra room to +# move during the initial stages of equilibration. However, you will have to +# run the simulation at NPT conditions later to compress the system to a +# more realistic density. diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/run.in.npt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/run.in.npt new file mode 100644 index 0000000000..ec9af62c40 --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/run.in.npt @@ -0,0 +1,103 @@ +# PREREQUISITES: +# +# You must use moltemplate.sh to create 3 files: +# system.data system.in.init system.in.settings +# (Follow the instructions in README_setup.sh, +# or run the file as a script using ./README_setup.sh) + +# ------------------------------- Initialization Section -------------------- + +include system.in.init + +# ------------------------------- Atom Definition Section ------------------- + +read_data system.data + +# ------------------------------- Settings Section -------------------------- + +include system.in.settings +include system.in.charges + +# ------------------------------- Run Section ------------------------------- + +# To avoid explosions, I have a 4-step equilibraion process (expand, minimize, +# reorient, compress). The system (as defined in the "system.data" file) +# is already expanded. That means there are 3 steps left: + +dump dumpeq1 all custom 50 traj_eq1_min.lammpstrj id mol type x y z ix iy iz +thermo_style custom step temp pe etotal epair ebond eangle edihed press vol +thermo 50 +thermo_modify norm yes + +# -- Equilibration: part 1: initial minimization -- + +# Note: In general, it's always a good idea to minimize the system at first. + +minimize 1.0e-5 1.0e-7 100000 400000 +undump dumpeq1 + +write_data system_after_eq1_min.data + +# -- Equilibration part 2: reorienting the molecules (NVT) -- + +timestep 1.0 +dump dumpeq2 all custom 200 traj_eq2_reorient.lammpstrj id mol type x y z ix iy iz + +# Run the system at high temperature (at constant volume) to reorient the +# the molecules (which would otherwise be pointing in the same direction). + +# To speed it up, I randomize the atomic positions for a few thousand steps +# using fix langevin (and fix nve). Then I switch to fix nvt (Nose-Hoover). +# (If I start with fix nvt (Nose-Hoover), it seems to get "stuck" for a while.) + + +fix fxlan all langevin 900.0 900.0 120 48279 +fix fxnve all nve + +run 4000 + +unfix fxlan +unfix fxnve +# Now continue the simulation at high temperature using fix nvt (Nose-Hoover). +fix fxnvt all nvt temp 900.0 900.0 100.0 + +run 10000 +undump dumpeq2 + + +write_data system_after_eq2_reorient.data + +unfix fxnvt + + +# -- equilibration part 3: Equilibrating the density (NPT) -- + +# Originally, the simulation box (in "system.data" and "system.lt") was +# unrealistically large. The spacing between the molecules was large also. +# I did this to enable the molecules to move freely and reorient themselves. +# After doing that, we should run the simulation under NPT conditions to +# allow the simulation box to contract to it's natural size. +# To help it collapse, we begin the simulation at a relatively high pressure +# Later on, we will slowly decrease it to 1 bar. + +# First cool the system. (Do this at high pressure to avoid bubble formation.) + +dump dumpeq3 all custom 200 traj_eq3_npt.lammpstrj id mol type x y z ix iy iz +fix fxnpt all npt temp 900.0 260.0 100.0 iso 500.0 500.0 1000.0 drag 2.0 + +timestep 1.0 +run 20000 + +# At the very end of the previous simulation, the temperature dropped below +# the boiling point. Run the simulation for longer at these conditions to +# give it a chance for the vapor -> liquid transition to complete. +# We will also slowly decrease the pressure to 1 bar. + +unfix fxnpt +fix fxnpt all npt temp 260.0 260.0 100.0 iso 500.0 1.0 1000.0 drag 2.0 + +timestep 1.0 +run 100000 + +write_data system_after_eq3_npt.data + diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/run.in.nvt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/run.in.nvt new file mode 100644 index 0000000000..ea3ac42167 --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/run.in.nvt @@ -0,0 +1,45 @@ +# PREREQUISITES: +# +# 1) You must use moltemplate.sh to create 3 files: +# system.data system.in.init system.in.settings +# (Follow the instructions in README_setup.sh, +# or run the file as a script using ./README_setup.sh) +# 2) You must equilibrate the system beforehand using "run.in.npt". +# This will create the file "system_after_npt.data" which this file reads. +# (Note: I have not verified that this equilibration protocol works well.) + +# ------------------------------- Initialization Section -------------------- + +include system.in.init + +# ------------------------------- Atom Definition Section ------------------- + + +# Read the coordinates generated by an earlier NPT simulation + +read_data system_after_eq3_npt.data + +# (The "write_restart" and "read_restart" commands were buggy in 2012, +# but they should work also. I prefer "write_data" and "read_data".) + + +# ------------------------------- Settings Section -------------------------- + +include system.in.settings +include system.in.charges + +# ------------------------------- Run Section ------------------------------- + +# -- simulation protocol -- + + +timestep 1.0 +dump 1 all custom 500 traj_nvt.lammpstrj id mol type x y z ix iy iz +fix fxnvt all nvt temp 260.0 260.0 500.0 tchain 1 +thermo_style custom step temp pe etotal epair ebond eangle edihed +thermo 100 +thermo_modify norm yes + +run 50000 + +write_data system_after_nvt.data diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/README.txt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/README.txt new file mode 100644 index 0000000000..5ffefbc7f3 --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/README.txt @@ -0,0 +1,42 @@ +This example is a simple simulation of many long alkane chains (hexadecane) in a +box near the boiling point at atmospheric pressure. Please read "WARNING.TXT". + +NOTE: This particular example uses the COMPASS force-field + However, moltemplate is not limited to COMPASS. + +1) Create the "system.data", "system.in.init", and "system.in.settings" +files which LAMMPS will read by running: + +moltemplate.sh system.lt + + +2) Run LAMMPS in this order: + +lmp_mpi -i run.in.npt # running the simulation at constant pressure +lmp_mpi -i run.in.nvt # running the simulation at constant temperature + +(The name of the LAMMPS executable, eg "lmp_mpi", may vary.) + +---- Details ---- + +The "Hexadecane" molecule, as well as the "CH2", and "CH3" monomers it contains +use the COMPASS force-field. This means that when we define these molecules, +we only specify the atom names, bond list, and coordinates. +We do not have to list the atom charges, angles, dihedrals, or impropers. +The rules for creating atomic charge and angle topology are contained in +the "compass_published.lt" file created by step 3) above. The "ch2group.lt", +"ch3group.lt", and "hexadecane.lt" files all refer to "compass_published.lt", +(as well as the "COMPASS" force-field object which it defines). Excerpt: + +import "compass_published.lt" +CH2 inherits COMPASS { ... +CH3 inherits COMPASS { ... +Hexadecane inherits COMPASS { ... + +Alternatively, you can manually define a list of angles, dihedrals, and +improper interactions in these files, instead of asking the force-field +to generate them for you. You can also specify some of the angles and +dihedrals explicitly, and let the force-field handle the rest. +(Many of the examples which come with moltemplate do this.) + + diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/README_remove_irrelevant_info.sh b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/README_remove_irrelevant_info.sh new file mode 100755 index 0000000000..5957289da9 --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/README_remove_irrelevant_info.sh @@ -0,0 +1,8 @@ + +# Note: By default, the system.data and system.in.settings files contain +# extra information for atoms defined in OPLSAA which you are not using +# in this simulation. +# This is harmless, but if you to delete this information from your +# system.in.settings and system.in.data files, run this script: + +cleanup_moltemplate.sh diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/README_run.sh b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/README_run.sh new file mode 100755 index 0000000000..4871a06495 --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/README_run.sh @@ -0,0 +1,21 @@ +# --- Running LAMMPS --- +# +# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS +# input scripts which link to the input scripts and data files +# you hopefully have created earlier with moltemplate.sh: +# system.in.init, system.in.settings, system.data +# If not, carry out the instructions in "README_setup.sh". +# +# -- Instructions: -- +# If "lmp_mpi" is the name of the command you use to invoke lammps, +# then you would run lammps on these files this way: + + +lmp_mpi -i run.in.npt # minimization and simulation at constant pressure +lmp_mpi -i run.in.nvt # simulation at constant volume + + +# If you have compiled the MPI version of lammps, you can run lammps in parallel +#mpirun -np 4 lmp_mpi -i run.in.npt +#mpirun -np 4 lmp_mpi -i run.in.nvt +# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/README_setup.sh b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/README_setup.sh new file mode 100755 index 0000000000..15a3a963c8 --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/README_setup.sh @@ -0,0 +1,34 @@ + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + + moltemplate.sh system.lt + + # Optional: + # To check for missing angle,dihedral params run moltemplate this way instead: + # moltemplate.sh -checkff system.lt + + + # Moltemplate generates various files with names ending in *.in* and *.data. + # Move them to the directory where you plan to run LAMMPS (in this case "../") + mv -f system.data system.in* ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ + + + + +# Optional: +# Note: The system.data and system.in.settings files contain extra information +# for atoms defined in OPLSAA which you are not using in this simulation. +# This is harmless, but if you to delete this information from your +# system.in.settings and system.in.data files, run this script: +# +# cleanup_moltemplate.sh diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/README_visualize.txt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/README_visualize.txt new file mode 100644 index 0000000000..a3e3ed620e --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/README_visualize.txt @@ -0,0 +1,87 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + Sometimes the solvent or membrane obscures the view of the solute. + It can help to shift the location of the periodic boundary box + To shift the box in the y direction (for example) do this: + + pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} + pbc box -shiftcenterrel {0.0 0.15 0.0} + + Distances are measured in units of box-length fractions, not Angstroms. + + Alternately if you have a solute whose atoms are all of type 1, + then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) + You should check if your periodic boundary conditions are too small. + To do that: + select Graphics->Representations menu option + click on the "Periodic" tab, and + click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. + +5) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/WARNING.txt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/WARNING.txt new file mode 100644 index 0000000000..ab508fc894 --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/WARNING.txt @@ -0,0 +1,13 @@ +# -------- WARNING: -------- + +This software is experimental, and the force-fields and equilbration protocols +have not been tested carefully by me. There is no gaurantee that the simulation +will reproduce the behavior of real hexadecane molecules, + +# -------- REQUEST FOR HELP: -------- + +However, if you notice a problem with this example, please report it. +Peer-review is the only way to improve this software (or any software). +Other suggestions are also welcome! + +(Contact jewett.aij@gmail.com, 2017-10-03) diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/images/hexadecane_12x12x2_t=0_LR.jpg b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/images/hexadecane_12x12x2_t=0_LR.jpg new file mode 100644 index 0000000000..b0d31f8845 Binary files /dev/null and b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/images/hexadecane_12x12x2_t=0_LR.jpg differ diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/images/hexadecane_12x12x2_t=10ps_npt_LR.jpg b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/images/hexadecane_12x12x2_t=10ps_npt_LR.jpg new file mode 100644 index 0000000000..f7c13d0989 Binary files /dev/null and b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/images/hexadecane_12x12x2_t=10ps_npt_LR.jpg differ diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/images/hexadecane_LR.jpg b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/images/hexadecane_LR.jpg new file mode 100644 index 0000000000..a4151a5fd3 Binary files /dev/null and b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/images/hexadecane_LR.jpg differ diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/moltemplate_files/ch2group.lt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/moltemplate_files/ch2group.lt new file mode 100644 index 0000000000..db7ccabdc9 --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/moltemplate_files/ch2group.lt @@ -0,0 +1,70 @@ +# This file contains a definition for the "CH2" molecular subunit. +# First, load the COMPASS force field parameters we will need: + +import "compass_published.lt" # <-- defines the "COMPASS" force field + +# (The "compass_published.lt" file is located in the "force_fields" +# subdirectory distributed with moltemplate.) +# Then define "CH2": + + + + +CH2 inherits COMPASS { + + # atom-id mol-id atom-type charge x y z + + write("Data Atoms") { + $atom:C $mol:... @atom:c4 0.0 0.000000 0.000000 0.000000 + $atom:H1 $mol:... @atom:h1 0.0 0.000000 0.631044 0.892431 + $atom:H2 $mol:... @atom:h1 0.0 0.000000 0.631044 -0.892431 + } + + write('Data Bond List') { + $bond:CH1 $atom:C $atom:H1 + $bond:CH2 $atom:C $atom:H2 + } + +} # CH2 + + + + +# COMMENTS: +# 1) Atom type names (eg. "c4", "h1") are defined in "compass_published.lt". +# 2) In this example, the atomic charge of an atom is calculated by summing +# partial charge contributions from neighboring atoms bonded to this atom. +# (according to the rules in "compass_published.lt"). For this reason, +# we can ignore the "charge" column in the "Data Atoms" section. Just +# leave theses charges as "0.0" for now. Moltemplate will recalculate them. +# 3) The "..." in "$mol:..." tells moltemplate that this molecule may be part +# of a larger molecule, and (if so) to use the larger parent object's +# molecule id number as it's own. + + + + + +# Optional: Shift all the coordinates in the +Y direction by 0.4431163. +# This way, the carbon atom is no longer located at 0,0,0, but the +# axis of an alkane chain containing this monomer is at 0,0,0. +# (This makes it more convenient to construct a polymer later. +# If this is confusing, then simply add 0.4431163 to the Y +# coordinates in the "Data Atoms" section above.) + +CH2.move(0,0.4431163,0) + + + + + +######### (scratchwork calculations for the atomic coordinates) ######### +# +# Lcc = 1.5350 # length of the C-C bond (Sp3) +# Lch = 1.0930 # length of the C-H bond +# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle) +# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594 +# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754 +# # 0.5*DeltaYc = 0.4431163 +# DeltaZh = Lch*sin(theta/2) # = 0.892431 +# DeltaYh = Lch*cos(theta/2) # = 0.631044 diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/moltemplate_files/ch3group.lt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/moltemplate_files/ch3group.lt new file mode 100644 index 0000000000..394080230a --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/moltemplate_files/ch3group.lt @@ -0,0 +1,70 @@ +# This file contains a definition for the "CH3" molecular subunit. +# First, load the COMPASS force field parameters we will need: + +import "compass_published.lt" # <-- defines the "COMPASS" force field + +# (The "compass_published.lt" file is located in the "force_fields" +# subdirectory distributed with moltemplate.) +# Then define "CH3": + + + + +CH3 inherits COMPASS { + + # atom-id mol-id atom-type charge x y z + + write("Data Atoms") { + $atom:C $mol:... @atom:c4 0.0 0.000000 0.000000 0.000000 + $atom:H1 $mol:... @atom:h1 0.0 0.000000 0.631044 0.892431 + $atom:H2 $mol:... @atom:h1 0.0 0.000000 0.631044 -0.892431 + $atom:H3 $mol:... @atom:h1 0.0 -0.892431 -0.631044 0.000000 + } + + write('Data Bond List') { + $bond:CH1 $atom:C $atom:H1 + $bond:CH2 $atom:C $atom:H2 + $bond:CH3 $atom:C $atom:H3 + } + +} # CH3 + + + + +# COMMENTS: +# 1) Atom type names (eg. "c4", "h1") are defined in "compass_published.lt". +# 2) In this example, the atomic charge of an atom is calculated by summing +# partial charge contributions from neighboring atoms bonded to this atom. +# (according to the rules in "compass_published.lt"). For this reason, +# we can ignore the "charge" column in the "Data Atoms" section. Just +# leave theses charges as "0.0" for now. Moltemplate will recalculate them. +# 3) The "..." in "$mol:..." tells moltemplate that this molecule may be part +# of a larger molecule, and (if so) to use the larger parent object's +# molecule id number as it's own. + + + + +# Optional: Shift all the coordinates in the +Y direction by 0.4431163. +# This way, the carbon atom is no longer located at 0,0,0, but the +# axis of an alkane chain containing this monomer is at 0,0,0. +# (This makes it more convenient to construct a polymer later. +# If this is confusing, then simply add 0.4431163 to the Y +# coordinates in the "Data Atoms" section above.) + +CH3.move(0,0.4431163,0) + + + + +######### (scratchwork calculations for the atomic coordinates) ######### +# +# Lcc = 1.5350 # length of the C-C bond (Sp3) +# Lch = 1.0930 # length of the C-H bond +# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle) +# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594 +# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754 +# # 0.5*DeltaYc = 0.4431163 +# DeltaZh = Lch*sin(theta/2) # = 0.892431 +# DeltaYh = Lch*cos(theta/2) # = 0.631044 diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/moltemplate_files/hexadecane.lt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/moltemplate_files/hexadecane.lt new file mode 100644 index 0000000000..23d1c229a1 --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/moltemplate_files/hexadecane.lt @@ -0,0 +1,79 @@ +# This example looks complicated because I split the +# hexadecane molecule into individual CH2 and CH3 monomers. +# +# I defined it this way so that you can easily modify +# it to change the length of the alkane chain. + + +import "compass_published.lt" # load the "COMPASS" force-field information +import "ch2group.lt" # load the definition of the "CH2" object +import "ch3group.lt" # load the definition of the "CH3" object + + + +Hexadecane inherits COMPASS { + + + create_var {$mol} # optional:force all monomers to share the same molecule-ID + + + # Now create an array of 16 "CH2" objects distributed along the X axis + + monomers = new CH2 [16].rot(180,1,0,0).move(1.2533223,0,0) + + # Each monomer is rotated 180 degrees with respect to the previous + # monomer, and then moved 1.2533223 Angstroms down the X axis. + + # ---- Now, modify the ends: --- + # Delete the CH2 groups at the beginning and end, and replace them with CH3. + + delete monomers[0] + delete monomers[15] + + monomers[0] = new CH3 + monomers[15] = new CH3 + + # Move the CH3 groups to the correct location at either end of the chain: + + monomers[15].rot(180.0,0,0,1).move(18.7998345,0,0) + # Note: 18.7998345 = (16-1) * 1.2533223 + + + # Now add a list of bonds connecting the carbon atoms together: + + write('Data Bond List') { + $bond:b1 $atom:monomers[0]/C $atom:monomers[1]/C + $bond:b2 $atom:monomers[1]/C $atom:monomers[2]/C + $bond:b3 $atom:monomers[2]/C $atom:monomers[3]/C + $bond:b4 $atom:monomers[3]/C $atom:monomers[4]/C + $bond:b5 $atom:monomers[4]/C $atom:monomers[5]/C + $bond:b6 $atom:monomers[5]/C $atom:monomers[6]/C + $bond:b7 $atom:monomers[6]/C $atom:monomers[7]/C + $bond:b8 $atom:monomers[7]/C $atom:monomers[8]/C + $bond:b9 $atom:monomers[8]/C $atom:monomers[9]/C + $bond:b10 $atom:monomers[9]/C $atom:monomers[10]/C + $bond:b11 $atom:monomers[10]/C $atom:monomers[11]/C + $bond:b12 $atom:monomers[11]/C $atom:monomers[12]/C + $bond:b13 $atom:monomers[12]/C $atom:monomers[13]/C + $bond:b14 $atom:monomers[13]/C $atom:monomers[14]/C + $bond:b15 $atom:monomers[14]/C $atom:monomers[15]/C + } + +} # Hexadecane + + + + + + + + +######### (scratchwork calculations for the atomic coordinates) ######### +# Lcc = 1.5350 # length of the C-C bond (Sp3) +# Lch = 1.0930 # length of the C-H bond +# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle) +# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594 +# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754 +# # 0.5*DeltaYc = 0.4431163316030377 +# DeltaZh = Lch*sin(theta/2) # = 0.8924307629540046 +# DeltaYh = Lch*cos(theta/2) # = 0.6310438442242609 diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/moltemplate_files/system.lt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/moltemplate_files/system.lt new file mode 100644 index 0000000000..9d90d39c20 --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/moltemplate_files/system.lt @@ -0,0 +1,20 @@ +import "hexadecane.lt" # <- defines the "Hexadecane" molecule type. + +# Periodic boundary conditions: +write_once("Data Boundary") { + 0.0 62.4 xlo xhi + 0.0 62.4 ylo yhi + 0.0 62.4 zlo zhi +} + +molecules = new Hexadecane [12].move(0, 0, 5.2) + [12].move(0, 5.2, 0) + [2].move(31.2, 0, 0) + + + + +# NOTE: The spacing between molecules is large. There should be extra room to +# move during the initial stages of equilibration. However, you will have to +# run the simulation at NPT conditions later to compress the system to a +# more realistic density. diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/run.in.npt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/run.in.npt new file mode 100644 index 0000000000..2e9c496817 --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/run.in.npt @@ -0,0 +1,102 @@ +# PREREQUISITES: +# +# You must use moltemplate.sh to create 3 files: +# system.data system.in.init system.in.settings +# (Follow the instructions in README_setup.sh, +# or run the file as a script using ./README_setup.sh) + +# ------------------------------- Initialization Section -------------------- + +include system.in.init + +# ------------------------------- Atom Definition Section ------------------- + +read_data system.data + +# ------------------------------- Settings Section -------------------------- + +include system.in.settings +include system.in.charges + +# ------------------------------- Run Section ------------------------------- + +# To avoid explosions, I have a 4-step equilibraion process (expand, minimize, +# reorient, compress). The system (as defined in the "system.data" file) +# is already expanded. That means there are 3 steps left: + +dump dumpeq1 all custom 50 traj_eq1_min.lammpstrj id mol type x y z ix iy iz +thermo_style custom step temp pe etotal epair ebond eangle edihed press vol +thermo 50 +thermo_modify norm yes + +# -- Equilibration: part 1: initial minimization -- + +# Note: In general, it's always a good idea to minimize the system at first. + +minimize 1.0e-5 1.0e-7 100000 400000 +undump dumpeq1 + +write_data system_after_eq1_min.data + +# -- Equilibration part 2: reorienting the molecules (NVT) -- + +timestep 1.0 +dump dumpeq2 all custom 200 traj_eq2_reorient.lammpstrj id mol type x y z ix iy iz + +# Run the system at high temperature (at constant volume) to reorient the +# the molecules (which would otherwise be pointing in the same direction). + +# To speed it up, I randomize the atomic positions for a few thousand steps +# using fix langevin (and fix nve). Then I switch to fix nvt (Nose-Hoover). +# (If I start with fix nvt (Nose-Hoover), it seems to get "stuck" for a while.) + + +fix fxlan all langevin 900.0 900.0 120 48279 +fix fxnve all nve + +run 4000 + +unfix fxlan +unfix fxnve +# Now continue the simulation at high temperature using fix nvt (Nose-Hoover). +fix fxnvt all nvt temp 900.0 900.0 100.0 + +run 50000 +undump dumpeq2 + + +write_data system_after_eq2_reorient.data + +unfix fxnvt + +# -- equilibration part 3: Equilibrating the density (NPT) -- + +# Originally, the simulation box (in "system.data" and "system.lt") was +# unrealistically large. The spacing between the molecules was large also. +# I did this to enable the molecules to move freely and reorient themselves. +# After doing that, we should run the simulation under NPT conditions to +# allow the simulation box to contract to it's natural size. We do that here: +# To help it collapse, we begin the simulation at a relatively high pressure +# Later on, we will slowly decrease it to 1 bar. + +# First cool the system. (Do this at high pressure to avoid bubble formation.) + +dump dumpeq3 all custom 200 traj_eq3_npt.lammpstrj id mol type x y z ix iy iz +fix fxnpt all npt temp 900.0 260.0 100.0 iso 500.0 500.0 1000.0 drag 2.0 + +timestep 1.0 +run 20000 + +# At the very end of the previous simulation, the temperature dropped below +# the boiling point. Run the simulation for longer at these conditions to +# give it a chance for the vapor -> liquid transition to complete. +# We will also slowly decrease the pressure to 1 bar. + +unfix fxnpt +fix fxnpt all npt temp 260.0 260.0 100.0 iso 500.0 1.0 1000.0 drag 2.0 + +timestep 1.0 +run 100000 + +write_data system_after_eq3_npt.data + diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/run.in.nvt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/run.in.nvt new file mode 100644 index 0000000000..7393961924 --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/run.in.nvt @@ -0,0 +1,45 @@ +# PREREQUISITES: +# +# 1) You must use moltemplate.sh to create 3 files: +# system.data system.in.init system.in.settings +# (Follow the instructions in README_setup.sh, +# or run the file as a script using ./README_setup.sh) +# 2) You must equilibrate the system beforehand using "run.in.npt". +# This will create the file "system_after_npt.data" which this file reads. +# (Note: I have not verified that this equilibration protocol works well.) + +# ------------------------------- Initialization Section -------------------- + +include system.in.init + +# ------------------------------- Atom Definition Section ------------------- + + +# Read the coordinates generated by an earlier NPT simulation + +read_data system_after_eq3_npt.data + +# (The "write_restart" and "read_restart" commands were buggy in 2012, +# but they should work also. I prefer "write_data" and "read_data".) + + +# ------------------------------- Settings Section -------------------------- + +include system.in.settings +include system.in.charges + +# ------------------------------- Run Section ------------------------------- + +# -- simulation protocol -- + + +timestep 1.0 +dump 1 all custom 500 traj_nvt.lammpstrj id mol type x y z ix iy iz +fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1 +thermo_style custom step temp pe etotal epair ebond eangle edihed +thermo 100 +thermo_modify norm yes + +run 50000 + +write_data system_after_nvt.data diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/README.txt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/README.txt new file mode 100644 index 0000000000..4a6377569d --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/README.txt @@ -0,0 +1,37 @@ +This example is a simple simulation of many short alkane chains (butane) in a +box near the boiling point at atmospheric pressure. Please read "WARNING.TXT". + +1) Create the "system.data", "system.in.init", and "system.in.settings" +files which LAMMPS will read by running: + +moltemplate.sh system.lt + + +2) Run LAMMPS in this order: + +lmp_mpi -i run.in.npt # running the simulation at constant pressure +lmp_mpi -i run.in.nvt # running the simulation at constant temperature + +(The name of the LAMMPS executable, eg "lmp_mpi", may vary.) + +---- Details ---- + +The "Butane50" molecule, as well as the "CH2", and "CH3" monomers it contains +use the OPLSAA force-field. This means that when we define these molecules, +we only specify the atom names, bond list, and coordinates. +We do not have to list the atom charges, angles, dihedrals, or impropers. +The rules for creating atomic charge and angle topology are contained in +the "oplsaa.lt" file created by step 3) above. The "ch2group.lt", +"ch3group.lt", and "butane.lt" files all refer to "oplsaa.lt", +(as well as the "OPLSAA" force-field object which it defines). Excerpt: + +import "oplsaa.lt" +CH2 inherits OPLSAA { ... +CH3 inherits OPLSAA { ... +Butane inherits OPLSAA { ... + +Alternatively, you can manually define a list of angles, dihedrals, and +improper interactions in these files, instead of asking the force-field +to generate them for you. You can also specify some of the angles and +dihedrals explicitly, and let the force-field handle the rest. +(Many of the examples which come with moltemplate do this.) diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/README_remove_irrelevant_info.sh b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/README_remove_irrelevant_info.sh new file mode 100755 index 0000000000..5957289da9 --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/README_remove_irrelevant_info.sh @@ -0,0 +1,8 @@ + +# Note: By default, the system.data and system.in.settings files contain +# extra information for atoms defined in OPLSAA which you are not using +# in this simulation. +# This is harmless, but if you to delete this information from your +# system.in.settings and system.in.data files, run this script: + +cleanup_moltemplate.sh diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/README_run.sh b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/README_run.sh new file mode 100755 index 0000000000..94d6de972c --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/README_run.sh @@ -0,0 +1,34 @@ +# --- Running LAMMPS --- +# +# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS +# input scripts which link to the input scripts and data files +# you hopefully have created earlier with moltemplate.sh: +# system.in.init, system.in.settings, system.data +# If not, carry out the instructions in "README_setup.sh". +# +# -- Instructions: -- +# If "lmp_mpi" is the name of the command you use to invoke lammps, +# then you would run lammps on these files this way: + + +lmp_mpi -i run.in.min # minimization +lmp_mpi -i run.in.nvt # minimization and simulation at constant volume + +#(Note: The constant volume simulation lacks pressure equilibration. These are +# completely separate simulations. The results of the constant pressure +# simulation might be ignored when beginning the simulation at constant +# volume. (This is because restart files in LAMMPS don't always work, +# and I was spending a lot of time trying to convince people it was a +# LAMMPS bug, instead of a moltemplate bug, so I disabled restart files.) +# Read the "run.in.nvt" file to find out how to use the "read_restart" +# command to load the results of the pressure-equilibration simulation, +# before beginning a constant-volume run. + + + + + +# If you have compiled the MPI version of lammps, you can run lammps in parallel +#mpirun -np 4 lmp_mpi -i run.in.npt +#mpirun -np 4 lmp_mpi -i run.in.nvt +# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/README_setup.sh b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/README_setup.sh new file mode 100755 index 0000000000..5cd2142a41 --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/README_setup.sh @@ -0,0 +1,34 @@ + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + + moltemplate.sh system.lt + + # Optional: + # To check for missing angle,dihedral params run moltemplate this way instead: + # moltemplate.sh -checkff system.lt + + + # Moltemplate generates various files with names ending in *.in* and *.data. + # Move them to the directory where you plan to run LAMMPS (in this case "../") + mv -f system.data system.in* ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ + + + + +# Optional: +# Note: The system.data and system.in.settings files contain extra information +# for atoms defined in OPLSAA which you are not using in this simulation. +# This is harmless, but if you to delete this information from your +# system.in.settings and system.in.data files, run this script: +# +# cleanup_moltemplate.sh diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/README_visualize.txt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/README_visualize.txt new file mode 100644 index 0000000000..b39d8901ad --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/README_visualize.txt @@ -0,0 +1,87 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + Sometimes the solvent or membrane obscures the view of the solute. + It can help to shift the location of the periodic boundary box + To shift the box in the y direction (for example) do this: + + pbc wrap -compound res -all -shiftcenterrel {-0.05 -0.05 -0.05} + pbc box -shiftcenterrel {-0.05 -0.05 -0.05} + + Distances are measured in units of box-length fractions, not Angstroms. + + Alternately if you have a solute whose atoms are all of type 1, + then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) + You should check if your periodic boundary conditions are too small. + To do that: + select Graphics->Representations menu option + click on the "Periodic" tab, and + click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. + +5) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/images/after_pressure_equilibration_LR.jpg b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/images/after_pressure_equilibration_LR.jpg new file mode 100644 index 0000000000..093f557dd9 Binary files /dev/null and b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/images/after_pressure_equilibration_LR.jpg differ diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/images/butane.jpg b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/images/butane.jpg new file mode 100644 index 0000000000..a1bcb4aee6 Binary files /dev/null and b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/images/butane.jpg differ diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/images/ch2_ry90.jpg b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/images/ch2_ry90.jpg new file mode 100644 index 0000000000..39a8879557 Binary files /dev/null and b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/images/ch2_ry90.jpg differ diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/images/ch3_ry60.jpg b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/images/ch3_ry60.jpg new file mode 100644 index 0000000000..ab140a8f9e Binary files /dev/null and b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/images/ch3_ry60.jpg differ diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/images/initial_configuration_LR.jpg b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/images/initial_configuration_LR.jpg new file mode 100644 index 0000000000..9fa7d195f3 Binary files /dev/null and b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/images/initial_configuration_LR.jpg differ diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/moltemplate_files/butane.lt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/moltemplate_files/butane.lt new file mode 100644 index 0000000000..8c21db265c --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/moltemplate_files/butane.lt @@ -0,0 +1,42 @@ +import "ch2group.lt" # load the definition of the "CH2" object +import "ch3group.lt" # load the definition of the "CH3" object + + +Butane inherits OPLSAA { + + create_var {$mol} # optional:force all monomers to share the same molecule-ID + + # Create an array of 4 objects distributed along the X axis + + monomer1 = new CH3 + monomer2 = new CH2.rot(180,1,0,0).move(1.2533223,0,0) + monomer3 = new CH2.move(2.5066446,0,0) + monomer4 = new CH3.rot(180,0,0,1).move(3.7599669,0,0) + + # Now add a list of bonds connecting the carbon atoms together: + # (Angles, dihedrals, impropers will be automatically added later.) + + write('Data Bond List') { + $bond:b1 $atom:monomer1/C $atom:monomer2/C + $bond:b2 $atom:monomer2/C $atom:monomer3/C + $bond:b3 $atom:monomer3/C $atom:monomer4/C + } + +} # Butane + + + + + + + + +######### (scratchwork calculations for the atomic coordinates) ######### +# Lcc = 1.5350 # length of the C-C bond (Sp3) +# Lch = 1.0930 # length of the C-H bond +# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle) +# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594 +# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754 +# # 0.5*DeltaYc = 0.4431163316030377 +# DeltaZh = Lch*sin(theta/2) # = 0.8924307629540046 +# DeltaYh = Lch*cos(theta/2) # = 0.6310438442242609 diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/moltemplate_files/ch2group.lt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/moltemplate_files/ch2group.lt new file mode 100644 index 0000000000..665e8e6607 --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/moltemplate_files/ch2group.lt @@ -0,0 +1,67 @@ +# This file contains a definition for the "CH2" molecular subunit. + +# First, load the OPLS force field parameters we will need. +# This file is located in the "force_fields" subdirectory +# of the moltemplate distribution. + +import "oplsaa.lt" # <-- defines the standard "OPLSAA" force field + + +# Then define "CH2": + + +CH2 inherits OPLSAA { + + # atom-id mol-id atom-type charge x y z + + write("Data Atoms") { + $atom:C $mol:... @atom:81 0.0 0.000000 0.000000 0.000000 + $atom:H1 $mol:... @atom:85 0.0 0.000000 0.631044 0.892431 + $atom:H2 $mol:... @atom:85 0.0 0.000000 0.631044 -0.892431 + } + + write('Data Bond List') { + $bond:CH1 $atom:C $atom:H1 + $bond:CH2 $atom:C $atom:H2 + } + +} # CH2 + + + + +# Optional: Shift all the coordinates in the +Y direction by 0.4431163. +# This way, the carbon atom is no longer located at 0,0,0, but the +# axis of an alkane chain containing this monomer is at 0,0,0. +# (This makes it more convenient to construct a polymer later. +# If this is confusing, then simply add 0.4431163 to the Y +# coordinates in the "Data Atoms" section above.) + +CH2.move(0,0.4431163,0) + + + + +# ---- NOTES: ---- +# +# Atom type numbers (@atom:80,81,85) are defined in "oplsaa.lt", +# @atom:80 "Alkane CH3-" +# @atom:81 "Alkane -CH2-" +# @atom:85 "Alkane H-C CH3" +# @atom:85 "Alkane H-C CH2" +# In this example, atomic charges are generated by atom type (according to the +# rules in oplsaa.lt), and can be omitted. Just leave them as "0.00" for now. +# The "..." in "$mol:..." tells moltemplate that this molecule may be part +# of a larger molecule, and (if so) to use the larger parent object's +# molecule id number as it's own. +# +######### (scratchwork calculations for the atomic coordinates) ######### +# +# Lcc = 1.5350 # length of the C-C bond (Sp3) +# Lch = 1.0930 # length of the C-H bond +# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle) +# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594 +# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754 +# # 0.5*DeltaYc = 0.4431163 +# DeltaZh = Lch*sin(theta/2) # = 0.892431 +# DeltaYh = Lch*cos(theta/2) # = 0.631044 diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/moltemplate_files/ch3group.lt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/moltemplate_files/ch3group.lt new file mode 100644 index 0000000000..bf802b3162 --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/moltemplate_files/ch3group.lt @@ -0,0 +1,69 @@ +# This file contains a definition for the "CH3" molecular subunit. + +# First, load the OPLS force field parameters we will need. +# This file is located in the "force_fields" subdirectory +# of the moltemplate distribution. + +import "oplsaa.lt" # <-- defines the standard "OPLSAA" force field + + +# Then define "CH3": + + +CH3 inherits OPLSAA { + + # atom-id mol-id atom-type charge x y z + + write("Data Atoms") { + $atom:C $mol:... @atom:80 0.0 0.000000 0.000000 0.000000 + $atom:H1 $mol:... @atom:85 0.0 0.000000 0.631044 0.892431 + $atom:H2 $mol:... @atom:85 0.0 0.000000 0.631044 -0.892431 + $atom:H3 $mol:... @atom:85 0.0 -0.892431 -0.631044 0.000000 + } + + write('Data Bond List') { + $bond:CH1 $atom:C $atom:H1 + $bond:CH2 $atom:C $atom:H2 + $bond:CH3 $atom:C $atom:H3 + } + +} # CH3 + + + + +# Optional: Shift all the coordinates in the +Y direction by 0.4431163. +# This way, the carbon atom is no longer located at 0,0,0, but the +# axis of an alkane chain containing this monomer is at 0,0,0. +# (This makes it more convenient to construct a polymer later. +# If this is confusing, then simply add 0.4431163 to the Y +# coordinates in the "Data Atoms" section above.) + +CH3.move(0,0.4431163,0) + + + + +# ---- NOTES: ---- +# +# Atom type numbers (@atom:80,81,85) are defined in "oplsaa.lt", +# @atom:80 "Alkane CH3-" +# @atom:81 "Alkane -CH2-" +# @atom:85 "Alkane H-C CH3" +# @atom:85 "Alkane H-C CH2" +# In this example, atomic charges are generated by atom type (according to the +# rules in oplsaa.lt), and can be omitted. Just leave them as "0.00" for now. +# The "..." in "$mol:..." tells moltemplate that this molecule may be part +# of a larger molecule, and (if so) to use the larger parent object's +# molecule id number as it's own. +# +######### (scratchwork calculations for the atomic coordinates) ######### +# +# Lcc = 1.5350 # length of the C-C bond (Sp3) +# Lch = 1.0930 # length of the C-H bond +# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle) +# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594 +# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754 +# # 0.5*DeltaYc = 0.4431163 +# DeltaZh = Lch*sin(theta/2) # = 0.892431 +# DeltaYh = Lch*cos(theta/2) # = 0.631044 diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/moltemplate_files/system.lt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/moltemplate_files/system.lt new file mode 100644 index 0000000000..52b5126494 --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/moltemplate_files/system.lt @@ -0,0 +1,25 @@ +import "butane.lt" # <- defines the "Butane" molecule type. + +# Periodic boundary conditions: +write_once("Data Boundary") { + 0.0 62.4 xlo xhi + 0.0 62.4 ylo yhi + 0.0 62.4 zlo zhi +} + + + +# Generate an array of 864 = 12 x 12 x 6 Butane molecules +# which (more or less) uniformly fills the simulation box: + +molecules = new Butane [12].move(0, 0, 5.2) + [12].move(0, 5.2, 0) + [6].move(10.4, 0, 0) + + + + +# NOTE: The spacing between molecules is large. There should be extra room to +# move during the initial stages of equilibration. However, you will have to +# run the simulation at NPT conditions later to compress the system to a +# more realistic density. diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/run.in.npt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/run.in.npt new file mode 100644 index 0000000000..ec9af62c40 --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/run.in.npt @@ -0,0 +1,103 @@ +# PREREQUISITES: +# +# You must use moltemplate.sh to create 3 files: +# system.data system.in.init system.in.settings +# (Follow the instructions in README_setup.sh, +# or run the file as a script using ./README_setup.sh) + +# ------------------------------- Initialization Section -------------------- + +include system.in.init + +# ------------------------------- Atom Definition Section ------------------- + +read_data system.data + +# ------------------------------- Settings Section -------------------------- + +include system.in.settings +include system.in.charges + +# ------------------------------- Run Section ------------------------------- + +# To avoid explosions, I have a 4-step equilibraion process (expand, minimize, +# reorient, compress). The system (as defined in the "system.data" file) +# is already expanded. That means there are 3 steps left: + +dump dumpeq1 all custom 50 traj_eq1_min.lammpstrj id mol type x y z ix iy iz +thermo_style custom step temp pe etotal epair ebond eangle edihed press vol +thermo 50 +thermo_modify norm yes + +# -- Equilibration: part 1: initial minimization -- + +# Note: In general, it's always a good idea to minimize the system at first. + +minimize 1.0e-5 1.0e-7 100000 400000 +undump dumpeq1 + +write_data system_after_eq1_min.data + +# -- Equilibration part 2: reorienting the molecules (NVT) -- + +timestep 1.0 +dump dumpeq2 all custom 200 traj_eq2_reorient.lammpstrj id mol type x y z ix iy iz + +# Run the system at high temperature (at constant volume) to reorient the +# the molecules (which would otherwise be pointing in the same direction). + +# To speed it up, I randomize the atomic positions for a few thousand steps +# using fix langevin (and fix nve). Then I switch to fix nvt (Nose-Hoover). +# (If I start with fix nvt (Nose-Hoover), it seems to get "stuck" for a while.) + + +fix fxlan all langevin 900.0 900.0 120 48279 +fix fxnve all nve + +run 4000 + +unfix fxlan +unfix fxnve +# Now continue the simulation at high temperature using fix nvt (Nose-Hoover). +fix fxnvt all nvt temp 900.0 900.0 100.0 + +run 10000 +undump dumpeq2 + + +write_data system_after_eq2_reorient.data + +unfix fxnvt + + +# -- equilibration part 3: Equilibrating the density (NPT) -- + +# Originally, the simulation box (in "system.data" and "system.lt") was +# unrealistically large. The spacing between the molecules was large also. +# I did this to enable the molecules to move freely and reorient themselves. +# After doing that, we should run the simulation under NPT conditions to +# allow the simulation box to contract to it's natural size. +# To help it collapse, we begin the simulation at a relatively high pressure +# Later on, we will slowly decrease it to 1 bar. + +# First cool the system. (Do this at high pressure to avoid bubble formation.) + +dump dumpeq3 all custom 200 traj_eq3_npt.lammpstrj id mol type x y z ix iy iz +fix fxnpt all npt temp 900.0 260.0 100.0 iso 500.0 500.0 1000.0 drag 2.0 + +timestep 1.0 +run 20000 + +# At the very end of the previous simulation, the temperature dropped below +# the boiling point. Run the simulation for longer at these conditions to +# give it a chance for the vapor -> liquid transition to complete. +# We will also slowly decrease the pressure to 1 bar. + +unfix fxnpt +fix fxnpt all npt temp 260.0 260.0 100.0 iso 500.0 1.0 1000.0 drag 2.0 + +timestep 1.0 +run 100000 + +write_data system_after_eq3_npt.data + diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/run.in.nvt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/run.in.nvt new file mode 100644 index 0000000000..ea3ac42167 --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/run.in.nvt @@ -0,0 +1,45 @@ +# PREREQUISITES: +# +# 1) You must use moltemplate.sh to create 3 files: +# system.data system.in.init system.in.settings +# (Follow the instructions in README_setup.sh, +# or run the file as a script using ./README_setup.sh) +# 2) You must equilibrate the system beforehand using "run.in.npt". +# This will create the file "system_after_npt.data" which this file reads. +# (Note: I have not verified that this equilibration protocol works well.) + +# ------------------------------- Initialization Section -------------------- + +include system.in.init + +# ------------------------------- Atom Definition Section ------------------- + + +# Read the coordinates generated by an earlier NPT simulation + +read_data system_after_eq3_npt.data + +# (The "write_restart" and "read_restart" commands were buggy in 2012, +# but they should work also. I prefer "write_data" and "read_data".) + + +# ------------------------------- Settings Section -------------------------- + +include system.in.settings +include system.in.charges + +# ------------------------------- Run Section ------------------------------- + +# -- simulation protocol -- + + +timestep 1.0 +dump 1 all custom 500 traj_nvt.lammpstrj id mol type x y z ix iy iz +fix fxnvt all nvt temp 260.0 260.0 500.0 tchain 1 +thermo_style custom step temp pe etotal epair ebond eangle edihed +thermo 100 +thermo_modify norm yes + +run 50000 + +write_data system_after_nvt.data diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/README.txt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/README.txt index f744e1718f..470df87550 100644 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/README.txt +++ b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/README.txt @@ -1,8 +1,5 @@ This is an example of how to use the OPLSAA force-field in LAMMPS -As of 2016-11-21, this code has not been tested for accuracy. -(See the WARNING.TXT file.) - step 1) To build the files which LAMMPS needs, follow the instructions in: README_setup.sh diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/README_visualize.txt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/README_visualize.txt index a3e3ed620e..642c85c24c 100644 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/README_visualize.txt +++ b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/README_visualize.txt @@ -60,8 +60,8 @@ d) Try entering these commands: It can help to shift the location of the periodic boundary box To shift the box in the y direction (for example) do this: - pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} - pbc box -shiftcenterrel {0.0 0.15 0.0} + pbc wrap -compound res -all -shiftcenterrel {-0.05 -0.05 -0.05} + pbc box -shiftcenterrel {-0.05 -0.05 -0.05} -width 0.5 Distances are measured in units of box-length fractions, not Angstroms. diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/images/ethylene+benzene_50bar_t=100000_LR.jpg b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/images/ethylene+benzene_50bar_t=100000_LR.jpg new file mode 100644 index 0000000000..b9ff053fcb Binary files /dev/null and b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/images/ethylene+benzene_50bar_t=100000_LR.jpg differ diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/images/ethylene+benzene_box80x80x80_LR.jpg b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/images/ethylene+benzene_box80x80x80_LR.jpg deleted file mode 100644 index 00c82d3d9f..0000000000 Binary files a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/images/ethylene+benzene_box80x80x80_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/images/ethylene+benzene_t=0_LR.jpg b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/images/ethylene+benzene_t=0_LR.jpg new file mode 100644 index 0000000000..65949a4684 Binary files /dev/null and b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/images/ethylene+benzene_t=0_LR.jpg differ diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/moltemplate_files/benzene.lt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/moltemplate_files/benzene.lt index 1293cb1e4d..5f5e8d904a 100644 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/moltemplate_files/benzene.lt +++ b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/moltemplate_files/benzene.lt @@ -1,7 +1,7 @@ import "oplsaa.lt" -# The "oplsaa.lt" file contains force-field definitions and masses for the -# atoms in your system. See oplsaa_lt_generator/README.TXT for details. +# The "oplsaa.lt" file contains force-field definitions, +# partial charges and masses for the atoms in your system. # Note: # Atom type @atom:90 corresponds to "Aromatic C" @@ -9,25 +9,32 @@ import "oplsaa.lt" Benzene inherits OPLSAA { - write('Data Atoms') { - $atom:C1 $mol @atom:90 0.00 5.274 1.999 -8.568 # "Aromatic C" - $atom:C2 $mol @atom:90 0.00 6.627 2.018 -8.209 # "Aromatic C" - $atom:C3 $mol @atom:90 0.00 7.366 0.829 -8.202 # "Aromatic C" - $atom:C4 $mol @atom:90 0.00 6.752 -0.379 -8.554 # "Aromatic C" - $atom:C5 $mol @atom:90 0.00 5.399 -0.398 -8.912 # "Aromatic C" - $atom:C6 $mol @atom:90 0.00 4.660 0.791 -8.919 # "Aromatic C" - $atom:H11 $mol @atom:91 0.00 4.704 2.916 -8.573 # "Aromatic H-C" - $atom:H21 $mol @atom:91 0.00 7.101 2.950 -7.938 # "Aromatic H-C" - $atom:H31 $mol @atom:91 0.00 8.410 0.844 -7.926 # "Aromatic H-C" - $atom:H41 $mol @atom:91 0.00 7.322 -1.296 -8.548 # "Aromatic H-C" - $atom:H51 $mol @atom:91 0.00 4.925 -1.330 -9.183 # "Aromatic H-C" - $atom:H61 $mol @atom:91 0.00 3.616 0.776 -9.196 # "Aromatic H-C" + # atom-id mol-id atom-type charge X Y Z # comment + + write("Data Atoms") { + $atom:C1 $mol @atom:90 0.00 -0.739 1.189 -0.00733 # 90 = "Aromatic C" + $atom:C2 $mol @atom:90 0.00 0.614 1.208 0.35167 # 90 = "Aromatic C" + $atom:C3 $mol @atom:90 0.00 1.353 0.019 0.35867 # 90 = "Aromatic C" + $atom:C4 $mol @atom:90 0.00 0.739 -1.189 0.00667 # 90 = "Aromatic C" + $atom:C5 $mol @atom:90 0.00 -0.614 -1.208 -0.35133 # 90 = "Aromatic C" + $atom:C6 $mol @atom:90 0.00 -1.353 -0.019 -0.35833 # 90 = "Aromatic C" + $atom:H11 $mol @atom:91 0.00 -1.309 2.106 -0.01233 # 91 = "Aromatic H-C" + $atom:H21 $mol @atom:91 0.00 1.088 2.14 0.62267 # 91 = "Aromatic H-C" + $atom:H31 $mol @atom:91 0.00 2.397 0.034 0.63467 # 91 = "Aromatic H-C" + $atom:H41 $mol @atom:91 0.00 1.309 -2.106 0.01267 # 91 = "Aromatic H-C" + $atom:H51 $mol @atom:91 0.00 -1.088 -2.14 -0.62233 # 91 = "Aromatic H-C" + $atom:H61 $mol @atom:91 0.00 -2.397 -0.034 -0.63533 # 91 = "Aromatic H-C" } # Note: You don't have to specify the charge in this example because # we are using the OPLSAA force-field assigns this by atom-type. # Just leave these numbers as 0.00 for now. + # Note: LAMMPS expects an integer in the 2nd column (the Molecule-ID number). + # If we put "$mol" there, moltemplate will generate this integer for you - write('Data Bond List') { + # A list of the bonds in the molecule + # BondID AtomID1 AtomID2 + + write("Data Bond List") { $bond:C12 $atom:C1 $atom:C2 $bond:C23 $atom:C2 $atom:C3 $bond:C34 $atom:C3 $atom:C4 @@ -42,4 +49,7 @@ Benzene inherits OPLSAA { $bond:C6H6 $atom:C6 $atom:H61 } + # In the "Data Bond List" section we don't have to specify the bond type. + # The bond-type will be determined by the atom type (according to "oplsaa.lt") + } # Benzene diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/moltemplate_files/ethylene.lt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/moltemplate_files/ethylene.lt index 626c731b02..3515702d1d 100644 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/moltemplate_files/ethylene.lt +++ b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/moltemplate_files/ethylene.lt @@ -1,7 +1,7 @@ import "oplsaa.lt" -# The "oplsaa.lt" file contains force-field definitions and masses for the -# atoms in your system. See oplsaa_lt_generator/README.TXT for details. +# The "oplsaa.lt" file contains force-field definitions, +# partial charges and masses for the atoms in your system. # Note: # Atom type 88 corresponds to "Alkene H2-C=" @@ -11,19 +11,24 @@ import "oplsaa.lt" Ethylene inherits OPLSAA { - # atom-id mol-id atom-type charge X Y Z + # atom-id mol-id atom-type charge X Y Z # comment write('Data Atoms') { - $atom:C1 $mol @atom:88 0.00 -0.6695 0.000000 0.000000 - $atom:C2 $mol @atom:88 0.00 0.6695 0.000000 0.000000 - $atom:H11 $mol @atom:89 0.00 -1.234217 -0.854458 0.000000 - $atom:H12 $mol @atom:89 0.00 -1.234217 0.854458 0.000000 - $atom:H21 $mol @atom:89 0.00 1.234217 -0.854458 0.000000 - $atom:H22 $mol @atom:89 0.00 1.234217 0.854458 0.000000 + $atom:C1 $mol @atom:88 0.00 -0.6695 0.00000 0.000 #88 = "Alkene H2-C=" + $atom:C2 $mol @atom:88 0.00 0.6695 0.00000 0.000 #88 = "Alkene H2-C=" + $atom:H11 $mol @atom:89 0.00 -1.23422 -0.85446 0.000 #89 = "Alkene H-C=" + $atom:H12 $mol @atom:89 0.00 -1.23422 0.85446 0.000 #89 = "Alkene H-C=" + $atom:H21 $mol @atom:89 0.00 1.23422 -0.85446 0.000 #89 = "Alkene H-C=" + $atom:H22 $mol @atom:89 0.00 1.23422 0.85446 0.000 #89 = "Alkene H-C=" } # Note: You don't have to specify the charge in this example because # we are using the OPLSAA force-field assigns this by atom-type. # Just leave these numbers as 0.00 for now. + # Note: LAMMPS expects an integer in the 2nd column (the Molecule-ID number). + # If we put "$mol" there, moltemplate will generate this integer for you + + # A list of the bonds in the molecule + # BondID AtomID1 AtomID2 write('Data Bond List') { $bond:C12 $atom:C1 $atom:C2 @@ -33,11 +38,8 @@ Ethylene inherits OPLSAA { $bond:C2H2 $atom:C2 $atom:H22 } + # In the "Data Bond List" section we don't have to specify the bond type. + # The bond-type will be determined by the atom type (according to "oplsaa.lt") + } # Ethylene - - -# Note: You don't need to supply the partial partial charges of the atoms. -# If you like, just fill the fourth column with zeros ("0.000"). -# Moltemplate and LAMMPS will automatically assign the charge later - diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/moltemplate_files/system.lt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/moltemplate_files/system.lt index 49458a5b42..a28fd9f4af 100644 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/moltemplate_files/system.lt +++ b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/moltemplate_files/system.lt @@ -4,20 +4,20 @@ import "benzene.lt" # <- defines the "Benzene" molecule type. # Periodic boundary conditions: write_once("Data Boundary") { - 0.0 80.00 xlo xhi - 0.0 80.00 ylo yhi - 0.0 80.00 zlo zhi + 0.0 48.00 xlo xhi + 0.0 48.00 ylo yhi + 0.0 48.00 zlo zhi } -# Create 1000 ethylenes and 500 benzenes +# Create 216 ethylenes and 108 benzenes -ethylenes = new Ethylene[10].move(8.0, 0, 0) - [10].move(0, 8.0, 0) - [10].move(0, 0, 8.0) +ethylenes = new Ethylene[6].move(8.0, 0, 0) + [6].move(0, 8.0, 0) + [6].move(0, 0, 8.0) -benzenes = new Benzene[10].move(8.0, 0, 0) - [10].move(0, 8.0, 0) - [5].move(0, 0, 16.0) +benzenes = new Benzene[6].move(8.0, 0, 0) + [6].move(0, 8.0, 0) + [3].move(0, 0, 16.0) # Now shift the positions of all of the benzene molecules, # to reduce the chance that they overlap with the ethylene molecules. diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/run.in.nvt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/run.in.nvt index 2f3b81c186..09b6a6b146 100644 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/run.in.nvt +++ b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/run.in.nvt @@ -40,7 +40,7 @@ include system.in.settings # -- simulation protocol -- -timestep 1.0 +timestep 2.0 dump 1 all custom 5000 traj_nvt.lammpstrj id mol type x y z ix iy iz fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1 thermo 500 diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/benzene.lt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/benzene.lt index f240a091fe..5f5e8d904a 100644 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/benzene.lt +++ b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/benzene.lt @@ -1,7 +1,7 @@ import "oplsaa.lt" -# The "oplsaa.lt" file contains force-field definitions and masses for the -# atoms in your system. See oplsaa_lt_generator/README.TXT for details. +# The "oplsaa.lt" file contains force-field definitions, +# partial charges and masses for the atoms in your system. # Note: # Atom type @atom:90 corresponds to "Aromatic C" @@ -9,31 +9,32 @@ import "oplsaa.lt" Benzene inherits OPLSAA { - # We just need a list of atom types and bonds. - # - # You don't have to specify the charge in this example because we are - # using the OPLSAA force-field assigns this by atom-type. - # - # You also don't have to specify the coordinates, because - # you are using PACKMOL to generate them for you. - # Just leave these numbers as 0.00 for now.. + # atom-id mol-id atom-type charge X Y Z # comment - write('Data Atoms') { - $atom:C1 $mol @atom:90 0.00 0.00 0.00 0.00 # "Aromatic C" - $atom:C2 $mol @atom:90 0.00 0.00 0.00 0.00 # "Aromatic C" - $atom:C3 $mol @atom:90 0.00 0.00 0.00 0.00 # "Aromatic C" - $atom:C4 $mol @atom:90 0.00 0.00 0.00 0.00 # "Aromatic C" - $atom:C5 $mol @atom:90 0.00 0.00 0.00 0.00 # "Aromatic C" - $atom:C6 $mol @atom:90 0.00 0.00 0.00 0.00 # "Aromatic C" - $atom:H11 $mol @atom:91 0.00 0.00 0.00 0.00 # "Aromatic H-C" - $atom:H21 $mol @atom:91 0.00 0.00 0.00 0.00 # "Aromatic H-C" - $atom:H31 $mol @atom:91 0.00 0.00 0.00 0.00 # "Aromatic H-C" - $atom:H41 $mol @atom:91 0.00 0.00 0.00 0.00 # "Aromatic H-C" - $atom:H51 $mol @atom:91 0.00 0.00 0.00 0.00 # "Aromatic H-C" - $atom:H61 $mol @atom:91 0.00 0.00 0.00 0.00 # "Aromatic H-C" + write("Data Atoms") { + $atom:C1 $mol @atom:90 0.00 -0.739 1.189 -0.00733 # 90 = "Aromatic C" + $atom:C2 $mol @atom:90 0.00 0.614 1.208 0.35167 # 90 = "Aromatic C" + $atom:C3 $mol @atom:90 0.00 1.353 0.019 0.35867 # 90 = "Aromatic C" + $atom:C4 $mol @atom:90 0.00 0.739 -1.189 0.00667 # 90 = "Aromatic C" + $atom:C5 $mol @atom:90 0.00 -0.614 -1.208 -0.35133 # 90 = "Aromatic C" + $atom:C6 $mol @atom:90 0.00 -1.353 -0.019 -0.35833 # 90 = "Aromatic C" + $atom:H11 $mol @atom:91 0.00 -1.309 2.106 -0.01233 # 91 = "Aromatic H-C" + $atom:H21 $mol @atom:91 0.00 1.088 2.14 0.62267 # 91 = "Aromatic H-C" + $atom:H31 $mol @atom:91 0.00 2.397 0.034 0.63467 # 91 = "Aromatic H-C" + $atom:H41 $mol @atom:91 0.00 1.309 -2.106 0.01267 # 91 = "Aromatic H-C" + $atom:H51 $mol @atom:91 0.00 -1.088 -2.14 -0.62233 # 91 = "Aromatic H-C" + $atom:H61 $mol @atom:91 0.00 -2.397 -0.034 -0.63533 # 91 = "Aromatic H-C" } + # Note: You don't have to specify the charge in this example because + # we are using the OPLSAA force-field assigns this by atom-type. + # Just leave these numbers as 0.00 for now. + # Note: LAMMPS expects an integer in the 2nd column (the Molecule-ID number). + # If we put "$mol" there, moltemplate will generate this integer for you - write('Data Bond List') { + # A list of the bonds in the molecule + # BondID AtomID1 AtomID2 + + write("Data Bond List") { $bond:C12 $atom:C1 $atom:C2 $bond:C23 $atom:C2 $atom:C3 $bond:C34 $atom:C3 $atom:C4 @@ -48,4 +49,7 @@ Benzene inherits OPLSAA { $bond:C6H6 $atom:C6 $atom:H61 } + # In the "Data Bond List" section we don't have to specify the bond type. + # The bond-type will be determined by the atom type (according to "oplsaa.lt") + } # Benzene diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/ethylene.lt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/ethylene.lt index 45adb1faef..3515702d1d 100644 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/ethylene.lt +++ b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/ethylene.lt @@ -1,7 +1,7 @@ import "oplsaa.lt" -# The "oplsaa.lt" file contains force-field definitions and masses for the -# atoms in your system. See oplsaa_lt_generator/README.TXT for details. +# The "oplsaa.lt" file contains force-field definitions, +# partial charges and masses for the atoms in your system. # Note: # Atom type 88 corresponds to "Alkene H2-C=" @@ -11,16 +11,24 @@ import "oplsaa.lt" Ethylene inherits OPLSAA { - # atom-id mol-id atom-type charge X Y Z + # atom-id mol-id atom-type charge X Y Z # comment write('Data Atoms') { - $atom:C1 $mol @atom:88 0.000 -0.6695 0.000000 0.000000 - $atom:C2 $mol @atom:88 0.000 0.6695 0.000000 0.000000 - $atom:H11 $mol @atom:89 0.000 -1.234217 -0.854458 0.000000 - $atom:H12 $mol @atom:89 0.000 -1.234217 0.854458 0.000000 - $atom:H21 $mol @atom:89 0.000 1.234217 -0.854458 0.000000 - $atom:H22 $mol @atom:89 0.000 1.234217 0.854458 0.000000 + $atom:C1 $mol @atom:88 0.00 -0.6695 0.00000 0.000 #88 = "Alkene H2-C=" + $atom:C2 $mol @atom:88 0.00 0.6695 0.00000 0.000 #88 = "Alkene H2-C=" + $atom:H11 $mol @atom:89 0.00 -1.23422 -0.85446 0.000 #89 = "Alkene H-C=" + $atom:H12 $mol @atom:89 0.00 -1.23422 0.85446 0.000 #89 = "Alkene H-C=" + $atom:H21 $mol @atom:89 0.00 1.23422 -0.85446 0.000 #89 = "Alkene H-C=" + $atom:H22 $mol @atom:89 0.00 1.23422 0.85446 0.000 #89 = "Alkene H-C=" } + # Note: You don't have to specify the charge in this example because + # we are using the OPLSAA force-field assigns this by atom-type. + # Just leave these numbers as 0.00 for now. + # Note: LAMMPS expects an integer in the 2nd column (the Molecule-ID number). + # If we put "$mol" there, moltemplate will generate this integer for you + + # A list of the bonds in the molecule + # BondID AtomID1 AtomID2 write('Data Bond List') { $bond:C12 $atom:C1 $atom:C2 @@ -30,11 +38,8 @@ Ethylene inherits OPLSAA { $bond:C2H2 $atom:C2 $atom:H22 } + # In the "Data Bond List" section we don't have to specify the bond type. + # The bond-type will be determined by the atom type (according to "oplsaa.lt") + } # Ethylene - - -# Note: You don't need to supply the partial partial charges of the atoms. -# If you like, just fill the fourth column with zeros ("0.000"). -# Moltemplate and LAMMPS will automatically assign the charge later - diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/packmol_files/benzene.xyz b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/packmol_files/benzene.xyz index 1a727ff40c..76af485144 100644 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/packmol_files/benzene.xyz +++ b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/packmol_files/benzene.xyz @@ -1,14 +1,14 @@ 12 Benzene -C1 5.274 1.999 -8.568 -C2 6.627 2.018 -8.209 -C3 7.366 0.829 -8.202 -C4 6.752 -0.379 -8.554 -C5 5.399 -0.398 -8.912 -C6 4.660 0.791 -8.919 -H11 4.704 2.916 -8.573 -H21 7.101 2.950 -7.938 -H31 8.410 0.844 -7.926 -H41 7.322 -1.296 -8.548 -H51 4.925 -1.330 -9.183 -H61 3.616 0.776 -9.196 +C1 -0.739 1.189 -0.00733 +C2 0.614 1.208 0.35167 +C3 1.353 0.019 0.35867 +C4 0.739 -1.189 0.00667 +C5 -0.614 -1.208 -0.35133 +C6 -1.353 -0.019 -0.35833 +H11 -1.309 2.106 -0.01233 +H21 1.088 2.14 0.62267 +H31 2.397 0.034 0.63467 +H41 1.309 -2.106 0.01267 +H51 -1.088 -2.14 -0.62233 +H61 -2.397 -0.034 -0.63533 diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/README.txt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/README.txt index 1450f1dd59..bfd39e8f47 100644 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/README.txt +++ b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/README.txt @@ -1,5 +1,5 @@ This example is a simple simulation of many long alkane chains (hexadecane) in a -box at room temperature and atmospheric pressure. Please read "WARNING.TXT". +box near the boiling point atmospheric pressure. Please read "WARNING.TXT". NOTE: This particular example uses the OPLSAA force-field However, moltemplate is not limited to OPLSAA. @@ -12,7 +12,6 @@ moltemplate.sh system.lt 2) Run LAMMPS in this order: -lmp_mpi -i run.in.min # minimize the energy (to avoid atom overlap) before... lmp_mpi -i run.in.npt # running the simulation at constant pressure lmp_mpi -i run.in.nvt # running the simulation at constant temperature diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/WARNING.txt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/WARNING.txt index e06bf0caa1..215e7fcf91 100644 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/WARNING.txt +++ b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/WARNING.txt @@ -2,9 +2,7 @@ This software is experimental, and the force-fields and equilbration protocols have not been tested carefully by me. There is no gaurantee that the simulation -will reproduce the behavior of real hexadecane molecules, -(or even of hexadecane molecules simulated using AMBER, which should - be using the same force-field). +will reproduce the behavior of real hexadecane molecules # -------- REQUEST FOR HELP: -------- diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/images/ch2_ry60_LR.jpg b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/images/ch2_ry60_LR.jpg new file mode 100644 index 0000000000..5a5a188aed Binary files /dev/null and b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/images/ch2_ry60_LR.jpg differ diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/images/ch3_ry60_LR.jpg b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/images/ch3_ry60_LR.jpg new file mode 100644 index 0000000000..65e20353ca Binary files /dev/null and b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/images/ch3_ry60_LR.jpg differ diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/images/hexadecane_LR.jpg b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/images/hexadecane_LR.jpg index 3ad353dbb4..a4151a5fd3 100644 Binary files a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/images/hexadecane_LR.jpg and b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/images/hexadecane_LR.jpg differ diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/moltemplate_files/ch2group.lt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/moltemplate_files/ch2group.lt index 05091ba39c..c800d56679 100644 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/moltemplate_files/ch2group.lt +++ b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/moltemplate_files/ch2group.lt @@ -2,7 +2,7 @@ # First, load the OPLS force field parameters we will need. # These 2 files are located in the "force_fields" subdirectory -# of the moltemplate distribution. +# distributed with moltemplate. import "oplsaa.lt" # <-- defines the standard "OPLSAA" force field import "loplsaa.lt" # <-- custom parameters for long alkane chains taken from diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/run.in.npt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/run.in.npt index 1b1a28fabc..f30c796b47 100644 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/run.in.npt +++ b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/run.in.npt @@ -74,11 +74,24 @@ unfix fxnvt # I did this to enable the molecules to move freely and reorient themselves. # After doing that, we should run the simulation under NPT conditions to # allow the simulation box to contract to it's natural size. We do that here: -# We begin the simulation at 100 barr (a relatively low pressure), and -# slowly decrease it to 1 barr, maintianing the temperature at 300K. +# To help it collapse, we begin the simulation at a relatively high pressure +# Later on, we will slowly decrease it to 1 bar. + +# First cool the system. (Do this at high pressure to avoid bubble formation.) dump dumpeq3 all custom 200 traj_eq3_npt.lammpstrj id mol type x y z ix iy iz -fix fxnpt all npt temp 900.0 300.0 100.0 iso 100.0 1.0 1000.0 drag 2.0 +fix fxnpt all npt temp 900.0 260.0 100.0 iso 500.0 500.0 1000.0 drag 2.0 + +timestep 1.0 +run 20000 + +# At the very end of the previous simulation, the temperature dropped below +# the boiling point. Run the simulation for longer at these conditions to +# give it a chance for the vapor -> liquid transition to complete. +# We will also slowly decrease the pressure to 1 bar. + +unfix fxnpt +fix fxnpt all npt temp 260.0 260.0 100.0 iso 500.0 1.0 1000.0 drag 2.0 timestep 1.0 run 100000 diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/run.in.nvt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/run.in.nvt index 38815745c5..6f74ef0870 100644 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/run.in.nvt +++ b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/run.in.nvt @@ -35,9 +35,10 @@ include system.in.charges timestep 1.0 dump 1 all custom 500 traj_nvt.lammpstrj id mol type x y z ix iy iz -fix fxnvt all nvt temp 350.0 350.0 500.0 tchain 1 +fix fxnvt all nvt temp 270.0 270.0 500.0 tchain 1 +thermo_style custom step temp pe etotal epair ebond eangle edihed thermo 100 -#thermo_modify flush yes +thermo_modify norm yes run 50000 diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/ice_crystal/moltemplate_files/spce.lt b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/ice_crystal/moltemplate_files/spce.lt index 2b550b6309..1f0f0f61b5 100644 --- a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/ice_crystal/moltemplate_files/spce.lt +++ b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/ice_crystal/moltemplate_files/spce.lt @@ -6,18 +6,6 @@ SPCE { - write_once("In Init") { - # -- Default styles (for solo "SPCE" water) -- - units real - atom_style full - # (Hybrid force fields were not necessary but are used for portability.) - pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0 - bond_style hybrid harmonic - angle_style hybrid harmonic - kspace_style pppm 0.0001 - pair_modify mix arithmetic - } - write("Data Atoms") { $atom:O $mol:. @atom:O -0.8476 0.0000000 0.00000 0.000000 $atom:H1 $mol:. @atom:H 0.4238 0.8164904 0.00000 0.5773590 @@ -39,13 +27,25 @@ SPCE { } write_once("In Settings") { - bond_coeff @bond:OH harmonic 1000.0 1.0 - angle_coeff @angle:HOH harmonic 1000.0 109.47 + bond_coeff @bond:OH harmonic 600.0 1.0 + angle_coeff @angle:HOH harmonic 75.0 109.47 pair_coeff @atom:O @atom:O lj/charmm/coul/long 0.1553 3.166 - pair_coeff @atom:H @atom:H lj/charmm/coul/long 0.0 2.058 + pair_coeff @atom:H @atom:H lj/charmm/coul/long 0.0 0.0 group spce type @atom:O @atom:H - fix fSHAKE spce shake 0.0001 10 100 b @bond:OH a @angle:HOH - # (Remember to "unfix" fSHAKE during minimization.) + fix fShakeSPCE spce shake 0.0001 10 100 b @bond:OH a @angle:HOH + # (Remember to "unfix" fShakeSPCE during minimization.) + } + + write_once("In Init") { + # -- Default styles (for solo "SPCE" water) -- + units real + atom_style full + # (Hybrid force fields were not necessary but are used for portability.) + pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0 + bond_style hybrid harmonic + angle_style hybrid harmonic + kspace_style pppm 0.0001 + #pair_modify mix arithmetic # LEAVE THIS UNSPECIFIED! } } # end of definition of "SPCE" water molecule type diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/ice_crystal/run.in.npt b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/ice_crystal/run.in.npt index c10893b411..efa4fca484 100644 --- a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/ice_crystal/run.in.npt +++ b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/ice_crystal/run.in.npt @@ -27,7 +27,7 @@ include system.in.settings # Note: The minimization step is not necessary in this example. However # in general, it's always a good idea to minimize the system beforehand. # fSHAKE was defined in system.in.settings. It is incompatible with "minimize". -unfix fSHAKE +unfix fShakeSPCE minimize 1.0e-5 1.0e-7 100000 400000 # Now read "system.in.settings" in order to redefine fSHAKE again: include system.in.settings diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/moltemplate_files/spce.lt b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/moltemplate_files/spce.lt index e1bf2390a0..d40da62b99 100644 --- a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/moltemplate_files/spce.lt +++ b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/moltemplate_files/spce.lt @@ -29,8 +29,8 @@ SPCE { write_once("In Settings") { bond_coeff @bond:OH harmonic 600.0 1.0 angle_coeff @angle:HOH harmonic 75.0 109.47 - pair_coeff @atom:O @atom:O lj/cut/coul/long 0.1553 3.166 - pair_coeff @atom:H @atom:H lj/cut/coul/long 0.0 2.058 + pair_coeff @atom:O @atom:O lj/cut/coul/long 0.1553 3.166 + pair_coeff @atom:H @atom:H lj/cut/coul/long 0.0 0.0 group spce type @atom:O @atom:H fix fShakeSPCE spce shake 0.0001 10 100 b @bond:OH a @angle:HOH # (Remember to "unfix" fShakeSPCE during minimization.) diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/moltemplate_files/watmw.lt b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/moltemplate_files/watmw.lt deleted file mode 100644 index c7aaecebbc..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/moltemplate_files/watmw.lt +++ /dev/null @@ -1,54 +0,0 @@ -# This file stores LAMMPS data for the "mW" water model. -# (Molinero, V. and Moore, E.B., J. Phys. Chem. B 2009, 113, 4008-4016) -# -# In this model, each water molecule is represented by a single "mW" particle. -# These particles interact with their neighbors via 3-body Stillinger-Weber -# forces whose parameters are tuned to mimic directional hydrogen-bonding -# in liquid water (as well as hexagonal ice, type II ice, and -# low-density super-cooled liquid/amorphous water phases). - -WatMW { - write("Data Atoms") { - $atom:mW $mol:. @atom:mW 0.0 0.0 0.0 0.0 - } - - write_once("Data Masses") { - @atom:mW 18.02 - } - - write_once("system.in.sw") { - mW mW mW 6.189 2.3925 1.8 23.15 1.2 -0.333333333 7.049556277 0.602224558 4 0 0 - } - - write_once("In Init") { - # -- Default styles for "WatMW" -- - units real - pair_style sw - } - - write_once("In Settings") { - # --Now indicate which atom type(s) are simulated using the "sw" pair style - # -- In this case only one of the atom types is used (the mW water "atom"). - - pair_coeff * * sw system.in.sw mW NULL NULL NULL - - # -- Unfortunately LAMMPS itself does not understand molemlate syntax, so - # -- the atoms are identified by order in the list, not by name. (The "mW" - # -- refers to to an identifier in the system.in.sw file, not watmw.lt.) - # -- This command says that the first atom type corresponds to the "mW" - # -- atom in system.in.sw, and to ignore the remaining three atom types - # -- (correspond to the CH2, CH3, CH4 atom types defined in trappe1998.lt. - # -- We don't want to use the "sw" force field for interactions involving - # -- these atom types, so we put "NULL" there.) - # -- Note: For this to work, you should probably run moltemplate this way: - # -- moltemplate.sh -a "@atom:WatMW/mW 1" system.lt - # -- This assigns the atom type named @atom:WatMW/mW to 1 (the first atom) - } - - # -- optional -- - - write_once("In Settings") { - group WatMW type @atom:mW #(Atoms of this type belong to the "WatMW" group) - } - -} # WatMW diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/README_visualize.txt b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/README_visualize.txt index a3e3ed620e..e345be951d 100644 --- a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/README_visualize.txt +++ b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/README_visualize.txt @@ -60,8 +60,8 @@ d) Try entering these commands: It can help to shift the location of the periodic boundary box To shift the box in the y direction (for example) do this: - pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} - pbc box -shiftcenterrel {0.0 0.15 0.0} + pbc wrap -compound res -all -shiftcenterrel {-0.05 0.14 -0.05} + pbc box -shiftcenterrel {-0.05 0.14 -0.05} -width 0.5 -style tubes Distances are measured in units of box-length fractions, not Angstroms. diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/images/waterSPCE+Na+Cl_t=0.jpg b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/images/waterSPCE+Na+Cl_t=0.jpg index 2c34754c4c..bf00edc9c4 100644 Binary files a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/images/waterSPCE+Na+Cl_t=0.jpg and b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/images/waterSPCE+Na+Cl_t=0.jpg differ diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/images/waterSPCE+Na+Cl_t=100ps.jpg b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/images/waterSPCE+Na+Cl_t=100ps.jpg index 220a717271..af70c23997 100644 Binary files a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/images/waterSPCE+Na+Cl_t=100ps.jpg and b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/images/waterSPCE+Na+Cl_t=100ps.jpg differ diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/moltemplate_files/ions.lt b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/moltemplate_files/ions.lt index 8d36341253..ff52a7db97 100644 --- a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/moltemplate_files/ions.lt +++ b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/moltemplate_files/ions.lt @@ -1,5 +1,57 @@ # We define two molecule classes to represent Na+ and Cl- ions, respectively. -# This may seem like overkill since they both only consist of one atom each. +# They both contain only one atom. + +# In moltemplate each molecule type is stored in a file whose format mimics the +# format of a LAMMPS "data" file, with "Atoms", "Bonds", and "Angles" sections. +# Once defined, these molecules may be copied and moved to build larger systems. + + +NaIon { + + # ---- Definition of "NaIon" ---- + + # AtomID MolID AtomType charge X Y Z + write("Data Atoms") { + $atom:Na $mol @atom:Na 1.0 0.00000 0.00000 0.000000 + } + + write_once("Data Masses") { + @atom:Na 22.9898 + } + + write_once("In Settings") { + pair_coeff @atom:Na @atom:Na 0.3526418 1.079769246386 + } + # (explanation: http://lammps.sandia.gov/doc/pair_charmm.html) + +} # NaIon + + + + +ClIon { + + # ---- Definition of "ClIon" ---- + + # AtomID MolID AtomType charge X Y Z + write("Data Atoms") { + $atom:Cl $mol @atom:Cl -1.0 0.00000 0.00000 0.000000 + } + + write_once("Data Masses") { + @atom:Cl 35.453 + } + + write_once("In Settings") { + pair_coeff @atom:Cl @atom:Cl 0.0127850 2.711 + } + # (explanation: http://lammps.sandia.gov/doc/pair_charmm.html) + +} # ClIon + + + + # Note: Monovalent ion parameters for Ewald and SPC/E water @@ -7,61 +59,10 @@ # These Lennard Jones parameters match the parameters for ions # in SPC/E water in the "frcmod.ionsjc_spce" file distributed # with Amber (the 2010 version). - - -NaIon { - - # The epsilong & sigma parameters from that paper were 0.3526418 & 1.212. - # However sigma must be divided by 2^(1/6), because they use the alternate - # Lennard-Jones convention: U(r)=epsilon*((s/r)^12 - 2*(s/r)^6), and - # pair_style lj/charmm/coul/long uses U(r)=4*epsilon*((s/r)^12 - (s/r)^6) - # (Note: This change does not effect the epsilon parameter.) - - write_once("In Settings") { - pair_coeff @atom:Na @atom:Na lj/charmm/coul/long 0.3526418 1.079769246386 - } - - write_once("Data Masses") { - @atom:Na 22.9898 - } - - # assumes "full" atom style - write("Data Atoms") { - $atom:Na $mol @atom:Na 1.0 0.00000 0.00000 0.000000 - } -} # NaIon - - -ClIon { - write_once("In Settings") { - pair_coeff @atom:Cl @atom:Cl lj/charmm/coul/long 0.0127850 2.711 - } - - write_once("Data Masses") { - @atom:Cl 35.453 - } - - # assumes "full" atom style - write("Data Atoms") { - $atom:Cl $mol @atom:Cl -1.0 0.00000 0.00000 0.000000 - } -} # ClIon - - -write_once("In Init") { - # -- Default styles for ions -- - units real - atom_style full - # (Hybrid force fields were not necessary but are used for portability.) - pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0 - kspace_style pppm 0.0001 - pair_modify mix arithmetic -} - -# Optional: Define a group named "ions" consisting of either Na or Cl ions. -write_once("In Settings") { - group ionNa type @atom:NaIon/Na @atom:NaIon/Na - group ionCl type @atom:ClIon/Cl @atom:ClIon/Cl - group ions type @atom:NaIon/Na @atom:ClIon/Cl -} +# +# The epsilong & sigma parameters from that paper were 0.3526418 & 1.212. +# However sigma must be divided by 2^(1/6), because they use the alternate +# Lennard-Jones convention: U(r)=epsilon*((s/r)^12 - 2*(s/r)^6), and +# pair_style lj/charmm/coul/long uses U(r)=4*epsilon*((s/r)^12 - (s/r)^6) +# (Note: This change does not effect the epsilon parameter.) diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/moltemplate_files/spce.lt b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/moltemplate_files/spce.lt index 019911c19b..db5e7df3b3 100644 --- a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/moltemplate_files/spce.lt +++ b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/moltemplate_files/spce.lt @@ -1,51 +1,113 @@ +# In moltemplate each molecule type is stored in a file whose format mimics the +# format of a LAMMPS "data" file, with "Atoms", "Bonds", and "Angles" sections. +# Once defined, these molecules can be copied and moved to build larger systems. +# +# "SPCE" ("extended simple point charge") is one of several popular water models +# (See Berendsen H.J.C et al., J.Phys.Chem. Vol91 pp.6269-6271,1987 for details) +# # file "spce.lt" # # H1 H2 # \ / # O + SPCE { - write_once("In Init") { - # -- Default styles (for solo "SPCE" water) -- - units real - atom_style full - # (Hybrid force fields were not necessary but are used for portability.) - pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0 - bond_style hybrid harmonic - angle_style hybrid harmonic - kspace_style pppm 0.0001 - pair_modify mix arithmetic - } + # ---- Definition of the "SPCE" (water molecule type) ---- + + # The "Data Atoms" section is a list of atom attributes (type, charge, x,y,z) + # AtomID MoleculeID AtomType Charge X Y Z write("Data Atoms") { - $atom:O $mol:. @atom:O -0.8476 0.0000000 0.00000 0.000000 - $atom:H1 $mol:. @atom:H 0.4238 0.8164904 0.00000 0.5773590 - $atom:H2 $mol:. @atom:H 0.4238 -0.8164904 0.00000 0.5773590 + $atom:o $mol @atom:O -0.8476 0.0000000 0.00000 0.000000 + $atom:h1 $mol @atom:H 0.4238 0.8164904 0.00000 0.5773590 + $atom:h2 $mol @atom:H 0.4238 -0.8164904 0.00000 0.5773590 } + # Note: LAMMPS expects an integer in the 2nd column (the Molecule-ID number). + # If we put "$mol" there, moltemplate will generate this integer for you + + # A list of the bonds in the molecule: + # BondID BondType AtomID1 AtomID2 + + write("Data Bonds") { + $bond:OH1 @bond:OH $atom:o $atom:h1 + $bond:OH2 @bond:OH $atom:o $atom:h2 + } + + # A list of the angles in the molecule: + # AngleID AngleType AtomID1 AtomID2 AtomID3 + + write("Data Angles") { + $angle:HOH @angle:HOH $atom:h1 $atom:o $atom:h2 + } + + # The mass of each atom type: write_once("Data Masses") { @atom:O 15.9994 @atom:H 1.008 } - write("Data Bonds") { - $bond:OH1 @bond:OH $atom:O $atom:H1 - $bond:OH2 @bond:OH $atom:O $atom:H2 - } - write("Data Angles") { - $angle:HOH @angle:HOH $atom:H1 $atom:O $atom:H2 - } + # ---- Where to put force field parameters? ---- + # Moltemplate allows you to specify force-field parameters anywhere you want. + # Sometimes it is convenient to nest them within a molecule's definition. + # For more complicated simulations, it's convenient to define a "ForceField" + # object containing force field parameters shared by many different types of + # molecules. (Since this is a simple example, there is no need to do that.) + + # The "In Settings" section contains LAMMPS commands which typically define + # force-field parameters (eg "pair_coeff") and constraints (eg "fix shake") write_once("In Settings") { - bond_coeff @bond:OH harmonic 1000.0 1.0 - angle_coeff @angle:HOH harmonic 1000.0 109.47 - pair_coeff @atom:O @atom:O lj/charmm/coul/long 0.1553 3.166 - pair_coeff @atom:H @atom:H lj/charmm/coul/long 0.0 2.058 - group spce type @atom:O @atom:H - fix fShakeSPCE spce shake 0.0001 10 100 b @bond:OH a @angle:HOH - # (Remember to "unfix" fShakeSPCE during minimization.) + bond_coeff @bond:OH 1000.0 1.0 + # explanation: http://lammps.sandia.gov/doc/bond_harmonic.html + + angle_coeff @angle:HOH 1000.0 109.47 + # explanation: http://lammps.sandia.gov/doc/angle_harmonic.html + + pair_coeff @atom:O @atom:O 0.1553 3.166 + pair_coeff @atom:H @atom:H 0.0 2.058 + # explanation: http://lammps.sandia.gov/doc/pair_charmm.html + + # OPTIONAL: We want the water molecules to behave like rigid objects, so + # we apply the "SHAKE" constraint to the group of atoms in water molecules. + # (SHAKE is used to make bonds and angles rigid.) + + group gSPCE type @atom:O @atom:H + # explanation: http://lammps.sandia.gov/doc/group.html + + fix fShakeSPCE gSPCE shake 0.0001 10 100 b @bond:OH a @angle:HOH + # explanation: http://lammps.sandia.gov/doc/fix_shake.html + # (Remember to "unfix" fSHAKE during minimization.) + + } + + # LAMMPS requires that some commands must be issued in a certain order. + # (IE. You must inform LAMMPS the kind of simulation you wish to run + # before supplying LAMMPS with numeric parameters for that simulation.) + # The "In Init" section is where you put commands which must be run before + # all other commands in the simulation (such as the commands in "In Settings") + + write_once("In Init") { + + units real + # explanation: http://lammps.sandia.gov/doc/units.html + + # Specify the attributes of the particles in our system (eg. "full") + atom_style full + # explanation: http://lammps.sandia.gov/doc/atom_style.html + + # Specify the kinds of formulas we want to use to calculate + # the forces in our system (ie. force-field "styles") + bond_style harmonic + angle_style harmonic + pair_style lj/charmm/coul/long 9.0 10.0 10.0 + pair_modify mix arithmetic + # explanation: http://lammps.sandia.gov/doc/pair_modify.html + kspace_style pppm 0.0001 + # explanation: http://lammps.sandia.gov/doc/kspace_style.html } } # end of definition of "SPCE" water molecule type diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/moltemplate_files/system.lt b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/moltemplate_files/system.lt index af38795022..284d042d73 100644 --- a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/moltemplate_files/system.lt +++ b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/moltemplate_files/system.lt @@ -1,6 +1,4 @@ -import "spce.lt" # <- This defines the SPCE water molecule. This file is - # located in the "force_fields" subdirectory - # distributed with moltemplate +import "spce.lt" # <- This defines the SPCE water molecule. import "ions.lt" # <- This defines the ions "NaIon" and "ClIon". @@ -16,8 +14,8 @@ write_once("Data Boundary") { # spacing 3.45 Angstroms. (The pressure must be equilibrated later.) wat = new SPCE [10].move(0.00, 0.00, 3.45) - [10].move(0.00, 3.45, 0.00) - [10].move(3.45, 0.00, 0.00) + [10].move(0.00, 3.45, 0.01) + [10].move(3.45, 0.01, 0.01) # We now create a 2x2x2 lattice of Na+ and Cl- ions: @@ -30,14 +28,16 @@ cl = new ClIon [2].move(0,0,17.25) [2].move(0,17.25,0) [2].move(17.25,0,0) -na[*][*][*].move(5.175,5.175,5.6) -cl[*][*][*].move(12.075,12.075,12.5) +na[*][*][*].move(5,5,5) +cl[*][*][*].move(12,12,12) -# (The (5.175,5.175,5.175) and (12.075,12.075,12.075) translational shifts +# (The (5,5,5) and (12,12,12) translational shifts # prevent the Na and Cl ions from overlapping # with the water molecules or each other.) + + # Comment: Fortunately the ions and the water in this example share the # same force-field styles (so their was no need to use "hybrid" styles). # If this were not the case, you might need to add something like this. diff --git a/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/README.txt b/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/README.txt new file mode 100644 index 0000000000..b2996dab29 --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/README.txt @@ -0,0 +1,11 @@ +This is an example of all-atom methanol immersed in coarse grained ELBA water. +It was provided by Oscar Matus Rivas at McGill University. + + +References: +1. Orsi, Mario, Wei Ding, and Michail Palaiokostas. "Direct mixing of atomistic solutes and coarse-grained water." Journal of chemical theory and computation 10.10 (2014): 4684-4693. + +2. Orsi, Mario. "Comparative assessment of the ELBA coarse-grained model for water." Molecular Physics 112.11 (2014): 1566-1576. + +3. ELBA coarse-grained water model tutorial: +https://github.com/orsim/elba-lammps/tree/master/examples/water-bulk diff --git a/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/README_run.sh b/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/README_run.sh new file mode 100644 index 0000000000..91e79124e1 --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/README_run.sh @@ -0,0 +1,20 @@ +# --- Running LAMMPS --- +# +# The file "run.in.npt" is a LAMMPS +# input script which link to the input scripts and data files +# you hopefully have created earlier with moltemplate.sh: +# system.in.init, system.in.settings, system.data +# If not, carry out the instructions in "README_setup.sh". +# +# -- Instructions: -- +# If "lmp_mpi" is the name of the command you use to invoke lammps, +# then you would run lammps on these files this way: + +lmp_mpi -i run.in.npt # simulation at constant pressure + +# (Note: The "lmp_mpi" program is also frequently called "lmp_ubuntu", +# and has many other names depending upon how it was compiled.) + +# If you have compiled the MPI version of lammps, you can run lammps in parallel +#mpirun -np 4 lmp_mpi -i run.in.npt +# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/README_setup.sh b/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/README_setup.sh new file mode 100755 index 0000000000..20d5eac231 --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/README_setup.sh @@ -0,0 +1,28 @@ + +# Create the coordinates of the atoms using PACKMOL +cd packmol_files + + packmol < input.packmol + mv -f system.xyz ../moltemplate_files/ + +cd .. + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + moltemplate.sh -atomstyle "hybrid sphere dipole molecular" \ + -xyz system.xyz system.lt + + + # This will generate various files with names ending in *.in* and *.data. + # Move them to the directory where you plan to run LAMMPS (in this case "../") + mv -f system.data system.in* ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ system.xyz + +cd ../ + diff --git a/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/images/ELBAwater+methanol_rendered_with_ovito.jpg b/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/images/ELBAwater+methanol_rendered_with_ovito.jpg new file mode 100644 index 0000000000..88773055a1 Binary files /dev/null and b/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/images/ELBAwater+methanol_rendered_with_ovito.jpg differ diff --git a/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/moltemplate_files/elba.lt b/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/moltemplate_files/elba.lt new file mode 100644 index 0000000000..e5a35fbfd9 --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/moltemplate_files/elba.lt @@ -0,0 +1,39 @@ + +ElbaFF { + + write_once("Data Masses") { + @atom:W 18.0153 # Water + } + + write_once("In Settings") { + pair_coeff @atom:W @atom:W lj/sf/dipole/sf 0.55 3.05 + } + + # select the LAMMPS force field styles and other settings we will need + write_once("In Init") { + units real + atom_style hybrid sphere dipole molecular + bond_style hybrid harmonic + angle_style hybrid harmonic + dihedral_style hybrid harmonic + pair_style hybrid lj/sf/dipole/sf 12.0 lj/charmm/coul/long 11.0 12.0 + kspace_style pppm/cg 1.0e-5 + pair_modify mix arithmetic + special_bonds amber + } + +} # end of definition of "ElbaFF" + + +ElbaWater inherits ElbaFF { + + # atom-ID atom-Type x y z diameter density q mux muy muz molecule-ID + write("Data Atoms") { + $atom:id1 @atom:W 0.0 0.0 0.0 4.080749 0.5063179 0.0 0.541 0.0 0.0 $mol:. + } + + write_once("In Settings") { + group gElbaWater type @atom:W + } + +} # end of definition of "ElbaWater" diff --git a/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/moltemplate_files/methanol.lt b/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/moltemplate_files/methanol.lt new file mode 100644 index 0000000000..1d556ab13b --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/moltemplate_files/methanol.lt @@ -0,0 +1,84 @@ +# This version of the methanol molecule uses the GAFF force +# field. (BCC) Charges were assigned using AmberTools + +Methanol { + + write_once("In Settings") { + pair_coeff @atom:type1 @atom:type1 lj/charmm/coul/long 0.2104000002486992 3.066473387458142 0.2104000002486992 3.066473387458142 + pair_coeff @atom:type2 @atom:type2 lj/charmm/coul/long 0.10939999991572773 3.399669508450741 0.10939999991572773 3.399669508450741 + pair_coeff @atom:type3 @atom:type3 lj/charmm/coul/long 0.01570000009846142 2.4713530426421655 0.01570000009846142 2.4713530426421655 + pair_coeff @atom:type4 @atom:type4 lj/charmm/coul/long 0.0 0.0 0.0 0.0 + } + + write_once("In Settings") { + bond_coeff @bond:type1 harmonic 316.7 1.4233 + bond_coeff @bond:type2 harmonic 371.4 0.973 + bond_coeff @bond:type3 harmonic 330.6 1.0969 + } + + write_once("In Settings") { + angle_coeff @angle:type1 harmonic 50.93 110.260047369346 + angle_coeff @angle:type2 harmonic 47.38 107.26004608361897 + angle_coeff @angle:type3 harmonic 39.24 108.46004659790978 + } + + write_once("In Settings") { + dihedral_coeff @dihedral:type1 harmonic 0.166666667 1 3 + } + + + ### DATA sections + + + write_once("Data Masses") { + @atom:type1 16.0 + @atom:type2 12.01 + @atom:type3 1.008 + @atom:type4 1.008 + } + + + # NOTE: This molecule uses atom_style hybrid sphere dipole molecular + # (This is the same atom_style used by ELBA.) Hence the extra + # columns for "diam", "mux", "muy", "muz" are not relevant + # for this molecule and can be ignored. + + write("Data Atoms") { + # atom-ID atom-Type x y z diam dens q mux muy muz molecule-ID + $atom:id1 @atom:type1 0.708 0.0 0.0 0.0 16.0 -0.598800 0.0 0.0 0.0 $mol:id0 + $atom:id2 @atom:type2 -0.708 0.0 0.0 0.0 12.01 0.116700 0.0 0.0 0.0 $mol:id0 + $atom:id3 @atom:type3 -1.073 -0.769 0.685 0.0 1.008 0.028700 0.0 0.0 0.0 $mol:id0 + $atom:id4 @atom:type3 -1.073 -0.195 -1.011 0.0 1.008 0.028700 0.0 0.0 0.0 $mol:id0 + $atom:id5 @atom:type3 -1.063 0.979 0.331 0.0 1.008 0.028700 0.0 0.0 0.0 $mol:id0 + $atom:id6 @atom:type4 0.994 -0.88 -0.298 0.0 1.008 0.396000 0.0 0.0 0.0 $mol:id0 + } + + write("Data Bonds") { + $bond:id1 @bond:type2 $atom:id1 $atom:id6 + $bond:id2 @bond:type3 $atom:id2 $atom:id3 + $bond:id3 @bond:type3 $atom:id2 $atom:id4 + $bond:id4 @bond:type3 $atom:id2 $atom:id5 + $bond:id5 @bond:type1 $atom:id1 $atom:id2 + } + + write("Data Angles") { + $angle:id1 @angle:type1 $atom:id1 $atom:id2 $atom:id3 + $angle:id2 @angle:type1 $atom:id1 $atom:id2 $atom:id4 + $angle:id3 @angle:type1 $atom:id1 $atom:id2 $atom:id5 + $angle:id4 @angle:type2 $atom:id2 $atom:id1 $atom:id6 + $angle:id5 @angle:type3 $atom:id3 $atom:id2 $atom:id4 + $angle:id6 @angle:type3 $atom:id3 $atom:id2 $atom:id5 + $angle:id7 @angle:type3 $atom:id4 $atom:id2 $atom:id5 + } + + write("Data Dihedrals") { + $dihedral:id1 @dihedral:type1 $atom:id6 $atom:id1 $atom:id2 $atom:id3 + $dihedral:id2 @dihedral:type1 $atom:id6 $atom:id1 $atom:id2 $atom:id4 + $dihedral:id3 @dihedral:type1 $atom:id6 $atom:id1 $atom:id2 $atom:id5 + } + + write_once("In Settings") { + group gMethanol type @atom:type1 @atom:type2 @atom:type3 @atom:type4 + } + +} # end of "Methanol" type definition diff --git a/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/moltemplate_files/system.lt b/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/moltemplate_files/system.lt new file mode 100644 index 0000000000..1a077a92f1 --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/moltemplate_files/system.lt @@ -0,0 +1,29 @@ +import "methanol.lt" + +import "elba.lt" + +write_once("Data Boundary") { + -15.5 15.5 xlo xhi + -15.5 15.5 ylo yhi + -15.5 15.5 zlo zhi +} + +solute = new Methanol [1] + +solvent = new ElbaWater [1000] + +# Lorentz-Berthelot mixing +write_once("In Settings") { + pair_coeff @atom:Methanol/type1 @atom:Methanol/type2 lj/charmm/coul/long 0.151716 3.233071 0.151716 3.233071 + pair_coeff @atom:Methanol/type1 @atom:Methanol/type3 lj/charmm/coul/long 0.057474 2.768913 0.057474 2.768913 + pair_coeff @atom:Methanol/type1 @atom:Methanol/type4 lj/charmm/coul/long 0.000000 1.533237 0.000000 1.533237 + pair_coeff @atom:Methanol/type1 @atom:ElbaFF/W lj/sf/dipole/sf 0.340176 3.058237 + pair_coeff @atom:Methanol/type2 @atom:Methanol/type3 lj/charmm/coul/long 0.041444 2.935511 0.041444 2.935511 + pair_coeff @atom:Methanol/type2 @atom:Methanol/type4 lj/charmm/coul/long 0.000000 1.699835 0.000000 1.699835 + pair_coeff @atom:Methanol/type2 @atom:ElbaFF/W lj/sf/dipole/sf 0.245296 3.224835 + pair_coeff @atom:Methanol/type3 @atom:Methanol/type4 lj/charmm/coul/long 0.000000 1.235677 0.000000 1.235677 + pair_coeff @atom:Methanol/type3 @atom:ElbaFF/W lj/sf/dipole/sf 0.092925 2.760677 + pair_coeff @atom:Methanol/type4 @atom:ElbaFF/W lj/sf/dipole/sf 0.000000 1.525000 +} + +} diff --git a/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/packmol_files/README.txt b/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/packmol_files/README.txt new file mode 100644 index 0000000000..3d310d44d3 --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/packmol_files/README.txt @@ -0,0 +1,12 @@ +Packmol is a program that generates non-overlapping atomic coordinates for +mixtures of molecules. + +Usage: + + packmol < input.packmol + +Ouput: + + system.xyz + +(a file containing the coordinates of all of the molecules packed together.) diff --git a/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/packmol_files/coord.xyz b/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/packmol_files/coord.xyz new file mode 100644 index 0000000000..fc495c0564 --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/packmol_files/coord.xyz @@ -0,0 +1,1008 @@ + 1006 + Built with Packmol + O 1.077217 0.144250 0.048817 + C -0.338583 0.144250 0.048817 + H -0.703883 -0.624750 0.734017 + H -0.703783 -0.050450 -0.962483 + H -0.693883 1.122850 0.380017 + H 1.362917 -0.736150 -0.249183 + OW -1.412297 -7.446504 10.904602 + OW 4.452292 7.235571 -6.250955 + OW -6.020558 -4.280954 1.868432 + OW -5.179618 11.632347 -13.999700 + OW 3.301355 8.558586 5.180801 + OW -12.174570 -4.025488 11.826522 + OW -12.212121 7.659684 7.004107 + OW 12.507397 4.123302 -9.139812 + OW -4.390714 -13.339157 -13.935723 + OW -2.347127 -13.464377 -11.186378 + OW -0.390430 -4.494023 -0.873365 + OW 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-5.121617 + OW 11.791809 -5.933214 7.596812 + OW 7.815492 1.001428 -9.412914 + OW -13.535245 -11.141362 0.465505 diff --git a/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/packmol_files/elba_water.xyz b/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/packmol_files/elba_water.xyz new file mode 100644 index 0000000000..3ed22d1fad --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/packmol_files/elba_water.xyz @@ -0,0 +1,4 @@ +1 + + OW 0.000000 0.000000 0.000000 + diff --git a/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/packmol_files/input.packmol b/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/packmol_files/input.packmol new file mode 100644 index 0000000000..9c640263d9 --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/packmol_files/input.packmol @@ -0,0 +1,17 @@ +tolerance 2.5 +filetype xyz +output system.xyz + +# Methanol +structure methanol.xyz + number 1 + center + fixed 0. 0. 0. 0. 0. 0. +end structure + +# ELBA Solvent +structure elba_water.xyz + number 1000 + inside box -14.0 -14.0 -14.0 14.0 14.0 14.0 +end structure + diff --git a/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/packmol_files/methanol.xyz b/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/packmol_files/methanol.xyz new file mode 100644 index 0000000000..b06d93fa5f --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/packmol_files/methanol.xyz @@ -0,0 +1,8 @@ +6 + +O 0.70790 0.00000 0.00000 +C -0.70790 0.00000 0.00000 +H -1.07320 -0.76900 0.68520 +H -1.07310 -0.19470 -1.01130 +H -1.06320 0.97860 0.33120 +H 0.99360 -0.88040 -0.29800 diff --git a/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/run.in.npt b/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/run.in.npt new file mode 100644 index 0000000000..ad8076d7fd --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/run.in.npt @@ -0,0 +1,54 @@ +# PREREQUISITES: +# +# You must use moltemplate.sh (& packmol?) to create 3 files: +# system.data system.in.init system.in.settings +# +# See "README_setup.sh" for instructions how to use moltemplate.sh +# Note: This input script file only covers equilibration of the system. +# +# ------------------------------- Initialization Section -------------------- + +include "system.in.init" + +# ------------------------------- Atom Definition Section ------------------- + +read_data "system.data" + +# ------------------------------- Settings Section -------------------------- + +include "system.in.settings" + +# ------------------------------- Run Section ------------------------------- + +# -- simulation protocol -- + +# (Groups "gElbaWater" and "gMethanol" are defined in "system.in.settings" +# Rename them to "gSolvent" and "gSolute") +group gSolvent union gElbaWater gElbaWater +group gSolute union gMethanol gMethanol + +# Randomize the direction of the solvent dipoles +set group gSolvent dipole/random 9876 0.541 + +velocity all create 298.0 9876 + +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +timestep 2.0 + +fix 1 gSolute nve # integrate gSolute +fix 2 gSolvent nve/sphere update dipole # integrate gSolvent +fix 3 gSolute langevin 298.0 298.0 1000 9876 # thermostat gSolute +fix 4 gSolvent langevin 298.0 298.0 1000 9876 omega yes zero yes # thermostat gSolvent +fix 5 all press/berendsen iso 1.0 1.0 1000 modulus 21740 # barostat +fix 6 all momentum 500 linear 1 1 1 +fix 7 gSolute shake 1.0e-6 100 0 m 1.0 + +dump 1 all custom 1000 traj_nvt.lammpstrj id mol type x y z mux muy muz ix iy iz + +thermo_style custom step temp etotal pe epair press +thermo_modify norm yes flush yes +thermo 100 + +run 10000 diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/DOPC_bilayer_example/packmol_files/README.txt b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/DOPC_bilayer_example/packmol_files/README.txt new file mode 100644 index 0000000000..c61369a225 --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/DOPC_bilayer_example/packmol_files/README.txt @@ -0,0 +1,8 @@ +You can use packmol to create a file containing the atomic coordinates +for a system of coarse-grained lipids mixed with water using this command: + +If it takes too long for packmol to run, try lowering the tolerance. +(tolerance 2.0 should work) + +packmol < mix_lipids+water.inp + diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/DOPC_bilayer_example/packmol_files/dopc.xyz b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/DOPC_bilayer_example/packmol_files/dopc.xyz new file mode 100644 index 0000000000..7caffdc159 --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/DOPC_bilayer_example/packmol_files/dopc.xyz @@ -0,0 +1,14 @@ +12 + DOPC +Q0 0.596 0.518 2.453 +Qa 0.413 0.591 2.167 +Na 0.525 0.626 1.829 +Na 0.749 0.434 1.795 +C1 0.428 0.686 1.448 +C3 0.395 0.491 1.197 +C1 0.389 0.575 0.899 +C1 0.423 0.497 0.555 +C1 0.944 0.505 1.503 +C3 0.906 0.476 1.192 +C1 0.899 0.567 0.905 +C1 0.921 0.637 0.557 diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/DOPC_bilayer_example/packmol_files/mix_lipids+water.inp b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/DOPC_bilayer_example/packmol_files/mix_lipids+water.inp new file mode 100644 index 0000000000..9e1388a137 --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/DOPC_bilayer_example/packmol_files/mix_lipids+water.inp @@ -0,0 +1,35 @@ +# +# A mixture of coarse-grained (martini) DPPC (lipid) and water. +# + +# All the atoms from diferent molecules will be separated at least 3.0 +# Anstroms at the solution. + +tolerance 3.0 # minimal distance between atoms in different molecules + # (you should also consider changing the "discale" + # parameter. I think discale=1.0 by default.) + +seed 12345 # seed for random number generator + +# The file type of input and output files is XYZ + +filetype xyz + +# The name of the output file + +output system.xyz + +# DPPC (lipid) molecules and water molecules will be put in a box +# defined by the minimum coordinates x, y and z = 0 0 0. and maximum +# coordinates 100 100 100. (Box size: 100x100x100) + +structure dopc.xyz + number 300 + inside box 0.0 0.0 0.0 100.0 100.0 100.0 +end structure + +structure water.xyz + number 6000 + inside box 0.0 0.0 0.0 100.0 100.0 100.0 +end structure + diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/DOPC_bilayer_example/packmol_files/water.xyz b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/DOPC_bilayer_example/packmol_files/water.xyz new file mode 100644 index 0000000000..84fe1f74c2 --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/DOPC_bilayer_example/packmol_files/water.xyz @@ -0,0 +1,3 @@ +1 + water +W 0 0 0 diff --git a/tools/moltemplate/examples/coarse_grained/abstract_2bead_heteropolymer/moltemplate_files/forcefield.lt b/tools/moltemplate/examples/coarse_grained/abstract_2bead_heteropolymer/moltemplate_files/forcefield.lt index aad330df20..e177c136e3 100644 --- a/tools/moltemplate/examples/coarse_grained/abstract_2bead_heteropolymer/moltemplate_files/forcefield.lt +++ b/tools/moltemplate/examples/coarse_grained/abstract_2bead_heteropolymer/moltemplate_files/forcefield.lt @@ -1,8 +1,11 @@ -# The "HPForceField" is a force-field environment object containing -# force-field data, atomic masses, and bond rules. -# Later, when we define molecules (such as "H" and "P"), we can inherit -# atom types and bond-rules from this force-field. This will automatically -# assign bonds and angular interactions according to atom (and bond) type. +# Define a "ForceField" object. +# A force field in moltemplate is any object containing mostly pair_coeff, +# bond_coeff, angle_coeff, dihedral_coeff, "Bonds By Type", "Angles By Type", +# "Dihedrals By Type", "Impropers By Type", "Data Masses" (and "In Charges") +# information. Later, when we define molecules (such as "H" and "P"), we can +# borrow these atom types, bond-rules and force field parameters. This way, +# bonds and angular interactions are generated automatically according to +# atom (and bond) type. # (You can also assign charge by atom type. However in this example I assigned # charge to each atom manually (not by type). The OPLSAA examples in the # "all_atoms" directory demonstrate how to assign charge by atom type.) @@ -11,6 +14,31 @@ HPForceField { + # LAMMPS supports a large number of "styles" (ie. equations for calculating + # forces between particles). At some point, we must eventually select the + # formulas we want to use. This can be done anywhere, but we might as + # well specify that now. Later on we will specify the parameters + # which go into these equations. + + write_once("In Init") { + units real + atom_style full + bond_style harmonic + angle_style harmonic + dihedral_style charmm + pair_style lj/cut 11.0 + + # If charges are needed, (assuming biopolymers), try one of: + #dielectric 80.0 + #pair_style lj/cut/coul/debye 0.1 11.0 + # or (for short distances, below a couple nm) + #pair_style lj/charmm/coul/charmm/implicit 9.0 11.0 + + pair_modify mix arithmetic + special_bonds lj 0.0 0.0 0.0 + } + + # There are 3 atom types: write_once("Data Masses") { @@ -22,16 +50,17 @@ HPForceField { # 2-body (non-bonded) interactions: # # Uij(r) = 4*eps_ij * ( (sig_ij/r)^12 - (sig_ij/r)^6 ) + # (for details see http://lammps.sandia.gov/doc/pair_lj.html) # # Hydrophobic side-chain (R) atoms are attractive (large epsilon parameter). # Polar side-chains and backbone atoms are not attractive (small epsilon). # - # i j pairstylename eps sig + # i j eps sig # write_once("In Settings") { - pair_coeff @atom:CA @atom:CA lj/cut 0.10 2.0 - pair_coeff @atom:HR @atom:HR lj/cut 2.50 3.6 - pair_coeff @atom:PR @atom:PR lj/cut 0.10 3.6 + pair_coeff @atom:CA @atom:CA 0.10 2.0 + pair_coeff @atom:HR @atom:HR 2.50 3.6 + pair_coeff @atom:PR @atom:PR 0.10 3.6 } # (By default, interactions between different AtomTypes use "arithmetic"rules: @@ -50,15 +79,16 @@ HPForceField { # 2-body (bonded) interactions: # # Ubond(r) = (k/2)*(r-0)^2 + # (for details see http://lammps.sandia.gov/doc/bond_harmonic.html) # # The corresponding command is: # - # bond_coeff bondType bondstylename k r0 + # bond_coeff bondType k r0 # write_once("In Settings") { - bond_coeff @bond:Sidechain harmonic 30.0 3.4 - bond_coeff @bond:Backbone harmonic 30.0 3.7 + bond_coeff @bond:Sidechain 30.0 3.4 + bond_coeff @bond:Backbone 30.0 3.7 } @@ -83,14 +113,15 @@ HPForceField { # # Uangle(theta) = (k/2)*(theta-theta0)^2 # (k in kcal/mol/rad^2, theta0 in degrees) + # (for details see http://lammps.sandia.gov/doc/angle_harmonic.html) # # The corresponding command is: # - # angle_coeff angleType anglestylename k theta0 + # angle_coeff angleType k theta0 write_once("In Settings") { - angle_coeff @angle:Backbone harmonic 30.00 114 - angle_coeff @angle:Sidechain harmonic 30.00 123 + angle_coeff @angle:Backbone 30.00 114 + angle_coeff @angle:Sidechain 30.00 123 } @@ -100,40 +131,16 @@ HPForceField { # Udihedral(phi) = K * (1 + cos(n*phi - d)) # # The d parameter is in degrees, K is in kcal/mol/rad^2. + # (for details, see http://lammps.sandia.gov/doc/dihedral_charmm.html) # # The corresponding command is - # dihedral_coeff dihedralType dihedralstylename K n d w (ignore "w") + # dihedral_coeff dihedralType K n d w (ignore "w") write_once("In Settings") { - dihedral_coeff @dihedral:CCCC charmm -0.5 1 -180 0.0 - dihedral_coeff @dihedral:RCCR charmm -1.5 1 -180 0.0 + dihedral_coeff @dihedral:CCCC -0.5 1 -180 0.0 + dihedral_coeff @dihedral:RCCR -1.5 1 -180 0.0 } # write_once("In Settings") - # LAMMPS supports a large number of force-field styles. We must select - # which ones we need. This information belongs in the "In Init" section. - # (Hybrid styles used for portability. These choices can be overridden later.) - - write_once("In Init") { - # -- Default styles for "2bead" -- - # (Hybrid force fields were not necessary but are used for portability.) - units real - atom_style full - bond_style hybrid harmonic - angle_style hybrid harmonic - dihedral_style hybrid charmm - pair_style hybrid lj/cut 11.0 - - # If charges are needed, (assuming biopolymers), try one of: - #dielectric 80.0 - #pair_style hybrid lj/cut/coul/debye 0.1 11.0 - # or (for short distances, below a couple nm) - #pair_style hybrid lj/charmm/coul/charmm/implicit 9.0 11.0 - - pair_modify mix arithmetic - special_bonds lj 0.0 0.0 0.0 - } - - } # HPForceField diff --git a/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/README.txt b/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/README.txt new file mode 100644 index 0000000000..eca0a1b7f4 --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/README.txt @@ -0,0 +1,17 @@ + +This directory contains an example of a couarse-grained (vaguely protein-like) +heteropolymer consisting of 14 residues, each of which has 2 atoms +(one backbone atom, one residue atom.) + +There are two types of residues, H and P. +The R-atom for the H residue are attracted to eachother. +All other atoms are repulsive. + +Instructions on how to build LAMMPS input files and +run a short simulation are provided in other README files. + +step 1) +README_setup.sh + +step2) +README_run.sh diff --git a/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/README_run.sh b/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/README_run.sh new file mode 100755 index 0000000000..8bf8e27648 --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/README_run.sh @@ -0,0 +1,20 @@ +# --- Running LAMMPS --- +# -- Prerequisites: -- +# The "run.in.nvt" file is a LAMMPS input script containing +# references to the input scripts and data files +# you hopefully have created earlier with moltemplate.sh: +# system.in.init, system.in.settings, system.data +# If not, carry out the instructions in "README_setup.sh". +# +# -- Instructions: -- +# If "lmp_mpi" is the name of the command you use to invoke lammps, +# then you would run lammps on these files this way: + + +lmp_mpi -i run.in.nvt + + + +# If you have compiled the MPI version of lammps, you can run lammps in parallel +#mpirun -np 4 lmp_mpi -i run.in.nvt +# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/README_setup.sh b/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/README_setup.sh new file mode 100755 index 0000000000..cf22ee0fa1 --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/README_setup.sh @@ -0,0 +1,23 @@ +# Use these commands to generate the LAMMPS input script and data file +# (and other auxilliary files): + + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + + moltemplate.sh system.lt + + # This will generate various files with names ending in *.in* and *.data. + # These files are the input files directly read by LAMMPS. Move them to + # the parent directory (or wherever you plan to run the simulation). + + mv -f system.in* system.data ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ diff --git a/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/README_visualize.txt b/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/README_visualize.txt new file mode 100644 index 0000000000..518df2c20a --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/README_visualize.txt @@ -0,0 +1,86 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + It can help to shift the location of the periodic boundary box + To shift the box in the y direction (for example) do this: + + pbc wrap -compound res -all -shiftcenterrel {-0.05 -0.15 -0.05} + pbc box -shiftcenterrel {-0.05 -0.15 -0.05} -width 1.6 -style tubes + + Distances are measured in units of box-length fractions, not Angstroms. + + Alternately if you have a solute whose atoms are all of type 1, + then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) + You should check if your periodic boundary conditions are too small. + To do that: + select Graphics->Representations menu option + click on the "Periodic" tab, and + click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. + +5) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/images/2bead_monomer.jpg b/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/images/2bead_monomer.jpg new file mode 100644 index 0000000000..35af99387e Binary files /dev/null and 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b/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/images/2bead_t=4850000_LR.jpg new file mode 100644 index 0000000000..18ca16001c Binary files /dev/null and b/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/images/2bead_t=4850000_LR.jpg differ diff --git a/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/moltemplate_files/README.sh b/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/moltemplate_files/README.sh new file mode 100755 index 0000000000..bcc5947b1f --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/moltemplate_files/README.sh @@ -0,0 +1,6 @@ +# Use these commands to generate the LAMMPS input script and data file +# (and other auxilliary files): +moltemplate.sh system.lt + +# This will generate various files with names ending in *.in* and *.data. + diff --git a/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/moltemplate_files/README.txt b/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/moltemplate_files/README.txt new file mode 100644 index 0000000000..3d9fdab320 --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/moltemplate_files/README.txt @@ -0,0 +1,19 @@ +# In this example, we construct a large molecule ("Polymer") +# from multiple smaller molecular subunits ("Monomer"). +# The "Monomer" molecule contains two atoms (type "CA", and "R") +# +# "Monomer" +# +# @R +# | +# @CA +# +# Eventually, we will connect multiple "Monomer" molecular subunits +# together to form a polymer, as shown below: +# +# @R @R +# | | +# _@CA_ _@CA_ +# ... -.@CA-' `-@CA-' ` ... +# | | +# @R @R diff --git a/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/moltemplate_files/forcefield.lt b/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/moltemplate_files/forcefield.lt new file mode 100644 index 0000000000..8dfdf98a41 --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/moltemplate_files/forcefield.lt @@ -0,0 +1,110 @@ + +# Define a "ForceField" object. +# A force field in moltemplate is any object containing mostly pair_coeff, +# bond_coeff, angle_coeff, dihedral_coeff, "Bonds By Type", "Angles By Type", +# "Dihedrals By Type", "Impropers By Type", "Data Masses" (and "In Charges") +# information. Later on when we define molecule objects, we can access all +# of the atom types and force field parameters here using "inherits ForceField". +# (See "monomer.lt" for example.) + + +ForceField { + + + # LAMMPS supports a large number of "styles" (ie. equations for calculating + # forces between particles). At some point, we must eventually select the + # formulas we want to use. This can be done anywhere, but we might as + # well specify that now. Later on we will specify the parameters + # which go into these equations. + + write_once("In Init") { + # -- Styles used in "ForceField" -- + # -- (Changing these styles will change the formulas above) -- + units real + atom_style full + bond_style harmonic + angle_style harmonic + dihedral_style charmm + pair_style lj/cut 11.0 + } + + + # There are 2 atom types: "CA" and "R" + write_once("Data Masses") { + @atom:CA 13.0 + @atom:R 50.0 + } + + # ---- 2-body (non-bonded) interactions: ---- + # U(r) = 4*epsilon((sigma/r)^12 - (sigma/r)^6) + # (for details see http://lammps.sandia.gov/doc/pair_lj.html) + # atom-type atom-type epsilon sigma + + write_once("In Settings") { + # Pairwise (non-bonded) interactions: + # atomType1 atomType2 epsilon sigma + pair_coeff @atom:CA @atom:CA 0.10 2.0 + pair_coeff @atom:R @atom:R 0.50 3.6 + # (Interactions between different atoms are determined by mixing rules.) + } + + # ---- 2-body (bonded) interactions: ---- + # + # Ubond(r) = k*(r-r0)^2 + # (for details see http://lammps.sandia.gov/doc/bond_harmonic.html) + # + write_once("In Settings") { + # bond-type k r0 + bond_coeff @bond:Sidechain 15.0 3.4 + bond_coeff @bond:Backbone 15.0 3.7 + } + + # ---- 3-body angle (hinge) interactions: ---- + + # Rules for determining 3-body (angle) interactions by atom & bond type: + # angle-type atomType1 atomType2 atomType3 bondType1 bondType2 + + write_once("Data Angles By Type") { + @angle:Backbone @atom:CA @atom:CA @atom:CA @bond:* @bond:* + @angle:Sidechain @atom:CA @atom:CA @atom:R @bond:* @bond:* + } + + # Force-field parameters for 3-body (angle) interactions: + # + # Uangle(theta) = k*(theta-theta0)^2 + # (for details see http://lammps.sandia.gov/doc/angle_harmonic.html) + # + write_once("In Settings") { + # angle-type k theta0 + angle_coeff @angle:Backbone 30.00 114 + angle_coeff @angle:Sidechain 30.00 132 + } + + # ---- 4-body dihedral interactions ---- + + # 4-body interactions in this example are listed by atomType + # Rules for determining 4-body (dihedral) interactions by atom & bond type: + write_once("Data Dihedrals By Type") { + # dihedralType atmType1 atmType2 atmType3 atmType4 bondType1 bType2 bType3 + @dihedral:CCCC @atom:CA @atom:CA @atom:CA @atom:CA @bond:* @bond:* @bond:* + @dihedral:RCCR @atom:R @atom:CA @atom:CA @atom:R @bond:* @bond:* @bond:* + } + + # The forumula used is: + # + # Udihedral(phi) = K * (1 + cos(n*phi - d)) + # + # The d parameter is in degrees, K is in kcal/mol/rad^2. + # (for details, see http://lammps.sandia.gov/doc/dihedral_charmm.html) + # + # The corresponding command is + # dihedral_coeff dihedralType K n d w(ignored) + + write_once("In Settings") { + dihedral_coeff @dihedral:CCCC -0.5 1 -180 0.0 + dihedral_coeff @dihedral:RCCR -1.5 1 -180 0.0 + } + +} # "ForceField" + + diff --git a/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/moltemplate_files/monomer.lt b/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/moltemplate_files/monomer.lt new file mode 100644 index 0000000000..286eb12ff4 --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/moltemplate_files/monomer.lt @@ -0,0 +1,20 @@ +import "forcefield.lt" # contains force-field parameters + +Monomer inherits ForceField { + + write("Data Atoms") { + # atomId molId atomType charge x y z + $atom:ca $mol:... @atom:CA 0.0 0.000 1.0000 0.0000000 + $atom:r $mol:... @atom:R 0.0 0.000 4.4000 0.0000000 + } + write("Data Bonds") { + # bond-id bond-type atom-id1 atom-id2 + $bond:cr @bond:Sidechain $atom:ca $atom:r + } +} + + + +# NOTE: The "..." in "$mol:..." tells moltemplate that this molecule is part +# of a larger molecule, and to use the larger parent object's +# molecule id number as it's own. diff --git a/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/moltemplate_files/polymer.lt b/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/moltemplate_files/polymer.lt new file mode 100644 index 0000000000..5ca8eb03e9 --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/moltemplate_files/polymer.lt @@ -0,0 +1,27 @@ +import "monomer.lt" # <-- defines "Monomer" and "ForceField" + +Polymer inherits ForceField { + + # The next line is optional + create_var {$mol} # force all monomers to share the same molecule-ID + + # Now create some monomers + + mon1 = new Monomer + mon2 = new Monomer.rot(180.0, 1,0,0).move(3.2,0,0) + mon3 = new Monomer.move(6.4,0,0) + mon4 = new Monomer.rot(180.0, 1,0,0).move(9.6,0,0) + mon5 = new Monomer.move(12.8,0,0) + mon6 = new Monomer.rot(180.0, 1,0,0).move(16.0,0,0) + mon7 = new Monomer.move(19.2,0,0) + + # Now, link the monomers together this way: + write("Data Bonds") { + $bond:backbone1 @bond:Backbone $atom:mon1/ca $atom:mon2/ca + $bond:backbone2 @bond:Backbone $atom:mon2/ca $atom:mon3/ca + $bond:backbone3 @bond:Backbone $atom:mon3/ca $atom:mon4/ca + $bond:backbone4 @bond:Backbone $atom:mon4/ca $atom:mon5/ca + $bond:backbone5 @bond:Backbone $atom:mon5/ca $atom:mon6/ca + $bond:backbone6 @bond:Backbone $atom:mon6/ca $atom:mon7/ca + } +} diff --git a/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/moltemplate_files/system.lt b/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/moltemplate_files/system.lt new file mode 100644 index 0000000000..480f8c0216 --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/moltemplate_files/system.lt @@ -0,0 +1,29 @@ +import "polymer.lt" + + +# Specify the periodic boundary conditions: +write_once("Data Boundary") { + 0 90.0 xlo xhi + 0 90.0 ylo yhi + 0 90.0 zlo zhi +} + +# Create 27 polymers in a rectangular grid + +polymers = new Polymer [3].move(0, 0, 30.0) + [3].move(0, 30.0, 0) + [3].move(30.0, 0, 0) + + + +# ------------ Optional: ------------ +# Now (for fun) shift some of the polymers +# in the x direction by a distance of 20.0 +# Suppose we want to move the middle slice +# (which has constant Z). We do that this way: +# polymers[1][*][*].move(20,0,0) +# more examples: +# polymers[*][1][*].move(0,0,20) +# polymers[*][*][1].move(0,20,0) + + diff --git a/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/run.in.nvt b/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/run.in.nvt new file mode 100644 index 0000000000..e9fdbf41fd --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/run.in.nvt @@ -0,0 +1,32 @@ +# -- Init Section -- + +include system.in.init + +# -- Atom Definition Section -- + +read_data system.data + +# -- Settings Section -- + +include system.in.settings + +# -- Run Section -- + + +timestep 2.0 +dump 1 all custom 5000 traj_nvt.lammpstrj id mol type x y z ix iy iz + +# To use Langevin dynamics in LAMMPS you need both "fix langevin" and "fix nve". +# (See http://lammps.sandia.gov/doc/fix_langevin.html for details.) + +fix fxlan all langevin 300.0 300.0 5000.0 48279 +fix fxnve all nve + + +thermo_style custom step temp pe etotal press vol epair ebond eangle edihed +thermo 1000 # time interval for printing out "thermo" data + +run 40000000 + +write_data system_after_nvt.data + diff --git a/tools/moltemplate/examples/coarse_grained/abstract_translocation/moltemplate_files/monomer.lt b/tools/moltemplate/examples/coarse_grained/abstract_translocation/moltemplate_files/monomer.lt index a8a35339f5..88c1f6e322 100644 --- a/tools/moltemplate/examples/coarse_grained/abstract_translocation/moltemplate_files/monomer.lt +++ b/tools/moltemplate/examples/coarse_grained/abstract_translocation/moltemplate_files/monomer.lt @@ -10,7 +10,10 @@ # ---------------------------------------------------------------------- -Monomer { +import "polymer_forcefield.lt" # contains force-field parameters + + +Monomer inherits ForceField { # atom-id mol-id atom-type charge x y z @@ -24,88 +27,14 @@ Monomer { # be a part of a larger molecule, and (if so) to use the larger # parent object's molecule id number as it's own - - # atom-type mass - - write_once("Data Masses") { - @atom:CA 13.0 - @atom:R 50.0 - } - - # atom-type atom-type epsilon sigma - - write_once("In Settings") { - pair_coeff @atom:CA @atom:CA 0.05 2.0 - pair_coeff @atom:R @atom:R 0.50 2.0 - } - # bond-id bond-type atom-id1 atom-id2 write("Data Bonds") { $bond:CR1 @bond:sidechain $atom:CA $atom:R1 $bond:CR2 @bond:sidechain $atom:CA $atom:R2 } - - write_once("In Settings") { - # bond-type k r0 - bond_coeff @bond:sidechain 30.0 1.2 - bond_coeff @bond:bb 30.0 2.0 # "bb" shorthand for "backbone" - } - - # For a compound molecule consisting of smaller building blocks (such as a - # polymer built from monomers), it is tedious to explicitly list all of the - # angles, dihedrals in the entire molecule. Instead, you can define rules - # for automatically generating all the angular interactions between bonded - # atoms according to their connectivity and the atom/bond type. - # Later, when you connect multiple monomers together to form a polymer, - # appropriate bond-angle forces will be applied to these atoms automatically - # (as well as dihedral and improper forces, if defined). - - # Rules for determining 3 and 4-body bonded interactions by type - - # angle-type atomType1 atomType2 atomType3 bondType1 bondType2 - - write_once("Data Angles By Type") { - @angle:backbone @atom:CA @atom:CA @atom:CA @bond:* @bond:* - @angle:sidechain @atom:CA @atom:CA @atom:R @bond:* @bond:* - @angle:RCR @atom:R @atom:CA @atom:R @bond:* @bond:* - } - - # ("@angle:RCR" defines the angle between the R-C-R atoms within a monomer. - # The other angular interactions are between atoms in neighboring monomers.) - - - # dihedral-type AtomType1 AtomType2 AtomType3 AtomType4 bondType1 btyp2 btyp3 - - write_once("Data Dihedrals By Type") { - @dihedral:backbn @atom:CA @atom:CA @atom:CA @atom:CA @bond:* @bond:* @bond:* - } - - # Parameters for these new angular interactions must be defined. (I recommend - # putting all force-field parameters (coeffs) in the "In Settings" section.) - - write_once("In Settings") { - # angle-type k theta0 - angle_coeff @angle:backbone 50.00 160 - angle_coeff @angle:sidechain 50.00 120 - angle_coeff @angle:RCR 50.00 120 - # dihedral-type K1 K2 K3 K4 - dihedral_coeff @dihedral:backbn 1.411036 -0.271016 3.145034 0.0 - } + # atom-type mass } # Monomer - - - - -# ------------------------------------------------------------------------- -# Heteropolymers: -# -# There is a similar example for heteropolymers which is distributed online -# bundled with the moltemplate software. It is named "2bead_heteropolymer", -# and it demonstrates how to share backbone (CA) atoms, bonds and angles -# (so that you don't have to define them seperately for each type of monomer). -# ------------------------------------------------------------------------- - diff --git a/tools/moltemplate/examples/coarse_grained/abstract_translocation/moltemplate_files/polymer.lt b/tools/moltemplate/examples/coarse_grained/abstract_translocation/moltemplate_files/polymer.lt index 31a36d07ce..5eae2abe29 100644 --- a/tools/moltemplate/examples/coarse_grained/abstract_translocation/moltemplate_files/polymer.lt +++ b/tools/moltemplate/examples/coarse_grained/abstract_translocation/moltemplate_files/polymer.lt @@ -1,9 +1,9 @@ -import "monomer.lt" +import "monomer.lt" # <-- defines "Monomer" and "ForceField" -Polymer { +Polymer inherits ForceField { create_var {$mol} # optional:force all monomers to share the same molecule-ID - # (The "Data Atoms" in Monomer must use "$mol:..." notation.) + #(The "Data Atoms" in Monomer must use "$mol:..." notation.) # Make a chain of monomers monomers = new Monomer [12].rot(180, 1,0,0).move(2.0, 0, 0) @@ -29,4 +29,4 @@ Polymer { # Angle, dihedral and improper interactions will be generated -# automatically according to the instructions in "monomer.lt" +# automatically according to the instructions in "forcefield.lt" diff --git a/tools/moltemplate/examples/coarse_grained/abstract_translocation/moltemplate_files/polymer_forcefield.lt b/tools/moltemplate/examples/coarse_grained/abstract_translocation/moltemplate_files/polymer_forcefield.lt new file mode 100644 index 0000000000..ef7efe24e4 --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained/abstract_translocation/moltemplate_files/polymer_forcefield.lt @@ -0,0 +1,120 @@ +# Define a "ForceField" object. +# A force field in moltemplate is any object containing mostly pair_coeff, +# bond_coeff, angle_coeff, dihedral_coeff, "Bonds By Type", "Angles By Type", +# "Dihedrals By Type", "Impropers By Type", "Data Masses" (and "In Charges") +# information. Later on when we define molecule objects, we can access all +# of the atom types and force field parameters here using "inherits ForceField". +# (See "monomer.lt" for example.) + + +ForceField { + + # LAMMPS supports a large number of "styles" (ie. equations for calculating + # forces between particles). At some point, we must eventually select the + # formulas we want to use. This can be done anywhere, but we might as + # well specify that now. Later on we will specify the parameters + # which go into these equations. + + write_once("In Init") { + # -- Styles used in "ForceField" -- + # -- (Changing these styles will change the formulas above) -- + units real + atom_style full + bond_style harmonic + angle_style harmonic + dihedral_style opls + pair_style lj/cut 11.0 + } + + + # There are 2 atom types: "CA" and "R" + + write_once("Data Masses") { + @atom:CA 13.0 + @atom:R 50.0 + } + + # ---- 2-body (non-bonded) interactions: ---- + # U(r) = 4*epsilon((sigma/r)^12 - (sigma/r)^6) + # (for details see http://lammps.sandia.gov/doc/pair_lj.html) + # atom-type atom-type epsilon sigma + + write_once("In Settings") { + pair_coeff @atom:CA @atom:CA 0.05 2.0 + pair_coeff @atom:R @atom:R 0.50 2.0 + # (Interactions between different atoms are determined by mixing rules.) + } + + # ---- 2-body (bonded) interactions: ---- + # + # Ubond(r) = k*(r-r0)^2 + # (for details see http://lammps.sandia.gov/doc/bond_harmonic.html) + # + write_once("In Settings") { + # bond-type k r0 + bond_coeff @bond:sidechain 30.0 1.2 + bond_coeff @bond:bb 30.0 2.0 # "bb" shorthand for "backbone" + } + + # For a compound molecule consisting of smaller building blocks (such as a + # polymer built from monomers), it is tedious to explicitly list all of the + # angles, dihedrals in the entire molecule. Instead, you can define rules + # for automatically generating all the angular interactions between bonded + # atoms according to their connectivity and the atom/bond type. + # Later, when you connect multiple monomers together to form a polymer, + # appropriate bond-angle forces will be applied to these atoms automatically + # (as well as dihedral and improper forces, if defined). + + # ---- 3-body angle (hinge) interactions ---- + # Rules for determining 3-body interactions by type + + # angle-type atomType1 atomType2 atomType3 bondType1 bondType2 + + write_once("Data Angles By Type") { + @angle:backbone @atom:CA @atom:CA @atom:CA @bond:* @bond:* + @angle:sidechain @atom:CA @atom:CA @atom:R @bond:* @bond:* + @angle:RCR @atom:R @atom:CA @atom:R @bond:* @bond:* + } + + # ("@angle:RCR" defines the angle between the R-C-R atoms within a monomer. + # The other angular interactions are between atoms in neighboring monomers.) + + # Force-field parameters for 3-body (angle) interactions: + # + # Uangle(theta) = k*(theta-theta0)^2 + # (for details see http://lammps.sandia.gov/doc/angle_harmonic.html) + # + write_once("In Settings") { + # angle-type k theta0 + angle_coeff @angle:backbone 50.00 160 + angle_coeff @angle:sidechain 50.00 120 + angle_coeff @angle:RCR 50.00 120 + } + + # ---- 4-body dihedral interactions ---- + + # Rules for determining 4-body (dihedral) interactions by atom & bond type: + # dihedralType atmType1 atmType2 atmType3 atmType4 bondType1 bType2 bType3 + + write_once("Data Dihedrals By Type") { + @dihedral:backbn @atom:CA @atom:CA @atom:CA @atom:CA @bond:* @bond:* @bond:* + } + # (A more realistic force field would have more dihedral and angle types) + + + # The forumula used for dihedral interactions is: + # + # Udihedral(phi) = (K1/2)*(1+cos(phi)) + (K2/2)*(1+cos(2*phi)) + + # ... (K3/2)*(1+cos(3*phi)) + (K4/2)*(1+cos(4*phi)) + # (for details, see http://lammps.sandia.gov/doc/dihedral_opls.html) + # + # The corresponding command is + + write_once("In Settings") { + # dihedral-type K1 K2 K3 K4 + dihedral_coeff @dihedral:backbn 1.411036 -0.271016 3.145034 0.0 + } + +} # "ForceField" + + diff --git a/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/README.txt b/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/README.txt new file mode 100644 index 0000000000..c3c4faecb1 --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/README.txt @@ -0,0 +1,20 @@ +# CG model of benzene where each molecule is represented as an ellipsoid +# and the intermolecular interactions are described with the Gay-Berne potential +# +# Do not expect realistic behaviour from this example. +# The long-range electrostatic interactions are missing. +# +# To build the files which LAMMPS needs, follow the instructions in +# README_setup.sh +# +# To run the simulation in LAMMPS, follow the instructions in: +# README_run.sh +# +# Finally, to view the simulation results in OVITO, follow the instructions in: +# README_visualization_OVITO.txt +# README_visualization_OVITO_ellipsoids.png +# +# +# This example was provided by Otello M. Roscion (U.Southampton) +# and Matteo Ricci(U.Bologna) Many thanks for editing and debugging +# moltemplate code to get this working! diff --git a/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/README_run.sh b/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/README_run.sh new file mode 100755 index 0000000000..91e79124e1 --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/README_run.sh @@ -0,0 +1,20 @@ +# --- Running LAMMPS --- +# +# The file "run.in.npt" is a LAMMPS +# input script which link to the input scripts and data files +# you hopefully have created earlier with moltemplate.sh: +# system.in.init, system.in.settings, system.data +# If not, carry out the instructions in "README_setup.sh". +# +# -- Instructions: -- +# If "lmp_mpi" is the name of the command you use to invoke lammps, +# then you would run lammps on these files this way: + +lmp_mpi -i run.in.npt # simulation at constant pressure + +# (Note: The "lmp_mpi" program is also frequently called "lmp_ubuntu", +# and has many other names depending upon how it was compiled.) + +# If you have compiled the MPI version of lammps, you can run lammps in parallel +#mpirun -np 4 lmp_mpi -i run.in.npt +# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/README_setup.sh b/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/README_setup.sh new file mode 100755 index 0000000000..3a5a6d2e67 --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/README_setup.sh @@ -0,0 +1,19 @@ +# Create LAMMPS input files this way: +cd moltemplate_files + + # Run moltemplate with the "-allow-wildcards" and "-nocheck" arguments + # as well as a custom -atomstyle + + moltemplate.sh -atomstyle "atomid atomtype flag density x y z" system.lt \ + -allow-wildcards -nocheck + + # This will generate various files with names ending in *.in* and *.data. + # Move them to the directory where you plan to run LAMMPS (in this case "../") + mv -f system.data system.in* ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ diff --git a/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/README_visualization_OVITO.txt b/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/README_visualization_OVITO.txt new file mode 100644 index 0000000000..cd2498b1a1 --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/README_visualization_OVITO.txt @@ -0,0 +1,12 @@ +You can visualize the trajectory (dump file) with the program OVITO (www.ovito.org). You will have to define few parameters, thought. Invoke ovito using: + +ovito traj.lammpstrj + +On the right panel of ovito, under the section "LAMMPS dump" click on the button "Edit column mapping" and enter the fields as specified in the attached png file. On the same panel, tick "File contains a time series" to display the entire trajectory. + +A screenshot of these settings is available: +README_visualization_OVITO_ellipsoids.png + + +Otello M. Roscioni +roscioni@gmail.com diff --git a/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/README_visualization_OVITO_ellipsoids.png b/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/README_visualization_OVITO_ellipsoids.png new file mode 100644 index 0000000000..15e5e77c4b Binary files /dev/null and b/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/README_visualization_OVITO_ellipsoids.png differ diff --git a/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/images/benzene_cg_ellipsoid.png b/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/images/benzene_cg_ellipsoid.png new file mode 100644 index 0000000000..89629bde48 Binary files /dev/null and b/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/images/benzene_cg_ellipsoid.png differ diff --git a/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/images/t=0.jpg b/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/images/t=0.jpg new file mode 100644 index 0000000000..b3514f4c8a Binary files /dev/null and b/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/images/t=0.jpg differ diff --git a/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/images/t=14900.jpg b/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/images/t=14900.jpg new file mode 100644 index 0000000000..7c35039c01 Binary files /dev/null and b/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/images/t=14900.jpg differ diff --git a/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/moltemplate_files/benzene_cg.lt b/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/moltemplate_files/benzene_cg.lt new file mode 100644 index 0000000000..036847ea4a --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/moltemplate_files/benzene_cg.lt @@ -0,0 +1,62 @@ +# CG model of benzene where each molecule is represented as an ellipsoid +# and the intermolecular interactions are described with the Gay-Berne potential +# +# Do not expect a physical behaviour from this sample: long-range electrostatic +# interactions are missing. +# +# Otello M. Roscioni +# roscioni@gmail.com + +# Run with the command: +# moltemplate.sh -atomstyle "atomid atomtype flag density x y z" system.lt -allow-wildcards -nocheck + + +BENZ { + + # atom-ID atom-type ellipsoidflag density x y z + write("Data Atoms"){ + $atom:ben @atom:b1 1 1.14337 0.0 0.0 0.0 + } + + # atom-ID width1 width2 width3 qw qx qy qz + write("Data Ellipsoids"){ + $atom:ben 6.3888 6.3888 3.1967 1.0 0.0 0.0 0.0 + } + + write_once("In Init") { + units real + atom_style ellipsoid + pair_style gayberne 1.0 1.0 -3.0 25.0 + pair_modify mix arithmetic + + # Neighbour list. (Can be overridden) + neighbor 1.0 bin + neigh_modify check yes one 5000 + } + + + write_once("In Settings") { + # Gay-Berne parameters. + pair_coeff @atom:b1 @atom:b1 1.0 3.7275 0.7797 0.7797 3.6200 0.7797 0.7797 3.6200 25.0 + } + + + write_once("In Settings") { # <-- append to "In Settings" + + # It's probably useful to put the following computes and settings here since + # I imagine that most people who use this model would find them useful: + + compute q all property/atom quatw quati quatj quatk + compute shape all property/atom shapex shapey shapez + compute temp_trasl all temp + compute temp_rototrasl all temp/asphere dof all + compute press_trasl all pressure temp_trasl + compute myMSD all msd com yes + + # Modify temperature to include ellipsoidal degrees of freedom. + thermo_modify temp temp_rototrasl + thermo_modify press press_trasl + } + +} #BENZ + diff --git a/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/moltemplate_files/system.lt b/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/moltemplate_files/system.lt new file mode 100644 index 0000000000..00d669063b --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/moltemplate_files/system.lt @@ -0,0 +1,24 @@ +# Run with the command: +# moltemplate.sh -atomstyle "atomid atomtype flag density x y z" benzene_sample01.lt -allow-wildcards -nocheck + +import "benzene_cg.lt" + +# Specify the periodic boundary conditions: +write_once("Data Boundary") { + 0 35.0 xlo xhi + 0 35.0 ylo yhi + 0 35.0 zlo zhi +} + +bulk = new BENZ [5].move(7, 0, 0) + [5].move(0, 7, 0).rot(10,0,1,0) + [5].move(0, 0, 7) + +# NOTE: +# I included a .rot() rotation command above in order to demonstrate +# that moltemplate can control ellipsoid orientation as well as position. +# Unfortunately, this example may be difficult to understand. Explanation: +# When ".rot(10,0,1,0)" appears in the middle of a 3-D array declaration, +# it applies a rotation of 10 degrees around the y axis ("0,1,0", into the +# screen) each time the middle index ("j" in "BENZ[i][j][k]") increases by one. +# This will cause the k-columns to be twisted around the y axis as y increases. diff --git a/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/run.in b/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/run.in new file mode 100644 index 0000000000..94ad81659b --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/run.in @@ -0,0 +1,37 @@ +# PREREQUISITES: +# +# You must use moltemplate.sh (& packmol?) to create 3 files: +# system.data system.in.init system.in.settings +# +# See "README_setup.sh" for instructions how to use moltemplate.sh +# Note: This input script file only covers equilibration of the system. +# +# ------------------------------- Initialization Section -------------------- + +include "system.in.init" +boundary p p p + +# ------------------------------- Atom Definition Section ------------------- + +read_data "system.data" + +# ------------------------------- Settings Section -------------------------- + +include "system.in.settings" + +# ------------------------------- Run Section ------------------------------- + +# Output: +thermo 100 +thermo_style custom step etotal evdwl ke pe temp press vol density & + c_myMSD[1] c_myMSD[2] c_myMSD[3] c_myMSD[4] cpu +dump 1 all custom 100 traj.lammpstrj & +id type x y z c_q[1] c_q[2] c_q[3] c_q[4] & +c_shape[1] c_shape[2] c_shape[3] & +angmomx angmomy angmomz + +# Dynamics: +timestep 10.0 +fix 2 all npt/asphere temp 300. 300. 1000. iso 1. 1. 10000. +fix_modify 2 press press_trasl +run 20000 diff --git a/tools/moltemplate/examples/coarse_grained/membrane+protein/run.in.min b/tools/moltemplate/examples/coarse_grained/membrane+protein/run.in.min index 2fc8fbba75..9e1ccb360a 100644 --- a/tools/moltemplate/examples/coarse_grained/membrane+protein/run.in.min +++ b/tools/moltemplate/examples/coarse_grained/membrane+protein/run.in.min @@ -28,7 +28,7 @@ include system.in.settings # -- Run section -- -dump 1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz +dump 1 all custom 50 traj.lammpstrj id mol type x y z ix iy iz minimize 1.0e-5 1.0e-7 500 2000 diff --git a/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/spce.lt b/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/spce.lt index 019911c19b..1f0f0f61b5 100644 --- a/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/spce.lt +++ b/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/spce.lt @@ -6,18 +6,6 @@ SPCE { - write_once("In Init") { - # -- Default styles (for solo "SPCE" water) -- - units real - atom_style full - # (Hybrid force fields were not necessary but are used for portability.) - pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0 - bond_style hybrid harmonic - angle_style hybrid harmonic - kspace_style pppm 0.0001 - pair_modify mix arithmetic - } - write("Data Atoms") { $atom:O $mol:. @atom:O -0.8476 0.0000000 0.00000 0.000000 $atom:H1 $mol:. @atom:H 0.4238 0.8164904 0.00000 0.5773590 @@ -39,14 +27,26 @@ SPCE { } write_once("In Settings") { - bond_coeff @bond:OH harmonic 1000.0 1.0 - angle_coeff @angle:HOH harmonic 1000.0 109.47 + bond_coeff @bond:OH harmonic 600.0 1.0 + angle_coeff @angle:HOH harmonic 75.0 109.47 pair_coeff @atom:O @atom:O lj/charmm/coul/long 0.1553 3.166 - pair_coeff @atom:H @atom:H lj/charmm/coul/long 0.0 2.058 + pair_coeff @atom:H @atom:H lj/charmm/coul/long 0.0 0.0 group spce type @atom:O @atom:H fix fShakeSPCE spce shake 0.0001 10 100 b @bond:OH a @angle:HOH # (Remember to "unfix" fShakeSPCE during minimization.) } + write_once("In Init") { + # -- Default styles (for solo "SPCE" water) -- + units real + atom_style full + # (Hybrid force fields were not necessary but are used for portability.) + pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0 + bond_style hybrid harmonic + angle_style hybrid harmonic + kspace_style pppm 0.0001 + #pair_modify mix arithmetic # LEAVE THIS UNSPECIFIED! + } + } # end of definition of "SPCE" water molecule type diff --git a/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/README.txt b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/README.txt new file mode 100644 index 0000000000..5f5fd61bd3 --- /dev/null +++ b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/README.txt @@ -0,0 +1,25 @@ +This example using the electron Force Field (eFF) was created by +Andres Jaramillo-Botero and distributed with LAMMPS in the +"examples/USERS/eff/CH4" subdirectory. +The files from that example were converted into moltemplate format using +"ltemplify.py" and then edited by hand (to rename the atom types, +and replace all of the "pair_coeff ..." commands with "pair_coeff * *") + + +--- Original README: --- +Methane, valence electron ionization and full molecule tests (spe, dynamics). +Note: electron mass set to 1 + + +----- +WARNING: Regarding the "run.in.ch4_ionized" file + As of 2014-3-12, the "pair_style eff/cut 5000.0 0 0" command + located in "orig_files/in.ch4_ionized.dynamics" (as well as the + files "moltemplate_files/ch4_ionized.lt" and "system.in.settings", + which are both derived from it) causes LAMMPS to hang. + Running LAMMPS on Andres' original eFF example has the same behavior. + This appears to be an eFF/LAMMPS issue (not a moltemplate issue). + The "pair_style eff/cut 100" command works, so + try reducing the cutoff (or ask Andres Jaramillo-Botero for help). + Please let me know if you solve this issue (jewett.aij -at- g mail) + diff --git a/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/README_run.sh b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/README_run.sh new file mode 100644 index 0000000000..527ff19442 --- /dev/null +++ b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/README_run.sh @@ -0,0 +1,3 @@ + +lmp_mpi -i run.in.ch4 + diff --git a/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/README_setup.sh b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/README_setup.sh new file mode 100644 index 0000000000..8433d10fa2 --- /dev/null +++ b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/README_setup.sh @@ -0,0 +1,14 @@ +cd moltemplate_files/ + + moltemplate.sh -atomstyle electron system_ch4.lt + + # This will generate 3 files: + # "system_ch4.data", "system_ch4.in.init", "system_ch4.in.settings" + + mv -f system_ch4.data system_ch4.in.init system_ch4.in.settings ../ + + # optional: delete temporary files + + rm -rf output_ttree + +cd ../ diff --git a/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/moltemplate_files/ch4.lt b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/moltemplate_files/ch4.lt new file mode 100644 index 0000000000..b5989e5a1b --- /dev/null +++ b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/moltemplate_files/ch4.lt @@ -0,0 +1,45 @@ + +CH4 { + + write_once("Data Masses") { + @atom:C 12.01070 + @atom:H 1.000794 + @atom:e 1.000000 + } + + # id type q spin eradius x y z + + write("Data Atoms") { + $atom:c @atom:C 6.0 0 0.0 0.0 0.0 0.0 + $atom:h1 @atom:H 1.0 0 0.0 1.0 1.0 1.0 + $atom:h2 @atom:H 1.0 0 0.0 -1.0 -1.0 1.0 + $atom:h3 @atom:H 1.0 0 0.0 1.0 -1.0 -1.0 + $atom:h4 @atom:H 1.0 0 0.0 -1.0 1.0 -1.0 + $atom:esr @atom:e 0.0 -1 0.5 0.0 0.0 0.0 + $atom:esR1 @atom:e 0.0 -1 1.0 1.0 1.0 1.0 + $atom:esR2 @atom:e 0.0 -1 1.0 -1.0 -1.0 1.0 + $atom:esR3 @atom:e 0.0 -1 1.0 1.0 -1.0 -1.0 + $atom:esR4 @atom:e 0.0 -1 1.0 -1.0 1.0 -1.0 + $atom:eSr @atom:e 0.0 1 0.5 0.0 0.0 0.0 + $atom:eSR1 @atom:e 0.0 1 1.0 1.0 1.0 1.0 + $atom:eSR2 @atom:e 0.0 1 1.0 -1.0 -1.0 1.0 + $atom:eSR2 @atom:e 0.0 1 1.0 1.0 -1.0 -1.0 + $atom:eSR3 @atom:e 0.0 1 1.0 -1.0 1.0 -1.0 + } + + # -- styles and force-field parameters -- + # (these can be overridden later) + + write_once("In Init") { + atom_style electron + units electron + pair_style eff/cut 100.0 + newton on + comm_modify vel yes + } + write_once("In Settings") { + pair_coeff * * + } + +} # end of "CH4" object definition + diff --git a/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/moltemplate_files/ch4_ionized.lt b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/moltemplate_files/ch4_ionized.lt new file mode 100644 index 0000000000..62865418e8 --- /dev/null +++ b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/moltemplate_files/ch4_ionized.lt @@ -0,0 +1,55 @@ +# WARNING: As of 2014-3-12, the "pair_style eff/cut 5000.0 0 0" command +# located in "orig_files/in.ch4_ionized.dynamics" (as well as the +# files "moltemplate_files/ch4_ionized.lt" (this file) +# ...causes LAMMPS to hang. +# Running LAMMPS on Andres' original eFF example has the same behavior. +# This appears to be an eFF/LAMMPS issue, not a moltemplate issue. +# The "pair_style eff/cut 100" command works, so +# try reducing the cutoff (or ask Andres Jaramillo-Botero for help). +# Please let me know if you solve this issue (jewett.aij -at- g mail ) + + +CH4_ionized { + + write_once("Data Masses") { + @atom:C 12.01070 + @atom:H 1.000794 + @atom:e 1.000000 + } + + # id type q spin eradius x y z + + write("Data Atoms") { + $atom:c @atom:C 6.000000 0 0.0 0.000000 -0.000000 0.000000 + $atom:h1 @atom:H 1.000000 0 0.0 1.247211 1.247211 1.247211 + $atom:h2 @atom:H 1.000000 0 0.0 -1.247211 -1.247211 1.247211 + $atom:h3 @atom:H 1.000000 0 0.0 1.247211 -1.247211 -1.247211 + $atom:h4 @atom:H 1.000000 0 0.0 -1.247211 1.247211 -1.247211 + $atom:esr @atom:e 0.000000 -1 0.329128 -0.000000 0.000000 -0.000000 + $atom:esR1 @atom:e 0.000000 -1 1.486181 0.979221 0.979221 0.979221 + $atom:esR2 @atom:e 0.000000 -1 1.486181 -0.979221 -0.979221 0.979221 + $atom:esR3 @atom:e 0.000000 -1 1.486181 0.979221 -0.979221 -0.979221 + $atom:esR4 @atom:e 0.000000 -1 1.486181 -0.979221 0.979221 -0.979221 + $atom:eSr @atom:e 0.000000 1 0.329128 -0.000000 0.000000 0.000000 + $atom:eSR1 @atom:e 0.000000 1 1.486181 -0.979221 -0.979221 0.979221 + $atom:eSR2 @atom:e 0.000000 1 1.486181 0.979221 -0.979221 -0.979221 + $atom:eSR3 @atom:e 0.000000 1 1.486181 -0.979221 0.979221 -0.979221 + } + + # -- styles and force-field parameters -- + # (these can be overridden later) + + write_once("In Init") { + atom_style electron + units electron + pair_style eff/cut 5000.0 0 0 + newton on + comm_modify vel yes + } + + write_once("In Settings") { + pair_coeff * * + } + +} # end of "CH4_ionized" object definition + diff --git a/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/moltemplate_files/system_ch4.in b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/moltemplate_files/system_ch4.in new file mode 100644 index 0000000000..8ba9365a9b --- /dev/null +++ b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/moltemplate_files/system_ch4.in @@ -0,0 +1,42 @@ + + +# ----------------- Init Section ----------------- + +include "system_ch4.in.init" + + +# ----------------- Atom Definition Section ----------------- + +read_data "system_ch4.data" + +# ----------------- Settings Section ----------------- + +include "system_ch4.in.settings" + + +# ----------------- Run Section ----------------- + +# The lines above define the system you want to simulate. +# What you do next is up to you. +# Typically a user would minimize and equilibrate +# the system using commands similar to the following: +# ---- examples ---- +# +# -- minimize -- +# minimize 1.0e-5 1.0e-7 1000 10000 +# (Note: Some fixes, for example "shake", interfere with the minimize command, +# You can use the "unfix" command to disable them before minimization.) +# -- declare time step for normal MD -- +# timestep 1.0 +# -- run at constant pressure (Nose-Hoover)-- +# fix fxnpt all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0 drag 1.0 +# -- ALTERNATELY, run at constant volume (Nose-Hoover) -- +# fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1 +# -- ALTERNATELY, run at constant volume using Langevin dynamics. -- +# -- (This is good for sparse CG polymers in implicit solvent.) -- +# fix fxLAN all langevin 300.0 300.0 5000 48279 +# fix fxNVE all nve #(<--needed by fix langevin) +# -- Now, finally run the simulation -- +# run 50000 +# ---- (end of examples) ---- + diff --git a/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/moltemplate_files/system_ch4.lt b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/moltemplate_files/system_ch4.lt new file mode 100644 index 0000000000..3b0e6d7894 --- /dev/null +++ b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/moltemplate_files/system_ch4.lt @@ -0,0 +1,28 @@ + +import "ch4.lt" # <-- defines "CH4" + + +# instantiate one or more copies of the "CH4" object: + +# Instantiate two copies of CH4: + +molecule1 = new CH4.move(-5.0,0,0) +molecule2 = new CH4.move(5.0,0,0) +# : : : + + +# alternate example: +# instantiate 2*2*2 = 8 copies, separated by 10.0 in each direction: +# molecules = new CH4 [2].move(0,0,10) [2].move(0,10,0) [2].move(10,0,0) +# molecules[*][*][*].move(-5,-5,-5) + + +# optional "Boundary" (goes in header of generated DATA file) +# (-200 200 by default) + +write_once("Data Boundary") { + -500.0 500.0 xlo xhi + -500.0 500.0 ylo yhi + -500.0 500.0 zlo zhi +} + diff --git a/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/moltemplate_files/system_ch4_ionized.lt b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/moltemplate_files/system_ch4_ionized.lt new file mode 100644 index 0000000000..cd44be380e --- /dev/null +++ b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/moltemplate_files/system_ch4_ionized.lt @@ -0,0 +1,29 @@ + +import "ch4.lt" # <-- defines "CH4" +import "ch4_ionized.lt" # <-- defines "CH4_ionized" + + +# instantiate one or more copies of the "CH4" object: + +# Instantiate two copies of CH4: + +molecule1 = new CH4_ionized.move(-5.0,0,0) +molecule2 = new CH4_ionized.move(5.0,0,0) +# : : : + + +# alternate example: +# instantiate 2*2*2 = 8 copies, separated by 10.0 in each direction: +# molecules = new CH4 [2].move(0,0,10) [2].move(0,10,0) [2].move(10,0,0) +# molecules[*][*][*].move(-5,-5,-5) + + +# optional "Boundary" (goes in header of generated DATA file) +# (-200 200 by default) + +write_once("Data Boundary") { + -500.0 500.0 xlo xhi + -500.0 500.0 ylo yhi + -500.0 500.0 zlo zhi +} + diff --git a/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/orig_files/README b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/orig_files/README new file mode 100644 index 0000000000..20714b24c0 --- /dev/null +++ b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/orig_files/README @@ -0,0 +1,2 @@ +Methane, valence electron ionization and full molecule tests (spe, min, dynamics). +Note: electron mass set to 1 diff --git a/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/orig_files/data.ch4 b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/orig_files/data.ch4 new file mode 100644 index 0000000000..ebe29be4ed --- /dev/null +++ b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/orig_files/data.ch4 @@ -0,0 +1,32 @@ +Created by AJB + +15 atoms +3 atom types + +-500.0 500.0 xlo xhi +-500.0 500.0 ylo yhi +-500.0 500.0 zlo zhi + +Masses + +1 12.01070 # C nuclei mass +2 1.000794 # H nuclei mass +3 1.000000 # electron mass + +Atoms +#id|type|q|spin|eradius|x|y|z| +1 1 6.0 0 0.0 0.0 0.0 0.0 +2 2 1.0 0 0.0 1.0 1.0 1.0 +3 2 1.0 0 0.0 -1.0 -1.0 1.0 +4 2 1.0 0 0.0 1.0 -1.0 -1.0 +5 2 1.0 0 0.0 -1.0 1.0 -1.0 +6 3 0.0 -1 0.5 0.0 0.0 0.0 +7 3 0.0 -1 1.0 1.0 1.0 1.0 +8 3 0.0 -1 1.0 -1.0 -1.0 1.0 +9 3 0.0 -1 1.0 1.0 -1.0 -1.0 +10 3 0.0 -1 1.0 -1.0 1.0 -1.0 +11 3 0.0 1 0.5 0.0 0.0 0.0 +12 3 0.0 1 1.0 1.0 1.0 1.0 +13 3 0.0 1 1.0 -1.0 -1.0 1.0 +14 3 0.0 1 1.0 1.0 -1.0 -1.0 +15 3 0.0 1 1.0 -1.0 1.0 -1.0 diff --git a/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/orig_files/data.ch4_ionized b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/orig_files/data.ch4_ionized new file mode 100644 index 0000000000..8c21a281a1 --- /dev/null +++ b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/orig_files/data.ch4_ionized @@ -0,0 +1,31 @@ +Created by AJB + +14 atoms +3 atom types + +-5000.0 5000.0 xlo xhi +-5000.0 5000.0 ylo yhi +-5000.0 5000.0 zlo zhi + +Masses + +1 12.01070 # C nuclei mass +2 1.000794 # H nuclei mass +3 1.000000 # electron mass + +Atoms + +1 1 6.000000 0 0.0 0.000000 -0.000000 0.000000 +2 2 1.000000 0 0.0 1.247211 1.247211 1.247211 +3 2 1.000000 0 0.0 -1.247211 -1.247211 1.247211 +4 2 1.000000 0 0.0 1.247211 -1.247211 -1.247211 +5 2 1.000000 0 0.0 -1.247211 1.247211 -1.247211 +6 3 0.000000 -1 0.329128 -0.000000 0.000000 -0.000000 +7 3 0.000000 -1 1.486181 0.979221 0.979221 0.979221 +8 3 0.000000 -1 1.486181 -0.979221 -0.979221 0.979221 +9 3 0.000000 -1 1.486181 0.979221 -0.979221 -0.979221 +10 3 0.000000 -1 1.486181 -0.979221 0.979221 -0.979221 +11 3 0.000000 1 0.329128 -0.000000 0.000000 0.000000 +12 3 0.000000 1 1.486181 -0.979221 -0.979221 0.979221 +13 3 0.000000 1 1.486181 0.979221 -0.979221 -0.979221 +14 3 0.000000 1 1.486181 -0.979221 0.979221 -0.979221 diff --git a/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/orig_files/in.ch4.dynamics b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/orig_files/in.ch4.dynamics new file mode 100644 index 0000000000..2536fa8f48 --- /dev/null +++ b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/orig_files/in.ch4.dynamics @@ -0,0 +1,41 @@ +variable sname index ch4 +log ${sname}.nve.log + +units electron +newton on +boundary f f f + +atom_style electron + +read_data data.${sname} + +pair_style eff/cut 100.0 +pair_coeff * * + +comm_modify vel yes + +# Minimize +min_style cg +compute 1 all property/atom spin eradius +dump 1 all custom 1 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z +min_modify line quadratic dmax 0.1 +minimize 0 1.0e-6 1000 10000 + +# Dynamics + +compute effTemp all temp/eff + +thermo 1000 +thermo_style custom step pe temp press +thermo_modify temp effTemp + +velocity all create 300.0 4928459 dist gaussian rot yes mom yes + +timestep 0.005 +fix 1 all nve/eff + +# the custom dump includes the radii +dump 2 all custom 1000 ${sname}.nve.lammpstrj id type q c_1[1] c_1[2] x y z +dump 3 all xyz 1000 ${sname}.nve.xyz + +run 100000 diff --git a/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/orig_files/in.ch4.min b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/orig_files/in.ch4.min new file mode 100644 index 0000000000..69b7c15bd4 --- /dev/null +++ b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/orig_files/in.ch4.min @@ -0,0 +1,32 @@ +variable sname index ch4 +log ${sname}.nve.log + +units electron +newton on +boundary f f f + +atom_style electron + +read_data data.${sname} + +pair_style eff/cut 100.0 +pair_coeff * * + +comm_modify vel yes + +compute effTemp all temp/eff + +compute energies all pair eff/cut +variable eke equal c_energies[1] +variable epauli equal c_energies[2] +variable ecoul equal c_energies[3] +variable erres equal c_energies[4] + +thermo 1 +thermo_style custom step etotal pe ke v_eke v_epauli v_ecoul v_erres + +min_style cg +compute 1 all property/atom spin eradius erforce +dump 2 all custom 10 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3] +minimize 0 1e-6 2000 4000 + diff --git a/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/orig_files/in.ch4_ionized.dynamics b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/orig_files/in.ch4_ionized.dynamics new file mode 100644 index 0000000000..14f214296f --- /dev/null +++ b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/orig_files/in.ch4_ionized.dynamics @@ -0,0 +1,42 @@ +variable sname index ch4_ionized +log ${sname}.nvt.log + +units electron +newton on +boundary f f f + +atom_style electron + +read_data data.${sname} + +pair_style eff/cut 5000.0 0 0 +pair_coeff * * + +comm_modify vel yes + +# minimize +min_style cg +min_modify line quadratic +minimize 0 1.0e-6 10000 100000 + +# dynamics +compute effTemp all temp/eff + +thermo 100 +thermo_style custom step etotal pe ke temp press +thermo_modify temp effTemp + +# equilibrate +timestep 0.001 +fix 1 all nvt/eff temp 300.0 300.0 0.1 + +# the custom dump includes the radii +compute 1 all property/atom spin eradius +dump 1 all custom 100 ${sname}.nvt.lammpstrj id type x y z c_1[1] c_1[2] +dump 2 all xyz 100 ${sname}.nvt.xyz + +run 1000000 + +fix 2 all nve/eff + +run 1000000 diff --git a/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/run.in.ch4 b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/run.in.ch4 new file mode 100644 index 0000000000..a822608768 --- /dev/null +++ b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/run.in.ch4 @@ -0,0 +1,49 @@ +# PREREQUISITES: +# system_ch4.data, system_ch4.in.init, system.in.settings +# Generate these files using: +# cd moltemplate_files/ +# moltemplate.sh -atomstyle electron system_ch4.lt + + +variable sname index ch4 +log ${sname}.nve.log + + +boundary f f f +include system_${sname}.in.init + + +read_data system_${sname}.data + + +include system_${sname}.in.settings + + + +# Minimize + +min_style cg +compute 1 all property/atom spin eradius +dump 1 all custom 1 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z +min_modify line quadratic dmax 0.1 +minimize 0 1.0e-6 1000 10000 + + +# Dynamics + +compute effTemp all temp/eff + +thermo 1000 +thermo_style custom step pe temp press +thermo_modify temp effTemp + +velocity all create 300.0 4928459 dist gaussian rot yes mom yes + +timestep 0.005 +fix 1 all nve/eff + +# the custom dump includes the radii +dump 2 all custom 1000 ${sname}.nve.lammpstrj id type q c_1[1] c_1[2] x y z +dump 3 all xyz 1000 ${sname}.nve.xyz + +run 100000 diff --git a/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/run.in.ch4_ionized b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/run.in.ch4_ionized new file mode 100644 index 0000000000..73e93b1cd2 --- /dev/null +++ b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/run.in.ch4_ionized @@ -0,0 +1,62 @@ +# PREREQUISITES: +# system_ch4_ionized.data, system_ch4_ionized.in.init, system.in.settings +# Generate these files using: +# cd moltemplate_files/ +# moltemplate.sh -atomstyle electron system_ch4_ionized.lt + +# WARNING: As of 2014-3-12, the "pair_style eff/cut 5000.0 0 0" command +# located in "orig_files/in.ch4_ionized.dynamics" (as well as the +# files "moltemplate_files/ch4_ionized.lt" and "system.in.settings", +# which are both derived from it) causes LAMMPS to hang. +# Running LAMMPS on Andres' original eFF example has the same behavior. +# This appears to be an eFF/LAMMPS issue, not a moltemplate issue. +# The "pair_style eff/cut 100" command works, so +# try reducing the cutoff (or ask Andres Jaramillo-Botero for help). +# Please let me know if you solve this issue (jewett.aij -at- g mail ) + + +variable sname index ch4 +log ${sname}.nve.log + + +boundary f f f +include system_${sname}.in.init + + +read_data system_${sname}.data + + +include system_${sname}.in.settings + + + +# Minimize + +min_style cg +min_modify line quadratic +minimize 0 1.0e-6 10000 100000 + + + +# Dynamics + +compute effTemp all temp/eff + +thermo 100 +thermo_style custom step etotal pe ke temp press +thermo_modify temp effTemp + +# Equilibrate +timestep 0.001 +fix 1 all nvt/eff temp 300.0 300.0 0.1 + +# the custom dump includes the radii +compute 1 all property/atom spin eradius +dump 1 all custom 100 ${sname}.nvt.lammpstrj id type x y z c_1[1] c_1[2] +dump 2 all xyz 100 ${sname}.nvt.xyz + +run 1000000 + +fix 2 all nve/eff + +run 1000000 diff --git a/tools/moltemplate/moltemplate/__init__.py b/tools/moltemplate/moltemplate/__init__.py index b9601769e1..ccd228a8c1 100644 --- a/tools/moltemplate/moltemplate/__init__.py +++ b/tools/moltemplate/moltemplate/__init__.py @@ -1,11 +1,11 @@ from .ttree import BasicUISettings, BasicUIParseArgs, EraseTemplateFiles, \ StackableCommand, PopCommand, PopRightCommand, PopLeftCommand, \ PushCommand, PushLeftCommand, PushRightCommand, ScopeCommand, \ - WriteVarBindingsFile, StaticObj, InstanceObj, \ + WriteVarBindingsFile, StaticObj, InstanceObj, ExtractFormattingCommands, \ BasicUI, ScopeBegin, ScopeEnd, WriteFileCommand, Render from .ttree_lex import TtreeShlex, split, LineLex, SplitQuotedString, \ EscCharStrToChar, SafelyEncodeString, RemoveOuterQuotes, MaxLenStr, \ - HasWildCard, InputError, ErrorLeader, SrcLoc, OSrcLoc, TextBlock, VarRef, \ + HasWildcard, InputError, ErrorLeader, SrcLoc, OSrcLoc, TextBlock, VarRef, \ VarNPtr, VarBinding, SplitTemplate, SplitTemplateMulti, TableFromTemplate, \ ExtractCatName, DeleteLinesWithBadVars, TemplateLexer from .lttree_styles import AtomStyle2ColNames, ColNames2AidAtypeMolid, \ diff --git a/tools/moltemplate/moltemplate/bonds_by_type.py b/tools/moltemplate/moltemplate/bonds_by_type.py index 6b36911f21..3df4a26582 100755 --- a/tools/moltemplate/moltemplate/bonds_by_type.py +++ b/tools/moltemplate/moltemplate/bonds_by_type.py @@ -32,7 +32,7 @@ import sys try: from . import ttree_lex from .lttree_styles import AtomStyle2ColNames, ColNames2AidAtypeMolid -except (SystemError, ValueError): +except (ImportError, SystemError, ValueError): # not installed as a package import ttree_lex from lttree_styles import AtomStyle2ColNames, ColNames2AidAtypeMolid diff --git a/tools/moltemplate/moltemplate/charge_by_bond.py b/tools/moltemplate/moltemplate/charge_by_bond.py index b8d7c75646..83acb83935 100755 --- a/tools/moltemplate/moltemplate/charge_by_bond.py +++ b/tools/moltemplate/moltemplate/charge_by_bond.py @@ -1,11 +1,13 @@ #!/usr/bin/env python - # Author: Andrew Jewett (jewett.aij at g mail) -# http://www.chem.ucsb.edu/~sheagroup # License: 3-clause BSD License (See LICENSE.TXT) -# Copyright (c) 2011, Regents of the University of California +# Copyright (c) 2017, California Institute of Technology # All rights reserved. +g_program_name = __file__.split('/')[-1] # = 'charge_by_bond.py' +g_date_str = '2017-10-03' +g_version_str = '0.14.0' + import sys import re @@ -14,7 +16,7 @@ from collections import defaultdict try: from . import ttree_lex from .lttree_styles import AtomStyle2ColNames, ColNames2AidAtypeMolid -except (SystemError, ValueError): +except (ImportError, SystemError, ValueError): # not installed as a package import ttree_lex from lttree_styles import AtomStyle2ColNames, ColNames2AidAtypeMolid @@ -23,6 +25,7 @@ except (SystemError, ValueError): def LookupChargePairs(chargebyatomid, # bond_ids, + # bond_types, # bond_pairs, lines_atoms, lines_bonds, @@ -137,7 +140,7 @@ def LookupChargePairs(chargebyatomid, # else: # raise(ttree_lex.InputError('Incorrect number of columns on line '+str(ie+1)+' of \"'+section_name+'\" section.')) - assert(len(bond_types) == 0) + #assert(len(bond_types) == 0) typepattern_to_chargepairs = [] warning_unassigned_chargepairs = None @@ -191,18 +194,20 @@ def LookupChargePairs(chargebyatomid, atomtype1 = atomids2types[atomid1] atomtype2 = atomids2types[atomid2] + found = False for typepattern, chargepair in typepattern_to_chargepairs: # use string comparisons to check if atom types match the pattern if ttree_lex.MatchesAll((atomtype1, atomtype2), typepattern): # ("MatchesAll()" defined in "ttree_lex.py") chargebyatomid[atomid1] += chargepair[0] chargebyatomid[atomid2] += chargepair[1] + found = True elif ttree_lex.MatchesAll((atomtype2, atomtype1), typepattern): chargebyatomid[atomid1] += chargepair[1] chargebyatomid[atomid2] += chargepair[0] - else: - if not warning_unassigned_chargepairs: - warning_unassigned_chargepairs = (atomid1, atomid2) + found = True + if (not found) and (not warning_unassigned_chargepairs): + warning_unassigned_chargepairs = (atomid1, atomid2) if warning_unassigned_chargepairs: sys.stderr.write('---------------------------------------------------------------------------\n' @@ -239,10 +244,6 @@ def main(): """ - g_program_name = __file__.split('/')[-1] # = 'charge_pairs_by_type.py' - g_date_str = '2016-12-22' - g_version_str = '0.13.0' - ####### Main Code Below: ####### sys.stderr.write(g_program_name + ' v' + g_version_str + ' ' + g_date_str + ' ') @@ -344,7 +345,7 @@ def main(): (' '.join(problem_args)) + '\n\n' ' (The actual problem may be earlier in the argument list.)\n') - bond_types = [] + #bond_types = [] fatoms = open(fname_atoms, 'r') lines_bonds = [] lines_bond_list = [] diff --git a/tools/moltemplate/moltemplate/dump2data.py b/tools/moltemplate/moltemplate/dump2data.py index 4c122d8eba..249e6c9b2e 100755 --- a/tools/moltemplate/moltemplate/dump2data.py +++ b/tools/moltemplate/moltemplate/dump2data.py @@ -22,8 +22,8 @@ A reference DATA file is needed (argument). # All rights reserved. g_program_name = 'dump2data.py' -g_date_str = '2017-7-27' -g_version_str = '0.53.0' +g_date_str = '2017-9-12' +g_version_str = '0.54.1' import sys from collections import defaultdict @@ -584,6 +584,7 @@ def WriteFrameToData(out_file, descr_str, misc_settings, data_settings, + dump_column_names, natoms, coords, coords_ixiyiz, @@ -677,13 +678,13 @@ def WriteFrameToData(out_file, # In principle, depending on the atom_style, # there could be multiple vectors per atom. for I in range(0, len(data_settings.ii_vects)): + i_vx = data_settings.ii_vects[I][0] + i_vy = data_settings.ii_vects[I][1] + i_vz = data_settings.ii_vects[I][2] if atomid in vects: vxvyvz = vects[atomid][I] assert((type(vxvyvz) is tuple) and (len(vxvyvz) == 3)) - i_vx = data_settings.ii_vects[I][0] - i_vy = data_settings.ii_vects[I][1] - i_vz = data_settings.ii_vects[I][2] if ((i_vx >= len(tokens)) or (i_vy >= len(tokens)) or (i_vz >= len(tokens))): @@ -697,8 +698,9 @@ def WriteFrameToData(out_file, tokens[i_vz] = vxvyvz[2] else: - if data_settings.column_names[ - i_vx] not in dump_column_names: + if (dump_column_names and + (data_settings.column_names[ + i_vx] not in dump_column_names)): raise InputError('Error(dump2data): You have a vector coordinate in your DATA file named \"' + data_settings.column_names[i_vx] + '\"\n' ' However there are no columns with this name in your DUMP file\n' ' (or the column was not in the expected place).\n' @@ -1273,6 +1275,7 @@ def main(): descr_str, misc_settings, data_settings, + dump_column_names, frame_natoms, frame_coords, frame_coords_ixiyiz, diff --git a/tools/moltemplate/moltemplate/ettree.py b/tools/moltemplate/moltemplate/ettree.py index c8d90c7e42..20353a86ef 100755 --- a/tools/moltemplate/moltemplate/ettree.py +++ b/tools/moltemplate/moltemplate/ettree.py @@ -56,7 +56,7 @@ try: iEsptAtomCoords, iEsptAtomVects, iEsptAtomType, iEsptAtomID from .ttree_matrix_stack import AffineTransform, MultiAffineStack, \ LinTransform -except (SystemError, ValueError): +except (ImportError, SystemError, ValueError): # not installed as a package from ttree import * from ttree_lex import * @@ -482,7 +482,7 @@ def WriteFiles(files_content, suffix='', write_to_stdout=True): -def main() +def main(): """ This is is a "main module" wrapper for invoking ettree.py as a stand alone program. This program: @@ -495,8 +495,8 @@ def main() """ g_program_name = 'ettree.py' - g_date_str = '2016-12-22' - g_version_str = '0.36.0' + g_date_str = '2018-6-26' + g_version_str = '0.37.0' SimpleCounter.default_n0 = 0 # counters in Espresso begin at 0, not 1 diff --git a/tools/moltemplate/moltemplate/force_fields/README.txt b/tools/moltemplate/moltemplate/force_fields/README.txt new file mode 100644 index 0000000000..d0650a0f72 --- /dev/null +++ b/tools/moltemplate/moltemplate/force_fields/README.txt @@ -0,0 +1,13 @@ + +If moltemplate is unable to locate an .LT file that the user has requested +(ie. using the "import" command) in the current local directory, +moltemplate will search for that file here. + +This directory contains moltemplate files (.LT files) containing common +force fields (including parameters and rules for creating bonded interactions), +as well as definitions of molecules which are frequently used (for example +SPCE water). + +The scripts used to convert these force fields are located here as well, along +with the original files containing the force field parameters (when available). + diff --git a/tools/moltemplate/moltemplate/force_fields/SDK_lipid+chol.lt b/tools/moltemplate/moltemplate/force_fields/SDK_lipid+chol.lt deleted file mode 100644 index dd54c6b697..0000000000 --- a/tools/moltemplate/moltemplate/force_fields/SDK_lipid+chol.lt +++ /dev/null @@ -1,423 +0,0 @@ -# Autogenerated by EMC 2 LT tool v0.2 on 2017-02-28 -# -# ./emcprm2lt.py --pair-style=lj/sdk/coul/long --bond-style=harmonic --angle-style=sdk sdk_lipids.prm sdk_cholesterol.prm --name=SDK_lipid+chol --units -# -# Adapted from EMC by Pieter J. in 't Veld -# Originally written as, FFNAME:SDK STYLE:COARSE VERSION:1.0 on Oct 2014 - -SDK { - write_once("Data Masses") { - @atom:CM 42.080400 # CM - @atom:CMD2 26.037800 # CMD2 - @atom:CT 43.088300 # CT - @atom:CT2 29.061500 # CT2 - @atom:EST1 58.036600 # EST1 - @atom:EST2 58.036600 # EST2 - @atom:GL 41.072500 # GL - @atom:NC 87.164400 # NC - @atom:NH 44.076100 # NH - @atom:PH 94.971600 # PH - @atom:PHE 94.971600 # PHE - @atom:W 54.045600 # W - @atom:C2T 43.090000 # C2T - @atom:CM2 28.050000 # CM2 - @atom:CM2R 28.050000 # CM2R - @atom:CMDB 39.060000 # CMDB - @atom:CMB 40.060000 # CMB - @atom:CMR 41.070000 # CMR - @atom:CMR5 41.070000 # CMR5 - @atom:CTB 42.080000 # CTB - @atom:CTBA 27.050000 # CTBA - @atom:CTBB 27.050000 # CTBB - @atom:OAB 30.030000 # OAB - } # end of atom masses - - # ----- EQUIVALENCE CATEGORIES for bonded interaction lookup ----- - replace{ @atom:CM @atom:CM_bCM_aCM_dCM_iCM} - replace{ @atom:CMD2 @atom:CMD2_bCMD2_aCMD2_dCMD2_iCMD2} - replace{ @atom:CT @atom:CT_bCT_aCT_dCT_iCT} - replace{ @atom:CT2 @atom:CT2_bCT2_aCT2_dCT2_iCT2} - replace{ @atom:EST1 @atom:EST1_bEST1_aEST1_dEST1_iEST1} - replace{ @atom:EST2 @atom:EST2_bEST2_aEST2_dEST2_iEST2} - replace{ @atom:GL @atom:GL_bGL_aGL_dGL_iGL} - replace{ @atom:NC @atom:NC_bNC_aNC_dNC_iNC} - replace{ @atom:NH @atom:NH_bNH_aNH_dNH_iNH} - replace{ @atom:PH @atom:PH_bPH_aPH_dPH_iPH} - replace{ @atom:PHE @atom:PHE_bPHE_aPHE_dPHE_iPHE} - replace{ @atom:W @atom:W_bW_aW_dW_iW} - replace{ @atom:C2T @atom:C2T_bC2T_aC2T_dC2T_iC2T} - replace{ @atom:CM2 @atom:CM2_bCM2_aCM2_dCM2_iCM2} - replace{ @atom:CM2R @atom:CM2R_bCM2R_aCM2R_dCM2R_iCM2R} - replace{ @atom:CMDB @atom:CMDB_bCMDB_aCMDB_dCMDB_iCMDB} - replace{ @atom:CMB @atom:CMB_bCMB_aCMB_dCMB_iCMB} - replace{ @atom:CMR @atom:CMR_bCMR_aCMR_dCMR_iCMR} - replace{ @atom:CMR5 @atom:CMR5_bCMR5_aCMR5_dCMR5_iCMR5} - replace{ @atom:CTB @atom:CTB_bCTB_aCTB_dCTB_iCTB} - replace{ @atom:CTBA @atom:CTBA_bCTBA_aCTBA_dCTBA_iCTBA} - replace{ @atom:CTBB @atom:CTBB_bCTBB_aCTBB_dCTBB_iCTBB} - replace{ @atom:OAB @atom:OAB_bOAB_aOAB_dOAB_iOAB} - # END EQUIVALENCE - - write_once("In Settings") { - # ----- Non-Bonded interactions ----- - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:CM_bCM_aCM_dCM_iCM lj9_6 0.420000 4.506000 # CM-CM - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:CMD2_bCMD2_aCMD2_dCMD2_iCMD2 lj9_6 0.312000 4.255500 # CM-CMD2 - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:CT_bCT_aCT_dCT_iCT lj9_6 0.444000 4.545500 # CM-CT - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:CT2_bCT2_aCT2_dCT2_iCT2 lj9_6 0.362000 4.363500 # CM-CT2 - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:EST1_bEST1_aEST1_dEST1_iEST1 lj9_6 0.470000 4.403000 # CM-EST1 - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:EST2_bEST2_aEST2_dEST2_iEST2 lj9_6 0.470000 4.403000 # CM-EST2 - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:GL_bGL_aGL_dGL_iGL lj9_6 0.420000 4.506000 # CM-GL - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:NC_bNC_aNC_dNC_iNC lj9_6 0.400000 5.128000 # CM-NC - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:NH_bNH_aNH_dNH_iNH lj9_6 0.330000 4.553000 # CM-NH - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:PH_bPH_aPH_dPH_iPH lj9_6 0.300000 4.953000 # CM-PH - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:PHE_bPHE_aPHE_dPHE_iPHE lj9_6 0.300000 4.953000 # CM-PHE - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:W_bW_aW_dW_iW lj12_4 0.340000 4.438500 # CM-W - pair_coeff @atom:CMD2_bCMD2_aCMD2_dCMD2_iCMD2 @atom:CMD2_bCMD2_aCMD2_dCMD2_iCMD2 lj9_6 0.232000 4.005000 # CMD2-CMD2 - pair_coeff @atom:CMD2_bCMD2_aCMD2_dCMD2_iCMD2 @atom:CT_bCT_aCT_dCT_iCT lj9_6 0.330000 4.295000 # CMD2-CT - pair_coeff @atom:CMD2_bCMD2_aCMD2_dCMD2_iCMD2 @atom:CT2_bCT2_aCT2_dCT2_iCT2 lj9_6 0.269000 4.113000 # CMD2-CT2 - pair_coeff @atom:CMD2_bCMD2_aCMD2_dCMD2_iCMD2 @atom:EST1_bEST1_aEST1_dEST1_iEST1 lj9_6 0.440000 4.005000 # CMD2-EST1 - pair_coeff @atom:CMD2_bCMD2_aCMD2_dCMD2_iCMD2 @atom:EST2_bEST2_aEST2_dEST2_iEST2 lj9_6 0.440000 4.005000 # CMD2-EST2 - pair_coeff @atom:CMD2_bCMD2_aCMD2_dCMD2_iCMD2 @atom:GL_bGL_aGL_dGL_iGL lj9_6 0.312000 4.255500 # CMD2-GL - pair_coeff @atom:CMD2_bCMD2_aCMD2_dCMD2_iCMD2 @atom:NC_bNC_aNC_dNC_iNC lj9_6 0.350000 4.877500 # CMD2-NC - pair_coeff @atom:CMD2_bCMD2_aCMD2_dCMD2_iCMD2 @atom:NH_bNH_aNH_dNH_iNH lj9_6 0.300000 4.302500 # CMD2-NH - pair_coeff @atom:CMD2_bCMD2_aCMD2_dCMD2_iCMD2 @atom:PH_bPH_aPH_dPH_iPH lj9_6 0.300000 4.702500 # CMD2-PH - pair_coeff @atom:CMD2_bCMD2_aCMD2_dCMD2_iCMD2 @atom:PHE_bPHE_aPHE_dPHE_iPHE lj9_6 0.300000 4.702500 # CMD2-PHE - pair_coeff @atom:CMD2_bCMD2_aCMD2_dCMD2_iCMD2 @atom:W_bW_aW_dW_iW lj12_4 0.270000 4.188000 # CMD2-W - pair_coeff @atom:CT_bCT_aCT_dCT_iCT @atom:CT_bCT_aCT_dCT_iCT lj9_6 0.469000 4.585000 # CT-CT - pair_coeff @atom:CT_bCT_aCT_dCT_iCT @atom:CT2_bCT2_aCT2_dCT2_iCT2 lj9_6 0.383000 4.403000 # CT-CT2 - pair_coeff @atom:CT_bCT_aCT_dCT_iCT @atom:EST1_bEST1_aEST1_dEST1_iEST1 lj9_6 0.470000 4.442500 # CT-EST1 - pair_coeff @atom:CT_bCT_aCT_dCT_iCT @atom:EST2_bEST2_aEST2_dEST2_iEST2 lj9_6 0.470000 4.442500 # CT-EST2 - pair_coeff @atom:CT_bCT_aCT_dCT_iCT @atom:GL_bGL_aGL_dGL_iGL lj9_6 0.444000 4.545500 # CT-GL - pair_coeff @atom:CT_bCT_aCT_dCT_iCT @atom:NC_bNC_aNC_dNC_iNC lj9_6 0.420000 5.167500 # CT-NC - pair_coeff @atom:CT_bCT_aCT_dCT_iCT @atom:NH_bNH_aNH_dNH_iNH lj9_6 0.340000 4.925000 # CT-NH - pair_coeff @atom:CT_bCT_aCT_dCT_iCT @atom:PH_bPH_aPH_dPH_iPH lj9_6 0.320000 4.992500 # CT-PH - pair_coeff @atom:CT_bCT_aCT_dCT_iCT @atom:PHE_bPHE_aPHE_dPHE_iPHE lj9_6 0.320000 4.992500 # CT-PHE - pair_coeff @atom:CT_bCT_aCT_dCT_iCT @atom:W_bW_aW_dW_iW lj12_4 0.360000 4.478000 # CT-W - pair_coeff @atom:CT2_bCT2_aCT2_dCT2_iCT2 @atom:CT2_bCT2_aCT2_dCT2_iCT2 lj9_6 0.312000 4.221000 # CT2-CT2 - pair_coeff @atom:CT2_bCT2_aCT2_dCT2_iCT2 @atom:EST1_bEST1_aEST1_dEST1_iEST1 lj9_6 0.390000 4.260500 # CT2-EST1 - pair_coeff @atom:CT2_bCT2_aCT2_dCT2_iCT2 @atom:EST2_bEST2_aEST2_dEST2_iEST2 lj9_6 0.390000 4.260500 # CT2-EST2 - pair_coeff @atom:CT2_bCT2_aCT2_dCT2_iCT2 @atom:GL_bGL_aGL_dGL_iGL lj9_6 0.362000 4.365000 # CT2-GL - pair_coeff @atom:CT2_bCT2_aCT2_dCT2_iCT2 @atom:NC_bNC_aNC_dNC_iNC lj9_6 0.320000 4.985500 # CT2-NC - pair_coeff @atom:CT2_bCT2_aCT2_dCT2_iCT2 @atom:NH_bNH_aNH_dNH_iNH lj9_6 0.320000 4.410500 # CT2-NH - pair_coeff @atom:CT2_bCT2_aCT2_dCT2_iCT2 @atom:PH_bPH_aPH_dPH_iPH lj9_6 0.280000 4.810500 # CT2-PH - pair_coeff @atom:CT2_bCT2_aCT2_dCT2_iCT2 @atom:PHE_bPHE_aPHE_dPHE_iPHE lj9_6 0.280000 4.810500 # CT2-PHE - pair_coeff @atom:CT2_bCT2_aCT2_dCT2_iCT2 @atom:W_bW_aW_dW_iW lj12_4 0.290000 4.296000 # CT2-W - pair_coeff @atom:EST1_bEST1_aEST1_dEST1_iEST1 @atom:EST1_bEST1_aEST1_dEST1_iEST1 lj9_6 0.495000 4.300000 # EST1-EST1 - pair_coeff @atom:EST1_bEST1_aEST1_dEST1_iEST1 @atom:EST2_bEST2_aEST2_dEST2_iEST2 lj9_6 0.495000 4.300000 # EST1-EST2 - pair_coeff @atom:EST1_bEST1_aEST1_dEST1_iEST1 @atom:GL_bGL_aGL_dGL_iGL lj9_6 0.470000 4.403000 # EST1-GL - pair_coeff @atom:EST1_bEST1_aEST1_dEST1_iEST1 @atom:NC_bNC_aNC_dNC_iNC lj9_6 0.750000 4.475000 # EST1-NC - pair_coeff @atom:EST1_bEST1_aEST1_dEST1_iEST1 @atom:NH_bNH_aNH_dNH_iNH lj9_6 0.850000 4.110000 # EST1-NH - pair_coeff @atom:EST1_bEST1_aEST1_dEST1_iEST1 @atom:PH_bPH_aPH_dPH_iPH lj9_6 0.500000 4.550000 # EST1-PH - pair_coeff @atom:EST1_bEST1_aEST1_dEST1_iEST1 @atom:PHE_bPHE_aPHE_dPHE_iPHE lj9_6 0.500000 4.550000 # EST1-PHE - pair_coeff @atom:EST1_bEST1_aEST1_dEST1_iEST1 @atom:W_bW_aW_dW_iW lj12_4 0.820000 4.290000 # EST1-W - pair_coeff @atom:EST2_bEST2_aEST2_dEST2_iEST2 @atom:EST2_bEST2_aEST2_dEST2_iEST2 lj9_6 0.495000 4.300000 # EST2-EST2 - pair_coeff @atom:EST2_bEST2_aEST2_dEST2_iEST2 @atom:GL_bGL_aGL_dGL_iGL lj9_6 0.470000 4.403000 # EST2-GL - pair_coeff @atom:EST2_bEST2_aEST2_dEST2_iEST2 @atom:NC_bNC_aNC_dNC_iNC lj9_6 0.750000 4.475000 # EST2-NC - pair_coeff @atom:EST2_bEST2_aEST2_dEST2_iEST2 @atom:NH_bNH_aNH_dNH_iNH lj9_6 0.850000 4.110000 # EST2-NH - pair_coeff @atom:EST2_bEST2_aEST2_dEST2_iEST2 @atom:PH_bPH_aPH_dPH_iPH lj9_6 0.500000 4.550000 # EST2-PH - pair_coeff @atom:EST2_bEST2_aEST2_dEST2_iEST2 @atom:PHE_bPHE_aPHE_dPHE_iPHE lj9_6 0.500000 4.550000 # EST2-PHE - pair_coeff @atom:EST2_bEST2_aEST2_dEST2_iEST2 @atom:W_bW_aW_dW_iW lj12_4 0.820000 4.290000 # EST2-W - pair_coeff @atom:GL_bGL_aGL_dGL_iGL @atom:GL_bGL_aGL_dGL_iGL lj9_6 0.420000 4.506000 # GL-GL - pair_coeff @atom:GL_bGL_aGL_dGL_iGL @atom:NC_bNC_aNC_dNC_iNC lj9_6 0.650000 4.620000 # GL-NC - pair_coeff @atom:GL_bGL_aGL_dGL_iGL @atom:NH_bNH_aNH_dNH_iNH lj9_6 0.750000 4.190000 # GL-NH - pair_coeff @atom:GL_bGL_aGL_dGL_iGL @atom:PH_bPH_aPH_dPH_iPH lj9_6 0.300000 4.750000 # GL-PH - pair_coeff @atom:GL_bGL_aGL_dGL_iGL @atom:PHE_bPHE_aPHE_dPHE_iPHE lj9_6 0.300000 4.750000 # GL-PHE - pair_coeff @atom:GL_bGL_aGL_dGL_iGL @atom:W_bW_aW_dW_iW lj12_4 0.640000 4.438500 # GL-W - pair_coeff @atom:NC_bNC_aNC_dNC_iNC @atom:NC_bNC_aNC_dNC_iNC lj9_6 0.700000 5.750000 # NC-NC - pair_coeff @atom:NC_bNC_aNC_dNC_iNC @atom:NH_bNH_aNH_dNH_iNH lj9_6 0.880000 5.175000 # NC-NH - pair_coeff @atom:NC_bNC_aNC_dNC_iNC @atom:PH_bPH_aPH_dPH_iPH lj9_6 1.150000 4.200000 # NC-PH - pair_coeff @atom:NC_bNC_aNC_dNC_iNC @atom:PHE_bPHE_aPHE_dPHE_iPHE lj9_6 1.150000 4.200000 # NC-PHE - pair_coeff @atom:NC_bNC_aNC_dNC_iNC @atom:W_bW_aW_dW_iW lj12_4 0.900000 4.610000 # NC-W - pair_coeff @atom:NH_bNH_aNH_dNH_iNH @atom:NH_bNH_aNH_dNH_iNH lj9_6 1.100000 4.600000 # NH-NH - pair_coeff @atom:NH_bNH_aNH_dNH_iNH @atom:PH_bPH_aPH_dPH_iPH lj9_6 1.200000 3.800000 # NH-PH - pair_coeff @atom:NH_bNH_aNH_dNH_iNH @atom:PHE_bPHE_aPHE_dPHE_iPHE lj9_6 1.200000 3.800000 # NH-PHE - pair_coeff @atom:NH_bNH_aNH_dNH_iNH @atom:W_bW_aW_dW_iW lj12_4 0.800000 3.950000 # NH-W - pair_coeff @atom:PH_bPH_aPH_dPH_iPH @atom:PH_bPH_aPH_dPH_iPH lj9_6 1.400000 5.400000 # PH-PH - pair_coeff @atom:PH_bPH_aPH_dPH_iPH @atom:PHE_bPHE_aPHE_dPHE_iPHE lj9_6 1.400000 5.000000 # PH-PHE - pair_coeff @atom:PH_bPH_aPH_dPH_iPH @atom:W_bW_aW_dW_iW lj12_4 1.000000 4.030000 # PH-W - pair_coeff @atom:PHE_bPHE_aPHE_dPHE_iPHE @atom:PHE_bPHE_aPHE_dPHE_iPHE lj9_6 1.400000 4.600000 # PHE-PHE - pair_coeff @atom:PHE_bPHE_aPHE_dPHE_iPHE @atom:W_bW_aW_dW_iW lj12_4 1.000000 4.030000 # PHE-W - pair_coeff @atom:W_bW_aW_dW_iW @atom:W_bW_aW_dW_iW lj12_4 0.895000 4.371000 # W-W - pair_coeff @atom:C2T_bC2T_aC2T_dC2T_iC2T @atom:NC_bNC_aNC_dNC_iNC lj9_6 0.420000 5.167500 # C2T-NC - pair_coeff @atom:CMR5_bCMR5_aCMR5_dCMR5_iCMR5 @atom:CT_bCT_aCT_dCT_iCT lj9_6 0.444000 4.545500 # CMR5-CT - pair_coeff @atom:C2T_bC2T_aC2T_dC2T_iC2T @atom:CTBA_bCTBA_aCTBA_dCTBA_iCTBA lj9_6 0.252000 4.767700 # C2T-CTBA - pair_coeff @atom:CT_bCT_aCT_dCT_iCT @atom:CTB_bCTB_aCTB_dCTB_iCTB lj9_6 0.469000 4.585000 # CT-CTB - pair_coeff @atom:C2T_bC2T_aC2T_dC2T_iC2T @atom:CMR_bCMR_aCMR_dCMR_iCMR lj9_6 0.331000 4.771400 # C2T-CMR - pair_coeff @atom:CT_bCT_aCT_dCT_iCT @atom:CTBA_bCTBA_aCTBA_dCTBA_iCTBA lj9_6 0.383000 4.403000 # CT-CTBA - pair_coeff @atom:C2T_bC2T_aC2T_dC2T_iC2T @atom:CTBB_bCTBB_aCTBB_dCTBB_iCTBB lj9_6 0.252000 4.767700 # C2T-CTBB - pair_coeff @atom:CT_bCT_aCT_dCT_iCT @atom:CTBB_bCTBB_aCTBB_dCTBB_iCTBB lj9_6 0.383000 4.403000 # CT-CTBB - pair_coeff @atom:C2T_bC2T_aC2T_dC2T_iC2T @atom:GL_bGL_aGL_dGL_iGL lj9_6 0.444000 4.545500 # C2T-GL - pair_coeff @atom:CT_bCT_aCT_dCT_iCT @atom:OAB_bOAB_aOAB_dOAB_iOAB lj9_6 0.437000 4.033000 # CT-OAB - pair_coeff @atom:C2T_bC2T_aC2T_dC2T_iC2T @atom:CM2R_bCM2R_aCM2R_dCM2R_iCM2R lj9_6 0.254000 4.610100 # C2T-CM2R - pair_coeff @atom:CT2_bCT2_aCT2_dCT2_iCT2 @atom:CTB_bCTB_aCTB_dCTB_iCTB lj9_6 0.383000 4.403000 # CT2-CTB - pair_coeff @atom:C2T_bC2T_aC2T_dC2T_iC2T @atom:CMD2_bCMD2_aCMD2_dCMD2_iCMD2 lj9_6 0.330000 4.295000 # C2T-CMD2 - pair_coeff @atom:CT2_bCT2_aCT2_dCT2_iCT2 @atom:CTBA_bCTBA_aCTBA_dCTBA_iCTBA lj9_6 0.312000 4.221000 # CT2-CTBA - pair_coeff @atom:C2T_bC2T_aC2T_dC2T_iC2T @atom:CMR5_bCMR5_aCMR5_dCMR5_iCMR5 lj9_6 0.331000 4.771400 # C2T-CMR5 - pair_coeff @atom:CT2_bCT2_aCT2_dCT2_iCT2 @atom:CTBB_bCTBB_aCTBB_dCTBB_iCTBB lj9_6 0.312000 4.221000 # CT2-CTBB - pair_coeff @atom:C2T_bC2T_aC2T_dC2T_iC2T @atom:W_bW_aW_dW_iW lj12_4 0.360000 4.478000 # C2T-W - pair_coeff @atom:CT2_bCT2_aCT2_dCT2_iCT2 @atom:OAB_bOAB_aOAB_dOAB_iOAB lj9_6 0.415000 3.950500 # CT2-OAB - pair_coeff @atom:C2T_bC2T_aC2T_dC2T_iC2T @atom:C2T_bC2T_aC2T_dC2T_iC2T lj9_6 0.400000 4.811500 # C2T-C2T - pair_coeff @atom:CTB_bCTB_aCTB_dCTB_iCTB @atom:CTB_bCTB_aCTB_dCTB_iCTB lj9_6 0.269000 5.015500 # CTB-CTB - pair_coeff @atom:C2T_bC2T_aC2T_dC2T_iC2T @atom:OAB_bOAB_aOAB_dOAB_iOAB lj9_6 0.437000 4.033000 # C2T-OAB - pair_coeff @atom:CTB_bCTB_aCTB_dCTB_iCTB @atom:EST1_bEST1_aEST1_dEST1_iEST1 lj9_6 0.470000 4.442500 # CTB-EST1 - pair_coeff @atom:C2T_bC2T_aC2T_dC2T_iC2T @atom:PH_bPH_aPH_dPH_iPH lj9_6 0.320000 4.992500 # C2T-PH - pair_coeff @atom:CTB_bCTB_aCTB_dCTB_iCTB @atom:EST2_bEST2_aEST2_dEST2_iEST2 lj9_6 0.470000 4.442500 # CTB-EST2 - pair_coeff @atom:C2T_bC2T_aC2T_dC2T_iC2T @atom:CMDB_bCMDB_aCMDB_dCMDB_iCMDB lj9_6 0.354000 4.894100 # C2T-CMDB - pair_coeff @atom:CTB_bCTB_aCTB_dCTB_iCTB @atom:NC_bNC_aNC_dNC_iNC lj9_6 0.420000 5.167500 # CTB-NC - pair_coeff @atom:C2T_bC2T_aC2T_dC2T_iC2T @atom:CT2_bCT2_aCT2_dCT2_iCT2 lj9_6 0.297000 4.527200 # C2T-CT2 - pair_coeff @atom:CTB_bCTB_aCTB_dCTB_iCTB @atom:CTBA_bCTBA_aCTBA_dCTBA_iCTBA lj9_6 0.265000 4.464800 # CTB-CTBA - pair_coeff @atom:C2T_bC2T_aC2T_dC2T_iC2T @atom:CM2_bCM2_aCM2_dCM2_iCM2 lj9_6 0.291000 4.588000 # C2T-CM2 - pair_coeff @atom:CTB_bCTB_aCTB_dCTB_iCTB @atom:CTBB_bCTBB_aCTBB_dCTBB_iCTBB lj9_6 0.265000 4.464800 # CTB-CTBB - pair_coeff @atom:C2T_bC2T_aC2T_dC2T_iC2T @atom:CM_bCM_aCM_dCM_iCM lj9_6 0.391000 4.545500 # C2T-CM - pair_coeff @atom:CTB_bCTB_aCTB_dCTB_iCTB @atom:GL_bGL_aGL_dGL_iGL lj9_6 0.444000 4.545500 # CTB-GL - pair_coeff @atom:C2T_bC2T_aC2T_dC2T_iC2T @atom:CT_bCT_aCT_dCT_iCT lj9_6 0.409000 4.860100 # C2T-CT - pair_coeff @atom:CTB_bCTB_aCTB_dCTB_iCTB @atom:W_bW_aW_dW_iW lj12_4 0.360000 4.478000 # CTB-W - pair_coeff @atom:C2T_bC2T_aC2T_dC2T_iC2T @atom:CTB_bCTB_aCTB_dCTB_iCTB lj9_6 0.283000 4.910900 # C2T-CTB - pair_coeff @atom:CTB_bCTB_aCTB_dCTB_iCTB @atom:OAB_bOAB_aOAB_dOAB_iOAB lj9_6 0.437000 4.033000 # CTB-OAB - pair_coeff @atom:C2T_bC2T_aC2T_dC2T_iC2T @atom:CMB_bCMB_aCMB_dCMB_iCMB lj9_6 0.310000 4.656400 # C2T-CMB - pair_coeff @atom:CTB_bCTB_aCTB_dCTB_iCTB @atom:PH_bPH_aPH_dPH_iPH lj9_6 0.320000 4.992500 # CTB-PH - pair_coeff @atom:C2T_bC2T_aC2T_dC2T_iC2T @atom:EST1_bEST1_aEST1_dEST1_iEST1 lj9_6 0.470000 4.442500 # C2T-EST1 - pair_coeff @atom:CTBA_bCTBA_aCTBA_dCTBA_iCTBA @atom:NC_bNC_aNC_dNC_iNC lj9_6 0.320000 4.985500 # CTBA-NC - pair_coeff @atom:C2T_bC2T_aC2T_dC2T_iC2T @atom:EST2_bEST2_aEST2_dEST2_iEST2 lj9_6 0.470000 4.442500 # C2T-EST2 - pair_coeff @atom:CTBA_bCTBA_aCTBA_dCTBA_iCTBA @atom:EST1_bEST1_aEST1_dEST1_iEST1 lj9_6 0.390000 4.260500 # CTBA-EST1 - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:CMR_bCMR_aCMR_dCMR_iCMR lj9_6 0.420000 4.506000 # CM-CMR - pair_coeff @atom:CTBA_bCTBA_aCTBA_dCTBA_iCTBA @atom:EST2_bEST2_aEST2_dEST2_iEST2 lj9_6 0.390000 4.260500 # CTBA-EST2 - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:CM2R_bCM2R_aCM2R_dCM2R_iCM2R lj9_6 0.390000 4.434200 # CM-CM2R - pair_coeff @atom:CTBA_bCTBA_aCTBA_dCTBA_iCTBA @atom:W_bW_aW_dW_iW lj12_4 0.290000 4.296000 # CTBA-W - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:CMR5_bCMR5_aCMR5_dCMR5_iCMR5 lj9_6 0.420000 4.506000 # CM-CMR5 - pair_coeff @atom:CTBA_bCTBA_aCTBA_dCTBA_iCTBA @atom:GL_bGL_aGL_dGL_iGL lj9_6 0.362000 4.363500 # CTBA-GL - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:OAB_bOAB_aOAB_dOAB_iOAB lj9_6 0.561000 4.093000 # CM-OAB - pair_coeff @atom:CTBA_bCTBA_aCTBA_dCTBA_iCTBA @atom:CTBA_bCTBA_aCTBA_dCTBA_iCTBA lj9_6 0.265000 4.461000 # CTBA-CTBA - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:CMDB_bCMDB_aCMDB_dCMDB_iCMDB lj9_6 0.362000 4.379000 # CM-CMDB - pair_coeff @atom:CTBA_bCTBA_aCTBA_dCTBA_iCTBA @atom:CTBB_bCTBB_aCTBB_dCTBB_iCTBB lj9_6 0.265000 4.461000 # CTBA-CTBB - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:CM2_bCM2_aCM2_dCM2_iCM2 lj9_6 0.336000 4.461900 # CM-CM2 - pair_coeff @atom:CTBA_bCTBA_aCTBA_dCTBA_iCTBA @atom:PH_bPH_aPH_dPH_iPH lj9_6 0.280000 4.810500 # CTBA-PH - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:CTB_bCTB_aCTB_dCTB_iCTB lj9_6 0.444000 4.545500 # CM-CTB - pair_coeff @atom:CTBA_bCTBA_aCTBA_dCTBA_iCTBA @atom:OAB_bOAB_aOAB_dOAB_iOAB lj9_6 0.380000 3.840000 # CTBA-OAB - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:CMB_bCMB_aCMB_dCMB_iCMB lj9_6 0.420000 4.506000 # CM-CMB - pair_coeff @atom:CTBB_bCTBB_aCTBB_dCTBB_iCTBB @atom:W_bW_aW_dW_iW lj12_4 0.290000 4.296000 # CTBB-W - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:CTBA_bCTBA_aCTBA_dCTBA_iCTBA lj9_6 0.362000 4.363500 # CM-CTBA - pair_coeff @atom:CTBB_bCTBB_aCTBB_dCTBB_iCTBB @atom:NC_bNC_aNC_dNC_iNC lj9_6 0.320000 4.985500 # CTBB-NC - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:CTBB_bCTBB_aCTBB_dCTBB_iCTBB lj9_6 0.362000 4.363500 # CM-CTBB - pair_coeff @atom:CTBB_bCTBB_aCTBB_dCTBB_iCTBB @atom:GL_bGL_aGL_dGL_iGL lj9_6 0.362000 4.363500 # CTBB-GL - pair_coeff @atom:CM2_bCM2_aCM2_dCM2_iCM2 @atom:PH_bPH_aPH_dPH_iPH lj9_6 0.248000 4.936800 # CM2-PH - pair_coeff @atom:CTBB_bCTBB_aCTBB_dCTBB_iCTBB @atom:EST1_bEST1_aEST1_dEST1_iEST1 lj9_6 0.390000 4.260500 # CTBB-EST1 - pair_coeff @atom:CM2_bCM2_aCM2_dCM2_iCM2 @atom:OAB_bOAB_aOAB_dOAB_iOAB lj9_6 0.413000 4.066900 # CM2-OAB - pair_coeff @atom:CTBB_bCTBB_aCTBB_dCTBB_iCTBB @atom:EST2_bEST2_aEST2_dEST2_iEST2 lj9_6 0.390000 4.260500 # CTBB-EST2 - pair_coeff @atom:CM2_bCM2_aCM2_dCM2_iCM2 @atom:CM2R_bCM2R_aCM2R_dCM2R_iCM2R lj9_6 0.237000 4.440300 # CM2-CM2R - pair_coeff @atom:CTBB_bCTBB_aCTBB_dCTBB_iCTBB @atom:PH_bPH_aPH_dPH_iPH lj9_6 0.280000 4.810500 # CTBB-PH - pair_coeff @atom:CM2_bCM2_aCM2_dCM2_iCM2 @atom:CMD2_bCMD2_aCMD2_dCMD2_iCMD2 lj9_6 0.248000 4.231300 # CM2-CMD2 - pair_coeff @atom:CTBB_bCTBB_aCTBB_dCTBB_iCTBB @atom:OAB_bOAB_aOAB_dOAB_iOAB lj9_6 0.380000 3.840000 # CTBB-OAB - pair_coeff @atom:CM2_bCM2_aCM2_dCM2_iCM2 @atom:CMR5_bCMR5_aCMR5_dCMR5_iCMR5 lj9_6 0.333000 4.484600 # CM2-CMR5 - pair_coeff @atom:CTBB_bCTBB_aCTBB_dCTBB_iCTBB @atom:CTBB_bCTBB_aCTBB_dCTBB_iCTBB lj9_6 0.265000 4.461000 # CTBB-CTBB - pair_coeff @atom:CM2_bCM2_aCM2_dCM2_iCM2 @atom:CT2_bCT2_aCT2_dCT2_iCT2 lj9_6 0.228000 4.319900 # CM2-CT2 - pair_coeff @atom:EST1_bEST1_aEST1_dEST1_iEST1 @atom:OAB_bOAB_aOAB_dOAB_iOAB lj9_6 1.100000 3.990000 # EST1-OAB - pair_coeff @atom:CM2_bCM2_aCM2_dCM2_iCM2 @atom:CM2_bCM2_aCM2_dCM2_iCM2 lj9_6 0.265000 4.461000 # CM2-CM2 - pair_coeff @atom:EST2_bEST2_aEST2_dEST2_iEST2 @atom:OAB_bOAB_aOAB_dOAB_iOAB lj9_6 1.100000 3.990000 # EST2-OAB - pair_coeff @atom:CM2_bCM2_aCM2_dCM2_iCM2 @atom:CMDB_bCMDB_aCMDB_dCMDB_iCMDB lj9_6 0.267000 4.369700 # CM2-CMDB - pair_coeff @atom:GL_bGL_aGL_dGL_iGL @atom:OAB_bOAB_aOAB_dOAB_iOAB lj9_6 0.669000 4.093000 # GL-OAB - pair_coeff @atom:CM2_bCM2_aCM2_dCM2_iCM2 @atom:CT_bCT_aCT_dCT_iCT lj9_6 0.301000 4.454600 # CM2-CT - pair_coeff @atom:NC_bNC_aNC_dNC_iNC @atom:OAB_bOAB_aOAB_dOAB_iOAB lj9_6 0.637000 3.931900 # NC-OAB - pair_coeff @atom:CM2_bCM2_aCM2_dCM2_iCM2 @atom:CTB_bCTB_aCTB_dCTB_iCTB lj9_6 0.353000 4.524600 # CM2-CTB - pair_coeff @atom:OAB_bOAB_aOAB_dOAB_iOAB @atom:W_bW_aW_dW_iW lj9_6 1.026000 4.025500 # OAB-W - pair_coeff @atom:CM2_bCM2_aCM2_dCM2_iCM2 @atom:CMB_bCMB_aCMB_dCMB_iCMB lj9_6 0.333000 4.484600 # CM2-CMB - pair_coeff @atom:OAB_bOAB_aOAB_dOAB_iOAB @atom:PH_bPH_aPH_dPH_iPH lj9_6 0.928000 3.616600 # OAB-PH - pair_coeff @atom:CM2_bCM2_aCM2_dCM2_iCM2 @atom:NC_bNC_aNC_dNC_iNC lj9_6 0.306000 5.113800 # CM2-NC - pair_coeff @atom:OAB_bOAB_aOAB_dOAB_iOAB @atom:OAB_bOAB_aOAB_dOAB_iOAB lj9_6 0.580000 3.680000 # OAB-OAB - pair_coeff @atom:CM2_bCM2_aCM2_dCM2_iCM2 @atom:EST1_bEST1_aEST1_dEST1_iEST1 lj9_6 0.366000 4.380500 # CM2-EST1 - pair_coeff @atom:CM2_bCM2_aCM2_dCM2_iCM2 @atom:EST2_bEST2_aEST2_dEST2_iEST2 lj9_6 0.366000 4.380500 # CM2-EST2 - } # end of nonbonded parameters - - write_once("In Settings") { - # ----- Bonds ----- - bond_coeff @bond:CM-CM harmonic 6.160000 3.640000 - bond_coeff @bond:CM-CMD2 harmonic 8.000000 3.030000 - bond_coeff @bond:CM-CT harmonic 6.160000 3.650000 - bond_coeff @bond:CM-CT2 harmonic 9.000000 3.130000 - bond_coeff @bond:CM-EST1 harmonic 4.700000 3.550000 - bond_coeff @bond:CM-EST2 harmonic 5.100000 3.610000 - bond_coeff @bond:CM-PHE harmonic 12.000000 3.690000 - bond_coeff @bond:CM-SO4 harmonic 11.000000 3.630000 - bond_coeff @bond:CMD2-CT harmonic 8.000000 3.090000 - bond_coeff @bond:CMD2-CT2 harmonic 60.000000 2.540000 - bond_coeff @bond:CT-CT harmonic 6.955000 3.710000 - bond_coeff @bond:EST1-GL harmonic 30.000000 2.880000 - bond_coeff @bond:EST2-GL harmonic 8.400000 3.480000 - bond_coeff @bond:GL-PHE harmonic 8.900000 3.520000 - bond_coeff @bond:NC-PHE harmonic 4.800000 4.250000 - bond_coeff @bond:NH-PHE harmonic 9.400000 3.600000 - bond_coeff @bond:PHE1-PHE2 harmonic 2.500000 150.000000 - bond_coeff @bond:C2T-CM2 harmonic 55.000000 2.500000 - bond_coeff @bond:CM2-CTB harmonic 42.500000 2.900000 - bond_coeff @bond:CM2R-CTBA harmonic 45.000000 2.400000 - bond_coeff @bond:CM2R-OAB harmonic 50.000000 2.600000 - bond_coeff @bond:CMB-CMDB harmonic 75.000000 3.500000 - bond_coeff @bond:CMB-CMR5 harmonic 50.000000 3.000000 - bond_coeff @bond:CMB-CTBA harmonic 35.000000 3.400000 - bond_coeff @bond:CMB-CTBB harmonic 50.000000 3.000000 - bond_coeff @bond:CMDB-CTBA harmonic 40.000000 2.500000 - bond_coeff @bond:CMDB-OAB harmonic 55.000000 3.100000 - bond_coeff @bond:CMR5-CTBB harmonic 60.000000 2.300000 - bond_coeff @bond:CMR-CTBA harmonic 50.000000 3.000000 - bond_coeff @bond:CMR-CTBB harmonic 55.000000 2.500000 - bond_coeff @bond:CTB-CTBB harmonic 22.500000 3.400000 - bond_coeff @bond:CMR5-CTB harmonic 35.000000 3.100000 - } - - write_once("Data Bonds By Type") { - @bond:CM-CM @atom:*_bCM_a*_d*_i* @atom:*_bCM_a*_d*_i* - @bond:CM-CMD2 @atom:*_bCM_a*_d*_i* @atom:*_bCMD2_a*_d*_i* - @bond:CM-CT @atom:*_bCM_a*_d*_i* @atom:*_bCT_a*_d*_i* - @bond:CM-CT2 @atom:*_bCM_a*_d*_i* @atom:*_bCT2_a*_d*_i* - @bond:CM-EST1 @atom:*_bCM_a*_d*_i* @atom:*_bEST1_a*_d*_i* - @bond:CM-EST2 @atom:*_bCM_a*_d*_i* @atom:*_bEST2_a*_d*_i* - @bond:CM-PHE @atom:*_bCM_a*_d*_i* @atom:*_bPHE_a*_d*_i* - @bond:CM-SO4 @atom:*_bCM_a*_d*_i* @atom:*_bSO4_a*_d*_i* - @bond:CMD2-CT @atom:*_bCMD2_a*_d*_i* @atom:*_bCT_a*_d*_i* - @bond:CMD2-CT2 @atom:*_bCMD2_a*_d*_i* @atom:*_bCT2_a*_d*_i* - @bond:CT-CT @atom:*_bCT_a*_d*_i* @atom:*_bCT_a*_d*_i* - @bond:EST1-GL @atom:*_bEST1_a*_d*_i* @atom:*_bGL_a*_d*_i* - @bond:EST2-GL @atom:*_bEST2_a*_d*_i* @atom:*_bGL_a*_d*_i* - @bond:GL-PHE @atom:*_bGL_a*_d*_i* @atom:*_bPHE_a*_d*_i* - @bond:NC-PHE @atom:*_bNC_a*_d*_i* @atom:*_bPHE_a*_d*_i* - @bond:NH-PHE @atom:*_bNH_a*_d*_i* @atom:*_bPHE_a*_d*_i* - @bond:PHE1-PHE2 @atom:*_bPHE1_a*_d*_i* @atom:*_bPHE2_a*_d*_i* - @bond:C2T-CM2 @atom:*_bC2T_a*_d*_i* @atom:*_bCM2_a*_d*_i* - @bond:CM2-CTB @atom:*_bCM2_a*_d*_i* @atom:*_bCTB_a*_d*_i* - @bond:CM2R-CTBA @atom:*_bCM2R_a*_d*_i* @atom:*_bCTBA_a*_d*_i* - @bond:CM2R-OAB @atom:*_bCM2R_a*_d*_i* @atom:*_bOAB_a*_d*_i* - @bond:CMB-CMDB @atom:*_bCMB_a*_d*_i* @atom:*_bCMDB_a*_d*_i* - @bond:CMB-CMR5 @atom:*_bCMB_a*_d*_i* @atom:*_bCMR5_a*_d*_i* - @bond:CMB-CTBA @atom:*_bCMB_a*_d*_i* @atom:*_bCTBA_a*_d*_i* - @bond:CMB-CTBB @atom:*_bCMB_a*_d*_i* @atom:*_bCTBB_a*_d*_i* - @bond:CMDB-CTBA @atom:*_bCMDB_a*_d*_i* @atom:*_bCTBA_a*_d*_i* - @bond:CMDB-OAB @atom:*_bCMDB_a*_d*_i* @atom:*_bOAB_a*_d*_i* - @bond:CMR5-CTBB @atom:*_bCMR5_a*_d*_i* @atom:*_bCTBB_a*_d*_i* - @bond:CMR-CTBA @atom:*_bCMR_a*_d*_i* @atom:*_bCTBA_a*_d*_i* - @bond:CMR-CTBB @atom:*_bCMR_a*_d*_i* @atom:*_bCTBB_a*_d*_i* - @bond:CTB-CTBB @atom:*_bCTB_a*_d*_i* @atom:*_bCTBB_a*_d*_i* - @bond:CMR5-CTB @atom:*_bCMR5_a*_d*_i* @atom:*_bCTB_a*_d*_i* - } # end of bonds - - write_once("In Settings") { - # ----- Angles ----- - angle_coeff @angle:CM-CM-CM sdk 1.190000 173.000000 - angle_coeff @angle:CM-CM-CMD2 sdk 1.900000 161.000000 - angle_coeff @angle:CM-CM-CT sdk 1.190000 175.000000 - angle_coeff @angle:CM-CM-CT2 sdk 1.600000 172.000000 - angle_coeff @angle:CM-CM-EST1 sdk 1.000000 178.000000 - angle_coeff @angle:CM-CM-EST2 sdk 1.000000 178.000000 - angle_coeff @angle:CM-CM-PHE sdk 1.100000 178.000000 - angle_coeff @angle:CM-CMD2-CM sdk 6.000000 110.000000 - angle_coeff @angle:CM-EST1-GL sdk 0.800000 168.000000 - angle_coeff @angle:CM-EST2-GL sdk 0.800000 172.000000 - angle_coeff @angle:CM-PHE-NC sdk 3.300000 112.000000 - angle_coeff @angle:CT-CM-CT sdk 1.093000 175.500000 - angle_coeff @angle:CT-CM-CT2 sdk 1.600000 172.000000 - angle_coeff @angle:CT-CMD2-CT sdk 7.700000 116.000000 - angle_coeff @angle:CT2-CM-CT2 sdk 1.700000 173.000000 - angle_coeff @angle:CT2-CMD2-CT2 sdk 12.000000 110.000000 - angle_coeff @angle:EST1-GL-EST2 sdk 1.000000 95.000000 - angle_coeff @angle:EST1-GL-PHE sdk 1.400000 124.000000 - angle_coeff @angle:EST2-GL-PHE sdk 2.000000 138.000000 - angle_coeff @angle:GL-PHE-NC sdk 3.100000 112.000000 - angle_coeff @angle:GL-PHE-NH sdk 4.000000 102.000000 - angle_coeff @angle:C2T-CM2-CTB sdk 8.000000 160.000000 - angle_coeff @angle:CM2-CTB-CTBB sdk 4.000000 130.000000 - angle_coeff @angle:CM2R-CTBA-CMB harmonic 40.000000 112.500000 - angle_coeff @angle:CM2R-CTBA-CMDB harmonic 22.500000 75.900000 - angle_coeff @angle:CM2R-CTBA-CMR harmonic 35.000000 98.700000 - angle_coeff @angle:CM2R-OAB-CMDB harmonic 40.000000 63.900000 - angle_coeff @angle:CMB-CMDB-CTBA harmonic 45.000000 68.600000 - angle_coeff @angle:CMB-CMDB-OAB harmonic 65.000000 146.600000 - angle_coeff @angle:CMB-CMR5-CTBB harmonic 35.000000 67.800000 - angle_coeff @angle:CMB-CTBA-CMDB harmonic 25.000000 68.900000 - angle_coeff @angle:CMB-CTBA-CMR harmonic 75.000000 47.800000 - angle_coeff @angle:CMB-CTBB-CMR5 harmonic 25.000000 68.200000 - angle_coeff @angle:CMB-CTBB-CMR harmonic 50.000000 56.300000 - angle_coeff @angle:CMB-CTBB-CTB sdk 35.000000 120.700000 - angle_coeff @angle:CMDB-CMB-CMR5 harmonic 150.000000 175.600000 - angle_coeff @angle:CMDB-CMB-CTBA harmonic 62.500000 42.500000 - angle_coeff @angle:CMDB-CMB-CTBB harmonic 25.000000 134.200000 - angle_coeff @angle:CMDB-CTBA-CMR harmonic 50.000000 108.600000 - angle_coeff @angle:CMR5-CNB-CTBA harmonic 15.000000 135.800000 - angle_coeff @angle:CMR5-CMB-CTBB harmonic 45.000000 44.000000 - angle_coeff @angle:CMR5-CTBB-CTB harmonic 20.000000 62.700000 - angle_coeff @angle:CMR-CTBB-CMR5 harmonic 75.000000 107.000000 - angle_coeff @angle:CMR-CTBB-CTB sdk 37.500000 110.100000 - angle_coeff @angle:CTBA-CM2R-OAB harmonic 25.000000 107.400000 - angle_coeff @angle:CTBA-CMB-CTBB harmonic 20.000000 92.200000 - angle_coeff @angle:CTBA-CMDB-OAB harmonic 20.000000 91.800000 - angle_coeff @angle:CTBA-CMR-CTBB harmonic 15.000000 115.000000 - angle_coeff @angle:CMB-CMR5-CTB harmonic 88.000000 131.700000 - angle_coeff @angle:CTBB-CMR5-CTB harmonic 20.000000 77.400000 - angle_coeff @angle:CM2-CTB-CMR5 sdk 20.000000 118.000000 - angle_coeff @angle:CMR5-CTB-CTBB harmonic 62.500000 39.700000 - } - - write_once("Data Angles By Type") { - @angle:CM-CM-CM @atom:*_b*_aCM_d*_i* @atom:*_b*_aCM_d*_i* @atom:*_b*_aCM_d*_i* - @angle:CM-CM-CMD2 @atom:*_b*_aCM_d*_i* @atom:*_b*_aCM_d*_i* @atom:*_b*_aCMD2_d*_i* - @angle:CM-CM-CT @atom:*_b*_aCM_d*_i* @atom:*_b*_aCM_d*_i* @atom:*_b*_aCT_d*_i* - @angle:CM-CM-CT2 @atom:*_b*_aCM_d*_i* @atom:*_b*_aCM_d*_i* @atom:*_b*_aCT2_d*_i* - @angle:CM-CM-EST1 @atom:*_b*_aCM_d*_i* @atom:*_b*_aCM_d*_i* @atom:*_b*_aEST1_d*_i* - @angle:CM-CM-EST2 @atom:*_b*_aCM_d*_i* @atom:*_b*_aCM_d*_i* @atom:*_b*_aEST2_d*_i* - @angle:CM-CM-PHE @atom:*_b*_aCM_d*_i* @atom:*_b*_aCM_d*_i* @atom:*_b*_aPHE_d*_i* - @angle:CM-CMD2-CM @atom:*_b*_aCM_d*_i* @atom:*_b*_aCMD2_d*_i* @atom:*_b*_aCM_d*_i* - @angle:CM-EST1-GL @atom:*_b*_aCM_d*_i* @atom:*_b*_aEST1_d*_i* @atom:*_b*_aGL_d*_i* - @angle:CM-EST2-GL @atom:*_b*_aCM_d*_i* @atom:*_b*_aEST2_d*_i* @atom:*_b*_aGL_d*_i* - @angle:CM-PHE-NC @atom:*_b*_aCM_d*_i* @atom:*_b*_aPHE_d*_i* @atom:*_b*_aNC_d*_i* - @angle:CT-CM-CT @atom:*_b*_aCT_d*_i* @atom:*_b*_aCM_d*_i* @atom:*_b*_aCT_d*_i* - @angle:CT-CM-CT2 @atom:*_b*_aCT_d*_i* @atom:*_b*_aCM_d*_i* @atom:*_b*_aCT2_d*_i* - @angle:CT-CMD2-CT @atom:*_b*_aCT_d*_i* @atom:*_b*_aCMD2_d*_i* @atom:*_b*_aCT_d*_i* - @angle:CT2-CM-CT2 @atom:*_b*_aCT2_d*_i* @atom:*_b*_aCM_d*_i* @atom:*_b*_aCT2_d*_i* - @angle:CT2-CMD2-CT2 @atom:*_b*_aCT2_d*_i* @atom:*_b*_aCMD2_d*_i* @atom:*_b*_aCT2_d*_i* - @angle:EST1-GL-EST2 @atom:*_b*_aEST1_d*_i* @atom:*_b*_aGL_d*_i* @atom:*_b*_aEST2_d*_i* - @angle:EST1-GL-PHE @atom:*_b*_aEST1_d*_i* @atom:*_b*_aGL_d*_i* @atom:*_b*_aPHE_d*_i* - @angle:EST2-GL-PHE @atom:*_b*_aEST2_d*_i* @atom:*_b*_aGL_d*_i* @atom:*_b*_aPHE_d*_i* - @angle:GL-PHE-NC @atom:*_b*_aGL_d*_i* @atom:*_b*_aPHE_d*_i* @atom:*_b*_aNC_d*_i* - @angle:GL-PHE-NH @atom:*_b*_aGL_d*_i* @atom:*_b*_aPHE_d*_i* @atom:*_b*_aNH_d*_i* - @angle:C2T-CM2-CTB @atom:*_b*_aC2T_d*_i* @atom:*_b*_aCM2_d*_i* @atom:*_b*_aCTB_d*_i* - @angle:CM2-CTB-CTBB @atom:*_b*_aCM2_d*_i* @atom:*_b*_aCTB_d*_i* @atom:*_b*_aCTBB_d*_i* - @angle:CM2R-CTBA-CMB @atom:*_b*_aCM2R_d*_i* @atom:*_b*_aCTBA_d*_i* @atom:*_b*_aCMB_d*_i* - @angle:CM2R-CTBA-CMDB @atom:*_b*_aCM2R_d*_i* @atom:*_b*_aCTBA_d*_i* @atom:*_b*_aCMDB_d*_i* - @angle:CM2R-CTBA-CMR @atom:*_b*_aCM2R_d*_i* @atom:*_b*_aCTBA_d*_i* @atom:*_b*_aCMR_d*_i* - @angle:CM2R-OAB-CMDB @atom:*_b*_aCM2R_d*_i* @atom:*_b*_aOAB_d*_i* @atom:*_b*_aCMDB_d*_i* - @angle:CMB-CMDB-CTBA @atom:*_b*_aCMB_d*_i* @atom:*_b*_aCMDB_d*_i* @atom:*_b*_aCTBA_d*_i* - @angle:CMB-CMDB-OAB @atom:*_b*_aCMB_d*_i* @atom:*_b*_aCMDB_d*_i* @atom:*_b*_aOAB_d*_i* - @angle:CMB-CMR5-CTBB @atom:*_b*_aCMB_d*_i* @atom:*_b*_aCMR5_d*_i* @atom:*_b*_aCTBB_d*_i* - @angle:CMB-CTBA-CMDB @atom:*_b*_aCMB_d*_i* @atom:*_b*_aCTBA_d*_i* @atom:*_b*_aCMDB_d*_i* - @angle:CMB-CTBA-CMR @atom:*_b*_aCMB_d*_i* @atom:*_b*_aCTBA_d*_i* @atom:*_b*_aCMR_d*_i* - @angle:CMB-CTBB-CMR5 @atom:*_b*_aCMB_d*_i* @atom:*_b*_aCTBB_d*_i* @atom:*_b*_aCMR5_d*_i* - @angle:CMB-CTBB-CMR @atom:*_b*_aCMB_d*_i* @atom:*_b*_aCTBB_d*_i* @atom:*_b*_aCMR_d*_i* - @angle:CMB-CTBB-CTB @atom:*_b*_aCMB_d*_i* @atom:*_b*_aCTBB_d*_i* @atom:*_b*_aCTB_d*_i* - @angle:CMDB-CMB-CMR5 @atom:*_b*_aCMDB_d*_i* @atom:*_b*_aCMB_d*_i* @atom:*_b*_aCMR5_d*_i* - @angle:CMDB-CMB-CTBA @atom:*_b*_aCMDB_d*_i* @atom:*_b*_aCMB_d*_i* @atom:*_b*_aCTBA_d*_i* - @angle:CMDB-CMB-CTBB @atom:*_b*_aCMDB_d*_i* @atom:*_b*_aCMB_d*_i* @atom:*_b*_aCTBB_d*_i* - @angle:CMDB-CTBA-CMR @atom:*_b*_aCMDB_d*_i* @atom:*_b*_aCTBA_d*_i* @atom:*_b*_aCMR_d*_i* - @angle:CMR5-CNB-CTBA @atom:*_b*_aCMR5_d*_i* @atom:*_b*_aCNB_d*_i* @atom:*_b*_aCTBA_d*_i* - @angle:CMR5-CMB-CTBB @atom:*_b*_aCMR5_d*_i* @atom:*_b*_aCMB_d*_i* @atom:*_b*_aCTBB_d*_i* - @angle:CMR5-CTBB-CTB @atom:*_b*_aCMR5_d*_i* @atom:*_b*_aCTBB_d*_i* @atom:*_b*_aCTB_d*_i* - @angle:CMR-CTBB-CMR5 @atom:*_b*_aCMR_d*_i* @atom:*_b*_aCTBB_d*_i* @atom:*_b*_aCMR5_d*_i* - @angle:CMR-CTBB-CTB @atom:*_b*_aCMR_d*_i* @atom:*_b*_aCTBB_d*_i* @atom:*_b*_aCTB_d*_i* - @angle:CTBA-CM2R-OAB @atom:*_b*_aCTBA_d*_i* @atom:*_b*_aCM2R_d*_i* @atom:*_b*_aOAB_d*_i* - @angle:CTBA-CMB-CTBB @atom:*_b*_aCTBA_d*_i* @atom:*_b*_aCMB_d*_i* @atom:*_b*_aCTBB_d*_i* - @angle:CTBA-CMDB-OAB @atom:*_b*_aCTBA_d*_i* @atom:*_b*_aCMDB_d*_i* @atom:*_b*_aOAB_d*_i* - @angle:CTBA-CMR-CTBB @atom:*_b*_aCTBA_d*_i* @atom:*_b*_aCMR_d*_i* @atom:*_b*_aCTBB_d*_i* - @angle:CMB-CMR5-CTB @atom:*_b*_aCMB_d*_i* @atom:*_b*_aCMR5_d*_i* @atom:*_b*_aCTB_d*_i* - @angle:CTBB-CMR5-CTB @atom:*_b*_aCTBB_d*_i* @atom:*_b*_aCMR5_d*_i* @atom:*_b*_aCTB_d*_i* - @angle:CM2-CTB-CMR5 @atom:*_b*_aCM2_d*_i* @atom:*_b*_aCTB_d*_i* @atom:*_b*_aCMR5_d*_i* - @angle:CMR5-CTB-CTBB @atom:*_b*_aCMR5_d*_i* @atom:*_b*_aCTB_d*_i* @atom:*_b*_aCTBB_d*_i* - } # end of angles - - write_once("In Init") { - # Warning: This is a very generic "In Init" section, further - # modification prior to any simulation is extremely likely - units real - atom_style full - bond_style hybrid harmonic - angle_style hybrid sdk - pair_style hybrid lj/sdk/coul/long 9.000000 12.000000 - special_bonds lj/coul 0.0 0.0 0.0 - } # end init -} # SDK diff --git a/tools/moltemplate/moltemplate/force_fields/__init__.py b/tools/moltemplate/moltemplate/force_fields/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/tools/moltemplate/moltemplate/force_fields/compass_original_format/README.txt b/tools/moltemplate/moltemplate/force_fields/compass_original_format/README.txt new file mode 100644 index 0000000000..d228c3c18f --- /dev/null +++ b/tools/moltemplate/moltemplate/force_fields/compass_original_format/README.txt @@ -0,0 +1,30 @@ +This directoroy contains the COMPASS force field parameters in the original +MSI file format ("compass_published.frc" which is distributed with "msi2lmp"). +It can be converted into moltemplate format using the following command: + +msifrc2lt.py -name COMPASS < compass_published.frc > compass_published.lt + +--- Credits: ---- + This is an incomplete version of the COMPASS force field based on available +public sources. Parameters for some common chemical groups are missing +(for example, the NH2 amine group). The commercial version of COMPASS is +much larger and presumably includes more up to date parameters and parameters +for a wider range of atom types and molecule types. (However files +containing those force field parameters are not publicly available.) + + This file has been graciously made available by Materials Design Inc. + + Here is a comment from "compass_published.frc": + + "This file created by Materials Design, Inc. (www.materialsdesign.com) +Please realize that we neither support this version, nor make any warranty +as to the correctness of the parameters. We have checked the numbers against +the literature, but of course there may still be errors, including errors of +interpretation. Also, the current version of COMPASS may well be different +that that originally published. + If you have comments or suggestions, feel free to email Paul Saxe +at psaxe (at) materialsdesign.com" + +(Note: This file predates moltemplate and was intended for use with other + software. Paul Saxe cannot be expected to answer questions related to + moltemplate.) diff --git a/tools/moltemplate/moltemplate/force_fields/compass_original_format/compass_published.frc b/tools/moltemplate/moltemplate/force_fields/compass_original_format/compass_published.frc new file mode 100644 index 0000000000..6c2e681b5c --- /dev/null +++ b/tools/moltemplate/moltemplate/force_fields/compass_original_format/compass_published.frc @@ -0,0 +1,1381 @@ +!BIOSYM forcefield 1 + +#version compass_published.frc 1.1 30-Jun-09 +#version compass_published.frc 1.0 01-Jun-09 + +#define compass + +!Ver Ref Function Label +!---- --- --------------------------------- ------ + 1.0 1 atom_types compass + 1.0 1 equivalence compass + 1.0 1 quartic_bond compass + 1.0 1 quartic_angle compass + 1.0 1 bond-bond compass + 1.0 1 bond-bond_1_3 compass + 1.0 1 bond-angle compass + 1.0 1 torsion_3 compass + 1.0 1 end_bond-torsion_3 compass + 1.0 1 middle_bond-torsion_3 compass + 1.0 1 angle-torsion_3 compass + 1.0 1 wilson_out_of_plane compass + 1.0 1 angle-angle compass + 1.0 1 angle-angle-torsion_1 compass + 1.0 1 nonbond(9-6) compass + 1.0 1 bond_increments compass + 1.0 1 templates compass + +#atom_types compass + +> Atom type definitions for any variant of compass +> Masses from CRC 1973/74 pages B-250. + +!Ver Ref Type Mass Element Comment +!---- --- ---- ---------- ------- ----------------------------------------- + 1.0 5 ar 39.94400 Ar argon + 1.0 1 c3a 12.01115 C aromatic carbon + 1.0 5 c1o 12.01115 C carbon in CO + 1.0 5 c2= 12.01115 C carbon in CO2 and CS2 + 1.0 7 c3' 12.01115 C carbonyl carbon [one polar substituent] + 1.0 1 c4 12.01115 C generic sp3 carbon + 1.0 8 c41o 12.01115 C carbon, sp3, in methanol + 1.0 8 c43o 12.01115 C carbon, sp3 in secondary alcohols + 1.0 1 c43 12.01115 C sp3 carbon with three heavy atoms attached + 1.0 1 c44 12.01115 C sp3 carbon with four heavy atoms attached + 1.0 3 c4o 12.01115 C alpha carbon + 1.0 9 c4z 12.01115 C carbon, sp3, bonded to -N3 + 1.0 1 h1 1.00797 H nonpolar hydrogen + 1.0 5 h1h 1.00797 H hydrogen in H2 + 1.0 3 h1o 1.00797 H strongly polar hydrogen, bonded to O,F + 1.0 5 he 4.00300 He helium + 1.0 5 kr 83.80000 Kr krypton + 1.0 5 n1n 14.00670 N nitrogen in N2 + 1.0 5 n1o 14.00670 N nitrogen in NO + 1.0 5 n1z 14.00670 N nitrogen, terminal atom in -N3 + 1.0 4 n2= 14.00670 N nitrogen + 1.0 5 n2o 14.00670 N nitrogen in NO2 + 1.0 9 n2t 14.00670 N nitrogen, central atom in -N3 + 1.0 9 n2z 14.00670 N nitrogen, first atom in -N3 + 1.0 7 n3m 14.00670 N sp3 nitrogen in amides without hydrogen + 1.0 6 n3o 14.00670 N nitrogen in nitro group + 1.0 5 ne 20.18300 Ne neon + 1.0 5 o1= 15.99940 O oxygen in NO2 and SO2 [and carbonyl] + 1.0 5 o1=* 15.99940 O oxygen in CO2 + 1.0 6 o12 15.99940 O oxygen in nitro group (-NO2) + 1.0 5 o1c 15.99940 O oxygen in CO + 1.0 5 o1n 15.99940 O oxygen in NO + 1.0 5 o1o 15.99940 O oxygen in O2 + 1.0 2 o2 15.99940 O generic oxygen with two bonds attached + 1.0 3 o2e 15.99940 O ether oxygen + 1.0 3 o2h 15.99940 O hydroxyl oxygen + 1.0 6 o2n 15.99940 O oxygen in nitrates + 1.0 7 o2s 15.99940 O ester oxygen + 1.0 2 o2z 15.99940 O oxygen, in siloxanes and zeolites + 1.0 4 p4= 30.97380 P phosphorous + 1.0 5 s1= 32.06400 S sulfur in CS2 + 1.0 5 s2= 32.06400 S sulfur in SO2 + 1.0 2 si4 28.08600 Si generic silicon with four bonds attached + 1.0 2 si4c 28.08600 Si a subset of si4, non-hydrogen atom attached [siloxanes] + 1.0 5 xe 131.30000 Xe xenon + + +#equivalence compass + +! Equivalences +! ----------------------------------------- +!Ver Ref Type NonB Bond Angle Torsion OOP +!---- --- ---- ---- ---- ----- ------- ---- + 1.0 5 ar ar ar ar ar ar + 1.0 5 c1o c1o c1o c1o c1o c1o + 1.0 5 c2= c2= c2= c2= c2= c2= + 1.0 1 c3a c3a c3a c3a c3a c3a + 1.0 7 c3' c3' c3' c3' c3' c3' + 1.0 1 c4 c4 c4 c4 c4 c4 + 1.0 8 c41o c41o c4 c4 c4 c4 + 1.0 8 c43o c43o c4 c4 c4 c4 + 1.0 1 c43 c43 c4 c4 c4 c4 + 1.0 1 c44 c44 c4 c4 c4 c4 + 1.0 3 c4o c4o c4 c4 c4 c4 + 1.0 9 c4z c4z c4 c4 c4 c4 + 1.0 1 h1 h1 h1 h1 h1 h1 + 1.0 5 h1h h1h h1h h1 h1 h1 + 1.0 3 h1o h1o h1 h1 h1 h1 + 1.0 5 he he he he he he + 1.0 5 kr kr kr kr kr kr + 1.0 5 n1n n1n n1n n1n n1n n1n + 1.0 5 n1o n1o n1o n1o n1o n1o + 1.0 9 n1z n1z n1t n1t n1t n1t + 1.0 4 n2= n2= n2= n2= n2= n2= + 1.0 5 n2o n2o n2o n2o n2o n2o + 1.0 9 n2t n2t n2t n2t n2t n2t + 1.0 9 n2z n2z n2z n2z n2z n2z + 1.0 7 n3m n3m n3m n3m n3m n3m + 1.0 6 n3o n3o n3o n3o n3o n3o + 1.0 5 ne ne ne ne ne ne + 1.0 5 o1= o1= o1= o1= o1= o1= + 1.0 5 o1=* o1=* o1= o1= o1= o1= + 1.0 6 o12 o12 o1= o1= o1= o1= + 1.0 5 o1c o1c o1c o1c o1c o1c + 1.0 5 o1n o1n o1n o1n o1n o1n + 1.0 5 o1o o1o o1o o1o o1o o1o + 1.0 2 o2 o2 o2 o2 o2 o2 + 1.0 3 o2h o2h o2h o2 o2 o2 + 1.0 3 o2e o2e o2e o2 o2 o2 + 1.0 6 o2n o2n o2n o2n o2 o2 + 1.0 7 o2s o2s o2e o2 o2 o2 + 1.0 2 o2z o2z o2z o2z o2z o2z + 1.0 4 p4= p4= p4= p4= p4= p4= + 1.0 5 s1= s1= s1= s1= s1= s1= + 1.0 5 s2= s2= s2= s2= s2= s2= + 1.0 2 si4 si4 si4 si4 si4 si4 + 1.0 2 si4c si4c si4 si4 si4 si4 + 1.0 5 xe xe xe xe xe xe + + +#quartic_bond compass + +> E = K2 * (R - R0)^2 + K3 * (R - R0)^3 + K4 * (R - R0)^4 + +!Ver Ref I J R0 K2 K3 K4 +!---- --- ---- ---- ------- -------- --------- -------- + 1.0 1 c3a c3a 1.4170 470.8361 -627.6179 1327.6345 + 1.0 1 c3a c4 1.5010 321.9021 -521.8208 572.1628 + 1.0 1 c3a h1 1.0982 372.8251 -803.4526 894.3173 + 1.0 1 c4 c4 1.5300 299.6700 -501.7700 679.8100 + 1.0 1 c4 h1 1.1010 345.0000 -691.8900 844.6000 + 1.0 2 o2z si4 1.6400 350.1232 -517.3424 673.7067 + 1.0 3 c3a o2 1.3768 428.8798 -738.2350 1114.9655 + 1.0 3 c3a o2e 1.3768 428.8798 -738.2351 1114.9655 + 1.0 3 c3a o2h 1.3768 428.8798 -738.2351 1114.9655 + 1.0 3 c4 o2e 1.4200 400.3954 -835.1951 1313.0142 + 1.0 3 c4 o2h 1.4200 400.3954 -835.1951 1313.0142 + 1.0 3 h1 o2h 0.9494 540.3633 -1311.8663 2132.4446 + 1.0 4 c3a n2= 1.4000 350.0000 0.0000 0.0000 + 1.0 4 c3a p4= 1.7890 197.7020 -332.2510 325.7160 + 1.0 4 c4 n2= 1.4740 337.0600 -147.3700 213.6330 + 1.0 4 c4 p4= 1.8000 218.1400 -329.5110 290.3490 + 1.0 4 cl1p p4= 2.0000 158.7770 -239.1290 210.0840 + 1.0 4 f1p p4= 1.5650 340.0000 -882.3840 1197.9190 + 1.0 4 h1 n2= 1.0310 540.1120 -1500.2952 2431.0080 + 1.0 4 h1 p4= 1.4300 285.2040 -575.6850 677.8460 + 1.0 4 n2= p4= 1.5980 393.0060 -751.4050 767.4310 + 1.0 4 n3 p4= 1.6780 329.0000 -713.7950 902.9190 + 1.0 4 o2 p4= 1.6000 333.0980 -726.6230 924.6200 + 1.0 5 h1h h1h 0.7412 414.2185 -805.6549 914.1296 + 1.0 5 n1n n1n 1.0977 1651.3730 -4069.3178 5984.9629 + 1.0 5 o1o o1o 1.2074 846.7150 -2247.1760 3478.9900 + 1.0 5 c1o o1c 1.1283 1368.7676 -3157.0007 4247.5298 + 1.0 5 n1o o1n 1.1506 1147.8362 -3167.7349 5099.5811 + 1.0 5 o1= s2= 1.4308 730.8387 -1531.7910 1859.7753 + 1.0 5 c2= o1= 1.1600 1161.3421 -2564.5706 3932.8735 + 1.0 5 n2o o1= 1.1930 620.0000 -1808.6018 3077.5918 + 1.0 5 c2= s1= 1.5540 559.0065 -1348.6633 1248.8604 + 1.0 6 c3a n3o 1.4300 313.8329 -568.6087 600.9597 + 1.0 6 c4 n3o 1.4740 301.6051 -535.7028 555.0420 + 1.0 6 c4 o2n 1.4350 400.3954 -835.1951 1313.0142 + 1.0 6 h1 n3o 1.0400 439.9346 -943.7307 1180.9318 + 1.0 6 n3o o1= 1.2100 765.0664 -2070.2830 2793.3218 + 1.0 6 n3o o2n 1.4020 300.0000 -1000.0000 2000.0000 + 1.0 7 c3' o2e 1.3750 368.7309 -832.4784 1274.0231 + 1.0 7 c3' c4 1.5140 312.3719 -465.8290 473.8300 + 1.0 7 c3' o1= 1.2160 823.7948 -1878.7939 2303.5310 + 1.0 7 c3' c3a 1.4890 339.3574 -655.7236 670.2362 + 1.0 7 c3' n3m 1.3850 359.1591 -558.4730 1146.3810 + 1.0 7 c3a n3m 1.3950 344.0452 -652.1208 1022.2242 + 1.0 9 n1t n1t 1.1354 1337.7450 -2675.4900 3121.4049 + 1.0 9 n2z n2t 1.2343 720.3345 -1542.6689 1799.7804 + 1.0 9 n2t n1t 1.1354 1198.7450 -2675.4900 3121.4049 + 1.0 9 n2z c4 1.4814 324.4578 -648.9156 757.0681 + 1.0 9 n2z h1 1.0221 440.1623 -960.3246 1120.3787 + 1.0 10 c3a si4 1.8634 233.2433 -276.8692 161.6659 + 1.0 10 c4 si4 1.8995 189.6536 -279.4210 307.5135 + 1.0 10 h1 si4 1.4783 202.7798 -305.3603 280.2685 + 1.0 10 si4 si4 2.3384 114.2164 -140.4212 80.7084 + 1.0 10 c4 n3m 1.4000 350.0000 0.0000 0.0000 + + +#quartic_angle compass + +> Delta = Theta - Theta0 +> E = K2 * Delta^2 + K3 * Delta^3 + K4 * Delta^4 + +!Ver Ref I J K Theta0 K2 K3 K4 +!---- --- ---- ---- ---- -------- ------- -------- -------- + 1.0 1 c3a c3a c3a 118.9000 61.0226 -34.9931 0.0000 + 1.0 1 c3a c3a c4 120.0500 44.7148 -22.7352 0.0000 + 1.0 1 c3a c3a h1 117.9400 35.1558 -12.4682 0.0000 + 1.0 1 c3a c4 c3a 111.0000 44.3234 -9.4454 0.0000 + 1.0 1 c3a c4 c4 108.4000 43.9594 -8.3924 -9.3379 + 1.0 1 c3a c4 h1 111.0000 44.3234 -9.4454 0.0000 + 1.0 1 c4 c4 c4 112.6700 39.5160 -7.4430 -9.5583 + 1.0 1 c4 c4 h1 110.7700 41.4530 -10.6040 5.1290 + 1.0 1 h1 c4 h1 107.6600 39.6410 -12.9210 -2.4318 + 1.0 2 h1 o2z si4 122.8000 23.7764 -19.8152 9.6331 + 1.0 2 si4 o2z si4 159.0000 8.5000 -13.4188 -4.1785 + 1.0 2 c3a si4 o2z 114.9060 23.0218 -31.3993 24.9814 + 1.0 2 c4 si4 o2z 114.9060 23.0218 -31.3993 24.9814 + 1.0 2 h1 si4 o2z 107.4000 57.6643 -10.6506 4.6274 + 1.0 2 o2z si4 o2z 110.7000 70.3069 -6.9375 0.0000 + 1.0 3 c3a c3a o2 123.4200 73.6781 -21.6787 0.0000 + 1.0 3 c4 c4 o2 111.2700 54.5381 -8.3642 -13.0838 + 1.0 3 h1 c4 o2 108.7280 58.5446 -10.8088 -12.4006 + 1.0 3 c3a o2 c4 102.9695 38.9739 -6.2595 -8.1710 + 1.0 3 c3a o2 h1 108.1900 53.1250 -8.5016 0.0000 + 1.0 3 c4 o2 c4 104.5000 35.7454 -10.0067 -6.2729 + 1.0 3 c4 o2 h1 105.8000 52.7061 -12.1090 -9.8681 + 1.0 4 c3a c3a n2= 120.0000 60.0000 0.0000 0.0000 + 1.0 4 c3a c3a p4= 120.0010 47.8410 -15.2290 -10.9070 + 1.0 4 c4 c4 n2= 117.3170 55.2420 0.0000 0.0000 + 1.0 4 h1 c4 n2= 107.4990 62.7310 0.0000 0.0000 + 1.0 4 h1 c4 p4= 110.8860 33.8300 -7.0430 -7.2460 + 1.0 4 c4 n2= h1 117.2000 37.2620 0.0000 0.0000 + 1.0 4 h1 n2= h1 110.9100 31.0910 0.0000 0.0000 + 1.0 4 h1 n2= p4= 120.0000 26.0680 -8.2980 -5.9430 + 1.0 4 p4= n2= p4= 135.0000 23.8680 -8.7360 0.0000 + 1.0 4 c4 n3 p4= 120.0830 25.0010 -6.1170 -5.4570 + 1.0 4 h1 n3 p4= 120.0830 25.0010 -6.1170 -5.4570 + 1.0 4 c4 o2 p4= 118.2830 35.0010 -10.3600 -7.8700 + 1.0 4 h1 o2 p4= 117.0000 26.0310 -5.8280 -5.6200 + 1.0 4 c3a p4= c3a 110.2310 56.1850 -17.3160 -12.7280 + 1.0 4 c3a p4= h1 108.2310 36.1850 -6.4880 -7.6460 + 1.0 4 c3a p4= n2= 109.6000 63.0620 -19.7400 -14.3290 + 1.0 4 c3a p4= n3 108.1650 70.9770 -11.5480 -15.1090 + 1.0 4 c3a p4= o2 107.3650 71.9770 -10.9430 -15.2900 + 1.0 4 c4 p4= c4 102.5000 48.2320 -5.7980 -9.9660 + 1.0 4 c4 p4= h1 102.9000 52.0710 -6.4680 -10.7730 + 1.0 4 c4 p4= n2= 119.3000 47.3660 -14.6410 -10.7360 + 1.0 4 h1 p4= h1 101.4080 39.6950 -5.1340 -8.2270 + 1.0 4 h1 p4= n2= 110.0330 45.9780 -14.0520 -10.3990 + 1.0 4 h1 p4= n3 103.9780 68.2570 -9.2210 -14.1740 + 1.0 4 h1 p4= o2 103.9780 73.2570 -9.8970 -15.2120 + 1.0 4 n2= p4= n2= 125.0000 90.5230 -20.8010 -19.6020 + 1.0 4 n2= p4= n3 123.2150 89.9230 -32.6120 -21.0960 + 1.0 4 n2= p4= o2 112.2150 99.9230 -32.0930 -22.8210 + 1.0 4 n3 p4= n3 107.1000 85.7690 -5.7790 -17.4890 + 1.0 4 n3 p4= o2 108.3000 86.7690 -5.1750 -17.6710 + 1.0 4 o2 p4= o2 107.5000 86.7690 -4.5700 -17.8520 + 1.0 5 o1= c2= o1= 180.0000 57.1000 0.0000 0.0000 + 1.0 5 s1= c2= s1= 180.0000 48.0000 0.0000 0.0000 + 1.0 5 o1= n2o o1= 134.1000 150.0000 -82.1013 -40.0005 + 1.0 5 o1= s2= o1= 119.3000 115.2627 -35.6278 -26.1261 + 1.0 6 c3a c3a n3o 118.8000 29.2436 -8.8495 -6.6020 + 1.0 6 h1 c4 n3o 107.0000 54.9318 -9.1333 -11.5434 + 1.0 6 h1 c4 o2n 108.7280 58.5446 -10.8088 -12.4006 + 1.0 6 c3a n3o o1= 117.7000 63.9404 -18.4524 -14.3129 + 1.0 6 c4 n3o o1= 117.5000 64.5228 -18.4582 -14.4215 + 1.0 6 h1 n3o o1= 115.7000 53.8034 -14.1991 -11.8708 + 1.0 6 o1= n3o o1= 128.0000 95.1035 -47.4240 -27.9164 + 1.0 6 c4 o2n n3o 108.5000 55.7454 -10.0067 -6.2729 + 1.0 6 c4 c4 o2n 105.0000 54.5381 -8.3642 -13.0838 + 1.0 6 o2n n3o o1= 112.8000 85.5228 -18.4582 -14.4215 + 1.0 7 c3' o2 c4 109.0000 38.9739 -6.2595 -8.1710 + 1.0 7 c3' c4 h1 107.8594 38.0833 -17.5074 0.0000 + 1.0 7 c3' n3m c3' 121.9556 76.3105 -26.3166 -17.6944 + 1.0 7 c3a c3a c3' 116.0640 71.2598 -15.8273 2.0506 + 1.0 7 c3a c3' n3m 108.4400 84.8377 -19.9640 2.7405 + 1.0 7 c3a c3' o1= 125.5320 72.3167 -16.0650 2.0818 + 1.0 7 c3a c3a n3m 120.7640 73.2738 -27.4033 13.3920 + 1.0 7 c3a n3m c3' 120.0700 47.1131 -32.5592 13.1257 + 1.0 7 o1= c3' o2 118.9855 98.6813 -22.2485 10.3673 + 1.0 7 o1= c3' c4 119.3000 65.1016 -17.9766 0.0000 + 1.0 7 o2 c3' c4 100.3182 88.8631 -3.8323 -7.9802 + 1.0 7 n3m c3' o1= 121.5420 92.5720 -34.4800 -11.1871 + 1.0 9 n2z n2t n1t 171.6211 47.7899 0.0000 0.0000 + 1.0 9 n2t n2z h1 110.0345 55.7635 0.6618 0.0022 + 1.0 9 n2t n2z c4 113.5017 82.6294 0.9845 0.0033 + 1.0 9 n2z c4 h1 107.9744 52.7803 0.6615 0.0023 + 1.0 9 n2z c4 c4 110.9900 77.9387 0.9499 0.0033 + 1.0 10 c3a c3a si4 120.0000 30.4689 -23.5439 0.0000 + 1.0 10 c4 c4 si4 112.6700 39.5160 -7.4430 0.0000 + 1.0 10 h1 c4 si4 112.0355 28.7721 -13.9523 0.0000 + 1.0 10 c3a si4 h1 109.5932 41.9497 -42.3639 48.1442 + 1.0 10 c4 si4 c4 113.1855 36.2069 -20.3939 20.0172 + 1.0 10 c4 si4 h1 112.0977 36.4832 -12.8094 0.0000 + 1.0 10 h1 si4 h1 108.6051 32.5415 -8.3164 0.0000 + 1.0 10 c4 si4 si4 113.0000 19.4692 -34.3471 0.0000 + 1.0 10 h1 si4 si4 112.0893 22.5062 -11.5926 0.0000 + 1.0 10 si4 si4 si4 114.2676 24.9501 -19.5949 0.0000 + +#bond-bond compass + +> E = K(b,b') * (R - R0) * (R' - R0') + +!Ver Ref I J K K(b,b') +!---- --- ---- ---- ---- ------- + 1.0 1 c3a c3a c3a 68.2856 + 1.0 1 c3a c3a c4 12.0676 + 1.0 1 c3a c3a h1 1.0795 + 1.0 1 c3a c4 h1 2.9168 + 1.0 1 c4 c4 h1 3.3872 + 1.0 1 h1 c4 h1 5.3316 + 1.1 2 h1 c4 si4 6.3820 + 1.0 2 h1 o2z si4 6.3820 + 1.0 2 si4 o2z si4 41.1143 + 1.0 2 c4 si4 o2z 5.4896 + 1.0 2 h1 si4 o2z 11.6183 + 1.0 2 o2z si4 o2z 41.1143 + 1.0 3 c3a c3a o2 48.4754 + 1.0 3 h1 c3a o2 4.5800 + 1.0 3 c4 c4 o2 11.4318 + 1.0 3 h1 c4 o2 23.1979 + 1.0 3 o2 c4 o2 8.2983 + 1.0 3 c3a o2 h1 20.6577 + 1.0 3 c4 o2 c4 -7.1131 + 1.0 3 c4 o2 h1 -9.6879 + 1.0 4 c4 c4 n2= 22.7100 + 1.0 4 h1 c4 n2= 5.6640 + 1.0 4 h1 c4 p4= 1.0500 + 1.0 4 c4 n2= h1 12.5630 + 1.0 4 h1 n2= h1 1.4570 + 1.0 4 h1 n2= p4= -18.2870 + 1.0 4 p4= n2= p4= 20.0000 + 1.0 4 c4 p4= c4 6.2460 + 1.0 4 c4 p4= h1 3.8820 + 1.0 4 c4 p4= n2= 1.0720 + 1.0 4 h1 p4= h1 20.0000 + 1.0 4 h1 p4= n2= 12.5700 + 1.0 4 n2= p4= n2= 20.0000 + 1.0 5 o1= c2= o1= 275.4350 + 1.0 5 s1= c2= s1= 100.7369 + 1.0 5 o1= n2o o1= 20.0000 + 1.0 5 o1= s2= o1= 20.0000 + 1.0 6 c3a c3a n3o 21.0495 + 1.0 6 c4 c4 o2n 11.4318 + 1.0 6 h1 c4 n3o 3.3770 + 1.0 6 h1 c4 o2n 23.1979 + 1.0 6 c3a n3o o1= 93.7948 + 1.0 6 o2n n3o o1= 80.0000 + 1.0 6 c4 n3o o1= 48.1403 + 1.0 6 h1 n3o o1= 14.8226 + 1.0 6 o1= n3o o1= 265.7106 + 1.0 7 c3' o2 c3a 69.5999 + 1.0 7 c3' c4 h1 2.2522 + 1.0 7 c3' n3m c3' 25.9530 + 1.0 7 c3a c4 o2 0.0000 + 1.0 7 c3a o2 c3a 0.0000 + 1.0 7 c3' c3a c3a 37.8749 + 1.0 7 c3a c3' n3m 0.0000 + 1.0 7 c3a c3' o1= 116.9445 + 1.0 7 c3a c3a n3m 37.8749 + 1.0 7 c3a n3m c3' 0.0000 + 1.0 7 o1= c3' o2 210.1813 + 1.0 7 c4 c3' o1= 77.5201 + 1.0 7 c4 c3' o2 19.1069 + 1.0 7 n3m c3' o1= 138.4954 + 1.0 9 h1 n2z n2t 14.9026 + 1.0 9 n2z n2t n1t 204.9909 + 1.0 9 n2t n2z c4 84.2075 + 1.0 9 n2z c4 h1 18.4621 + 1.0 9 n2z c4 c4 36.9309 + 1.0 10 h1 c4 si4 1.6561 + 1.0 10 c3a c3a si4 21.3938 + 1.0 10 c3a si4 h1 3.9264 + 1.0 10 c4 si4 c4 3.7419 + 1.0 10 c4 si4 h1 3.9340 + 1.0 10 c4 si4 si4 2.3030 + 1.0 10 h1 si4 h1 4.6408 + 1.0 10 h1 si4 si4 3.5172 + 1.0 10 si4 si4 si4 6.0704 + + +#bond-bond_1_3 compass + +> E = K(b,b') * (R - R0) * (R' - R0') + +!Ver Ref I J K L K(b,b') +!--- --- ----- ----- ----- ----- -------- + 1.0 1 c3a c3a c3a c3a 53.0000 + 1.0 1 c3a c3a c3a c4 2.5085 + 1.0 1 c3a c3a c3a h1 -6.2741 + 1.0 1 c4 c3a c3a h1 0.8743 + 1.0 1 h1 c3a c3a h1 -1.7077 + 1.0 1 c3a c3a c4 h1 -3.4826 + 1.0 3 c3a c3a c3a o2 -2.2436 + 1.0 3 h1 c3a c3a o2 -2.0517 + 1.0 3 c3a c3a o2 h1 1.1590 + + +#bond-angle compass + +> E = K * (R - R0) * (Theta - Theta0) + +!Ver Ref I J K K(b,theta) K(b',theta) +!---- --- ---- ---- ---- ---------- ----------- + 1.0 1 c3a c3a c3a 28.8708 + 1.0 1 c3a c3a c4 31.0771 47.0579 + 1.0 1 c3a c3a h1 20.0033 24.2183 + 1.0 1 c3a c4 h1 26.4608 11.7717 + 1.0 1 c4 c4 c4 8.0160 + 1.0 1 c4 c4 h1 20.7540 11.4210 + 1.0 1 h1 c4 h1 18.1030 + 1.0 2 h1 o2z si4 18.0902 31.0726 + 1.0 2 si4 o2z si4 28.6686 + 1.0 2 c4 si4 o2z 6.4278 20.5669 + 1.0 2 h1 si4 o2z 6.4278 20.5669 + 1.0 2 o2z si4 o2z 23.4380 + 1.0 3 c3a c3a o2 58.4790 107.6806 + 1.0 3 c4 c4 o2 2.6868 20.4033 + 1.0 3 h1 c4 o2 4.6189 55.3270 + 1.0 3 c3a o2 h1 53.8614 23.9224 + 1.0 3 c4 o2 c4 -2.8112 + 1.0 3 c4 o2 h1 28.5800 18.9277 + 1.0 4 c4 c4 n2= 19.2440 59.4220 + 1.0 4 h1 c4 n2= 6.4070 46.3730 + 1.0 4 h1 c4 p4= 19.8120 16.9400 + 1.0 4 c4 n2= h1 18.4860 7.8370 + 1.0 4 h1 n2= h1 8.4900 + 1.0 4 h1 n2= p4= 40.0630 90.7910 + 1.0 4 c4 p4= c4 12.8050 + 1.0 4 c4 p4= h1 11.1260 -19.4700 + 1.0 4 c4 p4= n2= -7.1280 26.3530 + 1.0 4 h1 p4= n2= -24.3830 72.9250 + 1.0 5 o1= n2o o1= -50.0000 + 1.0 5 o1= s2= o1= 45.0585 + 1.0 6 c3a c3a n3o 30.5211 59.8025 + 1.0 6 c4 c4 o2n 2.6868 20.4033 + 1.0 6 h1 c4 n3o 12.2491 30.5314 + 1.0 6 h1 c4 o2n 4.6189 55.3270 + 1.0 6 c3a n3o o1= 40.3757 92.1955 + 1.0 6 c4 n3o o1= 27.2141 93.9927 + 1.0 6 h1 n3o o1= -8.6275 58.6036 + 1.0 6 o1= n3o o1= 95.6936 + 1.0 7 c3' o2 c4 21.5366 -16.6748 + 1.0 7 c3' c4 h1 15.5988 14.6287 + 1.0 7 c3' n3m c3' 20.0533 + 1.0 7 c3' c3a c3a 23.6977 45.8865 + 1.0 7 c3a c3a n3m 35.8865 53.6977 + 1.0 7 c3a c3' o1= 72.8758 76.1093 + 1.0 7 o1= c3' o2 79.4497 57.0987 + 1.0 7 c4 c3' o1= 31.8455 46.6613 + 1.0 7 c4 c3' o2 1.3435 4.6978 + 1.0 7 n3m c3' o1= 62.7124 52.4045 + 1.0 9 h1 n2z n2t 37.4419 141.1218 + 1.0 9 n2z n2t n1t 25.5611 1.2222 + 1.0 9 n2t n2z c4 195.9722 88.2679 + 1.0 9 n2z c4 h1 61.9652 3.3182 + 1.0 9 n2z c4 c4 67.8888 34.8803 + 1.0 10 c3a c3a si4 14.5831 23.7679 + 1.0 10 h1 c4 si4 16.6908 18.2764 + 1.0 10 c3a si4 h1 22.5947 8.7811 + 1.0 10 c4 si4 c4 18.5805 + 1.0 10 c4 si4 h1 13.3961 7.4104 + 1.0 10 c4 si4 si4 16.9455 11.4377 + 1.0 10 h1 si4 h1 9.3467 + 1.0 10 h1 si4 si4 5.6630 2.0706 + 1.0 10 si4 si4 si4 8.9899 + + +#torsion_3 compass + +> E = SUM(n=1,3) { V(n) * [ 1 - cos(n*Phi - Phi0(n)) ] } + +!Ver Ref I J K L V1 Phi0 V2 Phi0 V3 Phi0 +!---- --- ---- ---- ---- ---- ------- ------ ------- ------ ------- ------ + 1.0 1 c3a c3a c3a c3a 8.3667 0.0 1.2000 0.0 0.0000 0.0 + 1.0 1 c3a c3a c3a c4 0.0000 0.0 4.4072 0.0 0.0000 0.0 + 1.0 1 c3a c3a c3a h1 0.0000 0.0 3.9661 0.0 0.0000 0.0 + 1.0 1 c4 c3a c3a h1 0.0000 0.0 1.5590 0.0 0.0000 0.0 + 1.0 1 h1 c3a c3a h1 0.0000 0.0 2.3500 0.0 0.0000 0.0 + 1.0 1 c3a c3a c4 c3a -0.2802 0.0 -0.0678 0.0 -0.0122 0.0 + 1.0 1 c3a c3a c4 c4 -0.2802 0.0 -0.0678 0.0 -0.0122 0.0 + 1.0 1 c3a c3a c4 h1 -0.2802 0.0 -0.0678 0.0 -0.0122 0.0 + 1.0 1 c3a c4 c4 h1 -0.0228 0.0 0.0280 0.0 -0.1863 0.0 + 1.0 1 c4 c4 c4 c4 0.0000 0.0 0.0514 0.0 -0.1430 0.0 + 1.0 1 c4 c4 c4 h1 0.0000 0.0 0.0316 0.0 -0.1681 0.0 + 1.0 1 h1 c4 c4 h1 -0.1432 0.0 0.0617 0.0 -0.1530 0.0 + 1.0 1 * c3a c3a * 0.0000 0.0 4.5000 0.0 0.0000 0.0 + 1.0 1 * c4 c4 * 0.0000 0.0 0.0000 0.0 -0.1530 0.0 + 1.0 2 h1 o2z si4 c4 0.0000 0.0 0.0000 0.0 -0.0500 0.0 + 1.0 2 h1 o2z si4 h1 0.0000 0.0 0.0000 0.0 -0.0500 0.0 + 1.0 2 h1 o2z si4 o2z 0.0000 0.0 0.0000 0.0 -0.0500 0.0 + 1.0 2 si4 o2z si4 c4 0.0000 0.0 0.0000 0.0 -0.0100 0.0 + 1.0 2 si4 o2z si4 h1 0.0000 0.0 0.0000 0.0 -0.0100 0.0 + 1.0 2 si4 o2z si4 o2z -0.2250 0.0 0.0000 0.0 -0.0100 0.0 + 1.0 2 * o2z si4 * 0.0000 0.0 0.0000 0.0 -0.0100 0.0 + 1.0 3 c3a c3a c3a o2 0.0000 0.0 4.8498 0.0 0.0000 0.0 + 1.0 3 h1 c3a c3a o2 0.0000 0.0 1.7234 0.0 0.0000 0.0 + 1.0 3 c3a c3a o2 c4 0.0000 0.0 1.5000 0.0 0.0000 0.0 + 1.0 3 c3a c3a o2 h1 -0.6900 0.0 0.5097 0.0 0.0095 0.0 + 1.0 3 c4 c4 c4 o2 0.7137 0.0 0.2660 0.0 -0.2545 0.0 + 1.0 3 h1 c4 c4 o2 -0.1435 0.0 0.2530 0.0 -0.0905 0.0 + 1.0 3 o2 c4 c4 o2 1.1000 0.0 -0.0500 0.0 -0.1441 0.0 + 1.0 3 c4 c4 o2 c4 -0.4000 0.0 -0.4028 0.0 -0.2450 0.0 + 1.0 3 c4 c4 o2 h1 -0.6732 0.0 -0.4778 0.0 -0.1670 0.0 + 1.0 3 h1 c4 o2 c3a 0.9513 0.0 0.1155 0.0 0.0720 0.0 + 1.0 3 h1 c4 o2 c4 0.5302 0.0 0.0000 0.0 -0.3966 0.0 + 1.0 3 h1 c4 o2 h1 0.1863 0.0 -0.4338 0.0 -0.2121 0.0 + 1.0 4 c3a c3a c3a p4= 0.0000 0.0 5.4770 0.0 0.0000 0.0 + 1.0 4 h1 c3a c3a p4= 0.0000 0.0 2.2700 0.0 0.0000 0.0 + 1.0 4 c3a c3a p4= h1 -0.2720 0.0 1.1900 0.0 0.0000 0.0 + 1.0 4 c3a c3a p4= n2= -0.2720 0.0 1.1900 0.0 0.0000 0.0 + 1.0 4 c4 c4 c4 n2= 0.0970 0.0 0.0720 0.0 -0.2580 0.0 + 1.0 4 h1 c4 c4 n2= -0.1510 0.0 0.0100 0.0 -0.1860 0.0 + 1.0 4 c4 c4 n2= h1 -5.0720 0.0 -0.4980 0.0 -0.4380 0.0 + 1.0 4 h1 c4 n2= h1 1.2660 0.0 -0.7740 0.0 0.0380 0.0 + 1.0 4 h1 c4 p4= c4 0.0000 0.0 0.0000 0.0 -0.0680 0.0 + 1.0 4 h1 c4 p4= h1 0.0000 0.0 0.0000 0.0 -0.0680 0.0 + 1.0 4 h1 c4 p4= n2= 0.0000 0.0 0.0000 0.0 -0.0680 0.0 + 1.0 4 h1 n2= p4= c3a 0.0000 0.0 0.0000 0.0 -0.3500 0.0 + 1.0 4 h1 n2= p4= c4 0.0000 0.0 0.0000 0.0 -0.3690 0.0 + 1.0 4 h1 n2= p4= h1 0.0000 0.0 0.0000 0.0 -0.3500 0.0 + 1.0 4 h1 n2= p4= o2 0.0000 0.0 0.0000 0.0 -0.3500 0.0 + 1.0 4 p4= n2= p4= h1 0.0000 0.0 0.0000 0.0 0.0000 0.0 + 1.0 4 p4= n2= p4= n2= 1.8000 0.0 0.5000 0.0 2.0000 0.0 + 1.0 4 h1 n3 p4= h1 0.0000 0.0 0.0000 0.0 0.0000 0.0 + 1.0 4 h1 n3 p4= n2= 0.0000 0.0 0.0000 0.0 0.0000 0.0 + 1.0 4 h1 n3 p4= o2 0.0000 0.0 0.0000 0.0 0.0000 0.0 + 1.0 4 h1 o2 p4= h1 5.7080 0.0 2.1180 0.0 0.0000 0.0 + 1.0 4 h1 o2 p4= n2= 5.7080 0.0 2.1180 0.0 0.0000 0.0 + 1.0 4 h1 o2 p4= o2 5.7080 0.0 2.1180 0.0 0.0000 0.0 + 1.0 4 * o2 p4= * 5.7080 0.0 2.1180 0.0 0.0000 0.0 + 1.0 4 * c3a n2= * 0.0000 0.0 1.0000 0.0 0.0000 0.0 + 1.0 4 * c3a p4= * -0.2720 0.0 1.1900 0.0 0.0000 0.0 + 1.0 4 * c4 n2= * 0.0000 0.0 0.0000 0.0 -0.0200 0.0 + 1.0 4 * c4 p4= * 0.0000 0.0 0.0000 0.0 -0.0680 0.0 + 1.0 4 * n2= p4= * 0.0000 0.0 0.0000 0.0 -0.3500 0.0 + 1.0 4 * n3 p4= * 0.0000 0.0 0.0000 0.0 0.0000 0.0 + 1.0 6 c3a c3a c3a n3o 0.0000 0.0 7.2124 0.0 0.0000 0.0 + 1.0 6 h1 c3a c3a n3o 0.0000 0.0 2.9126 0.0 0.0000 0.0 + 1.0 6 c3a c3a n3o o1= 0.0000 0.0 1.1600 0.0 0.0000 0.0 + 1.0 6 c4 c4 n3o o1= 0.0000 0.0 0.0000 0.0 -0.3500 0.0 + 1.0 6 h1 c4 n3o o1= 0.0000 0.0 0.0000 0.0 -0.3500 0.0 + 1.0 6 c4 c4 o2 n3o 0.0000 0.0 -0.4000 0.0 -0.2000 0.0 + 1.0 6 o1= n3o o2 c4 0.0000 0.0 2.0000 0.0 0.0000 0.0 + 1.0 7 c3' c3a c3a c3a 0.0000 0.0 4.6282 0.0 0.0000 0.0 + 1.0 7 c3' c3a c3a h1 0.0000 0.0 2.1670 0.0 0.0000 0.0 + 1.0 7 c3' n3m c3a c3a 0.0000 0.0 0.6500 0.0 0.0000 0.0 + 1.0 7 c3' n3m c3' o1 -0.4066 0.0 1.2513 0.0 -0.7507 0.0 + 1.0 7 c3' o2 c4 c4 0.1302 0.0 -0.3250 0.0 0.1134 0.0 + 1.0 7 c3' o2 c4 h1 0.9513 0.0 0.1155 0.0 0.0000 0.0 + 1.0 7 c3a c3a c3' o1= 0.0000 0.0 0.7800 0.0 0.0000 0.0 + 1.0 7 c3a c3a c3a n3m 0.0000 0.0 3.4040 0.0 0.0000 0.0 + 1.0 7 c3a n3m c3' o1= 0.0000 0.0 2.0521 0.0 0.0000 0.0 + 1.0 7 c4 o2 c3' c4 -2.5594 0.0 2.2013 0.0 0.0325 0.0 + 1.0 7 c4 o2 c3' o1= 0.8905 0.0 3.2644 0.0 0.2646 0.0 + 1.0 7 o1= c3' c4 h1 0.0000 0.0 0.0000 0.0 0.0000 0.0 + 1.0 7 o2 c3' c4 h1 0.0000 0.0 0.0000 0.0 0.0000 0.0 + 1.0 7 n3m c3a c3a h1 0.0000 0.0 3.4040 0.0 0.0000 0.0 + 1.0 9 h1 n2z n2t n1t 0.0000 0.0 0.0000 0.0 -0.2637 0.0 + 1.0 9 c4 n2z n2t n1t 0.0000 0.0 0.0000 0.0 -0.1823 0.0 + 1.0 9 n2t n2z c4 h1 0.0000 0.0 0.0000 0.0 -0.2181 0.0 + 1.0 9 n2t n2z c4 c4 0.0000 0.0 0.0000 0.0 -0.2021 0.0 + 1.0 9 n2z c4 c4 h1 0.0000 0.0 0.0000 0.0 -0.2259 0.0 + 1.0 10 c3a c3a c3a si4 0.0000 0.0 4.3270 0.0 0.0000 0.0 + 1.0 10 h1 c3a c3a si4 0.0000 0.0 1.5093 0.0 0.0000 0.0 + 1.0 10 c3a c3a si4 * 0.0000 0.0 0.0000 0.0 -0.0231 0.0 + 1.0 10 c4 c4 si4 si4 -0.3500 0.0 0.0000 0.0 -0.0657 0.0 + 1.0 10 * c4 si4 * 0.0000 0.0 0.0000 0.0 -0.0657 0.0 + 1.0 10 * si4 si4 * 0.0000 0.0 0.0000 0.0 -0.0657 0.0 + + +#end_bond-torsion_3 compass + +> E = (R - R0) * +> { F(1) * cos(phi) + F(2) * cos(2 * phi) + F(3) * cos(3 * phi) } + +! LEFT RIGHT +! ------------------------------- ------------------------------- +!Ver Ref I J K L F(1) F(2) F(3) F(1) F(2) F(3) +!---- --- ---- ---- ---- ---- ------- ------- ------- ------- ------- ------- + 1.0 1 c3a c3a c3a c3a -0.1185 6.3204 0.0000 + 1.0 1 c3a c3a c3a c4 0.0000 -0.6918 0.0000 0.0000 0.2421 0.0000 + 1.0 1 c3a c3a c3a h1 0.0000 -6.8958 0.0000 0.0000 -0.4669 0.0000 + 1.0 1 c4 c3a c3a h1 0.0000 -1.7970 0.0000 0.0000 -0.4879 0.0000 + 1.0 1 h1 c3a c3a h1 0.0000 -0.6890 0.0000 + 1.0 1 c3a c3a c4 c4 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 + 1.0 1 c3a c3a c4 h1 -0.5835 1.1220 0.3978 1.3997 0.7756 0.0000 + 1.0 1 c3a c4 c4 h1 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 + 1.0 1 c4 c4 c4 c4 -0.0732 0.0000 0.0000 + 1.0 1 c4 c4 c4 h1 0.2486 0.2422 -0.0925 0.0814 0.0591 0.2219 + 1.0 1 h1 c4 c4 h1 0.2130 0.3120 0.0777 + 1.0 3 c3a c3a c3a o2 0.0000 0.2655 0.0000 0.0000 4.8905 0.0000 + 1.0 3 h1 c3a c3a o2 0.0000 -1.5867 0.0000 0.0000 4.2641 0.0000 + 1.0 3 c3a c3a o2 h1 0.9000 -1.3456 1.1900 3.4132 0.5873 -0.1323 + 1.0 3 c4 c4 c4 o2 -0.3190 0.4411 -0.7174 1.1538 0.8409 -0.9138 + 1.0 3 h1 c4 c4 o2 0.9681 0.9551 0.0436 0.5903 0.6669 0.8584 + 1.0 3 o2 c4 c4 o2 1.0165 0.7553 -0.4609 + 1.0 3 c4 c4 o2 c4 -0.2456 1.0517 -0.7795 0.4741 1.2635 0.5576 + 1.0 3 c4 c4 o2 h1 -0.5800 0.9004 0.0000 0.0000 0.5343 0.9025 + 1.0 3 h1 c4 o2 c4 -0.6054 1.3339 0.9648 -0.1620 0.1564 -1.1408 + 1.0 3 h1 c4 o2 h1 -1.7554 1.3145 0.2263 0.2493 0.6803 0.0000 + 1.0 7 o1= c3' n3m c3' -0.7019 0.8305 -0.6874 0.1726 -0.4823 0.2666 + 1.0 7 c4 c4 o2 c3' -1.2164 -0.1715 -0.0964 0.2560 0.8133 -0.0728 + 1.0 7 h1 c4 o2 c3' 0.9589 0.9190 -0.6015 0.2282 2.2998 -0.4473 + 1.0 7 c4 c3' o2 c4 0.1928 1.3187 0.8599 0.0004 -1.0975 0.4831 + 1.0 7 o1= c3' o2 c4 -4.2421 10.1102 1.6824 0.0882 -2.4309 -0.7426 + 1.0 7 o1= c3' c4 h1 0.0536 0.0354 0.3853 2.9036 0.5307 0.1439 + 1.0 7 o2 c3' c4 h1 0.4160 -0.1140 0.7099 0.7800 1.3339 0.3268 + + +#middle_bond-torsion_3 compass + +> E = (R - R0) * +> { F(1) * cos(phi) + F(2) * cos(2 * phi) + F(3) * cos(3 * phi) } + +!Ver Ref I J K L F(1) F(2) F(3) +!---- --- ---- ---- ---- ---- -------- ------- ------- + 1.0 1 c3a c3a c3a c3a 27.5989 -2.3120 0.0000 + 1.0 1 c3a c3a c3a c4 0.0000 9.1792 0.0000 + 1.0 1 c3a c3a c3a h1 0.0000 -1.1521 0.0000 + 1.0 1 c4 c3a c3a h1 0.0000 3.9421 0.0000 + 1.0 1 h1 c3a c3a h1 0.0000 4.8228 0.0000 + 1.0 1 c3a c3a c4 c4 0.0000 0.0000 0.0000 + 1.0 1 c3a c3a c4 h1 -5.5679 1.4083 0.3010 + 1.0 1 c3a c4 c4 h1 0.0000 0.0000 0.0000 + 1.0 1 c4 c4 c4 c4 -17.7870 -7.1877 0.0000 + 1.0 1 c4 c4 c4 h1 -14.8790 -3.6581 -0.3138 + 1.0 1 h1 c4 c4 h1 -14.2610 -0.5322 -0.4864 + 1.0 3 c3a c3a c3a o2 0.0000 4.8255 0.0000 + 1.0 3 h1 c3a c3a o2 0.0000 5.5432 0.0000 + 1.0 3 c3a c3a o2 h1 1.1580 3.2697 3.5132 + 1.0 3 c4 c4 c4 o2 -21.8842 -7.6764 -0.6868 + 1.0 3 h1 c4 c4 o2 -16.7975 -1.2296 -0.2750 + 1.0 3 o2 c4 c4 o2 -17.2585 -3.6157 -0.8364 + 1.0 3 c4 c4 o2 c4 -5.9288 -2.7007 -0.3175 + 1.0 3 c4 c4 o2 h1 1.2472 0.0000 0.7485 + 1.0 3 h1 c4 o2 c4 -6.8007 -4.6546 -1.4101 + 1.0 3 h1 c4 o2 h1 0.0000 0.9241 -0.5889 + 1.0 4 c4 c4 c4 n2= 0.0000 0.0000 0.0000 + 1.0 4 h1 c4 c4 n2= -3.5150 -2.2980 -1.2770 + 1.0 4 c4 c4 n2= h1 -2.3800 2.5290 -0.7300 + 1.0 4 h1 c4 n2= h1 -0.4140 -2.8620 0.0070 + 1.0 4 p4= n2= p4= n2= 0.0000 0.0000 0.0000 + 1.0 7 c3' c3a c3a c3a 0.0000 3.8762 0.0000 + 1.0 7 o1= c3' n3m c3' -0.1118 -1.1990 0.6784 + 1.0 7 c4 c4 o2 c3' 9.9416 2.6421 2.2333 + 1.0 7 h1 c4 o2 c3' 7.7147 4.2557 -1.0118 + 1.0 7 o1= c3' c3a c3a 0.0000 2.4002 0.0000 + 1.0 7 c3a c3a c3a n3m 0.0000 5.2012 0.0000 + 1.0 7 c4 c3' o2 c4 1.3445 3.5515 -4.9202 + 1.0 7 o1= c3' o2 c4 0.4552 7.3091 0.2842 + 1.0 7 o1= c3' c4 h1 0.0000 0.0000 -1.0000 + 1.0 7 o2 c3' c4 h1 -13.7686 -2.5959 1.1934 + 1.0 7 h1 c3a c3a n3m 0.0000 5.2012 0.0000 + 1.0 10 c3a c3a c3a si4 0.0000 11.1576 0.0000 + 1.0 10 h1 c3a c3a si4 0.0000 6.2168 0.0000 + 1.0 10 c3a c3a si4 h1 0.0000 0.0000 -0.3146 + 1.0 10 h1 c4 si4 h1 0.0000 0.0000 -0.5906 + 1.0 10 h1 c4 si4 si4 0.0000 0.0000 -0.1909 + 1.0 10 c4 si4 si4 h1 0.0000 0.0000 -0.6941 + 1.0 10 h1 si4 si4 h1 0.0000 0.0000 -0.6302 + + +#angle-torsion_3 compass + +> E = (Theta - Theta0) * +> { F(1) * cos(phi) + F(2) * cos(2 * phi) + F(3) * cos(3 * phi) } + +! LEFT RIGHT +! ------------------------------- ------------------------------- +!Ver Ref I J K L F(1) F(2) F(3) F(1) F(2) F(3) +!---- --- ---- ---- ---- ---- ------- ------- ------- ------- ------- ------- + 1.0 1 c3a c3a c3a c3a 1.9767 1.0239 0.0000 + 1.0 1 c3a c3a c3a c4 0.0000 3.8987 0.0000 0.0000 -4.4683 0.0000 + 1.0 1 c3a c3a c3a h1 0.0000 2.5014 0.0000 0.0000 2.7147 0.0000 + 1.0 1 c4 c3a c3a h1 0.0000 -0.1242 0.0000 0.0000 3.4601 0.0000 + 1.0 1 h1 c3a c3a h1 0.0000 2.4501 0.0000 + 1.0 1 c3a c3a c4 c4 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 + 1.0 1 c3a c3a c4 h1 0.2251 0.6548 0.1237 4.6266 0.1632 0.0461 + 1.0 1 c3a c4 c4 h1 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 + 1.0 1 c4 c4 c4 c4 0.3886 -0.3139 0.1389 + 1.0 1 c4 c4 c4 h1 -0.2454 0.0000 -0.1136 0.3113 0.4516 -0.1988 + 1.0 1 h1 c4 c4 h1 -0.8085 0.5569 -0.2466 + 1.0 3 c3a c3a c3a o2 0.0000 10.0155 0.0000 0.0000 1.7404 0.0000 + 1.0 3 h1 c3a c3a o2 0.0000 1.8729 0.0000 0.0000 2.5706 0.0000 + 1.0 3 c3a c3a o2 h1 -5.1360 -1.0122 0.0000 4.6852 0.0230 -0.5980 + 1.0 3 c4 c4 c4 o2 0.5623 -0.3041 -0.4015 0.9672 -0.7566 -1.2331 + 1.0 3 h1 c4 c4 o2 2.3668 2.4920 -1.0122 -0.1892 0.4918 0.7273 + 1.0 3 o2 c4 c4 o2 0.5511 0.9737 -0.6673 + 1.0 3 c4 c4 o2 c4 -2.7466 1.4877 -0.8955 0.5676 0.9450 0.0703 + 1.0 3 c4 c4 o2 h1 -3.5903 2.5225 0.4888 0.8726 -0.3577 0.3888 + 1.0 3 h1 c4 o2 c4 -1.8234 1.6393 0.5144 -0.7777 0.4340 -0.6653 + 1.0 3 h1 c4 o2 h1 -3.4060 1.6396 0.0737 0.0000 -0.2810 -0.5944 + 1.0 4 c4 c4 c4 n2= -2.0980 1.8610 -1.6890 -0.1220 1.8930 -0.5670 + 1.0 4 h1 c4 c4 n2= -2.0980 1.8610 -1.6890 -0.1220 1.8930 -0.5670 + 1.0 4 c4 c4 n2= h1 -2.5230 2.8480 2.0590 -3.6920 4.0610 -1.5440 + 1.0 4 h1 c4 n2= h1 -1.8950 1.2210 -0.7460 0.1100 0.0650 0.1090 + 1.0 6 c3a c3a c3a n3o 0.0000 7.7594 0.0000 0.0000 0.0000 0.0000 + 1.0 6 h1 c3a c3a n3o 0.0000 -8.0369 0.0000 0.0000 0.0000 0.0000 + 1.0 6 c3a c3a n3o o1= 0.0000 0.0000 0.0000 0.0000 -3.4207 0.0000 + 1.0 6 h1 c4 n3o o1= 0.0000 -0.3086 0.0000 0.0000 1.0352 0.0000 + 1.0 6 o1= n3o o2 c4 -3.0000 0.0000 0.0000 0.0000 0.0000 0.0000 + 1.0 7 o1= c3' n3m c3' -1.5747 2.3997 -0.2851 -0.3038 -0.0548 -0.3188 + 1.0 7 c4 c4 o2 c3' -0.4620 1.4492 -0.6765 -0.0890 -0.9159 0.7229 + 1.0 7 h1 c4 o2 c3' -0.4990 2.8061 -0.0401 -0.3142 -0.8699 0.0971 + 1.0 7 c4 c3' o2 c4 0.9701 -2.5169 1.7195 0.8831 -0.8203 0.2405 + 1.0 7 o1= c3' o2 c4 5.9732 2.7261 1.9052 2.3573 1.0059 -0.0327 + 1.0 7 o1= c3' c4 h1 -2.0667 0.7308 -0.2083 14.4728 0.3339 0.0800 + 1.0 7 o2 c3' c4 h1 -0.0241 1.4427 0.1212 13.2959 0.8005 -0.0071 + 1.0 10 c3a c3a c3a si4 0.0000 -5.5448 0.0000 0.0000 4.3281 0.0000 + 1.0 10 h1 c3a c3a si4 0.0000 4.5914 0.0000 0.0000 1.1079 0.0000 + 1.0 10 c3a c3a si4 h1 0.0000 0.0000 -0.2779 0.0000 0.0000 -0.1932 + 1.0 10 h1 c4 si4 c4 0.0000 0.0000 0.3382 0.0000 0.0000 0.4272 + + +#wilson_out_of_plane compass + +> E = K * (Chi - Chi0)^2 + +!Ver Ref I J K L K Chi0 +!---- --- ---- ---- ---- ---- ------- ---- + 1.0 1 c3a c3a c3a c3a 7.1794 0.0 + 1.0 1 c3a c3a c3a c4 7.8153 0.0 + 1.0 1 c3a c3a c3a h1 4.8912 0.0 + 1.0 3 c3a c3a c3a o2 13.0421 0.0 + 1.0 4 c3a c3a c3a n2= 8.0000 0.0 + 1.0 4 c3a c3a c3a p4= 6.7090 0.0 + 1.0 6 c3a c3a c3a n3o 0.9194 0.0 + 1.0 6 c3a n3o o1= o1= 36.2612 0.0 + 1.0 6 c4 n3o o1= o1= 44.3062 0.0 + 1.0 6 h1 n3o o1= o1= 38.5581 0.0 + 1.0 6 o1= n3o o1= o2 45.0000 0.0 + 1.0 7 c3' c3' n3m c3a 0.0000 0.0 + 1.0 7 c3' c3a c3a c3a 17.0526 0.0 + 1.0 7 c3' n3m c3' c3a 0.0000 0.0 + 1.0 7 c3a c3a n3m c3a 17.0526 0.0 +!1.0 7 c3a c3a c3a n3m 17.0526 0.0 + 1.0 7 c3a c3' n3m o1= 30.0000 0.0 +!1.0 7 c3a c3a c3' c3a 17.0526 0.0 +!1.0 7 c3a c3' o1= n3m 30.0000 0.0 + 1.0 7 c3a o1= c3' n3m 30.0000 0.0 + 1.0 7 c4 c3' o2 o1= 46.9264 0.0 + 1.0 10 c3a c3a si4 c3a 5.3654 0.0 + + +#angle-angle compass + +> E = K * (Theta - Theta0) * (Theta' - Theta0') + +! J' I' K' +!Ver Ref I J K K +!---- --- ---- ---- ---- ---- ------- + 1.0 1 c3a c3a c3a c3a 0.0000 + 1.0 1 c3a c3a c3a h1 0.0000 + 1.0 1 c3a c3a h1 c3a 0.0000 + 1.0 1 c4 c4 c3a h1 2.0403 + 1.0 1 h1 c4 c3a h1 3.0118 + 1.0 1 c3a c4 c4 h1 -1.8202 + 1.0 1 c4 c4 c4 c4 -0.1729 + 1.0 1 c4 c4 c4 h1 -1.3199 + 1.0 1 h1 c4 c4 h1 -0.4825 + 1.0 1 c3a c4 h1 c4 1.0827 + 1.0 1 c3a c4 h1 h1 2.3794 + 1.0 1 c4 c4 h1 c4 0.1184 + 1.0 1 c4 c4 h1 h1 0.2738 + 1.0 1 h1 c4 h1 h1 -0.3157 + 1.0 3 c3a c3a c3a o2 0.0000 + 1.0 3 c3a c3a o2 c3a 0.0000 + 1.0 3 c4 c4 c4 o2 -0.8330 + 1.0 3 h1 c4 c4 o2 2.5926 + 1.0 3 c4 c4 h1 o2 3.9177 + 1.0 3 h1 c4 h1 o2 2.4259 + 1.0 3 c4 c4 o2 c4 -3.5744 + 1.0 3 c4 c4 o2 h1 0.1689 + 1.0 3 h1 c4 o2 h1 2.1283 + 1.0 4 h1 c4 c4 n2= 1.0910 + 1.0 4 c4 c4 h1 n2= 2.7530 + 1.0 4 h1 c4 h1 n2= 1.7680 + 1.0 4 c4 c4 n2= h1 -1.3060 + 1.0 4 h1 c4 n2= h1 -2.9470 + 1.0 7 h1 c4 c3' o2 4.7955 + 1.0 7 c3' c4 h1 h1 -1.7653 + 1.0 11 h1 c4 c3' h1 0.0 + 1.0 10 h1 c4 h1 si4 0.0000 + 1.0 10 h1 c4 si4 h1 2.2050 + 1.0 10 c4 si4 c4 h1 3.3827 + 1.0 10 c4 si4 c4 si4 1.3465 + 1.0 10 h1 si4 c4 h1 4.6809 + 1.0 10 si4 si4 c4 si4 -5.6849 + 1.0 10 c4 si4 h1 c4 2.7963 + 1.0 10 c4 si4 h1 h1 4.4559 + 1.0 10 c4 si4 h1 si4 3.4758 + 1.0 10 h1 si4 h1 h1 2.0665 + 1.0 10 si4 si4 h1 si4 3.4924 + 1.0 10 c4 si4 si4 c4 2.0805 + 1.0 10 c4 si4 si4 h1 -2.9623 + 1.0 10 c4 si4 si4 si4 4.5272 + 1.0 10 h1 si4 si4 h1 1.6082 + 1.0 10 si4 si4 si4 h1 4.1996 + + +#angle-angle-torsion_1 compass + +> E = K * (Theta - Theta0) * (Theta' - Theta0') * cos(Phi) + +!Ver Ref I J K L K(Ang,Ang,Tor) +!---- --- ---- ---- ---- ---- -------------- + 1.0 1 c3a c3a c3a c3a 0.0000 + 1.0 1 c3a c3a c3a c4 -14.4097 + 1.0 1 c3a c3a c3a h1 -4.8141 + 1.0 1 c4 c3a c3a h1 4.4444 + 1.0 1 h1 c3a c3a h1 0.3598 + 1.0 1 c3a c3a c4 h1 -5.8888 + 1.0 1 c4 c4 c4 c4 -22.0450 + 1.0 1 c4 c4 c4 h1 -16.1640 + 1.0 1 h1 c4 c4 h1 -12.5640 + 1.0 3 c3a c3a c3a o2 -21.0247 + 1.0 3 h1 c3a c3a o2 4.2296 + 1.0 3 c3a c3a o2 h1 -4.6072 + 1.0 3 c4 c4 c4 o2 -29.0420 + 1.0 3 h1 c4 c4 o2 -20.2006 + 1.0 3 o2 c4 c4 o2 -14.0484 + 1.0 3 c4 c4 o2 c4 -19.0059 + 1.0 3 c4 c4 o2 h1 -12.1038 + 1.0 3 h1 c4 o2 c4 -16.4438 + 1.0 3 h1 c4 o2 h1 -10.5093 + 1.0 4 c4 c4 c4 n2= 0.0000 + 1.0 4 h1 c4 c4 n2= -27.5060 + 1.0 4 c4 c4 n2= h1 -8.8980 + 1.0 4 h1 c4 n2= h1 -9.6280 + 1.0 4 h1 c4 p4= c4 -25.5460 + 1.0 4 h1 c4 p4= h1 -16.0180 + 1.0 4 h1 c4 p4= n2= -19.9340 + 1.0 4 h1 n2= p4= c4 -11.1020 + 1.0 4 h1 n2= p4= h1 -3.7880 + 1.0 6 c3a c3a c3a n3o -34.9681 + 1.0 6 h1 c3a c3a n3o 2.1508 + 1.0 6 c3a c3a n3o o1= -18.0436 + 1.0 6 h1 c4 n3o o1= -16.2615 + 1.0 7 o1= c3' n3m c3' -3.3556 + 1.0 7 c4 c4 o2 c3' -15.7082 + 1.0 7 h1 c4 o2 c3' -13.1500 + 1.0 7 c4 c3' o2 c4 -12.2070 + 1.0 7 o1= c3' o2 c4 -32.9368 + 1.0 7 o1= c3' c4 h1 -23.1923 + 1.0 7 o2 c3' c4 h1 -13.9734 + 1.0 10 c4 si4 c4 h1 -17.5802 + 1.0 10 h1 si4 c4 h1 -12.9341 + 1.0 10 h1 c4 si4 si4 -13.3679 + 1.0 10 c4 si4 si4 h1 -16.9141 + 1.0 10 h1 si4 si4 h1 -10.8232 + 1.0 10 h1 si4 si4 si4 -12.2900 + + +#nonbond(9-6) compass + +> E = eps(ij) [2(r(ij)*/r(ij))**9 - 3(r(ij)*/r(ij))**6] +> where r(ij) = [(r(i)**6 + r(j)**6))/2]**(1/6) +> +> eps(ij) = 2 sqrt(eps(i) * eps(j)) * +> r(i)^3 * r(j)^3/[r(i)^6 + r(j)^6] + +@combination sixth-power +@type r-eps + +!Ver Ref I r eps +!---- --- ---- --------- --------- + 1.0 1 c3a 3.9150 0.0680 + 1.0 1 c4 3.8540 0.0620 + 1.0 1 c43 3.8540 0.0400 + 1.0 1 c44 3.8540 0.0200 + 1.0 1 h1 2.8780 0.0230 + 1.0 2 o2z 3.3000 0.0800 + 1.0 2 si4 4.4050 0.1980 + 1.0 2 si4c 4.2900 0.1310 + 1.0 3 c4o 3.8150 0.0680 + 1.0 3 h1o 1.0870 0.0080 + 1.0 3 o2 3.3000 0.0800 + 1.0 3 o2e 3.3000 0.1200 + 1.0 3 o2h 3.5800 0.0960 + 1.0 4 n2= 3.8300 0.0960 + 1.0 4 p4= 4.2950 0.0650 + 1.0 5 he 2.9000 0.0050 + 1.0 5 ne 3.2000 0.0550 + 1.0 5 ar 3.8800 0.2000 + 1.0 5 kr 4.3000 0.2800 + 1.0 5 xe 4.2600 0.3900 + 1.0 5 h1h 1.4210 0.0216 + 1.0 5 n1n 3.8008 0.0598 + 1.0 5 c1o 4.0120 0.0530 + 1.0 5 o1o 3.4758 0.0780 + 1.0 5 o1c 3.6020 0.0850 + 1.0 5 n1o 3.4600 0.1280 + 1.0 5 o1n 3.3000 0.1560 + 1.0 5 c2= 3.9150 0.0680 + 1.0 5 s2= 4.0470 0.1250 + 1.0 5 n2o 3.5290 0.3330 + 1.0 5 o1= 3.4300 0.1920 + 1.0 5 o1=* 3.3600 0.0670 + 1.0 5 s1= 4.0070 0.3130 + 1.0 6 n3o 3.7600 0.0480 + 1.0 6 o12 3.4000 0.0480 + 1.0 6 o2n 3.6500 0.2000 + 1.0 7 c3' 3.9000 0.0640 + 1.0 7 n3m 3.7200 0.1500 + 1.0 7 o2s 3.3000 0.0960 + 1.1 8 c4o 3.8700 0.0748 + 1.1 8 c41o 3.8700 0.1080 + 1.1 8 c43o 3.6700 0.0498 + 1.0 9 c4z 3.6500 0.0800 + 1.0 9 n1z 3.5200 0.0850 + 1.0 9 n2t 3.3000 0.0500 + 1.0 9 n2z 3.4000 0.1200 + + +#bond_increments compass + +!Ver Ref I J DeltaIJ DeltaJI +!---- --- ---- ---- ------- ------- + 1.0 1 c3a c3a 0.0000 0.0000 + 1.0 1 c3a c4 0.0000 0.0000 + 1.0 1 c3a h1 -0.1268 0.1268 + 1.0 1 c4 c4 0.0000 0.0000 + 1.0 1 c4 h1 -0.0530 0.0530 + 1.0 2 o2z si4 -0.2225 0.2225 + 1.0 3 c3a o2e 0.0420 -0.0420 + 1.0 3 c3a o2h 0.0420 -0.0420 + 1.0 3 c4 o2e 0.1600 -0.1600 + 1.0 3 c4 o2h 0.1600 -0.1600 + 1.0 3 h1 o2 0.4200 -0.4200 + 1.0 3 h1 o2h 0.4200 -0.4200 + 1.0 4 c3a n2= 0.1990 -0.1990 + 1.0 4 c3a p4= -0.0600 0.0600 + 1.0 4 c4 n2= 0.3450 -0.3450 + 1.0 4 c4 p4= -0.0500 0.0500 + 1.0 4 cl1p p4= -0.1200 0.1200 + 1.0 4 f1p p4= -0.1800 0.1800 + 1.0 4 h1 n2= 0.3280 -0.3280 + 1.0 4 h1 p4= -0.0500 0.0500 + 1.0 4 n2= n2= 0.0000 0.0000 + 1.0 4 n2= n3 0.0250 -0.0250 + 1.0 4 n2= o2 -0.0430 0.0430 + 1.0 4 n2= p4= -0.3500 0.3500 + 1.0 4 n3 p4= -0.1200 0.1200 + 1.0 4 o2 p4= -0.1400 0.1400 + 1.0 5 c1o o1c -0.0203 0.0203 + 1.0 5 c2= o1= 0.4000 -0.4000 + 1.0 5 c2= s1= 0.0258 -0.0258 + 1.0 5 n2o o1= 0.0730 -0.0730 + 1.0 5 h1h h1h 0.0000 0.0000 + 1.0 5 n1n n1n 0.0000 0.0000 + 1.0 5 n1o o1n 0.0288 -0.0288 + 1.0 5 o1= s2= -0.2351 0.2351 + 1.0 5 o1o o1o 0.0000 0.0000 + 1.0 6 c3a n3o 0.2390 -0.2390 + 1.0 6 c4 n3o 0.2100 -0.2100 + 1.0 6 c4 o2n 0.3170 -0.3170 + 1.0 6 h1 n3o 0.1880 -0.1880 + 1.0 6 n3o o1= 0.4280 -0.4280 + 1.0 6 n3o o2n 0.0010 -0.0010 + 1.0 7 c3' o2e 0.1120 -0.1120 + 1.0 7 c3' c4 0.0000 0.0000 + 1.0 7 c3' o1= 0.4500 -0.4500 + 1.0 7 c3' c3a 0.0350 -0.0350 + 1.0 7 c3' n3m 0.0000 0.0000 + 1.0 7 c3a n3m 0.0950 -0.0950 + 1.1 8 h1 o2h 0.4100 -0.4100 + 1.0 9 n2z c4 -0.3110 0.3110 + 1.0 9 n2z h1 -0.3350 0.3350 + 1.0 9 n2t n1t 0.3860 -0.3860 + 1.0 9 n2t n2z 0.2470 -0.2470 + 1.0 10 c3a si4 -0.1170 0.1170 + 1.0 10 c4 si4 -0.1350 0.1350 + 1.0 10 h1 si4 -0.1260 0.1260 + +#templates compass + +type: ? + ! anything + template: (>*) +end_type + +type: ar + ! Argon atom + template: (>Ar) +end_type + +type:c1o + ! Carbon in CO + template: [>C[~O]] +end_type + +type:c2= + ! Carbon in =C= (e.g. CO2, CS2) + template: [>C[~*][~*]] +end_type + +type:c3' + ! Carbonyl carbon [one polar substituent such as O,N] + ! e.g. amide, acid and ester + template: (>C (~O) (~*) (~*)) + atom_test:1 + hybridization:sp2 + end_test + atom_test:3 + allowed_elements: C, H + end_test + atom_test:4 + allowed_elements: O, N + end_test +end_type + +type:c3a + ! SP2 aromatic carbon + template:(>C(~*)(~*)(~*)) + atom_test:1 + hybridization: SP2 + aromaticity:AROMATIC + end_test +end_type + +type:c3a + ! Transferred from pcff - may not be required. + ! This is used for aromatic carbons that fail the aromaticity test because + ! the current ring checker is too lame to figure on a ring with more than + ! seven or eight sides. The NON_AROMATIC test is to eliminate the conflict + ! with the above 'c3a' definition. This can be removed when the ring checker + ! is made more robust. + template: [>C(-*)(:*)(:*)] + atom_test:1 + hybridization:SP2 + aromaticity:NON_AROMATIC + end_test +end_type + +type:c4 + ! generic SP3 carbon + template: (>C(-*)(-*)(-*)(-*)) + atom_test:1 + hybridization:SP3 + end_test +end_type + +type:c41o + ! Carbon, sp3, in methanol (and dimethyl ether?) + template: [>C(-O(-*))(-H)(-H)(-H)] + atom_test:1 + hybridization:SP3 + end_test + atom_test:3 + allowed_elements:C,H +end_type + +type: c43 + ! sp3 carbon with 1 h and 3 heavy atoms + template: (>C(-H)(-*)(-*)(-*)) + atom_test:1 + hybridization:SP3 + atom_test:3 + disallowed_elements:H + atom_test:4 + disallowed_elements:H + atom_test:5 + disallowed_elements:H + end_test +end_type + +type:c43o + ! Carbon, sp3, in secondary alcohols + template: [>C(-O(-H))(-H)(-C)(-C)] + atom_test:1 + hybridization:SP3 + end_test +end_type + +type: c44 + ! sp3 carbon with four heavy atoms attached + template: (>C(-*)(-*)(-*)(-*)) + atom_test:1 + hybridization:SP3 + atom_test:2 + disallowed_elements:H + atom_test:3 + disallowed_elements:H + atom_test:4 + disallowed_elements:H + atom_test:5 + disallowed_elements:H + end_test +end_type + +type: c4o + ! alpha carbon (e.g. alpha to oxygen in ethers and alcohols) + template: (>C(-O)(-*)(-*)(-*)) + atom_test:1 + hybridization:SP3 + end_test +end_type + +type: c4z + ! Carbon, sp3, bonded to -N3 (azides) + template: (>C(-N(~N(~N)))(-*)(-*)(-*)) + atom_test:1 + hybridization:SP3 + end_test +end_type + +type:h1 + ! nonpolar hydrogen + template: (>H (-*) ) + atom_test:2 + allowed_elements:C,Si + end_test +end_type + +type:h1h + ! Hydrogen in H2 + template: [>H[-H]] +end_type + +type:h1o + ! strongly polar hydrogen (bonded to fluorine, nitrogen, Oxygen - h* in pcff) + template: (>H(-*)) + atom_test:2 + allowed_elements:O,N,F + end_test +end_type + +type: he + ! Helium atom + template: (>He) +end_type + +type: kr + ! Krypton atom + template: (>Kr) +end_type + +type:n1n + ! Nitrogen in N2 + template: [>N[~N]] +end_type + +type:n1o + ! Nitrogen in NO + template: [>N[~O]] +end_type + +type:n1z + ! Nitrogen, terminal atom in -N3 + template: [>N[~N[~N(~*)]]] +end_type + +type:n2= + ! Nitrogen (in phosphazenes, or generic???) + template: [>N(~*)(~*)] +end_type + +type:n2o + ! Nitrogen in NO2 + template: [>N[~O][~O]] +end_type + +type:n2t + ! Nitrogen, central atom in -N3 + template: [>N[~N][~N(~*)]] +end_type + +type:n2z + ! Nitrogen, first atom in -N3 + template: (>N[~N[~N]](~*)) +end_type + +type: n3m + ! sp3 nitrogen in amides without hydrogen + template: (>N(-C[=O])(-C)(-C)) + atom_test:1 + hybridization:SP3 + end_test +end_type + +type: n3o + ! Nitrogen in nitro group + template: (>N[~O][~O](~O(~C))) +end_type + +type: ne + ! Neon atom + template: (>Ne) +end_type + +type:o1= + ! Oxygen in NO2 and SO2 [and carbonyl] + template: (>O(~*)) + atom_test:2 + allowed_elements:N,S,C + end_test +end_type + +type:o1=* + ! Oxygen in CO2 + template: [>O[~C[~O]]] +end_type + +type:o12 + ! Oxygen in nitro group -NO2 + template: [>O[~N[~O](~*)]] +end_type + +type:o1c + ! Oxygen in CO + template: [>O[~C]] +end_type + +type:o1n + ! Oxygen in NO + template: [>O[~N]] +end_type + +type:o1o + ! Oxygen in O2 + template: [>O[~O]] +end_type + +type:o2 + ! Generic oxygen with two bonds attached + template: [>O(~*)(~*)] +end_type + +type:o2e + ! Ether oxygen + template: [>O(-C)(-C)] + atom_test: 1 + aromaticity:NON_AROMATIC + end_test +end_type + +type:o2h + ! Hydroxyl oxygen + template: (>O[-H](~*)) +end_type + +type:o2n + ! Oxygen in nitrates + template: (>O[~N[~O][~O]](~C)) +end_type + +type:o2s + ! Ester oxygen + template: (>O[~C[~O](~*)](~C)) +end_type + +type: o2z + ! Oxygen in siloxanes and zeolites + template: (>O(-Si)(-*) ) + atom_test: 3 + allowed_elements: Si, H + end_test +end_type + +type: p4= + ! Phosphorous [in phosphazenes] + template: (>P(~*)(~*)(~*)(~*)) +end_type + +type:s1= + ! Sulfur in CS2 + template: [>S[~C[~S]]] +end_type + +type:s2= + ! Sulfur in SO2 + template: [>S[~O][~O]] +end_type + +type: si4 + ! Generic silicon with four bonds attached + template: (>Si(-*)(-*)(-*)(-*)) +end_type + +type: si4c + ! A subset of si4, non-hydrogen atom attached [siloxanes??] + template: (>Si(-O)(-*)(-*)(-*)) + atom_test: 3 + allowed_elements: O, C + end_test + atom_test: 4 + allowed_elements: O, C + end_test + atom_test: 5 + allowed_elements: O, C + end_test +end_type + +type: xe + ! Xenon atom + template: (>Xe) +end_type + +precedence: +(? + (ar) + (c1o) + (c2=) + (c3a) (c3') + (c4 (c43 (c43o)) (c44) (c4o(c41o)) (c4z) ) + (h1) (h1h) (h1o) + (he) + (kr) + (n1n) (n1o) (n1z) + (n2= (n2o) (n2t) (n2z) ) + (n3m) (n3o) + (ne) + (o1= (o1=*) (o12) (o1c) (o1n) ) (o1o) + (o2 (o2e(o2s)) (o2h) (o2n) (o2z) ) + (p4=) + (s1=) + (s2=) + (si4 (si4c) ) + (xe) +) +end_precedence + + + +#reference 1 +@Author tester +@Date 01-Jun-09 +Barebones compass for aromatic & aliphatic hydrocarbons from H. Sun JCP B102, 7361-2 (1998) + +This file created by Materials Design, Inc. (www.materialsdesign.com) Please realize that +we neither support this version, nor make any warranty as to the correctness of the parameters. +We have checked the numbers against the literature, but of course there may still be errors, +including errors of interpretation. Also, the current version of COMPASS may well be different +that that originally published. + +If you have comments or suggestions, feel free to email Paul Saxe at psaxe (at) materialsdesign.com + +#reference 2 +@Author tester +@Date 27-Jun-09 +Parameters for siloxanes from Sun/Rigby Spectrochim. Acta A53, 1301-23 (1997) (o2 later renamed to o2z) + +#reference 3 +@Author tester +@Date 27-Jun-09 +Parameters for ethers and alcohols from Rigby/Sun/Eichinger Polym. Int. 44, 311-330 (1997) + +#reference 4 +@Author tester +@Date 30-Jun-09 +Parameters for phosphazenes from Comput. Theor. Polym. Sci. 8, 229-246 (1998) + +#reference 5 +@Author tester +@Date 28-Jun-09 +Parameters for He,Ne,Ar,Kr,Xe,H2,O2,N2,NO,CO,CO2,NO2,CS2,SO2 from JPC B104, 4951-7 (2000) + +#reference 6 +@Author tester +@Date 29-Jun-09 +Parameters for nitrate esters from JPC B104, 2477-89 (2000) + +#reference 7 +@Author tester +@Date 30-Jun-09 +Parameters for Ultem (imides) from Polymer 43, 599-607 (2002) + +#reference 8 +@Author tester +@Date 30-Jun-09 +Parameters for 2y and 3y alcohols from Fluid Phase Equilibria 217, 77-87 (2004) + +#reference 9 +@Author tester +@Date 30-Jun-09 +Parameters for aliphatic azides from J. Comput. Chem. 25, 61-71 (2004) + +#reference 10 +@Author tester +@Date 02-Jul-09 +Ref 2 missing -C-Si- params; assume values from Macromols 28, 701-712 (1995) (see pcff) diff --git a/tools/moltemplate/moltemplate/force_fields/compass_published.lt b/tools/moltemplate/moltemplate/force_fields/compass_published.lt new file mode 100644 index 0000000000..3ec7595f28 --- /dev/null +++ b/tools/moltemplate/moltemplate/force_fields/compass_published.lt @@ -0,0 +1,4148 @@ +# This file was generated automatically using: +# msifrc2lt.py -name COMPASS < compass_published.frc > compass_published.lt + +# This is an incomplete version of the COMPASS force field based on available +# public sources. Parameters for common atoms and many groups are missing +# (for example, sp2 carbons and the NH2 amine group). The commercial version +# of COMPASS is much larger and presumably includes more up to date +# parameters and parameters for a wider range of atom types and molecule types. +# (However files containing those force field parameters have not been publicly +# disclosed.) We would like to thank Materials Design Inc. for collecting +# these force field parameters and making them publicly available. + +# USAGE: You can create molecules using this force-field this way: +# +# MyMolecule inherits COMPASS { +# # atom-id mol-id atom-type charge X Y Z +# write('Data Atoms') { +# $atom:C1 $mol @atom:c4 0.00 -0.6695 0.000000 0.000000 +# $atom:H11 $mol @atom:h1 0.00 -1.234217 -0.854458 0.000000 +# : : : : : : +# } +# } +# +# You can omit the atom charge in your molecule definition. +# (Partial charges will be assigned later according to the force field rules.) +# Responsibility for choosing the atom types (eg "@atom:c4", "@atom:h1") falls +# on the user. You must select the type of each atom in the molecule carefully +# by looking at the description in the "Data Masses" section of this file +# (see below), and looking for a reasonable match. If your simulation is +# non-neutral, or moltemplate complains that you have missing bond, angle, or +# dihedral types, this means at least one of your atom types is incorrect. + + + +COMPASS { + + + # AtomType Mass # "Description" (version, reference) + + write_once("Data Masses") { + @atom:ar 39.944 # Ar, "argon" (ver=1.0, ref=5) + @atom:c3a 12.01115 # C, "aromatic carbon" (ver=1.0, ref=1) + @atom:c1o 12.01115 # C, "carbon in CO" (ver=1.0, ref=5) + @atom:c2= 12.01115 # C, "carbon in CO2 and CS2" (ver=1.0, ref=5) + @atom:c3prime 12.01115 # C, "carbonyl carbon [one polar substituent]" (ver=1.0, ref=7) + @atom:c4 12.01115 # C, "generic sp3 carbon" (ver=1.0, ref=1) + @atom:c41o 12.01115 # C, "carbon, sp3, in methanol" (ver=1.0, ref=8) + @atom:c43o 12.01115 # C, "carbon, sp3 in secondary alcohols" (ver=1.0, ref=8) + @atom:c43 12.01115 # C, "sp3 carbon with three heavy atoms attached" (ver=1.0, ref=1) + @atom:c44 12.01115 # C, "sp3 carbon with four heavy atoms attached" (ver=1.0, ref=1) + @atom:c4o 12.01115 # C, "alpha carbon" (ver=1.0, ref=3) + @atom:c4z 12.01115 # C, "carbon, sp3, bonded to -N3" (ver=1.0, ref=9) + @atom:h1 1.00797 # H, "nonpolar hydrogen" (ver=1.0, ref=1) + @atom:h1h 1.00797 # H, "hydrogen in H2" (ver=1.0, ref=5) + @atom:h1o 1.00797 # H, "strongly polar hydrogen, bonded to O,F" (ver=1.0, ref=3) + @atom:he 4.003 # He, "helium" (ver=1.0, ref=5) + @atom:kr 83.8 # Kr, "krypton" (ver=1.0, ref=5) + @atom:n1n 14.0067 # N, "nitrogen in N2" (ver=1.0, ref=5) + @atom:n1o 14.0067 # N, "nitrogen in NO" (ver=1.0, ref=5) + @atom:n1z 14.0067 # N, "nitrogen, terminal atom in -N3" (ver=1.0, ref=5) + @atom:n2= 14.0067 # N, "nitrogen" (ver=1.0, ref=4) + @atom:n2o 14.0067 # N, "nitrogen in NO2" (ver=1.0, ref=5) + @atom:n2t 14.0067 # N, "nitrogen, central atom in -N3" (ver=1.0, ref=9) + @atom:n2z 14.0067 # N, "nitrogen, first atom in -N3" (ver=1.0, ref=9) + @atom:n3m 14.0067 # N, "sp3 nitrogen in amides without hydrogen" (ver=1.0, ref=7) + @atom:n3o 14.0067 # N, "nitrogen in nitro group" (ver=1.0, ref=6) + @atom:ne 20.183 # Ne, "neon" (ver=1.0, ref=5) + @atom:o1= 15.9994 # O, "oxygen in NO2 and SO2 [and carbonyl]" (ver=1.0, ref=5) + @atom:o1=star 15.9994 # O, "oxygen in CO2" (ver=1.0, ref=5) + @atom:o12 15.9994 # O, "oxygen in nitro group (-NO2)" (ver=1.0, ref=6) + @atom:o1c 15.9994 # O, "oxygen in CO" (ver=1.0, ref=5) + @atom:o1n 15.9994 # O, "oxygen in NO" (ver=1.0, ref=5) + @atom:o1o 15.9994 # O, "oxygen in O2" (ver=1.0, ref=5) + @atom:o2 15.9994 # O, "generic oxygen with two bonds attached" (ver=1.0, ref=2) + @atom:o2e 15.9994 # O, "ether oxygen" (ver=1.0, ref=3) + @atom:o2h 15.9994 # O, "hydroxyl oxygen" (ver=1.0, ref=3) + @atom:o2n 15.9994 # O, "oxygen in nitrates" (ver=1.0, ref=6) + @atom:o2s 15.9994 # O, "ester oxygen" (ver=1.0, ref=7) + @atom:o2z 15.9994 # O, "oxygen, in siloxanes and zeolites" (ver=1.0, ref=2) + @atom:p4= 30.9738 # P, "phosphorous" (ver=1.0, ref=4) + @atom:s1= 32.064 # S, "sulfur in CS2" (ver=1.0, ref=5) + @atom:s2= 32.064 # S, "sulfur in SO2" (ver=1.0, ref=5) + @atom:si4 28.086 # Si, "generic silicon with four bonds attached" (ver=1.0, ref=2) + @atom:si4c 28.086 # Si, "a subset of si4, non-hydrogen atom attached [siloxanes]" (ver=1.0, ref=2) + @atom:xe 131.3 # Xe, "xenon" (ver=1.0, ref=5) + } #(end of atom masses) + + + # ---------- EQUIVALENCE CATEGORIES for bonded interaction lookup ---------- + # Each type of atom has a separate ID used for looking up bond parameters + # and a separate ID for looking up 3-body angle interaction parameters + # and a separate ID for looking up 4-body dihedral interaction parameters + # and a separate ID for looking up 4-body improper interaction parameters + # The complete @atom type name includes ALL of these ID numbers. There's + # no need to force the end-user to type the complete name of each atom. + # The "replace" command used below informs moltemplate that the short + # @atom names we have been using abovee are equivalent to the complete + # @atom names used below: + + replace{ @atom:ar @atom:ar,par,bar,aar,dar,iar } + replace{ @atom:c3a @atom:c3a,pc3a,bc3a,ac3a,dc3a,ic3a } + replace{ @atom:c1o @atom:c1o,pc1o,bc1o,ac1o,dc1o,ic1o } + replace{ @atom:c2= @atom:c2=,pc2=,bc2=,ac2=,dc2=,ic2= } + replace{ @atom:c3prime @atom:c3prime,pc3prime,bc3prime,ac3prime,dc3prime,ic3prime } + replace{ @atom:c4 @atom:c4,pc4,bc4,ac4,dc4,ic4 } + replace{ @atom:c41o @atom:c41o,pc41o,bc4,ac4,dc4,ic4 } + replace{ @atom:c43o @atom:c43o,pc43o,bc4,ac4,dc4,ic4 } + replace{ @atom:c43 @atom:c43,pc43,bc4,ac4,dc4,ic4 } + replace{ @atom:c44 @atom:c44,pc44,bc4,ac4,dc4,ic4 } + replace{ @atom:c4o @atom:c4o,pc4o,bc4,ac4,dc4,ic4 } + replace{ @atom:c4z @atom:c4z,pc4z,bc4,ac4,dc4,ic4 } + replace{ @atom:h1 @atom:h1,ph1,bh1,ah1,dh1,ih1 } + replace{ @atom:h1h @atom:h1h,ph1h,bh1h,ah1,dh1,ih1 } + replace{ @atom:h1o @atom:h1o,ph1o,bh1,ah1,dh1,ih1 } + replace{ @atom:he @atom:he,phe,bhe,ahe,dhe,ihe } + replace{ @atom:kr @atom:kr,pkr,bkr,akr,dkr,ikr } + replace{ @atom:n1n @atom:n1n,pn1n,bn1n,an1n,dn1n,in1n } + replace{ @atom:n1o @atom:n1o,pn1o,bn1o,an1o,dn1o,in1o } + replace{ @atom:n1z @atom:n1z,pn1z,bn1t,an1t,dn1t,in1t } + replace{ @atom:n2= @atom:n2=,pn2=,bn2=,an2=,dn2=,in2= } + replace{ @atom:n2o @atom:n2o,pn2o,bn2o,an2o,dn2o,in2o } + replace{ @atom:n2t @atom:n2t,pn2t,bn2t,an2t,dn2t,in2t } + replace{ @atom:n2z @atom:n2z,pn2z,bn2z,an2z,dn2z,in2z } + replace{ @atom:n3m @atom:n3m,pn3m,bn3m,an3m,dn3m,in3m } + replace{ @atom:n3o @atom:n3o,pn3o,bn3o,an3o,dn3o,in3o } + replace{ @atom:ne @atom:ne,pne,bne,ane,dne,ine } + replace{ @atom:o1= @atom:o1=,po1=,bo1=,ao1=,do1=,io1= } + replace{ @atom:o1=star @atom:o1=star,po1=star,bo1=,ao1=,do1=,io1= } + replace{ @atom:o12 @atom:o12,po12,bo1=,ao1=,do1=,io1= } + replace{ @atom:o1c @atom:o1c,po1c,bo1c,ao1c,do1c,io1c } + replace{ @atom:o1n @atom:o1n,po1n,bo1n,ao1n,do1n,io1n } + replace{ @atom:o1o @atom:o1o,po1o,bo1o,ao1o,do1o,io1o } + replace{ @atom:o2 @atom:o2,po2,bo2,ao2,do2,io2 } + replace{ @atom:o2e @atom:o2e,po2e,bo2e,ao2,do2,io2 } + replace{ @atom:o2h @atom:o2h,po2h,bo2h,ao2,do2,io2 } + replace{ @atom:o2n @atom:o2n,po2n,bo2n,ao2n,do2,io2 } + replace{ @atom:o2s @atom:o2s,po2s,bo2e,ao2,do2,io2 } + replace{ @atom:o2z @atom:o2z,po2z,bo2z,ao2z,do2z,io2z } + replace{ @atom:p4= @atom:p4=,pp4=,bp4=,ap4=,dp4=,ip4= } + replace{ @atom:s1= @atom:s1=,ps1=,bs1=,as1=,ds1=,is1= } + replace{ @atom:s2= @atom:s2=,ps2=,bs2=,as2=,ds2=,is2= } + replace{ @atom:si4 @atom:si4,psi4,bsi4,asi4,dsi4,isi4 } + replace{ @atom:si4c @atom:si4c,psi4c,bsi4,asi4,dsi4,isi4 } + replace{ @atom:xe @atom:xe,pxe,bxe,axe,dxe,ixe } + + + + + # --------------- Non-Bonded Interactions: --------------------- + # Syntax: + # pair_coeff AtomType1 AtomType2 pair_style_name parameters... + + write_once("In Settings") { + pair_coeff @atom:*,pc3a,b*,a*,d*,i* @atom:*,pc3a,b*,a*,d*,i* lj/class2/coul/long 0.0680 3.9150 # (ver=1.0, ref=1) + pair_coeff @atom:*,pc4,b*,a*,d*,i* @atom:*,pc4,b*,a*,d*,i* lj/class2/coul/long 0.0620 3.8540 # (ver=1.0, ref=1) + pair_coeff @atom:*,pc43,b*,a*,d*,i* @atom:*,pc43,b*,a*,d*,i* lj/class2/coul/long 0.0400 3.8540 # (ver=1.0, ref=1) + pair_coeff @atom:*,pc44,b*,a*,d*,i* @atom:*,pc44,b*,a*,d*,i* lj/class2/coul/long 0.0200 3.8540 # (ver=1.0, ref=1) + pair_coeff @atom:*,ph1,b*,a*,d*,i* @atom:*,ph1,b*,a*,d*,i* lj/class2/coul/long 0.0230 2.8780 # (ver=1.0, ref=1) + pair_coeff @atom:*,po2z,b*,a*,d*,i* @atom:*,po2z,b*,a*,d*,i* lj/class2/coul/long 0.0800 3.3000 # (ver=1.0, ref=2) + pair_coeff @atom:*,psi4,b*,a*,d*,i* @atom:*,psi4,b*,a*,d*,i* lj/class2/coul/long 0.1980 4.4050 # (ver=1.0, ref=2) + pair_coeff @atom:*,psi4c,b*,a*,d*,i* @atom:*,psi4c,b*,a*,d*,i* lj/class2/coul/long 0.1310 4.2900 # (ver=1.0, ref=2) + pair_coeff @atom:*,pc4o,b*,a*,d*,i* @atom:*,pc4o,b*,a*,d*,i* lj/class2/coul/long 0.0748 3.8700 # (ver=1.1, ref=8) + pair_coeff @atom:*,ph1o,b*,a*,d*,i* @atom:*,ph1o,b*,a*,d*,i* lj/class2/coul/long 0.0080 1.0870 # (ver=1.0, ref=3) + pair_coeff @atom:*,po2,b*,a*,d*,i* @atom:*,po2,b*,a*,d*,i* lj/class2/coul/long 0.0800 3.3000 # (ver=1.0, ref=3) + pair_coeff @atom:*,po2e,b*,a*,d*,i* @atom:*,po2e,b*,a*,d*,i* lj/class2/coul/long 0.1200 3.3000 # (ver=1.0, ref=3) + pair_coeff @atom:*,po2h,b*,a*,d*,i* @atom:*,po2h,b*,a*,d*,i* lj/class2/coul/long 0.0960 3.5800 # (ver=1.0, ref=3) + pair_coeff @atom:*,pn2=,b*,a*,d*,i* @atom:*,pn2=,b*,a*,d*,i* lj/class2/coul/long 0.0960 3.8300 # (ver=1.0, ref=4) + pair_coeff @atom:*,pp4=,b*,a*,d*,i* @atom:*,pp4=,b*,a*,d*,i* lj/class2/coul/long 0.0650 4.2950 # (ver=1.0, ref=4) + pair_coeff @atom:*,phe,b*,a*,d*,i* @atom:*,phe,b*,a*,d*,i* lj/class2/coul/long 0.0050 2.9000 # (ver=1.0, ref=5) + pair_coeff @atom:*,pne,b*,a*,d*,i* @atom:*,pne,b*,a*,d*,i* lj/class2/coul/long 0.0550 3.2000 # (ver=1.0, ref=5) + pair_coeff @atom:*,par,b*,a*,d*,i* @atom:*,par,b*,a*,d*,i* lj/class2/coul/long 0.2000 3.8800 # (ver=1.0, ref=5) + pair_coeff @atom:*,pkr,b*,a*,d*,i* @atom:*,pkr,b*,a*,d*,i* lj/class2/coul/long 0.2800 4.3000 # (ver=1.0, ref=5) + pair_coeff @atom:*,pxe,b*,a*,d*,i* @atom:*,pxe,b*,a*,d*,i* lj/class2/coul/long 0.3900 4.2600 # (ver=1.0, ref=5) + pair_coeff @atom:*,ph1h,b*,a*,d*,i* @atom:*,ph1h,b*,a*,d*,i* lj/class2/coul/long 0.0216 1.4210 # (ver=1.0, ref=5) + pair_coeff @atom:*,pn1n,b*,a*,d*,i* @atom:*,pn1n,b*,a*,d*,i* lj/class2/coul/long 0.0598 3.8008 # (ver=1.0, ref=5) + pair_coeff @atom:*,pc1o,b*,a*,d*,i* @atom:*,pc1o,b*,a*,d*,i* lj/class2/coul/long 0.0530 4.0120 # (ver=1.0, ref=5) + pair_coeff @atom:*,po1o,b*,a*,d*,i* @atom:*,po1o,b*,a*,d*,i* lj/class2/coul/long 0.0780 3.4758 # (ver=1.0, ref=5) + pair_coeff @atom:*,po1c,b*,a*,d*,i* @atom:*,po1c,b*,a*,d*,i* lj/class2/coul/long 0.0850 3.6020 # (ver=1.0, ref=5) + pair_coeff @atom:*,pn1o,b*,a*,d*,i* @atom:*,pn1o,b*,a*,d*,i* lj/class2/coul/long 0.1280 3.4600 # (ver=1.0, ref=5) + pair_coeff @atom:*,po1n,b*,a*,d*,i* @atom:*,po1n,b*,a*,d*,i* lj/class2/coul/long 0.1560 3.3000 # (ver=1.0, ref=5) + pair_coeff @atom:*,pc2=,b*,a*,d*,i* @atom:*,pc2=,b*,a*,d*,i* lj/class2/coul/long 0.0680 3.9150 # (ver=1.0, ref=5) + pair_coeff @atom:*,ps2=,b*,a*,d*,i* @atom:*,ps2=,b*,a*,d*,i* lj/class2/coul/long 0.1250 4.0470 # (ver=1.0, ref=5) + pair_coeff @atom:*,pn2o,b*,a*,d*,i* @atom:*,pn2o,b*,a*,d*,i* lj/class2/coul/long 0.3330 3.5290 # (ver=1.0, ref=5) + pair_coeff @atom:*,po1=,b*,a*,d*,i* @atom:*,po1=,b*,a*,d*,i* lj/class2/coul/long 0.1920 3.4300 # (ver=1.0, ref=5) + pair_coeff @atom:*,po1=star,b*,a*,d*,i* @atom:*,po1=star,b*,a*,d*,i* lj/class2/coul/long 0.0670 3.3600 # (ver=1.0, ref=5) + pair_coeff @atom:*,ps1=,b*,a*,d*,i* @atom:*,ps1=,b*,a*,d*,i* lj/class2/coul/long 0.3130 4.0070 # (ver=1.0, ref=5) + pair_coeff @atom:*,pn3o,b*,a*,d*,i* @atom:*,pn3o,b*,a*,d*,i* lj/class2/coul/long 0.0480 3.7600 # (ver=1.0, ref=6) + pair_coeff @atom:*,po12,b*,a*,d*,i* @atom:*,po12,b*,a*,d*,i* lj/class2/coul/long 0.0480 3.4000 # (ver=1.0, ref=6) + pair_coeff @atom:*,po2n,b*,a*,d*,i* @atom:*,po2n,b*,a*,d*,i* lj/class2/coul/long 0.2000 3.6500 # (ver=1.0, ref=6) + pair_coeff @atom:*,pc3prime,b*,a*,d*,i* @atom:*,pc3prime,b*,a*,d*,i* lj/class2/coul/long 0.0640 3.9000 # (ver=1.0, ref=7) + pair_coeff @atom:*,pn3m,b*,a*,d*,i* @atom:*,pn3m,b*,a*,d*,i* lj/class2/coul/long 0.1500 3.7200 # (ver=1.0, ref=7) + pair_coeff @atom:*,po2s,b*,a*,d*,i* @atom:*,po2s,b*,a*,d*,i* lj/class2/coul/long 0.0960 3.3000 # (ver=1.0, ref=7) + pair_coeff @atom:*,pc41o,b*,a*,d*,i* @atom:*,pc41o,b*,a*,d*,i* lj/class2/coul/long 0.1080 3.8700 # (ver=1.1, ref=8) + pair_coeff @atom:*,pc43o,b*,a*,d*,i* @atom:*,pc43o,b*,a*,d*,i* lj/class2/coul/long 0.0498 3.6700 # (ver=1.1, ref=8) + pair_coeff @atom:*,pc4z,b*,a*,d*,i* @atom:*,pc4z,b*,a*,d*,i* lj/class2/coul/long 0.0800 3.6500 # (ver=1.0, ref=9) + pair_coeff @atom:*,pn1z,b*,a*,d*,i* @atom:*,pn1z,b*,a*,d*,i* lj/class2/coul/long 0.0850 3.5200 # (ver=1.0, ref=9) + pair_coeff @atom:*,pn2t,b*,a*,d*,i* @atom:*,pn2t,b*,a*,d*,i* lj/class2/coul/long 0.0500 3.3000 # (ver=1.0, ref=9) + pair_coeff @atom:*,pn2z,b*,a*,d*,i* @atom:*,pn2z,b*,a*,d*,i* lj/class2/coul/long 0.1200 3.4000 # (ver=1.0, ref=9) + } #(end of pair_coeffs) + + + + # ---------- Charge By Bond (a.k.a. "bond equivalences") ---------- + + + + write_once("Data Charge By Bond") { + @atom:*,p*,bh1,a*,d*,i* @atom:*,p*,bsi4,a*,d*,i* -0.1260 0.1260 # (ver=1.0, ref=10) + @atom:*,p*,bc4,a*,d*,i* @atom:*,p*,bsi4,a*,d*,i* -0.1350 0.1350 # (ver=1.0, ref=10) + @atom:*,p*,bc3a,a*,d*,i* @atom:*,p*,bsi4,a*,d*,i* -0.1170 0.1170 # (ver=1.0, ref=10) + @atom:*,p*,bn2t,a*,d*,i* @atom:*,p*,bn2z,a*,d*,i* 0.2470 -0.2470 # (ver=1.0, ref=9) + @atom:*,p*,bn1t,a*,d*,i* @atom:*,p*,bn2t,a*,d*,i* -0.3860 0.3860 # (ver=1.0, ref=9) + @atom:*,p*,bh1,a*,d*,i* @atom:*,p*,bn2z,a*,d*,i* 0.3350 -0.3350 # (ver=1.0, ref=9) + @atom:*,p*,bc4,a*,d*,i* @atom:*,p*,bn2z,a*,d*,i* 0.3110 -0.3110 # (ver=1.0, ref=9) + @atom:*,p*,bc3a,a*,d*,i* @atom:*,p*,bn3m,a*,d*,i* 0.0950 -0.0950 # (ver=1.0, ref=7) + @atom:*,p*,bc3prime,a*,d*,i* @atom:*,p*,bn3m,a*,d*,i* 0.0000 0.0000 # (ver=1.0, ref=7) + @atom:*,p*,bc3a,a*,d*,i* @atom:*,p*,bc3prime,a*,d*,i* -0.0350 0.0350 # (ver=1.0, ref=7) + @atom:*,p*,bc3prime,a*,d*,i* @atom:*,p*,bo1=,a*,d*,i* 0.4500 -0.4500 # (ver=1.0, ref=7) + @atom:*,p*,bc3prime,a*,d*,i* @atom:*,p*,bc4,a*,d*,i* 0.0000 0.0000 # (ver=1.0, ref=7) + @atom:*,p*,bc3prime,a*,d*,i* @atom:*,p*,bo2e,a*,d*,i* 0.1120 -0.1120 # (ver=1.0, ref=7) + @atom:*,p*,bn3o,a*,d*,i* @atom:*,p*,bo2n,a*,d*,i* 0.0010 -0.0010 # (ver=1.0, ref=6) + @atom:*,p*,bn3o,a*,d*,i* @atom:*,p*,bo1=,a*,d*,i* 0.4280 -0.4280 # (ver=1.0, ref=6) + @atom:*,p*,bh1,a*,d*,i* @atom:*,p*,bn3o,a*,d*,i* 0.1880 -0.1880 # (ver=1.0, ref=6) + @atom:*,p*,bc4,a*,d*,i* @atom:*,p*,bo2n,a*,d*,i* 0.3170 -0.3170 # (ver=1.0, ref=6) + @atom:*,p*,bc4,a*,d*,i* @atom:*,p*,bn3o,a*,d*,i* 0.2100 -0.2100 # (ver=1.0, ref=6) + @atom:*,p*,bc3a,a*,d*,i* @atom:*,p*,bn3o,a*,d*,i* 0.2390 -0.2390 # (ver=1.0, ref=6) + @atom:*,p*,bo1o,a*,d*,i* @atom:*,p*,bo1o,a*,d*,i* 0.0000 0.0000 # (ver=1.0, ref=5) + @atom:*,p*,bo1=,a*,d*,i* @atom:*,p*,bs2=,a*,d*,i* -0.2351 0.2351 # (ver=1.0, ref=5) + @atom:*,p*,bn1o,a*,d*,i* @atom:*,p*,bo1n,a*,d*,i* 0.0288 -0.0288 # (ver=1.0, ref=5) + @atom:*,p*,bn1n,a*,d*,i* @atom:*,p*,bn1n,a*,d*,i* 0.0000 0.0000 # (ver=1.0, ref=5) + @atom:*,p*,bh1h,a*,d*,i* @atom:*,p*,bh1h,a*,d*,i* 0.0000 0.0000 # (ver=1.0, ref=5) + @atom:*,p*,bn2o,a*,d*,i* @atom:*,p*,bo1=,a*,d*,i* 0.0730 -0.0730 # (ver=1.0, ref=5) + @atom:*,p*,bc2=,a*,d*,i* @atom:*,p*,bs1=,a*,d*,i* 0.0258 -0.0258 # (ver=1.0, ref=5) + @atom:*,p*,bc2=,a*,d*,i* @atom:*,p*,bo1=,a*,d*,i* 0.4000 -0.4000 # (ver=1.0, ref=5) + @atom:*,p*,bc1o,a*,d*,i* @atom:*,p*,bo1c,a*,d*,i* -0.0203 0.0203 # (ver=1.0, ref=5) + @atom:*,p*,bo2,a*,d*,i* @atom:*,p*,bp4=,a*,d*,i* -0.1400 0.1400 # (ver=1.0, ref=4) + @atom:*,p*,bn3,a*,d*,i* @atom:*,p*,bp4=,a*,d*,i* -0.1200 0.1200 # (ver=1.0, ref=4) + @atom:*,p*,bn2=,a*,d*,i* @atom:*,p*,bp4=,a*,d*,i* -0.3500 0.3500 # (ver=1.0, ref=4) + @atom:*,p*,bn2=,a*,d*,i* @atom:*,p*,bo2,a*,d*,i* -0.0430 0.0430 # (ver=1.0, ref=4) + @atom:*,p*,bn2=,a*,d*,i* @atom:*,p*,bn3,a*,d*,i* 0.0250 -0.0250 # (ver=1.0, ref=4) + @atom:*,p*,bn2=,a*,d*,i* @atom:*,p*,bn2=,a*,d*,i* 0.0000 0.0000 # (ver=1.0, ref=4) + @atom:*,p*,bh1,a*,d*,i* @atom:*,p*,bp4=,a*,d*,i* -0.0500 0.0500 # (ver=1.0, ref=4) + @atom:*,p*,bh1,a*,d*,i* @atom:*,p*,bn2=,a*,d*,i* 0.3280 -0.3280 # (ver=1.0, ref=4) + @atom:*,p*,bf1p,a*,d*,i* @atom:*,p*,bp4=,a*,d*,i* -0.1800 0.1800 # (ver=1.0, ref=4) + @atom:*,p*,bcl1p,a*,d*,i* @atom:*,p*,bp4=,a*,d*,i* -0.1200 0.1200 # (ver=1.0, ref=4) + @atom:*,p*,bc4,a*,d*,i* @atom:*,p*,bp4=,a*,d*,i* -0.0500 0.0500 # (ver=1.0, ref=4) + @atom:*,p*,bc4,a*,d*,i* @atom:*,p*,bn2=,a*,d*,i* 0.3450 -0.3450 # (ver=1.0, ref=4) + @atom:*,p*,bc3a,a*,d*,i* @atom:*,p*,bp4=,a*,d*,i* -0.0600 0.0600 # (ver=1.0, ref=4) + @atom:*,p*,bc3a,a*,d*,i* @atom:*,p*,bn2=,a*,d*,i* 0.1990 -0.1990 # (ver=1.0, ref=4) + @atom:*,p*,bh1,a*,d*,i* @atom:*,p*,bo2,a*,d*,i* 0.4200 -0.4200 # (ver=1.0, ref=3) + @atom:*,p*,bc4,a*,d*,i* @atom:*,p*,bo2h,a*,d*,i* 0.1600 -0.1600 # (ver=1.0, ref=3) + @atom:*,p*,bc4,a*,d*,i* @atom:*,p*,bo2e,a*,d*,i* 0.1600 -0.1600 # (ver=1.0, ref=3) + @atom:*,p*,bc3a,a*,d*,i* @atom:*,p*,bo2h,a*,d*,i* 0.0420 -0.0420 # (ver=1.0, ref=3) + @atom:*,p*,bc3a,a*,d*,i* @atom:*,p*,bo2e,a*,d*,i* 0.0420 -0.0420 # (ver=1.0, ref=3) + @atom:*,p*,bo2z,a*,d*,i* @atom:*,p*,bsi4,a*,d*,i* -0.2225 0.2225 # (ver=1.0, ref=2) + @atom:*,p*,bc4,a*,d*,i* @atom:*,p*,bh1,a*,d*,i* -0.0530 0.0530 # (ver=1.0, ref=1) + @atom:*,p*,bc4,a*,d*,i* @atom:*,p*,bc4,a*,d*,i* 0.0000 0.0000 # (ver=1.0, ref=1) + @atom:*,p*,bc3a,a*,d*,i* @atom:*,p*,bh1,a*,d*,i* -0.1268 0.1268 # (ver=1.0, ref=1) + @atom:*,p*,bc3a,a*,d*,i* @atom:*,p*,bc4,a*,d*,i* 0.0000 0.0000 # (ver=1.0, ref=1) + @atom:*,p*,bc3a,a*,d*,i* @atom:*,p*,bc3a,a*,d*,i* 0.0000 0.0000 # (ver=1.0, ref=1) + @atom:*,p*,bh1,a*,d*,i* @atom:*,p*,bo2h,a*,d*,i* 0.4100 -0.4100 # (ver=1.1, ref=8) + } #(end of Charge by Bond (bond equivalences)) + + + + + + # --------------- Bond Interactions: --------------------- + + + # -- Rules for generating (2-body) "bond" interactions: -- + # BondType AtomType1 AtomType2 + + write_once("Data Bonds By Type") { + @bond:c4,n3m @atom:*,bc4,a*,d*,i* @atom:*,bn3m,a*,d*,i* + @bond:si4,si4 @atom:*,bsi4,a*,d*,i* @atom:*,bsi4,a*,d*,i* + @bond:h1,si4 @atom:*,bh1,a*,d*,i* @atom:*,bsi4,a*,d*,i* + @bond:c4,si4 @atom:*,bc4,a*,d*,i* @atom:*,bsi4,a*,d*,i* + @bond:c3a,si4 @atom:*,bc3a,a*,d*,i* @atom:*,bsi4,a*,d*,i* + @bond:h1,n2z @atom:*,bh1,a*,d*,i* @atom:*,bn2z,a*,d*,i* + @bond:c4,n2z @atom:*,bc4,a*,d*,i* @atom:*,bn2z,a*,d*,i* + @bond:n1t,n2t @atom:*,bn1t,a*,d*,i* @atom:*,bn2t,a*,d*,i* + @bond:n2t,n2z @atom:*,bn2t,a*,d*,i* @atom:*,bn2z,a*,d*,i* + @bond:n1t,n1t @atom:*,bn1t,a*,d*,i* @atom:*,bn1t,a*,d*,i* + @bond:c3a,n3m @atom:*,bc3a,a*,d*,i* @atom:*,bn3m,a*,d*,i* + @bond:c3prime,n3m @atom:*,bc3prime,a*,d*,i* @atom:*,bn3m,a*,d*,i* + @bond:c3a,c3prime @atom:*,bc3a,a*,d*,i* @atom:*,bc3prime,a*,d*,i* + @bond:c3prime,o1= @atom:*,bc3prime,a*,d*,i* @atom:*,bo1=,a*,d*,i* + @bond:c3prime,c4 @atom:*,bc3prime,a*,d*,i* @atom:*,bc4,a*,d*,i* + @bond:c3prime,o2e @atom:*,bc3prime,a*,d*,i* @atom:*,bo2e,a*,d*,i* + @bond:n3o,o2n @atom:*,bn3o,a*,d*,i* @atom:*,bo2n,a*,d*,i* + @bond:n3o,o1= @atom:*,bn3o,a*,d*,i* @atom:*,bo1=,a*,d*,i* + @bond:h1,n3o @atom:*,bh1,a*,d*,i* @atom:*,bn3o,a*,d*,i* + @bond:c4,o2n @atom:*,bc4,a*,d*,i* @atom:*,bo2n,a*,d*,i* + @bond:c4,n3o @atom:*,bc4,a*,d*,i* @atom:*,bn3o,a*,d*,i* + @bond:c3a,n3o @atom:*,bc3a,a*,d*,i* @atom:*,bn3o,a*,d*,i* + @bond:c2=,s1= @atom:*,bc2=,a*,d*,i* @atom:*,bs1=,a*,d*,i* + @bond:n2o,o1= @atom:*,bn2o,a*,d*,i* @atom:*,bo1=,a*,d*,i* + @bond:c2=,o1= @atom:*,bc2=,a*,d*,i* @atom:*,bo1=,a*,d*,i* + @bond:o1=,s2= @atom:*,bo1=,a*,d*,i* @atom:*,bs2=,a*,d*,i* + @bond:n1o,o1n @atom:*,bn1o,a*,d*,i* @atom:*,bo1n,a*,d*,i* + @bond:c1o,o1c @atom:*,bc1o,a*,d*,i* @atom:*,bo1c,a*,d*,i* + @bond:o1o,o1o @atom:*,bo1o,a*,d*,i* @atom:*,bo1o,a*,d*,i* + @bond:n1n,n1n @atom:*,bn1n,a*,d*,i* @atom:*,bn1n,a*,d*,i* + @bond:h1h,h1h @atom:*,bh1h,a*,d*,i* @atom:*,bh1h,a*,d*,i* + @bond:o2,p4= @atom:*,bo2,a*,d*,i* @atom:*,bp4=,a*,d*,i* + @bond:n3,p4= @atom:*,bn3,a*,d*,i* @atom:*,bp4=,a*,d*,i* + @bond:n2=,p4= @atom:*,bn2=,a*,d*,i* @atom:*,bp4=,a*,d*,i* + @bond:h1,p4= @atom:*,bh1,a*,d*,i* @atom:*,bp4=,a*,d*,i* + @bond:h1,n2= @atom:*,bh1,a*,d*,i* @atom:*,bn2=,a*,d*,i* + @bond:f1p,p4= @atom:*,bf1p,a*,d*,i* @atom:*,bp4=,a*,d*,i* + @bond:cl1p,p4= @atom:*,bcl1p,a*,d*,i* @atom:*,bp4=,a*,d*,i* + @bond:c4,p4= @atom:*,bc4,a*,d*,i* @atom:*,bp4=,a*,d*,i* + @bond:c4,n2= @atom:*,bc4,a*,d*,i* @atom:*,bn2=,a*,d*,i* + @bond:c3a,p4= @atom:*,bc3a,a*,d*,i* @atom:*,bp4=,a*,d*,i* + @bond:c3a,n2= @atom:*,bc3a,a*,d*,i* @atom:*,bn2=,a*,d*,i* + @bond:h1,o2h @atom:*,bh1,a*,d*,i* @atom:*,bo2h,a*,d*,i* + @bond:c4,o2h @atom:*,bc4,a*,d*,i* @atom:*,bo2h,a*,d*,i* + @bond:c4,o2e @atom:*,bc4,a*,d*,i* @atom:*,bo2e,a*,d*,i* + @bond:c3a,o2h @atom:*,bc3a,a*,d*,i* @atom:*,bo2h,a*,d*,i* + @bond:c3a,o2e @atom:*,bc3a,a*,d*,i* @atom:*,bo2e,a*,d*,i* + @bond:c3a,o2 @atom:*,bc3a,a*,d*,i* @atom:*,bo2,a*,d*,i* + @bond:o2z,si4 @atom:*,bo2z,a*,d*,i* @atom:*,bsi4,a*,d*,i* + @bond:c4,h1 @atom:*,bc4,a*,d*,i* @atom:*,bh1,a*,d*,i* + @bond:c4,c4 @atom:*,bc4,a*,d*,i* @atom:*,bc4,a*,d*,i* + @bond:c3a,h1 @atom:*,bc3a,a*,d*,i* @atom:*,bh1,a*,d*,i* + @bond:c3a,c4 @atom:*,bc3a,a*,d*,i* @atom:*,bc4,a*,d*,i* + @bond:c3a,c3a @atom:*,bc3a,a*,d*,i* @atom:*,bc3a,a*,d*,i* + } # end of "Data Bonds By Type" section + + + + # ------------ Bond Parameters: ---------- + # For an explanation of these parameters, visit: + # http://lammps.sandia.gov/doc/bond_class2.html + + # Syntax: + # bond_coeff BondTypeName BondStyle parameters... + + + write_once("In Settings") { + bond_coeff @bond:c4,n3m class2 1.4000 350.0000 0.0000 0.0000 # (ver=1.0, ref=10) + bond_coeff @bond:si4,si4 class2 2.3384 114.2164 -140.4212 80.7084 # (ver=1.0, ref=10) + bond_coeff @bond:h1,si4 class2 1.4783 202.7798 -305.3603 280.2685 # (ver=1.0, ref=10) + bond_coeff @bond:c4,si4 class2 1.8995 189.6536 -279.4210 307.5135 # (ver=1.0, ref=10) + bond_coeff @bond:c3a,si4 class2 1.8634 233.2433 -276.8692 161.6659 # (ver=1.0, ref=10) + bond_coeff @bond:h1,n2z class2 1.0221 440.1623 -960.3246 1120.3787 # (ver=1.0, ref=9) + bond_coeff @bond:c4,n2z class2 1.4814 324.4578 -648.9156 757.0681 # (ver=1.0, ref=9) + bond_coeff @bond:n1t,n2t class2 1.1354 1198.7450 -2675.4900 3121.4049 # (ver=1.0, ref=9) + bond_coeff @bond:n2t,n2z class2 1.2343 720.3345 -1542.6689 1799.7804 # (ver=1.0, ref=9) + bond_coeff @bond:n1t,n1t class2 1.1354 1337.7450 -2675.4900 3121.4049 # (ver=1.0, ref=9) + bond_coeff @bond:c3a,n3m class2 1.3950 344.0452 -652.1208 1022.2242 # (ver=1.0, ref=7) + bond_coeff @bond:c3prime,n3m class2 1.3850 359.1591 -558.4730 1146.3810 # (ver=1.0, ref=7) + bond_coeff @bond:c3a,c3prime class2 1.4890 339.3574 -655.7236 670.2362 # (ver=1.0, ref=7) + bond_coeff @bond:c3prime,o1= class2 1.2160 823.7948 -1878.7939 2303.5310 # (ver=1.0, ref=7) + bond_coeff @bond:c3prime,c4 class2 1.5140 312.3719 -465.8290 473.8300 # (ver=1.0, ref=7) + bond_coeff @bond:c3prime,o2e class2 1.3750 368.7309 -832.4784 1274.0231 # (ver=1.0, ref=7) + bond_coeff @bond:n3o,o2n class2 1.4020 300.0000 -1000.0000 2000.0000 # (ver=1.0, ref=6) + bond_coeff @bond:n3o,o1= class2 1.2100 765.0664 -2070.2830 2793.3218 # (ver=1.0, ref=6) + bond_coeff @bond:h1,n3o class2 1.0400 439.9346 -943.7307 1180.9318 # (ver=1.0, ref=6) + bond_coeff @bond:c4,o2n class2 1.4350 400.3954 -835.1951 1313.0142 # (ver=1.0, ref=6) + bond_coeff @bond:c4,n3o class2 1.4740 301.6051 -535.7028 555.0420 # (ver=1.0, ref=6) + bond_coeff @bond:c3a,n3o class2 1.4300 313.8329 -568.6087 600.9597 # (ver=1.0, ref=6) + bond_coeff @bond:c2=,s1= class2 1.5540 559.0065 -1348.6633 1248.8604 # (ver=1.0, ref=5) + bond_coeff @bond:n2o,o1= class2 1.1930 620.0000 -1808.6018 3077.5918 # (ver=1.0, ref=5) + bond_coeff @bond:c2=,o1= class2 1.1600 1161.3421 -2564.5706 3932.8735 # (ver=1.0, ref=5) + bond_coeff @bond:o1=,s2= class2 1.4308 730.8387 -1531.7910 1859.7753 # (ver=1.0, ref=5) + bond_coeff @bond:n1o,o1n class2 1.1506 1147.8362 -3167.7349 5099.5811 # (ver=1.0, ref=5) + bond_coeff @bond:c1o,o1c class2 1.1283 1368.7676 -3157.0007 4247.5298 # (ver=1.0, ref=5) + bond_coeff @bond:o1o,o1o class2 1.2074 846.7150 -2247.1760 3478.9900 # (ver=1.0, ref=5) + bond_coeff @bond:n1n,n1n class2 1.0977 1651.3730 -4069.3178 5984.9629 # (ver=1.0, ref=5) + bond_coeff @bond:h1h,h1h class2 0.7412 414.2185 -805.6549 914.1296 # (ver=1.0, ref=5) + bond_coeff @bond:o2,p4= class2 1.6000 333.0980 -726.6230 924.6200 # (ver=1.0, ref=4) + bond_coeff @bond:n3,p4= class2 1.6780 329.0000 -713.7950 902.9190 # (ver=1.0, ref=4) + bond_coeff @bond:n2=,p4= class2 1.5980 393.0060 -751.4050 767.4310 # (ver=1.0, ref=4) + bond_coeff @bond:h1,p4= class2 1.4300 285.2040 -575.6850 677.8460 # (ver=1.0, ref=4) + bond_coeff @bond:h1,n2= class2 1.0310 540.1120 -1500.2952 2431.0080 # (ver=1.0, ref=4) + bond_coeff @bond:f1p,p4= class2 1.5650 340.0000 -882.3840 1197.9190 # (ver=1.0, ref=4) + bond_coeff @bond:cl1p,p4= class2 2.0000 158.7770 -239.1290 210.0840 # (ver=1.0, ref=4) + bond_coeff @bond:c4,p4= class2 1.8000 218.1400 -329.5110 290.3490 # (ver=1.0, ref=4) + bond_coeff @bond:c4,n2= class2 1.4740 337.0600 -147.3700 213.6330 # (ver=1.0, ref=4) + bond_coeff @bond:c3a,p4= class2 1.7890 197.7020 -332.2510 325.7160 # (ver=1.0, ref=4) + bond_coeff @bond:c3a,n2= class2 1.4000 350.0000 0.0000 0.0000 # (ver=1.0, ref=4) + bond_coeff @bond:h1,o2h class2 0.9494 540.3633 -1311.8663 2132.4446 # (ver=1.0, ref=3) + bond_coeff @bond:c4,o2h class2 1.4200 400.3954 -835.1951 1313.0142 # (ver=1.0, ref=3) + bond_coeff @bond:c4,o2e class2 1.4200 400.3954 -835.1951 1313.0142 # (ver=1.0, ref=3) + bond_coeff @bond:c3a,o2h class2 1.3768 428.8798 -738.2351 1114.9655 # (ver=1.0, ref=3) + bond_coeff @bond:c3a,o2e class2 1.3768 428.8798 -738.2351 1114.9655 # (ver=1.0, ref=3) + bond_coeff @bond:c3a,o2 class2 1.3768 428.8798 -738.2350 1114.9655 # (ver=1.0, ref=3) + bond_coeff @bond:o2z,si4 class2 1.6400 350.1232 -517.3424 673.7067 # (ver=1.0, ref=2) + bond_coeff @bond:c4,h1 class2 1.1010 345.0000 -691.8900 844.6000 # (ver=1.0, ref=1) + bond_coeff @bond:c4,c4 class2 1.5300 299.6700 -501.7700 679.8100 # (ver=1.0, ref=1) + bond_coeff @bond:c3a,h1 class2 1.0982 372.8251 -803.4526 894.3173 # (ver=1.0, ref=1) + bond_coeff @bond:c3a,c4 class2 1.5010 321.9021 -521.8208 572.1628 # (ver=1.0, ref=1) + bond_coeff @bond:c3a,c3a class2 1.4170 470.8361 -627.6179 1327.6345 # (ver=1.0, ref=1) + } # end of bond_coeff commands + + + # --------------- Angle Interactions: --------------------- + + + # -- Rules for generating (3-body) "angle" interactions: -- + # AngleType AtomType1 AtomType2 AtomType3 [BondType1 BondType2] + + write_once("Data Angles By Type") { + @angle:c3a,o2,c3a,c3a,o2h,c3a @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bo2h,ao2,d*,i* @atom:*,p*,bc3a,ac3a,d*,i* + @angle:c3a,o2,c3a,c3a,o2e,c3a @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bo2e,ao2,d*,i* @atom:*,p*,bc3a,ac3a,d*,i* + @angle:c3a,o2,c3a,c3a,o2,c3a @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bo2,ao2,d*,i* @atom:*,p*,bc3a,ac3a,d*,i* + @angle:c3a,c4,o2,c3a,c4,o2h @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bo2h,ao2,d*,i* + @angle:c3a,c4,o2,c3a,c4,o2e @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bo2e,ao2,d*,i* + @angle:c3a,o2,c3prime,c3a,o2e,c3prime @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bo2e,ao2,d*,i* @atom:*,p*,bc3prime,ac3prime,d*,i* + @angle:o2,c4,o2,o2h,c4,o2h @atom:*,p*,bo2h,ao2,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bo2h,ao2,d*,i* + @angle:o2,c4,o2,o2h,c4,o2e @atom:*,p*,bo2h,ao2,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bo2e,ao2,d*,i* + @angle:o2,c4,o2,o2e,c4,o2h @atom:*,p*,bo2e,ao2,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bo2h,ao2,d*,i* + @angle:o2,c4,o2,o2e,c4,o2e @atom:*,p*,bo2e,ao2,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bo2e,ao2,d*,i* + @angle:h1,c3a,o2,h1,c3a,o2h @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bo2h,ao2,d*,i* + @angle:h1,c3a,o2,h1,c3a,o2e @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bo2e,ao2,d*,i* + @angle:h1,c3a,o2,h1,c3a,o2 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bo2,ao2,d*,i* + @angle:si4,si4,si4,si4,si4,si4 @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bsi4,asi4,d*,i* + @angle:h1,si4,si4,h1,si4,si4 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bsi4,asi4,d*,i* + @angle:c4,si4,si4,c4,si4,si4 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bsi4,asi4,d*,i* + @angle:h1,si4,h1,h1,si4,h1 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bh1,ah1,d*,i* + @angle:c4,si4,h1,c4,si4,h1 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bh1,ah1,d*,i* + @angle:c4,si4,c4,c4,si4,c4 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bc4,ac4,d*,i* + @angle:c3a,si4,h1,c3a,si4,h1 @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bh1,ah1,d*,i* + @angle:h1,c4,si4,h1,c4,si4 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bsi4,asi4,d*,i* + @angle:c4,c4,si4,c4,c4,si4 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bsi4,asi4,d*,i* + @angle:c3a,c3a,si4,c3a,c3a,si4 @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bsi4,asi4,d*,i* + @angle:c4,c4,n2z,c4,c4,n2z @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bn2z,an2z,d*,i* + @angle:h1,c4,n2z,h1,c4,n2z @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bn2z,an2z,d*,i* + @angle:c4,n2z,n2t,c4,n2z,n2t @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bn2z,an2z,d*,i* @atom:*,p*,bn2t,an2t,d*,i* + @angle:h1,n2z,n2t,h1,n2z,n2t @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bn2z,an2z,d*,i* @atom:*,p*,bn2t,an2t,d*,i* + @angle:n1t,n2t,n2z,n1t,n2t,n2z @atom:*,p*,bn1t,an1t,d*,i* @atom:*,p*,bn2t,an2t,d*,i* @atom:*,p*,bn2z,an2z,d*,i* + @angle:n3m,c3prime,o1=,n3m,c3prime,o1= @atom:*,p*,bn3m,an3m,d*,i* @atom:*,p*,bc3prime,ac3prime,d*,i* @atom:*,p*,bo1=,ao1=,d*,i* + @angle:c4,c3prime,o2,c4,c3prime,o2e @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc3prime,ac3prime,d*,i* @atom:*,p*,bo2e,ao2,d*,i* + @angle:c4,c3prime,o1=,c4,c3prime,o1= @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc3prime,ac3prime,d*,i* @atom:*,p*,bo1=,ao1=,d*,i* + @angle:o1=,c3prime,o2,o1=,c3prime,o2e @atom:*,p*,bo1=,ao1=,d*,i* @atom:*,p*,bc3prime,ac3prime,d*,i* @atom:*,p*,bo2e,ao2,d*,i* + @angle:c3a,n3m,c3prime,c3a,n3m,c3prime @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bn3m,an3m,d*,i* @atom:*,p*,bc3prime,ac3prime,d*,i* + @angle:c3a,c3a,n3m,c3a,c3a,n3m @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bn3m,an3m,d*,i* + @angle:c3a,c3prime,o1=,c3a,c3prime,o1= @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3prime,ac3prime,d*,i* @atom:*,p*,bo1=,ao1=,d*,i* + @angle:c3a,c3prime,n3m,c3a,c3prime,n3m @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3prime,ac3prime,d*,i* @atom:*,p*,bn3m,an3m,d*,i* + @angle:c3a,c3a,c3prime,c3a,c3a,c3prime @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3prime,ac3prime,d*,i* + @angle:c3prime,n3m,c3prime,c3prime,n3m,c3prime @atom:*,p*,bc3prime,ac3prime,d*,i* @atom:*,p*,bn3m,an3m,d*,i* @atom:*,p*,bc3prime,ac3prime,d*,i* + @angle:c3prime,c4,h1,c3prime,c4,h1 @atom:*,p*,bc3prime,ac3prime,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bh1,ah1,d*,i* + @angle:c3prime,o2,c4,c3prime,o2e,c4 @atom:*,p*,bc3prime,ac3prime,d*,i* @atom:*,p*,bo2e,ao2,d*,i* @atom:*,p*,bc4,ac4,d*,i* + @angle:o1=,n3o,o2n,o1=,n3o,o2n @atom:*,p*,bo1=,ao1=,d*,i* @atom:*,p*,bn3o,an3o,d*,i* @atom:*,p*,bo2n,ao2n,d*,i* + @angle:c4,c4,o2n,c4,c4,o2n @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bo2n,ao2n,d*,i* + @angle:c4,o2n,n3o,c4,o2n,n3o @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bo2n,ao2n,d*,i* @atom:*,p*,bn3o,an3o,d*,i* + @angle:o1=,n3o,o1=,o1=,n3o,o1= @atom:*,p*,bo1=,ao1=,d*,i* @atom:*,p*,bn3o,an3o,d*,i* @atom:*,p*,bo1=,ao1=,d*,i* + @angle:h1,n3o,o1=,h1,n3o,o1= @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bn3o,an3o,d*,i* @atom:*,p*,bo1=,ao1=,d*,i* + @angle:c4,n3o,o1=,c4,n3o,o1= @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bn3o,an3o,d*,i* @atom:*,p*,bo1=,ao1=,d*,i* + @angle:c3a,n3o,o1=,c3a,n3o,o1= @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bn3o,an3o,d*,i* @atom:*,p*,bo1=,ao1=,d*,i* + @angle:h1,c4,o2n,h1,c4,o2n @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bo2n,ao2n,d*,i* + @angle:h1,c4,n3o,h1,c4,n3o @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bn3o,an3o,d*,i* + @angle:c3a,c3a,n3o,c3a,c3a,n3o @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bn3o,an3o,d*,i* + @angle:o1=,s2=,o1=,o1=,s2=,o1= @atom:*,p*,bo1=,ao1=,d*,i* @atom:*,p*,bs2=,as2=,d*,i* @atom:*,p*,bo1=,ao1=,d*,i* + @angle:o1=,n2o,o1=,o1=,n2o,o1= @atom:*,p*,bo1=,ao1=,d*,i* @atom:*,p*,bn2o,an2o,d*,i* @atom:*,p*,bo1=,ao1=,d*,i* + @angle:s1=,c2=,s1=,s1=,c2=,s1= @atom:*,p*,bs1=,as1=,d*,i* @atom:*,p*,bc2=,ac2=,d*,i* @atom:*,p*,bs1=,as1=,d*,i* + @angle:o1=,c2=,o1=,o1=,c2=,o1= @atom:*,p*,bo1=,ao1=,d*,i* @atom:*,p*,bc2=,ac2=,d*,i* @atom:*,p*,bo1=,ao1=,d*,i* + @angle:o2,p4=,o2,o2,p4=,o2 @atom:*,p*,bo2,ao2,d*,i* @atom:*,p*,bp4=,ap4=,d*,i* @atom:*,p*,bo2,ao2,d*,i* + @angle:n2=,p4=,o2,n2=,p4=,o2 @atom:*,p*,bn2=,an2=,d*,i* @atom:*,p*,bp4=,ap4=,d*,i* @atom:*,p*,bo2,ao2,d*,i* + @angle:n2=,p4=,n2=,n2=,p4=,n2= @atom:*,p*,bn2=,an2=,d*,i* @atom:*,p*,bp4=,ap4=,d*,i* @atom:*,p*,bn2=,an2=,d*,i* + @angle:h1,p4=,o2,h1,p4=,o2 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bp4=,ap4=,d*,i* @atom:*,p*,bo2,ao2,d*,i* + @angle:h1,p4=,n2=,h1,p4=,n2= @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bp4=,ap4=,d*,i* @atom:*,p*,bn2=,an2=,d*,i* + @angle:h1,p4=,h1,h1,p4=,h1 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bp4=,ap4=,d*,i* @atom:*,p*,bh1,ah1,d*,i* + @angle:c4,p4=,n2=,c4,p4=,n2= @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bp4=,ap4=,d*,i* @atom:*,p*,bn2=,an2=,d*,i* + @angle:c4,p4=,h1,c4,p4=,h1 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bp4=,ap4=,d*,i* @atom:*,p*,bh1,ah1,d*,i* + @angle:c4,p4=,c4,c4,p4=,c4 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bp4=,ap4=,d*,i* @atom:*,p*,bc4,ac4,d*,i* + @angle:c3a,p4=,o2,c3a,p4=,o2 @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bp4=,ap4=,d*,i* @atom:*,p*,bo2,ao2,d*,i* + @angle:c3a,p4=,n2=,c3a,p4=,n2= @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bp4=,ap4=,d*,i* @atom:*,p*,bn2=,an2=,d*,i* + @angle:c3a,p4=,h1,c3a,p4=,h1 @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bp4=,ap4=,d*,i* @atom:*,p*,bh1,ah1,d*,i* + @angle:c3a,p4=,c3a,c3a,p4=,c3a @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bp4=,ap4=,d*,i* @atom:*,p*,bc3a,ac3a,d*,i* + @angle:p4=,n2=,p4=,p4=,n2=,p4= @atom:*,p*,bp4=,ap4=,d*,i* @atom:*,p*,bn2=,an2=,d*,i* @atom:*,p*,bp4=,ap4=,d*,i* + @angle:h1,n2=,p4=,h1,n2=,p4= @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bn2=,an2=,d*,i* @atom:*,p*,bp4=,ap4=,d*,i* + @angle:h1,n2=,h1,h1,n2=,h1 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bn2=,an2=,d*,i* @atom:*,p*,bh1,ah1,d*,i* + @angle:c4,n2=,h1,c4,n2=,h1 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bn2=,an2=,d*,i* @atom:*,p*,bh1,ah1,d*,i* + @angle:h1,c4,p4=,h1,c4,p4= @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bp4=,ap4=,d*,i* + @angle:h1,c4,n2=,h1,c4,n2= @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bn2=,an2=,d*,i* + @angle:c4,c4,n2=,c4,c4,n2= @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bn2=,an2=,d*,i* + @angle:c3a,c3a,p4=,c3a,c3a,p4= @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bp4=,ap4=,d*,i* + @angle:c3a,c3a,n2=,c3a,c3a,n2= @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bn2=,an2=,d*,i* + @angle:c4,o2,h1,c4,o2h,h1 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bo2h,ao2,d*,i* @atom:*,p*,bh1,ah1,d*,i* + @angle:c4,o2,c4,c4,o2h,c4 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bo2h,ao2,d*,i* @atom:*,p*,bc4,ac4,d*,i* + @angle:c4,o2,c4,c4,o2e,c4 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bo2e,ao2,d*,i* @atom:*,p*,bc4,ac4,d*,i* + @angle:c3a,o2,h1,c3a,o2h,h1 @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bo2h,ao2,d*,i* @atom:*,p*,bh1,ah1,d*,i* + @angle:c3a,o2,c4,c3a,o2h,c4 @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bo2h,ao2,d*,i* @atom:*,p*,bc4,ac4,d*,i* + @angle:c3a,o2,c4,c3a,o2e,c4 @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bo2e,ao2,d*,i* @atom:*,p*,bc4,ac4,d*,i* + @angle:h1,c4,o2,h1,c4,o2h @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bo2h,ao2,d*,i* + @angle:h1,c4,o2,h1,c4,o2e @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bo2e,ao2,d*,i* + @angle:c4,c4,o2,c4,c4,o2h @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bo2h,ao2,d*,i* + @angle:c4,c4,o2,c4,c4,o2e @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bo2e,ao2,d*,i* + @angle:c3a,c3a,o2,c3a,c3a,o2h @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bo2h,ao2,d*,i* + @angle:c3a,c3a,o2,c3a,c3a,o2e @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bo2e,ao2,d*,i* + @angle:c3a,c3a,o2,c3a,c3a,o2 @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bo2,ao2,d*,i* + @angle:o2z,si4,o2z,o2z,si4,o2z @atom:*,p*,bo2z,ao2z,d*,i* @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bo2z,ao2z,d*,i* + @angle:h1,si4,o2z,h1,si4,o2z @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bo2z,ao2z,d*,i* + @angle:c4,si4,o2z,c4,si4,o2z @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bo2z,ao2z,d*,i* + @angle:c3a,si4,o2z,c3a,si4,o2z @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bo2z,ao2z,d*,i* + @angle:si4,o2z,si4,si4,o2z,si4 @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bo2z,ao2z,d*,i* @atom:*,p*,bsi4,asi4,d*,i* + @angle:h1,c4,h1,h1,c4,h1 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bh1,ah1,d*,i* + @angle:c4,c4,h1,c4,c4,h1 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bh1,ah1,d*,i* + @angle:c4,c4,c4,c4,c4,c4 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,d*,i* + @angle:c3a,c4,h1,c3a,c4,h1 @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bh1,ah1,d*,i* + @angle:c3a,c4,c4,c3a,c4,c4 @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,d*,i* + @angle:c3a,c4,c3a,c3a,c4,c3a @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc3a,ac3a,d*,i* + @angle:c3a,c3a,h1,c3a,c3a,h1 @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bh1,ah1,d*,i* + @angle:c3a,c3a,c4,c3a,c3a,c4 @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc4,ac4,d*,i* + @angle:c3a,c3a,c3a,c3a,c3a,c3a @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3a,ac3a,d*,i* + @angle:n3,p4=,o2,X,X,X @atom:*,p*,b*,an3,d*,i* @atom:*,p*,b*,ap4=,d*,i* @atom:*,p*,b*,ao2,d*,i* + @angle:n3,p4=,n3,X,X,X @atom:*,p*,b*,an3,d*,i* @atom:*,p*,b*,ap4=,d*,i* @atom:*,p*,b*,an3,d*,i* + @angle:n2=,p4=,n3,X,X,X @atom:*,p*,b*,an2=,d*,i* @atom:*,p*,b*,ap4=,d*,i* @atom:*,p*,b*,an3,d*,i* + @angle:h1,p4=,n3,X,X,X @atom:*,p*,b*,ah1,d*,i* @atom:*,p*,b*,ap4=,d*,i* @atom:*,p*,b*,an3,d*,i* + @angle:c3a,p4=,n3,X,X,X @atom:*,p*,b*,ac3a,d*,i* @atom:*,p*,b*,ap4=,d*,i* @atom:*,p*,b*,an3,d*,i* + @angle:h1,o2,p4=,X,X,X @atom:*,p*,b*,ah1,d*,i* @atom:*,p*,b*,ao2,d*,i* @atom:*,p*,b*,ap4=,d*,i* + @angle:c4,o2,p4=,X,X,X @atom:*,p*,b*,ac4,d*,i* @atom:*,p*,b*,ao2,d*,i* @atom:*,p*,b*,ap4=,d*,i* + @angle:h1,n3,p4=,X,X,X @atom:*,p*,b*,ah1,d*,i* @atom:*,p*,b*,an3,d*,i* @atom:*,p*,b*,ap4=,d*,i* + @angle:c4,n3,p4=,X,X,X @atom:*,p*,b*,ac4,d*,i* @atom:*,p*,b*,an3,d*,i* @atom:*,p*,b*,ap4=,d*,i* + @angle:h1,o2z,si4,X,X,X @atom:*,p*,b*,ah1,d*,i* @atom:*,p*,b*,ao2z,d*,i* @atom:*,p*,b*,asi4,d*,i* + } # end of "Data Angles By Type" section + + + + # ------- Angle Force Field Parameters: ------- # For an explanation of these parameters, visit: + # http://lammps.sandia.gov/doc/angle_class2.html + + # Syntax: + # angle_coeff AngleTypeName AngleStyle parameters... + + + write_once("In Settings") { + angle_coeff @angle:c3a,o2,c3a,c3a,o2h,c3a class2 0.0 0.0 0.0 0.0 # (ver=1.0, ref=7) + angle_coeff @angle:c3a,o2,c3a,c3a,o2h,c3a class2 bb 0.0000 1.3768 1.3768 # (ver=1.0, ref=7) + angle_coeff @angle:c3a,o2,c3a,c3a,o2h,c3a class2 ba 0.0 0.0 1.3768 1.3768 # (ver=1.0, ref=7) + angle_coeff @angle:c3a,o2,c3a,c3a,o2e,c3a class2 0.0 0.0 0.0 0.0 # (ver=1.0, ref=7) + angle_coeff @angle:c3a,o2,c3a,c3a,o2e,c3a class2 bb 0.0000 1.3768 1.3768 # (ver=1.0, ref=7) + angle_coeff @angle:c3a,o2,c3a,c3a,o2e,c3a class2 ba 0.0 0.0 1.3768 1.3768 # (ver=1.0, ref=7) + angle_coeff @angle:c3a,o2,c3a,c3a,o2,c3a class2 0.0 0.0 0.0 0.0 # (ver=1.0, ref=7) + angle_coeff @angle:c3a,o2,c3a,c3a,o2,c3a class2 bb 0.0000 1.3768 1.3768 # (ver=1.0, ref=7) + angle_coeff @angle:c3a,o2,c3a,c3a,o2,c3a class2 ba 0.0 0.0 1.3768 1.3768 # (ver=1.0, ref=7) + angle_coeff @angle:c3a,c4,o2,c3a,c4,o2h class2 0.0 0.0 0.0 0.0 # (ver=1.0, ref=7) + angle_coeff @angle:c3a,c4,o2,c3a,c4,o2h class2 bb 0.0000 1.5010 1.4200 # (ver=1.0, ref=7) + angle_coeff @angle:c3a,c4,o2,c3a,c4,o2h class2 ba 0.0 0.0 1.5010 1.4200 # (ver=1.0, ref=7) + angle_coeff @angle:c3a,c4,o2,c3a,c4,o2e class2 0.0 0.0 0.0 0.0 # (ver=1.0, ref=7) + angle_coeff @angle:c3a,c4,o2,c3a,c4,o2e class2 bb 0.0000 1.5010 1.4200 # (ver=1.0, ref=7) + angle_coeff @angle:c3a,c4,o2,c3a,c4,o2e class2 ba 0.0 0.0 1.5010 1.4200 # (ver=1.0, ref=7) + angle_coeff @angle:c3a,o2,c3prime,c3a,o2e,c3prime class2 0.0 0.0 0.0 0.0 # (ver=1.0, ref=7) + angle_coeff @angle:c3a,o2,c3prime,c3a,o2e,c3prime class2 bb 69.5999 1.3768 1.3750 # (ver=1.0, ref=7) + angle_coeff @angle:c3a,o2,c3prime,c3a,o2e,c3prime class2 ba 0.0 0.0 1.3768 1.3750 # (ver=1.0, ref=7) + angle_coeff @angle:o2,c4,o2,o2h,c4,o2h class2 0.0 0.0 0.0 0.0 # (ver=1.0, ref=3) + angle_coeff @angle:o2,c4,o2,o2h,c4,o2h class2 bb 8.2983 1.4200 1.4200 # (ver=1.0, ref=3) + angle_coeff @angle:o2,c4,o2,o2h,c4,o2h class2 ba 0.0 0.0 1.4200 1.4200 # (ver=1.0, ref=3) + angle_coeff @angle:o2,c4,o2,o2h,c4,o2e class2 0.0 0.0 0.0 0.0 # (ver=1.0, ref=3) + angle_coeff @angle:o2,c4,o2,o2h,c4,o2e class2 bb 8.2983 1.4200 1.4200 # (ver=1.0, ref=3) + angle_coeff @angle:o2,c4,o2,o2h,c4,o2e class2 ba 0.0 0.0 1.4200 1.4200 # (ver=1.0, ref=3) + angle_coeff @angle:o2,c4,o2,o2e,c4,o2h class2 0.0 0.0 0.0 0.0 # (ver=1.0, ref=3) + angle_coeff @angle:o2,c4,o2,o2e,c4,o2h class2 bb 8.2983 1.4200 1.4200 # (ver=1.0, ref=3) + angle_coeff @angle:o2,c4,o2,o2e,c4,o2h class2 ba 0.0 0.0 1.4200 1.4200 # (ver=1.0, ref=3) + angle_coeff @angle:o2,c4,o2,o2e,c4,o2e class2 0.0 0.0 0.0 0.0 # (ver=1.0, ref=3) + angle_coeff @angle:o2,c4,o2,o2e,c4,o2e class2 bb 8.2983 1.4200 1.4200 # (ver=1.0, ref=3) + angle_coeff @angle:o2,c4,o2,o2e,c4,o2e class2 ba 0.0 0.0 1.4200 1.4200 # (ver=1.0, ref=3) + angle_coeff @angle:h1,c3a,o2,h1,c3a,o2h class2 0.0 0.0 0.0 0.0 # (ver=1.0, ref=3) + angle_coeff @angle:h1,c3a,o2,h1,c3a,o2h class2 bb 4.5800 1.0982 1.3768 # (ver=1.0, ref=3) + angle_coeff @angle:h1,c3a,o2,h1,c3a,o2h class2 ba 0.0 0.0 1.0982 1.3768 # (ver=1.0, ref=3) + angle_coeff @angle:h1,c3a,o2,h1,c3a,o2e class2 0.0 0.0 0.0 0.0 # (ver=1.0, ref=3) + angle_coeff @angle:h1,c3a,o2,h1,c3a,o2e class2 bb 4.5800 1.0982 1.3768 # (ver=1.0, ref=3) + angle_coeff @angle:h1,c3a,o2,h1,c3a,o2e class2 ba 0.0 0.0 1.0982 1.3768 # (ver=1.0, ref=3) + angle_coeff @angle:h1,c3a,o2,h1,c3a,o2 class2 0.0 0.0 0.0 0.0 # (ver=1.0, ref=3) + angle_coeff @angle:h1,c3a,o2,h1,c3a,o2 class2 bb 4.5800 1.0982 1.3768 # (ver=1.0, ref=3) + angle_coeff @angle:h1,c3a,o2,h1,c3a,o2 class2 ba 0.0 0.0 1.0982 1.3768 # (ver=1.0, ref=3) + angle_coeff @angle:si4,si4,si4,si4,si4,si4 class2 114.2676 24.9501 -19.5949 0.0000 # (ver=1.0, ref=10) + angle_coeff @angle:si4,si4,si4,si4,si4,si4 class2 bb 6.0704 2.3384 2.3384 # (ver=1.0, ref=10) + angle_coeff @angle:si4,si4,si4,si4,si4,si4 class2 ba 8.9899 8.9899 2.3384 2.3384 # (ver=1.0, ref=10) + angle_coeff @angle:h1,si4,si4,h1,si4,si4 class2 112.0893 22.5062 -11.5926 0.0000 # (ver=1.0, ref=10) + angle_coeff @angle:h1,si4,si4,h1,si4,si4 class2 bb 3.5172 1.4783 2.3384 # (ver=1.0, ref=10) + angle_coeff @angle:h1,si4,si4,h1,si4,si4 class2 ba 5.6630 2.0706 1.4783 2.3384 # (ver=1.0, ref=10) + angle_coeff @angle:c4,si4,si4,c4,si4,si4 class2 113.0000 19.4692 -34.3471 0.0000 # (ver=1.0, ref=10) + angle_coeff @angle:c4,si4,si4,c4,si4,si4 class2 bb 2.3030 1.8995 2.3384 # (ver=1.0, ref=10) + angle_coeff @angle:c4,si4,si4,c4,si4,si4 class2 ba 16.9455 11.4377 1.8995 2.3384 # (ver=1.0, ref=10) + angle_coeff @angle:h1,si4,h1,h1,si4,h1 class2 108.6051 32.5415 -8.3164 0.0000 # (ver=1.0, ref=10) + angle_coeff @angle:h1,si4,h1,h1,si4,h1 class2 bb 4.6408 1.4783 1.4783 # (ver=1.0, ref=10) + angle_coeff @angle:h1,si4,h1,h1,si4,h1 class2 ba 9.3467 9.3467 1.4783 1.4783 # (ver=1.0, ref=10) + angle_coeff @angle:c4,si4,h1,c4,si4,h1 class2 112.0977 36.4832 -12.8094 0.0000 # (ver=1.0, ref=10) + angle_coeff @angle:c4,si4,h1,c4,si4,h1 class2 bb 3.9340 1.8995 1.4783 # (ver=1.0, ref=10) + angle_coeff @angle:c4,si4,h1,c4,si4,h1 class2 ba 13.3961 7.4104 1.8995 1.4783 # (ver=1.0, ref=10) + angle_coeff @angle:c4,si4,c4,c4,si4,c4 class2 113.1855 36.2069 -20.3939 20.0172 # (ver=1.0, ref=10) + angle_coeff @angle:c4,si4,c4,c4,si4,c4 class2 bb 3.7419 1.8995 1.8995 # (ver=1.0, ref=10) + angle_coeff @angle:c4,si4,c4,c4,si4,c4 class2 ba 18.5805 18.5805 1.8995 1.8995 # (ver=1.0, ref=10) + angle_coeff @angle:c3a,si4,h1,c3a,si4,h1 class2 109.5932 41.9497 -42.3639 48.1442 # (ver=1.0, ref=10) + angle_coeff @angle:c3a,si4,h1,c3a,si4,h1 class2 bb 3.9264 1.8634 1.4783 # (ver=1.0, ref=10) + angle_coeff @angle:c3a,si4,h1,c3a,si4,h1 class2 ba 22.5947 8.7811 1.8634 1.4783 # (ver=1.0, ref=10) + angle_coeff @angle:h1,c4,si4,h1,c4,si4 class2 112.0355 28.7721 -13.9523 0.0000 # (ver=1.0, ref=10) + angle_coeff @angle:h1,c4,si4,h1,c4,si4 class2 bb 1.6561 1.1010 1.8995 # (ver=1.0, ref=10) + angle_coeff @angle:h1,c4,si4,h1,c4,si4 class2 ba 16.6908 18.2764 1.1010 1.8995 # (ver=1.0, ref=10) + angle_coeff @angle:c4,c4,si4,c4,c4,si4 class2 112.6700 39.5160 -7.4430 0.0000 # (ver=1.0, ref=10) + angle_coeff @angle:c4,c4,si4,c4,c4,si4 class2 bb 0.0 1.5300 1.8995 # (ver=1.0, ref=10) + angle_coeff @angle:c4,c4,si4,c4,c4,si4 class2 ba 0.0 0.0 1.5300 1.8995 # (ver=1.0, ref=10) + angle_coeff @angle:c3a,c3a,si4,c3a,c3a,si4 class2 120.0000 30.4689 -23.5439 0.0000 # (ver=1.0, ref=10) + angle_coeff @angle:c3a,c3a,si4,c3a,c3a,si4 class2 bb 21.3938 1.4170 1.8634 # (ver=1.0, ref=10) + angle_coeff @angle:c3a,c3a,si4,c3a,c3a,si4 class2 ba 14.5831 23.7679 1.4170 1.8634 # (ver=1.0, ref=10) + angle_coeff @angle:c4,c4,n2z,c4,c4,n2z class2 110.9900 77.9387 0.9499 0.0033 # (ver=1.0, ref=9) + angle_coeff @angle:c4,c4,n2z,c4,c4,n2z class2 bb 36.9309 1.5300 1.4814 # (ver=1.0, ref=9) + angle_coeff @angle:c4,c4,n2z,c4,c4,n2z class2 ba 34.8803 67.8888 1.5300 1.4814 # (ver=1.0, ref=9) + angle_coeff @angle:h1,c4,n2z,h1,c4,n2z class2 107.9744 52.7803 0.6615 0.0023 # (ver=1.0, ref=9) + angle_coeff @angle:h1,c4,n2z,h1,c4,n2z class2 bb 18.4621 1.1010 1.4814 # (ver=1.0, ref=9) + angle_coeff @angle:h1,c4,n2z,h1,c4,n2z class2 ba 3.3182 61.9652 1.1010 1.4814 # (ver=1.0, ref=9) + angle_coeff @angle:c4,n2z,n2t,c4,n2z,n2t class2 113.5017 82.6294 0.9845 0.0033 # (ver=1.0, ref=9) + angle_coeff @angle:c4,n2z,n2t,c4,n2z,n2t class2 bb 84.2075 1.4814 1.2343 # (ver=1.0, ref=9) + angle_coeff @angle:c4,n2z,n2t,c4,n2z,n2t class2 ba 88.2679 195.9722 1.4814 1.2343 # (ver=1.0, ref=9) + angle_coeff @angle:h1,n2z,n2t,h1,n2z,n2t class2 110.0345 55.7635 0.6618 0.0022 # (ver=1.0, ref=9) + angle_coeff @angle:h1,n2z,n2t,h1,n2z,n2t class2 bb 14.9026 1.0221 1.2343 # (ver=1.0, ref=9) + angle_coeff @angle:h1,n2z,n2t,h1,n2z,n2t class2 ba 37.4419 141.1218 1.0221 1.2343 # (ver=1.0, ref=9) + angle_coeff @angle:n1t,n2t,n2z,n1t,n2t,n2z class2 171.6211 47.7899 0.0000 0.0000 # (ver=1.0, ref=9) + angle_coeff @angle:n1t,n2t,n2z,n1t,n2t,n2z class2 bb 204.9909 1.1354 1.2343 # (ver=1.0, ref=9) + angle_coeff @angle:n1t,n2t,n2z,n1t,n2t,n2z class2 ba 1.2222 25.5611 1.1354 1.2343 # (ver=1.0, ref=9) + angle_coeff @angle:n3m,c3prime,o1=,n3m,c3prime,o1= class2 121.5420 92.5720 -34.4800 -11.1871 # (ver=1.0, ref=7) + angle_coeff @angle:n3m,c3prime,o1=,n3m,c3prime,o1= class2 bb 138.4954 1.3850 1.2160 # (ver=1.0, ref=7) + angle_coeff @angle:n3m,c3prime,o1=,n3m,c3prime,o1= class2 ba 62.7124 52.4045 1.3850 1.2160 # (ver=1.0, ref=7) + angle_coeff @angle:c4,c3prime,o2,c4,c3prime,o2e class2 100.3182 88.8631 -3.8323 -7.9802 # (ver=1.0, ref=7) + angle_coeff @angle:c4,c3prime,o2,c4,c3prime,o2e class2 bb 19.1069 1.5140 1.3750 # (ver=1.0, ref=7) + angle_coeff @angle:c4,c3prime,o2,c4,c3prime,o2e class2 ba 1.3435 4.6978 1.5140 1.3750 # (ver=1.0, ref=7) + angle_coeff @angle:c4,c3prime,o1=,c4,c3prime,o1= class2 119.3000 65.1016 -17.9766 0.0000 # (ver=1.0, ref=7) + angle_coeff @angle:c4,c3prime,o1=,c4,c3prime,o1= class2 bb 77.5201 1.5140 1.2160 # (ver=1.0, ref=7) + angle_coeff @angle:c4,c3prime,o1=,c4,c3prime,o1= class2 ba 31.8455 46.6613 1.5140 1.2160 # (ver=1.0, ref=7) + angle_coeff @angle:o1=,c3prime,o2,o1=,c3prime,o2e class2 118.9855 98.6813 -22.2485 10.3673 # (ver=1.0, ref=7) + angle_coeff @angle:o1=,c3prime,o2,o1=,c3prime,o2e class2 bb 210.1813 1.2160 1.3750 # (ver=1.0, ref=7) + angle_coeff @angle:o1=,c3prime,o2,o1=,c3prime,o2e class2 ba 79.4497 57.0987 1.2160 1.3750 # (ver=1.0, ref=7) + angle_coeff @angle:c3a,n3m,c3prime,c3a,n3m,c3prime class2 120.0700 47.1131 -32.5592 13.1257 # (ver=1.0, ref=7) + angle_coeff @angle:c3a,n3m,c3prime,c3a,n3m,c3prime class2 bb 0.0000 1.3950 1.3850 # (ver=1.0, ref=7) + angle_coeff @angle:c3a,n3m,c3prime,c3a,n3m,c3prime class2 ba 0.0 0.0 1.3950 1.3850 # (ver=1.0, ref=7) + angle_coeff @angle:c3a,c3a,n3m,c3a,c3a,n3m class2 120.7640 73.2738 -27.4033 13.3920 # (ver=1.0, ref=7) + angle_coeff @angle:c3a,c3a,n3m,c3a,c3a,n3m class2 bb 37.8749 1.4170 1.3950 # (ver=1.0, ref=7) + angle_coeff @angle:c3a,c3a,n3m,c3a,c3a,n3m class2 ba 35.8865 53.6977 1.4170 1.3950 # (ver=1.0, ref=7) + angle_coeff @angle:c3a,c3prime,o1=,c3a,c3prime,o1= class2 125.5320 72.3167 -16.0650 2.0818 # (ver=1.0, ref=7) + angle_coeff @angle:c3a,c3prime,o1=,c3a,c3prime,o1= class2 bb 116.9445 1.4890 1.2160 # (ver=1.0, ref=7) + angle_coeff @angle:c3a,c3prime,o1=,c3a,c3prime,o1= class2 ba 72.8758 76.1093 1.4890 1.2160 # (ver=1.0, ref=7) + angle_coeff @angle:c3a,c3prime,n3m,c3a,c3prime,n3m class2 108.4400 84.8377 -19.9640 2.7405 # (ver=1.0, ref=7) + angle_coeff @angle:c3a,c3prime,n3m,c3a,c3prime,n3m class2 bb 0.0000 1.4890 1.3850 # (ver=1.0, ref=7) + angle_coeff @angle:c3a,c3prime,n3m,c3a,c3prime,n3m class2 ba 0.0 0.0 1.4890 1.3850 # (ver=1.0, ref=7) + angle_coeff @angle:c3a,c3a,c3prime,c3a,c3a,c3prime class2 116.0640 71.2598 -15.8273 2.0506 # (ver=1.0, ref=7) + angle_coeff @angle:c3a,c3a,c3prime,c3a,c3a,c3prime class2 bb 37.8749 1.4170 1.4890 # (ver=1.0, ref=7) + angle_coeff @angle:c3a,c3a,c3prime,c3a,c3a,c3prime class2 ba 45.8865 23.6977 1.4170 1.4890 # (ver=1.0, ref=7) + angle_coeff @angle:c3prime,n3m,c3prime,c3prime,n3m,c3prime class2 121.9556 76.3105 -26.3166 -17.6944 # (ver=1.0, ref=7) + angle_coeff @angle:c3prime,n3m,c3prime,c3prime,n3m,c3prime class2 bb 25.9530 1.3850 1.3850 # (ver=1.0, ref=7) + angle_coeff @angle:c3prime,n3m,c3prime,c3prime,n3m,c3prime class2 ba 20.0533 20.0533 1.3850 1.3850 # (ver=1.0, ref=7) + angle_coeff @angle:c3prime,c4,h1,c3prime,c4,h1 class2 107.8594 38.0833 -17.5074 0.0000 # (ver=1.0, ref=7) + angle_coeff @angle:c3prime,c4,h1,c3prime,c4,h1 class2 bb 2.2522 1.5140 1.1010 # (ver=1.0, ref=7) + angle_coeff @angle:c3prime,c4,h1,c3prime,c4,h1 class2 ba 15.5988 14.6287 1.5140 1.1010 # (ver=1.0, ref=7) + angle_coeff @angle:c3prime,o2,c4,c3prime,o2e,c4 class2 109.0000 38.9739 -6.2595 -8.1710 # (ver=1.0, ref=7) + angle_coeff @angle:c3prime,o2,c4,c3prime,o2e,c4 class2 bb 0.0 1.3750 1.4200 # (ver=1.0, ref=7) + angle_coeff @angle:c3prime,o2,c4,c3prime,o2e,c4 class2 ba 21.5366 -16.6748 1.3750 1.4200 # (ver=1.0, ref=7) + angle_coeff @angle:o1=,n3o,o2n,o1=,n3o,o2n class2 112.8000 85.5228 -18.4582 -14.4215 # (ver=1.0, ref=6) + angle_coeff @angle:o1=,n3o,o2n,o1=,n3o,o2n class2 bb 80.0000 1.2100 1.4020 # (ver=1.0, ref=6) + angle_coeff @angle:o1=,n3o,o2n,o1=,n3o,o2n class2 ba 0.0 0.0 1.2100 1.4020 # (ver=1.0, ref=6) + angle_coeff @angle:c4,c4,o2n,c4,c4,o2n class2 105.0000 54.5381 -8.3642 -13.0838 # (ver=1.0, ref=6) + angle_coeff @angle:c4,c4,o2n,c4,c4,o2n class2 bb 11.4318 1.5300 1.4350 # (ver=1.0, ref=6) + angle_coeff @angle:c4,c4,o2n,c4,c4,o2n class2 ba 2.6868 20.4033 1.5300 1.4350 # (ver=1.0, ref=6) + angle_coeff @angle:c4,o2n,n3o,c4,o2n,n3o class2 108.5000 55.7454 -10.0067 -6.2729 # (ver=1.0, ref=6) + angle_coeff @angle:c4,o2n,n3o,c4,o2n,n3o class2 bb 0.0 1.4350 1.4020 # (ver=1.0, ref=6) + angle_coeff @angle:c4,o2n,n3o,c4,o2n,n3o class2 ba 0.0 0.0 1.4350 1.4020 # (ver=1.0, ref=6) + angle_coeff @angle:o1=,n3o,o1=,o1=,n3o,o1= class2 128.0000 95.1035 -47.4240 -27.9164 # (ver=1.0, ref=6) + angle_coeff @angle:o1=,n3o,o1=,o1=,n3o,o1= class2 bb 265.7106 1.2100 1.2100 # (ver=1.0, ref=6) + angle_coeff @angle:o1=,n3o,o1=,o1=,n3o,o1= class2 ba 95.6936 95.6936 1.2100 1.2100 # (ver=1.0, ref=6) + angle_coeff @angle:h1,n3o,o1=,h1,n3o,o1= class2 115.7000 53.8034 -14.1991 -11.8708 # (ver=1.0, ref=6) + angle_coeff @angle:h1,n3o,o1=,h1,n3o,o1= class2 bb 14.8226 1.0400 1.2100 # (ver=1.0, ref=6) + angle_coeff @angle:h1,n3o,o1=,h1,n3o,o1= class2 ba -8.6275 58.6036 1.0400 1.2100 # (ver=1.0, ref=6) + angle_coeff @angle:c4,n3o,o1=,c4,n3o,o1= class2 117.5000 64.5228 -18.4582 -14.4215 # (ver=1.0, ref=6) + angle_coeff @angle:c4,n3o,o1=,c4,n3o,o1= class2 bb 48.1403 1.4740 1.2100 # (ver=1.0, ref=6) + angle_coeff @angle:c4,n3o,o1=,c4,n3o,o1= class2 ba 27.2141 93.9927 1.4740 1.2100 # (ver=1.0, ref=6) + angle_coeff @angle:c3a,n3o,o1=,c3a,n3o,o1= class2 117.7000 63.9404 -18.4524 -14.3129 # (ver=1.0, ref=6) + angle_coeff @angle:c3a,n3o,o1=,c3a,n3o,o1= class2 bb 93.7948 1.4300 1.2100 # (ver=1.0, ref=6) + angle_coeff @angle:c3a,n3o,o1=,c3a,n3o,o1= class2 ba 40.3757 92.1955 1.4300 1.2100 # (ver=1.0, ref=6) + angle_coeff @angle:h1,c4,o2n,h1,c4,o2n class2 108.7280 58.5446 -10.8088 -12.4006 # (ver=1.0, ref=6) + angle_coeff @angle:h1,c4,o2n,h1,c4,o2n class2 bb 23.1979 1.1010 1.4350 # (ver=1.0, ref=6) + angle_coeff @angle:h1,c4,o2n,h1,c4,o2n class2 ba 4.6189 55.3270 1.1010 1.4350 # (ver=1.0, ref=6) + angle_coeff @angle:h1,c4,n3o,h1,c4,n3o class2 107.0000 54.9318 -9.1333 -11.5434 # (ver=1.0, ref=6) + angle_coeff @angle:h1,c4,n3o,h1,c4,n3o class2 bb 3.3770 1.1010 1.4740 # (ver=1.0, ref=6) + angle_coeff @angle:h1,c4,n3o,h1,c4,n3o class2 ba 12.2491 30.5314 1.1010 1.4740 # (ver=1.0, ref=6) + angle_coeff @angle:c3a,c3a,n3o,c3a,c3a,n3o class2 118.8000 29.2436 -8.8495 -6.6020 # (ver=1.0, ref=6) + angle_coeff @angle:c3a,c3a,n3o,c3a,c3a,n3o class2 bb 21.0495 1.4170 1.4300 # (ver=1.0, ref=6) + angle_coeff @angle:c3a,c3a,n3o,c3a,c3a,n3o class2 ba 30.5211 59.8025 1.4170 1.4300 # (ver=1.0, ref=6) + angle_coeff @angle:o1=,s2=,o1=,o1=,s2=,o1= class2 119.3000 115.2627 -35.6278 -26.1261 # (ver=1.0, ref=5) + angle_coeff @angle:o1=,s2=,o1=,o1=,s2=,o1= class2 bb 20.0000 1.4308 1.4308 # (ver=1.0, ref=5) + angle_coeff @angle:o1=,s2=,o1=,o1=,s2=,o1= class2 ba 45.0585 45.0585 1.4308 1.4308 # (ver=1.0, ref=5) + angle_coeff @angle:o1=,n2o,o1=,o1=,n2o,o1= class2 134.1000 150.0000 -82.1013 -40.0005 # (ver=1.0, ref=5) + angle_coeff @angle:o1=,n2o,o1=,o1=,n2o,o1= class2 bb 20.0000 1.1930 1.1930 # (ver=1.0, ref=5) + angle_coeff @angle:o1=,n2o,o1=,o1=,n2o,o1= class2 ba -50.0000 -50.0000 1.1930 1.1930 # (ver=1.0, ref=5) + angle_coeff @angle:s1=,c2=,s1=,s1=,c2=,s1= class2 180.0000 48.0000 0.0000 0.0000 # (ver=1.0, ref=5) + angle_coeff @angle:s1=,c2=,s1=,s1=,c2=,s1= class2 bb 100.7369 1.5540 1.5540 # (ver=1.0, ref=5) + angle_coeff @angle:s1=,c2=,s1=,s1=,c2=,s1= class2 ba 0.0 0.0 1.5540 1.5540 # (ver=1.0, ref=5) + angle_coeff @angle:o1=,c2=,o1=,o1=,c2=,o1= class2 180.0000 57.1000 0.0000 0.0000 # (ver=1.0, ref=5) + angle_coeff @angle:o1=,c2=,o1=,o1=,c2=,o1= class2 bb 275.4350 1.1600 1.1600 # (ver=1.0, ref=5) + angle_coeff @angle:o1=,c2=,o1=,o1=,c2=,o1= class2 ba 0.0 0.0 1.1600 1.1600 # (ver=1.0, ref=5) + angle_coeff @angle:o2,p4=,o2,o2,p4=,o2 class2 107.5000 86.7690 -4.5700 -17.8520 # (ver=1.0, ref=4) + angle_coeff @angle:o2,p4=,o2,o2,p4=,o2 class2 bb 0.0 1.6000 1.6000 # (ver=1.0, ref=4) + angle_coeff @angle:o2,p4=,o2,o2,p4=,o2 class2 ba 0.0 0.0 1.6000 1.6000 # (ver=1.0, ref=4) + angle_coeff @angle:n2=,p4=,o2,n2=,p4=,o2 class2 112.2150 99.9230 -32.0930 -22.8210 # (ver=1.0, ref=4) + angle_coeff @angle:n2=,p4=,o2,n2=,p4=,o2 class2 bb 0.0 1.5980 1.6000 # (ver=1.0, ref=4) + angle_coeff @angle:n2=,p4=,o2,n2=,p4=,o2 class2 ba 0.0 0.0 1.5980 1.6000 # (ver=1.0, ref=4) + angle_coeff @angle:n2=,p4=,n2=,n2=,p4=,n2= class2 125.0000 90.5230 -20.8010 -19.6020 # (ver=1.0, ref=4) + angle_coeff @angle:n2=,p4=,n2=,n2=,p4=,n2= class2 bb 20.0000 1.5980 1.5980 # (ver=1.0, ref=4) + angle_coeff @angle:n2=,p4=,n2=,n2=,p4=,n2= class2 ba 0.0 0.0 1.5980 1.5980 # (ver=1.0, ref=4) + angle_coeff @angle:h1,p4=,o2,h1,p4=,o2 class2 103.9780 73.2570 -9.8970 -15.2120 # (ver=1.0, ref=4) + angle_coeff @angle:h1,p4=,o2,h1,p4=,o2 class2 bb 0.0 1.4300 1.6000 # (ver=1.0, ref=4) + angle_coeff @angle:h1,p4=,o2,h1,p4=,o2 class2 ba 0.0 0.0 1.4300 1.6000 # (ver=1.0, ref=4) + angle_coeff @angle:h1,p4=,n2=,h1,p4=,n2= class2 110.0330 45.9780 -14.0520 -10.3990 # (ver=1.0, ref=4) + angle_coeff @angle:h1,p4=,n2=,h1,p4=,n2= class2 bb 12.5700 1.4300 1.5980 # (ver=1.0, ref=4) + angle_coeff @angle:h1,p4=,n2=,h1,p4=,n2= class2 ba -24.3830 72.9250 1.4300 1.5980 # (ver=1.0, ref=4) + angle_coeff @angle:h1,p4=,h1,h1,p4=,h1 class2 101.4080 39.6950 -5.1340 -8.2270 # (ver=1.0, ref=4) + angle_coeff @angle:h1,p4=,h1,h1,p4=,h1 class2 bb 20.0000 1.4300 1.4300 # (ver=1.0, ref=4) + angle_coeff @angle:h1,p4=,h1,h1,p4=,h1 class2 ba 0.0 0.0 1.4300 1.4300 # (ver=1.0, ref=4) + angle_coeff @angle:c4,p4=,n2=,c4,p4=,n2= class2 119.3000 47.3660 -14.6410 -10.7360 # (ver=1.0, ref=4) + angle_coeff @angle:c4,p4=,n2=,c4,p4=,n2= class2 bb 1.0720 1.8000 1.5980 # (ver=1.0, ref=4) + angle_coeff @angle:c4,p4=,n2=,c4,p4=,n2= class2 ba -7.1280 26.3530 1.8000 1.5980 # (ver=1.0, ref=4) + angle_coeff @angle:c4,p4=,h1,c4,p4=,h1 class2 102.9000 52.0710 -6.4680 -10.7730 # (ver=1.0, ref=4) + angle_coeff @angle:c4,p4=,h1,c4,p4=,h1 class2 bb 3.8820 1.8000 1.4300 # (ver=1.0, ref=4) + angle_coeff @angle:c4,p4=,h1,c4,p4=,h1 class2 ba 11.1260 -19.4700 1.8000 1.4300 # (ver=1.0, ref=4) + angle_coeff @angle:c4,p4=,c4,c4,p4=,c4 class2 102.5000 48.2320 -5.7980 -9.9660 # (ver=1.0, ref=4) + angle_coeff @angle:c4,p4=,c4,c4,p4=,c4 class2 bb 6.2460 1.8000 1.8000 # (ver=1.0, ref=4) + angle_coeff @angle:c4,p4=,c4,c4,p4=,c4 class2 ba 12.8050 12.8050 1.8000 1.8000 # (ver=1.0, ref=4) + angle_coeff @angle:c3a,p4=,o2,c3a,p4=,o2 class2 107.3650 71.9770 -10.9430 -15.2900 # (ver=1.0, ref=4) + angle_coeff @angle:c3a,p4=,o2,c3a,p4=,o2 class2 bb 0.0 1.7890 1.6000 # (ver=1.0, ref=4) + angle_coeff @angle:c3a,p4=,o2,c3a,p4=,o2 class2 ba 0.0 0.0 1.7890 1.6000 # (ver=1.0, ref=4) + angle_coeff @angle:c3a,p4=,n2=,c3a,p4=,n2= class2 109.6000 63.0620 -19.7400 -14.3290 # (ver=1.0, ref=4) + angle_coeff @angle:c3a,p4=,n2=,c3a,p4=,n2= class2 bb 0.0 1.7890 1.5980 # (ver=1.0, ref=4) + angle_coeff @angle:c3a,p4=,n2=,c3a,p4=,n2= class2 ba 0.0 0.0 1.7890 1.5980 # (ver=1.0, ref=4) + angle_coeff @angle:c3a,p4=,h1,c3a,p4=,h1 class2 108.2310 36.1850 -6.4880 -7.6460 # (ver=1.0, ref=4) + angle_coeff @angle:c3a,p4=,h1,c3a,p4=,h1 class2 bb 0.0 1.7890 1.4300 # (ver=1.0, ref=4) + angle_coeff @angle:c3a,p4=,h1,c3a,p4=,h1 class2 ba 0.0 0.0 1.7890 1.4300 # (ver=1.0, ref=4) + angle_coeff @angle:c3a,p4=,c3a,c3a,p4=,c3a class2 110.2310 56.1850 -17.3160 -12.7280 # (ver=1.0, ref=4) + angle_coeff @angle:c3a,p4=,c3a,c3a,p4=,c3a class2 bb 0.0 1.7890 1.7890 # (ver=1.0, ref=4) + angle_coeff @angle:c3a,p4=,c3a,c3a,p4=,c3a class2 ba 0.0 0.0 1.7890 1.7890 # (ver=1.0, ref=4) + angle_coeff @angle:p4=,n2=,p4=,p4=,n2=,p4= class2 135.0000 23.8680 -8.7360 0.0000 # (ver=1.0, ref=4) + angle_coeff @angle:p4=,n2=,p4=,p4=,n2=,p4= class2 bb 20.0000 1.5980 1.5980 # (ver=1.0, ref=4) + angle_coeff @angle:p4=,n2=,p4=,p4=,n2=,p4= class2 ba 0.0 0.0 1.5980 1.5980 # (ver=1.0, ref=4) + angle_coeff @angle:h1,n2=,p4=,h1,n2=,p4= class2 120.0000 26.0680 -8.2980 -5.9430 # (ver=1.0, ref=4) + angle_coeff @angle:h1,n2=,p4=,h1,n2=,p4= class2 bb -18.2870 1.0310 1.5980 # (ver=1.0, ref=4) + angle_coeff @angle:h1,n2=,p4=,h1,n2=,p4= class2 ba 40.0630 90.7910 1.0310 1.5980 # (ver=1.0, ref=4) + angle_coeff @angle:h1,n2=,h1,h1,n2=,h1 class2 110.9100 31.0910 0.0000 0.0000 # (ver=1.0, ref=4) + angle_coeff @angle:h1,n2=,h1,h1,n2=,h1 class2 bb 1.4570 1.0310 1.0310 # (ver=1.0, ref=4) + angle_coeff @angle:h1,n2=,h1,h1,n2=,h1 class2 ba 8.4900 8.4900 1.0310 1.0310 # (ver=1.0, ref=4) + angle_coeff @angle:c4,n2=,h1,c4,n2=,h1 class2 117.2000 37.2620 0.0000 0.0000 # (ver=1.0, ref=4) + angle_coeff @angle:c4,n2=,h1,c4,n2=,h1 class2 bb 12.5630 1.4740 1.0310 # (ver=1.0, ref=4) + angle_coeff @angle:c4,n2=,h1,c4,n2=,h1 class2 ba 18.4860 7.8370 1.4740 1.0310 # (ver=1.0, ref=4) + angle_coeff @angle:h1,c4,p4=,h1,c4,p4= class2 110.8860 33.8300 -7.0430 -7.2460 # (ver=1.0, ref=4) + angle_coeff @angle:h1,c4,p4=,h1,c4,p4= class2 bb 1.0500 1.1010 1.8000 # (ver=1.0, ref=4) + angle_coeff @angle:h1,c4,p4=,h1,c4,p4= class2 ba 19.8120 16.9400 1.1010 1.8000 # (ver=1.0, ref=4) + angle_coeff @angle:h1,c4,n2=,h1,c4,n2= class2 107.4990 62.7310 0.0000 0.0000 # (ver=1.0, ref=4) + angle_coeff @angle:h1,c4,n2=,h1,c4,n2= class2 bb 5.6640 1.1010 1.4740 # (ver=1.0, ref=4) + angle_coeff @angle:h1,c4,n2=,h1,c4,n2= class2 ba 6.4070 46.3730 1.1010 1.4740 # (ver=1.0, ref=4) + angle_coeff @angle:c4,c4,n2=,c4,c4,n2= class2 117.3170 55.2420 0.0000 0.0000 # (ver=1.0, ref=4) + angle_coeff @angle:c4,c4,n2=,c4,c4,n2= class2 bb 22.7100 1.5300 1.4740 # (ver=1.0, ref=4) + angle_coeff @angle:c4,c4,n2=,c4,c4,n2= class2 ba 19.2440 59.4220 1.5300 1.4740 # (ver=1.0, ref=4) + angle_coeff @angle:c3a,c3a,p4=,c3a,c3a,p4= class2 120.0010 47.8410 -15.2290 -10.9070 # (ver=1.0, ref=4) + angle_coeff @angle:c3a,c3a,p4=,c3a,c3a,p4= class2 bb 0.0 1.4170 1.7890 # (ver=1.0, ref=4) + angle_coeff @angle:c3a,c3a,p4=,c3a,c3a,p4= class2 ba 0.0 0.0 1.4170 1.7890 # (ver=1.0, ref=4) + angle_coeff @angle:c3a,c3a,n2=,c3a,c3a,n2= class2 120.0000 60.0000 0.0000 0.0000 # (ver=1.0, ref=4) + angle_coeff @angle:c3a,c3a,n2=,c3a,c3a,n2= class2 bb 0.0 1.4170 1.4000 # (ver=1.0, ref=4) + angle_coeff @angle:c3a,c3a,n2=,c3a,c3a,n2= class2 ba 0.0 0.0 1.4170 1.4000 # (ver=1.0, ref=4) + angle_coeff @angle:c4,o2,h1,c4,o2h,h1 class2 105.8000 52.7061 -12.1090 -9.8681 # (ver=1.0, ref=3) + angle_coeff @angle:c4,o2,h1,c4,o2h,h1 class2 bb -9.6879 1.4200 0.9494 # (ver=1.0, ref=3) + angle_coeff @angle:c4,o2,h1,c4,o2h,h1 class2 ba 28.5800 18.9277 1.4200 0.9494 # (ver=1.0, ref=3) + angle_coeff @angle:c4,o2,c4,c4,o2h,c4 class2 104.5000 35.7454 -10.0067 -6.2729 # (ver=1.0, ref=3) + angle_coeff @angle:c4,o2,c4,c4,o2h,c4 class2 bb -7.1131 1.4200 1.4200 # (ver=1.0, ref=3) + angle_coeff @angle:c4,o2,c4,c4,o2h,c4 class2 ba -2.8112 -2.8112 1.4200 1.4200 # (ver=1.0, ref=3) + angle_coeff @angle:c4,o2,c4,c4,o2e,c4 class2 104.5000 35.7454 -10.0067 -6.2729 # (ver=1.0, ref=3) + angle_coeff @angle:c4,o2,c4,c4,o2e,c4 class2 bb -7.1131 1.4200 1.4200 # (ver=1.0, ref=3) + angle_coeff @angle:c4,o2,c4,c4,o2e,c4 class2 ba -2.8112 -2.8112 1.4200 1.4200 # (ver=1.0, ref=3) + angle_coeff @angle:c3a,o2,h1,c3a,o2h,h1 class2 108.1900 53.1250 -8.5016 0.0000 # (ver=1.0, ref=3) + angle_coeff @angle:c3a,o2,h1,c3a,o2h,h1 class2 bb 20.6577 1.3768 0.9494 # (ver=1.0, ref=3) + angle_coeff @angle:c3a,o2,h1,c3a,o2h,h1 class2 ba 53.8614 23.9224 1.3768 0.9494 # (ver=1.0, ref=3) + angle_coeff @angle:c3a,o2,c4,c3a,o2h,c4 class2 102.9695 38.9739 -6.2595 -8.1710 # (ver=1.0, ref=3) + angle_coeff @angle:c3a,o2,c4,c3a,o2h,c4 class2 bb 0.0 1.3768 1.4200 # (ver=1.0, ref=3) + angle_coeff @angle:c3a,o2,c4,c3a,o2h,c4 class2 ba 0.0 0.0 1.3768 1.4200 # (ver=1.0, ref=3) + angle_coeff @angle:c3a,o2,c4,c3a,o2e,c4 class2 102.9695 38.9739 -6.2595 -8.1710 # (ver=1.0, ref=3) + angle_coeff @angle:c3a,o2,c4,c3a,o2e,c4 class2 bb 0.0 1.3768 1.4200 # (ver=1.0, ref=3) + angle_coeff @angle:c3a,o2,c4,c3a,o2e,c4 class2 ba 0.0 0.0 1.3768 1.4200 # (ver=1.0, ref=3) + angle_coeff @angle:h1,c4,o2,h1,c4,o2h class2 108.7280 58.5446 -10.8088 -12.4006 # (ver=1.0, ref=3) + angle_coeff @angle:h1,c4,o2,h1,c4,o2h class2 bb 23.1979 1.1010 1.4200 # (ver=1.0, ref=3) + angle_coeff @angle:h1,c4,o2,h1,c4,o2h class2 ba 4.6189 55.3270 1.1010 1.4200 # (ver=1.0, ref=3) + angle_coeff @angle:h1,c4,o2,h1,c4,o2e class2 108.7280 58.5446 -10.8088 -12.4006 # (ver=1.0, ref=3) + angle_coeff @angle:h1,c4,o2,h1,c4,o2e class2 bb 23.1979 1.1010 1.4200 # (ver=1.0, ref=3) + angle_coeff @angle:h1,c4,o2,h1,c4,o2e class2 ba 4.6189 55.3270 1.1010 1.4200 # (ver=1.0, ref=3) + angle_coeff @angle:c4,c4,o2,c4,c4,o2h class2 111.2700 54.5381 -8.3642 -13.0838 # (ver=1.0, ref=3) + angle_coeff @angle:c4,c4,o2,c4,c4,o2h class2 bb 11.4318 1.5300 1.4200 # (ver=1.0, ref=3) + angle_coeff @angle:c4,c4,o2,c4,c4,o2h class2 ba 2.6868 20.4033 1.5300 1.4200 # (ver=1.0, ref=3) + angle_coeff @angle:c4,c4,o2,c4,c4,o2e class2 111.2700 54.5381 -8.3642 -13.0838 # (ver=1.0, ref=3) + angle_coeff @angle:c4,c4,o2,c4,c4,o2e class2 bb 11.4318 1.5300 1.4200 # (ver=1.0, ref=3) + angle_coeff @angle:c4,c4,o2,c4,c4,o2e class2 ba 2.6868 20.4033 1.5300 1.4200 # (ver=1.0, ref=3) + angle_coeff @angle:c3a,c3a,o2,c3a,c3a,o2h class2 123.4200 73.6781 -21.6787 0.0000 # (ver=1.0, ref=3) + angle_coeff @angle:c3a,c3a,o2,c3a,c3a,o2h class2 bb 48.4754 1.4170 1.3768 # (ver=1.0, ref=3) + angle_coeff @angle:c3a,c3a,o2,c3a,c3a,o2h class2 ba 58.4790 107.6806 1.4170 1.3768 # (ver=1.0, ref=3) + angle_coeff @angle:c3a,c3a,o2,c3a,c3a,o2e class2 123.4200 73.6781 -21.6787 0.0000 # (ver=1.0, ref=3) + angle_coeff @angle:c3a,c3a,o2,c3a,c3a,o2e class2 bb 48.4754 1.4170 1.3768 # (ver=1.0, ref=3) + angle_coeff @angle:c3a,c3a,o2,c3a,c3a,o2e class2 ba 58.4790 107.6806 1.4170 1.3768 # (ver=1.0, ref=3) + angle_coeff @angle:c3a,c3a,o2,c3a,c3a,o2 class2 123.4200 73.6781 -21.6787 0.0000 # (ver=1.0, ref=3) + angle_coeff @angle:c3a,c3a,o2,c3a,c3a,o2 class2 bb 48.4754 1.4170 1.3768 # (ver=1.0, ref=3) + angle_coeff @angle:c3a,c3a,o2,c3a,c3a,o2 class2 ba 58.4790 107.6806 1.4170 1.3768 # (ver=1.0, ref=3) + angle_coeff @angle:o2z,si4,o2z,o2z,si4,o2z class2 110.7000 70.3069 -6.9375 0.0000 # (ver=1.0, ref=2) + angle_coeff @angle:o2z,si4,o2z,o2z,si4,o2z class2 bb 41.1143 1.6400 1.6400 # (ver=1.0, ref=2) + angle_coeff @angle:o2z,si4,o2z,o2z,si4,o2z class2 ba 23.4380 23.4380 1.6400 1.6400 # (ver=1.0, ref=2) + angle_coeff @angle:h1,si4,o2z,h1,si4,o2z class2 107.4000 57.6643 -10.6506 4.6274 # (ver=1.0, ref=2) + angle_coeff @angle:h1,si4,o2z,h1,si4,o2z class2 bb 11.6183 1.4783 1.6400 # (ver=1.0, ref=2) + angle_coeff @angle:h1,si4,o2z,h1,si4,o2z class2 ba 6.4278 20.5669 1.4783 1.6400 # (ver=1.0, ref=2) + angle_coeff @angle:c4,si4,o2z,c4,si4,o2z class2 114.9060 23.0218 -31.3993 24.9814 # (ver=1.0, ref=2) + angle_coeff @angle:c4,si4,o2z,c4,si4,o2z class2 bb 5.4896 1.8995 1.6400 # (ver=1.0, ref=2) + angle_coeff @angle:c4,si4,o2z,c4,si4,o2z class2 ba 6.4278 20.5669 1.8995 1.6400 # (ver=1.0, ref=2) + angle_coeff @angle:c3a,si4,o2z,c3a,si4,o2z class2 114.9060 23.0218 -31.3993 24.9814 # (ver=1.0, ref=2) + angle_coeff @angle:c3a,si4,o2z,c3a,si4,o2z class2 bb 0.0 1.8634 1.6400 # (ver=1.0, ref=2) + angle_coeff @angle:c3a,si4,o2z,c3a,si4,o2z class2 ba 0.0 0.0 1.8634 1.6400 # (ver=1.0, ref=2) + angle_coeff @angle:si4,o2z,si4,si4,o2z,si4 class2 159.0000 8.5000 -13.4188 -4.1785 # (ver=1.0, ref=2) + angle_coeff @angle:si4,o2z,si4,si4,o2z,si4 class2 bb 41.1143 1.6400 1.6400 # (ver=1.0, ref=2) + angle_coeff @angle:si4,o2z,si4,si4,o2z,si4 class2 ba 28.6686 28.6686 1.6400 1.6400 # (ver=1.0, ref=2) + angle_coeff @angle:h1,c4,h1,h1,c4,h1 class2 107.6600 39.6410 -12.9210 -2.4318 # (ver=1.0, ref=1) + angle_coeff @angle:h1,c4,h1,h1,c4,h1 class2 bb 5.3316 1.1010 1.1010 # (ver=1.0, ref=1) + angle_coeff @angle:h1,c4,h1,h1,c4,h1 class2 ba 18.1030 18.1030 1.1010 1.1010 # (ver=1.0, ref=1) + angle_coeff @angle:c4,c4,h1,c4,c4,h1 class2 110.7700 41.4530 -10.6040 5.1290 # (ver=1.0, ref=1) + angle_coeff @angle:c4,c4,h1,c4,c4,h1 class2 bb 3.3872 1.5300 1.1010 # (ver=1.0, ref=1) + angle_coeff @angle:c4,c4,h1,c4,c4,h1 class2 ba 20.7540 11.4210 1.5300 1.1010 # (ver=1.0, ref=1) + angle_coeff @angle:c4,c4,c4,c4,c4,c4 class2 112.6700 39.5160 -7.4430 -9.5583 # (ver=1.0, ref=1) + angle_coeff @angle:c4,c4,c4,c4,c4,c4 class2 bb 0.0 1.5300 1.5300 # (ver=1.0, ref=1) + angle_coeff @angle:c4,c4,c4,c4,c4,c4 class2 ba 8.0160 8.0160 1.5300 1.5300 # (ver=1.0, ref=1) + angle_coeff @angle:c3a,c4,h1,c3a,c4,h1 class2 111.0000 44.3234 -9.4454 0.0000 # (ver=1.0, ref=1) + angle_coeff @angle:c3a,c4,h1,c3a,c4,h1 class2 bb 2.9168 1.5010 1.1010 # (ver=1.0, ref=1) + angle_coeff @angle:c3a,c4,h1,c3a,c4,h1 class2 ba 26.4608 11.7717 1.5010 1.1010 # (ver=1.0, ref=1) + angle_coeff @angle:c3a,c4,c4,c3a,c4,c4 class2 108.4000 43.9594 -8.3924 -9.3379 # (ver=1.0, ref=1) + angle_coeff @angle:c3a,c4,c4,c3a,c4,c4 class2 bb 0.0 1.5010 1.5300 # (ver=1.0, ref=1) + angle_coeff @angle:c3a,c4,c4,c3a,c4,c4 class2 ba 0.0 0.0 1.5010 1.5300 # (ver=1.0, ref=1) + angle_coeff @angle:c3a,c4,c3a,c3a,c4,c3a class2 111.0000 44.3234 -9.4454 0.0000 # (ver=1.0, ref=1) + angle_coeff @angle:c3a,c4,c3a,c3a,c4,c3a class2 bb 0.0 1.5010 1.5010 # (ver=1.0, ref=1) + angle_coeff @angle:c3a,c4,c3a,c3a,c4,c3a class2 ba 0.0 0.0 1.5010 1.5010 # (ver=1.0, ref=1) + angle_coeff @angle:c3a,c3a,h1,c3a,c3a,h1 class2 117.9400 35.1558 -12.4682 0.0000 # (ver=1.0, ref=1) + angle_coeff @angle:c3a,c3a,h1,c3a,c3a,h1 class2 bb 1.0795 1.4170 1.0982 # (ver=1.0, ref=1) + angle_coeff @angle:c3a,c3a,h1,c3a,c3a,h1 class2 ba 20.0033 24.2183 1.4170 1.0982 # (ver=1.0, ref=1) + angle_coeff @angle:c3a,c3a,c4,c3a,c3a,c4 class2 120.0500 44.7148 -22.7352 0.0000 # (ver=1.0, ref=1) + angle_coeff @angle:c3a,c3a,c4,c3a,c3a,c4 class2 bb 12.0676 1.4170 1.5010 # (ver=1.0, ref=1) + angle_coeff @angle:c3a,c3a,c4,c3a,c3a,c4 class2 ba 31.0771 47.0579 1.4170 1.5010 # (ver=1.0, ref=1) + angle_coeff @angle:c3a,c3a,c3a,c3a,c3a,c3a class2 118.9000 61.0226 -34.9931 0.0000 # (ver=1.0, ref=1) + angle_coeff @angle:c3a,c3a,c3a,c3a,c3a,c3a class2 bb 68.2856 1.4170 1.4170 # (ver=1.0, ref=1) + angle_coeff @angle:c3a,c3a,c3a,c3a,c3a,c3a class2 ba 28.8708 28.8708 1.4170 1.4170 # (ver=1.0, ref=1) + angle_coeff @angle:n3,p4=,o2,X,X,X class2 108.3000 86.7690 -5.1750 -17.6710 # (ver=1.0, ref=4) + angle_coeff @angle:n3,p4=,o2,X,X,X class2 bb 0.0 1.0 1.0 # (ver=1.0, ref=4) + angle_coeff @angle:n3,p4=,o2,X,X,X class2 ba 0.0 0.0 1.0 1.0 # (ver=1.0, ref=4) + angle_coeff @angle:n3,p4=,n3,X,X,X class2 107.1000 85.7690 -5.7790 -17.4890 # (ver=1.0, ref=4) + angle_coeff @angle:n3,p4=,n3,X,X,X class2 bb 0.0 1.0 1.0 # (ver=1.0, ref=4) + angle_coeff @angle:n3,p4=,n3,X,X,X class2 ba 0.0 0.0 1.0 1.0 # (ver=1.0, ref=4) + angle_coeff @angle:n2=,p4=,n3,X,X,X class2 123.2150 89.9230 -32.6120 -21.0960 # (ver=1.0, ref=4) + angle_coeff @angle:n2=,p4=,n3,X,X,X class2 bb 0.0 1.0 1.0 # (ver=1.0, ref=4) + angle_coeff @angle:n2=,p4=,n3,X,X,X class2 ba 0.0 0.0 1.0 1.0 # (ver=1.0, ref=4) + angle_coeff @angle:h1,p4=,n3,X,X,X class2 103.9780 68.2570 -9.2210 -14.1740 # (ver=1.0, ref=4) + angle_coeff @angle:h1,p4=,n3,X,X,X class2 bb 0.0 1.0 1.0 # (ver=1.0, ref=4) + angle_coeff @angle:h1,p4=,n3,X,X,X class2 ba 0.0 0.0 1.0 1.0 # (ver=1.0, ref=4) + angle_coeff @angle:c3a,p4=,n3,X,X,X class2 108.1650 70.9770 -11.5480 -15.1090 # (ver=1.0, ref=4) + angle_coeff @angle:c3a,p4=,n3,X,X,X class2 bb 0.0 1.0 1.0 # (ver=1.0, ref=4) + angle_coeff @angle:c3a,p4=,n3,X,X,X class2 ba 0.0 0.0 1.0 1.0 # (ver=1.0, ref=4) + angle_coeff @angle:h1,o2,p4=,X,X,X class2 117.0000 26.0310 -5.8280 -5.6200 # (ver=1.0, ref=4) + angle_coeff @angle:h1,o2,p4=,X,X,X class2 bb 0.0 1.0 1.0 # (ver=1.0, ref=4) + angle_coeff @angle:h1,o2,p4=,X,X,X class2 ba 0.0 0.0 1.0 1.0 # (ver=1.0, ref=4) + angle_coeff @angle:c4,o2,p4=,X,X,X class2 118.2830 35.0010 -10.3600 -7.8700 # (ver=1.0, ref=4) + angle_coeff @angle:c4,o2,p4=,X,X,X class2 bb 0.0 1.0 1.0 # (ver=1.0, ref=4) + angle_coeff @angle:c4,o2,p4=,X,X,X class2 ba 0.0 0.0 1.0 1.0 # (ver=1.0, ref=4) + angle_coeff @angle:h1,n3,p4=,X,X,X class2 120.0830 25.0010 -6.1170 -5.4570 # (ver=1.0, ref=4) + angle_coeff @angle:h1,n3,p4=,X,X,X class2 bb 0.0 1.0 1.0 # (ver=1.0, ref=4) + angle_coeff @angle:h1,n3,p4=,X,X,X class2 ba 0.0 0.0 1.0 1.0 # (ver=1.0, ref=4) + angle_coeff @angle:c4,n3,p4=,X,X,X class2 120.0830 25.0010 -6.1170 -5.4570 # (ver=1.0, ref=4) + angle_coeff @angle:c4,n3,p4=,X,X,X class2 bb 0.0 1.0 1.0 # (ver=1.0, ref=4) + angle_coeff @angle:c4,n3,p4=,X,X,X class2 ba 0.0 0.0 1.0 1.0 # (ver=1.0, ref=4) + angle_coeff @angle:h1,o2z,si4,X,X,X class2 122.8000 23.7764 -19.8152 9.6331 # (ver=1.0, ref=2) + angle_coeff @angle:h1,o2z,si4,X,X,X class2 bb 0.0 1.0 1.0 # (ver=1.0, ref=2) + angle_coeff @angle:h1,o2z,si4,X,X,X class2 ba 0.0 0.0 1.0 1.0 # (ver=1.0, ref=2) + } # end of angle_coeff commands + + + # --------------- Dihedral Interactions: --------------------- + + + # -- Rules for generating (4-body) "dihedral" interactions: -- + # DihedralType AtmType1 AtmType2 AtmType3 AtmType3 [BondType1 Bnd2 Bnd3] + + + write_once("Data Dihedrals By Type") { + @dihedral:h1,si4,si4,si4,h1,si4,si4,si4,h1,si4,si4,si4 @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bsi4,asi4,dsi4,i* + @dihedral:h1,si4,c4,h1,h1,si4,c4,h1,h1,si4,c4,h1 @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bh1,ah1,dh1,i* + @dihedral:c4,si4,c4,h1,c4,si4,c4,h1,c4,si4,c4,h1 @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bh1,ah1,dh1,i* + @dihedral:h1,si4,si4,h1,h1,si4,si4,h1,h1,si4,si4,h1 @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bh1,ah1,dh1,i* + @dihedral:c4,si4,si4,h1,c4,si4,si4,h1,c4,si4,si4,h1 @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bh1,ah1,dh1,i* + @dihedral:h1,c4,si4,si4,h1,c4,si4,si4,h1,c4,si4,si4 @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bsi4,asi4,dsi4,i* + @dihedral:h1,c4,si4,h1,h1,c4,si4,h1,h1,c4,si4,h1 @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bh1,ah1,dh1,i* + @dihedral:c3a,c3a,si4,h1,c3a,c3a,si4,h1,c3a,c3a,si4,h1 @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bh1,ah1,dh1,i* + @dihedral:c4,c3prime,o2,c4,c4,c3prime,o2e,c4,c4,c3prime,o2,c4 @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc3prime,ac3prime,dc3prime,i* @atom:*,p*,bo2e,ao2,do2,i* @atom:*,p*,bc4,ac4,dc4,i* + @dihedral:c3prime,n3m,c3prime,o1=,c3prime,n3m,c3prime,o1=,c3prime,n3m,c3prime,o1= @atom:*,p*,bc3prime,ac3prime,dc3prime,i* @atom:*,p*,bn3m,an3m,dn3m,i* @atom:*,p*,bc3prime,ac3prime,dc3prime,i* @atom:*,p*,bo1=,ao1=,do1=,i* + @dihedral:X,si4,si4,X,si4,si4,si4,si4,si4,si4,si4,si4 @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bsi4,asi4,d*,i* + @dihedral:X,si4,si4,X,si4,si4,si4,h1,si4,si4,si4,h1 @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bh1,ah1,d*,i* + @dihedral:X,si4,si4,X,si4,si4,si4,c4,si4,si4,si4,c4 @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bc4,ac4,d*,i* + @dihedral:X,si4,si4,X,h1,si4,si4,si4,h1,si4,si4,si4 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bsi4,asi4,d*,i* + @dihedral:X,si4,si4,X,h1,si4,si4,h1,h1,si4,si4,h1 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bh1,ah1,d*,i* + @dihedral:X,si4,si4,X,h1,si4,si4,c4,h1,si4,si4,c4 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bc4,ac4,d*,i* + @dihedral:X,si4,si4,X,c4,si4,si4,si4,c4,si4,si4,si4 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bsi4,asi4,d*,i* + @dihedral:X,si4,si4,X,c4,si4,si4,h1,c4,si4,si4,h1 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bh1,ah1,d*,i* + @dihedral:X,si4,si4,X,c4,si4,si4,c4,c4,si4,si4,c4 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bc4,ac4,d*,i* + @dihedral:X,c4,si4,X,h1,c4,si4,si4,h1,c4,si4,si4 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bsi4,asi4,d*,i* + @dihedral:X,c4,si4,X,h1,c4,si4,o2z,h1,c4,si4,o2z @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bo2z,ao2z,d*,i* + @dihedral:X,c4,si4,X,h1,c4,si4,h1,h1,c4,si4,h1 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bh1,ah1,d*,i* + @dihedral:X,c4,si4,X,h1,c4,si4,c4,h1,c4,si4,c4 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bc4,ac4,d*,i* + @dihedral:X,c4,si4,X,c4,c4,si4,si4,c4,c4,si4,si4 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bsi4,asi4,d*,i* + @dihedral:X,c4,si4,X,c4,c4,si4,o2z,c4,c4,si4,o2z @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bo2z,ao2z,d*,i* + @dihedral:X,c4,si4,X,c4,c4,si4,h1,c4,c4,si4,h1 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bh1,ah1,d*,i* + @dihedral:X,c4,si4,X,c4,c4,si4,c4,c4,c4,si4,c4 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bc4,ac4,d*,i* + @dihedral:c4,c4,si4,si4,c4,c4,si4,si4,c4,c4,si4,si4 @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bsi4,asi4,dsi4,i* + @dihedral:X,si4,c3a,c3a,o2z,si4,c3a,c3a,o2z,si4,c3a,c3a @atom:*,p*,bo2z,ao2z,d*,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* + @dihedral:X,si4,c3a,c3a,h1,si4,c3a,c3a,h1,si4,c3a,c3a @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* + @dihedral:h1,c3a,c3a,si4,h1,c3a,c3a,si4,h1,c3a,c3a,si4 @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bsi4,asi4,dsi4,i* + @dihedral:c3a,c3a,c3a,si4,c3a,c3a,c3a,si4,c3a,c3a,c3a,si4 @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bsi4,asi4,dsi4,i* + @dihedral:h1,c4,c4,n2z,h1,c4,c4,n2z,h1,c4,c4,n2z @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2z,an2z,dn2z,i* + @dihedral:c4,c4,n2z,n2t,c4,c4,n2z,n2t,c4,c4,n2z,n2t @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2z,an2z,dn2z,i* @atom:*,p*,bn2t,an2t,dn2t,i* + @dihedral:h1,c4,n2z,n2t,h1,c4,n2z,n2t,h1,c4,n2z,n2t @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2z,an2z,dn2z,i* @atom:*,p*,bn2t,an2t,dn2t,i* + @dihedral:c4,n2z,n2t,n1t,c4,n2z,n2t,n1t,c4,n2z,n2t,n1t @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2z,an2z,dn2z,i* @atom:*,p*,bn2t,an2t,dn2t,i* @atom:*,p*,bn1t,an1t,dn1t,i* + @dihedral:h1,n2z,n2t,n1t,h1,n2z,n2t,n1t,h1,n2z,n2t,n1t @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bn2z,an2z,dn2z,i* @atom:*,p*,bn2t,an2t,dn2t,i* @atom:*,p*,bn1t,an1t,dn1t,i* + @dihedral:h1,c3a,c3a,n3m,h1,c3a,c3a,n3m,h1,c3a,c3a,n3m @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bn3m,an3m,dn3m,i* + @dihedral:h1,c4,c3prime,o2,h1,c4,c3prime,o2e,h1,c4,c3prime,o2 @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc3prime,ac3prime,dc3prime,i* @atom:*,p*,bo2e,ao2,do2,i* + @dihedral:h1,c4,c3prime,o1=,h1,c4,c3prime,o1=,h1,c4,c3prime,o1= @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc3prime,ac3prime,dc3prime,i* @atom:*,p*,bo1=,ao1=,do1=,i* + @dihedral:c4,o2,c3prime,o1=,c4,o2e,c3prime,o1=,c4,o2,c3prime,o1= @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2e,ao2,do2,i* @atom:*,p*,bc3prime,ac3prime,dc3prime,i* @atom:*,p*,bo1=,ao1=,do1=,i* + @dihedral:c4,o2,c3prime,c4,c4,o2e,c3prime,c4,c4,o2,c3prime,c4 @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2e,ao2,do2,i* @atom:*,p*,bc3prime,ac3prime,dc3prime,i* @atom:*,p*,bc4,ac4,dc4,i* + @dihedral:c3a,n3m,c3prime,o1=,c3a,n3m,c3prime,o1=,c3a,n3m,c3prime,o1= @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bn3m,an3m,dn3m,i* @atom:*,p*,bc3prime,ac3prime,dc3prime,i* @atom:*,p*,bo1=,ao1=,do1=,i* + @dihedral:c3a,c3a,c3a,n3m,c3a,c3a,c3a,n3m,c3a,c3a,c3a,n3m @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bn3m,an3m,dn3m,i* + @dihedral:c3a,c3a,c3prime,o1=,c3a,c3a,c3prime,o1=,c3a,c3a,c3prime,o1= @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3prime,ac3prime,dc3prime,i* @atom:*,p*,bo1=,ao1=,do1=,i* + @dihedral:c3prime,o2,c4,h1,c3prime,o2e,c4,h1,c3prime,o2,c4,h1 @atom:*,p*,bc3prime,ac3prime,dc3prime,i* @atom:*,p*,bo2e,ao2,do2,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bh1,ah1,dh1,i* + @dihedral:c3prime,o2,c4,c4,c3prime,o2e,c4,c4,c3prime,o2,c4,c4 @atom:*,p*,bc3prime,ac3prime,dc3prime,i* @atom:*,p*,bo2e,ao2,do2,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* + @dihedral:c3a,c3a,n3m,c3prime,c3a,c3a,n3m,c3prime,c3a,c3a,n3m,c3prime @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bn3m,an3m,dn3m,i* @atom:*,p*,bc3prime,ac3prime,dc3prime,i* + @dihedral:c3prime,c3a,c3a,h1,c3prime,c3a,c3a,h1,c3prime,c3a,c3a,h1 @atom:*,p*,bc3prime,ac3prime,dc3prime,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bh1,ah1,dh1,i* + @dihedral:c3a,c3a,c3a,c3prime,c3a,c3a,c3a,c3prime,c3a,c3a,c3a,c3prime @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3prime,ac3prime,dc3prime,i* + @dihedral:c4,o2,n3o,o1=,c4,o2n,n3o,o1=,c4,o2n,n3o,o1= @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2n,ao2n,do2,i* @atom:*,p*,bn3o,an3o,dn3o,i* @atom:*,p*,bo1=,ao1=,do1=,i* + @dihedral:c4,c4,o2,n3o,c4,c4,o2n,n3o,c4,c4,o2n,n3o @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2n,ao2n,do2,i* @atom:*,p*,bn3o,an3o,dn3o,i* + @dihedral:h1,c4,n3o,o1=,h1,c4,n3o,o1=,h1,c4,n3o,o1= @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn3o,an3o,dn3o,i* @atom:*,p*,bo1=,ao1=,do1=,i* + @dihedral:c3a,c3a,n3o,o1=,c3a,c3a,n3o,o1=,c3a,c3a,n3o,o1= @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bn3o,an3o,dn3o,i* @atom:*,p*,bo1=,ao1=,do1=,i* + @dihedral:h1,c3a,c3a,n3o,h1,c3a,c3a,n3o,h1,c3a,c3a,n3o @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bn3o,an3o,dn3o,i* + @dihedral:c3a,c3a,c3a,n3o,c3a,c3a,c3a,n3o,c3a,c3a,c3a,n3o @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bn3o,an3o,dn3o,i* + @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,o2,p4=,n2=,p4=,o2 @atom:*,p*,bp4=,ap4=,d*,i* @atom:*,p*,bn2=,an2=,dn2=,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bo2,ao2,d*,i* + @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,n2=,p4=,n2=,p4=,n2= @atom:*,p*,bp4=,ap4=,d*,i* @atom:*,p*,bn2=,an2=,dn2=,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bn2=,an2=,d*,i* + @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,h1,p4=,n2=,p4=,h1 @atom:*,p*,bp4=,ap4=,d*,i* @atom:*,p*,bn2=,an2=,dn2=,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bh1,ah1,d*,i* + @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,c4,p4=,n2=,p4=,c4 @atom:*,p*,bp4=,ap4=,d*,i* @atom:*,p*,bn2=,an2=,dn2=,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bc4,ac4,d*,i* + @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,c3a,p4=,n2=,p4=,c3a @atom:*,p*,bp4=,ap4=,d*,i* @atom:*,p*,bn2=,an2=,dn2=,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bc3a,ac3a,d*,i* + @dihedral:X,n2=,p4=,X,h1,n2=,p4=,o2,h1,n2=,p4=,o2 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bn2=,an2=,dn2=,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bo2,ao2,d*,i* + @dihedral:X,n2=,p4=,X,h1,n2=,p4=,n2=,h1,n2=,p4=,n2= @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bn2=,an2=,dn2=,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bn2=,an2=,d*,i* + @dihedral:X,n2=,p4=,X,h1,n2=,p4=,h1,h1,n2=,p4=,h1 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bn2=,an2=,dn2=,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bh1,ah1,d*,i* + @dihedral:X,n2=,p4=,X,h1,n2=,p4=,c4,h1,n2=,p4=,c4 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bn2=,an2=,dn2=,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bc4,ac4,d*,i* + @dihedral:X,n2=,p4=,X,h1,n2=,p4=,c3a,h1,n2=,p4=,c3a @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bn2=,an2=,dn2=,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bc3a,ac3a,d*,i* + @dihedral:X,c4,p4=,X,h1,c4,p4=,n2=,h1,c4,p4=,n2= @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bn2=,an2=,d*,i* + @dihedral:X,c4,p4=,X,h1,c4,p4=,h1,h1,c4,p4=,h1 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bh1,ah1,d*,i* + @dihedral:X,c4,p4=,X,h1,c4,p4=,c4,h1,c4,p4=,c4 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bc4,ac4,d*,i* + @dihedral:X,c4,n2=,X,h1,c4,n2=,h1,h1,c4,n2=,h1 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2=,an2=,dn2=,i* @atom:*,p*,bh1,ah1,d*,i* + @dihedral:X,c4,n2=,X,c4,c4,n2=,h1,c4,c4,n2=,h1 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2=,an2=,dn2=,i* @atom:*,p*,bh1,ah1,d*,i* + @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,o2,c3a,c3a,p4=,o2 @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bo2,ao2,d*,i* + @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,n2=,c3a,c3a,p4=,n2= @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bn2=,an2=,d*,i* + @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,h1,c3a,c3a,p4=,h1 @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bh1,ah1,d*,i* + @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,c3a,c3a,c3a,p4=,c3a @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bc3a,ac3a,d*,i* + @dihedral:n2=,p4=,n2=,p4=,n2=,p4=,n2=,p4=,n2=,p4=,n2=,p4= @atom:*,p*,bn2=,an2=,dn2=,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bn2=,an2=,dn2=,i* @atom:*,p*,bp4=,ap4=,dp4=,i* + @dihedral:h1,p4=,n2=,p4=,h1,p4=,n2=,p4=,h1,p4=,n2=,p4= @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bn2=,an2=,dn2=,i* @atom:*,p*,bp4=,ap4=,dp4=,i* + @dihedral:h1,n2=,p4=,o2,h1,n2=,p4=,o2,h1,n2=,p4=,o2 @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bn2=,an2=,dn2=,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bo2,ao2,do2,i* + @dihedral:h1,n2=,p4=,h1,h1,n2=,p4=,h1,h1,n2=,p4=,h1 @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bn2=,an2=,dn2=,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bh1,ah1,dh1,i* + @dihedral:c4,p4=,n2=,h1,c4,p4=,n2=,h1,c4,p4=,n2=,h1 @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bn2=,an2=,dn2=,i* @atom:*,p*,bh1,ah1,dh1,i* + @dihedral:c3a,p4=,n2=,h1,c3a,p4=,n2=,h1,c3a,p4=,n2=,h1 @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bn2=,an2=,dn2=,i* @atom:*,p*,bh1,ah1,dh1,i* + @dihedral:h1,c4,p4=,n2=,h1,c4,p4=,n2=,h1,c4,p4=,n2= @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bn2=,an2=,dn2=,i* + @dihedral:h1,c4,p4=,h1,h1,c4,p4=,h1,h1,c4,p4=,h1 @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bh1,ah1,dh1,i* + @dihedral:c4,p4=,c4,h1,c4,p4=,c4,h1,c4,p4=,c4,h1 @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bh1,ah1,dh1,i* + @dihedral:h1,c4,n2=,h1,h1,c4,n2=,h1,h1,c4,n2=,h1 @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2=,an2=,dn2=,i* @atom:*,p*,bh1,ah1,dh1,i* + @dihedral:c4,c4,n2=,h1,c4,c4,n2=,h1,c4,c4,n2=,h1 @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2=,an2=,dn2=,i* @atom:*,p*,bh1,ah1,dh1,i* + @dihedral:h1,c4,c4,n2=,h1,c4,c4,n2=,h1,c4,c4,n2= @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2=,an2=,dn2=,i* + @dihedral:c4,c4,c4,n2=,c4,c4,c4,n2=,c4,c4,c4,n2= @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2=,an2=,dn2=,i* + @dihedral:c3a,c3a,p4=,n2=,c3a,c3a,p4=,n2=,c3a,c3a,p4=,n2= @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bn2=,an2=,dn2=,i* + @dihedral:c3a,c3a,p4=,h1,c3a,c3a,p4=,h1,c3a,c3a,p4=,h1 @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bh1,ah1,dh1,i* + @dihedral:h1,c3a,c3a,p4=,h1,c3a,c3a,p4=,h1,c3a,c3a,p4= @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bp4=,ap4=,dp4=,i* + @dihedral:c3a,c3a,c3a,p4=,c3a,c3a,c3a,p4=,c3a,c3a,c3a,p4= @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bp4=,ap4=,dp4=,i* + @dihedral:h1,c4,o2,h1,h1,c4,o2h,h1,h1,c4,o2,h1 @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2h,ao2,do2,i* @atom:*,p*,bh1,ah1,dh1,i* + @dihedral:c4,o2,c4,h1,c4,o2h,c4,h1,c4,o2,c4,h1 @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2h,ao2,do2,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bh1,ah1,dh1,i* + @dihedral:c4,o2,c4,h1,c4,o2e,c4,h1,c4,o2,c4,h1 @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2e,ao2,do2,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bh1,ah1,dh1,i* + @dihedral:c3a,o2,c4,h1,c3a,o2h,c4,h1,c3a,o2,c4,h1 @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bo2h,ao2,do2,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bh1,ah1,dh1,i* + @dihedral:c3a,o2,c4,h1,c3a,o2e,c4,h1,c3a,o2,c4,h1 @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bo2e,ao2,do2,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bh1,ah1,dh1,i* + @dihedral:c4,c4,o2,h1,c4,c4,o2h,h1,c4,c4,o2,h1 @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2h,ao2,do2,i* @atom:*,p*,bh1,ah1,dh1,i* + @dihedral:c4,c4,o2,c4,c4,c4,o2h,c4,c4,c4,o2,c4 @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2h,ao2,do2,i* @atom:*,p*,bc4,ac4,dc4,i* + @dihedral:c4,c4,o2,c4,c4,c4,o2e,c4,c4,c4,o2,c4 @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2e,ao2,do2,i* @atom:*,p*,bc4,ac4,dc4,i* + @dihedral:o2,c4,c4,o2,o2n,c4,c4,o2n,o2n,c4,c4,o2n @atom:*,p*,bo2n,ao2n,do2,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2n,ao2n,do2,i* + @dihedral:o2,c4,c4,o2,o2n,c4,c4,o2h,o2n,c4,c4,o2 @atom:*,p*,bo2n,ao2n,do2,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2h,ao2,do2,i* + @dihedral:o2,c4,c4,o2,o2n,c4,c4,o2e,o2n,c4,c4,o2 @atom:*,p*,bo2n,ao2n,do2,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2e,ao2,do2,i* + @dihedral:o2,c4,c4,o2,o2h,c4,c4,o2n,o2,c4,c4,o2n @atom:*,p*,bo2h,ao2,do2,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2n,ao2n,do2,i* + @dihedral:o2,c4,c4,o2,o2h,c4,c4,o2h,o2,c4,c4,o2 @atom:*,p*,bo2h,ao2,do2,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2h,ao2,do2,i* + @dihedral:o2,c4,c4,o2,o2h,c4,c4,o2e,o2,c4,c4,o2 @atom:*,p*,bo2h,ao2,do2,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2e,ao2,do2,i* + @dihedral:o2,c4,c4,o2,o2e,c4,c4,o2n,o2,c4,c4,o2n @atom:*,p*,bo2e,ao2,do2,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2n,ao2n,do2,i* + @dihedral:o2,c4,c4,o2,o2e,c4,c4,o2h,o2,c4,c4,o2 @atom:*,p*,bo2e,ao2,do2,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2h,ao2,do2,i* + @dihedral:o2,c4,c4,o2,o2e,c4,c4,o2e,o2,c4,c4,o2 @atom:*,p*,bo2e,ao2,do2,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2e,ao2,do2,i* + @dihedral:h1,c4,c4,o2,h1,c4,c4,o2n,h1,c4,c4,o2n @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2n,ao2n,do2,i* + @dihedral:h1,c4,c4,o2,h1,c4,c4,o2h,h1,c4,c4,o2 @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2h,ao2,do2,i* + @dihedral:h1,c4,c4,o2,h1,c4,c4,o2e,h1,c4,c4,o2 @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2e,ao2,do2,i* + @dihedral:c4,c4,c4,o2,c4,c4,c4,o2n,c4,c4,c4,o2n @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2n,ao2n,do2,i* + @dihedral:c4,c4,c4,o2,c4,c4,c4,o2h,c4,c4,c4,o2 @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2h,ao2,do2,i* + @dihedral:c4,c4,c4,o2,c4,c4,c4,o2e,c4,c4,c4,o2 @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2e,ao2,do2,i* + @dihedral:c3a,c3a,o2,c4,c3a,c3a,o2h,c4,c3a,c3a,o2,c4 @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bo2h,ao2,do2,i* @atom:*,p*,bc4,ac4,dc4,i* + @dihedral:c3a,c3a,o2,c4,c3a,c3a,o2e,c4,c3a,c3a,o2,c4 @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bo2e,ao2,do2,i* @atom:*,p*,bc4,ac4,dc4,i* + @dihedral:X,o2z,si4,X,si4,o2z,si4,o2z,si4,o2z,si4,o2z @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bo2z,ao2z,do2z,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bo2z,ao2z,d*,i* + @dihedral:X,o2z,si4,X,si4,o2z,si4,h1,si4,o2z,si4,h1 @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bo2z,ao2z,do2z,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bh1,ah1,d*,i* + @dihedral:X,o2z,si4,X,si4,o2z,si4,c4,si4,o2z,si4,c4 @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bo2z,ao2z,do2z,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bc4,ac4,d*,i* + @dihedral:X,o2z,si4,X,si4,o2z,si4,c3a,si4,o2z,si4,c3a @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bo2z,ao2z,do2z,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bc3a,ac3a,d*,i* + @dihedral:o2z,si4,o2z,si4,o2z,si4,o2z,si4,o2z,si4,o2z,si4 @atom:*,p*,bo2z,ao2z,do2z,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bo2z,ao2z,do2z,i* @atom:*,p*,bsi4,asi4,dsi4,i* + @dihedral:h1,si4,o2z,si4,h1,si4,o2z,si4,h1,si4,o2z,si4 @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bo2z,ao2z,do2z,i* @atom:*,p*,bsi4,asi4,dsi4,i* + @dihedral:c4,si4,o2z,si4,c4,si4,o2z,si4,c4,si4,o2z,si4 @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bo2z,ao2z,do2z,i* @atom:*,p*,bsi4,asi4,dsi4,i* + @dihedral:X,c4,c4,X,si4,c4,c4,si4,si4,c4,c4,si4 @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bsi4,asi4,d*,i* + @dihedral:X,c4,c4,X,si4,c4,c4,o2n,si4,c4,c4,o2n @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2n,ao2n,d*,i* + @dihedral:X,c4,c4,X,si4,c4,c4,o2h,si4,c4,c4,o2 @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2h,ao2,d*,i* + @dihedral:X,c4,c4,X,si4,c4,c4,o2e,si4,c4,c4,o2 @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2e,ao2,d*,i* + @dihedral:X,c4,c4,X,si4,c4,c4,n2z,si4,c4,c4,n2z @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2z,an2z,d*,i* + @dihedral:X,c4,c4,X,si4,c4,c4,n2=,si4,c4,c4,n2= @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2=,an2=,d*,i* + @dihedral:X,c4,c4,X,si4,c4,c4,h1,si4,c4,c4,h1 @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bh1,ah1,d*,i* + @dihedral:X,c4,c4,X,si4,c4,c4,c4,si4,c4,c4,c4 @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,d*,i* + @dihedral:X,c4,c4,X,si4,c4,c4,c3a,si4,c4,c4,c3a @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc3a,ac3a,d*,i* + @dihedral:X,c4,c4,X,o2n,c4,c4,si4,o2n,c4,c4,si4 @atom:*,p*,bo2n,ao2n,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bsi4,asi4,d*,i* + @dihedral:X,c4,c4,X,o2n,c4,c4,o2n,o2n,c4,c4,o2n @atom:*,p*,bo2n,ao2n,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2n,ao2n,d*,i* + @dihedral:X,c4,c4,X,o2n,c4,c4,o2h,o2n,c4,c4,o2 @atom:*,p*,bo2n,ao2n,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2h,ao2,d*,i* + @dihedral:X,c4,c4,X,o2n,c4,c4,o2e,o2n,c4,c4,o2 @atom:*,p*,bo2n,ao2n,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2e,ao2,d*,i* + @dihedral:X,c4,c4,X,o2n,c4,c4,n2z,o2n,c4,c4,n2z @atom:*,p*,bo2n,ao2n,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2z,an2z,d*,i* + @dihedral:X,c4,c4,X,o2n,c4,c4,n2=,o2n,c4,c4,n2= @atom:*,p*,bo2n,ao2n,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2=,an2=,d*,i* + @dihedral:X,c4,c4,X,o2n,c4,c4,h1,o2n,c4,c4,h1 @atom:*,p*,bo2n,ao2n,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bh1,ah1,d*,i* + @dihedral:X,c4,c4,X,o2n,c4,c4,c4,o2n,c4,c4,c4 @atom:*,p*,bo2n,ao2n,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,d*,i* + @dihedral:X,c4,c4,X,o2n,c4,c4,c3a,o2n,c4,c4,c3a @atom:*,p*,bo2n,ao2n,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc3a,ac3a,d*,i* + @dihedral:X,c4,c4,X,o2h,c4,c4,si4,o2,c4,c4,si4 @atom:*,p*,bo2h,ao2,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bsi4,asi4,d*,i* + @dihedral:X,c4,c4,X,o2h,c4,c4,o2n,o2,c4,c4,o2n @atom:*,p*,bo2h,ao2,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2n,ao2n,d*,i* + @dihedral:X,c4,c4,X,o2h,c4,c4,o2h,o2,c4,c4,o2 @atom:*,p*,bo2h,ao2,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2h,ao2,d*,i* + @dihedral:X,c4,c4,X,o2h,c4,c4,o2e,o2,c4,c4,o2 @atom:*,p*,bo2h,ao2,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2e,ao2,d*,i* + @dihedral:X,c4,c4,X,o2h,c4,c4,n2z,o2,c4,c4,n2z @atom:*,p*,bo2h,ao2,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2z,an2z,d*,i* + @dihedral:X,c4,c4,X,o2h,c4,c4,n2=,o2,c4,c4,n2= @atom:*,p*,bo2h,ao2,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2=,an2=,d*,i* + @dihedral:X,c4,c4,X,o2h,c4,c4,h1,o2,c4,c4,h1 @atom:*,p*,bo2h,ao2,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bh1,ah1,d*,i* + @dihedral:X,c4,c4,X,o2h,c4,c4,c4,o2,c4,c4,c4 @atom:*,p*,bo2h,ao2,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,d*,i* + @dihedral:X,c4,c4,X,o2h,c4,c4,c3a,o2,c4,c4,c3a @atom:*,p*,bo2h,ao2,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc3a,ac3a,d*,i* + @dihedral:X,c4,c4,X,o2e,c4,c4,si4,o2,c4,c4,si4 @atom:*,p*,bo2e,ao2,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bsi4,asi4,d*,i* + @dihedral:X,c4,c4,X,o2e,c4,c4,o2n,o2,c4,c4,o2n @atom:*,p*,bo2e,ao2,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2n,ao2n,d*,i* + @dihedral:X,c4,c4,X,o2e,c4,c4,o2h,o2,c4,c4,o2 @atom:*,p*,bo2e,ao2,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2h,ao2,d*,i* + @dihedral:X,c4,c4,X,o2e,c4,c4,o2e,o2,c4,c4,o2 @atom:*,p*,bo2e,ao2,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2e,ao2,d*,i* + @dihedral:X,c4,c4,X,o2e,c4,c4,n2z,o2,c4,c4,n2z @atom:*,p*,bo2e,ao2,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2z,an2z,d*,i* + @dihedral:X,c4,c4,X,o2e,c4,c4,n2=,o2,c4,c4,n2= @atom:*,p*,bo2e,ao2,d*,i* 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@atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bsi4,asi4,d*,i* + @dihedral:X,c4,c4,X,n2=,c4,c4,o2n,n2=,c4,c4,o2n @atom:*,p*,bn2=,an2=,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2n,ao2n,d*,i* + @dihedral:X,c4,c4,X,n2=,c4,c4,o2h,n2=,c4,c4,o2 @atom:*,p*,bn2=,an2=,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2h,ao2,d*,i* + @dihedral:X,c4,c4,X,n2=,c4,c4,o2e,n2=,c4,c4,o2 @atom:*,p*,bn2=,an2=,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2e,ao2,d*,i* + @dihedral:X,c4,c4,X,n2=,c4,c4,n2z,n2=,c4,c4,n2z @atom:*,p*,bn2=,an2=,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2z,an2z,d*,i* + @dihedral:X,c4,c4,X,n2=,c4,c4,n2=,n2=,c4,c4,n2= @atom:*,p*,bn2=,an2=,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2=,an2=,d*,i* + @dihedral:X,c4,c4,X,n2=,c4,c4,h1,n2=,c4,c4,h1 @atom:*,p*,bn2=,an2=,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bh1,ah1,d*,i* + @dihedral:X,c4,c4,X,n2=,c4,c4,c4,n2=,c4,c4,c4 @atom:*,p*,bn2=,an2=,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,d*,i* + @dihedral:X,c4,c4,X,n2=,c4,c4,c3a,n2=,c4,c4,c3a @atom:*,p*,bn2=,an2=,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc3a,ac3a,d*,i* + @dihedral:X,c4,c4,X,h1,c4,c4,si4,h1,c4,c4,si4 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bsi4,asi4,d*,i* + @dihedral:X,c4,c4,X,h1,c4,c4,o2n,h1,c4,c4,o2n @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2n,ao2n,d*,i* + @dihedral:X,c4,c4,X,h1,c4,c4,o2h,h1,c4,c4,o2 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2h,ao2,d*,i* + @dihedral:X,c4,c4,X,h1,c4,c4,o2e,h1,c4,c4,o2 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2e,ao2,d*,i* + @dihedral:X,c4,c4,X,h1,c4,c4,n2z,h1,c4,c4,n2z @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2z,an2z,d*,i* + @dihedral:X,c4,c4,X,h1,c4,c4,n2=,h1,c4,c4,n2= @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2=,an2=,d*,i* + @dihedral:X,c4,c4,X,h1,c4,c4,h1,h1,c4,c4,h1 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bh1,ah1,d*,i* + @dihedral:X,c4,c4,X,h1,c4,c4,c4,h1,c4,c4,c4 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,d*,i* + @dihedral:X,c4,c4,X,h1,c4,c4,c3a,h1,c4,c4,c3a @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc3a,ac3a,d*,i* + @dihedral:X,c4,c4,X,c4,c4,c4,si4,c4,c4,c4,si4 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bsi4,asi4,d*,i* + @dihedral:X,c4,c4,X,c4,c4,c4,o2n,c4,c4,c4,o2n @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2n,ao2n,d*,i* + @dihedral:X,c4,c4,X,c4,c4,c4,o2h,c4,c4,c4,o2 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2h,ao2,d*,i* + @dihedral:X,c4,c4,X,c4,c4,c4,o2e,c4,c4,c4,o2 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2e,ao2,d*,i* + @dihedral:X,c4,c4,X,c4,c4,c4,n2z,c4,c4,c4,n2z @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2z,an2z,d*,i* + @dihedral:X,c4,c4,X,c4,c4,c4,n2=,c4,c4,c4,n2= @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2=,an2=,d*,i* + @dihedral:X,c4,c4,X,c4,c4,c4,h1,c4,c4,c4,h1 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bh1,ah1,d*,i* + @dihedral:X,c4,c4,X,c4,c4,c4,c4,c4,c4,c4,c4 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,d*,i* + @dihedral:X,c4,c4,X,c4,c4,c4,c3a,c4,c4,c4,c3a @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc3a,ac3a,d*,i* + @dihedral:X,c4,c4,X,c3a,c4,c4,si4,c3a,c4,c4,si4 @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bsi4,asi4,d*,i* + @dihedral:X,c4,c4,X,c3a,c4,c4,o2n,c3a,c4,c4,o2n @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2n,ao2n,d*,i* + @dihedral:X,c4,c4,X,c3a,c4,c4,o2h,c3a,c4,c4,o2 @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2h,ao2,d*,i* + @dihedral:X,c4,c4,X,c3a,c4,c4,o2e,c3a,c4,c4,o2 @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2e,ao2,d*,i* + @dihedral:X,c4,c4,X,c3a,c4,c4,n2z,c3a,c4,c4,n2z @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2z,an2z,d*,i* + @dihedral:X,c4,c4,X,c3a,c4,c4,n2=,c3a,c4,c4,n2= @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* 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@atom:*,p*,bc3a,ac3a,d*,i* + @dihedral:h1,c4,c4,h1,h1,c4,c4,h1,h1,c4,c4,h1 @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bh1,ah1,dh1,i* + @dihedral:c4,c4,c4,h1,c4,c4,c4,h1,c4,c4,c4,h1 @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bh1,ah1,dh1,i* + @dihedral:c4,c4,c4,c4,c4,c4,c4,c4,c4,c4,c4,c4 @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* + @dihedral:c3a,c4,c4,h1,c3a,c4,c4,h1,c3a,c4,c4,h1 @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bh1,ah1,dh1,i* + @dihedral:c3a,c3a,c4,c4,c3a,c3a,c4,c4,c3a,c3a,c4,c4 @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* + @dihedral:c3a,c3a,c4,c3a,c3a,c3a,c4,c3a,c3a,c3a,c4,c3a @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc3a,ac3a,dc3a,i* + 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@atom:*,p*,bo2e,ao2,do2,i* + @dihedral:c3a,c3a,c3a,o2,c3a,c3a,c3a,o2,c3a,c3a,c3a,o2 @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bo2,ao2,do2,i* + @dihedral:c3a,c3a,c4,h1,c3a,c3a,c4,h1,c3a,c3a,c4,h1 @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bh1,ah1,dh1,i* + @dihedral:h1,c3a,c3a,h1,h1,c3a,c3a,h1,h1,c3a,c3a,h1 @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bh1,ah1,dh1,i* + @dihedral:c4,c3a,c3a,h1,c4,c3a,c3a,h1,c4,c3a,c3a,h1 @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bh1,ah1,dh1,i* + @dihedral:c3a,c3a,c3a,h1,c3a,c3a,c3a,h1,c3a,c3a,c3a,h1 @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bh1,ah1,dh1,i* + @dihedral:c3a,c3a,c3a,c4,c3a,c3a,c3a,c4,c3a,c3a,c3a,c4 @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc4,ac4,dc4,i* + @dihedral:c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* + @dihedral:c3prime,n3m,c3prime,o1,X,X,X,X,X,X,X,X @atom:*,p*,b*,a*,dc3prime,i* @atom:*,p*,b*,a*,dn3m,i* @atom:*,p*,b*,a*,dc3prime,i* @atom:*,p*,b*,a*,do1,i* + @dihedral:c4,c4,n3o,o1=,X,X,X,X,X,X,X,X @atom:*,p*,b*,a*,dc4,i* @atom:*,p*,b*,a*,dc4,i* @atom:*,p*,b*,a*,dn3o,i* @atom:*,p*,b*,a*,do1=,i* + @dihedral:X,n3,p4=,X,X,X,X,X,X,X,X,X @atom:*,p*,b*,a*,d*,i* @atom:*,p*,b*,a*,dn3,i* @atom:*,p*,b*,a*,dp4=,i* @atom:*,p*,b*,a*,d*,i* + @dihedral:X,c3a,n2=,X,X,X,X,X,X,X,X,X @atom:*,p*,b*,a*,d*,i* @atom:*,p*,b*,a*,dc3a,i* @atom:*,p*,b*,a*,dn2=,i* @atom:*,p*,b*,a*,d*,i* + @dihedral:X,o2,p4=,X,X,X,X,X,X,X,X,X @atom:*,p*,b*,a*,d*,i* @atom:*,p*,b*,a*,do2,i* @atom:*,p*,b*,a*,dp4=,i* @atom:*,p*,b*,a*,d*,i* + @dihedral:h1,o2,p4=,o2,X,X,X,X,X,X,X,X @atom:*,p*,b*,a*,dh1,i* @atom:*,p*,b*,a*,do2,i* @atom:*,p*,b*,a*,dp4=,i* @atom:*,p*,b*,a*,do2,i* + @dihedral:h1,o2,p4=,n2=,X,X,X,X,X,X,X,X @atom:*,p*,b*,a*,dh1,i* @atom:*,p*,b*,a*,do2,i* @atom:*,p*,b*,a*,dp4=,i* @atom:*,p*,b*,a*,dn2=,i* + @dihedral:h1,o2,p4=,h1,X,X,X,X,X,X,X,X @atom:*,p*,b*,a*,dh1,i* @atom:*,p*,b*,a*,do2,i* @atom:*,p*,b*,a*,dp4=,i* @atom:*,p*,b*,a*,dh1,i* + @dihedral:h1,n3,p4=,o2,X,X,X,X,X,X,X,X @atom:*,p*,b*,a*,dh1,i* @atom:*,p*,b*,a*,dn3,i* @atom:*,p*,b*,a*,dp4=,i* @atom:*,p*,b*,a*,do2,i* + @dihedral:h1,n3,p4=,n2=,X,X,X,X,X,X,X,X @atom:*,p*,b*,a*,dh1,i* @atom:*,p*,b*,a*,dn3,i* @atom:*,p*,b*,a*,dp4=,i* @atom:*,p*,b*,a*,dn2=,i* + @dihedral:h1,n3,p4=,h1,X,X,X,X,X,X,X,X @atom:*,p*,b*,a*,dh1,i* @atom:*,p*,b*,a*,dn3,i* @atom:*,p*,b*,a*,dp4=,i* @atom:*,p*,b*,a*,dh1,i* + @dihedral:h1,o2z,si4,o2z,X,X,X,X,X,X,X,X @atom:*,p*,b*,a*,dh1,i* @atom:*,p*,b*,a*,do2z,i* @atom:*,p*,b*,a*,dsi4,i* @atom:*,p*,b*,a*,do2z,i* + @dihedral:h1,o2z,si4,h1,X,X,X,X,X,X,X,X @atom:*,p*,b*,a*,dh1,i* @atom:*,p*,b*,a*,do2z,i* @atom:*,p*,b*,a*,dsi4,i* @atom:*,p*,b*,a*,dh1,i* + @dihedral:c4,si4,o2z,h1,X,X,X,X,X,X,X,X @atom:*,p*,b*,a*,dc4,i* @atom:*,p*,b*,a*,dsi4,i* @atom:*,p*,b*,a*,do2z,i* @atom:*,p*,b*,a*,dh1,i* + } # end of "Data Dihedrals By Type" section + + + + # ------- Dihedral Force Field Parameters: ------- + # For an explanation of these parameters, visit: + # http://lammps.sandia.gov/doc/dihedral_class2.html + + # Syntax: + # dihedral_coeff DihedralTypeName DihedralStyle parameters... + + + write_once("In Settings") { + dihedral_coeff @dihedral:h1,si4,si4,si4,h1,si4,si4,si4,h1,si4,si4,si4 class2 0.0 0.0 0.0 0.0 0.0 0.0 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,si4,si4,si4,h1,si4,si4,si4,h1,si4,si4,si4 class2 mbt 0.0 0.0 0.0 2.3384 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,si4,si4,si4,h1,si4,si4,si4,h1,si4,si4,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4783 2.3384 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,si4,si4,si4,h1,si4,si4,si4,h1,si4,si4,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.0893 114.2676 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,si4,si4,si4,h1,si4,si4,si4,h1,si4,si4,si4 class2 aat -12.2900 112.0893 114.2676 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,si4,si4,si4,h1,si4,si4,si4,h1,si4,si4,si4 class2 bb13 0.0 1.4783 2.3384 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,si4,c4,h1,h1,si4,c4,h1,h1,si4,c4,h1 class2 0.0 0.0 0.0 0.0 0.0 0.0 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,si4,c4,h1,h1,si4,c4,h1,h1,si4,c4,h1 class2 mbt 0.0 0.0 0.0 1.8995 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,si4,c4,h1,h1,si4,c4,h1,h1,si4,c4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4783 1.1010 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,si4,c4,h1,h1,si4,c4,h1,h1,si4,c4,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.0977 112.0355 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,si4,c4,h1,h1,si4,c4,h1,h1,si4,c4,h1 class2 aat -12.9341 112.0977 112.0355 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,si4,c4,h1,h1,si4,c4,h1,h1,si4,c4,h1 class2 bb13 0.0 1.4783 1.1010 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:c4,si4,c4,h1,c4,si4,c4,h1,c4,si4,c4,h1 class2 0.0 0.0 0.0 0.0 0.0 0.0 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:c4,si4,c4,h1,c4,si4,c4,h1,c4,si4,c4,h1 class2 mbt 0.0 0.0 0.0 1.8995 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:c4,si4,c4,h1,c4,si4,c4,h1,c4,si4,c4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8995 1.1010 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:c4,si4,c4,h1,c4,si4,c4,h1,c4,si4,c4,h1 class2 at 0.4272 0.0000 0.0000 0.3382 0.0000 0.0000 113.1855 112.0355 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:c4,si4,c4,h1,c4,si4,c4,h1,c4,si4,c4,h1 class2 aat -17.5802 113.1855 112.0355 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:c4,si4,c4,h1,c4,si4,c4,h1,c4,si4,c4,h1 class2 bb13 0.0 1.8995 1.1010 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,si4,si4,h1,h1,si4,si4,h1,h1,si4,si4,h1 class2 0.0 0.0 0.0 0.0 0.0 0.0 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,si4,si4,h1,h1,si4,si4,h1,h1,si4,si4,h1 class2 mbt 0.0000 0.0000 -0.6302 2.3384 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,si4,si4,h1,h1,si4,si4,h1,h1,si4,si4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4783 1.4783 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,si4,si4,h1,h1,si4,si4,h1,h1,si4,si4,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.0893 112.0893 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,si4,si4,h1,h1,si4,si4,h1,h1,si4,si4,h1 class2 aat -10.8232 112.0893 112.0893 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,si4,si4,h1,h1,si4,si4,h1,h1,si4,si4,h1 class2 bb13 0.0 1.4783 1.4783 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:c4,si4,si4,h1,c4,si4,si4,h1,c4,si4,si4,h1 class2 0.0 0.0 0.0 0.0 0.0 0.0 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:c4,si4,si4,h1,c4,si4,si4,h1,c4,si4,si4,h1 class2 mbt 0.0000 0.0000 -0.6941 2.3384 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:c4,si4,si4,h1,c4,si4,si4,h1,c4,si4,si4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8995 1.4783 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:c4,si4,si4,h1,c4,si4,si4,h1,c4,si4,si4,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 113.0000 112.0893 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:c4,si4,si4,h1,c4,si4,si4,h1,c4,si4,si4,h1 class2 aat -16.9141 113.0000 112.0893 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:c4,si4,si4,h1,c4,si4,si4,h1,c4,si4,si4,h1 class2 bb13 0.0 1.8995 1.4783 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,c4,si4,si4,h1,c4,si4,si4,h1,c4,si4,si4 class2 0.0 0.0 0.0 0.0 0.0 0.0 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,c4,si4,si4,h1,c4,si4,si4,h1,c4,si4,si4 class2 mbt 0.0000 0.0000 -0.1909 1.8995 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,c4,si4,si4,h1,c4,si4,si4,h1,c4,si4,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 2.3384 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,c4,si4,si4,h1,c4,si4,si4,h1,c4,si4,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.0355 113.0000 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,c4,si4,si4,h1,c4,si4,si4,h1,c4,si4,si4 class2 aat -13.3679 112.0355 113.0000 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,c4,si4,si4,h1,c4,si4,si4,h1,c4,si4,si4 class2 bb13 0.0 1.1010 2.3384 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,c4,si4,h1,h1,c4,si4,h1,h1,c4,si4,h1 class2 0.0 0.0 0.0 0.0 0.0 0.0 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,c4,si4,h1,h1,c4,si4,h1,h1,c4,si4,h1 class2 mbt 0.0000 0.0000 -0.5906 1.8995 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,c4,si4,h1,h1,c4,si4,h1,h1,c4,si4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.4783 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,c4,si4,h1,h1,c4,si4,h1,h1,c4,si4,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.0355 112.0977 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,c4,si4,h1,h1,c4,si4,h1,h1,c4,si4,h1 class2 aat 0.0 112.0355 112.0977 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,c4,si4,h1,h1,c4,si4,h1,h1,c4,si4,h1 class2 bb13 0.0 1.1010 1.4783 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:c3a,c3a,si4,h1,c3a,c3a,si4,h1,c3a,c3a,si4,h1 class2 0.0 0.0 0.0 0.0 0.0 0.0 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:c3a,c3a,si4,h1,c3a,c3a,si4,h1,c3a,c3a,si4,h1 class2 mbt 0.0000 0.0000 -0.3146 1.8634 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:c3a,c3a,si4,h1,c3a,c3a,si4,h1,c3a,c3a,si4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.4783 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:c3a,c3a,si4,h1,c3a,c3a,si4,h1,c3a,c3a,si4,h1 class2 at 0.0000 0.0000 -0.2779 0.0000 0.0000 -0.1932 120.0000 109.5932 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:c3a,c3a,si4,h1,c3a,c3a,si4,h1,c3a,c3a,si4,h1 class2 aat 0.0 120.0000 109.5932 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:c3a,c3a,si4,h1,c3a,c3a,si4,h1,c3a,c3a,si4,h1 class2 bb13 0.0 1.4170 1.4783 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:c4,c3prime,o2,c4,c4,c3prime,o2e,c4,c4,c3prime,o2,c4 class2 0.0 0.0 0.0 0.0 0.0 0.0 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c4,c3prime,o2,c4,c4,c3prime,o2e,c4,c4,c3prime,o2,c4 class2 mbt 1.3445 3.5515 -4.9202 1.3750 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c4,c3prime,o2,c4,c4,c3prime,o2e,c4,c4,c3prime,o2,c4 class2 ebt 0.1928 1.3187 0.8599 0.0004 -1.0975 0.4831 1.5140 1.4200 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c4,c3prime,o2,c4,c4,c3prime,o2e,c4,c4,c3prime,o2,c4 class2 at 0.9701 -2.5169 1.7195 0.8831 -0.8203 0.2405 100.3182 109.0000 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c4,c3prime,o2,c4,c4,c3prime,o2e,c4,c4,c3prime,o2,c4 class2 aat -12.2070 100.3182 109.0000 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c4,c3prime,o2,c4,c4,c3prime,o2e,c4,c4,c3prime,o2,c4 class2 bb13 0.0 1.5140 1.4200 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3prime,n3m,c3prime,o1=,c3prime,n3m,c3prime,o1=,c3prime,n3m,c3prime,o1= class2 0.0 0.0 0.0 0.0 0.0 0.0 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3prime,n3m,c3prime,o1=,c3prime,n3m,c3prime,o1=,c3prime,n3m,c3prime,o1= class2 mbt -0.1118 -1.1990 0.6784 1.3850 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3prime,n3m,c3prime,o1=,c3prime,n3m,c3prime,o1=,c3prime,n3m,c3prime,o1= class2 ebt 0.1726 -0.4823 0.2666 -0.7019 0.8305 -0.6874 1.3850 1.2160 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3prime,n3m,c3prime,o1=,c3prime,n3m,c3prime,o1=,c3prime,n3m,c3prime,o1= class2 at -0.3188 -0.0548 -0.3038 -0.2851 2.3997 -1.5747 121.9556 121.5420 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3prime,n3m,c3prime,o1=,c3prime,n3m,c3prime,o1=,c3prime,n3m,c3prime,o1= class2 aat -3.3556 121.9556 121.5420 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3prime,n3m,c3prime,o1=,c3prime,n3m,c3prime,o1=,c3prime,n3m,c3prime,o1= class2 bb13 0.0 1.3850 1.2160 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:X,si4,si4,X,si4,si4,si4,si4,si4,si4,si4,si4 class2 0.0000 0.0 0.0000 0.0 -0.0657 0.0 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,si4,si4,si4,si4,si4,si4,si4,si4 class2 mbt 0.0 0.0 0.0 2.3384 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,si4,si4,si4,si4,si4,si4,si4,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 2.3384 2.3384 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,si4,si4,si4,si4,si4,si4,si4,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 114.2676 114.2676 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,si4,si4,si4,si4,si4,si4,si4,si4 class2 aat 0.0 114.2676 114.2676 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,si4,si4,si4,si4,si4,si4,si4,si4 class2 bb13 0.0 2.3384 2.3384 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,si4,si4,si4,h1,si4,si4,si4,h1 class2 0.0000 0.0 0.0000 0.0 -0.0657 0.0 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,si4,si4,si4,h1,si4,si4,si4,h1 class2 mbt 0.0 0.0 0.0 2.3384 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,si4,si4,si4,h1,si4,si4,si4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 2.3384 1.4783 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,si4,si4,si4,h1,si4,si4,si4,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 114.2676 112.0893 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,si4,si4,si4,h1,si4,si4,si4,h1 class2 aat 0.0 114.2676 112.0893 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,si4,si4,si4,h1,si4,si4,si4,h1 class2 bb13 0.0 2.3384 1.4783 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,si4,si4,si4,c4,si4,si4,si4,c4 class2 0.0000 0.0 0.0000 0.0 -0.0657 0.0 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,si4,si4,si4,c4,si4,si4,si4,c4 class2 mbt 0.0 0.0 0.0 2.3384 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,si4,si4,si4,c4,si4,si4,si4,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 2.3384 1.8995 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,si4,si4,si4,c4,si4,si4,si4,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 114.2676 113.0000 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,si4,si4,si4,c4,si4,si4,si4,c4 class2 aat 0.0 114.2676 113.0000 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,si4,si4,si4,c4,si4,si4,si4,c4 class2 bb13 0.0 2.3384 1.8995 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,h1,si4,si4,si4,h1,si4,si4,si4 class2 0.0000 0.0 0.0000 0.0 -0.0657 0.0 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,h1,si4,si4,si4,h1,si4,si4,si4 class2 mbt 0.0 0.0 0.0 2.3384 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,h1,si4,si4,si4,h1,si4,si4,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4783 2.3384 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,h1,si4,si4,si4,h1,si4,si4,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.0893 114.2676 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,h1,si4,si4,si4,h1,si4,si4,si4 class2 aat 0.0 112.0893 114.2676 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,h1,si4,si4,si4,h1,si4,si4,si4 class2 bb13 0.0 1.4783 2.3384 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,h1,si4,si4,h1,h1,si4,si4,h1 class2 0.0000 0.0 0.0000 0.0 -0.0657 0.0 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,h1,si4,si4,h1,h1,si4,si4,h1 class2 mbt 0.0 0.0 0.0 2.3384 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,h1,si4,si4,h1,h1,si4,si4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4783 1.4783 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,h1,si4,si4,h1,h1,si4,si4,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.0893 112.0893 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,h1,si4,si4,h1,h1,si4,si4,h1 class2 aat 0.0 112.0893 112.0893 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,h1,si4,si4,h1,h1,si4,si4,h1 class2 bb13 0.0 1.4783 1.4783 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,h1,si4,si4,c4,h1,si4,si4,c4 class2 0.0000 0.0 0.0000 0.0 -0.0657 0.0 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,h1,si4,si4,c4,h1,si4,si4,c4 class2 mbt 0.0 0.0 0.0 2.3384 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,h1,si4,si4,c4,h1,si4,si4,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4783 1.8995 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,h1,si4,si4,c4,h1,si4,si4,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.0893 113.0000 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,h1,si4,si4,c4,h1,si4,si4,c4 class2 aat 0.0 112.0893 113.0000 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,h1,si4,si4,c4,h1,si4,si4,c4 class2 bb13 0.0 1.4783 1.8995 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,c4,si4,si4,si4,c4,si4,si4,si4 class2 0.0000 0.0 0.0000 0.0 -0.0657 0.0 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,c4,si4,si4,si4,c4,si4,si4,si4 class2 mbt 0.0 0.0 0.0 2.3384 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,c4,si4,si4,si4,c4,si4,si4,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8995 2.3384 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,c4,si4,si4,si4,c4,si4,si4,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 113.0000 114.2676 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,c4,si4,si4,si4,c4,si4,si4,si4 class2 aat 0.0 113.0000 114.2676 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,c4,si4,si4,si4,c4,si4,si4,si4 class2 bb13 0.0 1.8995 2.3384 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,c4,si4,si4,h1,c4,si4,si4,h1 class2 0.0000 0.0 0.0000 0.0 -0.0657 0.0 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,c4,si4,si4,h1,c4,si4,si4,h1 class2 mbt 0.0 0.0 0.0 2.3384 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,c4,si4,si4,h1,c4,si4,si4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8995 1.4783 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,c4,si4,si4,h1,c4,si4,si4,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 113.0000 112.0893 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,c4,si4,si4,h1,c4,si4,si4,h1 class2 aat 0.0 113.0000 112.0893 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,c4,si4,si4,h1,c4,si4,si4,h1 class2 bb13 0.0 1.8995 1.4783 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,c4,si4,si4,c4,c4,si4,si4,c4 class2 0.0000 0.0 0.0000 0.0 -0.0657 0.0 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,c4,si4,si4,c4,c4,si4,si4,c4 class2 mbt 0.0 0.0 0.0 2.3384 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,c4,si4,si4,c4,c4,si4,si4,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8995 1.8995 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,c4,si4,si4,c4,c4,si4,si4,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 113.0000 113.0000 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,c4,si4,si4,c4,c4,si4,si4,c4 class2 aat 0.0 113.0000 113.0000 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,c4,si4,si4,c4,c4,si4,si4,c4 class2 bb13 0.0 1.8995 1.8995 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,si4,h1,c4,si4,si4 class2 0.0000 0.0 0.0000 0.0 -0.0657 0.0 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,si4,h1,c4,si4,si4 class2 mbt 0.0 0.0 0.0 1.8995 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,si4,h1,c4,si4,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 2.3384 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,si4,h1,c4,si4,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.0355 113.0000 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,si4,h1,c4,si4,si4 class2 aat 0.0 112.0355 113.0000 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,si4,h1,c4,si4,si4 class2 bb13 0.0 1.1010 2.3384 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,o2z,h1,c4,si4,o2z class2 0.0000 0.0 0.0000 0.0 -0.0657 0.0 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,o2z,h1,c4,si4,o2z class2 mbt 0.0 0.0 0.0 1.8995 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,o2z,h1,c4,si4,o2z class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.6400 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,o2z,h1,c4,si4,o2z class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.0355 114.9060 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,o2z,h1,c4,si4,o2z class2 aat 0.0 112.0355 114.9060 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,o2z,h1,c4,si4,o2z class2 bb13 0.0 1.1010 1.6400 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,h1,h1,c4,si4,h1 class2 0.0000 0.0 0.0000 0.0 -0.0657 0.0 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,h1,h1,c4,si4,h1 class2 mbt 0.0 0.0 0.0 1.8995 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,h1,h1,c4,si4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.4783 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,h1,h1,c4,si4,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.0355 112.0977 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,h1,h1,c4,si4,h1 class2 aat 0.0 112.0355 112.0977 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,h1,h1,c4,si4,h1 class2 bb13 0.0 1.1010 1.4783 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,c4,h1,c4,si4,c4 class2 0.0000 0.0 0.0000 0.0 -0.0657 0.0 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,c4,h1,c4,si4,c4 class2 mbt 0.0 0.0 0.0 1.8995 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,c4,h1,c4,si4,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.8995 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,c4,h1,c4,si4,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.0355 113.1855 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,c4,h1,c4,si4,c4 class2 aat 0.0 112.0355 113.1855 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,c4,h1,c4,si4,c4 class2 bb13 0.0 1.1010 1.8995 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,si4,c4,c4,si4,si4 class2 0.0000 0.0 0.0000 0.0 -0.0657 0.0 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,si4,c4,c4,si4,si4 class2 mbt 0.0 0.0 0.0 1.8995 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,si4,c4,c4,si4,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5300 2.3384 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,si4,c4,c4,si4,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.6700 113.0000 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,si4,c4,c4,si4,si4 class2 aat 0.0 112.6700 113.0000 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,si4,c4,c4,si4,si4 class2 bb13 0.0 1.5300 2.3384 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,o2z,c4,c4,si4,o2z class2 0.0000 0.0 0.0000 0.0 -0.0657 0.0 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,o2z,c4,c4,si4,o2z class2 mbt 0.0 0.0 0.0 1.8995 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,o2z,c4,c4,si4,o2z class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5300 1.6400 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,o2z,c4,c4,si4,o2z class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.6700 114.9060 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,o2z,c4,c4,si4,o2z class2 aat 0.0 112.6700 114.9060 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,o2z,c4,c4,si4,o2z class2 bb13 0.0 1.5300 1.6400 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,h1,c4,c4,si4,h1 class2 0.0000 0.0 0.0000 0.0 -0.0657 0.0 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,h1,c4,c4,si4,h1 class2 mbt 0.0 0.0 0.0 1.8995 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,h1,c4,c4,si4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5300 1.4783 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,h1,c4,c4,si4,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.6700 112.0977 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,h1,c4,c4,si4,h1 class2 aat 0.0 112.6700 112.0977 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,h1,c4,c4,si4,h1 class2 bb13 0.0 1.5300 1.4783 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,c4,c4,c4,si4,c4 class2 0.0000 0.0 0.0000 0.0 -0.0657 0.0 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,c4,c4,c4,si4,c4 class2 mbt 0.0 0.0 0.0 1.8995 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,c4,c4,c4,si4,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5300 1.8995 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,c4,c4,c4,si4,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.6700 113.1855 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,c4,c4,c4,si4,c4 class2 aat 0.0 112.6700 113.1855 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,c4,c4,c4,si4,c4 class2 bb13 0.0 1.5300 1.8995 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:c4,c4,si4,si4,c4,c4,si4,si4,c4,c4,si4,si4 class2 -0.3500 0.0 0.0000 0.0 -0.0657 0.0 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:c4,c4,si4,si4,c4,c4,si4,si4,c4,c4,si4,si4 class2 mbt 0.0 0.0 0.0 1.8995 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:c4,c4,si4,si4,c4,c4,si4,si4,c4,c4,si4,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5300 2.3384 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:c4,c4,si4,si4,c4,c4,si4,si4,c4,c4,si4,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.6700 113.0000 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:c4,c4,si4,si4,c4,c4,si4,si4,c4,c4,si4,si4 class2 aat 0.0 112.6700 113.0000 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:c4,c4,si4,si4,c4,c4,si4,si4,c4,c4,si4,si4 class2 bb13 0.0 1.5300 2.3384 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,c3a,c3a,o2z,si4,c3a,c3a,o2z,si4,c3a,c3a class2 0.0000 0.0 0.0000 0.0 -0.0231 0.0 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,c3a,c3a,o2z,si4,c3a,c3a,o2z,si4,c3a,c3a class2 mbt 0.0 0.0 0.0 1.8634 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,c3a,c3a,o2z,si4,c3a,c3a,o2z,si4,c3a,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.6400 1.4170 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,c3a,c3a,o2z,si4,c3a,c3a,o2z,si4,c3a,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 114.9060 120.0000 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,c3a,c3a,o2z,si4,c3a,c3a,o2z,si4,c3a,c3a class2 aat 0.0 114.9060 120.0000 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,c3a,c3a,o2z,si4,c3a,c3a,o2z,si4,c3a,c3a class2 bb13 0.0 1.6400 1.4170 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,c3a,c3a,h1,si4,c3a,c3a,h1,si4,c3a,c3a class2 0.0000 0.0 0.0000 0.0 -0.0231 0.0 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,c3a,c3a,h1,si4,c3a,c3a,h1,si4,c3a,c3a class2 mbt 0.0 0.0 0.0 1.8634 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,c3a,c3a,h1,si4,c3a,c3a,h1,si4,c3a,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4783 1.4170 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,c3a,c3a,h1,si4,c3a,c3a,h1,si4,c3a,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 109.5932 120.0000 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,c3a,c3a,h1,si4,c3a,c3a,h1,si4,c3a,c3a class2 aat 0.0 109.5932 120.0000 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,c3a,c3a,h1,si4,c3a,c3a,h1,si4,c3a,c3a class2 bb13 0.0 1.4783 1.4170 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,c3a,c3a,si4,h1,c3a,c3a,si4,h1,c3a,c3a,si4 class2 0.0000 0.0 1.5093 0.0 0.0000 0.0 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,c3a,c3a,si4,h1,c3a,c3a,si4,h1,c3a,c3a,si4 class2 mbt 0.0000 6.2168 0.0000 1.4170 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,c3a,c3a,si4,h1,c3a,c3a,si4,h1,c3a,c3a,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0982 1.8634 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,c3a,c3a,si4,h1,c3a,c3a,si4,h1,c3a,c3a,si4 class2 at 0.0000 4.5914 0.0000 0.0000 1.1079 0.0000 117.9400 120.0000 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,c3a,c3a,si4,h1,c3a,c3a,si4,h1,c3a,c3a,si4 class2 aat 0.0 117.9400 120.0000 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,c3a,c3a,si4,h1,c3a,c3a,si4,h1,c3a,c3a,si4 class2 bb13 0.0 1.0982 1.8634 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:c3a,c3a,c3a,si4,c3a,c3a,c3a,si4,c3a,c3a,c3a,si4 class2 0.0000 0.0 4.3270 0.0 0.0000 0.0 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:c3a,c3a,c3a,si4,c3a,c3a,c3a,si4,c3a,c3a,c3a,si4 class2 mbt 0.0000 11.1576 0.0000 1.4170 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:c3a,c3a,c3a,si4,c3a,c3a,c3a,si4,c3a,c3a,c3a,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.8634 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:c3a,c3a,c3a,si4,c3a,c3a,c3a,si4,c3a,c3a,c3a,si4 class2 at 0.0000 -5.5448 0.0000 0.0000 4.3281 0.0000 118.9000 120.0000 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:c3a,c3a,c3a,si4,c3a,c3a,c3a,si4,c3a,c3a,c3a,si4 class2 aat 0.0 118.9000 120.0000 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:c3a,c3a,c3a,si4,c3a,c3a,c3a,si4,c3a,c3a,c3a,si4 class2 bb13 0.0 1.4170 1.8634 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,c4,c4,n2z,h1,c4,c4,n2z,h1,c4,c4,n2z class2 0.0000 0.0 0.0000 0.0 -0.2259 0.0 # (ver=1.0, ref=9) + dihedral_coeff @dihedral:h1,c4,c4,n2z,h1,c4,c4,n2z,h1,c4,c4,n2z class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=9) + dihedral_coeff @dihedral:h1,c4,c4,n2z,h1,c4,c4,n2z,h1,c4,c4,n2z class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.4814 # (ver=1.0, ref=9) + dihedral_coeff @dihedral:h1,c4,c4,n2z,h1,c4,c4,n2z,h1,c4,c4,n2z class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.7700 110.9900 # (ver=1.0, ref=9) + dihedral_coeff @dihedral:h1,c4,c4,n2z,h1,c4,c4,n2z,h1,c4,c4,n2z class2 aat 0.0 110.7700 110.9900 # (ver=1.0, ref=9) + dihedral_coeff @dihedral:h1,c4,c4,n2z,h1,c4,c4,n2z,h1,c4,c4,n2z class2 bb13 0.0 1.1010 1.4814 # (ver=1.0, ref=9) + dihedral_coeff @dihedral:c4,c4,n2z,n2t,c4,c4,n2z,n2t,c4,c4,n2z,n2t class2 0.0000 0.0 0.0000 0.0 -0.2021 0.0 # (ver=1.0, ref=9) + dihedral_coeff @dihedral:c4,c4,n2z,n2t,c4,c4,n2z,n2t,c4,c4,n2z,n2t class2 mbt 0.0 0.0 0.0 1.4814 # (ver=1.0, ref=9) + dihedral_coeff @dihedral:c4,c4,n2z,n2t,c4,c4,n2z,n2t,c4,c4,n2z,n2t class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5300 1.2343 # (ver=1.0, ref=9) + dihedral_coeff @dihedral:c4,c4,n2z,n2t,c4,c4,n2z,n2t,c4,c4,n2z,n2t class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.9900 113.5017 # (ver=1.0, ref=9) + dihedral_coeff @dihedral:c4,c4,n2z,n2t,c4,c4,n2z,n2t,c4,c4,n2z,n2t class2 aat 0.0 110.9900 113.5017 # (ver=1.0, ref=9) + dihedral_coeff @dihedral:c4,c4,n2z,n2t,c4,c4,n2z,n2t,c4,c4,n2z,n2t class2 bb13 0.0 1.5300 1.2343 # (ver=1.0, ref=9) + dihedral_coeff @dihedral:h1,c4,n2z,n2t,h1,c4,n2z,n2t,h1,c4,n2z,n2t class2 0.0000 0.0 0.0000 0.0 -0.2181 0.0 # (ver=1.0, ref=9) + dihedral_coeff @dihedral:h1,c4,n2z,n2t,h1,c4,n2z,n2t,h1,c4,n2z,n2t class2 mbt 0.0 0.0 0.0 1.4814 # (ver=1.0, ref=9) + dihedral_coeff @dihedral:h1,c4,n2z,n2t,h1,c4,n2z,n2t,h1,c4,n2z,n2t class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.2343 # (ver=1.0, ref=9) + dihedral_coeff @dihedral:h1,c4,n2z,n2t,h1,c4,n2z,n2t,h1,c4,n2z,n2t class2 at 0.0 0.0 0.0 0.0 0.0 0.0 107.9744 113.5017 # (ver=1.0, ref=9) + dihedral_coeff @dihedral:h1,c4,n2z,n2t,h1,c4,n2z,n2t,h1,c4,n2z,n2t class2 aat 0.0 107.9744 113.5017 # (ver=1.0, ref=9) + dihedral_coeff @dihedral:h1,c4,n2z,n2t,h1,c4,n2z,n2t,h1,c4,n2z,n2t class2 bb13 0.0 1.1010 1.2343 # (ver=1.0, ref=9) + dihedral_coeff @dihedral:c4,n2z,n2t,n1t,c4,n2z,n2t,n1t,c4,n2z,n2t,n1t class2 0.0000 0.0 0.0000 0.0 -0.1823 0.0 # (ver=1.0, ref=9) + dihedral_coeff @dihedral:c4,n2z,n2t,n1t,c4,n2z,n2t,n1t,c4,n2z,n2t,n1t class2 mbt 0.0 0.0 0.0 1.2343 # (ver=1.0, ref=9) + dihedral_coeff @dihedral:c4,n2z,n2t,n1t,c4,n2z,n2t,n1t,c4,n2z,n2t,n1t class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4814 1.1354 # (ver=1.0, ref=9) + dihedral_coeff @dihedral:c4,n2z,n2t,n1t,c4,n2z,n2t,n1t,c4,n2z,n2t,n1t class2 at 0.0 0.0 0.0 0.0 0.0 0.0 113.5017 171.6211 # (ver=1.0, ref=9) + dihedral_coeff @dihedral:c4,n2z,n2t,n1t,c4,n2z,n2t,n1t,c4,n2z,n2t,n1t class2 aat 0.0 113.5017 171.6211 # (ver=1.0, ref=9) + dihedral_coeff @dihedral:c4,n2z,n2t,n1t,c4,n2z,n2t,n1t,c4,n2z,n2t,n1t class2 bb13 0.0 1.4814 1.1354 # (ver=1.0, ref=9) + dihedral_coeff @dihedral:h1,n2z,n2t,n1t,h1,n2z,n2t,n1t,h1,n2z,n2t,n1t class2 0.0000 0.0 0.0000 0.0 -0.2637 0.0 # (ver=1.0, ref=9) + dihedral_coeff @dihedral:h1,n2z,n2t,n1t,h1,n2z,n2t,n1t,h1,n2z,n2t,n1t class2 mbt 0.0 0.0 0.0 1.2343 # (ver=1.0, ref=9) + dihedral_coeff @dihedral:h1,n2z,n2t,n1t,h1,n2z,n2t,n1t,h1,n2z,n2t,n1t class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0221 1.1354 # (ver=1.0, ref=9) + dihedral_coeff @dihedral:h1,n2z,n2t,n1t,h1,n2z,n2t,n1t,h1,n2z,n2t,n1t class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.0345 171.6211 # (ver=1.0, ref=9) + dihedral_coeff @dihedral:h1,n2z,n2t,n1t,h1,n2z,n2t,n1t,h1,n2z,n2t,n1t class2 aat 0.0 110.0345 171.6211 # (ver=1.0, ref=9) + dihedral_coeff @dihedral:h1,n2z,n2t,n1t,h1,n2z,n2t,n1t,h1,n2z,n2t,n1t class2 bb13 0.0 1.0221 1.1354 # (ver=1.0, ref=9) + dihedral_coeff @dihedral:h1,c3a,c3a,n3m,h1,c3a,c3a,n3m,h1,c3a,c3a,n3m class2 0.0000 0.0 3.4040 0.0 0.0000 0.0 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:h1,c3a,c3a,n3m,h1,c3a,c3a,n3m,h1,c3a,c3a,n3m class2 mbt 0.0000 5.2012 0.0000 1.4170 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:h1,c3a,c3a,n3m,h1,c3a,c3a,n3m,h1,c3a,c3a,n3m class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0982 1.3950 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:h1,c3a,c3a,n3m,h1,c3a,c3a,n3m,h1,c3a,c3a,n3m class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.9400 120.7640 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:h1,c3a,c3a,n3m,h1,c3a,c3a,n3m,h1,c3a,c3a,n3m class2 aat 0.0 117.9400 120.7640 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:h1,c3a,c3a,n3m,h1,c3a,c3a,n3m,h1,c3a,c3a,n3m class2 bb13 0.0 1.0982 1.3950 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:h1,c4,c3prime,o2,h1,c4,c3prime,o2e,h1,c4,c3prime,o2 class2 0.0000 0.0 0.0000 0.0 0.0000 0.0 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:h1,c4,c3prime,o2,h1,c4,c3prime,o2e,h1,c4,c3prime,o2 class2 mbt -13.7686 -2.5959 1.1934 1.5140 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:h1,c4,c3prime,o2,h1,c4,c3prime,o2e,h1,c4,c3prime,o2 class2 ebt 0.7800 1.3339 0.3268 0.4160 -0.1140 0.7099 1.1010 1.3750 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:h1,c4,c3prime,o2,h1,c4,c3prime,o2e,h1,c4,c3prime,o2 class2 at -0.0071 0.8005 13.2959 0.1212 1.4427 -0.0241 107.8594 100.3182 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:h1,c4,c3prime,o2,h1,c4,c3prime,o2e,h1,c4,c3prime,o2 class2 aat -13.9734 107.8594 100.3182 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:h1,c4,c3prime,o2,h1,c4,c3prime,o2e,h1,c4,c3prime,o2 class2 bb13 0.0 1.1010 1.3750 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:h1,c4,c3prime,o1=,h1,c4,c3prime,o1=,h1,c4,c3prime,o1= class2 0.0000 0.0 0.0000 0.0 0.0000 0.0 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:h1,c4,c3prime,o1=,h1,c4,c3prime,o1=,h1,c4,c3prime,o1= class2 mbt 0.0000 0.0000 -1.0000 1.5140 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:h1,c4,c3prime,o1=,h1,c4,c3prime,o1=,h1,c4,c3prime,o1= class2 ebt 2.9036 0.5307 0.1439 0.0536 0.0354 0.3853 1.1010 1.2160 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:h1,c4,c3prime,o1=,h1,c4,c3prime,o1=,h1,c4,c3prime,o1= class2 at 0.0800 0.3339 14.4728 -0.2083 0.7308 -2.0667 107.8594 119.3000 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:h1,c4,c3prime,o1=,h1,c4,c3prime,o1=,h1,c4,c3prime,o1= class2 aat -23.1923 107.8594 119.3000 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:h1,c4,c3prime,o1=,h1,c4,c3prime,o1=,h1,c4,c3prime,o1= class2 bb13 0.0 1.1010 1.2160 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c4,o2,c3prime,o1=,c4,o2e,c3prime,o1=,c4,o2,c3prime,o1= class2 0.8905 0.0 3.2644 0.0 0.2646 0.0 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c4,o2,c3prime,o1=,c4,o2e,c3prime,o1=,c4,o2,c3prime,o1= class2 mbt 0.4552 7.3091 0.2842 1.3750 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c4,o2,c3prime,o1=,c4,o2e,c3prime,o1=,c4,o2,c3prime,o1= class2 ebt 0.0882 -2.4309 -0.7426 -4.2421 10.1102 1.6824 1.4200 1.2160 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c4,o2,c3prime,o1=,c4,o2e,c3prime,o1=,c4,o2,c3prime,o1= class2 at -0.0327 1.0059 2.3573 1.9052 2.7261 5.9732 109.0000 118.9855 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c4,o2,c3prime,o1=,c4,o2e,c3prime,o1=,c4,o2,c3prime,o1= class2 aat -32.9368 109.0000 118.9855 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c4,o2,c3prime,o1=,c4,o2e,c3prime,o1=,c4,o2,c3prime,o1= class2 bb13 0.0 1.4200 1.2160 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c4,o2,c3prime,c4,c4,o2e,c3prime,c4,c4,o2,c3prime,c4 class2 -2.5594 0.0 2.2013 0.0 0.0325 0.0 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c4,o2,c3prime,c4,c4,o2e,c3prime,c4,c4,o2,c3prime,c4 class2 mbt 0.0 0.0 0.0 1.3750 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c4,o2,c3prime,c4,c4,o2e,c3prime,c4,c4,o2,c3prime,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4200 1.5140 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c4,o2,c3prime,c4,c4,o2e,c3prime,c4,c4,o2,c3prime,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 109.0000 100.3182 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c4,o2,c3prime,c4,c4,o2e,c3prime,c4,c4,o2,c3prime,c4 class2 aat 0.0 109.0000 100.3182 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c4,o2,c3prime,c4,c4,o2e,c3prime,c4,c4,o2,c3prime,c4 class2 bb13 0.0 1.4200 1.5140 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3a,n3m,c3prime,o1=,c3a,n3m,c3prime,o1=,c3a,n3m,c3prime,o1= class2 0.0000 0.0 2.0521 0.0 0.0000 0.0 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3a,n3m,c3prime,o1=,c3a,n3m,c3prime,o1=,c3a,n3m,c3prime,o1= class2 mbt 0.0 0.0 0.0 1.3850 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3a,n3m,c3prime,o1=,c3a,n3m,c3prime,o1=,c3a,n3m,c3prime,o1= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3950 1.2160 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3a,n3m,c3prime,o1=,c3a,n3m,c3prime,o1=,c3a,n3m,c3prime,o1= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0700 121.5420 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3a,n3m,c3prime,o1=,c3a,n3m,c3prime,o1=,c3a,n3m,c3prime,o1= class2 aat 0.0 120.0700 121.5420 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3a,n3m,c3prime,o1=,c3a,n3m,c3prime,o1=,c3a,n3m,c3prime,o1= class2 bb13 0.0 1.3950 1.2160 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3a,c3a,c3a,n3m,c3a,c3a,c3a,n3m,c3a,c3a,c3a,n3m class2 0.0000 0.0 3.4040 0.0 0.0000 0.0 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3a,c3a,c3a,n3m,c3a,c3a,c3a,n3m,c3a,c3a,c3a,n3m class2 mbt 0.0000 5.2012 0.0000 1.4170 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3a,c3a,c3a,n3m,c3a,c3a,c3a,n3m,c3a,c3a,c3a,n3m class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.3950 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3a,c3a,c3a,n3m,c3a,c3a,c3a,n3m,c3a,c3a,c3a,n3m class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.9000 120.7640 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3a,c3a,c3a,n3m,c3a,c3a,c3a,n3m,c3a,c3a,c3a,n3m class2 aat 0.0 118.9000 120.7640 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3a,c3a,c3a,n3m,c3a,c3a,c3a,n3m,c3a,c3a,c3a,n3m class2 bb13 0.0 1.4170 1.3950 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3a,c3a,c3prime,o1=,c3a,c3a,c3prime,o1=,c3a,c3a,c3prime,o1= class2 0.0000 0.0 0.7800 0.0 0.0000 0.0 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3a,c3a,c3prime,o1=,c3a,c3a,c3prime,o1=,c3a,c3a,c3prime,o1= class2 mbt 0.0000 2.4002 0.0000 1.4890 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3a,c3a,c3prime,o1=,c3a,c3a,c3prime,o1=,c3a,c3a,c3prime,o1= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.2160 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3a,c3a,c3prime,o1=,c3a,c3a,c3prime,o1=,c3a,c3a,c3prime,o1= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 116.0640 125.5320 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3a,c3a,c3prime,o1=,c3a,c3a,c3prime,o1=,c3a,c3a,c3prime,o1= class2 aat 0.0 116.0640 125.5320 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3a,c3a,c3prime,o1=,c3a,c3a,c3prime,o1=,c3a,c3a,c3prime,o1= class2 bb13 0.0 1.4170 1.2160 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3prime,o2,c4,h1,c3prime,o2e,c4,h1,c3prime,o2,c4,h1 class2 0.9513 0.0 0.1155 0.0 0.0000 0.0 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3prime,o2,c4,h1,c3prime,o2e,c4,h1,c3prime,o2,c4,h1 class2 mbt 7.7147 4.2557 -1.0118 1.4200 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3prime,o2,c4,h1,c3prime,o2e,c4,h1,c3prime,o2,c4,h1 class2 ebt 0.2282 2.2998 -0.4473 0.9589 0.9190 -0.6015 1.3750 1.1010 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3prime,o2,c4,h1,c3prime,o2e,c4,h1,c3prime,o2,c4,h1 class2 at 0.0971 -0.8699 -0.3142 -0.0401 2.8061 -0.4990 109.0000 108.7280 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3prime,o2,c4,h1,c3prime,o2e,c4,h1,c3prime,o2,c4,h1 class2 aat -13.1500 109.0000 108.7280 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3prime,o2,c4,h1,c3prime,o2e,c4,h1,c3prime,o2,c4,h1 class2 bb13 0.0 1.3750 1.1010 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3prime,o2,c4,c4,c3prime,o2e,c4,c4,c3prime,o2,c4,c4 class2 0.1302 0.0 -0.3250 0.0 0.1134 0.0 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3prime,o2,c4,c4,c3prime,o2e,c4,c4,c3prime,o2,c4,c4 class2 mbt 9.9416 2.6421 2.2333 1.4200 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3prime,o2,c4,c4,c3prime,o2e,c4,c4,c3prime,o2,c4,c4 class2 ebt 0.2560 0.8133 -0.0728 -1.2164 -0.1715 -0.0964 1.3750 1.5300 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3prime,o2,c4,c4,c3prime,o2e,c4,c4,c3prime,o2,c4,c4 class2 at 0.7229 -0.9159 -0.0890 -0.6765 1.4492 -0.4620 109.0000 111.2700 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3prime,o2,c4,c4,c3prime,o2e,c4,c4,c3prime,o2,c4,c4 class2 aat -15.7082 109.0000 111.2700 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3prime,o2,c4,c4,c3prime,o2e,c4,c4,c3prime,o2,c4,c4 class2 bb13 0.0 1.3750 1.5300 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3a,c3a,n3m,c3prime,c3a,c3a,n3m,c3prime,c3a,c3a,n3m,c3prime class2 0.0000 0.0 0.6500 0.0 0.0000 0.0 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3a,c3a,n3m,c3prime,c3a,c3a,n3m,c3prime,c3a,c3a,n3m,c3prime class2 mbt 0.0 0.0 0.0 1.3950 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3a,c3a,n3m,c3prime,c3a,c3a,n3m,c3prime,c3a,c3a,n3m,c3prime class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.3850 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3a,c3a,n3m,c3prime,c3a,c3a,n3m,c3prime,c3a,c3a,n3m,c3prime class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.7640 120.0700 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3a,c3a,n3m,c3prime,c3a,c3a,n3m,c3prime,c3a,c3a,n3m,c3prime class2 aat 0.0 120.7640 120.0700 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3a,c3a,n3m,c3prime,c3a,c3a,n3m,c3prime,c3a,c3a,n3m,c3prime class2 bb13 0.0 1.4170 1.3850 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3prime,c3a,c3a,h1,c3prime,c3a,c3a,h1,c3prime,c3a,c3a,h1 class2 0.0000 0.0 2.1670 0.0 0.0000 0.0 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3prime,c3a,c3a,h1,c3prime,c3a,c3a,h1,c3prime,c3a,c3a,h1 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3prime,c3a,c3a,h1,c3prime,c3a,c3a,h1,c3prime,c3a,c3a,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4890 1.0982 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3prime,c3a,c3a,h1,c3prime,c3a,c3a,h1,c3prime,c3a,c3a,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 116.0640 117.9400 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3prime,c3a,c3a,h1,c3prime,c3a,c3a,h1,c3prime,c3a,c3a,h1 class2 aat 0.0 116.0640 117.9400 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3prime,c3a,c3a,h1,c3prime,c3a,c3a,h1,c3prime,c3a,c3a,h1 class2 bb13 0.0 1.4890 1.0982 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3a,c3a,c3a,c3prime,c3a,c3a,c3a,c3prime,c3a,c3a,c3a,c3prime class2 0.0000 0.0 4.6282 0.0 0.0000 0.0 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3a,c3a,c3a,c3prime,c3a,c3a,c3a,c3prime,c3a,c3a,c3a,c3prime class2 mbt 0.0000 3.8762 0.0000 1.4170 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3a,c3a,c3a,c3prime,c3a,c3a,c3a,c3prime,c3a,c3a,c3a,c3prime class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.4890 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3a,c3a,c3a,c3prime,c3a,c3a,c3a,c3prime,c3a,c3a,c3a,c3prime class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.9000 116.0640 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3a,c3a,c3a,c3prime,c3a,c3a,c3a,c3prime,c3a,c3a,c3a,c3prime class2 aat 0.0 118.9000 116.0640 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3a,c3a,c3a,c3prime,c3a,c3a,c3a,c3prime,c3a,c3a,c3a,c3prime class2 bb13 0.0 1.4170 1.4890 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c4,o2,n3o,o1=,c4,o2n,n3o,o1=,c4,o2n,n3o,o1= class2 0.0000 0.0 2.0000 0.0 0.0000 0.0 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:c4,o2,n3o,o1=,c4,o2n,n3o,o1=,c4,o2n,n3o,o1= class2 mbt 0.0 0.0 0.0 1.4020 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:c4,o2,n3o,o1=,c4,o2n,n3o,o1=,c4,o2n,n3o,o1= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4350 1.2100 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:c4,o2,n3o,o1=,c4,o2n,n3o,o1=,c4,o2n,n3o,o1= class2 at 0.0000 0.0000 0.0000 0.0000 0.0000 -3.0000 108.5000 112.8000 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:c4,o2,n3o,o1=,c4,o2n,n3o,o1=,c4,o2n,n3o,o1= class2 aat 0.0 108.5000 112.8000 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:c4,o2,n3o,o1=,c4,o2n,n3o,o1=,c4,o2n,n3o,o1= class2 bb13 0.0 1.4350 1.2100 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:c4,c4,o2,n3o,c4,c4,o2n,n3o,c4,c4,o2n,n3o class2 0.0000 0.0 -0.4000 0.0 -0.2000 0.0 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:c4,c4,o2,n3o,c4,c4,o2n,n3o,c4,c4,o2n,n3o class2 mbt 0.0 0.0 0.0 1.4350 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:c4,c4,o2,n3o,c4,c4,o2n,n3o,c4,c4,o2n,n3o class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5300 1.4020 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:c4,c4,o2,n3o,c4,c4,o2n,n3o,c4,c4,o2n,n3o class2 at 0.0 0.0 0.0 0.0 0.0 0.0 105.0000 108.5000 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:c4,c4,o2,n3o,c4,c4,o2n,n3o,c4,c4,o2n,n3o class2 aat 0.0 105.0000 108.5000 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:c4,c4,o2,n3o,c4,c4,o2n,n3o,c4,c4,o2n,n3o class2 bb13 0.0 1.5300 1.4020 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:h1,c4,n3o,o1=,h1,c4,n3o,o1=,h1,c4,n3o,o1= class2 0.0000 0.0 0.0000 0.0 -0.3500 0.0 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:h1,c4,n3o,o1=,h1,c4,n3o,o1=,h1,c4,n3o,o1= class2 mbt 0.0 0.0 0.0 1.4740 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:h1,c4,n3o,o1=,h1,c4,n3o,o1=,h1,c4,n3o,o1= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.2100 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:h1,c4,n3o,o1=,h1,c4,n3o,o1=,h1,c4,n3o,o1= class2 at 0.0000 -0.3086 0.0000 0.0000 1.0352 0.0000 107.0000 117.5000 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:h1,c4,n3o,o1=,h1,c4,n3o,o1=,h1,c4,n3o,o1= class2 aat -16.2615 107.0000 117.5000 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:h1,c4,n3o,o1=,h1,c4,n3o,o1=,h1,c4,n3o,o1= class2 bb13 0.0 1.1010 1.2100 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:c3a,c3a,n3o,o1=,c3a,c3a,n3o,o1=,c3a,c3a,n3o,o1= class2 0.0000 0.0 1.1600 0.0 0.0000 0.0 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:c3a,c3a,n3o,o1=,c3a,c3a,n3o,o1=,c3a,c3a,n3o,o1= class2 mbt 0.0 0.0 0.0 1.4300 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:c3a,c3a,n3o,o1=,c3a,c3a,n3o,o1=,c3a,c3a,n3o,o1= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.2100 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:c3a,c3a,n3o,o1=,c3a,c3a,n3o,o1=,c3a,c3a,n3o,o1= class2 at 0.0000 0.0000 0.0000 0.0000 -3.4207 0.0000 118.8000 117.7000 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:c3a,c3a,n3o,o1=,c3a,c3a,n3o,o1=,c3a,c3a,n3o,o1= class2 aat -18.0436 118.8000 117.7000 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:c3a,c3a,n3o,o1=,c3a,c3a,n3o,o1=,c3a,c3a,n3o,o1= class2 bb13 0.0 1.4170 1.2100 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:h1,c3a,c3a,n3o,h1,c3a,c3a,n3o,h1,c3a,c3a,n3o class2 0.0000 0.0 2.9126 0.0 0.0000 0.0 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:h1,c3a,c3a,n3o,h1,c3a,c3a,n3o,h1,c3a,c3a,n3o class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:h1,c3a,c3a,n3o,h1,c3a,c3a,n3o,h1,c3a,c3a,n3o class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0982 1.4300 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:h1,c3a,c3a,n3o,h1,c3a,c3a,n3o,h1,c3a,c3a,n3o class2 at 0.0000 -8.0369 0.0000 0.0000 0.0000 0.0000 117.9400 118.8000 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:h1,c3a,c3a,n3o,h1,c3a,c3a,n3o,h1,c3a,c3a,n3o class2 aat 2.1508 117.9400 118.8000 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:h1,c3a,c3a,n3o,h1,c3a,c3a,n3o,h1,c3a,c3a,n3o class2 bb13 0.0 1.0982 1.4300 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:c3a,c3a,c3a,n3o,c3a,c3a,c3a,n3o,c3a,c3a,c3a,n3o class2 0.0000 0.0 7.2124 0.0 0.0000 0.0 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:c3a,c3a,c3a,n3o,c3a,c3a,c3a,n3o,c3a,c3a,c3a,n3o class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:c3a,c3a,c3a,n3o,c3a,c3a,c3a,n3o,c3a,c3a,c3a,n3o class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.4300 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:c3a,c3a,c3a,n3o,c3a,c3a,c3a,n3o,c3a,c3a,c3a,n3o class2 at 0.0000 7.7594 0.0000 0.0000 0.0000 0.0000 118.9000 118.8000 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:c3a,c3a,c3a,n3o,c3a,c3a,c3a,n3o,c3a,c3a,c3a,n3o class2 aat -34.9681 118.9000 118.8000 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:c3a,c3a,c3a,n3o,c3a,c3a,c3a,n3o,c3a,c3a,c3a,n3o class2 bb13 0.0 1.4170 1.4300 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,o2,p4=,n2=,p4=,o2 class2 0.0000 0.0 0.0000 0.0 -0.3500 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,o2,p4=,n2=,p4=,o2 class2 mbt 0.0 0.0 0.0 1.5980 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,o2,p4=,n2=,p4=,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5980 1.6000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,o2,p4=,n2=,p4=,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 135.0000 112.2150 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,o2,p4=,n2=,p4=,o2 class2 aat 0.0 135.0000 112.2150 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,o2,p4=,n2=,p4=,o2 class2 bb13 0.0 1.5980 1.6000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,n2=,p4=,n2=,p4=,n2= class2 0.0000 0.0 0.0000 0.0 -0.3500 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,n2=,p4=,n2=,p4=,n2= class2 mbt 0.0 0.0 0.0 1.5980 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,n2=,p4=,n2=,p4=,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5980 1.5980 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,n2=,p4=,n2=,p4=,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 135.0000 125.0000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,n2=,p4=,n2=,p4=,n2= class2 aat 0.0 135.0000 125.0000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,n2=,p4=,n2=,p4=,n2= class2 bb13 0.0 1.5980 1.5980 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,h1,p4=,n2=,p4=,h1 class2 0.0000 0.0 0.0000 0.0 -0.3500 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,h1,p4=,n2=,p4=,h1 class2 mbt 0.0 0.0 0.0 1.5980 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,h1,p4=,n2=,p4=,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5980 1.4300 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,h1,p4=,n2=,p4=,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 135.0000 110.0330 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,h1,p4=,n2=,p4=,h1 class2 aat 0.0 135.0000 110.0330 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,h1,p4=,n2=,p4=,h1 class2 bb13 0.0 1.5980 1.4300 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,c4,p4=,n2=,p4=,c4 class2 0.0000 0.0 0.0000 0.0 -0.3500 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,c4,p4=,n2=,p4=,c4 class2 mbt 0.0 0.0 0.0 1.5980 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,c4,p4=,n2=,p4=,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5980 1.8000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,c4,p4=,n2=,p4=,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 135.0000 119.3000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,c4,p4=,n2=,p4=,c4 class2 aat 0.0 135.0000 119.3000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,c4,p4=,n2=,p4=,c4 class2 bb13 0.0 1.5980 1.8000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,c3a,p4=,n2=,p4=,c3a class2 0.0000 0.0 0.0000 0.0 -0.3500 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,c3a,p4=,n2=,p4=,c3a class2 mbt 0.0 0.0 0.0 1.5980 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,c3a,p4=,n2=,p4=,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5980 1.7890 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,c3a,p4=,n2=,p4=,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 135.0000 109.6000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,c3a,p4=,n2=,p4=,c3a class2 aat 0.0 135.0000 109.6000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,c3a,p4=,n2=,p4=,c3a class2 bb13 0.0 1.5980 1.7890 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,o2,h1,n2=,p4=,o2 class2 0.0000 0.0 0.0000 0.0 -0.3500 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,o2,h1,n2=,p4=,o2 class2 mbt 0.0 0.0 0.0 1.5980 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,o2,h1,n2=,p4=,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0310 1.6000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,o2,h1,n2=,p4=,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 112.2150 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,o2,h1,n2=,p4=,o2 class2 aat 0.0 120.0000 112.2150 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,o2,h1,n2=,p4=,o2 class2 bb13 0.0 1.0310 1.6000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,n2=,h1,n2=,p4=,n2= class2 0.0000 0.0 0.0000 0.0 -0.3500 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,n2=,h1,n2=,p4=,n2= class2 mbt 0.0 0.0 0.0 1.5980 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,n2=,h1,n2=,p4=,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0310 1.5980 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,n2=,h1,n2=,p4=,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 125.0000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,n2=,h1,n2=,p4=,n2= class2 aat 0.0 120.0000 125.0000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,n2=,h1,n2=,p4=,n2= class2 bb13 0.0 1.0310 1.5980 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,h1,h1,n2=,p4=,h1 class2 0.0000 0.0 0.0000 0.0 -0.3500 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,h1,h1,n2=,p4=,h1 class2 mbt 0.0 0.0 0.0 1.5980 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,h1,h1,n2=,p4=,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0310 1.4300 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,h1,h1,n2=,p4=,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 110.0330 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,h1,h1,n2=,p4=,h1 class2 aat 0.0 120.0000 110.0330 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,h1,h1,n2=,p4=,h1 class2 bb13 0.0 1.0310 1.4300 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,c4,h1,n2=,p4=,c4 class2 0.0000 0.0 0.0000 0.0 -0.3500 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,c4,h1,n2=,p4=,c4 class2 mbt 0.0 0.0 0.0 1.5980 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,c4,h1,n2=,p4=,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0310 1.8000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,c4,h1,n2=,p4=,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 119.3000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,c4,h1,n2=,p4=,c4 class2 aat 0.0 120.0000 119.3000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,c4,h1,n2=,p4=,c4 class2 bb13 0.0 1.0310 1.8000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,c3a,h1,n2=,p4=,c3a class2 0.0000 0.0 0.0000 0.0 -0.3500 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,c3a,h1,n2=,p4=,c3a class2 mbt 0.0 0.0 0.0 1.5980 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,c3a,h1,n2=,p4=,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0310 1.7890 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,c3a,h1,n2=,p4=,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 109.6000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,c3a,h1,n2=,p4=,c3a class2 aat 0.0 120.0000 109.6000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,c3a,h1,n2=,p4=,c3a class2 bb13 0.0 1.0310 1.7890 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c4,p4=,X,h1,c4,p4=,n2=,h1,c4,p4=,n2= class2 0.0000 0.0 0.0000 0.0 -0.0680 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c4,p4=,X,h1,c4,p4=,n2=,h1,c4,p4=,n2= class2 mbt 0.0 0.0 0.0 1.8000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c4,p4=,X,h1,c4,p4=,n2=,h1,c4,p4=,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.5980 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c4,p4=,X,h1,c4,p4=,n2=,h1,c4,p4=,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.8860 119.3000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c4,p4=,X,h1,c4,p4=,n2=,h1,c4,p4=,n2= class2 aat 0.0 110.8860 119.3000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c4,p4=,X,h1,c4,p4=,n2=,h1,c4,p4=,n2= class2 bb13 0.0 1.1010 1.5980 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c4,p4=,X,h1,c4,p4=,h1,h1,c4,p4=,h1 class2 0.0000 0.0 0.0000 0.0 -0.0680 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c4,p4=,X,h1,c4,p4=,h1,h1,c4,p4=,h1 class2 mbt 0.0 0.0 0.0 1.8000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c4,p4=,X,h1,c4,p4=,h1,h1,c4,p4=,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.4300 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c4,p4=,X,h1,c4,p4=,h1,h1,c4,p4=,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.8860 102.9000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c4,p4=,X,h1,c4,p4=,h1,h1,c4,p4=,h1 class2 aat 0.0 110.8860 102.9000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c4,p4=,X,h1,c4,p4=,h1,h1,c4,p4=,h1 class2 bb13 0.0 1.1010 1.4300 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c4,p4=,X,h1,c4,p4=,c4,h1,c4,p4=,c4 class2 0.0000 0.0 0.0000 0.0 -0.0680 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c4,p4=,X,h1,c4,p4=,c4,h1,c4,p4=,c4 class2 mbt 0.0 0.0 0.0 1.8000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c4,p4=,X,h1,c4,p4=,c4,h1,c4,p4=,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.8000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c4,p4=,X,h1,c4,p4=,c4,h1,c4,p4=,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.8860 102.5000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c4,p4=,X,h1,c4,p4=,c4,h1,c4,p4=,c4 class2 aat 0.0 110.8860 102.5000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c4,p4=,X,h1,c4,p4=,c4,h1,c4,p4=,c4 class2 bb13 0.0 1.1010 1.8000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c4,n2=,X,h1,c4,n2=,h1,h1,c4,n2=,h1 class2 0.0000 0.0 0.0000 0.0 -0.0200 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c4,n2=,X,h1,c4,n2=,h1,h1,c4,n2=,h1 class2 mbt 0.0 0.0 0.0 1.4740 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c4,n2=,X,h1,c4,n2=,h1,h1,c4,n2=,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.0310 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c4,n2=,X,h1,c4,n2=,h1,h1,c4,n2=,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 107.4990 117.2000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c4,n2=,X,h1,c4,n2=,h1,h1,c4,n2=,h1 class2 aat 0.0 107.4990 117.2000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c4,n2=,X,h1,c4,n2=,h1,h1,c4,n2=,h1 class2 bb13 0.0 1.1010 1.0310 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c4,n2=,X,c4,c4,n2=,h1,c4,c4,n2=,h1 class2 0.0000 0.0 0.0000 0.0 -0.0200 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c4,n2=,X,c4,c4,n2=,h1,c4,c4,n2=,h1 class2 mbt 0.0 0.0 0.0 1.4740 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c4,n2=,X,c4,c4,n2=,h1,c4,c4,n2=,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5300 1.0310 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c4,n2=,X,c4,c4,n2=,h1,c4,c4,n2=,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.3170 117.2000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c4,n2=,X,c4,c4,n2=,h1,c4,c4,n2=,h1 class2 aat 0.0 117.3170 117.2000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c4,n2=,X,c4,c4,n2=,h1,c4,c4,n2=,h1 class2 bb13 0.0 1.5300 1.0310 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,o2,c3a,c3a,p4=,o2 class2 -0.2720 0.0 1.1900 0.0 0.0000 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,o2,c3a,c3a,p4=,o2 class2 mbt 0.0 0.0 0.0 1.7890 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,o2,c3a,c3a,p4=,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.6000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,o2,c3a,c3a,p4=,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0010 107.3650 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,o2,c3a,c3a,p4=,o2 class2 aat 0.0 120.0010 107.3650 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,o2,c3a,c3a,p4=,o2 class2 bb13 0.0 1.4170 1.6000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,n2=,c3a,c3a,p4=,n2= class2 -0.2720 0.0 1.1900 0.0 0.0000 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,n2=,c3a,c3a,p4=,n2= class2 mbt 0.0 0.0 0.0 1.7890 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,n2=,c3a,c3a,p4=,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.5980 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,n2=,c3a,c3a,p4=,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0010 109.6000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,n2=,c3a,c3a,p4=,n2= class2 aat 0.0 120.0010 109.6000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,n2=,c3a,c3a,p4=,n2= class2 bb13 0.0 1.4170 1.5980 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,h1,c3a,c3a,p4=,h1 class2 -0.2720 0.0 1.1900 0.0 0.0000 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,h1,c3a,c3a,p4=,h1 class2 mbt 0.0 0.0 0.0 1.7890 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,h1,c3a,c3a,p4=,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.4300 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,h1,c3a,c3a,p4=,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0010 108.2310 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,h1,c3a,c3a,p4=,h1 class2 aat 0.0 120.0010 108.2310 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,h1,c3a,c3a,p4=,h1 class2 bb13 0.0 1.4170 1.4300 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,c3a,c3a,c3a,p4=,c3a class2 -0.2720 0.0 1.1900 0.0 0.0000 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,c3a,c3a,c3a,p4=,c3a class2 mbt 0.0 0.0 0.0 1.7890 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,c3a,c3a,c3a,p4=,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.7890 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,c3a,c3a,c3a,p4=,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0010 110.2310 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,c3a,c3a,c3a,p4=,c3a class2 aat 0.0 120.0010 110.2310 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,c3a,c3a,c3a,p4=,c3a class2 bb13 0.0 1.4170 1.7890 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:n2=,p4=,n2=,p4=,n2=,p4=,n2=,p4=,n2=,p4=,n2=,p4= class2 1.8000 0.0 0.5000 0.0 2.0000 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:n2=,p4=,n2=,p4=,n2=,p4=,n2=,p4=,n2=,p4=,n2=,p4= class2 mbt 0.0000 0.0000 0.0000 1.5980 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:n2=,p4=,n2=,p4=,n2=,p4=,n2=,p4=,n2=,p4=,n2=,p4= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5980 1.5980 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:n2=,p4=,n2=,p4=,n2=,p4=,n2=,p4=,n2=,p4=,n2=,p4= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 125.0000 135.0000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:n2=,p4=,n2=,p4=,n2=,p4=,n2=,p4=,n2=,p4=,n2=,p4= class2 aat 0.0 125.0000 135.0000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:n2=,p4=,n2=,p4=,n2=,p4=,n2=,p4=,n2=,p4=,n2=,p4= class2 bb13 0.0 1.5980 1.5980 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,p4=,n2=,p4=,h1,p4=,n2=,p4=,h1,p4=,n2=,p4= class2 0.0000 0.0 0.0000 0.0 0.0000 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,p4=,n2=,p4=,h1,p4=,n2=,p4=,h1,p4=,n2=,p4= class2 mbt 0.0 0.0 0.0 1.5980 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,p4=,n2=,p4=,h1,p4=,n2=,p4=,h1,p4=,n2=,p4= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4300 1.5980 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,p4=,n2=,p4=,h1,p4=,n2=,p4=,h1,p4=,n2=,p4= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.0330 135.0000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,p4=,n2=,p4=,h1,p4=,n2=,p4=,h1,p4=,n2=,p4= class2 aat 0.0 110.0330 135.0000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,p4=,n2=,p4=,h1,p4=,n2=,p4=,h1,p4=,n2=,p4= class2 bb13 0.0 1.4300 1.5980 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,n2=,p4=,o2,h1,n2=,p4=,o2,h1,n2=,p4=,o2 class2 0.0000 0.0 0.0000 0.0 -0.3500 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,n2=,p4=,o2,h1,n2=,p4=,o2,h1,n2=,p4=,o2 class2 mbt 0.0 0.0 0.0 1.5980 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,n2=,p4=,o2,h1,n2=,p4=,o2,h1,n2=,p4=,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0310 1.6000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,n2=,p4=,o2,h1,n2=,p4=,o2,h1,n2=,p4=,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 112.2150 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,n2=,p4=,o2,h1,n2=,p4=,o2,h1,n2=,p4=,o2 class2 aat 0.0 120.0000 112.2150 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,n2=,p4=,o2,h1,n2=,p4=,o2,h1,n2=,p4=,o2 class2 bb13 0.0 1.0310 1.6000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,n2=,p4=,h1,h1,n2=,p4=,h1,h1,n2=,p4=,h1 class2 0.0000 0.0 0.0000 0.0 -0.3500 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,n2=,p4=,h1,h1,n2=,p4=,h1,h1,n2=,p4=,h1 class2 mbt 0.0 0.0 0.0 1.5980 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,n2=,p4=,h1,h1,n2=,p4=,h1,h1,n2=,p4=,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0310 1.4300 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,n2=,p4=,h1,h1,n2=,p4=,h1,h1,n2=,p4=,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 110.0330 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,n2=,p4=,h1,h1,n2=,p4=,h1,h1,n2=,p4=,h1 class2 aat -3.7880 120.0000 110.0330 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,n2=,p4=,h1,h1,n2=,p4=,h1,h1,n2=,p4=,h1 class2 bb13 0.0 1.0310 1.4300 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c4,p4=,n2=,h1,c4,p4=,n2=,h1,c4,p4=,n2=,h1 class2 0.0000 0.0 0.0000 0.0 -0.3690 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c4,p4=,n2=,h1,c4,p4=,n2=,h1,c4,p4=,n2=,h1 class2 mbt 0.0 0.0 0.0 1.5980 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c4,p4=,n2=,h1,c4,p4=,n2=,h1,c4,p4=,n2=,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8000 1.0310 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c4,p4=,n2=,h1,c4,p4=,n2=,h1,c4,p4=,n2=,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 119.3000 120.0000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c4,p4=,n2=,h1,c4,p4=,n2=,h1,c4,p4=,n2=,h1 class2 aat -11.1020 119.3000 120.0000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c4,p4=,n2=,h1,c4,p4=,n2=,h1,c4,p4=,n2=,h1 class2 bb13 0.0 1.8000 1.0310 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c3a,p4=,n2=,h1,c3a,p4=,n2=,h1,c3a,p4=,n2=,h1 class2 0.0000 0.0 0.0000 0.0 -0.3500 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c3a,p4=,n2=,h1,c3a,p4=,n2=,h1,c3a,p4=,n2=,h1 class2 mbt 0.0 0.0 0.0 1.5980 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c3a,p4=,n2=,h1,c3a,p4=,n2=,h1,c3a,p4=,n2=,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.7890 1.0310 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c3a,p4=,n2=,h1,c3a,p4=,n2=,h1,c3a,p4=,n2=,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 109.6000 120.0000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c3a,p4=,n2=,h1,c3a,p4=,n2=,h1,c3a,p4=,n2=,h1 class2 aat 0.0 109.6000 120.0000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c3a,p4=,n2=,h1,c3a,p4=,n2=,h1,c3a,p4=,n2=,h1 class2 bb13 0.0 1.7890 1.0310 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,c4,p4=,n2=,h1,c4,p4=,n2=,h1,c4,p4=,n2= class2 0.0000 0.0 0.0000 0.0 -0.0680 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,c4,p4=,n2=,h1,c4,p4=,n2=,h1,c4,p4=,n2= class2 mbt 0.0 0.0 0.0 1.8000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,c4,p4=,n2=,h1,c4,p4=,n2=,h1,c4,p4=,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.5980 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,c4,p4=,n2=,h1,c4,p4=,n2=,h1,c4,p4=,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.8860 119.3000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,c4,p4=,n2=,h1,c4,p4=,n2=,h1,c4,p4=,n2= class2 aat -19.9340 110.8860 119.3000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,c4,p4=,n2=,h1,c4,p4=,n2=,h1,c4,p4=,n2= class2 bb13 0.0 1.1010 1.5980 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,c4,p4=,h1,h1,c4,p4=,h1,h1,c4,p4=,h1 class2 0.0000 0.0 0.0000 0.0 -0.0680 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,c4,p4=,h1,h1,c4,p4=,h1,h1,c4,p4=,h1 class2 mbt 0.0 0.0 0.0 1.8000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,c4,p4=,h1,h1,c4,p4=,h1,h1,c4,p4=,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.4300 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,c4,p4=,h1,h1,c4,p4=,h1,h1,c4,p4=,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.8860 102.9000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,c4,p4=,h1,h1,c4,p4=,h1,h1,c4,p4=,h1 class2 aat -16.0180 110.8860 102.9000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,c4,p4=,h1,h1,c4,p4=,h1,h1,c4,p4=,h1 class2 bb13 0.0 1.1010 1.4300 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c4,p4=,c4,h1,c4,p4=,c4,h1,c4,p4=,c4,h1 class2 0.0000 0.0 0.0000 0.0 -0.0680 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c4,p4=,c4,h1,c4,p4=,c4,h1,c4,p4=,c4,h1 class2 mbt 0.0 0.0 0.0 1.8000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c4,p4=,c4,h1,c4,p4=,c4,h1,c4,p4=,c4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8000 1.1010 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c4,p4=,c4,h1,c4,p4=,c4,h1,c4,p4=,c4,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 102.5000 110.8860 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c4,p4=,c4,h1,c4,p4=,c4,h1,c4,p4=,c4,h1 class2 aat -25.5460 102.5000 110.8860 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c4,p4=,c4,h1,c4,p4=,c4,h1,c4,p4=,c4,h1 class2 bb13 0.0 1.8000 1.1010 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,c4,n2=,h1,h1,c4,n2=,h1,h1,c4,n2=,h1 class2 1.2660 0.0 -0.7740 0.0 0.0380 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,c4,n2=,h1,h1,c4,n2=,h1,h1,c4,n2=,h1 class2 mbt -0.4140 -2.8620 0.0070 1.4740 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,c4,n2=,h1,h1,c4,n2=,h1,h1,c4,n2=,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.0310 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,c4,n2=,h1,h1,c4,n2=,h1,h1,c4,n2=,h1 class2 at -1.8950 1.2210 -0.7460 0.1100 0.0650 0.1090 107.4990 117.2000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,c4,n2=,h1,h1,c4,n2=,h1,h1,c4,n2=,h1 class2 aat -9.6280 107.4990 117.2000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,c4,n2=,h1,h1,c4,n2=,h1,h1,c4,n2=,h1 class2 bb13 0.0 1.1010 1.0310 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c4,c4,n2=,h1,c4,c4,n2=,h1,c4,c4,n2=,h1 class2 -5.0720 0.0 -0.4980 0.0 -0.4380 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c4,c4,n2=,h1,c4,c4,n2=,h1,c4,c4,n2=,h1 class2 mbt -2.3800 2.5290 -0.7300 1.4740 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c4,c4,n2=,h1,c4,c4,n2=,h1,c4,c4,n2=,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5300 1.0310 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c4,c4,n2=,h1,c4,c4,n2=,h1,c4,c4,n2=,h1 class2 at -2.5230 2.8480 2.0590 -3.6920 4.0610 -1.5440 117.3170 117.2000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c4,c4,n2=,h1,c4,c4,n2=,h1,c4,c4,n2=,h1 class2 aat -8.8980 117.3170 117.2000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c4,c4,n2=,h1,c4,c4,n2=,h1,c4,c4,n2=,h1 class2 bb13 0.0 1.5300 1.0310 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,c4,c4,n2=,h1,c4,c4,n2=,h1,c4,c4,n2= class2 -0.1510 0.0 0.0100 0.0 -0.1860 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,c4,c4,n2=,h1,c4,c4,n2=,h1,c4,c4,n2= class2 mbt -3.5150 -2.2980 -1.2770 1.5300 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,c4,c4,n2=,h1,c4,c4,n2=,h1,c4,c4,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.4740 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,c4,c4,n2=,h1,c4,c4,n2=,h1,c4,c4,n2= class2 at -2.0980 1.8610 -1.6890 -0.1220 1.8930 -0.5670 110.7700 117.3170 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,c4,c4,n2=,h1,c4,c4,n2=,h1,c4,c4,n2= class2 aat -27.5060 110.7700 117.3170 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,c4,c4,n2=,h1,c4,c4,n2=,h1,c4,c4,n2= class2 bb13 0.0 1.1010 1.4740 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c4,c4,c4,n2=,c4,c4,c4,n2=,c4,c4,c4,n2= class2 0.0970 0.0 0.0720 0.0 -0.2580 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c4,c4,c4,n2=,c4,c4,c4,n2=,c4,c4,c4,n2= class2 mbt 0.0000 0.0000 0.0000 1.5300 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c4,c4,c4,n2=,c4,c4,c4,n2=,c4,c4,c4,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5300 1.4740 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c4,c4,c4,n2=,c4,c4,c4,n2=,c4,c4,c4,n2= class2 at -2.0980 1.8610 -1.6890 -0.1220 1.8930 -0.5670 112.6700 117.3170 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c4,c4,c4,n2=,c4,c4,c4,n2=,c4,c4,c4,n2= class2 aat 0.0000 112.6700 117.3170 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c4,c4,c4,n2=,c4,c4,c4,n2=,c4,c4,c4,n2= class2 bb13 0.0 1.5300 1.4740 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c3a,c3a,p4=,n2=,c3a,c3a,p4=,n2=,c3a,c3a,p4=,n2= class2 -0.2720 0.0 1.1900 0.0 0.0000 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c3a,c3a,p4=,n2=,c3a,c3a,p4=,n2=,c3a,c3a,p4=,n2= class2 mbt 0.0 0.0 0.0 1.7890 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c3a,c3a,p4=,n2=,c3a,c3a,p4=,n2=,c3a,c3a,p4=,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.5980 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c3a,c3a,p4=,n2=,c3a,c3a,p4=,n2=,c3a,c3a,p4=,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0010 109.6000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c3a,c3a,p4=,n2=,c3a,c3a,p4=,n2=,c3a,c3a,p4=,n2= class2 aat 0.0 120.0010 109.6000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c3a,c3a,p4=,n2=,c3a,c3a,p4=,n2=,c3a,c3a,p4=,n2= class2 bb13 0.0 1.4170 1.5980 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c3a,c3a,p4=,h1,c3a,c3a,p4=,h1,c3a,c3a,p4=,h1 class2 -0.2720 0.0 1.1900 0.0 0.0000 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c3a,c3a,p4=,h1,c3a,c3a,p4=,h1,c3a,c3a,p4=,h1 class2 mbt 0.0 0.0 0.0 1.7890 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c3a,c3a,p4=,h1,c3a,c3a,p4=,h1,c3a,c3a,p4=,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.4300 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c3a,c3a,p4=,h1,c3a,c3a,p4=,h1,c3a,c3a,p4=,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0010 108.2310 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c3a,c3a,p4=,h1,c3a,c3a,p4=,h1,c3a,c3a,p4=,h1 class2 aat 0.0 120.0010 108.2310 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c3a,c3a,p4=,h1,c3a,c3a,p4=,h1,c3a,c3a,p4=,h1 class2 bb13 0.0 1.4170 1.4300 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,c3a,c3a,p4=,h1,c3a,c3a,p4=,h1,c3a,c3a,p4= class2 0.0000 0.0 2.2700 0.0 0.0000 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,c3a,c3a,p4=,h1,c3a,c3a,p4=,h1,c3a,c3a,p4= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,c3a,c3a,p4=,h1,c3a,c3a,p4=,h1,c3a,c3a,p4= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0982 1.7890 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,c3a,c3a,p4=,h1,c3a,c3a,p4=,h1,c3a,c3a,p4= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.9400 120.0010 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,c3a,c3a,p4=,h1,c3a,c3a,p4=,h1,c3a,c3a,p4= class2 aat 0.0 117.9400 120.0010 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,c3a,c3a,p4=,h1,c3a,c3a,p4=,h1,c3a,c3a,p4= class2 bb13 0.0 1.0982 1.7890 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c3a,c3a,c3a,p4=,c3a,c3a,c3a,p4=,c3a,c3a,c3a,p4= class2 0.0000 0.0 5.4770 0.0 0.0000 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c3a,c3a,c3a,p4=,c3a,c3a,c3a,p4=,c3a,c3a,c3a,p4= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c3a,c3a,c3a,p4=,c3a,c3a,c3a,p4=,c3a,c3a,c3a,p4= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.7890 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c3a,c3a,c3a,p4=,c3a,c3a,c3a,p4=,c3a,c3a,c3a,p4= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.9000 120.0010 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c3a,c3a,c3a,p4=,c3a,c3a,c3a,p4=,c3a,c3a,c3a,p4= class2 aat 0.0 118.9000 120.0010 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c3a,c3a,c3a,p4=,c3a,c3a,c3a,p4=,c3a,c3a,c3a,p4= class2 bb13 0.0 1.4170 1.7890 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,c4,o2,h1,h1,c4,o2h,h1,h1,c4,o2,h1 class2 0.1863 0.0 -0.4338 0.0 -0.2121 0.0 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c4,o2,h1,h1,c4,o2h,h1,h1,c4,o2,h1 class2 mbt 0.0000 0.9241 -0.5889 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c4,o2,h1,h1,c4,o2h,h1,h1,c4,o2,h1 class2 ebt -1.7554 1.3145 0.2263 0.2493 0.6803 0.0000 1.1010 0.9494 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c4,o2,h1,h1,c4,o2h,h1,h1,c4,o2,h1 class2 at -3.4060 1.6396 0.0737 0.0000 -0.2810 -0.5944 108.7280 105.8000 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c4,o2,h1,h1,c4,o2h,h1,h1,c4,o2,h1 class2 aat -10.5093 108.7280 105.8000 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c4,o2,h1,h1,c4,o2h,h1,h1,c4,o2,h1 class2 bb13 0.0 1.1010 0.9494 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,o2,c4,h1,c4,o2h,c4,h1,c4,o2,c4,h1 class2 0.5302 0.0 0.0000 0.0 -0.3966 0.0 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,o2,c4,h1,c4,o2h,c4,h1,c4,o2,c4,h1 class2 mbt -6.8007 -4.6546 -1.4101 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,o2,c4,h1,c4,o2h,c4,h1,c4,o2,c4,h1 class2 ebt -0.1620 0.1564 -1.1408 -0.6054 1.3339 0.9648 1.4200 1.1010 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,o2,c4,h1,c4,o2h,c4,h1,c4,o2,c4,h1 class2 at -0.6653 0.4340 -0.7777 0.5144 1.6393 -1.8234 104.5000 108.7280 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,o2,c4,h1,c4,o2h,c4,h1,c4,o2,c4,h1 class2 aat -16.4438 104.5000 108.7280 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,o2,c4,h1,c4,o2h,c4,h1,c4,o2,c4,h1 class2 bb13 0.0 1.4200 1.1010 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,o2,c4,h1,c4,o2e,c4,h1,c4,o2,c4,h1 class2 0.5302 0.0 0.0000 0.0 -0.3966 0.0 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,o2,c4,h1,c4,o2e,c4,h1,c4,o2,c4,h1 class2 mbt -6.8007 -4.6546 -1.4101 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,o2,c4,h1,c4,o2e,c4,h1,c4,o2,c4,h1 class2 ebt -0.1620 0.1564 -1.1408 -0.6054 1.3339 0.9648 1.4200 1.1010 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,o2,c4,h1,c4,o2e,c4,h1,c4,o2,c4,h1 class2 at -0.6653 0.4340 -0.7777 0.5144 1.6393 -1.8234 104.5000 108.7280 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,o2,c4,h1,c4,o2e,c4,h1,c4,o2,c4,h1 class2 aat -16.4438 104.5000 108.7280 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,o2,c4,h1,c4,o2e,c4,h1,c4,o2,c4,h1 class2 bb13 0.0 1.4200 1.1010 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,o2,c4,h1,c3a,o2h,c4,h1,c3a,o2,c4,h1 class2 0.9513 0.0 0.1155 0.0 0.0720 0.0 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,o2,c4,h1,c3a,o2h,c4,h1,c3a,o2,c4,h1 class2 mbt 0.0 0.0 0.0 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,o2,c4,h1,c3a,o2h,c4,h1,c3a,o2,c4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.1010 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,o2,c4,h1,c3a,o2h,c4,h1,c3a,o2,c4,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 102.9695 108.7280 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,o2,c4,h1,c3a,o2h,c4,h1,c3a,o2,c4,h1 class2 aat 0.0 102.9695 108.7280 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,o2,c4,h1,c3a,o2h,c4,h1,c3a,o2,c4,h1 class2 bb13 0.0 1.3768 1.1010 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,o2,c4,h1,c3a,o2e,c4,h1,c3a,o2,c4,h1 class2 0.9513 0.0 0.1155 0.0 0.0720 0.0 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,o2,c4,h1,c3a,o2e,c4,h1,c3a,o2,c4,h1 class2 mbt 0.0 0.0 0.0 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,o2,c4,h1,c3a,o2e,c4,h1,c3a,o2,c4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.1010 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,o2,c4,h1,c3a,o2e,c4,h1,c3a,o2,c4,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 102.9695 108.7280 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,o2,c4,h1,c3a,o2e,c4,h1,c3a,o2,c4,h1 class2 aat 0.0 102.9695 108.7280 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,o2,c4,h1,c3a,o2e,c4,h1,c3a,o2,c4,h1 class2 bb13 0.0 1.3768 1.1010 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,o2,h1,c4,c4,o2h,h1,c4,c4,o2,h1 class2 -0.6732 0.0 -0.4778 0.0 -0.1670 0.0 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,o2,h1,c4,c4,o2h,h1,c4,c4,o2,h1 class2 mbt 1.2472 0.0000 0.7485 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,o2,h1,c4,c4,o2h,h1,c4,c4,o2,h1 class2 ebt -0.5800 0.9004 0.0000 0.0000 0.5343 0.9025 1.5300 0.9494 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,o2,h1,c4,c4,o2h,h1,c4,c4,o2,h1 class2 at -3.5903 2.5225 0.4888 0.8726 -0.3577 0.3888 111.2700 105.8000 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,o2,h1,c4,c4,o2h,h1,c4,c4,o2,h1 class2 aat -12.1038 111.2700 105.8000 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,o2,h1,c4,c4,o2h,h1,c4,c4,o2,h1 class2 bb13 0.0 1.5300 0.9494 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,o2,c4,c4,c4,o2h,c4,c4,c4,o2,c4 class2 -0.4000 0.0 -0.4028 0.0 -0.2450 0.0 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,o2,c4,c4,c4,o2h,c4,c4,c4,o2,c4 class2 mbt -5.9288 -2.7007 -0.3175 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,o2,c4,c4,c4,o2h,c4,c4,c4,o2,c4 class2 ebt -0.2456 1.0517 -0.7795 0.4741 1.2635 0.5576 1.5300 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,o2,c4,c4,c4,o2h,c4,c4,c4,o2,c4 class2 at -2.7466 1.4877 -0.8955 0.5676 0.9450 0.0703 111.2700 104.5000 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,o2,c4,c4,c4,o2h,c4,c4,c4,o2,c4 class2 aat -19.0059 111.2700 104.5000 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,o2,c4,c4,c4,o2h,c4,c4,c4,o2,c4 class2 bb13 0.0 1.5300 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,o2,c4,c4,c4,o2e,c4,c4,c4,o2,c4 class2 -0.4000 0.0 -0.4028 0.0 -0.2450 0.0 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,o2,c4,c4,c4,o2e,c4,c4,c4,o2,c4 class2 mbt -5.9288 -2.7007 -0.3175 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,o2,c4,c4,c4,o2e,c4,c4,c4,o2,c4 class2 ebt -0.2456 1.0517 -0.7795 0.4741 1.2635 0.5576 1.5300 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,o2,c4,c4,c4,o2e,c4,c4,c4,o2,c4 class2 at -2.7466 1.4877 -0.8955 0.5676 0.9450 0.0703 111.2700 104.5000 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,o2,c4,c4,c4,o2e,c4,c4,c4,o2,c4 class2 aat -19.0059 111.2700 104.5000 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,o2,c4,c4,c4,o2e,c4,c4,c4,o2,c4 class2 bb13 0.0 1.5300 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2n,c4,c4,o2n,o2n,c4,c4,o2n class2 1.1000 0.0 -0.0500 0.0 -0.1441 0.0 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2n,c4,c4,o2n,o2n,c4,c4,o2n class2 mbt -17.2585 -3.6157 -0.8364 1.5300 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2n,c4,c4,o2n,o2n,c4,c4,o2n class2 ebt 1.0165 0.7553 -0.4609 1.0165 0.7553 -0.4609 1.4350 1.4350 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2n,c4,c4,o2n,o2n,c4,c4,o2n class2 at 0.5511 0.9737 -0.6673 0.5511 0.9737 -0.6673 105.0000 105.0000 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2n,c4,c4,o2n,o2n,c4,c4,o2n class2 aat -14.0484 105.0000 105.0000 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2n,c4,c4,o2n,o2n,c4,c4,o2n class2 bb13 0.0 1.4350 1.4350 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2n,c4,c4,o2h,o2n,c4,c4,o2 class2 1.1000 0.0 -0.0500 0.0 -0.1441 0.0 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2n,c4,c4,o2h,o2n,c4,c4,o2 class2 mbt -17.2585 -3.6157 -0.8364 1.5300 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2n,c4,c4,o2h,o2n,c4,c4,o2 class2 ebt 1.0165 0.7553 -0.4609 1.0165 0.7553 -0.4609 1.4350 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2n,c4,c4,o2h,o2n,c4,c4,o2 class2 at 0.5511 0.9737 -0.6673 0.5511 0.9737 -0.6673 105.0000 111.2700 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2n,c4,c4,o2h,o2n,c4,c4,o2 class2 aat -14.0484 105.0000 111.2700 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2n,c4,c4,o2h,o2n,c4,c4,o2 class2 bb13 0.0 1.4350 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2n,c4,c4,o2e,o2n,c4,c4,o2 class2 1.1000 0.0 -0.0500 0.0 -0.1441 0.0 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2n,c4,c4,o2e,o2n,c4,c4,o2 class2 mbt -17.2585 -3.6157 -0.8364 1.5300 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2n,c4,c4,o2e,o2n,c4,c4,o2 class2 ebt 1.0165 0.7553 -0.4609 1.0165 0.7553 -0.4609 1.4350 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2n,c4,c4,o2e,o2n,c4,c4,o2 class2 at 0.5511 0.9737 -0.6673 0.5511 0.9737 -0.6673 105.0000 111.2700 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2n,c4,c4,o2e,o2n,c4,c4,o2 class2 aat -14.0484 105.0000 111.2700 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2n,c4,c4,o2e,o2n,c4,c4,o2 class2 bb13 0.0 1.4350 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2h,c4,c4,o2n,o2,c4,c4,o2n class2 1.1000 0.0 -0.0500 0.0 -0.1441 0.0 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2h,c4,c4,o2n,o2,c4,c4,o2n class2 mbt -17.2585 -3.6157 -0.8364 1.5300 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2h,c4,c4,o2n,o2,c4,c4,o2n class2 ebt 1.0165 0.7553 -0.4609 1.0165 0.7553 -0.4609 1.4200 1.4350 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2h,c4,c4,o2n,o2,c4,c4,o2n class2 at 0.5511 0.9737 -0.6673 0.5511 0.9737 -0.6673 111.2700 105.0000 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2h,c4,c4,o2n,o2,c4,c4,o2n class2 aat -14.0484 111.2700 105.0000 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2h,c4,c4,o2n,o2,c4,c4,o2n class2 bb13 0.0 1.4200 1.4350 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2h,c4,c4,o2h,o2,c4,c4,o2 class2 1.1000 0.0 -0.0500 0.0 -0.1441 0.0 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2h,c4,c4,o2h,o2,c4,c4,o2 class2 mbt -17.2585 -3.6157 -0.8364 1.5300 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2h,c4,c4,o2h,o2,c4,c4,o2 class2 ebt 1.0165 0.7553 -0.4609 1.0165 0.7553 -0.4609 1.4200 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2h,c4,c4,o2h,o2,c4,c4,o2 class2 at 0.5511 0.9737 -0.6673 0.5511 0.9737 -0.6673 111.2700 111.2700 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2h,c4,c4,o2h,o2,c4,c4,o2 class2 aat -14.0484 111.2700 111.2700 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2h,c4,c4,o2h,o2,c4,c4,o2 class2 bb13 0.0 1.4200 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2h,c4,c4,o2e,o2,c4,c4,o2 class2 1.1000 0.0 -0.0500 0.0 -0.1441 0.0 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2h,c4,c4,o2e,o2,c4,c4,o2 class2 mbt -17.2585 -3.6157 -0.8364 1.5300 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2h,c4,c4,o2e,o2,c4,c4,o2 class2 ebt 1.0165 0.7553 -0.4609 1.0165 0.7553 -0.4609 1.4200 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2h,c4,c4,o2e,o2,c4,c4,o2 class2 at 0.5511 0.9737 -0.6673 0.5511 0.9737 -0.6673 111.2700 111.2700 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2h,c4,c4,o2e,o2,c4,c4,o2 class2 aat -14.0484 111.2700 111.2700 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2h,c4,c4,o2e,o2,c4,c4,o2 class2 bb13 0.0 1.4200 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2e,c4,c4,o2n,o2,c4,c4,o2n class2 1.1000 0.0 -0.0500 0.0 -0.1441 0.0 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2e,c4,c4,o2n,o2,c4,c4,o2n class2 mbt -17.2585 -3.6157 -0.8364 1.5300 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2e,c4,c4,o2n,o2,c4,c4,o2n class2 ebt 1.0165 0.7553 -0.4609 1.0165 0.7553 -0.4609 1.4200 1.4350 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2e,c4,c4,o2n,o2,c4,c4,o2n class2 at 0.5511 0.9737 -0.6673 0.5511 0.9737 -0.6673 111.2700 105.0000 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2e,c4,c4,o2n,o2,c4,c4,o2n class2 aat -14.0484 111.2700 105.0000 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2e,c4,c4,o2n,o2,c4,c4,o2n class2 bb13 0.0 1.4200 1.4350 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2e,c4,c4,o2h,o2,c4,c4,o2 class2 1.1000 0.0 -0.0500 0.0 -0.1441 0.0 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2e,c4,c4,o2h,o2,c4,c4,o2 class2 mbt -17.2585 -3.6157 -0.8364 1.5300 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2e,c4,c4,o2h,o2,c4,c4,o2 class2 ebt 1.0165 0.7553 -0.4609 1.0165 0.7553 -0.4609 1.4200 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2e,c4,c4,o2h,o2,c4,c4,o2 class2 at 0.5511 0.9737 -0.6673 0.5511 0.9737 -0.6673 111.2700 111.2700 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2e,c4,c4,o2h,o2,c4,c4,o2 class2 aat -14.0484 111.2700 111.2700 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2e,c4,c4,o2h,o2,c4,c4,o2 class2 bb13 0.0 1.4200 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2e,c4,c4,o2e,o2,c4,c4,o2 class2 1.1000 0.0 -0.0500 0.0 -0.1441 0.0 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2e,c4,c4,o2e,o2,c4,c4,o2 class2 mbt -17.2585 -3.6157 -0.8364 1.5300 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2e,c4,c4,o2e,o2,c4,c4,o2 class2 ebt 1.0165 0.7553 -0.4609 1.0165 0.7553 -0.4609 1.4200 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2e,c4,c4,o2e,o2,c4,c4,o2 class2 at 0.5511 0.9737 -0.6673 0.5511 0.9737 -0.6673 111.2700 111.2700 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2e,c4,c4,o2e,o2,c4,c4,o2 class2 aat -14.0484 111.2700 111.2700 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2e,c4,c4,o2e,o2,c4,c4,o2 class2 bb13 0.0 1.4200 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c4,c4,o2,h1,c4,c4,o2n,h1,c4,c4,o2n class2 -0.1435 0.0 0.2530 0.0 -0.0905 0.0 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c4,c4,o2,h1,c4,c4,o2n,h1,c4,c4,o2n class2 mbt -16.7975 -1.2296 -0.2750 1.5300 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c4,c4,o2,h1,c4,c4,o2n,h1,c4,c4,o2n class2 ebt 0.9681 0.9551 0.0436 0.5903 0.6669 0.8584 1.1010 1.4350 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c4,c4,o2,h1,c4,c4,o2n,h1,c4,c4,o2n class2 at 2.3668 2.4920 -1.0122 -0.1892 0.4918 0.7273 110.7700 105.0000 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c4,c4,o2,h1,c4,c4,o2n,h1,c4,c4,o2n class2 aat -20.2006 110.7700 105.0000 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c4,c4,o2,h1,c4,c4,o2n,h1,c4,c4,o2n class2 bb13 0.0 1.1010 1.4350 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c4,c4,o2,h1,c4,c4,o2h,h1,c4,c4,o2 class2 -0.1435 0.0 0.2530 0.0 -0.0905 0.0 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c4,c4,o2,h1,c4,c4,o2h,h1,c4,c4,o2 class2 mbt -16.7975 -1.2296 -0.2750 1.5300 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c4,c4,o2,h1,c4,c4,o2h,h1,c4,c4,o2 class2 ebt 0.9681 0.9551 0.0436 0.5903 0.6669 0.8584 1.1010 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c4,c4,o2,h1,c4,c4,o2h,h1,c4,c4,o2 class2 at 2.3668 2.4920 -1.0122 -0.1892 0.4918 0.7273 110.7700 111.2700 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c4,c4,o2,h1,c4,c4,o2h,h1,c4,c4,o2 class2 aat -20.2006 110.7700 111.2700 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c4,c4,o2,h1,c4,c4,o2h,h1,c4,c4,o2 class2 bb13 0.0 1.1010 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c4,c4,o2,h1,c4,c4,o2e,h1,c4,c4,o2 class2 -0.1435 0.0 0.2530 0.0 -0.0905 0.0 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c4,c4,o2,h1,c4,c4,o2e,h1,c4,c4,o2 class2 mbt -16.7975 -1.2296 -0.2750 1.5300 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c4,c4,o2,h1,c4,c4,o2e,h1,c4,c4,o2 class2 ebt 0.9681 0.9551 0.0436 0.5903 0.6669 0.8584 1.1010 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c4,c4,o2,h1,c4,c4,o2e,h1,c4,c4,o2 class2 at 2.3668 2.4920 -1.0122 -0.1892 0.4918 0.7273 110.7700 111.2700 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c4,c4,o2,h1,c4,c4,o2e,h1,c4,c4,o2 class2 aat -20.2006 110.7700 111.2700 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c4,c4,o2,h1,c4,c4,o2e,h1,c4,c4,o2 class2 bb13 0.0 1.1010 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,c4,o2,c4,c4,c4,o2n,c4,c4,c4,o2n class2 0.7137 0.0 0.2660 0.0 -0.2545 0.0 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,c4,o2,c4,c4,c4,o2n,c4,c4,c4,o2n class2 mbt -21.8842 -7.6764 -0.6868 1.5300 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,c4,o2,c4,c4,c4,o2n,c4,c4,c4,o2n class2 ebt -0.3190 0.4411 -0.7174 1.1538 0.8409 -0.9138 1.5300 1.4350 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,c4,o2,c4,c4,c4,o2n,c4,c4,c4,o2n class2 at 0.5623 -0.3041 -0.4015 0.9672 -0.7566 -1.2331 112.6700 105.0000 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,c4,o2,c4,c4,c4,o2n,c4,c4,c4,o2n class2 aat -29.0420 112.6700 105.0000 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,c4,o2,c4,c4,c4,o2n,c4,c4,c4,o2n class2 bb13 0.0 1.5300 1.4350 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,c4,o2,c4,c4,c4,o2h,c4,c4,c4,o2 class2 0.7137 0.0 0.2660 0.0 -0.2545 0.0 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,c4,o2,c4,c4,c4,o2h,c4,c4,c4,o2 class2 mbt -21.8842 -7.6764 -0.6868 1.5300 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,c4,o2,c4,c4,c4,o2h,c4,c4,c4,o2 class2 ebt -0.3190 0.4411 -0.7174 1.1538 0.8409 -0.9138 1.5300 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,c4,o2,c4,c4,c4,o2h,c4,c4,c4,o2 class2 at 0.5623 -0.3041 -0.4015 0.9672 -0.7566 -1.2331 112.6700 111.2700 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,c4,o2,c4,c4,c4,o2h,c4,c4,c4,o2 class2 aat -29.0420 112.6700 111.2700 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,c4,o2,c4,c4,c4,o2h,c4,c4,c4,o2 class2 bb13 0.0 1.5300 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,c4,o2,c4,c4,c4,o2e,c4,c4,c4,o2 class2 0.7137 0.0 0.2660 0.0 -0.2545 0.0 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,c4,o2,c4,c4,c4,o2e,c4,c4,c4,o2 class2 mbt -21.8842 -7.6764 -0.6868 1.5300 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,c4,o2,c4,c4,c4,o2e,c4,c4,c4,o2 class2 ebt -0.3190 0.4411 -0.7174 1.1538 0.8409 -0.9138 1.5300 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,c4,o2,c4,c4,c4,o2e,c4,c4,c4,o2 class2 at 0.5623 -0.3041 -0.4015 0.9672 -0.7566 -1.2331 112.6700 111.2700 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,c4,o2,c4,c4,c4,o2e,c4,c4,c4,o2 class2 aat -29.0420 112.6700 111.2700 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,c4,o2,c4,c4,c4,o2e,c4,c4,c4,o2 class2 bb13 0.0 1.5300 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,o2,c4,c3a,c3a,o2h,c4,c3a,c3a,o2,c4 class2 0.0000 0.0 1.5000 0.0 0.0000 0.0 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,o2,c4,c3a,c3a,o2h,c4,c3a,c3a,o2,c4 class2 mbt 0.0 0.0 0.0 1.3768 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,o2,c4,c3a,c3a,o2h,c4,c3a,c3a,o2,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,o2,c4,c3a,c3a,o2h,c4,c3a,c3a,o2,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 102.9695 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,o2,c4,c3a,c3a,o2h,c4,c3a,c3a,o2,c4 class2 aat 0.0 123.4200 102.9695 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,o2,c4,c3a,c3a,o2h,c4,c3a,c3a,o2,c4 class2 bb13 0.0 1.4170 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,o2,c4,c3a,c3a,o2e,c4,c3a,c3a,o2,c4 class2 0.0000 0.0 1.5000 0.0 0.0000 0.0 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,o2,c4,c3a,c3a,o2e,c4,c3a,c3a,o2,c4 class2 mbt 0.0 0.0 0.0 1.3768 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,o2,c4,c3a,c3a,o2e,c4,c3a,c3a,o2,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,o2,c4,c3a,c3a,o2e,c4,c3a,c3a,o2,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 102.9695 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,o2,c4,c3a,c3a,o2e,c4,c3a,c3a,o2,c4 class2 aat 0.0 123.4200 102.9695 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,o2,c4,c3a,c3a,o2e,c4,c3a,c3a,o2,c4 class2 bb13 0.0 1.4170 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,o2z,si4,o2z,si4,o2z class2 0.0000 0.0 0.0000 0.0 -0.0100 0.0 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,o2z,si4,o2z,si4,o2z class2 mbt 0.0 0.0 0.0 1.6400 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,o2z,si4,o2z,si4,o2z class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.6400 1.6400 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,o2z,si4,o2z,si4,o2z class2 at 0.0 0.0 0.0 0.0 0.0 0.0 159.0000 110.7000 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,o2z,si4,o2z,si4,o2z class2 aat 0.0 159.0000 110.7000 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,o2z,si4,o2z,si4,o2z class2 bb13 0.0 1.6400 1.6400 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,h1,si4,o2z,si4,h1 class2 0.0000 0.0 0.0000 0.0 -0.0100 0.0 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,h1,si4,o2z,si4,h1 class2 mbt 0.0 0.0 0.0 1.6400 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,h1,si4,o2z,si4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.6400 1.4783 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,h1,si4,o2z,si4,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 159.0000 107.4000 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,h1,si4,o2z,si4,h1 class2 aat 0.0 159.0000 107.4000 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,h1,si4,o2z,si4,h1 class2 bb13 0.0 1.6400 1.4783 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,c4,si4,o2z,si4,c4 class2 0.0000 0.0 0.0000 0.0 -0.0100 0.0 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,c4,si4,o2z,si4,c4 class2 mbt 0.0 0.0 0.0 1.6400 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,c4,si4,o2z,si4,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.6400 1.8995 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,c4,si4,o2z,si4,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 159.0000 114.9060 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,c4,si4,o2z,si4,c4 class2 aat 0.0 159.0000 114.9060 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,c4,si4,o2z,si4,c4 class2 bb13 0.0 1.6400 1.8995 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,c3a,si4,o2z,si4,c3a class2 0.0000 0.0 0.0000 0.0 -0.0100 0.0 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,c3a,si4,o2z,si4,c3a class2 mbt 0.0 0.0 0.0 1.6400 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,c3a,si4,o2z,si4,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.6400 1.8634 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,c3a,si4,o2z,si4,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 159.0000 114.9060 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,c3a,si4,o2z,si4,c3a class2 aat 0.0 159.0000 114.9060 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,c3a,si4,o2z,si4,c3a class2 bb13 0.0 1.6400 1.8634 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:o2z,si4,o2z,si4,o2z,si4,o2z,si4,o2z,si4,o2z,si4 class2 -0.2250 0.0 0.0000 0.0 -0.0100 0.0 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:o2z,si4,o2z,si4,o2z,si4,o2z,si4,o2z,si4,o2z,si4 class2 mbt 0.0 0.0 0.0 1.6400 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:o2z,si4,o2z,si4,o2z,si4,o2z,si4,o2z,si4,o2z,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.6400 1.6400 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:o2z,si4,o2z,si4,o2z,si4,o2z,si4,o2z,si4,o2z,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.7000 159.0000 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:o2z,si4,o2z,si4,o2z,si4,o2z,si4,o2z,si4,o2z,si4 class2 aat 0.0 110.7000 159.0000 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:o2z,si4,o2z,si4,o2z,si4,o2z,si4,o2z,si4,o2z,si4 class2 bb13 0.0 1.6400 1.6400 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:h1,si4,o2z,si4,h1,si4,o2z,si4,h1,si4,o2z,si4 class2 0.0000 0.0 0.0000 0.0 -0.0100 0.0 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:h1,si4,o2z,si4,h1,si4,o2z,si4,h1,si4,o2z,si4 class2 mbt 0.0 0.0 0.0 1.6400 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:h1,si4,o2z,si4,h1,si4,o2z,si4,h1,si4,o2z,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4783 1.6400 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:h1,si4,o2z,si4,h1,si4,o2z,si4,h1,si4,o2z,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 107.4000 159.0000 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:h1,si4,o2z,si4,h1,si4,o2z,si4,h1,si4,o2z,si4 class2 aat 0.0 107.4000 159.0000 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:h1,si4,o2z,si4,h1,si4,o2z,si4,h1,si4,o2z,si4 class2 bb13 0.0 1.4783 1.6400 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:c4,si4,o2z,si4,c4,si4,o2z,si4,c4,si4,o2z,si4 class2 0.0000 0.0 0.0000 0.0 -0.0100 0.0 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:c4,si4,o2z,si4,c4,si4,o2z,si4,c4,si4,o2z,si4 class2 mbt 0.0 0.0 0.0 1.6400 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:c4,si4,o2z,si4,c4,si4,o2z,si4,c4,si4,o2z,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8995 1.6400 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:c4,si4,o2z,si4,c4,si4,o2z,si4,c4,si4,o2z,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 114.9060 159.0000 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:c4,si4,o2z,si4,c4,si4,o2z,si4,c4,si4,o2z,si4 class2 aat 0.0 114.9060 159.0000 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:c4,si4,o2z,si4,c4,si4,o2z,si4,c4,si4,o2z,si4 class2 bb13 0.0 1.8995 1.6400 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,si4,si4,c4,c4,si4 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,si4,si4,c4,c4,si4 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,si4,si4,c4,c4,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8995 1.8995 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,si4,si4,c4,c4,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.6700 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,si4,si4,c4,c4,si4 class2 aat 0.0 112.6700 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,si4,si4,c4,c4,si4 class2 bb13 0.0 1.8995 1.8995 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,o2n,si4,c4,c4,o2n class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,o2n,si4,c4,c4,o2n class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,o2n,si4,c4,c4,o2n class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8995 1.4350 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,o2n,si4,c4,c4,o2n class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.6700 105.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,o2n,si4,c4,c4,o2n class2 aat 0.0 112.6700 105.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,o2n,si4,c4,c4,o2n class2 bb13 0.0 1.8995 1.4350 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,o2h,si4,c4,c4,o2 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,o2h,si4,c4,c4,o2 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,o2h,si4,c4,c4,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8995 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,o2h,si4,c4,c4,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.6700 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,o2h,si4,c4,c4,o2 class2 aat 0.0 112.6700 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,o2h,si4,c4,c4,o2 class2 bb13 0.0 1.8995 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,o2e,si4,c4,c4,o2 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,o2e,si4,c4,c4,o2 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,o2e,si4,c4,c4,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8995 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,o2e,si4,c4,c4,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.6700 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,o2e,si4,c4,c4,o2 class2 aat 0.0 112.6700 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,o2e,si4,c4,c4,o2 class2 bb13 0.0 1.8995 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,n2z,si4,c4,c4,n2z class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,n2z,si4,c4,c4,n2z class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,n2z,si4,c4,c4,n2z class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8995 1.4814 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,n2z,si4,c4,c4,n2z class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.6700 110.9900 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,n2z,si4,c4,c4,n2z class2 aat 0.0 112.6700 110.9900 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,n2z,si4,c4,c4,n2z class2 bb13 0.0 1.8995 1.4814 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,n2=,si4,c4,c4,n2= class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,n2=,si4,c4,c4,n2= class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,n2=,si4,c4,c4,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8995 1.4740 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,n2=,si4,c4,c4,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.6700 117.3170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,n2=,si4,c4,c4,n2= class2 aat 0.0 112.6700 117.3170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,n2=,si4,c4,c4,n2= class2 bb13 0.0 1.8995 1.4740 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,h1,si4,c4,c4,h1 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,h1,si4,c4,c4,h1 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,h1,si4,c4,c4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8995 1.1010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,h1,si4,c4,c4,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.6700 110.7700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,h1,si4,c4,c4,h1 class2 aat 0.0 112.6700 110.7700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,h1,si4,c4,c4,h1 class2 bb13 0.0 1.8995 1.1010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,c4,si4,c4,c4,c4 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,c4,si4,c4,c4,c4 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,c4,si4,c4,c4,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8995 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,c4,si4,c4,c4,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.6700 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,c4,si4,c4,c4,c4 class2 aat 0.0 112.6700 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,c4,si4,c4,c4,c4 class2 bb13 0.0 1.8995 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,c3a,si4,c4,c4,c3a class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,c3a,si4,c4,c4,c3a class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,c3a,si4,c4,c4,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8995 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,c3a,si4,c4,c4,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.6700 108.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,c3a,si4,c4,c4,c3a class2 aat 0.0 112.6700 108.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,c3a,si4,c4,c4,c3a class2 bb13 0.0 1.8995 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,si4,o2n,c4,c4,si4 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,si4,o2n,c4,c4,si4 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,si4,o2n,c4,c4,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4350 1.8995 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,si4,o2n,c4,c4,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 105.0000 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,si4,o2n,c4,c4,si4 class2 aat 0.0 105.0000 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,si4,o2n,c4,c4,si4 class2 bb13 0.0 1.4350 1.8995 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,o2n,o2n,c4,c4,o2n class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,o2n,o2n,c4,c4,o2n class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,o2n,o2n,c4,c4,o2n class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4350 1.4350 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,o2n,o2n,c4,c4,o2n class2 at 0.0 0.0 0.0 0.0 0.0 0.0 105.0000 105.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,o2n,o2n,c4,c4,o2n class2 aat 0.0 105.0000 105.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,o2n,o2n,c4,c4,o2n class2 bb13 0.0 1.4350 1.4350 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,o2h,o2n,c4,c4,o2 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,o2h,o2n,c4,c4,o2 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,o2h,o2n,c4,c4,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4350 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,o2h,o2n,c4,c4,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 105.0000 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,o2h,o2n,c4,c4,o2 class2 aat 0.0 105.0000 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,o2h,o2n,c4,c4,o2 class2 bb13 0.0 1.4350 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,o2e,o2n,c4,c4,o2 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,o2e,o2n,c4,c4,o2 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,o2e,o2n,c4,c4,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4350 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,o2e,o2n,c4,c4,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 105.0000 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,o2e,o2n,c4,c4,o2 class2 aat 0.0 105.0000 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,o2e,o2n,c4,c4,o2 class2 bb13 0.0 1.4350 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,n2z,o2n,c4,c4,n2z class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,n2z,o2n,c4,c4,n2z class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,n2z,o2n,c4,c4,n2z class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4350 1.4814 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,n2z,o2n,c4,c4,n2z class2 at 0.0 0.0 0.0 0.0 0.0 0.0 105.0000 110.9900 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,n2z,o2n,c4,c4,n2z class2 aat 0.0 105.0000 110.9900 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,n2z,o2n,c4,c4,n2z class2 bb13 0.0 1.4350 1.4814 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,n2=,o2n,c4,c4,n2= class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,n2=,o2n,c4,c4,n2= class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,n2=,o2n,c4,c4,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4350 1.4740 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,n2=,o2n,c4,c4,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 105.0000 117.3170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,n2=,o2n,c4,c4,n2= class2 aat 0.0 105.0000 117.3170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,n2=,o2n,c4,c4,n2= class2 bb13 0.0 1.4350 1.4740 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,h1,o2n,c4,c4,h1 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,h1,o2n,c4,c4,h1 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,h1,o2n,c4,c4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4350 1.1010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,h1,o2n,c4,c4,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 105.0000 110.7700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,h1,o2n,c4,c4,h1 class2 aat 0.0 105.0000 110.7700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,h1,o2n,c4,c4,h1 class2 bb13 0.0 1.4350 1.1010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,c4,o2n,c4,c4,c4 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,c4,o2n,c4,c4,c4 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,c4,o2n,c4,c4,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4350 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,c4,o2n,c4,c4,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 105.0000 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,c4,o2n,c4,c4,c4 class2 aat 0.0 105.0000 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,c4,o2n,c4,c4,c4 class2 bb13 0.0 1.4350 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,c3a,o2n,c4,c4,c3a class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,c3a,o2n,c4,c4,c3a class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,c3a,o2n,c4,c4,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4350 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,c3a,o2n,c4,c4,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 105.0000 108.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,c3a,o2n,c4,c4,c3a class2 aat 0.0 105.0000 108.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,c3a,o2n,c4,c4,c3a class2 bb13 0.0 1.4350 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,si4,o2,c4,c4,si4 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,si4,o2,c4,c4,si4 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,si4,o2,c4,c4,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4200 1.8995 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,si4,o2,c4,c4,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 111.2700 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,si4,o2,c4,c4,si4 class2 aat 0.0 111.2700 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,si4,o2,c4,c4,si4 class2 bb13 0.0 1.4200 1.8995 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,o2n,o2,c4,c4,o2n class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,o2n,o2,c4,c4,o2n class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,o2n,o2,c4,c4,o2n class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4200 1.4350 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,o2n,o2,c4,c4,o2n class2 at 0.0 0.0 0.0 0.0 0.0 0.0 111.2700 105.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,o2n,o2,c4,c4,o2n class2 aat 0.0 111.2700 105.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,o2n,o2,c4,c4,o2n class2 bb13 0.0 1.4200 1.4350 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,o2h,o2,c4,c4,o2 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,o2h,o2,c4,c4,o2 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,o2h,o2,c4,c4,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4200 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,o2h,o2,c4,c4,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 111.2700 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,o2h,o2,c4,c4,o2 class2 aat 0.0 111.2700 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,o2h,o2,c4,c4,o2 class2 bb13 0.0 1.4200 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,o2e,o2,c4,c4,o2 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,o2e,o2,c4,c4,o2 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,o2e,o2,c4,c4,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4200 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,o2e,o2,c4,c4,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 111.2700 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,o2e,o2,c4,c4,o2 class2 aat 0.0 111.2700 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,o2e,o2,c4,c4,o2 class2 bb13 0.0 1.4200 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,n2z,o2,c4,c4,n2z class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,n2z,o2,c4,c4,n2z class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,n2z,o2,c4,c4,n2z class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4200 1.4814 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,n2z,o2,c4,c4,n2z class2 at 0.0 0.0 0.0 0.0 0.0 0.0 111.2700 110.9900 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,n2z,o2,c4,c4,n2z class2 aat 0.0 111.2700 110.9900 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,n2z,o2,c4,c4,n2z class2 bb13 0.0 1.4200 1.4814 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,n2=,o2,c4,c4,n2= class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,n2=,o2,c4,c4,n2= class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,n2=,o2,c4,c4,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4200 1.4740 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,n2=,o2,c4,c4,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 111.2700 117.3170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,n2=,o2,c4,c4,n2= class2 aat 0.0 111.2700 117.3170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,n2=,o2,c4,c4,n2= class2 bb13 0.0 1.4200 1.4740 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,h1,o2,c4,c4,h1 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,h1,o2,c4,c4,h1 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,h1,o2,c4,c4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4200 1.1010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,h1,o2,c4,c4,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 111.2700 110.7700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,h1,o2,c4,c4,h1 class2 aat 0.0 111.2700 110.7700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,h1,o2,c4,c4,h1 class2 bb13 0.0 1.4200 1.1010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,c4,o2,c4,c4,c4 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,c4,o2,c4,c4,c4 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,c4,o2,c4,c4,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4200 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,c4,o2,c4,c4,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 111.2700 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,c4,o2,c4,c4,c4 class2 aat 0.0 111.2700 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,c4,o2,c4,c4,c4 class2 bb13 0.0 1.4200 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,c3a,o2,c4,c4,c3a class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,c3a,o2,c4,c4,c3a class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,c3a,o2,c4,c4,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4200 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,c3a,o2,c4,c4,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 111.2700 108.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,c3a,o2,c4,c4,c3a class2 aat 0.0 111.2700 108.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,c3a,o2,c4,c4,c3a class2 bb13 0.0 1.4200 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,si4,o2,c4,c4,si4 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,si4,o2,c4,c4,si4 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,si4,o2,c4,c4,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4200 1.8995 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,si4,o2,c4,c4,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 111.2700 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,si4,o2,c4,c4,si4 class2 aat 0.0 111.2700 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,si4,o2,c4,c4,si4 class2 bb13 0.0 1.4200 1.8995 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,o2n,o2,c4,c4,o2n class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,o2n,o2,c4,c4,o2n class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,o2n,o2,c4,c4,o2n class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4200 1.4350 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,o2n,o2,c4,c4,o2n class2 at 0.0 0.0 0.0 0.0 0.0 0.0 111.2700 105.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,o2n,o2,c4,c4,o2n class2 aat 0.0 111.2700 105.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,o2n,o2,c4,c4,o2n class2 bb13 0.0 1.4200 1.4350 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,o2h,o2,c4,c4,o2 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,o2h,o2,c4,c4,o2 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,o2h,o2,c4,c4,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4200 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,o2h,o2,c4,c4,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 111.2700 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,o2h,o2,c4,c4,o2 class2 aat 0.0 111.2700 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,o2h,o2,c4,c4,o2 class2 bb13 0.0 1.4200 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,o2e,o2,c4,c4,o2 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,o2e,o2,c4,c4,o2 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,o2e,o2,c4,c4,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4200 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,o2e,o2,c4,c4,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 111.2700 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,o2e,o2,c4,c4,o2 class2 aat 0.0 111.2700 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,o2e,o2,c4,c4,o2 class2 bb13 0.0 1.4200 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,n2z,o2,c4,c4,n2z class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,n2z,o2,c4,c4,n2z class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,n2z,o2,c4,c4,n2z class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4200 1.4814 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,n2z,o2,c4,c4,n2z class2 at 0.0 0.0 0.0 0.0 0.0 0.0 111.2700 110.9900 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,n2z,o2,c4,c4,n2z class2 aat 0.0 111.2700 110.9900 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,n2z,o2,c4,c4,n2z class2 bb13 0.0 1.4200 1.4814 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,n2=,o2,c4,c4,n2= class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,n2=,o2,c4,c4,n2= class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,n2=,o2,c4,c4,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4200 1.4740 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,n2=,o2,c4,c4,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 111.2700 117.3170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,n2=,o2,c4,c4,n2= class2 aat 0.0 111.2700 117.3170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,n2=,o2,c4,c4,n2= class2 bb13 0.0 1.4200 1.4740 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,h1,o2,c4,c4,h1 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,h1,o2,c4,c4,h1 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,h1,o2,c4,c4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4200 1.1010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,h1,o2,c4,c4,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 111.2700 110.7700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,h1,o2,c4,c4,h1 class2 aat 0.0 111.2700 110.7700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,h1,o2,c4,c4,h1 class2 bb13 0.0 1.4200 1.1010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,c4,o2,c4,c4,c4 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,c4,o2,c4,c4,c4 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,c4,o2,c4,c4,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4200 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,c4,o2,c4,c4,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 111.2700 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,c4,o2,c4,c4,c4 class2 aat 0.0 111.2700 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,c4,o2,c4,c4,c4 class2 bb13 0.0 1.4200 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,c3a,o2,c4,c4,c3a class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,c3a,o2,c4,c4,c3a class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,c3a,o2,c4,c4,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4200 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,c3a,o2,c4,c4,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 111.2700 108.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,c3a,o2,c4,c4,c3a class2 aat 0.0 111.2700 108.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,c3a,o2,c4,c4,c3a class2 bb13 0.0 1.4200 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,si4,n2z,c4,c4,si4 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,si4,n2z,c4,c4,si4 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,si4,n2z,c4,c4,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4814 1.8995 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,si4,n2z,c4,c4,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.9900 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,si4,n2z,c4,c4,si4 class2 aat 0.0 110.9900 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,si4,n2z,c4,c4,si4 class2 bb13 0.0 1.4814 1.8995 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,o2n,n2z,c4,c4,o2n class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,o2n,n2z,c4,c4,o2n class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,o2n,n2z,c4,c4,o2n class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4814 1.4350 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,o2n,n2z,c4,c4,o2n class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.9900 105.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,o2n,n2z,c4,c4,o2n class2 aat 0.0 110.9900 105.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,o2n,n2z,c4,c4,o2n class2 bb13 0.0 1.4814 1.4350 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,o2h,n2z,c4,c4,o2 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,o2h,n2z,c4,c4,o2 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,o2h,n2z,c4,c4,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4814 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,o2h,n2z,c4,c4,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.9900 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,o2h,n2z,c4,c4,o2 class2 aat 0.0 110.9900 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,o2h,n2z,c4,c4,o2 class2 bb13 0.0 1.4814 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,o2e,n2z,c4,c4,o2 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,o2e,n2z,c4,c4,o2 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,o2e,n2z,c4,c4,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4814 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,o2e,n2z,c4,c4,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.9900 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,o2e,n2z,c4,c4,o2 class2 aat 0.0 110.9900 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,o2e,n2z,c4,c4,o2 class2 bb13 0.0 1.4814 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,n2z,n2z,c4,c4,n2z class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,n2z,n2z,c4,c4,n2z class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,n2z,n2z,c4,c4,n2z class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4814 1.4814 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,n2z,n2z,c4,c4,n2z class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.9900 110.9900 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,n2z,n2z,c4,c4,n2z class2 aat 0.0 110.9900 110.9900 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,n2z,n2z,c4,c4,n2z class2 bb13 0.0 1.4814 1.4814 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,n2=,n2z,c4,c4,n2= class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,n2=,n2z,c4,c4,n2= class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,n2=,n2z,c4,c4,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4814 1.4740 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,n2=,n2z,c4,c4,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.9900 117.3170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,n2=,n2z,c4,c4,n2= class2 aat 0.0 110.9900 117.3170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,n2=,n2z,c4,c4,n2= class2 bb13 0.0 1.4814 1.4740 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,h1,n2z,c4,c4,h1 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,h1,n2z,c4,c4,h1 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,h1,n2z,c4,c4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4814 1.1010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,h1,n2z,c4,c4,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.9900 110.7700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,h1,n2z,c4,c4,h1 class2 aat 0.0 110.9900 110.7700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,h1,n2z,c4,c4,h1 class2 bb13 0.0 1.4814 1.1010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,c4,n2z,c4,c4,c4 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,c4,n2z,c4,c4,c4 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,c4,n2z,c4,c4,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4814 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,c4,n2z,c4,c4,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.9900 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,c4,n2z,c4,c4,c4 class2 aat 0.0 110.9900 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,c4,n2z,c4,c4,c4 class2 bb13 0.0 1.4814 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,c3a,n2z,c4,c4,c3a class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,c3a,n2z,c4,c4,c3a class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,c3a,n2z,c4,c4,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4814 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,c3a,n2z,c4,c4,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.9900 108.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,c3a,n2z,c4,c4,c3a class2 aat 0.0 110.9900 108.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,c3a,n2z,c4,c4,c3a class2 bb13 0.0 1.4814 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,si4,n2=,c4,c4,si4 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,si4,n2=,c4,c4,si4 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,si4,n2=,c4,c4,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4740 1.8995 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,si4,n2=,c4,c4,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.3170 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,si4,n2=,c4,c4,si4 class2 aat 0.0 117.3170 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,si4,n2=,c4,c4,si4 class2 bb13 0.0 1.4740 1.8995 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,o2n,n2=,c4,c4,o2n class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,o2n,n2=,c4,c4,o2n class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,o2n,n2=,c4,c4,o2n class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4740 1.4350 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,o2n,n2=,c4,c4,o2n class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.3170 105.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,o2n,n2=,c4,c4,o2n class2 aat 0.0 117.3170 105.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,o2n,n2=,c4,c4,o2n class2 bb13 0.0 1.4740 1.4350 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,o2h,n2=,c4,c4,o2 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,o2h,n2=,c4,c4,o2 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,o2h,n2=,c4,c4,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4740 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,o2h,n2=,c4,c4,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.3170 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,o2h,n2=,c4,c4,o2 class2 aat 0.0 117.3170 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,o2h,n2=,c4,c4,o2 class2 bb13 0.0 1.4740 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,o2e,n2=,c4,c4,o2 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,o2e,n2=,c4,c4,o2 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,o2e,n2=,c4,c4,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4740 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,o2e,n2=,c4,c4,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.3170 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,o2e,n2=,c4,c4,o2 class2 aat 0.0 117.3170 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,o2e,n2=,c4,c4,o2 class2 bb13 0.0 1.4740 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,n2z,n2=,c4,c4,n2z class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,n2z,n2=,c4,c4,n2z class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,n2z,n2=,c4,c4,n2z class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4740 1.4814 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,n2z,n2=,c4,c4,n2z class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.3170 110.9900 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,n2z,n2=,c4,c4,n2z class2 aat 0.0 117.3170 110.9900 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,n2z,n2=,c4,c4,n2z class2 bb13 0.0 1.4740 1.4814 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,n2=,n2=,c4,c4,n2= class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,n2=,n2=,c4,c4,n2= class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,n2=,n2=,c4,c4,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4740 1.4740 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,n2=,n2=,c4,c4,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.3170 117.3170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,n2=,n2=,c4,c4,n2= class2 aat 0.0 117.3170 117.3170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,n2=,n2=,c4,c4,n2= class2 bb13 0.0 1.4740 1.4740 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,h1,n2=,c4,c4,h1 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,h1,n2=,c4,c4,h1 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,h1,n2=,c4,c4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4740 1.1010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,h1,n2=,c4,c4,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.3170 110.7700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,h1,n2=,c4,c4,h1 class2 aat 0.0 117.3170 110.7700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,h1,n2=,c4,c4,h1 class2 bb13 0.0 1.4740 1.1010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,c4,n2=,c4,c4,c4 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,c4,n2=,c4,c4,c4 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,c4,n2=,c4,c4,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4740 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,c4,n2=,c4,c4,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.3170 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,c4,n2=,c4,c4,c4 class2 aat 0.0 117.3170 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,c4,n2=,c4,c4,c4 class2 bb13 0.0 1.4740 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,c3a,n2=,c4,c4,c3a class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,c3a,n2=,c4,c4,c3a class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,c3a,n2=,c4,c4,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4740 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,c3a,n2=,c4,c4,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.3170 108.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,c3a,n2=,c4,c4,c3a class2 aat 0.0 117.3170 108.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,c3a,n2=,c4,c4,c3a class2 bb13 0.0 1.4740 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,si4,h1,c4,c4,si4 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,si4,h1,c4,c4,si4 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,si4,h1,c4,c4,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.8995 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,si4,h1,c4,c4,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.7700 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,si4,h1,c4,c4,si4 class2 aat 0.0 110.7700 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,si4,h1,c4,c4,si4 class2 bb13 0.0 1.1010 1.8995 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,o2n,h1,c4,c4,o2n class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,o2n,h1,c4,c4,o2n class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,o2n,h1,c4,c4,o2n class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.4350 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,o2n,h1,c4,c4,o2n class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.7700 105.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,o2n,h1,c4,c4,o2n class2 aat 0.0 110.7700 105.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,o2n,h1,c4,c4,o2n class2 bb13 0.0 1.1010 1.4350 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,o2h,h1,c4,c4,o2 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,o2h,h1,c4,c4,o2 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,o2h,h1,c4,c4,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,o2h,h1,c4,c4,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.7700 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,o2h,h1,c4,c4,o2 class2 aat 0.0 110.7700 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,o2h,h1,c4,c4,o2 class2 bb13 0.0 1.1010 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,o2e,h1,c4,c4,o2 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,o2e,h1,c4,c4,o2 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,o2e,h1,c4,c4,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,o2e,h1,c4,c4,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.7700 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,o2e,h1,c4,c4,o2 class2 aat 0.0 110.7700 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,o2e,h1,c4,c4,o2 class2 bb13 0.0 1.1010 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,n2z,h1,c4,c4,n2z class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,n2z,h1,c4,c4,n2z class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,n2z,h1,c4,c4,n2z class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.4814 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,n2z,h1,c4,c4,n2z class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.7700 110.9900 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,n2z,h1,c4,c4,n2z class2 aat 0.0 110.7700 110.9900 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,n2z,h1,c4,c4,n2z class2 bb13 0.0 1.1010 1.4814 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,n2=,h1,c4,c4,n2= class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,n2=,h1,c4,c4,n2= class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,n2=,h1,c4,c4,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.4740 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,n2=,h1,c4,c4,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.7700 117.3170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,n2=,h1,c4,c4,n2= class2 aat 0.0 110.7700 117.3170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,n2=,h1,c4,c4,n2= class2 bb13 0.0 1.1010 1.4740 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,h1,h1,c4,c4,h1 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,h1,h1,c4,c4,h1 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,h1,h1,c4,c4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.1010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,h1,h1,c4,c4,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.7700 110.7700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,h1,h1,c4,c4,h1 class2 aat 0.0 110.7700 110.7700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,h1,h1,c4,c4,h1 class2 bb13 0.0 1.1010 1.1010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,c4,h1,c4,c4,c4 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,c4,h1,c4,c4,c4 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,c4,h1,c4,c4,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,c4,h1,c4,c4,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.7700 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,c4,h1,c4,c4,c4 class2 aat 0.0 110.7700 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,c4,h1,c4,c4,c4 class2 bb13 0.0 1.1010 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,c3a,h1,c4,c4,c3a class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,c3a,h1,c4,c4,c3a class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,c3a,h1,c4,c4,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,c3a,h1,c4,c4,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.7700 108.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,c3a,h1,c4,c4,c3a class2 aat 0.0 110.7700 108.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,c3a,h1,c4,c4,c3a class2 bb13 0.0 1.1010 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,si4,c4,c4,c4,si4 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,si4,c4,c4,c4,si4 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,si4,c4,c4,c4,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5300 1.8995 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,si4,c4,c4,c4,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.6700 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,si4,c4,c4,c4,si4 class2 aat 0.0 112.6700 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,si4,c4,c4,c4,si4 class2 bb13 0.0 1.5300 1.8995 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,o2n,c4,c4,c4,o2n class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,o2n,c4,c4,c4,o2n class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,o2n,c4,c4,c4,o2n class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5300 1.4350 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,o2n,c4,c4,c4,o2n class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.6700 105.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,o2n,c4,c4,c4,o2n class2 aat 0.0 112.6700 105.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,o2n,c4,c4,c4,o2n class2 bb13 0.0 1.5300 1.4350 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,o2h,c4,c4,c4,o2 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,o2h,c4,c4,c4,o2 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,o2h,c4,c4,c4,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5300 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,o2h,c4,c4,c4,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.6700 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,o2h,c4,c4,c4,o2 class2 aat 0.0 112.6700 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,o2h,c4,c4,c4,o2 class2 bb13 0.0 1.5300 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,o2e,c4,c4,c4,o2 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,o2e,c4,c4,c4,o2 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,o2e,c4,c4,c4,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5300 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,o2e,c4,c4,c4,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.6700 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,o2e,c4,c4,c4,o2 class2 aat 0.0 112.6700 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,o2e,c4,c4,c4,o2 class2 bb13 0.0 1.5300 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,n2z,c4,c4,c4,n2z class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,n2z,c4,c4,c4,n2z class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,n2z,c4,c4,c4,n2z class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5300 1.4814 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,n2z,c4,c4,c4,n2z class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.6700 110.9900 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,n2z,c4,c4,c4,n2z class2 aat 0.0 112.6700 110.9900 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,n2z,c4,c4,c4,n2z class2 bb13 0.0 1.5300 1.4814 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,n2=,c4,c4,c4,n2= class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,n2=,c4,c4,c4,n2= class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,n2=,c4,c4,c4,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5300 1.4740 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,n2=,c4,c4,c4,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.6700 117.3170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,n2=,c4,c4,c4,n2= class2 aat 0.0 112.6700 117.3170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,n2=,c4,c4,c4,n2= class2 bb13 0.0 1.5300 1.4740 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,h1,c4,c4,c4,h1 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,h1,c4,c4,c4,h1 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,h1,c4,c4,c4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5300 1.1010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,h1,c4,c4,c4,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.6700 110.7700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,h1,c4,c4,c4,h1 class2 aat 0.0 112.6700 110.7700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,h1,c4,c4,c4,h1 class2 bb13 0.0 1.5300 1.1010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,c4,c4,c4,c4,c4 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,c4,c4,c4,c4,c4 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,c4,c4,c4,c4,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5300 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,c4,c4,c4,c4,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.6700 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,c4,c4,c4,c4,c4 class2 aat 0.0 112.6700 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,c4,c4,c4,c4,c4 class2 bb13 0.0 1.5300 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,c3a,c4,c4,c4,c3a class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,c3a,c4,c4,c4,c3a class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,c3a,c4,c4,c4,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5300 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,c3a,c4,c4,c4,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.6700 108.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,c3a,c4,c4,c4,c3a class2 aat 0.0 112.6700 108.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,c3a,c4,c4,c4,c3a class2 bb13 0.0 1.5300 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,si4,c3a,c4,c4,si4 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,si4,c3a,c4,c4,si4 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,si4,c3a,c4,c4,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5010 1.8995 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,si4,c3a,c4,c4,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 108.4000 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,si4,c3a,c4,c4,si4 class2 aat 0.0 108.4000 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,si4,c3a,c4,c4,si4 class2 bb13 0.0 1.5010 1.8995 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,o2n,c3a,c4,c4,o2n class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,o2n,c3a,c4,c4,o2n class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,o2n,c3a,c4,c4,o2n class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5010 1.4350 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,o2n,c3a,c4,c4,o2n class2 at 0.0 0.0 0.0 0.0 0.0 0.0 108.4000 105.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,o2n,c3a,c4,c4,o2n class2 aat 0.0 108.4000 105.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,o2n,c3a,c4,c4,o2n class2 bb13 0.0 1.5010 1.4350 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,o2h,c3a,c4,c4,o2 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,o2h,c3a,c4,c4,o2 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,o2h,c3a,c4,c4,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5010 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,o2h,c3a,c4,c4,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 108.4000 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,o2h,c3a,c4,c4,o2 class2 aat 0.0 108.4000 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,o2h,c3a,c4,c4,o2 class2 bb13 0.0 1.5010 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,o2e,c3a,c4,c4,o2 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,o2e,c3a,c4,c4,o2 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,o2e,c3a,c4,c4,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5010 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,o2e,c3a,c4,c4,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 108.4000 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,o2e,c3a,c4,c4,o2 class2 aat 0.0 108.4000 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,o2e,c3a,c4,c4,o2 class2 bb13 0.0 1.5010 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,n2z,c3a,c4,c4,n2z class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,n2z,c3a,c4,c4,n2z class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,n2z,c3a,c4,c4,n2z class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5010 1.4814 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,n2z,c3a,c4,c4,n2z class2 at 0.0 0.0 0.0 0.0 0.0 0.0 108.4000 110.9900 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,n2z,c3a,c4,c4,n2z class2 aat 0.0 108.4000 110.9900 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,n2z,c3a,c4,c4,n2z class2 bb13 0.0 1.5010 1.4814 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,n2=,c3a,c4,c4,n2= class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,n2=,c3a,c4,c4,n2= class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,n2=,c3a,c4,c4,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5010 1.4740 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,n2=,c3a,c4,c4,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 108.4000 117.3170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,n2=,c3a,c4,c4,n2= class2 aat 0.0 108.4000 117.3170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,n2=,c3a,c4,c4,n2= class2 bb13 0.0 1.5010 1.4740 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,h1,c3a,c4,c4,h1 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,h1,c3a,c4,c4,h1 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,h1,c3a,c4,c4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5010 1.1010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,h1,c3a,c4,c4,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 108.4000 110.7700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,h1,c3a,c4,c4,h1 class2 aat 0.0 108.4000 110.7700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,h1,c3a,c4,c4,h1 class2 bb13 0.0 1.5010 1.1010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,c4,c3a,c4,c4,c4 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,c4,c3a,c4,c4,c4 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,c4,c3a,c4,c4,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5010 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,c4,c3a,c4,c4,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 108.4000 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,c4,c3a,c4,c4,c4 class2 aat 0.0 108.4000 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,c4,c3a,c4,c4,c4 class2 bb13 0.0 1.5010 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,c3a,c3a,c4,c4,c3a class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,c3a,c3a,c4,c4,c3a class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,c3a,c3a,c4,c4,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5010 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,c3a,c3a,c4,c4,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 108.4000 108.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,c3a,c3a,c4,c4,c3a class2 aat 0.0 108.4000 108.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,c3a,c3a,c4,c4,c3a class2 bb13 0.0 1.5010 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,si4,si4,c3a,c3a,si4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,si4,si4,c3a,c3a,si4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,si4,si4,c3a,c3a,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8634 1.8634 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,si4,si4,c3a,c3a,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,si4,si4,c3a,c3a,si4 class2 aat 0.0 120.0000 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,si4,si4,c3a,c3a,si4 class2 bb13 0.0 1.8634 1.8634 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,p4=,si4,c3a,c3a,p4= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,p4=,si4,c3a,c3a,p4= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,p4=,si4,c3a,c3a,p4= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8634 1.7890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,p4=,si4,c3a,c3a,p4= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 120.0010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,p4=,si4,c3a,c3a,p4= class2 aat 0.0 120.0000 120.0010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,p4=,si4,c3a,c3a,p4= class2 bb13 0.0 1.8634 1.7890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,o2h,si4,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,o2h,si4,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,o2h,si4,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8634 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,o2h,si4,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,o2h,si4,c3a,c3a,o2 class2 aat 0.0 120.0000 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,o2h,si4,c3a,c3a,o2 class2 bb13 0.0 1.8634 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,o2e,si4,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,o2e,si4,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,o2e,si4,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8634 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,o2e,si4,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,o2e,si4,c3a,c3a,o2 class2 aat 0.0 120.0000 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,o2e,si4,c3a,c3a,o2 class2 bb13 0.0 1.8634 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,o2,si4,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,o2,si4,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,o2,si4,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8634 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,o2,si4,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,o2,si4,c3a,c3a,o2 class2 aat 0.0 120.0000 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,o2,si4,c3a,c3a,o2 class2 bb13 0.0 1.8634 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,n3o,si4,c3a,c3a,n3o class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,n3o,si4,c3a,c3a,n3o class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,n3o,si4,c3a,c3a,n3o class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8634 1.4300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,n3o,si4,c3a,c3a,n3o class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 118.8000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,n3o,si4,c3a,c3a,n3o class2 aat 0.0 120.0000 118.8000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,n3o,si4,c3a,c3a,n3o class2 bb13 0.0 1.8634 1.4300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,n3m,si4,c3a,c3a,n3m class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,n3m,si4,c3a,c3a,n3m class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,n3m,si4,c3a,c3a,n3m class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8634 1.3950 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,n3m,si4,c3a,c3a,n3m class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 120.7640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,n3m,si4,c3a,c3a,n3m class2 aat 0.0 120.0000 120.7640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,n3m,si4,c3a,c3a,n3m class2 bb13 0.0 1.8634 1.3950 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,n2=,si4,c3a,c3a,n2= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,n2=,si4,c3a,c3a,n2= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,n2=,si4,c3a,c3a,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8634 1.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,n2=,si4,c3a,c3a,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,n2=,si4,c3a,c3a,n2= class2 aat 0.0 120.0000 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,n2=,si4,c3a,c3a,n2= class2 bb13 0.0 1.8634 1.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,h1,si4,c3a,c3a,h1 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,h1,si4,c3a,c3a,h1 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,h1,si4,c3a,c3a,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8634 1.0982 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,h1,si4,c3a,c3a,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 117.9400 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,h1,si4,c3a,c3a,h1 class2 aat 0.0 120.0000 117.9400 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,h1,si4,c3a,c3a,h1 class2 bb13 0.0 1.8634 1.0982 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,c4,si4,c3a,c3a,c4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,c4,si4,c3a,c3a,c4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,c4,si4,c3a,c3a,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8634 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,c4,si4,c3a,c3a,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 120.0500 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,c4,si4,c3a,c3a,c4 class2 aat 0.0 120.0000 120.0500 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,c4,si4,c3a,c3a,c4 class2 bb13 0.0 1.8634 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,c3prime,si4,c3a,c3a,c3prime class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,c3prime,si4,c3a,c3a,c3prime class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,c3prime,si4,c3a,c3a,c3prime class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8634 1.4890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,c3prime,si4,c3a,c3a,c3prime class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 116.0640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,c3prime,si4,c3a,c3a,c3prime class2 aat 0.0 120.0000 116.0640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,c3prime,si4,c3a,c3a,c3prime class2 bb13 0.0 1.8634 1.4890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,c3a,si4,c3a,c3a,c3a class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,c3a,si4,c3a,c3a,c3a class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,c3a,si4,c3a,c3a,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8634 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,c3a,si4,c3a,c3a,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 118.9000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,c3a,si4,c3a,c3a,c3a class2 aat 0.0 120.0000 118.9000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,c3a,si4,c3a,c3a,c3a class2 bb13 0.0 1.8634 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,si4,p4=,c3a,c3a,si4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,si4,p4=,c3a,c3a,si4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,si4,p4=,c3a,c3a,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.7890 1.8634 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,si4,p4=,c3a,c3a,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0010 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,si4,p4=,c3a,c3a,si4 class2 aat 0.0 120.0010 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,si4,p4=,c3a,c3a,si4 class2 bb13 0.0 1.7890 1.8634 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,p4=,p4=,c3a,c3a,p4= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,p4=,p4=,c3a,c3a,p4= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,p4=,p4=,c3a,c3a,p4= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.7890 1.7890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,p4=,p4=,c3a,c3a,p4= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0010 120.0010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,p4=,p4=,c3a,c3a,p4= class2 aat 0.0 120.0010 120.0010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,p4=,p4=,c3a,c3a,p4= class2 bb13 0.0 1.7890 1.7890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,o2h,p4=,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,o2h,p4=,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,o2h,p4=,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.7890 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,o2h,p4=,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0010 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,o2h,p4=,c3a,c3a,o2 class2 aat 0.0 120.0010 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,o2h,p4=,c3a,c3a,o2 class2 bb13 0.0 1.7890 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,o2e,p4=,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,o2e,p4=,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,o2e,p4=,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.7890 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,o2e,p4=,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0010 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,o2e,p4=,c3a,c3a,o2 class2 aat 0.0 120.0010 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,o2e,p4=,c3a,c3a,o2 class2 bb13 0.0 1.7890 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,o2,p4=,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,o2,p4=,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,o2,p4=,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.7890 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,o2,p4=,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0010 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,o2,p4=,c3a,c3a,o2 class2 aat 0.0 120.0010 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,o2,p4=,c3a,c3a,o2 class2 bb13 0.0 1.7890 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,n3o,p4=,c3a,c3a,n3o class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,n3o,p4=,c3a,c3a,n3o class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,n3o,p4=,c3a,c3a,n3o class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.7890 1.4300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,n3o,p4=,c3a,c3a,n3o class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0010 118.8000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,n3o,p4=,c3a,c3a,n3o class2 aat 0.0 120.0010 118.8000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,n3o,p4=,c3a,c3a,n3o class2 bb13 0.0 1.7890 1.4300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,n3m,p4=,c3a,c3a,n3m class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,n3m,p4=,c3a,c3a,n3m class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,n3m,p4=,c3a,c3a,n3m class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.7890 1.3950 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,n3m,p4=,c3a,c3a,n3m class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0010 120.7640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,n3m,p4=,c3a,c3a,n3m class2 aat 0.0 120.0010 120.7640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,n3m,p4=,c3a,c3a,n3m class2 bb13 0.0 1.7890 1.3950 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,n2=,p4=,c3a,c3a,n2= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,n2=,p4=,c3a,c3a,n2= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,n2=,p4=,c3a,c3a,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.7890 1.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,n2=,p4=,c3a,c3a,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0010 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,n2=,p4=,c3a,c3a,n2= class2 aat 0.0 120.0010 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,n2=,p4=,c3a,c3a,n2= class2 bb13 0.0 1.7890 1.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,h1,p4=,c3a,c3a,h1 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,h1,p4=,c3a,c3a,h1 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,h1,p4=,c3a,c3a,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.7890 1.0982 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,h1,p4=,c3a,c3a,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0010 117.9400 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,h1,p4=,c3a,c3a,h1 class2 aat 0.0 120.0010 117.9400 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,h1,p4=,c3a,c3a,h1 class2 bb13 0.0 1.7890 1.0982 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,c4,p4=,c3a,c3a,c4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,c4,p4=,c3a,c3a,c4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,c4,p4=,c3a,c3a,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.7890 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,c4,p4=,c3a,c3a,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0010 120.0500 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,c4,p4=,c3a,c3a,c4 class2 aat 0.0 120.0010 120.0500 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,c4,p4=,c3a,c3a,c4 class2 bb13 0.0 1.7890 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,c3prime,p4=,c3a,c3a,c3prime class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,c3prime,p4=,c3a,c3a,c3prime class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,c3prime,p4=,c3a,c3a,c3prime class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.7890 1.4890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,c3prime,p4=,c3a,c3a,c3prime class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0010 116.0640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,c3prime,p4=,c3a,c3a,c3prime class2 aat 0.0 120.0010 116.0640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,c3prime,p4=,c3a,c3a,c3prime class2 bb13 0.0 1.7890 1.4890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,c3a,p4=,c3a,c3a,c3a class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,c3a,p4=,c3a,c3a,c3a class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,c3a,p4=,c3a,c3a,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.7890 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,c3a,p4=,c3a,c3a,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0010 118.9000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,c3a,p4=,c3a,c3a,c3a class2 aat 0.0 120.0010 118.9000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,c3a,p4=,c3a,c3a,c3a class2 bb13 0.0 1.7890 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,si4,o2,c3a,c3a,si4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,si4,o2,c3a,c3a,si4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,si4,o2,c3a,c3a,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.8634 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,si4,o2,c3a,c3a,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,si4,o2,c3a,c3a,si4 class2 aat 0.0 123.4200 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,si4,o2,c3a,c3a,si4 class2 bb13 0.0 1.3768 1.8634 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,p4=,o2,c3a,c3a,p4= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,p4=,o2,c3a,c3a,p4= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,p4=,o2,c3a,c3a,p4= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.7890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,p4=,o2,c3a,c3a,p4= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 120.0010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,p4=,o2,c3a,c3a,p4= class2 aat 0.0 123.4200 120.0010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,p4=,o2,c3a,c3a,p4= class2 bb13 0.0 1.3768 1.7890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,o2h,o2,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,o2h,o2,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,o2h,o2,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,o2h,o2,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,o2h,o2,c3a,c3a,o2 class2 aat 0.0 123.4200 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,o2h,o2,c3a,c3a,o2 class2 bb13 0.0 1.3768 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,o2e,o2,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,o2e,o2,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,o2e,o2,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,o2e,o2,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,o2e,o2,c3a,c3a,o2 class2 aat 0.0 123.4200 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,o2e,o2,c3a,c3a,o2 class2 bb13 0.0 1.3768 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,o2,o2,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,o2,o2,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,o2,o2,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,o2,o2,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,o2,o2,c3a,c3a,o2 class2 aat 0.0 123.4200 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,o2,o2,c3a,c3a,o2 class2 bb13 0.0 1.3768 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,n3o,o2,c3a,c3a,n3o class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,n3o,o2,c3a,c3a,n3o class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,n3o,o2,c3a,c3a,n3o class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.4300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,n3o,o2,c3a,c3a,n3o class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 118.8000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,n3o,o2,c3a,c3a,n3o class2 aat 0.0 123.4200 118.8000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,n3o,o2,c3a,c3a,n3o class2 bb13 0.0 1.3768 1.4300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,n3m,o2,c3a,c3a,n3m class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,n3m,o2,c3a,c3a,n3m class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,n3m,o2,c3a,c3a,n3m class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.3950 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,n3m,o2,c3a,c3a,n3m class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 120.7640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,n3m,o2,c3a,c3a,n3m class2 aat 0.0 123.4200 120.7640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,n3m,o2,c3a,c3a,n3m class2 bb13 0.0 1.3768 1.3950 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,n2=,o2,c3a,c3a,n2= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,n2=,o2,c3a,c3a,n2= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,n2=,o2,c3a,c3a,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,n2=,o2,c3a,c3a,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,n2=,o2,c3a,c3a,n2= class2 aat 0.0 123.4200 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,n2=,o2,c3a,c3a,n2= class2 bb13 0.0 1.3768 1.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,h1,o2,c3a,c3a,h1 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,h1,o2,c3a,c3a,h1 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,h1,o2,c3a,c3a,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.0982 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,h1,o2,c3a,c3a,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 117.9400 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,h1,o2,c3a,c3a,h1 class2 aat 0.0 123.4200 117.9400 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,h1,o2,c3a,c3a,h1 class2 bb13 0.0 1.3768 1.0982 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,c4,o2,c3a,c3a,c4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,c4,o2,c3a,c3a,c4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,c4,o2,c3a,c3a,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,c4,o2,c3a,c3a,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 120.0500 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,c4,o2,c3a,c3a,c4 class2 aat 0.0 123.4200 120.0500 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,c4,o2,c3a,c3a,c4 class2 bb13 0.0 1.3768 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,c3prime,o2,c3a,c3a,c3prime class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,c3prime,o2,c3a,c3a,c3prime class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,c3prime,o2,c3a,c3a,c3prime class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.4890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,c3prime,o2,c3a,c3a,c3prime class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 116.0640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,c3prime,o2,c3a,c3a,c3prime class2 aat 0.0 123.4200 116.0640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,c3prime,o2,c3a,c3a,c3prime class2 bb13 0.0 1.3768 1.4890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,c3a,o2,c3a,c3a,c3a class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,c3a,o2,c3a,c3a,c3a class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,c3a,o2,c3a,c3a,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,c3a,o2,c3a,c3a,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 118.9000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,c3a,o2,c3a,c3a,c3a class2 aat 0.0 123.4200 118.9000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,c3a,o2,c3a,c3a,c3a class2 bb13 0.0 1.3768 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,si4,o2,c3a,c3a,si4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,si4,o2,c3a,c3a,si4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,si4,o2,c3a,c3a,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.8634 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,si4,o2,c3a,c3a,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,si4,o2,c3a,c3a,si4 class2 aat 0.0 123.4200 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,si4,o2,c3a,c3a,si4 class2 bb13 0.0 1.3768 1.8634 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,p4=,o2,c3a,c3a,p4= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,p4=,o2,c3a,c3a,p4= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,p4=,o2,c3a,c3a,p4= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.7890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,p4=,o2,c3a,c3a,p4= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 120.0010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,p4=,o2,c3a,c3a,p4= class2 aat 0.0 123.4200 120.0010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,p4=,o2,c3a,c3a,p4= class2 bb13 0.0 1.3768 1.7890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,o2h,o2,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,o2h,o2,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,o2h,o2,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,o2h,o2,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,o2h,o2,c3a,c3a,o2 class2 aat 0.0 123.4200 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,o2h,o2,c3a,c3a,o2 class2 bb13 0.0 1.3768 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,o2e,o2,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,o2e,o2,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,o2e,o2,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,o2e,o2,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,o2e,o2,c3a,c3a,o2 class2 aat 0.0 123.4200 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,o2e,o2,c3a,c3a,o2 class2 bb13 0.0 1.3768 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,o2,o2,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,o2,o2,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,o2,o2,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,o2,o2,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,o2,o2,c3a,c3a,o2 class2 aat 0.0 123.4200 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,o2,o2,c3a,c3a,o2 class2 bb13 0.0 1.3768 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,n3o,o2,c3a,c3a,n3o class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,n3o,o2,c3a,c3a,n3o class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,n3o,o2,c3a,c3a,n3o class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.4300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,n3o,o2,c3a,c3a,n3o class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 118.8000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,n3o,o2,c3a,c3a,n3o class2 aat 0.0 123.4200 118.8000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,n3o,o2,c3a,c3a,n3o class2 bb13 0.0 1.3768 1.4300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,n3m,o2,c3a,c3a,n3m class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,n3m,o2,c3a,c3a,n3m class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,n3m,o2,c3a,c3a,n3m class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.3950 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,n3m,o2,c3a,c3a,n3m class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 120.7640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,n3m,o2,c3a,c3a,n3m class2 aat 0.0 123.4200 120.7640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,n3m,o2,c3a,c3a,n3m class2 bb13 0.0 1.3768 1.3950 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,n2=,o2,c3a,c3a,n2= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,n2=,o2,c3a,c3a,n2= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,n2=,o2,c3a,c3a,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,n2=,o2,c3a,c3a,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,n2=,o2,c3a,c3a,n2= class2 aat 0.0 123.4200 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,n2=,o2,c3a,c3a,n2= class2 bb13 0.0 1.3768 1.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,h1,o2,c3a,c3a,h1 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,h1,o2,c3a,c3a,h1 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,h1,o2,c3a,c3a,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.0982 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,h1,o2,c3a,c3a,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 117.9400 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,h1,o2,c3a,c3a,h1 class2 aat 0.0 123.4200 117.9400 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,h1,o2,c3a,c3a,h1 class2 bb13 0.0 1.3768 1.0982 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,c4,o2,c3a,c3a,c4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,c4,o2,c3a,c3a,c4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,c4,o2,c3a,c3a,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,c4,o2,c3a,c3a,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 120.0500 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,c4,o2,c3a,c3a,c4 class2 aat 0.0 123.4200 120.0500 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,c4,o2,c3a,c3a,c4 class2 bb13 0.0 1.3768 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,c3prime,o2,c3a,c3a,c3prime class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,c3prime,o2,c3a,c3a,c3prime class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,c3prime,o2,c3a,c3a,c3prime class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.4890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,c3prime,o2,c3a,c3a,c3prime class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 116.0640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,c3prime,o2,c3a,c3a,c3prime class2 aat 0.0 123.4200 116.0640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,c3prime,o2,c3a,c3a,c3prime class2 bb13 0.0 1.3768 1.4890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,c3a,o2,c3a,c3a,c3a class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,c3a,o2,c3a,c3a,c3a class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,c3a,o2,c3a,c3a,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,c3a,o2,c3a,c3a,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 118.9000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,c3a,o2,c3a,c3a,c3a class2 aat 0.0 123.4200 118.9000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,c3a,o2,c3a,c3a,c3a class2 bb13 0.0 1.3768 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,si4,o2,c3a,c3a,si4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,si4,o2,c3a,c3a,si4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,si4,o2,c3a,c3a,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.8634 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,si4,o2,c3a,c3a,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,si4,o2,c3a,c3a,si4 class2 aat 0.0 123.4200 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,si4,o2,c3a,c3a,si4 class2 bb13 0.0 1.3768 1.8634 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,p4=,o2,c3a,c3a,p4= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,p4=,o2,c3a,c3a,p4= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,p4=,o2,c3a,c3a,p4= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.7890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,p4=,o2,c3a,c3a,p4= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 120.0010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,p4=,o2,c3a,c3a,p4= class2 aat 0.0 123.4200 120.0010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,p4=,o2,c3a,c3a,p4= class2 bb13 0.0 1.3768 1.7890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,o2h,o2,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,o2h,o2,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,o2h,o2,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,o2h,o2,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,o2h,o2,c3a,c3a,o2 class2 aat 0.0 123.4200 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,o2h,o2,c3a,c3a,o2 class2 bb13 0.0 1.3768 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,o2e,o2,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,o2e,o2,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,o2e,o2,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,o2e,o2,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,o2e,o2,c3a,c3a,o2 class2 aat 0.0 123.4200 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,o2e,o2,c3a,c3a,o2 class2 bb13 0.0 1.3768 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,o2,o2,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,o2,o2,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,o2,o2,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,o2,o2,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,o2,o2,c3a,c3a,o2 class2 aat 0.0 123.4200 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,o2,o2,c3a,c3a,o2 class2 bb13 0.0 1.3768 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,n3o,o2,c3a,c3a,n3o class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,n3o,o2,c3a,c3a,n3o class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,n3o,o2,c3a,c3a,n3o class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.4300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,n3o,o2,c3a,c3a,n3o class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 118.8000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,n3o,o2,c3a,c3a,n3o class2 aat 0.0 123.4200 118.8000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,n3o,o2,c3a,c3a,n3o class2 bb13 0.0 1.3768 1.4300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,n3m,o2,c3a,c3a,n3m class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,n3m,o2,c3a,c3a,n3m class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,n3m,o2,c3a,c3a,n3m class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.3950 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,n3m,o2,c3a,c3a,n3m class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 120.7640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,n3m,o2,c3a,c3a,n3m class2 aat 0.0 123.4200 120.7640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,n3m,o2,c3a,c3a,n3m class2 bb13 0.0 1.3768 1.3950 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,n2=,o2,c3a,c3a,n2= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,n2=,o2,c3a,c3a,n2= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,n2=,o2,c3a,c3a,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,n2=,o2,c3a,c3a,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,n2=,o2,c3a,c3a,n2= class2 aat 0.0 123.4200 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,n2=,o2,c3a,c3a,n2= class2 bb13 0.0 1.3768 1.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,h1,o2,c3a,c3a,h1 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,h1,o2,c3a,c3a,h1 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,h1,o2,c3a,c3a,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.0982 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,h1,o2,c3a,c3a,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 117.9400 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,h1,o2,c3a,c3a,h1 class2 aat 0.0 123.4200 117.9400 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,h1,o2,c3a,c3a,h1 class2 bb13 0.0 1.3768 1.0982 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,c4,o2,c3a,c3a,c4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,c4,o2,c3a,c3a,c4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,c4,o2,c3a,c3a,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,c4,o2,c3a,c3a,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 120.0500 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,c4,o2,c3a,c3a,c4 class2 aat 0.0 123.4200 120.0500 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,c4,o2,c3a,c3a,c4 class2 bb13 0.0 1.3768 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,c3prime,o2,c3a,c3a,c3prime class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,c3prime,o2,c3a,c3a,c3prime class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,c3prime,o2,c3a,c3a,c3prime class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.4890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,c3prime,o2,c3a,c3a,c3prime class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 116.0640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,c3prime,o2,c3a,c3a,c3prime class2 aat 0.0 123.4200 116.0640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,c3prime,o2,c3a,c3a,c3prime class2 bb13 0.0 1.3768 1.4890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,c3a,o2,c3a,c3a,c3a class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,c3a,o2,c3a,c3a,c3a class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,c3a,o2,c3a,c3a,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,c3a,o2,c3a,c3a,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 118.9000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,c3a,o2,c3a,c3a,c3a class2 aat 0.0 123.4200 118.9000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,c3a,o2,c3a,c3a,c3a class2 bb13 0.0 1.3768 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,si4,n3o,c3a,c3a,si4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,si4,n3o,c3a,c3a,si4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,si4,n3o,c3a,c3a,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4300 1.8634 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,si4,n3o,c3a,c3a,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.8000 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,si4,n3o,c3a,c3a,si4 class2 aat 0.0 118.8000 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,si4,n3o,c3a,c3a,si4 class2 bb13 0.0 1.4300 1.8634 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,p4=,n3o,c3a,c3a,p4= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,p4=,n3o,c3a,c3a,p4= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,p4=,n3o,c3a,c3a,p4= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4300 1.7890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,p4=,n3o,c3a,c3a,p4= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.8000 120.0010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,p4=,n3o,c3a,c3a,p4= class2 aat 0.0 118.8000 120.0010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,p4=,n3o,c3a,c3a,p4= class2 bb13 0.0 1.4300 1.7890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,o2h,n3o,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,o2h,n3o,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,o2h,n3o,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4300 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,o2h,n3o,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.8000 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,o2h,n3o,c3a,c3a,o2 class2 aat 0.0 118.8000 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,o2h,n3o,c3a,c3a,o2 class2 bb13 0.0 1.4300 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,o2e,n3o,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,o2e,n3o,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,o2e,n3o,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4300 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,o2e,n3o,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.8000 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,o2e,n3o,c3a,c3a,o2 class2 aat 0.0 118.8000 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,o2e,n3o,c3a,c3a,o2 class2 bb13 0.0 1.4300 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,o2,n3o,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,o2,n3o,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,o2,n3o,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4300 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,o2,n3o,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.8000 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,o2,n3o,c3a,c3a,o2 class2 aat 0.0 118.8000 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,o2,n3o,c3a,c3a,o2 class2 bb13 0.0 1.4300 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,n3o,n3o,c3a,c3a,n3o class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,n3o,n3o,c3a,c3a,n3o class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,n3o,n3o,c3a,c3a,n3o class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4300 1.4300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,n3o,n3o,c3a,c3a,n3o class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.8000 118.8000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,n3o,n3o,c3a,c3a,n3o class2 aat 0.0 118.8000 118.8000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,n3o,n3o,c3a,c3a,n3o class2 bb13 0.0 1.4300 1.4300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,n3m,n3o,c3a,c3a,n3m class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,n3m,n3o,c3a,c3a,n3m class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,n3m,n3o,c3a,c3a,n3m class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4300 1.3950 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,n3m,n3o,c3a,c3a,n3m class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.8000 120.7640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,n3m,n3o,c3a,c3a,n3m class2 aat 0.0 118.8000 120.7640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,n3m,n3o,c3a,c3a,n3m class2 bb13 0.0 1.4300 1.3950 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,n2=,n3o,c3a,c3a,n2= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,n2=,n3o,c3a,c3a,n2= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,n2=,n3o,c3a,c3a,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4300 1.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,n2=,n3o,c3a,c3a,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.8000 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,n2=,n3o,c3a,c3a,n2= class2 aat 0.0 118.8000 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,n2=,n3o,c3a,c3a,n2= class2 bb13 0.0 1.4300 1.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,h1,n3o,c3a,c3a,h1 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,h1,n3o,c3a,c3a,h1 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,h1,n3o,c3a,c3a,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4300 1.0982 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,h1,n3o,c3a,c3a,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.8000 117.9400 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,h1,n3o,c3a,c3a,h1 class2 aat 0.0 118.8000 117.9400 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,h1,n3o,c3a,c3a,h1 class2 bb13 0.0 1.4300 1.0982 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,c4,n3o,c3a,c3a,c4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,c4,n3o,c3a,c3a,c4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,c4,n3o,c3a,c3a,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4300 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,c4,n3o,c3a,c3a,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.8000 120.0500 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,c4,n3o,c3a,c3a,c4 class2 aat 0.0 118.8000 120.0500 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,c4,n3o,c3a,c3a,c4 class2 bb13 0.0 1.4300 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,c3prime,n3o,c3a,c3a,c3prime class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,c3prime,n3o,c3a,c3a,c3prime class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,c3prime,n3o,c3a,c3a,c3prime class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4300 1.4890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,c3prime,n3o,c3a,c3a,c3prime class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.8000 116.0640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,c3prime,n3o,c3a,c3a,c3prime class2 aat 0.0 118.8000 116.0640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,c3prime,n3o,c3a,c3a,c3prime class2 bb13 0.0 1.4300 1.4890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,c3a,n3o,c3a,c3a,c3a class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,c3a,n3o,c3a,c3a,c3a class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,c3a,n3o,c3a,c3a,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4300 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,c3a,n3o,c3a,c3a,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.8000 118.9000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,c3a,n3o,c3a,c3a,c3a class2 aat 0.0 118.8000 118.9000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,c3a,n3o,c3a,c3a,c3a class2 bb13 0.0 1.4300 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,si4,n3m,c3a,c3a,si4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,si4,n3m,c3a,c3a,si4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,si4,n3m,c3a,c3a,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3950 1.8634 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,si4,n3m,c3a,c3a,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.7640 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,si4,n3m,c3a,c3a,si4 class2 aat 0.0 120.7640 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,si4,n3m,c3a,c3a,si4 class2 bb13 0.0 1.3950 1.8634 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,p4=,n3m,c3a,c3a,p4= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,p4=,n3m,c3a,c3a,p4= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,p4=,n3m,c3a,c3a,p4= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3950 1.7890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,p4=,n3m,c3a,c3a,p4= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.7640 120.0010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,p4=,n3m,c3a,c3a,p4= class2 aat 0.0 120.7640 120.0010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,p4=,n3m,c3a,c3a,p4= class2 bb13 0.0 1.3950 1.7890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,o2h,n3m,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,o2h,n3m,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,o2h,n3m,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3950 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,o2h,n3m,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.7640 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,o2h,n3m,c3a,c3a,o2 class2 aat 0.0 120.7640 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,o2h,n3m,c3a,c3a,o2 class2 bb13 0.0 1.3950 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,o2e,n3m,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,o2e,n3m,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,o2e,n3m,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3950 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,o2e,n3m,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.7640 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,o2e,n3m,c3a,c3a,o2 class2 aat 0.0 120.7640 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,o2e,n3m,c3a,c3a,o2 class2 bb13 0.0 1.3950 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,o2,n3m,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,o2,n3m,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,o2,n3m,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3950 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,o2,n3m,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.7640 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,o2,n3m,c3a,c3a,o2 class2 aat 0.0 120.7640 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,o2,n3m,c3a,c3a,o2 class2 bb13 0.0 1.3950 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,n3o,n3m,c3a,c3a,n3o class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,n3o,n3m,c3a,c3a,n3o class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,n3o,n3m,c3a,c3a,n3o class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3950 1.4300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,n3o,n3m,c3a,c3a,n3o class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.7640 118.8000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,n3o,n3m,c3a,c3a,n3o class2 aat 0.0 120.7640 118.8000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,n3o,n3m,c3a,c3a,n3o class2 bb13 0.0 1.3950 1.4300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,n3m,n3m,c3a,c3a,n3m class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,n3m,n3m,c3a,c3a,n3m class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,n3m,n3m,c3a,c3a,n3m class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3950 1.3950 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,n3m,n3m,c3a,c3a,n3m class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.7640 120.7640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,n3m,n3m,c3a,c3a,n3m class2 aat 0.0 120.7640 120.7640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,n3m,n3m,c3a,c3a,n3m class2 bb13 0.0 1.3950 1.3950 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,n2=,n3m,c3a,c3a,n2= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,n2=,n3m,c3a,c3a,n2= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,n2=,n3m,c3a,c3a,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3950 1.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,n2=,n3m,c3a,c3a,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.7640 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,n2=,n3m,c3a,c3a,n2= class2 aat 0.0 120.7640 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,n2=,n3m,c3a,c3a,n2= class2 bb13 0.0 1.3950 1.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,h1,n3m,c3a,c3a,h1 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,h1,n3m,c3a,c3a,h1 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,h1,n3m,c3a,c3a,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3950 1.0982 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,h1,n3m,c3a,c3a,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.7640 117.9400 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,h1,n3m,c3a,c3a,h1 class2 aat 0.0 120.7640 117.9400 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,h1,n3m,c3a,c3a,h1 class2 bb13 0.0 1.3950 1.0982 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,c4,n3m,c3a,c3a,c4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,c4,n3m,c3a,c3a,c4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,c4,n3m,c3a,c3a,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3950 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,c4,n3m,c3a,c3a,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.7640 120.0500 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,c4,n3m,c3a,c3a,c4 class2 aat 0.0 120.7640 120.0500 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,c4,n3m,c3a,c3a,c4 class2 bb13 0.0 1.3950 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,c3prime,n3m,c3a,c3a,c3prime class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,c3prime,n3m,c3a,c3a,c3prime class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,c3prime,n3m,c3a,c3a,c3prime class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3950 1.4890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,c3prime,n3m,c3a,c3a,c3prime class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.7640 116.0640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,c3prime,n3m,c3a,c3a,c3prime class2 aat 0.0 120.7640 116.0640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,c3prime,n3m,c3a,c3a,c3prime class2 bb13 0.0 1.3950 1.4890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,c3a,n3m,c3a,c3a,c3a class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,c3a,n3m,c3a,c3a,c3a class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,c3a,n3m,c3a,c3a,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3950 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,c3a,n3m,c3a,c3a,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.7640 118.9000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,c3a,n3m,c3a,c3a,c3a class2 aat 0.0 120.7640 118.9000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,c3a,n3m,c3a,c3a,c3a class2 bb13 0.0 1.3950 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,si4,n2=,c3a,c3a,si4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,si4,n2=,c3a,c3a,si4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,si4,n2=,c3a,c3a,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4000 1.8634 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,si4,n2=,c3a,c3a,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,si4,n2=,c3a,c3a,si4 class2 aat 0.0 120.0000 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,si4,n2=,c3a,c3a,si4 class2 bb13 0.0 1.4000 1.8634 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,p4=,n2=,c3a,c3a,p4= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,p4=,n2=,c3a,c3a,p4= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,p4=,n2=,c3a,c3a,p4= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4000 1.7890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,p4=,n2=,c3a,c3a,p4= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 120.0010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,p4=,n2=,c3a,c3a,p4= class2 aat 0.0 120.0000 120.0010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,p4=,n2=,c3a,c3a,p4= class2 bb13 0.0 1.4000 1.7890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,o2h,n2=,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,o2h,n2=,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,o2h,n2=,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4000 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,o2h,n2=,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,o2h,n2=,c3a,c3a,o2 class2 aat 0.0 120.0000 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,o2h,n2=,c3a,c3a,o2 class2 bb13 0.0 1.4000 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,o2e,n2=,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,o2e,n2=,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,o2e,n2=,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4000 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,o2e,n2=,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,o2e,n2=,c3a,c3a,o2 class2 aat 0.0 120.0000 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,o2e,n2=,c3a,c3a,o2 class2 bb13 0.0 1.4000 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,o2,n2=,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,o2,n2=,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,o2,n2=,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4000 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,o2,n2=,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,o2,n2=,c3a,c3a,o2 class2 aat 0.0 120.0000 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,o2,n2=,c3a,c3a,o2 class2 bb13 0.0 1.4000 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,n3o,n2=,c3a,c3a,n3o class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,n3o,n2=,c3a,c3a,n3o class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,n3o,n2=,c3a,c3a,n3o class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4000 1.4300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,n3o,n2=,c3a,c3a,n3o class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 118.8000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,n3o,n2=,c3a,c3a,n3o class2 aat 0.0 120.0000 118.8000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,n3o,n2=,c3a,c3a,n3o class2 bb13 0.0 1.4000 1.4300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,n3m,n2=,c3a,c3a,n3m class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,n3m,n2=,c3a,c3a,n3m class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,n3m,n2=,c3a,c3a,n3m class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4000 1.3950 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,n3m,n2=,c3a,c3a,n3m class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 120.7640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,n3m,n2=,c3a,c3a,n3m class2 aat 0.0 120.0000 120.7640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,n3m,n2=,c3a,c3a,n3m class2 bb13 0.0 1.4000 1.3950 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,n2=,n2=,c3a,c3a,n2= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,n2=,n2=,c3a,c3a,n2= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,n2=,n2=,c3a,c3a,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4000 1.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,n2=,n2=,c3a,c3a,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,n2=,n2=,c3a,c3a,n2= class2 aat 0.0 120.0000 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,n2=,n2=,c3a,c3a,n2= class2 bb13 0.0 1.4000 1.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,h1,n2=,c3a,c3a,h1 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,h1,n2=,c3a,c3a,h1 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,h1,n2=,c3a,c3a,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4000 1.0982 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,h1,n2=,c3a,c3a,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 117.9400 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,h1,n2=,c3a,c3a,h1 class2 aat 0.0 120.0000 117.9400 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,h1,n2=,c3a,c3a,h1 class2 bb13 0.0 1.4000 1.0982 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,c4,n2=,c3a,c3a,c4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,c4,n2=,c3a,c3a,c4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,c4,n2=,c3a,c3a,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4000 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,c4,n2=,c3a,c3a,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 120.0500 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,c4,n2=,c3a,c3a,c4 class2 aat 0.0 120.0000 120.0500 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,c4,n2=,c3a,c3a,c4 class2 bb13 0.0 1.4000 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,c3prime,n2=,c3a,c3a,c3prime class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,c3prime,n2=,c3a,c3a,c3prime class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,c3prime,n2=,c3a,c3a,c3prime class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4000 1.4890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,c3prime,n2=,c3a,c3a,c3prime class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 116.0640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,c3prime,n2=,c3a,c3a,c3prime class2 aat 0.0 120.0000 116.0640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,c3prime,n2=,c3a,c3a,c3prime class2 bb13 0.0 1.4000 1.4890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,c3a,n2=,c3a,c3a,c3a class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,c3a,n2=,c3a,c3a,c3a class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,c3a,n2=,c3a,c3a,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4000 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,c3a,n2=,c3a,c3a,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 118.9000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,c3a,n2=,c3a,c3a,c3a class2 aat 0.0 120.0000 118.9000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,c3a,n2=,c3a,c3a,c3a class2 bb13 0.0 1.4000 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,si4,h1,c3a,c3a,si4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,si4,h1,c3a,c3a,si4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,si4,h1,c3a,c3a,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0982 1.8634 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,si4,h1,c3a,c3a,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.9400 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,si4,h1,c3a,c3a,si4 class2 aat 0.0 117.9400 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,si4,h1,c3a,c3a,si4 class2 bb13 0.0 1.0982 1.8634 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,p4=,h1,c3a,c3a,p4= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,p4=,h1,c3a,c3a,p4= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,p4=,h1,c3a,c3a,p4= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0982 1.7890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,p4=,h1,c3a,c3a,p4= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.9400 120.0010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,p4=,h1,c3a,c3a,p4= class2 aat 0.0 117.9400 120.0010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,p4=,h1,c3a,c3a,p4= class2 bb13 0.0 1.0982 1.7890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,o2h,h1,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,o2h,h1,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,o2h,h1,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0982 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,o2h,h1,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.9400 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,o2h,h1,c3a,c3a,o2 class2 aat 0.0 117.9400 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,o2h,h1,c3a,c3a,o2 class2 bb13 0.0 1.0982 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,o2e,h1,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,o2e,h1,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,o2e,h1,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0982 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,o2e,h1,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.9400 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,o2e,h1,c3a,c3a,o2 class2 aat 0.0 117.9400 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,o2e,h1,c3a,c3a,o2 class2 bb13 0.0 1.0982 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,o2,h1,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,o2,h1,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,o2,h1,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0982 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,o2,h1,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.9400 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,o2,h1,c3a,c3a,o2 class2 aat 0.0 117.9400 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,o2,h1,c3a,c3a,o2 class2 bb13 0.0 1.0982 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,n3o,h1,c3a,c3a,n3o class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,n3o,h1,c3a,c3a,n3o class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,n3o,h1,c3a,c3a,n3o class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0982 1.4300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,n3o,h1,c3a,c3a,n3o class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.9400 118.8000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,n3o,h1,c3a,c3a,n3o class2 aat 0.0 117.9400 118.8000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,n3o,h1,c3a,c3a,n3o class2 bb13 0.0 1.0982 1.4300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,n3m,h1,c3a,c3a,n3m class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,n3m,h1,c3a,c3a,n3m class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,n3m,h1,c3a,c3a,n3m class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0982 1.3950 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,n3m,h1,c3a,c3a,n3m class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.9400 120.7640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,n3m,h1,c3a,c3a,n3m class2 aat 0.0 117.9400 120.7640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,n3m,h1,c3a,c3a,n3m class2 bb13 0.0 1.0982 1.3950 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,n2=,h1,c3a,c3a,n2= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,n2=,h1,c3a,c3a,n2= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,n2=,h1,c3a,c3a,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0982 1.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,n2=,h1,c3a,c3a,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.9400 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,n2=,h1,c3a,c3a,n2= class2 aat 0.0 117.9400 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,n2=,h1,c3a,c3a,n2= class2 bb13 0.0 1.0982 1.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,h1,h1,c3a,c3a,h1 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,h1,h1,c3a,c3a,h1 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,h1,h1,c3a,c3a,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0982 1.0982 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,h1,h1,c3a,c3a,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.9400 117.9400 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,h1,h1,c3a,c3a,h1 class2 aat 0.0 117.9400 117.9400 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,h1,h1,c3a,c3a,h1 class2 bb13 0.0 1.0982 1.0982 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,c4,h1,c3a,c3a,c4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,c4,h1,c3a,c3a,c4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,c4,h1,c3a,c3a,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0982 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,c4,h1,c3a,c3a,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.9400 120.0500 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,c4,h1,c3a,c3a,c4 class2 aat 0.0 117.9400 120.0500 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,c4,h1,c3a,c3a,c4 class2 bb13 0.0 1.0982 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,c3prime,h1,c3a,c3a,c3prime class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,c3prime,h1,c3a,c3a,c3prime class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,c3prime,h1,c3a,c3a,c3prime class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0982 1.4890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,c3prime,h1,c3a,c3a,c3prime class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.9400 116.0640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,c3prime,h1,c3a,c3a,c3prime class2 aat 0.0 117.9400 116.0640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,c3prime,h1,c3a,c3a,c3prime class2 bb13 0.0 1.0982 1.4890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,c3a,h1,c3a,c3a,c3a class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,c3a,h1,c3a,c3a,c3a class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,c3a,h1,c3a,c3a,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0982 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,c3a,h1,c3a,c3a,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.9400 118.9000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,c3a,h1,c3a,c3a,c3a class2 aat 0.0 117.9400 118.9000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,c3a,h1,c3a,c3a,c3a class2 bb13 0.0 1.0982 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,si4,c4,c3a,c3a,si4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,si4,c4,c3a,c3a,si4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,si4,c4,c3a,c3a,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5010 1.8634 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,si4,c4,c3a,c3a,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0500 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,si4,c4,c3a,c3a,si4 class2 aat 0.0 120.0500 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,si4,c4,c3a,c3a,si4 class2 bb13 0.0 1.5010 1.8634 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,p4=,c4,c3a,c3a,p4= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,p4=,c4,c3a,c3a,p4= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,p4=,c4,c3a,c3a,p4= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5010 1.7890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,p4=,c4,c3a,c3a,p4= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0500 120.0010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,p4=,c4,c3a,c3a,p4= class2 aat 0.0 120.0500 120.0010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,p4=,c4,c3a,c3a,p4= class2 bb13 0.0 1.5010 1.7890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,o2h,c4,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,o2h,c4,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,o2h,c4,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5010 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,o2h,c4,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0500 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,o2h,c4,c3a,c3a,o2 class2 aat 0.0 120.0500 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,o2h,c4,c3a,c3a,o2 class2 bb13 0.0 1.5010 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,o2e,c4,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,o2e,c4,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,o2e,c4,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5010 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,o2e,c4,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0500 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,o2e,c4,c3a,c3a,o2 class2 aat 0.0 120.0500 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,o2e,c4,c3a,c3a,o2 class2 bb13 0.0 1.5010 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,o2,c4,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,o2,c4,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,o2,c4,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5010 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,o2,c4,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0500 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,o2,c4,c3a,c3a,o2 class2 aat 0.0 120.0500 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,o2,c4,c3a,c3a,o2 class2 bb13 0.0 1.5010 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,n3o,c4,c3a,c3a,n3o class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,n3o,c4,c3a,c3a,n3o class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,n3o,c4,c3a,c3a,n3o class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5010 1.4300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,n3o,c4,c3a,c3a,n3o class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0500 118.8000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,n3o,c4,c3a,c3a,n3o class2 aat 0.0 120.0500 118.8000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,n3o,c4,c3a,c3a,n3o class2 bb13 0.0 1.5010 1.4300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,n3m,c4,c3a,c3a,n3m class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,n3m,c4,c3a,c3a,n3m class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,n3m,c4,c3a,c3a,n3m class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5010 1.3950 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,n3m,c4,c3a,c3a,n3m class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0500 120.7640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,n3m,c4,c3a,c3a,n3m class2 aat 0.0 120.0500 120.7640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,n3m,c4,c3a,c3a,n3m class2 bb13 0.0 1.5010 1.3950 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,n2=,c4,c3a,c3a,n2= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,n2=,c4,c3a,c3a,n2= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,n2=,c4,c3a,c3a,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5010 1.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,n2=,c4,c3a,c3a,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0500 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,n2=,c4,c3a,c3a,n2= class2 aat 0.0 120.0500 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,n2=,c4,c3a,c3a,n2= class2 bb13 0.0 1.5010 1.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,h1,c4,c3a,c3a,h1 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,h1,c4,c3a,c3a,h1 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,h1,c4,c3a,c3a,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5010 1.0982 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,h1,c4,c3a,c3a,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0500 117.9400 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,h1,c4,c3a,c3a,h1 class2 aat 0.0 120.0500 117.9400 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,h1,c4,c3a,c3a,h1 class2 bb13 0.0 1.5010 1.0982 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,c4,c4,c3a,c3a,c4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,c4,c4,c3a,c3a,c4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,c4,c4,c3a,c3a,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5010 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,c4,c4,c3a,c3a,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0500 120.0500 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,c4,c4,c3a,c3a,c4 class2 aat 0.0 120.0500 120.0500 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,c4,c4,c3a,c3a,c4 class2 bb13 0.0 1.5010 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,c3prime,c4,c3a,c3a,c3prime class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,c3prime,c4,c3a,c3a,c3prime class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,c3prime,c4,c3a,c3a,c3prime class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5010 1.4890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,c3prime,c4,c3a,c3a,c3prime class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0500 116.0640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,c3prime,c4,c3a,c3a,c3prime class2 aat 0.0 120.0500 116.0640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,c3prime,c4,c3a,c3a,c3prime class2 bb13 0.0 1.5010 1.4890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,c3a,c4,c3a,c3a,c3a class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,c3a,c4,c3a,c3a,c3a class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,c3a,c4,c3a,c3a,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5010 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,c3a,c4,c3a,c3a,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0500 118.9000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,c3a,c4,c3a,c3a,c3a class2 aat 0.0 120.0500 118.9000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,c3a,c4,c3a,c3a,c3a class2 bb13 0.0 1.5010 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,si4,c3prime,c3a,c3a,si4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,si4,c3prime,c3a,c3a,si4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,si4,c3prime,c3a,c3a,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4890 1.8634 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,si4,c3prime,c3a,c3a,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 116.0640 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,si4,c3prime,c3a,c3a,si4 class2 aat 0.0 116.0640 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,si4,c3prime,c3a,c3a,si4 class2 bb13 0.0 1.4890 1.8634 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,p4=,c3prime,c3a,c3a,p4= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,p4=,c3prime,c3a,c3a,p4= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,p4=,c3prime,c3a,c3a,p4= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4890 1.7890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,p4=,c3prime,c3a,c3a,p4= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 116.0640 120.0010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,p4=,c3prime,c3a,c3a,p4= class2 aat 0.0 116.0640 120.0010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,p4=,c3prime,c3a,c3a,p4= class2 bb13 0.0 1.4890 1.7890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,o2h,c3prime,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,o2h,c3prime,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,o2h,c3prime,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4890 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,o2h,c3prime,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 116.0640 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,o2h,c3prime,c3a,c3a,o2 class2 aat 0.0 116.0640 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,o2h,c3prime,c3a,c3a,o2 class2 bb13 0.0 1.4890 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,o2e,c3prime,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,o2e,c3prime,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,o2e,c3prime,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4890 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,o2e,c3prime,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 116.0640 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,o2e,c3prime,c3a,c3a,o2 class2 aat 0.0 116.0640 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,o2e,c3prime,c3a,c3a,o2 class2 bb13 0.0 1.4890 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,o2,c3prime,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,o2,c3prime,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,o2,c3prime,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4890 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,o2,c3prime,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 116.0640 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,o2,c3prime,c3a,c3a,o2 class2 aat 0.0 116.0640 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,o2,c3prime,c3a,c3a,o2 class2 bb13 0.0 1.4890 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,n3o,c3prime,c3a,c3a,n3o class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,n3o,c3prime,c3a,c3a,n3o class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,n3o,c3prime,c3a,c3a,n3o class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4890 1.4300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,n3o,c3prime,c3a,c3a,n3o class2 at 0.0 0.0 0.0 0.0 0.0 0.0 116.0640 118.8000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,n3o,c3prime,c3a,c3a,n3o class2 aat 0.0 116.0640 118.8000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,n3o,c3prime,c3a,c3a,n3o class2 bb13 0.0 1.4890 1.4300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,n3m,c3prime,c3a,c3a,n3m class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,n3m,c3prime,c3a,c3a,n3m class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,n3m,c3prime,c3a,c3a,n3m class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4890 1.3950 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,n3m,c3prime,c3a,c3a,n3m class2 at 0.0 0.0 0.0 0.0 0.0 0.0 116.0640 120.7640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,n3m,c3prime,c3a,c3a,n3m class2 aat 0.0 116.0640 120.7640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,n3m,c3prime,c3a,c3a,n3m class2 bb13 0.0 1.4890 1.3950 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,n2=,c3prime,c3a,c3a,n2= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,n2=,c3prime,c3a,c3a,n2= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,n2=,c3prime,c3a,c3a,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4890 1.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,n2=,c3prime,c3a,c3a,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 116.0640 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,n2=,c3prime,c3a,c3a,n2= class2 aat 0.0 116.0640 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,n2=,c3prime,c3a,c3a,n2= class2 bb13 0.0 1.4890 1.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,h1,c3prime,c3a,c3a,h1 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,h1,c3prime,c3a,c3a,h1 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,h1,c3prime,c3a,c3a,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4890 1.0982 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,h1,c3prime,c3a,c3a,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 116.0640 117.9400 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,h1,c3prime,c3a,c3a,h1 class2 aat 0.0 116.0640 117.9400 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,h1,c3prime,c3a,c3a,h1 class2 bb13 0.0 1.4890 1.0982 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,c4,c3prime,c3a,c3a,c4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,c4,c3prime,c3a,c3a,c4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,c4,c3prime,c3a,c3a,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4890 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,c4,c3prime,c3a,c3a,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 116.0640 120.0500 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,c4,c3prime,c3a,c3a,c4 class2 aat 0.0 116.0640 120.0500 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,c4,c3prime,c3a,c3a,c4 class2 bb13 0.0 1.4890 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,c3prime,c3prime,c3a,c3a,c3prime class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,c3prime,c3prime,c3a,c3a,c3prime class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,c3prime,c3prime,c3a,c3a,c3prime class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4890 1.4890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,c3prime,c3prime,c3a,c3a,c3prime class2 at 0.0 0.0 0.0 0.0 0.0 0.0 116.0640 116.0640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,c3prime,c3prime,c3a,c3a,c3prime class2 aat 0.0 116.0640 116.0640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,c3prime,c3prime,c3a,c3a,c3prime class2 bb13 0.0 1.4890 1.4890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,c3a,c3prime,c3a,c3a,c3a class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,c3a,c3prime,c3a,c3a,c3a class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,c3a,c3prime,c3a,c3a,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4890 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,c3a,c3prime,c3a,c3a,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 116.0640 118.9000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,c3a,c3prime,c3a,c3a,c3a class2 aat 0.0 116.0640 118.9000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,c3a,c3prime,c3a,c3a,c3a class2 bb13 0.0 1.4890 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,si4,c3a,c3a,c3a,si4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,si4,c3a,c3a,c3a,si4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,si4,c3a,c3a,c3a,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.8634 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,si4,c3a,c3a,c3a,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.9000 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,si4,c3a,c3a,c3a,si4 class2 aat 0.0 118.9000 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,si4,c3a,c3a,c3a,si4 class2 bb13 0.0 1.4170 1.8634 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,p4=,c3a,c3a,c3a,p4= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,p4=,c3a,c3a,c3a,p4= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,p4=,c3a,c3a,c3a,p4= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.7890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,p4=,c3a,c3a,c3a,p4= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.9000 120.0010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,p4=,c3a,c3a,c3a,p4= class2 aat 0.0 118.9000 120.0010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,p4=,c3a,c3a,c3a,p4= class2 bb13 0.0 1.4170 1.7890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,o2h,c3a,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,o2h,c3a,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,o2h,c3a,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,o2h,c3a,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.9000 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,o2h,c3a,c3a,c3a,o2 class2 aat 0.0 118.9000 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,o2h,c3a,c3a,c3a,o2 class2 bb13 0.0 1.4170 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,o2e,c3a,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,o2e,c3a,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,o2e,c3a,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,o2e,c3a,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.9000 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,o2e,c3a,c3a,c3a,o2 class2 aat 0.0 118.9000 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,o2e,c3a,c3a,c3a,o2 class2 bb13 0.0 1.4170 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,o2,c3a,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,o2,c3a,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,o2,c3a,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,o2,c3a,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.9000 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,o2,c3a,c3a,c3a,o2 class2 aat 0.0 118.9000 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,o2,c3a,c3a,c3a,o2 class2 bb13 0.0 1.4170 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,n3o,c3a,c3a,c3a,n3o class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,n3o,c3a,c3a,c3a,n3o class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,n3o,c3a,c3a,c3a,n3o class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.4300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,n3o,c3a,c3a,c3a,n3o class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.9000 118.8000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,n3o,c3a,c3a,c3a,n3o class2 aat 0.0 118.9000 118.8000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,n3o,c3a,c3a,c3a,n3o class2 bb13 0.0 1.4170 1.4300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,n3m,c3a,c3a,c3a,n3m class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,n3m,c3a,c3a,c3a,n3m class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,n3m,c3a,c3a,c3a,n3m class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.3950 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,n3m,c3a,c3a,c3a,n3m class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.9000 120.7640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,n3m,c3a,c3a,c3a,n3m class2 aat 0.0 118.9000 120.7640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,n3m,c3a,c3a,c3a,n3m class2 bb13 0.0 1.4170 1.3950 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,n2=,c3a,c3a,c3a,n2= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,n2=,c3a,c3a,c3a,n2= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,n2=,c3a,c3a,c3a,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,n2=,c3a,c3a,c3a,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.9000 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,n2=,c3a,c3a,c3a,n2= class2 aat 0.0 118.9000 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,n2=,c3a,c3a,c3a,n2= class2 bb13 0.0 1.4170 1.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,h1,c3a,c3a,c3a,h1 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,h1,c3a,c3a,c3a,h1 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,h1,c3a,c3a,c3a,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.0982 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,h1,c3a,c3a,c3a,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.9000 117.9400 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,h1,c3a,c3a,c3a,h1 class2 aat 0.0 118.9000 117.9400 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,h1,c3a,c3a,c3a,h1 class2 bb13 0.0 1.4170 1.0982 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,c4,c3a,c3a,c3a,c4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,c4,c3a,c3a,c3a,c4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,c4,c3a,c3a,c3a,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,c4,c3a,c3a,c3a,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.9000 120.0500 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,c4,c3a,c3a,c3a,c4 class2 aat 0.0 118.9000 120.0500 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,c4,c3a,c3a,c3a,c4 class2 bb13 0.0 1.4170 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,c3prime,c3a,c3a,c3a,c3prime class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,c3prime,c3a,c3a,c3a,c3prime class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,c3prime,c3a,c3a,c3a,c3prime class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.4890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,c3prime,c3a,c3a,c3a,c3prime class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.9000 116.0640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,c3prime,c3a,c3a,c3a,c3prime class2 aat 0.0 118.9000 116.0640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,c3prime,c3a,c3a,c3a,c3prime class2 bb13 0.0 1.4170 1.4890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.9000 118.9000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a class2 aat 0.0 118.9000 118.9000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a class2 bb13 0.0 1.4170 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:h1,c4,c4,h1,h1,c4,c4,h1,h1,c4,c4,h1 class2 -0.1432 0.0 0.0617 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:h1,c4,c4,h1,h1,c4,c4,h1,h1,c4,c4,h1 class2 mbt -14.2610 -0.5322 -0.4864 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:h1,c4,c4,h1,h1,c4,c4,h1,h1,c4,c4,h1 class2 ebt 0.2130 0.3120 0.0777 0.2130 0.3120 0.0777 1.1010 1.1010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:h1,c4,c4,h1,h1,c4,c4,h1,h1,c4,c4,h1 class2 at -0.8085 0.5569 -0.2466 -0.8085 0.5569 -0.2466 110.7700 110.7700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:h1,c4,c4,h1,h1,c4,c4,h1,h1,c4,c4,h1 class2 aat -12.5640 110.7700 110.7700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:h1,c4,c4,h1,h1,c4,c4,h1,h1,c4,c4,h1 class2 bb13 0.0 1.1010 1.1010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c4,c4,c4,h1,c4,c4,c4,h1,c4,c4,c4,h1 class2 0.0000 0.0 0.0316 0.0 -0.1681 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c4,c4,c4,h1,c4,c4,c4,h1,c4,c4,c4,h1 class2 mbt -14.8790 -3.6581 -0.3138 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c4,c4,c4,h1,c4,c4,c4,h1,c4,c4,c4,h1 class2 ebt 0.2486 0.2422 -0.0925 0.0814 0.0591 0.2219 1.5300 1.1010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c4,c4,c4,h1,c4,c4,c4,h1,c4,c4,c4,h1 class2 at -0.2454 0.0000 -0.1136 0.3113 0.4516 -0.1988 112.6700 110.7700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c4,c4,c4,h1,c4,c4,c4,h1,c4,c4,c4,h1 class2 aat -16.1640 112.6700 110.7700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c4,c4,c4,h1,c4,c4,c4,h1,c4,c4,c4,h1 class2 bb13 0.0 1.5300 1.1010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c4,c4,c4,c4,c4,c4,c4,c4,c4,c4,c4,c4 class2 0.0000 0.0 0.0514 0.0 -0.1430 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c4,c4,c4,c4,c4,c4,c4,c4,c4,c4,c4,c4 class2 mbt -17.7870 -7.1877 0.0000 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c4,c4,c4,c4,c4,c4,c4,c4,c4,c4,c4,c4 class2 ebt -0.0732 0.0000 0.0000 -0.0732 0.0000 0.0000 1.5300 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c4,c4,c4,c4,c4,c4,c4,c4,c4,c4,c4,c4 class2 at 0.3886 -0.3139 0.1389 0.3886 -0.3139 0.1389 112.6700 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c4,c4,c4,c4,c4,c4,c4,c4,c4,c4,c4,c4 class2 aat -22.0450 112.6700 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c4,c4,c4,c4,c4,c4,c4,c4,c4,c4,c4,c4 class2 bb13 0.0 1.5300 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c4,c4,h1,c3a,c4,c4,h1,c3a,c4,c4,h1 class2 -0.0228 0.0 0.0280 0.0 -0.1863 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c4,c4,h1,c3a,c4,c4,h1,c3a,c4,c4,h1 class2 mbt 0.0000 0.0000 0.0000 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c4,c4,h1,c3a,c4,c4,h1,c3a,c4,c4,h1 class2 ebt 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.5010 1.1010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c4,c4,h1,c3a,c4,c4,h1,c3a,c4,c4,h1 class2 at 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 108.4000 110.7700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c4,c4,h1,c3a,c4,c4,h1,c3a,c4,c4,h1 class2 aat 0.0 108.4000 110.7700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c4,c4,h1,c3a,c4,c4,h1,c3a,c4,c4,h1 class2 bb13 0.0 1.5010 1.1010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,c4,c4,c3a,c3a,c4,c4,c3a,c3a,c4,c4 class2 -0.2802 0.0 -0.0678 0.0 -0.0122 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,c4,c4,c3a,c3a,c4,c4,c3a,c3a,c4,c4 class2 mbt 0.0000 0.0000 0.0000 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,c4,c4,c3a,c3a,c4,c4,c3a,c3a,c4,c4 class2 ebt 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.4170 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,c4,c4,c3a,c3a,c4,c4,c3a,c3a,c4,c4 class2 at 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 120.0500 108.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,c4,c4,c3a,c3a,c4,c4,c3a,c3a,c4,c4 class2 aat 0.0 120.0500 108.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,c4,c4,c3a,c3a,c4,c4,c3a,c3a,c4,c4 class2 bb13 0.0 1.4170 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,c4,c3a,c3a,c3a,c4,c3a,c3a,c3a,c4,c3a class2 -0.2802 0.0 -0.0678 0.0 -0.0122 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,c4,c3a,c3a,c3a,c4,c3a,c3a,c3a,c4,c3a class2 mbt 0.0 0.0 0.0 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,c4,c3a,c3a,c3a,c4,c3a,c3a,c3a,c4,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,c4,c3a,c3a,c3a,c4,c3a,c3a,c3a,c4,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0500 111.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,c4,c3a,c3a,c3a,c4,c3a,c3a,c3a,c4,c3a class2 aat 0.0 120.0500 111.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,c4,c3a,c3a,c3a,c4,c3a,c3a,c3a,c4,c3a class2 bb13 0.0 1.4170 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,o2,h1,c3a,c3a,o2h,h1,c3a,c3a,o2,h1 class2 -0.6900 0.0 0.5097 0.0 0.0095 0.0 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,o2,h1,c3a,c3a,o2h,h1,c3a,c3a,o2,h1 class2 mbt 1.1580 3.2697 3.5132 1.3768 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,o2,h1,c3a,c3a,o2h,h1,c3a,c3a,o2,h1 class2 ebt 0.9000 -1.3456 1.1900 3.4132 0.5873 -0.1323 1.4170 0.9494 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,o2,h1,c3a,c3a,o2h,h1,c3a,c3a,o2,h1 class2 at -5.1360 -1.0122 0.0000 4.6852 0.0230 -0.5980 123.4200 108.1900 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,o2,h1,c3a,c3a,o2h,h1,c3a,c3a,o2,h1 class2 aat -4.6072 123.4200 108.1900 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,o2,h1,c3a,c3a,o2h,h1,c3a,c3a,o2,h1 class2 bb13 1.1590 1.4170 0.9494 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c3a,c3a,o2,h1,c3a,c3a,o2h,h1,c3a,c3a,o2 class2 0.0000 0.0 1.7234 0.0 0.0000 0.0 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c3a,c3a,o2,h1,c3a,c3a,o2h,h1,c3a,c3a,o2 class2 mbt 0.0000 5.5432 0.0000 1.4170 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c3a,c3a,o2,h1,c3a,c3a,o2h,h1,c3a,c3a,o2 class2 ebt 0.0000 -1.5867 0.0000 0.0000 4.2641 0.0000 1.0982 1.3768 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c3a,c3a,o2,h1,c3a,c3a,o2h,h1,c3a,c3a,o2 class2 at 0.0000 1.8729 0.0000 0.0000 2.5706 0.0000 117.9400 123.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c3a,c3a,o2,h1,c3a,c3a,o2h,h1,c3a,c3a,o2 class2 aat 4.2296 117.9400 123.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c3a,c3a,o2,h1,c3a,c3a,o2h,h1,c3a,c3a,o2 class2 bb13 -2.0517 1.0982 1.3768 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c3a,c3a,o2,h1,c3a,c3a,o2e,h1,c3a,c3a,o2 class2 0.0000 0.0 1.7234 0.0 0.0000 0.0 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c3a,c3a,o2,h1,c3a,c3a,o2e,h1,c3a,c3a,o2 class2 mbt 0.0000 5.5432 0.0000 1.4170 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c3a,c3a,o2,h1,c3a,c3a,o2e,h1,c3a,c3a,o2 class2 ebt 0.0000 -1.5867 0.0000 0.0000 4.2641 0.0000 1.0982 1.3768 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c3a,c3a,o2,h1,c3a,c3a,o2e,h1,c3a,c3a,o2 class2 at 0.0000 1.8729 0.0000 0.0000 2.5706 0.0000 117.9400 123.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c3a,c3a,o2,h1,c3a,c3a,o2e,h1,c3a,c3a,o2 class2 aat 4.2296 117.9400 123.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c3a,c3a,o2,h1,c3a,c3a,o2e,h1,c3a,c3a,o2 class2 bb13 -2.0517 1.0982 1.3768 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c3a,c3a,o2,h1,c3a,c3a,o2,h1,c3a,c3a,o2 class2 0.0000 0.0 1.7234 0.0 0.0000 0.0 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c3a,c3a,o2,h1,c3a,c3a,o2,h1,c3a,c3a,o2 class2 mbt 0.0000 5.5432 0.0000 1.4170 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c3a,c3a,o2,h1,c3a,c3a,o2,h1,c3a,c3a,o2 class2 ebt 0.0000 -1.5867 0.0000 0.0000 4.2641 0.0000 1.0982 1.3768 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c3a,c3a,o2,h1,c3a,c3a,o2,h1,c3a,c3a,o2 class2 at 0.0000 1.8729 0.0000 0.0000 2.5706 0.0000 117.9400 123.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c3a,c3a,o2,h1,c3a,c3a,o2,h1,c3a,c3a,o2 class2 aat 4.2296 117.9400 123.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c3a,c3a,o2,h1,c3a,c3a,o2,h1,c3a,c3a,o2 class2 bb13 -2.0517 1.0982 1.3768 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,c3a,o2,c3a,c3a,c3a,o2h,c3a,c3a,c3a,o2 class2 0.0000 0.0 4.8498 0.0 0.0000 0.0 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,c3a,o2,c3a,c3a,c3a,o2h,c3a,c3a,c3a,o2 class2 mbt 0.0000 4.8255 0.0000 1.4170 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,c3a,o2,c3a,c3a,c3a,o2h,c3a,c3a,c3a,o2 class2 ebt 0.0000 0.2655 0.0000 0.0000 4.8905 0.0000 1.4170 1.3768 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,c3a,o2,c3a,c3a,c3a,o2h,c3a,c3a,c3a,o2 class2 at 0.0000 10.0155 0.0000 0.0000 1.7404 0.0000 118.9000 123.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,c3a,o2,c3a,c3a,c3a,o2h,c3a,c3a,c3a,o2 class2 aat -21.0247 118.9000 123.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,c3a,o2,c3a,c3a,c3a,o2h,c3a,c3a,c3a,o2 class2 bb13 -2.2436 1.4170 1.3768 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,c3a,o2,c3a,c3a,c3a,o2e,c3a,c3a,c3a,o2 class2 0.0000 0.0 4.8498 0.0 0.0000 0.0 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,c3a,o2,c3a,c3a,c3a,o2e,c3a,c3a,c3a,o2 class2 mbt 0.0000 4.8255 0.0000 1.4170 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,c3a,o2,c3a,c3a,c3a,o2e,c3a,c3a,c3a,o2 class2 ebt 0.0000 0.2655 0.0000 0.0000 4.8905 0.0000 1.4170 1.3768 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,c3a,o2,c3a,c3a,c3a,o2e,c3a,c3a,c3a,o2 class2 at 0.0000 10.0155 0.0000 0.0000 1.7404 0.0000 118.9000 123.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,c3a,o2,c3a,c3a,c3a,o2e,c3a,c3a,c3a,o2 class2 aat -21.0247 118.9000 123.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,c3a,o2,c3a,c3a,c3a,o2e,c3a,c3a,c3a,o2 class2 bb13 -2.2436 1.4170 1.3768 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,c3a,o2,c3a,c3a,c3a,o2,c3a,c3a,c3a,o2 class2 0.0000 0.0 4.8498 0.0 0.0000 0.0 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,c3a,o2,c3a,c3a,c3a,o2,c3a,c3a,c3a,o2 class2 mbt 0.0000 4.8255 0.0000 1.4170 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,c3a,o2,c3a,c3a,c3a,o2,c3a,c3a,c3a,o2 class2 ebt 0.0000 0.2655 0.0000 0.0000 4.8905 0.0000 1.4170 1.3768 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,c3a,o2,c3a,c3a,c3a,o2,c3a,c3a,c3a,o2 class2 at 0.0000 10.0155 0.0000 0.0000 1.7404 0.0000 118.9000 123.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,c3a,o2,c3a,c3a,c3a,o2,c3a,c3a,c3a,o2 class2 aat -21.0247 118.9000 123.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,c3a,o2,c3a,c3a,c3a,o2,c3a,c3a,c3a,o2 class2 bb13 -2.2436 1.4170 1.3768 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,c4,h1,c3a,c3a,c4,h1,c3a,c3a,c4,h1 class2 -0.2802 0.0 -0.0678 0.0 -0.0122 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,c4,h1,c3a,c3a,c4,h1,c3a,c3a,c4,h1 class2 mbt -5.5679 1.4083 0.3010 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,c4,h1,c3a,c3a,c4,h1,c3a,c3a,c4,h1 class2 ebt -0.5835 1.1220 0.3978 1.3997 0.7756 0.0000 1.4170 1.1010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,c4,h1,c3a,c3a,c4,h1,c3a,c3a,c4,h1 class2 at 0.2251 0.6548 0.1237 4.6266 0.1632 0.0461 120.0500 111.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,c4,h1,c3a,c3a,c4,h1,c3a,c3a,c4,h1 class2 aat -5.8888 120.0500 111.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,c4,h1,c3a,c3a,c4,h1,c3a,c3a,c4,h1 class2 bb13 -3.4826 1.4170 1.1010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:h1,c3a,c3a,h1,h1,c3a,c3a,h1,h1,c3a,c3a,h1 class2 0.0000 0.0 2.3500 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:h1,c3a,c3a,h1,h1,c3a,c3a,h1,h1,c3a,c3a,h1 class2 mbt 0.0000 4.8228 0.0000 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:h1,c3a,c3a,h1,h1,c3a,c3a,h1,h1,c3a,c3a,h1 class2 ebt 0.0000 -0.6890 0.0000 0.0000 -0.6890 0.0000 1.0982 1.0982 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:h1,c3a,c3a,h1,h1,c3a,c3a,h1,h1,c3a,c3a,h1 class2 at 0.0000 2.4501 0.0000 0.0000 2.4501 0.0000 117.9400 117.9400 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:h1,c3a,c3a,h1,h1,c3a,c3a,h1,h1,c3a,c3a,h1 class2 aat 0.3598 117.9400 117.9400 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:h1,c3a,c3a,h1,h1,c3a,c3a,h1,h1,c3a,c3a,h1 class2 bb13 -1.7077 1.0982 1.0982 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c4,c3a,c3a,h1,c4,c3a,c3a,h1,c4,c3a,c3a,h1 class2 0.0000 0.0 1.5590 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c4,c3a,c3a,h1,c4,c3a,c3a,h1,c4,c3a,c3a,h1 class2 mbt 0.0000 3.9421 0.0000 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c4,c3a,c3a,h1,c4,c3a,c3a,h1,c4,c3a,c3a,h1 class2 ebt 0.0000 -1.7970 0.0000 0.0000 -0.4879 0.0000 1.5010 1.0982 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c4,c3a,c3a,h1,c4,c3a,c3a,h1,c4,c3a,c3a,h1 class2 at 0.0000 -0.1242 0.0000 0.0000 3.4601 0.0000 120.0500 117.9400 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c4,c3a,c3a,h1,c4,c3a,c3a,h1,c4,c3a,c3a,h1 class2 aat 4.4444 120.0500 117.9400 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c4,c3a,c3a,h1,c4,c3a,c3a,h1,c4,c3a,c3a,h1 class2 bb13 0.8743 1.5010 1.0982 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,c3a,h1,c3a,c3a,c3a,h1,c3a,c3a,c3a,h1 class2 0.0000 0.0 3.9661 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,c3a,h1,c3a,c3a,c3a,h1,c3a,c3a,c3a,h1 class2 mbt 0.0000 -1.1521 0.0000 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,c3a,h1,c3a,c3a,c3a,h1,c3a,c3a,c3a,h1 class2 ebt 0.0000 -6.8958 0.0000 0.0000 -0.4669 0.0000 1.4170 1.0982 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,c3a,h1,c3a,c3a,c3a,h1,c3a,c3a,c3a,h1 class2 at 0.0000 2.5014 0.0000 0.0000 2.7147 0.0000 118.9000 117.9400 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,c3a,h1,c3a,c3a,c3a,h1,c3a,c3a,c3a,h1 class2 aat -4.8141 118.9000 117.9400 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,c3a,h1,c3a,c3a,c3a,h1,c3a,c3a,c3a,h1 class2 bb13 -6.2741 1.4170 1.0982 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,c3a,c4,c3a,c3a,c3a,c4,c3a,c3a,c3a,c4 class2 0.0000 0.0 4.4072 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,c3a,c4,c3a,c3a,c3a,c4,c3a,c3a,c3a,c4 class2 mbt 0.0000 9.1792 0.0000 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,c3a,c4,c3a,c3a,c3a,c4,c3a,c3a,c3a,c4 class2 ebt 0.0000 -0.6918 0.0000 0.0000 0.2421 0.0000 1.4170 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,c3a,c4,c3a,c3a,c3a,c4,c3a,c3a,c3a,c4 class2 at 0.0000 3.8987 0.0000 0.0000 -4.4683 0.0000 118.9000 120.0500 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,c3a,c4,c3a,c3a,c3a,c4,c3a,c3a,c3a,c4 class2 aat -14.4097 118.9000 120.0500 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,c3a,c4,c3a,c3a,c3a,c4,c3a,c3a,c3a,c4 class2 bb13 2.5085 1.4170 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a class2 8.3667 0.0 1.2000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a class2 mbt 27.5989 -2.3120 0.0000 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a class2 ebt -0.1185 6.3204 0.0000 -0.1185 6.3204 0.0000 1.4170 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a class2 at 1.9767 1.0239 0.0000 1.9767 1.0239 0.0000 118.9000 118.9000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a class2 aat 0.0000 118.9000 118.9000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a class2 bb13 53.0000 1.4170 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3prime,n3m,c3prime,o1,X,X,X,X,X,X,X,X class2 -0.4066 0.0 1.2513 0.0 -0.7507 0.0 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3prime,n3m,c3prime,o1,X,X,X,X,X,X,X,X class2 mbt 0.0 0.0 0.0 1.0 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3prime,n3m,c3prime,o1,X,X,X,X,X,X,X,X class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0 1.0 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3prime,n3m,c3prime,o1,X,X,X,X,X,X,X,X class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0 120.0 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3prime,n3m,c3prime,o1,X,X,X,X,X,X,X,X class2 aat 0.0 120.0 120.0 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3prime,n3m,c3prime,o1,X,X,X,X,X,X,X,X class2 bb13 0.0 1.0 1.0 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c4,c4,n3o,o1=,X,X,X,X,X,X,X,X class2 0.0000 0.0 0.0000 0.0 -0.3500 0.0 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:c4,c4,n3o,o1=,X,X,X,X,X,X,X,X class2 mbt 0.0 0.0 0.0 1.0 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:c4,c4,n3o,o1=,X,X,X,X,X,X,X,X class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0 1.0 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:c4,c4,n3o,o1=,X,X,X,X,X,X,X,X class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0 120.0 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:c4,c4,n3o,o1=,X,X,X,X,X,X,X,X class2 aat 0.0 120.0 120.0 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:c4,c4,n3o,o1=,X,X,X,X,X,X,X,X class2 bb13 0.0 1.0 1.0 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:X,n3,p4=,X,X,X,X,X,X,X,X,X class2 0.0000 0.0 0.0000 0.0 0.0000 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n3,p4=,X,X,X,X,X,X,X,X,X class2 mbt 0.0 0.0 0.0 1.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n3,p4=,X,X,X,X,X,X,X,X,X class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0 1.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n3,p4=,X,X,X,X,X,X,X,X,X class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0 120.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n3,p4=,X,X,X,X,X,X,X,X,X class2 aat 0.0 120.0 120.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n3,p4=,X,X,X,X,X,X,X,X,X class2 bb13 0.0 1.0 1.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c3a,n2=,X,X,X,X,X,X,X,X,X class2 0.0000 0.0 1.0000 0.0 0.0000 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c3a,n2=,X,X,X,X,X,X,X,X,X class2 mbt 0.0 0.0 0.0 1.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c3a,n2=,X,X,X,X,X,X,X,X,X class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0 1.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c3a,n2=,X,X,X,X,X,X,X,X,X class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0 120.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c3a,n2=,X,X,X,X,X,X,X,X,X class2 aat 0.0 120.0 120.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c3a,n2=,X,X,X,X,X,X,X,X,X class2 bb13 0.0 1.0 1.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,o2,p4=,X,X,X,X,X,X,X,X,X class2 5.7080 0.0 2.1180 0.0 0.0000 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,o2,p4=,X,X,X,X,X,X,X,X,X class2 mbt 0.0 0.0 0.0 1.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,o2,p4=,X,X,X,X,X,X,X,X,X class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0 1.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,o2,p4=,X,X,X,X,X,X,X,X,X class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0 120.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,o2,p4=,X,X,X,X,X,X,X,X,X class2 aat 0.0 120.0 120.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,o2,p4=,X,X,X,X,X,X,X,X,X class2 bb13 0.0 1.0 1.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,o2,p4=,o2,X,X,X,X,X,X,X,X class2 5.7080 0.0 2.1180 0.0 0.0000 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,o2,p4=,o2,X,X,X,X,X,X,X,X class2 mbt 0.0 0.0 0.0 1.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,o2,p4=,o2,X,X,X,X,X,X,X,X class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0 1.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,o2,p4=,o2,X,X,X,X,X,X,X,X class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0 120.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,o2,p4=,o2,X,X,X,X,X,X,X,X class2 aat 0.0 120.0 120.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,o2,p4=,o2,X,X,X,X,X,X,X,X class2 bb13 0.0 1.0 1.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,o2,p4=,n2=,X,X,X,X,X,X,X,X class2 5.7080 0.0 2.1180 0.0 0.0000 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,o2,p4=,n2=,X,X,X,X,X,X,X,X class2 mbt 0.0 0.0 0.0 1.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,o2,p4=,n2=,X,X,X,X,X,X,X,X class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0 1.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,o2,p4=,n2=,X,X,X,X,X,X,X,X class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0 120.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,o2,p4=,n2=,X,X,X,X,X,X,X,X class2 aat 0.0 120.0 120.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,o2,p4=,n2=,X,X,X,X,X,X,X,X class2 bb13 0.0 1.0 1.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,o2,p4=,h1,X,X,X,X,X,X,X,X class2 5.7080 0.0 2.1180 0.0 0.0000 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,o2,p4=,h1,X,X,X,X,X,X,X,X class2 mbt 0.0 0.0 0.0 1.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,o2,p4=,h1,X,X,X,X,X,X,X,X class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0 1.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,o2,p4=,h1,X,X,X,X,X,X,X,X class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0 120.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,o2,p4=,h1,X,X,X,X,X,X,X,X class2 aat 0.0 120.0 120.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,o2,p4=,h1,X,X,X,X,X,X,X,X class2 bb13 0.0 1.0 1.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,n3,p4=,o2,X,X,X,X,X,X,X,X class2 0.0000 0.0 0.0000 0.0 0.0000 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,n3,p4=,o2,X,X,X,X,X,X,X,X class2 mbt 0.0 0.0 0.0 1.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,n3,p4=,o2,X,X,X,X,X,X,X,X class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0 1.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,n3,p4=,o2,X,X,X,X,X,X,X,X class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0 120.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,n3,p4=,o2,X,X,X,X,X,X,X,X class2 aat 0.0 120.0 120.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,n3,p4=,o2,X,X,X,X,X,X,X,X class2 bb13 0.0 1.0 1.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,n3,p4=,n2=,X,X,X,X,X,X,X,X class2 0.0000 0.0 0.0000 0.0 0.0000 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,n3,p4=,n2=,X,X,X,X,X,X,X,X class2 mbt 0.0 0.0 0.0 1.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,n3,p4=,n2=,X,X,X,X,X,X,X,X class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0 1.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,n3,p4=,n2=,X,X,X,X,X,X,X,X class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0 120.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,n3,p4=,n2=,X,X,X,X,X,X,X,X class2 aat 0.0 120.0 120.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,n3,p4=,n2=,X,X,X,X,X,X,X,X class2 bb13 0.0 1.0 1.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,n3,p4=,h1,X,X,X,X,X,X,X,X class2 0.0000 0.0 0.0000 0.0 0.0000 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,n3,p4=,h1,X,X,X,X,X,X,X,X class2 mbt 0.0 0.0 0.0 1.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,n3,p4=,h1,X,X,X,X,X,X,X,X class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0 1.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,n3,p4=,h1,X,X,X,X,X,X,X,X class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0 120.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,n3,p4=,h1,X,X,X,X,X,X,X,X class2 aat 0.0 120.0 120.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,n3,p4=,h1,X,X,X,X,X,X,X,X class2 bb13 0.0 1.0 1.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,o2z,si4,o2z,X,X,X,X,X,X,X,X class2 0.0000 0.0 0.0000 0.0 -0.0500 0.0 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:h1,o2z,si4,o2z,X,X,X,X,X,X,X,X class2 mbt 0.0 0.0 0.0 1.0 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:h1,o2z,si4,o2z,X,X,X,X,X,X,X,X class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0 1.0 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:h1,o2z,si4,o2z,X,X,X,X,X,X,X,X class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0 120.0 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:h1,o2z,si4,o2z,X,X,X,X,X,X,X,X class2 aat 0.0 120.0 120.0 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:h1,o2z,si4,o2z,X,X,X,X,X,X,X,X class2 bb13 0.0 1.0 1.0 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:h1,o2z,si4,h1,X,X,X,X,X,X,X,X class2 0.0000 0.0 0.0000 0.0 -0.0500 0.0 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:h1,o2z,si4,h1,X,X,X,X,X,X,X,X class2 mbt 0.0 0.0 0.0 1.0 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:h1,o2z,si4,h1,X,X,X,X,X,X,X,X class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0 1.0 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:h1,o2z,si4,h1,X,X,X,X,X,X,X,X class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0 120.0 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:h1,o2z,si4,h1,X,X,X,X,X,X,X,X class2 aat 0.0 120.0 120.0 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:h1,o2z,si4,h1,X,X,X,X,X,X,X,X class2 bb13 0.0 1.0 1.0 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:c4,si4,o2z,h1,X,X,X,X,X,X,X,X class2 0.0000 0.0 0.0000 0.0 -0.0500 0.0 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:c4,si4,o2z,h1,X,X,X,X,X,X,X,X class2 mbt 0.0 0.0 0.0 1.0 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:c4,si4,o2z,h1,X,X,X,X,X,X,X,X class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0 1.0 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:c4,si4,o2z,h1,X,X,X,X,X,X,X,X class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0 120.0 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:c4,si4,o2z,h1,X,X,X,X,X,X,X,X class2 aat 0.0 120.0 120.0 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:c4,si4,o2z,h1,X,X,X,X,X,X,X,X class2 bb13 0.0 1.0 1.0 # (ver=1.0, ref=2) + } # end of dihedral_coeff commands + + + # --------------- Improper Interactions: --------------------- + + + # -- Rules for generating (4-body) "improper" interactions: -- + # ImproperType AtmType1 AtmType2 AtmType3 AtmType3 [BondType1 Bnd2 Bnd3] + + write_once("Data Impropers By Type (cenJsortIKL)") { + @improper:c4,c4,c4,c4,c4,c4,c4,c4 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ac4,d*,ic4 + @improper:c3a,c4,h1,h1,c3a,c4,h1,h1 @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ah1,d*,ih1 @atom:*,p*,b*,ah1,d*,ih1 + @improper:c4,c4,h1,o2,c4,c4,h1,o2 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ah1,d*,ih1 @atom:*,p*,b*,ao2,d*,io2 + @improper:h1,c4,h1,n2=,h1,c4,h1,n2= @atom:*,p*,b*,ah1,d*,ih1 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ah1,d*,ih1 @atom:*,p*,b*,an2=,d*,in2= + @improper:h1,c4,h1,si4,h1,c4,h1,si4 @atom:*,p*,b*,ah1,d*,ih1 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ah1,d*,ih1 @atom:*,p*,b*,asi4,d*,isi4 + @improper:c4,si4,c4,h1,c4,si4,c4,h1 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,asi4,d*,isi4 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ah1,d*,ih1 + @improper:h1,c4,h1,h1,h1,c4,h1,h1 @atom:*,p*,b*,ah1,d*,ih1 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ah1,d*,ih1 @atom:*,p*,b*,ah1,d*,ih1 + @improper:c4,c4,c4,h1,c4,c4,c4,h1 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ah1,d*,ih1 + @improper:c4,si4,c4,si4,c4,si4,c4,si4 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,asi4,d*,isi4 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,asi4,d*,isi4 + @improper:c4,c4,h1,h1,c4,c4,h1,h1 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ah1,d*,ih1 @atom:*,p*,b*,ah1,d*,ih1 + @improper:h1,si4,h1,h1,h1,si4,h1,h1 @atom:*,p*,b*,ah1,d*,ih1 @atom:*,p*,b*,asi4,d*,isi4 @atom:*,p*,b*,ah1,d*,ih1 @atom:*,p*,b*,ah1,d*,ih1 + @improper:h1,si4,si4,si4,h1,si4,si4,si4 @atom:*,p*,b*,ah1,d*,ih1 @atom:*,p*,b*,asi4,d*,isi4 @atom:*,p*,b*,asi4,d*,isi4 @atom:*,p*,b*,asi4,d*,isi4 + @improper:c4,si4,si4,si4,c4,si4,si4,si4 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,asi4,d*,isi4 @atom:*,p*,b*,asi4,d*,isi4 @atom:*,p*,b*,asi4,d*,isi4 + @improper:c3a,c4,c4,h1,c3a,c4,c4,h1 @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ah1,d*,ih1 + @improper:c3prime,c4,h1,h1,c3prime,c4,h1,h1 @atom:*,p*,b*,ac3prime,d*,ic3prime @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ah1,d*,ih1 @atom:*,p*,b*,ah1,d*,ih1 + @improper:c4,si4,h1,si4,c4,si4,h1,si4 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,asi4,d*,isi4 @atom:*,p*,b*,ah1,d*,ih1 @atom:*,p*,b*,asi4,d*,isi4 + @improper:c4,c4,c4,o2,c4,c4,c4,o2 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ao2,d*,io2 + @improper:h1,c4,h1,o2,h1,c4,h1,o2 @atom:*,p*,b*,ah1,d*,ih1 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ah1,d*,ih1 @atom:*,p*,b*,ao2,d*,io2 + @improper:c4,c4,h1,n2=,c4,c4,h1,n2= @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ah1,d*,ih1 @atom:*,p*,b*,an2=,d*,in2= + @improper:c4,si4,h1,h1,c4,si4,h1,h1 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,asi4,d*,isi4 @atom:*,p*,b*,ah1,d*,ih1 @atom:*,p*,b*,ah1,d*,ih1 + @improper:h1,si4,h1,si4,h1,si4,h1,si4 @atom:*,p*,b*,ah1,d*,ih1 @atom:*,p*,b*,asi4,d*,isi4 @atom:*,p*,b*,ah1,d*,ih1 @atom:*,p*,b*,asi4,d*,isi4 + @improper:c3a,c3prime,n3m,o1=,c3a,c3prime,n3m,o1= @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac3prime,d*,ic3prime @atom:*,p*,b*,an3m,d*,in3m @atom:*,p*,b*,ao1=,d*,io1= + @improper:c3a,c3a,c3a,n2=,c3a,c3a,c3a,n2= @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,an2=,d*,in2= + @improper:c3a,n3m,c3prime,c3prime,c3a,n3m,c3prime,c3prime @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,an3m,d*,in3m @atom:*,p*,b*,ac3prime,d*,ic3prime @atom:*,p*,b*,ac3prime,d*,ic3prime + @improper:c3a,c3a,c3a,si4,c3a,c3a,c3a,si4 @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,asi4,d*,isi4 + @improper:c3a,c3a,c3a,p4=,c3a,c3a,c3a,p4= @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ap4=,d*,ip4= + @improper:c3a,c3a,c3a,c3prime,c3a,c3a,c3a,c3prime @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac3prime,d*,ic3prime + @improper:c3a,c3a,c3a,n3m,c3a,c3a,c3a,n3m @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,an3m,d*,in3m + @improper:c3a,c3a,c3a,n3o,c3a,c3a,c3a,n3o @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,an3o,d*,in3o + @improper:o1=,n3o,o1=,o2,o1=,n3o,o1=,o2n @atom:*,p*,b*,ao1=,d*,io1= @atom:*,p*,b*,an3o,d*,in3o @atom:*,p*,b*,ao1=,d*,io1= @atom:*,p*,b*,ao2n,d*,io2 + @improper:c3a,c3a,c3a,o2,c3a,c3a,c3a,o2 @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ao2,d*,io2 + @improper:h1,n3o,o1=,o1=,h1,n3o,o1=,o1= @atom:*,p*,b*,ah1,d*,ih1 @atom:*,p*,b*,an3o,d*,in3o @atom:*,p*,b*,ao1=,d*,io1= @atom:*,p*,b*,ao1=,d*,io1= + @improper:c3a,c3a,c3a,h1,c3a,c3a,c3a,h1 @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ah1,d*,ih1 + @improper:c4,c3prime,o1=,o2,c4,c3prime,o1=,o2 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ac3prime,d*,ic3prime @atom:*,p*,b*,ao1=,d*,io1= @atom:*,p*,b*,ao2,d*,io2 + @improper:c4,n3o,o1=,o1=,c4,n3o,o1=,o1= @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,an3o,d*,in3o @atom:*,p*,b*,ao1=,d*,io1= @atom:*,p*,b*,ao1=,d*,io1= + @improper:c3a,n3o,o1=,o1=,c3a,n3o,o1=,o1= @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,an3o,d*,in3o @atom:*,p*,b*,ao1=,d*,io1= @atom:*,p*,b*,ao1=,d*,io1= + @improper:c3a,c3a,c3a,c4,c3a,c3a,c3a,c4 @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac4,d*,ic4 + @improper:c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac3a,d*,ic3a + @improper:c3a,c3prime,c3prime,n3m,X,X,X,X @atom:*,p*,b*,a*,d*,ic3a @atom:*,p*,b*,a*,d*,ic3prime @atom:*,p*,b*,a*,d*,ic3prime @atom:*,p*,b*,a*,d*,in3m + @improper:c3a,o1=,c3prime,n3m,X,X,X,X @atom:*,p*,b*,a*,d*,ic3a @atom:*,p*,b*,a*,d*,io1= @atom:*,p*,b*,a*,d*,ic3prime @atom:*,p*,b*,a*,d*,in3m + } # end of "Data Impropers By Type" section + + + + # ------- Improper Force Field Parameters: ------- + # For an explanation of these parameters, visit: + # http://lammps.sandia.gov/doc/improper_class2.html + +# Syntax: + # improper_coeff ImproperTypeName ImproperStyle parameters... + + + write_once("In Settings") { + improper_coeff @improper:c4,c4,c4,c4,c4,c4,c4,c4 class2 0.0 0.0 # (ver=1.0, ref=1) + improper_coeff @improper:c4,c4,c4,c4,c4,c4,c4,c4 class2 aa -0.1729 -0.1729 -0.1729 112.6700 112.6700 112.6700 # (ver=1.0, ref=1) + improper_coeff @improper:c3a,c4,h1,h1,c3a,c4,h1,h1 class2 0.0 0.0 # (ver=1.0, ref=1) + improper_coeff @improper:c3a,c4,h1,h1,c3a,c4,h1,h1 class2 aa 2.3794 3.0118 2.3794 111.0000 111.0000 107.6600 # (ver=1.0, ref=1) + improper_coeff @improper:c4,c4,h1,o2,c4,c4,h1,o2 class2 0.0 0.0 # (ver=1.0, ref=3) + improper_coeff @improper:c4,c4,h1,o2,c4,c4,h1,o2 class2 aa 3.9177 2.5926 0.1689 110.7700 111.2700 108.7280 # (ver=1.0, ref=3) + improper_coeff @improper:h1,c4,h1,n2=,h1,c4,h1,n2= class2 0.0 0.0 # (ver=1.0, ref=4) + improper_coeff @improper:h1,c4,h1,n2=,h1,c4,h1,n2= class2 aa 1.7680 1.7680 -2.9470 107.6600 107.4990 107.4990 # (ver=1.0, ref=4) + improper_coeff @improper:h1,c4,h1,si4,h1,c4,h1,si4 class2 0.0 0.0 # (ver=1.0, ref=10) + improper_coeff @improper:h1,c4,h1,si4,h1,c4,h1,si4 class2 aa 0.0000 0.0000 2.2050 107.6600 112.0355 112.0355 # (ver=1.0, ref=10) + improper_coeff @improper:c4,si4,c4,h1,c4,si4,c4,h1 class2 0.0 0.0 # (ver=1.0, ref=10) + improper_coeff @improper:c4,si4,c4,h1,c4,si4,c4,h1 class2 aa 3.3827 3.3827 2.7963 113.1855 112.0977 112.0977 # (ver=1.0, ref=10) + improper_coeff @improper:h1,c4,h1,h1,h1,c4,h1,h1 class2 0.0 0.0 # (ver=1.0, ref=1) + improper_coeff @improper:h1,c4,h1,h1,h1,c4,h1,h1 class2 aa -0.3157 -0.3157 -0.3157 107.6600 107.6600 107.6600 # (ver=1.0, ref=1) + improper_coeff @improper:c4,c4,c4,h1,c4,c4,c4,h1 class2 0.0 0.0 # (ver=1.0, ref=1) + improper_coeff @improper:c4,c4,c4,h1,c4,c4,c4,h1 class2 aa -1.3199 -1.3199 0.1184 112.6700 110.7700 110.7700 # (ver=1.0, ref=1) + improper_coeff @improper:c4,si4,c4,si4,c4,si4,c4,si4 class2 0.0 0.0 # (ver=1.0, ref=10) + improper_coeff @improper:c4,si4,c4,si4,c4,si4,c4,si4 class2 aa 1.3465 1.3465 2.0805 113.1855 113.0000 113.0000 # (ver=1.0, ref=10) + improper_coeff @improper:c4,c4,h1,h1,c4,c4,h1,h1 class2 0.0 0.0 # (ver=1.0, ref=7) + improper_coeff @improper:c4,c4,h1,h1,c4,c4,h1,h1 class2 aa 0.2738 -0.4825 0.2738 110.7700 110.7700 107.6600 # (ver=1.0, ref=7) + improper_coeff @improper:h1,si4,h1,h1,h1,si4,h1,h1 class2 0.0 0.0 # (ver=1.0, ref=10) + improper_coeff @improper:h1,si4,h1,h1,h1,si4,h1,h1 class2 aa 2.0665 2.0665 2.0665 108.6051 108.6051 108.6051 # (ver=1.0, ref=10) + improper_coeff @improper:h1,si4,si4,si4,h1,si4,si4,si4 class2 0.0 0.0 # (ver=1.0, ref=10) + improper_coeff @improper:h1,si4,si4,si4,h1,si4,si4,si4 class2 aa 4.1996 3.4924 4.1996 112.0893 112.0893 114.2676 # (ver=1.0, ref=10) + improper_coeff @improper:c4,si4,si4,si4,c4,si4,si4,si4 class2 0.0 0.0 # (ver=1.0, ref=10) + improper_coeff @improper:c4,si4,si4,si4,c4,si4,si4,si4 class2 aa 4.5272 -5.6849 4.5272 113.0000 113.0000 114.2676 # (ver=1.0, ref=10) + improper_coeff @improper:c3a,c4,c4,h1,c3a,c4,c4,h1 class2 0.0 0.0 # (ver=1.0, ref=1) + improper_coeff @improper:c3a,c4,c4,h1,c3a,c4,c4,h1 class2 aa -1.8202 2.0403 1.0827 108.4000 111.0000 110.7700 # (ver=1.0, ref=1) + improper_coeff @improper:c3prime,c4,h1,h1,c3prime,c4,h1,h1 class2 0.0 0.0 # (ver=1.0, ref=7) + improper_coeff @improper:c3prime,c4,h1,h1,c3prime,c4,h1,h1 class2 aa -1.7653 0.0 -1.7653 107.8594 107.8594 107.6600 # (ver=1.0, ref=7) + improper_coeff @improper:c4,si4,h1,si4,c4,si4,h1,si4 class2 0.0 0.0 # (ver=1.0, ref=10) + improper_coeff @improper:c4,si4,h1,si4,c4,si4,h1,si4 class2 aa 3.4758 0.0 -2.9623 112.0977 113.0000 112.0893 # (ver=1.0, ref=10) + improper_coeff @improper:c4,c4,c4,o2,c4,c4,c4,o2 class2 0.0 0.0 # (ver=1.0, ref=3) + improper_coeff @improper:c4,c4,c4,o2,c4,c4,c4,o2 class2 aa -0.8330 -0.8330 -3.5744 112.6700 111.2700 111.2700 # (ver=1.0, ref=3) + improper_coeff @improper:h1,c4,h1,o2,h1,c4,h1,o2 class2 0.0 0.0 # (ver=1.0, ref=3) + improper_coeff @improper:h1,c4,h1,o2,h1,c4,h1,o2 class2 aa 2.4259 2.4259 2.1283 107.6600 108.7280 108.7280 # (ver=1.0, ref=3) + improper_coeff @improper:c4,c4,h1,n2=,c4,c4,h1,n2= class2 0.0 0.0 # (ver=1.0, ref=4) + improper_coeff @improper:c4,c4,h1,n2=,c4,c4,h1,n2= class2 aa 2.7530 1.0910 -1.3060 110.7700 117.3170 107.4990 # (ver=1.0, ref=4) + improper_coeff @improper:c4,si4,h1,h1,c4,si4,h1,h1 class2 0.0 0.0 # (ver=1.0, ref=10) + improper_coeff @improper:c4,si4,h1,h1,c4,si4,h1,h1 class2 aa 4.4559 4.6809 4.4559 112.0977 112.0977 108.6051 # (ver=1.0, ref=10) + improper_coeff @improper:h1,si4,h1,si4,h1,si4,h1,si4 class2 0.0 0.0 # (ver=1.0, ref=10) + improper_coeff @improper:h1,si4,h1,si4,h1,si4,h1,si4 class2 aa 0.0 0.0 1.6082 108.6051 112.0893 112.0893 # (ver=1.0, ref=10) + improper_coeff @improper:c3a,c3prime,n3m,o1=,c3a,c3prime,n3m,o1= class2 30.0000 -0.0 # (ver=1.0, ref=7) + improper_coeff @improper:c3a,c3prime,n3m,o1=,c3a,c3prime,n3m,o1= class2 aa 0.0 0.0 0.0 108.4400 125.5320 121.5420 # (ver=1.0, ref=7) + improper_coeff @improper:c3a,c3a,c3a,n2=,c3a,c3a,c3a,n2= class2 8.0000 -0.0 # (ver=1.0, ref=4) + improper_coeff @improper:c3a,c3a,c3a,n2=,c3a,c3a,c3a,n2= class2 aa 0.0 0.0 0.0 118.9000 120.0000 120.0000 # (ver=1.0, ref=4) + improper_coeff @improper:c3a,n3m,c3prime,c3prime,c3a,n3m,c3prime,c3prime class2 0.0000 -0.0 # (ver=1.0, ref=7) + improper_coeff @improper:c3a,n3m,c3prime,c3prime,c3a,n3m,c3prime,c3prime class2 aa 0.0 0.0 0.0 120.0700 120.0700 121.9556 # (ver=1.0, ref=7) + improper_coeff @improper:c3a,c3a,c3a,si4,c3a,c3a,c3a,si4 class2 5.3654 0.0 # (ver=1.0, ref=10) + improper_coeff @improper:c3a,c3a,c3a,si4,c3a,c3a,c3a,si4 class2 aa 0.0 0.0 0.0 118.9000 120.0000 120.0000 # (ver=1.0, ref=10) + improper_coeff @improper:c3a,c3a,c3a,p4=,c3a,c3a,c3a,p4= class2 6.7090 -0.0 # (ver=1.0, ref=4) + improper_coeff @improper:c3a,c3a,c3a,p4=,c3a,c3a,c3a,p4= class2 aa 0.0 0.0 0.0 118.9000 120.0010 120.0010 # (ver=1.0, ref=4) + improper_coeff @improper:c3a,c3a,c3a,c3prime,c3a,c3a,c3a,c3prime class2 17.0526 -0.0 # (ver=1.0, ref=7) + improper_coeff @improper:c3a,c3a,c3a,c3prime,c3a,c3a,c3a,c3prime class2 aa 0.0 0.0 0.0 118.9000 116.0640 116.0640 # (ver=1.0, ref=7) + improper_coeff @improper:c3a,c3a,c3a,n3m,c3a,c3a,c3a,n3m class2 17.0526 0.0 # (ver=1.0, ref=7) + improper_coeff @improper:c3a,c3a,c3a,n3m,c3a,c3a,c3a,n3m class2 aa 0.0 0.0 0.0 118.9000 120.7640 120.7640 # (ver=1.0, ref=7) + improper_coeff @improper:c3a,c3a,c3a,n3o,c3a,c3a,c3a,n3o class2 0.9194 -0.0 # (ver=1.0, ref=6) + improper_coeff @improper:c3a,c3a,c3a,n3o,c3a,c3a,c3a,n3o class2 aa 0.0 0.0 0.0 118.9000 118.8000 118.8000 # (ver=1.0, ref=6) + improper_coeff @improper:o1=,n3o,o1=,o2,o1=,n3o,o1=,o2n class2 45.0000 -0.0 # (ver=1.0, ref=6) + improper_coeff @improper:o1=,n3o,o1=,o2,o1=,n3o,o1=,o2n class2 aa 0.0 0.0 0.0 128.0000 112.8000 112.8000 # (ver=1.0, ref=6) + improper_coeff @improper:c3a,c3a,c3a,o2,c3a,c3a,c3a,o2 class2 13.0421 -0.0 # (ver=1.0, ref=3) + improper_coeff @improper:c3a,c3a,c3a,o2,c3a,c3a,c3a,o2 class2 aa 0.0000 0.0000 0.0000 118.9000 123.4200 123.4200 # (ver=1.0, ref=3) + improper_coeff @improper:h1,n3o,o1=,o1=,h1,n3o,o1=,o1= class2 38.5581 -0.0 # (ver=1.0, ref=6) + improper_coeff @improper:h1,n3o,o1=,o1=,h1,n3o,o1=,o1= class2 aa 0.0 0.0 0.0 115.7000 115.7000 128.0000 # (ver=1.0, ref=6) + improper_coeff @improper:c3a,c3a,c3a,h1,c3a,c3a,c3a,h1 class2 4.8912 -0.0 # (ver=1.0, ref=1) + improper_coeff @improper:c3a,c3a,c3a,h1,c3a,c3a,c3a,h1 class2 aa 0.0000 0.0000 0.0000 118.9000 117.9400 117.9400 # (ver=1.0, ref=1) + improper_coeff @improper:c4,c3prime,o1=,o2,c4,c3prime,o1=,o2 class2 46.9264 0.0 # (ver=1.0, ref=7) + improper_coeff @improper:c4,c3prime,o1=,o2,c4,c3prime,o1=,o2 class2 aa 0.0 0.0 0.0 119.3000 100.3182 118.9855 # (ver=1.0, ref=7) + improper_coeff @improper:c4,n3o,o1=,o1=,c4,n3o,o1=,o1= class2 44.3062 -0.0 # (ver=1.0, ref=6) + improper_coeff @improper:c4,n3o,o1=,o1=,c4,n3o,o1=,o1= class2 aa 0.0 0.0 0.0 117.5000 117.5000 128.0000 # (ver=1.0, ref=6) + improper_coeff @improper:c3a,n3o,o1=,o1=,c3a,n3o,o1=,o1= class2 36.2612 -0.0 # (ver=1.0, ref=6) + improper_coeff @improper:c3a,n3o,o1=,o1=,c3a,n3o,o1=,o1= class2 aa 0.0 0.0 0.0 117.7000 117.7000 128.0000 # (ver=1.0, ref=6) + improper_coeff @improper:c3a,c3a,c3a,c4,c3a,c3a,c3a,c4 class2 7.8153 -0.0 # (ver=1.0, ref=1) + improper_coeff @improper:c3a,c3a,c3a,c4,c3a,c3a,c3a,c4 class2 aa 0.0 0.0 0.0 118.9000 120.0500 120.0500 # (ver=1.0, ref=1) + improper_coeff @improper:c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a class2 7.1794 -0.0 # (ver=1.0, ref=1) + improper_coeff @improper:c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a class2 aa 0.0000 0.0000 0.0000 118.9000 118.9000 118.9000 # (ver=1.0, ref=1) + improper_coeff @improper:c3a,c3prime,c3prime,n3m,X,X,X,X class2 0.0000 -0.0 # (ver=1.0, ref=7) + improper_coeff @improper:c3a,c3prime,c3prime,n3m,X,X,X,X class2 aa 0.0 0.0 0.0 120.0 120.0 120.0 # (ver=1.0, ref=7) + improper_coeff @improper:c3a,o1=,c3prime,n3m,X,X,X,X class2 30.0000 -0.0 # (ver=1.0, ref=7) + improper_coeff @improper:c3a,o1=,c3prime,n3m,X,X,X,X class2 aa 0.0 0.0 0.0 120.0 120.0 120.0 # (ver=1.0, ref=7) + } # end of improper_coeff commands + + + + + + + # -------------------- Select LAMMPS style(s) ------------------ + + + # LAMMPS supports many different kinds of bonded and non-bonded + # interactions which can be selected at run time. Eventually + # we must inform LAMMPS which of them we will need. We specify + # this in the "In Init" section: + + write_once("In Init") { + units real + atom_style full + bond_style hybrid class2 + # http://lammps.sandia.gov/doc/bond_class2.html + + angle_style hybrid class2 + # http://lammps.sandia.gov/doc/angle_class2.html + + dihedral_style hybrid class2 + # http://lammps.sandia.gov/doc/dihedral_class2.html + + improper_style hybrid class2 + # http://lammps.sandia.gov/doc/improper_class2.html + + pair_style hybrid lj/class2/coul/long 10.0 + # http://lammps.sandia.gov/doc/pair_class2.html + + pair_modify mix sixthpower tail yes + special_bonds lj/coul 0.0 0.0 1.0 dihedral yes + kspace_style pppm 0.0001 + } #end of init parameters + +} # COMPASS + +# +# WARNING: The following 1-2, 1-3, and 1-4 weighting parameters were ASSUMED: +# special_bonds lj/coul 0.0 0.0 1.0 dihedral yes +# (See http://lammps.sandia.gov/doc/special_bonds.html for details) + + + + +# ---- templates from the original .frc file used for atom type selection: --- +# +# type: ? +# template: (>*) +# end_type +# +# type: ar +# template: (>Ar) +# end_type +# +# type:c1o +# template: [>C[~O]] +# end_type +# +# type:c2= +# template: [>C[~*][~*]] +# end_type +# +# type:c3' +# template: (>C (~O) (~*) (~*)) +# atom_test:1 +# hybridization:sp2 +# end_test +# atom_test:3 +# allowed_elements: C, H +# end_test +# atom_test:4 +# allowed_elements: O, N +# end_test +# end_type +# +# type:c3a +# template:(>C(~*)(~*)(~*)) +# atom_test:1 +# hybridization: SP2 +# aromaticity:AROMATIC +# end_test +# end_type +# +# type:c3a +# template: [>C(-*)(:*)(:*)] +# atom_test:1 +# hybridization:SP2 +# aromaticity:NON_AROMATIC +# end_test +# end_type +# +# type:c4 +# template: (>C(-*)(-*)(-*)(-*)) +# atom_test:1 +# hybridization:SP3 +# end_test +# end_type +# +# type:c41o +# template: [>C(-O(-*))(-H)(-H)(-H)] +# atom_test:1 +# hybridization:SP3 +# end_test +# atom_test:3 +# allowed_elements:C,H +# end_type +# +# type: c43 +# template: (>C(-H)(-*)(-*)(-*)) +# atom_test:1 +# hybridization:SP3 +# atom_test:3 +# disallowed_elements:H +# atom_test:4 +# disallowed_elements:H +# atom_test:5 +# disallowed_elements:H +# end_test +# end_type +# +# type:c43o +# template: [>C(-O(-H))(-H)(-C)(-C)] +# atom_test:1 +# hybridization:SP3 +# end_test +# end_type +# +# type: c44 +# template: (>C(-*)(-*)(-*)(-*)) +# atom_test:1 +# hybridization:SP3 +# atom_test:2 +# disallowed_elements:H +# atom_test:3 +# disallowed_elements:H +# atom_test:4 +# disallowed_elements:H +# atom_test:5 +# disallowed_elements:H +# end_test +# end_type +# +# type: c4o +# template: (>C(-O)(-*)(-*)(-*)) +# atom_test:1 +# hybridization:SP3 +# end_test +# end_type +# +# type: c4z +# template: (>C(-N(~N(~N)))(-*)(-*)(-*)) +# atom_test:1 +# hybridization:SP3 +# end_test +# end_type +# +# type:h1 +# template: (>H (-*) ) +# atom_test:2 +# allowed_elements:C,Si +# end_test +# end_type +# +# type:h1h +# template: [>H[-H]] +# end_type +# +# type:h1o +# template: (>H(-*)) +# atom_test:2 +# allowed_elements:O,N,F +# end_test +# end_type +# +# type: he +# template: (>He) +# end_type +# +# type: kr +# template: (>Kr) +# end_type +# +# type:n1n +# template: [>N[~N]] +# end_type +# +# type:n1o +# template: [>N[~O]] +# end_type +# +# type:n1z +# template: [>N[~N[~N(~*)]]] +# end_type +# +# type:n2= +# template: [>N(~*)(~*)] +# end_type +# +# type:n2o +# template: [>N[~O][~O]] +# end_type +# +# type:n2t +# template: [>N[~N][~N(~*)]] +# end_type +# +# type:n2z +# template: (>N[~N[~N]](~*)) +# end_type +# +# type: n3m +# template: (>N(-C[=O])(-C)(-C)) +# atom_test:1 +# hybridization:SP3 +# end_test +# end_type +# +# type: n3o +# template: (>N[~O][~O](~O(~C))) +# end_type +# +# type: ne +# template: (>Ne) +# end_type +# +# type:o1= +# template: (>O(~*)) +# atom_test:2 +# allowed_elements:N,S,C +# end_test +# end_type +# +# type:o1=* +# template: [>O[~C[~O]]] +# end_type +# +# type:o12 +# template: [>O[~N[~O](~*)]] +# end_type +# +# type:o1c +# template: [>O[~C]] +# end_type +# +# type:o1n +# template: [>O[~N]] +# end_type +# +# type:o1o +# template: [>O[~O]] +# end_type +# +# type:o2 +# template: [>O(~*)(~*)] +# end_type +# +# type:o2e +# template: [>O(-C)(-C)] +# atom_test: 1 +# aromaticity:NON_AROMATIC +# end_test +# end_type +# +# type:o2h +# template: (>O[-H](~*)) +# end_type +# +# type:o2n +# template: (>O[~N[~O][~O]](~C)) +# end_type +# +# type:o2s +# template: (>O[~C[~O](~*)](~C)) +# end_type +# +# type: o2z +# template: (>O(-Si)(-*) ) +# atom_test: 3 +# allowed_elements: Si, H +# end_test +# end_type +# +# type: p4= +# template: (>P(~*)(~*)(~*)(~*)) +# end_type +# +# type:s1= +# template: [>S[~C[~S]]] +# end_type +# +# type:s2= +# template: [>S[~O][~O]] +# end_type +# +# type: si4 +# template: (>Si(-*)(-*)(-*)(-*)) +# end_type +# +# type: si4c +# template: (>Si(-O)(-*)(-*)(-*)) +# atom_test: 3 +# allowed_elements: O, C +# end_test +# atom_test: 4 +# allowed_elements: O, C +# end_test +# atom_test: 5 +# allowed_elements: O, C +# end_test +# end_type +# +# type: xe +# template: (>Xe) +# end_type +# +# precedence: +# (? +# (ar) +# (c1o) +# (c2=) +# (c3a) (c3') +# (c4 (c43 (c43o)) (c44) (c4o(c41o)) (c4z) ) +# (h1) (h1h) (h1o) +# (he) +# (kr) +# (n1n) (n1o) (n1z) +# (n2= (n2o) (n2t) (n2z) ) +# (n3m) (n3o) +# (ne) +# (o1= (o1=*) (o12) (o1c) (o1n) ) (o1o) +# (o2 (o2e(o2s)) (o2h) (o2n) (o2z) ) +# (p4=) +# (s1=) +# (s2=) +# (si4 (si4c) ) +# (xe) +# ) +# end_precedence +# +# +# + + + + +# ---- references from the original .frc file: ---- + +# reference 1 +# @Author tester +# @Date 01-Jun-09 +# Barebones compass for aromatic & aliphatic hydrocarbons from H. Sun JCP B102, 7361-2 (1998) +# This file created by Materials Design, Inc. (www.materialsdesign.com) Please realize that +# we neither support this version, nor make any warranty as to the correctness of the parameters. +# We have checked the numbers against the literature, but of course there may still be errors, +# including errors of interpretation. Also, the current version of COMPASS may well be different +# that that originally published. +# If you have comments or suggestions, feel free to email Paul Saxe at psaxe (at) materialsdesign.com + +# reference 2 +# @Author tester +# @Date 27-Jun-09 +# Parameters for siloxanes from Sun/Rigby Spectrochim. Acta A53, 1301-23 (1997) (o2 later renamed to o2z) + +# reference 3 +# @Author tester +# @Date 27-Jun-09 +# Parameters for ethers and alcohols from Rigby/Sun/Eichinger Polym. Int. 44, 311-330 (1997) + +# reference 4 +# @Author tester +# @Date 30-Jun-09 +# Parameters for phosphazenes from Comput. Theor. Polym. Sci. 8, 229-246 (1998) + +# reference 5 +# @Author tester +# @Date 28-Jun-09 +# Parameters for He,Ne,Ar,Kr,Xe,H2,O2,N2,NO,CO,CO2,NO2,CS2,SO2 from JPC B104, 4951-7 (2000) + +# reference 6 +# @Author tester +# @Date 29-Jun-09 +# Parameters for nitrate esters from JPC B104, 2477-89 (2000) + +# reference 7 +# @Author tester +# @Date 30-Jun-09 +# Parameters for Ultem (imides) from Polymer 43, 599-607 (2002) + +# reference 8 +# @Author tester +# @Date 30-Jun-09 +# Parameters for 2y and 3y alcohols from Fluid Phase Equilibria 217, 77-87 (2004) + +# reference 9 +# @Author tester +# @Date 30-Jun-09 +# Parameters for aliphatic azides from J. Comput. Chem. 25, 61-71 (2004) + +# reference 10 +# @Author tester +# @Date 02-Jul-09 +# Ref 2 missing -C-Si- params; assume values from Macromols 28, 701-712 (1995) (see pcff) + + + + + +# ---- additional warnings: ---- +# WARNING: Undefined bond length (r0) in angle: h1 o2z si4 +# WARNING: Undefined bond length (r0) in angle: c4 n3 p4= +# WARNING: Undefined bond length (r0) in angle: h1 n3 p4= +# WARNING: Undefined bond length (r0) in angle: c4 o2 p4= +# WARNING: Undefined bond length (r0) in angle: h1 o2 p4= +# WARNING: Undefined bond length (r0) in angle: c3a p4= n3 +# WARNING: Undefined bond length (r0) in angle: h1 p4= n3 +# WARNING: Undefined bond length (r0) in angle: n2= p4= n3 +# WARNING: Undefined bond length (r0) in angle: n3 p4= n3 +# WARNING: Undefined bond length (r0) in angle: n3 p4= o2 +# WARNING: Undefined bond length (r0) or rest angle (theta0) in dihedral: c4 si4 o2z h1 +# WARNING: Undefined bond length (r0) or rest angle (theta0) in dihedral: h1 o2z si4 h1 +# WARNING: Undefined bond length (r0) or rest angle (theta0) in dihedral: h1 o2z si4 o2z +# WARNING: Undefined bond length (r0) or rest angle (theta0) in dihedral: h1 n3 p4= h1 +# WARNING: Undefined bond length (r0) or rest angle (theta0) in dihedral: h1 n3 p4= n2= +# WARNING: Undefined bond length (r0) or rest angle (theta0) in dihedral: h1 n3 p4= o2 +# WARNING: Undefined bond length (r0) or rest angle (theta0) in dihedral: h1 o2 p4= h1 +# WARNING: Undefined bond length (r0) or rest angle (theta0) in dihedral: h1 o2 p4= n2= +# WARNING: Undefined bond length (r0) or rest angle (theta0) in dihedral: h1 o2 p4= o2 +# WARNING: Undefined bond length (r0) or rest angle (theta0) in dihedral: X o2 p4= X +# WARNING: Undefined bond length (r0) or rest angle (theta0) in dihedral: X c3a n2= X +# WARNING: Undefined bond length (r0) or rest angle (theta0) in dihedral: X n3 p4= X +# WARNING: Undefined bond length (r0) or rest angle (theta0) in dihedral: c4 c4 n3o o1= +# WARNING: Undefined bond length (r0) or rest angle (theta0) in dihedral: c3prime n3m c3prime o1 +# WARNING: Undefined rest angle (theta0) in improper: c3a o1= c3prime n3m +# WARNING: Undefined rest angle (theta0) in improper: c3a c3prime c3prime n3m diff --git a/tools/moltemplate/moltemplate/force_fields/amber/README.txt b/tools/moltemplate/moltemplate/force_fields/convert_AMBER_files_to_LT_files/README.txt similarity index 100% rename from tools/moltemplate/moltemplate/force_fields/amber/README.txt rename to tools/moltemplate/moltemplate/force_fields/convert_AMBER_files_to_LT_files/README.txt diff --git a/tools/moltemplate/moltemplate/force_fields/amber/amberparm2lt.sh b/tools/moltemplate/moltemplate/force_fields/convert_AMBER_files_to_LT_files/amberparm2lt.sh similarity index 98% rename from tools/moltemplate/moltemplate/force_fields/amber/amberparm2lt.sh rename to tools/moltemplate/moltemplate/force_fields/convert_AMBER_files_to_LT_files/amberparm2lt.sh index 07442dbee7..98a77f3b05 100755 --- a/tools/moltemplate/moltemplate/force_fields/amber/amberparm2lt.sh +++ b/tools/moltemplate/moltemplate/force_fields/convert_AMBER_files_to_LT_files/amberparm2lt.sh @@ -61,6 +61,8 @@ echo "$MOLTEMPLATE_USAGE_MSG" echo "####################################################################" echo "# Moltemplate can not assign atom charge. You must assign atomic" echo "# charges yourself. (Moltemplate is only a simple text manipulation tool.)" +echo "# You can do this afterwards using commands like \"set atom 70 charge -0.212\"" +echo "# For details, see http://lammps.sandia.gov/doc/set.html)" echo "####################################################################" echo "" echo "" diff --git a/tools/moltemplate/moltemplate/force_fields/amber/amberparm_angle_to_lt.py b/tools/moltemplate/moltemplate/force_fields/convert_AMBER_files_to_LT_files/amberparm_angle_to_lt.py similarity index 91% rename from tools/moltemplate/moltemplate/force_fields/amber/amberparm_angle_to_lt.py rename to tools/moltemplate/moltemplate/force_fields/convert_AMBER_files_to_LT_files/amberparm_angle_to_lt.py index dd465841b5..447857675e 100755 --- a/tools/moltemplate/moltemplate/force_fields/amber/amberparm_angle_to_lt.py +++ b/tools/moltemplate/moltemplate/force_fields/convert_AMBER_files_to_LT_files/amberparm_angle_to_lt.py @@ -22,7 +22,11 @@ for i in range(0, len(lines_gaff)): keq = tokens[0] req = tokens[1] comments=' '.join(tokens[2:]) - sys.stdout.write(' angle_coeff '+angletype+' '+angle_style_name+' '+keq+' '+req+' # '+comments+'\n') + sys.stdout.write(' angle_coeff '+angletype+' '+angle_style_name+' '+keq+' '+req) + if len(comments.strip()) > 0: + sys.stdout.write(' # '+comments) + sys.stdout.write('\n') + sys.stdout.write(' } # (end of angle_coeffs)\n') sys.stdout.write('\n') diff --git a/tools/moltemplate/moltemplate/force_fields/amber/amberparm_bond_to_lt.py b/tools/moltemplate/moltemplate/force_fields/convert_AMBER_files_to_LT_files/amberparm_bond_to_lt.py similarity index 90% rename from tools/moltemplate/moltemplate/force_fields/amber/amberparm_bond_to_lt.py rename to tools/moltemplate/moltemplate/force_fields/convert_AMBER_files_to_LT_files/amberparm_bond_to_lt.py index bacc49b7d5..abfde23dab 100755 --- a/tools/moltemplate/moltemplate/force_fields/amber/amberparm_bond_to_lt.py +++ b/tools/moltemplate/moltemplate/force_fields/convert_AMBER_files_to_LT_files/amberparm_bond_to_lt.py @@ -21,7 +21,11 @@ for i in range(0, len(lines_gaff)): keq = tokens[0] req = tokens[1] comments=' '.join(tokens[2:]) - sys.stdout.write(' bond_coeff '+bondtype+' '+bond_style_name+' '+keq+' '+req+' # '+comments+'\n') + sys.stdout.write(' bond_coeff '+bondtype+' '+bond_style_name+' '+keq+' '+req) + if len(comments.strip()) > 0: + sys.stdout.write(' # '+comments) + sys.stdout.write('\n') + sys.stdout.write(' } # (end of bond_coeffs)\n') sys.stdout.write('\n') diff --git a/tools/moltemplate/moltemplate/force_fields/amber/amberparm_dihedral_to_lt.py b/tools/moltemplate/moltemplate/force_fields/convert_AMBER_files_to_LT_files/amberparm_dihedral_to_lt.py similarity index 97% rename from tools/moltemplate/moltemplate/force_fields/amber/amberparm_dihedral_to_lt.py rename to tools/moltemplate/moltemplate/force_fields/convert_AMBER_files_to_LT_files/amberparm_dihedral_to_lt.py index 8729e3fe16..f4f8e3a645 100755 --- a/tools/moltemplate/moltemplate/force_fields/amber/amberparm_dihedral_to_lt.py +++ b/tools/moltemplate/moltemplate/force_fields/convert_AMBER_files_to_LT_files/amberparm_dihedral_to_lt.py @@ -29,7 +29,9 @@ for i in range(0, len(lines_gaff)): # ...I THINK (?). (Very confusing. See documentation below...) dn = float(tokens[2]) n = int(float(tokens[3])) - comments=' # '+(' '.join(tokens[4:])) + comments=' '.join(tokens[4:]) + if len(comments.strip()) > 0: + comments = ' # ' + comments in_dihedral_coeffs.append([dihedraltype, Kn, n, dn, comments]) #print(Kn, n, dn) diff --git a/tools/moltemplate/moltemplate/force_fields/amber/amberparm_improper_to_lt.py b/tools/moltemplate/moltemplate/force_fields/convert_AMBER_files_to_LT_files/amberparm_improper_to_lt.py similarity index 94% rename from tools/moltemplate/moltemplate/force_fields/amber/amberparm_improper_to_lt.py rename to tools/moltemplate/moltemplate/force_fields/convert_AMBER_files_to_LT_files/amberparm_improper_to_lt.py index 8cc7828f89..ebf48d4f18 100755 --- a/tools/moltemplate/moltemplate/force_fields/amber/amberparm_improper_to_lt.py +++ b/tools/moltemplate/moltemplate/force_fields/convert_AMBER_files_to_LT_files/amberparm_improper_to_lt.py @@ -31,11 +31,13 @@ for i in range(0, len(lines_gaff)): dn = float(tokens[1]) n = int(float(tokens[2])) comments=' '.join(tokens[3:]) + if len(comments.strip()) > 0: + comments = ' # ' + comments if (dn < 0.001): - sys.stdout.write(' improper_coeff '+impropertype+' '+improper_style_name+' '+str(Kn)+' 1 '+str(n)+' # '+comments+'\n') + sys.stdout.write(' improper_coeff '+impropertype+' '+improper_style_name+' '+str(Kn)+' 1 '+str(n)+comments+'\n') elif (179.999 < abs(dn) < 180.001): - sys.stdout.write(' improper_coeff '+impropertype+' '+improper_style_name+' '+str(Kn)+' -1 '+str(n)+' # '+comments+'\n') + sys.stdout.write(' improper_coeff '+impropertype+' '+improper_style_name+' '+str(Kn)+' -1 '+str(n)+comments+'\n') else: sys.stderr.write('Error: Illegal bondImproper parameters:\n' ' As of 2013-8-03, LAMMPS doens hot have an improper style\n' diff --git a/tools/moltemplate/moltemplate/force_fields/amber/amberparm_mass_to_lt.py b/tools/moltemplate/moltemplate/force_fields/convert_AMBER_files_to_LT_files/amberparm_mass_to_lt.py similarity index 100% rename from tools/moltemplate/moltemplate/force_fields/amber/amberparm_mass_to_lt.py rename to tools/moltemplate/moltemplate/force_fields/convert_AMBER_files_to_LT_files/amberparm_mass_to_lt.py diff --git a/tools/moltemplate/moltemplate/force_fields/amber/amberparm_pair_to_lt.py b/tools/moltemplate/moltemplate/force_fields/convert_AMBER_files_to_LT_files/amberparm_pair_to_lt.py similarity index 93% rename from tools/moltemplate/moltemplate/force_fields/amber/amberparm_pair_to_lt.py rename to tools/moltemplate/moltemplate/force_fields/convert_AMBER_files_to_LT_files/amberparm_pair_to_lt.py index 61e7672589..f24a92b78f 100755 --- a/tools/moltemplate/moltemplate/force_fields/amber/amberparm_pair_to_lt.py +++ b/tools/moltemplate/moltemplate/force_fields/convert_AMBER_files_to_LT_files/amberparm_pair_to_lt.py @@ -51,7 +51,11 @@ for i in range(0, len(lines_gaff)): sig=str(float(tokens[1])*2.0*pow(2.0, (-1.0/6.0))) eps=tokens[2] comments=' '.join(tokens[3:]) - sys.stdout.write(' pair_coeff @atom:'+atype+' @atom:'+atype+' '+pair_style+' '+eps+' '+sig+' # '+comments+'\n') + sys.stdout.write(' pair_coeff @atom:'+atype+' @atom:'+atype+' '+pair_style+' '+eps+' '+sig) + if len(comments.strip()) > 0: + sys.stdout.write(' # '+comments) + sys.stdout.write('\n') + sys.stdout.write(' } # (end of pair_coeffs)\n') sys.stdout.write('\n') diff --git a/tools/moltemplate/moltemplate/force_fields/convert_EMC_files_to_LT_files/README.txt b/tools/moltemplate/moltemplate/force_fields/convert_EMC_files_to_LT_files/README.txt new file mode 100644 index 0000000000..f110af62ca --- /dev/null +++ b/tools/moltemplate/moltemplate/force_fields/convert_EMC_files_to_LT_files/README.txt @@ -0,0 +1,18 @@ +This directory contains a tool "emcprm2lt.py" which +converts ".PRM" files containing lists of force-field parameters +in EMC format into MOLTEMPLATE files in ".LT" format. +(Several force fields including MARTINI and SDK have been + converted into moltemplate format using this tool.) + +---- Credit: ---- + +The "emcprm2lt.py" converter was writtin by David Stelter. +The .PRM files we use were written by Pieter J. in 't Veld. + +---- Citation request: ---- + +Since we borrowed force field parameters from files distributed with EMC, +if you use files generated by "emcprm2lt.py", please also cite the EMC paper: +P. J. in ‘t Veld and G. C. Rutledge, Macromolecules 2003, 36, 7358 + + diff --git a/tools/moltemplate/moltemplate/force_fields/convert_EMC_files_to_LT_files/__init__.py b/tools/moltemplate/moltemplate/force_fields/convert_EMC_files_to_LT_files/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/tools/moltemplate/moltemplate/force_fields/sdk/emcprm2lt.py b/tools/moltemplate/moltemplate/force_fields/convert_EMC_files_to_LT_files/emcprm2lt.py similarity index 99% rename from tools/moltemplate/moltemplate/force_fields/sdk/emcprm2lt.py rename to tools/moltemplate/moltemplate/force_fields/convert_EMC_files_to_LT_files/emcprm2lt.py index c924ce64e0..7e97770899 100755 --- a/tools/moltemplate/moltemplate/force_fields/sdk/emcprm2lt.py +++ b/tools/moltemplate/moltemplate/force_fields/convert_EMC_files_to_LT_files/emcprm2lt.py @@ -508,7 +508,7 @@ for i in range(len(nonbond)): atom1name = None atom2name = None stylename = pstyle - if pstyle == 'lj/sdk' or 'lj/sdk/coul/long': + if pstyle == 'lj/sdk' or pstyle == 'lj/sdk/coul/long': stylename = 'lj%s_%s' % (nonbond[i][4], nonbond[i][5]) # Cross Terms + Diagonal, normal for j in range(len(equiv)): diff --git a/tools/moltemplate/moltemplate/force_fields/convert_MSI_files_to_LT_files/msifrc2lt.py b/tools/moltemplate/moltemplate/force_fields/convert_MSI_files_to_LT_files/msifrc2lt.py new file mode 100755 index 0000000000..7c4c6abc73 --- /dev/null +++ b/tools/moltemplate/moltemplate/force_fields/convert_MSI_files_to_LT_files/msifrc2lt.py @@ -0,0 +1,4536 @@ +#! /usr/bin/env python +# Author: Andrew Jewett (jewett.aij at g mail) +# License: 3-clause BSD License (See LICENSE.TXT) +# Copyright (c) 2017, California Institute of Technology +# All rights reserved. + +""" +This standalone python script can be used to convert force-field data +in FRC files (a.k.a. "MSI", "Accelrys", "BIOSYM", "DISCOVERY" files) +...into MOLTEMPLATE/LAMMPS compatible format (.LT files). + +Once converted into moltemplate (.LT) format, users can use these files with +MOLTEMPLATE to prepare LAMMPS simulations of molecules using these force fields +(without needing any additional software such as msi2lmp). + +There are several examples of MSI files in the "tools/msi2lmp/frc_files/" +directory which is distributed with LAMMPS. + +Limitations: + +Currently (2017-10) this script ignores the "template" information in .FRC files. +When defining a new type of molecule, the user must carefully choose the +complete atom type for each type of atom in the molecule. In other words, +MOLTEMPLATE will not attempt to determine (from local context) whether +a carbon atom somewhere in your molecule happens to be an SP3 carbon +(ie. "c4" in the COMPASS force-field), or an aromatic carbon ("c3a"), +or something else (for example). This information is typically contained +in the "templates" section of these files, and this script currently ignores +that information. Instead, the user must determine which type of carbon atom +it is manually, for all of the carbon atoms in that kind of molecule. +(This only needs to be done once per molecule definition. + Once a type of molecule is defined, it can be copied indefinitely.) + +""" + + +__author__ = 'Andrew Jewett' +__version__ = '0.2.1' +__date__ = '2017-10-15' + + +import sys +import os + +from collections import defaultdict, OrderedDict +from operator import itemgetter + + +g_program_name = __file__.split('/')[-1] + + +doc_msg = \ + "Typical Usage:\n\n" + \ + " " + g_program_name + " -name COMPASS < compass_published.frc > compass.lt\n\n" + \ + " where \"compass_published.frc\" is a force-field file in MSI format.\n" + \ + " \"comass.lt\" is the corresponding file converted to moltemplate format\n" + \ + " and \"COMPASS\" is the name that future moltemplate users will use to refer\n" + \ + " to this force-field (optional).\n" + \ + "Optional Arguments\n" + \ + " -name FORCEFIELDNAME # Give the force-field a name\n" + \ + " -file FILE_NAME # Read force field parameters from a file\n" + \ + " -url URL # Read force field parameters from a file on the web\n" + \ + " -atoms \"QUOTED LIST\" # Restrict output to a subset of atom types\n" + \ + " Sometimes an FRC file contains multiple versions. In that case,\n"+\ + " you can select between them using these optional arguments:\n"+\ + " -pair-style \"PAIRSTYLE ARGS\" # LAMMPS pair style and cutoff arg(s)\n" + \ + " -bond-style BONDSTYLE # desired LAMMPS bond style (default: \"class2\")\n" + \ + " -angle-style ANGLESTYLE # desired LAMMPS angle style\n" + \ + " -dihedral-style DIHEDRALSTYLE # desired LAMMPS dihedral style\n" + \ + " -improper-style IMPROPERSTYLE # desired LAMMPS improper style\n" + \ + " -hbond-style \"HBONDTYLE ARGS\" # LAMMPS hydrogen-bond style and args\n" + + +# " -auto # Consider auto_equivalences in the .frc file \n"+\ + + + +class InputError(Exception): + """ A generic exception object containing a string for error reporting. + (Raising this exception implies that the caller has provided + a faulty input file or argument.) + + """ + + def __init__(self, err_msg): + self.err_msg = err_msg + + def __str__(self): + return self.err_msg + + def __repr__(self): + return str(self) + +# It seems like there are no ordered sets in python, (a set that remembers the +# order that you added elements), so I built one by wrapping OrderedDict() + +class MyOrderedSet(object): + def __init__(self, l): + self.d = OrderedDict() + for x in l: + self.d[x] = True + def __add__(self, x): + self.d[x] = True + def __delitem__(self, x): + del self.d[x] + def __contains__(self, x): + return x in self.d + def __iter__(self): + self.p = iter(self.d) + return self + def __next__(self): + return next(self.p) + # the following wrappers might be necessary for python2/3 compatibility: + def add(self, x): + self.__add__(x) + def del_item(self, x): + self.__del_item__(x) + def iter(self): + return self.__iter__() + def next(self): + return self.__next__() + # no need to bother with set unions and intersections + + +def NSplitQuotedString(string, + nmax, + quotes, + delimiters=' \t\r\f\n', + escape='\\', + comment_char='#'): + """ + Split a quoted & commented string into at most "nmax" tokens (if nmax>0), + where each token is separated by one or more delimeter characters + in the origingal string, and quoted substrings are not split, + This function returns a list of strings. Once the string is split Nmax + times, any remaining text will be appended to the last entry of the list. + Comments are stripped from the string before splitting begins. + """ + tokens = [] + token = '' + reading_token = True + escaped_state = False + quote_state = None + for c in string: + + if (c in comment_char) and (not escaped_state) and (quote_state == None): + if len(token) > 0: + tokens.append(token) + return tokens + + elif (c in delimiters) and (not escaped_state) and (quote_state == None): + if reading_token: + if (nmax == 0) or (len(tokens) < nmax-1): + if len(token) > 0: + tokens.append(token) + token = '' + reading_token = False + else: + token += c + elif c in escape: + if escaped_state: + token += c + reading_token = True + escaped_state = False + else: + escaped_state = True + # and leave c (the '\' character) out of token + elif (c in quotes) and (not escaped_state): + if (quote_state != None): + if (c == quote_state): + quote_state = None + else: + quote_state = c + token += c + reading_token = True + else: + if (c == 'n') and (escaped_state == True): + c = '\n' + elif (c == 't') and (escaped_state == True): + c = '\t' + elif (c == 'r') and (escaped_state == True): + c = '\r' + elif (c == 'f') and (escaped_state == True): + c = '\f' + token += c + reading_token = True + escaped_state = False + + if len(token) > 0: + tokens.append(token) + return tokens + + + + +def SplitQuotedString(string, + quotes='\'\"', + delimiters=' \t\r\f\n', + escape='\\', + comment_char='#'): + + return NSplitQuotedString(string, + 0, + quotes, + delimiters, + escape, + comment_char) + + + + +def RemoveOuterQuotes(text, quotes='\"\''): + if ((len(text) >= 2) and (text[0] in quotes) and (text[-1] == text[0])): + return text[1:-1] + else: + return text + + +def SortByEnds(l_orig): + """ + Convenient to have a one-line macro for swapping list order if first>last + """ + l = [x for x in l_orig] + if l[0] > l[-1]: + l.reverse() + return l + + + +#def Repl(tokens, a, b): +# return [(b if x==a else x) for x in tokens] + +def DecodeAName(s): + if s.find('auto') == 0: + s = s[4:] + if s == 'X': # special case: deal with strings like 'X' + return '*' + return s + + +def EncodeAName(s): + """ + Handle * characters in MSI atom names + """ + + if s.find('auto') == 0: + s = s[4:] + # If the atom name begins with *, then it is a wildcard + if s[:1] == '*': # special case: deal with strings like *7 + return 'X' # These have special meaning. Throw away the integer. + # (and replace the * with an X) + + # If the * character occurs later on in the atom name, then it is actually + # part of the atom's name. (MSI force fields use many strange characters in + # atom names.) Here we change the * to \* to prevent the atom name from + # being interpreted as a wild card in the rules for generating bonds, + # angles, dihedrals, and impropers. + + return s.replace('*','star').replace('\'','prime').replace('"','dblpr') + # '*' is reserved for wildcards in moltemplate + # 'star' is a string that is unused in any + # of the force fields I have seen so far. + # Similarly quote characters (' and ") confuse + # moltemplate, so we replace them with something else. + + # The following approach doesn't work (mistakenly thinks '\*' = wildcard) + #return s.replace('*','\\*') # this prevents ttree_lex.MatchesAll() + # # from interpreting the '*' as a wildcard + + +def DetermineAutoPriority(anames): + """ + Given a list of atom names (including wildcards), generate a number + indicating the priority the interaction between these atoms should have: + Scan through list of strings anames, looking for patterns of the form + *n + where n is an integer. + Make sure this pattern only appears once and return n to the caller. + (These patterns are used by MSI software when using "auto_equivalences" + to look up force field parameters for bonded interactions. + The higher the integer, the lower the priority. + For details, see "Forcefield based simulations" PDF, Cerius2, p 87) + Ordinary wildcards ('*' characters not followed by integers) have the + lowest possible priority. (Each time a '*' string appears in the + list of arguments, the priority value increases by HUGE_VAL.) + """ + + # This is terrible code. + + n = -1.0 + num_blank_wildcards = 0 + for a in anames: + # Sometimes the first atom name contains the prefix 'auto'. Remove this + if a.find('auto') == 0: + a = a[4:] + if a[:1] == '*': + #if a[:1] == 'X': + if len(a) > 1: + if n == -1.0: + n = float(a[1:]) + elif n != float(a[1:]): + # Make sure if present, the number appears only once in the list of atom names + raise InputError('Error: Inconsistent priority integers in the following interaction:\n' + ' ' + ' '.join(anames) + '\n') + else: + num_blank_wildcards += 1 + + # A "blank" wildcard (not followed by a number eg '*') has a very low priority + # Give it a high number, because this corresponds to low priority. Very confusing + # For details, see "Forcefield based simulations" PDF, Cerius2, p 87) + HUGE_VAL = 1.0e5 + return n + num_blank_wildcards*HUGE_VAL + + + + +#def DeterminePriority(is_auto, +# anames, +# version): +# """ +# Determine the priority of an interaction from +# 1) whether or not it is an "auto" interaction +# 2) what is the force-field "version" (a number) +# 3) what are the names of the atoms (for auto_equivalences only, +# some atom "names" are wildcards followed by integers. use the integer) +# """ +# +# if is_auto: +# n = DetermineAutoPriority(anames) +# return (is_auto, n) +# else: +# return (is_auto, -version) + + +def DetermineNumericPriority(is_auto, + anames, + version): + """ + Determine the priority of an interaction from + 2) what is the force-field "version" (a number) + 3) what are the names of the atoms (for auto_equivalences only, + some atom "names" are wildcards followed by integers. use the integer) + """ + + if is_auto: + n = DetermineAutoPriority(anames) + return n # low priority integers <--> high priority () + else: + return -float(version) # later version numbers <--> higher priority + # (multiplying by -1 compensates for this) + # Note: this means auto interactions always have + # lower priority because their numeric priority + # will be a positive number. Otherwise the + # numeric priority will be a negative number + # (...corresponding to a higher priority + # I don't like this complicated priority system + # but I didn't invent it. It's not my fault.) + + +def IsAutoAtom(atom_name): + return atom_name[-1:] == '_' + + +#def PossibleAutoAtom(atom_name): +# """ Auto-equivalences are alternate atom names used in "auto" +# interactions. (These are low priority interactions used as a +# last resort when the interaction parameters could not be located +# by any other means). Each atom is given an alternate name which +# is used in this kind of interaction. These names typically end +# '_' followed by an optional integer. Example "auto" atom names +# are 'c3m_' and 'c=_3'. Unfortunately some ordinary atom names +# also end in an integer preceeded by a _ character. But they +# never end in a '_' character. Here we check for both.""" +# +# i = atom_name.rfind('_') +# if (i == -1) or str.isdigit(atom_name[i:]): +# return True +# return False + + + +def IsAutoInteraction(interaction_name): + return interaction_name.find('auto') == 0 + + +#def IsAutoInteraction(interaction_name): +# anames = ExtractAtomNames(interaction_name) +# for a in anames: +# if IsAutoAtom(a): +# return True +# if not PossibleAutoAtom(a): +# return False +# return True + + + + +def EncodeInteractionName(anames, + is_auto = False): + if is_auto == False: + is_auto = False + # Is the line containing anames from an "_auto" section of + # the FRC file? (I am trying to infer this from whether or + # not any of the atom names are followed by the '_' character.) + for s in anames: + if IsAutoAtom(s): + is_auto = True + if is_auto: + priority = DetermineAutoPriority(anames) + # (If an atom name is a wildcard '*' followed by + # an integer, DetermineAutoPriority() will return + # that integer. Otherwise it will return '') + #return str(priority)+'auto'+','.join(anames) + return 'auto'+','.join(anames) + + return ','.join(anames) + + + +def ExtractANames(interaction_name): + if IsAutoInteraction(interaction_name): + return interaction_name[4:].split(',') + return interaction_name.split(',') + + + +def OOPImproperNameSort(aorig): + assert(len(aorig) == 4) + atom_names = map(EncodeAName, aorig) + if atom_names[0] < atom_names[3]: + return (atom_names, [0,1,2,3]) + else: + return ([atom_names[3], + atom_names[1], + atom_names[2], + atom_names[0]], + [3,1,2,0]) + + +def Class2ImproperNameSort(aorig): + """ + This function takes a list of 4 strings as an argument representing 4 atom + names for atoms participating in an "improper" ("wilson-out-of-plane") + interaction. This function assumes the second atom is the central ("hub") + atom in the interaction, and it sorts the remaining atoms names. + This function also replaces any occurence of \"*\" with \"X\". + The new list is returned to the caller, along with the permutation. + """ + assert(len(aorig) == 4) + atom_names = [a for a in map(EncodeAName, aorig)] + z = [x for x in zip([atom_names[0], atom_names[2], atom_names[3]], + [0,2,3])] + z.sort() + l = [z[0][0], atom_names[1], z[1][0], z[2][0]] + p = [z[0][1], 1, z[1][1], z[2][1]] + return (l, p) + + + +def Parity(p): + """ compute the parity of a permutation + (credit: "Weeble") + """ + permutation = list(p) + length = len(permutation) + elements_seen = [False] * length + cycles = 0 + for index, already_seen in enumerate(elements_seen): + if already_seen: + continue + cycles += 1 + current = index + while not elements_seen[current]: + elements_seen[current] = True + current = permutation[current] + return (length-cycles) % 2 == 0 + + + +def ImCrossTermID(atom_names): + """ + # From a list of 4 atom names, corresponding two a pair + # of angles between atoms# 3,2,1 and 3,2,4, + # and replaces the list of atoms with a canonical tuple + # which eliminates order ambiguity. + # If you swap the first and last atom (#1 and #4), then + # the -pair- of angles is the same. Hence if atom #1 + # has a name which is lexicographically less than atom #4, + # swap atoms 1 and 4. + """ + if atom_names[0] <= atom_names[3]: + return (atom_names[0]+','+atom_names[1]+','+ + atom_names[2]+','+atom_names[3]) + else: + return (atom_names[3]+','+atom_names[1]+','+ + atom_names[2]+','+atom_names[0]) + + + + +def AtomsMatchPattern(anames, pattern): + """ + Check whether the list of atom names "anames" matches "pattern" + (Both arguments are lists of strings, but some of the strings + in pattern may contain wildcard characters followed by + "priority" numbers. Matches with lower priority numbers are + given preference whenever multiple distinct matches are found. + (Note: This function does not check patterns in reverse order.) + """ + #sys.stderr.write('DEBUG: checking whether '+str(anames)+' matches '+str(pattern)+'\n') + assert(len(anames) == len(pattern)) + matched = True + for d in range(0, len(pattern)): + if (pattern[d] == anames[d]) or (pattern[d][0] == '*'): + if pattern[d][0] == '*': + priority = int(pattern[d][1:]) + else: + priority = 0 + else: + matched = False + if matched: + #sys.stderr.write('DEBUG: '+str(anames)+' matches '+str(pattern)+'\n') + return priority + else: + return None + + +def LookupBondLength(a1, a2, + atom2equiv_bond, + bond2r0, + atom2auto_bond, + bond2r0_auto): + """ + Try to find bond parameters between atoms whose original + atom names (without equivalences) are a1 and a2. + Then return both the equilibrium bond length for that bond, + as well as the equivalent atom names used to lookup that bond. + (These could be stored in either atom2equiv_bond or atom2auto_bond.) + If a match was not found, return None. + """ + return_val = None + anames = (atom2equiv_bond[a1], atom2equiv_bond[a2]) + bond_name = EncodeInteractionName(SortByEnds(anames)) + if bond_name in bond2r0: + return_val = (bond2r0[bond_name], + [anames[0], anames[1]], + False) + # If no bond between these atoms is defined, + # check the bonds in the _auto section(s) + # This is a lot messier. + elif ((a1 in atom2auto_bond) and (a2 in atom2auto_bond)): + anames = [atom2auto_bond[a1], atom2auto_bond[a2]] + # Because _auto interactions can contain wildcards, + # there can be multiple entries in bond2r0_auto[] + # for the same list of atom names, and we have to + # consider all of them, and pick the one with the + # most priority (ie. whose priority number is lowest). + # (Note: The MSI file format uses low priority numbers + # to indicate high priority. Somewhat confusing. + # For details, see "Forcefield based simulations" PDF, Cerius2, p 87) + HUGE_VAL = 2000000000 + best_priority = HUGE_VAL + pattern = ['',''] + for (pattern[0],pattern[1]), r0 in bond2r0_auto.items(): + priority = AtomsMatchPattern(anames, pattern) + if (priority != None) and (priority < best_priority): + best_priority = priority + return_val = (r0, anames, True) + # try again with the atom type names in reverse order + priority = AtomsMatchPattern([anames[1],anames[0]], pattern) + if ((priority != None) and + (priority < best_priority)): #(note: low priority numbers = high priority) + best_priority = priority + return_val = (r0, anames, True) + #if return_val != None: + # sys.stderr.write('DEBUG: For atoms '+str((a1,a2))+' ... bond_length, batom_names = '+str(return_val)+'\n') + return return_val + + + + + + + + +def LookupBondAngle(a1, a2, a3, + atom2equiv_angle, + angle2theta0_or, + atom2auto_angle, + angle2theta0_auto_or): + """ + Try to find angle parameters between atoms whose original atom + names (without equivalences) are a1, a2, and a3. Then return + both the equilibrium rest angle for that 3body interaction + as well as the equivalent atom names used to look it up. (These + could be stored in either atom2equiv_angle or atom2auto_angle.) + If a match was not found, return None. + """ + return_val = None + anames = (atom2equiv_angle[a1], atom2equiv_angle[a2], atom2equiv_angle[a3]) + angle_name = EncodeInteractionName(SortByEnds(anames)) + if angle_name in angle2theta0_or: + return_val = (angle2theta0_or[angle_name], + [anames[0], anames[1], anames[2]], + False) + + # If no angle between these atoms is defined, + # check the angles in the _auto section(s) + # This is a lot messier. + elif ((a1 in atom2auto_angle[0]) and + (a2 in atom2auto_angle[1]) and + (a3 in atom2auto_angle[2])): + + anames = [atom2auto_angle[0][a1], + atom2auto_angle[1][a2], + atom2auto_angle[2][a3]] + #sys.stderr.write('DEBUG: LookupBondAngle(): a1,a2,a3=('+ + # a1+','+a2+','+a3+'), anames='+str(anames)+'\n') + + # Because _auto interactions can contain wildcards, + # there can be multiple entries in angle2theta0_auto_or[] + # for the same list of atom names, and we have to + # consider all of them, and pick the one with the + # most priority (ie. whose priority number is lowest). + # (Note: The MSI file format uses low priority numbers + # to indicate high priority. Somewhat confusing.) + HUGE_VAL = 2000000000 + best_priority = HUGE_VAL # (ie. low priority) + pattern = ['','',''] + for (pattern[0],pattern[1],pattern[2]), theta0 in angle2theta0_auto_or.items(): + priority = AtomsMatchPattern(anames, pattern) + if ((priority != None) and + (priority < best_priority)): #(note: low priority numbers = high priority) + best_priority = priority + return_val = (theta0, anames, True) + # try again with the atom type names in reverse order + priority = AtomsMatchPattern([anames[2],anames[1],anames[0]], pattern) + if (priority != None) and (priority < best_priority): + best_priority = priority + return_val = (theta0, anames, True) + #if return_val != None: + # sys.stderr.write('DEBUG: For atoms '+str((a1,a2,a3))+' ... rest_angle, anames = '+str(return_val)+'\n') + return return_val + + + + + + + + +def Equivalences2ffids(lines_equivalences, + atom_types, + atom2equiv_pair, + atom2equiv_bond, + atom2equiv_angle, + atom2equiv_dihedral, + atom2equiv_improper): + """ + This function reads a list of lines containing "equivalences" and + "auto_equivalences" from an MSI-formatted .FRC file. + Then, for each atom type, it generates a long string which includes the + original atom type name as well as all of the equivalences it belongs to. + Later on, when it is time to generate angles, dihedrals, or impropers, + moltemplate will search for patterns contained in these strings to decide + which type of interaction to generate. + This function returns a dictionary that converts the original atom type name + into these strings. + """ + for line in lines_equivalences: + #tokens = SplitQuotedString(line.strip(), + # comment_char='!>') + + # skip past both '!' and '>' characters + ic1 = line.find('!') + ic = ic1 + ic2 = line.find('>') + if ic2 != -1 and ic2 < ic1: + ic = ic2 + if ic != -1: + line = line[:ic] + else: + line = line.rstrip('\n') + tokens = line.strip().split() + #sys.stderr.write('DEBUG Equivalences2ffids():\n' + # ' tokens = '+str(tokens)+'\n') + atype = EncodeAName(tokens[2]) + atom2equiv_pair[atype] = EncodeAName(tokens[3]) + atom2equiv_bond[atype] = EncodeAName(tokens[4]) + atom2equiv_angle[atype] = EncodeAName(tokens[5]) + atom2equiv_dihedral[atype] = EncodeAName(tokens[6]) + atom2equiv_improper[atype] = EncodeAName(tokens[7]) + + atom2ffid = OrderedDict() + for atom in atom_types: + atom2ffid[atom] = (atom + + ',p'+atom2equiv_pair.get(atom,'') + + ',b'+atom2equiv_bond.get(atom,'') + + ',a'+atom2equiv_angle.get(atom,'') + + ',d'+atom2equiv_dihedral.get(atom,'') + + ',i'+atom2equiv_improper.get(atom,'')) + return atom2ffid + + + + + + +def AutoEquivalences2ffids(lines_equivalences, + lines_auto_equivalences, + atom_types, + atom2equiv_pair, + atom2equiv_bond, + atom2equiv_angle, + atom2equiv_dihedral, + atom2equiv_improper, + atom2auto_pair, + atom2auto_bondincr, + atom2auto_bond, + atom2auto_angleend, + atom2auto_anglecenter, + atom2auto_dihedralend, + atom2auto_dihedralcenter, + atom2auto_improperend, + atom2auto_impropercenter): + """ + This function is a variant of Equivalences2ffids() which also considers + "auto_equivalences". + This function returns a dictionary that converts the original atom type name + into a string that includes that atom's "equivalences", + as well as its "auto_equivalences". + moltemplate will search for patterns contained in these strings to decide + which type of interaction to generate. + """ + Equivalences2ffids(lines_equivalences, + atom_types, + atom2equiv_pair, + atom2equiv_bond, + atom2equiv_angle, + atom2equiv_dihedral, + atom2equiv_improper) + + # ------ The following lines are for processing "auto_equivalences" ----- + # + # What is the difference between "equivalences" and "auto_equivalences"? + # + # equivalences: + # Here is an excerpt from the Discover manual describing "equivalences": + # "Chemically distinct atoms often differ in some, but not all, + # of their forcefield parameters. For example, the bond parameters + # for the C-C bonds in ethene and in benzene are quite different, + # but the nonbond parameters for the carbon atoms are essentially + # the same. Rather than duplicating the nonbond parameters in the + # forcefield parameter file, the Discover program uses atom type + # equivalences to simplify the problem. In the example, the phenyl + # carbon atom type is equivalent to the pure sp2 carbons of ethene + # insofar as the nonbond parameters are concerned. The Discover + # program recognizes five types of equivalences for each atom + # type: nonbond, bond, angle, torsion, and out-of-plane. + # Cross terms such as bond-bond terms have the same equivalences + # (insofar as atom types are concerned) as the diagonal term of + # the topology of all the atoms defining the internal coordinates. + # For the bond-bond term, this means that the atom type + # equivalences for angles would be used + # + # auto_equivalences: + # Are similar to equivalences, but apparently with lower priority. + # In addition, it seems that, when looking up some of the class2 terms + # in the interaction according to atom type using "auto_equivalences" + # a distinction is made between end atoms and central atoms. + # The parameters for these interactions are also stored in different + # tables in the .frc file, with different comments/tags. + # (for example, "cff91_auto" as opposed to "cff91") + # An excerpt from the Discover manual is somewhat vague: + # "A forcefield may include automatic parameters for use when + # better-quality explicit parameters are not defined for a + # particular bond, angle, torsion, or out-of-plane interaction. + # These parameters are intended as temporary patches, to allow + # you to begin calculations immediately." + + for line in lines_auto_equivalences: + #tokens = SplitQuotedString(line.strip(), + # comment_char='!>') + + # skip past both '!' and '>' characters + ic1 = line.find('!') + ic = ic1 + ic2 = line.find('>') + if ic2 != -1 and ic2 < ic1: + ic = ic2 + if ic != -1: + line = line[:ic] + else: + line = line.rstrip('\n') + tokens = line.strip().split() + #sys.stderr.write('DEBUG Equivalences2ffids():\n' + # ' tokens = '+str(tokens)+'\n') + atype = EncodeAName(tokens[2]) + atom2auto_pair[atype] = EncodeAName(tokens[3]) + atom2auto_bondincr[atype] = EncodeAName(tokens[4]) + atom2auto_bond[atype] = EncodeAName(tokens[5]) + atom2auto_angleend[atype] = EncodeAName(tokens[6]) + atom2auto_anglecenter[atype] = EncodeAName(tokens[7]) + atom2auto_dihedralend[atype] = EncodeAName(tokens[8]) + atom2auto_dihedralcenter[atype] = EncodeAName(tokens[9]) + atom2auto_improperend[atype] = EncodeAName(tokens[10]) + atom2auto_impropercenter[atype] = EncodeAName(tokens[11]) + + atom2ffid = OrderedDict() + for atom in atom_types: + atom2ffid[atom] = (atom + + ',p'+atom2equiv_pair.get(atom,'') + + ',b'+atom2equiv_bond.get(atom,'') + + ',a'+atom2equiv_angle.get(atom,'') + + ',d'+atom2equiv_dihedral.get(atom,'') + + ',i'+atom2equiv_improper.get(atom,'') + + ',ap'+atom2auto_pair.get(atom,'') + + ',aq'+atom2auto_bondincr.get(atom,'') + + ',ab'+atom2auto_bond.get(atom,'') + + ',aae'+atom2auto_angleend.get(atom,'') + + ',aac'+atom2auto_anglecenter.get(atom,'') + + ',ade'+atom2auto_dihedralend.get(atom,'') + + ',adc'+atom2auto_dihedralcenter.get(atom,'') + + ',aie'+atom2auto_improperend.get(atom,'') + + ',aic'+atom2auto_impropercenter.get(atom,'') + + '' + ) + return atom2ffid + + + + + + +def main(): + try: + sys.stderr.write(g_program_name + ", version " + + __version__ + ", " + __date__ + "\n") + if sys.version < '2.6': + raise InputError('Error: Using python ' + sys.version + '\n' + + ' Alas, your version of python is too old.\n' + ' You must upgrade to a newer version of python (2.6 or later).') + + if sys.version < '2.7': + from ordereddict import OrderedDict + else: + from collections import OrderedDict + + if sys.version > '3': + import io + else: + import cStringIO + + # defaults: + ffname = 'BIOSYM_MSI_FORCE_FIELD' + type_subset = set([]) + filename_in = '' + file_in = sys.stdin + #file_in = open('pcff_repaired.frc','r') #CONTINUEHERE + include_auto_equivalences = False + #pair_style_name = 'lj/class2/coul/long' + #pair_style_params = "10.0 10.0" + pair_style2docs = {} + pair_style2args = defaultdict(str) + pair_style2docs['lj/cut/coul/long'] = 'http://lammps.sandia.gov/doc/pair_lj.html' + pair_style2args['lj/cut/coul/long'] = '10.0' + pair_style2docs['lj/class2/coul/long'] = 'http://lammps.sandia.gov/doc/pair_class2.html' + pair_style2args['lj/class2/coul/long'] = '10.0' + pair_style2docs['lj/class2/coul/cut'] = 'http://lammps.sandia.gov/doc/pair_class2.html' + pair_style2args['lj/class2/coul/cut'] = '10.0' + + bond_style2docs = {} + #bond_style2args = defaultdict(str) + bond_style2docs['harmonic'] = 'http://lammps.sandia.gov/doc/bond_harmonic.html' + bond_style2docs['class2'] = 'http://lammps.sandia.gov/doc/bond_class2.html' + bond_style2docs['morse'] = 'http://lammps.sandia.gov/doc/bond_morse.html' + bond_symmetry_subgraph = '' # default + + angle_style2docs = {} + #angle_style2args = defaultdict(str) + angle_style2docs['harmonic'] = 'http://lammps.sandia.gov/doc/angle_harmonic.html' + angle_style2docs['class2'] = 'http://lammps.sandia.gov/doc/angle_class2.html' + angle_symmetry_subgraph = '' # default + + dihedral_style2docs = {} + #dihedral_style2args = defaultdict(str) + dihedral_style2docs['charmm'] = 'http://lammps.sandia.gov/doc/dihedral_charmm.html' + dihedral_style2docs['class2'] = 'http://lammps.sandia.gov/doc/dihedral_class2.html' + dihedral_symmetry_subgraph = '' # default + + improper_style2docs = {} + #improper_style2args = defaultdict(str) + improper_style2docs['cvff'] = 'http://lammps.sandia.gov/doc/improper_cvff.html' + improper_style2docs['class2'] = 'http://lammps.sandia.gov/doc/improper_class2.html' + improper_symmetry_subgraph = {} #'cenJsortIKL' + + pair_mixing_style = 'sixthpower tail yes' + + special_bonds_command = 'special_bonds lj/coul 0.0 0.0 1.0 dihedral yes' + # Thanks to Paul Saxe for is suggestions + # http://lammps.sandia.gov/threads/msg11270.html + + + kspace_style = 'kspace_style pppm 0.0001' + pair_styles_selected = set([]) + #pair_style_link = 'http://lammps.sandia.gov/doc/pair_class2.html' + pair_style_args = {} + pair_cutoff = '10.0' + #pair_style_command = " pair_style hybrid " + \ + # pair_style_name + " " + pair_style_args + "\n" + bond_styles_selected = set([]) + #bond_style_link = bond_style2docs[bond_style_name] + #bond_style_args = '' + angle_styles_selected = set([]) + #angle_style_link = angle_style2docs[angle_style_name] + #angle_style_args = '' + dihedral_styles_selected = set([]) + #dihedral_style_link = dihedral_style2docs[dihedral_style_name] + #dihedral_style_args = '' + improper_styles_selected = set([]) + #improper_style_link = improper_style2docs[improper_style_name] + #improper_style_args = '' + hbond_style_name = '' + hbond_style_link = '' + hbond_style_args = '' + + lines_templates = [] + lines_references = defaultdict(list) + lines_warnings = [] + + + argv = [arg for arg in sys.argv] + + i = 1 + + while i < len(argv): + + #sys.stderr.write('argv['+str(i)+'] = \"'+argv[i]+'\"\n') + + if argv[i] == '-atoms': + if i + 1 >= len(argv): + raise InputError('Error: the \"' + argv[i] + '\" argument should be followed by a quoted string\n' + ' which contains a space-delimited list of of a subset of atom types\n' + ' you want to use from the original force-field.\n' + ' Make sure you enclose the entire list in quotes.\n') + type_subset = set(argv[i + 1].strip('\"\'').strip().split()) + del argv[i:i + 2] + + elif argv[i] == '-name': + if i + 1 >= len(argv): + raise InputError('Error: ' + argv[i] + ' flag should be followed by the name of the force-field\n') + ffname = argv[i + 1] + del argv[i:i + 2] + + elif argv[i] in ('-file', '-in-file'): + if i + 1 >= len(argv): + raise InputError('Error: ' + argv[i] + ' flag should be followed by the name of a force-field file\n') + filename_in = argv[i + 1] + try: + file_in = open(filename_in, 'r') + except IOError: + sys.stderr.write('Error: Unable to open file\n' + ' \"' + filename_in + '\"\n' + ' for reading.\n') + sys.exit(1) + del argv[i:i + 2] + + elif argv[i] == '-pair-cutoff': + if i + 1 >= len(argv): + raise InputError('Error: ' + argv[i] + ' flag should be followed by a number' + ' (the distance cutoff for non-bonded (pair) interactions)\n') + pair_style_cutoff = argv[i+1] + del argv[i:i + 2] + + elif argv[i] == '-pair-style': + if i + 1 >= len(argv): + raise InputError('Error: ' + argv[i] + ' flag should be followed by either \"lj/class2/coul/cut\" or \"lj/class2/coul/long\"\n') + pair_style_list = argv[i + 1].split(',') + for pair_style in pair_style_list: + if pair_style == '9-6': + pair_style = 'lj/class2/coul/long' + elif pair_style in ('12-6', 'lj', 'LJ'): + pair_style = 'lj/cut/coul/long' + + if pair_style.find('lj/class2/coul/long') == 0: + kspace_style = 'kspace_style pppm 0.0001' + elif pair_style.find('lj/cut/coul/long') == 0: + kspace_style = 'kspace_style pppm 0.0001' + elif pair_style.find('lj/class2/coul/cut') == 0: + pass + #kspace_style = '' + elif pair_style.find('lj/cut') == 0: + pass + #kspace_style = '' + else: + raise InputError('Error: ' + argv[i] + ' ' + pair_style + ' not supported.\n' + ' The following pair_styles are supported:\n' + ' lj/class2/coul/cut\n' + ' lj/class2/coul/long\n' + ' lj/cut\n' + ' lj/cut/coul/long\n') + pair_styles_selected.add(pair_style) + + del argv[i:i + 2] + + elif argv[i] == '-bond-style': + if i + 1 >= len(argv): + raise InputError('Error: ' + argv[i] + ' flag should be followed by\n' + ' a compatible bond_style.\n') + bond_styles = argv[i + 1].split(',') + for bond_style in bond_styles: + bond_styles_selected.add(bond_style) + #bond_style2args[bond_style] = argv[i + 1].split()[1:] + #if bond_style_name.find('harmonic') == 0: + # pass + # #bond_style_link = 'http://lammps.sandia.gov/doc/bond_harmonic.html' + #elif bond_style_name.find('morse') == 0: + # pass + # #bond_style_link = 'http://lammps.sandia.gov/doc/bond_morse.html' + #elif bond_style_name.find('class2') == 0: + # pass + # #bond_style_link = 'http://lammps.sandia.gov/doc/bond_class2.html' + #else: + # raise InputError('Error: ' + argv[i] + ' must be followed by either:\n' + # ' \"harmonic\", \"class2\", or \"morse\".\n') + del argv[i:i + 2] + + elif argv[i] == '-angle-style': + if i + 1 >= len(argv): + raise InputError('Error: ' + argv[i] + ' flag should be followed by\n' + ' a compatible angle_style.\n') + angle_styles = argv[i + 1].split(',') + for angle_style in angle_styles: + angle_styles_selected.add(angle_style) + #if angle_style_name.find('harmonic') == 0: + # pass + # #angle_style_link = 'http://lammps.sandia.gov/doc/angle_harmonic.html' + #elif angle_style_name.find('class2') == 0: + # pass + # #angle_style_link = 'http://lammps.sandia.gov/doc/angle_class2.html' + #else: + # raise InputError('Error: ' + argv[i] + ' must be followed by either:\n' + # ' \"harmonic\" or \"class2\"\n') + del argv[i:i + 2] + + elif argv[i] == '-dihedral-style': + if i + 1 >= len(argv): + raise InputError('Error: ' + argv[i] + ' flag should be followed by\n' + ' a compatible dihedral_style.\n') + dihedral_styles = argv[i + 1].split(',') + for dihedral_style in dihedral_styles: + dihedral_styles_selected.add(dihedral_style) + #if dihedral_style_name.find('charmm') == 0: + # pass + # #dihedral_style_link = 'http://lammps.sandia.gov/doc/dihedral_charmm.html' + #elif dihedral_style_name.find('class2') == 0: + # pass + # #dihedral_style_link = 'http://lammps.sandia.gov/doc/dihedral_class2.html' + #else: + # raise InputError('Error: ' + argv[i] + ' must be followed by either:\n' + # ' \"harmonic\" or \"class2\"\n') + del argv[i:i + 2] + + elif argv[i] == '-improper-style': + if i + 1 >= len(argv): + raise InputError('Error: ' + argv[i] + ' flag should be followed by\n' + ' a compatible impropoer_style.\n') + improper_styles = argv[i + 1].split(',') + for improper_style in improper_styles: + improper_styles_selected.add(improper_style) + #if impropoer_style_name.find('harmonic') == 0: + # pass + # #impropoer_style_link = 'http://lammps.sandia.gov/doc/impropoer_harmonic.html' + #elif impropoer_style_name.find('class2') == 0: + # pass + # #impropoer_style_link = 'http://lammps.sandia.gov/doc/impropoer_class2.html' + #else: + # raise InputError('Error: ' + argv[i] + ' must be followed by either:\n' + # ' \"harmonic\" or \"class2\"\n') + del argv[i:i + 2] + + elif argv[i] == '-hbond-style': + if i + 1 >= len(argv): + raise InputError('Error: ' + argv[i] + ' ' + hbond_style_name + '\n' + ' should be followed by a compatible pair_style.\n') + hbond_style_name = argv[i + 1] + hbond_style_link = 'http://lammps.sandia.gov/doc/pair_hbond_dreiding.html' + if hbond_style_name.find('none') == 0: + hbond_style_name = '' + hbond_style_args = '' + elif hbond_style_name.find('hbond/dreiding/lj') == 0: + n = len('hbond/dreiding/lj') + hbond_style_args = hbond_style_name[n+1:] + hbond_style_name = hbond_style_name[:n] + elif hbond_style_name.find('hbond/dreiding/morse') == 0: + n = len('hbond/dreiding/morse') + hbond_style_args = hbond_style_name[n+1:] + hbond_style_name = hbond_style_name[:n] + else: + raise InputError('Error: ' + argv[i] + ' flag should be followed by either\n' + ' \"hbond/dreiding/lj\" or \"hbond/dreiding/morse"\n') + del argv[i:i + 2] + + elif argv[i] in ('-url', '-in-url'): + import urllib2 + if i + 1 >= len(argv): + raise InputError('Error: ' + argv[i] + ' flag should be followed by a URL pointing to\n' + ' a file containing force-field information in msi/frc format.\n') + url = argv[i + 1] + try: + request = urllib2.Request(url) + file_in = urllib2.urlopen(request) + except urllib2.URLError: + sys.stdout.write("Error: Unable to open link:\n" + url + "\n") + sys.exit(1) + del argv[i:i + 2] + + elif argv[i] == '-auto': + include_auto_equivalences = True + del argv[i:i + 1] + + elif argv[i] in ('-help', '--help', '-?', '--?'): + sys.stderr.write(doc_msg) + sys.exit(0) + del argv[i:i + 1] + + else: + i += 1 + + if len(argv) != 1: + raise InputError('Error: Unrecongized arguments: ' + ' '.join(argv[1:]) + + '\n\n' + doc_msg) + + # Default styles: + if len(bond_styles_selected) == 0: + bond_styles_selected.add('class2') + if len(angle_styles_selected) == 0: + angle_styles_selected.add('class2') + if len(dihedral_styles_selected) == 0: + dihedral_styles_selected.add('class2') + if len(improper_styles_selected) == 0: + improper_styles_selected.add('class2') + if len(pair_styles_selected) == 0: + pair_styles_selected.add('lj/class2/coul/long') + + #sys.stderr.write("Reading parameter file...\n") + + lines = file_in.readlines() + atom2charge = OrderedDict() # lookup charge from atom type + atom2mass = OrderedDict() # lookup mass from atom type + # equivalences lookup + atom2ffid = OrderedDict() # lookup "force-field-ID" a string containing + # equivalences to lookup bonded interactions + atom2equiv_pair = OrderedDict() # lookup the equivalent symbol used for + # looking up pair interactions + atom2equiv_bond = OrderedDict() + atom2equiv_angle = OrderedDict() + atom2equiv_dihedral = OrderedDict() + atom2equiv_improper = OrderedDict() + # inverse equivalences lookup + equiv_pair2atom = defaultdict(set) + equiv_bond2atom = defaultdict(set) + equiv_angle2atom = defaultdict(set) + equiv_dihedral2atom = defaultdict(set) + equiv_improper2atom = defaultdict(set) + + # auto equivalences lookup + atom2auto_pair = OrderedDict() + atom2auto_bondincr = OrderedDict() + atom2auto_bond = OrderedDict() + atom2auto_angleend = OrderedDict() + atom2auto_anglecenter = OrderedDict() + atom2auto_dihedralend = OrderedDict() + atom2auto_dihedralcenter = OrderedDict() + atom2auto_improperend = OrderedDict() + atom2auto_impropercenter = OrderedDict() + # inverse auto equivalences lookup + auto_pair2atom = defaultdict(set) + auto_bondincr2atom = defaultdict(set) + auto_bond2atom = defaultdict(set) + auto_angleend2atom = defaultdict(set) + auto_anglecenter2atom = defaultdict(set) + auto_dihedralend2atom = defaultdict(set) + auto_dihedralcenter2atom = defaultdict(set) + auto_improperend2atom = defaultdict(set) + auto_impropercenter2atom = defaultdict(set) + + + atom2element = OrderedDict() # Optional: + # which element (eg 'C', 'O') ? (Note this + # is different from atom type: 'C1', 'Oh') + atom2numbonds = OrderedDict() # Optional: how many bonds emanate from + atom2descr = OrderedDict() # Optional: a brief description + atom2ver = OrderedDict() # atoms introduced in different versions of ff + atom2ref = OrderedDict() # reference to paper where atom introduced + lines_equivalences = [] # equivalences for force-field lookup + lines_auto_equivalences = [] # auto_equivalences have lower priority + + pair2params = OrderedDict() + pair2style = OrderedDict() + pair_styles = set([]) + pair2ver = OrderedDict() + pair2ref = OrderedDict() + + bond2chargepair = OrderedDict() # a.k.a "bond increments" + charge_pair_priority = OrderedDict() # priority in case multiple entries + # exist for the same pair of atoms + charge_pair_ver = OrderedDict() # which version of the force field? + charge_pair_ref = OrderedDict() # paper introducing this chargepair + + bond2params = OrderedDict() # store a tuple with the 2-body bond + # interaction type, and its parameters + # for every type of bond + bond2priority = OrderedDict() # What is the priority of this interaction? + bond2style = OrderedDict() # What LAMMPS bond style (formula) + # is used for a given interaction? + bond_styles = set([]) # Contains all bond styles used. + bond2ver = OrderedDict() + bond2ref = OrderedDict() + bond2r0 = OrderedDict() + bond2r0_auto = OrderedDict() + + angle2params = OrderedDict() # store a tuple with the 3-body angle + # interaction type, and its parameters + # for every type of angle + + angle2params_or = OrderedDict() + # http://lammps.sandia.gov/doc/angle_class2.html + #angle2class2_a = OrderedDict() # params for the "a" class2 terms + angle2class2_bb = OrderedDict() # params for the "bb" class2 terms + angle2class2_bb_or = OrderedDict() + angle2class2_ba = OrderedDict() # params for the "ba" class2 terms + angle2class2_ba_or = OrderedDict() + angle2priority = OrderedDict() # What is the priority of this interaction? + angle2priority_or = OrderedDict() + angle_is_secondary_or = OrderedDict() + angle2style = OrderedDict() # What LAMMPS angle style (formula) + # is used for a given interaction? + angle2style_or = OrderedDict() + angle_styles = set([]) # Contains all angle styles used. + angle2ref = OrderedDict() + angle2ver = OrderedDict() + angle2ref_or = OrderedDict() + angle2ver_or = OrderedDict() + angle2ver_bb = OrderedDict() + angle2ver_bb_or = OrderedDict() + angle2ref_bb = OrderedDict() + angle2ref_bb_or = OrderedDict() + angle2ver_ba = OrderedDict() + angle2ver_ba_or = OrderedDict() + angle2ref_ba = OrderedDict() + angle2ref_ba_or = OrderedDict() + angle2theta0_or = OrderedDict() + angle2theta0_auto_or = OrderedDict() + + # http://lammps.sandia.gov/doc/dihedral_class2.html + dihedral2params = OrderedDict() # store a tuple with the 4-body dihedral + # interaction type, and its parameters + # for every type of dihedral + dihedral2params_or = OrderedDict() + #dihedral2class2_d = OrderedDict() # params for the "d" class2 term + dihedral2class2_mbt = OrderedDict() # params for the "mbt" class2 term + dihedral2class2_mbt_or = OrderedDict() + dihedral2class2_ebt = OrderedDict() # params for the "ebt" class2 term + dihedral2class2_ebt_or = OrderedDict() + #dihedral2sym_ebt = OrderedDict() + dihedral2class2_at = OrderedDict() # params for the "at" class2 term + dihedral2class2_at_or = OrderedDict() + #dihedral2sym_at = OrderedDict() + dihedral2class2_aat = OrderedDict() # params for the "aat" class2 term + dihedral2class2_aat_or = OrderedDict() + #dihedral2sym_aat = OrderedDict() + dihedral2class2_bb13 = OrderedDict() # params for the "bb13" class2 term + dihedral2class2_bb13_or = OrderedDict() + #dihedral2sym_bb13 = OrderedDict() + dihedral2priority = OrderedDict() # What is the priority of this interaction? + dihedral2priority_or = OrderedDict() + dihedral_is_secondary_or = OrderedDict() + dihedral2style = OrderedDict() # What LAMMPS dihedral style (formula) + # is used for a given interaction? + dihedral2style_or = OrderedDict() + dihedral_styles = set([]) # Contains all dihedral styles used. + dihedral2ref = OrderedDict() + dihedral2ver = OrderedDict() + dihedral2ver_or = OrderedDict() + dihedral2ref_or = OrderedDict() + dihedral2ver_mbt = OrderedDict() + dihedral2ver_mbt_or = OrderedDict() + dihedral2ref_mbt = OrderedDict() + dihedral2ref_mbt_or = OrderedDict() + dihedral2ver_ebt = OrderedDict() + dihedral2ver_ebt_or = OrderedDict() + dihedral2ref_ebt = OrderedDict() + dihedral2ref_ebt_or = OrderedDict() + dihedral2ver_at = OrderedDict() + dihedral2ver_at_or = OrderedDict() + dihedral2ref_at = OrderedDict() + dihedral2ref_at_or = OrderedDict() + dihedral2ver_aat = OrderedDict() + dihedral2ver_aat_or = OrderedDict() + dihedral2ref_aat = OrderedDict() + dihedral2ref_aat_or = OrderedDict() + dihedral2ver_bb13 = OrderedDict() + dihedral2ver_bb13_or = OrderedDict() + dihedral2ref_bb13 = OrderedDict() + dihedral2ref_bb13_or = OrderedDict() + + + # http://lammps.sandia.gov/doc/improper_class2.html + improper2params = OrderedDict() # store a tuple with the 4-body improper + # interaction type, and its parameters + # for every type of imporpoer + improper2params_or = OrderedDict() + improper2class2_aa = OrderedDict() # params for the "aa" class2 term + improper2class2_aa_or = OrderedDict() + + improper2cross = defaultdict(dict) + # improper2cross[imp_name][atoms] stores the + # coefficient (K) for the angle-angle ("aa") + # improper interactions between a pair of + # neighboring 3-body angles (in the .FRC file). + # "imp_name" is the name of the improper interaction + # (which is a concatination of the central atom and + # the 3 surrounding leaf atoms (which are sorted)) + # "atoms" indicates, for that K value, the list of + # leaf atoms for that K value as they appear in the + # corresponding line of the .frc file (however the + # and last atom names are swapped if the first + # atom name is lexicographically > the last, to + # eliminate redundancy and ambiguity.) + + improper2sym = defaultdict(set) + # improper2sym[imp_name] indicates which subset of + # leaf atoms (from 0 to 2) are equivalent and can + # tolerate having their order rearranged without + # effecting the energy. Later on this will be used + # to reduce the number of improper interactions that + # will be generated by moltemplate. + + improper2priority = OrderedDict() # What is the priority of this interaction? + improper2priority_or = OrderedDict() + improper_is_secondary_or = OrderedDict() + improper2style = OrderedDict() # What LAMMPS improper style (formula) + # is used for a given interaction? + improper2style_or = OrderedDict() + improper_styles = set([]) # Contains all improper styles used. + improper2ver = OrderedDict() + improper2ver_or = OrderedDict() + improper2ref = OrderedDict() + improper2ref_or = OrderedDict() + improper2ver_aa = OrderedDict() + improper2ver_aa_or = OrderedDict() + improper2ref_aa = OrderedDict() + improper2ref_aa_or = OrderedDict() + + + # Warn users if force field contains terms which cannot yet + # be simulated with LAMMPS (as of 2017-10-13) + display_OOP_OOP_warning = False + display_torsion_torsion_1_warning = False + + + """ + --- these next few lines of code appear to be unnecessary. + --- I'll probably delete this code in a later version + hbond2params = OrderedDict() # lookup hbond parameters and atom types + hbond2donors = OrderedDict() # according to the identifier in the 2nd + hbond2acceptors = OrderedDict() # column of the "#hbond_definition" + hbond2hydrogens = OrderedDict() # section of an .frc file. + """ + + allowed_section_names = set(['#define', + # sections used in all MSI force-fields + '#atom_types', + '#equivalence', + '#auto_equivalence', + '#nonbond(9-6)', + '#nonbond(12-6)', + '#quadratic_bond', + '#quartic_bond', + '#morse_bond', + '#quadratic_angle', + '#quartic_angle', + '#bond-bond', + '#bond-angle', + '#torsion_1', + '#torsion_3', + '#middle_bond-torsion_3', + '#end_bond-torsion_3', + '#angle-torsion_3', + '#angle-angle-torsion_1',#(class2 dihedral) + '#bond-bond_1_3', #(a class2 dihedral term) + '#out_of_plane', + '#wilson_out_of_plane', + '#angle-angle', #(a class2 improper term) + '#out_of_plane-out_of_plane', # UNSUPPORTED + '#torsion-torsion_1', # UNSUPPORTED + '#bond_increments', + '#hbond_definition', # irrelevant? + '#templates', + '#reference', + '#end' + ]) + + icol_type = icol_mass = icol_elem = icol_nbonds = icol_comment = icol_ver = icol_ref = -1 + + section_name = '' + section_is_auto = False + + sys.stderr.write("parsing file pass1: look for atom types and equivalences...") + + for iline in range(0, len(lines)): + line = lines[iline] + sys.stderr.write('line=\"' + line.strip() + '\"\n') + tokens = SplitQuotedString(line.strip(), + quotes='', + comment_char='>') + #sys.stderr.write('tokens = ' + str(tokens) + '\n') + if line.lstrip().find('!') == 0 and tokens[0] != '!Ver': + continue + if line.lstrip(' ').find('#') == 0: + #sys.stderr.write('allowed_section_names = ' + + # str(allowed_section_names) + '\n') + if tokens[0] in allowed_section_names: + section_name = tokens[0] + section_is_auto = tokens[-1].endswith('_auto') + tokens_after_section_name = tokens[1:] + sys.stderr.write(' encountered section \"'+tokens[0]+'\"\n') + continue + elif not tokens[0] in ('#version', + '#define'): + raise InputError('Error: Line# '+str(iline) +'\n' + ' Unrecognized section name:\n' + ' \"' + tokens[0] + '\"\n') + elif (len(tokens) == 8) and (section_name == '#equivalence'): + if line.lstrip().find('!') == 0: + continue + lines_equivalences.append(line) + elif (len(tokens) == 12) and (section_name == '#auto_equivalence'): + if line.lstrip().find('!') == 0: + continue + lines_auto_equivalences.append(line) + elif (len(tokens) > 0) and (section_name == '#atom_types'): + # Different FRC files put this information in different + # columns. Column order is stored in the !Ver comment line: + if line.lstrip().find('!Ver') == 0: + tokens = line.strip().split() + for i in range(0, len(tokens)): + if tokens[i].lower() == 'type': + icol_type = i + elif tokens[i].lower() == 'mass': + icol_mass = i + elif tokens[i].lower() == 'element': + icol_elem = i + elif tokens[i].lower() == 'connections': + icol_nbonds = i + elif tokens[i].lower() == 'comment': + icol_comment = i + elif tokens[i].lower() == '!ver': #(version of ff) + icol_ver = i + elif tokens[i].lower() == 'ref': + icol_ref = i + assert(icol_ver == 0) + + if -1 in (icol_type, icol_mass): + raise InputError('Error: Invalid #atom_types section.\n' + ' The meaning of each column cannot be determined.\n' + ' This file needs a valid "!Ver..." comment.\n') + if icol_comment == -1: + icol_comment = max(icol_type, icol_mass, + icol_elem, icol_nbonds) + 1 + + sys.stderr.write('icol_ver = '+str(icol_ver)+'\n') + sys.stderr.write('icol_ref = '+str(icol_ref)+'\n') + sys.stderr.write('icol_mass = '+str(icol_mass)+'\n') + sys.stderr.write('icol_nelem = '+str(icol_elem)+'\n') + sys.stderr.write('icol_nbonds = '+str(icol_nbonds)+'\n') + sys.stderr.write('icol_comment = '+str(icol_comment)+'\n') + continue + + tokens = map(RemoveOuterQuotes, + NSplitQuotedString(line.strip(), + icol_comment+1, + quotes='', + comment_char='>')) + tokens = list(tokens) + + if (len(tokens) > 4): + if ((len(type_subset) == 0) or (tokens[1] in type_subset)): + aname = EncodeAName(tokens[icol_type]) + atom2mass[aname] = str(max(float(tokens[icol_mass]), 1.0e-06)) + # Some atoms in cvff.prm have zero mass. Unfortunately this + # causes LAMMPS to crash, even if these atoms are never used, + # so I give the mass a non-zero value instead. + + if icol_elem != -1: + atom2element[aname] = tokens[icol_elem] + if icol_nbonds != -1: + atom2numbonds[aname] = int(tokens[icol_nbonds]) + atom2descr[aname] = tokens[icol_comment] + atom2ver[aname] = tokens[icol_ver] + atom2ref[aname] = tokens[icol_ref] + + elif len(tokens) > 0: + raise InputError('Error: Invalid atom line: (line#'+str(iline)+')\n' + + '\"'+line.strip()+'\"') + + atom_types = [x for x in atom2mass] + + # Now construct the lookup tables and inverse tables + # we will need to understand the remainder of the file: + if not include_auto_equivalences: + atom2ffid = Equivalences2ffids(lines_equivalences, + atom_types, + atom2equiv_pair, + atom2equiv_bond, + atom2equiv_angle, + atom2equiv_dihedral, + atom2equiv_improper) + else: + atom2ffid = AutoEquivalences2ffids(lines_equivalences, + lines_auto_equivalences, + atom_types, + atom2equiv_pair, + atom2equiv_bond, + atom2equiv_angle, + atom2equiv_dihedral, + atom2equiv_improper, + atom2auto_pair, + atom2auto_bondincr, + atom2auto_bond, + atom2auto_angleend, + atom2auto_anglecenter, + atom2auto_dihedralend, + atom2auto_dihedralcenter, + atom2auto_improperend, + atom2auto_impropercenter) + + for a,e in atom2equiv_pair.items(): + equiv_pair2atom[e].add(a) + for a,e in atom2equiv_bond.items(): + equiv_bond2atom[e].add(a) + for a,e in atom2equiv_angle.items(): + equiv_angle2atom[e].add(a) + for a,e in atom2equiv_dihedral.items(): + equiv_dihedral2atom[e].add(a) + for a,e in atom2equiv_improper.items(): + equiv_improper2atom[e].add(a) + + # the inverse lookup for '*' matches all atom types + for a in atom_types: + #equiv_pair2atom['*'].add(EncodeAName(a)) + equiv_pair2atom['X'].add(EncodeAName(a)) + #equiv_bond2atom['*'].add(EncodeAName(a)) + equiv_bond2atom['X'].add(EncodeAName(a)) + #equiv_angle2atom['*'].add(EncodeAName(a)) + equiv_angle2atom['X'].add(EncodeAName(a)) + #equiv_dihedral2atom['*'].add(EncodeAName(a)) + equiv_dihedral2atom['X'].add(EncodeAName(a)) + #equiv_improper2atom['*'].add(EncodeAName(a)) + equiv_improper2atom['X'].add(EncodeAName(a)) + + for a,e in atom2auto_pair.items(): + auto_pair2atom[e].add(a) + for a,e in atom2auto_bondincr.items(): + auto_bondincr2atom[e].add(a) + for a,e in atom2auto_bond.items(): + auto_bond2atom[e].add(a) + for a,e in atom2auto_angleend.items(): + auto_angleend2atom[e].add(a) + #auto_angle[0][e].add(a) + #auto_angle[2][e].add(a) + for a,e in atom2auto_anglecenter.items(): + auto_anglecenter2atom[e].add(a) + #auto_angle[1][e].add(a) + for a,e in atom2auto_dihedralend.items(): + auto_dihedralend2atom[e].add(a) + #auto_dihedral2atom[0][e].add(a) + #auto_dihedral2atom[3][e].add(a) + for a,e in atom2auto_dihedralcenter.items(): + auto_dihedralcenter2atom[e].add(a) + #auto_dihedral2atom[1][e].add(a) + #auto_dihedral2atom[2][e].add(a) + for a,e in atom2auto_improperend.items(): + auto_improperend2atom[e].add(a) + for a,e in atom2auto_impropercenter.items(): + auto_impropercenter2atom[e].add(a) + + # the inverse lookup for '*' matches all atom types + for a in atom_types: + #auto_pair2atom['*'].add(EncodeAName(a)) + auto_pair2atom['X'].add(EncodeAName(a)) + #auto_bondincr2atom['*'].add(EncodeAName(a)) + auto_bondincr2atom['X'].add(EncodeAName(a)) + #auto_bond2atom['*'].add(EncodeAName(a)) + auto_bond2atom['X'].add(EncodeAName(a)) + #auto_angleend2atom['*'].add(EncodeAName(a)) + auto_angleend2atom['X'].add(EncodeAName(a)) + #auto_anglecenter2atom['*'].add(EncodeAName(a)) + auto_anglecenter2atom['X'].add(EncodeAName(a)) + #auto_dihedralend2atom['*'].add(EncodeAName(a)) + auto_dihedralend2atom['X'].add(EncodeAName(a)) + #auto_dihedralcenter2atom['*'].add(EncodeAName(a)) + auto_dihedralcenter2atom['X'].add(EncodeAName(a)) + #auto_improperend2atom['*'].add(EncodeAName(a)) + auto_improperend2atom['X'].add(EncodeAName(a)) + #auto_impropercenter2atom['*'].add(EncodeAName(a)) + auto_impropercenter2atom['X'].add(EncodeAName(a)) + + + + + + + + + sys.stderr.write("parsing file pass2: look for bonds, bond_increments and nonbonded (pair) interactions...") + + for iline in range(0, len(lines)): + line = lines[iline] + sys.stderr.write('line=\"' + line.strip() + '\"\n') + tokens = SplitQuotedString(line.strip(), + quotes='', + comment_char='>') + #sys.stderr.write('tokens = ' + str(tokens) + '\n') + if line.lstrip().find('!') == 0 and tokens[0] != '!Ver': + continue + if line.lstrip(' ').find('#') == 0: + #sys.stderr.write('allowed_section_names = ' + + # str(allowed_section_names) + '\n') + if (tokens[0] in allowed_section_names): + section_name = tokens[0] + section_is_auto = tokens[-1].endswith('_auto') + tokens_after_section_name = tokens[1:] + sys.stderr.write(' encountered section \"'+tokens[0]+'\"\n') + continue + elif (not tokens[0] in ('#version','#define')): + raise InputError('Error: Line# '+str(iline) +'\n' + ' Unrecognized section name:\n' + ' \"' + tokens[0] + '\"\n') + + + elif ((len(tokens) > 4) and (section_name == '#nonbond(12-6)') + and (pair_styles_selected & set(['lj','lj/cut','lj/cut/coul/long', + 'lj/cut/coul/cut','lj/cut/coul/debye', + 'lj/cut/coul/dsf','lj/cut/coul/msm', + '12-6','nonbond(12-6)']))): + + if line.lstrip().find('!') == 0: + continue + atom_name = EncodeAName(tokens[2]) + pair2ver[atom_name] = tokens[0] + pair2ref[atom_name] = tokens[1] + A = float(tokens[3]) + B = float(tokens[4]) + epsilon = B*B/(4*A) + sigma = pow(B/A, 1.0/6) + if sigma == 0.0: + sigma = 1.0 #(non-zero to avoid nan error later) + pair_styles.add('lj/cut/coul/long') + pair_style_args['lj/cut/coul/long'] = pair_cutoff + pair2style[atom_name] = 'lj/cut/coul/long' + pair2params[atom_name] = (str(epsilon)+' '+str(sigma)) + pair_mixing_style = 'geometric tail yes' + #if pair_style_name.find('lj/cut') == 0: + # pair2params[atom_name] = (str(epsilon)+' '+str(sigma)) + # pair_mixing_style = 'geometric tail yes' + + + elif ((len(tokens) > 4) and (section_name == '#nonbond(9-6)') + and (pair_styles_selected & + set(['class2', '9-6', 'nonbond(9-6)', + 'lj/class2/coul/long']))): + if line.lstrip().find('!') == 0: + continue + atom_name = EncodeAName(tokens[2]) + pair2ver[atom_name] = tokens[0] + pair2ref[atom_name] = tokens[1] + sigma = tokens[3] + epsilon = tokens[4] + pair_styles.add('lj/class2/coul/long') + pair_style_args['lj/class2/coul/long'] = pair_cutoff + pair2style[atom_name] = 'lj/class2/coul/long' + pair2params[atom_name] = (epsilon+' '+sigma) + pair_mixing_style = 'sixthpower tail yes' + #if pair_style_name.find('lj/class2') == 0: + # pair2params[atom_name] = (epsilon+' '+sigma) + # pair_mixing_style = 'sixthpower tail yes' + + + elif (len(tokens) == 6) and (section_name == '#bond_increments'): + if line.lstrip().find('!') == 0: + continue + aorig = [a for a in map(EncodeAName, tokens[2:4])] + delta_q = tokens[4:6] + atom_names = [a for a in aorig] + # swap the order of the atoms? + order_reversed = aorig[0] > aorig[-1] + if order_reversed: + delta_q.reverse() + atom_names.reverse() + bond_name = EncodeInteractionName(atom_names, section_is_auto) + charge_pair_ver[bond_name] = tokens[0] + charge_pair_ref[bond_name] = tokens[1] + charge_pair_priority[bond_name] = \ + (section_is_auto, + DetermineNumericPriority(section_is_auto, + tokens[2:4], + float(charge_pair_ver[bond_name]))) + bond2chargepair[bond_name] = (delta_q[0] + ' ' + delta_q[1]) + + + elif ((len(tokens) > 5) and (section_name == '#quadratic_bond') + and (bond_styles_selected & set(['harmonic','quadratic','quadratic_bond']))): + if line.lstrip().find('!') == 0: + continue + bond_styles.add('harmonic') + atom_names = SortByEnds(map(EncodeAName, tokens[2:4])) + bond_name = EncodeInteractionName(atom_names, section_is_auto) + bond2ver[bond_name] = tokens[0] + bond2ref[bond_name] = tokens[1] + bond2priority[bond_name] = \ + (section_is_auto, + DetermineNumericPriority(section_is_auto, + tokens[2:4], + float(bond2ver[bond_name]))) + r0 = tokens[4] + k = tokens[5] + if not section_is_auto: + bond2r0[bond_name] = r0 + sys.stderr.write('bond2r0['+bond_name+'] = ' + str(r0) + '\n') + else: + bond2r0_auto[(atom_names[0], atom_names[1])] = r0 + sys.stderr.write('bond2r0_auto['+str(atom_names)+'] = ' + str(r0) + '\n') + bond2style[bond_name] = 'harmonic' + bond2params[bond_name] = (k+' '+r0) + + + elif ((len(tokens) > 6) and (section_name == '#morse_bond') + and (bond_styles_selected & set(['morse','morse_bond']))): + if line.lstrip().find('!') == 0: + continue + bond_styles.add('morse') + atom_names = SortByEnds(map(EncodeAName, tokens[2:4])) + bond_name = EncodeInteractionName(atom_names, section_is_auto) + bond2ver[bond_name] = tokens[0] + bond2ref[bond_name] = tokens[1] + bond2priority[bond_name] = \ + (section_is_auto, + DetermineNumericPriority(section_is_auto, + tokens[2:4], + float(bond2ver[bond_name]))) + r0 = tokens[4] + D = tokens[5] + alpha = tokens[6] + sys.stderr.write('DEBUG: morse: atom_names = '+str(atom_names)+'\n') + if not section_is_auto: + bond2r0[bond_name] = r0 + sys.stderr.write('bond2r0['+bond_name+'] = ' + str(r0) + '\n') + else: + bond2r0_auto[(atom_names[0], atom_names[1])] = r0 + sys.stderr.write('bond2r0_auto['+str(atom_names)+'] = ' + str(r0) + '\n') + bond2style[bond_name] = 'morse' + bond2params[bond_name] = (D+' '+alpha+' '+r0) + + + + elif ((len(tokens) > 7) and (section_name == '#quartic_bond') + and (bond_styles_selected & set(['class2','quartic','quartic_bond']))): + if line.lstrip().find('!') == 0: + continue + bond_styles.add('class2') + atom_names = SortByEnds(map(EncodeAName, tokens[2:4])) + bond_name = EncodeInteractionName(atom_names, section_is_auto) + bond2ver[bond_name] = tokens[0] + bond2ref[bond_name] = tokens[1] + bond2priority[bond_name] = \ + (section_is_auto, + DetermineNumericPriority(section_is_auto, + tokens[2:4], + float(bond2ver[bond_name]))) + r0 = tokens[4] + if not section_is_auto: + bond2r0[bond_name] = r0 + sys.stderr.write('bond2r0['+bond_name+'] = ' + str(r0) + '\n') + else: + bond2r0_auto[(atom_names[0], atom_names[1])] = r0 + sys.stderr.write('bond2r0_auto['+str(atom_names)+'] = ' + str(r0) + '\n') + K2 = tokens[5] + K3 = tokens[6] + K4 = tokens[7] + bond2style[bond_name] = 'class2' + bond2params[bond_name] = (r0+' '+K2+' '+K3+' '+K4) + + + + + + sys.stderr.write("parsing file pass3: look for (3-body) angle interactions...") + + for iline in range(0, len(lines)): + line = lines[iline] + sys.stderr.write('line=\"' + line.strip() + '\"\n') + tokens = SplitQuotedString(line.strip(), + quotes='', + comment_char='>') + #sys.stderr.write('tokens = ' + str(tokens) + '\n') + if line.lstrip().find('!') == 0 and tokens[0] != '!Ver': + continue + if line.lstrip(' ').find('#') == 0: + #sys.stderr.write('allowed_section_names = ' + + # str(allowed_section_names) + '\n') + if (tokens[0] in allowed_section_names): + section_name = tokens[0] + section_is_auto = tokens[-1].endswith('_auto') + tokens_after_section_name = tokens[1:] + sys.stderr.write(' encountered section \"'+tokens[0]+'\"\n') + continue + elif (not tokens[0] in ('#version','#define')): + raise InputError('Error: Line# '+str(iline) +'\n' + ' Unrecognized section name:\n' + ' \"' + tokens[0] + '\"\n') + + + + + + + + elif (len(tokens) > 6) and (section_name == '#quadratic_angle'): + if line.lstrip().find('!') == 0: + continue + atom_names = SortByEnds(map(EncodeAName, tokens[2:5])) + angle_name = EncodeInteractionName(atom_names, section_is_auto) + + angle2ver[angle_name] = tokens[0] + angle2ref[angle_name] = tokens[1] + angle2priority_or[angle_name] = \ + DetermineNumericPriority(section_is_auto, + tokens[2:5], + float(angle2ver[angle_name])) + angle_is_secondary_or[angle_name] = False + angle2priority[angle_name] = \ + (section_is_auto, + angle_is_secondary_or[angle_name], + angle2priority_or[angle_name]) + theta0 = tokens[5] + k = tokens[6] + if not section_is_auto: + angle2theta0_or[angle_name] = theta0 + sys.stderr.write('angle2theta0_or['+angle_name+'] = ' + str(theta0) + '\n') + else: + angle2theta0_auto_or[(atom_names[0], atom_names[1], atom_names[2])] = theta0 + sys.stderr.write('angle2theta0_auto_or['+str(atom_names)+'] = ' + str(theta0) + '\n') + if (angle_styles_selected & set(['harmonic', + 'quadratic', + 'quadratic_angle'])): + angle_styles.add('harmonic') + angle2style[angle_name] = 'harmonic' + angle2params[angle_name] = (k+' '+theta0) + elif (angle_styles_selected & set(['class2', + 'quartic', + 'quartic_angle'])): + # Then this is a special case of the class2 angle where + # the (theta-theta0)^3 and (theta-theta0)^4 terms = 0 + angle_styles.add('class2') + angle2style_or[angle_name] = 'class2' + angle2params_or[angle_name] = (theta0+' '+k+' 0 0') + + + + elif ((len(tokens) > 8) and (section_name == '#quartic_angle') + and (angle_styles_selected & set(['class2','quartic','quartic_angle']))): + if line.lstrip().find('!') == 0: + continue + angle_styles.add('class2') + atom_names = SortByEnds(map(EncodeAName, tokens[2:5])) + ang_name_orig = EncodeInteractionName(atom_names, section_is_auto) + version = tokens[0] + reference = tokens[1] + angle2ver_or[ang_name_orig] = version + angle2ref_or[ang_name_orig] = reference + angle2priority_or[ang_name_orig] = \ + DetermineNumericPriority(section_is_auto, + tokens[2:5], + float(angle2ver_or[ang_name_orig])) + angle_is_secondary_or[ang_name_orig] = False + #angle2priority[ang_name_orig] = \ + # (section_is_auto, + # angle_is_secondary_or[ang_name_orig], + # angle2priority_or[ang_name_orig]) + theta0 = tokens[5] + if not section_is_auto: + angle2theta0_or[ang_name_orig] = theta0 + sys.stderr.write('angle2theta0_or['+ang_name_orig+'] = ' + str(theta0) + '\n') + else: + angle2theta0_auto_or[(atom_names[0], atom_names[1], atom_names[2])] = theta0 + sys.stderr.write('angle2theta0_auto_or['+str(atom_names)+'] = ' + str(theta0) + '\n') + K2 = tokens[6] + K3 = tokens[7] + K4 = tokens[8] + angle2style_or[ang_name_orig] = 'class2' + angle2params_or[ang_name_orig] = [theta0, K2, K3, K4] + if not ang_name_orig in angle2class2_bb_or: + angle2class2_bb_or[ang_name_orig] = '0.0' # default value + angle2ver_bb_or[ang_name_orig] = version # default value + angle2ref_bb_or[ang_name_orig] = reference # default value + if not ang_name_orig in angle2class2_ba_or: + angle2class2_ba_or[ang_name_orig] = ['0.0', '0.0'] # default value + angle2ver_ba_or[ang_name_orig] = version # default value + angle2ref_ba_or[ang_name_orig] = reference # default value + + elif ((len(tokens) > 5) and + (section_name in ('#bond-bond', '#bond-angle')) and + (angle_styles_selected & + set(['class2', 'quartic', 'quartic_angle']))): + if line.lstrip().find('!') == 0: + continue + version = tokens[0] + reference = tokens[1] + if line.lstrip().find('!') == 0: + continue + aorig = [a for a in map(EncodeAName, tokens[2:5])] + atom_names = SortByEnds(aorig) + ang_name_orig = EncodeInteractionName(atom_names, section_is_auto) + K = ['', ''] + K[0] = tokens[5] + K[1] = K[0] + if len(tokens) > 6: + K[1] = tokens[6] + order_reversed = aorig[0] > aorig[-1] + if order_reversed: + K.reverse() + if (section_name == '#bond-bond'): + angle2class2_bb_or[ang_name_orig] = K[0] + angle2ver_bb_or[ang_name_orig] = version + angle2ref_bb_or[ang_name_orig] = reference + elif (section_name == '#bond-angle'): + angle2class2_ba_or[ang_name_orig] = [k for k in K] + angle2ver_ba_or[ang_name_orig] = version + angle2ref_ba_or[ang_name_orig] = reference + if not ang_name_orig in angle2params_or: + angle_is_secondary_or[ang_name_orig] = True #only cross terms have been defined so far + angle2params_or[ang_name_orig] = ['0.0', '0.0', '0.0', '0.0'] # default value + angle2ver_or[ang_name_orig] = version + angle2ref_or[ang_name_orig] = reference + angle2priority_or[ang_name_orig] = 0.0 + + + + + + + + + + sys.stderr.write("parsing file pass4: look for dihedrals(torsions) and impropers(out_of_plane)...") + + for iline in range(0, len(lines)): + line = lines[iline] + sys.stderr.write('line=\"' + line.strip() + '\"\n') + tokens = SplitQuotedString(line.strip(), + quotes='', + comment_char='>') + #sys.stderr.write('tokens = ' + str(tokens) + '\n') + if line.lstrip().find('!') == 0 and tokens[0] != '!Ver': + continue + + + if line.lstrip(' ').find('#') == 0: + #sys.stderr.write('allowed_section_names = ' + + # str(allowed_section_names) + '\n') + if (tokens[0] in allowed_section_names): + section_name = tokens[0] + section_is_auto = tokens[-1].endswith('_auto') + tokens_after_section_name = tokens[1:] + sys.stderr.write(' encountered section \"'+tokens[0]+'\"\n') + continue + elif (not tokens[0] in ('#version','#define')): + raise InputError('Error: Line# '+str(iline) +'\n' + ' Unrecognized section name:\n' + ' \"' + tokens[0] + '\"\n') + + + + + elif (len(tokens) > 8) and (section_name == '#torsion_1'): + if line.lstrip().find('!') == 0: + continue + atom_names = SortByEnds(map(EncodeAName, tokens[2:6])) + dihedral_name = EncodeInteractionName(atom_names, section_is_auto) + dihedral2ver[dihedral_name] = tokens[0] + dihedral2ref[dihedral_name] = tokens[1] + dihedral2priority_or[dihedral_name] = \ + DetermineNumericPriority(section_is_auto, + tokens[2:6], + float(dihedral2ver[dihedral_name])) + dihedral_is_secondary_or[dihedral_name] = False + dihedral2priority[dihedral_name] = \ + (section_is_auto, + dihedral_is_secondary_or[dihedral_name], + dihedral2priority_or[dihedral_name]) + K = tokens[6] + n = tokens[7] + d = tokens[8] + + w = '0.0' #ignore: this is only used by the CHARMM force field + + if (dihedral_styles_selected & set(['charmm','torsion_1'])): + dihedral_styles.add('charmm') + dihedral2style[dihedral_name] = 'charmm' + #dihedral2params_or[dihedral_name] = [K,n,d,w] + dihedral2params[dihedral_name] = (K+' '+n+' '+d+' '+w) + elif (dihedral_styles_selected & set(['class2','torsion_3'])): + # Then this is a special case of the class2 angle + # lacking the higher terms in the Fourier series + dihedral_styles.add('class2') + dihedral2style[dihedral_name] = 'class2' + dihedral2params_or[dihedral_name] = [K,d,0,0,0,0] + + + + + elif ((len(tokens) > 7) and (section_name == '#torsion_3') + and (dihedral_styles_selected & set(['class2','torsion_3']))): + if line.lstrip().find('!') == 0: + continue + dihedral_styles.add('class2') + atom_names = SortByEnds(map(EncodeAName, tokens[2:6])) + dih_name_orig = EncodeInteractionName(atom_names, section_is_auto) + version = tokens[0] + reference = tokens[1] + dihedral2priority_or[dih_name_orig] = \ + DetermineNumericPriority(section_is_auto, + tokens[2:6], + float(version)) + dihedral_is_secondary_or[dih_name_orig] = False + #dihedral2priority[dih_name_orig] = \ + # (section_is_auto, + # dihedral_is_secondary_or[dih_name_orig], + # dihedral2priority_or[dih_name_orig]) + V1 = tokens[6] + phi0_1 = tokens[7] + V2 = phi0_2 = V3 = phi0_3 = '0.0' + if len(tokens) > 9: + V2 = tokens[8] + phi0_2 = tokens[9] + if len(tokens) > 11: + V3 = tokens[10] + phi0_3 = tokens[11] + dihedral2style_or[dih_name_orig] = 'class2' + dihedral2ver_or[dih_name_orig] = version + dihedral2ref_or[dih_name_orig] = reference + dihedral2params_or[dih_name_orig] = [V1, phi0_1, V2, phi0_2, V3, phi0_3] + # default values for cross terms: + if not dih_name_orig in dihedral2class2_mbt_or: + dihedral2class2_mbt_or[dih_name_orig] = ['0.0','0.0','0.0'] # default value + dihedral2ver_mbt_or[dih_name_orig] = version + dihedral2ref_mbt_or[dih_name_orig] = reference + if not dih_name_orig in dihedral2class2_ebt_or: + dihedral2class2_ebt_or[dih_name_orig] = [['0.0','0.0','0.0'],['0.0','0.0','0.0']] # default value + dihedral2ver_ebt_or[dih_name_orig] = version + dihedral2ref_ebt_or[dih_name_orig] = reference + if not dih_name_orig in dihedral2class2_bb13_or: + dihedral2class2_bb13_or[dih_name_orig] = '0.0' # default value + dihedral2ver_bb13_or[dih_name_orig] = version + dihedral2ref_bb13_or[dih_name_orig] = reference + if not dih_name_orig in dihedral2class2_at_or: + dihedral2class2_at_or[dih_name_orig] = [['0.0','0.0','0.0'],['0.0','0.0','0.0']] # default value + dihedral2ver_at_or[dih_name_orig] = version + dihedral2ref_at_or[dih_name_orig] = reference + if not dih_name_orig in dihedral2class2_aat_or: + dihedral2class2_aat_or[dih_name_orig] = '0.0' # default value + dihedral2ver_aat_or[dih_name_orig] = version + dihedral2ref_aat_or[dih_name_orig] = reference + + + + + + elif ((len(tokens) > 6) and (section_name == '#middle_bond-torsion_3') + and (dihedral_styles_selected & set(['class2','torsion_3']))): + if line.lstrip().find('!') == 0: + continue + dihedral_styles.add('class2') + version = tokens[0] + reference = tokens[1] + if line.lstrip().find('!') == 0: + continue + aorig = [a for a in map(EncodeAName, tokens[2:6])] + atom_names = SortByEnds(aorig) + + Fmbt = [tokens[6], '0.0', '0.0'] + if len(tokens) > 7: + Fmbt[1] = tokens[7] + if len(tokens) > 8: + Fmbt[2] = tokens[8] + + dih_name_orig = EncodeInteractionName(atom_names, section_is_auto) + + #sys.stderr.write('DEBUG: (a2,a3) = '+str((a2,a3))+', ' + # ' (b1,b2) = '+str(batoms)+'\n') + dihedral2style[dih_name_orig] = 'class2' + dihedral2class2_mbt_or[dih_name_orig] = [F for F in Fmbt] + dihedral2ver_mbt_or[dih_name_orig] = version + dihedral2ref_mbt_or[dih_name_orig] = reference + if not dih_name_orig in dihedral2params_or: + dihedral_is_secondary_or[dih_name_orig] = True #only cross terms have been defined so far + dihedral2params_or[dih_name_orig] = ['0.0', '0.0', '0.0', '0.0', '0.0', '0.0'] + dihedral2ver_or[dih_name_orig] = version + dihedral2ref_or[dih_name_orig] = reference + dihedral2priority_or[dih_name_orig] = 0.0 + + + + + elif ((len(tokens) > 6) and + (section_name in ('#end_bond-torsion_3', + '#bond-bond_1_3')) and + (dihedral_styles_selected & + set(['class2', 'torsion_3']))): + if line.lstrip().find('!') == 0: + continue + dihedral_styles.add('class2') + version = tokens[0] + reference = tokens[1] + if line.lstrip().find('!') == 0: + continue + aorig = [a for a in map(EncodeAName, tokens[2:6])] + atom_names = SortByEnds(aorig) + + dih_name_orig = EncodeInteractionName(atom_names, section_is_auto) + + dihedral2style[dih_name_orig] = 'class2' + if section_name == '#end_bond-torsion_3': + Febt = [[0.0, 0.0, 0.0], [0.0, 0.0, 0.0]] + Febt[0][0] = tokens[6] + if len(tokens) > 7: + Febt[0][1] = tokens[7] + if len(tokens) > 8: + Febt[0][2] = tokens[8] + Febt[1][0] = Febt[0][0] + Febt[1][1] = Febt[0][1] + Febt[1][2] = Febt[0][2] + if len(tokens) > 9: + Febt[1][0] = tokens[9] + if len(tokens) > 10: + Febt[1][1] = tokens[10] + if len(tokens) > 11: + Febt[1][2] = tokens[11] + order_reversed = aorig[0] > aorig[-1] + if order_reversed: + Febt.reverse() + dihedral2class2_ebt_or[dih_name_orig] = [ [F_ij for F_ij in F_i] for F_i in Febt] #deep copy of Febt[][] + dihedral2ver_ebt_or[dih_name_orig] = version + dihedral2ref_ebt_or[dih_name_orig] = reference + + elif section_name == '#bond-bond_1_3': + Kbb13 = tokens[6] + #dihedral2ver_bb13[dih_name_orig] = version + dihedral2class2_bb13_or[dih_name_orig] = Kbb13 + dihedral2ver_bb13_or[dih_name_orig] = version + dihedral2ref_bb13_or[dih_name_orig] = reference + else: + assert(False) + if not dih_name_orig in dihedral2params_or: + dihedral_is_secondary_or[dih_name_orig] = True #only cross terms have been defined so far + dihedral2params_or[dih_name_orig] = ['0.0', '0.0', '0.0', '0.0', '0.0', '0.0'] + dihedral2ver_or[dih_name_orig] = version + dihedral2ref_or[dih_name_orig] = reference + dihedral2priority_or[dih_name_orig] = 0.0 + + + + + + + + + + + elif ((len(tokens) > 6) and + (section_name in ('#angle-torsion_3', + '#angle-angle-torsion_1')) and + (dihedral_styles_selected & + set(['class2', 'torsion_3']))): + if line.lstrip().find('!') == 0: + continue + dihedral_styles.add('class2') + version = tokens[0] + reference = tokens[1] + if line.lstrip().find('!') == 0: + continue + aorig = [a for a in map(EncodeAName, tokens[2:6])] + atom_names = SortByEnds(aorig) + + dih_name_orig = EncodeInteractionName(atom_names, section_is_auto) + + dihedral2style[dih_name_orig] = 'class2' + + if section_name == '#angle-torsion_3': + Fat = [[0.0, 0.0, 0.0], [0.0, 0.0, 0.0]] + Fat[0][0] = tokens[6] + if len(tokens) > 7: + Fat[0][1] = tokens[7] + if len(tokens) > 8: + Fat[0][2] = tokens[8] + Fat[1][0] = Fat[0][0] + Fat[1][1] = Fat[0][1] + Fat[1][2] = Fat[0][2] + if len(tokens) > 9: + Fat[1][0] = tokens[9] + if len(tokens) > 10: + Fat[1][1] = tokens[10] + if len(tokens) > 11: + Fat[1][2] = tokens[11] + order_reversed = aorig[0] > aorig[-1] + if order_reversed: + Fat.reverse() + Fat[0].reverse() + Fat[1].reverse() + dihedral2class2_at_or[dih_name_orig] = [ [F_ij for F_ij in F_i] for F_i in Fat] #deep copy of Fat + dihedral2ver_at_or[dih_name_orig] = version + dihedral2ref_at_or[dih_name_orig] = reference + elif section_name == '#angle-angle-torsion_1': + Kaat = tokens[6] + dihedral2class2_aat_or[dih_name_orig] = Kaat + dihedral2ver_aat_or[dih_name_orig] = version + dihedral2ref_aat_or[dih_name_orig] = reference + else: + assert(False) + + if not dih_name_orig in dihedral2params_or: + dihedral_is_secondary_or[dih_name_orig] = True #only cross terms have been defined so far + dihedral2params_or[dih_name_orig] = ['0.0', '0.0', '0.0', '0.0', '0.0', '0.0'] # default value + dihedral2ver_or[dih_name_orig] = version + dihedral2ref_or[dih_name_orig] = reference + dihedral2priority_or[dih_name_orig] = 0.0 + + + + + + + + + + + elif ((len(tokens) > 8) and (section_name == '#out_of_plane') + and (improper_styles_selected & set(['cvff','out_of_plane']))): + if line.lstrip().find('!') == 0: + continue + improper_styles.add('cvff') + aorig = [a for a in map(EncodeAName, tokens[2:6])] + atom_names,_ignore = OOPImproperNameSort(tokens[2:6]) + improper_name = EncodeInteractionName(atom_names, section_is_auto) + imsym = improper_symmetry_subgraph[improper_name] = 'cenJflipIL' + subgraph2impname['cenJflipIL'].add(improper_name) CONTINUEHERE + improper2ver[imsym][improper_name] = tokens[0] + improper2ref[imsym][improper_name] = tokens[1] + improper2priority_or[imsym][improper_name] = \ + DetermineNumericPriority(section_is_auto, + tokens[2:6], + float(improper2ver[imsym][improper_name])) + improper_is_secondary_or[imsym][imp_name_orig] = False + improper2priority[imsym][improper_name] = \ + (section_is_auto, + improper_is_secondary_or[imsym][imp_name_orig], + improper2priority_or[imsym][improper_name]) + K = tokens[6] + n = tokens[7] + chi0 = tokens[8] + improper2style[imsym][improper_name] = 'cvff' + improper2params[imsym][improper_name] = (Kchi+' '+n+' '+chi0) + #if improper_style_name == 'cvff': + # improper2params[improper_name] = (Kchi+' '+n+' '+chi0) + # improper_symmetry_subgraph[improper_name] = 'cenJswapIL' + + + elif ((len(tokens) > 7) and (section_name == '#wilson_out_of_plane') + and (improper_styles_selected and set(['class2','wilson_out_of_plane']))): + if line.lstrip().find('!') == 0: + continue + improper_styles.add('class2') + sys.stderr.write('tokens = ' + str(tokens) + '\n') + + version = tokens[0] + reference = tokens[1] + aorig = [a for a in map(EncodeAName, tokens[2:6])] + + # To avoid redundancy, it is necessary to order the atoms + # in the interaction so that two equivalent ways of ordering + # the atoms in an improper interaction do not get misinterpreted + # as two different types of improper interactions. So we sort + # the 3 "leaf" atoms surrounding the central "hub" by name. + + atom_names, permutation = Class2ImproperNameSort(tokens[2:6]) + + # This will effect the formula for the energy. + # (specifically the "chi0" parameter) + # When we lookup the various cross-term interactions for that + # same improper interaction, we will be sure to sort them + # in the same way to make sure those interactions are + # associated with the same improper interaction. + + imp_name_orig = EncodeInteractionName(atom_names, section_is_auto) + #improper_symmetry_subgraph_or[improper_name] = 'dihedrals_nosym' (<--no) + imsym = improper_symmetry_subgraph_or[imp_name_orig] = 'cenJsortIKL' + improper2ver_or[imsym][imp_name_orig] = version + improper2ref_or[imsym][imp_name_orig] = reference + improper2priority_or[imsym][imp_name_orig] = \ + DetermineNumericPriority(section_is_auto, + tokens[2:6], + float(improper2ver_or[imp_name_orig])) + improper_is_secondary_or[imsym][imp_name_orig] = False + #improper2priority[imp_name_orig] = \ + # (section_is_auto, + # improper_is_secondary_or[imp_name_orig], + # improper2priority_or[imp_name_orig]) + K = tokens[6] + chi0 = tokens[7] + + if Parity(permutation) != 0: + # Each time the order of a pair of atoms is swapped in + # the interaction, all 3 of the "X" (chi) angles change sign + # The formula for the ordinary term in the improper + # interaction is Ei = K*((Xijkl + Xkjli + Xljik)/3 - chi0)^2 + # This formula is invariant if we change the sign of all + # Xijkl, Xkjli, Xljik, chi0 + # Hence, we can account for a change in atom order by + # changing the sign of the "chi0" parameter. + # We calculate the "Parity" of the permutation (ie whether + # the permutation has an even or odd number of swaps) + # and multiply chi0 by -1 for each swap. + # It's not clear if this is necessary since in practice + # the "chi0" parameter is usually zero. + + chi0 = str(-1.0*float(chi0)) # same as ('-' + chi0) + + improper2style_or[imsym][imp_name_orig] = 'class2' + improper2params_or[imsym][imp_name_orig] = [K, chi0] + #improper2params[imp_name_orig] = K + ' ' + chi0 + # default values for cross terms: + if not imp_name_orig in improper2class2_aa_or: + improper2class2_aa_or[imsym][imp_name_orig] = '0.0' #(default) + improper2ver_aa_or[imsym][imp_name_orig] = version + improper2ref_aa_or[imsym][imp_name_orig] = reference + # Initially, set all of the angle-angle cross terms to zero + # Start with the first cross term between aorig[0],aorig[1],aorig[2] & aorig[2],aorig[1],aorig[3] + improper2cross[imp_name_orig][ImCrossTermID([aorig[0],aorig[1],aorig[2],aorig[3]])] = '0.0' + # ...then cyclically permute the 3 "leaf" atoms (aorig[0], aorig[2], aorig[3]) around the "hub" atom (aorig[1]) + improper2cross[imp_name_orig][ImCrossTermID([aorig[2],aorig[1],aorig[3],aorig[0]])] = '0.0' + improper2cross[imp_name_orig][ImCrossTermID([aorig[3],aorig[1],aorig[0],aorig[2]])] = '0.0' + + elif ((len(tokens) > 6) and (section_name == '#angle-angle') + and (improper_styles_selected and set(['class2','wilson_out_of_plane']))): + if line.lstrip().find('!') == 0: + continue + improper_styles.add('class2') + version = tokens[0] + reference = tokens[1] + aorig = [a for a in map(EncodeAName, tokens[2:6])] + atom_names, permutation = Class2ImproperNameSort(tokens[2:6]) + imp_name_orig = EncodeInteractionName(atom_names, section_is_auto) + imsym = improper_symmetry_subgraph_or[imp_name_orig] = 'cenJsortIKL' + improper2ver_aa_or[imsym][imp_name_orig] = version + improper2ref_aa_or[imsym][imp_name_orig] = reference + K = tokens[6] + improper2style_or[imsym][imp_name_orig] = 'class2' + if not imp_name_orig in improper2params_or: + improper_is_secondary_or[imsym][imp_name_orig] = True #only cross terms have been defined so far + improper2params_or[imsym][imp_name_orig] = ['0.0', '0.0'] + improper2ver_or[imsym][imp_name_orig] = version + improper2ref_or[imsym][imp_name_orig] = reference + improper2priority_or[imsym][imp_name_orig] = 0.0 + if not imp_name_orig in improper2cross: + # then initialize all of the cross terms to zero + improper2cross[imp_name_orig][ImCrossTermID([aorig[0],aorig[1],aorig[2],aorig[3]])] = '0.0' + # ...then cyclically permute the 3 "leaf" atoms (aorig[0], aorig[2], aorig[3]) around the "hub" atom (aorig[1]) + improper2cross[imp_name_orig][ImCrossTermID([aorig[2],aorig[1],aorig[3],aorig[0]])] = '0.0' + improper2cross[imp_name_orig][ImCrossTermID([aorig[3],aorig[1],aorig[0],aorig[2]])] = '0.0' + #improper2class2_aa_or[imp_name_orig] = K (not needed) + improper2cross[imp_name_orig][ImCrossTermID(aorig)] = K + + elif (len(tokens) > 0) and (section_name == '#out_of_plane-out_of_plane'): + if line.lstrip().find('!') == 0: + continue + display_OOP_OOP_warning = True + + elif (len(tokens) > 0) and (section_name == '#torsion-torsion_1'): + if line.lstrip().find('!') == 0: + continue + display_torsion_torsion_1_warning = True + + elif section_name == '#templates': + #if line.lstrip().find('!') == 0: + # continue + lines_templates.append(line) + + elif section_name == '#reference': + if line.lstrip().find('!') == 0: + continue + if len(tokens_after_section_name) > 0: + ref_number = int(tokens_after_section_name[0]) + if len(line.strip()) > 0: + lines_references[ref_number].append(line) + + + + """ + --- these next few lines of code appear to be unnecessary. + --- I'll probably delete this code in a later version + elif (len(tokens) > 3) and (section_name == '#hbond_definition'): + hbondID = tokens[1] + if tokens[2] == 'distance': + hbond2distance[hbondID] = tokens[3] + if tokens[2] == 'angle': + hbond2angle[hbondID] = tokens[3] + if tokens[2] == 'donors': + hbond2donors[hbondID] = map(EncodeAName, tokens[2:]) + if tokens[2] == 'acceptors': + hbond2acceptors[hbondID] = map(EncodeAname(),tokens[2:]) + """ + + + if display_OOP_OOP_warning: + lines_warnings.append('###########################################################\n' + '# WARNING\n' + '# ALL \"out-of-plane_out-of_plane\" INTERACTIONS ARE IGNORED.\n' + '# CHECK THAT THESE TERMS ARE NEGLEGIBLY SMALL.\n' + '# \"out-of-plane_out-of_plane\" interactions are not yet supported in LAMMPS\n' + '# (...as of 2017-10-13) There is no way that moltemplate can produce\n' + '# LAMMPS compatible parameter files for these interactions.\n' + '###########################################################\n') + + if display_torsion_torsion_1_warning: + lines_warnings.append('###########################################################\n' + '# WARNING\n' + '# ALL \"torsion_torsion_1\" INTERACTIONS ARE IGNORED.\n' + '# CHECK THAT THESE TERMS ARE NEGLEGIBLY SMALL.\n' + '# \"torsion_torsion_1\" interactions are not yet supported in LAMMPS\n' + '# (...as of 2017-10-13) There is no way that moltemplate can produce\n' + '# LAMMPS compatible parameter files for these interactions.\n' + '###########################################################\n') + + + sys.stderr.write(' done.\n' + 'building lookup tables...') + + + + + + + + """ + --- these next few lines of code appear to be unnecessary. + --- I'll probably delete them eventually + if len(hbond2params) > 0: + sys.stdout.write('\n\n write_once("In Settings") {\n') + if hbond_style == 'hbond/dreiding/lj': + for hbondID, angle in hbond2angle: + hbond2params[hbondID] = hbond2distance[hbondID]+' '+hbond2angle[hbondID] ##<--this is not correct + for hbondID, params in hbond2params: + for donor in hbond2donors[hbondID]: + for acceptor in hbond2acceptors[hbondID]: + for hydrogen in hbond2hydrogens[hbondID]: + sys.stdout.write('pair_coeff @atom:'+donor+' @atom:'+acceptor+' '+hbond_style+' @atom:'+hydrogen+' i '+params+'\n') + sys.stdout.write(' } # (DREIDING style H-bond parameters)\n\n\n') + """ + + + + + + + sys.stderr.write(" done.\n") + sys.stderr.write("Trying all combinations of atom types...") + + + + + + + + ##################### POST-PROCESSING ######################## + + + + + + for ang_name_orig in angle2params_or: + + is_auto = (ang_name_orig.find('auto_') == 0) + + atom_names = ExtractANames(ang_name_orig) + + num_angles = 0 + + atom_combos = [set([]), set([]), set([])] + + # We must consider every possible combination of atom types + # which satisfy BOTH angle_equivalences and bond_equivalences. + # ...AND we must consider BOTH regular AND auto equivalences. + # For each combination generate a separate @angle interaction. + # (I fear this will make the resulting .LT file large.) + + # Use different auto equivalence lookup tables for different + # atoms in the interaction. (ie the "center" and "end" atoms) + auto_angle2atom = [auto_angleend2atom, + auto_anglecenter2atom, + auto_angleend2atom] + + for i in range(0, 3): + angle_atom_name = atom_names[i] + sys.stderr.write('DEBUG: angle_atom_name = '+angle_atom_name+'\n') + if not is_auto: + assert(angle_atom_name[-1] != '_') + # assume regular equivalences when looking up atom types + sys.stderr.write('DEBUG: equiv_angle2atom['+angle_atom_name+'] = '+ + str(equiv_angle2atom[angle_atom_name])+'\n') + for a in equiv_angle2atom[angle_atom_name]: + atom_combos[i].add(a) + else: + #assert((angle_atom_name[-1] == '_') or (angle_atom_name[0] == '*')) (<--some exceptions. don't assert this) + + # assume "auto" equivalences when looking up atom types + sys.stderr.write('DEBUG: auto_angle2atom['+str(i)+']['+angle_atom_name+'] = \n' + ' '+str(equiv_angle2atom[i][angle_atom_name])+'\n') + for a in auto_angle2atom[i][angle_atom_name]: + atom_combos[i].add(a) + + found_at_least_one = False + #for a1 in atom_combos[0]: + for a1 in sorted(list(atom_combos[0])): + #for a2 in atom_combos[1]: + for a2 in sorted(list(atom_combos[1])): + #sys.stderr.write('atom2auto_bond = '+str(atom2auto_bond)+'\n') + bond_data1 = LookupBondLength(a1, a2, + atom2equiv_bond, + bond2r0, + atom2auto_bond, + bond2r0_auto) + if bond_data1 == None: # Save time by continuing only if a + continue # bond was defined between a1 and a2 + + #for a3 in atom_combos[2]: + for a3 in sorted(list(atom_combos[2])): + bond_data2 = LookupBondLength(a2, a3, + atom2equiv_bond, + bond2r0, + atom2auto_bond, + bond2r0_auto) + if bond_data2 == None: + continue + + #bond lengths: + r0s = [0.0, 0.0] + #equivalent atom names used to lookup the bonds: + batoms = [['', ''], ['', '']] + #were "auto" equivalences needed to lookup the bond length? + b_is_auto = [False, False] + r0s[0], batoms[0], b_is_auto[0] = bond_data1 + r0s[1], batoms[1], b_is_auto[1] = bond_data2 + order_reversed = aorig[0] > aorig[-1] + if order_reversed: + batoms.reverse() + batoms[0].reverse() + batoms[1].reverse() + b_is_auto.reverse() + ang_name_full = (ang_name_orig + ',' + + EncodeInteractionName(batoms[0], b_is_auto[0]) + ',' + + EncodeInteractionName(batoms[1], b_is_auto[1])) + + + #sys.stderr.write('DEBUG: (a1,a2,a3) = '+str((a1,a2,a3))+', ' + # ' (b11,b12,b21,b22) = '+str(batoms)+'\n') + angle2ref_or[ang_name_full] = reference + angle2style_or[ang_name_full] = 'class2' + theta0_K_params = angle2params_or[ang_name_orig] + angle2params[ang_name_full] = ' '.join(theta0_K_params) + if ang_name_orig in angle2class2_bb_or: + Kbb = angle2class2_bb_or[ang_name_orig] + assert(ang_name_orig in angle2ver_bb_or) + assert(ang_name_orig in angle2ref_bb_or) + else: #(use default values) + Kbb = '0.0' + angle2class2_bb_or[ang_name_orig] = Kbb + angle2ver_bb_or[ang_name_orig] = angle2ver_or[ang_name_orig] + angle2ref_bb_or[ang_name_orig] = angle2ref_or[ang_name_orig] + angle2class2_bb[ang_name_full] = (Kbb+' '+r0s[0]+' '+r0s[1]) + angle2priority_bb = \ + DetermineNumericPriority(is_auto, + batoms[0] + batoms[1], + float(angle2ver_bb_or[ang_name_orig])) + angle2ver_bb[ang_name_full] = angle2ver_bb_or[ang_name_orig] + angle2ref_bb[ang_name_full] = angle2ref_bb_or[ang_name_orig] + + if ang_name_orig in angle2class2_ba_or: + Kba = angle2class2_ba_or[ang_name_orig] + assert(ang_name_orig in angle2ver_ba_or) + assert(ang_name_orig in angle2ref_ba_or) + else: #(use default values) + Kba = ['0.0', '0.0'] + angle2class2_ba_or[ang_name_orig] = Kba + angle2ver_ba_or[ang_name_orig] = angle2ver_or[ang_name_orig] + angle2ref_ba_or[ang_name_orig] = angle2ref_or[ang_name_orig] + angle2class2_ba[ang_name_full] = (Kba[0]+' '+Kba[1]+' '+r0s[0]+' '+r0s[1]) + angle2sym_ba = (Kba[0] == Kba[1]) + angle2priority_ba = \ + DetermineNumericPriority(is_auto, + batoms[0] + batoms[1], + angle2ver_ba_or[ang_name_orig]) + angle2ver_ba[ang_name_full] = angle2ver_ba_or[ang_name_orig] + angle2ref_ba[ang_name_full] = angle2ref_ba_or[ang_name_orig] + + version = max((angle2ver_or[ang_name_orig], + angle2ver_bb_or[ang_name_orig], + angle2ver_ba_or[ang_name_orig])) + angle2ver[ang_name_full] = version + angle2ref[ang_name_full] = angle2ref_or[ang_name_orig] + angle2style[ang_name_full] = 'class2' + angle2priority[ang_name_full] = \ + (is_auto, + angle_is_secondary_or[ang_name_orig], + angle2priority_or[ang_name_orig], + angle2priority_bb, + angle2priority_ba) + + if num_angles < len(angle2params): + sys.stderr.write('DEBUG: '+section_name[1:]+' r0 ('+ang_name_full+') = ('+r0s[0]+', '+r0s[1]+')\n') + sys.stderr.write('DEBUG: len(angle2class2_bb) = '+str(len(angle2class2_bb))+'\n') + sys.stderr.write('DEBUG: '+section_name[1:]+' r0 ('+ang_name_full+') = ('+r0s[0]+', '+r0s[1]+')\n') + #sys.stderr.write('DEBUG: len(angle2class2_ba) = '+str(len(angle2class2_ba))+'\n') + num_angles = len(angle2params) + + if ((not angle2sym_ba) + and + (atom_names[0] == atom_names[2])): + raise InputError('Error: Unsupported angle interaction: \"@angle:'+str(ang_name_orig)+'\"\n' + ' This interaction has symmetric atom names:\n' + ', '.join(atom_names)+'\n' + ' and yet it lacks symmetry in the corresponding force field parameters.\n' + ' (If this is not a mistake in the .frc file, then explain\n' + ' why to andrew so he can fix this.)\n') + + + found_at_least_one = True + + + if not found_at_least_one: + lines_warnings.append('# WARNING: Undefined bond length (r0) in angle: ' + + ' '.join(atom_names)+'\n') + # Then we were unable to define cross terms for this interaction + # because at least one of the bond lengths could not be determined. + # This usually occurs because most of the .FRC files which are + # in circulation are incomplete. We have to handle this gracefully. + ang_name_full = (ang_name_orig + ',X,X,X,X,X,X') + version = angle2ver_or[ang_name_orig] + reference = angle2ref_or[ang_name_orig] + angle2ref[ang_name_full] = reference + angle2ver[ang_name_full] = version + angle2style[ang_name_full] = 'class2' + angle2params[ang_name_full] = ' '.join(angle2params_or[ang_name_orig]) + # substitute zeros for all the cross term interactions + angle2priority[ang_name_full] = angle2priority_or[ang_name_orig] + angle2class2_bb[ang_name_full] = '0.0 1.0 1.0' + angle2ref_bb[ang_name_full] = reference + angle2ver_bb[ang_name_full] = version + angle2class2_ba[ang_name_full] = '0.0 0.0 1.0 1.0' + angle2ref_ba[ang_name_full] = reference + angle2ver_ba[ang_name_full] = version + #sys.stderr.write('bond_names = ' + str(bond_names) + '\n') + + + + + + ############ POST-PROCESSING DIHEDRALS ########### + + + + for dih_name_orig in dihedral2params_or: + #assert(dih_name_orig in dihedral2class2_mbt_or) + #assert(dih_name_orig in dihedral2class2_ebt_or) + #assert(dih_name_orig in dihedral2class2_bb13_or) + #assert(dih_name_orig in dihedral2class2_at_or) + #assert(dih_name_orig in dihedral2class2_aat_or) + + is_auto = (dih_name_orig.find('auto_') == 0) + + atom_names = ExtractANames(dih_name_orig) + + num_dihedrals = 0 + + atom_combos = [set([]), set([]), set([]), set([])] + + # We must consider every possible combination of atom types + # which satisfy all three: + # dihedral_equivalences + # bond_equivalences + # angle_equivalences + # ...AND we must consider BOTH regular AND auto equivalences. + # For each combination generate a separate @dihedral interaction. + # (I fear this will make the resulting .LT file large.) + + # Use different auto equivalence lookup tables for different + # atoms in the interaction. (ie the "center" and "end" atoms) + auto_dihedral2atom = [auto_dihedralend2atom, + auto_dihedralcenter2atom, + auto_dihedralcenter2atom, + auto_dihedralend2atom] + + for i in range(0, 4): + dihedral_atom_name = atom_names[i] + sys.stderr.write('DEBUG: dihedral_atom_name = '+dihedral_atom_name+'\n') + if not is_auto: + assert(dihedral_atom_name[-1] != '_') + # assume regular equivalences when looking up atom types + sys.stderr.write('DEBUG: equiv_dihedral2atom['+dihedral_atom_name+'] = '+ + str(equiv_dihedral2atom[dihedral_atom_name])+'\n') + for a in equiv_dihedral2atom[dihedral_atom_name]: + atom_combos[i].add(a) + else: + assert((dihedral_atom_name[-1] == '_') or (ange_atom_name[0] == '*')) + # assume "auto" equivalences when looking up atom types + sys.stderr.write('DEBUG: auto_dihedral2atom['+str(i)+']['+dihedral_atom_name+'] = \n' + ' '+str(equiv_dihedral2atom[i][dihedral_atom_name])+'\n') + for a in auto_dihedral2atom[i][dihedral_atom_name]: + atom_combos[i].add(a) + + found_at_least_one = False + + #for a1 in atom_combos[0]: + for a1 in sorted(list(atom_combos[0])): + + #for a2 in atom_combos[1]: + for a2 in sorted(list(atom_combos[1])): + + #sys.stderr.write('atom2auto_bond = '+str(atom2auto_bond)+'\n') + bond_data12 = LookupBondLength(a1, a2, + atom2equiv_bond, + bond2r0, + atom2auto_bond, + bond2r0_auto) + if bond_data12 == None: + # Save time by only continuing if a bond was + # found between a1 and a2 + continue + #for a3 in atom_combos[2]: + for a3 in sorted(list(atom_combos[2])): + bond_data23 = LookupBondLength(a2, a3, + atom2equiv_bond, + bond2r0, + atom2auto_bond, + bond2r0_auto) + if bond_data23 == None: + # Save time by only continuing if a bond was + # found between a2 and a3 + continue + + angle_data123 = LookupBondAngle(a1, a2, a3, + atom2equiv_angle, + angle2theta0_or, + [atom2auto_angleend, + atom2auto_anglecenter, + atom2auto_anglecenter], + angle2theta0_auto_or) + if angle_data123 == None: + # Save time by only continuing if an angle was + # found between a1, a2, a3 + continue + + + #for a4 in atom_combos[3]: + for a4 in sorted(list(atom_combos[3])): + bond_data34 = LookupBondLength(a3, a4, + atom2equiv_bond, + bond2r0, + atom2auto_bond, + bond2r0_auto) + if bond_data34 == None: + # Save time by only continuing if a bond was + # found between a3 and a4 + continue + + #rest bond lengths: + r0s = [0.0, 0.0, 0,0] + #equivalent atom names used to lookup the bonds: + batoms = [['', ''], ['', ''], ['','']] + #are these bond interactions "auto" interactions? + #were "auto" equivalences needed to lookup the bond length? + b_is_auto = [False, False, False] + r0s[0], batoms[0], b_is_auto[0] = bond_data12 + r0s[1], batoms[1], b_is_auto[1] = bond_data23 + r0s[2], batoms[2], b_is_auto[2] = bond_data34 + + angle_data234 = LookupBondAngle(a2, a3, a4, + atom2equiv_angle, + angle2theta0_or, + [atom2auto_angleend, + atom2auto_anglecenter, + atom2auto_anglecenter], + angle2theta0_auto_or) + if angle_data234 == None: + # Save time by only continuing if an angle was + # found between a2, a3, a4 + continue + + #rest angles: + theta0s = [0.0, 0.0] + #equivalent atom names used to lookup angles: + aatoms = [['', '',''], ['', '','']] + #were "auto" equivalences needed to lookup the bond-angle? + a_is_auto = [False, False] + theta0s[0], aatoms[0], a_is_auto[0] = angle_data123 + theta0s[1], aatoms[1], a_is_auto[1] = angle_data234 + order_reversed = aorig[0] > aorig[-1] + if order_reversed: + batoms.reverse() + batoms[0].reverse() + batoms[1].reverse() + batoms[2].reverse() + b_is_auto.reverse() + theta0s.reverse() + aatoms.reverse() + aatoms[0].reverse() + aatoms[1].reverse() + a_is_auto.reverse() + + #if is_auto: + dih_name_full = (dih_name_orig + ',' + + EncodeInteractionName(batoms[0], b_is_auto[0]) + ',' + + EncodeInteractionName(batoms[1], b_is_auto[1]) + ',' + + EncodeInteractionName(batoms[2], b_is_auto[2]) + ',' + + EncodeInteractionName(aatoms[0], a_is_auto[0]) + ',' + + EncodeInteractionName(aatoms[1], a_is_auto[1])) + #else: + # assert(batoms[0][1] == batoms[1][0]) + # assert(batoms[1][1] == batoms[2][0]) + # assert(aatoms[0][1] == aatoms[1][0]) + # assert(aatoms[0][2] == aatoms[1][1]) + # dih_name_full = dih_name_orig + ',' + \ + # EncodeInteractionName([batoms[0][0], batoms[0][1] + # batoms[2][0], batoms[2][1], + # aatoms[0][0], aatoms[0][1], + # aatoms[0][2], aatoms[1][0]], + # False) + + ########### Fourier terms ########### + #if dih_name_orig in dihedral2param_or: + V_phi0_params = dihedral2params_or[dih_name_orig] + dihedral2params[dih_name_full] = ' '.join(V_phi0_params) + #else: + # dihedral2params[dih_name_full] = '0.0 0.0 0.0 0.0 0.0 0.0' + + ########### "mbt", "ebt", and "aat" terms ########### + # "mbt" terms: + if dih_name_orig in dihedral2class2_mbt_or: + Fmbt = dihedral2class2_mbt_or[dih_name_orig] + else: + Fmbt = ['0.0', '0.0', '0.0'] + dihedral2class2_mbt_or[dih_name_orig] = Fmbt + dihedral2ver_mbt_or[dih_name_orig] = dihedral2ver_or[dih_name_orig] + dihedral2ref_mbt_or[dih_name_orig] = dihedral2ref_or[dih_name_orig] + dihedral2class2_mbt[dih_name_full] = \ + (Fmbt[0]+' '+Fmbt[1]+' '+Fmbt[2]+' '+r0s[1]) + dihedral2priority_mbt = \ + DetermineNumericPriority(is_auto, + batoms[1], + float(dihedral2ver_mbt_or[dih_name_orig])) + dihedral2ver_mbt[dih_name_full] = dihedral2ver_mbt_or[dih_name_orig] + dihedral2ref_mbt[dih_name_full] = dihedral2ref_mbt_or[dih_name_orig] + + # "ebt" terms: + if dih_name_orig in dihedral2class2_ebt_or: + Febt = dihedral2class2_ebt_or[dih_name_orig] + dihedral2sym_ebt = ((Febt[0][0] == Febt[1][0]) and + (Febt[0][1] == Febt[1][1]) and + (Febt[0][2] == Febt[1][2])) + #and (r0s[0] == r0s[2])) + else: + Febt = [['0.0','0.0','0.0'], ['0.0','0.0','0.0']] + dihedral2class2_ebt_or[dih_name_orig] = Febt + dihedral2ver_ebt_or[dih_name_orig] = dihedral2ver_or[dih_name_orig] + dihedral2ref_ebt_or[dih_name_orig] = dihedral2ref_or[dih_name_orig] + dihedral2sym_ebt = True + dihedral2class2_ebt[dih_name_full]= (Febt[0][0] + ' ' + + Febt[0][1] + ' ' + + Febt[0][2] + ' ' + + Febt[1][0] + ' ' + + Febt[1][1] + ' ' + + Febt[1][2] + ' ' + + r0s[0]+' '+r0s[2]) + + dihedral2priority_ebt = \ + DetermineNumericPriority(is_auto, + batoms[0] + batoms[2], + float(dihedral2ver_ebt_or[dih_name_orig])) + dihedral2ver_ebt[dih_name_full] = dihedral2ver_ebt_or[dih_name_orig] + dihedral2ref_ebt[dih_name_full] = dihedral2ref_ebt_or[dih_name_orig] + + #(Note: large atom_priority number <==> low priority + # Only one of the atom priority numbers should be > 0) + + # "bb13" terms: + if dih_name_orig in dihedral2class2_bb13_or: + Kbb13 = dihedral2class2_bb13_or[dih_name_orig] + #dihedral2sym_bb13 = (r0s[0] == r0s[2]) + dihedral2sym_bb13 = True + else: + Kbb13 = '0.0' + dihedral2class2_bb13_or[dih_name_orig] = Kbb13 + dihedral2ver_bb13_or[dih_name_orig] = dihedral2ver_or[dih_name_orig] + dihedral2ref_bb13_or[dih_name_orig] = dihedral2ref_or[dih_name_orig] + dihedral2sym_bb13 = True + + dihedral2class2_bb13[dih_name_full] = (Kbb13+' '+r0s[0]+' '+r0s[2]) + dihedral2priority_bb13 = \ + DetermineNumericPriority(is_auto, + batoms[0] + batoms[2], + float(dihedral2ver_bb13_or[dih_name_orig])) + dihedral2ver_bb13[dih_name_full] = dihedral2ver_bb13_or[dih_name_orig] + dihedral2ref_bb13[dih_name_full] = dihedral2ref_bb13_or[dih_name_orig] + + + ########### "at" and "aat" terms ########### + # "at" terms: + if dih_name_orig in dihedral2class2_at_or: + Fat = dihedral2class2_at_or[dih_name_orig] + dihedral2sym_at = ((Fat[0][0] == Fat[1][0]) and + (Fat[0][1] == Fat[1][1]) and + (Fat[0][2] == Fat[1][2])) + #and (theta0[0] == theta0[1])) + else: + Fat = [['0.0','0.0','0.0'], ['0.0','0.0','0.0']] + dihedral2class2_at_or[dih_name_orig] = Fat + dihedral2ver_at_or[dih_name_orig] = dihedral2ver_or[dih_name_orig] + dihedral2ref_at_or[dih_name_orig] = dihedral2ref_or[dih_name_orig] + dihedral2sym_at = True + dihedral2class2_at[dih_name_full] = \ + (Fat[0][0] + ' ' + + Fat[0][1] + ' ' + + Fat[0][2] + ' ' + + Fat[1][0] + ' ' + + Fat[1][1] + ' ' + + Fat[1][2] + ' ' + + theta0s[0] + ' ' + + theta0s[1]) + dihedral2priority_at = \ + DetermineNumericPriority(is_auto, + aatoms[0] + aatoms[1], + float(dihedral2ver_at_or[dih_name_orig])) + dihedral2ver_at[dih_name_full] = dihedral2ver_at_or[dih_name_orig] + dihedral2ref_at[dih_name_full] = dihedral2ref_at_or[dih_name_orig] + + + # "aat" terms: + if dih_name_orig in dihedral2class2_aat_or: + Kaat = dihedral2class2_aat_or[dih_name_orig] + #dihedral2sym_aat = (theta0[0] == theta0[1]) + dihedral2sym_aat = True + else: + Kaat = '0.0' + dihedral2class2_aat_or[dih_name_orig] = Kaat + dihedral2ver_aat_or[dih_name_orig] = dihedral2ver_or[dih_name_orig] + dihedral2ref_aat_or[dih_name_orig] = dihedral2ref_or[dih_name_orig] + dihedral2sym_aat = True + dihedral2class2_aat[dih_name_full] = \ + (Kaat+' '+theta0s[0]+' '+theta0s[1]) + dihedral2priority_aat = \ + DetermineNumericPriority(is_auto, + aatoms[0] + aatoms[1], + float(dihedral2ver_aat_or[dih_name_orig])) + dihedral2ver_aat[dih_name_full] = dihedral2ver_aat_or[dih_name_orig] + dihedral2ref_aat[dih_name_full] = dihedral2ref_aat_or[dih_name_orig] + + if len(dihedral2params) > num_dihedrals: + sys.stderr.write('DEBUG: dihedral['+dih_name_full+']:\n' + '(r12,r23,r34) = (' + +r0s[0]+','+r0s[1]+','+r0s[2]+') \n' + '(theta123,theta234) = (' + +theta0s[0]+','+theta0s[1]+') \n') + sys.stderr.write('DEBUG: num_dihedrals = len(dihedral2params) = ' + +str(len(dihedral2params))+'\n') + version = max((dihedral2ver_or[dih_name_orig], + dihedral2ver_mbt_or[dih_name_orig], + dihedral2ver_ebt_or[dih_name_orig], + dihedral2ver_bb13_or[dih_name_orig], + dihedral2ver_at_or[dih_name_orig], + dihedral2ver_aat_or[dih_name_orig])) + + dihedral2style[dih_name_full] = 'class2' + dihedral2ver[dih_name_full] = version + dihedral2ref[dih_name_full] = dihedral2ref_or[dih_name_orig] + dihedral2priority[dih_name_full] = \ + (is_auto, + dihedral_is_secondary_or[dih_name_orig], + dihedral2priority_or[dih_name_orig], + dihedral2priority_mbt, + dihedral2priority_ebt, + dihedral2priority_bb13, + dihedral2priority_at, + dihedral2priority_aat) + + num_dihedrals = len(dihedral2params) + + if ((not (dihedral2sym_ebt and + #dihedral2sym_mbt and + # (note: symmetry doesn't make sense for mbt) + dihedral2sym_at and + dihedral2sym_aat and + dihedral2sym_bb13)) + and + ((atom_names[0] == atom_names[3]) and + (atom_names[1] == atom_names[2]))): + raise InputError('Error: Unsupported dihedral interaction: \"@dihedral:'+str(dih_name_orig)+'\"\n' + ' This interaction has symmetric atom names:\n'+ + ', '.join(atom_names)+'\n'+ + ' and yet it lacks symmetry in the corresponding force field parameters.\n'+ + ' (If this is not a mistake in the .frc file, then explain\n'+ + ' why to andrew so he can fix this.)\n') + + found_at_least_one = True + + + #sys.stderr.write('DEBUG: number of interactions = '+str(len(dihedral2class2_bb))+'\n') + if not found_at_least_one: + lines_warnings.append('# WARNING: Undefined bond length (r0) or rest angle (theta0) in dihedral: ' + + #'# the dihedral interaction between: ' + + ' '.join(atom_names)+'\n') + # Then we were unable to define cross terms for this interaction because + # at least one of the bond lengths or bond angles could not be determined. + # This usually occurs because most of the .FRC files which are + # in circulation are incomplete. We have to handle this gracefully. + dih_name_full = (dih_name_orig + ',X,X,X,X,X,X,X,X,X,X,X,X') + reference = dihedral2ref_or[dih_name_orig] + version = dihedral2ver_or[dih_name_orig] + dihedral2ref[dih_name_full] = reference + dihedral2ver[dih_name_full] = version + dihedral2style[dih_name_full] = 'class2' + dihedral2priority[dih_name_full] = dihedral2priority_or[dih_name_orig] + dihedral2params[dih_name_full] = ' '.join(dihedral2params_or[dih_name_orig]) + # substitute zeros for all the cross term interactions + + dihedral2class2_mbt[dih_name_full] = '0.0 0.0 0.0 1.0' + dihedral2ref_mbt[dih_name_full] = reference + dihedral2ver_mbt[dih_name_full] = version + + dihedral2class2_ebt[dih_name_full] = '0.0 0.0 0.0 0.0 0.0 0.0 1.0 1.0' + dihedral2ref_ebt[dih_name_full] = reference + dihedral2ver_ebt[dih_name_full] = version + + dihedral2class2_bb13[dih_name_full] = '0.0 1.0 1.0' + dihedral2ref_bb13[dih_name_full] = reference + dihedral2ver_bb13[dih_name_full] = version + + dihedral2class2_at[dih_name_full] = '0.0 0.0 0.0 0.0 0.0 0.0 120.0 120.0' + dihedral2ref_at[dih_name_full] = reference + dihedral2ver_at[dih_name_full] = version + + dihedral2class2_aat[dih_name_full] = '0.0 120.0 120.0' + dihedral2ref_aat[dih_name_full] = reference + dihedral2ver_aat[dih_name_full] = version + + + + + + + + + ############ POST-PROCESSING IMPROPERS ########### + + + + + imsym = 'cenJsortIKL' + for imp_name_orig in improper2cross[imsym]: + + if improper2style_or[imsym][imp_name_orig] != 'class2': + continue + + assert(imp_name_orig in improper2params_or[imsym]) + assert(imp_name_orig in improper2class2_aa_or[imsym]) + + is_auto = (imp_name_orig.find('auto') == 0) + + atom_names = ExtractANames(imp_name_orig) + + num_impropers = 0 + + atom_combos = [set([]), set([]), set([]), set([])] + + # We must consider every possible combination of atom types + # which satisfy both: + # improper_equivalences + # angle_equivalences + # ...AND we must consider BOTH regular AND auto equivalences. + # For each combination generate a separate @improper interaction. + # (I fear this will make the resulting .LT file large.) + + # Use different auto equivalence lookup tables for different + # atoms in the interaction. (ie the "center" and "end" atoms) + + auto_improper2atom = [auto_improperend2atom, + auto_impropercenter2atom, + auto_improperend2atom, + auto_improperend2atom] + + for i in range(0, 4): + improper_atom_name = atom_names[i] + sys.stderr.write('DEBUG: improper_atom_name = '+improper_atom_name+'\n') + if not is_auto: + assert(improper_atom_name[-1] != '_') + # assume regular equivalences when looking up atom types + sys.stderr.write('DEBUG: equiv_improper2atom['+improper_atom_name+'] = '+ + str(equiv_improper2atom[improper_atom_name])+'\n') + for a in equiv_improper2atom[improper_atom_name]: + atom_combos[i].add(a) + else: + assert((improper_atom_name[-1] == '_') or (improper_atom_name[0] == 'X')) + # assume "auto" equivalences when looking up atom types + sys.stderr.write('DEBUG: auto_improper2atom['+str(i)+']['+improper_atom_name+'] = \n' + ' '+str(auto_improper2atom[i][improper_atom_name])+'\n') + for a in auto_improper2atom[i][improper_atom_name]: + atom_combos[i].add(a) + + is_auto = IsAutoInteraction(imp_name_orig) # is this an "auto" interaction? + + atom_names = ExtractANames(imp_name_orig) # names of all 4 atoms + lnames = [atom_names[0], atom_names[2], atom_names[3]] # names of "leaf" atoms + + #M1 = improper2cross[imp_name_orig][ 2 ] + #M2 = improper2cross[imp_name_orig][ 0 ] + #M3 = improper2cross[imp_name_orig][ 3 ] + + #try: + M1 = improper2cross[imp_name_orig][ImCrossTermID([atom_names[0], + atom_names[1], + atom_names[2], + atom_names[3]])] + #except KeyError: + # M1 = '0.0' + + #try: + M2 = improper2cross[imp_name_orig][ImCrossTermID([atom_names[2], + atom_names[1], + atom_names[0], + atom_names[3]])] + #except KeyError: + # M2 = '0.0' + + #try: + M3 = improper2cross[imp_name_orig][ImCrossTermID([atom_names[0], + atom_names[1], + atom_names[3], + atom_names[2]])] + #except KeyError: + # M3 = '0.0' + + + + + + + # ###### Symmetry: ###### + # Unfortunately, it's time to wade into the messy issue of symmetry. + # We desire a way to detect whether an improper interaction + # between 4 atoms is invariant with respect to atom reordering + # of the 3 peripheral "leaf" atoms which surround the central atom. + # In principle, any rearrangement of atoms would require a separate + # class2 improper interaction. However, in some cases, when the + # parameters for these rearrangements are symmetric, we can detect + # that and warn moltemplate that it is not necessary to generate new + # improper interactions for every conceivable permutation of these + # atoms. Figuring out when it is safe to do that is a headache. + # (...but it's necessary. Otherwise each junction in the molecule + # will generate 3*2*1=6 improper interactions which are usually + # redundant. This will slow down the simulation significantly + # and may make it difficult to compare the resulting LAMMPS + # input files with those generated by other tools like msi2lmp.) + # + # To make this easier, I store the parameters in arrays which + # are arranged in a more symmetric way + M = [0.0, 0.0, 0.0] + theta0 = [0.0, 0.0, 0.0] + # noti3[i] = the sorted tuple of integers from the + # set {0,1,2} which remain after deleting i + noti3 = ((1,2), (0,2), (0,1)) + i_neigh = [ ([0,2,3][ noti3[i][0] ], # neighbor leaves of ith leaf + [0,2,3][ noti3[i][1] ]) for i in range(0,3)] + for i in range(0, 3): + # You will notice the pattern "[0,2,3][i]" appears often in the + # code below because for class 2 force-fields, the second atom + # (with index 1) is the central atom ("hub" atom), and the three + # that surround it ("leaf" atoms) have indices 0,2,3. I want + # to skip over the central atoms and loop over the leaf atoms + imTermID = ImCrossTermID([atom_names[ i_neigh[i][0] ], + atom_names[ 1 ], + atom_names[ [0,2,3][i] ], + atom_names[ i_neigh[i][1] ]]) + M[i] = float(improper2cross[imp_name_orig][imTermID]) + ##i_leaf = [0,2,3][i] + ##M[i] = float(improper2cross[imp_name_orig][ i_leaf ]) + #angle_name_l = SortByEnds([atom_names[i_neigh[i][0]], + # atom_names[ 1 ], + # atom_names[i_neigh[i][1]]]) + #angle_name = EncodeInteractionName(angle_name_l, is_auto) + #theta0[i] = float(angle2theta0_or[angle_name]) + + for i in range(0, 3): + if (M[ noti3[i][0] ] == M[ noti3[i][1] ]): + #and (theta0[ noti3[i][0] ] == theta0[ noti3[i][1] ])): + # Then it is safe to swap the order of these two atoms in + # the list of atoms when looking up force-field parameters + improper2sym[imp_name_orig].add(i_neigh[i][0]) + improper2sym[imp_name_orig].add(i_neigh[i][1]) + # Later, I can use these to decide whether or not I need to + # change the default script with symmetry rules. (I'm hoping + # that "cenJsortIKL.py" should work in most cases.) + # CONTINUEHERE: FIGURE OUT WHETHER TO WORRY ABOUT improper2sym + else: + if atom_names[i_neigh[i][0]] == atom_names[i_neigh[i][1]]: + raise InputError('Error: Unsupported improper interaction: \"@improper:'+str(imp_name_orig)+'\"\n' + ' This interaction has matching atom aliases:\n' + ' (@atom:'+str(atom_names[i_neigh[i][0]])+ + ', @atom:'+str(atom_names[i_neigh[i][1]])+')\n' + ' and yet it lacks symmetry in the corresponding force field parameters.\n' + ' (If this is not a mistake in the .frc file, then ask andrew to\n' + ' fix this limitation.)\n') + + + found_at_least_one = False + for a1 in sorted(list(atom_combos[0])): + for a2 in sorted(list(atom_combos[1])): + sys.stderr.write('DEBUG: improper '+imp_name_orig+' substitutions: '+a1+','+a2+',...\n') + for a3 in sorted(list(atom_combos[2])): + #(Note: sorting "atom_combos" makes it faster and easier + # to follow the loop's progress. This nested loop can be very slow.) + theta0s = ['0.0', '0.0', '0.0'] + aatoms = [['', '',''], ['', '',''], ['', '', '']] + #were "auto" equivalences needed to lookup the bond-angle? + a_is_auto = [False, False, False] + # Collect information from the different terms in a class2 improper: + # http://lammps.sandia.gov/doc/improper_class2.html + + # Loop over the neighbors of the central atom in each improper + # interaction and collect all the Mi and Ti parameters. Collect + # them in the order they appear in the formula for the Eaa + # term as it appears in the documentation for improper_style class2: + # + # http://lammps.sandia.gov/doc/improper_class2.html + # + # Eaa = M1 (Tijk - T0)(Tkjl - T2) + #common leaf node: k (index 2) + # M2 (Tijk - T0)(Tijl - T1) + #common leaf node: i (index 0) + # M3 (Tijl - T1)(Tkjl - T2) #common leaf node: l (index 3) + # (I'm trying to match the variable names used in this web page + # I wish the author had chosen the M1,M2,M3, T1,T2,T3 order in more + # symmetric way, or at least in a way that makes more sense to me.) + + #angle_name_l = SortByEnds([atom_names[0], atom_names[1], atom_names[2]]) + #angle_name = EncodeInteractionName(angle_name_l, is_auto) + #theta01 = angle2theta0_or[angle_name] + angle_data = LookupBondAngle(a1, a2, a3, + atom2equiv_angle, + angle2theta0_or, + [atom2auto_improperend, + atom2auto_impropercenter, + atom2auto_improperend], + angle2theta0_auto_or) + if angle_data == None: + # Save time by only continuing if an angle was + # found between a1, a2, a3 + continue + theta0s[0], aatoms[0], a_is_auto[0] = angle_data + + + for a4 in sorted(list(atom_combos[3])): + theta0s[1] = theta0s[2] = '0.0' + aatoms[1] = aatoms[2] = ['', '',''] + + #angle_name_l = SortByEnds(aatoms[0]) + #angle_name = EncodeInteractionName(angle_name_l[0], is_auto) + + #theta02 = angle2theta0_or[angle_name] + angle_data = LookupBondAngle(a1, a2, a4, + atom2equiv_angle, + angle2theta0_or, + [atom2auto_improperend, + atom2auto_impropercenter, + atom2auto_improperend], + angle2theta0_auto_or) + if angle_data == None: + # Save time by only continuing if an angle was + # found between a1, a2, a4 + continue + theta0s[1], aatoms[1], a_is_auto[1] = angle_data + + #angle_name_l = SortByEnds(aatoms[1]) + #angle_name = EncodeInteractionName(angle_name_l, is_auto) + + + #theta03 = angle2theta0_or[angle_name] + angle_data = LookupBondAngle(a3, a2, a4, + atom2equiv_angle, + angle2theta0_or, + [atom2auto_improperend, + atom2auto_impropercenter, + atom2auto_improperend], + angle2theta0_auto_or) + if angle_data == None: + # Save time by only continuing if an angle was + # found between a3, a2, a4 + continue + theta0s[2], aatoms[2], a_is_auto[2] = angle_data + + + # The following asserts checks that the two theta0s + # are defined whenever the corresponding M is defined. + # (Note: The order is LAMMPS-implementation specific. + # See http://lammps.sandia.gov/doc/improper_class2.html) + assert((float(theta0s[0]) != 0) or (float(M1) == 0)) + assert((float(theta0s[2]) != 0) or (float(M1) == 0)) + assert((float(theta0s[0]) != 0) or (float(M2) == 0)) + assert((float(theta0s[1]) != 0) or (float(M2) == 0)) + assert((float(theta0s[1]) != 0) or (float(M3) == 0)) + assert((float(theta0s[2]) != 0) or (float(M3) == 0)) + + #angle_name_l = SortByEnds(aatoms[2]) + #angle_name = EncodeInteractionName(angle_name_l, is_auto) + + + imp_name_full = (imp_name_orig + ',' + + EncodeInteractionName(aatoms[0], a_is_auto[0]) + ',' + + EncodeInteractionName(aatoms[1], a_is_auto[1]) + ',' + + EncodeInteractionName(aatoms[2], a_is_auto[2])) + + #if imp_name_orig in improper2params_or[imsym][imp_name_orig]: + improper2params[imsym][imp_name_full] = ' '.join(improper2params_or[imsym][imp_name_orig]) + #else: + # improper2params[imsym][imp_name_full] = '0.0 0.0' + + #if imp_name_orig in improper2cross: + improper2class2_aa[imsym][imp_name_full] = \ + (str(M1)+' '+str(M2)+' '+str(M3)+' '+ + str(theta0s[0])+' '+str(theta0s[1])+' '+str(theta0s[2])) + #else: + # improper2class2_aa[imsym][imp_name_full] = '0.0 0.0 0.0 0.0 0.0 0.0' + # improper2ver_aa_or[imsym][imp_name_orig] = improper2ver_or[imsym][imp_name_orig] + # improper2ref_aa_or[imsym][imp_name_orig] = improper2ref_or[imsym][imp_name_orig] + + improper2priority_aa = \ + DetermineNumericPriority(is_auto, + aatoms[0] + aatoms[1] + aatoms[2], + float(improper2ver_aa_or[imsym][imp_name_orig])) + improper2ver_aa[imsym][imp_name_full] = improper2ver_aa_or[imsym][imp_name_orig] + improper2ref_aa[imsym][imp_name_full] = improper2ref_aa_or[imsym][imp_name_orig] + + + version = max((improper2ver_or[imsym][imp_name_orig], + improper2ver_aa_or[imsym][imp_name_orig])) + improper2style[imsym][imp_name_full] = 'class2' + improper2ref[imsym][imp_name_full] = improper2ref_or[imsym][imp_name_orig] + improper2ver[imsym][imp_name_full] = version + improper2priority[imsym][imp_name_full] = \ + (is_auto, + improper_is_secondary_or[imsym][imp_name_orig], + improper2priority_or[imsym][imp_name_orig], + improper2priority_aa) + + if len(improper2params) > num_impropers: + sys.stderr.write('DEBUG: improper['+imp_name_full+']:\n' + 'theta0 = (' + +theta0s[0]+','+theta0s[1]+','+theta0s[2]+')\n') + sys.stderr.write('DEBUG: num_impropers = len(improper2params) = ' + +str(len(improper2params))+'\n') + num_impropers = len(improper2params) + + + found_at_least_one = True + + + if not found_at_least_one: + lines_warnings.append('# WARNING: Undefined rest angle (theta0) in improper: ' + + #'# the improper interaction between: ' + + ' '.join(atom_names)+'\n') + # Then we were unable to define cross terms for this interaction because + # at least one of the equilibrium rest angles could not be determined. + # This usually occurs because most of the .FRC files which are + # in circulation are incomplete. We have to handle this gracefully. + imp_name_full = (imp_name_orig + ',X,X,X,X,X,X,X,X,X') + reference = improper2ref_or[imsym][imp_name_orig] + version = improper2ver_or[imsym][imp_name_orig] + improper2ref[imsym][imp_name_full] = reference + improper2ver[imsym][imp_name_full] = version + improper2params[imsym][imp_name_full] = ' '.join(improper2params_or[imp_name_orig]) + CONTINUEHERE + improper2style[imp_name_full] = 'class2' + improper2priority[imp_name_full] = improper2priority_or[imp_name_orig] + # substitute zeros for the cross term interactions + improper2class2_aa[imp_name_full] = '0.0 0.0 0.0 120.0 120.0 120.0' + improper2ref_aa[imp_name_full] = reference + improper2ver_aa[imp_name_full] = version + + + + + + sys.stderr.write("done\n") + sys.stderr.write("Converting to moltemplate format...\n") + + + + + + ##################### BEGIN WRITING FILE ##################### + + + + + + sys.stdout.write("# This file was generated automatically using:\n") + sys.stdout.write("# " + g_program_name + " " + " ".join(sys.argv[1:]) + "\n") + sys.stdout.write("\n\n") + sys.stdout.write(ffname + " {\n\n") + + sys.stdout.write("\n" + " # AtomType Mass # \"Description\" (version, reference)\n\n") + sys.stdout.write(" write_once(\"Data Masses\") {\n") + for atype in atom2mass: + sys.stdout.write(" @atom:" + atype + " " + str(atom2mass[atype])) + sys.stdout.write(" # ") + if atype in atom2element: + sys.stdout.write(atom2element[atype] + ", ") + #sys.stdout.write(atom2descr[atype]) + sys.stdout.write("\"" + atom2descr[atype] + "\"") + sys.stdout.write(" (") + if atype in atom2numbonds: + sys.stdout.write("nbonds="+str(atom2numbonds[atype])+", ") + sys.stdout.write("ver=" + atom2ver[atype] + + ", ref=" + atom2ref[atype]) + sys.stdout.write(")\n") + sys.stdout.write(" } #(end of atom masses)\n\n\n") + + + + + + + + + + + + + sys.stdout.write(" # ---------- EQUIVALENCE CATEGORIES for bonded interaction lookup ----------\n" + " # Each type of atom has a separate ID used for looking up bond parameters\n" + " # and a separate ID for looking up 3-body angle interaction parameters\n" + " # and a separate ID for looking up 4-body dihedral interaction parameters\n" + " # and a separate ID for looking up 4-body improper interaction parameters\n" + #" # (This is because there are several different types of sp3 carbon atoms\n" + #" # which have the same torsional properties when within an alkane molecule,\n" + #" # for example. If they share the same dihedral-ID, then this frees us\n" + #" # from being forced define separate dihedral interaction parameters\n" + #" # for all of them.)\n" + " # The complete @atom type name includes ALL of these ID numbers. There's\n" + " # no need to force the end-user to type the complete name of each atom.\n" + " # The \"replace\" command used below informs moltemplate that the short\n" + " # @atom names we have been using abovee are equivalent to the complete\n" + " # @atom names used below:\n\n") + + for atype in atom2ffid: + #ffid = atype + "_ffid" + atom2ffid[atype] + sys.stdout.write(" replace{ @atom:" + atype + + " @atom:" + atom2ffid[atype] + " }\n") + + sys.stdout.write("\n\n\n\n") + + + sys.stdout.write(" # --------------- Non-Bonded Interactions: ---------------------\n" + " # Syntax:\n" + " # pair_coeff AtomType1 AtomType2 pair_style_name parameters...\n\n") + + sys.stdout.write(" write_once(\"In Settings\") {\n") + + for atype in pair2params: + assert(atype in pair2style) + if IsAutoInteraction(bond_name): + assert(atype in atom2auto_pair) + if include_auto_equivalences: + sys.stdout.write(' pair_coeff @atom:*,ap' + atom2auto_pair[atype] + + ',aq*,ab*,aae*,aac*,ade*,adc*,aie*,aic*' + + ' @atom:*,ap' + atom2auto_pair[atype] + + ',aq*,ab*,aae*,aac*,ade*,adc*,aie*,aic* ' + + pair2style[atype] + ' ' + + pair2params[atype] + + ' # (ver=' + pair2ver[atype] + + ', ref=' +pair2ref[atype] + ')\n') + else: + continue + else: + assert(atype in atom2equiv_pair) + sys.stdout.write(' pair_coeff ' + + '@atom:*,p' + atom2equiv_pair[atype] + ',b*,a*,d*,i* ' + + '@atom:*,p' + atom2equiv_pair[atype] + ',b*,a*,d*,i* ' + + pair2style[atype] + ' ' + + pair2params[atype] + + ' # (ver=' + pair2ver[atype] + + ', ref=' +pair2ref[atype] + ')\n') + sys.stdout.write(" } #(end of pair_coeffs)\n\n\n\n") + + + + + + + + ################# Print Charge By Bond Interactions ################## + charge_pair_priority_high_to_low = [x[0] for x in + sorted([x for x in reversed(charge_pair_priority.items())], + key=itemgetter(1), + reverse=True)] + + if len(charge_pair_priority) > 0: + sys.stdout.write(" # ---------- Charge By Bond (a.k.a. \"bond equivalences\") ----------\n") + # Print rules for generating (2-body) "bond" interactions: + sys.stdout.write('\n\n\n' + ' write_once("Data Charge By Bond") {\n') + for bond_name in charge_pair_priority_high_to_low: + anames = ['*' if x=='X' else x + for x in ExtractANames(bond_name)] + # Did the user ask us to include "auto" interactions? + if IsAutoInteraction(bond_name): + if include_auto_equivalences: + sys.stdout.write(' @atom:*,ap*,aq' + anames[0] + + ',ab*,aae*,aac*,ade*,adc*,aie*,aic*' + + ' @atom:*,ap*,aq' + anames[1] + + ',ab*,aae*,aac*,ade*,adc*,aie*,aic*' + + ' ' + bond2chargepair[bond_name] + + " # (ver=" + charge_pair_ver[bond_name] + + ", ref=" + charge_pair_ref[bond_name] + ")\n") + else: + continue + else: + sys.stdout.write(' @atom:*,p*,b' + anames[0] + ',a*,d*,i* ' + + ' @atom:*,p*,b' + anames[1] + ',a*,d*,i* ' + + ' ' + bond2chargepair[bond_name] + + " # (ver=" + charge_pair_ver[bond_name] + + ", ref=" + charge_pair_ref[bond_name] + ")\n") + sys.stdout.write(' } #(end of Charge by Bond (bond equivalences))\n\n' + '\n\n\n\n') + + + + + + + + ################# Print 2-body Bond Interactions ################## + + bond_names_priority_high_to_low = [x[0] for x in + sorted([x for x in reversed(bond2priority.items())], + key=itemgetter(1), + reverse=True)] + + if len(bond2priority) > 0: + sys.stdout.write(" # --------------- Bond Interactions: ---------------------\n") + sys.stdout.write('\n' + '\n' + ' # -- Rules for generating (2-body) "bond" interactions: --\n' + ' # BondType AtomType1 AtomType2\n') + sys.stdout.write('\n' + ' write_once("Data Bonds By Type') + if bond_symmetry_subgraph != '': + sys.stdout.write(' ('+bond_symmetry_subgraph+')') + sys.stdout.write('") {\n') + for bond_name in bond_names_priority_high_to_low: + if not (bond2style[bond_name] in + bond_styles_selected): + continue + anames = ['*' if x=='X' else x + for x in ExtractANames(bond_name)] + # Did the user ask us to include "auto" interactions? + if IsAutoInteraction(bond_name): + if include_auto_equivalences: + sys.stdout.write(' @bond:' + bond_name + ' ' + + ' @atom:*,ap*,aq*,ab' + anames[0] + + ',aae*,aac*,ade*,adc*,aie*,aic*' + + ' @atom:*,ap*,aq*,ab' + anames[1] + + ',aae*,aac*,ade*,adc*,aie*,aic*' + + '\n') + else: + continue + else: + sys.stdout.write(' @bond:' + bond_name + ' ' + + ' @atom:*,b' + anames[0] + ',a*,d*,i* ' + + ' @atom:*,b' + anames[1] + ',a*,d*,i* ' + + '\n') + + sys.stdout.write(' } # end of "Data Bonds By Type" section\n' + '\n') + + # Print the force-field parameters for these bond interactions: + sys.stdout.write('\n\n' + ' # ------------ Bond Parameters: ----------\n') + sys.stdout.write(' # For an explanation of these parameters, visit:\n') + for bond_style in bond_styles: + if not (bond_style in bond_styles_selected): + continue + sys.stdout.write(' # '+bond_style2docs[bond_style]+'\n') + sys.stdout.write('\n' + ' # Syntax: \n' + ' # bond_coeff BondTypeName BondStyle parameters...\n\n') + sys.stdout.write('\n' + ' write_once("In Settings") {\n') + for bond_name in bond_names_priority_high_to_low: + if not (bond2style[bond_name] in + bond_styles_selected): + continue + # Did the user ask us to include "auto" interactions? + if (IsAutoInteraction(bond_name) and + (not include_auto_equivalences)): + continue + sys.stdout.write(' bond_coeff @bond:'+bond_name+' '+ + bond2style[bond_name] + ' ' + + bond2params[bond_name] + + " # (ver=" + bond2ver[bond_name] + + ", ref=" +bond2ref[bond_name] + ")\n") + + sys.stdout.write(' } # end of bond_coeff commands\n' + '\n\n') + + + + + + + ################# Print 3-body Angle Interactions ################## + + ang_names_priority_high_to_low = [x[0] for x in + sorted([x for x in reversed(angle2priority.items())], + key=itemgetter(1), + reverse=True)] + + ang_name_abbr = {} #optional abbreviated name for each interaction + ang_name_abbr_used = set([]) #make sure we don't reuse these abbreviated names + + if len(angle2priority) > 0: + sys.stdout.write(" # --------------- Angle Interactions: ---------------------\n") + sys.stdout.write('\n' + '\n' + ' # -- Rules for generating (3-body) "angle" interactions: --\n' + ' # AngleType AtomType1 AtomType2 AtomType3 [BondType1 BondType2]\n') + sys.stdout.write('\n' + ' write_once("Data Angles By Type') + if angle_symmetry_subgraph != '': + sys.stdout.write(' ('+angle_symmetry_subgraph+')') + sys.stdout.write('") {\n') + for angle_name in ang_names_priority_high_to_low: + if not (angle2style[angle_name] in + angle_styles_selected): + continue + anames = ['*' if x=='X' else x + for x in ExtractANames(angle_name)] + + angle_is_auto = IsAutoInteraction(angle_name) + if angle2style[angle_name] == 'class2': + anm = [a for a in map(DecodeAName, anames)] + bnames = [[a for a in map(DecodeAName, anames[3:5])], + [a for a in map(DecodeAName, anames[5:7])]] + bond_is_auto1 = IsAutoInteraction(anames[3]) + bond_is_auto2 = IsAutoInteraction(anames[5]) + + if ((angle_is_auto or bond_is_auto1 or bond_is_auto2) and + (not include_auto_equivalences)): + continue + + # Can we ignore "auto" interactions? + # (If so, life is much easier) + if not (angle_is_auto or bond_is_auto1 or bond_is_auto2): + if angle2style[angle_name] == 'class2': + assert(bnames[0][1] == bnames[1][0]) + # Optional: Shorten the angle name since some of the atom's bond names are redundant: + ang_name_abbr[angle_name] = EncodeInteractionName(map(EncodeAName, + anm[0:3] + + #[anm[3],anm[4],anm[6]], + [bnames[0][0],bnames[0][1],bnames[1][1]]), + angle_is_auto) + sys.stdout.write(' @angle:' + ang_name_abbr[angle_name] + ' ' + + ' @atom:*,p*,b'+bnames[0][0]+',a'+anames[0]+',d*,i* ' + + ' @atom:*,p*,b'+bnames[0][1]+',a'+anames[1]+',d*,i* ' + + ' @atom:*,p*,b'+bnames[1][1]+',a'+anames[2]+',d*,i*' + '\n') + else: + ang_name_abbr[angle_name] = angle_name + sys.stdout.write(' @angle:' + ang_name_abbr[angle_name] + ' ' + + ' @atom:*,p*,b*,a'+anames[0]+',d*,i* ' + + ' @atom:*,p*,b*,a'+anames[1]+',d*,i* ' + + ' @atom:*,p*,b*,a'+anames[2]+',d*,i*' + '\n') + else: + # Consider "auto" interactions and "auto" atom equivalences + ang_name_abbr[angle_name] = angle_name #(full name) + sys.stdout.write(' @angle:' + ang_name_abbr[angle_name] + ' ') + + if angle2style[angle_name] == 'class2': + + bshared = 'b*' #(default. overidden below) + abshared = 'ab*' #(default. overidden below) + + if angle_is_auto: + a1 = a2 = a3 = 'a*' #Then, dont use regular equivalences for these atoms. + aa1 = 'aae' + anames[0] + ',aac*' #Instead use the corresponding "auto" equivalence names + aa2 = 'aae*,aac*' + anames[1] #for these atoms. (There are different auto equivalence names depending + aa3 = 'aae' + anames[2] + ',aac*' #on if the atom appears in the center (c) or end(e) of the 3-body angle) + else: + a1 = 'a' + anames[0] #In this case, use use (regular) equivalence names + a2 = 'a' + anames[1] #for these atoms + a3 = 'a' + anames[2] + aa1 = aa2 = aa3 = 'aae*,aac*' + + if not bond_is_auto1: + b11 = 'b' + bnames[0][0] #(bond atom equivalent name) + b12 = 'b' + bnames[0][1] #(bond atom equivalent name) + bshared = 'b' + bnames[0][1] #(bond atom equivalent name) + ab11 = ab12 = 'ab*' + else: + b11 = b12 = 'b*' + ab11 = 'ab' + bnames[0][0] #(auto bond atom name) + ab12 = 'ab' + bnames[0][1] #(auto bond atom name) + abshared = 'ab' + bnames[0][1] #(auto bond atom name) + # print atom 1 information: + sys.stdout.write(' @atom:*,p*,'+b11+','+a1+',d*,i*,' + + 'ap*,aq*,'+ab11+','+aa1+ + ',ade*,adc*,aie*,aic*') + if not bond_is_auto2: + b21 = 'b' + bnames[1][0] #(bond atom equivalent name) + b22 = 'b' + bnames[1][1] #(bond atom equivalent name) + assert((bshared == 'b*') or (bshared == 'b' + bnames[1][0])) + bshared = 'b' + bnames[1][0] + ab21 = ab22 = 'ab*' + else: + b21 = b22 = 'b*' + ab21 = 'ab' + bnames[1][0] #(auto bond atom name) + ab22 = 'ab' + bnames[1][1] #(auto bond atom name) + assert((abshared == 'ab*') or (abshared == 'ab' + bnames[1][0])) + abshared = 'ab' + bnames[1][0] + # print atom 2 information: + sys.stdout.write(' @atom:*,p*,'+bshared+','+a2+',d*,i*,' + + 'ap*,aq*,'+abshared+','+aa2+ + ',ade*,adc*,aie*,aic*') + # print atom 3 information: + sys.stdout.write(' @atom:*,p*,'+b22+','+a3+',d*,i*,' + + 'ap*,aq*,'+ab22+','+aa3+ + ',ade*,adc*,aie*,aic*') + sys.stdout.write('\n') + else: + sys.stdout.write(' @angle:' + ang_name_abbr[angle_name] + ' ' + + ' @atom:*,p*,b*,d*,i*,' + + 'ap*,aq*,ab*,aae'+anames[0]+'aac*,ade*,adc*,aie*,aic* ' + ' @atom:*,p*,b*,d*,i*,' + + 'ap*,aq*,ab*,aae*,aac'+anames[1]+',ade*,adc*,aie*,aic* ' + ' @atom:*,p*,b*,d*,i*,' + + 'ap*,aq*,ab*,aae'+anames[2]+'aac*,ade*,adc*,aie*,aic* ' + '\n') + + assert(ang_name_abbr[angle_name] not in ang_name_abbr_used) + ang_name_abbr_used.add(ang_name_abbr[angle_name]) + + sys.stdout.write(' } # end of "Data Angles By Type" section\n' + '\n') + + # Print the force-field parameters for these angle interactions: + sys.stdout.write('\n\n' + ' # ------- Angle Force Field Parameters: -------') + sys.stdout.write(' # For an explanation of these parameters, visit:\n') + for angle_style in angle_styles: + if not (angle_style in angle_styles_selected): + continue + sys.stdout.write(' # '+angle_style2docs[angle_style]+'\n') + sys.stdout.write('\n' + ' # Syntax: \n' + ' # angle_coeff AngleTypeName AngleStyle parameters...\n\n') + sys.stdout.write('\n' + ' write_once("In Settings") {\n') + for angle_name in ang_names_priority_high_to_low: + anames = ['*' if x=='X' else x + for x in ExtractANames(angle_name)] + if not (angle2style[angle_name] in + angle_styles_selected): + continue + + + # Did the user ask us to include "auto" interactions? + #if (IsAutoInteraction(angle_name) and + # (not include_auto_equivalences)): + # continue + # the if statement above is covered by the following: + if angle_name not in ang_name_abbr: + continue + + sys.stdout.write(' angle_coeff @angle:'+ang_name_abbr[angle_name]+' '+ + angle2style[angle_name] + ' ' + + angle2params[angle_name] + + " # (ver=" + angle2ver[angle_name] + + ", ref=" + angle2ref[angle_name] + ")\n") + if angle_name in angle2class2_bb: + sys.stdout.write(' angle_coeff @angle:'+ang_name_abbr[angle_name]+' '+ + angle2style[angle_name] + ' bb ' + + angle2class2_bb[angle_name] + + " # (ver=" + angle2ver_bb[angle_name] + + ", ref=" + angle2ref_bb[angle_name] + ")\n") + + assert(angle_name in angle2class2_ba) + sys.stdout.write(' angle_coeff @angle:'+ang_name_abbr[angle_name]+' '+ + angle2style[angle_name] + ' ba ' + + angle2class2_ba[angle_name] + + " # (ver=" + angle2ver_ba[angle_name] + + ", ref=" + angle2ref_ba[angle_name] + ")\n") + sys.stdout.write(' } # end of angle_coeff commands\n' + '\n\n') + + + + + + + + ################# Print 4-body Dihedral Interactions ################## + + dih_names_priority_high_to_low = [x[0] for x in + sorted([x for x in reversed(dihedral2priority.items())], + key=itemgetter(1), + reverse=True)] + + dih_name_abbr = {} #optional abbreviated name for each interaction + dih_name_abbr_used = set([]) #make sure we don't reuse these abbreviated names + + if len(dih_names_priority_high_to_low) > 0: + sys.stdout.write(' # --------------- Dihedral Interactions: ---------------------\n') + sys.stdout.write('\n' + '\n' + ' # -- Rules for generating (4-body) "dihedral" interactions: --\n' + ' # DihedralType AtmType1 AtmType2 AtmType3 AtmType3 [BondType1 Bnd2 Bnd3]\n') + sys.stdout.write('\n\n' + ' write_once("Data Dihedrals By Type') + if dihedral_symmetry_subgraph != '': + sys.stdout.write(' ('+dihedral_symmetry_subgraph+')') + sys.stdout.write('") {\n') + + + + for dihedral_name in dih_names_priority_high_to_low: + if not (dihedral2style[dihedral_name] in + dihedral_styles_selected): + continue + anames = ['*' if x=='X' else x + for x in ExtractANames(dihedral_name)] + + dihedral_is_auto = IsAutoInteraction(dihedral_name) + if dihedral2style[dihedral_name] == 'class2': + anm = [a for a in map(DecodeAName, anames)] + bnames = [[a for a in map(DecodeAName, anames[4:6])], + [a for a in map(DecodeAName, anames[6:8])], + [a for a in map(DecodeAName, anames[8:10])]] + bond_is_auto1 = IsAutoInteraction(anames[4]) + bond_is_auto2 = IsAutoInteraction(anames[6]) + bond_is_auto3 = IsAutoInteraction(anames[8]) + ang_names = [[a for a in map(DecodeAName, anames[10:13])], + [a for a in map(DecodeAName, anames[13:16])]] + angle_is_auto1 = IsAutoInteraction(anames[10]) + angle_is_auto2 = IsAutoInteraction(anames[13]) + + if ((dihedral_is_auto or + angle_is_auto1 or angle_is_auto2 or + bond_is_auto1 or bond_is_auto2 or bond_is_auto3) and + (not include_auto_equivalences)): + continue + + # Can we ignore "auto" interactions? + # (If so, life is much easier) + if not (dihedral_is_auto or + angle_is_auto1 or angle_is_auto2 or + bond_is_auto1 or bond_is_auto2 or bond_is_auto3): + + if dihedral2style[dihedral_name] == 'class2': + assert(bnames[0][1] == bnames[1][0]) + assert(bnames[1][1] == bnames[2][0]) + assert(ang_names[0][1] == ang_names[1][0]) + assert(ang_names[0][2] == ang_names[1][1]) + + # Optional: Shorten the dihedral name since some of the atom's bond names are redundant: + dih_name_abbr[dihedral_name] = EncodeInteractionName(map(EncodeAName, + anm[0:4] + + #[bnames[0][0], bnames[0][1], + # bnames[1][1], bnames[2][1]] + [anm[4],anm[5],anm[7],anm[9]]+ + #[ang_names[0][0], + # ang_names[0][1], + # ang_names[0][2], + # ang_names[1][2]] + [anm[10],anm[11],anm[12],anm[15]]), + is_auto) + + sys.stdout.write(' @dihedral:' + dih_name_abbr[dihedral_name] + ' ' + + ' @atom:*,p*,b'+bnames[0][0]+',a'+ang_names[0][0]+',d'+anames[0]+',i* ' + + ' @atom:*,p*,b'+bnames[0][1]+',a'+ang_names[0][1]+',d'+anames[1]+',i* ' + + ' @atom:*,p*,b'+bnames[1][1]+',a'+ang_names[0][2]+',d'+anames[2]+',i* ' + ' @atom:*,p*,b'+bnames[2][1]+',a'+ang_names[1][2]+',d'+anames[3]+',i*' + '\n') + else: + dih_name_abbr[dihedral_name] = dihedral_name + sys.stdout.write(' @dihedral:' + dih_name_abbr[dihedral_name] + ' ' + + ' @atom:*,p*,b*,a*,d'+anames[0]+',i* ' + + ' @atom:*,p*,b*,a*,d'+anames[1]+',i* ' + + ' @atom:*,p*,b*,a*,d'+anames[2]+',i* ' + ' @atom:*,p*,b*,a*,d'+anames[3]+',i*' + + '\n') + else: + # Consider "auto" interactions and "auto" atom equivalences + dih_name_abbr[dihedral_name] = dihedral_name #(full name) + sys.stdout.write(' @dihedral:' + dih_name_abbr[dihedral_name] + ' ') + + if dihedral2style[dihedral_name] == 'class2': + + # equivalent names of atoms shared by more than one bond: + # (names ending in * mean they were unspecified for this + # dihedral interaction. By default, this is the case.) + bshared1 = 'b*' #(default. overidden below) + bshared2 = 'b*' #(default. overidden below) + abshared1 = 'ab*' #(default. overidden below) + abshared2 = 'ab*' #(default. overidden below) + + # equivalent names of atoms shared by more than one angle interaction: + # (names ending in * mean they were unspecified for this + # dihedral interaction. By default, this is the case.) + ashared1 = 'a*' #(default. overidden below) + ashared2 = 'a*' #(default. overidden below) + aac_shared1 = 'aac*' #(default. overidden below) + aae_shared1 = 'aae*' #(default. overidden below) + aac_shared2 = 'aac*' #(default. overidden below) + aae_shared2 = 'aae*' #(default. overidden below) + + if dihedral_is_auto: + d1 = d2 = d3 = d4 = 'd*' #Then, dont use regular equivalences for these atoms. + ad1 = 'ade' + anames[0] + ',adc*' #Instead use the corresponding "auto" + ad2 = 'ade*,adc*' + anames[1] #equivalence names for these atoms. + ad3 = 'ade*,adc*' + anames[1] #(There are different auto equivalence names depending upon + ad4 = 'ade' + anames[2] + ',adc*' # if the atom appears in the center (c) or end(e) of the dihedral) + else: + d1 = 'd' + anames[0] # In this case, use use (regular) equivalence names + d2 = 'd' + anames[1] # for these atoms + d3 = 'd' + anames[2] + d4 = 'd' + anames[3] + ad1 = ad2 = ad3 = ad4 = 'ade*,adc*' + + if not bond_is_auto1: + b11 = 'b' + bnames[0][0] #(bond atom equivalent name) + b12 = 'b' + bnames[0][1] #(bond atom equivalent name) + bshared1 = 'b' + bnames[0][1] #(bond atom equivalent name) + ab11 = ab12 = 'ab*' + else: + b11 = b12 = 'b*' + ab11 = 'ab' + bnames[0][0] #(auto bond atom name) + ab12 = 'ab' + bnames[0][1] #(auto bond atom name) + abshared1 = 'ab' + bnames[0][1] #(auto bond atom name) + + if not bond_is_auto2: + b21 = 'b' + bnames[1][0] #(bond atom equivalent name) + b22 = 'b' + bnames[1][1] #(bond atom equivalent name) + assert((bshared1 == 'b*') or (bshared1 == 'b' + bnames[1][0])) + bshared1 = 'b' + bnames[1][0] #(bond atom equivalent name) + assert((bshared2 == 'b*') or (bshared2 == 'b' + bnames[1][1])) + bshared2 = 'b' + bnames[1][1] #(bond atom equivalent name) + ab21 = ab22 = 'ab*' + else: + b21 = b22 = 'b*' + ab21 = 'ab' + bnames[1][0] #(auto bond atom name) + ab22 = 'ab' + bnames[1][1] #(auto bond atom name) + assert((abshared1 == 'ab*') or (abshared1 == 'ab' + bnames[1][0])) + abshared1 = 'ab' + bnames[1][0] #(auto bond atom name) + assert((abshared2 == 'ab*') or (abshared2 == 'ab' + bnames[1][1])) + abshared2 = 'ab' + bnames[1][1] #(auto bond atom name) + + if not bond_is_auto3: + b31 = 'b' + bnames[2][0] #(bond atom equivalent name) + b32 = 'b' + bnames[2][1] #(bond atom equivalent name) + assert((bshared2 == 'b*') or (bshared2 == 'b' + bnames[2][0])) + bshared2 = 'b' + bnames[2][0] #(bond atom equivalent name) + ab31 = ab32 = 'ab*' + else: + b31 = b32 = 'b*' + ab31 = 'ab' + bnames[2][0] #(auto bond atom name) + ab32 = 'ab' + bnames[2][1] #(auto bond atom name) + assert((abshared2 == 'ab*') or (abshared2 == 'ab' + bnames[2][0])) + abshared2 = 'ab' + bnames[2][0] #(auto bond atom name) + + if not angle_is_auto1: + a11 = 'a' + ang_names[0][0] #(angle atom equivalent name) + a12 = 'a' + ang_names[0][1] #(angle atom equivalent name) + a13 = 'a' + ang_names[0][2] #(angle atom equivalent name) + ashared1 = 'a' + ang_names[0][1] #(angle atom equivalent name) + ashared2 = 'a' + ang_names[0][2] #(angle atom equivalent name) + aa11 = 'aae*,aac*' + aa12 = 'aae*,aac*' + aa13 = 'aae*,aac*' + else: + a11 = a12 = a13 = 'a*' + aa11 = 'aae'+ang_names[0][0]+'aac*' #(auto angle atom name) + aa12 = 'aae*,aac'+ang_names[0][1] #(auto angle atom name) + aa13 = 'aae'+ang_names[0][2]+'aac*' #(auto angle atom name) + aac_shared1 = 'aac'+ang_names[0][1] #(auto angle atom name) + aae_shared2 = 'aae'+ang_names[0][2] #(auto angle atom name) + + if not angle_is_auto2: + a21 = 'a' + ang_names[1][0] #(angle atom equivalent name) + a22 = 'a' + ang_names[1][1] #(angle atom equivalent name) + a23 = 'a' + ang_names[1][2] #(angle atom equivalent name) + assert((ashared1 == 'a*') or (ashared1 == 'a' + ang_names[1][0])) + ashared1 = 'a' + ang_names[1][0] #(angle atom equivalent name) + assert((ashared2 == 'a*') or (ashared2 == 'a' + ang_names[1][1])) + ashared2 = 'a' + ang_names[1][1] #(angle atom equivalent name) + aa21 = 'aae*,aac*' + aa22 = 'aae*,aac*' + aa23 = 'aae*,aac*' + else: + a21 = a22 = a23 = 'a*' + aa21 = 'aae'+ang_names[1][0]+',aac*' #(auto angle atom name) + aa22 = 'aae*,aac'+ang_names[1][1] #(auto angle atom name) + aa23 = 'aae'+ang_names[1][2]+',aac*' #(auto angle atom name) + aae_shared1 = 'aae'+ang_names[1][0] #(auto angle atom name) + aac_shared2 = 'aac'+ang_names[1][1] #(auto angle atom name) + + + # print atom 1 information: + sys.stdout.write(' @atom:*,p*,'+b11+','+a11+','+d1+',i*,' + + 'ap*,aq*,'+ab11+','+aa11+',' + + ad1+',aie*,aic*') + # print atom 2 information: + sys.stdout.write(' @atom:*,p*,'+bshared1+','+ashared1+','+d2+',i*,' + + 'ap*,aq*,'+abshared1+','+aae_shared1+','+aac_shared1+',' + + ad2+',aie*,aic*') + # print atom 3 information: + sys.stdout.write(' @atom:*,p*,'+bshared2+','+ashared2+','+d3+',i*,' + + 'ap*,aq*,'+abshared2+','+aae_shared2+','+aac_shared2+',' + + ad3+',aie*,aic*') + # print atom 4 information: + sys.stdout.write(' @atom:*,p*,'+b32+','+a23+','+d4+',i*,' + + 'ap*,aq*,'+ab32+','+aa23+',' + + ad4+',aie*,aic*') + sys.stdout.write('\n') + else: + assert(dihedral_is_auto) #(so we should use "auto" equivalence names for these atoms) + sys.stdout.write(' @dihedral:' + dih_name_abbr[dihedral_name] + ' ' + + ' @atom:*,p*,b*,d*,i*,' + + 'ap*,aq*,ab*,aae*,aac*,ade'+anames[0]+',adc*,aie*,aic* ' + ' @atom:*,p*,b*,d*,i*,' + + 'ap*,aq*,ab*,aae*,aac*,ade*,adc'+anames[1]+',aie*,aic* ' + ' @atom:*,p*,b*,d*,i*,' + + 'ap*,aq*,ab*,aae*,aac*,ade*,adc'+anames[2]+',aie*,aic* ' + ' @atom:*,p*,b*,d*,i*,' + + 'ap*,aq*,ab*,aae*,aac*,ade'+anames[3]+',adc*,aie*,aic* ' + '\n') + + + + + assert(dih_name_abbr[dihedral_name] not in dih_name_abbr_used) + dih_name_abbr_used.add(dih_name_abbr[dihedral_name]) + + sys.stdout.write(' } # end of "Data Dihedrals By Type" section\n' + '\n') + + # Print the force-field parameters for these dihedral interactions: + sys.stdout.write('\n\n' + ' # ------- Dihedral Force Field Parameters: -------\n') + sys.stdout.write(' # For an explanation of these parameters, visit:\n') + for dihedral_style in dihedral_styles: + if not (dihedral_style in dihedral_styles_selected): + continue + sys.stdout.write(' # '+dihedral_style2docs[dihedral_style]+'\n') + sys.stdout.write('\n' + ' # Syntax: \n' + ' # dihedral_coeff DihedralTypeName DihedralStyle parameters...\n\n') + sys.stdout.write('\n' + ' write_once("In Settings") {\n') + for dihedral_name in dih_names_priority_high_to_low: + anames = ['*' if x=='X' else x + for x in ExtractANames(dihedral_name)] + #if (len(anames) == 4) and dihedral2style[dihedral_name] == 'class2': + # continue + if not (dihedral2style[dihedral_name] in + dihedral_styles_selected): + continue + + # Did the user ask us to include "auto" interactions? + #if (IsAutoInteraction(dihedral_name) and + # (not include_auto_equivalences)): + # continue + # the if statement above is covered by the following: + if dihedral_name not in dih_name_abbr: + continue + + sys.stdout.write(' dihedral_coeff @dihedral:'+dih_name_abbr[dihedral_name]+' '+ + dihedral2style[dihedral_name] + ' ' + + dihedral2params[dihedral_name] + + " # (ver=" + dihedral2ver[dihedral_name] + + ", ref=" + dihedral2ref[dihedral_name] + ")\n") + if dihedral_name in dihedral2class2_mbt: + sys.stdout.write(' dihedral_coeff @dihedral:'+dih_name_abbr[dihedral_name]+' '+ + dihedral2style[dihedral_name] + ' mbt ' + + dihedral2class2_mbt[dihedral_name] + + " # (ver=" + dihedral2ver_mbt[dihedral_name] + + ", ref=" + dihedral2ref_mbt[dihedral_name] + ")\n") + + assert(dihedral_name in dihedral2class2_ebt) + sys.stdout.write(' dihedral_coeff @dihedral:'+dih_name_abbr[dihedral_name]+' '+ + dihedral2style[dihedral_name] + ' ebt ' + + dihedral2class2_ebt[dihedral_name] + + " # (ver=" + dihedral2ver_ebt[dihedral_name] + + ", ref=" + dihedral2ref_ebt[dihedral_name] + ")\n") + + assert(dihedral_name in dihedral2class2_at) + sys.stdout.write(' dihedral_coeff @dihedral:'+dih_name_abbr[dihedral_name]+' '+ + dihedral2style[dihedral_name] + ' at ' + + dihedral2class2_at[dihedral_name] + + " # (ver=" + dihedral2ver_at[dihedral_name] + + ", ref=" + dihedral2ref_at[dihedral_name] + ")\n") + + assert(dihedral_name in dihedral2class2_aat) + sys.stdout.write(' dihedral_coeff @dihedral:'+dih_name_abbr[dihedral_name]+' '+ + dihedral2style[dihedral_name] + ' aat ' + + dihedral2class2_aat[dihedral_name] + + " # (ver=" + dihedral2ver_aat[dihedral_name] + + ", ref=" + dihedral2ref_aat[dihedral_name] + ")\n") + assert(dihedral_name in dihedral2class2_bb13) + sys.stdout.write(' dihedral_coeff @dihedral:'+dih_name_abbr[dihedral_name]+' '+ + dihedral2style[dihedral_name] + ' bb13 ' + + dihedral2class2_bb13[dihedral_name] + + " # (ver=" + dihedral2ver_bb13[dihedral_name] + + ", ref=" + dihedral2ref_bb13[dihedral_name] + ")\n") + sys.stdout.write(' } # end of dihedral_coeff commands\n' + '\n\n') + + + + + + ################# Print 4-body Improper Interactions ################## + + imp_names_priority_high_to_low = [x[0] for x in + sorted([x for x in reversed(improper2priority.items())], + key=itemgetter(1), + reverse=True)] + + imp_name_abbr = {} #optional abbreviated name for each interaction + imp_name_abbr_used = set([]) #make sure we don't reuse these abbreviated names + + if len(imp_names_priority_high_to_low) > 0: + sys.stdout.write(" # --------------- Improper Interactions: ---------------------\n") + sys.stdout.write('\n' + '\n' + ' # -- Rules for generating (4-body) "improper" interactions: --\n' + ' # ImproperType AtmType1 AtmType2 AtmType3 AtmType3 [BondType1 Bnd2 Bnd3]\n') + sys.stdout.write('\n' + ' write_once("Data Impropers By Type') + if improper_symmetry_subgraph != '': + sys.stdout.write(' ('+improper_symmetry_subgraph+')') + sys.stdout.write('") {\n') + for improper_name in imp_names_priority_high_to_low: + if not (improper2style[improper_name] in + improper_styles_selected): + continue + anames = ['*' if x=='X' else x + for x in ExtractANames(improper_name)] + #if (len(anames) == 4) and improper2style[improper_name] == 'class2': + # continue + ang_names = [[a for a in map(DecodeAName, anames[4:7])], + [a for a in map(DecodeAName, anames[7:10])], + [a for a in map(DecodeAName, anames[10:13])]] + anm = [a for a in map(DecodeAName, anames)] + + improper_is_auto = IsAutoInteraction(improper_name) + if improper2style[improper_name] == 'class2': + angle_is_auto1 = IsAutoInteraction(anames[4]) + angle_is_auto2 = IsAutoInteraction(anames[7]) + angle_is_auto3 = IsAutoInteraction(anames[10]) + + if ((improper_is_auto or + angle_is_auto1 or + angle_is_auto2 or + angle_is_auto3) and + (not include_auto_equivalences)): + continue + + # Can we ignore "auto" interactions? + # (If so, life is much easier) + if not (improper_is_auto or + angle_is_auto1 or + angle_is_auto2 or + angle_is_auto3): + if improper2style[improper_name] == 'class2': + # NOTE: atom orderings here are LAMMPS implementation specific. + # http://lammps.sandia.gov/doc/improper_class2.html + #ang_names[0] <==> (a1, a2, a3) <==> (i, j, k) + #ang_names[1] <==> (a1, a2, a4) <==> (i, j, l) + #ang_names[2] <==> (a3, a2, a4) <==> (k, j, l) + assert(ang_names[0][1] == ang_names[1][1] == ang_names[2][1]) + assert(ang_names[0][0] == ang_names[1][0]) + assert(ang_names[1][2] == ang_names[2][2]) + assert(ang_names[2][0] == ang_names[0][2]) + + # Optional: Shorten the improper name since some of the atom's bond names are redundant: + imp_name_abbr[improper_name] = EncodeInteractionName(map(EncodeAName, anm[0:4] + + [ang_names[0][0], + ang_names[0][1], + ang_names[0][2], + ang_names[1][2]]), + #[anm[4],anm[5],anm[6], + #anm[9]], + improper_is_auto) + sys.stdout.write(' @improper:' + imp_name_abbr[improper_name] + ' ' + + ' @atom:*,p*,b*,a'+ang_names[0][0]+',d*,i' + anames[0] + + ' @atom:*,p*,b*,a'+ang_names[0][1]+',d*,i' + anames[1] + + ' @atom:*,p*,b*,a'+ang_names[0][2]+',d*,i' + anames[2] + + ' @atom:*,p*,b*,a'+ang_names[1][2]+',d*,i' + anames[3] + + '\n') + else: + imp_name_abbr[improper_name] = improper_name + sys.stdout.write(' @improper:' + imp_name_abbr[improper_name] + ' ' + + ' @atom:*,p*,b*,a*,d*,i' + anames[0] + + ' @atom:*,p*,b*,a*,d*,i' + anames[1] + + ' @atom:*,p*,b*,a*,d*,i' + anames[2] + + ' @atom:*,p*,b*,a*,d*,i' + anames[3] + + '\n') + else: + # Consider "auto" interactions and "auto" atom equivalences + imp_name_abbr[improper_name] = improper_name #(full name) + sys.stdout.write(' @improper:' + imp_name_abbr[improper_name] + ' ') + + if improper2style[improper_name] == 'class2': + + #ang_names[0] <==> (a1, a2, a3) <==> (i, j, k) + #ang_names[1] <==> (a1, a2, a4) <==> (i, j, l) + #ang_names[2] <==> (a3, a2, a4) <==> (k, j, l) + + # default angle atom equivalence names: + ashared1 = 'a*' #(default for a1 <-> ang_names[0][0], ang_names[1][0]) + ashared2 = 'a*' #(default for a2 <-> ang_names[0][1], ang_names[1][1], ang_names[2][1]) + ashared3 = 'a*' #(default for a3 <-> ang_names[2][0], ang_names[0][2]) + ashared4 = 'a*' #(default for a4 <-> ang_names[1][2], ang_names[2][2]) + + # default auto angle atom equivalence names: + aashared1 = 'aae*,aac*' #(default for a1 <-> ang_names[0][0], ang_names[1][0]) + aashared2 = 'aae*,aac*' #(default for a2 <-> ang_names[0][1], ang_names[1][1], ang_names[2][1]) + aashared3 = 'aae*,aac*' #(default for a3 <-> ang_names[2][0], ang_names[0][2]) + aashared4 = 'aae*,aac*' #(default for a4 <-> ang_names[1][2], ang_names[2][2]) + + if improper_is_auto: + i1 = i2 = i3 = i4 = 'i*' #Then, dont use regular equivalences for these atoms. + ai1 = 'aie' + anames[0] + ',aic*' #Instead use the corresponding "auto" equivalence names + ai2 = 'aie*,aic*' + anames[1] #for these atoms. (There are different auto equivalence names depending + ai3 = 'aie' + anames[2] + ',aic*' #on if the atom appears in the center (c) or end(e) + ai4 = 'aie' + anames[3] + ',aic*' + else: + i1 = 'i' + anames[0] #In this case, use use (regular) equivalence names + i2 = 'i' + anames[1] #for these atoms + i3 = 'i' + anames[2] + i4 = 'i' + anames[3] + ai1 = ai2 = ai3 = 'aie*,aic*' + + #For reference, LAMMPS-specific atom ordering: + #ang_names[0] <==> (a1, a2, a3) <==> (i, j, k) + #ang_names[1] <==> (a1, a2, a4) <==> (i, j, l) + #ang_names[2] <==> (a3, a2, a4) <==> (k, j, l) + if not angle_is_auto1: + ashared1 = 'a' + ang_names[0][0] + ashared2 = 'a' + ang_names[0][1] + ashared3 = 'a' + ang_names[0][2] + else: + aashared1 = 'aae' + ang_names[0][0] + ',aac*' + aashared2 = 'aae*,aac' + ang_names[0][1] + aashared3 = 'aae' + ang_names[0][2] + ',aac*' + + #For reference, LAMMPS-specific atom ordering: + #ang_names[0] <==> (a1, a2, a3) <==> (i, j, k) + #ang_names[1] <==> (a1, a2, a4) <==> (i, j, l) + #ang_names[2] <==> (a3, a2, a4) <==> (k, j, l) + if not angle_is_auto2: + assert((ashared1 == 'a*') or (ashared1 == 'a' + ang_names[1][0])) + ashared1 = 'a' + ang_names[1][0] + assert((ashared2 == 'a*') or (ashared2 == 'a' + ang_names[1][1])) + ashared2 = 'a' + ang_names[1][1] + ashared4 = 'a' + ang_names[1][2] + else: + assert((aashared1 == 'aae*,aac*') or (aashared1 == 'aae' + ang_names[1][0] + ',aac*')) + aashared1 = 'aae' + ang_names[1][0] + ',aac*' + assert((aashared2 == 'aae*,aac*') or (aashared2 == 'aae*,aac' + ang_names[1][1])) + aashared2 = 'aae*,aac' + ang_names[1][1] + aashared4 = 'aae' + ang_names[1][2] + ',aac*' + + #For reference, LAMMPS-specific atom ordering: + #ang_names[0] <==> (a1, a2, a3) <==> (i, j, k) + #ang_names[1] <==> (a1, a2, a4) <==> (i, j, l) + #ang_names[2] <==> (a3, a2, a4) <==> (k, j, l) + if not angle_is_auto3: + assert((ashared3 == 'a*') or (ashared3 == 'a' + ang_names[2][0])) + ashared3 = 'a' + ang_names[2][0] + assert((ashared2 == 'a*') or (ashared2 == 'a' + ang_names[2][1])) + ashared2 = 'a' + ang_names[2][1] + assert((ashared4 == 'a*') or (ashared4 == 'a' + ang_names[2][2])) + ashared4 = 'a' + ang_names[2][2] + else: + assert((aashared3 == 'aae*,aac*') or (aashared3 == 'aae' + ang_names[2][0] + ',aac*')) + aashared3 = 'aae' + ang_names[2][0] + ',aac*' + assert((aashared2 == 'aae*,aac*') or (aashared2 == 'aae*,aac' + ang_names[2][1])) + aashared2 = 'aae*,aac' + ang_names[2][1] + assert((aashared4 == 'aae*,aac*') or (aashared4 == 'aae' + ang_names[2][2] + ',aac*')) + aashared4 = 'aae' + ang_names[2][2] + ',aac*' + + # print atom 1 information: + sys.stdout.write(' @atom:*,p*,b*,'+ashared1+',d*,'+i1+','+ + 'ap*,aq*,ab*,'+aashared1+',ad*,'+ai1) + # print atom 2 information: + sys.stdout.write(' @atom:*,p*,b*,'+ashared2+',d*,'+i2+','+ + 'ap*,aq*,ab*,'+aashared2+',ad*,'+ai2) + # print atom 3 information: + sys.stdout.write(' @atom:*,p*,b*,'+ashared3+',d*,'+i3+','+ + 'ap*,aq*,ab*,'+aashared3+',ad*,'+ai3) + # print atom 4 information: + sys.stdout.write(' @atom:*,p*,b*,'+ashared4+',d*,'+i4+','+ + 'ap*,aq*,ab*,'+aashared4+',ad*,'+ai4) + sys.stdout.write('\n') + else: + sys.stdout.write(' @improper:' + imp_name_abbr[improper_name] + ' ' + + ' @atom:*,p*,b*,d*,i*,' + + 'ap*,aq*,ab*,aae*,aac*,ade*,adc*,aie*,aie'+anames[0]+',aic*' + ' @atom:*,p*,b*,d*,i*,' + + 'ap*,aq*,ab*,aae*,aac*,ade*,adc*,aie*,aie*,aic'+anames[1]+ + ' @atom:*,p*,b*,d*,i*,' + + 'ap*,aq*,ab*,aae*,aac*,ade*,adc*,aie*,aie'+anames[2]+',aic*' + ' @atom:*,p*,b*,d*,i*,' + + 'ap*,aq*,ab*,aae*,aac*,ade*,adc*,aie*,aie'+anames[3]+',aic*' + '\n') + + assert(imp_name_abbr[improper_name] not in imp_name_abbr_used) + imp_name_abbr_used.add(imp_name_abbr[improper_name]) + + + + + sys.stdout.write(' } # end of "Data Impropers By Type" section\n' + '\n') + + # Print the force-field parameters for these improper interactions: + sys.stdout.write('\n\n' + ' # ------- Improper Force Field Parameters: -------\n') + sys.stdout.write(' # For an explanation of these parameters, visit:\n') + for improper_style in improper_styles: + if not (improper_style in improper_styles_selected): + continue + sys.stdout.write(' # '+improper_style2docs[improper_style]+'\n') + sys.stdout.write('\n' + '# Syntax: \n' + ' # improper_coeff ImproperTypeName ImproperStyle parameters...\n\n') + sys.stdout.write('\n' + ' write_once("In Settings") {\n') + for improper_name in imp_names_priority_high_to_low: + anames = ['*' if x=='X' else x + for x in ExtractANames(improper_name)] + #if (len(anames) == 4) and improper2style[improper_name] == 'class2': + # continue + # Optional: Shorten the angle name since some of the bnames are redundant: + + is_auto = IsAutoInteraction(improper_name) + + if not (improper2style[improper_name] in + improper_styles_selected): + continue + + # Did the user ask us to include "auto" interactions? + #if (IsAutoInteraction(improper_name) and + # (not include_auto_equivalences)): + # continue + # the if statement above is covered by the following: + if improper_name not in imp_name_abbr: + continue + + sys.stdout.write(' improper_coeff @improper:'+imp_name_abbr[improper_name]+' '+ + improper2style[improper_name] + ' ' + + improper2params[improper_name] + + " # (ver=" + improper2ver[improper_name] + + ", ref=" + improper2ref[improper_name] + ")\n") + if improper_name in improper2class2_aa: + sys.stdout.write(' improper_coeff @improper:'+imp_name_abbr[improper_name]+' '+ + improper2style[improper_name] + ' aa ' + + improper2class2_aa[improper_name] + + " # (ver=" + improper2ver_aa[improper_name] + + ", ref=" + improper2ref[improper_name] + ")\n") + sys.stdout.write(' } # end of improper_coeff commands\n' + '\n\n') + + + + sys.stdout.write('\n\n\n\n' + ' # -------------------- Select LAMMPS style(s) ------------------\n' + '\n') + + + sys.stdout.write('\n' + ' # LAMMPS supports many different kinds of bonded and non-bonded\n' + ' # interactions which can be selected at run time. Eventually\n' + ' # we must inform LAMMPS which of them we will need. We specify\n' + ' # this in the "In Init" section: \n\n') + + sys.stdout.write(' write_once("In Init") {\n') + sys.stdout.write(' units real\n') + sys.stdout.write(' atom_style full\n') + + if len(bond_styles) > 0: + sys.stdout.write(' bond_style hybrid') + for bond_style in bond_styles: + if not (bond_style in bond_styles_selected): + continue + sys.stdout.write(' ' + bond_style) + sys.stdout.write('\n') + for bond_style in bond_styles: + if not (bond_style in bond_styles_selected): + continue + sys.stdout.write(' # '+bond_style2docs[bond_style]+'\n') + sys.stdout.write('\n') + + if len(angle_styles) > 0: + sys.stdout.write(' angle_style hybrid') + for angle_style in angle_styles: + if not (angle_style in angle_styles_selected): + continue + sys.stdout.write(' ' + angle_style) + sys.stdout.write('\n') + for angle_style in angle_styles: + if not (angle_style in angle_styles_selected): + continue + sys.stdout.write(' # '+angle_style2docs[angle_style]+'\n') + sys.stdout.write('\n') + + if len(dihedral_styles) > 0: + sys.stdout.write(' dihedral_style hybrid') + for dihedral_style in dihedral_styles: + if not (dihedral_style in dihedral_styles_selected): + continue + sys.stdout.write(' ' + dihedral_style) + sys.stdout.write('\n') + for dihedral_style in dihedral_styles: + if not (dihedral_style in dihedral_styles_selected): + continue + sys.stdout.write(' # '+dihedral_style2docs[dihedral_style]+'\n') + sys.stdout.write('\n') + + if len(improper_styles) > 0: + sys.stdout.write(' improper_style hybrid') + for improper_style in improper_styles: + if not (improper_style in improper_styles_selected): + continue + sys.stdout.write(' ' + improper_style) + sys.stdout.write('\n') + for improper_style in improper_styles: + if not (improper_style in improper_styles_selected): + continue + sys.stdout.write(' # '+improper_style2docs[improper_style]+'\n') + sys.stdout.write('\n') + + if len(pair_styles) > 0: + sys.stdout.write(' pair_style hybrid') + for pair_style in pair_styles: + if not (pair_style in pair_styles_selected): + continue + sys.stdout.write(' ' + pair_style + + ' ' + pair_style_args[pair_style]) + sys.stdout.write('\n') + for pair_style in pair_styles: + sys.stdout.write(' # '+pair_style2docs[pair_style]+'\n') + sys.stdout.write('\n') + + sys.stdout.write(' pair_modify mix ' + pair_mixing_style + '\n') + sys.stdout.write(' ' + special_bonds_command + '\n') + sys.stdout.write(' ' + kspace_style + '\n') + sys.stdout.write(' } #end of init parameters\n\n') + sys.stdout.write('} # ' + ffname + '\n\n') + + + sys.stdout.write("#\n" + "# WARNING: The following 1-2, 1-3, and 1-4 weighting parameters were ASSUMED:\n") + sys.stdout.write("# " + special_bonds_command + "\n") + sys.stdout.write("# (See http://lammps.sandia.gov/doc/special_bonds.html for details)\n") + + #sys.stderr.write(' done.\n') + + + if len(lines_templates) > 0: + sys.stdout.write('\n\n\n\n' + '# ---- templates from the original .frc file used for atom type selection: ---\n') + for line in lines_templates: + sys.stdout.write('# '+line) + + if len(lines_references) > 0: + sys.stdout.write('\n\n\n\n' + '# ---- references from the original .frc file: ----\n\n') + for ref_number,lines in sorted(lines_references.items()): + sys.stdout.write('# reference '+str(ref_number)+'\n') + for line in lines: + sys.stdout.write('# '+line) + sys.stdout.write('\n') + + + if len(lines_warnings) > 0: + sys.stdout.write('\n\n\n\n' + '# ---- additional warnings: ----\n') + for line in lines_warnings: + sys.stdout.write(line) + + + if filename_in != '': + file_in.close() + + + + + except InputError as err: + sys.stderr.write('\n\n' + str(err) + '\n') + sys.exit(1) + + + +if __name__ == '__main__': + main() diff --git a/tools/moltemplate/moltemplate/force_fields/convert_TINKER_files_to_LT_files/__init__.py b/tools/moltemplate/moltemplate/force_fields/convert_TINKER_files_to_LT_files/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/tools/moltemplate/moltemplate/force_fields/tinker/tinkerparm2lt.py b/tools/moltemplate/moltemplate/force_fields/convert_TINKER_files_to_LT_files/tinkerparm2lt.py similarity index 76% rename from tools/moltemplate/moltemplate/force_fields/tinker/tinkerparm2lt.py rename to tools/moltemplate/moltemplate/force_fields/convert_TINKER_files_to_LT_files/tinkerparm2lt.py index acb3db5e5c..c5bf317e52 100755 --- a/tools/moltemplate/moltemplate/force_fields/tinker/tinkerparm2lt.py +++ b/tools/moltemplate/moltemplate/force_fields/convert_TINKER_files_to_LT_files/tinkerparm2lt.py @@ -17,8 +17,8 @@ to my knowledge, have not yet been implemented in LAMMPS as of 2017-2-01.) __author__ = 'Jason Lambert and Andrew Jewett' # (some additional corrections by Miguel Gonzalez, Yue Chun Chiu and others) -__version__ = '0.2.1' -__date__ = '2017-17-18' +__version__ = '0.3.2' +__date__ = '2018-6-15' import sys @@ -38,10 +38,12 @@ doc_msg = \ " and \"OPLS\" is the name that future moltemplate users will use to refer to\n" + \ " this force-field (optional).\n" + \ "Optional Arguments\n" + \ - " -name FORCEFIELDNAME # Give the force-field a name\n" + \ + " -name FORCEFIELDNAME # Give the force-field a name (recommended)\n" + \ " -file FILE_NAME # Read force field parameters from a file\n" + \ - " -url URL # Read force field parameters from a file on the web\n" + \ - " -atoms \"QUOTED LIST\" # Restrict output to a subset of atom types\n" + " -url URL # Read force field parameters from a file online\n" + \ + " -atoms \"QUOTED LIST\" # Restrict output to a subset of atom types\n" + \ + " -hybrid # Optional LAMMPS \"hybrid\" style compatibility\n" + \ + " -zeropad N # Optional zero-padding for bonded interactions\n" def SplitQuotedString(string, @@ -142,9 +144,13 @@ def main(): dihedral_style_link = "http://lammps.sandia.gov/doc/dihedral_fourier.html" improper_style_name = "harmonic" improper_style_link = "http://lammps.sandia.gov/doc/improper_harmonic.html" + #improper_style_name = "cvff" + #improper_style_link = "http://lammps.sandia.gov/doc/improper_cvff.html" special_bonds_command = "special_bonds lj/coul 0.0 0.0 0.5" mixing_style = "geometric" + use_hybrid = False contains_united_atoms = False + zeropad_ffid = 1 argv = [arg for arg in sys.argv] @@ -183,7 +189,7 @@ def main(): ' for reading.\n') sys.exit(1) del argv[i:i + 2] - + elif argv[i] == '-dihedral-style': if i + 1 >= len(argv): raise Exception( @@ -201,8 +207,9 @@ def main(): elif argv[i] in ('-url', '-in-url'): import urllib2 if i + 1 >= len(argv): - raise Exception( - 'Error: ' + argv[i] + ' flag should be followed by the name of a force-field file.\n') + raise InputError('Error: ' + argv[i] + ' flag should be followed by a URL pointing to\n' + + ' a TINKER file containing force-field information.\n') url = argv[i + 1] try: request = urllib2.Request(url) @@ -211,6 +218,17 @@ def main(): sys.stdout.write("Error: Unable to open link:\n" + url + "\n") sys.exit(1) del argv[i:i + 2] + + elif argv[i] == '-hybrid': + use_hybrid = True + del argv[i:i + 1] + + elif (argv[i] == '-zeropad' or argv[i] == '-zero-pad'): + if (i + 1 >= len(argv)) or (argv[i+1][1:] == '-'): + raise Exception( + 'Error: ' + argv[i] + ' flag should be followed by a positive integer\n') + zeropad_ffid = int(argv[i+1]) + del argv[i:i + 2] elif argv[i] in ('-help', '--help', '-?', '--?'): sys.stderr.write(doc_msg) @@ -276,11 +294,14 @@ def main(): elif (len(tokens) > 4) and (tokens[0] == 'bond'): k = float(tokens[3]) r0 = float(tokens[4]) - bonds_by_type[tokens[1], tokens[2]] = (k, r0) + bonds_by_type[tokens[1].rjust(zeropad_ffid,'0'), + tokens[2].rjust(zeropad_ffid,'0')] = (k, r0) elif (len(tokens) > 5) and (tokens[0] == 'angle'): k = float(tokens[4]) angle0 = float(tokens[5]) - angles_by_type[tokens[1], tokens[2], tokens[3]] = (k, angle0) + angles_by_type[tokens[1].rjust(zeropad_ffid,'0'), + tokens[2].rjust(zeropad_ffid,'0'), + tokens[3].rjust(zeropad_ffid,'0')] = (k, angle0) elif (len(tokens) > 11) and (tokens[0] == 'torsion'): if dihedral_style_name == 'fourier': # http://lammps.sandia.gov/doc/dihedral_fourier.html @@ -292,8 +313,10 @@ def main(): K[i] = float(tokens[5 + 3 * i]) d[i] = float(tokens[5 + 3 * i + 1]) n[i] = float(tokens[5 + 3 * i + 2]) - dihedrals_by_type[tokens[1], tokens[2], - tokens[3], tokens[4]] = (K, n, d) + dihedrals_by_type[tokens[1].rjust(zeropad_ffid,'0'), + tokens[2].rjust(zeropad_ffid,'0'), + tokens[3].rjust(zeropad_ffid,'0'), + tokens[4].rjust(zeropad_ffid,'0')] = (K, n, d) elif dihedral_style_name == 'opls': # http://lammps.sandia.gov/doc/dihedral_opls.html K1 = float(tokens[5]) @@ -311,8 +334,10 @@ def main(): (float(tokens[16]) != 4.0)))): raise Exception("Error: This parameter file is incompatible with -dihedral-style \"" + dihedral_style_name + "\"\n" + " (See line number " + str(iline + 1) + " of parameter file.)\n") - dihedrals_by_type[tokens[1], tokens[2], - tokens[3], tokens[4]] = (K1, K2, K3, K4) + dihedrals_by_type[tokens[1].rjust(zeropad_ffid,'0'), + tokens[2].rjust(zeropad_ffid,'0'), + tokens[3].rjust(zeropad_ffid,'0'), + tokens[4].rjust(zeropad_ffid,'0')] = (K1, K2, K3, K4) else: assert(False) @@ -320,8 +345,10 @@ def main(): k = float(tokens[5]) angle0 = float(tokens[6]) multiplicity = float(tokens[7]) - impropers_by_type[tokens[1], tokens[2], tokens[ - 3], tokens[4]] = (k / multiplicity, angle0) + impropers_by_type[tokens[1].rjust(zeropad_ffid,'0'), + tokens[2].rjust(zeropad_ffid,'0'), + tokens[3].rjust(zeropad_ffid,'0'), + tokens[4].rjust(zeropad_ffid,'0')] = (k / multiplicity, angle0) elif ((len(tokens) > 0) and (tokens[0] == 'biotype')): # I'm not sure what to do with these, so I'll store them for now and # append them as comments to the .lt file generated by the program. @@ -351,13 +378,28 @@ def main(): " to consider alternate mixing rules.\n\n" + "The offending line from the file is line number " + str(iline) + ":\n" + line + "\n") - - - + + # Zero-pad the atom2ffid values so that they have the same number + # of digits. This is usually not necessary, but it can be helpful + # to remove uncertainty about the meaning of '4*' which could + # pattern match with '4', '4L', '47', '47L'... If you replace '4' + # with '04', '04*' becomes distinguishable from '47*'. + # This can be useful if you want to augment the force field later, + # (for example, adding additional atoms to the LOPLSAA variant of OPLSAA) + + for k in atom2ffid.keys(): + atom2ffid[k] = atom2ffid[k].rjust(zeropad_ffid, '0') + + # Horrible hack: for LOPLSAA, uncomment the next 3 lines: + #ki = atom2ffid[k].find('L') + #if ki!=-1: + # atom2ffid[k] = atom2ffid[k].rjust(zeropad_ffid + len(atom2ffid[k]) - ki, '0') + + #sys.stderr.write(" done.\n") #sys.stderr.write("Converting to moltemplate format...\n") - - + + system_is_charged = False for atom_type in atom2charge: if atom2charge[atom_type] != 0.0: @@ -373,10 +415,9 @@ def main(): pair_style_params = "10.0" kspace_style = "" pair_style_link = "http://lammps.sandia.gov/doc/pair_lj.html" - - pair_style_command = " pair_style hybrid " + \ - pair_style_name + " " + pair_style_params + "\n" - + + pair_style_command = " pair_style " + ("hybrid " if use_hybrid else "") + \ + pair_style_name + " " + pair_style_params + "\n" sys.stdout.write("# This file was generated automatically using:\n") sys.stdout.write("# " + g_program_name + " " + " ".join(sys.argv[1:]) + "\n") @@ -442,8 +483,10 @@ def main(): sys.stdout.write(" # --------------- Non-Bonded interactions: ---------------------\n" " # " + pair_style_link + "\n" " # Syntax:\n" - " # pair_coeff AtomType1 AtomType2 pair_style_name parameters...\n\n") - + " # pair_coeff AtomType1 AtomType2 " + + ("PairStyleName " if use_hybrid else "") + + "parameters...\n\n") + sys.stdout.write(" write_once(\"In Settings\") {\n") for atype in atom2vdw_e: assert(atype in atom2vdw_s) @@ -454,7 +497,7 @@ def main(): "@atom:" + atype + "_b" + atom2ffid[atype] + "_a" + atom2ffid[ atype] + "_d" + atom2ffid[atype] + "_i" + atom2ffid[atype] + " " "@atom:" + atype + "_b" + atom2ffid[atype] + "_a" + atom2ffid[atype] + "_d" + atom2ffid[atype] + "_i" + atom2ffid[atype] + " " + - pair_style_name + + (pair_style_name if use_hybrid else "") + " " + str(atom2vdw_e[atype]) + " " + str(atom2vdw_s[atype]) + "\n") sys.stdout.write(" } #(end of pair_coeffs)\n\n\n\n") @@ -463,15 +506,18 @@ def main(): sys.stdout.write(" # ------- Bonded Interactions: -------\n" " # " + bond_style_link + "\n" " # Syntax: \n" - " # bond_coeff BondTypeName BondStyle parameters...\n\n") + " # bond_coeff BondTypeName " + + ("BondStyleName " if use_hybrid else "") + + "parameters...\n\n") sys.stdout.write(" write_once(\"In Settings\") {\n") for btype in bonds_by_type: - ffid1 = btype[0] if btype[0] != "0" else "X" - ffid2 = btype[1] if btype[1] != "0" else "X" + ffid1 = btype[0] if btype[0] != ("0"*zeropad_ffid) else "X" + ffid2 = btype[1] if btype[1] != ("0"*zeropad_ffid) else "X" (k, r0) = bonds_by_type[btype] - sys.stdout.write(" bond_coeff @bond:" + ffid1 + "-" + ffid2 + " " + - bond_style_name + " " + str(k) + " " + str(r0) + "\n") + sys.stdout.write(" bond_coeff @bond:" + ffid1 + "_" + ffid2 + " " + + (bond_style_name if use_hybrid else "") + + " " + str(k) + " " + str(r0) + "\n") sys.stdout.write(" } #(end of bond_coeffs)\n\n") sys.stdout.write(" # Rules for assigning bond types by atom type:\n" @@ -480,13 +526,13 @@ def main(): sys.stdout.write(" write_once(\"Data Bonds By Type\") {\n") for btype in bonds_by_type: - ffid1 = btype[0] if btype[0] != "0" else "X" - ffid2 = btype[1] if btype[1] != "0" else "X" - sys.stdout.write(" @bond:" + ffid1 + "-" + ffid2) + ffid1 = btype[0] if btype[0] != ("0"*zeropad_ffid) else "X" + ffid2 = btype[1] if btype[1] != ("0"*zeropad_ffid) else "X" + sys.stdout.write(" @bond:" + ffid1 + "_" + ffid2) ffid1 = "@atom:*_b" + btype[0] + \ - "_a*_d*_i*" if btype[0] != "0" else "@atom:*" + "*_a*_d*_i*" if btype[0] != ("0"*zeropad_ffid) else "@atom:*" ffid2 = "@atom:*_b" + btype[1] + \ - "_a*_d*_i*" if btype[1] != "0" else "@atom:*" + "*_a*_d*_i*" if btype[1] != ("0"*zeropad_ffid) else "@atom:*" sys.stdout.write(" " + ffid1 + " " + ffid2 + "\n") sys.stdout.write(" } #(end of bonds by type)\n\n\n\n\n") @@ -494,16 +540,19 @@ def main(): sys.stdout.write(" # ------- Angle Interactions: -------\n" " # " + angle_style_link + "\n" " # Syntax: \n" - " # angle_coeff AngleTypeName AngleStyle parameters...\n\n") + " # angle_coeff AngleTypeName "+ + ("AngleStyleName " if use_hybrid else "") + + "parameters...\n\n") sys.stdout.write(" write_once(\"In Settings\") {\n") for atype in angles_by_type: - ffid1 = atype[0] if atype[0] != "0" else "X" - ffid2 = atype[1] if atype[1] != "0" else "X" - ffid3 = atype[2] if atype[2] != "0" else "X" + ffid1 = atype[0] if atype[0] != ("0"*zeropad_ffid) else "X" + ffid2 = atype[1] if atype[1] != ("0"*zeropad_ffid) else "X" + ffid3 = atype[2] if atype[2] != ("0"*zeropad_ffid) else "X" (k, angle0) = angles_by_type[atype] - sys.stdout.write(" angle_coeff @angle:" + ffid1 + "-" + ffid2 + "-" + ffid3 + " " + - angle_style_name + " " + str(k) + " " + str(angle0) + "\n") + sys.stdout.write(" angle_coeff @angle:" + ffid1 + "_" + ffid2 + "_" + ffid3 + " " + + (angle_style_name if use_hybrid else "") + + " " + str(k) + " " + str(angle0) + "\n") sys.stdout.write(" } #(end of angle_coeffs)\n\n") @@ -513,16 +562,16 @@ def main(): sys.stdout.write(" write_once(\"Data Angles By Type\") {\n") for atype in angles_by_type: - ffid1 = atype[0] if atype[0] != "0" else "X" - ffid2 = atype[1] if atype[1] != "0" else "X" - ffid3 = atype[2] if atype[2] != "0" else "X" - sys.stdout.write(" @angle:" + ffid1 + "-" + ffid2 + "-" + ffid3) + ffid1 = atype[0] if atype[0] != ("0"*zeropad_ffid) else "X" + ffid2 = atype[1] if atype[1] != ("0"*zeropad_ffid) else "X" + ffid3 = atype[2] if atype[2] != ("0"*zeropad_ffid) else "X" + sys.stdout.write(" @angle:" + ffid1 + "_" + ffid2 + "_" + ffid3) ffid1 = "@atom:*_b*_a" + atype[0] + \ - "_d*_i*" if atype[0] != "0" else "@atom:*" + "*_d*_i*" if atype[0] != ("0"*zeropad_ffid) else "@atom:*" ffid2 = "@atom:*_b*_a" + atype[1] + \ - "_d*_i*" if atype[1] != "0" else "@atom:*" + "*_d*_i*" if atype[1] != ("0"*zeropad_ffid) else "@atom:*" ffid3 = "@atom:*_b*_a" + atype[2] + \ - "_d*_i*" if atype[2] != "0" else "@atom:*" + "*_d*_i*" if atype[2] != ("0"*zeropad_ffid) else "@atom:*" sys.stdout.write(" " + ffid1 + " " + ffid2 + " " + ffid3 + "\n") sys.stdout.write(" } #(end of angles by type)\n\n\n\n\n") @@ -530,17 +579,20 @@ def main(): sys.stdout.write(" # ----------- Dihedral Interactions: ------------\n" " # " + dihedral_style_link + "\n" " # Syntax:\n" - " # dihedral_coeff DihedralTypeName DihedralStyle parameters...\n\n") + " # dihedral_coeff DihedralTypeName " + + ("DihedralStyleName " if use_hybrid else "") + + "parameters...\n\n") sys.stdout.write(" write_once(\"In Settings\") {\n") for dtype in dihedrals_by_type: - ffid1 = dtype[0] if dtype[0] != "0" else "X" - ffid2 = dtype[1] if dtype[1] != "0" else "X" - ffid3 = dtype[2] if dtype[2] != "0" else "X" - ffid4 = dtype[3] if dtype[3] != "0" else "X" + ffid1 = dtype[0] if dtype[0] != ("0"*zeropad_ffid) else "X" + ffid2 = dtype[1] if dtype[1] != ("0"*zeropad_ffid) else "X" + ffid3 = dtype[2] if dtype[2] != ("0"*zeropad_ffid) else "X" + ffid4 = dtype[3] if dtype[3] != ("0"*zeropad_ffid) else "X" sys.stdout.write(" dihedral_coeff @dihedral:" + - ffid1 + "-" + ffid2 + "-" + ffid3 + "-" + ffid4 + " " + - dihedral_style_name + " ") + ffid1 + "_" + ffid2 + "_" + ffid3 + "_" + ffid4 + " " + + (dihedral_style_name if use_hybrid else "") + + " ") if dihedral_style_name == 'fourier': # http://lammps.sandia.gov/doc/dihedral_fourier.html (K, n, d) = dihedrals_by_type[dtype] @@ -567,20 +619,22 @@ def main(): sys.stdout.write(" write_once(\"Data Dihedrals By Type\") {\n") for dtype in dihedrals_by_type: - ffid1 = dtype[0] if dtype[0] != "0" else "X" - ffid2 = dtype[1] if dtype[1] != "0" else "X" - ffid3 = dtype[2] if dtype[2] != "0" else "X" - ffid4 = dtype[3] if dtype[3] != "0" else "X" - sys.stdout.write(" @dihedral:" + ffid1 + "-" + - ffid2 + "-" + ffid3 + "-" + ffid4) + ffid1 = dtype[0] if dtype[0] != ("0"*zeropad_ffid) else "X" + ffid2 = dtype[1] if dtype[1] != ("0"*zeropad_ffid) else "X" + ffid3 = dtype[2] if dtype[2] != ("0"*zeropad_ffid) else "X" + ffid4 = dtype[3] if dtype[3] != ("0"*zeropad_ffid) else "X" + sys.stdout.write(" @dihedral:" + + ffid1 + "_" + ffid2 + "_" + + ffid3 + "_" + ffid4) ffid1 = "@atom:*_b*_a*_d" + dtype[0] + \ - "_i*" if dtype[0] != "0" else "@atom:*" + "*_i*" if dtype[0] != ("0"*zeropad_ffid) else "@atom:*" ffid2 = "@atom:*_b*_a*_d" + dtype[1] + \ - "_i*" if dtype[1] != "0" else "@atom:*" + "*_i*" if dtype[1] != ("0"*zeropad_ffid) else "@atom:*" ffid3 = "@atom:*_b*_a*_d" + dtype[2] + \ - "_i*" if dtype[2] != "0" else "@atom:*" + "*_i*" if dtype[2] != ("0"*zeropad_ffid) else "@atom:*" ffid4 = "@atom:*_b*_a*_d" + dtype[3] + \ - "_i*" if dtype[3] != "0" else "@atom:*" + "*_i*" if dtype[3] != ("0"*zeropad_ffid) else "@atom:*" + sys.stdout.write(" " + ffid1 + " " + ffid2 + " " + ffid3 + " " + ffid4 + "\n") sys.stdout.write(" } #(end of dihedrals by type)\n\n\n\n\n") @@ -589,37 +643,41 @@ def main(): sys.stdout.write(" # ---------- Improper Interactions: ----------\n" " # " + improper_style_link + "\n" " # Syntax:\n" - " # improper_coeff ImproperTypeName ImproperStyle parameters\n\n") + " # improper_coeff ImproperTypeName " + + ("ImproperStyleName " if use_hybrid else "") + + "parameters\n\n") sys.stdout.write(" write_once(\"In Settings\") {\n") for itype in impropers_by_type: - ffid1 = itype[0] if itype[0] != "0" else "X" - ffid2 = itype[1] if itype[1] != "0" else "X" - ffid3 = itype[2] if itype[2] != "0" else "X" - ffid4 = itype[3] if itype[3] != "0" else "X" + ffid1 = itype[0] if itype[0] != ("0"*zeropad_ffid) else "X" + ffid2 = itype[1] if itype[1] != ("0"*zeropad_ffid) else "X" + ffid3 = itype[2] if itype[2] != ("0"*zeropad_ffid) else "X" + ffid4 = itype[3] if itype[3] != ("0"*zeropad_ffid) else "X" (k, angle0) = impropers_by_type[itype] sys.stdout.write(" improper_coeff @improper:" + - ffid1 + "-" + ffid2 + "-" + ffid3 + "-" + ffid4 + " " + - improper_style_name + " " + str(k) + " " + str(angle0) + "\n") + ffid1 + "_" + ffid2 + "_" + ffid3 + "_" + ffid4 + " " + + (improper_style_name if use_hybrid else "") + + " " + str(k) + " " + str(angle0) + "\n") sys.stdout.write(" } #(end of improper_coeffs)\n\n") - sys.stdout.write(" # Rules for creating dihedral interactions according to atom type:\n" + sys.stdout.write(" # Rules for creating improper interactions according to atom type:\n" " # ImproperTypeName AtomType1 AtomType2 AtomType3 AtomType4\n" " # (* = wildcard)\n") sys.stdout.write(" write_once(\"Data Impropers By Type (opls_imp.py)\") {\n") for itype in impropers_by_type: - ffid1 = itype[0] if itype[0] != "0" else "X" - ffid2 = itype[1] if itype[1] != "0" else "X" - ffid3 = itype[2] if itype[2] != "0" else "X" - ffid4 = itype[3] if itype[3] != "0" else "X" - sys.stdout.write(" @improper:" + ffid1 + "-" + - ffid2 + "-" + ffid3 + "-" + ffid4) - ffid1 = "@atom:*_b*_a*_d*_i" + itype[0] if itype[0] != "0" else "@atom:*" - ffid2 = "@atom:*_b*_a*_d*_i" + itype[1] if itype[1] != "0" else "@atom:*" - ffid3 = "@atom:*_b*_a*_d*_i" + itype[2] if itype[2] != "0" else "@atom:*" - ffid4 = "@atom:*_b*_a*_d*_i" + itype[3] if itype[3] != "0" else "@atom:*" + ffid1 = itype[0] if itype[0] != ("0"*zeropad_ffid) else "X" + ffid2 = itype[1] if itype[1] != ("0"*zeropad_ffid) else "X" + ffid3 = itype[2] if itype[2] != ("0"*zeropad_ffid) else "X" + ffid4 = itype[3] if itype[3] != ("0"*zeropad_ffid) else "X" + sys.stdout.write(" @improper:" + + ffid1 + "_" + ffid2 + "_" + + ffid3 + "_" + ffid4) + ffid1 = "@atom:*_b*_a*_d*_i" + itype[0]+"*" if itype[0] != ("0"*zeropad_ffid) else "@atom:*" + ffid2 = "@atom:*_b*_a*_d*_i" + itype[1]+"*" if itype[1] != ("0"*zeropad_ffid) else "@atom:*" + ffid3 = "@atom:*_b*_a*_d*_i" + itype[2]+"*" if itype[2] != ("0"*zeropad_ffid) else "@atom:*" + ffid4 = "@atom:*_b*_a*_d*_i" + itype[3]+"*" if itype[3] != ("0"*zeropad_ffid) else "@atom:*" sys.stdout.write(" " + ffid1 + " " + ffid2 + " " + ffid3 + " " + ffid4 + "\n") sys.stdout.write(" } #(end of impropers by type)\n\n\n\n\n") @@ -639,10 +697,18 @@ def main(): sys.stdout.write(" write_once(\"In Init\") {\n") sys.stdout.write(" units real\n") sys.stdout.write(" atom_style full\n") - sys.stdout.write(" bond_style hybrid " + bond_style_name + "\n") - sys.stdout.write(" angle_style hybrid " + angle_style_name + "\n") - sys.stdout.write(" dihedral_style hybrid " + dihedral_style_name + "\n") - sys.stdout.write(" improper_style hybrid " + improper_style_name + "\n") + sys.stdout.write(" bond_style " + + ("hybrid " if use_hybrid else "") + + bond_style_name + "\n") + sys.stdout.write(" angle_style " + + ("hybrid " if use_hybrid else "") + + angle_style_name + "\n") + sys.stdout.write(" dihedral_style " + + ("hybrid " if use_hybrid else "") + + dihedral_style_name + "\n") + sys.stdout.write(" improper_style " + + ("hybrid " if use_hybrid else "") + + improper_style_name + "\n") sys.stdout.write(pair_style_command) sys.stdout.write(" pair_modify mix " + mixing_style + "\n") sys.stdout.write(" " + special_bonds_command + "\n") diff --git a/tools/moltemplate/moltemplate/force_fields/cooke_deserno/README b/tools/moltemplate/moltemplate/force_fields/cooke_deserno_supporting_files/README similarity index 100% rename from tools/moltemplate/moltemplate/force_fields/cooke_deserno/README rename to tools/moltemplate/moltemplate/force_fields/cooke_deserno_supporting_files/README diff --git a/tools/moltemplate/moltemplate/force_fields/cooke_deserno/gen_potential-cooke.py b/tools/moltemplate/moltemplate/force_fields/cooke_deserno_supporting_files/gen_potential-cooke.py similarity index 100% rename from tools/moltemplate/moltemplate/force_fields/cooke_deserno/gen_potential-cooke.py rename to tools/moltemplate/moltemplate/force_fields/cooke_deserno_supporting_files/gen_potential-cooke.py diff --git a/tools/moltemplate/moltemplate/force_fields/cooke_deserno/tabulated_potential.dat b/tools/moltemplate/moltemplate/force_fields/cooke_deserno_supporting_files/tabulated_potential.dat similarity index 100% rename from tools/moltemplate/moltemplate/force_fields/cooke_deserno/tabulated_potential.dat rename to tools/moltemplate/moltemplate/force_fields/cooke_deserno_supporting_files/tabulated_potential.dat diff --git a/tools/moltemplate/moltemplate/force_fields/gaff.lt b/tools/moltemplate/moltemplate/force_fields/gaff.lt index 683dbf4ee4..d9e367e8ce 100644 --- a/tools/moltemplate/moltemplate/force_fields/gaff.lt +++ b/tools/moltemplate/moltemplate/force_fields/gaff.lt @@ -30,15 +30,14 @@ #(See "Inheritance" and "short names vs. full names" in the moltemplate manual.) #################################################################### # Moltemplate can not assign atom charge. You must assign atomic -# charges yourself. (Moltemplate is only a simple text manipulation tool.) +# charges yourself. (Moltemplate is only a simple text manipulation tool. +# You can do this afterwards using commands like "set atom 70 charge -0.212" +# For details, see http://lammps.sandia.gov/doc/set.html) #################################################################### - - - GAFF { # ---------------------------------------------------------------------- diff --git a/tools/moltemplate/moltemplate/force_fields/gaff2.lt b/tools/moltemplate/moltemplate/force_fields/gaff2.lt new file mode 100644 index 0000000000..9063b28cb9 --- /dev/null +++ b/tools/moltemplate/moltemplate/force_fields/gaff2.lt @@ -0,0 +1,13357 @@ +# This is the 2.1 version of GAFF (April 2016) +#################################################################### +# This moltemplate (LT) file was generated automatically using +# amberparm2lt.sh gaff2.dat GAFF2 > gaff2.lt +#################################################################### +# WARNING: As of 2017-10-03 this file has not yet been tested with +# moltemplate. Please report issues to jewett.aij -at- gmail.com +#################################################################### +# Background information and usage explanation: +# This file contanis a list of atom types and rules for generating bonded +# interactions between these atoms (hopefully) according to AMBER conventions. +# By using the atom types shown below in your own molecules, bonds and angular +# interactions will be automatically generated. +# AMBER (GAFF) force-field parameters will also be assigned to each angle +# interaction (according to these atom types). +# One way to apply the GAFF force field to a particular type of molecule, is +# to use the "inherits" keyword when you define that molecule. For example: +# import("gaff.lt") +# MoleculeType inherits GAFF { +# write_once("Data Atoms") { +# $atom:C1 $mol:... @atom:cx 0.0 4.183 3.194 13.285 +# $atom:C2 $mol:... @atom:cx 0.0 4.291 4.618 13.382 +# : : : +# } +# } +#(See "Inheritance" and "short names vs. full names" in the moltemplate manual.) +#################################################################### +# Moltemplate can not assign atom charge. You must assign atomic +# charges yourself. (Moltemplate is only a simple text manipulation tool. +# You can do this afterwards using commands like "set atom 70 charge -0.212" +# For details, see http://lammps.sandia.gov/doc/set.html) +#################################################################### + + +GAFF2 { + + # ---------------------------------------------------------------------- + # The basic atom nomenclature and conventions are explained here: + # http://ambermd.org/antechamber/gaff.pdf + # For reference, the original gaff.dat file and format documentation are here: + # http://ambermd.org/AmberTools-get.html + # http://ambermd.org/formats.html#parm.dat + # ---------------------------------------------------------------------- + + write_once("Data Masses") { + @atom:c 12.01 # Sp2 C carbonyl group + @atom:cs 12.01 # Sp2 C in c=S + @atom:c1 12.01 # Sp C + @atom:c2 12.01 # Sp2 C + @atom:c3 12.01 # Sp3 C + @atom:ca 12.01 # Sp2 C in pure aromatic systems + @atom:cp 12.01 # Head Sp2 C that connect two rings in biphenyl sys. + @atom:cq 12.01 # Head Sp2 C that connect two rings in biphenyl sys. identical to cp + @atom:cc 12.01 # Sp2 carbons in non-pure aromatic systems + @atom:cd 12.01 # Sp2 carbons in non-pure aromatic systems, identical to cc + @atom:ce 12.01 # Inner Sp2 carbons in conjugated systems + @atom:cf 12.01 # Inner Sp2 carbons in conjugated systems, identical to ce + @atom:cg 12.01 # Inner Sp carbons in conjugated systems + @atom:ch 12.01 # Inner Sp carbons in conjugated systems, identical to cg + @atom:cx 12.01 # Sp3 carbons in triangle systems + @atom:cy 12.01 # Sp3 carbons in square systems + @atom:cu 12.01 # Sp2 carbons in triangle systems + @atom:cv 12.01 # Sp2 carbons in square systems + @atom:cz 12.01 # Sp2 carbon in guanidine group + @atom:h1 1.008 # H bonded to aliphatic carbon with 1 electrwd. group + @atom:h2 1.008 # H bonded to aliphatic carbon with 2 electrwd. group + @atom:h3 1.008 # H bonded to aliphatic carbon with 3 electrwd. group + @atom:h4 1.008 # H bonded to non-sp3 carbon with 1 electrwd. group + @atom:h5 1.008 # H bonded to non-sp3 carbon with 2 electrwd. group + @atom:ha 1.008 # H bonded to aromatic carbon + @atom:hc 1.008 # H bonded to aliphatic carbon without electrwd. group + @atom:hn 1.008 # H bonded to nitrogen atoms + @atom:ho 1.008 # Hydroxyl group + @atom:hp 1.008 # H bonded to phosphate + @atom:hs 1.008 # Hydrogen bonded to sulphur + @atom:hw 1.008 # Hydrogen in water + @atom:hx 1.008 # H bonded to C next to positively charged group + @atom:f 19.00 # Fluorine + @atom:cl 35.45 # Chlorine + @atom:br 79.90 # Bromine + @atom:i 126.9 # Iodine + @atom:n 14.01 # Sp2 nitrogen in amide groups + @atom:n1 14.01 # Sp N + @atom:n2 14.01 # aliphatic Sp2 N with two connected atoms + @atom:n3 14.01 # Sp3 N with three connected atoms + @atom:n4 14.01 # Sp3 N with four connected atoms + @atom:na 14.01 # Sp2 N with three connected atoms + @atom:nb 14.01 # Sp2 N in pure aromatic systems + @atom:nc 14.01 # Sp2 N in non-pure aromatic systems + @atom:nd 14.01 # Sp2 N in non-pure aromatic systems, identical to nc + @atom:ne 14.01 # Inner Sp2 N in conjugated systems + @atom:nf 14.01 # Inner Sp2 N in conjugated systems, identical to ne + @atom:nh 14.01 # Amine N connected one or more aromatic rings + @atom:no 14.01 # Nitro N + @atom:ns 14.01 # amind N, with 1 attached hydrogen atom + @atom:nt 14.01 # amide N, with 2 attached hydrogen atoms + @atom:nx 14.01 # like n4, but only has one hydrogen atom + @atom:ny 14.01 # like n4, but only has two hydrogen atoms + @atom:nz 14.01 # like n4, but only has three three hydrogen atoms + @atom:n+ 14.01 # NH4+ + @atom:nu 14.01 # like nh, but only has one attached hydrogen atom + @atom:nv 14.01 # like nh, but only has two attached hydrogen atoms + @atom:n7 14.01 # like n3, but only has one attached hydrogen atom + @atom:n8 14.01 # like n3, but only has two attached hydrogen atoms + @atom:n9 14.01 # NH3 + @atom:o 16.00 # Oxygen with one connected atom + @atom:oh 16.00 # Oxygen in hydroxyl group + @atom:os 16.00 # Ether and ester oxygen + @atom:ow 16.00 # Oxygen in water + @atom:p2 30.97 # Phosphate with two connected atoms + @atom:p3 30.97 # Phosphate with three connected atoms, such as PH3 + @atom:p4 30.97 # Phosphate with three connected atoms, such as O=P(CH3)2 + @atom:p5 30.97 # Phosphate with four connected atoms, such as O=P(OH)3 + @atom:pb 30.97 # Sp2 P in pure aromatic systems + @atom:pc 30.97 # Sp2 P in non-pure aromatic systems + @atom:pd 30.97 # Sp2 P in non-pure aromatic systems, identical to pc + @atom:pe 30.97 # Inner Sp2 P in conjugated systems + @atom:pf 30.97 # Inner Sp2 P in conjugated systems, identical to pe + @atom:px 30.97 # Special p4 in conjugated systems + @atom:py 30.97 # Special p5 in conjugated systems + @atom:s 32.06 # S with one connected atom + @atom:s2 32.06 # S with two connected atom, involved at least one double bond + @atom:s4 32.06 # S with three connected atoms + @atom:s6 32.06 # S with four connected atoms + @atom:sh 32.06 # Sp3 S connected with hydrogen + @atom:ss 32.06 # Sp3 S in thio-ester and thio-ether + @atom:sx 32.06 # Special s4 in conjugated systems + @atom:sy 32.06 # Special s6 in conjugated systems + } # (end of masses) + + write_once("In Settings") { + pair_coeff @atom:hc @atom:hc lj/charmm/coul/long 0.0208 2.60017699876 + pair_coeff @atom:ha @atom:ha lj/charmm/coul/long 0.0161 2.62547852236 + pair_coeff @atom:hn @atom:hn lj/charmm/coul/long 0.0100 1.10649620793 + pair_coeff @atom:ho @atom:ho lj/charmm/coul/long 0.0047 0.537924646013 + pair_coeff @atom:hs @atom:hs lj/charmm/coul/long 0.0124 1.08903459305 + pair_coeff @atom:hp @atom:hp lj/charmm/coul/long 0.0144 1.07460203382 + pair_coeff @atom:o @atom:o lj/charmm/coul/long 0.1463 3.04812087425 + pair_coeff @atom:os @atom:os lj/charmm/coul/long 0.0726 3.15609779888 + pair_coeff @atom:oh @atom:oh lj/charmm/coul/long 0.0930 3.24287133403 + pair_coeff @atom:c3 @atom:c3 lj/charmm/coul/long 0.1078 3.39770953124 + pair_coeff @atom:c2 @atom:c2 lj/charmm/coul/long 0.0988 3.31521230994 + pair_coeff @atom:c1 @atom:c1 lj/charmm/coul/long 0.1596 3.47895949434 + pair_coeff @atom:n @atom:n lj/charmm/coul/long 0.1636 3.18086478325 + pair_coeff @atom:s @atom:s lj/charmm/coul/long 0.2824 3.53241341743 + pair_coeff @atom:p2 @atom:p2 lj/charmm/coul/long 0.2295 3.6940224449 + pair_coeff @atom:f @atom:f lj/charmm/coul/long 0.0832 3.03422285424 + pair_coeff @atom:cl @atom:cl lj/charmm/coul/long 0.2638 3.46595237305 + pair_coeff @atom:br @atom:br lj/charmm/coul/long 0.3932 3.61259430206 + pair_coeff @atom:i @atom:i lj/charmm/coul/long 0.4955 3.84119891313 + pair_coeff @atom:n1 @atom:n1 lj/charmm/coul/long 0.1098 3.27351824993 + pair_coeff @atom:n2 @atom:n2 lj/charmm/coul/long 0.0941 3.38416787073 + pair_coeff @atom:n3 @atom:n3 lj/charmm/coul/long 0.0858 3.36510263816 + pair_coeff @atom:na @atom:na lj/charmm/coul/long 0.2042 3.20580994736 + pair_coeff @atom:nh @atom:nh lj/charmm/coul/long 0.2150 3.18995195017 + pair_coeff @atom:n+ @atom:n+ lj/charmm/coul/long 0.7828 2.85586493087 + pair_coeff @atom:n9 @atom:n9 lj/charmm/coul/long 0.0095 4.04468018036 + pair_coeff @atom:h1 @atom:h1 lj/charmm/coul/long 0.0208 2.42199725514 + pair_coeff @atom:h2 @atom:h2 lj/charmm/coul/long 0.0208 2.24381751151 + pair_coeff @atom:h3 @atom:h3 lj/charmm/coul/long 0.0208 2.06563776788 + pair_coeff @atom:hx @atom:hx lj/charmm/coul/long 0.0208 1.88745802425 + pair_coeff @atom:h4 @atom:h4 lj/charmm/coul/long 0.0161 2.53638865055 + pair_coeff @atom:h5 @atom:h5 lj/charmm/coul/long 0.0161 2.44729877873 + pair_coeff @atom:cx @atom:cx lj/charmm/coul/long 0.1078 3.39770953124 + pair_coeff @atom:cy @atom:cy lj/charmm/coul/long 0.1078 3.39770953124 + pair_coeff @atom:c @atom:c lj/charmm/coul/long 0.0988 3.31521230994 + pair_coeff @atom:cs @atom:cs lj/charmm/coul/long 0.0988 3.31521230994 + pair_coeff @atom:ca @atom:ca lj/charmm/coul/long 0.0988 3.31521230994 + pair_coeff @atom:cc @atom:cc lj/charmm/coul/long 0.0988 3.31521230994 + pair_coeff @atom:cd @atom:cd lj/charmm/coul/long 0.0988 3.31521230994 + pair_coeff @atom:ce @atom:ce lj/charmm/coul/long 0.0988 3.31521230994 + pair_coeff @atom:cf @atom:cf lj/charmm/coul/long 0.0988 3.31521230994 + pair_coeff @atom:cp @atom:cp lj/charmm/coul/long 0.0988 3.31521230994 + pair_coeff @atom:cq @atom:cq lj/charmm/coul/long 0.0988 3.31521230994 + pair_coeff @atom:cz @atom:cz lj/charmm/coul/long 0.0988 3.31521230994 + pair_coeff @atom:cg @atom:cg lj/charmm/coul/long 0.1596 3.47895949434 + pair_coeff @atom:ch @atom:ch lj/charmm/coul/long 0.1596 3.47895949434 + pair_coeff @atom:cu @atom:cu lj/charmm/coul/long 0.0988 3.31521230994 + pair_coeff @atom:cv @atom:cv lj/charmm/coul/long 0.0988 3.31521230994 + pair_coeff @atom:nb @atom:nb lj/charmm/coul/long 0.0941 3.38416787073 + pair_coeff @atom:nc @atom:nc lj/charmm/coul/long 0.0941 3.38416787073 + pair_coeff @atom:nd @atom:nd lj/charmm/coul/long 0.0941 3.38416787073 + pair_coeff @atom:ne @atom:ne lj/charmm/coul/long 0.0941 3.38416787073 + pair_coeff @atom:nf @atom:nf lj/charmm/coul/long 0.0941 3.38416787073 + pair_coeff @atom:no @atom:no lj/charmm/coul/long 0.0858 3.36510263816 + pair_coeff @atom:n7 @atom:n7 lj/charmm/coul/long 0.0522 3.50764643306 + pair_coeff @atom:n8 @atom:n8 lj/charmm/coul/long 0.0323 3.65019022796 + pair_coeff @atom:n4 @atom:n4 lj/charmm/coul/long 3.8748 2.49950544361 + pair_coeff @atom:nx @atom:nx lj/charmm/coul/long 2.5453 2.58859531543 + pair_coeff @atom:ny @atom:ny lj/charmm/coul/long 1.6959 2.67768518724 + pair_coeff @atom:nz @atom:nz lj/charmm/coul/long 1.1450 2.76677505906 + pair_coeff @atom:ns @atom:ns lj/charmm/coul/long 0.1174 3.26995465506 + pair_coeff @atom:nt @atom:nt lj/charmm/coul/long 0.0851 3.35904452688 + pair_coeff @atom:nu @atom:nu lj/charmm/coul/long 0.1545 3.27904182199 + pair_coeff @atom:nv @atom:nv lj/charmm/coul/long 0.1120 3.3681316938 + pair_coeff @atom:s2 @atom:s2 lj/charmm/coul/long 0.2824 3.53241341743 + pair_coeff @atom:s4 @atom:s4 lj/charmm/coul/long 0.2824 3.53241341743 + pair_coeff @atom:s6 @atom:s6 lj/charmm/coul/long 0.2824 3.53241341743 + pair_coeff @atom:sx @atom:sx lj/charmm/coul/long 0.2824 3.53241341743 + pair_coeff @atom:sy @atom:sy lj/charmm/coul/long 0.2824 3.53241341743 + pair_coeff @atom:sh @atom:sh lj/charmm/coul/long 0.2824 3.53241341743 + pair_coeff @atom:ss @atom:ss lj/charmm/coul/long 0.2824 3.53241341743 + pair_coeff @atom:p3 @atom:p3 lj/charmm/coul/long 0.2295 3.6940224449 + pair_coeff @atom:p4 @atom:p4 lj/charmm/coul/long 0.2295 3.6940224449 + pair_coeff @atom:p5 @atom:p5 lj/charmm/coul/long 0.2295 3.6940224449 + pair_coeff @atom:pb @atom:pb lj/charmm/coul/long 0.2295 3.6940224449 + pair_coeff @atom:px @atom:px lj/charmm/coul/long 0.2295 3.6940224449 + pair_coeff @atom:py @atom:py lj/charmm/coul/long 0.2295 3.6940224449 + pair_coeff @atom:pc @atom:pc lj/charmm/coul/long 0.2295 3.6940224449 + pair_coeff @atom:pd @atom:pd lj/charmm/coul/long 0.2295 3.6940224449 + pair_coeff @atom:pe @atom:pe lj/charmm/coul/long 0.2295 3.6940224449 + pair_coeff @atom:pf @atom:pf lj/charmm/coul/long 0.2295 3.6940224449 + } # (end of pair_coeffs) + + write_once("In Settings") { + bond_coeff @bond:ow-hw harmonic 612.98 0.957 # TIP3P_Water 1 + bond_coeff @bond:hw-hw harmonic 15.17 1.514 # TIP3P_Water 1 + bond_coeff @bond:br-br harmonic 81.01 2.542 # SOURCE1 4 + bond_coeff @bond:br-c1 harmonic 227.01 1.787 # SOURCE2 4 0.0024 + bond_coeff @bond:br-c2 harmonic 168.91 1.893 # SOURCE1_SOURCE5 25 0.0078 + bond_coeff @bond:br-c harmonic 146.48 1.946 # SOURCE2 2 0.0285 + bond_coeff @bond:br-c3 harmonic 134.73 1.978 # SOURCE1_SOURCE5 146 0.0118 + bond_coeff @bond:br-ca harmonic 162.15 1.908 # SOURCE1_SOURCE5 462 0.0052 + bond_coeff @bond:br-cc harmonic 172.53 1.885 # SOURCE4_SOURCE5 128 0.0078 + bond_coeff @bond:br-cx harmonic 154.63 1.926 # SOURCE1_SOURCE5 11 0.0019 + bond_coeff @bond:br-n1 harmonic 141.51 1.860 # SOUECE3 1 + bond_coeff @bond:br-n2 harmonic 88.47 2.038 # SOURCE3 5 0.1082 + bond_coeff @bond:br-n harmonic 136.53 1.873 # SOURCE3 4 0.0046 + bond_coeff @bond:br-n3 harmonic 110.41 1.952 # SOURCE3 2 + bond_coeff @bond:br-n4 harmonic 118.29 1.926 # SOURCE3 3 0.0013 + bond_coeff @bond:br-na harmonic 96.95 2.002 # SOURCE3 7 0.2156 + bond_coeff @bond:br-nh harmonic 112.77 1.944 # SOURCE3 1 + bond_coeff @bond:br-no harmonic 75.65 2.101 # SOURCE3 1 + bond_coeff @bond:br-o harmonic 193.58 1.800 # SOUECE3 1 + bond_coeff @bond:br-oh harmonic 160.87 1.866 # SOURCE3 1 + bond_coeff @bond:br-os harmonic 151.88 1.887 # SOURCE3 2 + bond_coeff @bond:br-p2 harmonic 133.12 2.210 # SOURCE3 9 0.0510 + bond_coeff @bond:br-p3 harmonic 126.80 2.231 # SOURCE3 3 0.0101 + bond_coeff @bond:br-p4 harmonic 145.88 2.171 # SOUECE3 1 + bond_coeff @bond:br-p5 harmonic 137.54 2.196 # SOURCE3 3 0.0099 + bond_coeff @bond:br-s harmonic 169.20 2.220 # SOUECE3 1 + bond_coeff @bond:br-s4 harmonic 128.80 2.341 # SOURCE3 1 + bond_coeff @bond:br-s6 harmonic 171.57 2.214 # SOURCE3 3 0.0443 + bond_coeff @bond:br-sh harmonic 173.58 2.209 # SOURCE3 1 + bond_coeff @bond:br-ss harmonic 176.02 2.203 # SOURCE3 3 0.0035 + bond_coeff @bond:c1-c1 harmonic 837.28 1.198 # SOURCE1_SOURCE5 659 0.0039 + bond_coeff @bond:c1-c2 harmonic 535.85 1.307 # SOURCE1 18 + bond_coeff @bond:c1-c3 harmonic 295.86 1.467 # SOURCE1_SOURCE5 795 0.0034 + bond_coeff @bond:c1-ca harmonic 325.62 1.440 # SOUECE3 1 + bond_coeff @bond:c1-ce harmonic 518.69 1.315 # SOURCE4 6 0.0086 + bond_coeff @bond:c1-cg harmonic 776.82 1.216 # SOURCE3_SOURCE5 179 0.0036 + bond_coeff @bond:c1-ch harmonic 765.43 1.219 # SOURCE3_SOURCE5 13 0.0016 + bond_coeff @bond:c1-cl harmonic 261.49 1.631 # SOURCE2 6 0.0050 + bond_coeff @bond:c1-cx harmonic 320.55 1.444 # SOURCE1_SOURCE5 24 0.0043 + bond_coeff @bond:c1-f harmonic 482.19 1.270 # SOURCE2 2 0.0085 + bond_coeff @bond:c1-ha harmonic 433.72 1.067 # SOURCE3_SOURCE5 343 0.0013 + bond_coeff @bond:c1-hc harmonic 448.21 1.060 # SOUECE3 1 + bond_coeff @bond:c1-i harmonic 153.51 1.989 # SOURCE2 4 0.0032 + bond_coeff @bond:c1-n1 harmonic 891.54 1.153 # SOURCE1_SOURCE5 481 0.0035 + bond_coeff @bond:c1-n2 harmonic 736.75 1.197 # SOURCE3_SOURCE5 36 0.0076 + bond_coeff @bond:c1-n3 harmonic 400.99 1.347 # SOURCE2_SOURCE5 10 0.0093 + bond_coeff @bond:c1-n4 harmonic 309.65 1.417 # SOURCE3 3 0.0032 + bond_coeff @bond:c1-n harmonic 428.86 1.330 # SOUECE3 1 + bond_coeff @bond:c1-na harmonic 379.52 1.362 # SOURCE3 8 0.0034 + bond_coeff @bond:c1-ne harmonic 720.51 1.202 # SOURCE4_SOURCE5 31 0.0124 + bond_coeff @bond:c1-nf harmonic 720.51 1.202 # SOURCE4_SOURCE5 21 0.0141 + bond_coeff @bond:c1-nh harmonic 409.04 1.342 # SOURCE4_SOURCE5 33 0.0061 + bond_coeff @bond:c1-no harmonic 323.48 1.405 # SOURCE3 3 0.0005 + bond_coeff @bond:c1-o harmonic 794.98 1.172 # SOURCE2_SOURCE5 31 0.0068 + bond_coeff @bond:c1-oh harmonic 422.21 1.326 # SOURCE3 1 + bond_coeff @bond:c1-os harmonic 435.38 1.318 # SOURCE3_SOURCE5 8 0.0079 + bond_coeff @bond:c1-p2 harmonic 215.98 1.770 # SOUECE3 1 + bond_coeff @bond:c1-p3 harmonic 203.86 1.790 # SOUECE3 1 + bond_coeff @bond:c1-p4 harmonic 203.86 1.790 # SOUECE3 1 + bond_coeff @bond:c1-p5 harmonic 226.96 1.753 # SOURCE3 2 + bond_coeff @bond:c1-s2 harmonic 380.51 1.595 # SOURCE3 1 + bond_coeff @bond:c1-s harmonic 370.61 1.603 # SOURCE1_SOURCE5 37 0.0043 + bond_coeff @bond:c1-s4 harmonic 239.03 1.746 # SOURCE3 2 + bond_coeff @bond:c1-s6 harmonic 256.65 1.722 # SOURCE3 2 + bond_coeff @bond:c1-sh harmonic 291.39 1.680 # SOUECE3 1 + bond_coeff @bond:c1-ss harmonic 282.80 1.690 # SOURCE1_SOURCE5 49 0.0113 + bond_coeff @bond:c2-c2 harmonic 481.83 1.334 # SOURCE1_SOURCE5 3727 0.0053 + bond_coeff @bond:c2-c3 harmonic 255.56 1.510 # SOURCE1_SOURCE5 10204 0.0042 + bond_coeff @bond:c2-ca harmonic 398.37 1.385 # SOUECE3_SOURCE5 9 0.0149 + bond_coeff @bond:c2-cc harmonic 437.98 1.359 # SOURCE1_SOURCE5 882 0.0181 + bond_coeff @bond:c2-cd harmonic 437.98 1.359 # SOURCE1_SOURCE5 882 0.0181 + bond_coeff @bond:c2-ce harmonic 460.51 1.346 # SOURCE3_SOURCE5 3239 0.0058 + bond_coeff @bond:c2-cf harmonic 460.51 1.346 # SOURCE3_SOURCE5 3177 0.0057 + bond_coeff @bond:c2-cl harmonic 192.70 1.731 # SOURCE1_SOURCE5 290 0.0098 + bond_coeff @bond:c2-cu harmonic 500.05 1.325 # SOURCE2_SOURCE5 11 0.0010 + bond_coeff @bond:c2-cx harmonic 278.37 1.485 # SOURCE4_SOURCE5 102 0.0061 + bond_coeff @bond:c2-cy harmonic 255.91 1.509 # SOURCE4_SOURCE5 30 0.0063 + bond_coeff @bond:c2-f harmonic 368.08 1.339 # SOURCE1_SOURCE5 35 0.0085 + bond_coeff @bond:c2-h4 harmonic 394.23 1.087 # SOURCE3_SOURCE5 517 0.0028 + bond_coeff @bond:c2-h5 harmonic 386.13 1.091 # SOURCE4_SOURCE5 116 0.0021 + bond_coeff @bond:c2-ha harmonic 392.18 1.088 # SOURCE3_SOURCE5 5991 0.0019 + bond_coeff @bond:c2-hc harmonic 393.86 1.087 # SOURCE3 789 0.0046 + bond_coeff @bond:c2-hx harmonic 401.39 1.083 # SOURCE3 3 0.0008 + bond_coeff @bond:c2-i harmonic 98.09 2.170 # SOURCE3_SOURCE5 7 0.0194 + bond_coeff @bond:c2-n1 harmonic 470.94 1.306 # SOURCE3 4 0.0161 + bond_coeff @bond:c2-n2 harmonic 518.67 1.282 # SOURCE1_SOURCE5 1004 0.0051 + bond_coeff @bond:c2-n3 harmonic 412.66 1.340 # SOUECE3 1 + bond_coeff @bond:c2-n harmonic 330.19 1.399 # SOURCE3_SOURCE5 174 0.0100 + bond_coeff @bond:c2-n4 harmonic 221.45 1.512 # SOURCE3_SOURCE5 21 0.0133 + bond_coeff @bond:c2-na harmonic 327.66 1.401 # SOURCE3_SOURCE5 65 0.0179 + bond_coeff @bond:c2-nc harmonic 458.17 1.313 # SOURCE1 99 0.0095 + bond_coeff @bond:c2-nd harmonic 458.17 1.313 # SOURCE1 99 + bond_coeff @bond:c2-ne harmonic 498.75 1.292 # SOURCE3_SOURCE5 310 0.0099 + bond_coeff @bond:c2-nf harmonic 498.75 1.292 # SOURCE3_SOURCE5 273 0.0098 + bond_coeff @bond:c2-nh harmonic 345.39 1.387 # SOURCE3_SOURCE5 1559 0.0120 + bond_coeff @bond:c2-no harmonic 276.95 1.448 # SOURCE4_SOURCE5 27 0.0139 + bond_coeff @bond:c2-o harmonic 635.23 1.225 # SOURCE4_SOURCE5 35 0.0033 + bond_coeff @bond:c2-oh harmonic 402.33 1.339 # SOURCE1_SOURCE5 85 0.0126 + bond_coeff @bond:c2-os harmonic 371.26 1.360 # SOURCE1_SOURCE5 548 0.0107 + bond_coeff @bond:c2-p2 harmonic 292.48 1.669 # SOURCE3_SOURCE5 87 0.0126 + bond_coeff @bond:c2-p3 harmonic 179.93 1.834 # SOURCE3 5 0.0042 + bond_coeff @bond:c2-p4 harmonic 186.11 1.822 # SOUECE3 1 + bond_coeff @bond:c2-p5 harmonic 166.18 1.863 # SOURCE4_SOURCE5 15 0.0083 + bond_coeff @bond:c2-pe harmonic 275.11 1.689 # SOURCE3_SOURCE5 60 0.0472 + bond_coeff @bond:c2-pf harmonic 275.11 1.689 # SOURCE3_SOURCE5 8 0.0019 + bond_coeff @bond:c2-s2 harmonic 362.64 1.610 # SOURCE2 1 + bond_coeff @bond:c2-s harmonic 247.65 1.734 # SOURCE3 4 0.0034 + bond_coeff @bond:c2-s4 harmonic 229.42 1.760 # SOUECE3 1 + bond_coeff @bond:c2-s6 harmonic 229.42 1.760 # SOUECE3 1 + bond_coeff @bond:c2-sh harmonic 215.23 1.782 # SOURCE4_SOURCE5 13 0.0077 + bond_coeff @bond:c2-ss harmonic 246.19 1.736 # SOURCE1 209 0.0155 + bond_coeff @bond:c3-c3 harmonic 232.52 1.538 # SOURCE1_SOURCE5 88072 0.0058 + bond_coeff @bond:c3-ca harmonic 250.32 1.516 # SOURCE1_SOURCE5 10699 0.0054 + bond_coeff @bond:c3-cc harmonic 262.64 1.502 # SOURCE3_SOURCE5 3926 0.0049 + bond_coeff @bond:c3-cd harmonic 262.64 1.502 # SOURCE3_SOURCE5 3926 0.0049 + bond_coeff @bond:c3-ce harmonic 250.06 1.516 # SOURCE3_SOURCE5 1210 0.0060 + bond_coeff @bond:c3-cf harmonic 250.23 1.516 # SOURCE3_SOURCE5 345 0.0071 + bond_coeff @bond:c3-cl harmonic 155.52 1.804 # SOURCE1_SOURCE5 1173 0.0119 + bond_coeff @bond:c3-cu harmonic 284.82 1.478 # SOURCE1 7 + bond_coeff @bond:c3-cv harmonic 274.17 1.489 # SOURCE1 11 + bond_coeff @bond:c3-cx harmonic 247.95 1.518 # SOURCE1_SOURCE5 1561 0.0054 + bond_coeff @bond:c3-cy harmonic 236.93 1.532 # SOURCE1_SOURCE5 522 0.0055 + bond_coeff @bond:c3-f harmonic 352.65 1.350 # SOURCE1_SOURCE5 2188 0.0139 + bond_coeff @bond:c3-h1 harmonic 375.92 1.097 # SOURCE3_SOURCE5 112144 0.0055 + bond_coeff @bond:c3-h2 harmonic 377.33 1.096 # SOURCE3_SOURCE5 2681 0.0032 + bond_coeff @bond:c3-h3 harmonic 379.47 1.095 # SOURCE4_SOURCE5 64 0.0028 + bond_coeff @bond:c3-hc harmonic 375.92 1.097 # SOURCE3_SOURCE5 133628 0.0015 + bond_coeff @bond:c3-hx harmonic 386.49 1.091 # SOURCE3_SOURCE5 6495 0.0022 + bond_coeff @bond:c3-i harmonic 88.97 2.212 # SOURCE1_SOURCE5 35 0.0128 + bond_coeff @bond:c3-n1 harmonic 292.28 1.433 # SOURCE3_SOURCE5 7 0.0033 + bond_coeff @bond:c3-n2 harmonic 259.91 1.466 # SOURCE1_SOURCE5 816 0.0087 + bond_coeff @bond:c3-n harmonic 263.77 1.462 # SOURCE1_SOURCE5 4576 0.0061 + bond_coeff @bond:c3-n3 harmonic 261.19 1.465 # SOURCE1_SOURCE5 15206 0.0039 + bond_coeff @bond:c3-n4 harmonic 222.58 1.511 # SOURCE1_SOURCE5 2375 0.0125 + bond_coeff @bond:c3-na harmonic 262.85 1.463 # SOURCE3_SOURCE5 1732 0.0077 + bond_coeff @bond:c3-nc harmonic 269.31 1.456 # SOURCE3 9 0.0109 + bond_coeff @bond:c3-nd harmonic 269.31 1.456 # SOURCE3 9 + bond_coeff @bond:c3-nh harmonic 261.84 1.464 # SOURCE3_SOURCE5 3492 0.0064 + bond_coeff @bond:c3-no harmonic 206.37 1.533 # SOURCE1_SOURCE5 150 0.0187 + bond_coeff @bond:c3-o harmonic 438.11 1.317 # SOURCE4 8 0.0193 + bond_coeff @bond:c3-oh harmonic 293.40 1.423 # SOURCE1_SOURCE5 8884 0.0067 + bond_coeff @bond:c3-os harmonic 284.76 1.432 # SOURCE1_SOURCE5 17971 0.0103 + bond_coeff @bond:c3-p2 harmonic 169.71 1.855 # SOURCE3 9 0.0125 + bond_coeff @bond:c3-p3 harmonic 168.21 1.858 # SOURCE3_SOURCE5 221 0.0094 + bond_coeff @bond:c3-p4 harmonic 177.58 1.839 # SOURCE3_SOURCE5 45 0.0106 + bond_coeff @bond:c3-p5 harmonic 177.19 1.839 # SOURCE1_SOURCE5 408 0.0183 + bond_coeff @bond:c3-px harmonic 182.68 1.829 # SOURCE3_SOURCE5 35 0.0083 + bond_coeff @bond:c3-py harmonic 177.09 1.840 # SOURCE3_SOURCE5 39 0.0126 + bond_coeff @bond:c3-s harmonic 180.03 1.845 # SOURCE3 4 0.0185 + bond_coeff @bond:c3-s4 harmonic 187.48 1.831 # SOURCE1_SOURCE5 326 0.0096 + bond_coeff @bond:c3-s6 harmonic 200.07 1.808 # SOURCE1_SOURCE5 644 0.0143 + bond_coeff @bond:c3-sh harmonic 180.78 1.843 # SOURCE3_SOURCE5 189 0.0058 + bond_coeff @bond:c3-ss harmonic 182.96 1.839 # SOURCE1_SOURCE5 2732 0.0105 + bond_coeff @bond:c3-sx harmonic 181.64 1.842 # SOURCE3_SOURCE5 99 0.0121 + bond_coeff @bond:c3-sy harmonic 199.39 1.809 # SOURCE3_SOURCE5 162 0.0094 + bond_coeff @bond:ca-ca harmonic 378.57 1.398 # SOURCE1_SOURCE5 121206 0.0061 + bond_coeff @bond:ca-cc harmonic 308.19 1.456 # SOURCE1_SOURCE5 2424 0.0121 + bond_coeff @bond:ca-cd harmonic 308.19 1.456 # SOURCE1_SOURCE5 2424 0.0121 + bond_coeff @bond:ca-ce harmonic 286.51 1.476 # SOURCE1_SOURCE5 1750 0.0089 + bond_coeff @bond:ca-cf harmonic 286.51 1.476 # SOURCE1_SOURCE5 1750 0.0089 + bond_coeff @bond:ca-cg harmonic 334.12 1.433 # SOURCE1_SOURCE5 318 0.0029 + bond_coeff @bond:ca-ch harmonic 334.12 1.433 # SOURCE1_SOURCE5 318 0.0029 + bond_coeff @bond:ca-cl harmonic 181.97 1.750 # SOURCE1_SOURCE5 2919 0.0059 + bond_coeff @bond:ca-cp harmonic 368.44 1.406 # CORR_SOURCE5 2042 0.0049 + bond_coeff @bond:ca-cq harmonic 368.44 1.406 # CORR_SOURCE5 2042 0.0049 + bond_coeff @bond:ca-cx harmonic 273.13 1.490 # SOURCE1_SOURCE5 165 0.0091 + bond_coeff @bond:ca-cy harmonic 250.49 1.515 # SOURCE4_SOURCE5 35 0.0055 + bond_coeff @bond:ca-f harmonic 353.59 1.349 # SOURCE1_SOURCE5 1239 0.0057 + bond_coeff @bond:ca-h4 harmonic 390.15 1.089 # SOURCE3_SOURCE5 2643 0.0010 + bond_coeff @bond:ca-h5 harmonic 392.37 1.088 # SOURCE3_SOURCE5 299 0.0007 + bond_coeff @bond:ca-ha harmonic 395.72 1.086 # SOURCE3_SOURCE5 65456 0.0010 + bond_coeff @bond:ca-i harmonic 108.27 2.129 # SOURCE1_SOURCE5 61 0.0076 + bond_coeff @bond:ca-n1 harmonic 420.66 1.335 # SOURCE3_SOURCE5 6 0.0078 + bond_coeff @bond:ca-n2 harmonic 476.53 1.303 # SOURCE4 7 0.0058 + bond_coeff @bond:ca-n harmonic 315.21 1.412 # SOURCE3_SOURCE5 1254 0.0090 + bond_coeff @bond:ca-n4 harmonic 244.03 1.484 # SOURCE1_SOURCE5 28 0.0065 + bond_coeff @bond:ca-na harmonic 349.52 1.384 # SOURCE1_SOURCE5 2751 0.0095 + bond_coeff @bond:ca-nb harmonic 414.24 1.339 # SOURCE3_SOURCE5 6806 0.0055 + bond_coeff @bond:ca-nc harmonic 394.62 1.352 # SOURCE1_SOURCE5 2672 0.0030 + bond_coeff @bond:ca-nd harmonic 394.62 1.352 # SOURCE1_SOURCE5 2672 0.0030 + bond_coeff @bond:ca-ne harmonic 320.07 1.408 # SOURCE1_SOURCE5 276 0.0093 + bond_coeff @bond:ca-nf harmonic 320.07 1.408 # SOURCE1_SOURCE5 276 0.0093 + bond_coeff @bond:ca-nh harmonic 347.06 1.386 # SOURCE1_SOURCE5 2785 0.0134 + bond_coeff @bond:ca-no harmonic 257.38 1.469 # SOURCE1_SOURCE5 454 0.0049 + bond_coeff @bond:ca-o harmonic 606.45 1.236 # SOURCE4_SOURCE5 17 0.0088 + bond_coeff @bond:ca-oh harmonic 365.55 1.364 # SOURCE1_SOURCE5 3637 0.0062 + bond_coeff @bond:ca-os harmonic 357.53 1.370 # SOURCE1_SOURCE5 6900 0.0064 + bond_coeff @bond:ca-p2 harmonic 176.94 1.840 # SOUECE3 1 + bond_coeff @bond:ca-p3 harmonic 184.18 1.826 # SOURCE1_SOURCE5 156 0.0180 + bond_coeff @bond:ca-p4 harmonic 194.74 1.806 # SOUECE3 1 + bond_coeff @bond:ca-p5 harmonic 200.84 1.795 # SOURCE1_SOURCE5 577 0.0028 + bond_coeff @bond:ca-pe harmonic 182.48 1.829 # SOURCE3 10 0.0042 + bond_coeff @bond:ca-pf harmonic 182.48 1.829 # SOURCE3 10 0.0042 + bond_coeff @bond:ca-px harmonic 184.54 1.825 # SOURCE3 5 0.0168 + bond_coeff @bond:ca-py harmonic 189.18 1.816 # SOURCE4_SOURCE5 34 0.0098 + bond_coeff @bond:ca-s harmonic 244.02 1.739 # SOURCE3 2 + bond_coeff @bond:ca-s4 harmonic 211.54 1.788 # SOURCE1 51 0.0048 + bond_coeff @bond:ca-s6 harmonic 224.85 1.767 # SOURCE1_SOURCE5 258 0.0041 + bond_coeff @bond:ca-sh harmonic 215.91 1.781 # SOURCE4_SOURCE5 40 0.0053 + bond_coeff @bond:ca-ss harmonic 216.10 1.781 # SOURCE1_SOURCE5 1016 0.0068 + bond_coeff @bond:ca-sx harmonic 190.35 1.825 # SOURCE4_SOURCE5 90 0.0050 + bond_coeff @bond:ca-sy harmonic 209.78 1.791 # SOURCE3_SOURCE5 703 0.0076 + bond_coeff @bond:c-c1 harmonic 303.33 1.460 # SOUECE3 1 + bond_coeff @bond:c-c2 harmonic 368.17 1.406 # SOURCE3 2 0.0370 + bond_coeff @bond:c-c harmonic 224.38 1.548 # SOURCE1_SOURCE5 254 0.0090 + bond_coeff @bond:c-c3 harmonic 243.22 1.524 # SOURCE1_SOURCE5 12697 0.0077 + bond_coeff @bond:c-ca harmonic 272.66 1.491 # SOURCE1_SOURCE5 4357 0.0085 + bond_coeff @bond:c-cc harmonic 295.35 1.468 # SOURCE3_SOURCE5 1864 0.0130 + bond_coeff @bond:cc-cc harmonic 340.18 1.428 # SOURCE1_SOURCE5 4559 0.0096 + bond_coeff @bond:cc-cd harmonic 416.13 1.373 # SOURCE3_SOURCE5 8451 0.0091 + bond_coeff @bond:cc-ce harmonic 309.82 1.454 # CORR_SOURCE5 396 0.0089 + bond_coeff @bond:cc-cf harmonic 427.69 1.366 # CORR_SOURCE5 156 0.0107 + bond_coeff @bond:cc-cg harmonic 342.76 1.426 # SOURCE1_SOURCE5 109 0.0049 + bond_coeff @bond:cc-ch harmonic 341.16 1.427 # SOURCE1 560 + bond_coeff @bond:cc-cl harmonic 190.08 1.735 # CORR_SOURCE5 137 0.0076 + bond_coeff @bond:cc-cx harmonic 290.53 1.472 # CORR_SOURCE5 37 0.0035 + bond_coeff @bond:c-cd harmonic 295.35 1.468 # SOURCE3_SOURCE5 1864 0.0130 + bond_coeff @bond:c-ce harmonic 280.40 1.482 # SOURCE1_SOURCE5 3022 0.0115 + bond_coeff @bond:c-cf harmonic 280.40 1.482 # SOURCE1_SOURCE5 3022 0.0115 + bond_coeff @bond:cc-f harmonic 364.99 1.341 # SOURCE4_SOURCE5 70 0.0039 + bond_coeff @bond:c-cg harmonic 312.91 1.451 # SOURCE3_SOURCE5 11 0.0089 + bond_coeff @bond:c-ch harmonic 312.91 1.451 # SOURCE3_SOURCE5 11 0.0089 + bond_coeff @bond:cc-h4 harmonic 403.88 1.082 # SOURCE3_SOURCE5 4457 0.0016 + bond_coeff @bond:cc-h5 harmonic 403.49 1.082 # SOURCE3_SOURCE5 879 0.0012 + bond_coeff @bond:cc-ha harmonic 400.06 1.084 # SOURCE3_SOURCE5 4706 0.0018 + bond_coeff @bond:c-cl harmonic 156.23 1.803 # SOURCE3_SOURCE5 16 0.0187 + bond_coeff @bond:cc-n2 harmonic 500.74 1.290 # CORR_SOURCE5 156 0.0074 + bond_coeff @bond:cc-n harmonic 353.83 1.381 # SOURCE3_SOURCE5 1142 0.0085 + bond_coeff @bond:cc-n4 harmonic 236.72 1.493 # SOURCE4 7 0.0148 + bond_coeff @bond:cc-na harmonic 354.49 1.380 # SOURCE3_SOURCE5 6739 0.0088 + bond_coeff @bond:cc-nc harmonic 369.10 1.369 # SOURCE1_SOURCE5 2269 0.0086 + bond_coeff @bond:cc-nd harmonic 450.71 1.317 # SOURCE3_SOURCE5 4612 0.0083 + bond_coeff @bond:cc-ne harmonic 356.61 1.379 # SOURCE4_SOURCE5 82 0.0119 + bond_coeff @bond:cc-nf harmonic 485.08 1.298 # CORR_SOURCE5 41 0.0113 + bond_coeff @bond:cc-nh harmonic 363.47 1.373 # SOURCE3_SOURCE5 976 0.0106 + bond_coeff @bond:cc-no harmonic 296.62 1.429 # SOURCE4_SOURCE5 386 0.0074 + bond_coeff @bond:cc-oh harmonic 389.45 1.347 # CORR_SOURCE5 248 0.0073 + bond_coeff @bond:cc-os harmonic 367.90 1.362 # SOURCE3_SOURCE5 1859 0.0083 + bond_coeff @bond:cc-pd harmonic 240.75 1.733 # SOURCE3 84 0.0161 + bond_coeff @bond:cc-sh harmonic 223.28 1.769 # SOURCE4_SOURCE5 22 0.0030 + bond_coeff @bond:cc-ss harmonic 231.98 1.756 # SOURCE3_SOURCE5 2011 0.0134 + bond_coeff @bond:cc-sx harmonic 198.26 1.811 # SOURCE4_SOURCE5 44 0.0033 + bond_coeff @bond:cc-sy harmonic 214.05 1.784 # CORR_SOURCE5 73 0.0082 + bond_coeff @bond:c-cu harmonic 360.20 1.412 # SOURCE2 1 + bond_coeff @bond:c-cx harmonic 265.90 1.498 # SOURCE1_SOURCE5 246 0.0109 + bond_coeff @bond:c-cy harmonic 222.38 1.551 # SOURCE1_SOURCE5 374 0.0059 + bond_coeff @bond:cd-cd harmonic 340.18 1.428 # SOURCE1_SOURCE5 4559 0.0096 + bond_coeff @bond:cd-ce harmonic 427.69 1.366 # CORR_SOURCE5 156 0.0107 + bond_coeff @bond:cd-cf harmonic 309.82 1.454 # CORR_SOURCE5 396 0.0089 + bond_coeff @bond:cd-cg harmonic 341.16 1.427 # SOURCE1 560 + bond_coeff @bond:cd-ch harmonic 342.76 1.426 # SOURCE1_SOURCE5 109 0.0049 + bond_coeff @bond:cd-cl harmonic 190.08 1.735 # CORR_SOURCE5 137 0.0076 + bond_coeff @bond:cd-cx harmonic 290.53 1.472 # CORR_SOURCE5 37 0.0035 + bond_coeff @bond:cd-cy harmonic 259.34 1.505 # SOURCE4_SOURCE5 21 0.0007 + bond_coeff @bond:cd-h4 harmonic 403.88 1.082 # SOURCE3_SOURCE5 4457 0.0016 + bond_coeff @bond:cd-h5 harmonic 403.68 1.082 # SOURCE3_SOURCE5 578 0.0013 + bond_coeff @bond:cd-ha harmonic 400.06 1.084 # SOURCE3_SOURCE5 4706 0.0018 + bond_coeff @bond:cd-n2 harmonic 500.74 1.290 # CORR_SOURCE5 156 0.0074 + bond_coeff @bond:cd-n harmonic 353.83 1.381 # SOURCE3_SOURCE5 1142 0.0085 + bond_coeff @bond:cd-na harmonic 354.49 1.380 # SOURCE3_SOURCE5 6739 0.0088 + bond_coeff @bond:cd-nc harmonic 450.71 1.317 # SOURCE3_SOURCE5 4612 0.0083 + bond_coeff @bond:cd-nd harmonic 369.10 1.369 # SOURCE1_SOURCE5 2269 0.0086 + bond_coeff @bond:cd-ne harmonic 485.08 1.298 # CORR_SOURCE5 41 0.0113 + bond_coeff @bond:cd-nh harmonic 363.47 1.373 # SOURCE3_SOURCE5 976 0.0106 + bond_coeff @bond:cd-oh harmonic 389.45 1.347 # CORR_SOURCE5 248 0.0073 + bond_coeff @bond:cd-os harmonic 367.90 1.362 # SOURCE3_SOURCE5 1859 0.0083 + bond_coeff @bond:cd-pc harmonic 240.75 1.733 # SOURCE3 84 + bond_coeff @bond:cd-ss harmonic 231.98 1.756 # SOURCE3_SOURCE5 2011 0.0134 + bond_coeff @bond:cd-sy harmonic 214.05 1.784 # CORR_SOURCE5 73 0.0082 + bond_coeff @bond:ce-ce harmonic 306.13 1.457 # SOURCE1_SOURCE5 1000 0.0092 + bond_coeff @bond:ce-cf harmonic 452.16 1.351 # SOURCE1_SOURCE5 1908 0.0059 + bond_coeff @bond:ce-cg harmonic 341.16 1.427 # SOURCE1_SOURCE5 238 0.0053 + bond_coeff @bond:ce-ch harmonic 336.29 1.431 # SOURCE1 22 + bond_coeff @bond:ce-cl harmonic 174.72 1.764 # SOURCE4_SOURCE5 90 0.0111 + bond_coeff @bond:ce-cx harmonic 261.83 1.502 # SOURCE4_SOURCE5 31 0.0075 + bond_coeff @bond:ce-cy harmonic 250.06 1.516 # SOURCE4_SOURCE5 53 0.0043 + bond_coeff @bond:ce-h4 harmonic 385.40 1.092 # CORR_SOURCE5 315 0.0033 + bond_coeff @bond:ce-ha harmonic 391.44 1.088 # SOURCE3_SOURCE5 2751 0.0014 + bond_coeff @bond:ce-n1 harmonic 461.59 1.311 # CORR_SOURCE5 16 0.0049 + bond_coeff @bond:ce-n2 harmonic 506.97 1.287 # SOURCE1_SOURCE5 896 0.0038 + bond_coeff @bond:ce-n harmonic 301.69 1.424 # CORR_SOURCE5 209 0.0059 + bond_coeff @bond:ce-na harmonic 305.30 1.421 # SOURCE4_SOURCE5 11 0.0050 + bond_coeff @bond:ce-ne harmonic 336.57 1.394 # SOURCE3_SOURCE5 69 0.0151 + bond_coeff @bond:ce-nf harmonic 489.14 1.296 # CORR_SOURCE5 101 0.0097 + bond_coeff @bond:ce-nh harmonic 341.71 1.390 # CORR_SOURCE5 300 0.0133 + bond_coeff @bond:ce-oh harmonic 384.73 1.350 # CORR_SOURCE5 58 0.0102 + bond_coeff @bond:ce-os harmonic 355.66 1.371 # CORR_SOURCE5 96 0.0128 + bond_coeff @bond:ce-p2 harmonic 190.37 1.814 # SOUECE3 1 + bond_coeff @bond:ce-pe harmonic 188.22 1.818 # SOURCE3 8 0.0108 + bond_coeff @bond:ce-px harmonic 186.64 1.821 # SOURCE3 6 0.0046 + bond_coeff @bond:ce-py harmonic 194.96 1.806 # SOURCE3_SOURCE5 22 0.0142 + bond_coeff @bond:ce-s harmonic 291.39 1.680 # SOUECE3 1 + bond_coeff @bond:ce-ss harmonic 215.60 1.781 # SOURCE4_SOURCE5 56 0.0098 + bond_coeff @bond:ce-sx harmonic 193.92 1.819 # SOURCE3_SOURCE5 30 0.0101 + bond_coeff @bond:ce-sy harmonic 211.48 1.788 # SOURCE3_SOURCE5 41 0.0169 + bond_coeff @bond:c-f harmonic 387.77 1.325 # SOURCE2 6 0.0147 + bond_coeff @bond:cf-cf harmonic 306.13 1.457 # SOURCE1_SOURCE5 1000 0.0092 + bond_coeff @bond:cf-cg harmonic 336.29 1.431 # SOURCE1 22 + bond_coeff @bond:cf-ch harmonic 341.16 1.427 # SOURCE1_SOURCE5 238 0.0053 + bond_coeff @bond:cf-h4 harmonic 385.40 1.092 # CORR_SOURCE5 315 0.0033 + bond_coeff @bond:cf-ha harmonic 391.44 1.088 # SOURCE3_SOURCE5 2751 0.0014 + bond_coeff @bond:cf-n1 harmonic 461.59 1.311 # CORR_SOURCE5 16 0.0049 + bond_coeff @bond:cf-n2 harmonic 506.97 1.287 # SOURCE1_SOURCE5 896 0.0038 + bond_coeff @bond:cf-n harmonic 301.69 1.424 # CORR_SOURCE5 209 0.0059 + bond_coeff @bond:cf-ne harmonic 489.14 1.296 # CORR_SOURCE5 101 0.0097 + bond_coeff @bond:cf-nf harmonic 336.57 1.394 # SOURCE3_SOURCE5 62 0.0156 + bond_coeff @bond:cf-nh harmonic 341.71 1.390 # CORR_SOURCE5 300 0.0133 + bond_coeff @bond:cf-oh harmonic 384.73 1.350 # CORR_SOURCE5 58 0.0102 + bond_coeff @bond:cf-os harmonic 355.66 1.371 # CORR_SOURCE5 96 0.0128 + bond_coeff @bond:cf-p2 harmonic 190.37 1.814 # SOUECE3 1 + bond_coeff @bond:cf-pf harmonic 188.22 1.818 # SOURCE3 8 + bond_coeff @bond:cf-px harmonic 186.64 1.821 # SOURCE3 6 + bond_coeff @bond:cf-py harmonic 194.96 1.806 # SOURCE3_SOURCE5 17 0.0171 + bond_coeff @bond:cf-s harmonic 291.39 1.680 # SOUECE3 1 + bond_coeff @bond:cf-sx harmonic 193.92 1.819 # SOURCE3_SOURCE5 25 0.0105 + bond_coeff @bond:cf-sy harmonic 211.48 1.788 # SOURCE3_SOURCE5 36 0.0177 + bond_coeff @bond:cg-cg harmonic 421.79 1.369 # SOURCE1_SOURCE5 62 0.0025 + bond_coeff @bond:cg-ch harmonic 811.54 1.206 # SOURCE1_SOURCE5 156 0.0023 + bond_coeff @bond:cg-n1 harmonic 879.32 1.157 # SOURCE1_SOURCE5 879 0.0015 + bond_coeff @bond:cg-ne harmonic 435.38 1.326 # SOURCE4_SOURCE5 68 0.0013 + bond_coeff @bond:cg-pe harmonic 339.39 1.621 # SOURCE3 11 0.2008 + bond_coeff @bond:c-h4 harmonic 350.25 1.112 # SOURCE4_SOURCE5 506 0.0025 + bond_coeff @bond:c-h5 harmonic 361.80 1.105 # SOURCE4_SOURCE5 163 0.0038 + bond_coeff @bond:c-ha harmonic 368.78 1.101 # SOURCE3 53 0.0102 + bond_coeff @bond:ch-ch harmonic 421.79 1.369 # SOURCE1_SOURCE5 62 0.0025 + bond_coeff @bond:ch-n1 harmonic 879.32 1.157 # SOURCE1_SOURCE5 879 0.0015 + bond_coeff @bond:ch-nf harmonic 435.38 1.326 # SOURCE4_SOURCE5 51 0.0014 + bond_coeff @bond:ch-pf harmonic 339.39 1.621 # SOURCE3 11 + bond_coeff @bond:c-i harmonic 89.53 2.209 # SOURCE3 4 0.0365 + bond_coeff @bond:cl-cl harmonic 79.29 2.267 # SOURCE1 2 0.0395 + bond_coeff @bond:cl-cx harmonic 172.69 1.768 # SOURCE1_SOURCE5 42 0.0071 + bond_coeff @bond:cl-cy harmonic 161.13 1.792 # SOURCE2_SOURCE5 28 0.0103 + bond_coeff @bond:cl-n1 harmonic 217.59 1.630 # SOUECE3 1 + bond_coeff @bond:cl-n2 harmonic 123.81 1.819 # SOURCE3 6 0.1020 + bond_coeff @bond:cl-n3 harmonic 139.52 1.777 # SOURCE4_SOURCE5 16 0.0044 + bond_coeff @bond:cl-n harmonic 167.01 1.716 # SOURCE4_SOURCE5 17 0.0049 + bond_coeff @bond:cl-n4 harmonic 149.71 1.753 # SOURCE3 4 0.0098 + bond_coeff @bond:cl-na harmonic 118.36 1.835 # SOURCE3 7 0.2083 + bond_coeff @bond:cl-nh harmonic 145.39 1.763 # SOURCE3 1 + bond_coeff @bond:cl-no harmonic 116.71 1.840 # SOURCE2 1 + bond_coeff @bond:cl-o harmonic 331.00 1.483 # SOURCE3 4 + bond_coeff @bond:cl-oh harmonic 169.11 1.690 # SOURCE2 1 + bond_coeff @bond:cl-os harmonic 149.95 1.730 # SOURCE3 4 + bond_coeff @bond:cl-p2 harmonic 143.51 2.070 # SOURCE3 6 0.0108 + bond_coeff @bond:cl-p3 harmonic 167.79 2.008 # SOURCE1 111 + bond_coeff @bond:cl-p4 harmonic 167.79 2.008 # SOURCE1 111 + bond_coeff @bond:cl-p5 harmonic 167.79 2.008 # SOURCE1 111 + bond_coeff @bond:cl-pb harmonic 172.59 1.997 # SOURCE1 46 + bond_coeff @bond:cl-s harmonic 230.41 2.072 # SOURCE1 6 + bond_coeff @bond:cl-s2 harmonic 185.62 2.161 # SOURCE2 1 + bond_coeff @bond:cl-s4 harmonic 230.41 2.072 # SOURCE1 6 + bond_coeff @bond:cl-s6 harmonic 230.41 2.072 # SOURCE1 6 + bond_coeff @bond:cl-sh harmonic 230.41 2.072 # SOURCE1 6 + bond_coeff @bond:cl-ss harmonic 230.41 2.072 # SOURCE1 6 + bond_coeff @bond:cl-sx harmonic 230.41 2.072 # SOURCE1 6 + bond_coeff @bond:cl-sy harmonic 230.41 2.072 # SOURCE1 6 + bond_coeff @bond:c-n2 harmonic 306.30 1.420 # SOUECE3 1 + bond_coeff @bond:c-n4 harmonic 197.87 1.546 # SOURCE3 4 0.0388 + bond_coeff @bond:c-n harmonic 356.21 1.379 # SOURCE1_SOURCE5 9463 0.0137 + bond_coeff @bond:c-nc harmonic 346.03 1.387 # CORR_SOURCE5 179 0.0121 + bond_coeff @bond:c-nd harmonic 346.03 1.387 # CORR_SOURCE5 179 0.0121 + bond_coeff @bond:c-ne harmonic 340.70 1.391 # CORR_SOURCE5 87 0.0140 + bond_coeff @bond:c-nf harmonic 340.70 1.391 # CORR_SOURCE5 87 0.0140 + bond_coeff @bond:c-no harmonic 201.86 1.540 # SOUECE3 1 + bond_coeff @bond:c-o harmonic 652.57 1.218 # SOURCE1_SOURCE5 27083 0.0110 + bond_coeff @bond:c-oh harmonic 383.13 1.351 # SOURCE1_SOURCE5 3610 0.0055 + bond_coeff @bond:c-os harmonic 372.94 1.358 # SOURCE1_SOURCE5 5555 0.0163 + bond_coeff @bond:c-p2 harmonic 150.04 1.900 # SOUECE3 1 + bond_coeff @bond:c-p3 harmonic 157.13 1.883 # SOURCE3 6 0.0129 + bond_coeff @bond:c-p4 harmonic 158.42 1.880 # SOUECE3 1 + bond_coeff @bond:c-p5 harmonic 157.64 1.882 # SOURCE4_SOURCE5 25 0.0081 + bond_coeff @bond:cp-cp harmonic 277.60 1.485 # SOURCE1_SOURCE5 728 0.0059 + bond_coeff @bond:cp-cq harmonic 309.60 1.454 # SOURCE4_SOURCE5 34 0.0159 + bond_coeff @bond:c-pe harmonic 145.65 1.911 # SOURCE3 3 0.0025 + bond_coeff @bond:c-pf harmonic 145.65 1.911 # SOURCE3 3 + bond_coeff @bond:cp-na harmonic 349.52 1.384 # SOURCE4 7 0.0181 + bond_coeff @bond:cp-nb harmonic 414.72 1.339 # SOURCE4_SOURCE5 190 0.0068 + bond_coeff @bond:c-px harmonic 148.42 1.904 # SOURCE3 1 + bond_coeff @bond:c-py harmonic 164.17 1.867 # SOURCE3_SOURCE5 17 0.0103 + bond_coeff @bond:cq-cq harmonic 277.60 1.485 # SOURCE1_SOURCE5 728 0.0059 + bond_coeff @bond:c-s harmonic 298.35 1.672 # SOURCE1_SOURCE5 875 0.0114 + bond_coeff @bond:c-s4 harmonic 167.99 1.870 # SOUECE3 1 + bond_coeff @bond:c-s6 harmonic 167.99 1.870 # SOUECE3 1 + bond_coeff @bond:c-sh harmonic 206.09 1.797 # SOURCE3_SOURCE5 39 0.0097 + bond_coeff @bond:c-ss harmonic 204.39 1.800 # SOURCE1_SOURCE5 249 0.0157 + bond_coeff @bond:c-sx harmonic 161.23 1.885 # SOURCE3 5 0.0088 + bond_coeff @bond:c-sy harmonic 170.32 1.865 # SOURCE3 5 0.0085 + bond_coeff @bond:cu-cu harmonic 564.10 1.294 # SOURCE1 10 + bond_coeff @bond:cu-cx harmonic 277.70 1.485 # SOURCE1_SOURCE5 31 0.0066 + bond_coeff @bond:cu-ha harmonic 405.22 1.081 # SOURCE2 3 0.0111 + bond_coeff @bond:cv-cv harmonic 480.53 1.335 # SOURCE1 25 + bond_coeff @bond:cv-cy harmonic 250.66 1.515 # SOURCE1_SOURCE5 19 0.0057 + bond_coeff @bond:cv-ha harmonic 393.86 1.087 # SOURCE3 2 + bond_coeff @bond:cx-cv harmonic 256.87 1.508 # SOURCE1 2536 + bond_coeff @bond:cx-cx harmonic 260.31 1.504 # SOURCE1_SOURCE5 2781 0.0136 + bond_coeff @bond:cx-cy harmonic 250.83 1.515 # SOURCE3 2 + bond_coeff @bond:cx-f harmonic 339.01 1.360 # SOURCE2_SOURCE5 10 0.0045 + bond_coeff @bond:cx-h1 harmonic 390.15 1.089 # SOURCE3_SOURCE5 1142 0.0013 + bond_coeff @bond:cx-h2 harmonic 395.91 1.086 # SOURCE3_SOURCE5 5 0.0014 + bond_coeff @bond:cx-hc harmonic 393.86 1.087 # SOURCE3_SOURCE5 1702 0.0009 + bond_coeff @bond:cx-hx harmonic 397.60 1.085 # SOURCE4_SOURCE5 19 0.0002 + bond_coeff @bond:cx-n2 harmonic 245.89 1.482 # SOURCE3 2 + bond_coeff @bond:cx-n3 harmonic 256.30 1.470 # SOURCE1_SOURCE5 227 0.0050 + bond_coeff @bond:cx-n harmonic 283.33 1.442 # SOURCE4_SOURCE5 39 0.0103 + bond_coeff @bond:cx-na harmonic 264.52 1.461 # SOURCE4_SOURCE5 49 0.0026 + bond_coeff @bond:cx-nh harmonic 270.65 1.455 # SOURCE4_SOURCE5 192 0.0076 + bond_coeff @bond:cx-oh harmonic 369.30 1.361 # SOURCE3 3 0.0018 + bond_coeff @bond:cx-os harmonic 279.50 1.437 # SOURCE3_SOURCE5 703 0.0071 + bond_coeff @bond:cx-p3 harmonic 164.17 1.867 # SOURCE2 1 + bond_coeff @bond:cx-s4 harmonic 192.02 1.822 # SOURCE2 1 + bond_coeff @bond:cx-s6 harmonic 249.87 1.731 # SOURCE2 1 + bond_coeff @bond:cx-ss harmonic 186.43 1.833 # SOURCE2_SOURCE5 5 0.0011 + bond_coeff @bond:cy-cy harmonic 218.51 1.556 # SOURCE1_SOURCE5 1665 0.0053 + bond_coeff @bond:cy-f harmonic 344.83 1.356 # SOURCE4_SOURCE5 36 0.0095 + bond_coeff @bond:cy-h1 harmonic 379.11 1.095 # SOURCE3_SOURCE5 477 0.0019 + bond_coeff @bond:cy-h2 harmonic 382.87 1.093 # SOURCE4_SOURCE5 210 0.0017 + bond_coeff @bond:cy-hc harmonic 379.47 1.095 # SOURCE3_SOURCE5 840 0.0011 + bond_coeff @bond:cy-n harmonic 256.66 1.470 # SOURCE4_SOURCE5 618 0.0101 + bond_coeff @bond:cy-n3 harmonic 248.73 1.479 # SOURCE1_SOURCE5 67 0.0083 + bond_coeff @bond:cy-oh harmonic 305.23 1.412 # SOURCE3_SOURCE5 13 0.0082 + bond_coeff @bond:cy-os harmonic 277.32 1.439 # SOURCE4_SOURCE5 81 0.0141 + bond_coeff @bond:cy-s6 harmonic 177.00 1.851 # SOURCE4_SOURCE5 39 0.0142 + bond_coeff @bond:cy-ss harmonic 177.89 1.849 # SOURCE4_SOURCE5 201 0.0086 + bond_coeff @bond:cz-nh harmonic 414.24 1.339 # SOURCE4_SOURCE5 85 0.0046 + bond_coeff @bond:f-n1 harmonic 167.33 1.410 # SOUECE3 1 + bond_coeff @bond:f-n2 harmonic 148.04 1.444 # SOURCE3 5 0.0377 + bond_coeff @bond:f-n3 harmonic 169.79 1.406 # SOURCE1 9 + bond_coeff @bond:f-n harmonic 175.49 1.397 # SOURCE3 3 0.0112 + bond_coeff @bond:f-n4 harmonic 246.14 1.308 # SOURCE3 2 + bond_coeff @bond:f-na harmonic 166.72 1.411 # SOURCE3 7 0.0611 + bond_coeff @bond:f-nh harmonic 157.90 1.426 # SOURCE3 3 0.0085 + bond_coeff @bond:f-no harmonic 136.49 1.467 # SOURCE2 1 + bond_coeff @bond:f-o harmonic 198.07 1.330 # SOUECE3 1 + bond_coeff @bond:f-oh harmonic 129.79 1.444 # SOURCE3 1 + bond_coeff @bond:f-os harmonic 139.94 1.423 # SOURCE3 2 + bond_coeff @bond:f-p2 harmonic 522.31 1.536 # SOURCE3 7 0.2054 + bond_coeff @bond:f-p3 harmonic 454.68 1.578 # SOURCE2 8 0.0103 + bond_coeff @bond:f-p4 harmonic 437.32 1.590 # SOUECE3 1 + bond_coeff @bond:f-p5 harmonic 442.73 1.586 # SOURCE1_SOURCE5 18 0.0161 + bond_coeff @bond:f-s2 harmonic 363.47 1.643 # SOURCE2 1 + bond_coeff @bond:f-s harmonic 344.73 1.660 # SOUECE3 1 + bond_coeff @bond:f-s4 harmonic 428.80 1.591 # SOURCE2 4 0.0065 + bond_coeff @bond:f-s6 harmonic 400.85 1.612 # SOURCE2_SOURCE5 15 0.0133 + bond_coeff @bond:f-sh harmonic 356.72 1.649 # SOURCE3 1 + bond_coeff @bond:f-ss harmonic 373.87 1.634 # SOURCE3 3 0.0156 + bond_coeff @bond:hn-n1 harmonic 605.55 0.986 # SOURCE2 1 + bond_coeff @bond:hn-n2 harmonic 501.09 1.023 # SOURCE3_SOURCE5 732 0.0030 + bond_coeff @bond:hn-n3 harmonic 511.28 1.019 # SOURCE3_SOURCE5 5944 0.0012 + bond_coeff @bond:hn-n harmonic 527.31 1.013 # SOURCE3_SOURCE5 7593 0.0034 + bond_coeff @bond:hn-n4 harmonic 482.87 1.030 # SOURCE3_SOURCE5 756 0.0122 + bond_coeff @bond:hn-na harmonic 535.14 1.010 # SOURCE3_SOURCE5 1755 0.0019 + bond_coeff @bond:hn-nh harmonic 529.46 1.012 # SOURCE3_SOURCE5 7230 0.0022 + bond_coeff @bond:hn-no harmonic 501.09 1.023 # SOURCE3 1 + bond_coeff @bond:ho-o harmonic 540.28 0.981 # SOURCE3 1 + bond_coeff @bond:ho-oh harmonic 563.51 0.973 # SOURCE3_SOURCE5 21237 0.0034 + bond_coeff @bond:hp-p2 harmonic 266.54 1.336 # SOURCE3 87 0.1706 + bond_coeff @bond:hp-p3 harmonic 200.57 1.412 # SOURCE3_SOURCE5 123 0.0510 + bond_coeff @bond:hp-p4 harmonic 253.60 1.349 # SOURCE3 17 0.1577 + bond_coeff @bond:hp-p5 harmonic 196.39 1.418 # SOURCE3_SOURCE5 31 0.0077 + bond_coeff @bond:hs-s harmonic 288.27 1.353 # SOURCE3 1 + bond_coeff @bond:hs-s4 harmonic 265.33 1.375 # SOURCE3 5 0.0004 + bond_coeff @bond:hs-s6 harmonic 281.78 1.359 # SOURCE3 5 0.0015 + bond_coeff @bond:hs-sh harmonic 294.59 1.347 # SOURCE3_SOURCE5 477 0.0118 + bond_coeff @bond:i-i harmonic 50.27 2.917 # SOURCE1 1 + bond_coeff @bond:i-n1 harmonic 105.51 2.060 # SOUECE3 1 + bond_coeff @bond:i-n2 harmonic 59.35 2.304 # SOURCE3 6 0.1186 + bond_coeff @bond:i-n harmonic 96.05 2.098 # SOURCE3 5 0.0156 + bond_coeff @bond:i-n3 harmonic 77.95 2.185 # SOURCE3 3 0.0437 + bond_coeff @bond:i-n4 harmonic 83.69 2.155 # SOURCE3 3 0.0168 + bond_coeff @bond:i-na harmonic 89.07 2.129 # SOURCE3 8 0.1276 + bond_coeff @bond:i-nh harmonic 84.69 2.150 # SOURCE3 1 + bond_coeff @bond:i-no harmonic 70.03 2.231 # SOURCE3 1 + bond_coeff @bond:i-o harmonic 106.33 1.980 # SOUECE3 1 + bond_coeff @bond:i-oh harmonic 78.38 2.101 # SOURCE3 2 + bond_coeff @bond:i-os harmonic 73.23 2.129 # SOURCE3 3 0.0146 + bond_coeff @bond:i-p2 harmonic 66.30 2.643 # SOURCE3 6 0.0297 + bond_coeff @bond:i-p3 harmonic 77.18 2.566 # SOURCE3 3 0.0016 + bond_coeff @bond:i-p4 harmonic 120.75 2.352 # SOURCE3 4 0.2600 + bond_coeff @bond:i-p5 harmonic 72.70 2.596 # SOURCE3 3 0.0143 + bond_coeff @bond:i-s harmonic 115.77 2.430 # SOUECE3 1 + bond_coeff @bond:i-s4 harmonic 49.21 2.870 # SOUECE3 1 + bond_coeff @bond:i-s6 harmonic 49.21 2.870 # SOURCE3 1 + bond_coeff @bond:i-sh harmonic 88.56 2.560 # SOUECE3 1 + bond_coeff @bond:i-ss harmonic 86.63 2.571 # SOURCE3 3 0.0065 + bond_coeff @bond:n1-n1 harmonic 750.98 1.135 # SOURCE1_SOURCE5 78 0.0044 + bond_coeff @bond:n1-n2 harmonic 494.86 1.230 # SOURCE1_SOURCE5 36 0.0029 + bond_coeff @bond:n1-n3 harmonic 307.19 1.350 # SOUECE3 1 + bond_coeff @bond:n1-n4 harmonic 295.75 1.360 # SOUECE3 1 + bond_coeff @bond:n1-na harmonic 307.19 1.350 # SOUECE3 1 + bond_coeff @bond:n1-nc harmonic 525.73 1.216 # SOURCE1 38 + bond_coeff @bond:n1-nd harmonic 525.73 1.216 # SOURCE1 38 + bond_coeff @bond:n1-ne harmonic 452.52 1.252 # SOURCE2 1 + bond_coeff @bond:n1-nf harmonic 452.52 1.252 # SOURCE2 1 + bond_coeff @bond:n1-nh harmonic 319.16 1.340 # SOUECE3 1 + bond_coeff @bond:n1-no harmonic 254.81 1.400 # SOUECE3 1 + bond_coeff @bond:n1-o harmonic 298.40 1.277 # SOURCE3 5 0.0438 + bond_coeff @bond:n1-oh harmonic 272.24 1.300 # SOUECE3 1 + bond_coeff @bond:n1-os harmonic 261.73 1.310 # SOUECE3 1 + bond_coeff @bond:n1-p2 harmonic 268.95 1.678 # SOURCE3 2 0.0282 + bond_coeff @bond:n1-p3 harmonic 284.28 1.660 # SOUECE3 1 + bond_coeff @bond:n1-p4 harmonic 267.31 1.680 # SOURCE3 0 + bond_coeff @bond:n1-p5 harmonic 377.36 1.571 # SOURCE1 132 + bond_coeff @bond:n1-s2 harmonic 681.10 1.449 # SOURCE2 2 0.0010 + bond_coeff @bond:n1-s harmonic 339.70 1.659 # SOURCE3 6 0.0789 + bond_coeff @bond:n1-s4 harmonic 349.33 1.650 # SOUECE3 1 + bond_coeff @bond:n1-s6 harmonic 766.72 1.416 # SOURCE2 2 + bond_coeff @bond:n1-sh harmonic 396.29 1.610 # SOUECE3 1 + bond_coeff @bond:n1-ss harmonic 396.29 1.610 # SOUECE3 1 + bond_coeff @bond:n2-n2 harmonic 425.99 1.267 # SOURCE3_SOURCE5 40 0.0268 + bond_coeff @bond:n2-n3 harmonic 332.97 1.329 # SOURCE2 1 + bond_coeff @bond:n2-n4 harmonic 100.13 1.679 # SOURCE3 7 0.3138 + bond_coeff @bond:n2-na harmonic 287.40 1.368 # SOURCE4_SOURCE5 49 0.0087 + bond_coeff @bond:n2-nc harmonic 446.98 1.255 # SOURCE1 13 + bond_coeff @bond:n2-nd harmonic 446.98 1.255 # SOURCE1 13 + bond_coeff @bond:n2-ne harmonic 418.13 1.271 # SOURCE3_SOURCE5 57 0.0194 + bond_coeff @bond:n2-nf harmonic 418.13 1.271 # SOURCE3_SOURCE5 27 0.0074 + bond_coeff @bond:n2-nh harmonic 304.40 1.352 # SOURCE3_SOURCE5 210 0.0159 + bond_coeff @bond:n2-no harmonic 224.76 1.435 # SOURCE3_SOURCE5 15 0.0628 + bond_coeff @bond:n2-o harmonic 381.83 1.217 # SOURCE3_SOURCE5 112 0.0102 + bond_coeff @bond:n2-oh harmonic 192.13 1.391 # SOURCE1_SOURCE5 149 0.0171 + bond_coeff @bond:n2-os harmonic 184.98 1.401 # SOURCE3_SOURCE5 108 0.0101 + bond_coeff @bond:n2-p2 harmonic 338.04 1.605 # SOURCE3 35 0.0737 + bond_coeff @bond:n2-p3 harmonic 208.02 1.764 # SOURCE3 7 0.0374 + bond_coeff @bond:n2-p4 harmonic 234.05 1.724 # SOUECE3 1 + bond_coeff @bond:n2-p5 harmonic 344.61 1.599 # SOURCE1 7 + bond_coeff @bond:n2-pe harmonic 418.07 1.540 # SOURCE3 20 0.1392 + bond_coeff @bond:n2-pf harmonic 418.07 1.540 # SOURCE3 20 + bond_coeff @bond:n2-s2 harmonic 491.26 1.544 # SOURCE2_SOURCE5 11 0.0086 + bond_coeff @bond:n2-s4 harmonic 396.29 1.610 # SOUECE3 1 + bond_coeff @bond:n2-s harmonic 496.36 1.541 # SOURCE1 37 + bond_coeff @bond:n2-s6 harmonic 475.70 1.554 # SOURCE4_SOURCE5 16 0.0041 + bond_coeff @bond:n2-sh harmonic 267.45 1.738 # SOURCE3 5 0.0511 + bond_coeff @bond:n2-ss harmonic 342.87 1.656 # SOURCE1 36 + bond_coeff @bond:n3-n3 harmonic 219.29 1.442 # SOURCE1_SOURCE5 48 0.0063 + bond_coeff @bond:n3-n4 harmonic 228.50 1.430 # SOURCE1_SOURCE5 9 0.0040 + bond_coeff @bond:n3-na harmonic 236.90 1.420 # SOURCE1 68 + bond_coeff @bond:n3-nh harmonic 240.71 1.416 # SOURCE1_SOURCE5 66 0.0085 + bond_coeff @bond:n3-no harmonic 256.88 1.398 # SOURCE3_SOURCE5 19 0.0132 + bond_coeff @bond:n3-o harmonic 269.04 1.303 # SOURCE3 4 0.1217 + bond_coeff @bond:n3-oh harmonic 176.15 1.415 # SOURCE1_SOURCE5 17 0.0055 + bond_coeff @bond:n3-os harmonic 160.59 1.441 # SOURCE1_SOURCE5 84 0.0191 + bond_coeff @bond:n3-p2 harmonic 275.64 1.670 # SOUECE3 1 + bond_coeff @bond:n3-p3 harmonic 229.90 1.730 # SOURCE1 40 + bond_coeff @bond:n3-p4 harmonic 253.83 1.697 # SOURCE1 88 + bond_coeff @bond:n3-p5 harmonic 275.98 1.670 # SOURCE1_SOURCE5 680 0.0109 + bond_coeff @bond:n3-py harmonic 256.22 1.694 # SOURCE4_SOURCE5 16 0.0080 + bond_coeff @bond:n3-s harmonic 228.53 1.792 # SOURCE3 3 0.0178 + bond_coeff @bond:n3-s4 harmonic 254.85 1.754 # SOURCE3_SOURCE5 15 0.0416 + bond_coeff @bond:n3-s6 harmonic 326.04 1.672 # SOURCE1_SOURCE5 243 0.0144 + bond_coeff @bond:n3-sh harmonic 266.66 1.739 # SOURCE3 3 0.0154 + bond_coeff @bond:n3-ss harmonic 279.14 1.724 # SOURCE3_SOURCE5 25 0.0197 + bond_coeff @bond:n3-sy harmonic 303.10 1.696 # SOURCE4_SOURCE5 511 0.0083 + bond_coeff @bond:n4-n4 harmonic 188.86 1.484 # SOURCE3 4 0.0089 + bond_coeff @bond:n4-na harmonic 224.44 1.435 # SOURCE3 9 0.0390 + bond_coeff @bond:n4-nh harmonic 201.09 1.466 # SOURCE3 5 0.0108 + bond_coeff @bond:n4-no harmonic 191.50 1.480 # SOUECE3 1 + bond_coeff @bond:n4-o harmonic 215.08 1.361 # SOURCE3 3 0.0041 + bond_coeff @bond:n4-oh harmonic 186.01 1.400 # SOURCE3 3 0.0115 + bond_coeff @bond:n4-os harmonic 172.30 1.421 # SOURCE3 5 0.0249 + bond_coeff @bond:n4-p2 harmonic 126.91 1.942 # SOURCE3 10 0.0643 + bond_coeff @bond:n4-p3 harmonic 149.95 1.880 # SOURCE3 5 0.0146 + bond_coeff @bond:n4-p4 harmonic 128.26 1.938 # SOURCE3 1 + bond_coeff @bond:n4-p5 harmonic 172.23 1.830 # SOURCE3 5 0.0087 + bond_coeff @bond:n4-py harmonic 141.24 1.902 # SOURCE3 4 + bond_coeff @bond:n4-s harmonic 204.02 1.832 # SOURCE3 3 0.0004 + bond_coeff @bond:n4-s4 harmonic 139.73 1.972 # SOURCE3 3 0.0198 + bond_coeff @bond:n4-s6 harmonic 162.90 1.914 # SOURCE3 5 0.0432 + bond_coeff @bond:n4-sh harmonic 216.47 1.811 # SOURCE3 3 0.0027 + bond_coeff @bond:n4-ss harmonic 215.86 1.812 # SOURCE3 5 0.0064 + bond_coeff @bond:na-na harmonic 253.88 1.401 # SOURCE1 40 + bond_coeff @bond:na-nb harmonic 310.48 1.347 # SOURCE4_SOURCE5 26 0.0093 + bond_coeff @bond:na-nc harmonic 300.49 1.356 # SOURCE3_SOURCE5 899 0.0083 + bond_coeff @bond:na-nd harmonic 302.44 1.354 # SOURCE3_SOURCE5 362 0.0113 + bond_coeff @bond:na-nh harmonic 254.81 1.400 # SOURCE1_SOURCE5 20 0.0066 + bond_coeff @bond:na-no harmonic 224.76 1.435 # SOURCE3_SOURCE5 16 0.0192 + bond_coeff @bond:na-o harmonic 347.95 1.239 # SOURCE1_SOURCE5 93 0.0208 + bond_coeff @bond:na-oh harmonic 191.21 1.393 # SOURCE3_SOURCE5 18 0.0144 + bond_coeff @bond:na-os harmonic 158.65 1.444 # SOURCE3 45 0.0423 + bond_coeff @bond:na-p2 harmonic 217.35 1.749 # SOURCE3 11 0.0192 + bond_coeff @bond:na-p3 harmonic 209.23 1.762 # SOURCE3 8 0.0113 + bond_coeff @bond:na-p4 harmonic 386.12 1.564 # SOURCE3 5 0.2161 + bond_coeff @bond:na-p5 harmonic 240.43 1.715 # SOURCE3 11 0.0238 + bond_coeff @bond:na-pc harmonic 228.54 1.732 # SOURCE3 81 0.0207 + bond_coeff @bond:na-pd harmonic 228.54 1.732 # SOURCE3 81 + bond_coeff @bond:na-py harmonic 242.60 1.712 # SOURCE3 2 + bond_coeff @bond:na-s harmonic 247.08 1.765 # SOURCE3 8 0.0095 + bond_coeff @bond:na-s4 harmonic 227.88 1.793 # SOURCE3 10 0.0421 + bond_coeff @bond:na-s6 harmonic 279.89 1.723 # SOURCE3_SOURCE5 15 0.0153 + bond_coeff @bond:na-sh harmonic 281.31 1.721 # SOURCE3 9 0.0113 + bond_coeff @bond:na-ss harmonic 271.85 1.732 # SOURCE3_SOURCE5 50 0.0325 + bond_coeff @bond:na-sy harmonic 276.32 1.727 # SOURCE3 1 + bond_coeff @bond:nb-nb harmonic 327.23 1.333 # SOURCE1_SOURCE5 98 0.0106 + bond_coeff @bond:nb-pb harmonic 358.21 1.587 # SOURCE1 162 0.0091 + bond_coeff @bond:nc-nc harmonic 290.67 1.365 # SOURCE3_SOURCE5 271 0.0065 + bond_coeff @bond:nc-nd harmonic 374.73 1.299 # SOURCE3_SOURCE5 185 0.0074 + bond_coeff @bond:nc-os harmonic 185.12 1.401 # SOURCE1_SOURCE5 243 0.0096 + bond_coeff @bond:nc-ss harmonic 376.65 1.626 # SOURCE1_SOURCE5 114 0.0148 + bond_coeff @bond:nc-sy harmonic 473.81 1.555 # SOURCE3 2 + bond_coeff @bond:nd-nd harmonic 290.67 1.365 # SOURCE3_SOURCE5 271 0.0065 + bond_coeff @bond:nd-os harmonic 185.12 1.401 # SOURCE1_SOURCE5 243 0.0096 + bond_coeff @bond:nd-ss harmonic 376.65 1.626 # SOURCE1_SOURCE5 114 0.0148 + bond_coeff @bond:nd-sy harmonic 473.81 1.555 # SOURCE3 2 + bond_coeff @bond:ne-ne harmonic 235.02 1.422 # SOURCE3_SOURCE5 47 0.0776 + bond_coeff @bond:ne-nf harmonic 432.27 1.263 # SOURCE4_SOURCE5 78 0.0037 + bond_coeff @bond:ne-o harmonic 360.78 1.231 # SOURCE3_SOURCE5 55 0.0223 + bond_coeff @bond:ne-p2 harmonic 387.40 1.563 # SOURCE3 14 0.1325 + bond_coeff @bond:ne-pe harmonic 242.60 1.712 # SOURCE3 28 0.1076 + bond_coeff @bond:ne-px harmonic 250.02 1.702 # SOURCE3 11 0.0883 + bond_coeff @bond:ne-py harmonic 338.14 1.605 # SOURCE4_SOURCE5 94 0.0111 + bond_coeff @bond:ne-s harmonic 503.04 1.537 # SOURCE3 22 0.1708 + bond_coeff @bond:ne-sx harmonic 200.62 1.838 # SOURCE3 7 0.1060 + bond_coeff @bond:ne-sy harmonic 326.04 1.672 # SOURCE3_SOURCE5 49 0.0285 + bond_coeff @bond:nf-nf harmonic 235.02 1.422 # SOURCE3_SOURCE5 28 0.0146 + bond_coeff @bond:nf-o harmonic 360.78 1.231 # SOURCE3_SOURCE5 15 0.0138 + bond_coeff @bond:nf-p2 harmonic 387.40 1.563 # SOURCE3 14 + bond_coeff @bond:nf-pf harmonic 242.60 1.712 # SOURCE3 28 + bond_coeff @bond:nf-px harmonic 250.02 1.702 # SOURCE3 11 + bond_coeff @bond:nf-py harmonic 338.14 1.605 # SOURCE4_SOURCE5 84 0.0113 + bond_coeff @bond:nf-s harmonic 503.04 1.537 # SOURCE3 22 + bond_coeff @bond:nf-sx harmonic 200.62 1.838 # SOURCE3 7 + bond_coeff @bond:nf-sy harmonic 326.04 1.672 # SOURCE3_SOURCE5 42 0.0197 + bond_coeff @bond:nh-nh harmonic 252.77 1.402 # SOURCE1_SOURCE5 8 0.0109 + bond_coeff @bond:nh-no harmonic 267.93 1.386 # SOURCE4_SOURCE5 22 0.0046 + bond_coeff @bond:nh-o harmonic 316.06 1.263 # SOURCE3_SOURCE5 18 0.0143 + bond_coeff @bond:nh-oh harmonic 175.33 1.416 # SOURCE4_SOURCE5 63 0.0072 + bond_coeff @bond:nh-os harmonic 175.90 1.415 # SOURCE4_SOURCE5 26 0.0063 + bond_coeff @bond:nh-p2 harmonic 268.13 1.679 # SOURCE3 17 0.0872 + bond_coeff @bond:nh-p3 harmonic 229.90 1.730 # SOURCE3 3 0.0016 + bond_coeff @bond:nh-p4 harmonic 247.02 1.706 # SOURCE3 3 0.0008 + bond_coeff @bond:nh-p5 harmonic 274.79 1.671 # SOURCE3 3 0.0007 + bond_coeff @bond:nh-s harmonic 233.85 1.784 # SOURCE3 3 0.0076 + bond_coeff @bond:nh-s4 harmonic 258.92 1.749 # SOURCE3 3 0.0203 + bond_coeff @bond:nh-s6 harmonic 301.91 1.698 # SOURCE4_SOURCE5 93 0.0076 + bond_coeff @bond:nh-sh harmonic 292.49 1.708 # SOURCE3 1 + bond_coeff @bond:nh-ss harmonic 291.53 1.709 # SOURCE1_SOURCE5 58 0.0020 + bond_coeff @bond:nh-sy harmonic 287.18 1.714 # SOURCE4_SOURCE5 239 0.0099 + bond_coeff @bond:n-n1 harmonic 319.16 1.340 # SOUECE3 1 + bond_coeff @bond:n-n2 harmonic 295.31 1.360 # SOURCE3_SOURCE5 272 0.0114 + bond_coeff @bond:n-n3 harmonic 250.92 1.404 # SOURCE3_SOURCE5 87 0.0076 + bond_coeff @bond:n-n4 harmonic 226.87 1.432 # SOURCE3 5 0.0098 + bond_coeff @bond:n-n harmonic 250.83 1.404 # SOURCE3_SOURCE5 47 0.0125 + bond_coeff @bond:n-na harmonic 248.27 1.407 # SOURCE3_SOURCE5 56 0.0060 + bond_coeff @bond:n-nc harmonic 295.87 1.360 # CORR_SOURCE5 121 0.0130 + bond_coeff @bond:n-nd harmonic 295.87 1.360 # CORR_SOURCE5 121 0.0130 + bond_coeff @bond:n-nh harmonic 253.32 1.402 # SOURCE4_SOURCE5 51 0.0075 + bond_coeff @bond:n-no harmonic 208.29 1.456 # SOURCE3 4 0.0327 + bond_coeff @bond:n-o harmonic 342.80 1.243 # SOURCE3_SOURCE5 16 0.0255 + bond_coeff @bond:n-oh harmonic 181.83 1.406 # SOURCE3_SOURCE5 119 0.0062 + bond_coeff @bond:no-no harmonic 65.41 1.824 # SOURCE3 1 + bond_coeff @bond:no-o harmonic 367.95 1.226 # SOURCE1_SOURCE5 4403 0.0099 + bond_coeff @bond:no-oh harmonic 181.96 1.406 # SOURCE2 1 + bond_coeff @bond:no-os harmonic 172.24 1.421 # SOURCE4_SOURCE5 138 0.0070 + bond_coeff @bond:no-p2 harmonic 224.52 1.738 # SOURCE3 10 0.2231 + bond_coeff @bond:no-p3 harmonic 165.61 1.844 # SOURCE3 3 0.0005 + bond_coeff @bond:no-p4 harmonic 154.11 1.870 # SOURCE3 3 0.0006 + bond_coeff @bond:no-p5 harmonic 170.31 1.834 # SOURCE3 4 0.0020 + bond_coeff @bond:no-s harmonic 264.31 1.742 # SOURCE3 2 + bond_coeff @bond:n-os harmonic 180.04 1.409 # SOURCE4_SOURCE5 73 0.0121 + bond_coeff @bond:no-s4 harmonic 131.30 1.996 # SOURCE3 3 0.0313 + bond_coeff @bond:no-s6 harmonic 138.28 1.976 # SOURCE3 3 0.0520 + bond_coeff @bond:no-sh harmonic 220.82 1.804 # SOURCE3 1 + bond_coeff @bond:no-ss harmonic 206.32 1.828 # SOURCE3 3 0.0244 + bond_coeff @bond:n-p2 harmonic 227.87 1.733 # SOURCE3 8 0.0217 + bond_coeff @bond:n-p3 harmonic 204.42 1.770 # SOURCE3 9 0.0118 + bond_coeff @bond:n-p4 harmonic 227.19 1.734 # SOURCE3 1 + bond_coeff @bond:n-p5 harmonic 238.92 1.717 # SOURCE4_SOURCE5 25 0.0133 + bond_coeff @bond:n-pc harmonic 223.19 1.740 # SOURCE3 3 0.0010 + bond_coeff @bond:n-pd harmonic 223.19 1.740 # SOURCE3 3 + bond_coeff @bond:n-s harmonic 245.64 1.767 # SOURCE3 3 0.0011 + bond_coeff @bond:n-s4 harmonic 244.86 1.768 # SOURCE3_SOURCE5 9 0.0163 + bond_coeff @bond:n-s6 harmonic 283.34 1.719 # SOURCE4_SOURCE5 45 0.0154 + bond_coeff @bond:n-sh harmonic 275.50 1.728 # SOURCE3 4 0.0128 + bond_coeff @bond:n-ss harmonic 277.23 1.726 # SOURCE3_SOURCE5 22 0.0103 + bond_coeff @bond:n-sy harmonic 285.29 1.716 # SOURCE4_SOURCE5 126 0.0086 + bond_coeff @bond:oh-oh harmonic 123.13 1.469 # SOURCE3 1 + bond_coeff @bond:oh-os harmonic 129.12 1.456 # SOURCE4_SOURCE5 49 0.0046 + bond_coeff @bond:oh-p2 harmonic 329.87 1.630 # SOURCE3 8 0.0916 + bond_coeff @bond:oh-p3 harmonic 285.03 1.677 # SOURCE3 3 0.0148 + bond_coeff @bond:oh-p4 harmonic 318.66 1.641 # SOURCE3 4 0.0092 + bond_coeff @bond:oh-p5 harmonic 346.03 1.615 # SOURCE3_SOURCE5 1121 0.0129 + bond_coeff @bond:oh-py harmonic 344.61 1.616 # SOURCE3_SOURCE5 112 0.0110 + bond_coeff @bond:oh-s harmonic 219.79 1.812 # SOURCE3 2 + bond_coeff @bond:oh-s4 harmonic 309.00 1.696 # SOURCE4_SOURCE5 29 0.0100 + bond_coeff @bond:oh-s6 harmonic 373.26 1.635 # SOURCE3_SOURCE5 193 0.0162 + bond_coeff @bond:oh-sh harmonic 312.59 1.692 # SOURCE3 2 0.0003 + bond_coeff @bond:oh-ss harmonic 316.41 1.688 # SOURCE3_SOURCE5 12 0.0167 + bond_coeff @bond:oh-sy harmonic 356.03 1.650 # SOURCE4_SOURCE5 123 0.0037 + bond_coeff @bond:o-o harmonic 141.39 1.430 # SOURCE3 2 0.0500 + bond_coeff @bond:o-oh harmonic 104.37 1.517 # SOURCE3 2 + bond_coeff @bond:o-os harmonic 109.10 1.504 # SOURCE3 3 0.0117 + bond_coeff @bond:o-p2 harmonic 492.04 1.508 # SOURCE3 17 0.0306 + bond_coeff @bond:o-p3 harmonic 480.47 1.515 # SOURCE3 35 0.0297 + bond_coeff @bond:o-p4 harmonic 498.98 1.504 # SOURCE3_SOURCE5 60 0.0565 + bond_coeff @bond:o-p5 harmonic 529.55 1.487 # SOURCE1_SOURCE5 1318 0.0133 + bond_coeff @bond:o-pe harmonic 470.81 1.521 # SOURCE3 20 0.0171 + bond_coeff @bond:o-pf harmonic 470.81 1.521 # SOURCE3 20 + bond_coeff @bond:o-px harmonic 499.66 1.504 # SOURCE3_SOURCE5 45 0.0136 + bond_coeff @bond:o-py harmonic 527.91 1.488 # SOURCE3_SOURCE5 119 0.0072 + bond_coeff @bond:o-s harmonic 226.13 1.802 # SOURCE3 2 + bond_coeff @bond:o-s2 harmonic 417.99 1.599 # SOURCE3 3 0.0707 + bond_coeff @bond:o-s4 harmonic 572.26 1.504 # SOURCE1_SOURCE5 137 0.0127 + bond_coeff @bond:o-s6 harmonic 683.03 1.453 # SOURCE1_SOURCE5 2456 0.0105 + bond_coeff @bond:o-sh harmonic 410.02 1.605 # SOURCE3 2 + bond_coeff @bond:os-os harmonic 124.74 1.465 # SOURCE1_SOURCE5 69 0.0090 + bond_coeff @bond:os-p2 harmonic 396.10 1.573 # SOURCE1 16 + bond_coeff @bond:os-p3 harmonic 287.31 1.674 # SOURCE3_SOURCE5 22 0.0105 + bond_coeff @bond:os-p4 harmonic 323.70 1.636 # SOURCE3 4 0.0057 + bond_coeff @bond:os-p5 harmonic 346.25 1.615 # SOURCE1_SOURCE5 1200 0.0218 + bond_coeff @bond:os-py harmonic 342.10 1.619 # SOURCE3_SOURCE5 68 0.0106 + bond_coeff @bond:os-s harmonic 227.43 1.800 # SOURCE3 3 0.0052 + bond_coeff @bond:o-ss harmonic 567.21 1.507 # SOURCE3_SOURCE5 22 0.0235 + bond_coeff @bond:os-s4 harmonic 312.40 1.692 # SOURCE3_SOURCE5 25 0.0189 + bond_coeff @bond:os-s6 harmonic 387.79 1.623 # SOURCE1_SOURCE5 242 0.0147 + bond_coeff @bond:os-sh harmonic 333.31 1.671 # SOURCE3 3 0.0106 + bond_coeff @bond:os-ss harmonic 301.43 1.704 # SOURCE3 9 0.0277 + bond_coeff @bond:os-sy harmonic 306.02 1.699 # SOURCE3 1 + bond_coeff @bond:o-sx harmonic 555.55 1.513 # SOURCE3_SOURCE5 136 0.0072 + bond_coeff @bond:o-sy harmonic 653.16 1.466 # SOURCE3_SOURCE5 2007 0.0061 + bond_coeff @bond:p2-p2 harmonic 307.63 1.786 # SOURCE3 25 0.3488 + bond_coeff @bond:p2-p3 harmonic 118.00 2.152 # SOURCE3 9 0.1777 + bond_coeff @bond:p2-p4 harmonic 110.68 2.179 # SOUECE3 1 + bond_coeff @bond:p2-p5 harmonic 110.42 2.180 # SOUECE3 1 + bond_coeff @bond:p2-pe harmonic 244.92 1.867 # SOURCE3 16 0.3571 + bond_coeff @bond:p2-pf harmonic 244.92 1.867 # SOURCE3 16 + bond_coeff @bond:p2-s harmonic 375.05 1.772 # SOURCE3 26 0.3014 + bond_coeff @bond:p2-s4 harmonic 126.27 2.190 # SOUECE3 1 + bond_coeff @bond:p2-s6 harmonic 129.28 2.180 # SOUECE3 1 + bond_coeff @bond:p2-sh harmonic 217.02 1.971 # SOURCE3 10 0.2829 + bond_coeff @bond:p2-ss harmonic 219.87 1.966 # SOURCE3 10 0.2739 + bond_coeff @bond:p3-p3 harmonic 101.97 2.214 # SOURCE1 41 + bond_coeff @bond:p3-p4 harmonic 101.50 2.216 # SOURCE3 3 0.0011 + bond_coeff @bond:p3-p5 harmonic 102.21 2.213 # SOURCE3 9 0.0265 + bond_coeff @bond:p3-s harmonic 168.70 2.070 # SOUECE3 1 + bond_coeff @bond:p3-s4 harmonic 161.75 2.087 # SOURCE3 8 0.2235 + bond_coeff @bond:p3-s6 harmonic 165.79 2.077 # SOURCE3 11 0.1420 + bond_coeff @bond:p3-sh harmonic 144.95 2.132 # SOURCE3 3 0.0078 + bond_coeff @bond:p3-ss harmonic 148.86 2.121 # SOURCE3 3 0.0059 + bond_coeff @bond:p4-p4 harmonic 157.68 2.034 # SOURCE1 1 + bond_coeff @bond:p4-p5 harmonic 96.70 2.237 # SOUECE3 1 + bond_coeff @bond:p4-s harmonic 140.16 2.146 # SOURCE3 5 0.0601 + bond_coeff @bond:p4-s4 harmonic 109.64 2.251 # SOUECE3 1 + bond_coeff @bond:p4-s6 harmonic 105.24 2.269 # SOUECE3 1 + bond_coeff @bond:p4-sh harmonic 151.04 2.115 # SOURCE3 4 0.0008 + bond_coeff @bond:p4-ss harmonic 155.14 2.104 # SOURCE3 4 0.0044 + bond_coeff @bond:p5-p5 harmonic 149.95 2.054 # SOURCE1 1 + bond_coeff @bond:p5-s harmonic 239.16 1.934 # SOURCE1_SOURCE5 173 0.0138 + bond_coeff @bond:p5-s4 harmonic 181.84 2.040 # SOUECE3 1 + bond_coeff @bond:p5-s6 harmonic 181.84 2.040 # SOUECE3 1 + bond_coeff @bond:p5-sh harmonic 163.76 2.082 # SOURCE3 3 0.0035 + bond_coeff @bond:p5-ss harmonic 150.09 2.118 # SOURCE4_SOURCE5 70 0.0117 + bond_coeff @bond:pe-pe harmonic 136.46 2.092 # SOURCE3 7 0.1369 + bond_coeff @bond:pe-pf harmonic 149.57 2.055 # SOURCE3 1 + bond_coeff @bond:pe-px harmonic 169.76 2.005 # SOURCE3 12 0.2609 + bond_coeff @bond:pe-py harmonic 161.32 2.025 # SOURCE3 12 0.2617 + bond_coeff @bond:pe-s harmonic 390.65 1.758 # SOURCE3 31 0.3197 + bond_coeff @bond:pe-sx harmonic 133.00 2.168 # SOURCE3 9 0.1743 + bond_coeff @bond:pe-sy harmonic 119.67 2.213 # SOURCE3 6 0.0127 + bond_coeff @bond:pf-pf harmonic 136.46 2.092 # SOURCE3 7 + bond_coeff @bond:pf-px harmonic 169.76 2.005 # SOURCE3 12 + bond_coeff @bond:pf-py harmonic 161.32 2.025 # SOURCE3 12 + bond_coeff @bond:pf-s harmonic 390.65 1.758 # SOURCE3 31 + bond_coeff @bond:pf-sx harmonic 133.00 2.168 # SOURCE3 9 + bond_coeff @bond:pf-sy harmonic 119.67 2.213 # SOURCE3 6 + bond_coeff @bond:px-py harmonic 105.60 2.199 # SOURCE3 5 0.0238 + bond_coeff @bond:px-sx harmonic 111.92 2.242 # SOURCE3 3 0.0119 + bond_coeff @bond:px-sy harmonic 110.14 2.249 # SOURCE3 3 0.0272 + bond_coeff @bond:py-py harmonic 108.87 2.186 # SOURCE3 8 0.0132 + bond_coeff @bond:py-sx harmonic 107.66 2.259 # SOURCE3 7 0.0603 + bond_coeff @bond:py-sy harmonic 128.67 2.182 # SOURCE3 5 0.0047 + bond_coeff @bond:s4-s4 harmonic 243.62 2.080 # SOUECE3 1 + bond_coeff @bond:s4-s6 harmonic 243.62 2.080 # SOUECE3 1 + bond_coeff @bond:s4-sh harmonic 196.89 2.168 # SOURCE3 3 0.0227 + bond_coeff @bond:s4-ss harmonic 197.83 2.166 # SOURCE3 5 0.0247 + bond_coeff @bond:s6-s6 harmonic 243.62 2.080 # SOUECE3 1 + bond_coeff @bond:s6-sh harmonic 227.44 2.108 # SOURCE3 3 0.0144 + bond_coeff @bond:s6-ss harmonic 221.98 2.118 # SOURCE3 5 0.0209 + bond_coeff @bond:sh-sh harmonic 257.31 2.058 # SOURCE2 1 + bond_coeff @bond:sh-ss harmonic 251.60 2.067 # SOURCE3 3 0.0029 + bond_coeff @bond:s-s harmonic 276.08 2.030 # SOURCE3 1 + bond_coeff @bond:s-s2 harmonic 391.11 1.897 # SOURCE1 5 + bond_coeff @bond:s-s4 harmonic 246.05 2.076 # SOURCE3 4 0.0345 + bond_coeff @bond:s-s6 harmonic 270.56 2.038 # SOURCE3 3 0.0311 + bond_coeff @bond:s-sh harmonic 226.34 2.110 # SOURCE3 2 + bond_coeff @bond:s-ss harmonic 238.28 2.089 # SOURCE3 1 + bond_coeff @bond:ss-ss harmonic 248.01 2.073 # SOURCE1_SOURCE5 457 0.0074 + bond_coeff @bond:sx-sx harmonic 119.03 2.391 # SOURCE3 3 0.0185 + bond_coeff @bond:sx-sy harmonic 160.84 2.255 # SOURCE3 5 0.0737 + bond_coeff @bond:sy-sy harmonic 162.69 2.250 # SOURCE3 3 0.0289 + bond_coeff @bond:br-cd harmonic 172.53 1.885 # SOURCE4_SOURCE5 89 0.0082 + bond_coeff @bond:c1-cf harmonic 518.69 1.315 # SOURCE4 6 + bond_coeff @bond:cd-f harmonic 364.99 1.341 # SOURCE4_SOURCE5 46 0.0041 + bond_coeff @bond:cd-n4 harmonic 236.72 1.493 # SOURCE4 7 + bond_coeff @bond:cd-nf harmonic 356.61 1.379 # SOURCE4_SOURCE5 52 0.0115 + bond_coeff @bond:cd-no harmonic 296.62 1.429 # SOURCE4_SOURCE5 253 0.0081 + bond_coeff @bond:cd-sh harmonic 223.28 1.769 # SOURCE4_SOURCE5 14 0.0031 + bond_coeff @bond:cd-sx harmonic 198.26 1.811 # SOURCE4_SOURCE5 28 0.0024 + bond_coeff @bond:cc-cy harmonic 259.34 1.505 # SOURCE4_SOURCE5 11 0.0006 + bond_coeff @bond:cf-cl harmonic 174.72 1.764 # SOURCE4_SOURCE5 66 0.0129 + bond_coeff @bond:cf-cx harmonic 261.83 1.502 # SOURCE4_SOURCE5 26 0.0077 + bond_coeff @bond:cf-cy harmonic 250.06 1.516 # SOURCE4_SOURCE5 36 0.0052 + bond_coeff @bond:cf-na harmonic 305.30 1.421 # SOURCE4_SOURCE5 6 0.0049 + bond_coeff @bond:cf-ss harmonic 215.60 1.781 # SOURCE4_SOURCE5 46 0.0106 + bond_coeff @bond:cq-na harmonic 349.52 1.384 # SOURCE4 7 + bond_coeff @bond:cq-nb harmonic 414.72 1.339 # SOURCE4_SOURCE5 120 0.0071 + bond_coeff @bond:cl-py harmonic 152.76 2.045 # SOURCE5 45 0.0072 + bond_coeff @bond:f-py harmonic 456.16 1.577 # SOURCE5 25 0.0035 + bond_coeff @bond:py-s harmonic 215.89 1.973 # SOURCE5 17 0.0159 + bond_coeff @bond:cy-nh harmonic 251.08 1.476 # SOURCE5 16 0.0050 + bond_coeff @bond:cy-hx harmonic 386.49 1.091 # SOURCE5 13 0.0007 + bond_coeff @bond:br-ce harmonic 163.42 1.905 # SOURCE5 12 0.0099 + bond_coeff @bond:cc-i harmonic 110.60 2.120 # SOURCE5 11 0.0086 + bond_coeff @bond:cy-n4 harmonic 214.44 1.522 # SOURCE5 11 0.0076 + bond_coeff @bond:cy-p3 harmonic 146.83 1.908 # SOURCE5 10 0.0056 + bond_coeff @bond:cy-na harmonic 279.03 1.446 # SOURCE5 8 0.0049 + bond_coeff @bond:cx-n4 harmonic 234.29 1.496 # SOURCE5 9 0.0009 + bond_coeff @bond:ne-s4 harmonic 338.65 1.660 # SOURCE5 6 0.0027 + bond_coeff @bond:cv-ss harmonic 228.75 1.761 # SOURCE5 8 0.0086 + bond_coeff @bond:cy-no harmonic 216.62 1.519 # SOURCE5 7 0.0035 + bond_coeff @bond:ce-cv harmonic 436.82 1.360 # SOURCE5 6 0.0111 + bond_coeff @bond:cd-i harmonic 111.95 2.115 # SOURCE5 7 0.0138 + bond_coeff @bond:cy-s4 harmonic 149.47 1.913 # SOURCE5 5 0.0068 + bond_coeff @bond:n2-sy harmonic 491.42 1.544 # SOURCE5 7 0.0042 + bond_coeff @bond:cc-s6 harmonic 196.41 1.814 # SOURCE5 6 0.0108 + bond_coeff @bond:i-s2 harmonic 48.08 2.883 # SOURCE5 5 0.0165 + bond_coeff @bond:br-cy harmonic 144.56 1.951 # SOURCE5 5 0.0056 + bond_coeff @bond:br-cf harmonic 163.42 1.905 # SOURCE5 12 0.0099 + bond_coeff @bond:nf-s4 harmonic 338.65 1.660 # SOURCE5 6 0.0027 + bond_coeff @bond:cf-cv harmonic 436.82 1.360 # SOURCE5 6 0.0111 + bond_coeff @bond:cd-s6 harmonic 196.41 1.814 # SOURCE5 6 0.0108 + bond_coeff @bond:ss-sy harmonic 177.36 2.212 # SOURCE5 4 0.0105 + bond_coeff @bond:h5-ce harmonic 390.52 1.089 # SOURCE5 4 0.0006 + bond_coeff @bond:h5-cf harmonic 390.52 1.089 # SOURCE5 4 0.0006 + bond_coeff @bond:ce-s4 harmonic 226.75 1.764 # SOURCE5 4 0.0087 + bond_coeff @bond:cf-s4 harmonic 226.69 1.764 # SOURCE5 4 0.0087 + bond_coeff @bond:cy-py harmonic 136.02 1.937 # SOURCE5 4 0.0000 + bond_coeff @bond:cd-o harmonic 649.55 1.219 # SOURCE5 4 0.0015 + bond_coeff @bond:ne-s6 harmonic 412.23 1.598 # SOURCE5 3 0.0054 + bond_coeff @bond:nf-s6 harmonic 412.23 1.598 # SOURCE5 3 0.0054 + bond_coeff @bond:ce-no harmonic 262.66 1.463 # SOURCE5 3 0.0129 + bond_coeff @bond:cf-no harmonic 262.66 1.463 # SOURCE5 3 0.0129 + } # (end of bond_coeffs) + + write_once("Data Bonds By Type") { + @bond:ow-hw @atom:ow @atom:hw + @bond:hw-hw @atom:hw @atom:hw + @bond:br-br @atom:br @atom:br + @bond:br-c1 @atom:br @atom:c1 + @bond:br-c2 @atom:br @atom:c2 + @bond:br-c @atom:br @atom:c + @bond:br-c3 @atom:br @atom:c3 + @bond:br-ca @atom:br @atom:ca + @bond:br-cc @atom:br @atom:cc + @bond:br-cx @atom:br @atom:cx + @bond:br-n1 @atom:br @atom:n1 + @bond:br-n2 @atom:br @atom:n2 + @bond:br-n @atom:br @atom:n + @bond:br-n3 @atom:br @atom:n3 + @bond:br-n4 @atom:br @atom:n4 + @bond:br-na @atom:br @atom:na + @bond:br-nh @atom:br @atom:nh + @bond:br-no @atom:br @atom:no + @bond:br-o @atom:br @atom:o + @bond:br-oh @atom:br @atom:oh + @bond:br-os @atom:br @atom:os + @bond:br-p2 @atom:br @atom:p2 + @bond:br-p3 @atom:br @atom:p3 + @bond:br-p4 @atom:br @atom:p4 + @bond:br-p5 @atom:br @atom:p5 + @bond:br-s @atom:br @atom:s + @bond:br-s4 @atom:br @atom:s4 + @bond:br-s6 @atom:br @atom:s6 + @bond:br-sh @atom:br @atom:sh + @bond:br-ss @atom:br @atom:ss + @bond:c1-c1 @atom:c1 @atom:c1 + @bond:c1-c2 @atom:c1 @atom:c2 + @bond:c1-c3 @atom:c1 @atom:c3 + @bond:c1-ca @atom:c1 @atom:ca + @bond:c1-ce @atom:c1 @atom:ce + @bond:c1-cg @atom:c1 @atom:cg + @bond:c1-ch @atom:c1 @atom:ch + @bond:c1-cl @atom:c1 @atom:cl + @bond:c1-cx @atom:c1 @atom:cx + @bond:c1-f @atom:c1 @atom:f + @bond:c1-ha @atom:c1 @atom:ha + @bond:c1-hc @atom:c1 @atom:hc + @bond:c1-i @atom:c1 @atom:i + @bond:c1-n1 @atom:c1 @atom:n1 + @bond:c1-n2 @atom:c1 @atom:n2 + @bond:c1-n3 @atom:c1 @atom:n3 + @bond:c1-n4 @atom:c1 @atom:n4 + @bond:c1-n @atom:c1 @atom:n + @bond:c1-na @atom:c1 @atom:na + @bond:c1-ne @atom:c1 @atom:ne + @bond:c1-nf @atom:c1 @atom:nf + @bond:c1-nh @atom:c1 @atom:nh + @bond:c1-no @atom:c1 @atom:no + @bond:c1-o @atom:c1 @atom:o + @bond:c1-oh @atom:c1 @atom:oh + @bond:c1-os @atom:c1 @atom:os + @bond:c1-p2 @atom:c1 @atom:p2 + @bond:c1-p3 @atom:c1 @atom:p3 + @bond:c1-p4 @atom:c1 @atom:p4 + @bond:c1-p5 @atom:c1 @atom:p5 + @bond:c1-s2 @atom:c1 @atom:s2 + @bond:c1-s @atom:c1 @atom:s + @bond:c1-s4 @atom:c1 @atom:s4 + @bond:c1-s6 @atom:c1 @atom:s6 + @bond:c1-sh @atom:c1 @atom:sh + @bond:c1-ss @atom:c1 @atom:ss + @bond:c2-c2 @atom:c2 @atom:c2 + @bond:c2-c3 @atom:c2 @atom:c3 + @bond:c2-ca @atom:c2 @atom:ca + @bond:c2-cc @atom:c2 @atom:cc + @bond:c2-cd @atom:c2 @atom:cd + @bond:c2-ce @atom:c2 @atom:ce + @bond:c2-cf @atom:c2 @atom:cf + @bond:c2-cl @atom:c2 @atom:cl + @bond:c2-cu @atom:c2 @atom:cu + @bond:c2-cx @atom:c2 @atom:cx + @bond:c2-cy @atom:c2 @atom:cy + @bond:c2-f @atom:c2 @atom:f + @bond:c2-h4 @atom:c2 @atom:h4 + @bond:c2-h5 @atom:c2 @atom:h5 + @bond:c2-ha @atom:c2 @atom:ha + @bond:c2-hc @atom:c2 @atom:hc + @bond:c2-hx @atom:c2 @atom:hx + @bond:c2-i @atom:c2 @atom:i + @bond:c2-n1 @atom:c2 @atom:n1 + @bond:c2-n2 @atom:c2 @atom:n2 + @bond:c2-n3 @atom:c2 @atom:n3 + @bond:c2-n @atom:c2 @atom:n + @bond:c2-n4 @atom:c2 @atom:n4 + @bond:c2-na @atom:c2 @atom:na + @bond:c2-nc @atom:c2 @atom:nc + @bond:c2-nd @atom:c2 @atom:nd + @bond:c2-ne @atom:c2 @atom:ne + @bond:c2-nf @atom:c2 @atom:nf + @bond:c2-nh @atom:c2 @atom:nh + @bond:c2-no @atom:c2 @atom:no + @bond:c2-o @atom:c2 @atom:o + @bond:c2-oh @atom:c2 @atom:oh + @bond:c2-os @atom:c2 @atom:os + @bond:c2-p2 @atom:c2 @atom:p2 + @bond:c2-p3 @atom:c2 @atom:p3 + @bond:c2-p4 @atom:c2 @atom:p4 + @bond:c2-p5 @atom:c2 @atom:p5 + @bond:c2-pe @atom:c2 @atom:pe + @bond:c2-pf @atom:c2 @atom:pf + @bond:c2-s2 @atom:c2 @atom:s2 + @bond:c2-s @atom:c2 @atom:s + @bond:c2-s4 @atom:c2 @atom:s4 + @bond:c2-s6 @atom:c2 @atom:s6 + @bond:c2-sh @atom:c2 @atom:sh + @bond:c2-ss @atom:c2 @atom:ss + @bond:c3-c3 @atom:c3 @atom:c3 + @bond:c3-ca @atom:c3 @atom:ca + @bond:c3-cc @atom:c3 @atom:cc + @bond:c3-cd @atom:c3 @atom:cd + @bond:c3-ce @atom:c3 @atom:ce + @bond:c3-cf @atom:c3 @atom:cf + @bond:c3-cl @atom:c3 @atom:cl + @bond:c3-cu @atom:c3 @atom:cu + @bond:c3-cv @atom:c3 @atom:cv + @bond:c3-cx @atom:c3 @atom:cx + @bond:c3-cy @atom:c3 @atom:cy + @bond:c3-f @atom:c3 @atom:f + @bond:c3-h1 @atom:c3 @atom:h1 + @bond:c3-h2 @atom:c3 @atom:h2 + @bond:c3-h3 @atom:c3 @atom:h3 + @bond:c3-hc @atom:c3 @atom:hc + @bond:c3-hx @atom:c3 @atom:hx + @bond:c3-i @atom:c3 @atom:i + @bond:c3-n1 @atom:c3 @atom:n1 + @bond:c3-n2 @atom:c3 @atom:n2 + @bond:c3-n @atom:c3 @atom:n + @bond:c3-n3 @atom:c3 @atom:n3 + @bond:c3-n4 @atom:c3 @atom:n4 + @bond:c3-na @atom:c3 @atom:na + @bond:c3-nc @atom:c3 @atom:nc + @bond:c3-nd @atom:c3 @atom:nd + @bond:c3-nh @atom:c3 @atom:nh + @bond:c3-no @atom:c3 @atom:no + @bond:c3-o @atom:c3 @atom:o + @bond:c3-oh @atom:c3 @atom:oh + @bond:c3-os @atom:c3 @atom:os + @bond:c3-p2 @atom:c3 @atom:p2 + @bond:c3-p3 @atom:c3 @atom:p3 + @bond:c3-p4 @atom:c3 @atom:p4 + @bond:c3-p5 @atom:c3 @atom:p5 + @bond:c3-px @atom:c3 @atom:px + @bond:c3-py @atom:c3 @atom:py + @bond:c3-s @atom:c3 @atom:s + @bond:c3-s4 @atom:c3 @atom:s4 + @bond:c3-s6 @atom:c3 @atom:s6 + @bond:c3-sh @atom:c3 @atom:sh + @bond:c3-ss @atom:c3 @atom:ss + @bond:c3-sx @atom:c3 @atom:sx + @bond:c3-sy @atom:c3 @atom:sy + @bond:ca-ca @atom:ca @atom:ca + @bond:ca-cc @atom:ca @atom:cc + @bond:ca-cd @atom:ca @atom:cd + @bond:ca-ce @atom:ca @atom:ce + @bond:ca-cf @atom:ca @atom:cf + @bond:ca-cg @atom:ca @atom:cg + @bond:ca-ch @atom:ca @atom:ch + @bond:ca-cl @atom:ca @atom:cl + @bond:ca-cp @atom:ca @atom:cp + @bond:ca-cq @atom:ca @atom:cq + @bond:ca-cx @atom:ca @atom:cx + @bond:ca-cy @atom:ca @atom:cy + @bond:ca-f @atom:ca @atom:f + @bond:ca-h4 @atom:ca @atom:h4 + @bond:ca-h5 @atom:ca @atom:h5 + @bond:ca-ha @atom:ca @atom:ha + @bond:ca-i @atom:ca @atom:i + @bond:ca-n1 @atom:ca @atom:n1 + @bond:ca-n2 @atom:ca @atom:n2 + @bond:ca-n @atom:ca @atom:n + @bond:ca-n4 @atom:ca @atom:n4 + @bond:ca-na @atom:ca @atom:na + @bond:ca-nb @atom:ca @atom:nb + @bond:ca-nc @atom:ca @atom:nc + @bond:ca-nd @atom:ca @atom:nd + @bond:ca-ne @atom:ca @atom:ne + @bond:ca-nf @atom:ca @atom:nf + @bond:ca-nh @atom:ca @atom:nh + @bond:ca-no @atom:ca @atom:no + @bond:ca-o @atom:ca @atom:o + @bond:ca-oh @atom:ca @atom:oh + @bond:ca-os @atom:ca @atom:os + @bond:ca-p2 @atom:ca @atom:p2 + @bond:ca-p3 @atom:ca @atom:p3 + @bond:ca-p4 @atom:ca @atom:p4 + @bond:ca-p5 @atom:ca @atom:p5 + @bond:ca-pe @atom:ca @atom:pe + @bond:ca-pf @atom:ca @atom:pf + @bond:ca-px @atom:ca @atom:px + @bond:ca-py @atom:ca @atom:py + @bond:ca-s @atom:ca @atom:s + @bond:ca-s4 @atom:ca @atom:s4 + @bond:ca-s6 @atom:ca @atom:s6 + @bond:ca-sh @atom:ca @atom:sh + @bond:ca-ss @atom:ca @atom:ss + @bond:ca-sx @atom:ca @atom:sx + @bond:ca-sy @atom:ca @atom:sy + @bond:c-c1 @atom:c @atom:c1 + @bond:c-c2 @atom:c @atom:c2 + @bond:c-c @atom:c @atom:c + @bond:c-c3 @atom:c @atom:c3 + @bond:c-ca @atom:c @atom:ca + @bond:c-cc @atom:c @atom:cc + @bond:cc-cc @atom:cc @atom:cc + @bond:cc-cd @atom:cc @atom:cd + @bond:cc-ce @atom:cc @atom:ce + @bond:cc-cf @atom:cc @atom:cf + @bond:cc-cg @atom:cc @atom:cg + @bond:cc-ch @atom:cc @atom:ch + @bond:cc-cl @atom:cc @atom:cl + @bond:cc-cx @atom:cc @atom:cx + @bond:c-cd @atom:c @atom:cd + @bond:c-ce @atom:c @atom:ce + @bond:c-cf @atom:c @atom:cf + @bond:cc-f @atom:cc @atom:f + @bond:c-cg @atom:c @atom:cg + @bond:c-ch @atom:c @atom:ch + @bond:cc-h4 @atom:cc @atom:h4 + @bond:cc-h5 @atom:cc @atom:h5 + @bond:cc-ha @atom:cc @atom:ha + @bond:c-cl @atom:c @atom:cl + @bond:cc-n2 @atom:cc @atom:n2 + @bond:cc-n @atom:cc @atom:n + @bond:cc-n4 @atom:cc @atom:n4 + @bond:cc-na @atom:cc @atom:na + @bond:cc-nc @atom:cc @atom:nc + @bond:cc-nd @atom:cc @atom:nd + @bond:cc-ne @atom:cc @atom:ne + @bond:cc-nf @atom:cc @atom:nf + @bond:cc-nh @atom:cc @atom:nh + @bond:cc-no @atom:cc @atom:no + @bond:cc-oh @atom:cc @atom:oh + @bond:cc-os @atom:cc @atom:os + @bond:cc-pd @atom:cc @atom:pd + @bond:cc-sh @atom:cc @atom:sh + @bond:cc-ss @atom:cc @atom:ss + @bond:cc-sx @atom:cc @atom:sx + @bond:cc-sy @atom:cc @atom:sy + @bond:c-cu @atom:c @atom:cu + @bond:c-cx @atom:c @atom:cx + @bond:c-cy @atom:c @atom:cy + @bond:cd-cd @atom:cd @atom:cd + @bond:cd-ce @atom:cd @atom:ce + @bond:cd-cf @atom:cd @atom:cf + @bond:cd-cg @atom:cd @atom:cg + @bond:cd-ch @atom:cd @atom:ch + @bond:cd-cl @atom:cd @atom:cl + @bond:cd-cx @atom:cd @atom:cx + @bond:cd-cy @atom:cd @atom:cy + @bond:cd-h4 @atom:cd @atom:h4 + @bond:cd-h5 @atom:cd @atom:h5 + @bond:cd-ha @atom:cd @atom:ha + @bond:cd-n2 @atom:cd @atom:n2 + @bond:cd-n @atom:cd @atom:n + @bond:cd-na @atom:cd @atom:na + @bond:cd-nc @atom:cd @atom:nc + @bond:cd-nd @atom:cd @atom:nd + @bond:cd-ne @atom:cd @atom:ne + @bond:cd-nh @atom:cd @atom:nh + @bond:cd-oh @atom:cd @atom:oh + @bond:cd-os @atom:cd @atom:os + @bond:cd-pc @atom:cd @atom:pc + @bond:cd-ss @atom:cd @atom:ss + @bond:cd-sy @atom:cd @atom:sy + @bond:ce-ce @atom:ce @atom:ce + @bond:ce-cf @atom:ce @atom:cf + @bond:ce-cg @atom:ce @atom:cg + @bond:ce-ch @atom:ce @atom:ch + @bond:ce-cl @atom:ce @atom:cl + @bond:ce-cx @atom:ce @atom:cx + @bond:ce-cy @atom:ce @atom:cy + @bond:ce-h4 @atom:ce @atom:h4 + @bond:ce-ha @atom:ce @atom:ha + @bond:ce-n1 @atom:ce @atom:n1 + @bond:ce-n2 @atom:ce @atom:n2 + @bond:ce-n @atom:ce @atom:n + @bond:ce-na @atom:ce @atom:na + @bond:ce-ne @atom:ce @atom:ne + @bond:ce-nf @atom:ce @atom:nf + @bond:ce-nh @atom:ce @atom:nh + @bond:ce-oh @atom:ce @atom:oh + @bond:ce-os @atom:ce @atom:os + @bond:ce-p2 @atom:ce @atom:p2 + @bond:ce-pe @atom:ce @atom:pe + @bond:ce-px @atom:ce @atom:px + @bond:ce-py @atom:ce @atom:py + @bond:ce-s @atom:ce @atom:s + @bond:ce-ss @atom:ce @atom:ss + @bond:ce-sx @atom:ce @atom:sx + @bond:ce-sy @atom:ce @atom:sy + @bond:c-f @atom:c @atom:f + @bond:cf-cf @atom:cf @atom:cf + @bond:cf-cg @atom:cf @atom:cg + @bond:cf-ch @atom:cf @atom:ch + @bond:cf-h4 @atom:cf @atom:h4 + @bond:cf-ha @atom:cf @atom:ha + @bond:cf-n1 @atom:cf @atom:n1 + @bond:cf-n2 @atom:cf @atom:n2 + @bond:cf-n @atom:cf @atom:n + @bond:cf-ne @atom:cf @atom:ne + @bond:cf-nf @atom:cf @atom:nf + @bond:cf-nh @atom:cf @atom:nh + @bond:cf-oh @atom:cf @atom:oh + @bond:cf-os @atom:cf @atom:os + @bond:cf-p2 @atom:cf @atom:p2 + @bond:cf-pf @atom:cf @atom:pf + @bond:cf-px @atom:cf @atom:px + @bond:cf-py @atom:cf @atom:py + @bond:cf-s @atom:cf @atom:s + @bond:cf-sx @atom:cf @atom:sx + @bond:cf-sy @atom:cf @atom:sy + @bond:cg-cg @atom:cg @atom:cg + @bond:cg-ch @atom:cg @atom:ch + @bond:cg-n1 @atom:cg @atom:n1 + @bond:cg-ne @atom:cg @atom:ne + @bond:cg-pe @atom:cg @atom:pe + @bond:c-h4 @atom:c @atom:h4 + @bond:c-h5 @atom:c @atom:h5 + @bond:c-ha @atom:c @atom:ha + @bond:ch-ch @atom:ch @atom:ch + @bond:ch-n1 @atom:ch @atom:n1 + @bond:ch-nf @atom:ch @atom:nf + @bond:ch-pf @atom:ch @atom:pf + @bond:c-i @atom:c @atom:i + @bond:cl-cl @atom:cl @atom:cl + @bond:cl-cx @atom:cl @atom:cx + @bond:cl-cy @atom:cl @atom:cy + @bond:cl-n1 @atom:cl @atom:n1 + @bond:cl-n2 @atom:cl @atom:n2 + @bond:cl-n3 @atom:cl @atom:n3 + @bond:cl-n @atom:cl @atom:n + @bond:cl-n4 @atom:cl @atom:n4 + @bond:cl-na @atom:cl @atom:na + @bond:cl-nh @atom:cl @atom:nh + @bond:cl-no @atom:cl @atom:no + @bond:cl-o @atom:cl @atom:o + @bond:cl-oh @atom:cl @atom:oh + @bond:cl-os @atom:cl @atom:os + @bond:cl-p2 @atom:cl @atom:p2 + @bond:cl-p3 @atom:cl @atom:p3 + @bond:cl-p4 @atom:cl @atom:p4 + @bond:cl-p5 @atom:cl @atom:p5 + @bond:cl-pb @atom:cl @atom:pb + @bond:cl-s @atom:cl @atom:s + @bond:cl-s2 @atom:cl @atom:s2 + @bond:cl-s4 @atom:cl @atom:s4 + @bond:cl-s6 @atom:cl @atom:s6 + @bond:cl-sh @atom:cl @atom:sh + @bond:cl-ss @atom:cl @atom:ss + @bond:cl-sx @atom:cl @atom:sx + @bond:cl-sy @atom:cl @atom:sy + @bond:c-n2 @atom:c @atom:n2 + @bond:c-n4 @atom:c @atom:n4 + @bond:c-n @atom:c @atom:n + @bond:c-nc @atom:c @atom:nc + @bond:c-nd @atom:c @atom:nd + @bond:c-ne @atom:c @atom:ne + @bond:c-nf @atom:c @atom:nf + @bond:c-no @atom:c @atom:no + @bond:c-o @atom:c @atom:o + @bond:c-oh @atom:c @atom:oh + @bond:c-os @atom:c @atom:os + @bond:c-p2 @atom:c @atom:p2 + @bond:c-p3 @atom:c @atom:p3 + @bond:c-p4 @atom:c @atom:p4 + @bond:c-p5 @atom:c @atom:p5 + @bond:cp-cp @atom:cp @atom:cp + @bond:cp-cq @atom:cp @atom:cq + @bond:c-pe @atom:c @atom:pe + @bond:c-pf @atom:c @atom:pf + @bond:cp-na @atom:cp @atom:na + @bond:cp-nb @atom:cp @atom:nb + @bond:c-px @atom:c @atom:px + @bond:c-py @atom:c @atom:py + @bond:cq-cq @atom:cq @atom:cq + @bond:c-s @atom:c @atom:s + @bond:c-s4 @atom:c @atom:s4 + @bond:c-s6 @atom:c @atom:s6 + @bond:c-sh @atom:c @atom:sh + @bond:c-ss @atom:c @atom:ss + @bond:c-sx @atom:c @atom:sx + @bond:c-sy @atom:c @atom:sy + @bond:cu-cu @atom:cu @atom:cu + @bond:cu-cx @atom:cu @atom:cx + @bond:cu-ha @atom:cu @atom:ha + @bond:cv-cv @atom:cv @atom:cv + @bond:cv-cy @atom:cv @atom:cy + @bond:cv-ha @atom:cv @atom:ha + @bond:cx-cv @atom:cx @atom:cv + @bond:cx-cx @atom:cx @atom:cx + @bond:cx-cy @atom:cx @atom:cy + @bond:cx-f @atom:cx @atom:f + @bond:cx-h1 @atom:cx @atom:h1 + @bond:cx-h2 @atom:cx @atom:h2 + @bond:cx-hc @atom:cx @atom:hc + @bond:cx-hx @atom:cx @atom:hx + @bond:cx-n2 @atom:cx @atom:n2 + @bond:cx-n3 @atom:cx @atom:n3 + @bond:cx-n @atom:cx @atom:n + @bond:cx-na @atom:cx @atom:na + @bond:cx-nh @atom:cx @atom:nh + @bond:cx-oh @atom:cx @atom:oh + @bond:cx-os @atom:cx @atom:os + @bond:cx-p3 @atom:cx @atom:p3 + @bond:cx-s4 @atom:cx @atom:s4 + @bond:cx-s6 @atom:cx @atom:s6 + @bond:cx-ss @atom:cx @atom:ss + @bond:cy-cy @atom:cy @atom:cy + @bond:cy-f @atom:cy @atom:f + @bond:cy-h1 @atom:cy @atom:h1 + @bond:cy-h2 @atom:cy @atom:h2 + @bond:cy-hc @atom:cy @atom:hc + @bond:cy-n @atom:cy @atom:n + @bond:cy-n3 @atom:cy @atom:n3 + @bond:cy-oh @atom:cy @atom:oh + @bond:cy-os @atom:cy @atom:os + @bond:cy-s6 @atom:cy @atom:s6 + @bond:cy-ss @atom:cy @atom:ss + @bond:cz-nh @atom:cz @atom:nh + @bond:f-n1 @atom:f @atom:n1 + @bond:f-n2 @atom:f @atom:n2 + @bond:f-n3 @atom:f @atom:n3 + @bond:f-n @atom:f @atom:n + @bond:f-n4 @atom:f @atom:n4 + @bond:f-na @atom:f @atom:na + @bond:f-nh @atom:f @atom:nh + @bond:f-no @atom:f @atom:no + @bond:f-o @atom:f @atom:o + @bond:f-oh @atom:f @atom:oh + @bond:f-os @atom:f @atom:os + @bond:f-p2 @atom:f @atom:p2 + @bond:f-p3 @atom:f @atom:p3 + @bond:f-p4 @atom:f @atom:p4 + @bond:f-p5 @atom:f @atom:p5 + @bond:f-s2 @atom:f @atom:s2 + @bond:f-s @atom:f @atom:s + @bond:f-s4 @atom:f @atom:s4 + @bond:f-s6 @atom:f @atom:s6 + @bond:f-sh @atom:f @atom:sh + @bond:f-ss @atom:f @atom:ss + @bond:hn-n1 @atom:hn @atom:n1 + @bond:hn-n2 @atom:hn @atom:n2 + @bond:hn-n3 @atom:hn @atom:n3 + @bond:hn-n @atom:hn @atom:n + @bond:hn-n4 @atom:hn @atom:n4 + @bond:hn-na @atom:hn @atom:na + @bond:hn-nh @atom:hn @atom:nh + @bond:hn-no @atom:hn @atom:no + @bond:ho-o @atom:ho @atom:o + @bond:ho-oh @atom:ho @atom:oh + @bond:hp-p2 @atom:hp @atom:p2 + @bond:hp-p3 @atom:hp @atom:p3 + @bond:hp-p4 @atom:hp @atom:p4 + @bond:hp-p5 @atom:hp @atom:p5 + @bond:hs-s @atom:hs @atom:s + @bond:hs-s4 @atom:hs @atom:s4 + @bond:hs-s6 @atom:hs @atom:s6 + @bond:hs-sh @atom:hs @atom:sh + @bond:i-i @atom:i @atom:i + @bond:i-n1 @atom:i @atom:n1 + @bond:i-n2 @atom:i @atom:n2 + @bond:i-n @atom:i @atom:n + @bond:i-n3 @atom:i @atom:n3 + @bond:i-n4 @atom:i @atom:n4 + @bond:i-na @atom:i @atom:na + @bond:i-nh @atom:i @atom:nh + @bond:i-no @atom:i @atom:no + @bond:i-o @atom:i @atom:o + @bond:i-oh @atom:i @atom:oh + @bond:i-os @atom:i @atom:os + @bond:i-p2 @atom:i @atom:p2 + @bond:i-p3 @atom:i @atom:p3 + @bond:i-p4 @atom:i @atom:p4 + @bond:i-p5 @atom:i @atom:p5 + @bond:i-s @atom:i @atom:s + @bond:i-s4 @atom:i @atom:s4 + @bond:i-s6 @atom:i @atom:s6 + @bond:i-sh @atom:i @atom:sh + @bond:i-ss @atom:i @atom:ss + @bond:n1-n1 @atom:n1 @atom:n1 + @bond:n1-n2 @atom:n1 @atom:n2 + @bond:n1-n3 @atom:n1 @atom:n3 + @bond:n1-n4 @atom:n1 @atom:n4 + @bond:n1-na @atom:n1 @atom:na + @bond:n1-nc @atom:n1 @atom:nc + @bond:n1-nd @atom:n1 @atom:nd + @bond:n1-ne @atom:n1 @atom:ne + @bond:n1-nf @atom:n1 @atom:nf + @bond:n1-nh @atom:n1 @atom:nh + @bond:n1-no @atom:n1 @atom:no + @bond:n1-o @atom:n1 @atom:o + @bond:n1-oh @atom:n1 @atom:oh + @bond:n1-os @atom:n1 @atom:os + @bond:n1-p2 @atom:n1 @atom:p2 + @bond:n1-p3 @atom:n1 @atom:p3 + @bond:n1-p4 @atom:n1 @atom:p4 + @bond:n1-p5 @atom:n1 @atom:p5 + @bond:n1-s2 @atom:n1 @atom:s2 + @bond:n1-s @atom:n1 @atom:s + @bond:n1-s4 @atom:n1 @atom:s4 + @bond:n1-s6 @atom:n1 @atom:s6 + @bond:n1-sh @atom:n1 @atom:sh + @bond:n1-ss @atom:n1 @atom:ss + @bond:n2-n2 @atom:n2 @atom:n2 + @bond:n2-n3 @atom:n2 @atom:n3 + @bond:n2-n4 @atom:n2 @atom:n4 + @bond:n2-na @atom:n2 @atom:na + @bond:n2-nc @atom:n2 @atom:nc + @bond:n2-nd @atom:n2 @atom:nd + @bond:n2-ne @atom:n2 @atom:ne + @bond:n2-nf @atom:n2 @atom:nf + @bond:n2-nh @atom:n2 @atom:nh + @bond:n2-no @atom:n2 @atom:no + @bond:n2-o @atom:n2 @atom:o + @bond:n2-oh @atom:n2 @atom:oh + @bond:n2-os @atom:n2 @atom:os + @bond:n2-p2 @atom:n2 @atom:p2 + @bond:n2-p3 @atom:n2 @atom:p3 + @bond:n2-p4 @atom:n2 @atom:p4 + @bond:n2-p5 @atom:n2 @atom:p5 + @bond:n2-pe @atom:n2 @atom:pe + @bond:n2-pf @atom:n2 @atom:pf + @bond:n2-s2 @atom:n2 @atom:s2 + @bond:n2-s4 @atom:n2 @atom:s4 + @bond:n2-s @atom:n2 @atom:s + @bond:n2-s6 @atom:n2 @atom:s6 + @bond:n2-sh @atom:n2 @atom:sh + @bond:n2-ss @atom:n2 @atom:ss + @bond:n3-n3 @atom:n3 @atom:n3 + @bond:n3-n4 @atom:n3 @atom:n4 + @bond:n3-na @atom:n3 @atom:na + @bond:n3-nh @atom:n3 @atom:nh + @bond:n3-no @atom:n3 @atom:no + @bond:n3-o @atom:n3 @atom:o + @bond:n3-oh @atom:n3 @atom:oh + @bond:n3-os @atom:n3 @atom:os + @bond:n3-p2 @atom:n3 @atom:p2 + @bond:n3-p3 @atom:n3 @atom:p3 + @bond:n3-p4 @atom:n3 @atom:p4 + @bond:n3-p5 @atom:n3 @atom:p5 + @bond:n3-py @atom:n3 @atom:py + @bond:n3-s @atom:n3 @atom:s + @bond:n3-s4 @atom:n3 @atom:s4 + @bond:n3-s6 @atom:n3 @atom:s6 + @bond:n3-sh @atom:n3 @atom:sh + @bond:n3-ss @atom:n3 @atom:ss + @bond:n3-sy @atom:n3 @atom:sy + @bond:n4-n4 @atom:n4 @atom:n4 + @bond:n4-na @atom:n4 @atom:na + @bond:n4-nh @atom:n4 @atom:nh + @bond:n4-no @atom:n4 @atom:no + @bond:n4-o @atom:n4 @atom:o + @bond:n4-oh @atom:n4 @atom:oh + @bond:n4-os @atom:n4 @atom:os + @bond:n4-p2 @atom:n4 @atom:p2 + @bond:n4-p3 @atom:n4 @atom:p3 + @bond:n4-p4 @atom:n4 @atom:p4 + @bond:n4-p5 @atom:n4 @atom:p5 + @bond:n4-py @atom:n4 @atom:py + @bond:n4-s @atom:n4 @atom:s + @bond:n4-s4 @atom:n4 @atom:s4 + @bond:n4-s6 @atom:n4 @atom:s6 + @bond:n4-sh @atom:n4 @atom:sh + @bond:n4-ss @atom:n4 @atom:ss + @bond:na-na @atom:na @atom:na + @bond:na-nb @atom:na @atom:nb + @bond:na-nc @atom:na @atom:nc + @bond:na-nd @atom:na @atom:nd + @bond:na-nh @atom:na @atom:nh + @bond:na-no @atom:na @atom:no + @bond:na-o @atom:na @atom:o + @bond:na-oh @atom:na @atom:oh + @bond:na-os @atom:na @atom:os + @bond:na-p2 @atom:na @atom:p2 + @bond:na-p3 @atom:na @atom:p3 + @bond:na-p4 @atom:na @atom:p4 + @bond:na-p5 @atom:na @atom:p5 + @bond:na-pc @atom:na @atom:pc + @bond:na-pd @atom:na @atom:pd + @bond:na-py @atom:na @atom:py + @bond:na-s @atom:na @atom:s + @bond:na-s4 @atom:na @atom:s4 + @bond:na-s6 @atom:na @atom:s6 + @bond:na-sh @atom:na @atom:sh + @bond:na-ss @atom:na @atom:ss + @bond:na-sy @atom:na @atom:sy + @bond:nb-nb @atom:nb @atom:nb + @bond:nb-pb @atom:nb @atom:pb + @bond:nc-nc @atom:nc @atom:nc + @bond:nc-nd @atom:nc @atom:nd + @bond:nc-os @atom:nc @atom:os + @bond:nc-ss @atom:nc @atom:ss + @bond:nc-sy @atom:nc @atom:sy + @bond:nd-nd @atom:nd @atom:nd + @bond:nd-os @atom:nd @atom:os + @bond:nd-ss @atom:nd @atom:ss + @bond:nd-sy @atom:nd @atom:sy + @bond:ne-ne @atom:ne @atom:ne + @bond:ne-nf @atom:ne @atom:nf + @bond:ne-o @atom:ne @atom:o + @bond:ne-p2 @atom:ne @atom:p2 + @bond:ne-pe @atom:ne @atom:pe + @bond:ne-px @atom:ne @atom:px + @bond:ne-py @atom:ne @atom:py + @bond:ne-s @atom:ne @atom:s + @bond:ne-sx @atom:ne @atom:sx + @bond:ne-sy @atom:ne @atom:sy + @bond:nf-nf @atom:nf @atom:nf + @bond:nf-o @atom:nf @atom:o + @bond:nf-p2 @atom:nf @atom:p2 + @bond:nf-pf @atom:nf @atom:pf + @bond:nf-px @atom:nf @atom:px + @bond:nf-py @atom:nf @atom:py + @bond:nf-s @atom:nf @atom:s + @bond:nf-sx @atom:nf @atom:sx + @bond:nf-sy @atom:nf @atom:sy + @bond:nh-nh @atom:nh @atom:nh + @bond:nh-no @atom:nh @atom:no + @bond:nh-o @atom:nh @atom:o + @bond:nh-oh @atom:nh @atom:oh + @bond:nh-os @atom:nh @atom:os + @bond:nh-p2 @atom:nh @atom:p2 + @bond:nh-p3 @atom:nh @atom:p3 + @bond:nh-p4 @atom:nh @atom:p4 + @bond:nh-p5 @atom:nh @atom:p5 + @bond:nh-s @atom:nh @atom:s + @bond:nh-s4 @atom:nh @atom:s4 + @bond:nh-s6 @atom:nh @atom:s6 + @bond:nh-sh @atom:nh @atom:sh + @bond:nh-ss @atom:nh @atom:ss + @bond:nh-sy @atom:nh @atom:sy + @bond:n-n1 @atom:n @atom:n1 + @bond:n-n2 @atom:n @atom:n2 + @bond:n-n3 @atom:n @atom:n3 + @bond:n-n4 @atom:n @atom:n4 + @bond:n-n @atom:n @atom:n + @bond:n-na @atom:n @atom:na + @bond:n-nc @atom:n @atom:nc + @bond:n-nd @atom:n @atom:nd + @bond:n-nh @atom:n @atom:nh + @bond:n-no @atom:n @atom:no + @bond:n-o @atom:n @atom:o + @bond:n-oh @atom:n @atom:oh + @bond:no-no @atom:no @atom:no + @bond:no-o @atom:no @atom:o + @bond:no-oh @atom:no @atom:oh + @bond:no-os @atom:no @atom:os + @bond:no-p2 @atom:no @atom:p2 + @bond:no-p3 @atom:no @atom:p3 + @bond:no-p4 @atom:no @atom:p4 + @bond:no-p5 @atom:no @atom:p5 + @bond:no-s @atom:no @atom:s + @bond:n-os @atom:n @atom:os + @bond:no-s4 @atom:no @atom:s4 + @bond:no-s6 @atom:no @atom:s6 + @bond:no-sh @atom:no @atom:sh + @bond:no-ss @atom:no @atom:ss + @bond:n-p2 @atom:n @atom:p2 + @bond:n-p3 @atom:n @atom:p3 + @bond:n-p4 @atom:n @atom:p4 + @bond:n-p5 @atom:n @atom:p5 + @bond:n-pc @atom:n @atom:pc + @bond:n-pd @atom:n @atom:pd + @bond:n-s @atom:n @atom:s + @bond:n-s4 @atom:n @atom:s4 + @bond:n-s6 @atom:n @atom:s6 + @bond:n-sh @atom:n @atom:sh + @bond:n-ss @atom:n @atom:ss + @bond:n-sy @atom:n @atom:sy + @bond:oh-oh @atom:oh @atom:oh + @bond:oh-os @atom:oh @atom:os + @bond:oh-p2 @atom:oh @atom:p2 + @bond:oh-p3 @atom:oh @atom:p3 + @bond:oh-p4 @atom:oh @atom:p4 + @bond:oh-p5 @atom:oh @atom:p5 + @bond:oh-py @atom:oh @atom:py + @bond:oh-s @atom:oh @atom:s + @bond:oh-s4 @atom:oh @atom:s4 + @bond:oh-s6 @atom:oh @atom:s6 + @bond:oh-sh @atom:oh @atom:sh + @bond:oh-ss @atom:oh @atom:ss + @bond:oh-sy @atom:oh @atom:sy + @bond:o-o @atom:o @atom:o + @bond:o-oh @atom:o @atom:oh + @bond:o-os @atom:o @atom:os + @bond:o-p2 @atom:o @atom:p2 + @bond:o-p3 @atom:o @atom:p3 + @bond:o-p4 @atom:o @atom:p4 + @bond:o-p5 @atom:o @atom:p5 + @bond:o-pe @atom:o @atom:pe + @bond:o-pf @atom:o @atom:pf + @bond:o-px @atom:o @atom:px + @bond:o-py @atom:o @atom:py + @bond:o-s @atom:o @atom:s + @bond:o-s2 @atom:o @atom:s2 + @bond:o-s4 @atom:o @atom:s4 + @bond:o-s6 @atom:o @atom:s6 + @bond:o-sh @atom:o @atom:sh + @bond:os-os @atom:os @atom:os + @bond:os-p2 @atom:os @atom:p2 + @bond:os-p3 @atom:os @atom:p3 + @bond:os-p4 @atom:os @atom:p4 + @bond:os-p5 @atom:os @atom:p5 + @bond:os-py @atom:os @atom:py + @bond:os-s @atom:os @atom:s + @bond:o-ss @atom:o @atom:ss + @bond:os-s4 @atom:os @atom:s4 + @bond:os-s6 @atom:os @atom:s6 + @bond:os-sh @atom:os @atom:sh + @bond:os-ss @atom:os @atom:ss + @bond:os-sy @atom:os @atom:sy + @bond:o-sx @atom:o @atom:sx + @bond:o-sy @atom:o @atom:sy + @bond:p2-p2 @atom:p2 @atom:p2 + @bond:p2-p3 @atom:p2 @atom:p3 + @bond:p2-p4 @atom:p2 @atom:p4 + @bond:p2-p5 @atom:p2 @atom:p5 + @bond:p2-pe @atom:p2 @atom:pe + @bond:p2-pf @atom:p2 @atom:pf + @bond:p2-s @atom:p2 @atom:s + @bond:p2-s4 @atom:p2 @atom:s4 + @bond:p2-s6 @atom:p2 @atom:s6 + @bond:p2-sh @atom:p2 @atom:sh + @bond:p2-ss @atom:p2 @atom:ss + @bond:p3-p3 @atom:p3 @atom:p3 + @bond:p3-p4 @atom:p3 @atom:p4 + @bond:p3-p5 @atom:p3 @atom:p5 + @bond:p3-s @atom:p3 @atom:s + @bond:p3-s4 @atom:p3 @atom:s4 + @bond:p3-s6 @atom:p3 @atom:s6 + @bond:p3-sh @atom:p3 @atom:sh + @bond:p3-ss @atom:p3 @atom:ss + @bond:p4-p4 @atom:p4 @atom:p4 + @bond:p4-p5 @atom:p4 @atom:p5 + @bond:p4-s @atom:p4 @atom:s + @bond:p4-s4 @atom:p4 @atom:s4 + @bond:p4-s6 @atom:p4 @atom:s6 + @bond:p4-sh @atom:p4 @atom:sh + @bond:p4-ss @atom:p4 @atom:ss + @bond:p5-p5 @atom:p5 @atom:p5 + @bond:p5-s @atom:p5 @atom:s + @bond:p5-s4 @atom:p5 @atom:s4 + @bond:p5-s6 @atom:p5 @atom:s6 + @bond:p5-sh @atom:p5 @atom:sh + @bond:p5-ss @atom:p5 @atom:ss + @bond:pe-pe @atom:pe @atom:pe + @bond:pe-pf @atom:pe @atom:pf + @bond:pe-px @atom:pe @atom:px + @bond:pe-py @atom:pe @atom:py + @bond:pe-s @atom:pe @atom:s + @bond:pe-sx @atom:pe @atom:sx + @bond:pe-sy @atom:pe @atom:sy + @bond:pf-pf @atom:pf @atom:pf + @bond:pf-px @atom:pf @atom:px + @bond:pf-py @atom:pf @atom:py + @bond:pf-s @atom:pf @atom:s + @bond:pf-sx @atom:pf @atom:sx + @bond:pf-sy @atom:pf @atom:sy + @bond:px-py @atom:px @atom:py + @bond:px-sx @atom:px @atom:sx + @bond:px-sy @atom:px @atom:sy + @bond:py-py @atom:py @atom:py + @bond:py-sx @atom:py @atom:sx + @bond:py-sy @atom:py @atom:sy + @bond:s4-s4 @atom:s4 @atom:s4 + @bond:s4-s6 @atom:s4 @atom:s6 + @bond:s4-sh @atom:s4 @atom:sh + @bond:s4-ss @atom:s4 @atom:ss + @bond:s6-s6 @atom:s6 @atom:s6 + @bond:s6-sh @atom:s6 @atom:sh + @bond:s6-ss @atom:s6 @atom:ss + @bond:sh-sh @atom:sh @atom:sh + @bond:sh-ss @atom:sh @atom:ss + @bond:s-s @atom:s @atom:s + @bond:s-s2 @atom:s @atom:s2 + @bond:s-s4 @atom:s @atom:s4 + @bond:s-s6 @atom:s @atom:s6 + @bond:s-sh @atom:s @atom:sh + @bond:s-ss @atom:s @atom:ss + @bond:ss-ss @atom:ss @atom:ss + @bond:sx-sx @atom:sx @atom:sx + @bond:sx-sy @atom:sx @atom:sy + @bond:sy-sy @atom:sy @atom:sy + @bond:br-cd @atom:br @atom:cd + @bond:c1-cf @atom:c1 @atom:cf + @bond:cd-f @atom:cd @atom:f + @bond:cd-n4 @atom:cd @atom:n4 + @bond:cd-nf @atom:cd @atom:nf + @bond:cd-no @atom:cd @atom:no + @bond:cd-sh @atom:cd @atom:sh + @bond:cd-sx @atom:cd @atom:sx + @bond:cc-cy @atom:cc @atom:cy + @bond:cf-cl @atom:cf @atom:cl + @bond:cf-cx @atom:cf @atom:cx + @bond:cf-cy @atom:cf @atom:cy + @bond:cf-na @atom:cf @atom:na + @bond:cf-ss @atom:cf @atom:ss + @bond:cq-na @atom:cq @atom:na + @bond:cq-nb @atom:cq @atom:nb + @bond:cl-py @atom:cl @atom:py + @bond:f-py @atom:f @atom:py + @bond:py-s @atom:py @atom:s + @bond:cy-nh @atom:cy @atom:nh + @bond:cy-hx @atom:cy @atom:hx + @bond:br-ce @atom:br @atom:ce + @bond:cc-i @atom:cc @atom:i + @bond:cy-n4 @atom:cy @atom:n4 + @bond:cy-p3 @atom:cy @atom:p3 + @bond:cy-na @atom:cy @atom:na + @bond:cx-n4 @atom:cx @atom:n4 + @bond:ne-s4 @atom:ne @atom:s4 + @bond:cv-ss @atom:cv @atom:ss + @bond:cy-no @atom:cy @atom:no + @bond:ce-cv @atom:ce @atom:cv + @bond:cd-i @atom:cd @atom:i + @bond:cy-s4 @atom:cy @atom:s4 + @bond:n2-sy @atom:n2 @atom:sy + @bond:cc-s6 @atom:cc @atom:s6 + @bond:i-s2 @atom:i @atom:s2 + @bond:br-cy @atom:br @atom:cy + @bond:br-cf @atom:br @atom:cf + @bond:nf-s4 @atom:nf @atom:s4 + @bond:cf-cv @atom:cf @atom:cv + @bond:cd-s6 @atom:cd @atom:s6 + @bond:ss-sy @atom:ss @atom:sy + @bond:h5-ce @atom:h5 @atom:ce + @bond:h5-cf @atom:h5 @atom:cf + @bond:ce-s4 @atom:ce @atom:s4 + @bond:cf-s4 @atom:cf @atom:s4 + @bond:cy-py @atom:cy @atom:py + @bond:cd-o @atom:cd @atom:o + @bond:ne-s6 @atom:ne @atom:s6 + @bond:nf-s6 @atom:nf @atom:s6 + @bond:ce-no @atom:ce @atom:no + @bond:cf-no @atom:cf @atom:no + } # (end of Bonds By Type) + + write_once("In Settings") { + angle_coeff @angle:hw-ow-hw harmonic 43.276 104.520 # AMBER 1 TIP3P_water + angle_coeff @angle:hw-hw-ow harmonic 0.000 127.740 # AMBER 1 (found_in_crystallographic_water_with_3_bonds) + angle_coeff @angle:br-c1-br harmonic 58.432 180.000 # Guess 0 + angle_coeff @angle:br-c1-c1 harmonic 56.125 180.000 # SOURCE3 1 + angle_coeff @angle:c1-c1-c1 harmonic 65.529 180.000 # SOURCE3 1 + angle_coeff @angle:c1-c1-c2 harmonic 62.451 180.000 # SOURCE3 2 + angle_coeff @angle:c1-c1-c3 harmonic 57.975 178.510 # SOURCE4_SOURCE5 618 0.7369 + angle_coeff @angle:c1-c1-ca harmonic 58.535 180.000 # SOURCE3 1 + angle_coeff @angle:c1-c1-cl harmonic 63.947 180.000 # SOURCE3 1 + angle_coeff @angle:c1-c1-f harmonic 80.686 180.000 # SOURCE3 1 + angle_coeff @angle:c1-c1-ha harmonic 44.782 179.110 # SOURCE3_SOURCE5 219 0.5885 + angle_coeff @angle:c1-c1-hc harmonic 44.772 180.000 # SOURCE3 1 + angle_coeff @angle:c1-c1-i harmonic 52.986 180.000 # SOURCE3 1 + angle_coeff @angle:c1-c1-n1 harmonic 83.562 180.000 # SOURCE3 1 + angle_coeff @angle:c1-c1-n2 harmonic 82.100 180.000 # SOURCE3 1 + angle_coeff @angle:c1-c1-n3 harmonic 76.721 180.000 # SOURCE3 1 + angle_coeff @angle:c1-c1-n4 harmonic 74.244 179.560 # SOURCE3 3 0.3096 + angle_coeff @angle:c1-c1-n harmonic 77.977 177.180 # SOURCE3 1 + angle_coeff @angle:c1-c1-na harmonic 76.884 176.750 # SOURCE3 8 2.9328 + angle_coeff @angle:c1-c1-nh harmonic 77.069 179.270 # SOURCE3 3 0.2357 + angle_coeff @angle:c1-c1-no harmonic 74.597 180.000 # SOURCE3 3 + angle_coeff @angle:c1-c1-o harmonic 82.936 180.000 # SOURCE3 1 + angle_coeff @angle:c1-c1-oh harmonic 78.242 176.650 # SOURCE3 1 + angle_coeff @angle:c1-c1-os harmonic 78.471 176.930 # SOURCE3_SOURCE5 5 1.1927 + angle_coeff @angle:c1-c1-p2 harmonic 68.155 180.000 # SOURCE3 1 + angle_coeff @angle:c1-c1-p3 harmonic 69.444 169.630 # SOURCE3 2 + angle_coeff @angle:c1-c1-p4 harmonic 67.414 180.000 # SOURCE3 1 + angle_coeff @angle:c1-c1-p5 harmonic 69.535 176.170 # SOURCE3 2 + angle_coeff @angle:c1-c1-s4 harmonic 55.785 167.470 # SOURCE3 2 + angle_coeff @angle:c1-c1-s6 harmonic 55.388 174.380 # SOURCE3 2 + angle_coeff @angle:c1-c1-s harmonic 58.129 179.970 # SOURCE3 1 + angle_coeff @angle:c1-c1-sh harmonic 55.773 180.000 # SOURCE3 1 + angle_coeff @angle:c1-c1-ss harmonic 56.169 175.600 # SOURCE3_SOURCE5 19 1.3679 + angle_coeff @angle:c2-c1-c2 harmonic 60.185 179.370 # SOURCE3_SOURCE5 14 0.3391 + angle_coeff @angle:c2-c1-ce harmonic 60.047 179.050 # SOURCE4_SOURCE5 15 0.4210 + angle_coeff @angle:c2-c1-n1 harmonic 79.308 180.000 # HF/6-31G* 1 + angle_coeff @angle:c2-c1-o harmonic 78.963 179.500 # SOURCE2 1 + angle_coeff @angle:c2-c1-s2 harmonic 58.516 172.980 # SOURCE3 1 + angle_coeff @angle:c3-c1-c3 harmonic 53.523 180.000 # Guess 0 + angle_coeff @angle:c3-c1-cg harmonic 57.770 178.430 # SOURCE4_SOURCE5 134 0.5502 + angle_coeff @angle:c3-c1-n1 harmonic 73.216 178.580 # SOURCE4_SOURCE5 245 0.5409 + angle_coeff @angle:ca-c1-ca harmonic 54.530 180.000 # Guess 0 + angle_coeff @angle:c-c1-c1 harmonic 57.944 180.000 # SOURCE3 1 + angle_coeff @angle:cg-c1-ha harmonic 44.392 178.830 # SOURCE3_SOURCE5 60 1.1251 + angle_coeff @angle:ch-c1-ha harmonic 44.307 178.830 # SOURCE3_SOURCE5 38 0.3321 + angle_coeff @angle:cl-c1-cl harmonic 70.163 180.000 # Guess 0 + angle_coeff @angle:f-c1-f harmonic 99.768 180.000 # Guess 0 + angle_coeff @angle:i-c1-i harmonic 58.397 180.000 # Guess 0 + angle_coeff @angle:n1-c1-n1 harmonic 141.802 102.010 # SOURCE3 1 + angle_coeff @angle:n1-c1-n3 harmonic 98.388 176.010 # SOURCE2_SOURCE5 5 0.1498 + angle_coeff @angle:n1-c1-nh harmonic 98.195 177.650 # SOURCE4_SOURCE5 18 0.7845 + angle_coeff @angle:n1-c1-os harmonic 99.150 178.590 # SOURCE3 1 + angle_coeff @angle:n1-c1-p3 harmonic 86.562 171.200 # SOURCE2 1 + angle_coeff @angle:n1-c1-ss harmonic 70.134 177.470 # SOURCE3_SOURCE5 15 0.7211 + angle_coeff @angle:n2-c1-n2 harmonic 102.862 180.000 # Guess 0 + angle_coeff @angle:n2-c1-o harmonic 106.076 172.730 # SOURCE3_SOURCE5 10 0.3647 + angle_coeff @angle:n2-c1-s harmonic 73.638 175.910 # SOURCE4_SOURCE5 29 0.2046 + angle_coeff @angle:n3-c1-n3 harmonic 91.381 180.000 # Guess 0 + angle_coeff @angle:n4-c1-n4 harmonic 86.899 180.000 # Guess 0 + angle_coeff @angle:na-c1-na harmonic 90.408 180.000 # Guess 0 + angle_coeff @angle:ne-c1-o harmonic 105.956 172.330 # SOURCE3 1 + angle_coeff @angle:ne-c1-s harmonic 73.610 175.820 # SOURCE4_SOURCE5 23 0.2168 + angle_coeff @angle:nf-c1-o harmonic 105.956 172.330 # SOURCE3 1 + angle_coeff @angle:nh-c1-nh harmonic 91.735 180.000 # Guess 0 + angle_coeff @angle:n-c1-n harmonic 92.583 180.000 # Guess 0 + angle_coeff @angle:no-c1-no harmonic 87.641 180.000 # Guess 0 + angle_coeff @angle:oh-c1-oh harmonic 92.863 180.000 # Guess 0 + angle_coeff @angle:o-c1-o harmonic 105.029 180.000 # Guess 0 + angle_coeff @angle:os-c1-os harmonic 93.419 180.000 # Guess 0 + angle_coeff @angle:p2-c1-p2 harmonic 85.393 180.000 # Guess 0 + angle_coeff @angle:p3-c1-p3 harmonic 84.439 180.000 # Guess 0 + angle_coeff @angle:p4-c1-p4 harmonic 84.439 180.000 # Guess 0 + angle_coeff @angle:p5-c1-p5 harmonic 86.221 180.000 # Guess 0 + angle_coeff @angle:s2-c1-s2 harmonic 57.538 180.000 # Guess 0 + angle_coeff @angle:s4-c1-s4 harmonic 52.562 180.000 # Guess 0 + angle_coeff @angle:s6-c1-s6 harmonic 53.295 180.000 # Guess 0 + angle_coeff @angle:sh-c1-sh harmonic 54.627 180.000 # Guess 0 + angle_coeff @angle:s-c1-s harmonic 57.244 180.000 # Guess 0 + angle_coeff @angle:ss-c1-ss harmonic 54.310 180.000 # Guess 0 + angle_coeff @angle:br-c2-br harmonic 68.999 115.060 # SOURCE3 1 + angle_coeff @angle:br-c2-c2 harmonic 64.458 121.030 # SOURCE4_SOURCE5 18 0.8426 + angle_coeff @angle:br-c2-c3 harmonic 64.834 115.320 # SOURCE4_SOURCE5 18 0.6855 + angle_coeff @angle:br-c2-ce harmonic 64.279 121.530 # SOURCE4_SOURCE5 18 0.7036 + angle_coeff @angle:br-c2-h4 harmonic 42.846 113.730 # SOURCE4_SOURCE5 17 0.5888 + angle_coeff @angle:br-c2-ha harmonic 42.937 113.280 # SOURCE3 1 + angle_coeff @angle:c1-c2-c1 harmonic 74.593 116.770 # SOURCE3 1 + angle_coeff @angle:c1-c2-c2 harmonic 72.319 121.620 # SOURCE3 1 + angle_coeff @angle:c1-c2-c3 harmonic 66.250 124.900 # SOURCE4_SOURCE5 44 0.7045 + angle_coeff @angle:c1-c2-f harmonic 90.501 124.900 # SOURCE2 1 + angle_coeff @angle:c1-c2-ha harmonic 51.141 120.420 # SOURCE3_SOURCE5 30 0.4602 + angle_coeff @angle:c2-c2-c2 harmonic 71.539 121.810 # SOURCE3 10 0.3843 + angle_coeff @angle:c2-c2-c3 harmonic 66.132 123.630 # SOURCE3_SOURCE5 4623 2.2803 + angle_coeff @angle:c2-c2-ca harmonic 71.595 117.000 # SOURCE3 1 + angle_coeff @angle:c2-c2-cc harmonic 72.240 117.210 # SOURCE3 2 0.3418 + angle_coeff @angle:c2-c2-cd harmonic 72.240 117.210 # SOURCE3 2 + angle_coeff @angle:c2-c2-cl harmonic 72.331 123.110 # SOURCE4_SOURCE5 103 1.0574 + angle_coeff @angle:c2-c2-cx harmonic 66.489 124.950 # SOURCE4_SOURCE5 51 1.8521 + angle_coeff @angle:c2-c2-cy harmonic 67.939 117.180 # SOURCE2_SOURCE5 11 1.7549 + angle_coeff @angle:c2-c2-f harmonic 90.338 122.870 # SOURCE4_SOURCE5 37 0.6494 + angle_coeff @angle:c2-c2-h4 harmonic 49.914 122.670 # SOURCE4_SOURCE5 266 1.3387 + angle_coeff @angle:c2-c2-ha harmonic 50.363 120.430 # SOURCE3_SOURCE5 3764 1.3300 + angle_coeff @angle:c2-c2-hc harmonic 50.527 119.700 # SOURCE3 1 + angle_coeff @angle:c2-c2-hx harmonic 49.204 126.450 # SOURCE3 3 0.0219 + angle_coeff @angle:c2-c2-i harmonic 59.321 121.030 # SOURCE3 2 + angle_coeff @angle:c2-c2-n1 harmonic 90.093 122.980 # HF/6-31G* 1 + angle_coeff @angle:c2-c2-n2 harmonic 89.778 126.010 # SOURCE3 1 + angle_coeff @angle:c2-c2-n3 harmonic 88.404 124.550 # SOURCE3 1 + angle_coeff @angle:c2-c2-n4 harmonic 83.421 121.520 # SOURCE3 5 1.2656 + angle_coeff @angle:c2-c2-n harmonic 86.693 123.670 # SOURCE4_SOURCE5 48 1.8326 + angle_coeff @angle:c2-c2-na harmonic 87.232 121.940 # SOURCE3_SOURCE5 35 5.4059 + angle_coeff @angle:c2-c2-nh harmonic 86.653 124.990 # SOURCE3 7 0.9929 + angle_coeff @angle:c2-c2-no harmonic 85.060 123.460 # SOURCE4_SOURCE5 26 1.6311 + angle_coeff @angle:c2-c2-o harmonic 89.793 130.890 # SOURCE3 2 0.0201 + angle_coeff @angle:c2-c2-oh harmonic 89.312 122.170 # SOURCE4_SOURCE5 18 1.1206 + angle_coeff @angle:c2-c2-os harmonic 88.706 121.870 # SOURCE4_SOURCE5 114 1.6810 + angle_coeff @angle:c2-c2-p2 harmonic 88.516 115.100 # SOURCE3 1 + angle_coeff @angle:c2-c2-p3 harmonic 78.573 124.830 # SOURCE3 5 2.1222 + angle_coeff @angle:c2-c2-p4 harmonic 80.685 119.760 # SOURCE3 1 + angle_coeff @angle:c2-c2-p5 harmonic 77.141 125.970 # SOURCE3 1 + angle_coeff @angle:c2-c2-s4 harmonic 64.747 119.840 # SOURCE3 1 + angle_coeff @angle:c2-c2-s6 harmonic 64.702 120.010 # SOURCE3 1 + angle_coeff @angle:c2-c2-s harmonic 63.092 129.370 # SOURCE3 2 + angle_coeff @angle:c2-c2-sh harmonic 62.559 125.700 # SOURCE3 3 1.3390 + angle_coeff @angle:c2-c2-ss harmonic 64.815 122.350 # SOURCE4_SOURCE5 54 2.2017 + angle_coeff @angle:c3-c2-c3 harmonic 64.898 115.650 # SOURCE3_SOURCE5 1743 1.5647 + angle_coeff @angle:c3-c2-cc harmonic 65.283 125.190 # CORR_SOURCE5 50 1.5929 + angle_coeff @angle:c3-c2-cd harmonic 65.283 125.190 # CORR_SOURCE5 50 1.5929 + angle_coeff @angle:c3-c2-ce harmonic 66.056 123.150 # CORR_SOURCE5 2644 2.0746 + angle_coeff @angle:c3-c2-cf harmonic 66.056 123.150 # CORR_SOURCE5 2644 2.0746 + angle_coeff @angle:c3-c2-h4 harmonic 45.760 119.020 # SOURCE4_SOURCE5 63 1.6077 + angle_coeff @angle:c3-c2-ha harmonic 46.411 115.680 # SOURCE3_SOURCE5 3991 1.1961 + angle_coeff @angle:c3-c2-hc harmonic 45.572 120.000 # SOURCE3 1 + angle_coeff @angle:c3-c2-n2 harmonic 83.960 123.430 # SOURCE4_SOURCE5 388 2.3609 + angle_coeff @angle:c3-c2-n harmonic 84.414 114.800 # SOURCE4 12 1.8112 + angle_coeff @angle:c3-c2-na harmonic 83.495 117.200 # SOURCE3_SOURCE5 5 0.8937 + angle_coeff @angle:c3-c2-ne harmonic 84.706 120.710 # SOURCE3_SOURCE5 11 0.9157 + angle_coeff @angle:c3-c2-nf harmonic 84.706 120.710 # SOURCE3_SOURCE5 7 1.3134 + angle_coeff @angle:c3-c2-nh harmonic 84.195 116.210 # SOURCE3_SOURCE5 339 2.4814 + angle_coeff @angle:c3-c2-o harmonic 85.206 122.820 # SOURCE4_SOURCE5 12 1.1220 + angle_coeff @angle:c3-c2-oh harmonic 85.711 115.160 # SOURCE4_SOURCE5 90 2.0675 + angle_coeff @angle:c3-c2-os harmonic 86.117 112.800 # SOURCE4_SOURCE5 148 2.4217 + angle_coeff @angle:c3-c2-p2 harmonic 82.609 122.740 # SOURCE3 2 + angle_coeff @angle:c3-c2-s harmonic 64.740 115.440 # SOURCE3 2 0.0115 + angle_coeff @angle:c3-c2-ss harmonic 63.539 119.660 # SOURCE4_SOURCE5 137 2.1299 + angle_coeff @angle:ca-c2-ca harmonic 70.080 117.880 # SOURCE3 1 + angle_coeff @angle:ca-c2-hc harmonic 48.375 123.300 # SOURCE3 1 + angle_coeff @angle:c-c2-c2 harmonic 69.891 120.700 # SOURCE3 1 + angle_coeff @angle:c-c2-c3 harmonic 65.889 119.700 # SOURCE3 1 + angle_coeff @angle:c-c2-c harmonic 68.722 118.880 # SOURCE3 1 + angle_coeff @angle:cc-c2-h4 harmonic 49.786 119.850 # SOURCE4_SOURCE5 23 0.5829 + angle_coeff @angle:cc-c2-ha harmonic 50.004 118.750 # SOURCE3_SOURCE5 72 1.1667 + angle_coeff @angle:cc-c2-nh harmonic 86.562 123.120 # SOURCE4_SOURCE5 27 1.0384 + angle_coeff @angle:cc-c2-o harmonic 91.352 123.590 # SOURCE4_SOURCE5 12 0.0560 + angle_coeff @angle:cd-c2-ha harmonic 50.004 118.750 # SOURCE3_SOURCE5 72 1.1667 + angle_coeff @angle:ce-c2-cl harmonic 72.107 123.470 # SOURCE4_SOURCE5 41 0.8440 + angle_coeff @angle:ce-c2-h4 harmonic 49.654 122.310 # SOURCE4_SOURCE5 220 1.5462 + angle_coeff @angle:ce-c2-ha harmonic 50.024 120.450 # SOURCE3_SOURCE5 2139 1.1520 + angle_coeff @angle:ce-c2-na harmonic 86.108 124.170 # SOURCE4_SOURCE5 12 1.9766 + angle_coeff @angle:ce-c2-nh harmonic 87.822 120.710 # SOURCE4_SOURCE5 243 2.3407 + angle_coeff @angle:ce-c2-no harmonic 86.097 119.650 # SOURCE4_SOURCE5 10 0.9817 + angle_coeff @angle:ce-c2-o harmonic 91.992 123.370 # SOURCE4_SOURCE5 14 0.7592 + angle_coeff @angle:ce-c2-oh harmonic 88.571 123.130 # SOURCE4_SOURCE5 104 1.7734 + angle_coeff @angle:ce-c2-os harmonic 87.995 122.800 # SOURCE4_SOURCE5 149 2.3406 + angle_coeff @angle:cf-c2-ha harmonic 50.024 120.450 # SOURCE3_SOURCE5 2017 1.1895 + angle_coeff @angle:c-c2-ha harmonic 48.160 121.330 # SOURCE3 4 0.2462 + angle_coeff @angle:c-c2-hc harmonic 48.494 119.700 # SOURCE3 1 + angle_coeff @angle:cl-c2-cl harmonic 82.957 114.340 # SOURCE4_SOURCE5 29 0.6417 + angle_coeff @angle:cl-c2-h4 harmonic 49.503 113.540 # SOURCE4_SOURCE5 33 0.7337 + angle_coeff @angle:cl-c2-ha harmonic 49.579 113.200 # SOURCE3 1 + angle_coeff @angle:cx-c2-ha harmonic 47.006 116.150 # SOURCE4_SOURCE5 64 0.8729 + angle_coeff @angle:f-c2-f harmonic 120.199 111.640 # SOURCE2_SOURCE5 12 0.8567 + angle_coeff @angle:f-c2-ha harmonic 66.780 110.000 # SOURCE2 1 + angle_coeff @angle:h4-c2-n2 harmonic 64.810 120.990 # SOURCE4_SOURCE5 77 1.9305 + angle_coeff @angle:h4-c2-n harmonic 62.621 113.440 # SOURCE4_SOURCE5 78 1.0580 + angle_coeff @angle:h4-c2-na harmonic 62.675 112.970 # SOURCE4_SOURCE5 27 0.6876 + angle_coeff @angle:h4-c2-ne harmonic 64.858 119.510 # SOURCE4_SOURCE5 52 1.6395 + angle_coeff @angle:h4-c2-nh harmonic 62.613 115.080 # SOURCE4_SOURCE5 109 1.1974 + angle_coeff @angle:h4-c2-no harmonic 60.883 113.380 # SOURCE4_SOURCE5 20 0.1373 + angle_coeff @angle:h4-c2-os harmonic 63.989 113.730 # SOURCE3_SOURCE5 89 1.3113 + angle_coeff @angle:h4-c2-ss harmonic 43.595 116.670 # SOURCE3_SOURCE5 49 1.4612 + angle_coeff @angle:h5-c2-n2 harmonic 64.543 121.700 # SOURCE4_SOURCE5 71 2.1538 + angle_coeff @angle:h5-c2-na harmonic 59.208 126.390 # SOURCE3 4 0.3299 + angle_coeff @angle:h5-c2-ne harmonic 64.691 119.850 # SOURCE4_SOURCE5 44 1.3576 + angle_coeff @angle:h5-c2-nh harmonic 62.882 113.910 # SOURCE4_SOURCE5 119 0.8516 + angle_coeff @angle:ha-c2-ha harmonic 37.684 116.900 # SOURCE3_SOURCE5 1456 0.6313 + angle_coeff @angle:ha-c2-n1 harmonic 63.987 120.760 # SOURCE3 8 0.6632 + angle_coeff @angle:ha-c2-n2 harmonic 64.911 120.540 # SOURCE3 92 1.4571 + angle_coeff @angle:ha-c2-n3 harmonic 64.744 113.540 # SOURCE3 1 + angle_coeff @angle:ha-c2-n harmonic 62.620 113.400 # SOURCE3 4 1.2182 + angle_coeff @angle:ha-c2-na harmonic 62.816 112.420 # SOURCE3 8 0.6507 + angle_coeff @angle:ha-c2-ne harmonic 64.391 121.180 # SOURCE3 68 0.6824 + angle_coeff @angle:ha-c2-nf harmonic 64.391 121.180 # SOURCE3 68 + angle_coeff @angle:ha-c2-nh harmonic 62.169 116.680 # SOURCE3 13 2.5734 + angle_coeff @angle:ha-c2-no harmonic 61.209 112.140 # SOURCE3 2 0.0264 + angle_coeff @angle:ha-c2-o harmonic 67.875 117.230 # SOURCE3 2 0.0201 + angle_coeff @angle:ha-c2-oh harmonic 64.058 116.180 # SOURCE3 2 + angle_coeff @angle:ha-c2-os harmonic 64.269 112.690 # SOURCE3 13 2.5851 + angle_coeff @angle:ha-c2-p2 harmonic 57.111 121.480 # SOURCE3 122 0.4329 + angle_coeff @angle:ha-c2-p3 harmonic 53.276 114.310 # SOURCE3 3 + angle_coeff @angle:ha-c2-p4 harmonic 52.849 117.860 # SOURCE3 1 + angle_coeff @angle:ha-c2-p5 harmonic 51.984 116.000 # SOURCE3_SOURCE5 6 0.1220 + angle_coeff @angle:ha-c2-pe harmonic 56.443 121.400 # SOURCE3_SOURCE5 119 0.8904 + angle_coeff @angle:ha-c2-pf harmonic 56.443 121.400 # SOURCE3_SOURCE5 15 1.6416 + angle_coeff @angle:ha-c2-s2 harmonic 46.632 118.740 # SOURCE3 2 + angle_coeff @angle:ha-c2-s4 harmonic 43.223 115.300 # SOURCE3 2 + angle_coeff @angle:ha-c2-s harmonic 43.832 115.700 # SOURCE3 2 + angle_coeff @angle:ha-c2-s6 harmonic 42.982 116.600 # SOURCE3 2 + angle_coeff @angle:ha-c2-sh harmonic 43.327 111.740 # SOURCE3 1 + angle_coeff @angle:ha-c2-ss harmonic 43.588 116.720 # SOURCE3 7 2.7543 + angle_coeff @angle:hc-c2-hc harmonic 37.394 118.920 # SOURCE3 1 + angle_coeff @angle:hc-c2-n2 harmonic 64.965 120.400 # SOURCE3 1 + angle_coeff @angle:hc-c2-n harmonic 62.454 114.040 # SOURCE3 1 + angle_coeff @angle:hc-c2-na harmonic 61.038 119.100 # SOURCE3 1 + angle_coeff @angle:hc-c2-nh harmonic 63.084 113.360 # SOURCE3 1 + angle_coeff @angle:hc-c2-no harmonic 61.222 112.120 # SOURCE3 1 + angle_coeff @angle:hc-c2-oh harmonic 64.060 116.220 # SOURCE3 1 + angle_coeff @angle:hc-c2-os harmonic 63.327 116.110 # SOURCE3 1 + angle_coeff @angle:hc-c2-p3 harmonic 52.613 117.190 # SOURCE3 1 + angle_coeff @angle:hc-c2-p5 harmonic 51.195 119.580 # SOURCE3 1 + angle_coeff @angle:hc-c2-s4 harmonic 43.068 116.120 # SOURCE3 1 + angle_coeff @angle:hc-c2-s6 harmonic 43.193 115.450 # SOURCE3 1 + angle_coeff @angle:hc-c2-sh harmonic 42.589 115.630 # SOURCE3 1 + angle_coeff @angle:hc-c2-ss harmonic 43.793 115.620 # SOURCE3 1 + angle_coeff @angle:hx-c2-n4 harmonic 58.717 113.030 # SOURCE3 3 0.3873 + angle_coeff @angle:i-c2-i harmonic 66.122 117.940 # SOURCE3 1 + angle_coeff @angle:n1-c2-n1 harmonic 113.528 124.150 # HF/6-31G* 1 + angle_coeff @angle:n2-c2-n2 harmonic 120.816 113.820 # SOURCE3 1 + angle_coeff @angle:n2-c2-n4 harmonic 109.745 112.970 # SOURCE4_SOURCE5 13 0.4034 + angle_coeff @angle:n2-c2-na harmonic 110.312 123.620 # SOURCE3 1 + angle_coeff @angle:n2-c2-nh harmonic 110.708 124.270 # SOURCE3 12 2.4114 + angle_coeff @angle:n2-c2-oh harmonic 114.021 122.080 # SOURCE3 1 + angle_coeff @angle:n2-c2-os harmonic 114.100 119.780 # SOURCE4_SOURCE5 55 1.3881 + angle_coeff @angle:n2-c2-ss harmonic 79.299 129.770 # SOURCE3 1 + angle_coeff @angle:n3-c2-n3 harmonic 113.269 118.470 # SOURCE3 1 + angle_coeff @angle:n4-c2-n4 harmonic 102.331 113.930 # SOURCE3 1 + angle_coeff @angle:n4-c2-ss harmonic 80.666 116.270 # SOURCE4_SOURCE5 14 2.4226 + angle_coeff @angle:na-c2-na harmonic 112.735 109.330 # SOURCE3 3 3.0187 + angle_coeff @angle:ne-c2-nh harmonic 110.728 123.460 # CORR_SOURCE5 241 2.3941 + angle_coeff @angle:ne-c2-os harmonic 114.213 118.760 # SOURCE4 5 0.3382 + angle_coeff @angle:ne-c2-ss harmonic 82.205 120.510 # SOURCE4_SOURCE5 32 2.1160 + angle_coeff @angle:nf-c2-nh harmonic 110.728 123.460 # CORR_SOURCE5 241 2.3941 + angle_coeff @angle:nh-c2-nh harmonic 112.122 112.820 # SOURCE4_SOURCE5 689 1.9577 + angle_coeff @angle:nh-c2-oh harmonic 111.944 117.110 # SOURCE4_SOURCE5 15 0.8639 + angle_coeff @angle:nh-c2-os harmonic 112.490 114.300 # SOURCE4_SOURCE5 50 1.3395 + angle_coeff @angle:nh-c2-ss harmonic 84.343 111.550 # SOURCE4 37 1.1778 + angle_coeff @angle:n-c2-n2 harmonic 110.772 122.820 # SOURCE3_SOURCE5 46 2.2661 + angle_coeff @angle:n-c2-n harmonic 110.943 113.230 # SOURCE3 1 + angle_coeff @angle:n-c2-na harmonic 114.893 105.420 # SOURCE3 1 + angle_coeff @angle:n-c2-ne harmonic 109.323 125.340 # SOURCE4_SOURCE5 25 1.6082 + angle_coeff @angle:n-c2-nh harmonic 113.384 109.350 # SOURCE4_SOURCE5 61 1.6924 + angle_coeff @angle:no-c2-no harmonic 106.896 113.900 # SOURCE3 1 + angle_coeff @angle:n-c2-ss harmonic 84.310 111.190 # SOURCE4_SOURCE5 24 0.6195 + angle_coeff @angle:oh-c2-oh harmonic 115.431 114.330 # SOURCE3 1 + angle_coeff @angle:o-c2-o harmonic 122.282 121.690 # SOURCE3 1 + angle_coeff @angle:o-c2-oh harmonic 116.614 121.230 # SOURCE4_SOURCE5 12 0.0958 + angle_coeff @angle:o-c2-s harmonic 80.412 127.680 # SOURCE3 2 0.0547 + angle_coeff @angle:os-c2-os harmonic 113.284 115.050 # SOURCE3_SOURCE5 6 1.2203 + angle_coeff @angle:p2-c2-p2 harmonic 106.670 129.800 # SOURCE3 1 + angle_coeff @angle:p3-c2-p3 harmonic 102.865 115.540 # SOURCE3 1 + angle_coeff @angle:p5-c2-p5 harmonic 98.628 121.850 # SOURCE3 1 + angle_coeff @angle:s4-c2-s4 harmonic 63.778 120.320 # SOURCE3 1 + angle_coeff @angle:s4-c2-s6 harmonic 63.877 119.950 # SOURCE3 1 + angle_coeff @angle:s6-c2-s6 harmonic 63.871 119.970 # SOURCE3 1 + angle_coeff @angle:sh-c2-sh harmonic 65.736 110.480 # SOURCE3 1 + angle_coeff @angle:sh-c2-ss harmonic 64.466 117.820 # SOURCE3 1 + angle_coeff @angle:s-c2-s harmonic 64.374 121.670 # SOURCE3 1 + angle_coeff @angle:ss-c2-ss harmonic 65.740 116.400 # SOURCE3_SOURCE5 22 2.3993 + angle_coeff @angle:br-c3-br harmonic 67.612 109.740 # SOURCE4_SOURCE5 24 0.9971 + angle_coeff @angle:br-c3-c1 harmonic 63.834 111.800 # SOURCE2 3 0.2160 + angle_coeff @angle:br-c3-c3 harmonic 63.860 110.010 # SOURCE3_SOURCE5 216 1.1568 + angle_coeff @angle:br-c3-c harmonic 64.284 108.920 # SOURCE4_SOURCE5 35 2.3703 + angle_coeff @angle:br-c3-h1 harmonic 42.433 105.070 # SOURCE3_SOURCE5 175 0.8275 + angle_coeff @angle:br-c3-h2 harmonic 42.082 106.800 # SOURCE4_SOURCE5 25 0.8044 + angle_coeff @angle:br-c3-hc harmonic 42.147 106.500 # SOURCE3 1 + angle_coeff @angle:c1-c3-c1 harmonic 68.433 110.110 # SOURCE2_SOURCE5 11 0.3454 + angle_coeff @angle:c1-c3-c2 harmonic 67.184 110.920 # SOURCE4_SOURCE5 35 0.5903 + angle_coeff @angle:c1-c3-c3 harmonic 66.276 111.710 # SOURCE4_SOURCE5 624 1.1320 + angle_coeff @angle:c1-c3-ca harmonic 67.047 110.890 # SOURCE4_SOURCE5 78 1.1306 + angle_coeff @angle:c1-c3-cc harmonic 66.403 114.190 # CORR_SOURCE5 15 0.1283 + angle_coeff @angle:c1-c3-cd harmonic 66.403 114.190 # CORR_SOURCE5 15 0.1283 + angle_coeff @angle:c1-c3-cl harmonic 72.363 110.630 # SOURCE2 3 1.2257 + angle_coeff @angle:c1-c3-h1 harmonic 48.917 109.240 # SOURCE4_SOURCE5 436 0.5758 + angle_coeff @angle:c1-c3-hc harmonic 48.879 109.410 # SOURCE3_SOURCE5 495 0.5104 + angle_coeff @angle:c1-c3-hx harmonic 48.339 112.040 # SOURCE4_SOURCE5 52 0.3815 + angle_coeff @angle:c1-c3-n3 harmonic 84.763 112.730 # SOURCE4_SOURCE5 99 0.7675 + angle_coeff @angle:c1-c3-n4 harmonic 83.658 112.060 # SOURCE4_SOURCE5 25 0.5395 + angle_coeff @angle:c1-c3-n harmonic 84.975 112.380 # SOURCE4_SOURCE5 55 0.9540 + angle_coeff @angle:c1-c3-nh harmonic 84.843 112.570 # SOURCE4_SOURCE5 21 0.9525 + angle_coeff @angle:c1-c3-oh harmonic 87.220 109.440 # SOURCE4_SOURCE5 127 0.9878 + angle_coeff @angle:c1-c3-os harmonic 87.159 109.000 # SOURCE4_SOURCE5 87 0.9531 + angle_coeff @angle:c2-c3-c2 harmonic 65.947 112.000 # SOURCE4_SOURCE5 453 0.8153 + angle_coeff @angle:c2-c3-c3 harmonic 65.459 111.560 # SOURCE4_SOURCE5 9345 1.7373 + angle_coeff @angle:c2-c3-ca harmonic 65.670 112.490 # SOURCE4_SOURCE5 475 1.6791 + angle_coeff @angle:c2-c3-cc harmonic 66.148 111.910 # CORR_SOURCE5 65 1.7402 + angle_coeff @angle:c2-c3-cd harmonic 66.148 111.910 # CORR_SOURCE5 65 1.7402 + angle_coeff @angle:c2-c3-ce harmonic 65.863 111.810 # CORR_SOURCE5 85 1.8411 + angle_coeff @angle:c2-c3-cf harmonic 65.867 111.810 # CORR_SOURCE5 85 1.8411 + angle_coeff @angle:c2-c3-cl harmonic 71.864 110.510 # SOURCE4_SOURCE5 60 1.4762 + angle_coeff @angle:c2-c3-cx harmonic 65.673 112.270 # SOURCE4_SOURCE5 76 1.2985 + angle_coeff @angle:c2-c3-cy harmonic 68.713 101.630 # SOURCE4_SOURCE5 164 1.0542 + angle_coeff @angle:c2-c3-f harmonic 88.392 110.760 # SOURCE4_SOURCE5 69 0.5776 + angle_coeff @angle:c2-c3-h1 harmonic 47.561 109.960 # SOURCE3_SOURCE5 2169 0.9645 + angle_coeff @angle:c2-c3-h2 harmonic 47.195 111.690 # SOURCE4_SOURCE5 49 0.9061 + angle_coeff @angle:c2-c3-hc harmonic 47.475 110.360 # SOURCE3_SOURCE5 11033 0.8531 + angle_coeff @angle:c2-c3-hx harmonic 47.293 111.340 # SOURCE4_SOURCE5 56 0.8089 + angle_coeff @angle:c2-c3-n2 harmonic 85.005 108.720 # SOURCE4_SOURCE5 36 1.3485 + angle_coeff @angle:c2-c3-n3 harmonic 84.006 111.420 # SOURCE4_SOURCE5 447 1.5436 + angle_coeff @angle:c2-c3-n harmonic 84.129 111.290 # SOURCE4_SOURCE5 180 1.8899 + angle_coeff @angle:c2-c3-na harmonic 83.365 113.270 # SOURCE4_SOURCE5 78 1.2929 + angle_coeff @angle:c2-c3-nh harmonic 84.408 110.410 # SOURCE4_SOURCE5 134 1.7670 + angle_coeff @angle:c2-c3-oh harmonic 85.495 110.350 # SOURCE4_SOURCE5 793 1.4429 + angle_coeff @angle:c2-c3-os harmonic 85.982 108.560 # SOURCE4_SOURCE5 763 1.7474 + angle_coeff @angle:c2-c3-s4 harmonic 63.867 109.890 # SOURCE4_SOURCE5 19 0.8365 + angle_coeff @angle:c2-c3-ss harmonic 65.117 104.970 # SOURCE3 2 2.2248 + angle_coeff @angle:c3-c3-c3 harmonic 64.888 111.510 # SOURCE3_SOURCE5 61999 1.8007 + angle_coeff @angle:c3-c3-ca harmonic 65.183 112.070 # SOURCE4_SOURCE5 11982 1.5875 + angle_coeff @angle:c3-c3-cc harmonic 65.515 111.930 # CORR_SOURCE5 2280 1.5614 + angle_coeff @angle:c3-c3-cd harmonic 65.515 111.930 # CORR_SOURCE5 2280 1.5614 + angle_coeff @angle:c3-c3-ce harmonic 65.514 110.920 # CORR_SOURCE5 1159 1.8552 + angle_coeff @angle:c3-c3-cf harmonic 65.518 110.920 # CORR_SOURCE5 1159 1.8552 + angle_coeff @angle:c3-c3-cl harmonic 71.515 110.410 # SOURCE3_SOURCE5 824 0.9824 + angle_coeff @angle:c3-c3-cx harmonic 65.198 111.820 # SOURCE4 179 2.4814 + angle_coeff @angle:c3-c3-cy harmonic 64.751 112.390 # SOURCE3_SOURCE5 322 1.3623 + angle_coeff @angle:c3-c3-f harmonic 87.947 109.240 # SOURCE3_SOURCE5 785 1.1106 + angle_coeff @angle:c3-c3-h1 harmonic 46.868 109.560 # SOURCE3_SOURCE5 55294 0.8125 + angle_coeff @angle:c3-c3-h2 harmonic 46.730 110.220 # SOURCE3_SOURCE5 1083 0.9457 + angle_coeff @angle:c3-c3-hc harmonic 46.816 109.800 # SOURCE3_SOURCE5 179054 0.7972 + angle_coeff @angle:c3-c3-hx harmonic 46.677 110.560 # SOURCE3_SOURCE5 1758 0.9658 + angle_coeff @angle:c3-c3-i harmonic 60.771 111.150 # SOURCE3_SOURCE5 48 1.3033 + angle_coeff @angle:c3-c3-n1 harmonic 84.875 108.980 # SOURCE4_SOURCE5 20 0.8416 + angle_coeff @angle:c3-c3-n2 harmonic 84.123 108.800 # SOURCE3_SOURCE5 665 2.1214 + angle_coeff @angle:c3-c3-n3 harmonic 83.305 111.040 # SOURCE3_SOURCE5 12086 1.5519 + angle_coeff @angle:c3-c3-n4 harmonic 80.976 114.210 # SOURCE4_SOURCE5 1537 2.4293 + angle_coeff @angle:c3-c3-n harmonic 83.161 111.610 # SOURCE3_SOURCE5 3543 1.6672 + angle_coeff @angle:c3-c3-na harmonic 82.668 112.880 # SOURCE4_SOURCE5 1677 1.4742 + angle_coeff @angle:c3-c3-nh harmonic 83.541 110.460 # SOURCE4_SOURCE5 3983 1.4189 + angle_coeff @angle:c3-c3-no harmonic 82.142 109.410 # SOURCE4_SOURCE5 111 1.3831 + angle_coeff @angle:c3-c3-o harmonic 85.929 113.010 # SOURCE4_SOURCE5 31 1.2728 + angle_coeff @angle:c3-c3-oh harmonic 84.642 110.190 # SOURCE3_SOURCE5 10188 1.4761 + angle_coeff @angle:c3-c3-os harmonic 85.306 107.970 # SOURCE3_SOURCE5 11384 1.3754 + angle_coeff @angle:c3-c3-p3 harmonic 79.425 113.360 # SOURCE4_SOURCE5 47 0.9033 + angle_coeff @angle:c3-c3-p5 harmonic 80.490 112.020 # SOURCE4_SOURCE5 346 1.5599 + angle_coeff @angle:c3-c3-s4 harmonic 63.481 110.120 # SOURCE4_SOURCE5 117 0.9869 + angle_coeff @angle:c3-c3-s6 harmonic 64.024 110.220 # SOURCE4_SOURCE5 420 1.6420 + angle_coeff @angle:c3-c3-sh harmonic 62.313 113.130 # SOURCE4_SOURCE5 226 1.3868 + angle_coeff @angle:c3-c3-ss harmonic 63.222 110.270 # SOURCE3_SOURCE5 1315 1.5441 + angle_coeff @angle:c3-c3-sy harmonic 64.081 109.920 # SOURCE4_SOURCE5 62 0.8825 + angle_coeff @angle:ca-c3-ca harmonic 65.611 112.240 # SOURCE4_SOURCE5 1062 1.7394 + angle_coeff @angle:ca-c3-cc harmonic 65.728 112.880 # CORR_SOURCE5 146 1.4369 + angle_coeff @angle:ca-c3-cd harmonic 65.728 112.880 # CORR_SOURCE5 146 1.4369 + angle_coeff @angle:ca-c3-ce harmonic 65.614 112.210 # SOURCE4_SOURCE5 144 1.2359 + angle_coeff @angle:ca-c3-cl harmonic 71.631 110.980 # SOURCE4_SOURCE5 62 0.7657 + angle_coeff @angle:ca-c3-cx harmonic 65.472 112.510 # SOURCE4_SOURCE5 24 2.0281 + angle_coeff @angle:ca-c3-f harmonic 87.765 111.770 # SOURCE4_SOURCE5 1080 0.3344 + angle_coeff @angle:ca-c3-h1 harmonic 47.477 109.560 # SOURCE3_SOURCE5 3349 0.8812 + angle_coeff @angle:ca-c3-h2 harmonic 47.451 109.700 # SOURCE4_SOURCE5 86 1.1507 + angle_coeff @angle:ca-c3-hc harmonic 47.281 110.470 # SOURCE3_SOURCE5 13973 0.8325 + angle_coeff @angle:ca-c3-hx harmonic 47.099 111.450 # SOURCE4_SOURCE5 113 0.5046 + angle_coeff @angle:ca-c3-n2 harmonic 83.424 112.390 # SOURCE4_SOURCE5 58 1.2061 + angle_coeff @angle:ca-c3-n3 harmonic 83.546 112.160 # SOURCE4_SOURCE5 1125 1.2435 + angle_coeff @angle:ca-c3-n4 harmonic 81.721 113.800 # SOURCE4_SOURCE5 79 2.4049 + angle_coeff @angle:ca-c3-n harmonic 83.537 112.380 # SOURCE4_SOURCE5 512 1.5411 + angle_coeff @angle:ca-c3-na harmonic 83.330 112.870 # SOURCE4_SOURCE5 240 1.5673 + angle_coeff @angle:ca-c3-nc harmonic 85.966 106.510 # SOURCE3 1 + angle_coeff @angle:ca-c3-nd harmonic 85.966 106.510 # SOURCE3 1 + angle_coeff @angle:ca-c3-nh harmonic 83.853 111.390 # SOURCE4_SOURCE5 349 0.9955 + angle_coeff @angle:ca-c3-oh harmonic 85.192 110.620 # SOURCE4_SOURCE5 1007 1.2078 + angle_coeff @angle:ca-c3-os harmonic 85.631 108.950 # SOURCE4_SOURCE5 1123 1.1238 + angle_coeff @angle:ca-c3-p5 harmonic 80.237 113.600 # SOURCE4_SOURCE5 41 1.4171 + angle_coeff @angle:ca-c3-s6 harmonic 63.909 111.540 # SOURCE4_SOURCE5 38 1.2112 + angle_coeff @angle:ca-c3-ss harmonic 63.252 111.020 # SOURCE4_SOURCE5 226 1.6105 + angle_coeff @angle:ca-c3-sx harmonic 63.255 110.780 # SOURCE4_SOURCE5 40 0.6145 + angle_coeff @angle:c-c3-c1 harmonic 66.399 112.380 # SOURCE4_SOURCE5 32 1.1114 + angle_coeff @angle:c-c3-c2 harmonic 65.824 111.330 # SOURCE4_SOURCE5 282 2.0882 + angle_coeff @angle:c-c3-c3 harmonic 65.307 111.040 # SOURCE3_SOURCE5 8161 1.7693 + angle_coeff @angle:c-c3-c harmonic 65.424 111.630 # SOURCE4_SOURCE5 409 2.2030 + angle_coeff @angle:c-c3-ca harmonic 65.788 111.010 # SOURCE4_SOURCE5 1282 1.7239 + angle_coeff @angle:c-c3-cc harmonic 65.455 113.170 # CORR_SOURCE5 164 1.3730 + angle_coeff @angle:cc-c3-cc harmonic 66.183 112.390 # CORR_SOURCE5 14 0.8688 + angle_coeff @angle:cc-c3-cd harmonic 66.037 112.890 # SOURCE3_SOURCE5 10 1.0674 + angle_coeff @angle:cc-c3-cx harmonic 65.894 112.100 # SOURCE4_SOURCE5 12 1.5999 + angle_coeff @angle:c-c3-cd harmonic 65.455 113.170 # CORR_SOURCE5 164 1.3730 + angle_coeff @angle:c-c3-ce harmonic 65.523 111.890 # SOURCE4_SOURCE5 75 1.6968 + angle_coeff @angle:cc-c3-f harmonic 88.472 111.310 # CORR_SOURCE5 105 0.4710 + angle_coeff @angle:cc-c3-h1 harmonic 47.855 109.640 # SOURCE3_SOURCE5 1145 0.8896 + angle_coeff @angle:cc-c3-hc harmonic 47.671 110.490 # SOURCE3_SOURCE5 6781 0.7714 + angle_coeff @angle:cc-c3-hx harmonic 47.588 111.010 # SOURCE4_SOURCE5 19 0.7303 + angle_coeff @angle:c-c3-cl harmonic 71.700 110.410 # SOURCE4_SOURCE5 146 1.5057 + angle_coeff @angle:cc-c3-n2 harmonic 84.630 110.310 # SOURCE4_SOURCE5 32 0.5465 + angle_coeff @angle:cc-c3-n3 harmonic 84.370 111.090 # CORR_SOURCE5 192 1.4026 + angle_coeff @angle:cc-c3-n4 harmonic 81.467 115.580 # SOURCE4_SOURCE5 12 1.1723 + angle_coeff @angle:cc-c3-n harmonic 84.192 111.760 # CORR_SOURCE5 51 1.5321 + angle_coeff @angle:cc-c3-na harmonic 83.647 113.150 # SOURCE4_SOURCE5 18 0.7152 + angle_coeff @angle:cc-c3-nc harmonic 86.190 107.040 # SOURCE3 2 + angle_coeff @angle:cc-c3-nh harmonic 83.918 112.340 # CORR_SOURCE5 25 1.8212 + angle_coeff @angle:cc-c3-oh harmonic 85.441 111.160 # CORR_SOURCE5 187 1.3741 + angle_coeff @angle:cc-c3-os harmonic 86.104 108.900 # CORR_SOURCE5 213 1.1488 + angle_coeff @angle:cc-c3-p5 harmonic 79.513 116.230 # SOURCE4_SOURCE5 12 0.7766 + angle_coeff @angle:cc-c3-sh harmonic 62.454 114.020 # SOURCE3 1 + angle_coeff @angle:cc-c3-ss harmonic 63.363 111.160 # CORR_SOURCE5 65 0.8483 + angle_coeff @angle:c-c3-cx harmonic 65.687 111.150 # SOURCE4_SOURCE5 48 1.8520 + angle_coeff @angle:cd-c3-cd harmonic 66.183 112.390 # CORR_SOURCE5 14 0.8688 + angle_coeff @angle:cd-c3-f harmonic 88.472 111.310 # CORR_SOURCE5 105 0.4710 + angle_coeff @angle:cd-c3-h1 harmonic 47.855 109.640 # SOURCE3_SOURCE5 1145 0.8896 + angle_coeff @angle:cd-c3-hc harmonic 47.671 110.490 # SOURCE3_SOURCE5 6781 0.7714 + angle_coeff @angle:cd-c3-n3 harmonic 84.370 111.090 # CORR_SOURCE5 192 1.4026 + angle_coeff @angle:cd-c3-n harmonic 84.192 111.760 # CORR_SOURCE5 51 1.5321 + angle_coeff @angle:cd-c3-nd harmonic 86.190 107.040 # SOURCE3 2 + angle_coeff @angle:cd-c3-nh harmonic 83.918 112.340 # CORR_SOURCE5 25 1.8212 + angle_coeff @angle:cd-c3-oh harmonic 85.441 111.160 # CORR_SOURCE5 187 1.3741 + angle_coeff @angle:cd-c3-os harmonic 86.104 108.900 # CORR_SOURCE5 213 1.1488 + angle_coeff @angle:cd-c3-sh harmonic 62.454 114.020 # SOURCE3 1 + angle_coeff @angle:cd-c3-ss harmonic 63.363 111.160 # CORR_SOURCE5 65 0.8483 + angle_coeff @angle:ce-c3-ce harmonic 65.825 111.470 # SOURCE4_SOURCE5 53 0.5207 + angle_coeff @angle:ce-c3-cy harmonic 68.161 102.860 # CORR_SOURCE5 72 0.2321 + angle_coeff @angle:ce-c3-h1 harmonic 47.473 109.540 # CORR_SOURCE5 252 0.8257 + angle_coeff @angle:ce-c3-hc harmonic 47.247 110.590 # SOURCE3_SOURCE5 2438 0.7216 + angle_coeff @angle:ce-c3-n3 harmonic 83.687 111.760 # CORR_SOURCE5 83 0.9878 + angle_coeff @angle:ce-c3-n harmonic 84.343 110.220 # SOURCE4_SOURCE5 16 1.1101 + angle_coeff @angle:ce-c3-oh harmonic 84.964 111.190 # SOURCE4_SOURCE5 74 1.5577 + angle_coeff @angle:ce-c3-os harmonic 85.406 109.500 # SOURCE4_SOURCE5 71 1.9041 + angle_coeff @angle:ce-c3-ss harmonic 63.335 110.720 # SOURCE4_SOURCE5 19 1.8179 + angle_coeff @angle:c-c3-f harmonic 88.148 110.000 # SOURCE4_SOURCE5 101 0.9951 + angle_coeff @angle:cf-c3-cy harmonic 68.165 102.860 # CORR_SOURCE5 72 0.2321 + angle_coeff @angle:cf-c3-h1 harmonic 47.479 109.540 # CORR_SOURCE5 252 0.8257 + angle_coeff @angle:cf-c3-hc harmonic 47.253 110.590 # SOURCE3_SOURCE5 2411 0.7279 + angle_coeff @angle:cf-c3-n3 harmonic 83.693 111.760 # CORR_SOURCE5 83 0.9878 + angle_coeff @angle:c-c3-h1 harmonic 47.531 108.220 # SOURCE3_SOURCE5 3484 0.9857 + angle_coeff @angle:c-c3-h2 harmonic 47.215 109.690 # SOURCE4_SOURCE5 100 1.0452 + angle_coeff @angle:c-c3-hc harmonic 47.411 108.770 # SOURCE3_SOURCE5 11750 0.9577 + angle_coeff @angle:c-c3-hx harmonic 47.419 108.850 # SOURCE4_SOURCE5 172 0.8753 + angle_coeff @angle:cl-c3-cl harmonic 81.372 109.330 # SOURCE2_SOURCE5 325 0.5772 + angle_coeff @angle:cl-c3-f harmonic 94.073 109.110 # SOURCE4_SOURCE5 57 0.3048 + angle_coeff @angle:cl-c3-h1 harmonic 48.859 106.780 # SOURCE3_SOURCE5 860 0.4999 + angle_coeff @angle:cl-c3-h2 harmonic 48.808 106.990 # SOURCE4_SOURCE5 147 0.6435 + angle_coeff @angle:cl-c3-hc harmonic 48.661 107.650 # SOURCE2 2 2.2500 + angle_coeff @angle:cl-c3-os harmonic 91.033 110.860 # SOURCE4_SOURCE5 26 1.1129 + angle_coeff @angle:cl-c3-ss harmonic 71.130 112.530 # SOURCE4_SOURCE5 39 1.6937 + angle_coeff @angle:c-c3-n2 harmonic 84.195 109.670 # SOURCE4_SOURCE5 157 1.3668 + angle_coeff @angle:c-c3-n3 harmonic 83.673 111.140 # SOURCE4_SOURCE5 1652 1.6694 + angle_coeff @angle:c-c3-n4 harmonic 82.611 110.730 # SOURCE4_SOURCE5 103 1.8311 + angle_coeff @angle:c-c3-n harmonic 84.540 109.060 # SOURCE3_SOURCE5 905 1.7615 + angle_coeff @angle:c-c3-na harmonic 83.584 111.500 # SOURCE4_SOURCE5 87 1.4027 + angle_coeff @angle:c-c3-nh harmonic 84.373 109.350 # SOURCE4_SOURCE5 106 1.8043 + angle_coeff @angle:c-c3-oh harmonic 85.627 108.790 # SOURCE4_SOURCE5 824 1.3178 + angle_coeff @angle:c-c3-os harmonic 85.254 109.210 # SOURCE3_SOURCE5 429 1.7229 + angle_coeff @angle:c-c3-p5 harmonic 81.107 110.850 # SOURCE4_SOURCE5 32 1.9944 + angle_coeff @angle:c-c3-s6 harmonic 64.058 110.670 # SOURCE4_SOURCE5 14 2.0336 + angle_coeff @angle:c-c3-sh harmonic 63.714 108.720 # SOURCE4_SOURCE5 31 0.7714 + angle_coeff @angle:c-c3-ss harmonic 63.788 108.840 # SOURCE3_SOURCE5 149 1.5563 + angle_coeff @angle:cx-c3-cx harmonic 65.100 113.590 # SOURCE4_SOURCE5 27 1.6971 + angle_coeff @angle:cx-c3-h1 harmonic 47.373 109.680 # SOURCE4_SOURCE5 611 0.9276 + angle_coeff @angle:cx-c3-hc harmonic 47.265 110.180 # SOURCE4_SOURCE5 1366 0.9055 + angle_coeff @angle:cx-c3-hx harmonic 46.751 112.740 # SOURCE4_SOURCE5 30 0.2036 + angle_coeff @angle:cx-c3-n3 harmonic 83.086 113.180 # SOURCE4_SOURCE5 97 1.4360 + angle_coeff @angle:cx-c3-n4 harmonic 86.467 101.460 # SOURCE4_SOURCE5 26 0.1569 + angle_coeff @angle:cx-c3-n harmonic 83.435 112.430 # SOURCE4_SOURCE5 68 0.9548 + angle_coeff @angle:cx-c3-oh harmonic 85.349 109.980 # SOURCE4_SOURCE5 145 1.5821 + angle_coeff @angle:cx-c3-os harmonic 85.968 107.870 # SOURCE4_SOURCE5 126 1.4698 + angle_coeff @angle:cy-c3-h1 harmonic 47.300 108.280 # SOURCE4_SOURCE5 415 1.0438 + angle_coeff @angle:cy-c3-hc harmonic 46.770 110.750 # SOURCE3_SOURCE5 539 0.9100 + angle_coeff @angle:cy-c3-n3 harmonic 82.598 113.410 # SOURCE4_SOURCE5 17 1.2266 + angle_coeff @angle:cy-c3-oh harmonic 84.330 111.490 # SOURCE4_SOURCE5 347 0.5753 + angle_coeff @angle:cy-c3-os harmonic 85.847 107.070 # SOURCE4_SOURCE5 16 1.1669 + angle_coeff @angle:f-c3-f harmonic 121.555 107.360 # SOURCE2_SOURCE5 1178 0.5429 + angle_coeff @angle:f-c3-h1 harmonic 66.869 107.900 # SOURCE3_SOURCE5 181 0.5803 + angle_coeff @angle:f-c3-h2 harmonic 66.607 108.790 # SOURCE3_SOURCE5 66 0.6474 + angle_coeff @angle:f-c3-h3 harmonic 66.233 110.080 # SOURCE4_SOURCE5 45 0.6178 + angle_coeff @angle:f-c3-hc harmonic 66.555 108.920 # SOURCE2 5 3.0534 + angle_coeff @angle:f-c3-n2 harmonic 112.898 110.400 # SOURCE2 3 2.6470 + angle_coeff @angle:f-c3-os harmonic 114.397 110.580 # SOURCE4_SOURCE5 114 1.2792 + angle_coeff @angle:f-c3-p5 harmonic 107.070 107.610 # SOURCE4_SOURCE5 35 1.1282 + angle_coeff @angle:f-c3-s6 harmonic 83.906 109.680 # SOURCE4_SOURCE5 57 0.4273 + angle_coeff @angle:f-c3-ss harmonic 81.883 111.750 # SOURCE4_SOURCE5 38 1.8571 + angle_coeff @angle:h1-c3-h1 harmonic 38.802 108.460 # SOURCE3_SOURCE5 50971 0.8222 + angle_coeff @angle:h1-c3-n1 harmonic 62.841 107.990 # HF/6-31G*_SOURCE5 7 0.3554 + angle_coeff @angle:h1-c3-n2 harmonic 61.133 109.810 # SOURCE3_SOURCE5 957 1.0346 + angle_coeff @angle:h1-c3-n3 harmonic 61.163 109.880 # SOURCE3_SOURCE5 20428 1.2681 + angle_coeff @angle:h1-c3-n harmonic 61.544 108.880 # SOURCE3_SOURCE5 6816 1.0842 + angle_coeff @angle:h1-c3-na harmonic 61.536 108.780 # SOURCE3_SOURCE5 2896 0.9339 + angle_coeff @angle:h1-c3-nc harmonic 61.844 108.570 # SOURCE3 6 0.0764 + angle_coeff @angle:h1-c3-nd harmonic 61.844 108.570 # SOURCE3 6 + angle_coeff @angle:h1-c3-nh harmonic 61.213 109.790 # SOURCE3_SOURCE5 6106 1.0471 + angle_coeff @angle:h1-c3-no harmonic 59.962 105.470 # SOURCE4_SOURCE5 73 0.6459 + angle_coeff @angle:h1-c3-o harmonic 64.637 116.450 # SOURCE3_SOURCE5 25 1.4798 + angle_coeff @angle:h1-c3-oh harmonic 62.540 110.260 # SOURCE3_SOURCE5 7971 1.1355 + angle_coeff @angle:h1-c3-os harmonic 62.377 109.780 # SOURCE3_SOURCE5 19982 1.1092 + angle_coeff @angle:h1-c3-p5 harmonic 54.608 108.270 # SOURCE4_SOURCE5 222 1.1376 + angle_coeff @angle:h1-c3-s4 harmonic 42.850 107.920 # SOURCE3_SOURCE5 496 0.6942 + angle_coeff @angle:h1-c3-s harmonic 41.631 112.370 # SOURCE3_SOURCE5 14 0.4580 + angle_coeff @angle:h1-c3-s6 harmonic 43.600 107.150 # SOURCE3_SOURCE5 1022 0.8992 + angle_coeff @angle:h1-c3-sh harmonic 42.420 108.420 # SOURCE3_SOURCE5 259 1.4350 + angle_coeff @angle:h1-c3-ss harmonic 42.463 108.760 # SOURCE3_SOURCE5 3369 1.0506 + angle_coeff @angle:h1-c3-sx harmonic 42.605 107.700 # SOURCE3_SOURCE5 201 0.7977 + angle_coeff @angle:h1-c3-sy harmonic 43.421 107.880 # SOURCE3_SOURCE5 377 1.1089 + angle_coeff @angle:h2-c3-h2 harmonic 38.523 110.200 # SOURCE3_SOURCE5 677 0.8586 + angle_coeff @angle:h2-c3-i harmonic 39.064 104.990 # SOURCE3 2 + angle_coeff @angle:h2-c3-n2 harmonic 61.031 110.200 # SOURCE3_SOURCE5 69 0.8494 + angle_coeff @angle:h2-c3-n3 harmonic 61.318 109.350 # SOURCE4_SOURCE5 660 0.9086 + angle_coeff @angle:h2-c3-n harmonic 62.008 107.280 # SOURCE4_SOURCE5 692 1.3634 + angle_coeff @angle:h2-c3-na harmonic 61.963 107.310 # SOURCE3_SOURCE5 428 0.9670 + angle_coeff @angle:h2-c3-nc harmonic 61.596 109.470 # SOURCE3 10 0.3133 + angle_coeff @angle:h2-c3-nd harmonic 61.596 109.470 # SOURCE3 10 + angle_coeff @angle:h2-c3-nh harmonic 61.159 110.010 # SOURCE4_SOURCE5 274 1.1061 + angle_coeff @angle:h2-c3-no harmonic 59.186 108.270 # SOURCE3_SOURCE5 13 0.4528 + angle_coeff @angle:h2-c3-o harmonic 66.832 108.970 # SOURCE3 4 + angle_coeff @angle:h2-c3-oh harmonic 62.785 109.430 # SOURCE3_SOURCE5 258 1.6998 + angle_coeff @angle:h2-c3-os harmonic 62.442 109.580 # SOURCE3_SOURCE5 2823 0.6377 + angle_coeff @angle:h2-c3-s4 harmonic 42.969 107.310 # SOURCE3_SOURCE5 29 0.3344 + angle_coeff @angle:h2-c3-s harmonic 42.709 106.750 # SOURCE3 4 + angle_coeff @angle:h2-c3-s6 harmonic 43.728 106.510 # SOURCE4_SOURCE5 67 1.0466 + angle_coeff @angle:h2-c3-sh harmonic 42.525 107.870 # SOURCE3 6 0.4376 + angle_coeff @angle:h2-c3-ss harmonic 42.544 108.330 # SOURCE3_SOURCE5 279 1.1804 + angle_coeff @angle:h3-c3-n3 harmonic 61.502 108.730 # SOURCE4_SOURCE5 32 1.8953 + angle_coeff @angle:h3-c3-nc harmonic 61.634 109.370 # SOURCE3 1 + angle_coeff @angle:h3-c3-nd harmonic 61.634 109.370 # SOURCE3 1 + angle_coeff @angle:h3-c3-nh harmonic 61.116 110.200 # SOURCE4_SOURCE5 11 1.4222 + angle_coeff @angle:h3-c3-os harmonic 61.911 111.510 # SOURCE4_SOURCE5 44 1.4444 + angle_coeff @angle:h3-c3-ss harmonic 42.391 109.090 # SOURCE4_SOURCE5 19 0.8547 + angle_coeff @angle:hc-c3-hc harmonic 38.960 107.580 # SOURCE3_SOURCE5 92717 0.5328 + angle_coeff @angle:hc-c3-i harmonic 39.071 104.990 # SOURCE3 1 + angle_coeff @angle:hc-c3-n2 harmonic 61.220 109.500 # SOURCE3 1 + angle_coeff @angle:hc-c3-n3 harmonic 61.186 109.800 # SOURCE2 5 2.0070 + angle_coeff @angle:hc-c3-n4 harmonic 60.071 107.900 # SOURCE3 1 + angle_coeff @angle:hc-c3-n harmonic 61.369 109.500 # SOURCE3 1 + angle_coeff @angle:hc-c3-na harmonic 61.334 109.500 # SOURCE3 1 + angle_coeff @angle:hc-c3-nh harmonic 60.731 111.540 # SOURCE3 1 + angle_coeff @angle:hc-c3-no harmonic 59.477 107.200 # SOURCE2 1 + angle_coeff @angle:hc-c3-oh harmonic 62.756 109.500 # SOURCE3 1 + angle_coeff @angle:hc-c3-os harmonic 62.686 108.700 # SOURCE2 13 2.3739 + angle_coeff @angle:hc-c3-p2 harmonic 53.633 110.180 # SOURCE3 25 0.4057 + angle_coeff @angle:hc-c3-p3 harmonic 53.601 109.890 # SOURCE3_SOURCE5 528 0.6740 + angle_coeff @angle:hc-c3-p4 harmonic 54.339 109.450 # SOURCE3_SOURCE5 128 0.4042 + angle_coeff @angle:hc-c3-p5 harmonic 54.567 108.430 # SOURCE3_SOURCE5 513 1.0539 + angle_coeff @angle:hc-c3-px harmonic 54.606 109.700 # SOURCE3_SOURCE5 103 0.3664 + angle_coeff @angle:hc-c3-py harmonic 54.373 109.180 # SOURCE3_SOURCE5 74 0.4506 + angle_coeff @angle:hc-c3-s4 harmonic 42.934 107.500 # SOURCE2 1 + angle_coeff @angle:hc-c3-s6 harmonic 43.388 108.200 # SOURCE3 1 + angle_coeff @angle:hc-c3-sh harmonic 42.529 107.870 # SOURCE2 3 2.0981 + angle_coeff @angle:hc-c3-ss harmonic 42.463 108.760 # SOURCE2 3 1.6891 + angle_coeff @angle:hx-c3-hx harmonic 38.782 109.750 # SOURCE3_SOURCE5 5075 0.8234 + angle_coeff @angle:hx-c3-n4 harmonic 60.076 108.010 # SOURCE3_SOURCE5 6129 1.3658 + angle_coeff @angle:i-c3-i harmonic 66.247 113.120 # SOURCE3 1 + angle_coeff @angle:n1-c3-n1 harmonic 112.470 105.070 # HF/6-31G* 1 + angle_coeff @angle:n2-c3-n2 harmonic 107.595 109.680 # SOURCE3_SOURCE5 6 0.6095 + angle_coeff @angle:n2-c3-nh harmonic 106.900 111.270 # SOURCE4_SOURCE5 19 0.9194 + angle_coeff @angle:n2-c3-oh harmonic 108.058 111.890 # SOURCE4_SOURCE5 31 0.2948 + angle_coeff @angle:n2-c3-os harmonic 108.177 111.040 # SOURCE4_SOURCE5 16 1.7109 + angle_coeff @angle:n3-c3-n3 harmonic 106.945 111.230 # SOURCE4_SOURCE5 123 1.3731 + angle_coeff @angle:n3-c3-nc harmonic 106.282 113.290 # SOURCE3 1 + angle_coeff @angle:n3-c3-nd harmonic 106.282 113.290 # SOURCE3 1 + angle_coeff @angle:n3-c3-nh harmonic 107.270 110.610 # SOURCE4_SOURCE5 58 1.2027 + angle_coeff @angle:n3-c3-oh harmonic 108.693 110.700 # SOURCE4_SOURCE5 52 0.9667 + angle_coeff @angle:n3-c3-os harmonic 109.486 108.510 # SOURCE4_SOURCE5 53 1.7879 + angle_coeff @angle:n3-c3-p5 harmonic 103.225 109.410 # SOURCE4_SOURCE5 26 1.5078 + angle_coeff @angle:n3-c3-ss harmonic 81.202 107.380 # SOURCE4_SOURCE5 50 1.6843 + angle_coeff @angle:n4-c3-n4 harmonic 102.708 113.320 # SOURCE3 1 + angle_coeff @angle:na-c3-na harmonic 106.005 113.490 # SOURCE3 1 + angle_coeff @angle:na-c3-os harmonic 109.296 109.030 # SOURCE4_SOURCE5 495 0.5894 + angle_coeff @angle:nc-c3-nc harmonic 107.885 110.610 # SOURCE3 1 + angle_coeff @angle:nc-c3-nh harmonic 106.714 112.430 # SOURCE3 1 + angle_coeff @angle:nc-c3-os harmonic 106.495 115.410 # SOURCE3 3 1.0288 + angle_coeff @angle:nd-c3-nd harmonic 107.885 110.610 # SOURCE3 1 + angle_coeff @angle:nd-c3-nh harmonic 106.714 112.430 # SOURCE3 1 + angle_coeff @angle:nd-c3-os harmonic 106.495 115.410 # SOURCE3 3 + angle_coeff @angle:nh-c3-nh harmonic 109.672 105.870 # SOURCE3 1 + angle_coeff @angle:nh-c3-oh harmonic 107.958 112.270 # SOURCE4_SOURCE5 43 0.9258 + angle_coeff @angle:nh-c3-os harmonic 109.202 109.130 # SOURCE4_SOURCE5 47 1.3529 + angle_coeff @angle:nh-c3-p5 harmonic 101.809 112.500 # SOURCE4 5 1.7371 + angle_coeff @angle:nh-c3-ss harmonic 80.602 109.010 # SOURCE4_SOURCE5 19 2.2237 + angle_coeff @angle:n-c3-n2 harmonic 106.958 111.310 # SOURCE4_SOURCE5 12 1.5991 + angle_coeff @angle:n-c3-n3 harmonic 107.105 111.110 # SOURCE4_SOURCE5 37 1.6907 + angle_coeff @angle:n-c3-n harmonic 106.473 112.650 # SOURCE3_SOURCE5 30 2.1166 + angle_coeff @angle:n-c3-nh harmonic 108.332 108.660 # SOURCE4_SOURCE5 26 1.9779 + angle_coeff @angle:n-c3-oh harmonic 107.902 112.560 # SOURCE4_SOURCE5 75 1.1310 + angle_coeff @angle:no-c3-no harmonic 105.051 105.180 # SOURCE4_SOURCE5 23 1.9192 + angle_coeff @angle:n-c3-os harmonic 109.285 109.130 # SOURCE4_SOURCE5 432 0.8256 + angle_coeff @angle:n-c3-p5 harmonic 102.749 110.520 # SOURCE4_SOURCE5 12 1.2739 + angle_coeff @angle:oh-c3-oh harmonic 110.720 109.900 # SOURCE4_SOURCE5 20 1.5118 + angle_coeff @angle:oh-c3-os harmonic 110.658 109.380 # SOURCE4_SOURCE5 280 1.2270 + angle_coeff @angle:oh-c3-p5 harmonic 104.174 108.680 # SOURCE4_SOURCE5 77 1.3087 + angle_coeff @angle:oh-c3-sh harmonic 78.616 115.460 # SOURCE3 1 + angle_coeff @angle:o-c3-o harmonic 113.472 122.300 # SOURCE3 1 + angle_coeff @angle:os-c3-os harmonic 110.893 108.290 # SOURCE3_SOURCE5 723 1.0283 + angle_coeff @angle:os-c3-p5 harmonic 104.392 107.990 # SOURCE4_SOURCE5 63 2.0205 + angle_coeff @angle:os-c3-ss harmonic 81.130 108.590 # SOURCE4_SOURCE5 54 1.6231 + angle_coeff @angle:p2-c3-p2 harmonic 104.003 110.480 # SOURCE3 1 + angle_coeff @angle:p3-c3-p3 harmonic 103.975 110.160 # SOURCE3 1 + angle_coeff @angle:p5-c3-p5 harmonic 105.046 110.130 # SOURCE4 33 2.4116 + angle_coeff @angle:p5-c3-ss harmonic 81.364 111.480 # SOURCE4_SOURCE5 12 1.9291 + angle_coeff @angle:s4-c3-s4 harmonic 63.477 112.290 # SOURCE3 2 1.2724 + angle_coeff @angle:s4-c3-s6 harmonic 63.526 113.520 # SOURCE3 1 + angle_coeff @angle:s6-c3-s6 harmonic 64.593 111.220 # SOURCE3_SOURCE5 6 1.7567 + angle_coeff @angle:sh-c3-sh harmonic 61.944 116.260 # SOURCE3 1 + angle_coeff @angle:sh-c3-ss harmonic 63.545 110.730 # SOURCE3 1 + angle_coeff @angle:s-c3-s harmonic 60.088 123.350 # SOURCE3 1 + angle_coeff @angle:ss-c3-ss harmonic 63.417 111.440 # SOURCE4_SOURCE5 66 1.6272 + angle_coeff @angle:br-ca-br harmonic 67.710 117.600 # SOURCE3 1 + angle_coeff @angle:br-ca-ca harmonic 64.160 119.300 # SOURCE3_SOURCE5 640 0.4898 + angle_coeff @angle:c1-ca-c1 harmonic 66.786 120.000 # SOURCE3 1 + angle_coeff @angle:c1-ca-ca harmonic 67.736 120.000 # SOURCE3 1 + angle_coeff @angle:c2-ca-c2 harmonic 69.458 120.000 # SOURCE3 1 + angle_coeff @angle:c2-ca-ca harmonic 68.938 120.600 # SOURCE3 1 + angle_coeff @angle:c3-ca-c2 harmonic 66.051 120.000 # SOURCE3 1 + angle_coeff @angle:c3-ca-c3 harmonic 64.318 116.800 # SOURCE3 1 + angle_coeff @angle:c3-ca-ca harmonic 65.583 120.770 # SOURCE3_SOURCE5 23865 1.2220 + angle_coeff @angle:c3-ca-cp harmonic 65.482 120.630 # CORR 120 + angle_coeff @angle:c3-ca-cq harmonic 65.482 120.630 # CORR 120 + angle_coeff @angle:c3-ca-na harmonic 83.171 118.720 # SOURCE4_SOURCE5 145 1.1124 + angle_coeff @angle:c3-ca-nb harmonic 84.916 116.680 # SOURCE4_SOURCE5 1062 0.9093 + angle_coeff @angle:ca-ca-ca harmonic 68.767 120.020 # SOURCE3_SOURCE5 108055 0.7701 + angle_coeff @angle:ca-ca-cc harmonic 67.122 120.790 # SOURCE3_SOURCE5 2048 2.0941 + angle_coeff @angle:ca-ca-cd harmonic 67.122 120.790 # SOURCE3_SOURCE5 2048 2.0941 + angle_coeff @angle:ca-ca-ce harmonic 66.584 120.820 # SOURCE3_SOURCE5 3962 1.5682 + angle_coeff @angle:ca-ca-cf harmonic 66.584 120.820 # SOURCE3_SOURCE5 3948 1.5732 + angle_coeff @angle:ca-ca-cg harmonic 67.841 120.270 # SOURCE3_SOURCE5 453 0.4194 + angle_coeff @angle:ca-ca-ch harmonic 67.841 120.270 # SOURCE3_SOURCE5 447 0.4218 + angle_coeff @angle:ca-ca-cl harmonic 72.112 119.390 # SOURCE4_SOURCE5 6669 0.5363 + angle_coeff @angle:ca-ca-cp harmonic 68.394 120.690 # CORR_SOURCE5 1915 0.8596 + angle_coeff @angle:ca-ca-cq harmonic 68.394 120.690 # CORR_SOURCE5 1915 0.8596 + angle_coeff @angle:ca-ca-cx harmonic 66.227 120.830 # SOURCE4 71 1.3062 + angle_coeff @angle:ca-ca-cy harmonic 65.564 120.860 # SOURCE4 17 2.0287 + angle_coeff @angle:ca-ca-f harmonic 89.261 118.960 # SOURCE4_SOURCE5 2636 0.3804 + angle_coeff @angle:ca-ca-h4 harmonic 48.561 120.340 # SOURCE3_SOURCE5 2590 0.5568 + angle_coeff @angle:ca-ca-ha harmonic 48.680 119.880 # SOURCE3_SOURCE5 126779 0.4424 + angle_coeff @angle:ca-ca-i harmonic 61.098 119.110 # SOURCE3_SOURCE5 123 0.9416 + angle_coeff @angle:ca-ca-n1 harmonic 88.104 119.780 # HF/6-31G*_SOURCE5 14 0.4655 + angle_coeff @angle:ca-ca-n2 harmonic 89.100 119.570 # SOURCE3 1 + angle_coeff @angle:ca-ca-n4 harmonic 83.650 119.310 # SOURCE3_SOURCE5 63 1.4960 + angle_coeff @angle:ca-ca-n harmonic 85.629 120.190 # SOURCE3_SOURCE5 3041 2.2480 + angle_coeff @angle:ca-ca-na harmonic 87.167 118.340 # SOURCE3 54 3.6168 + angle_coeff @angle:ca-ca-nb harmonic 86.849 122.940 # SOURCE3_SOURCE5 5507 1.1495 + angle_coeff @angle:ca-ca-nc harmonic 87.635 119.720 # SOURCE3 22 3.3994 + angle_coeff @angle:ca-ca-nd harmonic 87.635 119.720 # SOURCE3 22 3.3994 + angle_coeff @angle:ca-ca-ne harmonic 85.610 120.610 # SOURCE3_SOURCE5 349 2.0914 + angle_coeff @angle:ca-ca-nf harmonic 85.610 120.610 # SOURCE3_SOURCE5 349 2.0914 + angle_coeff @angle:ca-ca-nh harmonic 86.163 120.950 # SOURCE3_SOURCE5 4970 1.2168 + angle_coeff @angle:ca-ca-no harmonic 84.250 119.010 # SOURCE3_SOURCE5 854 0.7071 + angle_coeff @angle:ca-ca-o harmonic 89.534 123.260 # SOURCE4_SOURCE5 35 1.2620 + angle_coeff @angle:ca-ca-oh harmonic 87.211 119.900 # SOURCE3_SOURCE5 6384 1.7827 + angle_coeff @angle:ca-ca-os harmonic 87.289 119.200 # SOURCE3 52 0.5240 + angle_coeff @angle:ca-ca-p2 harmonic 81.329 114.360 # SOURCE3 1 + angle_coeff @angle:ca-ca-p3 harmonic 79.908 120.010 # SOURCE3_SOURCE5 24 1.1566 + angle_coeff @angle:ca-ca-p4 harmonic 80.525 120.300 # SOURCE3 1 + angle_coeff @angle:ca-ca-p5 harmonic 80.938 120.240 # SOURCE4_SOURCE5 15 0.0746 + angle_coeff @angle:ca-ca-pe harmonic 79.643 120.450 # SOURCE3 20 0.2719 + angle_coeff @angle:ca-ca-pf harmonic 79.643 120.450 # SOURCE3 20 0.2719 + angle_coeff @angle:ca-ca-px harmonic 79.761 120.530 # SOURCE3 10 0.4509 + angle_coeff @angle:ca-ca-py harmonic 80.172 120.250 # SOURCE3_SOURCE5 75 1.5353 + angle_coeff @angle:ca-ca-s4 harmonic 63.561 119.150 # SOURCE3 1 + angle_coeff @angle:ca-ca-s6 harmonic 63.822 120.430 # SOURCE4_SOURCE5 89 1.1843 + angle_coeff @angle:ca-ca-s harmonic 64.056 122.550 # SOURCE3 4 + angle_coeff @angle:ca-ca-sh harmonic 63.072 121.780 # SOURCE4_SOURCE5 54 1.3490 + angle_coeff @angle:ca-ca-ss harmonic 63.530 120.060 # SOURCE3_SOURCE5 1341 2.1632 + angle_coeff @angle:ca-ca-sx harmonic 62.473 119.280 # SOURCE3_SOURCE5 140 1.1919 + angle_coeff @angle:ca-ca-sy harmonic 63.407 119.420 # SOURCE3_SOURCE5 1489 0.7572 + angle_coeff @angle:c-ca-c3 harmonic 64.497 118.060 # SOURCE3 1 + angle_coeff @angle:c-ca-c harmonic 64.519 120.000 # SOURCE3 1 + angle_coeff @angle:c-ca-ca harmonic 66.351 120.330 # SOURCE3_SOURCE5 8320 1.9221 + angle_coeff @angle:cc-ca-cp harmonic 66.010 124.300 # SOURCE4_SOURCE5 20 0.6423 + angle_coeff @angle:cc-ca-nb harmonic 86.709 117.750 # CORR_SOURCE5 42 1.7067 + angle_coeff @angle:cd-ca-nb harmonic 86.709 117.750 # CORR_SOURCE5 42 1.7067 + angle_coeff @angle:ce-ca-na harmonic 84.062 119.920 # SOURCE4_SOURCE5 38 0.5659 + angle_coeff @angle:ce-ca-nb harmonic 86.028 117.560 # CORR_SOURCE5 91 0.8492 + angle_coeff @angle:cf-ca-nb harmonic 86.028 117.560 # CORR_SOURCE5 91 0.8492 + angle_coeff @angle:cg-ca-cp harmonic 67.320 121.530 # SOURCE4_SOURCE5 24 0.1831 + angle_coeff @angle:c-ca-ha harmonic 46.900 115.900 # SOURCE3 1 + angle_coeff @angle:cl-ca-cl harmonic 80.510 118.720 # SOURCE3 1 + angle_coeff @angle:cl-ca-cp harmonic 71.726 120.390 # SOURCE4_SOURCE5 52 0.5449 + angle_coeff @angle:cl-ca-nb harmonic 92.329 116.180 # SOURCE4_SOURCE5 152 0.5909 + angle_coeff @angle:c-ca-nb harmonic 85.429 117.780 # SOURCE4_SOURCE5 262 1.1507 + angle_coeff @angle:c-ca-nc harmonic 80.781 130.800 # SOURCE3 1 + angle_coeff @angle:c-ca-nd harmonic 80.781 130.800 # SOURCE3 1 + angle_coeff @angle:cp-ca-f harmonic 88.831 119.420 # SOURCE4_SOURCE5 46 0.2425 + angle_coeff @angle:cp-ca-h4 harmonic 48.404 120.090 # SOURCE4_SOURCE5 62 0.4243 + angle_coeff @angle:cp-ca-ha harmonic 48.475 119.860 # CORR_SOURCE5 1240 0.5472 + angle_coeff @angle:cp-ca-na harmonic 90.665 108.790 # SOURCE4_SOURCE5 514 0.5055 + angle_coeff @angle:cp-ca-nb harmonic 86.369 123.580 # SOURCE4_SOURCE5 129 0.8391 + angle_coeff @angle:cp-ca-nh harmonic 85.714 121.560 # SOURCE4_SOURCE5 30 0.5872 + angle_coeff @angle:cp-ca-oh harmonic 86.623 120.850 # SOURCE4_SOURCE5 41 1.3658 + angle_coeff @angle:cp-ca-ss harmonic 65.950 111.170 # SOURCE4_SOURCE5 24 1.8180 + angle_coeff @angle:cp-ca-sy harmonic 65.646 111.180 # CORR 4 + angle_coeff @angle:cq-ca-ha harmonic 48.475 119.860 # CORR_SOURCE5 1240 0.5472 + angle_coeff @angle:cq-ca-sy harmonic 65.646 111.180 # CORR 4 + angle_coeff @angle:f-ca-f harmonic 116.252 117.500 # SOURCE3 1 + angle_coeff @angle:f-ca-nb harmonic 116.437 114.670 # SOURCE4_SOURCE5 42 0.4295 + angle_coeff @angle:h4-ca-n harmonic 61.444 116.020 # SOURCE3 1 + angle_coeff @angle:h4-ca-na harmonic 62.367 116.320 # SOURCE3_SOURCE5 394 0.4031 + angle_coeff @angle:h4-ca-nb harmonic 64.066 116.030 # SOURCE3_SOURCE5 2217 0.2861 + angle_coeff @angle:h4-ca-nc harmonic 62.978 118.360 # SOURCE3 1 + angle_coeff @angle:h4-ca-nd harmonic 62.978 118.360 # SOURCE3 1 + angle_coeff @angle:h4-ca-os harmonic 64.330 111.150 # SOURCE3 1 + angle_coeff @angle:h4-ca-ss harmonic 42.528 116.190 # SOURCE3 1 + angle_coeff @angle:h5-ca-nb harmonic 64.141 115.820 # SOURCE3_SOURCE5 618 0.3893 + angle_coeff @angle:h5-ca-nc harmonic 62.019 122.110 # SOURCE3 1 + angle_coeff @angle:h5-ca-nd harmonic 62.019 122.110 # SOURCE3 1 + angle_coeff @angle:ha-ca-n2 harmonic 65.427 116.000 # SOURCE2 1 + angle_coeff @angle:ha-ca-p2 harmonic 51.256 122.560 # SOURCE3 1 + angle_coeff @angle:i-ca-i harmonic 67.026 119.280 # SOURCE3 1 + angle_coeff @angle:n1-ca-n1 harmonic 114.391 117.030 # HF/6-31G* 1 + angle_coeff @angle:n2-ca-n2 harmonic 115.741 120.000 # SOURCE3 1 + angle_coeff @angle:n2-ca-na harmonic 112.235 119.600 # SOURCE3 1 + angle_coeff @angle:n4-ca-n4 harmonic 102.984 116.820 # SOURCE3 1 + angle_coeff @angle:na-ca-na harmonic 115.064 107.620 # SOURCE4_SOURCE5 11 0.8382 + angle_coeff @angle:na-ca-nb harmonic 107.575 127.090 # SOURCE4_SOURCE5 708 1.9791 + angle_coeff @angle:na-ca-nh harmonic 109.505 118.660 # SOURCE4_SOURCE5 73 0.9977 + angle_coeff @angle:nb-ca-nb harmonic 109.369 127.260 # SOURCE4_SOURCE5 1586 1.1854 + angle_coeff @angle:nb-ca-nc harmonic 109.175 126.500 # CORR_SOURCE5 33 1.0453 + angle_coeff @angle:nb-ca-nd harmonic 109.175 126.500 # CORR_SOURCE5 33 1.0453 + angle_coeff @angle:nb-ca-nh harmonic 112.063 116.940 # SOURCE4_SOURCE5 2042 0.7868 + angle_coeff @angle:nb-ca-oh harmonic 112.676 117.680 # SOURCE4_SOURCE5 182 0.7979 + angle_coeff @angle:nb-ca-os harmonic 111.458 119.720 # SOURCE4_SOURCE5 194 0.7211 + angle_coeff @angle:nb-ca-sh harmonic 80.990 117.610 # SOURCE4_SOURCE5 35 1.3741 + angle_coeff @angle:nb-ca-ss harmonic 80.595 118.800 # SOURCE4_SOURCE5 111 1.8247 + angle_coeff @angle:nc-ca-nc harmonic 107.717 128.740 # SOURCE3 1 + angle_coeff @angle:nc-ca-nh harmonic 110.670 118.860 # SOURCE3 1 + angle_coeff @angle:nd-ca-nd harmonic 107.717 128.740 # SOURCE3 1 + angle_coeff @angle:nd-ca-nh harmonic 110.670 118.860 # SOURCE3 1 + angle_coeff @angle:nh-ca-nh harmonic 108.376 120.980 # SOURCE3 1 + angle_coeff @angle:n-ca-nc harmonic 107.316 123.860 # SOURCE3 1 + angle_coeff @angle:n-ca-nd harmonic 107.316 123.860 # SOURCE3 1 + angle_coeff @angle:n-ca-nh harmonic 109.547 116.160 # SOURCE3 1 + angle_coeff @angle:no-ca-no harmonic 103.915 117.140 # SOURCE3 1 + angle_coeff @angle:oh-ca-oh harmonic 110.589 120.000 # SOURCE3 1 + angle_coeff @angle:o-ca-o harmonic 118.708 126.820 # SOURCE3 1 + angle_coeff @angle:os-ca-os harmonic 113.107 113.730 # SOURCE3 1 + angle_coeff @angle:p2-ca-p2 harmonic 100.107 121.200 # SOURCE3 1 + angle_coeff @angle:p3-ca-p3 harmonic 100.783 121.460 # SOURCE3 1 + angle_coeff @angle:p5-ca-p5 harmonic 103.117 120.000 # SOURCE3 1 + angle_coeff @angle:s4-ca-s4 harmonic 66.946 105.810 # SOURCE3 1 + angle_coeff @angle:s6-ca-s6 harmonic 67.745 105.810 # SOURCE3 1 + angle_coeff @angle:sh-ca-sh harmonic 63.051 120.240 # SOURCE3 1 + angle_coeff @angle:s-ca-s harmonic 63.293 125.140 # SOURCE3 1 + angle_coeff @angle:ss-ca-ss harmonic 64.440 115.150 # SOURCE3 1 + angle_coeff @angle:br-c-br harmonic 67.692 113.100 # SOURCE3 1 + angle_coeff @angle:br-c-c3 harmonic 64.598 110.740 # SOURCE3 1 + angle_coeff @angle:br-c-o harmonic 78.490 121.460 # SOURCE3 5 1.6264 + angle_coeff @angle:c1-c-c1 harmonic 67.194 115.320 # SOURCE3 1 + angle_coeff @angle:c1-c-o harmonic 87.628 122.340 # SOURCE3 1 + angle_coeff @angle:c2-c-c2 harmonic 69.337 116.780 # SOURCE3 1 + angle_coeff @angle:c2-c-ha harmonic 49.151 115.950 # SOURCE3 1 + angle_coeff @angle:c2-c-o harmonic 91.182 119.120 # SOURCE3 2 + angle_coeff @angle:c2-c-s harmonic 66.780 119.160 # SOURCE3 2 + angle_coeff @angle:c3-c-c3 harmonic 64.041 116.500 # SOURCE3_SOURCE5 720 1.3034 + angle_coeff @angle:c3-c-ca harmonic 64.216 118.400 # SOURCE4_SOURCE5 749 1.4991 + angle_coeff @angle:c3-c-cc harmonic 64.984 117.290 # CORR_SOURCE5 118 1.7737 + angle_coeff @angle:c3-c-cd harmonic 64.984 117.290 # CORR_SOURCE5 118 1.7737 + angle_coeff @angle:c3-c-ce harmonic 64.919 116.440 # CORR_SOURCE5 543 1.3559 + angle_coeff @angle:c3-c-cf harmonic 64.919 116.440 # CORR_SOURCE5 543 1.3559 + angle_coeff @angle:c3-c-cg harmonic 65.958 115.000 # SOURCE2 1 + angle_coeff @angle:c3-c-ch harmonic 65.958 115.000 # SOURCE2 1 + angle_coeff @angle:c3-c-cl harmonic 71.237 111.990 # SOURCE3 2 0.0125 + angle_coeff @angle:c3-c-f harmonic 88.418 110.700 # SOURCE2 1 + angle_coeff @angle:c3-c-h4 harmonic 46.112 114.640 # SOURCE4_SOURCE5 193 0.4989 + angle_coeff @angle:c3-c-ha harmonic 46.047 115.220 # SOURCE3 15 0.3181 + angle_coeff @angle:c3-c-i harmonic 60.388 112.940 # SOURCE3 1 + angle_coeff @angle:c3-c-n2 harmonic 83.534 114.530 # SOURCE3 1 + angle_coeff @angle:c3-c-n4 harmonic 81.106 112.260 # SOURCE3 2 + angle_coeff @angle:c3-c-n harmonic 84.266 115.180 # SOURCE3_SOURCE5 2997 1.3885 + angle_coeff @angle:c3-c-ne harmonic 84.941 112.610 # CORR_SOURCE5 19 2.4426 + angle_coeff @angle:c3-c-nf harmonic 84.941 112.610 # CORR_SOURCE5 19 2.4426 + angle_coeff @angle:c3-c-o harmonic 84.552 123.200 # SOURCE3_SOURCE5 10083 1.8011 + angle_coeff @angle:c3-c-oh harmonic 85.803 112.730 # SOURCE3_SOURCE5 1989 1.3796 + angle_coeff @angle:c3-c-os harmonic 86.419 110.720 # SOURCE3_SOURCE5 1786 0.9391 + angle_coeff @angle:c3-c-p3 harmonic 77.773 116.420 # SOURCE3 3 0.1291 + angle_coeff @angle:c3-c-p5 harmonic 76.995 118.900 # SOURCE3 1 + angle_coeff @angle:c3-c-pe harmonic 77.418 114.850 # SOURCE3 1 + angle_coeff @angle:c3-c-pf harmonic 77.418 114.850 # SOURCE3 1 + angle_coeff @angle:c3-c-px harmonic 77.387 115.600 # SOURCE3 1 + angle_coeff @angle:c3-c-py harmonic 77.698 118.160 # SOURCE3 3 1.0735 + angle_coeff @angle:c3-c-s4 harmonic 61.352 114.790 # SOURCE3 1 + angle_coeff @angle:c3-c-s6 harmonic 61.371 114.720 # SOURCE3 1 + angle_coeff @angle:c3-c-s harmonic 63.941 123.150 # SOURCE3_SOURCE5 66 1.3121 + angle_coeff @angle:c3-c-sh harmonic 63.752 112.650 # SOURCE3_SOURCE5 9 1.5127 + angle_coeff @angle:c3-c-ss harmonic 63.438 113.510 # SOURCE3_SOURCE5 65 0.9334 + angle_coeff @angle:c3-c-sx harmonic 61.201 113.970 # SOURCE3 3 0.0610 + angle_coeff @angle:c3-c-sy harmonic 61.612 114.280 # SOURCE3 3 0.7341 + angle_coeff @angle:ca-c-ca harmonic 65.033 118.110 # SOURCE4_SOURCE5 506 1.8633 + angle_coeff @angle:ca-c-cc harmonic 66.124 116.000 # CORR_SOURCE5 670 1.7109 + angle_coeff @angle:ca-c-cd harmonic 66.124 116.000 # CORR_SOURCE5 670 1.7109 + angle_coeff @angle:ca-c-ce harmonic 64.959 119.020 # CORR_SOURCE5 83 1.3943 + angle_coeff @angle:ca-c-cf harmonic 64.959 119.020 # CORR_SOURCE5 83 1.3943 + angle_coeff @angle:ca-c-h4 harmonic 46.911 115.140 # SOURCE4_SOURCE5 122 0.7683 + angle_coeff @angle:ca-c-ha harmonic 47.184 114.120 # SOURCE3 1 + angle_coeff @angle:ca-c-n harmonic 85.392 115.250 # SOURCE4_SOURCE5 1494 1.4889 + angle_coeff @angle:ca-c-ne harmonic 85.290 114.710 # SOURCE4_SOURCE5 14 0.5855 + angle_coeff @angle:ca-c-o harmonic 86.207 122.600 # SOURCE3_SOURCE5 3960 1.5802 + angle_coeff @angle:ca-c-oh harmonic 86.748 113.450 # SOURCE4_SOURCE5 656 0.8414 + angle_coeff @angle:ca-c-os harmonic 86.963 112.440 # SOURCE3_SOURCE5 493 0.8365 + angle_coeff @angle:ca-c-s harmonic 64.593 122.680 # SOURCE4_SOURCE5 32 1.3788 + angle_coeff @angle:ca-c-sh harmonic 62.515 118.630 # SOURCE3 1 + angle_coeff @angle:ca-c-ss harmonic 63.406 115.050 # SOURCE4_SOURCE5 37 1.0695 + angle_coeff @angle:br-cc-c harmonic 65.156 116.280 # SOURCE4_SOURCE5 32 1.1116 + angle_coeff @angle:br-cc-cc harmonic 63.389 124.050 # SOURCE4_SOURCE5 31 1.9388 + angle_coeff @angle:br-cc-cd harmonic 63.686 124.230 # SOURCE4_SOURCE5 116 2.3356 + angle_coeff @angle:br-cc-na harmonic 80.565 121.580 # SOURCE4_SOURCE5 19 0.8500 + angle_coeff @angle:c2-cc-c3 harmonic 65.262 126.110 # SOURCE3 2 + angle_coeff @angle:c2-cc-ca harmonic 66.952 124.420 # CORR_SOURCE5 25 1.8245 + angle_coeff @angle:c2-cc-cc harmonic 68.308 122.190 # CORR_SOURCE5 46 2.3853 + angle_coeff @angle:c2-cc-cd harmonic 71.286 117.020 # SOURCE3 2 0.0703 + angle_coeff @angle:c2-cc-ha harmonic 49.231 122.720 # SOURCE3 2 0.0092 + angle_coeff @angle:c2-cc-n harmonic 86.150 124.910 # SOURCE3_SOURCE5 5 1.6803 + angle_coeff @angle:c2-cc-os harmonic 87.991 121.420 # CORR_SOURCE5 24 0.9570 + angle_coeff @angle:c-c-c3 harmonic 63.621 116.170 # SOURCE3_SOURCE5 58 1.1332 + angle_coeff @angle:c3-cc-ca harmonic 63.318 126.520 # CORR_SOURCE5 370 1.8946 + angle_coeff @angle:c3-cc-cc harmonic 66.709 115.970 # SOURCE3 4 3.0507 + angle_coeff @angle:c3-cc-cd harmonic 66.802 119.450 # SOURCE3 35 8.2040 + angle_coeff @angle:c3-cc-cf harmonic 67.395 117.840 # CORR 2 + angle_coeff @angle:c3-cc-ha harmonic 45.517 121.520 # SOURCE3 32 3.2091 + angle_coeff @angle:c3-cc-n2 harmonic 83.336 125.690 # CORR_SOURCE5 12 1.9935 + angle_coeff @angle:c3-cc-n harmonic 83.558 119.190 # CORR_SOURCE5 107 2.1078 + angle_coeff @angle:c3-cc-na harmonic 82.356 122.730 # CORR_SOURCE5 961 1.6482 + angle_coeff @angle:c3-cc-nc harmonic 83.215 120.950 # CORR_SOURCE5 456 0.8756 + angle_coeff @angle:c3-cc-nd harmonic 83.886 122.410 # CORR_SOURCE5 653 1.6992 + angle_coeff @angle:c3-cc-os harmonic 84.855 116.800 # CORR_SOURCE5 306 0.8990 + angle_coeff @angle:c3-cc-ss harmonic 62.656 121.530 # CORR_SOURCE5 270 1.0948 + angle_coeff @angle:c-c-c harmonic 64.391 111.680 # SOURCE3 2 6.1226 + angle_coeff @angle:c-c-ca harmonic 63.623 118.600 # SOURCE4_SOURCE5 90 1.0263 + angle_coeff @angle:ca-cc-cc harmonic 69.336 111.040 # SOURCE3 9 7.9455 + angle_coeff @angle:ca-cc-cd harmonic 69.802 113.510 # SOURCE3 26 7.4229 + angle_coeff @angle:ca-cc-ce harmonic 64.258 127.010 # SOURCE4_SOURCE5 38 1.6763 + angle_coeff @angle:ca-cc-h4 harmonic 45.368 129.250 # SOURCE3_SOURCE5 54 1.5632 + angle_coeff @angle:ca-cc-ha harmonic 46.300 124.040 # SOURCE3 34 3.6691 + angle_coeff @angle:ca-cc-n harmonic 85.642 117.670 # CORR 18 + angle_coeff @angle:ca-cc-nc harmonic 84.897 120.590 # CORR_SOURCE5 224 1.0853 + angle_coeff @angle:ca-cc-nd harmonic 85.294 123.240 # CORR_SOURCE5 246 2.3557 + angle_coeff @angle:ca-cc-nh harmonic 84.253 122.130 # SOURCE4_SOURCE5 20 1.7636 + angle_coeff @angle:ca-cc-oh harmonic 86.577 117.550 # CORR_SOURCE5 35 1.9318 + angle_coeff @angle:ca-cc-os harmonic 87.229 114.750 # CORR_SOURCE5 247 2.0579 + angle_coeff @angle:ca-cc-ss harmonic 63.408 120.800 # CORR_SOURCE5 80 2.1212 + angle_coeff @angle:c-cc-c2 harmonic 67.513 121.170 # CORR_SOURCE5 28 1.6484 + angle_coeff @angle:c-cc-c3 harmonic 65.378 117.760 # CORR_SOURCE5 566 1.9588 + angle_coeff @angle:c-cc-c harmonic 65.240 121.070 # CORR_SOURCE5 128 0.8902 + angle_coeff @angle:c-c-cc harmonic 66.020 111.670 # SOURCE3 4 5.5146 + angle_coeff @angle:c-cc-ca harmonic 65.005 122.950 # SOURCE3 1 + angle_coeff @angle:c-cc-cc harmonic 65.674 122.690 # SOURCE3 2 + angle_coeff @angle:cc-c-cc harmonic 66.696 115.840 # CORR_SOURCE5 115 1.4659 + angle_coeff @angle:cc-cc-cc harmonic 70.129 110.700 # SOURCE3 54 3.4091 + angle_coeff @angle:cc-cc-cd harmonic 70.348 114.190 # SOURCE3 517 6.5960 + angle_coeff @angle:cc-cc-ce harmonic 64.853 127.060 # CORR_SOURCE5 61 2.3233 + angle_coeff @angle:cc-cc-cf harmonic 68.022 122.720 # CORR_SOURCE5 66 1.9701 + angle_coeff @angle:cc-cc-cg harmonic 65.805 125.910 # CORR_SOURCE5 41 1.1646 + angle_coeff @angle:c-cc-cd harmonic 67.187 121.350 # CORR_SOURCE5 3554 2.2084 + angle_coeff @angle:cc-c-cd harmonic 67.592 112.790 # SOURCE3 1 + angle_coeff @angle:c-cc-ce harmonic 65.406 121.570 # CORR_SOURCE5 29 1.1305 + angle_coeff @angle:cc-c-ce harmonic 66.433 115.570 # SOURCE4_SOURCE5 14 1.2088 + angle_coeff @angle:cc-cc-f harmonic 88.377 119.190 # SOURCE4_SOURCE5 26 0.8983 + angle_coeff @angle:c-cc-cg harmonic 67.046 117.880 # SOURCE4_SOURCE5 26 0.6759 + angle_coeff @angle:cc-cc-h4 harmonic 46.348 127.960 # SOURCE3_SOURCE5 391 2.1732 + angle_coeff @angle:cc-cc-ha harmonic 47.634 121.070 # CORR_SOURCE5 2414 2.2010 + angle_coeff @angle:c-cc-cl harmonic 72.591 116.380 # CORR_SOURCE5 50 1.2099 + angle_coeff @angle:cc-cc-n2 harmonic 87.356 122.210 # CORR_SOURCE5 37 1.6493 + angle_coeff @angle:cc-cc-n harmonic 85.753 119.890 # SOURCE3 36 0.2095 + angle_coeff @angle:cc-cc-na harmonic 86.536 117.770 # SOURCE3_SOURCE5 865 1.5665 + angle_coeff @angle:cc-cc-nc harmonic 85.332 121.980 # CORR_SOURCE5 141 1.9633 + angle_coeff @angle:cc-cc-nd harmonic 90.306 112.560 # SOURCE3 141 4.2871 + angle_coeff @angle:cc-cc-nh harmonic 86.018 119.720 # CORR_SOURCE5 348 1.7785 + angle_coeff @angle:cc-cc-oh harmonic 86.201 121.270 # CORR_SOURCE5 11 2.2744 + angle_coeff @angle:cc-cc-os harmonic 87.213 117.340 # CORR_SOURCE5 217 1.9304 + angle_coeff @angle:cc-cc-pd harmonic 84.517 115.360 # SOURCE3 84 + angle_coeff @angle:cc-cc-ss harmonic 63.877 120.210 # CORR_SOURCE5 52 2.1160 + angle_coeff @angle:cc-cc-sy harmonic 61.106 128.250 # SOURCE4_SOURCE5 20 0.9014 + angle_coeff @angle:c-c-cd harmonic 66.020 111.670 # SOURCE3 4 5.5146 + angle_coeff @angle:cd-cc-cd harmonic 70.027 120.080 # CORR_SOURCE5 119 1.6139 + angle_coeff @angle:cd-cc-ce harmonic 65.759 128.050 # CORR_SOURCE5 350 2.4628 + angle_coeff @angle:cd-cc-cl harmonic 71.687 123.410 # CORR_SOURCE5 115 2.1217 + angle_coeff @angle:cd-cc-f harmonic 89.570 121.190 # SOURCE4_SOURCE5 82 0.7206 + angle_coeff @angle:cd-cc-h4 harmonic 47.759 128.480 # SOURCE3_SOURCE5 3291 2.3189 + angle_coeff @angle:cd-cc-ha harmonic 49.040 121.760 # SOURCE3_SOURCE5 4433 1.8701 + angle_coeff @angle:cd-cc-n harmonic 86.990 121.330 # SOURCE3_SOURCE5 821 1.9126 + angle_coeff @angle:cd-cc-na harmonic 92.653 106.990 # SOURCE3_SOURCE5 3003 2.3845 + angle_coeff @angle:cd-cc-nc harmonic 91.057 111.650 # CORR_SOURCE5 1656 1.8430 + angle_coeff @angle:cd-cc-nh harmonic 86.331 123.840 # CORR_SOURCE5 152 2.2360 + angle_coeff @angle:cd-cc-no harmonic 82.947 128.690 # SOURCE4_SOURCE5 314 1.4409 + angle_coeff @angle:cd-cc-oh harmonic 87.177 123.780 # CORR_SOURCE5 251 1.1988 + angle_coeff @angle:cd-cc-os harmonic 87.957 120.300 # SOURCE3 64 5.4354 + angle_coeff @angle:cd-cc-ss harmonic 66.887 111.550 # CORR_SOURCE5 1048 1.8648 + angle_coeff @angle:cd-cc-sy harmonic 62.501 124.550 # CORR_SOURCE5 56 1.7107 + angle_coeff @angle:ce-cc-na harmonic 83.371 124.350 # CORR_SOURCE5 87 1.3591 + angle_coeff @angle:ce-cc-nc harmonic 84.769 121.100 # CORR_SOURCE5 43 1.2959 + angle_coeff @angle:ce-cc-nd harmonic 85.887 121.700 # CORR_SOURCE5 58 1.4179 + angle_coeff @angle:ce-cc-os harmonic 85.796 118.760 # CORR_SOURCE5 92 1.3159 + angle_coeff @angle:ce-cc-ss harmonic 63.222 121.580 # CORR_SOURCE5 54 1.3126 + angle_coeff @angle:c-cc-f harmonic 87.759 116.980 # SOURCE4_SOURCE5 49 0.4690 + angle_coeff @angle:cg-cc-na harmonic 84.878 122.610 # SOURCE4_SOURCE5 12 0.9695 + angle_coeff @angle:cg-cc-ss harmonic 63.762 120.730 # SOURCE4_SOURCE5 27 0.9221 + angle_coeff @angle:cc-c-h4 harmonic 47.598 114.830 # SOURCE4_SOURCE5 25 0.5124 + angle_coeff @angle:c-cc-ha harmonic 47.405 116.640 # SOURCE3_SOURCE5 896 1.3075 + angle_coeff @angle:cl-cc-na harmonic 90.511 121.120 # SOURCE4_SOURCE5 37 0.7206 + angle_coeff @angle:cl-cc-nd harmonic 90.963 122.070 # CORR_SOURCE5 19 1.6973 + angle_coeff @angle:cl-cc-ss harmonic 71.934 119.850 # SOURCE4_SOURCE5 27 0.9529 + angle_coeff @angle:c-cc-n2 harmonic 85.228 123.930 # CORR_SOURCE5 6 0.0993 + angle_coeff @angle:c-cc-n harmonic 85.713 116.370 # CORR_SOURCE5 41 2.4875 + angle_coeff @angle:cc-c-n harmonic 87.145 112.700 # SOURCE3_SOURCE5 1124 1.8431 + angle_coeff @angle:c-cc-nc harmonic 83.549 123.320 # CORR_SOURCE5 27 2.2025 + angle_coeff @angle:cc-c-nd harmonic 85.602 116.240 # CORR_SOURCE5 38 1.0053 + angle_coeff @angle:c-cc-nd harmonic 85.323 121.880 # CORR_SOURCE5 54 2.0672 + angle_coeff @angle:c-cc-ne harmonic 84.503 119.880 # SOURCE4 6 0.3139 + angle_coeff @angle:cc-c-o harmonic 86.736 123.930 # SOURCE3_SOURCE5 3463 2.3073 + angle_coeff @angle:c-cc-oh harmonic 87.608 113.660 # CORR_SOURCE5 190 1.6462 + angle_coeff @angle:cc-c-oh harmonic 87.815 112.840 # CORR_SOURCE5 184 0.7264 + angle_coeff @angle:c-cc-os harmonic 85.149 119.260 # CORR_SOURCE5 104 2.4145 + angle_coeff @angle:cc-c-os harmonic 87.108 114.200 # SOURCE3_SOURCE5 427 2.2749 + angle_coeff @angle:cc-c-s harmonic 64.011 126.280 # SOURCE4_SOURCE5 69 1.9867 + angle_coeff @angle:cc-c-ss harmonic 64.406 112.400 # SOURCE4_SOURCE5 42 0.9902 + angle_coeff @angle:cx-cc-nd harmonic 83.147 127.820 # SOURCE4_SOURCE5 27 1.6288 + angle_coeff @angle:cx-cc-os harmonic 85.414 118.070 # SOURCE4_SOURCE5 23 0.0923 + angle_coeff @angle:cd-c-cd harmonic 66.696 115.840 # CORR_SOURCE5 115 1.4659 + angle_coeff @angle:cd-c-cx harmonic 65.553 117.430 # SOURCE4_SOURCE5 37 0.1506 + angle_coeff @angle:cd-c-n harmonic 87.145 112.700 # SOURCE3_SOURCE5 1124 1.8431 + angle_coeff @angle:cd-c-nc harmonic 85.602 116.240 # CORR_SOURCE5 38 1.0053 + angle_coeff @angle:cd-c-nd harmonic 86.534 113.750 # SOURCE4_SOURCE5 28 0.0860 + angle_coeff @angle:cd-c-o harmonic 86.736 123.930 # SOURCE3_SOURCE5 3463 2.3073 + angle_coeff @angle:cd-c-oh harmonic 87.815 112.840 # CORR_SOURCE5 184 0.7264 + angle_coeff @angle:cd-c-os harmonic 87.108 114.200 # SOURCE3_SOURCE5 427 2.2749 + angle_coeff @angle:ce-c-ce harmonic 66.032 115.820 # CORR_SOURCE5 103 0.7143 + angle_coeff @angle:ce-c-cf harmonic 65.875 116.370 # SOURCE4_SOURCE5 31 1.3157 + angle_coeff @angle:ce-c-cx harmonic 65.246 117.390 # SOURCE4_SOURCE5 19 0.7227 + angle_coeff @angle:ce-c-h4 harmonic 47.181 114.890 # SOURCE4_SOURCE5 113 0.4718 + angle_coeff @angle:ce-c-ha harmonic 47.181 115.220 # SOURCE3 7 2.4188 + angle_coeff @angle:ce-c-n harmonic 85.680 115.220 # CORR_SOURCE5 38 1.1173 + angle_coeff @angle:ce-c-o harmonic 86.348 123.200 # SOURCE3_SOURCE5 2306 2.0617 + angle_coeff @angle:ce-c-oh harmonic 86.976 113.620 # CORR_SOURCE5 273 1.4501 + angle_coeff @angle:ce-c-os harmonic 87.846 110.930 # CORR_SOURCE5 445 1.6899 + angle_coeff @angle:ce-c-s harmonic 64.731 122.630 # SOURCE3_SOURCE5 11 1.3034 + angle_coeff @angle:ce-c-ss harmonic 64.794 110.490 # SOURCE4_SOURCE5 13 0.5852 + angle_coeff @angle:cf-c-cf harmonic 66.032 115.820 # CORR_SOURCE5 103 0.7143 + angle_coeff @angle:cf-c-ha harmonic 47.181 115.220 # SOURCE3 7 + angle_coeff @angle:cf-c-n harmonic 85.680 115.220 # CORR_SOURCE5 38 1.1173 + angle_coeff @angle:cf-c-o harmonic 86.348 123.200 # SOURCE3_SOURCE5 2306 2.0617 + angle_coeff @angle:cf-c-oh harmonic 86.976 113.620 # CORR_SOURCE5 273 1.4501 + angle_coeff @angle:cf-c-os harmonic 87.846 110.930 # CORR_SOURCE5 445 1.6899 + angle_coeff @angle:cf-c-s harmonic 64.731 122.630 # SOURCE3_SOURCE5 11 1.3034 + angle_coeff @angle:cg-c-cg harmonic 67.584 115.380 # SOURCE3 1 + angle_coeff @angle:cg-c-ha harmonic 48.322 113.900 # SOURCE2 1 + angle_coeff @angle:cg-c-o harmonic 88.213 121.780 # SOURCE3_SOURCE5 13 0.8393 + angle_coeff @angle:c-c-h4 harmonic 45.243 115.800 # SOURCE4_SOURCE5 17 0.7492 + angle_coeff @angle:h4-cc-n harmonic 62.742 115.690 # SOURCE3_SOURCE5 425 0.9142 + angle_coeff @angle:h4-cc-na harmonic 61.487 120.530 # SOURCE3_SOURCE5 1801 1.3882 + angle_coeff @angle:h4-cc-nc harmonic 61.716 121.140 # SOURCE3_SOURCE5 574 0.5658 + angle_coeff @angle:h4-cc-nd harmonic 64.296 118.470 # SOURCE3_SOURCE5 435 1.3360 + angle_coeff @angle:h4-cc-os harmonic 63.640 114.900 # SOURCE3_SOURCE5 456 0.8638 + angle_coeff @angle:h4-cc-ss harmonic 42.456 119.970 # SOURCE3_SOURCE5 496 0.7119 + angle_coeff @angle:h5-cc-n harmonic 62.737 115.700 # CORR_SOURCE5 41 0.7665 + angle_coeff @angle:h5-cc-na harmonic 61.226 121.550 # SOURCE3_SOURCE5 1138 0.7136 + angle_coeff @angle:h5-cc-nc harmonic 61.265 122.920 # SOURCE3_SOURCE5 136 0.3532 + angle_coeff @angle:h5-cc-nd harmonic 62.461 125.520 # SOURCE3_SOURCE5 1309 0.7276 + angle_coeff @angle:h5-cc-os harmonic 63.110 116.830 # SOURCE3_SOURCE5 42 1.3051 + angle_coeff @angle:h5-cc-ss harmonic 42.272 121.020 # SOURCE3_SOURCE5 46 0.6462 + angle_coeff @angle:c-c-ha harmonic 45.358 115.430 # SOURCE2 3 0.6549 + angle_coeff @angle:ha-cc-na harmonic 61.218 121.500 # SOURCE2 1 + angle_coeff @angle:ha-cc-nc harmonic 62.898 116.540 # SOURCE3 5 1.4482 + angle_coeff @angle:ha-cc-nd harmonic 64.154 118.880 # SOURCE3 20 2.8923 + angle_coeff @angle:ha-cc-os harmonic 64.764 110.860 # SOURCE3 7 1.3846 + angle_coeff @angle:ha-cc-pd harmonic 54.856 121.760 # SOURCE3 84 + angle_coeff @angle:ha-cc-ss harmonic 42.168 121.640 # SOURCE2 5 1.3276 + angle_coeff @angle:ch-c-ch harmonic 67.584 115.380 # SOURCE3 1 + angle_coeff @angle:ch-c-ha harmonic 48.322 113.900 # SOURCE2 1 + angle_coeff @angle:ch-c-o harmonic 88.213 121.780 # SOURCE3_SOURCE5 13 0.8393 + angle_coeff @angle:cl-c-cl harmonic 80.720 111.300 # SOURCE2 1 + angle_coeff @angle:cl-c-f harmonic 93.155 112.000 # SOURCE2 1 + angle_coeff @angle:cl-c-ha harmonic 48.221 109.900 # SOURCE2 1 + angle_coeff @angle:cl-c-o harmonic 89.044 120.690 # SOURCE3_SOURCE5 14 1.1076 + angle_coeff @angle:cl-c-s harmonic 69.852 127.600 # SOURCE2 1 + angle_coeff @angle:c-c-n harmonic 84.329 112.740 # SOURCE4_SOURCE5 157 2.1770 + angle_coeff @angle:na-cc-nc harmonic 108.812 121.950 # CORR_SOURCE5 321 1.6221 + angle_coeff @angle:na-cc-nd harmonic 115.504 112.220 # SOURCE3_SOURCE5 2726 1.5103 + angle_coeff @angle:na-cc-no harmonic 105.313 124.590 # SOURCE4_SOURCE5 162 0.8093 + angle_coeff @angle:na-cc-oh harmonic 111.744 117.480 # SOURCE4_SOURCE5 39 0.9806 + angle_coeff @angle:na-cc-sx harmonic 79.683 117.020 # SOURCE4_SOURCE5 32 0.3937 + angle_coeff @angle:na-cc-sy harmonic 79.507 120.460 # SOURCE4_SOURCE5 15 1.7292 + angle_coeff @angle:nc-cc-nd harmonic 114.185 115.830 # CORR_SOURCE5 309 1.2424 + angle_coeff @angle:nc-cc-nh harmonic 111.255 117.230 # CORR_SOURCE5 51 1.7463 + angle_coeff @angle:nc-cc-no harmonic 106.922 121.730 # SOURCE4_SOURCE5 17 0.8729 + angle_coeff @angle:nc-cc-ss harmonic 79.922 122.640 # SOURCE3_SOURCE5 10 1.3100 + angle_coeff @angle:nd-cc-nd harmonic 110.827 128.070 # SOURCE4_SOURCE5 17 0.2580 + angle_coeff @angle:nd-cc-ne harmonic 107.796 129.010 # SOURCE4_SOURCE5 20 1.2478 + angle_coeff @angle:nd-cc-nh harmonic 111.697 120.650 # SOURCE3_SOURCE5 554 1.6769 + angle_coeff @angle:nd-cc-no harmonic 108.240 122.750 # SOURCE4_SOURCE5 80 0.3006 + angle_coeff @angle:nd-cc-oh harmonic 112.660 121.120 # CORR_SOURCE5 31 1.3923 + angle_coeff @angle:nd-cc-os harmonic 114.076 116.740 # CORR_SOURCE5 156 2.0183 + angle_coeff @angle:nd-cc-sh harmonic 79.198 124.970 # SOURCE4_SOURCE5 18 0.8493 + angle_coeff @angle:nd-cc-ss harmonic 83.264 114.510 # SOURCE3 8 0.3449 + angle_coeff @angle:nd-cc-sx harmonic 76.768 127.740 # SOURCE4_SOURCE5 33 0.6804 + angle_coeff @angle:nd-cc-sy harmonic 79.255 123.030 # SOURCE4_SOURCE5 33 1.1587 + angle_coeff @angle:ne-cc-ss harmonic 81.707 117.030 # SOURCE4_SOURCE5 17 0.2106 + angle_coeff @angle:nh-cc-nh harmonic 111.696 115.960 # SOURCE3 1 + angle_coeff @angle:nh-cc-os harmonic 111.815 116.680 # CORR_SOURCE5 36 0.7439 + angle_coeff @angle:nh-cc-ss harmonic 80.147 121.810 # CORR_SOURCE5 128 1.0728 + angle_coeff @angle:n-cc-n2 harmonic 112.932 119.420 # SOURCE4_SOURCE5 28 1.2985 + angle_coeff @angle:n-cc-na harmonic 108.295 122.120 # CORR_SOURCE5 15 1.1276 + angle_coeff @angle:n-cc-nc harmonic 106.932 126.230 # CORR_SOURCE5 118 0.4381 + angle_coeff @angle:n-cc-nd harmonic 110.304 123.000 # CORR_SOURCE5 354 1.4352 + angle_coeff @angle:n-cc-nh harmonic 110.935 116.940 # CORR_SOURCE5 126 0.5956 + angle_coeff @angle:no-cc-os harmonic 109.068 117.550 # SOURCE4_SOURCE5 144 0.2521 + angle_coeff @angle:no-cc-ss harmonic 79.693 121.060 # SOURCE4_SOURCE5 33 0.2051 + angle_coeff @angle:n-cc-ss harmonic 79.713 122.880 # CORR_SOURCE5 82 1.5666 + angle_coeff @angle:c-c-o harmonic 84.325 120.850 # SOURCE4_SOURCE5 712 2.3365 + angle_coeff @angle:c-c-oh harmonic 85.170 112.070 # SOURCE3_SOURCE5 45 0.4339 + angle_coeff @angle:c-c-os harmonic 85.272 111.410 # SOURCE4_SOURCE5 34 0.4577 + angle_coeff @angle:os-cc-ss harmonic 81.124 119.280 # SOURCE3_SOURCE5 10 1.6753 + angle_coeff @angle:ss-cc-ss harmonic 63.639 121.370 # CORR 22 + angle_coeff @angle:ss-cc-sy harmonic 63.048 121.700 # CORR_SOURCE5 43 0.4842 + angle_coeff @angle:cx-c-cx harmonic 87.506 64.600 # SOURCE2 1 + angle_coeff @angle:cx-c-n harmonic 85.409 114.530 # SOURCE4_SOURCE5 60 1.3306 + angle_coeff @angle:cx-c-o harmonic 85.839 122.750 # SOURCE4_SOURCE5 366 2.2300 + angle_coeff @angle:cx-c-oh harmonic 86.840 112.520 # SOURCE4_SOURCE5 43 1.3576 + angle_coeff @angle:cx-c-os harmonic 87.109 111.390 # SOURCE4_SOURCE5 64 2.0118 + angle_coeff @angle:cy-c-cy harmonic 70.855 91.910 # SOURCE2_SOURCE5 12 0.9858 + angle_coeff @angle:cy-c-n harmonic 93.471 91.560 # SOURCE4_SOURCE5 619 0.5374 + angle_coeff @angle:cy-c-o harmonic 79.625 135.160 # SOURCE4_SOURCE5 665 1.3860 + angle_coeff @angle:cy-c-oh harmonic 85.029 112.180 # SOURCE4_SOURCE5 17 0.7869 + angle_coeff @angle:cy-c-os harmonic 92.339 94.790 # SOURCE4_SOURCE5 25 0.5353 + angle_coeff @angle:c2-cd-c3 harmonic 65.262 126.110 # SOURCE3 2 + angle_coeff @angle:c2-cd-ca harmonic 66.952 124.420 # CORR_SOURCE5 25 1.8245 + angle_coeff @angle:c2-cd-cc harmonic 71.286 117.020 # SOURCE3 2 + angle_coeff @angle:c2-cd-cd harmonic 68.308 122.190 # CORR_SOURCE5 46 2.3853 + angle_coeff @angle:c2-cd-ha harmonic 49.231 122.720 # SOURCE3 2 + angle_coeff @angle:c2-cd-n harmonic 86.150 124.910 # SOURCE3_SOURCE5 5 1.6803 + angle_coeff @angle:c2-cd-os harmonic 87.991 121.420 # CORR_SOURCE5 24 0.9570 + angle_coeff @angle:c3-cd-ca harmonic 63.318 126.520 # CORR_SOURCE5 370 1.8946 + angle_coeff @angle:c3-cd-cc harmonic 66.802 119.450 # SOURCE3 35 8.2040 + angle_coeff @angle:c3-cd-cd harmonic 66.709 115.970 # SOURCE3 4 3.0507 + angle_coeff @angle:c3-cd-ce harmonic 67.395 117.840 # CORR 2 + angle_coeff @angle:c3-cd-ha harmonic 45.517 121.520 # SOURCE3 32 3.2091 + angle_coeff @angle:c3-cd-n2 harmonic 83.336 125.690 # CORR_SOURCE5 12 1.9935 + angle_coeff @angle:c3-cd-n harmonic 83.558 119.190 # CORR_SOURCE5 107 2.1078 + angle_coeff @angle:c3-cd-na harmonic 82.356 122.730 # CORR_SOURCE5 961 1.6482 + angle_coeff @angle:c3-cd-nc harmonic 83.886 122.410 # CORR_SOURCE5 653 1.6992 + angle_coeff @angle:c3-cd-nd harmonic 83.215 120.950 # CORR_SOURCE5 456 0.8756 + angle_coeff @angle:c3-cd-os harmonic 84.855 116.800 # CORR_SOURCE5 306 0.8990 + angle_coeff @angle:c3-cd-ss harmonic 62.656 121.530 # CORR_SOURCE5 270 1.0948 + angle_coeff @angle:ca-cd-cc harmonic 69.802 113.510 # SOURCE3 26 7.4229 + angle_coeff @angle:ca-cd-cd harmonic 69.336 111.040 # SOURCE3 9 7.9455 + angle_coeff @angle:ca-cd-ce harmonic 66.694 124.900 # SOURCE4_SOURCE5 41 1.7178 + angle_coeff @angle:ca-cd-h4 harmonic 45.368 129.250 # SOURCE3_SOURCE5 54 1.5632 + angle_coeff @angle:ca-cd-ha harmonic 46.300 124.040 # SOURCE3 34 3.6691 + angle_coeff @angle:ca-cd-n harmonic 85.642 117.670 # CORR 18 + angle_coeff @angle:ca-cd-na harmonic 83.626 123.450 # SOURCE4 39 1.9138 + angle_coeff @angle:ca-cd-nc harmonic 85.294 123.240 # CORR_SOURCE5 246 2.3557 + angle_coeff @angle:ca-cd-nd harmonic 84.897 120.590 # CORR_SOURCE5 224 1.0853 + angle_coeff @angle:ca-cd-oh harmonic 86.577 117.550 # CORR_SOURCE5 35 1.9318 + angle_coeff @angle:ca-cd-os harmonic 87.229 114.750 # CORR_SOURCE5 247 2.0579 + angle_coeff @angle:ca-cd-ss harmonic 63.408 120.800 # CORR_SOURCE5 80 2.1212 + angle_coeff @angle:c-cd-c2 harmonic 67.513 121.170 # CORR_SOURCE5 28 1.6484 + angle_coeff @angle:c-cd-c3 harmonic 65.378 117.760 # CORR_SOURCE5 566 1.9588 + angle_coeff @angle:c-cd-c harmonic 65.240 121.070 # CORR_SOURCE5 128 0.8902 + angle_coeff @angle:c-cd-ca harmonic 65.005 122.950 # SOURCE3 1 + angle_coeff @angle:c-cd-cc harmonic 67.187 121.350 # CORR_SOURCE5 3554 2.2084 + angle_coeff @angle:cc-cd-cc harmonic 70.027 120.080 # CORR_SOURCE5 119 1.6139 + angle_coeff @angle:cc-cd-cd harmonic 70.348 114.190 # SOURCE3 517 6.5960 + angle_coeff @angle:cc-cd-cf harmonic 65.759 128.050 # CORR_SOURCE5 350 2.4628 + angle_coeff @angle:cc-cd-ch harmonic 67.080 125.790 # SOURCE4_SOURCE5 84 1.6445 + angle_coeff @angle:cc-cd-cl harmonic 71.687 123.410 # CORR_SOURCE5 115 2.1217 + angle_coeff @angle:cc-cd-cy harmonic 65.987 122.050 # SOURCE4_SOURCE5 22 0.8483 + angle_coeff @angle:c-cd-cd harmonic 65.674 122.690 # SOURCE3 2 + angle_coeff @angle:c-cd-cf harmonic 65.406 121.570 # CORR_SOURCE5 29 1.1305 + angle_coeff @angle:cc-cd-h4 harmonic 47.759 128.480 # SOURCE3_SOURCE5 3291 2.3189 + angle_coeff @angle:cc-cd-ha harmonic 49.040 121.760 # SOURCE3_SOURCE5 4433 1.8701 + angle_coeff @angle:c-cd-cl harmonic 72.591 116.380 # CORR_SOURCE5 50 1.2099 + angle_coeff @angle:cc-cd-n harmonic 86.990 121.330 # SOURCE3_SOURCE5 821 1.9126 + angle_coeff @angle:cc-cd-na harmonic 92.653 106.990 # SOURCE3_SOURCE5 3003 2.3845 + angle_coeff @angle:cc-cd-nc harmonic 88.069 123.820 # SOURCE4_SOURCE5 28 0.3678 + angle_coeff @angle:cc-cd-nd harmonic 91.057 111.650 # CORR_SOURCE5 1656 1.8430 + angle_coeff @angle:cc-cd-nh harmonic 86.331 123.840 # CORR_SOURCE5 152 2.2360 + angle_coeff @angle:cc-cd-oh harmonic 87.177 123.780 # CORR_SOURCE5 251 1.1988 + angle_coeff @angle:cc-cd-os harmonic 87.957 120.300 # SOURCE3 64 5.4354 + angle_coeff @angle:cc-cd-ss harmonic 66.887 111.550 # CORR_SOURCE5 1048 1.8648 + angle_coeff @angle:cc-cd-sy harmonic 62.501 124.550 # CORR_SOURCE5 56 1.7107 + angle_coeff @angle:cd-cd-cd harmonic 70.129 110.700 # SOURCE3 54 3.4091 + angle_coeff @angle:cd-cd-ce harmonic 68.022 122.720 # CORR_SOURCE5 66 1.9701 + angle_coeff @angle:cd-cd-cf harmonic 64.853 127.060 # CORR_SOURCE5 61 2.3233 + angle_coeff @angle:cd-cd-ch harmonic 65.805 125.910 # CORR_SOURCE5 41 1.1646 + angle_coeff @angle:cd-cd-cy harmonic 64.938 122.040 # SOURCE4_SOURCE5 13 0.6868 + angle_coeff @angle:cd-cd-h4 harmonic 46.348 127.960 # SOURCE3_SOURCE5 391 2.1732 + angle_coeff @angle:cd-cd-ha harmonic 47.634 121.070 # CORR_SOURCE5 2414 2.2010 + angle_coeff @angle:cd-cd-n2 harmonic 87.356 122.210 # CORR_SOURCE5 37 1.6493 + angle_coeff @angle:cd-cd-n harmonic 85.753 119.890 # SOURCE3 36 0.2095 + angle_coeff @angle:cd-cd-na harmonic 86.536 117.770 # SOURCE3_SOURCE5 832 1.6037 + angle_coeff @angle:cd-cd-nc harmonic 90.306 112.560 # SOURCE3 141 4.2871 + angle_coeff @angle:cd-cd-nd harmonic 85.332 121.980 # CORR_SOURCE5 141 1.9633 + angle_coeff @angle:cd-cd-nh harmonic 86.018 119.720 # CORR_SOURCE5 348 1.7785 + angle_coeff @angle:cd-cd-oh harmonic 86.201 121.270 # CORR_SOURCE5 11 2.2744 + angle_coeff @angle:cd-cd-os harmonic 87.213 117.340 # CORR_SOURCE5 217 1.9304 + angle_coeff @angle:cd-cd-pc harmonic 84.517 115.360 # SOURCE3 84 3.2889 + angle_coeff @angle:cd-cd-ss harmonic 63.877 120.210 # CORR_SOURCE5 52 2.1160 + angle_coeff @angle:ce-cd-nd harmonic 86.641 123.980 # SOURCE4_SOURCE5 10 2.4097 + angle_coeff @angle:cf-cd-na harmonic 83.371 124.350 # CORR_SOURCE5 87 1.3591 + angle_coeff @angle:cf-cd-nc harmonic 85.887 121.700 # CORR_SOURCE5 58 1.4179 + angle_coeff @angle:cf-cd-nd harmonic 84.769 121.100 # CORR_SOURCE5 43 1.2959 + angle_coeff @angle:cf-cd-os harmonic 85.796 118.760 # CORR_SOURCE5 92 1.3159 + angle_coeff @angle:cf-cd-ss harmonic 63.222 121.580 # CORR_SOURCE5 54 1.3126 + angle_coeff @angle:c-cd-h4 harmonic 47.105 118.190 # SOURCE4_SOURCE5 16 0.2226 + angle_coeff @angle:c-cd-ha harmonic 47.405 116.640 # SOURCE3_SOURCE5 896 1.3075 + angle_coeff @angle:cl-cd-nc harmonic 90.963 122.070 # CORR_SOURCE5 19 1.6973 + angle_coeff @angle:c-cd-n2 harmonic 85.228 123.930 # CORR_SOURCE5 6 0.0993 + angle_coeff @angle:c-cd-n harmonic 85.713 116.370 # CORR_SOURCE5 41 2.4875 + angle_coeff @angle:c-cd-nc harmonic 85.323 121.880 # CORR_SOURCE5 54 2.0672 + angle_coeff @angle:c-cd-nd harmonic 83.549 123.320 # CORR_SOURCE5 27 2.2025 + angle_coeff @angle:c-cd-oh harmonic 87.608 113.660 # CORR_SOURCE5 190 1.6462 + angle_coeff @angle:c-cd-os harmonic 85.149 119.260 # CORR_SOURCE5 104 2.4145 + angle_coeff @angle:h4-cd-n harmonic 62.742 115.690 # SOURCE3_SOURCE5 425 0.9142 + angle_coeff @angle:h4-cd-na harmonic 61.487 120.530 # SOURCE3_SOURCE5 1801 1.3882 + angle_coeff @angle:h4-cd-nc harmonic 64.296 118.470 # SOURCE3_SOURCE5 435 1.3360 + angle_coeff @angle:h4-cd-nd harmonic 61.716 121.140 # SOURCE3_SOURCE5 574 0.5658 + angle_coeff @angle:h4-cd-os harmonic 63.640 114.900 # SOURCE3_SOURCE5 456 0.8638 + angle_coeff @angle:h4-cd-ss harmonic 42.456 119.970 # SOURCE3_SOURCE5 496 0.7119 + angle_coeff @angle:h5-cd-n harmonic 62.738 115.700 # CORR_SOURCE5 41 0.7665 + angle_coeff @angle:h5-cd-na harmonic 61.227 121.550 # SOURCE3_SOURCE5 1138 0.7136 + angle_coeff @angle:h5-cd-nc harmonic 62.462 125.520 # SOURCE3_SOURCE5 1309 0.7276 + angle_coeff @angle:h5-cd-nd harmonic 61.266 122.920 # SOURCE3_SOURCE5 136 0.3532 + angle_coeff @angle:h5-cd-os harmonic 63.111 116.830 # SOURCE3_SOURCE5 42 1.3051 + angle_coeff @angle:h5-cd-ss harmonic 42.271 121.020 # SOURCE3_SOURCE5 46 0.6462 + angle_coeff @angle:ha-cd-na harmonic 61.218 121.500 # SOURCE2 1 + angle_coeff @angle:ha-cd-nc harmonic 64.154 118.880 # SOURCE3 20 2.8923 + angle_coeff @angle:ha-cd-nd harmonic 62.898 116.540 # SOURCE3 5 1.4482 + angle_coeff @angle:ha-cd-os harmonic 64.764 110.860 # SOURCE3 7 1.3846 + angle_coeff @angle:ha-cd-pc harmonic 54.856 121.760 # SOURCE3 84 2.2216 + angle_coeff @angle:ha-cd-ss harmonic 42.168 121.640 # SOURCE2 5 + angle_coeff @angle:na-cd-nc harmonic 115.504 112.220 # SOURCE3_SOURCE5 2726 1.5103 + angle_coeff @angle:na-cd-nd harmonic 108.812 121.950 # CORR_SOURCE5 321 1.6221 + angle_coeff @angle:na-cd-nh harmonic 110.794 117.280 # SOURCE4_SOURCE5 100 1.6359 + angle_coeff @angle:na-cd-ss harmonic 83.703 111.460 # SOURCE4 20 0.8600 + angle_coeff @angle:nc-cd-nd harmonic 114.185 115.830 # CORR_SOURCE5 309 1.2424 + angle_coeff @angle:nc-cd-nh harmonic 111.697 120.650 # SOURCE3_SOURCE5 554 1.6769 + angle_coeff @angle:nc-cd-oh harmonic 112.660 121.120 # CORR_SOURCE5 31 1.3923 + angle_coeff @angle:nc-cd-os harmonic 114.076 116.740 # CORR_SOURCE5 156 2.0183 + angle_coeff @angle:nc-cd-ss harmonic 83.264 114.510 # SOURCE3 8 0.3449 + angle_coeff @angle:nd-cd-nd harmonic 107.603 125.700 # SOURCE4_SOURCE5 31 0.5900 + angle_coeff @angle:nd-cd-nh harmonic 111.255 117.230 # CORR_SOURCE5 51 1.7463 + angle_coeff @angle:nd-cd-ss harmonic 79.922 122.640 # SOURCE3_SOURCE5 10 1.3100 + angle_coeff @angle:nh-cd-nh harmonic 111.696 115.960 # SOURCE3 1 + angle_coeff @angle:nh-cd-os harmonic 111.815 116.680 # CORR_SOURCE5 36 0.7439 + angle_coeff @angle:nh-cd-ss harmonic 80.147 121.810 # CORR_SOURCE5 128 1.0728 + angle_coeff @angle:n-cd-na harmonic 108.295 122.120 # CORR_SOURCE5 15 1.1276 + angle_coeff @angle:n-cd-nc harmonic 110.304 123.000 # CORR_SOURCE5 354 1.4352 + angle_coeff @angle:n-cd-nd harmonic 106.932 126.230 # CORR_SOURCE5 118 0.4381 + angle_coeff @angle:n-cd-nh harmonic 110.935 116.940 # CORR_SOURCE5 126 0.5956 + angle_coeff @angle:n-cd-ss harmonic 79.713 122.880 # CORR_SOURCE5 82 1.5666 + angle_coeff @angle:oh-cd-os harmonic 115.442 111.610 # SOURCE4_SOURCE5 12 1.1909 + angle_coeff @angle:os-cd-ss harmonic 81.124 119.280 # SOURCE3_SOURCE5 10 1.6753 + angle_coeff @angle:ss-cd-ss harmonic 63.639 121.370 # CORR 22 + angle_coeff @angle:ss-cd-sy harmonic 63.048 121.700 # CORR_SOURCE5 43 0.4842 + angle_coeff @angle:c2-ce-c3 harmonic 66.042 122.530 # SOURCE3_SOURCE5 882 1.9288 + angle_coeff @angle:c2-ce-ca harmonic 67.362 121.780 # SOURCE3_SOURCE5 11 1.7099 + angle_coeff @angle:c2-ce-cc harmonic 67.560 123.320 # CORR_SOURCE5 132 1.9068 + angle_coeff @angle:c2-ce-ce harmonic 67.482 123.260 # SOURCE3_SOURCE5 791 1.8772 + angle_coeff @angle:c2-ce-cg harmonic 68.647 122.090 # CORR_SOURCE5 54 1.3612 + angle_coeff @angle:c2-ce-cl harmonic 72.080 119.760 # SOURCE4_SOURCE5 62 1.3986 + angle_coeff @angle:c2-ce-h4 harmonic 49.154 124.550 # SOURCE4_SOURCE5 43 1.6498 + angle_coeff @angle:c2-ce-ha harmonic 50.126 119.940 # SOURCE3_SOURCE5 1439 1.4338 + angle_coeff @angle:c2-ce-n1 harmonic 91.289 118.230 # SOURCE4_SOURCE5 18 0.9047 + angle_coeff @angle:c2-ce-n2 harmonic 88.228 128.700 # SOURCE3 1 + angle_coeff @angle:c2-ce-na harmonic 87.216 119.190 # SOURCE4_SOURCE5 10 0.8452 + angle_coeff @angle:c2-ce-ne harmonic 88.464 118.320 # SOURCE3 7 1.0468 + angle_coeff @angle:c2-ce-oh harmonic 87.984 123.700 # SOURCE4_SOURCE5 27 1.7525 + angle_coeff @angle:c2-ce-p2 harmonic 81.422 118.240 # SOURCE3 1 + angle_coeff @angle:c2-ce-pe harmonic 81.089 118.760 # SOURCE3 8 2.3984 + angle_coeff @angle:c2-ce-px harmonic 80.647 119.720 # SOURCE3 6 0.5213 + angle_coeff @angle:c2-ce-py harmonic 80.419 122.180 # SOURCE3_SOURCE5 12 1.9482 + angle_coeff @angle:c2-ce-sx harmonic 63.052 119.210 # SOURCE3_SOURCE5 14 0.9863 + angle_coeff @angle:c2-ce-sy harmonic 63.705 120.200 # SOURCE3_SOURCE5 17 1.3599 + angle_coeff @angle:c3-ce-ca harmonic 64.464 119.240 # CORR_SOURCE5 312 1.7689 + angle_coeff @angle:c3-ce-cc harmonic 65.246 118.030 # CORR_SOURCE5 77 1.5840 + angle_coeff @angle:c3-ce-ce harmonic 65.430 117.120 # CORR_SOURCE5 524 1.4790 + angle_coeff @angle:c3-ce-cf harmonic 65.999 122.380 # CORR_SOURCE5 490 2.0752 + angle_coeff @angle:c3-ce-cg harmonic 66.008 117.220 # SOURCE4_SOURCE5 34 1.7153 + angle_coeff @angle:c3-ce-n2 harmonic 83.839 122.730 # CORR_SOURCE5 149 1.8752 + angle_coeff @angle:c3-ce-nf harmonic 84.370 120.680 # SOURCE4_SOURCE5 13 2.1196 + angle_coeff @angle:c3-ce-nh harmonic 82.726 119.560 # SOURCE4_SOURCE5 10 1.0079 + angle_coeff @angle:ca-ce-ca harmonic 65.741 117.830 # CORR_SOURCE5 210 0.9675 + angle_coeff @angle:ca-ce-cc harmonic 66.149 118.130 # CORR_SOURCE5 30 0.7112 + angle_coeff @angle:ca-ce-ce harmonic 65.684 119.540 # SOURCE4_SOURCE5 32 1.9209 + angle_coeff @angle:ca-ce-cf harmonic 65.738 127.520 # CORR_SOURCE5 599 1.6916 + angle_coeff @angle:ca-ce-cl harmonic 72.181 114.590 # SOURCE4_SOURCE5 14 1.1195 + angle_coeff @angle:ca-ce-h4 harmonic 47.047 116.990 # SOURCE4_SOURCE5 255 1.0051 + angle_coeff @angle:ca-ce-ha harmonic 47.444 115.130 # CORR_SOURCE5 720 0.9389 + angle_coeff @angle:ca-ce-n2 harmonic 86.084 120.720 # SOURCE3 1 + angle_coeff @angle:ca-ce-nf harmonic 85.534 121.710 # CORR_SOURCE5 49 2.1313 + angle_coeff @angle:ca-ce-nh harmonic 85.466 115.580 # SOURCE4_SOURCE5 240 1.0372 + angle_coeff @angle:ca-ce-oh harmonic 86.291 116.100 # CORR_SOURCE5 15 0.6417 + angle_coeff @angle:ca-ce-os harmonic 85.838 115.910 # SOURCE4_SOURCE5 25 1.4247 + angle_coeff @angle:ca-ce-ss harmonic 63.378 117.520 # SOURCE4_SOURCE5 14 1.2435 + angle_coeff @angle:c-ce-c2 harmonic 67.566 120.420 # SOURCE3 13 1.8877 + angle_coeff @angle:c-ce-c3 harmonic 64.889 117.220 # CORR_SOURCE5 558 2.2754 + angle_coeff @angle:c-ce-c harmonic 64.277 122.230 # CORR_SOURCE5 52 2.1518 + angle_coeff @angle:c-ce-ca harmonic 65.478 118.280 # SOURCE4_SOURCE5 25 1.6999 + angle_coeff @angle:cc-ce-cd harmonic 65.259 130.610 # SOURCE4_SOURCE5 24 1.1422 + angle_coeff @angle:cc-ce-cf harmonic 66.704 126.140 # CORR_SOURCE5 122 1.8142 + angle_coeff @angle:c-ce-cd harmonic 67.092 120.770 # CORR_SOURCE5 15 1.8896 + angle_coeff @angle:c-ce-ce harmonic 65.150 120.980 # SOURCE4_SOURCE5 53 2.2319 + angle_coeff @angle:c-ce-cf harmonic 65.856 126.410 # SOURCE3 2 5.7847 + angle_coeff @angle:c-ce-cg harmonic 66.500 118.420 # SOURCE4_SOURCE5 49 1.0600 + angle_coeff @angle:cc-ce-h4 harmonic 47.935 115.680 # SOURCE4_SOURCE5 77 0.8454 + angle_coeff @angle:cc-ce-ha harmonic 48.006 115.440 # CORR_SOURCE5 179 0.9381 + angle_coeff @angle:c-ce-cl harmonic 71.821 115.470 # SOURCE4_SOURCE5 25 1.2041 + angle_coeff @angle:cc-ce-n2 harmonic 86.868 120.960 # CORR_SOURCE5 102 2.2421 + angle_coeff @angle:cc-ce-nh harmonic 85.299 118.050 # SOURCE4_SOURCE5 21 1.8052 + angle_coeff @angle:c-ce-cy harmonic 74.704 88.440 # SOURCE4_SOURCE5 53 0.9126 + angle_coeff @angle:cd-ce-ce harmonic 66.791 124.350 # CORR_SOURCE5 18 1.4583 + angle_coeff @angle:cd-ce-ha harmonic 50.638 114.950 # CORR_SOURCE5 95 1.4175 + angle_coeff @angle:ce-ce-ce harmonic 65.416 122.110 # SOURCE3_SOURCE5 9 2.4680 + angle_coeff @angle:ce-ce-cf harmonic 67.119 124.240 # CORR_SOURCE5 866 1.6941 + angle_coeff @angle:ce-ce-cl harmonic 71.617 117.220 # SOURCE4_SOURCE5 35 0.8344 + angle_coeff @angle:ce-ce-h4 harmonic 47.341 118.130 # CORR_SOURCE5 44 1.1161 + angle_coeff @angle:ce-ce-ha harmonic 47.662 116.650 # SOURCE3_SOURCE5 1159 0.9686 + angle_coeff @angle:ce-ce-n1 harmonic 84.049 127.150 # CORR 4 + angle_coeff @angle:ce-ce-n2 harmonic 87.472 118.930 # CORR_SOURCE5 13 1.3210 + angle_coeff @angle:ce-ce-oh harmonic 86.685 116.850 # SOURCE4_SOURCE5 30 1.7182 + angle_coeff @angle:cf-ce-cg harmonic 68.252 123.130 # CORR_SOURCE5 115 2.1292 + angle_coeff @angle:cf-ce-cy harmonic 62.247 137.580 # SOURCE4_SOURCE5 31 0.9919 + angle_coeff @angle:cf-ce-h4 harmonic 49.339 122.950 # SOURCE4_SOURCE5 23 1.1580 + angle_coeff @angle:cf-ce-ha harmonic 50.352 118.220 # CORR_SOURCE5 1522 1.3445 + angle_coeff @angle:cf-ce-n1 harmonic 90.464 119.940 # SOURCE4_SOURCE5 13 1.8896 + angle_coeff @angle:cf-ce-n harmonic 91.197 108.390 # CORR_SOURCE5 86 1.0066 + angle_coeff @angle:cf-ce-nh harmonic 87.337 121.380 # SOURCE4_SOURCE5 39 1.7667 + angle_coeff @angle:cf-ce-oh harmonic 88.551 121.690 # CORR_SOURCE5 37 1.2824 + angle_coeff @angle:cg-ce-cg harmonic 68.393 116.520 # CORR_SOURCE5 35 1.1031 + angle_coeff @angle:cg-ce-ha harmonic 48.557 116.460 # CORR_SOURCE5 58 0.6523 + angle_coeff @angle:cg-ce-n1 harmonic 87.835 119.500 # CORR 2 + angle_coeff @angle:cg-ce-n2 harmonic 87.851 121.140 # SOURCE4_SOURCE5 14 0.8974 + angle_coeff @angle:c-ce-ha harmonic 47.000 116.460 # SOURCE3_SOURCE5 1028 1.3091 + angle_coeff @angle:c-ce-n harmonic 83.338 118.450 # CORR_SOURCE5 213 1.4857 + angle_coeff @angle:c-ce-nh harmonic 85.341 115.360 # CORR_SOURCE5 28 2.1980 + angle_coeff @angle:c-ce-oh harmonic 86.196 115.760 # SOURCE4_SOURCE5 20 2.0254 + angle_coeff @angle:c-ce-os harmonic 86.086 114.670 # SOURCE4_SOURCE5 47 2.1291 + angle_coeff @angle:h4-ce-n1 harmonic 64.863 116.640 # SOURCE4_SOURCE5 19 0.4343 + angle_coeff @angle:h4-ce-n2 harmonic 64.393 121.480 # CORR_SOURCE5 257 1.1842 + angle_coeff @angle:h4-ce-ne harmonic 62.153 115.650 # SOURCE4_SOURCE5 19 1.8165 + angle_coeff @angle:ha-ce-n1 harmonic 65.106 115.960 # CORR 4 + angle_coeff @angle:ha-ce-n2 harmonic 64.979 119.510 # SOURCE3 2 0.4623 + angle_coeff @angle:ha-ce-ne harmonic 61.414 118.590 # SOURCE3 5 1.1113 + angle_coeff @angle:ha-ce-nh harmonic 62.516 114.990 # CORR 2 + angle_coeff @angle:ha-ce-p2 harmonic 52.606 120.110 # SOURCE3 1 + angle_coeff @angle:ha-ce-pe harmonic 52.651 119.330 # SOURCE3 6 0.8966 + angle_coeff @angle:ha-ce-px harmonic 52.873 117.900 # SOURCE3 6 0.1809 + angle_coeff @angle:ha-ce-py harmonic 53.346 117.990 # SOURCE3_SOURCE5 11 0.7169 + angle_coeff @angle:ha-ce-sx harmonic 41.698 115.450 # SOURCE3 3 0.6640 + angle_coeff @angle:ha-ce-sy harmonic 42.578 114.860 # SOURCE3 3 0.4717 + angle_coeff @angle:n2-ce-nh harmonic 110.010 125.090 # CORR_SOURCE5 163 1.6803 + angle_coeff @angle:n2-ce-os harmonic 114.215 117.950 # SOURCE4_SOURCE5 19 0.3524 + angle_coeff @angle:n2-ce-ss harmonic 81.512 117.230 # SOURCE4 6 2.0518 + angle_coeff @angle:ne-ce-ne harmonic 106.467 123.870 # SOURCE3 1 + angle_coeff @angle:ne-ce-nh harmonic 111.319 113.640 # SOURCE4_SOURCE5 41 1.4024 + angle_coeff @angle:nf-ce-nh harmonic 112.342 119.270 # SOURCE4_SOURCE5 23 1.5487 + angle_coeff @angle:pe-ce-pe harmonic 97.908 129.790 # SOURCE3 1 + angle_coeff @angle:py-ce-py harmonic 108.039 108.060 # SOURCE3 1 + angle_coeff @angle:sx-ce-sx harmonic 61.727 120.320 # SOURCE3 1 + angle_coeff @angle:sy-ce-sy harmonic 62.867 119.970 # SOURCE3 1 + angle_coeff @angle:c2-cf-c3 harmonic 66.048 122.530 # SOURCE3_SOURCE5 875 1.9359 + angle_coeff @angle:c2-cf-ca harmonic 67.362 121.780 # SOURCE3_SOURCE5 5 1.1712 + angle_coeff @angle:c2-cf-cd harmonic 67.560 123.320 # CORR_SOURCE5 132 1.9068 + angle_coeff @angle:c2-cf-cf harmonic 67.482 123.260 # SOURCE3_SOURCE5 779 1.8961 + angle_coeff @angle:c2-cf-ch harmonic 68.647 122.090 # CORR_SOURCE5 54 1.3612 + angle_coeff @angle:c2-cf-ha harmonic 50.126 119.940 # SOURCE3_SOURCE5 1393 1.4017 + angle_coeff @angle:c2-cf-n2 harmonic 88.228 128.700 # SOURCE3 1 + angle_coeff @angle:c2-cf-nf harmonic 88.464 118.320 # SOURCE3 7 + angle_coeff @angle:c2-cf-p2 harmonic 81.422 118.240 # SOURCE3 1 + angle_coeff @angle:c2-cf-pf harmonic 81.089 118.760 # SOURCE3 8 + angle_coeff @angle:c2-cf-px harmonic 80.647 119.720 # SOURCE3 6 + angle_coeff @angle:c2-cf-py harmonic 80.419 122.180 # SOURCE3_SOURCE5 7 1.0992 + angle_coeff @angle:c2-cf-sx harmonic 63.052 119.210 # SOURCE3_SOURCE5 9 1.0588 + angle_coeff @angle:c2-cf-sy harmonic 63.705 120.200 # SOURCE3_SOURCE5 12 1.7015 + angle_coeff @angle:c3-cf-ca harmonic 64.468 119.240 # CORR_SOURCE5 312 1.7689 + angle_coeff @angle:c3-cf-cd harmonic 65.251 118.030 # CORR_SOURCE5 77 1.5840 + angle_coeff @angle:c3-cf-ce harmonic 66.005 122.380 # CORR_SOURCE5 490 2.0752 + angle_coeff @angle:c3-cf-cf harmonic 65.435 117.120 # CORR_SOURCE5 524 1.4790 + angle_coeff @angle:c3-cf-n2 harmonic 83.846 122.730 # CORR_SOURCE5 149 1.8752 + angle_coeff @angle:ca-cf-ca harmonic 65.741 117.830 # CORR_SOURCE5 210 0.9675 + angle_coeff @angle:ca-cf-cc harmonic 64.611 130.880 # SOURCE4_SOURCE5 41 1.2386 + angle_coeff @angle:ca-cf-cd harmonic 66.149 118.130 # CORR_SOURCE5 30 0.7112 + angle_coeff @angle:ca-cf-ce harmonic 65.738 127.520 # CORR_SOURCE5 599 1.6916 + angle_coeff @angle:ca-cf-ha harmonic 47.444 115.130 # CORR_SOURCE5 720 0.9389 + angle_coeff @angle:ca-cf-n2 harmonic 86.084 120.720 # SOURCE3 1 + angle_coeff @angle:ca-cf-ne harmonic 85.534 121.710 # CORR_SOURCE5 49 2.1313 + angle_coeff @angle:ca-cf-oh harmonic 86.291 116.100 # CORR_SOURCE5 15 0.6417 + angle_coeff @angle:c-cf-c2 harmonic 67.566 120.420 # SOURCE3 13 + angle_coeff @angle:c-cf-c3 harmonic 64.893 117.220 # CORR_SOURCE5 558 2.2754 + angle_coeff @angle:c-cf-c harmonic 64.277 122.230 # CORR_SOURCE5 52 2.1518 + angle_coeff @angle:c-cf-cc harmonic 67.092 120.770 # CORR_SOURCE5 15 1.8896 + angle_coeff @angle:cc-cf-cf harmonic 66.791 124.350 # CORR_SOURCE5 18 1.4583 + angle_coeff @angle:c-cf-cd harmonic 66.092 117.820 # SOURCE4_SOURCE5 29 1.0204 + angle_coeff @angle:c-cf-ce harmonic 65.856 126.410 # SOURCE3 2 + angle_coeff @angle:cc-cf-ha harmonic 50.638 114.950 # CORR_SOURCE5 95 1.4175 + angle_coeff @angle:cd-cf-ce harmonic 66.704 126.140 # CORR_SOURCE5 122 1.8142 + angle_coeff @angle:cd-cf-ha harmonic 48.006 115.440 # CORR_SOURCE5 179 0.9381 + angle_coeff @angle:cd-cf-n2 harmonic 86.868 120.960 # CORR_SOURCE5 102 2.2421 + angle_coeff @angle:ce-cf-cf harmonic 67.119 124.240 # CORR_SOURCE5 866 1.6941 + angle_coeff @angle:ce-cf-ch harmonic 68.252 123.130 # CORR_SOURCE5 115 2.1292 + angle_coeff @angle:ce-cf-ha harmonic 50.352 118.220 # CORR_SOURCE5 1522 1.3445 + angle_coeff @angle:ce-cf-n harmonic 91.197 108.390 # CORR_SOURCE5 86 1.0066 + angle_coeff @angle:ce-cf-oh harmonic 88.551 121.690 # CORR_SOURCE5 37 1.2824 + angle_coeff @angle:cf-cf-cf harmonic 65.416 122.110 # SOURCE3_SOURCE5 9 2.4680 + angle_coeff @angle:cf-cf-h4 harmonic 47.341 118.130 # CORR_SOURCE5 44 1.1161 + angle_coeff @angle:cf-cf-ha harmonic 47.662 116.650 # SOURCE3_SOURCE5 1159 0.9686 + angle_coeff @angle:cf-cf-n1 harmonic 84.049 127.150 # CORR 4 + angle_coeff @angle:cf-cf-n2 harmonic 87.472 118.930 # CORR_SOURCE5 13 1.3210 + angle_coeff @angle:c-cf-ha harmonic 47.000 116.460 # SOURCE3_SOURCE5 1028 1.3091 + angle_coeff @angle:ch-cf-ch harmonic 68.393 116.520 # CORR_SOURCE5 35 1.1031 + angle_coeff @angle:ch-cf-ha harmonic 48.557 116.460 # CORR_SOURCE5 58 0.6523 + angle_coeff @angle:ch-cf-n1 harmonic 87.835 119.500 # CORR 2 + angle_coeff @angle:c-cf-n2 harmonic 88.177 114.410 # SOURCE4_SOURCE5 13 1.4243 + angle_coeff @angle:c-cf-n harmonic 83.338 118.450 # CORR_SOURCE5 213 1.4857 + angle_coeff @angle:c-cf-nh harmonic 85.341 115.360 # CORR_SOURCE5 28 2.1980 + angle_coeff @angle:f-c-f harmonic 123.826 107.350 # SOURCE2 2 0.2500 + angle_coeff @angle:h4-cf-n2 harmonic 64.393 121.480 # CORR_SOURCE5 257 1.1842 + angle_coeff @angle:h4-cf-ne harmonic 64.320 120.560 # SOURCE4_SOURCE5 39 0.8435 + angle_coeff @angle:ha-cf-n1 harmonic 65.106 115.960 # CORR 4 + angle_coeff @angle:ha-cf-n2 harmonic 64.979 119.510 # SOURCE3 2 + angle_coeff @angle:ha-cf-nf harmonic 61.414 118.590 # SOURCE3 5 + angle_coeff @angle:ha-cf-nh harmonic 62.516 114.990 # CORR 2 + angle_coeff @angle:ha-cf-p2 harmonic 52.606 120.110 # SOURCE3 1 + angle_coeff @angle:ha-cf-pf harmonic 52.651 119.330 # SOURCE3 6 + angle_coeff @angle:ha-cf-px harmonic 52.873 117.900 # SOURCE3 6 + angle_coeff @angle:ha-cf-py harmonic 53.346 117.990 # SOURCE3_SOURCE5 8 0.8708 + angle_coeff @angle:ha-cf-sx harmonic 41.698 115.450 # SOURCE3 3 + angle_coeff @angle:ha-cf-sy harmonic 42.578 114.860 # SOURCE3 3 + angle_coeff @angle:n2-cf-nh harmonic 110.010 125.090 # CORR_SOURCE5 163 1.6803 + angle_coeff @angle:nf-cf-nf harmonic 106.467 123.870 # SOURCE3 1 + angle_coeff @angle:f-c-o harmonic 118.196 123.440 # SOURCE3 1 + angle_coeff @angle:pf-cf-pf harmonic 97.908 129.790 # SOURCE3 1 + angle_coeff @angle:py-cf-py harmonic 108.039 108.060 # SOURCE3 1 + angle_coeff @angle:f-c-s harmonic 84.396 124.000 # SOURCE2 1 + angle_coeff @angle:sx-cf-sx harmonic 61.727 120.320 # SOURCE3 1 + angle_coeff @angle:sy-cf-sy harmonic 62.867 119.970 # SOURCE3 1 + angle_coeff @angle:c1-cg-ca harmonic 58.572 179.570 # CORR_SOURCE5 38 0.4711 + angle_coeff @angle:c1-cg-cc harmonic 58.934 178.610 # SOURCE4_SOURCE5 13 0.3677 + angle_coeff @angle:c1-cg-ce harmonic 58.989 178.050 # CORR_SOURCE5 15 0.1905 + angle_coeff @angle:c1-cg-cg harmonic 60.378 179.670 # CORR_SOURCE5 90 0.1487 + angle_coeff @angle:c1-cg-ne harmonic 79.305 170.020 # SOURCE3 4 1.1724 + angle_coeff @angle:c1-cg-pe harmonic 75.149 173.290 # SOURCE3 11 4.9305 + angle_coeff @angle:ca-cg-ch harmonic 58.741 179.430 # CORR_SOURCE5 40 0.6103 + angle_coeff @angle:ca-cg-n1 harmonic 74.346 179.490 # CORR_SOURCE5 186 0.6659 + angle_coeff @angle:c-cg-c1 harmonic 58.113 179.140 # SOURCE3 2 + angle_coeff @angle:cc-cg-n1 harmonic 74.809 178.620 # CORR_SOURCE5 43 0.6454 + angle_coeff @angle:ce-cg-ch harmonic 59.157 177.940 # CORR 17 + angle_coeff @angle:ce-cg-n1 harmonic 74.894 177.970 # CORR_SOURCE5 184 1.2220 + angle_coeff @angle:n1-cg-ne harmonic 99.946 174.030 # CORR_SOURCE5 30 0.6173 + angle_coeff @angle:h4-c-o harmonic 66.570 120.700 # SOURCE4_SOURCE5 491 0.4811 + angle_coeff @angle:h5-c-n harmonic 63.496 112.160 # SOURCE4_SOURCE5 98 0.3632 + angle_coeff @angle:h5-c-o harmonic 65.930 123.650 # SOURCE4_SOURCE5 150 0.7654 + angle_coeff @angle:ha-c-ha harmonic 37.443 115.610 # SOURCE3 4 0.0458 + angle_coeff @angle:ha-c-i harmonic 38.168 110.580 # SOURCE3 1 + angle_coeff @angle:ha-c-n harmonic 63.490 112.370 # SOURCE3 4 0.6424 + angle_coeff @angle:ha-c-o harmonic 66.484 121.940 # SOURCE3 51 2.3235 + angle_coeff @angle:ha-c-oh harmonic 64.638 111.820 # SOURCE3 4 1.9375 + angle_coeff @angle:ha-c-os harmonic 64.813 110.340 # SOURCE3 8 1.9344 + angle_coeff @angle:ha-c-s harmonic 44.760 119.560 # SOURCE3 3 0.7586 + angle_coeff @angle:c1-ch-ca harmonic 58.522 179.570 # CORR_SOURCE5 38 0.4711 + angle_coeff @angle:c1-ch-cf harmonic 58.938 178.050 # CORR_SOURCE5 15 0.1905 + angle_coeff @angle:c1-ch-ch harmonic 60.316 179.670 # CORR_SOURCE5 90 0.1487 + angle_coeff @angle:c1-ch-nf harmonic 79.216 170.020 # SOURCE3 4 + angle_coeff @angle:c1-ch-pf harmonic 75.117 173.290 # SOURCE3 11 + angle_coeff @angle:ca-ch-cg harmonic 58.741 179.430 # CORR_SOURCE5 40 0.6103 + angle_coeff @angle:ca-ch-n1 harmonic 74.346 179.490 # CORR_SOURCE5 186 0.6659 + angle_coeff @angle:c-ch-c1 harmonic 58.066 179.140 # SOURCE3 2 + angle_coeff @angle:cd-ch-n1 harmonic 74.807 178.630 # CORR_SOURCE5 49 0.3708 + angle_coeff @angle:cf-ch-cg harmonic 59.157 177.940 # CORR 17 + angle_coeff @angle:cf-ch-n1 harmonic 74.894 177.970 # CORR_SOURCE5 184 1.2220 + angle_coeff @angle:cg-ch-ch harmonic 60.571 179.580 # SOURCE4_SOURCE5 55 0.2973 + angle_coeff @angle:n1-ch-nf harmonic 99.946 174.030 # CORR_SOURCE5 30 0.6173 + angle_coeff @angle:i-c-i harmonic 65.372 116.450 # SOURCE3 1 + angle_coeff @angle:i-c-o harmonic 71.718 122.020 # SOURCE3 4 1.2961 + angle_coeff @angle:f-cl-f harmonic 0.000 87.500 # SOURCE2 1 + angle_coeff @angle:n2-c-n2 harmonic 110.771 110.310 # SOURCE3 1 + angle_coeff @angle:n2-c-o harmonic 111.836 122.500 # SOURCE3 1 + angle_coeff @angle:n4-c-n4 harmonic 99.803 114.640 # SOURCE3 1 + angle_coeff @angle:n4-c-o harmonic 106.610 118.830 # SOURCE3 4 3.8516 + angle_coeff @angle:nc-c-o harmonic 113.330 123.180 # CORR_SOURCE5 172 1.0508 + angle_coeff @angle:nd-c-o harmonic 113.330 123.180 # CORR_SOURCE5 172 1.0508 + angle_coeff @angle:ne-c-ne harmonic 113.088 110.310 # CORR 2 + angle_coeff @angle:ne-c-o harmonic 111.914 125.810 # CORR_SOURCE5 65 1.1135 + angle_coeff @angle:nf-c-nf harmonic 113.088 110.310 # CORR 2 + angle_coeff @angle:nf-c-o harmonic 111.914 125.810 # CORR_SOURCE5 65 1.1135 + angle_coeff @angle:n-c-n harmonic 112.428 113.560 # SOURCE4_SOURCE5 1747 1.4619 + angle_coeff @angle:n-c-nc harmonic 110.397 117.110 # CORR_SOURCE5 131 0.7717 + angle_coeff @angle:n-c-nd harmonic 110.397 117.110 # CORR_SOURCE5 131 0.7717 + angle_coeff @angle:n-c-ne harmonic 113.600 110.260 # SOURCE4_SOURCE5 25 1.7043 + angle_coeff @angle:n-c-o harmonic 113.811 123.050 # SOURCE3_SOURCE5 8454 1.5552 + angle_coeff @angle:n-c-oh harmonic 113.913 112.820 # SOURCE4_SOURCE5 14 1.4518 + angle_coeff @angle:no-c-no harmonic 102.620 109.280 # SOURCE3 1 + angle_coeff @angle:no-c-o harmonic 104.115 125.360 # SOURCE3 1 + angle_coeff @angle:n-c-os harmonic 115.486 109.220 # SOURCE4_SOURCE5 821 0.9352 + angle_coeff @angle:n-c-s harmonic 82.398 124.050 # SOURCE3_SOURCE5 514 1.4099 + angle_coeff @angle:n-c-sh harmonic 81.620 112.970 # SOURCE4_SOURCE5 26 1.1725 + angle_coeff @angle:n-c-ss harmonic 82.496 110.290 # SOURCE4_SOURCE5 160 1.6051 + angle_coeff @angle:oh-c-oh harmonic 116.271 110.560 # SOURCE3 2 0.5498 + angle_coeff @angle:oh-c-s harmonic 83.019 123.440 # SOURCE3 1 + angle_coeff @angle:o-c-o harmonic 118.817 130.250 # SOURCE4_SOURCE5 1037 1.2396 + angle_coeff @angle:o-c-oh harmonic 115.745 122.100 # SOURCE3_SOURCE5 2859 0.8497 + angle_coeff @angle:o-c-os harmonic 114.822 123.250 # SOURCE4_SOURCE5 5492 1.1411 + angle_coeff @angle:o-c-p2 harmonic 96.161 123.100 # SOURCE3 1 + angle_coeff @angle:o-c-p3 harmonic 97.971 120.790 # SOURCE3 1 + angle_coeff @angle:o-c-p5 harmonic 97.881 121.170 # SOURCE4_SOURCE5 18 1.1433 + angle_coeff @angle:o-c-pe harmonic 95.623 123.020 # SOURCE3 3 0.1404 + angle_coeff @angle:o-c-pf harmonic 95.623 123.020 # SOURCE3 3 + angle_coeff @angle:o-c-px harmonic 97.552 119.100 # SOURCE3 1 + angle_coeff @angle:o-c-py harmonic 98.325 122.010 # SOURCE4_SOURCE5 14 1.0132 + angle_coeff @angle:o-c-s4 harmonic 76.764 121.150 # SOURCE3 1 + angle_coeff @angle:o-c-s6 harmonic 77.308 119.450 # SOURCE3 1 + angle_coeff @angle:o-c-s harmonic 85.589 120.440 # SOURCE3 2 + angle_coeff @angle:o-c-sh harmonic 79.543 122.050 # SOURCE3_SOURCE5 10 1.1120 + angle_coeff @angle:os-c-os harmonic 115.283 111.290 # SOURCE4_SOURCE5 32 0.8183 + angle_coeff @angle:o-c-ss harmonic 79.009 123.320 # SOURCE3_SOURCE5 190 1.2053 + angle_coeff @angle:os-c-s harmonic 82.392 125.010 # SOURCE4_SOURCE5 62 1.0980 + angle_coeff @angle:os-c-ss harmonic 82.286 111.400 # SOURCE4_SOURCE5 23 1.7283 + angle_coeff @angle:o-c-sx harmonic 76.145 121.150 # SOURCE3 5 3.6452 + angle_coeff @angle:o-c-sy harmonic 77.559 119.320 # SOURCE3 5 2.4495 + angle_coeff @angle:p2-c-p2 harmonic 100.070 113.750 # SOURCE3 1 + angle_coeff @angle:p3-c-p3 harmonic 99.122 118.040 # SOURCE3 1 + angle_coeff @angle:p3-c-py harmonic 113.947 90.080 # SOURCE3 1 + angle_coeff @angle:p5-c-p5 harmonic 96.866 123.760 # SOURCE3 1 + angle_coeff @angle:ca-cp-ca harmonic 68.877 118.380 # CORR_SOURCE5 959 0.6763 + angle_coeff @angle:ca-cp-cp harmonic 66.121 121.110 # CORR_SOURCE5 1631 1.6425 + angle_coeff @angle:ca-cp-na harmonic 86.507 119.500 # SOURCE4_SOURCE5 59 0.7877 + angle_coeff @angle:ca-cp-nb harmonic 87.071 121.620 # SOURCE4_SOURCE5 174 0.6998 + angle_coeff @angle:cp-cp-cp harmonic 74.761 90.000 # SOURCE3 4 + angle_coeff @angle:cp-cp-cq harmonic 64.283 124.270 # CORR_SOURCE5 8 2.0477 + angle_coeff @angle:cp-cp-nb harmonic 86.053 116.610 # SOURCE4_SOURCE5 235 1.1595 + angle_coeff @angle:pe-c-pe harmonic 99.485 113.770 # SOURCE3 1 + angle_coeff @angle:pf-c-pf harmonic 99.485 113.770 # SOURCE3 1 + angle_coeff @angle:nb-cp-nb harmonic 110.031 125.790 # SOURCE4_SOURCE5 11 0.6658 + angle_coeff @angle:py-c-py harmonic 97.618 123.800 # SOURCE3 1 + angle_coeff @angle:ca-cq-ca harmonic 68.877 118.380 # CORR_SOURCE5 959 0.6763 + angle_coeff @angle:ca-cq-cq harmonic 66.121 121.110 # CORR_SOURCE5 1631 1.6425 + angle_coeff @angle:ca-cq-nb harmonic 87.071 121.620 # SOURCE4_SOURCE5 111 0.7244 + angle_coeff @angle:cp-cq-cq harmonic 64.278 124.290 # CORR_SOURCE5 8 1.4947 + angle_coeff @angle:cq-cq-cq harmonic 74.761 90.000 # SOURCE3 4 + angle_coeff @angle:cq-cq-nb harmonic 86.053 116.610 # SOURCE4_SOURCE5 147 1.1420 + angle_coeff @angle:s4-c-s4 harmonic 63.122 108.810 # SOURCE3 1 + angle_coeff @angle:s6-c-s6 harmonic 61.200 115.750 # SOURCE3 1 + angle_coeff @angle:sh-c-sh harmonic 63.799 115.330 # SOURCE3 1 + angle_coeff @angle:s-c-s harmonic 65.463 126.500 # SOURCE3_SOURCE5 14 1.3489 + angle_coeff @angle:s-c-sh harmonic 63.925 122.650 # SOURCE4_SOURCE5 37 1.5614 + angle_coeff @angle:s-c-ss harmonic 63.724 123.190 # SOURCE3_SOURCE5 85 1.7112 + angle_coeff @angle:ss-c-ss harmonic 64.515 112.420 # SOURCE3_SOURCE5 17 0.4533 + angle_coeff @angle:sx-c-sx harmonic 62.622 108.800 # SOURCE3 1 + angle_coeff @angle:sy-c-sy harmonic 61.356 115.780 # SOURCE3 1 + angle_coeff @angle:c2-cu-cx harmonic 61.131 148.500 # SOURCE4_SOURCE5 23 1.5654 + angle_coeff @angle:c-cu-cu harmonic 98.040 62.600 # SOURCE2 1 + angle_coeff @angle:cu-cu-cx harmonic 105.362 50.800 # SOURCE2 1 + angle_coeff @angle:cu-cu-ha harmonic 46.590 147.730 # SOURCE2 3 2.0950 + angle_coeff @angle:cv-cv-cy harmonic 75.476 94.410 # SOURCE3_SOURCE5 6 0.2122 + angle_coeff @angle:cv-cv-ha harmonic 47.789 133.700 # SOURCE3 2 + angle_coeff @angle:cx-cv-cx harmonic 87.395 63.900 # SOURCE2 1 + angle_coeff @angle:cy-cv-ha harmonic 43.281 132.140 # SOURCE3 2 + angle_coeff @angle:c1-cx-cx harmonic 65.298 119.570 # SOURCE4_SOURCE5 51 1.0503 + angle_coeff @angle:c2-cx-cx harmonic 64.271 120.300 # SOURCE4_SOURCE5 207 2.3490 + angle_coeff @angle:c2-cx-h1 harmonic 47.059 115.860 # SOURCE4_SOURCE5 34 0.6256 + angle_coeff @angle:c2-cx-hc harmonic 47.215 115.150 # SOURCE4_SOURCE5 45 0.9609 + angle_coeff @angle:c2-cx-os harmonic 83.614 116.550 # SOURCE4_SOURCE5 48 1.1122 + angle_coeff @angle:c3-cx-c3 harmonic 64.915 114.240 # SOURCE4_SOURCE5 207 2.2113 + angle_coeff @angle:c3-cx-cx harmonic 63.608 120.100 # SOURCE4_SOURCE5 1739 2.3197 + angle_coeff @angle:c3-cx-h1 harmonic 46.234 115.320 # SOURCE4_SOURCE5 326 1.1035 + angle_coeff @angle:c3-cx-hc harmonic 46.430 114.390 # SOURCE4_SOURCE5 291 1.4379 + angle_coeff @angle:c3-cx-n3 harmonic 81.063 118.500 # SOURCE4 17 2.4897 + angle_coeff @angle:c3-cx-os harmonic 82.886 115.680 # SOURCE4_SOURCE5 616 1.2862 + angle_coeff @angle:ca-cx-cx harmonic 63.720 121.950 # SOURCE4_SOURCE5 197 1.8192 + angle_coeff @angle:ca-cx-h1 harmonic 47.143 114.700 # SOURCE4_SOURCE5 19 0.6393 + angle_coeff @angle:ca-cx-hc harmonic 47.377 113.620 # SOURCE4_SOURCE5 57 0.9227 + angle_coeff @angle:ca-cx-oh harmonic 86.728 112.930 # SOURCE3 1 + angle_coeff @angle:ca-cx-os harmonic 82.823 118.310 # SOURCE4_SOURCE5 18 0.7292 + angle_coeff @angle:c-cx-c3 harmonic 64.445 117.470 # SOURCE4_SOURCE5 71 1.9181 + angle_coeff @angle:cc-cx-cx harmonic 64.711 119.620 # CORR_SOURCE5 73 1.1478 + angle_coeff @angle:cc-cx-hc harmonic 47.813 113.930 # SOURCE4_SOURCE5 44 0.6781 + angle_coeff @angle:c-cx-cx harmonic 64.620 117.970 # SOURCE4_SOURCE5 554 2.1023 + angle_coeff @angle:cd-cx-cx harmonic 64.711 119.620 # CORR_SOURCE5 73 1.1478 + angle_coeff @angle:c-cx-h1 harmonic 46.552 116.550 # SOURCE4_SOURCE5 86 1.1535 + angle_coeff @angle:c-cx-hc harmonic 46.546 116.630 # SOURCE4_SOURCE5 122 1.5743 + angle_coeff @angle:cl-cx-cl harmonic 82.588 110.550 # SOURCE2_SOURCE5 14 0.4864 + angle_coeff @angle:cl-cx-cx harmonic 70.087 119.850 # SOURCE4_SOURCE5 84 0.7070 + angle_coeff @angle:cl-cx-h1 harmonic 48.861 111.430 # SOURCE3 1 + angle_coeff @angle:cl-cx-hc harmonic 47.924 115.800 # SOURCE2 1 + angle_coeff @angle:c-cx-os harmonic 83.552 115.590 # SOURCE4 36 0.8227 + angle_coeff @angle:cu-cx-cu harmonic 95.990 54.600 # SOURCE2 1 + angle_coeff @angle:cu-cx-cx harmonic 92.184 58.450 # SOURCE4_SOURCE5 35 0.3844 + angle_coeff @angle:cu-cx-hc harmonic 46.510 118.570 # SOURCE4_SOURCE5 36 0.6733 + angle_coeff @angle:cx-cx-cx harmonic 90.424 60.000 # SOURCE4_SOURCE5 2370 0.7579 + angle_coeff @angle:cx-cx-cy harmonic 69.603 100.530 # SOURCE3 4 + angle_coeff @angle:cx-cx-f harmonic 85.391 118.550 # SOURCE4_SOURCE5 24 1.1971 + angle_coeff @angle:cx-cx-h1 harmonic 45.959 118.700 # SOURCE3_SOURCE5 1351 1.3656 + angle_coeff @angle:cx-cx-hc harmonic 46.163 117.700 # SOURCE3_SOURCE5 3574 0.9510 + angle_coeff @angle:cx-cx-hx harmonic 45.802 119.610 # SOURCE4_SOURCE5 29 0.1468 + angle_coeff @angle:cx-cx-n3 harmonic 114.892 59.590 # SOURCE4_SOURCE5 400 0.3281 + angle_coeff @angle:cx-cx-na harmonic 79.232 126.020 # SOURCE4_SOURCE5 69 1.6659 + angle_coeff @angle:cx-cx-nh harmonic 115.868 59.170 # SOURCE4_SOURCE5 276 0.6810 + angle_coeff @angle:cx-cx-os harmonic 116.592 59.090 # SOURCE4_SOURCE5 1094 0.5727 + angle_coeff @angle:cy-cx-hc harmonic 44.429 125.430 # SOURCE3 2 + angle_coeff @angle:f-cx-f harmonic 120.884 106.900 # SOURCE2 2 1.4000 + angle_coeff @angle:f-cx-h1 harmonic 65.454 111.680 # SOURCE3 1 + angle_coeff @angle:f-cx-hc harmonic 65.300 112.300 # SOURCE2 1 + angle_coeff @angle:h1-cx-h1 harmonic 37.880 115.460 # SOURCE4_SOURCE5 585 0.3332 + angle_coeff @angle:h1-cx-n3 harmonic 59.281 116.470 # SOURCE4_SOURCE5 463 1.4379 + angle_coeff @angle:h1-cx-n harmonic 60.648 115.050 # SOURCE4_SOURCE5 36 1.2404 + angle_coeff @angle:h1-cx-na harmonic 61.785 108.360 # SOURCE4_SOURCE5 35 1.1443 + angle_coeff @angle:h1-cx-nh harmonic 59.869 116.290 # SOURCE4_SOURCE5 349 1.0287 + angle_coeff @angle:h1-cx-os harmonic 60.853 114.930 # SOURCE3_SOURCE5 531 0.5509 + angle_coeff @angle:h2-cx-h2 harmonic 37.352 119.430 # SOURCE3 1 + angle_coeff @angle:h2-cx-n2 harmonic 58.708 117.180 # SOURCE3 4 + angle_coeff @angle:hc-cx-hc harmonic 38.120 114.430 # SOURCE3_SOURCE5 595 0.4830 + angle_coeff @angle:hc-cx-os harmonic 61.092 114.100 # SOURCE2 1 + angle_coeff @angle:hx-cx-n4 harmonic 58.913 114.470 # SOURCE4_SOURCE5 28 0.1963 + angle_coeff @angle:n2-cx-n2 harmonic 157.396 50.160 # SOURCE3 1 + angle_coeff @angle:n-cx-oh harmonic 107.552 119.750 # SOURCE3 2 + angle_coeff @angle:n-cx-os harmonic 141.311 65.980 # SOURCE3 1 + angle_coeff @angle:oh-cx-oh harmonic 116.883 107.850 # SOURCE3 1 + angle_coeff @angle:oh-cx-os harmonic 108.501 118.120 # SOURCE3 4 1.3581 + angle_coeff @angle:os-cx-os harmonic 106.734 116.050 # SOURCE4_SOURCE5 15 2.1532 + angle_coeff @angle:c2-cy-cy harmonic 68.568 100.400 # SOURCE2 1 + angle_coeff @angle:c3-cy-c3 harmonic 65.146 111.440 # SOURCE4_SOURCE5 53 1.0307 + angle_coeff @angle:c3-cy-cy harmonic 62.618 118.700 # SOURCE4 293 1.8510 + angle_coeff @angle:c3-cy-h1 harmonic 46.561 111.780 # SOURCE4_SOURCE5 309 0.4521 + angle_coeff @angle:c3-cy-hc harmonic 46.907 110.140 # SOURCE3_SOURCE5 291 0.5598 + angle_coeff @angle:c3-cy-n3 harmonic 82.158 113.650 # SOURCE3_SOURCE5 15 2.3547 + angle_coeff @angle:c3-cy-n harmonic 86.069 104.130 # SOURCE4_SOURCE5 306 0.5952 + angle_coeff @angle:c3-cy-os harmonic 83.640 112.310 # SOURCE4_SOURCE5 40 1.1099 + angle_coeff @angle:c-cy-c3 harmonic 63.261 116.710 # SOURCE4_SOURCE5 332 0.5683 + angle_coeff @angle:cc-cy-cy harmonic 62.477 121.220 # CORR_SOURCE5 27 0.4901 + angle_coeff @angle:c-cy-cy harmonic 73.514 85.090 # SOURCE4_SOURCE5 672 0.9017 + angle_coeff @angle:cd-cy-cy harmonic 62.477 121.220 # CORR_SOURCE5 27 0.4901 + angle_coeff @angle:ce-cy-h2 harmonic 45.874 117.400 # SOURCE4_SOURCE5 38 0.5598 + angle_coeff @angle:ce-cy-n harmonic 94.195 87.940 # SOURCE4_SOURCE5 38 0.1933 + angle_coeff @angle:ce-cy-ss harmonic 60.454 120.540 # SOURCE4_SOURCE5 34 1.4182 + angle_coeff @angle:c-cy-h1 harmonic 45.784 113.030 # SOURCE4_SOURCE5 167 0.8137 + angle_coeff @angle:c-cy-hc harmonic 46.135 111.320 # SOURCE3_SOURCE5 246 1.1605 + angle_coeff @angle:cl-cy-cy harmonic 69.535 117.010 # SOURCE3_SOURCE5 41 1.1740 + angle_coeff @angle:cl-cy-h1 harmonic 49.261 106.590 # SOURCE3 1 + angle_coeff @angle:cl-cy-hc harmonic 47.632 114.000 # SOURCE2 1 + angle_coeff @angle:c-cy-n harmonic 80.522 117.340 # SOURCE4_SOURCE5 164 1.1278 + angle_coeff @angle:c-cy-os harmonic 82.061 115.000 # SOURCE4_SOURCE5 17 1.7766 + angle_coeff @angle:cv-cy-cy harmonic 73.645 86.710 # SOURCE4_SOURCE5 30 1.1538 + angle_coeff @angle:cv-cy-hc harmonic 46.478 114.420 # SOURCE4_SOURCE5 25 1.1899 + angle_coeff @angle:cx-cy-cy harmonic 68.163 101.230 # SOURCE3 4 + angle_coeff @angle:cx-cy-hc harmonic 45.715 118.300 # SOURCE2 3 5.7799 + angle_coeff @angle:cy-cy-cy harmonic 72.002 88.400 # SOURCE3_SOURCE5 746 1.4921 + angle_coeff @angle:cy-cy-f harmonic 85.702 112.870 # SOURCE4 13 1.6772 + angle_coeff @angle:cy-cy-h1 harmonic 45.598 113.240 # SOURCE3_SOURCE5 501 1.2112 + angle_coeff @angle:cy-cy-h2 harmonic 44.908 116.780 # SOURCE4_SOURCE5 206 0.8496 + angle_coeff @angle:cy-cy-hc harmonic 45.290 114.790 # SOURCE3_SOURCE5 1632 2.3030 + angle_coeff @angle:cy-cy-n3 harmonic 92.778 87.580 # SOURCE3 4 0.6135 + angle_coeff @angle:cy-cy-n harmonic 91.445 90.630 # SOURCE3_SOURCE5 429 2.2980 + angle_coeff @angle:cy-cy-na harmonic 80.160 119.560 # SOURCE4_SOURCE5 26 0.4777 + angle_coeff @angle:cy-cy-oh harmonic 82.786 114.190 # SOURCE3 4 + angle_coeff @angle:cy-cy-os harmonic 83.069 111.770 # SOURCE4 18 2.1334 + angle_coeff @angle:cy-cy-s6 harmonic 60.829 117.220 # SOURCE4_SOURCE5 19 1.2938 + angle_coeff @angle:cy-cy-ss harmonic 60.567 118.400 # SOURCE4_SOURCE5 183 1.7650 + angle_coeff @angle:h1-cy-h1 harmonic 38.688 109.460 # SOURCE3_SOURCE5 73 0.6101 + angle_coeff @angle:h1-cy-n3 harmonic 59.591 113.930 # SOURCE3_SOURCE5 104 0.9602 + angle_coeff @angle:h1-cy-n harmonic 60.615 111.280 # SOURCE4_SOURCE5 377 0.6736 + angle_coeff @angle:h1-cy-oh harmonic 62.604 111.490 # SOURCE3 2 + angle_coeff @angle:h1-cy-os harmonic 62.029 110.130 # SOURCE3_SOURCE5 45 0.8913 + angle_coeff @angle:h1-cy-s6 harmonic 41.611 111.620 # SOURCE4_SOURCE5 16 1.2135 + angle_coeff @angle:h2-cy-n harmonic 59.772 114.500 # SOURCE4_SOURCE5 213 0.6904 + angle_coeff @angle:h2-cy-os harmonic 62.315 109.190 # SOURCE4_SOURCE5 19 0.6835 + angle_coeff @angle:h2-cy-s6 harmonic 41.906 110.010 # SOURCE4_SOURCE5 29 1.6175 + angle_coeff @angle:h2-cy-ss harmonic 41.997 109.770 # SOURCE4_SOURCE5 214 0.7540 + angle_coeff @angle:hc-cy-hc harmonic 38.780 108.980 # SOURCE3_SOURCE5 313 0.5379 + angle_coeff @angle:n-cy-os harmonic 109.575 107.420 # SOURCE4_SOURCE5 24 2.2897 + angle_coeff @angle:n-cy-s6 harmonic 82.361 103.180 # SOURCE4_SOURCE5 18 0.8204 + angle_coeff @angle:n-cy-ss harmonic 81.655 105.130 # SOURCE4_SOURCE5 165 0.4214 + angle_coeff @angle:nh-cz-nh harmonic 112.563 120.140 # SOURCE4_SOURCE5 67 0.3910 + angle_coeff @angle:br-n1-c1 harmonic 52.125 180.000 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-c1 harmonic 65.921 179.920 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-c2 harmonic 61.737 177.730 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-c3 harmonic 57.795 177.720 # HF/6-31G*_SOURCE5 6 0.4473 + angle_coeff @angle:c1-n1-ca harmonic 60.455 179.990 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-cl harmonic 62.197 179.950 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-f harmonic 73.857 179.960 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-hn harmonic 45.538 179.980 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-i harmonic 49.085 179.950 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-n1 harmonic 83.205 180.000 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-n2 harmonic 81.640 171.560 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-n3 harmonic 76.060 175.590 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-n4 harmonic 74.800 179.690 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-na harmonic 75.122 180.000 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-nh harmonic 76.286 176.350 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-o harmonic 77.945 179.950 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-oh harmonic 78.300 174.310 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-os harmonic 77.399 176.610 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-p2 harmonic 70.987 172.830 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-p3 harmonic 71.573 173.510 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-p4 harmonic 70.741 173.640 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-p5 harmonic 74.438 177.280 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-s2 harmonic 61.878 178.110 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-s4 harmonic 56.730 169.600 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-s harmonic 54.789 179.990 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-s6 harmonic 63.372 175.920 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-sh harmonic 57.243 174.250 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-ss harmonic 56.948 176.060 # HF/6-31G* 1 + angle_coeff @angle:c2-n1-n1 harmonic 77.250 180.000 # HF/6-31G* 1 + angle_coeff @angle:c2-n1-o harmonic 91.430 116.940 # SOURCE3 2 0.0060 + angle_coeff @angle:c2-n1-s harmonic 66.557 118.000 # SOURCE3 2 0.0121 + angle_coeff @angle:c3-n1-n1 harmonic 72.180 180.000 # HF/6-31G* 1 + angle_coeff @angle:ca-n1-n1 harmonic 76.091 180.000 # HF/6-31G* 1 + angle_coeff @angle:ce-n1-o harmonic 89.183 122.400 # CORR 2 + angle_coeff @angle:ce-n1-s harmonic 66.690 117.340 # CORR 2 + angle_coeff @angle:cf-n1-o harmonic 89.183 122.400 # CORR 2 + angle_coeff @angle:cf-n1-s harmonic 66.690 117.340 # CORR 2 + angle_coeff @angle:cl-n1-n1 harmonic 77.983 179.940 # HF/6-31G* 1 + angle_coeff @angle:f-n1-n1 harmonic 92.867 179.930 # HF/6-31G* 1 + angle_coeff @angle:hn-n1-n1 harmonic 57.688 179.910 # HF/6-31G* 1 + angle_coeff @angle:i-n1-n1 harmonic 61.297 179.940 # HF/6-31G* 1 + angle_coeff @angle:n1-n1-n1 harmonic 105.090 179.970 # HF/6-31G* 1 + angle_coeff @angle:n1-n1-n2 harmonic 102.546 172.850 # HF/6-31G*_SOURCE5 38 0.7957 + angle_coeff @angle:n1-n1-n3 harmonic 95.850 175.090 # HF/6-31G* 1 + angle_coeff @angle:n1-n1-n4 harmonic 94.056 179.910 # HF/6-31G* 1 + angle_coeff @angle:n1-n1-na harmonic 94.541 179.970 # HF/6-31G* 1 + angle_coeff @angle:n1-n1-nh harmonic 96.108 176.000 # HF/6-31G* 1 + angle_coeff @angle:n1-n1-o harmonic 98.200 179.940 # HF/6-31G* 1 + angle_coeff @angle:n1-n1-oh harmonic 98.761 173.770 # HF/6-31G* 1 + angle_coeff @angle:n1-n1-os harmonic 97.594 176.120 # HF/6-31G* 1 + angle_coeff @angle:n1-n1-p2 harmonic 88.474 174.710 # HF/6-31G* 1 + angle_coeff @angle:n1-n1-p3 harmonic 89.510 174.270 # HF/6-31G* 1 + angle_coeff @angle:n1-n1-s harmonic 68.668 180.000 # SOURCE3 1 + angle_coeff @angle:n1-n1-sh harmonic 71.618 175.070 # HF/6-31G* 1 + angle_coeff @angle:n1-n1-ss harmonic 71.507 175.610 # HF/6-31G* 1 + angle_coeff @angle:o-n1-p2 harmonic 107.306 116.050 # SOURCE3 1 + angle_coeff @angle:p2-n1-s harmonic 83.718 119.930 # SOURCE3 1 + angle_coeff @angle:br-n2-br harmonic 64.457 106.600 # SOURCE3 1 + angle_coeff @angle:br-n2-c2 harmonic 60.247 112.400 # SOURCE3 1 + angle_coeff @angle:br-n2-n2 harmonic 76.071 110.420 # SOURCE3 1 + angle_coeff @angle:br-n2-o harmonic 74.480 114.470 # SOURCE3 1 + angle_coeff @angle:br-n2-p2 harmonic 82.651 111.030 # SOURCE3 1 + angle_coeff @angle:br-n2-s harmonic 63.537 115.780 # SOURCE3 1 + angle_coeff @angle:c1-n2-c1 harmonic 77.425 121.100 # SOURCE3 1 + angle_coeff @angle:c1-n2-c3 harmonic 60.897 151.880 # SOURCE3 4 15.8282 + angle_coeff @angle:c1-n2-cl harmonic 68.804 118.800 # SOURCE2 1 + angle_coeff @angle:c1-n2-hn harmonic 52.343 126.500 # SOURCE2 3 7.6267 + angle_coeff @angle:c1-n2-n2 harmonic 97.203 113.400 # SOURCE3 1 + angle_coeff @angle:c1-n2-o harmonic 99.262 113.590 # SOURCE3 1 + angle_coeff @angle:c1-n2-p2 harmonic 88.534 119.570 # SOURCE3 1 + angle_coeff @angle:c1-n2-s harmonic 71.943 117.670 # SOURCE3 1 + angle_coeff @angle:c2-n2-c2 harmonic 73.202 118.180 # SOURCE3 1 + angle_coeff @angle:c2-n2-c3 harmonic 68.517 115.300 # SOURCE3 8 4.2940 + angle_coeff @angle:c2-n2-ca harmonic 72.054 119.940 # SOURCE3 1 + angle_coeff @angle:c2-n2-cl harmonic 70.470 112.640 # SOURCE3 1 + angle_coeff @angle:c2-n2-f harmonic 90.773 108.140 # SOURCE3 1 + angle_coeff @angle:c2-n2-hn harmonic 53.185 110.800 # SOURCE3_SOURCE5 419 0.5563 + angle_coeff @angle:c2-n2-i harmonic 54.902 114.740 # SOURCE3 2 0.0139 + angle_coeff @angle:c2-n2-n1 harmonic 94.708 115.090 # HF/6-31G* 1 + angle_coeff @angle:c2-n2-n2 harmonic 98.476 103.590 # SOURCE3 2 + angle_coeff @angle:c2-n2-n3 harmonic 89.963 118.140 # SOURCE3 1 + angle_coeff @angle:c2-n2-n4 harmonic 78.566 112.220 # SOURCE3 3 0.0406 + angle_coeff @angle:c2-n2-n harmonic 88.873 117.930 # SOURCE4_SOURCE5 32 1.2067 + angle_coeff @angle:c2-n2-na harmonic 88.734 117.580 # SOURCE3 8 1.6671 + angle_coeff @angle:c2-n2-nh harmonic 89.294 117.610 # SOURCE3 6 3.2642 + angle_coeff @angle:c2-n2-no harmonic 86.019 118.020 # SOURCE3_SOURCE5 8 0.7772 + angle_coeff @angle:c2-n2-o harmonic 94.405 116.940 # SOURCE3 1 + angle_coeff @angle:c2-n2-oh harmonic 90.358 111.120 # SOURCE4_SOURCE5 59 1.2303 + angle_coeff @angle:c2-n2-os harmonic 90.019 110.960 # SOURCE4_SOURCE5 46 1.0478 + angle_coeff @angle:c2-n2-p2 harmonic 88.774 116.000 # SOURCE3 1 + angle_coeff @angle:c2-n2-p3 harmonic 80.914 119.300 # SOURCE3 3 2.8489 + angle_coeff @angle:c2-n2-p4 harmonic 82.737 118.770 # SOURCE3 1 + angle_coeff @angle:c2-n2-s4 harmonic 70.138 112.290 # SOURCE3 1 + angle_coeff @angle:c2-n2-s6 harmonic 70.821 116.240 # SOURCE3 1 + angle_coeff @angle:c2-n2-s harmonic 70.719 118.000 # SOURCE3 1 + angle_coeff @angle:c2-n2-sh harmonic 64.926 115.480 # SOURCE3 1 + angle_coeff @angle:c2-n2-ss harmonic 66.888 118.040 # SOURCE3 4 2.2804 + angle_coeff @angle:c3-n2-c3 harmonic 66.122 110.700 # SOURCE3 1 + angle_coeff @angle:c3-n2-ca harmonic 68.205 115.050 # SOURCE4_SOURCE5 12 1.0676 + angle_coeff @angle:c3-n2-ce harmonic 67.437 118.670 # CORR_SOURCE5 270 1.8559 + angle_coeff @angle:c3-n2-cf harmonic 67.437 118.670 # CORR_SOURCE5 270 1.8559 + angle_coeff @angle:c3-n2-hn harmonic 45.854 118.400 # SOURCE3 1 + angle_coeff @angle:c3-n2-n1 harmonic 86.587 116.100 # SOURCE4_SOURCE5 33 0.4557 + angle_coeff @angle:c3-n2-n2 harmonic 87.844 110.840 # SOURCE3_SOURCE5 20 1.2862 + angle_coeff @angle:c3-n2-nh harmonic 86.138 109.990 # SOURCE3 1 + angle_coeff @angle:c3-n2-o harmonic 88.263 112.400 # SOURCE2 1 + angle_coeff @angle:c3-n2-p2 harmonic 85.879 114.210 # SOURCE3 2 2.2772 + angle_coeff @angle:c3-n2-s6 harmonic 68.328 113.840 # SOURCE3 1 + angle_coeff @angle:c3-n2-s harmonic 67.797 116.720 # SOURCE3 1 + angle_coeff @angle:ca-n2-ca harmonic 73.899 112.200 # SOURCE3 1 + angle_coeff @angle:ca-n2-hn harmonic 50.447 120.000 # SOURCE3 1 + angle_coeff @angle:ca-n2-n2 harmonic 93.256 113.530 # SOURCE3 1 + angle_coeff @angle:ca-n2-o harmonic 93.893 116.000 # SOURCE2 1 + angle_coeff @angle:ca-n2-p2 harmonic 87.640 118.110 # SOURCE3 1 + angle_coeff @angle:ca-n2-s harmonic 69.770 120.110 # SOURCE3 1 + angle_coeff @angle:c-n2-c2 harmonic 68.290 120.970 # SOURCE3 1 + angle_coeff @angle:c-n2-c harmonic 64.555 123.800 # SOURCE3 1 + angle_coeff @angle:c-n2-ca harmonic 67.993 120.500 # SOURCE3 1 + angle_coeff @angle:cc-n2-cl harmonic 69.467 115.790 # CORR 2 + angle_coeff @angle:cc-n2-hn harmonic 52.795 111.250 # CORR_SOURCE5 44 0.9238 + angle_coeff @angle:cc-n2-na harmonic 91.793 109.240 # SOURCE4_SOURCE5 23 1.5921 + angle_coeff @angle:cc-n2-nh harmonic 88.704 118.470 # SOURCE4_SOURCE5 13 1.7276 + angle_coeff @angle:cd-n2-cl harmonic 69.467 115.790 # CORR 2 + angle_coeff @angle:cd-n2-hn harmonic 52.795 111.250 # CORR_SOURCE5 44 0.9238 + angle_coeff @angle:ce-n2-hn harmonic 52.954 111.000 # CORR_SOURCE5 129 0.3980 + angle_coeff @angle:ce-n2-n harmonic 88.686 117.980 # CORR_SOURCE5 153 0.9604 + angle_coeff @angle:ce-n2-nh harmonic 88.846 118.340 # CORR_SOURCE5 99 1.0308 + angle_coeff @angle:ce-n2-o harmonic 96.153 112.160 # SOURCE3 1 + angle_coeff @angle:ce-n2-oh harmonic 89.527 112.790 # CORR_SOURCE5 124 1.4261 + angle_coeff @angle:ce-n2-os harmonic 89.131 112.790 # CORR_SOURCE5 58 1.1282 + angle_coeff @angle:ce-n2-s harmonic 71.153 116.280 # SOURCE3 1 + angle_coeff @angle:cf-n2-hn harmonic 52.942 111.050 # CORR_SOURCE5 5 0.7460 + angle_coeff @angle:cf-n2-n harmonic 88.686 117.980 # CORR_SOURCE5 153 0.9604 + angle_coeff @angle:cf-n2-nh harmonic 88.846 118.340 # CORR_SOURCE5 99 1.0308 + angle_coeff @angle:cf-n2-o harmonic 96.153 112.160 # SOURCE3 1 + angle_coeff @angle:cf-n2-oh harmonic 89.527 112.790 # CORR_SOURCE5 124 1.4261 + angle_coeff @angle:cf-n2-os harmonic 89.131 112.790 # CORR_SOURCE5 58 1.1282 + angle_coeff @angle:cf-n2-s harmonic 71.153 116.280 # SOURCE3 1 + angle_coeff @angle:cl-n2-n1 harmonic 90.032 108.700 # SOURCE2 1 + angle_coeff @angle:cl-n2-n2 harmonic 89.183 110.470 # SOURCE3 1 + angle_coeff @angle:cl-n2-o harmonic 87.927 114.030 # SOURCE3 1 + angle_coeff @angle:cl-n2-p2 harmonic 93.146 112.980 # SOURCE3 1 + angle_coeff @angle:cl-n2-s harmonic 72.639 115.770 # SOURCE3 1 + angle_coeff @angle:cx-n2-n2 harmonic 113.932 64.920 # SOURCE3 2 + angle_coeff @angle:f-n2-n2 harmonic 110.866 114.600 # SOURCE2 1 + angle_coeff @angle:f-n2-o harmonic 114.530 110.100 # SOURCE2 1 + angle_coeff @angle:f-n2-p2 harmonic 113.300 107.100 # SOURCE3 1 + angle_coeff @angle:f-n2-s harmonic 88.996 110.730 # SOURCE3 1 + angle_coeff @angle:hn-n2-hn harmonic 38.294 120.000 # SOURCE3 1 + angle_coeff @angle:hn-n2-n1 harmonic 67.682 114.100 # SOURCE2 1 + angle_coeff @angle:hn-n2-n2 harmonic 69.032 105.010 # SOURCE3 19 1.5183 + angle_coeff @angle:hn-n2-ne harmonic 67.706 108.560 # SOURCE3 29 5.5708 + angle_coeff @angle:hn-n2-nf harmonic 67.706 108.560 # SOURCE3 29 + angle_coeff @angle:hn-n2-o harmonic 70.317 107.370 # SOURCE3 1 + angle_coeff @angle:hn-n2-p2 harmonic 59.815 112.090 # SOURCE3 18 4.0663 + angle_coeff @angle:hn-n2-p4 harmonic 55.602 111.330 # SOURCE3 1 + angle_coeff @angle:hn-n2-p5 harmonic 57.476 122.340 # SOURCE3 1 + angle_coeff @angle:hn-n2-pe harmonic 62.556 111.410 # SOURCE3 20 4.9895 + angle_coeff @angle:hn-n2-pf harmonic 62.556 111.410 # SOURCE3 20 + angle_coeff @angle:hn-n2-s2 harmonic 47.686 115.800 # SOURCE2 1 + angle_coeff @angle:hn-n2-s4 harmonic 46.643 111.210 # SOURCE3 1 + angle_coeff @angle:hn-n2-s harmonic 49.437 108.170 # SOURCE3 1 + angle_coeff @angle:hn-n2-s6 harmonic 48.367 111.170 # SOURCE3_SOURCE5 7 0.7012 + angle_coeff @angle:i-n2-n2 harmonic 69.513 111.790 # SOURCE3 1 + angle_coeff @angle:i-n2-o harmonic 67.472 116.820 # SOURCE3 1 + angle_coeff @angle:i-n2-p2 harmonic 77.614 113.260 # SOURCE3 1 + angle_coeff @angle:i-n2-s harmonic 59.644 116.850 # SOURCE3 1 + angle_coeff @angle:n1-n2-n1 harmonic 122.832 112.000 # HF/6-31G* 1 + angle_coeff @angle:n2-n2-n1 harmonic 95.438 180.000 # dac_for_azides 0 + angle_coeff @angle:n2-n2-n2 harmonic 120.662 109.490 # SOURCE3 2 + angle_coeff @angle:n2-n2-n3 harmonic 117.964 108.880 # SOURCE3 1 + angle_coeff @angle:n2-n2-n4 harmonic 101.207 106.450 # SOURCE3 1 + angle_coeff @angle:n2-n2-na harmonic 114.285 112.230 # SOURCE3 1 + angle_coeff @angle:n2-n2-nh harmonic 115.311 111.700 # SOURCE3 5 0.3475 + angle_coeff @angle:n2-n2-no harmonic 114.147 105.970 # SOURCE3 1 + angle_coeff @angle:n2-n2-o harmonic 122.449 110.430 # SOURCE3 1 + angle_coeff @angle:n2-n2-oh harmonic 113.470 111.510 # SOURCE3 1 + angle_coeff @angle:n2-n2-os harmonic 114.570 108.380 # SOURCE3 1 + angle_coeff @angle:n2-n2-p2 harmonic 114.892 109.150 # SOURCE3 1 + angle_coeff @angle:n2-n2-p3 harmonic 104.216 113.050 # SOURCE3 1 + angle_coeff @angle:n2-n2-p4 harmonic 103.768 118.770 # SOURCE3 1 + angle_coeff @angle:n2-n2-p5 harmonic 114.546 110.460 # SOURCE3 1 + angle_coeff @angle:n2-n2-s4 harmonic 90.072 107.300 # SOURCE3 1 + angle_coeff @angle:n2-n2-s6 harmonic 90.924 111.250 # SOURCE3 1 + angle_coeff @angle:n2-n2-s harmonic 89.630 115.910 # SOURCE3 1 + angle_coeff @angle:n2-n2-sh harmonic 83.010 111.100 # SOURCE3 1 + angle_coeff @angle:n2-n2-ss harmonic 86.115 112.140 # SOURCE3 1 + angle_coeff @angle:n3-n2-n3 harmonic 112.191 115.070 # SOURCE3 1 + angle_coeff @angle:n3-n2-o harmonic 117.213 114.000 # SOURCE2 1 + angle_coeff @angle:n3-n2-p2 harmonic 110.501 115.340 # SOURCE3 1 + angle_coeff @angle:n3-n2-s harmonic 87.944 117.130 # SOURCE3 1 + angle_coeff @angle:n4-n2-n4 harmonic 92.222 106.700 # SOURCE3 1 + angle_coeff @angle:n4-n2-o harmonic 99.103 112.200 # SOURCE3 1 + angle_coeff @angle:n4-n2-p2 harmonic 101.387 113.070 # SOURCE3 1 + angle_coeff @angle:n4-n2-s harmonic 78.497 118.500 # SOURCE3 1 + angle_coeff @angle:na-n2-na harmonic 113.061 107.000 # SOURCE3 1 + angle_coeff @angle:na-n2-o harmonic 115.589 113.090 # SOURCE3 1 + angle_coeff @angle:na-n2-p2 harmonic 107.835 119.160 # SOURCE3 1 + angle_coeff @angle:na-n2-s harmonic 86.691 118.260 # SOURCE3 1 + angle_coeff @angle:ne-n2-nh harmonic 114.300 113.340 # CORR_SOURCE5 18 1.2157 + angle_coeff @angle:ne-n2-o harmonic 122.270 110.310 # SOURCE3 1 + angle_coeff @angle:ne-n2-s harmonic 89.426 116.220 # SOURCE3 1 + angle_coeff @angle:nf-n2-nh harmonic 114.300 113.340 # CORR_SOURCE5 18 1.2157 + angle_coeff @angle:nf-n2-o harmonic 122.270 110.310 # SOURCE3 1 + angle_coeff @angle:nf-n2-s harmonic 89.426 116.220 # SOURCE3 1 + angle_coeff @angle:nh-n2-nh harmonic 107.426 121.200 # SOURCE3 1 + angle_coeff @angle:nh-n2-o harmonic 116.027 113.850 # SOURCE4_SOURCE5 33 1.0590 + angle_coeff @angle:nh-n2-p2 harmonic 108.341 118.830 # SOURCE3 2 0.1024 + angle_coeff @angle:nh-n2-s harmonic 87.530 116.900 # SOURCE3 2 0.2276 + angle_coeff @angle:n-n2-n2 harmonic 116.779 108.160 # SOURCE4_SOURCE5 18 0.3340 + angle_coeff @angle:n-n2-o harmonic 114.959 115.110 # SOURCE4_SOURCE5 85 0.2779 + angle_coeff @angle:no-n2-no harmonic 109.483 103.700 # SOURCE3 1 + angle_coeff @angle:no-n2-o harmonic 118.569 100.760 # SOURCE3 1 + angle_coeff @angle:no-n2-p2 harmonic 109.507 111.950 # SOURCE3 1 + angle_coeff @angle:n-n2-p2 harmonic 108.858 117.300 # SOURCE3 1 + angle_coeff @angle:n-n2-s harmonic 87.790 115.740 # SOURCE3 1 + angle_coeff @angle:oh-n2-oh harmonic 114.003 101.700 # SOURCE3 1 + angle_coeff @angle:oh-n2-p2 harmonic 109.132 115.110 # SOURCE3 1 + angle_coeff @angle:oh-n2-s harmonic 86.961 116.080 # SOURCE3 1 + angle_coeff @angle:o-n2-o harmonic 122.337 115.370 # SOURCE3 1 + angle_coeff @angle:o-n2-oh harmonic 114.777 112.150 # SOURCE2 2 1.4500 + angle_coeff @angle:o-n2-os harmonic 115.139 110.350 # SOURCE3 2 0.0042 + angle_coeff @angle:o-n2-p2 harmonic 112.237 116.080 # SOURCE3 1 + angle_coeff @angle:o-n2-p3 harmonic 104.358 113.430 # SOURCE3 1 + angle_coeff @angle:o-n2-p4 harmonic 107.967 110.610 # SOURCE3 1 + angle_coeff @angle:o-n2-p5 harmonic 116.129 109.110 # SOURCE3 1 + angle_coeff @angle:o-n2-pe harmonic 107.813 134.560 # SOURCE3 1 + angle_coeff @angle:o-n2-pf harmonic 107.813 134.560 # SOURCE3 1 + angle_coeff @angle:o-n2-s4 harmonic 90.054 108.910 # SOURCE3 1 + angle_coeff @angle:o-n2-s6 harmonic 91.703 111.340 # SOURCE3 1 + angle_coeff @angle:o-n2-s harmonic 89.978 117.180 # SOURCE3 1 + angle_coeff @angle:o-n2-sh harmonic 81.901 114.980 # SOURCE3 1 + angle_coeff @angle:os-n2-os harmonic 108.669 110.290 # SOURCE3 1 + angle_coeff @angle:os-n2-p2 harmonic 111.268 110.200 # SOURCE3 1 + angle_coeff @angle:o-n2-ss harmonic 85.259 115.770 # SOURCE3_SOURCE5 7 0.2342 + angle_coeff @angle:os-n2-s harmonic 88.194 112.230 # SOURCE3 1 + angle_coeff @angle:p2-n2-p2 harmonic 113.183 116.800 # SOURCE3 1 + angle_coeff @angle:p2-n2-p3 harmonic 103.997 124.480 # SOURCE3 1 + angle_coeff @angle:p2-n2-p4 harmonic 103.837 128.370 # SOURCE3 1 + angle_coeff @angle:p2-n2-p5 harmonic 110.289 123.470 # SOURCE3 1 + angle_coeff @angle:p2-n2-s4 harmonic 89.884 112.100 # SOURCE3 1 + angle_coeff @angle:p2-n2-s6 harmonic 90.002 115.700 # SOURCE3 1 + angle_coeff @angle:p2-n2-s harmonic 89.517 117.840 # SOURCE3 1 + angle_coeff @angle:p2-n2-sh harmonic 83.828 118.450 # SOURCE3 1 + angle_coeff @angle:p2-n2-ss harmonic 85.455 120.430 # SOURCE3 1 + angle_coeff @angle:p3-n2-p3 harmonic 101.430 120.400 # SOURCE3 1 + angle_coeff @angle:p3-n2-s harmonic 83.445 120.860 # SOURCE3 1 + angle_coeff @angle:p4-n2-s harmonic 81.102 131.840 # SOURCE3 1 + angle_coeff @angle:p5-n2-p5 harmonic 111.803 120.600 # SOURCE3 1 + angle_coeff @angle:p5-n2-s harmonic 88.930 119.890 # SOURCE3 1 + angle_coeff @angle:pe-n2-s harmonic 92.311 115.730 # SOURCE3 1 + angle_coeff @angle:pf-n2-s harmonic 92.311 115.730 # SOURCE3 1 + angle_coeff @angle:s4-n2-s4 harmonic 67.822 119.180 # SOURCE3 1 + angle_coeff @angle:s4-n2-s6 harmonic 68.983 119.180 # SOURCE3 1 + angle_coeff @angle:s6-n2-s6 harmonic 70.275 119.180 # SOURCE3 1 + angle_coeff @angle:sh-n2-sh harmonic 61.611 123.930 # SOURCE3 1 + angle_coeff @angle:sh-n2-ss harmonic 63.026 123.930 # SOURCE3 1 + angle_coeff @angle:s-n2-s harmonic 70.359 120.880 # SOURCE3 1 + angle_coeff @angle:s-n2-s4 harmonic 71.109 113.000 # SOURCE3 1 + angle_coeff @angle:s-n2-s6 harmonic 70.436 119.610 # SOURCE3 1 + angle_coeff @angle:s-n2-sh harmonic 65.341 122.050 # SOURCE3 1 + angle_coeff @angle:s-n2-ss harmonic 68.418 118.190 # SOURCE3 1 + angle_coeff @angle:ss-n2-ss harmonic 64.662 123.930 # SOURCE3 1 + angle_coeff @angle:br-n3-br harmonic 67.124 107.150 # SOURCE3 1 + angle_coeff @angle:br-n3-c3 harmonic 63.925 106.930 # SOURCE3 2 + angle_coeff @angle:c1-n3-c1 harmonic 68.156 123.340 # SOURCE3 1 + angle_coeff @angle:c1-n3-f harmonic 91.888 104.700 # SOURCE2 1 + angle_coeff @angle:c1-n3-hn harmonic 50.216 114.780 # SOURCE3_SOURCE5 7 0.4776 + angle_coeff @angle:c1-n3-o harmonic 89.192 116.630 # SOURCE3 1 + angle_coeff @angle:c2-n3-c2 harmonic 68.168 124.680 # SOURCE3 1 + angle_coeff @angle:c2-n3-hn harmonic 49.470 119.380 # SOURCE3 1 + angle_coeff @angle:c3-n3-c3 harmonic 65.697 112.350 # SOURCE3_SOURCE5 10425 1.3688 + angle_coeff @angle:c3-n3-cl harmonic 72.005 107.230 # SOURCE3 3 0.3673 + angle_coeff @angle:c3-n3-cx harmonic 64.536 116.000 # SOURCE4_SOURCE5 93 0.9654 + angle_coeff @angle:c3-n3-cy harmonic 63.919 117.550 # SOURCE4_SOURCE5 52 1.6649 + angle_coeff @angle:c3-n3-f harmonic 88.810 103.130 # SOURCE3 2 + angle_coeff @angle:c3-n3-hn harmonic 47.782 109.290 # SOURCE3_SOURCE5 6742 0.6614 + angle_coeff @angle:c3-n3-i harmonic 60.375 108.480 # SOURCE3 2 + angle_coeff @angle:c3-n3-n2 harmonic 83.514 118.750 # SOURCE2 2 2.6500 + angle_coeff @angle:c3-n3-n3 harmonic 83.494 110.800 # SOURCE3_SOURCE5 91 1.4698 + angle_coeff @angle:c3-n3-n4 harmonic 84.250 109.650 # SOURCE3 3 0.1146 + angle_coeff @angle:c3-n3-n harmonic 84.170 111.710 # SOURCE4_SOURCE5 108 1.7154 + angle_coeff @angle:c3-n3-nh harmonic 83.840 111.770 # SOURCE4_SOURCE5 54 1.2232 + angle_coeff @angle:c3-n3-no harmonic 82.437 116.930 # SOURCE3_SOURCE5 25 0.8475 + angle_coeff @angle:c3-n3-o harmonic 86.116 113.310 # SOURCE3 5 8.9081 + angle_coeff @angle:c3-n3-oh harmonic 85.913 106.490 # SOURCE4_SOURCE5 51 1.1723 + angle_coeff @angle:c3-n3-os harmonic 85.469 105.800 # SOURCE4_SOURCE5 28 1.5996 + angle_coeff @angle:c3-n3-p3 harmonic 79.872 119.670 # SOURCE3_SOURCE5 17 1.9089 + angle_coeff @angle:c3-n3-p5 harmonic 81.775 119.860 # SOURCE4_SOURCE5 188 2.0452 + angle_coeff @angle:c3-n3-s4 harmonic 62.997 114.490 # SOURCE3_SOURCE5 8 1.8120 + angle_coeff @angle:c3-n3-s6 harmonic 64.550 116.550 # SOURCE4_SOURCE5 179 1.8765 + angle_coeff @angle:c3-n3-s harmonic 63.268 110.020 # SOURCE3 1 + angle_coeff @angle:c3-n3-sh harmonic 63.898 112.700 # SOURCE3 1 + angle_coeff @angle:c3-n3-ss harmonic 63.312 116.250 # SOURCE3_SOURCE5 14 1.9512 + angle_coeff @angle:c3-n3-sy harmonic 64.295 115.250 # SOURCE4_SOURCE5 250 1.7586 + angle_coeff @angle:cl-n3-cl harmonic 80.378 108.280 # SOURCE3 1 + angle_coeff @angle:cl-n3-hn harmonic 48.266 104.390 # SOURCE3 2 + angle_coeff @angle:cl-n3-n3 harmonic 90.354 107.650 # SOURCE3 1 + angle_coeff @angle:cx-n3-cx harmonic 89.029 60.730 # SOURCE4_SOURCE5 147 0.2518 + angle_coeff @angle:cx-n3-hn harmonic 47.500 109.830 # SOURCE4_SOURCE5 76 0.6684 + angle_coeff @angle:cx-n3-p5 harmonic 81.827 119.410 # SOURCE4_SOURCE5 173 1.2386 + angle_coeff @angle:cx-n3-py harmonic 80.259 121.750 # SOURCE4_SOURCE5 20 1.0295 + angle_coeff @angle:cy-n3-cy harmonic 72.263 91.110 # SOURCE4_SOURCE5 36 0.9119 + angle_coeff @angle:cy-n3-hn harmonic 47.059 110.670 # SOURCE4_SOURCE5 48 0.9592 + angle_coeff @angle:f-n3-f harmonic 115.777 102.220 # SOURCE2 4 0.7562 + angle_coeff @angle:f-n3-hn harmonic 65.935 99.800 # SOURCE2 1 + angle_coeff @angle:hn-n3-hn harmonic 40.828 106.400 # SOURCE3_SOURCE5 2019 0.9777 + angle_coeff @angle:hn-n3-i harmonic 36.749 109.980 # SOURCE3 2 + angle_coeff @angle:hn-n3-n1 harmonic 64.085 110.170 # HF/6-31G* 1 + angle_coeff @angle:hn-n3-n2 harmonic 63.293 115.940 # SOURCE3 1 + angle_coeff @angle:hn-n3-n3 harmonic 61.180 107.680 # SOURCE3_SOURCE5 107 1.7630 + angle_coeff @angle:hn-n3-n4 harmonic 61.852 106.910 # SOURCE3_SOURCE5 18 0.7068 + angle_coeff @angle:hn-n3-n harmonic 62.520 108.120 # SOURCE3_SOURCE5 90 1.1435 + angle_coeff @angle:hn-n3-na harmonic 61.963 107.890 # SOURCE3 1 + angle_coeff @angle:hn-n3-nh harmonic 62.016 108.310 # SOURCE3_SOURCE5 85 1.2609 + angle_coeff @angle:hn-n3-no harmonic 63.767 104.780 # SOURCE3 3 1.1126 + angle_coeff @angle:hn-n3-o harmonic 65.058 113.320 # SOURCE3 3 4.3945 + angle_coeff @angle:hn-n3-oh harmonic 63.840 102.300 # SOURCE3_SOURCE5 14 0.6850 + angle_coeff @angle:hn-n3-os harmonic 62.667 102.750 # SOURCE3_SOURCE5 43 0.6086 + angle_coeff @angle:hn-n3-p2 harmonic 55.368 120.260 # SOURCE3 1 + angle_coeff @angle:hn-n3-p3 harmonic 54.032 116.890 # SOURCE3 9 3.8816 + angle_coeff @angle:hn-n3-p4 harmonic 56.121 113.050 # SOURCE3 2 + angle_coeff @angle:hn-n3-p5 harmonic 56.803 114.320 # SOURCE3_SOURCE5 63 1.6600 + angle_coeff @angle:hn-n3-s4 harmonic 42.895 109.140 # SOURCE3_SOURCE5 13 1.2903 + angle_coeff @angle:hn-n3-s harmonic 41.811 109.470 # SOURCE3 1 + angle_coeff @angle:hn-n3-s6 harmonic 45.126 109.600 # SOURCE4_SOURCE5 234 1.2605 + angle_coeff @angle:hn-n3-sh harmonic 43.414 108.670 # SOURCE3 3 2.5025 + angle_coeff @angle:hn-n3-ss harmonic 43.417 110.830 # SOURCE3_SOURCE5 14 1.1613 + angle_coeff @angle:hn-n3-sy harmonic 44.457 109.500 # SOURCE4_SOURCE5 617 0.8005 + angle_coeff @angle:i-n3-i harmonic 65.458 111.270 # SOURCE3 1 + angle_coeff @angle:n1-n3-n1 harmonic 111.350 113.210 # HF/6-31G* 1 + angle_coeff @angle:n2-n3-n2 harmonic 110.449 118.730 # SOURCE3 1 + angle_coeff @angle:n2-n3-o harmonic 113.356 114.910 # SOURCE3 1 + angle_coeff @angle:n3-n3-n3 harmonic 107.918 105.710 # SOURCE3 3 0.3561 + angle_coeff @angle:n4-n3-n4 harmonic 104.995 113.480 # SOURCE3 1 + angle_coeff @angle:n4-n3-nh harmonic 108.598 107.140 # SOURCE3 1 + angle_coeff @angle:na-n3-na harmonic 106.431 112.000 # SOURCE3 1 + angle_coeff @angle:nh-n3-nh harmonic 109.151 107.150 # SOURCE3 1 + angle_coeff @angle:n-n3-n harmonic 108.332 110.550 # SOURCE3 1 + angle_coeff @angle:no-n3-no harmonic 106.581 115.260 # SOURCE3 1 + angle_coeff @angle:oh-n3-oh harmonic 109.190 107.180 # SOURCE3 1 + angle_coeff @angle:o-n3-o harmonic 109.294 126.140 # SOURCE3 1 + angle_coeff @angle:o-n3-p2 harmonic 106.891 117.020 # SOURCE3 1 + angle_coeff @angle:o-n3-p4 harmonic 105.671 116.650 # SOURCE3 1 + angle_coeff @angle:o-n3-s4 harmonic 80.957 114.090 # SOURCE3 1 + angle_coeff @angle:o-n3-s6 harmonic 84.368 113.800 # SOURCE3 1 + angle_coeff @angle:o-n3-s harmonic 77.548 119.810 # SOURCE3 1 + angle_coeff @angle:os-n3-os harmonic 107.574 106.520 # SOURCE3 1 + angle_coeff @angle:p2-n3-p2 harmonic 103.056 130.130 # SOURCE3 1 + angle_coeff @angle:p3-n3-p3 harmonic 104.144 118.740 # SOURCE3 3 3.3755 + angle_coeff @angle:p4-n3-p4 harmonic 107.254 116.350 # SOURCE3 1 + angle_coeff @angle:p5-n3-p5 harmonic 107.603 119.420 # SOURCE3 1 + angle_coeff @angle:s4-n3-s4 harmonic 62.022 120.020 # SOURCE3 1 + angle_coeff @angle:s4-n3-s6 harmonic 63.190 120.950 # SOURCE3 1 + angle_coeff @angle:s6-n3-s6 harmonic 65.471 118.540 # SOURCE3_SOURCE5 18 1.1456 + angle_coeff @angle:sh-n3-sh harmonic 62.936 118.630 # SOURCE3 1 + angle_coeff @angle:sh-n3-ss harmonic 62.938 119.670 # SOURCE3 1 + angle_coeff @angle:s-n3-s harmonic 58.040 131.360 # SOURCE3 1 + angle_coeff @angle:ss-n3-ss harmonic 63.249 119.570 # SOURCE3 1 + angle_coeff @angle:br-n4-br harmonic 65.719 114.820 # SOURCE3 1 + angle_coeff @angle:br-n4-hn harmonic 41.251 108.440 # SOURCE3 7 0.5630 + angle_coeff @angle:c1-n4-c1 harmonic 67.454 113.870 # SOURCE3 1 + angle_coeff @angle:c1-n4-hn harmonic 48.997 110.190 # SOURCE3 7 1.0847 + angle_coeff @angle:c2-n4-c2 harmonic 63.556 112.580 # SOURCE3 1 + angle_coeff @angle:c2-n4-c3 harmonic 64.050 110.960 # SOURCE4 13 2.4632 + angle_coeff @angle:c2-n4-hn harmonic 46.094 110.370 # SOURCE3_SOURCE5 39 1.1227 + angle_coeff @angle:c3-n4-c3 harmonic 64.460 109.660 # SOURCE3_SOURCE5 2931 1.1695 + angle_coeff @angle:c3-n4-ca harmonic 64.770 110.530 # SOURCE4_SOURCE5 127 1.4968 + angle_coeff @angle:c3-n4-cc harmonic 64.438 111.040 # SOURCE4_SOURCE5 18 1.4876 + angle_coeff @angle:c3-n4-cl harmonic 71.792 108.040 # SOURCE3 3 + angle_coeff @angle:c3-n4-hn harmonic 46.193 110.110 # SOURCE3 100 1.3136 + angle_coeff @angle:c3-n4-n3 harmonic 83.568 107.700 # SOURCE3_SOURCE5 11 1.5498 + angle_coeff @angle:c3-n4-n4 harmonic 79.845 114.070 # SOURCE3 4 + angle_coeff @angle:c3-n4-n harmonic 82.738 109.740 # SOURCE4_SOURCE5 17 2.0520 + angle_coeff @angle:c3-n4-nh harmonic 81.141 111.730 # SOURCE3 1 + angle_coeff @angle:c3-n4-no harmonic 81.756 109.080 # SOURCE3 1 + angle_coeff @angle:c3-n4-o harmonic 84.145 110.520 # SOURCE3_SOURCE5 7 0.8910 + angle_coeff @angle:c3-n4-oh harmonic 82.047 113.730 # SOURCE3 1 + angle_coeff @angle:c3-n4-os harmonic 83.903 107.420 # SOURCE3 3 3.5920 + angle_coeff @angle:c3-n4-p2 harmonic 74.897 112.520 # SOURCE3 1 + angle_coeff @angle:c3-n4-p3 harmonic 77.458 110.730 # SOURCE3 3 2.1084 + angle_coeff @angle:c3-n4-p5 harmonic 78.172 113.220 # SOURCE3 3 0.4021 + angle_coeff @angle:c3-n4-s4 harmonic 58.766 108.230 # SOURCE3 3 0.4195 + angle_coeff @angle:c3-n4-s6 harmonic 59.297 111.560 # SOURCE3 3 1.8851 + angle_coeff @angle:c3-n4-s harmonic 60.776 113.550 # SOURCE3 1 + angle_coeff @angle:c3-n4-sh harmonic 60.690 115.810 # SOURCE3 1 + angle_coeff @angle:c3-n4-ss harmonic 61.231 113.680 # SOURCE3 3 1.1405 + angle_coeff @angle:ca-n4-ca harmonic 64.228 114.480 # SOURCE3 1 + angle_coeff @angle:ca-n4-hn harmonic 46.901 110.500 # SOURCE3_SOURCE5 23 1.4863 + angle_coeff @angle:c-n4-c harmonic 63.305 108.610 # SOURCE3 1 + angle_coeff @angle:c-n4-hn harmonic 44.970 111.120 # SOURCE3_SOURCE5 17 0.9627 + angle_coeff @angle:cl-n4-cl harmonic 79.101 114.910 # SOURCE3 1 + angle_coeff @angle:cl-n4-hn harmonic 48.065 108.870 # SOURCE3 7 0.7719 + angle_coeff @angle:f-n4-f harmonic 120.491 109.050 # SOURCE3 1 + angle_coeff @angle:f-n4-hn harmonic 67.122 108.390 # SOURCE3 4 + angle_coeff @angle:hn-n4-hn harmonic 40.020 108.300 # SOURCE3_SOURCE5 588 1.8224 + angle_coeff @angle:hn-n4-i harmonic 37.762 108.720 # SOURCE3 7 1.2717 + angle_coeff @angle:hn-n4-n1 harmonic 63.803 109.390 # HF/6-31G* 1 + angle_coeff @angle:hn-n4-n2 harmonic 52.071 109.680 # SOURCE3 19 0.6266 + angle_coeff @angle:hn-n4-n3 harmonic 60.801 110.400 # SOURCE3 11 0.7307 + angle_coeff @angle:hn-n4-n4 harmonic 59.235 108.660 # SOURCE3 18 1.2967 + angle_coeff @angle:hn-n4-n harmonic 61.091 109.080 # SOURCE3 13 1.6047 + angle_coeff @angle:hn-n4-na harmonic 60.973 109.090 # SOURCE3_SOURCE5 31 1.0459 + angle_coeff @angle:hn-n4-nh harmonic 59.568 109.920 # SOURCE3 12 0.7304 + angle_coeff @angle:hn-n4-no harmonic 60.590 104.380 # SOURCE3 2 + angle_coeff @angle:hn-n4-o harmonic 63.200 111.350 # SOURCE3_SOURCE5 11 1.4866 + angle_coeff @angle:hn-n4-oh harmonic 62.612 108.090 # SOURCE3 6 1.6728 + angle_coeff @angle:hn-n4-os harmonic 61.427 109.390 # SOURCE3 10 1.4403 + angle_coeff @angle:hn-n4-p2 harmonic 48.678 110.500 # SOURCE3 25 1.0664 + angle_coeff @angle:hn-n4-p3 harmonic 50.742 109.890 # SOURCE3 10 2.3870 + angle_coeff @angle:hn-n4-p4 harmonic 48.617 111.330 # SOURCE3 3 + angle_coeff @angle:hn-n4-p5 harmonic 52.339 110.000 # SOURCE3 10 1.0282 + angle_coeff @angle:hn-n4-py harmonic 48.319 117.890 # SOURCE3 8 + angle_coeff @angle:hn-n4-s4 harmonic 37.298 110.100 # SOURCE3 6 0.8471 + angle_coeff @angle:hn-n4-s harmonic 41.320 106.890 # SOURCE3 6 1.0775 + angle_coeff @angle:hn-n4-s6 harmonic 38.875 108.940 # SOURCE3 10 0.5715 + angle_coeff @angle:hn-n4-sh harmonic 41.549 108.560 # SOURCE3 6 0.8535 + angle_coeff @angle:hn-n4-ss harmonic 41.406 109.170 # SOURCE3 10 0.8455 + angle_coeff @angle:i-n4-i harmonic 64.315 118.490 # SOURCE3 1 + angle_coeff @angle:n1-n4-n1 harmonic 111.792 110.670 # HF/6-31G* 1 + angle_coeff @angle:n2-n4-n2 harmonic 91.394 108.640 # SOURCE3 1 + angle_coeff @angle:n3-n4-n3 harmonic 106.128 111.070 # SOURCE3 1 + angle_coeff @angle:n4-n4-n4 harmonic 100.290 115.490 # SOURCE3 1 + angle_coeff @angle:na-n4-na harmonic 101.917 119.600 # SOURCE3 1 + angle_coeff @angle:nh-n4-nh harmonic 104.319 109.380 # SOURCE3 1 + angle_coeff @angle:n-n4-n harmonic 102.552 118.620 # SOURCE3 1 + angle_coeff @angle:oh-n4-oh harmonic 109.836 108.190 # SOURCE3 1 + angle_coeff @angle:o-n4-o harmonic 106.848 120.970 # SOURCE3 1 + angle_coeff @angle:os-n4-os harmonic 110.159 104.400 # SOURCE3 1 + angle_coeff @angle:p2-n4-p2 harmonic 94.721 113.910 # SOURCE3 2 + angle_coeff @angle:p3-n4-p3 harmonic 94.786 121.380 # SOURCE3 1 + angle_coeff @angle:p5-n4-p5 harmonic 103.704 107.020 # SOURCE3 1 + angle_coeff @angle:py-n4-py harmonic 123.558 69.790 # SOURCE3 2 + angle_coeff @angle:s4-n4-s4 harmonic 56.264 115.430 # SOURCE3 1 + angle_coeff @angle:s6-n4-s6 harmonic 59.515 109.510 # SOURCE3 1 + angle_coeff @angle:sh-n4-sh harmonic 62.034 112.590 # SOURCE3 1 + angle_coeff @angle:s-n4-s harmonic 58.304 124.550 # SOURCE3 1 + angle_coeff @angle:ss-n4-ss harmonic 62.955 109.200 # SOURCE3 1 + angle_coeff @angle:br-na-br harmonic 61.086 123.000 # SOURCE3 1 + angle_coeff @angle:br-na-c2 harmonic 64.788 100.480 # SOURCE3 2 1.0536 + angle_coeff @angle:br-na-ca harmonic 58.177 124.810 # SOURCE3 1 + angle_coeff @angle:br-na-cc harmonic 58.230 124.620 # SOURCE3 3 0.5348 + angle_coeff @angle:br-na-cd harmonic 58.230 124.620 # SOURCE3 3 + angle_coeff @angle:br-na-nc harmonic 74.547 119.420 # SOURCE3 4 1.6703 + angle_coeff @angle:br-na-nd harmonic 74.550 119.420 # SOURCE3 4 + angle_coeff @angle:br-na-os harmonic 79.164 104.990 # SOURCE3 1 + angle_coeff @angle:br-na-p2 harmonic 78.377 121.010 # SOURCE3 1 + angle_coeff @angle:br-na-pc harmonic 78.871 120.260 # SOURCE3 3 2.1456 + angle_coeff @angle:br-na-pd harmonic 78.871 120.260 # SOURCE3 3 + angle_coeff @angle:br-na-ss harmonic 63.599 112.280 # SOURCE3 1 + angle_coeff @angle:c1-na-c1 harmonic 69.174 117.200 # SOURCE3 1 + angle_coeff @angle:c1-na-c2 harmonic 65.944 125.200 # SOURCE3 1 + angle_coeff @angle:c1-na-ca harmonic 67.645 120.570 # SOURCE3 1 + angle_coeff @angle:c1-na-cc harmonic 67.523 121.350 # SOURCE3 6 0.6517 + angle_coeff @angle:c1-na-cd harmonic 67.523 121.350 # SOURCE3 6 0.6517 + angle_coeff @angle:c1-na-nc harmonic 85.715 120.240 # SOURCE3 4 1.6849 + angle_coeff @angle:c1-na-nd harmonic 85.768 120.240 # SOURCE3 4 + angle_coeff @angle:c1-na-os harmonic 87.875 106.960 # SOURCE3 2 + angle_coeff @angle:c1-na-p2 harmonic 79.771 122.250 # SOURCE3 1 + angle_coeff @angle:c1-na-pc harmonic 80.652 121.480 # SOURCE3 3 2.1681 + angle_coeff @angle:c1-na-pd harmonic 80.652 121.480 # SOURCE3 3 + angle_coeff @angle:c1-na-ss harmonic 63.670 118.300 # SOURCE3 1 + angle_coeff @angle:c2-na-c2 harmonic 69.273 110.370 # SOURCE3 6 0.5121 + angle_coeff @angle:c2-na-c3 harmonic 65.723 117.200 # SOURCE3 2 + angle_coeff @angle:c2-na-ca harmonic 65.505 124.970 # SOURCE4_SOURCE5 19 0.9360 + angle_coeff @angle:c2-na-cc harmonic 65.181 126.550 # SOURCE3_SOURCE5 47 1.6996 + angle_coeff @angle:c2-na-cd harmonic 65.181 126.550 # SOURCE3_SOURCE5 47 1.6996 + angle_coeff @angle:c2-na-cl harmonic 73.039 101.010 # SOURCE3 2 1.5799 + angle_coeff @angle:c2-na-f harmonic 90.731 103.110 # SOURCE3 1 + angle_coeff @angle:c2-na-hn harmonic 47.660 119.280 # SOURCE3 14 6.6027 + angle_coeff @angle:c2-na-i harmonic 62.480 106.740 # SOURCE3 1 + angle_coeff @angle:c2-na-n1 harmonic 83.043 124.810 # HF/6-31G* 1 + angle_coeff @angle:c2-na-n2 harmonic 82.486 125.000 # SOURCE3 1 + angle_coeff @angle:c2-na-n3 harmonic 81.036 124.800 # SOURCE3 1 + angle_coeff @angle:c2-na-n4 harmonic 81.740 121.320 # SOURCE3 1 + angle_coeff @angle:c2-na-n harmonic 81.447 124.700 # SOURCE3 1 + angle_coeff @angle:c2-na-na harmonic 81.658 124.600 # SOURCE3 1 + angle_coeff @angle:c2-na-nc harmonic 84.246 120.800 # CORR_SOURCE5 5 1.0225 + angle_coeff @angle:c2-na-nd harmonic 84.294 120.800 # CORR_SOURCE5 5 1.0225 + angle_coeff @angle:c2-na-nh harmonic 81.563 124.980 # SOURCE3 1 + angle_coeff @angle:c2-na-no harmonic 80.798 124.200 # SOURCE3 1 + angle_coeff @angle:c2-na-o harmonic 85.559 125.900 # SOURCE3 1 + angle_coeff @angle:c2-na-oh harmonic 82.136 123.900 # SOURCE3 1 + angle_coeff @angle:c2-na-os harmonic 85.429 110.330 # SOURCE3 4 3.2172 + angle_coeff @angle:c2-na-p2 harmonic 79.329 122.140 # SOURCE3 1 + angle_coeff @angle:c2-na-p3 harmonic 77.626 126.100 # SOURCE3 1 + angle_coeff @angle:c2-na-p4 harmonic 84.849 125.000 # SOURCE3 1 + angle_coeff @angle:c2-na-p5 harmonic 79.565 125.100 # SOURCE3 1 + angle_coeff @angle:c2-na-pc harmonic 80.116 121.560 # SOURCE3 3 1.6252 + angle_coeff @angle:c2-na-pd harmonic 80.116 121.560 # SOURCE3 3 + angle_coeff @angle:c2-na-s4 harmonic 59.943 124.900 # SOURCE3 1 + angle_coeff @angle:c2-na-s6 harmonic 61.964 124.400 # SOURCE3 1 + angle_coeff @angle:c2-na-s harmonic 60.479 125.800 # SOURCE3 1 + angle_coeff @angle:c2-na-sh harmonic 61.837 125.100 # SOURCE3 1 + angle_coeff @angle:c2-na-ss harmonic 64.023 115.530 # SOURCE3 5 1.4036 + angle_coeff @angle:c3-na-c3 harmonic 62.214 125.590 # SOURCE3 1 + angle_coeff @angle:c3-na-ca harmonic 64.155 124.360 # SOURCE3 5 4.2557 + angle_coeff @angle:c3-na-cc harmonic 63.695 126.460 # SOURCE3_SOURCE5 2025 1.8293 + angle_coeff @angle:c3-na-cd harmonic 63.695 126.460 # SOURCE3_SOURCE5 2025 1.8293 + angle_coeff @angle:c3-na-cp harmonic 65.414 119.620 # SOURCE4_SOURCE5 17 0.4924 + angle_coeff @angle:c3-na-n2 harmonic 82.460 119.240 # SOURCE4_SOURCE5 15 0.8410 + angle_coeff @angle:c3-na-n harmonic 83.711 112.880 # SOURCE4_SOURCE5 34 0.6363 + angle_coeff @angle:c3-na-nc harmonic 82.430 120.180 # SOURCE3_SOURCE5 266 0.9487 + angle_coeff @angle:c3-na-nd harmonic 82.472 120.180 # SOURCE3_SOURCE5 266 0.9487 + angle_coeff @angle:c3-na-os harmonic 86.002 104.390 # SOURCE3 3 1.2017 + angle_coeff @angle:c3-na-p2 harmonic 78.161 123.120 # SOURCE3 1 + angle_coeff @angle:c3-na-pc harmonic 79.034 122.110 # SOURCE3 3 2.8504 + angle_coeff @angle:c3-na-pd harmonic 79.034 122.110 # SOURCE3 3 + angle_coeff @angle:c3-na-sh harmonic 65.096 110.280 # SOURCE3 1 + angle_coeff @angle:c3-na-ss harmonic 64.618 110.870 # SOURCE3 3 0.8260 + angle_coeff @angle:ca-na-ca harmonic 67.261 120.050 # SOURCE4_SOURCE5 899 1.7177 + angle_coeff @angle:ca-na-cc harmonic 69.377 113.150 # SOURCE3 18 9.8644 + angle_coeff @angle:ca-na-cd harmonic 69.377 113.150 # SOURCE3 18 9.8644 + angle_coeff @angle:ca-na-cl harmonic 65.846 124.790 # SOURCE3 1 + angle_coeff @angle:ca-na-cp harmonic 67.035 120.860 # SOURCE4_SOURCE5 58 1.3836 + angle_coeff @angle:ca-na-cx harmonic 64.141 124.590 # SOURCE4_SOURCE5 51 1.7589 + angle_coeff @angle:ca-na-f harmonic 85.915 116.400 # SOURCE3 1 + angle_coeff @angle:ca-na-hn harmonic 46.979 125.540 # SOURCE4_SOURCE5 1396 1.1217 + angle_coeff @angle:ca-na-i harmonic 58.530 121.620 # SOURCE3 1 + angle_coeff @angle:ca-na-n2 harmonic 85.072 119.070 # SOURCE4_SOURCE5 19 2.0667 + angle_coeff @angle:ca-na-n4 harmonic 82.602 120.190 # SOURCE3 1 + angle_coeff @angle:ca-na-n harmonic 82.849 122.000 # SOURCE3 1 + angle_coeff @angle:ca-na-na harmonic 82.443 123.760 # SOURCE3 1 + angle_coeff @angle:ca-na-nb harmonic 84.426 122.640 # SOURCE4_SOURCE5 30 1.1363 + angle_coeff @angle:ca-na-nc harmonic 85.867 117.850 # SOURCE3 6 3.6536 + angle_coeff @angle:ca-na-nd harmonic 85.918 117.850 # SOURCE3 6 + angle_coeff @angle:ca-na-nh harmonic 82.258 124.410 # SOURCE4_SOURCE5 15 1.3695 + angle_coeff @angle:ca-na-o harmonic 88.288 120.170 # SOURCE4_SOURCE5 161 1.3927 + angle_coeff @angle:ca-na-oh harmonic 83.969 120.050 # SOURCE3_SOURCE5 6 2.2969 + angle_coeff @angle:ca-na-os harmonic 86.259 109.460 # SOURCE3 1 + angle_coeff @angle:ca-na-p2 harmonic 78.367 125.850 # SOURCE3 1 + angle_coeff @angle:ca-na-p3 harmonic 78.367 124.380 # SOURCE3 1 + angle_coeff @angle:ca-na-p4 harmonic 85.239 124.970 # SOURCE3 1 + angle_coeff @angle:ca-na-p5 harmonic 80.389 123.300 # SOURCE3 1 + angle_coeff @angle:ca-na-pc harmonic 80.162 122.130 # SOURCE3 3 2.2393 + angle_coeff @angle:ca-na-pd harmonic 80.162 122.130 # SOURCE3 3 + angle_coeff @angle:ca-na-py harmonic 75.307 140.880 # SOURCE3 2 + angle_coeff @angle:ca-na-s4 harmonic 62.021 117.230 # SOURCE3 1 + angle_coeff @angle:ca-na-s6 harmonic 63.097 120.690 # SOURCE3 1 + angle_coeff @angle:ca-na-s harmonic 60.676 125.640 # SOURCE3 1 + angle_coeff @angle:ca-na-sh harmonic 61.938 125.440 # SOURCE3 1 + angle_coeff @angle:ca-na-ss harmonic 60.549 129.920 # SOURCE4_SOURCE5 17 0.1432 + angle_coeff @angle:cc-na-cc harmonic 70.492 109.900 # SOURCE3 109 1.5547 + angle_coeff @angle:cc-na-cd harmonic 65.316 128.010 # SOURCE3 1 + angle_coeff @angle:cc-na-ce harmonic 64.694 126.610 # SOURCE4_SOURCE5 16 0.5158 + angle_coeff @angle:cc-na-cl harmonic 65.922 124.610 # SOURCE3 3 0.5208 + angle_coeff @angle:cc-na-f harmonic 85.431 118.030 # SOURCE3 4 0.3081 + angle_coeff @angle:cc-na-hn harmonic 47.101 125.500 # CORR_SOURCE5 1758 1.2247 + angle_coeff @angle:cc-na-i harmonic 57.570 125.700 # SOURCE3 6 0.7821 + angle_coeff @angle:cc-na-n2 harmonic 84.478 121.090 # SOURCE3_SOURCE5 21 1.2340 + angle_coeff @angle:cc-na-n4 harmonic 82.458 120.910 # SOURCE3_SOURCE5 16 2.5151 + angle_coeff @angle:cc-na-n harmonic 87.346 110.050 # SOURCE3_SOURCE5 63 1.0193 + angle_coeff @angle:cc-na-na harmonic 84.774 117.360 # SOURCE3_SOURCE5 38 0.6452 + angle_coeff @angle:cc-na-nc harmonic 88.067 112.360 # SOURCE3_SOURCE5 209 2.0210 + angle_coeff @angle:cc-na-nd harmonic 83.137 126.230 # CORR_SOURCE5 157 1.3576 + angle_coeff @angle:cc-na-nh harmonic 82.640 123.590 # SOURCE3_SOURCE5 33 0.7437 + angle_coeff @angle:cc-na-no harmonic 81.621 123.440 # SOURCE3_SOURCE5 15 0.5273 + angle_coeff @angle:cc-na-o harmonic 86.644 125.210 # SOURCE3 10 0.0124 + angle_coeff @angle:cc-na-oh harmonic 83.278 122.380 # SOURCE3 10 0.1570 + angle_coeff @angle:cc-na-os harmonic 83.586 116.860 # CORR 48 + angle_coeff @angle:cc-na-p2 harmonic 78.409 125.860 # SOURCE3 14 2.2993 + angle_coeff @angle:cc-na-p3 harmonic 78.138 125.250 # SOURCE3 8 0.1998 + angle_coeff @angle:cc-na-p4 harmonic 84.394 127.730 # SOURCE3 7 3.6077 + angle_coeff @angle:cc-na-p5 harmonic 79.988 124.700 # SOURCE3 13 1.4225 + angle_coeff @angle:cc-na-s4 harmonic 61.070 121.030 # SOURCE3 10 0.5589 + angle_coeff @angle:cc-na-s6 harmonic 62.402 123.550 # SOURCE3_SOURCE5 18 0.8360 + angle_coeff @angle:cc-na-s harmonic 60.705 125.660 # SOURCE3 8 0.1880 + angle_coeff @angle:cc-na-sh harmonic 62.346 123.960 # SOURCE3 10 0.3424 + angle_coeff @angle:cc-na-ss harmonic 62.745 121.130 # CORR_SOURCE5 13 0.6360 + angle_coeff @angle:cd-na-cd harmonic 70.492 109.900 # SOURCE3 109 1.5547 + angle_coeff @angle:cd-na-cl harmonic 65.922 124.610 # SOURCE3 3 + angle_coeff @angle:cd-na-f harmonic 85.431 118.030 # SOURCE3 4 0.3081 + angle_coeff @angle:cd-na-hn harmonic 47.101 125.500 # CORR_SOURCE5 1758 1.2247 + angle_coeff @angle:cd-na-i harmonic 57.570 125.700 # SOURCE3 6 0.7821 + angle_coeff @angle:cd-na-n2 harmonic 84.478 121.090 # SOURCE3_SOURCE5 21 1.2340 + angle_coeff @angle:cd-na-n4 harmonic 82.458 120.910 # SOURCE3_SOURCE5 16 2.5151 + angle_coeff @angle:cd-na-n harmonic 87.346 110.050 # SOURCE3_SOURCE5 63 1.0193 + angle_coeff @angle:cd-na-na harmonic 84.774 117.360 # SOURCE3_SOURCE5 38 0.6452 + angle_coeff @angle:cd-na-nc harmonic 83.088 126.230 # CORR_SOURCE5 157 1.3576 + angle_coeff @angle:cd-na-nd harmonic 88.120 112.360 # SOURCE3_SOURCE5 209 2.0210 + angle_coeff @angle:cd-na-nh harmonic 82.624 123.640 # SOURCE3_SOURCE5 34 0.8283 + angle_coeff @angle:cd-na-no harmonic 81.621 123.440 # SOURCE3_SOURCE5 15 0.5273 + angle_coeff @angle:cd-na-o harmonic 86.644 125.210 # SOURCE3 10 0.0124 + angle_coeff @angle:cd-na-oh harmonic 83.278 122.380 # SOURCE3 10 0.1570 + angle_coeff @angle:cd-na-os harmonic 83.586 116.860 # CORR 48 + angle_coeff @angle:cd-na-p2 harmonic 78.409 125.860 # SOURCE3 14 2.2993 + angle_coeff @angle:cd-na-p3 harmonic 78.138 125.250 # SOURCE3 8 0.1998 + angle_coeff @angle:cd-na-p4 harmonic 84.394 127.730 # SOURCE3 7 + angle_coeff @angle:cd-na-p5 harmonic 79.988 124.700 # SOURCE3 13 1.4225 + angle_coeff @angle:cd-na-s4 harmonic 61.070 121.030 # SOURCE3 10 0.5589 + angle_coeff @angle:cd-na-s6 harmonic 62.402 123.550 # SOURCE3_SOURCE5 18 0.8360 + angle_coeff @angle:cd-na-s harmonic 60.705 125.660 # SOURCE3 8 0.1880 + angle_coeff @angle:cd-na-sh harmonic 62.346 123.960 # SOURCE3 10 0.3424 + angle_coeff @angle:cd-na-ss harmonic 62.745 121.130 # CORR_SOURCE5 13 0.6360 + angle_coeff @angle:cl-na-cl harmonic 73.099 122.800 # SOURCE3 1 + angle_coeff @angle:cl-na-nc harmonic 84.560 119.360 # SOURCE3 4 1.7128 + angle_coeff @angle:cl-na-nd harmonic 84.574 119.360 # SOURCE3 4 + angle_coeff @angle:cl-na-os harmonic 88.543 106.580 # SOURCE3 1 + angle_coeff @angle:cl-na-p2 harmonic 86.459 121.290 # SOURCE3 1 + angle_coeff @angle:cl-na-pc harmonic 87.107 120.510 # SOURCE3 3 2.1985 + angle_coeff @angle:cl-na-pd harmonic 87.107 120.510 # SOURCE3 3 + angle_coeff @angle:cl-na-ss harmonic 70.427 111.910 # SOURCE3 1 + angle_coeff @angle:f-na-f harmonic 106.388 120.200 # SOURCE3 1 + angle_coeff @angle:f-na-nc harmonic 107.856 118.050 # SOURCE3 4 1.7931 + angle_coeff @angle:f-na-nd harmonic 107.917 118.050 # SOURCE3 4 + angle_coeff @angle:f-na-os harmonic 111.494 103.860 # SOURCE3 1 + angle_coeff @angle:f-na-p2 harmonic 101.527 119.950 # SOURCE3 1 + angle_coeff @angle:f-na-pc harmonic 102.647 119.100 # SOURCE3 3 2.3967 + angle_coeff @angle:f-na-pd harmonic 102.647 119.100 # SOURCE3 3 + angle_coeff @angle:f-na-ss harmonic 83.972 108.010 # SOURCE3 1 + angle_coeff @angle:hn-na-hn harmonic 39.315 116.800 # SOURCE3 1 + angle_coeff @angle:hn-na-n harmonic 61.525 111.440 # SOURCE4_SOURCE5 14 1.2883 + angle_coeff @angle:hn-na-nc harmonic 61.377 119.550 # SOURCE3_SOURCE5 196 1.0024 + angle_coeff @angle:hn-na-nd harmonic 61.443 119.550 # SOURCE3_SOURCE5 196 1.0024 + angle_coeff @angle:hn-na-os harmonic 62.765 102.120 # SOURCE3_SOURCE5 20 2.5614 + angle_coeff @angle:hn-na-p2 harmonic 52.077 122.520 # SOURCE3 1 + angle_coeff @angle:hn-na-pc harmonic 52.878 121.480 # SOURCE3 3 2.9355 + angle_coeff @angle:hn-na-pd harmonic 52.878 121.480 # SOURCE3 3 + angle_coeff @angle:hn-na-ss harmonic 42.530 113.950 # SOURCE3 1 + angle_coeff @angle:i-na-i harmonic 63.587 124.200 # SOURCE3 1 + angle_coeff @angle:i-na-nc harmonic 73.745 120.030 # SOURCE3 4 2.0032 + angle_coeff @angle:i-na-nd harmonic 73.742 120.030 # SOURCE3 4 + angle_coeff @angle:i-na-os harmonic 77.062 109.910 # SOURCE3 1 + angle_coeff @angle:i-na-p2 harmonic 78.740 122.280 # SOURCE3 1 + angle_coeff @angle:i-na-pc harmonic 79.219 121.400 # SOURCE3 3 2.4763 + angle_coeff @angle:i-na-pd harmonic 79.219 121.400 # SOURCE3 3 + angle_coeff @angle:i-na-ss harmonic 62.502 118.400 # SOURCE3 1 + angle_coeff @angle:n2-na-n2 harmonic 108.256 116.710 # SOURCE3 1 + angle_coeff @angle:n2-na-nc harmonic 107.238 119.960 # SOURCE3 4 4.5041 + angle_coeff @angle:n2-na-nd harmonic 107.304 119.960 # SOURCE3 4 + angle_coeff @angle:n2-na-os harmonic 107.573 111.530 # SOURCE3 1 + angle_coeff @angle:n2-na-p2 harmonic 98.756 124.880 # SOURCE3 1 + angle_coeff @angle:n2-na-pc harmonic 100.212 123.180 # SOURCE3 3 4.7947 + angle_coeff @angle:n2-na-pd harmonic 100.212 123.180 # SOURCE3 3 + angle_coeff @angle:n2-na-ss harmonic 77.611 124.640 # SOURCE3 1 + angle_coeff @angle:n3-na-n3 harmonic 101.150 124.000 # SOURCE3 1 + angle_coeff @angle:n4-na-n4 harmonic 105.460 111.700 # SOURCE3 1 + angle_coeff @angle:n4-na-nc harmonic 106.051 116.440 # SOURCE3 4 3.6604 + angle_coeff @angle:n4-na-nd harmonic 106.108 116.440 # SOURCE3 4 + angle_coeff @angle:n4-na-os harmonic 109.494 102.970 # SOURCE3 1 + angle_coeff @angle:n4-na-p2 harmonic 98.207 123.560 # SOURCE3 1 + angle_coeff @angle:n4-na-pc harmonic 99.557 121.980 # SOURCE3 3 4.4884 + angle_coeff @angle:n4-na-pd harmonic 99.557 121.980 # SOURCE3 3 + angle_coeff @angle:na-na-na harmonic 102.688 123.600 # SOURCE3 1 + angle_coeff @angle:na-na-nc harmonic 106.027 119.640 # SOURCE3 4 1.6920 + angle_coeff @angle:na-na-nd harmonic 106.088 119.640 # SOURCE3 4 + angle_coeff @angle:na-na-os harmonic 107.416 109.470 # SOURCE3 1 + angle_coeff @angle:na-na-p2 harmonic 99.520 121.720 # SOURCE3 1 + angle_coeff @angle:na-na-pc harmonic 100.604 120.910 # SOURCE3 3 2.3033 + angle_coeff @angle:na-na-pd harmonic 100.604 120.910 # SOURCE3 3 + angle_coeff @angle:na-na-ss harmonic 79.845 116.500 # SOURCE3 1 + angle_coeff @angle:nc-na-nc harmonic 109.391 116.300 # SOURCE3_SOURCE5 57 1.3191 + angle_coeff @angle:nc-na-nd harmonic 106.540 122.760 # SOURCE4_SOURCE5 12 0.1496 + angle_coeff @angle:nc-na-nh harmonic 105.667 120.550 # SOURCE3 8 1.1436 + angle_coeff @angle:nc-na-no harmonic 104.829 119.210 # SOURCE3_SOURCE5 9 1.2751 + angle_coeff @angle:nc-na-o harmonic 110.789 122.790 # SOURCE3 6 1.3154 + angle_coeff @angle:nc-na-oh harmonic 106.562 119.220 # SOURCE3 4 1.7201 + angle_coeff @angle:nc-na-os harmonic 104.244 119.650 # SOURCE3 4 1.5019 + angle_coeff @angle:nc-na-p2 harmonic 100.917 119.990 # SOURCE3 4 3.6009 + angle_coeff @angle:nc-na-p3 harmonic 100.275 120.070 # SOURCE3 4 3.7188 + angle_coeff @angle:nc-na-p4 harmonic 109.789 119.770 # SOURCE3 3 0.3747 + angle_coeff @angle:nc-na-p5 harmonic 102.963 118.950 # SOURCE3 4 3.1194 + angle_coeff @angle:nc-na-pc harmonic 102.284 118.660 # SOURCE3 27 1.5082 + angle_coeff @angle:nc-na-s4 harmonic 77.292 119.200 # SOURCE3 4 2.3841 + angle_coeff @angle:nc-na-s6 harmonic 79.850 119.240 # SOURCE3 4 2.2262 + angle_coeff @angle:nc-na-s harmonic 77.325 122.260 # SOURCE3 4 0.9173 + angle_coeff @angle:nc-na-sh harmonic 79.494 120.500 # SOURCE3 4 1.5016 + angle_coeff @angle:nc-na-ss harmonic 79.073 120.500 # SOURCE3 4 1.5615 + angle_coeff @angle:nd-na-nd harmonic 109.528 116.300 # SOURCE3_SOURCE5 57 1.3191 + angle_coeff @angle:nd-na-nh harmonic 105.728 120.550 # SOURCE3 8 + angle_coeff @angle:nd-na-no harmonic 104.885 119.210 # SOURCE3_SOURCE5 5 1.0113 + angle_coeff @angle:nd-na-o harmonic 110.874 122.790 # SOURCE3 6 + angle_coeff @angle:nd-na-oh harmonic 106.624 119.220 # SOURCE3 4 + angle_coeff @angle:nd-na-os harmonic 104.299 119.650 # SOURCE3 4 + angle_coeff @angle:nd-na-p2 harmonic 100.941 119.990 # SOURCE3 4 + angle_coeff @angle:nd-na-p3 harmonic 100.297 120.070 # SOURCE3 4 + angle_coeff @angle:nd-na-p4 harmonic 109.833 119.770 # SOURCE3 3 + angle_coeff @angle:nd-na-p5 harmonic 102.991 118.950 # SOURCE3 4 + angle_coeff @angle:nd-na-pd harmonic 102.309 118.660 # SOURCE3 27 + angle_coeff @angle:nd-na-s4 harmonic 77.307 119.200 # SOURCE3 4 + angle_coeff @angle:nd-na-s6 harmonic 79.870 119.240 # SOURCE3 4 + angle_coeff @angle:nd-na-s harmonic 77.342 122.260 # SOURCE3 4 + angle_coeff @angle:nd-na-sh harmonic 79.514 120.500 # SOURCE3 4 + angle_coeff @angle:nd-na-ss harmonic 79.092 120.500 # SOURCE3 4 + angle_coeff @angle:nh-na-nh harmonic 102.761 123.600 # SOURCE3 1 + angle_coeff @angle:nh-na-os harmonic 106.530 111.370 # SOURCE3 1 + angle_coeff @angle:nh-na-p2 harmonic 99.889 120.860 # SOURCE3 1 + angle_coeff @angle:nh-na-pc harmonic 100.842 120.380 # SOURCE3 6 1.3513 + angle_coeff @angle:nh-na-pd harmonic 100.842 120.380 # SOURCE3 6 + angle_coeff @angle:nh-na-ss harmonic 81.320 112.350 # SOURCE3 2 5.2951 + angle_coeff @angle:n-na-n harmonic 102.160 123.800 # SOURCE3 1 + angle_coeff @angle:n-na-nc harmonic 105.685 119.850 # SOURCE3 4 1.6156 + angle_coeff @angle:n-na-nd harmonic 105.745 119.850 # SOURCE3 4 + angle_coeff @angle:no-na-no harmonic 100.609 122.800 # SOURCE3 1 + angle_coeff @angle:no-na-os harmonic 107.653 106.550 # SOURCE3 1 + angle_coeff @angle:no-na-pc harmonic 100.336 120.110 # SOURCE3 3 2.0821 + angle_coeff @angle:no-na-pd harmonic 100.336 120.110 # SOURCE3 3 + angle_coeff @angle:n-na-os harmonic 109.608 104.710 # SOURCE3 1 + angle_coeff @angle:no-na-ss harmonic 79.903 114.950 # SOURCE3 1 + angle_coeff @angle:n-na-p2 harmonic 99.572 121.350 # SOURCE3 1 + angle_coeff @angle:n-na-pc harmonic 100.611 120.640 # SOURCE3 3 2.0168 + angle_coeff @angle:n-na-pd harmonic 100.611 120.640 # SOURCE3 3 + angle_coeff @angle:n-na-ss harmonic 79.899 116.100 # SOURCE3 1 + angle_coeff @angle:oh-na-oh harmonic 103.905 122.200 # SOURCE3 1 + angle_coeff @angle:oh-na-p2 harmonic 100.050 120.760 # SOURCE3 1 + angle_coeff @angle:oh-na-pc harmonic 101.133 119.990 # SOURCE3 3 2.1734 + angle_coeff @angle:oh-na-pd harmonic 101.133 119.990 # SOURCE3 3 + angle_coeff @angle:oh-na-ss harmonic 81.173 113.040 # SOURCE3 1 + angle_coeff @angle:o-na-o harmonic 114.875 126.200 # SOURCE3 1 + angle_coeff @angle:o-na-os harmonic 108.116 118.780 # SOURCE3_SOURCE5 6 0.4047 + angle_coeff @angle:o-na-p2 harmonic 100.973 122.800 # SOURCE3 1 + angle_coeff @angle:o-na-pc harmonic 102.067 122.340 # SOURCE3 3 1.2908 + angle_coeff @angle:o-na-pd harmonic 102.067 122.340 # SOURCE3 3 + angle_coeff @angle:os-na-os harmonic 108.379 104.450 # SOURCE3 2 0.0983 + angle_coeff @angle:os-na-p2 harmonic 100.391 117.860 # SOURCE3 1 + angle_coeff @angle:os-na-p3 harmonic 105.930 104.700 # SOURCE3 1 + angle_coeff @angle:os-na-p5 harmonic 104.736 111.410 # SOURCE3 1 + angle_coeff @angle:os-na-pc harmonic 100.242 119.910 # SOURCE3 3 1.9002 + angle_coeff @angle:os-na-pd harmonic 100.242 119.910 # SOURCE3 3 + angle_coeff @angle:os-na-s4 harmonic 81.006 105.880 # SOURCE3 2 + angle_coeff @angle:os-na-s6 harmonic 81.137 112.000 # SOURCE3 2 + angle_coeff @angle:os-na-ss harmonic 81.670 109.640 # SOURCE3 3 4.1395 + angle_coeff @angle:p2-na-p2 harmonic 102.084 120.910 # SOURCE3 1 + angle_coeff @angle:p2-na-p3 harmonic 100.105 124.800 # SOURCE3 1 + angle_coeff @angle:p2-na-p5 harmonic 101.778 123.990 # SOURCE3 1 + angle_coeff @angle:p2-na-pc harmonic 102.658 120.720 # SOURCE3 3 0.2407 + angle_coeff @angle:p2-na-pd harmonic 102.658 120.720 # SOURCE3 3 + angle_coeff @angle:p2-na-s4 harmonic 78.032 122.470 # SOURCE3 1 + angle_coeff @angle:p2-na-s6 harmonic 79.617 122.500 # SOURCE3 1 + angle_coeff @angle:p2-na-s harmonic 78.874 121.850 # SOURCE3 1 + angle_coeff @angle:p2-na-sh harmonic 79.900 121.750 # SOURCE3 1 + angle_coeff @angle:p2-na-ss harmonic 79.600 121.880 # SOURCE3 1 + angle_coeff @angle:p3-na-p3 harmonic 99.027 126.600 # SOURCE3 1 + angle_coeff @angle:p3-na-pc harmonic 101.182 123.320 # SOURCE3 3 4.1781 + angle_coeff @angle:p3-na-pd harmonic 101.182 123.320 # SOURCE3 3 + angle_coeff @angle:p5-na-p5 harmonic 102.554 124.600 # SOURCE3 1 + angle_coeff @angle:p5-na-pc harmonic 102.835 122.690 # SOURCE3 3 3.6738 + angle_coeff @angle:p5-na-pd harmonic 102.835 122.690 # SOURCE3 3 + angle_coeff @angle:p5-na-ss harmonic 81.516 118.520 # SOURCE3 1 + angle_coeff @angle:pc-na-pc harmonic 103.141 120.780 # SOURCE3 27 1.6457 + angle_coeff @angle:pc-na-s4 harmonic 78.694 121.510 # SOURCE3 3 2.7242 + angle_coeff @angle:pc-na-s6 harmonic 80.329 121.550 # SOURCE3 3 2.7065 + angle_coeff @angle:pc-na-s harmonic 79.371 121.470 # SOURCE3 3 1.0668 + angle_coeff @angle:pc-na-sh harmonic 80.524 121.080 # SOURCE3 3 1.8942 + angle_coeff @angle:pc-na-ss harmonic 80.219 121.200 # SOURCE3 3 1.9295 + angle_coeff @angle:pd-na-pd harmonic 103.141 120.780 # SOURCE3 27 + angle_coeff @angle:pd-na-s4 harmonic 78.694 121.510 # SOURCE3 3 + angle_coeff @angle:pd-na-s6 harmonic 80.329 121.550 # SOURCE3 3 + angle_coeff @angle:pd-na-s harmonic 79.371 121.470 # SOURCE3 3 + angle_coeff @angle:pd-na-sh harmonic 80.524 121.080 # SOURCE3 3 + angle_coeff @angle:pd-na-ss harmonic 80.219 121.200 # SOURCE3 3 + angle_coeff @angle:py-na-py harmonic 129.638 78.250 # SOURCE3 1 + angle_coeff @angle:s4-na-s4 harmonic 59.656 124.200 # SOURCE3 1 + angle_coeff @angle:s4-na-s6 harmonic 63.782 112.860 # SOURCE3 1 + angle_coeff @angle:s4-na-ss harmonic 63.885 111.920 # SOURCE3 1 + angle_coeff @angle:s6-na-s6 harmonic 62.342 123.200 # SOURCE3 1 + angle_coeff @angle:s6-na-ss harmonic 63.225 119.100 # SOURCE3 1 + angle_coeff @angle:sh-na-sh harmonic 62.052 124.600 # SOURCE3 1 + angle_coeff @angle:sh-na-ss harmonic 63.339 118.790 # SOURCE3 1 + angle_coeff @angle:s-na-s harmonic 60.168 126.000 # SOURCE3 1 + angle_coeff @angle:s-na-ss harmonic 64.260 112.490 # SOURCE3 1 + angle_coeff @angle:ss-na-ss harmonic 64.658 113.240 # SOURCE3 2 6.6084 + angle_coeff @angle:sy-na-sy harmonic 62.187 123.200 # SOURCE3 1 + angle_coeff @angle:ca-nb-ca harmonic 70.356 117.220 # SOURCE3_SOURCE5 3343 1.0306 + angle_coeff @angle:ca-nb-cp harmonic 70.116 118.050 # SOURCE4_SOURCE5 160 0.7542 + angle_coeff @angle:ca-nb-cq harmonic 70.116 118.050 # SOURCE4_SOURCE5 102 0.7384 + angle_coeff @angle:ca-nb-nb harmonic 87.237 120.050 # SOURCE3_SOURCE5 159 0.6095 + angle_coeff @angle:cp-nb-nb harmonic 86.918 120.960 # SOURCE4_SOURCE5 32 0.5601 + angle_coeff @angle:nb-nb-nb harmonic 109.020 121.040 # SOURCE3 1 + angle_coeff @angle:br-n-br harmonic 67.176 116.200 # SOURCE3 1 + angle_coeff @angle:br-n-c harmonic 62.729 121.250 # SOURCE3_SOURCE5 10 1.6266 + angle_coeff @angle:br-n-ca harmonic 63.323 118.190 # SOURCE3 1 + angle_coeff @angle:br-n-cc harmonic 63.525 118.190 # SOURCE3 1 + angle_coeff @angle:br-n-cd harmonic 63.525 118.190 # SOURCE3 1 + angle_coeff @angle:c1-n-c1 harmonic 75.677 102.690 # SOURCE3 1 + angle_coeff @angle:c1-n-ca harmonic 68.108 118.880 # SOURCE3 1 + angle_coeff @angle:c1-n-cc harmonic 68.972 118.880 # SOURCE3 1 + angle_coeff @angle:c1-n-cd harmonic 68.972 118.880 # SOURCE3 1 + angle_coeff @angle:c2-n-c2 harmonic 67.455 116.750 # SOURCE3 1 + angle_coeff @angle:c2-n-c3 harmonic 64.992 120.100 # SOURCE4_SOURCE5 62 2.3796 + angle_coeff @angle:c2-n-ca harmonic 67.208 116.540 # SOURCE3 1 + angle_coeff @angle:c2-n-cc harmonic 67.963 116.540 # SOURCE3 1 + angle_coeff @angle:c2-n-cd harmonic 67.963 116.540 # SOURCE3 1 + angle_coeff @angle:c2-n-hn harmonic 47.988 117.900 # SOURCE4_SOURCE5 115 1.4688 + angle_coeff @angle:c3-n-c3 harmonic 64.880 115.640 # SOURCE4_SOURCE5 1017 2.0256 + angle_coeff @angle:c3-n-ca harmonic 64.801 119.830 # SOURCE4_SOURCE5 448 1.9961 + angle_coeff @angle:c3-n-cc harmonic 65.172 120.850 # CORR_SOURCE5 523 1.4176 + angle_coeff @angle:c3-n-cd harmonic 65.172 120.850 # CORR_SOURCE5 523 1.4176 + angle_coeff @angle:c3-n-cy harmonic 64.307 117.080 # SOURCE4_SOURCE5 120 1.3701 + angle_coeff @angle:c3-n-hn harmonic 46.147 117.680 # SOURCE3_SOURCE5 1934 1.5065 + angle_coeff @angle:c3-n-n2 harmonic 81.830 121.710 # SOURCE4_SOURCE5 131 1.2251 + angle_coeff @angle:c3-n-n harmonic 82.901 115.390 # SOURCE4_SOURCE5 28 1.0963 + angle_coeff @angle:c3-n-nc harmonic 84.094 115.280 # CORR_SOURCE5 61 0.8561 + angle_coeff @angle:c3-n-nd harmonic 84.094 115.280 # CORR_SOURCE5 61 0.8561 + angle_coeff @angle:c3-n-oh harmonic 83.734 112.970 # SOURCE4_SOURCE5 82 0.8203 + angle_coeff @angle:c3-n-os harmonic 83.821 112.540 # SOURCE4_SOURCE5 42 1.7642 + angle_coeff @angle:c3-n-sy harmonic 62.308 120.880 # SOURCE4_SOURCE5 13 1.1569 + angle_coeff @angle:ca-n-ca harmonic 66.671 117.370 # SOURCE4_SOURCE5 99 1.5139 + angle_coeff @angle:ca-n-cc harmonic 68.390 114.010 # CORR_SOURCE5 53 1.0051 + angle_coeff @angle:ca-n-cd harmonic 68.390 114.010 # CORR_SOURCE5 53 1.0051 + angle_coeff @angle:ca-n-cl harmonic 71.199 117.720 # SOURCE3 1 + angle_coeff @angle:ca-n-f harmonic 86.043 114.920 # SOURCE3 1 + angle_coeff @angle:ca-n-hn harmonic 47.989 116.000 # SOURCE4_SOURCE5 1451 1.8612 + angle_coeff @angle:ca-n-i harmonic 59.954 119.300 # SOURCE3 1 + angle_coeff @angle:ca-n-n2 harmonic 83.352 122.020 # SOURCE4_SOURCE5 12 0.9977 + angle_coeff @angle:ca-n-n4 harmonic 80.984 122.980 # SOURCE3 1 + angle_coeff @angle:ca-n-n harmonic 83.301 118.550 # SOURCE4_SOURCE5 46 0.3283 + angle_coeff @angle:ca-n-na harmonic 82.957 119.300 # SOURCE4_SOURCE5 47 0.3131 + angle_coeff @angle:ca-n-nc harmonic 85.318 116.500 # CORR_SOURCE5 14 1.6910 + angle_coeff @angle:ca-n-nd harmonic 85.318 116.500 # CORR_SOURCE5 14 1.6910 + angle_coeff @angle:ca-n-nh harmonic 84.129 116.450 # SOURCE3 1 + angle_coeff @angle:ca-n-p2 harmonic 83.158 112.320 # SOURCE3 1 + angle_coeff @angle:ca-n-p3 harmonic 77.529 125.110 # SOURCE3 1 + angle_coeff @angle:ca-n-s4 harmonic 62.152 118.400 # SOURCE3 1 + angle_coeff @angle:ca-n-s6 harmonic 63.800 117.320 # SOURCE3 1 + angle_coeff @angle:ca-n-ss harmonic 63.794 116.600 # SOURCE3 1 + angle_coeff @angle:c-n-c1 harmonic 69.561 117.040 # SOURCE3 1 + angle_coeff @angle:c-n-c2 harmonic 66.426 122.150 # SOURCE3 9 5.1016 + angle_coeff @angle:c-n-c3 harmonic 65.252 120.690 # SOURCE3_SOURCE5 4556 2.1510 + angle_coeff @angle:c3-nc-cd harmonic 69.940 109.510 # SOURCE3 9 5.4142 + angle_coeff @angle:c-n-c harmonic 65.616 127.080 # SOURCE4_SOURCE5 1415 2.1363 + angle_coeff @angle:c-n-ca harmonic 65.694 123.710 # SOURCE3 10 3.8159 + angle_coeff @angle:ca-nc-ca harmonic 71.962 109.950 # SOURCE3 1 + angle_coeff @angle:ca-nc-cd harmonic 74.608 104.880 # CORR_SOURCE5 766 1.8814 + angle_coeff @angle:ca-nc-n harmonic 92.070 104.690 # CORR 2 + angle_coeff @angle:ca-nc-na harmonic 93.072 102.760 # CORR_SOURCE5 25 0.7558 + angle_coeff @angle:ca-nc-os harmonic 90.719 104.480 # CORR_SOURCE5 16 0.1832 + angle_coeff @angle:ca-nc-ss harmonic 70.369 107.070 # SOURCE3_SOURCE5 17 0.3771 + angle_coeff @angle:c-n-cc harmonic 66.579 123.270 # SOURCE3_SOURCE5 805 2.2636 + angle_coeff @angle:c-nc-ca harmonic 67.794 120.660 # CORR 2 + angle_coeff @angle:cc-n-cc harmonic 70.783 108.920 # SOURCE3 11 0.3167 + angle_coeff @angle:cc-nc-cc harmonic 73.120 103.760 # CORR_SOURCE5 6 0.0439 + angle_coeff @angle:cc-nc-cd harmonic 73.871 105.490 # CORR_SOURCE5 1810 1.9032 + angle_coeff @angle:c-nc-cd harmonic 68.639 120.490 # CORR_SOURCE5 205 1.1318 + angle_coeff @angle:cc-n-cl harmonic 71.592 117.720 # SOURCE3 1 + angle_coeff @angle:cc-nc-na harmonic 92.369 102.970 # SOURCE3 1 + angle_coeff @angle:cc-nc-nd harmonic 91.732 108.620 # SOURCE3_SOURCE5 82 1.5614 + angle_coeff @angle:c-n-cd harmonic 66.579 123.270 # SOURCE3_SOURCE5 805 2.2636 + angle_coeff @angle:cd-nc-cd harmonic 71.496 117.300 # CORR_SOURCE5 18 0.3907 + angle_coeff @angle:cd-nc-n harmonic 88.099 117.190 # CORR 64 + angle_coeff @angle:cd-nc-na harmonic 93.753 103.820 # SOURCE3_SOURCE5 919 1.7445 + angle_coeff @angle:cd-nc-nc harmonic 91.676 107.820 # CORR_SOURCE5 457 1.5268 + angle_coeff @angle:cd-nc-os harmonic 91.671 104.670 # CORR_SOURCE5 184 0.8204 + angle_coeff @angle:cd-nc-ss harmonic 70.508 108.070 # CORR_SOURCE5 95 1.3804 + angle_coeff @angle:c-n-ce harmonic 63.457 131.380 # SOURCE4_SOURCE5 371 1.5975 + angle_coeff @angle:cc-n-f harmonic 87.015 114.920 # SOURCE3 1 + angle_coeff @angle:cc-n-hn harmonic 48.285 119.260 # CORR_SOURCE5 459 1.7223 + angle_coeff @angle:cc-n-i harmonic 59.973 119.300 # SOURCE3 1 + angle_coeff @angle:c-n-cl harmonic 72.034 116.350 # SOURCE4 11 0.6829 + angle_coeff @angle:cc-n-n2 harmonic 88.496 110.870 # SOURCE3 1 + angle_coeff @angle:cc-n-n harmonic 83.245 121.370 # SOURCE3 1 + angle_coeff @angle:cc-n-na harmonic 84.492 117.570 # SOURCE3 1 + angle_coeff @angle:cc-n-nc harmonic 88.107 111.890 # CORR_SOURCE5 20 0.7095 + angle_coeff @angle:cc-n-nh harmonic 84.683 117.520 # SOURCE3 1 + angle_coeff @angle:cc-n-no harmonic 83.522 115.920 # SOURCE3 1 + angle_coeff @angle:cc-n-o harmonic 88.192 120.540 # SOURCE3 1 + angle_coeff @angle:cc-n-oh harmonic 83.905 119.300 # SOURCE3_SOURCE5 7 0.3237 + angle_coeff @angle:cc-n-os harmonic 85.167 115.560 # SOURCE3 1 + angle_coeff @angle:cc-n-p2 harmonic 83.596 112.320 # SOURCE3 1 + angle_coeff @angle:cc-n-p3 harmonic 77.892 125.110 # SOURCE3 1 + angle_coeff @angle:cc-n-p5 harmonic 81.119 121.000 # SOURCE3 1 + angle_coeff @angle:cc-n-s4 harmonic 62.446 118.400 # SOURCE3 1 + angle_coeff @angle:cc-n-s6 harmonic 64.150 117.320 # SOURCE3 1 + angle_coeff @angle:cc-n-s harmonic 62.506 118.290 # SOURCE3 1 + angle_coeff @angle:cc-n-sh harmonic 63.393 119.130 # SOURCE3 1 + angle_coeff @angle:cc-n-ss harmonic 64.137 116.600 # SOURCE3 2 + angle_coeff @angle:c-n-cx harmonic 65.394 122.070 # SOURCE4 11 1.9478 + angle_coeff @angle:c-n-cy harmonic 73.625 94.220 # SOURCE4_SOURCE5 674 1.8186 + angle_coeff @angle:cd-n-cd harmonic 70.783 108.920 # SOURCE3 11 + angle_coeff @angle:cd-n-cl harmonic 71.592 117.720 # SOURCE3 1 + angle_coeff @angle:cd-n-f harmonic 87.015 114.920 # SOURCE3 1 + angle_coeff @angle:cd-n-hn harmonic 48.285 119.260 # CORR_SOURCE5 459 1.7223 + angle_coeff @angle:cd-n-i harmonic 59.973 119.300 # SOURCE3 1 + angle_coeff @angle:cd-n-n2 harmonic 88.496 110.870 # SOURCE3 1 + angle_coeff @angle:cd-n-n harmonic 83.245 121.370 # SOURCE3 1 + angle_coeff @angle:cd-n-na harmonic 84.492 117.570 # SOURCE3 1 + angle_coeff @angle:cd-n-nd harmonic 88.107 111.890 # CORR_SOURCE5 20 0.7095 + angle_coeff @angle:cd-n-nh harmonic 84.683 117.520 # SOURCE3 1 + angle_coeff @angle:cd-n-no harmonic 83.522 115.920 # SOURCE3 1 + angle_coeff @angle:cd-n-o harmonic 88.192 120.540 # SOURCE3 1 + angle_coeff @angle:cd-n-oh harmonic 83.905 119.300 # SOURCE3_SOURCE5 7 0.3237 + angle_coeff @angle:cd-n-os harmonic 85.167 115.560 # SOURCE3 1 + angle_coeff @angle:cd-n-p2 harmonic 83.596 112.320 # SOURCE3 1 + angle_coeff @angle:cd-n-p3 harmonic 77.892 125.110 # SOURCE3 1 + angle_coeff @angle:cd-n-p5 harmonic 81.119 121.000 # SOURCE3 1 + angle_coeff @angle:cd-n-s4 harmonic 62.446 118.400 # SOURCE3 1 + angle_coeff @angle:cd-n-s6 harmonic 64.150 117.320 # SOURCE3 1 + angle_coeff @angle:cd-n-s harmonic 62.506 118.290 # SOURCE3 1 + angle_coeff @angle:cd-n-sh harmonic 63.393 119.130 # SOURCE3 1 + angle_coeff @angle:cd-n-ss harmonic 64.137 116.600 # SOURCE3 2 1.8318 + angle_coeff @angle:ce-n-cy harmonic 66.660 111.710 # CORR_SOURCE5 226 2.0477 + angle_coeff @angle:c-n-f harmonic 89.555 108.630 # SOURCE3 3 4.6785 + angle_coeff @angle:cf-n-cy harmonic 66.660 111.710 # CORR_SOURCE5 226 2.0477 + angle_coeff @angle:c-n-hn harmonic 48.691 117.550 # SOURCE3_SOURCE5 5866 1.6058 + angle_coeff @angle:c-n-i harmonic 59.703 120.380 # SOURCE3 5 2.1600 + angle_coeff @angle:cl-n-cl harmonic 81.959 111.690 # SOURCE3 1 + angle_coeff @angle:c-n-n2 harmonic 85.152 119.910 # SOURCE3_SOURCE5 237 1.7782 + angle_coeff @angle:c-n-n3 harmonic 83.740 120.100 # SOURCE3_SOURCE5 90 1.4705 + angle_coeff @angle:c-n-n4 harmonic 85.688 112.320 # SOURCE3 5 1.2622 + angle_coeff @angle:c-n-n harmonic 84.328 118.420 # SOURCE3 10 2.8922 + angle_coeff @angle:c-n-na harmonic 86.815 111.500 # SOURCE3_SOURCE5 60 1.0005 + angle_coeff @angle:na-nc-nd harmonic 116.802 106.240 # SOURCE3_SOURCE5 145 0.6824 + angle_coeff @angle:c-n-nc harmonic 83.462 124.860 # CORR_SOURCE5 117 2.2930 + angle_coeff @angle:nc-nc-nd harmonic 113.624 111.460 # CORR_SOURCE5 97 0.5962 + angle_coeff @angle:c-n-nd harmonic 83.462 124.860 # CORR_SOURCE5 117 2.2930 + angle_coeff @angle:nd-nc-os harmonic 114.084 107.220 # SOURCE3 3 0.4707 + angle_coeff @angle:c-n-nh harmonic 84.310 118.710 # SOURCE4_SOURCE5 52 1.7764 + angle_coeff @angle:c-n-no harmonic 82.773 118.160 # SOURCE3 4 5.4870 + angle_coeff @angle:c-n-o harmonic 89.074 118.360 # SOURCE3_SOURCE5 14 3.9188 + angle_coeff @angle:c-n-oh harmonic 85.324 115.510 # SOURCE3_SOURCE5 128 0.8808 + angle_coeff @angle:c-n-os harmonic 86.126 113.140 # SOURCE3 7 3.0839 + angle_coeff @angle:c-n-p2 harmonic 79.405 124.560 # SOURCE3 8 3.6907 + angle_coeff @angle:c-n-p3 harmonic 78.725 122.540 # SOURCE3 9 4.4802 + angle_coeff @angle:c-n-p4 harmonic 79.728 123.440 # SOURCE3 1 + angle_coeff @angle:c-n-p5 harmonic 78.739 128.500 # SOURCE4 6 0.5353 + angle_coeff @angle:c-n-pc harmonic 79.905 122.230 # SOURCE3 3 2.8787 + angle_coeff @angle:c-n-pd harmonic 79.905 122.230 # SOURCE3 3 + angle_coeff @angle:c-n-s4 harmonic 61.938 120.410 # SOURCE3 4 3.1760 + angle_coeff @angle:c-n-s6 harmonic 62.226 124.760 # SOURCE4_SOURCE5 44 1.7490 + angle_coeff @angle:c-n-s harmonic 60.447 126.550 # SOURCE3 3 4.3365 + angle_coeff @angle:c-n-sh harmonic 63.302 119.540 # SOURCE3 4 1.7681 + angle_coeff @angle:c-n-ss harmonic 62.795 121.710 # SOURCE3_SOURCE5 23 1.8428 + angle_coeff @angle:c-n-sy harmonic 62.308 124.690 # SOURCE4_SOURCE5 124 1.1647 + angle_coeff @angle:cx-n-hn harmonic 46.588 118.500 # SOURCE4_SOURCE5 12 0.6959 + angle_coeff @angle:cx-n-os harmonic 121.869 54.040 # SOURCE3 1 + angle_coeff @angle:cy-n-hn harmonic 45.639 119.110 # SOURCE4_SOURCE5 156 1.4586 + angle_coeff @angle:c3-nd-cc harmonic 69.940 109.510 # SOURCE3 9 + angle_coeff @angle:ca-nd-ca harmonic 71.962 109.950 # SOURCE3 1 + angle_coeff @angle:ca-nd-cc harmonic 74.608 104.880 # CORR_SOURCE5 766 1.8814 + angle_coeff @angle:ca-nd-n harmonic 92.070 104.690 # CORR 2 + angle_coeff @angle:ca-nd-na harmonic 93.131 102.760 # CORR_SOURCE5 25 0.7558 + angle_coeff @angle:ca-nd-nc harmonic 92.520 108.340 # SOURCE4_SOURCE5 23 0.2293 + angle_coeff @angle:ca-nd-os harmonic 90.719 104.480 # CORR_SOURCE5 16 0.1832 + angle_coeff @angle:ca-nd-ss harmonic 70.369 107.070 # SOURCE3_SOURCE5 17 0.3771 + angle_coeff @angle:c-nd-ca harmonic 67.794 120.660 # CORR 2 + angle_coeff @angle:c-nd-cc harmonic 68.639 120.490 # CORR_SOURCE5 205 1.1318 + angle_coeff @angle:cc-nd-cc harmonic 71.496 117.300 # CORR_SOURCE5 18 0.3907 + angle_coeff @angle:cc-nd-cd harmonic 73.871 105.490 # CORR_SOURCE5 1810 1.9032 + angle_coeff @angle:cc-nd-n harmonic 88.099 117.190 # CORR 64 + angle_coeff @angle:cc-nd-na harmonic 93.815 103.820 # SOURCE3_SOURCE5 919 1.7445 + angle_coeff @angle:cc-nd-nd harmonic 91.676 107.820 # CORR_SOURCE5 457 1.5268 + angle_coeff @angle:cc-nd-os harmonic 91.671 104.670 # CORR_SOURCE5 184 0.8204 + angle_coeff @angle:cc-nd-ss harmonic 70.508 108.070 # CORR_SOURCE5 95 1.3804 + angle_coeff @angle:cd-nd-cd harmonic 73.120 103.760 # CORR_SOURCE5 6 0.0439 + angle_coeff @angle:cd-nd-na harmonic 92.426 102.970 # SOURCE3 1 + angle_coeff @angle:cd-nd-nc harmonic 91.732 108.620 # SOURCE3_SOURCE5 82 1.5614 + angle_coeff @angle:na-nd-nc harmonic 116.883 106.240 # SOURCE3_SOURCE5 145 0.6824 + angle_coeff @angle:nc-nd-nd harmonic 113.624 111.460 # CORR_SOURCE5 97 0.5962 + angle_coeff @angle:nc-nd-os harmonic 114.084 107.220 # SOURCE3 3 + angle_coeff @angle:c1-ne-ca harmonic 62.618 151.950 # CORR_SOURCE5 15 1.4352 + angle_coeff @angle:c1-ne-cg harmonic 67.861 140.000 # SOURCE2 1 + angle_coeff @angle:c2-ne-ca harmonic 68.492 120.830 # CORR_SOURCE5 103 1.9474 + angle_coeff @angle:c2-ne-ce harmonic 70.313 116.010 # SOURCE3_SOURCE5 34 2.0813 + angle_coeff @angle:c2-ne-cg harmonic 70.178 123.230 # SOURCE4_SOURCE5 39 1.0918 + angle_coeff @angle:c2-ne-n2 harmonic 93.623 113.310 # SOURCE3 1 + angle_coeff @angle:c2-ne-ne harmonic 88.990 110.860 # SOURCE3 7 4.5874 + angle_coeff @angle:c2-ne-p2 harmonic 84.105 134.030 # SOURCE3 1 + angle_coeff @angle:c2-ne-pe harmonic 82.533 120.520 # SOURCE3 8 8.1381 + angle_coeff @angle:c2-ne-px harmonic 83.910 117.750 # SOURCE3 5 0.8581 + angle_coeff @angle:c2-ne-py harmonic 88.230 117.040 # SOURCE3 3 1.4398 + angle_coeff @angle:c2-ne-sx harmonic 62.652 111.980 # SOURCE3 3 0.4090 + angle_coeff @angle:c2-ne-sy harmonic 65.555 120.600 # CORR_SOURCE5 19 1.1215 + angle_coeff @angle:ca-ne-cf harmonic 68.142 121.710 # CORR_SOURCE5 29 1.8572 + angle_coeff @angle:ca-ne-n2 harmonic 88.697 114.350 # CORR_SOURCE5 15 1.3133 + angle_coeff @angle:ca-ne-nf harmonic 88.592 115.170 # CORR_SOURCE5 98 0.8636 + angle_coeff @angle:ca-ne-o harmonic 89.200 115.690 # SOURCE3_SOURCE5 18 1.7090 + angle_coeff @angle:ca-ne-p2 harmonic 87.186 118.090 # SOURCE3 1 + angle_coeff @angle:ca-ne-s harmonic 68.068 120.110 # SOURCE3 1 + angle_coeff @angle:c-ne-c2 harmonic 69.660 118.530 # CORR 6 + angle_coeff @angle:ce-ne-n2 harmonic 90.497 111.190 # SOURCE3 1 + angle_coeff @angle:ce-ne-o harmonic 91.180 112.160 # SOURCE3 1 + angle_coeff @angle:ce-ne-p2 harmonic 87.896 117.020 # SOURCE3 1 + angle_coeff @angle:ce-ne-s harmonic 69.440 116.280 # SOURCE3 1 + angle_coeff @angle:cg-ne-n1 harmonic 90.226 120.200 # SOURCE2 1 + angle_coeff @angle:cg-ne-n2 harmonic 92.273 113.390 # SOURCE3 1 + angle_coeff @angle:cg-ne-o harmonic 93.028 114.700 # SOURCE2 1 + angle_coeff @angle:cg-ne-p2 harmonic 88.388 119.570 # SOURCE3 1 + angle_coeff @angle:cg-ne-s harmonic 70.232 117.700 # SOURCE3 1 + angle_coeff @angle:c-ne-sy harmonic 65.604 116.430 # SOURCE4_SOURCE5 16 1.7300 + angle_coeff @angle:n2-ne-n2 harmonic 121.491 107.220 # SOURCE3 1 + angle_coeff @angle:n2-ne-ne harmonic 112.157 110.720 # SOURCE3 9 6.1488 + angle_coeff @angle:n2-ne-o harmonic 119.624 114.100 # SOURCE3 1 + angle_coeff @angle:n2-ne-p2 harmonic 116.902 109.660 # SOURCE3 1 + angle_coeff @angle:n2-ne-pe harmonic 107.386 112.150 # SOURCE3 7 6.5273 + angle_coeff @angle:n2-ne-px harmonic 106.135 115.970 # SOURCE3 3 1.9854 + angle_coeff @angle:n2-ne-py harmonic 112.046 114.600 # SOURCE3 3 2.9261 + angle_coeff @angle:n2-ne-s harmonic 89.721 115.900 # SOURCE3 1 + angle_coeff @angle:n2-ne-sx harmonic 80.235 107.290 # SOURCE3 1 + angle_coeff @angle:n2-ne-sy harmonic 85.721 111.210 # SOURCE3 1 + angle_coeff @angle:ne-ne-o harmonic 113.544 110.450 # SOURCE3 10 1.8535 + angle_coeff @angle:ne-ne-p2 harmonic 110.510 114.390 # SOURCE3 6 4.0528 + angle_coeff @angle:ne-ne-s harmonic 86.406 115.950 # SOURCE3 6 3.4604 + angle_coeff @angle:o-ne-o harmonic 116.666 124.090 # SOURCE3 2 8.7534 + angle_coeff @angle:o-ne-pe harmonic 99.245 132.320 # SOURCE3 11 23.9559 + angle_coeff @angle:o-ne-px harmonic 109.115 110.620 # SOURCE3 1 + angle_coeff @angle:o-ne-py harmonic 114.678 110.790 # SOURCE3 4 1.6818 + angle_coeff @angle:o-ne-s harmonic 89.941 117.190 # SOURCE3 2 0.0225 + angle_coeff @angle:o-ne-sx harmonic 79.732 108.920 # SOURCE3 1 + angle_coeff @angle:o-ne-sy harmonic 86.078 111.340 # SOURCE3 1 + angle_coeff @angle:p2-ne-pe harmonic 110.473 116.810 # SOURCE3 1 + angle_coeff @angle:p2-ne-px harmonic 105.767 128.350 # SOURCE3 1 + angle_coeff @angle:p2-ne-py harmonic 111.507 123.470 # SOURCE3 1 + angle_coeff @angle:p2-ne-sx harmonic 83.857 112.120 # SOURCE3 1 + angle_coeff @angle:p2-ne-sy harmonic 87.708 115.730 # SOURCE3 1 + angle_coeff @angle:pe-ne-s harmonic 87.031 115.730 # SOURCE3 1 + angle_coeff @angle:px-ne-s harmonic 81.843 131.840 # SOURCE3 1 + angle_coeff @angle:py-ne-s harmonic 90.262 116.180 # SOURCE3 4 3.7135 + angle_coeff @angle:s-ne-s harmonic 70.545 120.870 # SOURCE3 1 + angle_coeff @angle:s-ne-sx harmonic 65.416 112.960 # SOURCE3 1 + angle_coeff @angle:s-ne-sy harmonic 67.679 119.630 # SOURCE3 1 + angle_coeff @angle:c1-nf-ca harmonic 62.618 151.950 # CORR_SOURCE5 15 1.4352 + angle_coeff @angle:c1-nf-ch harmonic 67.861 140.000 # SOURCE2 1 + angle_coeff @angle:c2-nf-ca harmonic 68.492 120.830 # CORR_SOURCE5 103 1.9474 + angle_coeff @angle:c2-nf-cf harmonic 70.313 116.010 # SOURCE3_SOURCE5 31 2.1630 + angle_coeff @angle:c2-nf-n2 harmonic 93.623 113.310 # SOURCE3 1 + angle_coeff @angle:c2-nf-nf harmonic 88.990 110.860 # SOURCE3 7 + angle_coeff @angle:c2-nf-p2 harmonic 84.105 134.030 # SOURCE3 1 + angle_coeff @angle:c2-nf-pf harmonic 82.533 120.520 # SOURCE3 8 + angle_coeff @angle:c2-nf-px harmonic 83.910 117.750 # SOURCE3 5 + angle_coeff @angle:c2-nf-py harmonic 88.230 117.040 # SOURCE3 3 + angle_coeff @angle:c2-nf-sx harmonic 62.652 111.980 # SOURCE3 3 + angle_coeff @angle:c2-nf-sy harmonic 65.555 120.600 # CORR_SOURCE5 19 1.1215 + angle_coeff @angle:ca-nf-ce harmonic 68.142 121.710 # CORR_SOURCE5 29 1.8572 + angle_coeff @angle:ca-nf-n2 harmonic 88.697 114.350 # CORR_SOURCE5 15 1.3133 + angle_coeff @angle:ca-nf-ne harmonic 88.592 115.170 # CORR_SOURCE5 98 0.8636 + angle_coeff @angle:ca-nf-o harmonic 89.200 115.690 # SOURCE3_SOURCE5 15 1.8257 + angle_coeff @angle:ca-nf-p2 harmonic 87.186 118.090 # SOURCE3 1 + angle_coeff @angle:ca-nf-s harmonic 68.068 120.110 # SOURCE3 1 + angle_coeff @angle:c-nf-c2 harmonic 69.660 118.530 # CORR 6 + angle_coeff @angle:cf-nf-n2 harmonic 90.497 111.190 # SOURCE3 1 + angle_coeff @angle:cf-nf-o harmonic 91.180 112.160 # SOURCE3 1 + angle_coeff @angle:cf-nf-p2 harmonic 87.896 117.020 # SOURCE3 1 + angle_coeff @angle:cf-nf-s harmonic 69.440 116.280 # SOURCE3 1 + angle_coeff @angle:ch-nf-n1 harmonic 90.226 120.200 # SOURCE2 1 + angle_coeff @angle:ch-nf-n2 harmonic 92.273 113.390 # SOURCE3 1 + angle_coeff @angle:ch-nf-o harmonic 93.028 114.700 # SOURCE2 1 + angle_coeff @angle:ch-nf-p2 harmonic 88.388 119.570 # SOURCE3 1 + angle_coeff @angle:ch-nf-s harmonic 70.232 117.700 # SOURCE3 1 + angle_coeff @angle:f-n-f harmonic 116.092 102.980 # SOURCE3 1 + angle_coeff @angle:n2-nf-n2 harmonic 121.491 107.220 # SOURCE3 1 + angle_coeff @angle:n2-nf-nf harmonic 112.157 110.720 # SOURCE3 9 + angle_coeff @angle:n2-nf-o harmonic 119.624 114.100 # SOURCE3 1 + angle_coeff @angle:n2-nf-p2 harmonic 116.902 109.660 # SOURCE3 1 + angle_coeff @angle:n2-nf-pf harmonic 107.386 112.150 # SOURCE3 7 + angle_coeff @angle:n2-nf-px harmonic 106.135 115.970 # SOURCE3 3 + angle_coeff @angle:n2-nf-py harmonic 112.046 114.600 # SOURCE3 3 + angle_coeff @angle:n2-nf-s harmonic 89.721 115.900 # SOURCE3 1 + angle_coeff @angle:n2-nf-sx harmonic 80.235 107.290 # SOURCE3 1 + angle_coeff @angle:n2-nf-sy harmonic 85.721 111.210 # SOURCE3 1 + angle_coeff @angle:nf-nf-o harmonic 113.544 110.450 # SOURCE3 10 + angle_coeff @angle:nf-nf-p2 harmonic 110.510 114.390 # SOURCE3 6 + angle_coeff @angle:nf-nf-s harmonic 86.406 115.950 # SOURCE3 6 + angle_coeff @angle:o-nf-o harmonic 116.666 124.090 # SOURCE3 2 + angle_coeff @angle:o-nf-pf harmonic 99.245 132.320 # SOURCE3 11 + angle_coeff @angle:o-nf-px harmonic 109.115 110.620 # SOURCE3 1 + angle_coeff @angle:o-nf-py harmonic 114.678 110.790 # SOURCE3 4 + angle_coeff @angle:o-nf-s harmonic 89.941 117.190 # SOURCE3 2 + angle_coeff @angle:o-nf-sx harmonic 79.732 108.920 # SOURCE3 1 + angle_coeff @angle:o-nf-sy harmonic 86.078 111.340 # SOURCE3 1 + angle_coeff @angle:p2-nf-pf harmonic 110.473 116.810 # SOURCE3 1 + angle_coeff @angle:p2-nf-px harmonic 105.767 128.350 # SOURCE3 1 + angle_coeff @angle:p2-nf-py harmonic 111.507 123.470 # SOURCE3 1 + angle_coeff @angle:p2-nf-sx harmonic 83.857 112.120 # SOURCE3 1 + angle_coeff @angle:p2-nf-sy harmonic 87.708 115.730 # SOURCE3 1 + angle_coeff @angle:pf-nf-s harmonic 87.031 115.730 # SOURCE3 1 + angle_coeff @angle:px-nf-s harmonic 81.843 131.840 # SOURCE3 1 + angle_coeff @angle:py-nf-s harmonic 90.262 116.180 # SOURCE3 4 + angle_coeff @angle:s-nf-s harmonic 70.545 120.870 # SOURCE3 1 + angle_coeff @angle:s-nf-sx harmonic 65.416 112.960 # SOURCE3 1 + angle_coeff @angle:s-nf-sy harmonic 67.679 119.630 # SOURCE3 1 + angle_coeff @angle:br-nh-br harmonic 67.679 106.270 # SOURCE3 1 + angle_coeff @angle:br-nh-ca harmonic 63.138 111.880 # SOURCE3 1 + angle_coeff @angle:br-nh-hn harmonic 41.986 101.560 # SOURCE3 1 + angle_coeff @angle:c1-nh-c1 harmonic 70.255 116.980 # SOURCE3 1 + angle_coeff @angle:c1-nh-c2 harmonic 67.255 123.350 # SOURCE4_SOURCE5 17 1.3108 + angle_coeff @angle:c1-nh-ca harmonic 67.561 122.360 # SOURCE3 3 1.2016 + angle_coeff @angle:c1-nh-hn harmonic 49.868 117.400 # SOURCE4_SOURCE5 22 0.6517 + angle_coeff @angle:c2-nh-c2 harmonic 65.835 124.730 # SOURCE4_SOURCE5 107 1.4158 + angle_coeff @angle:c2-nh-c3 harmonic 64.232 123.710 # SOURCE3 8 3.5348 + angle_coeff @angle:c2-nh-ca harmonic 65.131 127.560 # SOURCE4_SOURCE5 258 2.3985 + angle_coeff @angle:c2-nh-cc harmonic 65.733 126.350 # CORR_SOURCE5 14 0.8394 + angle_coeff @angle:c2-nh-cd harmonic 65.733 126.350 # CORR_SOURCE5 14 0.8394 + angle_coeff @angle:c2-nh-cx harmonic 64.299 124.350 # SOURCE4_SOURCE5 21 1.6877 + angle_coeff @angle:c2-nh-hn harmonic 48.954 115.090 # SOURCE4_SOURCE5 2743 1.5424 + angle_coeff @angle:c2-nh-n2 harmonic 85.013 120.220 # SOURCE4_SOURCE5 101 1.0922 + angle_coeff @angle:c2-nh-n3 harmonic 84.289 116.870 # SOURCE4_SOURCE5 35 1.4173 + angle_coeff @angle:c2-nh-no harmonic 82.173 125.620 # SOURCE4_SOURCE5 19 0.8850 + angle_coeff @angle:c2-nh-oh harmonic 86.014 112.180 # SOURCE4_SOURCE5 38 1.3409 + angle_coeff @angle:c2-nh-os harmonic 85.749 112.950 # SOURCE4_SOURCE5 14 0.4455 + angle_coeff @angle:c2-nh-sy harmonic 63.190 121.130 # SOURCE4_SOURCE5 20 0.5133 + angle_coeff @angle:c3-nh-c3 harmonic 65.106 114.510 # SOURCE4_SOURCE5 1386 2.1206 + angle_coeff @angle:c3-nh-ca harmonic 65.249 119.980 # SOURCE3_SOURCE5 1640 2.1716 + angle_coeff @angle:c3-nh-cc harmonic 65.571 119.720 # CORR_SOURCE5 638 2.4802 + angle_coeff @angle:c3-nh-cd harmonic 65.571 119.720 # CORR_SOURCE5 638 2.4802 + angle_coeff @angle:c3-nh-cf harmonic 65.126 120.120 # SOURCE4_SOURCE5 52 2.0459 + angle_coeff @angle:c3-nh-cz harmonic 64.716 125.460 # SOURCE4_SOURCE5 25 0.5651 + angle_coeff @angle:c3-nh-hn harmonic 46.421 115.990 # SOURCE3_SOURCE5 1206 1.7716 + angle_coeff @angle:c3-nh-n2 harmonic 85.302 112.350 # SOURCE3 9 4.0058 + angle_coeff @angle:c3-nh-n harmonic 84.428 111.270 # SOURCE4_SOURCE5 20 2.2657 + angle_coeff @angle:c3-nh-na harmonic 84.049 112.390 # SOURCE4_SOURCE5 18 1.3421 + angle_coeff @angle:c3-nh-p2 harmonic 80.321 123.350 # SOURCE3 1 + angle_coeff @angle:c3-nh-sy harmonic 63.547 116.320 # SOURCE4_SOURCE5 31 1.3018 + angle_coeff @angle:ca-nh-ca harmonic 65.187 127.460 # SOURCE3 2 0.0002 + angle_coeff @angle:ca-nh-cc harmonic 64.885 129.800 # CORR_SOURCE5 49 1.2126 + angle_coeff @angle:ca-nh-cd harmonic 64.885 129.800 # CORR_SOURCE5 49 1.2126 + angle_coeff @angle:ca-nh-cl harmonic 71.441 113.150 # SOURCE3 1 + angle_coeff @angle:ca-nh-cx harmonic 64.495 123.700 # SOURCE4_SOURCE5 80 0.6122 + angle_coeff @angle:ca-nh-f harmonic 89.432 106.090 # SOURCE3 3 1.0660 + angle_coeff @angle:ca-nh-hn harmonic 48.787 116.070 # SOURCE4_SOURCE5 5026 1.3182 + angle_coeff @angle:ca-nh-i harmonic 58.875 117.830 # SOURCE3 1 + angle_coeff @angle:ca-nh-n1 harmonic 86.539 117.130 # HF/6-31G* 1 + angle_coeff @angle:ca-nh-n2 harmonic 84.736 121.130 # SOURCE4_SOURCE5 61 1.2262 + angle_coeff @angle:ca-nh-n3 harmonic 83.982 117.830 # SOURCE3_SOURCE5 31 1.9504 + angle_coeff @angle:ca-nh-n4 harmonic 85.682 108.940 # SOURCE3 5 0.6562 + angle_coeff @angle:ca-nh-n harmonic 85.070 116.030 # SOURCE4_SOURCE5 31 1.0216 + angle_coeff @angle:ca-nh-na harmonic 85.145 115.960 # SOURCE3_SOURCE5 14 0.6985 + angle_coeff @angle:ca-nh-nh harmonic 85.491 114.840 # SOURCE3_SOURCE5 14 1.2270 + angle_coeff @angle:ca-nh-no harmonic 86.330 113.920 # SOURCE3 4 2.9561 + angle_coeff @angle:ca-nh-o harmonic 86.968 121.920 # SOURCE3 2 3.9630 + angle_coeff @angle:ca-nh-oh harmonic 85.751 112.970 # SOURCE3_SOURCE5 7 0.3980 + angle_coeff @angle:ca-nh-os harmonic 86.208 111.850 # SOURCE3_SOURCE5 8 0.6032 + angle_coeff @angle:ca-nh-p2 harmonic 81.008 125.270 # SOURCE3 8 5.1798 + angle_coeff @angle:ca-nh-p3 harmonic 79.062 125.700 # SOURCE3 3 5.7796 + angle_coeff @angle:ca-nh-p4 harmonic 80.454 124.010 # SOURCE3 3 2.5810 + angle_coeff @angle:ca-nh-p5 harmonic 80.367 128.170 # SOURCE3_SOURCE5 9 0.9847 + angle_coeff @angle:ca-nh-s4 harmonic 63.691 115.620 # SOURCE3 3 0.3434 + angle_coeff @angle:ca-nh-s6 harmonic 63.224 122.850 # SOURCE4_SOURCE5 92 2.1278 + angle_coeff @angle:ca-nh-s harmonic 60.896 122.540 # SOURCE3 3 2.7001 + angle_coeff @angle:ca-nh-sh harmonic 63.303 121.410 # SOURCE3 1 + angle_coeff @angle:ca-nh-ss harmonic 63.248 121.500 # SOURCE3 3 2.6255 + angle_coeff @angle:ca-nh-sy harmonic 62.161 125.230 # SOURCE4_SOURCE5 116 1.6241 + angle_coeff @angle:cc-nh-cx harmonic 64.747 123.700 # CORR_SOURCE5 82 1.6057 + angle_coeff @angle:cc-nh-hn harmonic 49.267 115.630 # SOURCE3_SOURCE5 1084 1.8598 + angle_coeff @angle:cc-nh-n2 harmonic 85.504 120.090 # SOURCE4_SOURCE5 21 1.0306 + angle_coeff @angle:cc-nh-sy harmonic 62.976 122.520 # SOURCE4_SOURCE5 60 1.2839 + angle_coeff @angle:cd-nh-cx harmonic 64.747 123.700 # CORR_SOURCE5 82 1.6057 + angle_coeff @angle:cd-nh-hn harmonic 49.267 115.630 # SOURCE3_SOURCE5 1084 1.8598 + angle_coeff @angle:ce-nh-hn harmonic 48.739 115.680 # CORR_SOURCE5 360 1.2286 + angle_coeff @angle:ce-nh-o harmonic 84.249 129.430 # CORR 2 + angle_coeff @angle:ce-nh-sy harmonic 65.279 113.390 # SOURCE4_SOURCE5 15 1.0862 + angle_coeff @angle:cf-nh-hn harmonic 48.739 115.680 # CORR_SOURCE5 360 1.2286 + angle_coeff @angle:cf-nh-o harmonic 84.249 129.430 # CORR 2 + angle_coeff @angle:cl-nh-cl harmonic 81.661 106.600 # SOURCE3 1 + angle_coeff @angle:cl-nh-hn harmonic 48.722 104.140 # SOURCE3 1 + angle_coeff @angle:cx-nh-cx harmonic 89.045 62.010 # SOURCE4_SOURCE5 98 0.5911 + angle_coeff @angle:cx-nh-hn harmonic 46.132 118.880 # SOURCE4_SOURCE5 23 0.1930 + angle_coeff @angle:cz-nh-hn harmonic 49.192 121.150 # SOURCE4_SOURCE5 116 0.7805 + angle_coeff @angle:f-nh-f harmonic 114.444 101.700 # SOURCE3 1 + angle_coeff @angle:f-nh-hn harmonic 64.681 101.230 # SOURCE3 1 + angle_coeff @angle:hn-nh-hn harmonic 39.519 115.120 # SOURCE4_SOURCE5 3024 2.1393 + angle_coeff @angle:hn-nh-i harmonic 37.873 107.570 # SOURCE3 1 + angle_coeff @angle:hn-nh-n1 harmonic 64.440 110.570 # HF/6-31G* 1 + angle_coeff @angle:hn-nh-n2 harmonic 61.856 118.140 # SOURCE4_SOURCE5 220 2.1956 + angle_coeff @angle:hn-nh-n3 harmonic 60.496 113.970 # SOURCE3_SOURCE5 53 1.8422 + angle_coeff @angle:hn-nh-n4 harmonic 61.193 104.400 # SOURCE3 3 0.5056 + angle_coeff @angle:hn-nh-n harmonic 62.655 108.170 # SOURCE4_SOURCE5 39 1.1076 + angle_coeff @angle:hn-nh-na harmonic 62.699 108.240 # SOURCE3_SOURCE5 48 1.3913 + angle_coeff @angle:hn-nh-nh harmonic 61.867 110.860 # SOURCE4_SOURCE5 20 1.2814 + angle_coeff @angle:hn-nh-no harmonic 62.754 109.940 # SOURCE4_SOURCE5 17 0.1843 + angle_coeff @angle:hn-nh-o harmonic 65.877 116.450 # SOURCE3 2 0.6063 + angle_coeff @angle:hn-nh-oh harmonic 62.561 106.490 # SOURCE4_SOURCE5 45 1.2492 + angle_coeff @angle:hn-nh-os harmonic 62.721 106.070 # SOURCE3_SOURCE5 11 1.1257 + angle_coeff @angle:hn-nh-p2 harmonic 55.498 118.180 # SOURCE3 21 3.6927 + angle_coeff @angle:hn-nh-p3 harmonic 54.152 116.190 # SOURCE3 3 3.0539 + angle_coeff @angle:hn-nh-p4 harmonic 55.870 112.600 # SOURCE3 3 0.8237 + angle_coeff @angle:hn-nh-p5 harmonic 56.530 115.090 # SOURCE3_SOURCE5 12 1.4234 + angle_coeff @angle:hn-nh-s4 harmonic 43.338 107.480 # SOURCE3 3 1.3960 + angle_coeff @angle:hn-nh-s harmonic 41.075 114.370 # SOURCE3 1 + angle_coeff @angle:hn-nh-s6 harmonic 44.306 109.920 # SOURCE4_SOURCE5 70 0.7219 + angle_coeff @angle:hn-nh-sh harmonic 43.546 112.250 # SOURCE3 1 + angle_coeff @angle:hn-nh-ss harmonic 43.161 114.100 # SOURCE3_SOURCE5 9 0.8638 + angle_coeff @angle:hn-nh-sy harmonic 43.636 110.910 # SOURCE4_SOURCE5 174 1.2855 + angle_coeff @angle:i-nh-i harmonic 65.204 115.820 # SOURCE3 1 + angle_coeff @angle:n1-nh-n1 harmonic 115.547 106.710 # HF/6-31G* 1 + angle_coeff @angle:n2-nh-n2 harmonic 109.104 117.500 # SOURCE3 2 1.1907 + angle_coeff @angle:n2-nh-n3 harmonic 105.802 119.060 # SOURCE3_SOURCE5 5 1.1057 + angle_coeff @angle:n2-nh-o harmonic 108.688 126.060 # SOURCE3 1 + angle_coeff @angle:n3-nh-n3 harmonic 107.251 110.980 # SOURCE3 1 + angle_coeff @angle:n4-nh-n4 harmonic 104.809 108.360 # SOURCE3 1 + angle_coeff @angle:na-nh-na harmonic 107.947 112.010 # SOURCE3 1 + angle_coeff @angle:hn-n-hn harmonic 39.011 117.950 # SOURCE3_SOURCE5 619 1.1004 + angle_coeff @angle:nh-nh-nh harmonic 107.672 112.230 # SOURCE3 1 + angle_coeff @angle:hn-n-i harmonic 37.457 117.240 # SOURCE3 2 0.4435 + angle_coeff @angle:hn-n-n2 harmonic 61.294 119.080 # SOURCE3_SOURCE5 133 1.1985 + angle_coeff @angle:hn-n-n3 harmonic 60.078 117.240 # SOURCE4_SOURCE5 85 1.3614 + angle_coeff @angle:hn-n-n4 harmonic 60.201 112.680 # SOURCE3 3 1.9746 + angle_coeff @angle:hn-n-n harmonic 61.137 113.200 # SOURCE3_SOURCE5 44 1.5099 + angle_coeff @angle:hn-n-na harmonic 60.720 114.350 # SOURCE3_SOURCE5 14 1.6595 + angle_coeff @angle:hn-n-nc harmonic 62.278 115.420 # SOURCE4_SOURCE5 34 0.6814 + angle_coeff @angle:hn-n-nh harmonic 61.240 113.210 # SOURCE4_SOURCE5 34 1.4195 + angle_coeff @angle:hn-n-no harmonic 59.968 110.110 # SOURCE3 1 + angle_coeff @angle:hn-n-o harmonic 66.701 116.320 # SOURCE3 2 0.0175 + angle_coeff @angle:n-nh-o harmonic 111.046 115.630 # SOURCE3 1 + angle_coeff @angle:hn-n-oh harmonic 61.737 110.740 # SOURCE4_SOURCE5 106 1.1526 + angle_coeff @angle:no-nh-no harmonic 110.729 108.550 # SOURCE3 1 + angle_coeff @angle:hn-n-os harmonic 61.835 110.010 # SOURCE4_SOURCE5 28 0.8603 + angle_coeff @angle:hn-n-p2 harmonic 53.625 118.050 # SOURCE3 7 3.0564 + angle_coeff @angle:hn-n-p3 harmonic 52.013 119.630 # SOURCE3 2 + angle_coeff @angle:hn-n-p4 harmonic 54.129 115.710 # SOURCE3 1 + angle_coeff @angle:hn-n-p5 harmonic 55.227 113.610 # SOURCE4_SOURCE5 12 0.8598 + angle_coeff @angle:hn-n-s4 harmonic 41.853 112.460 # SOURCE3 1 + angle_coeff @angle:hn-n-s harmonic 41.432 114.920 # SOURCE3 2 0.0260 + angle_coeff @angle:hn-n-s6 harmonic 43.193 112.560 # SOURCE4_SOURCE5 18 0.6934 + angle_coeff @angle:hn-n-sh harmonic 42.490 114.910 # SOURCE3 1 + angle_coeff @angle:hn-n-ss harmonic 42.420 115.600 # SOURCE3 3 0.6414 + angle_coeff @angle:hn-n-sy harmonic 43.301 112.330 # SOURCE4_SOURCE5 87 0.6324 + angle_coeff @angle:oh-nh-oh harmonic 109.556 106.270 # SOURCE3 1 + angle_coeff @angle:o-nh-o harmonic 111.924 128.060 # SOURCE3 1 + angle_coeff @angle:os-nh-os harmonic 110.145 105.270 # SOURCE3 1 + angle_coeff @angle:p2-nh-p2 harmonic 103.624 127.330 # SOURCE3 2 2.7857 + angle_coeff @angle:p3-nh-p3 harmonic 101.470 125.080 # SOURCE3 1 + angle_coeff @angle:p5-nh-p5 harmonic 110.643 112.760 # SOURCE3 1 + angle_coeff @angle:s4-nh-s4 harmonic 64.290 112.390 # SOURCE3 1 + angle_coeff @angle:s6-nh-s6 harmonic 64.034 120.270 # SOURCE3 1 + angle_coeff @angle:sh-nh-sh harmonic 63.979 119.000 # SOURCE3 1 + angle_coeff @angle:s-nh-s harmonic 61.323 118.730 # SOURCE3 1 + angle_coeff @angle:ss-nh-ss harmonic 63.871 119.250 # SOURCE3 1 + angle_coeff @angle:i-n-i harmonic 66.144 118.200 # SOURCE3 1 + angle_coeff @angle:n2-n-n2 harmonic 108.745 116.890 # SOURCE3 1 + angle_coeff @angle:n3-n-n3 harmonic 104.883 117.940 # SOURCE3 1 + angle_coeff @angle:n4-n-n4 harmonic 105.215 112.690 # SOURCE3 1 + angle_coeff @angle:na-n-na harmonic 104.916 117.380 # SOURCE3 1 + angle_coeff @angle:nc-n-nc harmonic 109.009 116.410 # CORR 2 + angle_coeff @angle:nc-n-p2 harmonic 102.805 117.210 # CORR 2 + angle_coeff @angle:nc-n-pc harmonic 102.474 117.210 # CORR 2 + angle_coeff @angle:nd-n-nd harmonic 109.009 116.410 # CORR 2 + angle_coeff @angle:nd-n-p2 harmonic 102.805 117.210 # CORR 2 + angle_coeff @angle:nd-n-pd harmonic 102.474 117.210 # CORR 2 + angle_coeff @angle:nh-n-nh harmonic 106.329 115.180 # SOURCE3 1 + angle_coeff @angle:n-n-n harmonic 106.384 114.620 # SOURCE3 1 + angle_coeff @angle:no-n-no harmonic 105.383 108.660 # SOURCE3 1 + angle_coeff @angle:br-no-o harmonic 72.469 113.190 # SOURCE3 2 + angle_coeff @angle:c1-no-o harmonic 89.075 116.630 # SOURCE3 6 + angle_coeff @angle:c2-no-o harmonic 86.856 117.670 # SOURCE3_SOURCE5 49 0.7530 + angle_coeff @angle:c3-no-o harmonic 83.512 116.930 # SOURCE3_SOURCE5 182 0.7108 + angle_coeff @angle:ca-no-o harmonic 85.942 117.760 # SOURCE3_SOURCE5 886 0.2929 + angle_coeff @angle:cc-no-o harmonic 87.737 117.490 # SOURCE4_SOURCE5 624 0.5662 + angle_coeff @angle:cl-no-o harmonic 86.532 115.080 # SOURCE3 2 + angle_coeff @angle:c-no-o harmonic 83.834 115.260 # SOURCE3 1 + angle_coeff @angle:hn-no-o harmonic 67.449 115.490 # SOURCE3 2 + angle_coeff @angle:oh-n-oh harmonic 109.825 107.260 # SOURCE3 1 + angle_coeff @angle:i-no-o harmonic 70.372 116.310 # SOURCE3 2 + angle_coeff @angle:n1-no-o harmonic 112.600 115.000 # HF/6-31G* 1 + angle_coeff @angle:n2-no-o harmonic 110.021 116.520 # SOURCE2_SOURCE5 17 2.4833 + angle_coeff @angle:n3-no-o harmonic 111.860 116.770 # SOURCE3_SOURCE5 35 0.4158 + angle_coeff @angle:n4-no-o harmonic 111.250 109.000 # SOURCE3 2 + angle_coeff @angle:na-no-o harmonic 110.472 115.570 # SOURCE3_SOURCE5 29 0.5293 + angle_coeff @angle:nh-no-o harmonic 112.798 116.080 # SOURCE3_SOURCE5 32 0.8573 + angle_coeff @angle:n-no-o harmonic 109.317 115.590 # SOURCE3_SOURCE5 14 0.7108 + angle_coeff @angle:no-no-o harmonic 91.614 112.380 # SOURCE3 4 + angle_coeff @angle:o-n-o harmonic 113.464 128.610 # SOURCE3 3 1.0626 + angle_coeff @angle:o-no-o harmonic 116.649 125.080 # SOURCE4_SOURCE5 1464 0.8585 + angle_coeff @angle:o-no-oh harmonic 112.426 114.700 # SOURCE3 2 + angle_coeff @angle:o-no-os harmonic 111.586 114.760 # SOURCE3_SOURCE5 147 2.2227 + angle_coeff @angle:o-no-p2 harmonic 103.970 117.380 # SOURCE3 20 0.8083 + angle_coeff @angle:o-no-p3 harmonic 98.510 116.780 # SOURCE3 6 0.4929 + angle_coeff @angle:o-no-p4 harmonic 97.206 116.640 # SOURCE3 6 0.0089 + angle_coeff @angle:o-no-p5 harmonic 99.077 116.690 # SOURCE3 8 0.4507 + angle_coeff @angle:o-no-s4 harmonic 71.457 114.490 # SOURCE3 6 0.5674 + angle_coeff @angle:o-no-s6 harmonic 72.259 114.390 # SOURCE3 6 0.8311 + angle_coeff @angle:o-no-s harmonic 80.020 119.810 # SOURCE3 4 0.0042 + angle_coeff @angle:o-no-sh harmonic 78.649 116.100 # SOURCE3 2 + angle_coeff @angle:o-no-ss harmonic 77.822 115.580 # SOURCE3 6 0.5860 + angle_coeff @angle:os-n-os harmonic 109.989 106.530 # SOURCE3 1 + angle_coeff @angle:p2-n-p2 harmonic 103.580 119.620 # SOURCE3 1 + angle_coeff @angle:p3-n-p3 harmonic 106.372 108.730 # SOURCE3 3 0.2591 + angle_coeff @angle:p4-n-p4 harmonic 108.671 108.550 # SOURCE3 1 + angle_coeff @angle:p5-n-p5 harmonic 114.341 99.990 # SOURCE3 1 + angle_coeff @angle:pc-n-pc harmonic 103.163 119.620 # SOURCE3 1 + angle_coeff @angle:pd-n-pd harmonic 103.163 119.620 # SOURCE3 1 + angle_coeff @angle:s4-n-s4 harmonic 63.214 113.750 # SOURCE3 1 + angle_coeff @angle:s6-n-s6 harmonic 63.403 119.680 # SOURCE3 1 + angle_coeff @angle:sh-n-sh harmonic 63.230 119.030 # SOURCE3 1 + angle_coeff @angle:s-n-s harmonic 60.100 126.000 # SOURCE3 1 + angle_coeff @angle:ss-n-ss harmonic 63.451 118.490 # SOURCE3 1 + angle_coeff @angle:br-oh-ho harmonic 43.172 101.600 # SOURCE3 1 + angle_coeff @angle:c1-oh-ho harmonic 51.954 108.760 # SOURCE3 1 + angle_coeff @angle:c2-oh-ho harmonic 51.795 107.630 # SOURCE3_SOURCE5 86 1.5038 + angle_coeff @angle:c3-oh-ho harmonic 49.027 107.260 # SOURCE3_SOURCE5 7781 0.7665 + angle_coeff @angle:ca-oh-ho harmonic 50.712 108.580 # SOURCE3_SOURCE5 3580 0.7052 + angle_coeff @angle:cc-oh-ho harmonic 51.627 107.120 # CORR_SOURCE5 226 1.6427 + angle_coeff @angle:cd-oh-ho harmonic 51.627 107.120 # CORR_SOURCE5 226 1.6427 + angle_coeff @angle:ce-oh-ho harmonic 51.587 106.830 # CORR_SOURCE5 48 1.2629 + angle_coeff @angle:cf-oh-ho harmonic 51.587 106.830 # CORR_SOURCE5 48 1.2629 + angle_coeff @angle:c-oh-ho harmonic 51.617 106.550 # SOURCE3_SOURCE5 2765 1.0627 + angle_coeff @angle:cl-oh-ho harmonic 50.601 102.400 # SOURCE2 1 + angle_coeff @angle:cx-oh-ho harmonic 51.376 106.170 # SOURCE3 3 0.0644 + angle_coeff @angle:cy-oh-ho harmonic 49.289 107.690 # SOURCE4_SOURCE5 21 0.5952 + angle_coeff @angle:f-oh-ho harmonic 64.650 96.800 # SOURCE2 1 + angle_coeff @angle:ho-oh-ho harmonic 42.178 106.490 # SOURCE2_SOURCE5 23 1.3050 + angle_coeff @angle:ho-oh-i harmonic 37.979 107.980 # SOURCE3 2 + angle_coeff @angle:ho-oh-n1 harmonic 66.474 107.810 # HF/6-31G* 1 + angle_coeff @angle:ho-oh-n2 harmonic 63.987 103.090 # SOURCE3_SOURCE5 185 1.2900 + angle_coeff @angle:ho-oh-n3 harmonic 63.233 102.260 # SOURCE3_SOURCE5 28 0.5790 + angle_coeff @angle:ho-oh-n4 harmonic 62.546 106.630 # SOURCE3 3 0.2770 + angle_coeff @angle:ho-oh-n harmonic 63.907 101.290 # SOURCE3_SOURCE5 114 1.0315 + angle_coeff @angle:ho-oh-na harmonic 63.538 104.370 # SOURCE3_SOURCE5 16 0.9188 + angle_coeff @angle:ho-oh-nh harmonic 63.021 102.770 # SOURCE4_SOURCE5 57 0.7554 + angle_coeff @angle:ho-oh-no harmonic 63.640 102.170 # SOURCE3 1 + angle_coeff @angle:ho-oh-o harmonic 59.432 100.870 # SOURCE3 1 + angle_coeff @angle:ho-oh-oh harmonic 62.055 98.720 # SOURCE3 2 + angle_coeff @angle:ho-oh-os harmonic 62.321 99.680 # SOURCE4_SOURCE5 45 0.3142 + angle_coeff @angle:ho-oh-p2 harmonic 58.567 109.450 # SOURCE3 8 3.3491 + angle_coeff @angle:ho-oh-p3 harmonic 56.437 110.640 # SOURCE3 3 0.5191 + angle_coeff @angle:ho-oh-p4 harmonic 57.939 110.190 # SOURCE3 4 0.2372 + angle_coeff @angle:ho-oh-p5 harmonic 58.997 110.080 # SOURCE3_SOURCE5 1074 1.1258 + angle_coeff @angle:ho-oh-py harmonic 58.835 110.490 # SOURCE3_SOURCE5 115 1.4927 + angle_coeff @angle:ho-oh-s4 harmonic 44.189 106.850 # SOURCE4_SOURCE5 28 0.5669 + angle_coeff @angle:ho-oh-s harmonic 42.242 100.150 # SOURCE3 2 + angle_coeff @angle:ho-oh-s6 harmonic 45.957 107.260 # SOURCE3_SOURCE5 180 0.7965 + angle_coeff @angle:ho-oh-sh harmonic 44.429 106.240 # SOURCE3 2 0.0661 + angle_coeff @angle:ho-oh-ss harmonic 44.367 107.110 # SOURCE3_SOURCE5 12 1.0472 + angle_coeff @angle:ho-oh-sy harmonic 45.671 106.420 # SOURCE4_SOURCE5 121 0.3216 + angle_coeff @angle:br-os-br harmonic 67.436 110.630 # SOURCE3 1 + angle_coeff @angle:c1-os-c1 harmonic 71.202 115.020 # SOURCE3 1 + angle_coeff @angle:c1-os-c3 harmonic 68.518 113.390 # SOURCE3 1 + angle_coeff @angle:c2-os-c2 harmonic 69.600 113.140 # SOURCE3 6 2.1932 + angle_coeff @angle:c2-os-c3 harmonic 66.993 115.590 # SOURCE3_SOURCE5 149 2.3501 + angle_coeff @angle:c2-os-ca harmonic 67.843 118.200 # SOURCE3_SOURCE5 13 0.6779 + angle_coeff @angle:c2-os-n2 harmonic 83.963 118.130 # SOURCE3 1 + angle_coeff @angle:c2-os-na harmonic 88.073 103.850 # SOURCE3 4 0.6297 + angle_coeff @angle:c2-os-os harmonic 87.781 102.770 # SOURCE3 1 + angle_coeff @angle:c2-os-p5 harmonic 82.312 126.370 # SOURCE4 7 1.7939 + angle_coeff @angle:c2-os-ss harmonic 66.609 108.130 # SOURCE3 1 + angle_coeff @angle:c3-os-c3 harmonic 66.293 112.480 # SOURCE4_SOURCE5 4012 1.7399 + angle_coeff @angle:c3-os-ca harmonic 66.103 117.960 # SOURCE4_SOURCE5 7354 1.4497 + angle_coeff @angle:c3-os-cc harmonic 66.432 117.370 # CORR_SOURCE5 411 1.1548 + angle_coeff @angle:c3-os-cd harmonic 66.432 117.370 # CORR_SOURCE5 411 1.1548 + angle_coeff @angle:c3-os-ce harmonic 66.603 116.090 # CORR_SOURCE5 59 1.9942 + angle_coeff @angle:c3-os-cf harmonic 66.603 116.090 # CORR_SOURCE5 59 1.9942 + angle_coeff @angle:c3-os-cl harmonic 71.832 110.500 # SOURCE2 1 + angle_coeff @angle:c3-os-cy harmonic 66.337 111.750 # SOURCE4_SOURCE5 19 0.7990 + angle_coeff @angle:c3-os-i harmonic 59.723 113.700 # SOURCE3 1 + angle_coeff @angle:c3-os-n1 harmonic 85.969 113.500 # HF/6-31G* 1 + angle_coeff @angle:c3-os-n2 harmonic 85.118 109.230 # SOURCE3_SOURCE5 93 0.8090 + angle_coeff @angle:c3-os-n3 harmonic 83.747 109.830 # SOURCE4_SOURCE5 46 1.7350 + angle_coeff @angle:c3-os-n4 harmonic 84.065 110.500 # SOURCE3 3 0.5426 + angle_coeff @angle:c3-os-n harmonic 84.730 109.680 # SOURCE4_SOURCE5 42 0.9897 + angle_coeff @angle:c3-os-na harmonic 83.212 110.980 # SOURCE3_SOURCE5 17 1.2781 + angle_coeff @angle:c3-os-nc harmonic 83.792 112.730 # SOURCE3 2 1.0358 + angle_coeff @angle:c3-os-nd harmonic 83.792 112.730 # SOURCE3 2 + angle_coeff @angle:c3-os-nh harmonic 84.502 109.790 # SOURCE4_SOURCE5 22 0.2157 + angle_coeff @angle:c3-os-no harmonic 82.802 113.890 # SOURCE4_SOURCE5 112 0.3140 + angle_coeff @angle:c3-os-o harmonic 84.510 103.000 # SOURCE3 1 + angle_coeff @angle:c3-os-oh harmonic 83.965 108.110 # SOURCE4_SOURCE5 34 0.5701 + angle_coeff @angle:c3-os-os harmonic 83.957 107.370 # SOURCE3_SOURCE5 55 0.9835 + angle_coeff @angle:c3-os-p2 harmonic 86.122 115.470 # SOURCE3 8 2.6374 + angle_coeff @angle:c3-os-p3 harmonic 81.943 117.510 # SOURCE3_SOURCE5 11 0.9552 + angle_coeff @angle:c3-os-p4 harmonic 83.257 117.480 # SOURCE3 4 0.3850 + angle_coeff @angle:c3-os-p5 harmonic 83.251 119.540 # SOURCE3_SOURCE5 665 1.1338 + angle_coeff @angle:c3-os-py harmonic 83.113 119.570 # SOURCE3_SOURCE5 59 1.1952 + angle_coeff @angle:c3-os-s4 harmonic 64.572 113.210 # SOURCE3_SOURCE5 18 1.1865 + angle_coeff @angle:c3-os-s6 harmonic 65.683 115.870 # SOURCE4_SOURCE5 144 1.2750 + angle_coeff @angle:c3-os-s harmonic 62.691 109.550 # SOURCE3 1 + angle_coeff @angle:c3-os-sh harmonic 65.257 112.820 # SOURCE3 1 + angle_coeff @angle:c3-os-ss harmonic 64.028 114.010 # SOURCE3_SOURCE5 8 0.2853 + angle_coeff @angle:ca-os-ca harmonic 67.119 119.890 # SOURCE4_SOURCE5 312 1.5712 + angle_coeff @angle:ca-os-cc harmonic 69.301 113.080 # CORR_SOURCE5 343 1.5098 + angle_coeff @angle:ca-os-cd harmonic 69.301 113.080 # CORR_SOURCE5 343 1.5098 + angle_coeff @angle:ca-os-n3 harmonic 84.583 112.190 # SOURCE3 1 + angle_coeff @angle:ca-os-na harmonic 85.998 108.240 # SOURCE3 1 + angle_coeff @angle:ca-os-nc harmonic 86.989 109.320 # SOURCE3_SOURCE5 7 0.0434 + angle_coeff @angle:ca-os-nd harmonic 86.989 109.320 # SOURCE3_SOURCE5 7 0.0434 + angle_coeff @angle:ca-os-p5 harmonic 83.193 123.180 # SOURCE4_SOURCE5 136 1.2191 + angle_coeff @angle:ca-os-s6 harmonic 66.238 117.180 # SOURCE4_SOURCE5 46 1.0420 + angle_coeff @angle:c-os-c2 harmonic 68.118 118.220 # SOURCE4_SOURCE5 22 0.6933 + angle_coeff @angle:c-os-c3 harmonic 66.906 115.980 # SOURCE3_SOURCE5 2731 1.0103 + angle_coeff @angle:c-os-c harmonic 67.462 120.640 # SOURCE4 7 1.5114 + angle_coeff @angle:c-os-ca harmonic 67.041 121.150 # SOURCE4_SOURCE5 731 1.7389 + angle_coeff @angle:c-os-cc harmonic 67.659 119.620 # SOURCE3 5 6.0675 + angle_coeff @angle:cc-os-cc harmonic 71.537 106.720 # CORR_SOURCE5 406 0.7345 + angle_coeff @angle:cc-os-cd harmonic 67.837 118.680 # SOURCE4_SOURCE5 49 2.2289 + angle_coeff @angle:c-os-cd harmonic 67.659 119.620 # SOURCE3 5 6.0675 + angle_coeff @angle:cc-os-na harmonic 84.874 111.660 # SOURCE3 28 4.1343 + angle_coeff @angle:cc-os-nc harmonic 87.598 108.370 # SOURCE3_SOURCE5 148 0.8594 + angle_coeff @angle:cc-os-os harmonic 85.382 108.470 # SOURCE3 2 + angle_coeff @angle:cc-os-ss harmonic 63.313 119.590 # SOURCE3 1 + angle_coeff @angle:c-os-cy harmonic 75.270 91.100 # SOURCE3 2 0.0155 + angle_coeff @angle:cd-os-cd harmonic 71.537 106.720 # CORR_SOURCE5 406 0.7345 + angle_coeff @angle:cd-os-na harmonic 84.874 111.660 # SOURCE3 28 4.1343 + angle_coeff @angle:cd-os-nd harmonic 87.598 108.370 # SOURCE3_SOURCE5 148 0.8594 + angle_coeff @angle:cd-os-os harmonic 85.382 108.470 # SOURCE3 2 + angle_coeff @angle:cd-os-ss harmonic 63.313 119.590 # SOURCE3 1 + angle_coeff @angle:cl-os-cl harmonic 80.567 110.760 # SOURCE3 2 + angle_coeff @angle:c-os-n2 harmonic 86.219 112.120 # SOURCE4_SOURCE5 16 0.1285 + angle_coeff @angle:c-os-n harmonic 85.927 112.240 # SOURCE4_SOURCE5 17 0.6206 + angle_coeff @angle:c-os-oh harmonic 85.021 110.500 # SOURCE3 1 + angle_coeff @angle:c-os-os harmonic 84.800 110.200 # SOURCE4_SOURCE5 22 1.3187 + angle_coeff @angle:c-os-p5 harmonic 83.749 122.130 # SOURCE4_SOURCE5 11 0.5685 + angle_coeff @angle:c-os-sy harmonic 65.179 113.490 # SOURCE3 1 + angle_coeff @angle:cx-os-cx harmonic 89.127 61.780 # SOURCE4_SOURCE5 379 0.2104 + angle_coeff @angle:cx-os-n harmonic 114.351 59.990 # SOURCE3 1 + angle_coeff @angle:cx-os-os harmonic 115.519 56.520 # SOURCE3 2 + angle_coeff @angle:cy-os-cy harmonic 72.980 91.860 # SOURCE2_SOURCE5 16 1.0042 + angle_coeff @angle:f-os-f harmonic 112.297 103.300 # SOURCE2 1 + angle_coeff @angle:f-os-os harmonic 105.904 109.500 # SOURCE2 1 + angle_coeff @angle:i-os-i harmonic 65.023 115.670 # SOURCE3 1 + angle_coeff @angle:n1-os-n1 harmonic 111.016 117.790 # HF/6-31G* 1 + angle_coeff @angle:n2-os-n2 harmonic 108.962 106.830 # SOURCE3 1 + angle_coeff @angle:n2-os-s6 harmonic 84.516 111.300 # SOURCE4_SOURCE5 14 0.5651 + angle_coeff @angle:n3-os-n3 harmonic 106.985 104.880 # SOURCE3 1 + angle_coeff @angle:n4-os-n4 harmonic 103.723 114.680 # SOURCE3 1 + angle_coeff @angle:na-os-na harmonic 104.414 109.590 # SOURCE3 1 + angle_coeff @angle:na-os-ss harmonic 83.603 104.340 # SOURCE3 1 + angle_coeff @angle:nc-os-nc harmonic 106.078 112.750 # SOURCE2_SOURCE5 12 0.7540 + angle_coeff @angle:nc-os-ss harmonic 81.743 110.970 # SOURCE3 1 + angle_coeff @angle:nd-os-nd harmonic 106.078 112.750 # SOURCE2_SOURCE5 12 0.7540 + angle_coeff @angle:nd-os-ss harmonic 81.743 110.970 # SOURCE3 1 + angle_coeff @angle:nh-os-nh harmonic 107.169 108.290 # SOURCE3 1 + angle_coeff @angle:n-os-n harmonic 107.646 108.310 # SOURCE3 1 + angle_coeff @angle:no-os-no harmonic 105.015 111.860 # SOURCE3 1 + angle_coeff @angle:n-os-s6 harmonic 83.504 113.630 # SOURCE4_SOURCE5 13 0.1799 + angle_coeff @angle:o-os-o harmonic 97.999 114.680 # SOURCE3 1 + angle_coeff @angle:p2-os-p2 harmonic 112.427 120.020 # SOURCE3 1 + angle_coeff @angle:p2-os-p5 harmonic 117.003 107.860 # SOURCE3 1 + angle_coeff @angle:p3-os-p3 harmonic 105.094 121.220 # SOURCE3 1 + angle_coeff @angle:p3-os-py harmonic 114.455 105.580 # SOURCE3 1 + angle_coeff @angle:p5-os-p5 harmonic 106.787 126.250 # SOURCE3 1 + angle_coeff @angle:s4-os-s4 harmonic 65.797 111.630 # SOURCE3 1 + angle_coeff @angle:s6-os-s6 harmonic 66.445 119.070 # SOURCE3 2 0.4318 + angle_coeff @angle:sh-os-sh harmonic 64.549 118.950 # SOURCE3 1 + angle_coeff @angle:s-os-s harmonic 60.143 118.080 # SOURCE3 1 + angle_coeff @angle:ss-os-ss harmonic 64.198 115.640 # SOURCE3 1 + angle_coeff @angle:br-p2-br harmonic 50.367 108.600 # SOURCE3 1 + angle_coeff @angle:br-p2-c2 harmonic 49.320 102.320 # SOURCE3 2 0.0146 + angle_coeff @angle:br-p2-n2 harmonic 61.779 103.330 # SOURCE3 1 + angle_coeff @angle:br-p2-o harmonic 59.925 110.870 # SOURCE3 1 + angle_coeff @angle:br-p2-p2 harmonic 63.559 115.460 # SOURCE3 4 7.8622 + angle_coeff @angle:br-p2-s harmonic 50.714 110.520 # SOURCE3 1 + angle_coeff @angle:c1-p2-c1 harmonic 49.523 99.040 # SOURCE3 1 + angle_coeff @angle:c1-p2-c2 harmonic 50.326 101.290 # SOURCE3 1 + angle_coeff @angle:c1-p2-n2 harmonic 63.856 101.790 # SOURCE3 1 + angle_coeff @angle:c1-p2-o harmonic 63.431 107.620 # SOURCE3 1 + angle_coeff @angle:c1-p2-p2 harmonic 68.223 99.540 # SOURCE3 1 + angle_coeff @angle:c1-p2-s harmonic 51.746 105.900 # SOURCE3 1 + angle_coeff @angle:c2-p2-c2 harmonic 51.141 104.500 # SOURCE3 1 + angle_coeff @angle:c2-p2-c3 harmonic 48.776 101.900 # SOURCE3 4 0.1132 + angle_coeff @angle:c2-p2-ca harmonic 49.013 101.950 # SOURCE3 1 + angle_coeff @angle:c2-p2-cl harmonic 54.318 102.720 # SOURCE3 2 + angle_coeff @angle:c2-p2-f harmonic 67.755 103.470 # SOURCE3 2 0.0136 + angle_coeff @angle:c2-p2-hp harmonic 37.280 97.190 # SOURCE3 3 0.0216 + angle_coeff @angle:c2-p2-i harmonic 44.010 101.940 # SOURCE3 2 0.0368 + angle_coeff @angle:c2-p2-n2 harmonic 66.728 99.880 # SOURCE3 1 + angle_coeff @angle:c2-p2-n3 harmonic 64.858 101.800 # SOURCE3 1 + angle_coeff @angle:c2-p2-n4 harmonic 60.347 98.260 # SOURCE3 6 0.1522 + angle_coeff @angle:c2-p2-n harmonic 63.154 103.280 # SOURCE3 4 3.3113 + angle_coeff @angle:c2-p2-na harmonic 62.619 103.990 # SOURCE3 8 1.6834 + angle_coeff @angle:c2-p2-nh harmonic 63.638 105.170 # SOURCE3 8 0.8263 + angle_coeff @angle:c2-p2-no harmonic 64.740 97.970 # SOURCE3 3 0.4175 + angle_coeff @angle:c2-p2-o harmonic 63.763 115.160 # SOURCE3 1 + angle_coeff @angle:c2-p2-oh harmonic 65.278 102.890 # SOURCE3 3 0.8191 + angle_coeff @angle:c2-p2-os harmonic 66.578 102.120 # SOURCE3 4 0.8783 + angle_coeff @angle:c2-p2-p2 harmonic 70.059 99.560 # SOURCE3 1 + angle_coeff @angle:c2-p2-p3 harmonic 61.583 99.270 # SOURCE3 4 1.1590 + angle_coeff @angle:c2-p2-p4 harmonic 61.685 96.940 # SOURCE3 1 + angle_coeff @angle:c2-p2-p5 harmonic 61.450 97.610 # SOURCE3 1 + angle_coeff @angle:c2-p2-s4 harmonic 48.314 95.150 # SOURCE3 1 + angle_coeff @angle:c2-p2-s6 harmonic 48.407 95.510 # SOURCE3 1 + angle_coeff @angle:c2-p2-s harmonic 53.268 105.530 # SOURCE3 1 + angle_coeff @angle:c2-p2-sh harmonic 50.735 101.490 # SOURCE3 3 0.0057 + angle_coeff @angle:c2-p2-ss harmonic 50.746 101.810 # SOURCE3 4 0.5883 + angle_coeff @angle:c3-p2-c3 harmonic 47.191 99.300 # SOURCE3 1 + angle_coeff @angle:c3-p2-n2 harmonic 62.233 100.820 # SOURCE3 1 + angle_coeff @angle:c3-p2-o harmonic 61.561 106.720 # SOURCE3 1 + angle_coeff @angle:c3-p2-os harmonic 62.459 101.340 # SOURCE3 1 + angle_coeff @angle:c3-p2-p2 harmonic 66.273 100.480 # SOURCE3 1 + angle_coeff @angle:c3-p2-s harmonic 50.533 105.680 # SOURCE3 1 + angle_coeff @angle:ca-p2-ca harmonic 47.481 99.700 # SOURCE3 1 + angle_coeff @angle:ca-p2-n2 harmonic 62.575 100.820 # SOURCE3 1 + angle_coeff @angle:ca-p2-n harmonic 64.349 89.970 # SOURCE3 1 + angle_coeff @angle:ca-p2-na harmonic 64.367 89.210 # SOURCE3 1 + angle_coeff @angle:ca-p2-o harmonic 61.891 106.880 # SOURCE3 1 + angle_coeff @angle:ca-p2-s harmonic 50.228 107.930 # SOURCE3 1 + angle_coeff @angle:c-p2-c2 harmonic 49.148 97.300 # SOURCE3 1 + angle_coeff @angle:c-p2-c harmonic 48.369 90.100 # SOURCE3 1 + angle_coeff @angle:ce-p2-o harmonic 62.381 107.440 # SOURCE3 1 + angle_coeff @angle:ce-p2-s harmonic 51.184 105.540 # SOURCE3 1 + angle_coeff @angle:cf-p2-o harmonic 62.381 107.440 # SOURCE3 1 + angle_coeff @angle:cf-p2-s harmonic 51.184 105.540 # SOURCE3 1 + angle_coeff @angle:cl-p2-cl harmonic 58.906 108.700 # SOURCE3 1 + angle_coeff @angle:cl-p2-n2 harmonic 68.360 103.380 # SOURCE3 1 + angle_coeff @angle:cl-p2-o harmonic 66.726 110.570 # SOURCE3 1 + angle_coeff @angle:cl-p2-p2 harmonic 73.823 103.110 # SOURCE3 1 + angle_coeff @angle:cl-p2-s harmonic 55.803 110.110 # SOURCE3 1 + angle_coeff @angle:f-p2-f harmonic 88.550 107.100 # SOURCE3 1 + angle_coeff @angle:f-p2-n2 harmonic 86.735 103.570 # SOURCE3 1 + angle_coeff @angle:f-p2-o harmonic 86.673 110.610 # SOURCE3 1 + angle_coeff @angle:f-p2-p2 harmonic 89.962 103.480 # SOURCE3 1 + angle_coeff @angle:f-p2-s harmonic 66.939 114.710 # SOURCE3 2 5.2794 + angle_coeff @angle:hp-p2-hp harmonic 27.644 98.760 # SOURCE3 1 + angle_coeff @angle:hp-p2-n1 harmonic 46.969 95.180 # SOURCE3 2 1.5708 + angle_coeff @angle:hp-p2-n2 harmonic 48.480 95.540 # SOURCE3 19 4.7352 + angle_coeff @angle:hp-p2-ne harmonic 48.264 100.100 # SOURCE3 14 6.1290 + angle_coeff @angle:hp-p2-nf harmonic 48.264 100.100 # SOURCE3 14 + angle_coeff @angle:hp-p2-o harmonic 48.141 105.580 # SOURCE3 1 + angle_coeff @angle:hp-p2-p2 harmonic 47.796 101.880 # SOURCE3 27 12.9535 + angle_coeff @angle:hp-p2-p4 harmonic 40.954 94.510 # SOURCE3 1 + angle_coeff @angle:hp-p2-p5 harmonic 42.165 89.070 # SOURCE3 1 + angle_coeff @angle:hp-p2-pe harmonic 47.048 97.250 # SOURCE3 16 8.8916 + angle_coeff @angle:hp-p2-pf harmonic 47.048 97.250 # SOURCE3 16 + angle_coeff @angle:hp-p2-s4 harmonic 32.527 89.990 # SOURCE3 1 + angle_coeff @angle:hp-p2-s harmonic 37.377 102.520 # SOURCE3 1 + angle_coeff @angle:hp-p2-s6 harmonic 33.031 88.130 # SOURCE3 1 + angle_coeff @angle:i-p2-i harmonic 47.836 104.160 # SOURCE3 1 + angle_coeff @angle:i-p2-n2 harmonic 55.025 101.770 # SOURCE3 1 + angle_coeff @angle:i-p2-o harmonic 52.674 109.510 # SOURCE3 1 + angle_coeff @angle:i-p2-p2 harmonic 60.877 102.630 # SOURCE3 1 + angle_coeff @angle:i-p2-s harmonic 45.705 110.600 # SOURCE3 1 + angle_coeff @angle:n1-p2-n1 harmonic 87.795 86.220 # HF/6-31G* 1 + angle_coeff @angle:n2-p2-n2 harmonic 86.095 98.000 # SOURCE3 1 + angle_coeff @angle:n2-p2-n3 harmonic 83.297 100.420 # SOURCE3 1 + angle_coeff @angle:n2-p2-n4 harmonic 78.374 93.420 # SOURCE3 1 + angle_coeff @angle:n2-p2-na harmonic 80.458 102.030 # SOURCE3 1 + angle_coeff @angle:n2-p2-nh harmonic 82.457 101.870 # SOURCE3 2 0.8491 + angle_coeff @angle:n2-p2-no harmonic 82.358 98.120 # SOURCE3 1 + angle_coeff @angle:n2-p2-o harmonic 81.674 115.340 # SOURCE3 1 + angle_coeff @angle:n2-p2-oh harmonic 80.728 109.720 # SOURCE3 1 + angle_coeff @angle:n2-p2-os harmonic 85.101 102.290 # SOURCE3 1 + angle_coeff @angle:n2-p2-p3 harmonic 77.520 99.510 # SOURCE3 1 + angle_coeff @angle:n2-p2-p4 harmonic 75.847 101.730 # SOURCE3 1 + angle_coeff @angle:n2-p2-p5 harmonic 79.007 93.680 # SOURCE3 1 + angle_coeff @angle:n2-p2-s4 harmonic 60.003 97.830 # SOURCE3 1 + angle_coeff @angle:n2-p2-s6 harmonic 60.149 98.140 # SOURCE3 1 + angle_coeff @angle:n2-p2-s harmonic 65.491 112.940 # SOURCE3 1 + angle_coeff @angle:n2-p2-sh harmonic 64.416 100.820 # SOURCE3 1 + angle_coeff @angle:n2-p2-ss harmonic 64.240 101.760 # SOURCE3 1 + angle_coeff @angle:n3-p2-n3 harmonic 79.448 106.300 # SOURCE3 1 + angle_coeff @angle:n3-p2-o harmonic 82.859 106.830 # SOURCE3 1 + angle_coeff @angle:n3-p2-p2 harmonic 87.256 100.580 # SOURCE3 1 + angle_coeff @angle:n3-p2-s harmonic 66.611 105.750 # SOURCE3 1 + angle_coeff @angle:n4-p2-n4 harmonic 74.750 88.800 # SOURCE3 1 + angle_coeff @angle:n4-p2-o harmonic 76.313 101.360 # SOURCE3 1 + angle_coeff @angle:n4-p2-p2 harmonic 82.466 96.530 # SOURCE3 1 + angle_coeff @angle:n4-p2-s harmonic 61.808 104.980 # SOURCE3 1 + angle_coeff @angle:na-p2-na harmonic 75.931 106.100 # SOURCE3 1 + angle_coeff @angle:na-p2-o harmonic 80.149 107.460 # SOURCE3 1 + angle_coeff @angle:na-p2-s harmonic 64.498 108.150 # SOURCE3 1 + angle_coeff @angle:ne-p2-o harmonic 85.784 107.710 # SOURCE3 1 + angle_coeff @angle:ne-p2-s harmonic 68.411 105.500 # SOURCE3 1 + angle_coeff @angle:nf-p2-o harmonic 85.784 107.710 # SOURCE3 1 + angle_coeff @angle:nf-p2-s harmonic 68.411 105.500 # SOURCE3 1 + angle_coeff @angle:nh-p2-nh harmonic 79.891 104.000 # SOURCE3 1 + angle_coeff @angle:nh-p2-o harmonic 82.088 108.110 # SOURCE3 2 0.6773 + angle_coeff @angle:nh-p2-p2 harmonic 84.120 107.730 # SOURCE3 3 3.1678 + angle_coeff @angle:nh-p2-s harmonic 65.274 109.620 # SOURCE3 2 1.7725 + angle_coeff @angle:n-p2-n2 harmonic 82.195 98.850 # SOURCE3 1 + angle_coeff @angle:n-p2-o harmonic 81.559 105.080 # SOURCE3 1 + angle_coeff @angle:no-p2-no harmonic 79.425 98.200 # SOURCE3 1 + angle_coeff @angle:no-p2-o harmonic 81.482 104.870 # SOURCE3 1 + angle_coeff @angle:no-p2-p2 harmonic 82.518 108.570 # SOURCE3 3 8.2121 + angle_coeff @angle:no-p2-s harmonic 64.423 109.060 # SOURCE3 2 5.4074 + angle_coeff @angle:n-p2-p2 harmonic 85.198 102.120 # SOURCE3 1 + angle_coeff @angle:n-p2-s harmonic 63.562 112.340 # SOURCE3 1 + angle_coeff @angle:oh-p2-oh harmonic 83.880 100.100 # SOURCE3 1 + angle_coeff @angle:oh-p2-p2 harmonic 85.099 107.820 # SOURCE3 2 2.6708 + angle_coeff @angle:oh-p2-s harmonic 66.041 109.750 # SOURCE3 1 + angle_coeff @angle:o-p2-o harmonic 82.822 119.960 # SOURCE3 1 + angle_coeff @angle:o-p2-oh harmonic 82.704 110.460 # SOURCE3 1 + angle_coeff @angle:o-p2-os harmonic 85.052 108.810 # SOURCE3 1 + angle_coeff @angle:o-p2-p2 harmonic 84.879 114.230 # SOURCE3 1 + angle_coeff @angle:o-p2-p3 harmonic 75.364 106.690 # SOURCE3 1 + angle_coeff @angle:o-p2-p4 harmonic 75.313 104.370 # SOURCE3 1 + angle_coeff @angle:o-p2-p5 harmonic 75.237 104.490 # SOURCE3 1 + angle_coeff @angle:o-p2-pe harmonic 72.675 145.960 # SOURCE3 1 + angle_coeff @angle:o-p2-pf harmonic 72.675 145.960 # SOURCE3 1 + angle_coeff @angle:o-p2-s4 harmonic 57.795 106.590 # SOURCE3 1 + angle_coeff @angle:o-p2-s6 harmonic 58.473 105.040 # SOURCE3 1 + angle_coeff @angle:o-p2-s harmonic 65.598 117.420 # SOURCE3 1 + angle_coeff @angle:o-p2-sh harmonic 62.592 109.600 # SOURCE3 1 + angle_coeff @angle:os-p2-os harmonic 87.712 98.300 # SOURCE3 1 + angle_coeff @angle:os-p2-p2 harmonic 88.869 101.460 # SOURCE3 1 + angle_coeff @angle:o-p2-ss harmonic 62.723 109.600 # SOURCE3 1 + angle_coeff @angle:os-p2-s harmonic 67.319 108.470 # SOURCE3 3 1.7065 + angle_coeff @angle:p2-p2-n2 harmonic 90.057 97.400 # SOURCE3 1 + angle_coeff @angle:p2-p2-p3 harmonic 83.101 101.730 # SOURCE3 1 + angle_coeff @angle:p2-p2-p4 harmonic 82.238 101.980 # SOURCE3 1 + angle_coeff @angle:p2-p2-p5 harmonic 83.299 99.330 # SOURCE3 1 + angle_coeff @angle:p2-p2-s4 harmonic 65.891 95.730 # SOURCE3 1 + angle_coeff @angle:p2-p2-s6 harmonic 66.042 95.950 # SOURCE3 1 + angle_coeff @angle:p2-p2-s harmonic 69.717 111.280 # SOURCE3 1 + angle_coeff @angle:p2-p2-sh harmonic 64.935 113.940 # SOURCE3 3 8.5009 + angle_coeff @angle:p3-p2-p3 harmonic 77.638 101.000 # SOURCE3 1 + angle_coeff @angle:p3-p2-s harmonic 61.492 113.280 # SOURCE3 2 6.7035 + angle_coeff @angle:p4-p2-s harmonic 63.615 103.890 # SOURCE3 1 + angle_coeff @angle:p5-p2-p5 harmonic 81.461 89.400 # SOURCE3 1 + angle_coeff @angle:p5-p2-s harmonic 64.429 101.210 # SOURCE3 1 + angle_coeff @angle:pe-p2-s harmonic 69.635 106.350 # SOURCE3 1 + angle_coeff @angle:pf-p2-s harmonic 69.635 106.350 # SOURCE3 1 + angle_coeff @angle:s4-p2-s4 harmonic 50.406 85.300 # SOURCE3 1 + angle_coeff @angle:s6-p2-s6 harmonic 47.194 98.200 # SOURCE3 1 + angle_coeff @angle:sh-p2-sh harmonic 52.119 98.500 # SOURCE3 1 + angle_coeff @angle:s-p2-s harmonic 55.726 106.600 # SOURCE3 1 + angle_coeff @angle:s-p2-s4 harmonic 49.051 105.290 # SOURCE3 1 + angle_coeff @angle:s-p2-s6 harmonic 48.843 106.930 # SOURCE3 1 + angle_coeff @angle:s-p2-sh harmonic 51.478 110.730 # SOURCE3 2 0.0232 + angle_coeff @angle:s-p2-ss harmonic 50.784 114.140 # SOURCE3 4 5.9223 + angle_coeff @angle:ss-p2-ss harmonic 52.411 97.900 # SOURCE3 1 + angle_coeff @angle:br-p3-br harmonic 51.098 103.540 # SOURCE3 1 + angle_coeff @angle:br-p3-hp harmonic 32.984 96.360 # SOURCE3 4 0.6701 + angle_coeff @angle:c1-p3-c1 harmonic 48.612 100.500 # SOURCE3 1 + angle_coeff @angle:c1-p3-f harmonic 66.318 96.900 # SOURCE2 1 + angle_coeff @angle:c1-p3-hp harmonic 34.779 97.670 # SOURCE3 2 + angle_coeff @angle:c2-p3-c2 harmonic 47.149 101.770 # SOURCE3 3 + angle_coeff @angle:c2-p3-hp harmonic 34.073 97.850 # SOURCE3 4 + angle_coeff @angle:c3-p3-c3 harmonic 47.098 99.350 # SOURCE3_SOURCE5 108 0.9814 + angle_coeff @angle:c3-p3-ca harmonic 46.899 101.940 # SOURCE3 2 + angle_coeff @angle:c3-p3-cl harmonic 54.343 99.890 # SOURCE3 1 + angle_coeff @angle:c3-p3-f harmonic 64.355 97.800 # SOURCE2 1 + angle_coeff @angle:c3-p3-hp harmonic 33.769 97.480 # SOURCE3_SOURCE5 20 0.3444 + angle_coeff @angle:c3-p3-n2 harmonic 61.301 96.550 # SOURCE3 2 + angle_coeff @angle:c3-p3-n3 harmonic 60.308 101.410 # SOURCE3_SOURCE5 22 1.5604 + angle_coeff @angle:c3-p3-n4 harmonic 59.355 96.940 # SOURCE3 6 0.4815 + angle_coeff @angle:c3-p3-n harmonic 59.620 101.770 # SOURCE3 12 2.4449 + angle_coeff @angle:c3-p3-na harmonic 60.213 100.170 # SOURCE3 4 0.0554 + angle_coeff @angle:c3-p3-nh harmonic 59.410 104.500 # SOURCE3 2 + angle_coeff @angle:c3-p3-no harmonic 59.922 96.980 # SOURCE3 2 + angle_coeff @angle:c3-p3-o harmonic 60.035 111.670 # SOURCE3 28 5.3387 + angle_coeff @angle:c3-p3-oh harmonic 62.034 98.210 # SOURCE3 2 + angle_coeff @angle:c3-p3-os harmonic 61.657 99.530 # SOURCE3 3 1.7678 + angle_coeff @angle:c3-p3-p3 harmonic 58.575 99.880 # SOURCE3_SOURCE5 26 1.6230 + angle_coeff @angle:c3-p3-p5 harmonic 58.297 100.900 # SOURCE3 10 2.7070 + angle_coeff @angle:c3-p3-s4 harmonic 47.756 98.880 # SOURCE3 8 6.2235 + angle_coeff @angle:c3-p3-s6 harmonic 47.355 101.180 # SOURCE3 12 6.4536 + angle_coeff @angle:c3-p3-sh harmonic 47.131 98.710 # SOURCE3 2 + angle_coeff @angle:c3-p3-ss harmonic 47.137 99.370 # SOURCE3 2 + angle_coeff @angle:ca-p3-ca harmonic 47.814 99.860 # SOURCE3 1 + angle_coeff @angle:ca-p3-hp harmonic 34.261 97.500 # SOURCE3 2 + angle_coeff @angle:c-p3-c3 harmonic 47.331 97.060 # SOURCE3 3 1.1490 + angle_coeff @angle:c-p3-c harmonic 46.120 100.900 # SOURCE3 1 + angle_coeff @angle:c-p3-hp harmonic 33.554 96.550 # SOURCE3 6 0.5223 + angle_coeff @angle:cl-p3-cl harmonic 62.437 102.820 # SOURCE3 1 + angle_coeff @angle:cl-p3-f harmonic 72.784 99.200 # SOURCE2 1 + angle_coeff @angle:cl-p3-hp harmonic 38.308 96.300 # SOURCE3 3 0.6203 + angle_coeff @angle:c-p3-os harmonic 67.637 81.320 # SOURCE3 1 + angle_coeff @angle:cx-p3-hp harmonic 34.036 95.200 # SOURCE2 1 + angle_coeff @angle:f-p3-f harmonic 90.383 97.400 # SOURCE2 8 1.6636 + angle_coeff @angle:f-p3-hp harmonic 48.664 96.410 # SOURCE3 2 + angle_coeff @angle:f-p3-n3 harmonic 83.292 100.600 # SOURCE2 1 + angle_coeff @angle:f-p3-os harmonic 85.509 99.230 # SOURCE2_SOURCE5 5 0.5316 + angle_coeff @angle:f-p3-p3 harmonic 77.745 97.200 # SOURCE2 1 + angle_coeff @angle:hp-p3-hp harmonic 26.638 95.220 # SOURCE3_SOURCE5 51 2.1059 + angle_coeff @angle:hp-p3-i harmonic 29.813 96.190 # SOURCE3 4 0.6454 + angle_coeff @angle:hp-p3-n1 harmonic 47.221 92.980 # HF/6-31G* 1 + angle_coeff @angle:hp-p3-n2 harmonic 43.917 98.280 # SOURCE3 10 1.8860 + angle_coeff @angle:hp-p3-n3 harmonic 45.466 94.460 # SOURCE3 2 + angle_coeff @angle:hp-p3-n4 harmonic 42.822 93.210 # SOURCE3 2 + angle_coeff @angle:hp-p3-n harmonic 44.516 95.150 # SOURCE3 2 + angle_coeff @angle:hp-p3-na harmonic 44.183 97.270 # SOURCE3 12 0.9318 + angle_coeff @angle:hp-p3-nh harmonic 45.553 94.100 # SOURCE3 2 + angle_coeff @angle:hp-p3-no harmonic 43.557 93.060 # SOURCE3 2 + angle_coeff @angle:hp-p3-o harmonic 48.052 101.020 # SOURCE3 2 + angle_coeff @angle:hp-p3-oh harmonic 46.151 95.950 # SOURCE3 2 + angle_coeff @angle:hp-p3-os harmonic 45.868 97.350 # SOURCE3 6 2.8326 + angle_coeff @angle:hp-p3-p2 harmonic 40.595 99.110 # SOURCE3 16 4.3022 + angle_coeff @angle:hp-p3-p3 harmonic 40.175 95.520 # SOURCE3 4 0.0844 + angle_coeff @angle:hp-p3-p4 harmonic 40.047 95.950 # SOURCE3 6 0.0489 + angle_coeff @angle:hp-p3-p5 harmonic 40.189 95.540 # SOURCE3 2 + angle_coeff @angle:hp-p3-s4 harmonic 33.215 95.490 # SOURCE3 2 + angle_coeff @angle:hp-p3-s6 harmonic 33.822 92.950 # SOURCE3 2 + angle_coeff @angle:hp-p3-sh harmonic 32.748 94.210 # SOURCE3 2 + angle_coeff @angle:hp-p3-ss harmonic 32.846 94.610 # SOURCE3 2 + angle_coeff @angle:i-p3-i harmonic 49.016 105.250 # SOURCE3 1 + angle_coeff @angle:n1-p3-n1 harmonic 86.652 90.440 # HF/6-31G* 1 + angle_coeff @angle:n2-p3-n2 harmonic 76.240 103.460 # SOURCE3 1 + angle_coeff @angle:n3-p3-n3 harmonic 74.122 113.800 # SOURCE3 1 + angle_coeff @angle:n3-p3-o harmonic 80.756 107.100 # SOURCE3 4 + angle_coeff @angle:n3-p3-oh harmonic 80.929 98.360 # SOURCE3 1 + angle_coeff @angle:n4-p3-n4 harmonic 72.570 100.530 # SOURCE3 1 + angle_coeff @angle:na-p3-na harmonic 75.328 106.220 # SOURCE3 1 + angle_coeff @angle:nh-p3-nh harmonic 75.698 109.110 # SOURCE3 1 + angle_coeff @angle:n-p3-n harmonic 75.573 104.580 # SOURCE3 1 + angle_coeff @angle:n-p3-o harmonic 80.307 104.990 # SOURCE3 4 + angle_coeff @angle:no-p3-no harmonic 74.810 98.330 # SOURCE3 1 + angle_coeff @angle:oh-p3-oh harmonic 79.802 104.480 # SOURCE3 1 + angle_coeff @angle:o-p3-o harmonic 81.687 122.180 # SOURCE3 2 7.8556 + angle_coeff @angle:o-p3-p3 harmonic 70.126 116.740 # SOURCE3 14 0.7525 + angle_coeff @angle:o-p3-p5 harmonic 73.068 107.620 # SOURCE3 4 + angle_coeff @angle:o-p3-s4 harmonic 59.257 110.700 # SOURCE3 4 0.7259 + angle_coeff @angle:o-p3-s6 harmonic 60.626 106.660 # SOURCE3 6 3.4017 + angle_coeff @angle:os-p3-os harmonic 81.795 99.760 # SOURCE3_SOURCE5 8 1.2613 + angle_coeff @angle:p2-p3-p2 harmonic 76.665 103.580 # SOURCE3 1 + angle_coeff @angle:p3-p3-p3 harmonic 73.903 105.310 # SOURCE3 4 3.5864 + angle_coeff @angle:p4-p3-p4 harmonic 76.119 99.090 # SOURCE3 1 + angle_coeff @angle:p5-p3-p5 harmonic 76.218 99.100 # SOURCE3 1 + angle_coeff @angle:s4-p3-s4 harmonic 49.282 98.260 # SOURCE3 1 + angle_coeff @angle:s6-p3-s6 harmonic 49.641 97.780 # SOURCE3 1 + angle_coeff @angle:sh-p3-sh harmonic 46.105 107.580 # SOURCE3 1 + angle_coeff @angle:s-p3-s harmonic 42.980 131.320 # SOURCE3 1 + angle_coeff @angle:ss-p3-ss harmonic 45.990 109.240 # SOURCE3 1 + angle_coeff @angle:br-p4-br harmonic 50.850 110.410 # SOURCE3 1 + angle_coeff @angle:br-p4-o harmonic 57.453 124.800 # SOURCE3 1 + angle_coeff @angle:c2-p4-c2 harmonic 46.901 104.210 # SOURCE3 1 + angle_coeff @angle:c2-p4-hp harmonic 34.221 99.500 # SOURCE3 2 + angle_coeff @angle:c2-p4-o harmonic 60.517 113.590 # SOURCE3 1 + angle_coeff @angle:c3-p4-c3 harmonic 46.849 102.550 # SOURCE3 4 0.0192 + angle_coeff @angle:c3-p4-n2 harmonic 60.249 103.170 # SOURCE3 1 + angle_coeff @angle:c3-p4-n3 harmonic 60.876 102.370 # SOURCE3 1 + angle_coeff @angle:c3-p4-n4 harmonic 57.893 99.570 # SOURCE3 1 + angle_coeff @angle:c3-p4-n harmonic 60.075 103.260 # SOURCE3 1 + angle_coeff @angle:c3-p4-na harmonic 58.423 117.670 # SOURCE3 5 19.0404 + angle_coeff @angle:c3-p4-nh harmonic 60.622 102.790 # SOURCE3 1 + angle_coeff @angle:c3-p4-no harmonic 58.960 99.800 # SOURCE3 3 0.2151 + angle_coeff @angle:c3-p4-o harmonic 59.565 115.670 # SOURCE3_SOURCE5 41 1.9882 + angle_coeff @angle:c3-p4-oh harmonic 62.836 98.560 # SOURCE3 2 0.4558 + angle_coeff @angle:c3-p4-os harmonic 63.080 98.010 # SOURCE3 2 0.0931 + angle_coeff @angle:c3-p4-p2 harmonic 56.813 109.270 # SOURCE3 1 + angle_coeff @angle:c3-p4-p3 harmonic 57.663 103.530 # SOURCE3 1 + angle_coeff @angle:c3-p4-p4 harmonic 61.536 102.120 # SOURCE3 1 + angle_coeff @angle:c3-p4-p5 harmonic 57.093 104.150 # SOURCE3 1 + angle_coeff @angle:c3-p4-sh harmonic 47.201 100.170 # SOURCE3 2 0.0815 + angle_coeff @angle:c3-p4-ss harmonic 47.127 101.190 # SOURCE3 1 + angle_coeff @angle:ca-p4-ca harmonic 46.528 107.770 # SOURCE3 1 + angle_coeff @angle:ca-p4-o harmonic 61.439 111.640 # SOURCE3 1 + angle_coeff @angle:cl-p4-cl harmonic 62.229 103.510 # SOURCE3 1 + angle_coeff @angle:cl-p4-o harmonic 66.762 116.530 # SOURCE3 2 + angle_coeff @angle:hp-p4-hp harmonic 27.316 99.210 # SOURCE3 4 6.4572 + angle_coeff @angle:hp-p4-n1 harmonic 45.702 99.910 # HF/6-31G* 1 + angle_coeff @angle:hp-p4-o harmonic 47.223 109.350 # SOURCE3 6 10.8284 + angle_coeff @angle:hp-p4-p3 harmonic 39.333 98.960 # SOURCE3 4 + angle_coeff @angle:hp-p4-s harmonic 30.046 110.240 # SOURCE3 4 4.1081 + angle_coeff @angle:i-p4-i harmonic 51.559 113.220 # SOURCE3 2 6.7916 + angle_coeff @angle:i-p4-o harmonic 59.585 110.220 # SOURCE3 4 9.7726 + angle_coeff @angle:n1-p4-n1 harmonic 81.177 100.610 # HF/6-31G* 1 + angle_coeff @angle:n1-p4-o harmonic 79.782 114.590 # HF/6-31G* 1 + angle_coeff @angle:n2-p4-n2 harmonic 78.358 102.540 # SOURCE3 1 + angle_coeff @angle:n2-p4-o harmonic 76.567 120.280 # SOURCE3 1 + angle_coeff @angle:n3-p4-o harmonic 79.727 113.270 # SOURCE3 1 + angle_coeff @angle:n4-p4-o harmonic 74.226 107.610 # SOURCE3 1 + angle_coeff @angle:na-p4-o harmonic 84.731 110.600 # SOURCE3 5 1.3133 + angle_coeff @angle:nh-p4-nh harmonic 82.137 95.300 # SOURCE3 1 + angle_coeff @angle:nh-p4-o harmonic 78.559 115.860 # SOURCE3 3 3.2712 + angle_coeff @angle:n-p4-o harmonic 77.006 117.990 # SOURCE3 1 + angle_coeff @angle:no-p4-o harmonic 73.956 114.690 # SOURCE3 3 0.1070 + angle_coeff @angle:oh-p4-oh harmonic 85.208 95.710 # SOURCE3 1 + angle_coeff @angle:o-p4-o harmonic 84.013 117.220 # SOURCE3 6 2.7792 + angle_coeff @angle:o-p4-oh harmonic 79.987 117.390 # SOURCE3 4 1.0083 + angle_coeff @angle:o-p4-os harmonic 80.383 116.670 # SOURCE3 4 0.6923 + angle_coeff @angle:o-p4-p2 harmonic 69.856 121.350 # SOURCE3 1 + angle_coeff @angle:o-p4-p3 harmonic 70.923 114.000 # SOURCE3 3 0.6663 + angle_coeff @angle:o-p4-p4 harmonic 75.914 116.430 # SOURCE3 1 + angle_coeff @angle:o-p4-p5 harmonic 71.622 109.760 # SOURCE3 1 + angle_coeff @angle:o-p4-s4 harmonic 54.866 112.190 # SOURCE3 1 + angle_coeff @angle:o-p4-s6 harmonic 54.029 113.890 # SOURCE3 1 + angle_coeff @angle:o-p4-s harmonic 57.277 112.780 # SOURCE3 2 + angle_coeff @angle:o-p4-sh harmonic 56.730 118.090 # SOURCE3 1 + angle_coeff @angle:os-p4-os harmonic 83.473 100.340 # SOURCE3 1 + angle_coeff @angle:o-p4-ss harmonic 57.476 116.140 # SOURCE3 4 1.0636 + angle_coeff @angle:p2-p4-p2 harmonic 73.236 110.710 # SOURCE3 1 + angle_coeff @angle:p3-p4-p3 harmonic 70.664 114.980 # SOURCE3 1 + angle_coeff @angle:p4-p4-p4 harmonic 79.664 107.380 # SOURCE3 1 + angle_coeff @angle:p5-p4-p5 harmonic 72.301 107.780 # SOURCE3 1 + angle_coeff @angle:s4-p4-s4 harmonic 46.168 96.240 # SOURCE3 1 + angle_coeff @angle:s6-p4-s6 harmonic 44.412 102.360 # SOURCE3 1 + angle_coeff @angle:sh-p4-sh harmonic 48.494 98.810 # SOURCE3 1 + angle_coeff @angle:s-p4-s harmonic 46.079 106.300 # SOURCE3 2 25.0119 + angle_coeff @angle:ss-p4-ss harmonic 47.422 104.410 # SOURCE3 1 + angle_coeff @angle:br-p5-br harmonic 51.952 103.380 # SOURCE3 1 + angle_coeff @angle:br-p5-o harmonic 59.322 114.650 # SOURCE3 3 1.0910 + angle_coeff @angle:br-p5-oh harmonic 62.204 102.920 # SOURCE3 4 0.5468 + angle_coeff @angle:c1-p5-c1 harmonic 49.058 102.890 # SOURCE3 1 + angle_coeff @angle:c1-p5-o harmonic 61.836 115.770 # SOURCE3 2 + angle_coeff @angle:c1-p5-oh harmonic 63.769 102.790 # SOURCE3 2 + angle_coeff @angle:c2-p5-c2 harmonic 45.370 106.560 # SOURCE3 1 + angle_coeff @angle:c2-p5-o harmonic 60.781 109.520 # SOURCE4_SOURCE5 15 2.0293 + angle_coeff @angle:c2-p5-oh harmonic 61.672 101.690 # SOURCE3 1 + angle_coeff @angle:c2-p5-os harmonic 63.109 97.120 # SOURCE3_SOURCE5 6 0.9178 + angle_coeff @angle:c3-p5-c3 harmonic 46.061 106.000 # SOURCE3_SOURCE5 107 1.6965 + angle_coeff @angle:c3-p5-hp harmonic 33.063 103.260 # SOURCE4_SOURCE5 20 1.3795 + angle_coeff @angle:c3-p5-n3 harmonic 60.649 104.400 # SOURCE3_SOURCE5 10 1.8148 + angle_coeff @angle:c3-p5-o harmonic 60.550 112.500 # SOURCE3 23 4.4203 + angle_coeff @angle:c3-p5-oh harmonic 61.886 102.690 # SOURCE3_SOURCE5 389 1.5370 + angle_coeff @angle:c3-p5-os harmonic 62.476 100.770 # SOURCE4 51 2.0928 + angle_coeff @angle:c3-p5-p4 harmonic 56.514 106.270 # SOURCE3 1 + angle_coeff @angle:c3-p5-s harmonic 46.672 114.400 # SOURCE3_SOURCE5 36 1.0844 + angle_coeff @angle:c3-p5-ss harmonic 45.854 105.940 # SOURCE3_SOURCE5 24 1.6358 + angle_coeff @angle:ca-p5-ca harmonic 46.780 107.900 # SOURCE3_SOURCE5 5 0.5519 + angle_coeff @angle:ca-p5-o harmonic 61.263 113.980 # SOURCE3 1 + angle_coeff @angle:ca-p5-oh harmonic 63.154 101.770 # SOURCE3 1 + angle_coeff @angle:ca-p5-os harmonic 62.551 103.750 # SOURCE3 1 + angle_coeff @angle:c-p5-c harmonic 45.421 104.160 # SOURCE3 1 + angle_coeff @angle:cl-p5-cl harmonic 62.172 103.700 # SOURCE2 1 + angle_coeff @angle:cl-p5-o harmonic 68.012 112.650 # SOURCE3_SOURCE5 7 1.0635 + angle_coeff @angle:cl-p5-oh harmonic 70.253 102.440 # SOURCE3 2 + angle_coeff @angle:c-p5-o harmonic 60.972 107.100 # SOURCE4_SOURCE5 37 0.4646 + angle_coeff @angle:c-p5-oh harmonic 61.112 102.120 # SOURCE3 1 + angle_coeff @angle:f-p5-f harmonic 92.407 92.220 # SOURCE2_SOURCE5 19 1.3661 + angle_coeff @angle:f-p5-o harmonic 85.135 112.070 # SOURCE4_SOURCE5 15 0.5195 + angle_coeff @angle:f-p5-oh harmonic 85.837 101.980 # SOURCE3 2 + angle_coeff @angle:f-p5-os harmonic 85.720 102.270 # SOURCE4_SOURCE5 16 1.0230 + angle_coeff @angle:f-p5-s harmonic 61.598 117.400 # SOURCE2 1 + angle_coeff @angle:hp-p5-hp harmonic 25.816 100.550 # SOURCE3_SOURCE5 11 0.5508 + angle_coeff @angle:hp-p5-n1 harmonic 46.858 101.320 # HF/6-31G* 1 + angle_coeff @angle:hp-p5-o harmonic 45.433 115.080 # SOURCE3_SOURCE5 27 1.7749 + angle_coeff @angle:hp-p5-oh harmonic 45.976 101.570 # SOURCE3_SOURCE5 16 1.3736 + angle_coeff @angle:hp-p5-s harmonic 31.882 119.200 # SOURCE2 1 + angle_coeff @angle:i-p5-i harmonic 48.013 107.170 # SOURCE3 1 + angle_coeff @angle:i-p5-o harmonic 52.148 115.930 # SOURCE3 3 0.0415 + angle_coeff @angle:i-p5-oh harmonic 55.980 102.260 # SOURCE3 4 1.9577 + angle_coeff @angle:n1-p5-n1 harmonic 86.407 101.550 # HF/6-31G* 1 + angle_coeff @angle:n1-p5-o harmonic 83.757 113.780 # HF/6-31G* 1 + angle_coeff @angle:n2-p5-n2 harmonic 82.960 106.340 # SOURCE3 1 + angle_coeff @angle:n2-p5-o harmonic 82.994 113.530 # SOURCE3 1 + angle_coeff @angle:n2-p5-oh harmonic 84.118 102.400 # SOURCE3 1 + angle_coeff @angle:n3-p5-n3 harmonic 80.585 103.370 # SOURCE4 47 2.1009 + angle_coeff @angle:n3-p5-nh harmonic 80.369 103.840 # SOURCE4_SOURCE5 11 1.8670 + angle_coeff @angle:n3-p5-o harmonic 80.416 114.640 # SOURCE4 76 2.2728 + angle_coeff @angle:n3-p5-oh harmonic 81.248 104.990 # SOURCE3_SOURCE5 18 0.6974 + angle_coeff @angle:n3-p5-os harmonic 82.342 102.230 # SOURCE4_SOURCE5 90 2.1717 + angle_coeff @angle:n3-p5-s harmonic 60.056 116.560 # SOURCE4_SOURCE5 28 0.9342 + angle_coeff @angle:n4-p5-n4 harmonic 73.942 102.200 # SOURCE3 1 + angle_coeff @angle:n4-p5-o harmonic 77.060 109.780 # SOURCE3 5 2.7519 + angle_coeff @angle:n4-p5-oh harmonic 79.407 98.480 # SOURCE3 6 0.4104 + angle_coeff @angle:n4-p5-os harmonic 81.044 94.550 # SOURCE3 2 + angle_coeff @angle:na-p5-na harmonic 76.550 108.570 # SOURCE3 1 + angle_coeff @angle:na-p5-o harmonic 79.422 113.430 # SOURCE3 11 0.8968 + angle_coeff @angle:na-p5-oh harmonic 81.176 102.070 # SOURCE3 16 1.4144 + angle_coeff @angle:na-p5-os harmonic 80.790 103.060 # SOURCE3 4 0.7463 + angle_coeff @angle:nh-p5-nh harmonic 82.064 99.510 # SOURCE3 1 + angle_coeff @angle:nh-p5-o harmonic 80.296 114.860 # SOURCE3_SOURCE5 11 1.6006 + angle_coeff @angle:nh-p5-oh harmonic 82.027 102.910 # SOURCE3_SOURCE5 6 0.9034 + angle_coeff @angle:nh-p5-os harmonic 81.134 105.200 # SOURCE3_SOURCE5 6 2.0688 + angle_coeff @angle:n-p5-n3 harmonic 79.065 104.310 # SOURCE4_SOURCE5 28 1.2397 + angle_coeff @angle:n-p5-n harmonic 78.462 103.090 # SOURCE3 1 + angle_coeff @angle:n-p5-o harmonic 79.797 112.180 # SOURCE4_SOURCE5 14 1.5068 + angle_coeff @angle:n-p5-oh harmonic 80.973 102.440 # SOURCE3 4 0.0999 + angle_coeff @angle:no-p5-no harmonic 76.253 95.680 # SOURCE3 1 + angle_coeff @angle:no-p5-o harmonic 75.912 112.750 # SOURCE3 4 3.3684 + angle_coeff @angle:no-p5-oh harmonic 78.162 101.350 # SOURCE3 2 + angle_coeff @angle:no-p5-os harmonic 78.031 101.700 # SOURCE3 4 0.0565 + angle_coeff @angle:n-p5-os harmonic 81.763 100.480 # SOURCE3 2 + angle_coeff @angle:oh-p5-oh harmonic 83.590 102.690 # SOURCE3_SOURCE5 359 1.1644 + angle_coeff @angle:oh-p5-os harmonic 83.902 101.940 # SOURCE3_SOURCE5 591 1.1251 + angle_coeff @angle:oh-p5-p2 harmonic 75.094 103.530 # SOURCE3 1 + angle_coeff @angle:oh-p5-p3 harmonic 74.007 103.830 # SOURCE3 13 0.4303 + angle_coeff @angle:oh-p5-p4 harmonic 74.032 101.790 # SOURCE3 1 + angle_coeff @angle:oh-p5-p5 harmonic 80.103 100.450 # SOURCE3 1 + angle_coeff @angle:oh-p5-s4 harmonic 61.903 103.240 # SOURCE3 1 + angle_coeff @angle:oh-p5-s6 harmonic 62.438 101.480 # SOURCE3 1 + angle_coeff @angle:oh-p5-s harmonic 62.070 111.300 # SOURCE3_SOURCE5 8 1.1112 + angle_coeff @angle:oh-p5-sh harmonic 61.449 101.410 # SOURCE3 2 + angle_coeff @angle:oh-p5-ss harmonic 59.814 104.090 # SOURCE3_SOURCE5 23 1.4682 + angle_coeff @angle:o-p5-o harmonic 85.510 115.800 # SOURCE3 17 5.7902 + angle_coeff @angle:o-p5-oh harmonic 81.901 115.210 # SOURCE4_SOURCE5 1716 1.3221 + angle_coeff @angle:o-p5-os harmonic 81.819 115.460 # SOURCE3_SOURCE5 843 2.3835 + angle_coeff @angle:o-p5-p2 harmonic 71.892 114.600 # SOURCE3 1 + angle_coeff @angle:o-p5-p3 harmonic 70.584 115.480 # SOURCE3 9 2.1084 + angle_coeff @angle:o-p5-p4 harmonic 70.090 114.660 # SOURCE3 1 + angle_coeff @angle:o-p5-p5 harmonic 76.354 113.440 # SOURCE3 1 + angle_coeff @angle:o-p5-s4 harmonic 60.725 110.230 # SOURCE3 1 + angle_coeff @angle:o-p5-s6 harmonic 60.311 111.750 # SOURCE3 1 + angle_coeff @angle:o-p5-s harmonic 61.702 116.940 # SOURCE3 3 2.9506 + angle_coeff @angle:o-p5-sh harmonic 58.488 114.560 # SOURCE3 3 1.7645 + angle_coeff @angle:os-p5-os harmonic 83.949 101.840 # SOURCE4_SOURCE5 608 1.9896 + angle_coeff @angle:os-p5-p3 harmonic 74.065 103.670 # SOURCE3 2 + angle_coeff @angle:os-p5-p5 harmonic 78.545 104.480 # SOURCE3 1 + angle_coeff @angle:os-p5-s4 harmonic 62.122 102.520 # SOURCE3 1 + angle_coeff @angle:os-p5-s6 harmonic 62.313 101.890 # SOURCE3 1 + angle_coeff @angle:o-p5-ss harmonic 57.641 114.340 # SOURCE3_SOURCE5 37 1.7416 + angle_coeff @angle:os-p5-s harmonic 60.508 117.130 # SOURCE4_SOURCE5 200 0.8203 + angle_coeff @angle:os-p5-sh harmonic 61.258 102.050 # SOURCE3_SOURCE5 7 0.5915 + angle_coeff @angle:os-p5-ss harmonic 60.283 102.480 # SOURCE4_SOURCE5 70 1.4633 + angle_coeff @angle:p2-p5-p2 harmonic 74.412 107.140 # SOURCE3 1 + angle_coeff @angle:p3-p5-p3 harmonic 73.965 105.230 # SOURCE3 3 5.1024 + angle_coeff @angle:p4-p5-p4 harmonic 74.460 101.620 # SOURCE3 1 + angle_coeff @angle:p5-p5-p5 harmonic 76.997 112.720 # SOURCE3 1 + angle_coeff @angle:s6-p5-s6 harmonic 48.731 105.180 # SOURCE3 1 + angle_coeff @angle:sh-p5-sh harmonic 47.889 104.560 # SOURCE3 1 + angle_coeff @angle:sh-p5-ss harmonic 46.903 107.130 # SOURCE3 1 + angle_coeff @angle:s-p5-s harmonic 49.342 114.130 # SOURCE3 1 + angle_coeff @angle:ss-p5-ss harmonic 45.986 109.610 # SOURCE3 1 + angle_coeff @angle:cd-pc-n harmonic 66.016 90.800 # SOURCE3 3 2.3423 + angle_coeff @angle:cd-pc-na harmonic 66.396 90.180 # SOURCE3 81 2.7619 + angle_coeff @angle:cc-pd-n harmonic 66.016 90.800 # SOURCE3 3 + angle_coeff @angle:cc-pd-na harmonic 66.396 90.180 # SOURCE3 81 + angle_coeff @angle:c2-pe-ca harmonic 49.088 101.440 # SOURCE3 3 0.7177 + angle_coeff @angle:c2-pe-ce harmonic 48.888 103.010 # SOURCE3 4 1.4470 + angle_coeff @angle:c2-pe-cg harmonic 51.641 104.030 # SOURCE3 3 3.8740 + angle_coeff @angle:c2-pe-n2 harmonic 69.448 94.140 # SOURCE3 1 + angle_coeff @angle:c2-pe-ne harmonic 64.662 98.700 # SOURCE3 12 5.3383 + angle_coeff @angle:c2-pe-o harmonic 63.086 115.160 # SOURCE3 2 0.0149 + angle_coeff @angle:c2-pe-p2 harmonic 65.232 107.820 # SOURCE3 1 + angle_coeff @angle:c2-pe-pe harmonic 61.668 102.990 # SOURCE3 9 8.2860 + angle_coeff @angle:c2-pe-px harmonic 65.444 97.370 # SOURCE3 4 0.6655 + angle_coeff @angle:c2-pe-py harmonic 65.200 96.710 # SOURCE3 4 1.2755 + angle_coeff @angle:c2-pe-s harmonic 51.862 111.160 # SOURCE3 2 + angle_coeff @angle:c2-pe-sx harmonic 48.622 95.110 # SOURCE3 4 0.2676 + angle_coeff @angle:c2-pe-sy harmonic 47.698 95.560 # SOURCE3 2 0.0462 + angle_coeff @angle:ca-pe-n2 harmonic 63.263 102.030 # SOURCE3 1 + angle_coeff @angle:ca-pe-o harmonic 62.025 106.880 # SOURCE3 2 0.0018 + angle_coeff @angle:ca-pe-p2 harmonic 65.219 100.790 # SOURCE3 1 + angle_coeff @angle:ca-pe-pf harmonic 61.993 99.700 # SOURCE3 2 + angle_coeff @angle:ca-pe-s harmonic 50.574 107.930 # SOURCE3 1 + angle_coeff @angle:c-pe-c2 harmonic 48.762 97.300 # SOURCE3 3 0.0335 + angle_coeff @angle:ce-pe-n2 harmonic 64.000 100.550 # SOURCE3 1 + angle_coeff @angle:ce-pe-o harmonic 62.134 107.440 # SOURCE3 1 + angle_coeff @angle:ce-pe-p2 harmonic 65.808 99.560 # SOURCE3 1 + angle_coeff @angle:ce-pe-s harmonic 51.312 105.540 # SOURCE3 1 + angle_coeff @angle:cg-pe-n2 harmonic 68.416 101.790 # SOURCE3 1 + angle_coeff @angle:cg-pe-o harmonic 66.891 107.620 # SOURCE3 1 + angle_coeff @angle:cg-pe-p2 harmonic 67.155 104.680 # SOURCE3 2 5.1435 + angle_coeff @angle:cg-pe-s harmonic 53.387 108.600 # SOURCE3 4 2.6981 + angle_coeff @angle:n2-pe-n2 harmonic 85.418 108.140 # SOURCE3 1 + angle_coeff @angle:n2-pe-ne harmonic 80.952 106.800 # SOURCE3 6 4.5981 + angle_coeff @angle:n2-pe-o harmonic 83.198 115.390 # SOURCE3 1 + angle_coeff @angle:n2-pe-p2 harmonic 82.679 111.600 # SOURCE3 1 + angle_coeff @angle:n2-pe-pe harmonic 76.187 109.400 # SOURCE3 1 + angle_coeff @angle:n2-pe-px harmonic 78.660 110.300 # SOURCE3 3 6.0548 + angle_coeff @angle:n2-pe-py harmonic 84.653 93.680 # SOURCE3 1 + angle_coeff @angle:n2-pe-s harmonic 66.247 114.840 # SOURCE3 3 3.6512 + angle_coeff @angle:n2-pe-sx harmonic 60.809 97.830 # SOURCE3 1 + angle_coeff @angle:n2-pe-sy harmonic 59.570 98.140 # SOURCE3 1 + angle_coeff @angle:ne-pe-o harmonic 80.037 110.240 # SOURCE3 3 3.8478 + angle_coeff @angle:ne-pe-p2 harmonic 82.546 104.480 # SOURCE3 2 7.1207 + angle_coeff @angle:ne-pe-s harmonic 65.116 109.190 # SOURCE3 5 3.6708 + angle_coeff @angle:o-pe-o harmonic 82.114 119.960 # SOURCE3 1 + angle_coeff @angle:o-pe-p2 harmonic 81.980 114.230 # SOURCE3 1 + angle_coeff @angle:o-pe-pe harmonic 66.057 145.960 # SOURCE3 1 + angle_coeff @angle:o-pe-px harmonic 81.034 104.370 # SOURCE3 1 + angle_coeff @angle:o-pe-py harmonic 80.312 104.490 # SOURCE3 1 + angle_coeff @angle:o-pe-s harmonic 65.783 117.420 # SOURCE3 2 0.0426 + angle_coeff @angle:o-pe-sx harmonic 58.314 106.590 # SOURCE3 1 + angle_coeff @angle:o-pe-sy harmonic 57.621 105.040 # SOURCE3 1 + angle_coeff @angle:p2-pe-pe harmonic 85.030 98.240 # SOURCE3 1 + angle_coeff @angle:p2-pe-px harmonic 83.137 108.280 # SOURCE3 2 6.2959 + angle_coeff @angle:p2-pe-py harmonic 81.676 110.870 # SOURCE3 3 8.1645 + angle_coeff @angle:p2-pe-s harmonic 68.307 111.280 # SOURCE3 1 + angle_coeff @angle:p2-pe-sx harmonic 65.549 95.730 # SOURCE3 1 + angle_coeff @angle:p2-pe-sy harmonic 64.541 95.950 # SOURCE3 1 + angle_coeff @angle:pe-pe-s harmonic 64.452 107.910 # SOURCE3 2 1.5577 + angle_coeff @angle:px-pe-s harmonic 66.458 107.620 # SOURCE3 2 3.7266 + angle_coeff @angle:py-pe-s harmonic 65.679 108.730 # SOURCE3 3 5.3201 + angle_coeff @angle:s-pe-s harmonic 43.414 178.440 # SOURCE3 1 + angle_coeff @angle:s-pe-sx harmonic 48.826 108.320 # SOURCE3 2 3.0318 + angle_coeff @angle:s-pe-sy harmonic 48.370 106.930 # SOURCE3 1 + angle_coeff @angle:c2-pf-ca harmonic 49.088 101.440 # SOURCE3 3 + angle_coeff @angle:c2-pf-cf harmonic 48.888 103.010 # SOURCE3 4 + angle_coeff @angle:c2-pf-ch harmonic 51.641 104.030 # SOURCE3 3 + angle_coeff @angle:c2-pf-n2 harmonic 69.448 94.140 # SOURCE3 1 + angle_coeff @angle:c2-pf-nf harmonic 64.662 98.700 # SOURCE3 12 + angle_coeff @angle:c2-pf-o harmonic 63.086 115.160 # SOURCE3 2 + angle_coeff @angle:c2-pf-p2 harmonic 65.232 107.820 # SOURCE3 1 + angle_coeff @angle:c2-pf-pf harmonic 61.668 102.990 # SOURCE3 9 + angle_coeff @angle:c2-pf-px harmonic 65.444 97.370 # SOURCE3 4 + angle_coeff @angle:c2-pf-py harmonic 65.200 96.710 # SOURCE3 4 + angle_coeff @angle:c2-pf-s harmonic 51.862 111.160 # SOURCE3 2 + angle_coeff @angle:c2-pf-sx harmonic 48.622 95.110 # SOURCE3 4 + angle_coeff @angle:c2-pf-sy harmonic 47.698 95.560 # SOURCE3 2 + angle_coeff @angle:ca-pf-n2 harmonic 63.263 102.030 # SOURCE3 1 + angle_coeff @angle:ca-pf-o harmonic 62.025 106.880 # SOURCE3 2 + angle_coeff @angle:ca-pf-p2 harmonic 65.219 100.790 # SOURCE3 1 + angle_coeff @angle:ca-pf-pe harmonic 61.993 99.700 # SOURCE3 2 + angle_coeff @angle:ca-pf-s harmonic 50.574 107.930 # SOURCE3 1 + angle_coeff @angle:c-pf-c2 harmonic 48.762 97.300 # SOURCE3 3 + angle_coeff @angle:cf-pf-n2 harmonic 64.000 100.550 # SOURCE3 1 + angle_coeff @angle:cf-pf-o harmonic 62.134 107.440 # SOURCE3 1 + angle_coeff @angle:cf-pf-p2 harmonic 65.808 99.560 # SOURCE3 1 + angle_coeff @angle:cf-pf-s harmonic 51.312 105.540 # SOURCE3 1 + angle_coeff @angle:ch-pf-n2 harmonic 68.416 101.790 # SOURCE3 1 + angle_coeff @angle:ch-pf-o harmonic 66.891 107.620 # SOURCE3 1 + angle_coeff @angle:ch-pf-p2 harmonic 67.155 104.680 # SOURCE3 2 + angle_coeff @angle:ch-pf-s harmonic 53.387 108.600 # SOURCE3 4 + angle_coeff @angle:n2-pf-n2 harmonic 85.418 108.140 # SOURCE3 1 + angle_coeff @angle:n2-pf-nf harmonic 80.952 106.800 # SOURCE3 6 + angle_coeff @angle:n2-pf-o harmonic 83.198 115.390 # SOURCE3 1 + angle_coeff @angle:n2-pf-p2 harmonic 82.679 111.600 # SOURCE3 1 + angle_coeff @angle:n2-pf-pf harmonic 76.187 109.400 # SOURCE3 1 + angle_coeff @angle:n2-pf-px harmonic 78.660 110.300 # SOURCE3 3 + angle_coeff @angle:n2-pf-py harmonic 84.653 93.680 # SOURCE3 1 + angle_coeff @angle:n2-pf-s harmonic 66.247 114.840 # SOURCE3 3 + angle_coeff @angle:n2-pf-sx harmonic 60.809 97.830 # SOURCE3 1 + angle_coeff @angle:n2-pf-sy harmonic 59.570 98.140 # SOURCE3 1 + angle_coeff @angle:nf-pf-o harmonic 80.037 110.240 # SOURCE3 3 + angle_coeff @angle:nf-pf-p2 harmonic 82.546 104.480 # SOURCE3 2 + angle_coeff @angle:nf-pf-s harmonic 65.116 109.190 # SOURCE3 5 + angle_coeff @angle:o-pf-o harmonic 82.114 119.960 # SOURCE3 1 + angle_coeff @angle:o-pf-p2 harmonic 81.980 114.230 # SOURCE3 1 + angle_coeff @angle:o-pf-pf harmonic 66.057 145.960 # SOURCE3 1 + angle_coeff @angle:o-pf-px harmonic 81.034 104.370 # SOURCE3 1 + angle_coeff @angle:o-pf-py harmonic 80.312 104.490 # SOURCE3 1 + angle_coeff @angle:o-pf-s harmonic 65.783 117.420 # SOURCE3 2 + angle_coeff @angle:o-pf-sx harmonic 58.314 106.590 # SOURCE3 1 + angle_coeff @angle:o-pf-sy harmonic 57.621 105.040 # SOURCE3 1 + angle_coeff @angle:p2-pf-pf harmonic 85.030 98.240 # SOURCE3 1 + angle_coeff @angle:p2-pf-px harmonic 83.137 108.280 # SOURCE3 2 + angle_coeff @angle:p2-pf-py harmonic 81.676 110.870 # SOURCE3 3 + angle_coeff @angle:p2-pf-s harmonic 68.307 111.280 # SOURCE3 1 + angle_coeff @angle:p2-pf-sx harmonic 65.549 95.730 # SOURCE3 1 + angle_coeff @angle:p2-pf-sy harmonic 64.541 95.950 # SOURCE3 1 + angle_coeff @angle:pf-pf-s harmonic 64.452 107.910 # SOURCE3 2 + angle_coeff @angle:px-pf-s harmonic 66.458 107.620 # SOURCE3 2 + angle_coeff @angle:py-pf-s harmonic 65.679 108.730 # SOURCE3 3 + angle_coeff @angle:s-pf-s harmonic 43.414 178.440 # SOURCE3 1 + angle_coeff @angle:s-pf-sx harmonic 48.826 108.320 # SOURCE3 2 + angle_coeff @angle:s-pf-sy harmonic 48.370 106.930 # SOURCE3 1 + angle_coeff @angle:c3-px-ca harmonic 46.648 104.790 # SOURCE3 1 + angle_coeff @angle:c3-px-ce harmonic 46.683 104.860 # SOURCE3 4 0.6354 + angle_coeff @angle:c3-px-cf harmonic 46.683 104.860 # SOURCE3 4 + angle_coeff @angle:c3-px-ne harmonic 60.976 102.460 # SOURCE3 7 1.8685 + angle_coeff @angle:c3-px-nf harmonic 60.976 102.460 # SOURCE3 7 + angle_coeff @angle:c3-px-o harmonic 60.307 113.790 # SOURCE3_SOURCE5 33 4.2352 + angle_coeff @angle:c3-px-pe harmonic 61.145 105.730 # SOURCE3 10 4.4059 + angle_coeff @angle:c3-px-pf harmonic 61.145 105.730 # SOURCE3 10 + angle_coeff @angle:c3-px-py harmonic 58.192 103.110 # SOURCE3 3 0.8680 + angle_coeff @angle:c3-px-sx harmonic 45.492 99.550 # SOURCE3 1 + angle_coeff @angle:c3-px-sy harmonic 44.530 103.410 # SOURCE3 1 + angle_coeff @angle:ca-px-ca harmonic 46.837 104.150 # SOURCE3 2 3.6168 + angle_coeff @angle:ca-px-o harmonic 62.137 107.500 # SOURCE3 5 5.7355 + angle_coeff @angle:c-px-c3 harmonic 46.307 101.720 # SOURCE3 1 + angle_coeff @angle:ce-px-ce harmonic 46.926 104.210 # SOURCE3 1 + angle_coeff @angle:ce-px-o harmonic 60.493 113.790 # SOURCE3 6 0.3877 + angle_coeff @angle:cf-px-cf harmonic 46.926 104.210 # SOURCE3 1 + angle_coeff @angle:cf-px-o harmonic 60.493 113.790 # SOURCE3 6 + angle_coeff @angle:c-px-o harmonic 58.294 114.470 # SOURCE3 1 + angle_coeff @angle:ne-px-ne harmonic 79.109 103.220 # SOURCE3 2 0.6807 + angle_coeff @angle:ne-px-o harmonic 79.281 114.130 # SOURCE3 11 8.9737 + angle_coeff @angle:nf-px-nf harmonic 79.109 103.220 # SOURCE3 2 + angle_coeff @angle:nf-px-o harmonic 79.281 114.130 # SOURCE3 11 + angle_coeff @angle:o-px-pe harmonic 76.837 116.500 # SOURCE3 12 8.2925 + angle_coeff @angle:o-px-pf harmonic 76.837 116.500 # SOURCE3 12 + angle_coeff @angle:o-px-py harmonic 71.388 114.200 # SOURCE3 5 1.7165 + angle_coeff @angle:o-px-sx harmonic 54.930 112.810 # SOURCE3 3 0.8799 + angle_coeff @angle:o-px-sy harmonic 54.586 113.540 # SOURCE3 3 0.5010 + angle_coeff @angle:pe-px-pe harmonic 79.592 110.710 # SOURCE3 1 + angle_coeff @angle:pf-px-pf harmonic 79.592 110.710 # SOURCE3 1 + angle_coeff @angle:py-px-py harmonic 73.550 107.780 # SOURCE3 1 + angle_coeff @angle:sx-px-sx harmonic 46.354 96.240 # SOURCE3 1 + angle_coeff @angle:sy-px-sy harmonic 44.807 102.360 # SOURCE3 1 + angle_coeff @angle:c3-py-n4 harmonic 57.271 103.830 # SOURCE3 4 + angle_coeff @angle:c3-py-na harmonic 59.344 106.890 # SOURCE3 2 + angle_coeff @angle:c3-py-o harmonic 59.442 116.680 # SOURCE3_SOURCE5 22 1.9051 + angle_coeff @angle:c3-py-oh harmonic 62.641 100.160 # SOURCE3 2 + angle_coeff @angle:c3-py-os harmonic 61.038 105.390 # SOURCE3 1 + angle_coeff @angle:c3-py-px harmonic 57.225 106.270 # SOURCE3 2 + angle_coeff @angle:c3-py-py harmonic 56.530 109.830 # SOURCE3_SOURCE5 16 1.4525 + angle_coeff @angle:c3-py-sx harmonic 43.696 106.360 # SOURCE3 4 + angle_coeff @angle:ca-py-ca harmonic 46.314 107.550 # SOURCE3 1 + angle_coeff @angle:ca-py-o harmonic 60.635 114.330 # SOURCE3_SOURCE5 20 1.3895 + angle_coeff @angle:ca-py-oh harmonic 62.332 102.870 # SOURCE4_SOURCE5 16 1.4519 + angle_coeff @angle:ca-py-os harmonic 62.763 101.360 # SOURCE3_SOURCE5 12 1.6676 + angle_coeff @angle:c-py-c3 harmonic 44.799 110.360 # SOURCE3 1 + angle_coeff @angle:c-py-c harmonic 45.772 104.200 # SOURCE3 1 + angle_coeff @angle:ce-py-ce harmonic 46.806 106.540 # SOURCE3 1 + angle_coeff @angle:ce-py-o harmonic 60.977 114.040 # SOURCE3_SOURCE5 17 2.0725 + angle_coeff @angle:ce-py-oh harmonic 61.997 104.770 # SOURCE3 6 2.1852 + angle_coeff @angle:ce-py-os harmonic 61.932 104.880 # SOURCE3_SOURCE5 7 1.2571 + angle_coeff @angle:cf-py-cf harmonic 46.806 106.540 # SOURCE3 1 + angle_coeff @angle:cf-py-o harmonic 60.977 114.040 # SOURCE3_SOURCE5 12 1.5779 + angle_coeff @angle:cf-py-oh harmonic 61.997 104.770 # SOURCE3 6 + angle_coeff @angle:cf-py-os harmonic 61.932 104.880 # SOURCE3_SOURCE5 7 1.2571 + angle_coeff @angle:c-py-o harmonic 59.457 114.000 # SOURCE3_SOURCE5 17 1.4765 + angle_coeff @angle:c-py-oh harmonic 61.100 103.220 # SOURCE3_SOURCE5 16 1.4543 + angle_coeff @angle:c-py-os harmonic 62.044 100.010 # SOURCE3_SOURCE5 14 3.2269 + angle_coeff @angle:n3-py-ne harmonic 79.409 108.760 # SOURCE4_SOURCE5 30 1.0660 + angle_coeff @angle:n4-py-o harmonic 72.867 115.580 # SOURCE3 4 + angle_coeff @angle:n4-py-py harmonic 98.929 55.100 # SOURCE3 4 + angle_coeff @angle:na-py-o harmonic 76.532 122.400 # SOURCE3 2 + angle_coeff @angle:na-py-py harmonic 105.838 50.880 # SOURCE3 2 + angle_coeff @angle:ne-py-ne harmonic 78.402 118.190 # SOURCE3_SOURCE5 35 1.2083 + angle_coeff @angle:ne-py-o harmonic 82.910 113.210 # SOURCE3 15 3.8894 + angle_coeff @angle:ne-py-oh harmonic 83.005 104.700 # SOURCE3 26 2.7513 + angle_coeff @angle:ne-py-os harmonic 81.559 108.290 # SOURCE3_SOURCE5 23 1.6881 + angle_coeff @angle:nf-py-nf harmonic 78.402 118.190 # SOURCE3_SOURCE5 35 1.2083 + angle_coeff @angle:nf-py-o harmonic 82.910 113.210 # SOURCE3 15 + angle_coeff @angle:nf-py-oh harmonic 83.005 104.700 # SOURCE3 26 + angle_coeff @angle:nf-py-os harmonic 81.559 108.290 # SOURCE3_SOURCE5 23 1.6881 + angle_coeff @angle:oh-py-oh harmonic 83.937 101.680 # SOURCE3_SOURCE5 49 1.9218 + angle_coeff @angle:oh-py-pe harmonic 79.277 104.840 # SOURCE3 22 2.0337 + angle_coeff @angle:oh-py-pf harmonic 79.277 104.840 # SOURCE3 22 + angle_coeff @angle:oh-py-px harmonic 74.246 104.300 # SOURCE3 8 1.2772 + angle_coeff @angle:oh-py-py harmonic 76.047 100.450 # SOURCE3 6 + angle_coeff @angle:oh-py-sx harmonic 57.417 100.940 # SOURCE3 4 + angle_coeff @angle:oh-py-sy harmonic 59.053 101.470 # SOURCE3 6 0.2490 + angle_coeff @angle:o-py-oh harmonic 81.623 115.830 # SOURCE3_SOURCE5 105 1.8918 + angle_coeff @angle:o-py-os harmonic 81.496 115.990 # SOURCE3_SOURCE5 47 1.2146 + angle_coeff @angle:o-py-pe harmonic 76.936 114.560 # SOURCE3 12 3.6114 + angle_coeff @angle:o-py-pf harmonic 76.936 114.560 # SOURCE3 12 + angle_coeff @angle:o-py-px harmonic 72.318 111.370 # SOURCE3 5 0.3803 + angle_coeff @angle:o-py-py harmonic 69.944 120.430 # SOURCE3 16 6.0629 + angle_coeff @angle:os-py-os harmonic 83.760 101.820 # SOURCE3_SOURCE5 27 1.5502 + angle_coeff @angle:os-py-py harmonic 74.513 104.590 # SOURCE3_SOURCE5 5 0.4023 + angle_coeff @angle:os-py-sx harmonic 56.596 103.860 # SOURCE3 2 + angle_coeff @angle:os-py-sy harmonic 58.853 102.120 # SOURCE3 2 + angle_coeff @angle:o-py-sx harmonic 53.190 118.560 # SOURCE3 7 6.2976 + angle_coeff @angle:o-py-sy harmonic 56.689 111.710 # SOURCE3 5 1.1937 + angle_coeff @angle:pe-py-pe harmonic 80.108 107.140 # SOURCE3 1 + angle_coeff @angle:pf-py-pf harmonic 80.108 107.140 # SOURCE3 1 + angle_coeff @angle:py-py-py harmonic 72.354 112.700 # SOURCE3 1 + angle_coeff @angle:py-py-sx harmonic 75.004 61.540 # SOURCE3 4 + angle_coeff @angle:sy-py-sy harmonic 45.561 105.170 # SOURCE3 1 + angle_coeff @angle:c1-s2-o harmonic 94.269 117.250 # SOURCE3 1 + angle_coeff @angle:c2-s2-n2 harmonic 98.098 110.840 # SOURCE3 1 + angle_coeff @angle:c2-s2-o harmonic 94.864 114.700 # SOURCE2 1 + angle_coeff @angle:cl-s2-n1 harmonic 92.974 117.700 # SOURCE2 1 + angle_coeff @angle:f-s2-n1 harmonic 122.911 116.900 # SOURCE2 1 + angle_coeff @angle:n1-s2-o harmonic 127.997 108.460 # HF/6-31G* 1 + angle_coeff @angle:n2-s2-o harmonic 117.918 121.200 # SOURCE2 2 0.8000 + angle_coeff @angle:o-s2-o harmonic 118.448 116.170 # SOURCE3 1 + angle_coeff @angle:o-s2-s harmonic 91.358 118.300 # SOURCE2 1 + angle_coeff @angle:s-s2-s harmonic 74.776 115.040 # SOURCE3 1 + angle_coeff @angle:br-s4-br harmonic 74.689 98.020 # SOURCE3 1 + angle_coeff @angle:br-s4-c3 harmonic 72.437 92.980 # SOURCE3 1 + angle_coeff @angle:br-s4-o harmonic 84.014 112.070 # SOURCE3 1 + angle_coeff @angle:c1-s4-c1 harmonic 77.086 93.550 # SOURCE3 1 + angle_coeff @angle:c1-s4-o harmonic 94.436 110.360 # SOURCE3 2 + angle_coeff @angle:c2-s4-c2 harmonic 73.133 102.290 # SOURCE3 1 + angle_coeff @angle:c2-s4-c3 harmonic 74.359 94.950 # SOURCE3 1 + angle_coeff @angle:c2-s4-o harmonic 95.340 107.090 # SOURCE3 1 + angle_coeff @angle:c3-s4-c3 harmonic 72.538 96.120 # SOURCE3_SOURCE5 72 1.2506 + angle_coeff @angle:c3-s4-ca harmonic 73.801 95.000 # SOURCE3 1 + angle_coeff @angle:c3-s4-f harmonic 99.956 91.700 # SOURCE3 1 + angle_coeff @angle:c3-s4-hs harmonic 53.159 90.600 # SOURCE3 1 + angle_coeff @angle:c3-s4-i harmonic 64.204 90.530 # SOURCE3 1 + angle_coeff @angle:c3-s4-n2 harmonic 98.749 90.590 # SOURCE3 1 + angle_coeff @angle:c3-s4-n3 harmonic 92.849 95.770 # SOURCE3_SOURCE5 10 1.8721 + angle_coeff @angle:c3-s4-n harmonic 92.379 96.070 # SOURCE3 4 1.0354 + angle_coeff @angle:c3-s4-n4 harmonic 88.918 92.470 # SOURCE3 1 + angle_coeff @angle:c3-s4-na harmonic 93.247 93.070 # SOURCE3 10 1.8813 + angle_coeff @angle:c3-s4-nh harmonic 92.347 97.080 # SOURCE3 1 + angle_coeff @angle:c3-s4-no harmonic 89.712 89.530 # SOURCE3 1 + angle_coeff @angle:c3-s4-o harmonic 92.851 106.710 # SOURCE3_SOURCE5 233 1.1391 + angle_coeff @angle:c3-s4-oh harmonic 97.024 90.280 # SOURCE4_SOURCE5 21 0.2709 + angle_coeff @angle:c3-s4-os harmonic 97.226 90.060 # SOURCE3 4 0.4484 + angle_coeff @angle:c3-s4-p2 harmonic 91.018 94.370 # SOURCE3 1 + angle_coeff @angle:c3-s4-p3 harmonic 93.042 96.540 # SOURCE3 4 1.3634 + angle_coeff @angle:c3-s4-p4 harmonic 87.791 97.400 # SOURCE3 1 + angle_coeff @angle:c3-s4-p5 harmonic 93.163 99.180 # SOURCE3 1 + angle_coeff @angle:c3-s4-s4 harmonic 75.465 89.500 # SOURCE3 1 + angle_coeff @angle:c3-s4-s harmonic 71.946 98.720 # SOURCE3 2 0.0185 + angle_coeff @angle:c3-s4-s6 harmonic 72.311 97.480 # SOURCE3 1 + angle_coeff @angle:c3-s4-sh harmonic 71.328 94.660 # SOURCE3 1 + angle_coeff @angle:c3-s4-ss harmonic 71.131 95.310 # SOURCE3 3 1.4101 + angle_coeff @angle:ca-s4-ca harmonic 74.616 95.210 # SOURCE3 1 + angle_coeff @angle:ca-s4-o harmonic 94.489 106.630 # SOURCE3 1 + angle_coeff @angle:c-s4-c3 harmonic 72.142 95.070 # SOURCE3 1 + angle_coeff @angle:c-s4-c harmonic 74.707 86.830 # SOURCE3 1 + angle_coeff @angle:cl-s4-cl harmonic 92.643 97.680 # SOURCE3 1 + angle_coeff @angle:cl-s4-o harmonic 100.538 108.340 # SOURCE3 2 + angle_coeff @angle:c-s4-o harmonic 91.597 106.170 # SOURCE3 1 + angle_coeff @angle:cx-s4-cx harmonic 102.278 48.800 # SOURCE2 1 + angle_coeff @angle:cx-s4-o harmonic 91.767 110.000 # SOURCE2 1 + angle_coeff @angle:f-s4-f harmonic 137.119 92.710 # SOURCE2 3 0.1490 + angle_coeff @angle:f-s4-o harmonic 129.265 106.810 # SOURCE2 2 0.0100 + angle_coeff @angle:f-s4-s harmonic 90.806 107.500 # SOURCE2 1 + angle_coeff @angle:hs-s4-hs harmonic 42.707 87.000 # SOURCE3 2 0.0202 + angle_coeff @angle:hs-s4-n1 harmonic 72.280 90.510 # HF/6-31G* 1 + angle_coeff @angle:hs-s4-o harmonic 69.666 110.270 # SOURCE3 5 0.1908 + angle_coeff @angle:i-s4-i harmonic 68.021 97.290 # SOURCE3 1 + angle_coeff @angle:i-s4-o harmonic 69.889 113.910 # SOURCE3 1 + angle_coeff @angle:n1-s4-n1 harmonic 127.594 94.020 # HF/6-31G* 1 + angle_coeff @angle:n1-s4-o harmonic 122.838 110.090 # HF/6-31G* 1 + angle_coeff @angle:n2-s4-n2 harmonic 133.526 90.170 # SOURCE3 1 + angle_coeff @angle:n2-s4-o harmonic 126.113 107.570 # SOURCE3 1 + angle_coeff @angle:n3-s4-n3 harmonic 121.849 91.190 # SOURCE3 1 + angle_coeff @angle:n3-s4-o harmonic 117.831 110.430 # SOURCE3_SOURCE5 13 1.9165 + angle_coeff @angle:n4-s4-n4 harmonic 106.426 94.610 # SOURCE3 1 + angle_coeff @angle:n4-s4-o harmonic 110.589 104.910 # SOURCE3 3 0.4370 + angle_coeff @angle:na-s4-na harmonic 112.128 103.100 # SOURCE3 1 + angle_coeff @angle:na-s4-o harmonic 116.397 109.750 # SOURCE3 10 2.6919 + angle_coeff @angle:nh-s4-nh harmonic 121.527 92.240 # SOURCE3 1 + angle_coeff @angle:nh-s4-o harmonic 119.657 107.540 # SOURCE3 3 0.0401 + angle_coeff @angle:n-s4-n harmonic 120.832 91.300 # SOURCE3 1 + angle_coeff @angle:n-s4-o harmonic 118.814 107.440 # SOURCE3_SOURCE5 9 1.2433 + angle_coeff @angle:no-s4-no harmonic 111.990 83.400 # SOURCE3 1 + angle_coeff @angle:no-s4-o harmonic 110.173 103.580 # SOURCE3 3 1.5109 + angle_coeff @angle:oh-s4-oh harmonic 120.174 100.340 # SOURCE3 1 + angle_coeff @angle:o-s4-o harmonic 127.045 114.110 # SOURCE3_SOURCE5 14 2.6371 + angle_coeff @angle:o-s4-oh harmonic 120.725 110.100 # SOURCE4_SOURCE5 30 0.8834 + angle_coeff @angle:o-s4-os harmonic 121.937 108.220 # SOURCE3_SOURCE5 19 1.5128 + angle_coeff @angle:o-s4-p2 harmonic 110.606 106.770 # SOURCE3 1 + angle_coeff @angle:o-s4-p3 harmonic 115.784 106.510 # SOURCE3 8 4.0943 + angle_coeff @angle:o-s4-p4 harmonic 109.471 103.360 # SOURCE3 1 + angle_coeff @angle:o-s4-p5 harmonic 123.827 96.950 # SOURCE3 1 + angle_coeff @angle:o-s4-s4 harmonic 91.337 104.550 # SOURCE3 1 + angle_coeff @angle:o-s4-s harmonic 88.312 112.220 # SOURCE3 4 2.8682 + angle_coeff @angle:o-s4-s6 harmonic 92.094 102.840 # SOURCE3 1 + angle_coeff @angle:o-s4-sh harmonic 86.714 107.510 # SOURCE3 3 0.7511 + angle_coeff @angle:os-s4-os harmonic 124.379 94.070 # SOURCE3_SOURCE5 7 2.3843 + angle_coeff @angle:o-s4-ss harmonic 86.001 109.490 # SOURCE3 5 1.8509 + angle_coeff @angle:p2-s4-p2 harmonic 118.888 92.620 # SOURCE3 1 + angle_coeff @angle:p3-s4-p3 harmonic 122.725 95.710 # SOURCE3 2 1.2239 + angle_coeff @angle:p5-s4-p5 harmonic 126.784 93.860 # SOURCE3 1 + angle_coeff @angle:s4-s4-s4 harmonic 77.030 90.170 # SOURCE3 1 + angle_coeff @angle:s4-s4-s6 harmonic 77.030 90.170 # SOURCE3 1 + angle_coeff @angle:s6-s4-s6 harmonic 75.638 93.520 # SOURCE3 1 + angle_coeff @angle:sh-s4-sh harmonic 69.229 102.760 # SOURCE3 1 + angle_coeff @angle:sh-s4-ss harmonic 69.301 102.640 # SOURCE3 1 + angle_coeff @angle:s-s4-s harmonic 70.495 108.080 # SOURCE3 1 + angle_coeff @angle:ss-s4-ss harmonic 71.889 95.470 # SOURCE3 1 + angle_coeff @angle:br-s6-br harmonic 77.581 101.570 # SOURCE3 1 + angle_coeff @angle:br-s6-c3 harmonic 73.519 98.990 # SOURCE3 1 + angle_coeff @angle:br-s6-f harmonic 94.581 100.600 # SOURCE2 1 + angle_coeff @angle:br-s6-o harmonic 90.691 107.580 # SOURCE3 6 0.3000 + angle_coeff @angle:c1-s6-c1 harmonic 75.601 99.990 # SOURCE3 1 + angle_coeff @angle:c1-s6-o harmonic 97.406 107.980 # SOURCE3_SOURCE5 7 0.4450 + angle_coeff @angle:c2-s6-c2 harmonic 72.969 102.750 # SOURCE3 1 + angle_coeff @angle:c2-s6-c3 harmonic 71.521 104.050 # SOURCE3 1 + angle_coeff @angle:c2-s6-o harmonic 96.507 106.580 # SOURCE3 1 + angle_coeff @angle:c3-s6-c3 harmonic 70.681 103.830 # SOURCE3_SOURCE5 74 2.0698 + angle_coeff @angle:c3-s6-ca harmonic 71.693 103.170 # SOURCE3 1 + angle_coeff @angle:c3-s6-cy harmonic 73.114 94.680 # SOURCE4_SOURCE5 19 0.4776 + angle_coeff @angle:c3-s6-f harmonic 98.119 95.900 # SOURCE3_SOURCE5 9 2.4171 + angle_coeff @angle:c3-s6-hs harmonic 51.078 100.620 # SOURCE3 1 + angle_coeff @angle:c3-s6-i harmonic 61.761 97.740 # SOURCE3 1 + angle_coeff @angle:c3-s6-n2 harmonic 90.421 112.480 # SOURCE4_SOURCE5 27 1.7086 + angle_coeff @angle:c3-s6-n3 harmonic 92.504 101.970 # SOURCE4_SOURCE5 162 1.1030 + angle_coeff @angle:c3-s6-n harmonic 90.797 103.440 # SOURCE3_SOURCE5 15 0.8616 + angle_coeff @angle:c3-s6-n4 harmonic 87.728 99.400 # SOURCE3 3 0.4695 + angle_coeff @angle:c3-s6-na harmonic 90.979 102.810 # SOURCE3 10 3.1256 + angle_coeff @angle:c3-s6-nh harmonic 90.894 104.320 # SOURCE4_SOURCE5 92 1.5234 + angle_coeff @angle:c3-s6-no harmonic 86.016 99.570 # SOURCE3 1 + angle_coeff @angle:c3-s6-o harmonic 93.703 108.610 # SOURCE3_SOURCE5 1062 1.0758 + angle_coeff @angle:c3-s6-oh harmonic 94.842 98.740 # SOURCE4_SOURCE5 121 0.7363 + angle_coeff @angle:c3-s6-os harmonic 96.240 96.420 # SOURCE4_SOURCE5 70 0.5868 + angle_coeff @angle:c3-s6-p2 harmonic 86.273 106.470 # SOURCE3 1 + angle_coeff @angle:c3-s6-p3 harmonic 90.571 103.400 # SOURCE3 3 0.8516 + angle_coeff @angle:c3-s6-p4 harmonic 84.641 104.120 # SOURCE3 1 + angle_coeff @angle:c3-s6-p5 harmonic 91.629 103.460 # SOURCE3 1 + angle_coeff @angle:c3-s6-s4 harmonic 72.386 98.100 # SOURCE3 1 + angle_coeff @angle:c3-s6-s harmonic 71.088 104.500 # SOURCE3 1 + angle_coeff @angle:c3-s6-s6 harmonic 71.006 101.950 # SOURCE3 1 + angle_coeff @angle:c3-s6-sh harmonic 70.399 101.840 # SOURCE3 1 + angle_coeff @angle:c3-s6-ss harmonic 69.952 102.470 # SOURCE3 3 1.7451 + angle_coeff @angle:ca-s6-ca harmonic 72.567 103.080 # SOURCE3 1 + angle_coeff @angle:ca-s6-o harmonic 97.373 104.090 # SOURCE4_SOURCE5 137 0.5743 + angle_coeff @angle:c-s6-c3 harmonic 70.322 101.240 # SOURCE3 1 + angle_coeff @angle:c-s6-c harmonic 69.677 99.820 # SOURCE3 1 + angle_coeff @angle:cc-s6-o harmonic 95.603 103.760 # SOURCE4_SOURCE5 24 0.8201 + angle_coeff @angle:cl-s6-cl harmonic 90.995 101.250 # SOURCE3 1 + angle_coeff @angle:cl-s6-f harmonic 105.577 99.000 # SOURCE2 1 + angle_coeff @angle:cl-s6-o harmonic 101.239 107.520 # SOURCE3_SOURCE5 6 0.2106 + angle_coeff @angle:c-s6-o harmonic 91.492 107.970 # SOURCE3 1 + angle_coeff @angle:c-s6-os harmonic 91.455 102.120 # SOURCE3 1 + angle_coeff @angle:cx-s6-cx harmonic 101.683 54.700 # SOURCE2 1 + angle_coeff @angle:cy-s6-o harmonic 91.172 110.520 # SOURCE4_SOURCE5 71 0.9427 + angle_coeff @angle:f-s6-f harmonic 137.577 89.710 # SOURCE2_SOURCE5 22 1.8574 + angle_coeff @angle:f-s6-o harmonic 130.197 106.540 # SOURCE3_SOURCE5 7 0.0793 + angle_coeff @angle:hs-s6-hs harmonic 40.502 99.020 # SOURCE3 2 0.0595 + angle_coeff @angle:hs-s6-n1 harmonic 77.206 97.270 # HF/6-31G* 1 + angle_coeff @angle:hs-s6-o harmonic 72.305 107.680 # SOURCE3_SOURCE5 17 0.0882 + angle_coeff @angle:i-s6-i harmonic 67.346 99.250 # SOURCE3 1 + angle_coeff @angle:i-s6-o harmonic 70.931 108.820 # SOURCE3_SOURCE5 6 0.6545 + angle_coeff @angle:n1-s6-n1 harmonic 147.507 95.520 # HF/6-31G* 1 + angle_coeff @angle:n1-s6-o harmonic 137.179 107.520 # HF/6-31G* 1 + angle_coeff @angle:n2-s6-n2 harmonic 132.302 98.610 # SOURCE3 1 + angle_coeff @angle:n2-s6-o harmonic 124.131 119.100 # SOURCE3_SOURCE5 11 3.0533 + angle_coeff @angle:n2-s6-oh harmonic 123.655 106.960 # SOURCE3 2 + angle_coeff @angle:n2-s6-os harmonic 126.381 103.250 # SOURCE3 1 + angle_coeff @angle:n3-s6-n3 harmonic 123.034 98.440 # SOURCE4_SOURCE5 16 0.3984 + angle_coeff @angle:n3-s6-o harmonic 124.794 107.430 # SOURCE3_SOURCE5 319 1.1452 + angle_coeff @angle:n3-s6-os harmonic 124.070 99.660 # SOURCE4_SOURCE5 27 0.8063 + angle_coeff @angle:n4-s6-n4 harmonic 105.682 101.850 # SOURCE3 1 + angle_coeff @angle:n4-s6-o harmonic 115.123 102.920 # SOURCE3 10 1.5434 + angle_coeff @angle:na-s6-na harmonic 119.677 98.040 # SOURCE3 1 + angle_coeff @angle:na-s6-o harmonic 123.180 105.820 # SOURCE3_SOURCE5 31 0.6987 + angle_coeff @angle:nh-s6-nh harmonic 123.669 94.560 # SOURCE3 1 + angle_coeff @angle:nh-s6-o harmonic 123.651 107.210 # SOURCE3_SOURCE5 106 1.3795 + angle_coeff @angle:n-s6-n harmonic 116.385 104.160 # SOURCE3 1 + angle_coeff @angle:n-s6-o harmonic 122.694 107.020 # SOURCE3_SOURCE5 63 1.7044 + angle_coeff @angle:no-s6-no harmonic 107.924 91.630 # SOURCE3 1 + angle_coeff @angle:no-s6-o harmonic 109.649 107.430 # SOURCE3 6 1.5494 + angle_coeff @angle:n-s6-os harmonic 122.468 99.230 # SOURCE4_SOURCE5 10 0.9794 + angle_coeff @angle:oh-s6-oh harmonic 124.674 100.340 # SOURCE3 6 0.0076 + angle_coeff @angle:oh-s6-os harmonic 127.394 96.810 # SOURCE4_SOURCE5 74 0.8201 + angle_coeff @angle:oh-s6-p2 harmonic 108.695 109.670 # SOURCE3 2 + angle_coeff @angle:o-s6-o harmonic 128.200 120.050 # SOURCE4_SOURCE5 971 1.8153 + angle_coeff @angle:o-s6-oh harmonic 126.323 108.050 # SOURCE3_SOURCE5 306 0.8954 + angle_coeff @angle:o-s6-os harmonic 126.629 108.560 # SOURCE3_SOURCE5 346 1.4469 + angle_coeff @angle:o-s6-p2 harmonic 111.304 106.610 # SOURCE3 1 + angle_coeff @angle:o-s6-p3 harmonic 116.333 107.070 # SOURCE3 22 1.0550 + angle_coeff @angle:o-s6-p4 harmonic 107.389 105.670 # SOURCE3 1 + angle_coeff @angle:o-s6-p5 harmonic 118.512 106.640 # SOURCE3 1 + angle_coeff @angle:o-s6-s4 harmonic 90.199 107.850 # SOURCE3 1 + angle_coeff @angle:o-s6-s harmonic 90.887 110.290 # SOURCE3 6 2.2405 + angle_coeff @angle:o-s6-s6 harmonic 90.953 106.070 # SOURCE3 1 + angle_coeff @angle:o-s6-sh harmonic 89.506 106.810 # SOURCE3 6 0.6292 + angle_coeff @angle:os-s6-os harmonic 126.643 98.700 # SOURCE3 1 + angle_coeff @angle:o-s6-ss harmonic 88.847 107.430 # SOURCE3 10 1.1423 + angle_coeff @angle:p3-s6-p3 harmonic 114.939 110.170 # SOURCE3 4 5.3678 + angle_coeff @angle:p5-s6-p5 harmonic 120.162 104.490 # SOURCE3 1 + angle_coeff @angle:s4-s6-s4 harmonic 72.429 101.990 # SOURCE3 1 + angle_coeff @angle:s4-s6-s6 harmonic 77.030 90.170 # SOURCE3 1 + angle_coeff @angle:s6-s6-s6 harmonic 71.972 103.290 # SOURCE3 1 + angle_coeff @angle:sh-s6-sh harmonic 69.961 106.430 # SOURCE3 1 + angle_coeff @angle:sh-s6-ss harmonic 71.071 102.640 # SOURCE3 1 + angle_coeff @angle:s-s6-s harmonic 71.394 109.340 # SOURCE3 1 + angle_coeff @angle:ss-s6-ss harmonic 71.189 101.820 # SOURCE3 1 + angle_coeff @angle:br-sh-hs harmonic 49.791 95.640 # SOURCE3 1 + angle_coeff @angle:c1-sh-hs harmonic 55.580 95.990 # calculated_based_on_C#C-SH 0 + angle_coeff @angle:c2-sh-hs harmonic 52.778 96.790 # SOURCE4_SOURCE5 12 0.5703 + angle_coeff @angle:c3-sh-hs harmonic 51.361 96.400 # SOURCE3_SOURCE5 191 0.6428 + angle_coeff @angle:ca-sh-hs harmonic 53.161 95.500 # SOURCE4_SOURCE5 44 0.8350 + angle_coeff @angle:cc-sh-hs harmonic 53.591 95.010 # SOURCE4_SOURCE5 23 1.3099 + angle_coeff @angle:c-sh-hs harmonic 53.042 94.470 # SOURCE3_SOURCE5 41 0.9733 + angle_coeff @angle:f-sh-hs harmonic 71.420 96.500 # SOURCE3 1 + angle_coeff @angle:hs-sh-hs harmonic 42.155 93.000 # SOURCE3_SOURCE5 3 0.4777 + angle_coeff @angle:hs-sh-i harmonic 44.148 96.440 # SOURCE3 1 + angle_coeff @angle:hs-sh-n1 harmonic 72.794 93.510 # HF/6-31G* 1 + angle_coeff @angle:hs-sh-n2 harmonic 67.814 95.820 # SOURCE3 5 3.1495 + angle_coeff @angle:hs-sh-n harmonic 68.213 95.590 # SOURCE3 4 3.9065 + angle_coeff @angle:hs-sh-n3 harmonic 67.725 95.980 # SOURCE3 3 1.1735 + angle_coeff @angle:hs-sh-n4 harmonic 66.458 93.130 # SOURCE3 3 0.1675 + angle_coeff @angle:hs-sh-na harmonic 67.804 97.380 # SOURCE3 9 1.0223 + angle_coeff @angle:hs-sh-nh harmonic 66.944 101.110 # SOURCE3 1 + angle_coeff @angle:hs-sh-no harmonic 66.751 92.930 # SOURCE3 1 + angle_coeff @angle:hs-sh-o harmonic 67.503 109.230 # SOURCE3 2 0.0068 + angle_coeff @angle:hs-sh-oh harmonic 68.281 98.640 # SOURCE3 2 0.0605 + angle_coeff @angle:hs-sh-os harmonic 69.115 98.150 # SOURCE3 3 0.1661 + angle_coeff @angle:hs-sh-p2 harmonic 66.084 99.120 # SOURCE3 10 5.4110 + angle_coeff @angle:hs-sh-p3 harmonic 62.144 95.810 # SOURCE3 3 0.4396 + angle_coeff @angle:hs-sh-p4 harmonic 63.188 94.220 # SOURCE3 4 0.7605 + angle_coeff @angle:hs-sh-p5 harmonic 64.112 94.520 # SOURCE3 3 0.5589 + angle_coeff @angle:hs-sh-s harmonic 47.237 102.870 # SOURCE3 2 + angle_coeff @angle:hs-sh-s4 harmonic 48.513 92.160 # SOURCE3 3 1.6519 + angle_coeff @angle:hs-sh-s6 harmonic 49.509 93.830 # SOURCE3 3 1.2561 + angle_coeff @angle:hs-sh-sh harmonic 49.372 99.070 # SOURCE3 2 + angle_coeff @angle:hs-sh-ss harmonic 49.131 99.170 # SOURCE3 3 0.2457 + angle_coeff @angle:br-ss-br harmonic 77.455 102.920 # SOURCE3 1 + angle_coeff @angle:br-ss-c3 harmonic 73.438 99.030 # SOURCE3 1 + angle_coeff @angle:c1-ss-c1 harmonic 77.701 98.300 # SOURCE2 1 + angle_coeff @angle:c1-ss-c3 harmonic 72.838 101.860 # SOURCE2_SOURCE5 24 1.0923 + angle_coeff @angle:c2-ss-c2 harmonic 75.153 99.560 # SOURCE3 1 + angle_coeff @angle:c2-ss-c3 harmonic 72.568 100.370 # SOURCE4 100 2.3280 + angle_coeff @angle:c2-ss-cy harmonic 76.860 88.910 # SOURCE4_SOURCE5 51 0.4794 + angle_coeff @angle:c2-ss-n2 harmonic 92.922 106.760 # SOURCE3 1 + angle_coeff @angle:c2-ss-na harmonic 93.759 100.510 # SOURCE3 6 6.9702 + angle_coeff @angle:c2-ss-os harmonic 100.020 89.760 # SOURCE3 1 + angle_coeff @angle:c2-ss-ss harmonic 75.743 92.260 # SOURCE3 1 + angle_coeff @angle:c3-ss-c3 harmonic 71.051 99.240 # SOURCE3_SOURCE5 443 1.3973 + angle_coeff @angle:c3-ss-ca harmonic 71.145 102.100 # SOURCE4_SOURCE5 393 1.3148 + angle_coeff @angle:c3-ss-cc harmonic 72.106 100.640 # CORR_SOURCE5 118 1.6668 + angle_coeff @angle:c3-ss-cd harmonic 72.106 100.640 # CORR_SOURCE5 118 1.6668 + angle_coeff @angle:c3-ss-cl harmonic 80.033 99.400 # SOURCE2 1 + angle_coeff @angle:c3-ss-cy harmonic 72.699 94.270 # SOURCE4_SOURCE5 150 0.4649 + angle_coeff @angle:c3-ss-f harmonic 95.769 97.490 # SOURCE3 1 + angle_coeff @angle:c3-ss-i harmonic 67.953 100.000 # SOURCE3 1 + angle_coeff @angle:c3-ss-n1 harmonic 94.433 98.440 # HF/6-31G* 1 + angle_coeff @angle:c3-ss-n2 harmonic 94.643 96.080 # SOURCE3_SOURCE5 11 1.2317 + angle_coeff @angle:c3-ss-n3 harmonic 91.857 98.830 # SOURCE3 3 0.2909 + angle_coeff @angle:c3-ss-n harmonic 91.130 100.300 # SOURCE3 4 0.6579 + angle_coeff @angle:c3-ss-n4 harmonic 90.288 97.790 # SOURCE3 3 0.2002 + angle_coeff @angle:c3-ss-na harmonic 92.714 96.590 # SOURCE3_SOURCE5 21 1.0132 + angle_coeff @angle:c3-ss-nh harmonic 91.350 100.630 # SOURCE3 1 + angle_coeff @angle:c3-ss-no harmonic 89.523 98.620 # SOURCE3 1 + angle_coeff @angle:c3-ss-o harmonic 92.362 106.990 # SOURCE3_SOURCE5 11 1.0097 + angle_coeff @angle:c3-ss-oh harmonic 92.897 98.280 # SOURCE3 2 1.4326 + angle_coeff @angle:c3-ss-os harmonic 92.581 98.210 # SOURCE3 4 1.7097 + angle_coeff @angle:c3-ss-p2 harmonic 95.479 98.410 # SOURCE3 8 0.9454 + angle_coeff @angle:c3-ss-p3 harmonic 90.885 98.700 # SOURCE3 3 0.0356 + angle_coeff @angle:c3-ss-p4 harmonic 91.629 98.160 # SOURCE3 4 0.1361 + angle_coeff @angle:c3-ss-p5 harmonic 90.364 100.060 # SOURCE4_SOURCE5 62 1.0141 + angle_coeff @angle:c3-ss-s4 harmonic 70.640 96.370 # SOURCE3 3 0.0202 + angle_coeff @angle:c3-ss-s harmonic 70.410 101.900 # SOURCE3 1 + angle_coeff @angle:c3-ss-s6 harmonic 71.595 96.760 # SOURCE3 3 1.5680 + angle_coeff @angle:c3-ss-sh harmonic 70.887 101.930 # SOURCE3 1 + angle_coeff @angle:c3-ss-ss harmonic 70.258 103.390 # SOURCE4_SOURCE5 237 1.0715 + angle_coeff @angle:ca-ss-ca harmonic 73.541 98.830 # SOURCE4_SOURCE5 225 1.3938 + angle_coeff @angle:ca-ss-cc harmonic 77.818 89.470 # CORR_SOURCE5 200 1.1779 + angle_coeff @angle:ca-ss-cd harmonic 77.818 89.470 # CORR_SOURCE5 200 1.1779 + angle_coeff @angle:ca-ss-cl harmonic 80.234 101.050 # SOURCE3 1 + angle_coeff @angle:ca-ss-n harmonic 97.427 90.990 # SOURCE3_SOURCE5 5 0.5202 + angle_coeff @angle:ca-ss-na harmonic 93.087 99.320 # SOURCE3 1 + angle_coeff @angle:ca-ss-nc harmonic 97.913 94.760 # SOURCE3 1 + angle_coeff @angle:ca-ss-nd harmonic 97.913 94.760 # SOURCE3 1 + angle_coeff @angle:ca-ss-ss harmonic 70.425 105.130 # SOURCE4_SOURCE5 69 1.0007 + angle_coeff @angle:c-ss-c2 harmonic 76.536 92.430 # SOURCE3 1 + angle_coeff @angle:c-ss-c3 harmonic 71.828 99.160 # SOURCE3_SOURCE5 108 1.2072 + angle_coeff @angle:c-ss-c harmonic 71.820 101.400 # SOURCE3 1 + angle_coeff @angle:c-ss-cc harmonic 75.135 94.890 # SOURCE4_SOURCE5 32 1.7205 + angle_coeff @angle:cc-ss-cc harmonic 78.031 90.240 # SOURCE3_SOURCE5 652 1.5043 + angle_coeff @angle:cc-ss-cd harmonic 77.807 90.760 # SOURCE4_SOURCE5 157 1.7485 + angle_coeff @angle:cc-ss-n harmonic 96.775 93.580 # SOURCE3_SOURCE5 6 2.0175 + angle_coeff @angle:cc-ss-na harmonic 93.760 99.330 # SOURCE3 18 + angle_coeff @angle:cc-ss-nc harmonic 99.545 93.220 # CORR_SOURCE5 25 1.5563 + angle_coeff @angle:cc-ss-os harmonic 94.746 98.810 # SOURCE3 2 2.1583 + angle_coeff @angle:cc-ss-ss harmonic 74.869 93.800 # CORR_SOURCE5 31 0.9858 + angle_coeff @angle:cd-ss-cd harmonic 78.031 90.240 # SOURCE3_SOURCE5 652 1.5043 + angle_coeff @angle:cd-ss-n harmonic 96.775 93.580 # SOURCE3_SOURCE5 6 2.0175 + angle_coeff @angle:cd-ss-na harmonic 93.760 99.330 # SOURCE3 18 2.5847 + angle_coeff @angle:cd-ss-nd harmonic 99.545 93.220 # CORR_SOURCE5 25 1.5563 + angle_coeff @angle:cd-ss-os harmonic 94.746 98.810 # SOURCE3 2 + angle_coeff @angle:cd-ss-ss harmonic 74.869 93.800 # CORR_SOURCE5 31 0.9858 + angle_coeff @angle:cl-ss-cl harmonic 90.057 103.370 # SOURCE3 1 + angle_coeff @angle:cx-ss-cx harmonic 102.217 48.300 # SOURCE2 1 + angle_coeff @angle:f-ss-f harmonic 129.659 98.300 # SOURCE2 1 + angle_coeff @angle:f-ss-ss harmonic 90.124 108.300 # SOURCE2 1 + angle_coeff @angle:i-ss-i harmonic 72.646 106.290 # SOURCE3 1 + angle_coeff @angle:n1-ss-n1 harmonic 128.766 96.960 # HF/6-31G* 1 + angle_coeff @angle:n2-ss-n2 harmonic 125.325 96.750 # SOURCE3 1 + angle_coeff @angle:n3-ss-n3 harmonic 117.075 102.340 # SOURCE3 1 + angle_coeff @angle:n4-ss-n4 harmonic 111.994 101.190 # SOURCE3 1 + angle_coeff @angle:na-ss-na harmonic 116.207 102.810 # SOURCE3 1 + angle_coeff @angle:nc-ss-nc harmonic 126.827 97.990 # CORR_SOURCE5 29 0.5000 + angle_coeff @angle:nd-ss-nd harmonic 126.827 97.990 # CORR_SOURCE5 29 0.5000 + angle_coeff @angle:nh-ss-nh harmonic 114.991 107.890 # SOURCE3 1 + angle_coeff @angle:n-ss-n harmonic 116.487 103.100 # SOURCE3 1 + angle_coeff @angle:no-ss-no harmonic 108.247 106.430 # SOURCE3 1 + angle_coeff @angle:oh-ss-oh harmonic 118.444 104.250 # SOURCE3 1 + angle_coeff @angle:o-ss-o harmonic 124.036 119.300 # SOURCE2 1 + angle_coeff @angle:o-ss-p5 harmonic 114.305 106.410 # SOURCE3 1 + angle_coeff @angle:o-ss-s6 harmonic 89.483 105.390 # SOURCE3 1 + angle_coeff @angle:os-ss-os harmonic 118.047 102.990 # SOURCE3 1 + angle_coeff @angle:o-ss-ss harmonic 88.228 112.700 # SOURCE2 1 + angle_coeff @angle:p2-ss-p2 harmonic 127.760 99.520 # SOURCE3 1 + angle_coeff @angle:p3-ss-p3 harmonic 117.165 101.670 # SOURCE3 1 + angle_coeff @angle:p5-ss-p5 harmonic 126.593 87.370 # SOURCE3_SOURCE5 11 1.2491 + angle_coeff @angle:s4-ss-s4 harmonic 71.661 96.080 # SOURCE3 1 + angle_coeff @angle:s4-ss-s6 harmonic 70.568 101.260 # SOURCE3 1 + angle_coeff @angle:s6-ss-s6 harmonic 71.193 101.810 # SOURCE3 1 + angle_coeff @angle:sh-ss-sh harmonic 70.979 107.540 # SOURCE3 1 + angle_coeff @angle:sh-ss-ss harmonic 71.215 106.530 # SOURCE3 1 + angle_coeff @angle:s-ss-s harmonic 67.904 115.040 # SOURCE3 1 + angle_coeff @angle:ss-ss-ss harmonic 70.653 107.930 # SOURCE4_SOURCE5 72 1.6368 + angle_coeff @angle:c3-sx-ca harmonic 72.223 96.640 # SOURCE4_SOURCE5 41 0.4942 + angle_coeff @angle:c3-sx-cc harmonic 73.054 95.180 # SOURCE4_SOURCE5 41 0.6549 + angle_coeff @angle:c3-sx-ce harmonic 72.861 95.290 # SOURCE3_SOURCE5 10 0.5723 + angle_coeff @angle:c3-sx-cf harmonic 72.861 95.290 # SOURCE3_SOURCE5 7 0.8172 + angle_coeff @angle:c3-sx-ne harmonic 93.362 90.060 # SOURCE3 5 1.9627 + angle_coeff @angle:c3-sx-nf harmonic 93.362 90.060 # SOURCE3 5 + angle_coeff @angle:c3-sx-o harmonic 91.942 107.520 # SOURCE3_SOURCE5 84 0.7996 + angle_coeff @angle:c3-sx-pe harmonic 91.537 94.320 # SOURCE3 7 0.5547 + angle_coeff @angle:c3-sx-pf harmonic 91.537 94.320 # SOURCE3 7 + angle_coeff @angle:c3-sx-px harmonic 88.346 96.460 # SOURCE3 3 1.3351 + angle_coeff @angle:c3-sx-py harmonic 88.211 95.670 # SOURCE3 1 + angle_coeff @angle:c3-sx-sx harmonic 67.226 91.470 # SOURCE3 4 1.9919 + angle_coeff @angle:c3-sx-sy harmonic 68.899 95.470 # SOURCE3 3 2.8422 + angle_coeff @angle:ca-sx-ca harmonic 72.893 95.750 # SOURCE3_SOURCE5 14 1.8607 + angle_coeff @angle:ca-sx-o harmonic 92.722 107.150 # SOURCE4_SOURCE5 86 0.9103 + angle_coeff @angle:c-sx-c3 harmonic 72.536 92.710 # SOURCE3 3 0.3095 + angle_coeff @angle:c-sx-c harmonic 74.104 86.850 # SOURCE3 1 + angle_coeff @angle:cc-sx-o harmonic 94.293 104.810 # SOURCE4_SOURCE5 45 1.5594 + angle_coeff @angle:ce-sx-ce harmonic 73.461 94.960 # SOURCE3 1 + angle_coeff @angle:ce-sx-o harmonic 92.502 108.230 # SOURCE3_SOURCE5 27 0.8358 + angle_coeff @angle:cf-sx-cf harmonic 73.461 94.960 # SOURCE3 1 + angle_coeff @angle:cf-sx-o harmonic 92.502 108.230 # SOURCE3_SOURCE5 22 0.9547 + angle_coeff @angle:c-sx-o harmonic 90.915 106.170 # SOURCE3 5 0.9477 + angle_coeff @angle:ne-sx-ne harmonic 107.648 106.450 # SOURCE3_SOURCE5 5 1.4815 + angle_coeff @angle:ne-sx-o harmonic 114.103 109.810 # SOURCE3_SOURCE5 13 1.0385 + angle_coeff @angle:nf-sx-nf harmonic 107.648 106.450 # SOURCE3_SOURCE5 5 1.4815 + angle_coeff @angle:nf-sx-o harmonic 114.103 109.810 # SOURCE3_SOURCE5 6 0.5536 + angle_coeff @angle:o-sx-pe harmonic 111.805 106.430 # SOURCE3 9 2.8345 + angle_coeff @angle:o-sx-pf harmonic 111.805 106.430 # SOURCE3 9 + angle_coeff @angle:o-sx-px harmonic 109.143 104.770 # SOURCE3 3 1.9810 + angle_coeff @angle:o-sx-py harmonic 106.155 109.130 # SOURCE3 7 5.6840 + angle_coeff @angle:o-sx-sx harmonic 79.764 104.650 # SOURCE3 6 3.0524 + angle_coeff @angle:o-sx-sy harmonic 85.123 103.410 # SOURCE3 5 0.9618 + angle_coeff @angle:pe-sx-pe harmonic 120.095 92.620 # SOURCE3 1 + angle_coeff @angle:pf-sx-pf harmonic 120.095 92.620 # SOURCE3 1 + angle_coeff @angle:py-sx-py harmonic 133.313 69.230 # SOURCE3 3 17.4143 + angle_coeff @angle:sx-sx-sx harmonic 69.059 84.900 # SOURCE3 1 + angle_coeff @angle:sy-sx-sy harmonic 69.768 93.520 # SOURCE3 1 + angle_coeff @angle:c3-sy-ca harmonic 70.945 103.930 # SOURCE4_SOURCE5 136 0.4172 + angle_coeff @angle:c3-sy-cc harmonic 71.767 101.950 # SOURCE4_SOURCE5 32 1.4362 + angle_coeff @angle:c3-sy-ce harmonic 71.136 103.530 # SOURCE3_SOURCE5 11 1.3594 + angle_coeff @angle:c3-sy-cf harmonic 71.136 103.530 # SOURCE3_SOURCE5 8 1.7429 + angle_coeff @angle:c3-sy-ne harmonic 92.368 102.190 # SOURCE3_SOURCE5 11 3.1966 + angle_coeff @angle:c3-sy-nf harmonic 92.368 102.190 # SOURCE3_SOURCE5 6 2.3703 + angle_coeff @angle:c3-sy-o harmonic 93.792 107.850 # SOURCE3_SOURCE5 283 0.5690 + angle_coeff @angle:c3-sy-pe harmonic 85.480 106.030 # SOURCE3 6 2.6117 + angle_coeff @angle:c3-sy-pf harmonic 85.480 106.030 # SOURCE3 6 + angle_coeff @angle:c3-sy-px harmonic 85.416 103.620 # SOURCE3 3 0.7078 + angle_coeff @angle:c3-sy-py harmonic 87.474 103.390 # SOURCE3 3 0.4563 + angle_coeff @angle:c3-sy-sx harmonic 66.097 104.640 # SOURCE3 3 4.6276 + angle_coeff @angle:c3-sy-sy harmonic 67.466 100.780 # SOURCE3 4 1.1633 + angle_coeff @angle:ca-sy-ca harmonic 71.127 104.440 # SOURCE4_SOURCE5 55 1.7845 + angle_coeff @angle:ca-sy-cc harmonic 71.045 105.090 # SOURCE4_SOURCE5 10 0.3628 + angle_coeff @angle:ca-sy-n3 harmonic 92.241 102.440 # SOURCE4_SOURCE5 407 1.1038 + angle_coeff @angle:ca-sy-n harmonic 90.479 105.370 # SOURCE4_SOURCE5 122 1.2203 + angle_coeff @angle:ca-sy-ne harmonic 92.539 103.010 # SOURCE4_SOURCE5 36 2.1672 + angle_coeff @angle:ca-sy-nh harmonic 90.475 105.500 # SOURCE4_SOURCE5 205 1.5936 + angle_coeff @angle:ca-sy-o harmonic 94.276 108.350 # SOURCE3_SOURCE5 1362 0.6985 + angle_coeff @angle:ca-sy-oh harmonic 93.834 101.300 # SOURCE4_SOURCE5 94 0.8210 + angle_coeff @angle:ca-sy-os harmonic 96.750 92.980 # SOURCE3 1 + angle_coeff @angle:c-sy-c3 harmonic 70.399 101.250 # SOURCE3 3 1.1850 + angle_coeff @angle:c-sy-c harmonic 69.867 99.810 # SOURCE3 1 + angle_coeff @angle:cc-sy-n3 harmonic 92.404 102.530 # CORR_SOURCE5 35 0.5689 + angle_coeff @angle:cc-sy-o harmonic 94.752 107.890 # CORR_SOURCE5 130 0.8911 + angle_coeff @angle:cd-sy-n3 harmonic 92.404 102.530 # CORR_SOURCE5 35 0.5689 + angle_coeff @angle:cd-sy-nh harmonic 94.463 97.200 # SOURCE4_SOURCE5 12 0.2429 + angle_coeff @angle:cd-sy-o harmonic 94.752 107.890 # CORR_SOURCE5 130 0.8911 + angle_coeff @angle:ce-sy-ce harmonic 71.811 102.780 # SOURCE3 1 + angle_coeff @angle:ce-sy-o harmonic 94.373 108.380 # SOURCE3_SOURCE5 66 0.9753 + angle_coeff @angle:cf-sy-cf harmonic 71.811 102.780 # SOURCE3 1 + angle_coeff @angle:cf-sy-o harmonic 94.373 108.380 # SOURCE3_SOURCE5 56 1.0516 + angle_coeff @angle:c-sy-o harmonic 91.740 107.480 # SOURCE3_SOURCE5 16 0.7996 + angle_coeff @angle:n2-sy-o harmonic 121.876 123.530 # SOURCE4 6 1.2388 + angle_coeff @angle:n3-sy-ne harmonic 120.039 101.930 # SOURCE4_SOURCE5 15 1.4395 + angle_coeff @angle:n3-sy-o harmonic 123.426 107.130 # SOURCE4_SOURCE5 863 1.1609 + angle_coeff @angle:na-sy-na harmonic 119.379 98.040 # SOURCE3 1 + angle_coeff @angle:nc-sy-nc harmonic 132.584 98.040 # SOURCE3 2 + angle_coeff @angle:nd-sy-nd harmonic 132.584 98.040 # SOURCE3 2 + angle_coeff @angle:ne-sy-ne harmonic 122.921 98.620 # SOURCE3 1 + angle_coeff @angle:ne-sy-o harmonic 123.169 109.650 # SOURCE3_SOURCE5 101 1.9902 + angle_coeff @angle:nf-sy-nf harmonic 122.921 98.620 # SOURCE3 1 + angle_coeff @angle:nf-sy-o harmonic 123.169 109.650 # SOURCE3_SOURCE5 87 1.9451 + angle_coeff @angle:nh-sy-o harmonic 123.056 106.230 # SOURCE4_SOURCE5 319 1.7353 + angle_coeff @angle:n-sy-o harmonic 122.195 107.540 # SOURCE4_SOURCE5 155 1.8699 + angle_coeff @angle:o-sy-o harmonic 126.375 121.410 # SOURCE3_SOURCE5 734 0.8526 + angle_coeff @angle:o-sy-oh harmonic 125.990 106.680 # SOURCE3_SOURCE5 166 0.5588 + angle_coeff @angle:o-sy-os harmonic 123.063 107.520 # SOURCE4_SOURCE5 38 1.6656 + angle_coeff @angle:o-sy-pe harmonic 109.504 106.900 # SOURCE3 12 1.4524 + angle_coeff @angle:o-sy-pf harmonic 109.504 106.900 # SOURCE3 12 + angle_coeff @angle:o-sy-px harmonic 108.122 106.170 # SOURCE3 6 0.7059 + angle_coeff @angle:o-sy-py harmonic 111.153 106.670 # SOURCE3 10 0.6478 + angle_coeff @angle:o-sy-sx harmonic 83.961 106.330 # SOURCE3 10 2.0456 + angle_coeff @angle:o-sy-sy harmonic 84.205 106.190 # SOURCE3 12 0.1754 + angle_coeff @angle:py-sy-py harmonic 112.342 104.490 # SOURCE3 1 + angle_coeff @angle:sx-sy-sx harmonic 66.808 101.990 # SOURCE3 1 + angle_coeff @angle:sy-sy-sy harmonic 66.534 103.290 # SOURCE3 1 + angle_coeff @angle:c2-c1-cf harmonic 60.047 179.050 # SOURCE4_SOURCE5 9 0.3913 + angle_coeff @angle:c3-c1-ch harmonic 57.725 178.430 # SOURCE4_SOURCE5 95 0.5682 + angle_coeff @angle:nf-c1-s harmonic 73.610 175.820 # SOURCE4_SOURCE5 15 0.2067 + angle_coeff @angle:br-c2-cf harmonic 64.279 121.530 # SOURCE4_SOURCE5 11 0.7009 + angle_coeff @angle:cd-c2-h4 harmonic 49.786 119.850 # SOURCE4_SOURCE5 16 0.8001 + angle_coeff @angle:cd-c2-nh harmonic 86.562 123.120 # SOURCE4_SOURCE5 17 1.2171 + angle_coeff @angle:cd-c2-o harmonic 91.352 123.590 # SOURCE4_SOURCE5 6 0.0560 + angle_coeff @angle:cf-c2-cl harmonic 72.107 123.470 # SOURCE4_SOURCE5 30 1.0225 + angle_coeff @angle:cf-c2-h4 harmonic 49.654 122.310 # SOURCE4_SOURCE5 145 1.6214 + angle_coeff @angle:cf-c2-na harmonic 86.108 124.170 # SOURCE4_SOURCE5 6 1.9423 + angle_coeff @angle:cf-c2-nh harmonic 87.822 120.710 # SOURCE4_SOURCE5 150 2.3947 + angle_coeff @angle:cf-c2-no harmonic 86.097 119.650 # SOURCE4_SOURCE5 5 0.9817 + angle_coeff @angle:cf-c2-o harmonic 91.992 123.370 # SOURCE4_SOURCE5 9 1.0481 + angle_coeff @angle:cf-c2-oh harmonic 88.571 123.130 # SOURCE4_SOURCE5 62 1.7479 + angle_coeff @angle:cf-c2-os harmonic 87.995 122.800 # SOURCE4_SOURCE5 98 2.2743 + angle_coeff @angle:h4-c2-nf harmonic 64.858 119.510 # SOURCE4_SOURCE5 42 1.6302 + angle_coeff @angle:h5-c2-nf harmonic 64.691 119.850 # SOURCE4_SOURCE5 27 1.3790 + angle_coeff @angle:nf-c2-os harmonic 114.213 118.760 # SOURCE4 5 + angle_coeff @angle:nf-c2-ss harmonic 82.205 120.510 # SOURCE4_SOURCE5 23 2.4188 + angle_coeff @angle:n-c2-nf harmonic 109.323 125.340 # SOURCE4_SOURCE5 15 1.5591 + angle_coeff @angle:ca-c3-cf harmonic 65.618 112.210 # SOURCE4_SOURCE5 93 1.2595 + angle_coeff @angle:cd-c3-cx harmonic 65.894 112.100 # SOURCE4_SOURCE5 7 1.7201 + angle_coeff @angle:c-c3-cf harmonic 65.527 111.890 # SOURCE4_SOURCE5 59 1.5769 + angle_coeff @angle:cd-c3-hx harmonic 47.588 111.010 # SOURCE4_SOURCE5 10 0.7123 + angle_coeff @angle:cd-c3-n2 harmonic 84.630 110.310 # SOURCE4_SOURCE5 21 0.5628 + angle_coeff @angle:cd-c3-n4 harmonic 81.467 115.580 # SOURCE4_SOURCE5 6 1.1723 + angle_coeff @angle:cd-c3-na harmonic 83.647 113.150 # SOURCE4_SOURCE5 10 0.6466 + angle_coeff @angle:cd-c3-p5 harmonic 79.513 116.230 # SOURCE4_SOURCE5 6 0.7766 + angle_coeff @angle:cf-c3-cf harmonic 65.833 111.470 # SOURCE4_SOURCE5 35 0.5985 + angle_coeff @angle:cf-c3-n harmonic 84.349 110.220 # SOURCE4_SOURCE5 10 1.0919 + angle_coeff @angle:cf-c3-oh harmonic 84.971 111.190 # SOURCE4_SOURCE5 57 1.5702 + angle_coeff @angle:cf-c3-os harmonic 85.412 109.500 # SOURCE4_SOURCE5 55 1.8883 + angle_coeff @angle:cf-c3-ss harmonic 63.337 110.720 # SOURCE4_SOURCE5 12 1.7025 + angle_coeff @angle:cd-ca-cq harmonic 66.010 124.300 # SOURCE4_SOURCE5 10 0.6423 + angle_coeff @angle:cf-ca-na harmonic 84.062 119.920 # SOURCE4_SOURCE5 29 0.5242 + angle_coeff @angle:ch-ca-cq harmonic 67.320 121.530 # SOURCE4_SOURCE5 12 0.1831 + angle_coeff @angle:cl-ca-cq harmonic 71.726 120.390 # SOURCE4_SOURCE5 34 0.5366 + angle_coeff @angle:cq-ca-f harmonic 88.831 119.420 # SOURCE4_SOURCE5 30 0.2799 + angle_coeff @angle:cq-ca-h4 harmonic 48.404 120.090 # SOURCE4_SOURCE5 35 0.4098 + angle_coeff @angle:cq-ca-na harmonic 90.665 108.790 # SOURCE4_SOURCE5 349 0.5003 + angle_coeff @angle:cq-ca-nb harmonic 86.369 123.580 # SOURCE4_SOURCE5 79 0.8527 + angle_coeff @angle:cq-ca-nh harmonic 85.714 121.560 # SOURCE4_SOURCE5 19 0.6123 + angle_coeff @angle:cq-ca-oh harmonic 86.623 120.850 # SOURCE4_SOURCE5 29 1.4592 + angle_coeff @angle:cq-ca-ss harmonic 65.950 111.170 # SOURCE4_SOURCE5 16 2.4162 + angle_coeff @angle:ca-c-nf harmonic 85.290 114.710 # SOURCE4_SOURCE5 9 0.7464 + angle_coeff @angle:br-cd-c harmonic 65.156 116.280 # SOURCE4_SOURCE5 24 1.3164 + angle_coeff @angle:br-cd-cd harmonic 63.389 124.050 # SOURCE4_SOURCE5 23 1.9356 + angle_coeff @angle:br-cd-cc harmonic 63.686 124.230 # SOURCE4_SOURCE5 84 2.2845 + angle_coeff @angle:br-cd-na harmonic 80.565 121.580 # SOURCE4_SOURCE5 13 0.9881 + angle_coeff @angle:ca-cd-cf harmonic 64.258 127.010 # SOURCE4_SOURCE5 27 1.6430 + angle_coeff @angle:ca-cd-nh harmonic 84.253 122.130 # SOURCE4_SOURCE5 11 2.0536 + angle_coeff @angle:cd-c-cf harmonic 66.433 115.570 # SOURCE4_SOURCE5 8 1.2130 + angle_coeff @angle:cd-cd-f harmonic 88.377 119.190 # SOURCE4_SOURCE5 19 1.0481 + angle_coeff @angle:c-cd-ch harmonic 67.046 117.880 # SOURCE4_SOURCE5 19 0.6396 + angle_coeff @angle:cd-cd-sy harmonic 61.106 128.250 # SOURCE4_SOURCE5 12 0.8482 + angle_coeff @angle:cc-cd-f harmonic 89.570 121.190 # SOURCE4_SOURCE5 54 0.6386 + angle_coeff @angle:cc-cd-no harmonic 82.947 128.690 # SOURCE4_SOURCE5 197 1.4212 + angle_coeff @angle:c-cd-f harmonic 87.759 116.980 # SOURCE4_SOURCE5 33 0.4384 + angle_coeff @angle:ch-cd-na harmonic 84.878 122.610 # SOURCE4_SOURCE5 7 1.0826 + angle_coeff @angle:ch-cd-ss harmonic 63.762 120.730 # SOURCE4_SOURCE5 15 0.9326 + angle_coeff @angle:cd-c-h4 harmonic 47.598 114.830 # SOURCE4_SOURCE5 20 0.4400 + angle_coeff @angle:cl-cd-na harmonic 90.511 121.120 # SOURCE4_SOURCE5 25 0.9015 + angle_coeff @angle:cl-cd-ss harmonic 71.934 119.850 # SOURCE4_SOURCE5 16 0.8775 + angle_coeff @angle:c-cd-nf harmonic 84.503 119.880 # SOURCE4 6 + angle_coeff @angle:cd-c-s harmonic 64.011 126.280 # SOURCE4_SOURCE5 57 2.2083 + angle_coeff @angle:cd-c-ss harmonic 64.406 112.400 # SOURCE4_SOURCE5 32 1.0830 + angle_coeff @angle:cx-cd-nc harmonic 83.147 127.820 # SOURCE4_SOURCE5 15 1.5594 + angle_coeff @angle:cx-cd-os harmonic 85.414 118.070 # SOURCE4_SOURCE5 13 0.0898 + angle_coeff @angle:cc-c-cx harmonic 65.553 117.430 # SOURCE4_SOURCE5 24 0.1441 + angle_coeff @angle:cc-c-nc harmonic 86.534 113.750 # SOURCE4_SOURCE5 14 0.0860 + angle_coeff @angle:cf-c-cx harmonic 65.246 117.390 # SOURCE4_SOURCE5 13 0.7631 + angle_coeff @angle:cf-c-h4 harmonic 47.181 114.890 # SOURCE4_SOURCE5 94 0.4993 + angle_coeff @angle:cf-c-ss harmonic 64.794 110.490 # SOURCE4_SOURCE5 8 0.5728 + angle_coeff @angle:na-cd-no harmonic 105.313 124.590 # SOURCE4_SOURCE5 114 0.8160 + angle_coeff @angle:na-cd-oh harmonic 111.744 117.480 # SOURCE4_SOURCE5 23 1.0304 + angle_coeff @angle:na-cd-sx harmonic 79.683 117.020 # SOURCE4_SOURCE5 19 0.3766 + angle_coeff @angle:na-cd-sy harmonic 79.507 120.460 # SOURCE4_SOURCE5 8 1.7069 + angle_coeff @angle:nd-cd-no harmonic 106.922 121.730 # SOURCE4_SOURCE5 10 0.8384 + angle_coeff @angle:nc-cd-nc harmonic 110.827 128.070 # SOURCE4_SOURCE5 10 0.4198 + angle_coeff @angle:nc-cd-nf harmonic 107.796 129.010 # SOURCE4_SOURCE5 13 1.6879 + angle_coeff @angle:nc-cd-no harmonic 108.240 122.750 # SOURCE4_SOURCE5 64 0.2909 + angle_coeff @angle:nc-cd-sh harmonic 79.198 124.970 # SOURCE4_SOURCE5 13 0.8081 + angle_coeff @angle:nc-cd-sx harmonic 76.768 127.740 # SOURCE4_SOURCE5 19 0.3234 + angle_coeff @angle:nc-cd-sy harmonic 79.255 123.030 # SOURCE4_SOURCE5 20 1.2273 + angle_coeff @angle:nf-cd-ss harmonic 81.707 117.030 # SOURCE4_SOURCE5 10 0.2421 + angle_coeff @angle:n-cd-n2 harmonic 112.932 119.420 # SOURCE4_SOURCE5 13 0.1189 + angle_coeff @angle:no-cd-os harmonic 109.068 117.550 # SOURCE4_SOURCE5 82 0.2764 + angle_coeff @angle:no-cd-ss harmonic 79.693 121.060 # SOURCE4_SOURCE5 23 0.2526 + angle_coeff @angle:ca-cc-cf harmonic 66.694 124.900 # SOURCE4_SOURCE5 32 1.6591 + angle_coeff @angle:ca-cc-na harmonic 83.626 123.450 # SOURCE4 39 + angle_coeff @angle:cd-cc-cg harmonic 67.080 125.790 # SOURCE4_SOURCE5 54 1.7418 + angle_coeff @angle:cd-cc-cy harmonic 65.987 122.050 # SOURCE4_SOURCE5 12 0.8462 + angle_coeff @angle:cd-cc-nd harmonic 88.069 123.820 # SOURCE4_SOURCE5 14 0.3678 + angle_coeff @angle:cc-cc-cy harmonic 64.938 122.040 # SOURCE4_SOURCE5 7 0.2293 + angle_coeff @angle:cf-cc-nc harmonic 86.641 123.980 # SOURCE4_SOURCE5 5 2.4219 + angle_coeff @angle:c-cc-h4 harmonic 47.105 118.190 # SOURCE4_SOURCE5 8 0.2226 + angle_coeff @angle:na-cc-nh harmonic 110.794 117.280 # SOURCE4_SOURCE5 54 1.7570 + angle_coeff @angle:na-cc-ss harmonic 83.703 111.460 # SOURCE4 20 + angle_coeff @angle:nc-cc-nc harmonic 107.603 125.700 # SOURCE4_SOURCE5 18 0.6787 + angle_coeff @angle:oh-cc-os harmonic 115.442 111.610 # SOURCE4_SOURCE5 6 1.1909 + angle_coeff @angle:c2-cf-cl harmonic 72.080 119.760 # SOURCE4_SOURCE5 38 1.3369 + angle_coeff @angle:c2-cf-h4 harmonic 49.154 124.550 # SOURCE4_SOURCE5 32 1.8945 + angle_coeff @angle:c2-cf-n1 harmonic 91.289 118.230 # SOURCE4_SOURCE5 11 1.2780 + angle_coeff @angle:c2-cf-na harmonic 87.216 119.190 # SOURCE4_SOURCE5 5 0.8452 + angle_coeff @angle:c2-cf-oh harmonic 87.984 123.700 # SOURCE4_SOURCE5 17 1.7138 + angle_coeff @angle:c3-cf-ch harmonic 66.013 117.220 # SOURCE4_SOURCE5 26 1.7890 + angle_coeff @angle:c3-cf-ne harmonic 84.378 120.680 # SOURCE4_SOURCE5 7 2.0560 + angle_coeff @angle:c3-cf-nh harmonic 82.733 119.560 # SOURCE4_SOURCE5 5 1.0524 + angle_coeff @angle:ca-cf-cf harmonic 65.684 119.540 # SOURCE4_SOURCE5 18 1.9239 + angle_coeff @angle:ca-cf-cl harmonic 72.181 114.590 # SOURCE4_SOURCE5 8 0.9719 + angle_coeff @angle:ca-cf-h4 harmonic 47.047 116.990 # SOURCE4_SOURCE5 181 1.0407 + angle_coeff @angle:ca-cf-nh harmonic 85.466 115.580 # SOURCE4_SOURCE5 147 1.1060 + angle_coeff @angle:ca-cf-os harmonic 85.838 115.910 # SOURCE4_SOURCE5 17 1.5899 + angle_coeff @angle:ca-cf-ss harmonic 63.378 117.520 # SOURCE4_SOURCE5 9 1.2901 + angle_coeff @angle:c-cf-ca harmonic 65.478 118.280 # SOURCE4_SOURCE5 17 1.7879 + angle_coeff @angle:cd-cf-cc harmonic 65.259 130.610 # SOURCE4_SOURCE5 19 0.8270 + angle_coeff @angle:c-cf-cf harmonic 65.150 120.980 # SOURCE4_SOURCE5 37 2.3876 + angle_coeff @angle:c-cf-ch harmonic 66.500 118.420 # SOURCE4_SOURCE5 34 1.0602 + angle_coeff @angle:cd-cf-h4 harmonic 47.935 115.680 # SOURCE4_SOURCE5 48 0.8279 + angle_coeff @angle:c-cf-cl harmonic 71.821 115.470 # SOURCE4_SOURCE5 19 1.2383 + angle_coeff @angle:cd-cf-nh harmonic 85.299 118.050 # SOURCE4_SOURCE5 13 1.6005 + angle_coeff @angle:c-cf-cy harmonic 74.704 88.440 # SOURCE4_SOURCE5 34 1.2419 + angle_coeff @angle:cf-cf-cl harmonic 71.617 117.220 # SOURCE4_SOURCE5 23 1.1321 + angle_coeff @angle:cf-cf-oh harmonic 86.685 116.850 # SOURCE4_SOURCE5 19 1.5331 + angle_coeff @angle:ce-cf-cy harmonic 62.247 137.580 # SOURCE4_SOURCE5 18 1.4229 + angle_coeff @angle:ce-cf-h4 harmonic 49.339 122.950 # SOURCE4_SOURCE5 18 1.1766 + angle_coeff @angle:ce-cf-n1 harmonic 90.464 119.940 # SOURCE4_SOURCE5 7 1.8420 + angle_coeff @angle:ce-cf-nh harmonic 87.337 121.380 # SOURCE4_SOURCE5 27 1.6583 + angle_coeff @angle:ch-cf-n2 harmonic 87.851 121.140 # SOURCE4_SOURCE5 8 0.9418 + angle_coeff @angle:c-cf-oh harmonic 86.196 115.760 # SOURCE4_SOURCE5 15 2.2145 + angle_coeff @angle:c-cf-os harmonic 86.086 114.670 # SOURCE4_SOURCE5 26 2.3740 + angle_coeff @angle:h4-cf-n1 harmonic 64.863 116.640 # SOURCE4_SOURCE5 12 0.5604 + angle_coeff @angle:h4-cf-nf harmonic 62.153 115.650 # SOURCE4_SOURCE5 12 1.7190 + angle_coeff @angle:n2-cf-os harmonic 114.215 117.950 # SOURCE4_SOURCE5 13 0.4519 + angle_coeff @angle:n2-cf-ss harmonic 81.512 117.230 # SOURCE4 6 + angle_coeff @angle:nf-cf-nh harmonic 111.319 113.640 # SOURCE4_SOURCE5 29 1.5167 + angle_coeff @angle:ne-cf-nh harmonic 112.342 119.270 # SOURCE4_SOURCE5 17 1.8891 + angle_coeff @angle:ca-ce-cd harmonic 64.611 130.880 # SOURCE4_SOURCE5 29 1.2258 + angle_coeff @angle:c-ce-cc harmonic 66.092 117.820 # SOURCE4_SOURCE5 19 0.9022 + angle_coeff @angle:c-ce-n2 harmonic 88.177 114.410 # SOURCE4_SOURCE5 8 1.4615 + angle_coeff @angle:h4-ce-nf harmonic 64.320 120.560 # SOURCE4_SOURCE5 33 0.8495 + angle_coeff @angle:c1-ch-cd harmonic 58.883 178.610 # SOURCE4_SOURCE5 7 0.3553 + angle_coeff @angle:ch-cg-cg harmonic 60.571 179.580 # SOURCE4_SOURCE5 48 0.3197 + angle_coeff @angle:n-c-nf harmonic 113.600 110.260 # SOURCE4_SOURCE5 15 1.6743 + angle_coeff @angle:ca-cq-na harmonic 86.507 119.500 # SOURCE4_SOURCE5 38 0.8587 + angle_coeff @angle:nb-cq-nb harmonic 110.031 125.790 # SOURCE4_SOURCE5 6 0.6645 + angle_coeff @angle:cd-cx-hc harmonic 47.813 113.930 # SOURCE4_SOURCE5 29 0.6832 + angle_coeff @angle:cf-cy-h2 harmonic 45.874 117.400 # SOURCE4_SOURCE5 21 0.5798 + angle_coeff @angle:cf-cy-n harmonic 94.195 87.940 # SOURCE4_SOURCE5 24 0.2234 + angle_coeff @angle:cf-cy-ss harmonic 60.454 120.540 # SOURCE4_SOURCE5 21 2.1971 + angle_coeff @angle:cd-n2-na harmonic 91.793 109.240 # SOURCE4_SOURCE5 14 1.5712 + angle_coeff @angle:cd-n2-nh harmonic 88.704 118.470 # SOURCE4_SOURCE5 7 1.6660 + angle_coeff @angle:c3-n4-cd harmonic 64.438 111.040 # SOURCE4_SOURCE5 11 1.9847 + angle_coeff @angle:c3-na-cq harmonic 65.414 119.620 # SOURCE4_SOURCE5 10 0.5495 + angle_coeff @angle:ca-na-cq harmonic 67.035 120.860 # SOURCE4_SOURCE5 38 1.4370 + angle_coeff @angle:cd-na-cf harmonic 64.694 126.610 # SOURCE4_SOURCE5 8 0.5158 + angle_coeff @angle:cq-nb-nb harmonic 86.918 120.960 # SOURCE4_SOURCE5 20 0.6372 + angle_coeff @angle:c-n-cf harmonic 63.457 131.380 # SOURCE4_SOURCE5 225 1.7874 + angle_coeff @angle:ca-nc-nd harmonic 92.520 108.340 # SOURCE4_SOURCE5 14 0.2755 + angle_coeff @angle:c2-nf-ch harmonic 70.178 123.230 # SOURCE4_SOURCE5 27 1.1966 + angle_coeff @angle:c-nf-sy harmonic 65.604 116.430 # SOURCE4_SOURCE5 10 2.0084 + angle_coeff @angle:c3-nh-ce harmonic 65.126 120.120 # SOURCE4_SOURCE5 32 2.1639 + angle_coeff @angle:cd-nh-n2 harmonic 85.504 120.090 # SOURCE4_SOURCE5 16 0.9182 + angle_coeff @angle:cd-nh-sy harmonic 62.976 122.520 # SOURCE4_SOURCE5 37 1.3342 + angle_coeff @angle:cf-nh-sy harmonic 65.279 113.390 # SOURCE4_SOURCE5 8 1.1060 + angle_coeff @angle:hn-n-nd harmonic 62.278 115.420 # SOURCE4_SOURCE5 24 0.7584 + angle_coeff @angle:cd-no-o harmonic 87.737 117.490 # SOURCE4_SOURCE5 426 0.5387 + angle_coeff @angle:n3-py-nf harmonic 79.409 108.760 # SOURCE4_SOURCE5 18 1.1434 + angle_coeff @angle:cd-s6-o harmonic 95.603 103.760 # SOURCE4_SOURCE5 15 0.9562 + angle_coeff @angle:cd-sh-hs harmonic 53.591 95.010 # SOURCE4_SOURCE5 15 1.4000 + angle_coeff @angle:c-ss-cd harmonic 75.135 94.890 # SOURCE4_SOURCE5 18 1.2231 + angle_coeff @angle:c3-sx-cd harmonic 73.054 95.180 # SOURCE4_SOURCE5 24 0.6543 + angle_coeff @angle:cd-sx-o harmonic 94.293 104.810 # SOURCE4_SOURCE5 28 1.4279 + angle_coeff @angle:c3-sy-cd harmonic 71.767 101.950 # SOURCE4_SOURCE5 20 1.3784 + angle_coeff @angle:ca-sy-cd harmonic 71.045 105.090 # SOURCE4_SOURCE5 5 0.3628 + angle_coeff @angle:ca-sy-nf harmonic 92.539 103.010 # SOURCE4_SOURCE5 25 2.4137 + angle_coeff @angle:cc-sy-nh harmonic 94.463 97.200 # SOURCE4_SOURCE5 6 0.2429 + angle_coeff @angle:n3-sy-nf harmonic 120.039 101.930 # SOURCE4_SOURCE5 10 1.4898 + angle_coeff @angle:cl-py-ne harmonic 67.181 109.160 # SOURCE5 79 0.9726 + angle_coeff @angle:ce-ce-nh harmonic 85.786 116.410 # SOURCE5 70 1.9262 + angle_coeff @angle:cp-ca-os harmonic 87.894 116.910 # SOURCE5 38 1.2997 + angle_coeff @angle:ca-cc-ca harmonic 65.280 122.940 # SOURCE5 37 2.3284 + angle_coeff @angle:h1-c3-i harmonic 39.280 103.880 # SOURCE5 43 0.8359 + angle_coeff @angle:h4-c2-h4 harmonic 37.559 117.920 # SOURCE5 46 1.0787 + angle_coeff @angle:c-ss-ss harmonic 72.810 97.680 # SOURCE5 29 1.7788 + angle_coeff @angle:f-py-ne harmonic 83.682 108.600 # SOURCE5 47 0.7739 + angle_coeff @angle:ca-nh-ce harmonic 65.017 127.740 # SOURCE5 32 0.9569 + angle_coeff @angle:ce-cx-cx harmonic 64.347 118.620 # SOURCE5 40 1.7472 + angle_coeff @angle:py-ne-py harmonic 111.020 121.410 # SOURCE5 34 1.5196 + angle_coeff @angle:c-cd-ss harmonic 62.961 121.970 # SOURCE5 29 2.1476 + angle_coeff @angle:s-p5-ss harmonic 46.401 116.670 # SOURCE5 27 1.1060 + angle_coeff @angle:cx-c3-nh harmonic 86.752 103.860 # SOURCE5 29 2.2522 + angle_coeff @angle:cc-cc-cl harmonic 72.034 119.990 # SOURCE5 43 1.9574 + angle_coeff @angle:cd-na-cx harmonic 66.440 116.390 # SOURCE5 14 0.5535 + angle_coeff @angle:h1-cy-nh harmonic 59.704 113.860 # SOURCE5 31 0.8499 + angle_coeff @angle:h5-c-os harmonic 63.962 113.090 # SOURCE5 20 0.1826 + angle_coeff @angle:c2-c3-n4 harmonic 81.944 113.640 # SOURCE5 18 2.3563 + angle_coeff @angle:c2-cx-c3 harmonic 65.275 115.480 # SOURCE5 22 1.1986 + angle_coeff @angle:c3-c2-cx harmonic 64.810 117.870 # SOURCE5 20 2.2886 + angle_coeff @angle:br-cx-cx harmonic 62.999 119.040 # SOURCE5 21 0.7114 + angle_coeff @angle:cc-cf-ch harmonic 68.168 122.270 # SOURCE5 30 0.9028 + angle_coeff @angle:c3-c3-sx harmonic 63.092 110.500 # SOURCE5 14 1.4461 + angle_coeff @angle:ca-cy-hc harmonic 46.450 114.530 # SOURCE5 17 1.6221 + angle_coeff @angle:cx-c1-n1 harmonic 74.188 178.250 # SOURCE5 17 0.8798 + angle_coeff @angle:cl-py-cl harmonic 61.568 101.950 # SOURCE5 12 0.7596 + angle_coeff @angle:c2-ce-cx harmonic 66.366 122.740 # SOURCE5 23 1.5745 + angle_coeff @angle:c3-c-cx harmonic 64.715 116.040 # SOURCE5 14 1.1793 + angle_coeff @angle:cf-cc-os harmonic 87.197 123.070 # SOURCE5 15 1.3662 + angle_coeff @angle:cd-cd-cl harmonic 72.034 119.990 # SOURCE5 43 1.9574 + angle_coeff @angle:c3-py-ca harmonic 46.073 107.270 # SOURCE5 20 1.8136 + angle_coeff @angle:c3-c3-py harmonic 80.645 111.570 # SOURCE5 14 1.9142 + angle_coeff @angle:c3-py-s harmonic 46.250 113.850 # SOURCE5 14 0.3847 + angle_coeff @angle:ca-c-cx harmonic 64.997 117.660 # SOURCE5 20 1.5268 + angle_coeff @angle:ce-ce-os harmonic 86.756 115.190 # SOURCE5 15 2.1777 + angle_coeff @angle:c3-n4-cx harmonic 62.636 117.290 # SOURCE5 15 0.3164 + angle_coeff @angle:h4-ce-sy harmonic 42.563 115.000 # SOURCE5 20 1.1588 + angle_coeff @angle:hx-cy-n4 harmonic 58.977 110.620 # SOURCE5 14 1.8211 + angle_coeff @angle:cy-no-o harmonic 84.157 116.830 # SOURCE5 17 1.1181 + angle_coeff @angle:cc-cd-cx harmonic 66.301 124.150 # SOURCE5 10 1.8770 + angle_coeff @angle:ca-nb-na harmonic 87.254 118.780 # SOURCE5 10 0.6408 + angle_coeff @angle:cl-c3-cy harmonic 71.118 111.890 # SOURCE5 12 0.7377 + angle_coeff @angle:f-c2-h4 harmonic 66.183 112.050 # SOURCE5 13 0.7763 + angle_coeff @angle:ca-py-s harmonic 45.997 116.310 # SOURCE5 11 1.2602 + angle_coeff @angle:cl-c3-cx harmonic 71.664 110.760 # SOURCE5 9 1.3315 + angle_coeff @angle:ca-nh-cy harmonic 63.219 126.620 # SOURCE5 12 1.1353 + angle_coeff @angle:cy-cy-no harmonic 79.836 115.430 # SOURCE5 15 1.0848 + angle_coeff @angle:ce-n1-n1 harmonic 77.561 177.620 # SOURCE5 10 0.5740 + angle_coeff @angle:cy-cy-hx harmonic 45.080 115.920 # SOURCE5 9 1.5918 + angle_coeff @angle:ce-n-hn harmonic 48.071 113.830 # SOURCE5 11 1.3642 + angle_coeff @angle:c3-cx-cu harmonic 63.779 120.910 # SOURCE5 11 0.4272 + angle_coeff @angle:cf-cf-ne harmonic 86.585 120.790 # SOURCE5 9 1.8014 + angle_coeff @angle:f-p5-na harmonic 88.711 89.260 # SOURCE5 12 1.2991 + angle_coeff @angle:h4-ce-nh harmonic 62.318 115.580 # SOURCE5 10 0.8050 + angle_coeff @angle:ne-c-s harmonic 82.148 124.230 # SOURCE5 9 1.7990 + angle_coeff @angle:ca-os-py harmonic 83.011 123.310 # SOURCE5 12 0.8994 + angle_coeff @angle:cf-ce-cl harmonic 71.390 121.940 # SOURCE5 20 1.2372 + angle_coeff @angle:cy-cy-n4 harmonic 90.361 89.940 # SOURCE5 10 0.7009 + angle_coeff @angle:na-cc-sh harmonic 79.224 122.950 # SOURCE5 9 1.1542 + angle_coeff @angle:nb-na-o harmonic 113.391 118.130 # SOURCE5 11 0.6838 + angle_coeff @angle:c-cx-n3 harmonic 82.187 116.960 # SOURCE5 11 1.3298 + angle_coeff @angle:cd-cy-hc harmonic 48.302 107.200 # SOURCE5 8 0.5300 + angle_coeff @angle:f-c3-no harmonic 111.081 107.760 # SOURCE5 11 0.3179 + angle_coeff @angle:ce-cd-na harmonic 85.967 124.930 # SOURCE5 9 0.9918 + angle_coeff @angle:cq-cp-cq harmonic 69.705 108.020 # SOURCE5 24 0.5633 + angle_coeff @angle:os-py-s harmonic 59.825 116.220 # SOURCE5 11 0.4580 + angle_coeff @angle:c-c3-cy harmonic 65.476 110.880 # SOURCE5 9 1.4172 + angle_coeff @angle:cy-c2-ha harmonic 45.849 118.590 # SOURCE5 5 1.8406 + angle_coeff @angle:cp-cq-cp harmonic 69.705 108.020 # SOURCE5 24 0.5633 + angle_coeff @angle:cx-cu-cx harmonic 89.228 63.190 # SOURCE5 12 0.2140 + angle_coeff @angle:cu-c2-ha harmonic 50.414 121.490 # SOURCE5 12 0.1524 + angle_coeff @angle:cd-ce-cg harmonic 68.168 122.270 # SOURCE5 30 0.9028 + angle_coeff @angle:cf-ne-ne harmonic 87.949 113.170 # SOURCE5 15 1.6715 + angle_coeff @angle:c3-c2-no harmonic 82.781 115.940 # SOURCE5 9 0.9963 + angle_coeff @angle:f-cy-f harmonic 120.355 108.560 # SOURCE5 9 1.2393 + angle_coeff @angle:c2-cy-hc harmonic 46.979 112.800 # SOURCE5 10 0.5936 + angle_coeff @angle:c3-c2-cy harmonic 64.260 117.990 # SOURCE5 10 1.8958 + angle_coeff @angle:c-ce-h4 harmonic 46.659 118.080 # SOURCE5 8 2.4522 + angle_coeff @angle:cf-cc-n harmonic 86.203 124.200 # SOURCE5 10 0.8706 + angle_coeff @angle:cd-cc-i harmonic 60.056 124.280 # SOURCE5 14 1.7120 + angle_coeff @angle:ce-cf-cl harmonic 71.390 121.940 # SOURCE5 20 1.2372 + angle_coeff @angle:cl-c3-p5 harmonic 92.521 109.520 # SOURCE5 9 0.8307 + angle_coeff @angle:c2-c3-no harmonic 83.742 107.190 # SOURCE5 9 0.5470 + angle_coeff @angle:ce-nf-nf harmonic 87.949 113.170 # SOURCE5 15 1.6715 + angle_coeff @angle:c1-c3-cx harmonic 66.544 112.350 # SOURCE5 11 0.3186 + angle_coeff @angle:ce-c3-h2 harmonic 46.896 112.270 # SOURCE5 9 0.2011 + angle_coeff @angle:na-cd-na harmonic 115.931 106.600 # SOURCE5 10 1.3968 + angle_coeff @angle:cx-cx-n4 harmonic 113.255 60.300 # SOURCE5 10 0.1253 + angle_coeff @angle:c1-cx-hc harmonic 48.408 114.860 # SOURCE5 6 0.1269 + angle_coeff @angle:cg-ca-nb harmonic 87.852 116.870 # SOURCE5 10 0.6088 + angle_coeff @angle:ce-c2-f harmonic 90.032 122.620 # SOURCE5 11 1.4117 + angle_coeff @angle:cp-ca-cq harmonic 70.964 111.520 # SOURCE5 8 0.0849 + angle_coeff @angle:cl-py-nf harmonic 67.181 109.160 # SOURCE5 79 0.9726 + angle_coeff @angle:ca-c3-cy harmonic 65.233 112.320 # SOURCE5 7 0.8064 + angle_coeff @angle:ch-cd-nd harmonic 85.036 123.030 # SOURCE5 7 0.2371 + angle_coeff @angle:h1-cy-ss harmonic 41.667 111.560 # SOURCE5 6 1.1376 + angle_coeff @angle:h5-cc-n2 harmonic 63.976 123.280 # SOURCE5 5 1.2554 + angle_coeff @angle:cc-na-cy harmonic 64.047 126.730 # SOURCE5 13 0.8228 + angle_coeff @angle:c-c3-no harmonic 83.428 106.990 # SOURCE5 8 1.0618 + angle_coeff @angle:c3-py-c3 harmonic 46.116 105.720 # SOURCE5 10 2.4094 + angle_coeff @angle:hx-c3-n3 harmonic 60.702 111.730 # SOURCE5 10 0.1463 + angle_coeff @angle:cf-cf-nh harmonic 85.786 116.410 # SOURCE5 70 1.9262 + angle_coeff @angle:c3-n3-py harmonic 81.527 118.270 # SOURCE5 8 1.5513 + angle_coeff @angle:h5-c2-os harmonic 64.726 110.950 # SOURCE5 9 1.4177 + angle_coeff @angle:cc-c3-ce harmonic 66.308 110.890 # SOURCE5 7 2.0183 + angle_coeff @angle:n4-c3-p5 harmonic 104.054 106.090 # SOURCE5 10 1.7975 + angle_coeff @angle:ne-cd-ss harmonic 79.536 126.000 # SOURCE5 6 1.6775 + angle_coeff @angle:na-cd-ne harmonic 111.251 122.470 # SOURCE5 7 2.4448 + angle_coeff @angle:cl-c3-h3 harmonic 48.652 107.660 # SOURCE5 10 0.1942 + angle_coeff @angle:h5-c-s harmonic 44.037 123.510 # SOURCE5 6 0.5125 + angle_coeff @angle:cf-ce-ss harmonic 63.673 120.950 # SOURCE5 15 1.8784 + angle_coeff @angle:c3-c2-f harmonic 87.663 113.280 # SOURCE5 8 1.0861 + angle_coeff @angle:h4-c2-oh harmonic 64.512 114.610 # SOURCE5 8 1.2250 + angle_coeff @angle:ne-ce-nf harmonic 108.272 127.960 # SOURCE5 10 1.2321 + angle_coeff @angle:cc-n-cd harmonic 67.143 121.050 # SOURCE5 7 0.3580 + angle_coeff @angle:f-py-f harmonic 90.389 97.510 # SOURCE5 5 0.2281 + angle_coeff @angle:n-cc-os harmonic 110.414 119.020 # SOURCE5 8 1.4066 + angle_coeff @angle:cq-cp-nb harmonic 85.943 120.010 # SOURCE5 14 1.1266 + angle_coeff @angle:c-c-s harmonic 64.027 121.310 # SOURCE5 8 0.9033 + angle_coeff @angle:cf-ce-os harmonic 88.396 120.230 # SOURCE5 8 2.3122 + angle_coeff @angle:br-ce-c2 harmonic 64.169 120.520 # SOURCE5 8 0.4148 + angle_coeff @angle:cp-nb-na harmonic 87.511 118.110 # SOURCE5 5 0.5760 + angle_coeff @angle:n-s6-oh harmonic 123.280 97.300 # SOURCE5 8 0.9381 + angle_coeff @angle:cd-c3-h2 harmonic 47.679 110.470 # SOURCE5 12 1.1111 + angle_coeff @angle:nb-ca-sy harmonic 81.256 115.730 # SOURCE5 6 0.4033 + angle_coeff @angle:na-sy-o harmonic 122.952 105.300 # SOURCE5 5 1.0811 + angle_coeff @angle:hx-cx-hx harmonic 37.969 115.770 # SOURCE5 9 0.0901 + angle_coeff @angle:cd-cf-ne harmonic 86.147 122.390 # SOURCE5 7 1.4919 + angle_coeff @angle:h5-c-oh harmonic 65.262 109.490 # SOURCE5 7 0.3600 + angle_coeff @angle:cy-n-cy harmonic 71.371 94.550 # SOURCE5 5 0.6286 + angle_coeff @angle:br-c3-no harmonic 81.143 106.960 # SOURCE5 6 2.2092 + angle_coeff @angle:c2-ss-s4 harmonic 73.233 92.420 # SOURCE5 8 0.4009 + angle_coeff @angle:c3-nh-o harmonic 85.477 117.530 # SOURCE5 7 1.0041 + angle_coeff @angle:br-cc-ss harmonic 65.672 120.060 # SOURCE5 6 0.2609 + angle_coeff @angle:c-ce-ss harmonic 64.495 113.230 # SOURCE5 6 1.9344 + angle_coeff @angle:c3-n-n3 harmonic 82.135 117.560 # SOURCE5 6 2.4546 + angle_coeff @angle:h5-ca-na harmonic 62.521 115.800 # SOURCE5 8 0.4738 + angle_coeff @angle:n2-nh-oh harmonic 106.301 117.890 # SOURCE5 6 0.2008 + angle_coeff @angle:c2-c3-p5 harmonic 80.813 112.220 # SOURCE5 6 0.6523 + angle_coeff @angle:c3-cx-nh harmonic 82.121 116.580 # SOURCE5 7 1.1795 + angle_coeff @angle:c2-cc-ss harmonic 62.687 127.480 # SOURCE5 6 0.3389 + angle_coeff @angle:c-ca-na harmonic 84.333 117.810 # SOURCE5 7 2.2477 + angle_coeff @angle:cl-c2-n2 harmonic 91.772 121.450 # SOURCE5 8 0.8251 + angle_coeff @angle:n2-s4-ne harmonic 122.203 104.290 # SOURCE5 8 0.9503 + angle_coeff @angle:nc-c-s harmonic 82.136 124.470 # SOURCE5 7 1.3793 + angle_coeff @angle:o-sy-ss harmonic 85.092 107.590 # SOURCE5 7 2.0694 + angle_coeff @angle:c2-ce-ss harmonic 62.956 123.860 # SOURCE5 5 1.0553 + angle_coeff @angle:c3-cx-ca harmonic 64.734 117.010 # SOURCE5 6 1.1320 + angle_coeff @angle:cc-cc-nf harmonic 87.342 121.680 # SOURCE5 7 1.9093 + angle_coeff @angle:ca-nd-cd harmonic 73.420 104.240 # SOURCE5 8 0.2625 + angle_coeff @angle:cc-n2-oh harmonic 89.258 113.250 # SOURCE5 7 1.6484 + angle_coeff @angle:ca-os-sy harmonic 63.798 118.010 # SOURCE5 8 2.0392 + angle_coeff @angle:hx-c3-p5 harmonic 54.750 107.590 # SOURCE5 7 1.8329 + angle_coeff @angle:ca-ce-n harmonic 83.340 118.990 # SOURCE5 8 0.3821 + angle_coeff @angle:h4-ce-sx harmonic 41.742 115.270 # SOURCE5 5 0.1053 + angle_coeff @angle:c3-ce-ne harmonic 83.806 116.230 # SOURCE5 5 1.2988 + angle_coeff @angle:c1-n1-ce harmonic 61.729 176.870 # SOURCE5 7 0.6686 + angle_coeff @angle:c3-n2-cd harmonic 67.858 117.010 # SOURCE5 6 1.8279 + angle_coeff @angle:cc-c3-h2 harmonic 47.679 110.470 # SOURCE5 12 1.1111 + angle_coeff @angle:ca-ce-cg harmonic 67.208 116.470 # SOURCE5 5 1.0847 + angle_coeff @angle:c2-cc-na harmonic 86.738 123.270 # SOURCE5 6 1.9888 + angle_coeff @angle:ca-c3-s4 harmonic 63.907 109.520 # SOURCE5 7 1.3239 + angle_coeff @angle:n2-cf-nf harmonic 111.801 120.690 # SOURCE5 6 1.4522 + angle_coeff @angle:ce-cf-ss harmonic 63.673 120.950 # SOURCE5 15 1.8784 + angle_coeff @angle:c3-cx-ss harmonic 62.514 114.160 # SOURCE5 7 0.1562 + angle_coeff @angle:nh-ce-nh harmonic 108.620 119.710 # SOURCE5 6 0.4946 + angle_coeff @angle:cd-c-ne harmonic 87.008 112.220 # SOURCE5 6 0.1806 + angle_coeff @angle:na-c3-ss harmonic 82.873 103.150 # SOURCE5 8 0.3361 + angle_coeff @angle:cf-cf-os harmonic 86.756 115.190 # SOURCE5 15 2.1777 + angle_coeff @angle:cx-c3-h2 harmonic 46.468 114.010 # SOURCE5 8 0.8649 + angle_coeff @angle:cv-ss-cy harmonic 79.244 82.620 # SOURCE5 8 0.2654 + angle_coeff @angle:ss-cy-ss harmonic 68.296 95.040 # SOURCE5 6 0.9436 + angle_coeff @angle:ce-cx-os harmonic 82.835 117.210 # SOURCE5 6 1.3466 + angle_coeff @angle:nb-ca-ne harmonic 109.027 121.410 # SOURCE5 6 1.6965 + angle_coeff @angle:br-ca-nb harmonic 81.701 116.350 # SOURCE5 5 0.4508 + angle_coeff @angle:c3-nh-os harmonic 84.400 110.370 # SOURCE5 6 2.4123 + angle_coeff @angle:c2-nh-p5 harmonic 81.068 125.900 # SOURCE5 6 1.8594 + angle_coeff @angle:br-ca-cp harmonic 63.564 121.390 # SOURCE5 7 0.3403 + angle_coeff @angle:cc-ce-cc harmonic 67.224 116.170 # SOURCE5 6 0.4089 + angle_coeff @angle:c3-nh-s6 harmonic 63.928 116.490 # SOURCE5 6 0.5375 + angle_coeff @angle:cx-c3-na harmonic 82.551 114.780 # SOURCE5 7 1.7481 + angle_coeff @angle:ca-os-p3 harmonic 85.566 110.460 # SOURCE5 5 0.0025 + angle_coeff @angle:ce-cf-sy harmonic 62.892 123.190 # SOURCE5 5 0.3760 + angle_coeff @angle:ca-n2-n1 harmonic 92.483 118.480 # SOURCE5 5 0.1464 + angle_coeff @angle:cd-cd-no harmonic 82.299 125.950 # SOURCE5 5 2.2787 + angle_coeff @angle:na-n2-os harmonic 113.058 104.340 # SOURCE5 6 0.3185 + angle_coeff @angle:ce-c3-f harmonic 88.332 110.310 # SOURCE5 6 0.9204 + angle_coeff @angle:cx-cc-na harmonic 81.840 127.210 # SOURCE5 7 2.0873 + angle_coeff @angle:n-n2-na harmonic 113.870 106.040 # SOURCE5 6 0.3975 + angle_coeff @angle:c3-cf-cc harmonic 67.117 117.430 # SOURCE5 5 2.0116 + angle_coeff @angle:ca-na-cy harmonic 63.636 128.060 # SOURCE5 7 0.2603 + angle_coeff @angle:h1-c3-py harmonic 54.323 109.380 # SOURCE5 7 0.4767 + angle_coeff @angle:cy-s6-cy harmonic 75.496 86.770 # SOURCE5 5 1.5405 + angle_coeff @angle:ce-ce-s4 harmonic 63.624 119.120 # SOURCE5 6 0.0093 + angle_coeff @angle:c3-p3-cy harmonic 45.442 103.850 # SOURCE5 6 0.6245 + angle_coeff @angle:h2-cx-os harmonic 60.942 114.700 # SOURCE5 7 1.4166 + angle_coeff @angle:c-c-ce harmonic 64.646 115.440 # SOURCE5 5 1.0373 + angle_coeff @angle:ce-cy-h1 harmonic 46.242 115.490 # SOURCE5 5 0.2559 + angle_coeff @angle:cx-c3-ss harmonic 64.879 105.420 # SOURCE5 7 0.4078 + angle_coeff @angle:cg-ce-ss harmonic 63.731 118.190 # SOURCE5 5 1.0760 + angle_coeff @angle:br-cy-cy harmonic 61.847 119.270 # SOURCE5 6 1.4624 + angle_coeff @angle:c-cy-cl harmonic 71.094 112.180 # SOURCE5 5 2.4165 + angle_coeff @angle:c-cx-n harmonic 81.704 120.510 # SOURCE5 7 1.7811 + angle_coeff @angle:br-c3-f harmonic 82.493 109.620 # SOURCE5 7 0.6251 + angle_coeff @angle:c3-n4-cy harmonic 63.514 112.130 # SOURCE5 5 0.7180 + angle_coeff @angle:ce-cv-ss harmonic 61.912 130.090 # SOURCE5 7 2.1973 + angle_coeff @angle:cc-cd-i harmonic 60.200 124.280 # SOURCE5 14 1.7120 + angle_coeff @angle:c2-ss-ca harmonic 73.005 102.780 # SOURCE5 5 0.7426 + angle_coeff @angle:c-cx-ce harmonic 64.969 116.840 # SOURCE5 7 1.2393 + angle_coeff @angle:cy-nh-cy harmonic 71.537 93.310 # SOURCE5 6 0.3047 + angle_coeff @angle:cx-c-h4 harmonic 46.665 115.380 # SOURCE5 7 0.1819 + angle_coeff @angle:c-n4-c3 harmonic 63.969 108.760 # SOURCE5 7 1.5097 + angle_coeff @angle:f-cy-py harmonic 99.595 113.190 # SOURCE5 8 0.9744 + angle_coeff @angle:n2-c3-ss harmonic 80.436 109.390 # SOURCE5 5 1.4343 + angle_coeff @angle:c3-ss-cf harmonic 71.418 101.280 # SOURCE5 6 2.4411 + angle_coeff @angle:ce-cy-hc harmonic 46.374 114.840 # SOURCE5 5 0.4991 + angle_coeff @angle:br-cc-nc harmonic 82.466 116.250 # SOURCE5 5 0.0824 + angle_coeff @angle:h3-c3-n harmonic 61.280 109.880 # SOURCE5 6 0.7497 + angle_coeff @angle:ca-ne-cd harmonic 67.557 123.670 # SOURCE5 5 2.0742 + angle_coeff @angle:cx-n-cy harmonic 64.984 116.210 # SOURCE5 6 0.4758 + angle_coeff @angle:cl-c3-s4 harmonic 71.477 111.990 # SOURCE5 6 1.5116 + angle_coeff @angle:cp-cq-nb harmonic 85.943 120.010 # SOURCE5 14 1.1266 + angle_coeff @angle:cc-cd-o harmonic 86.659 136.060 # SOURCE5 5 0.5251 + angle_coeff @angle:hx-cy-hx harmonic 38.598 110.800 # SOURCE5 5 0.4155 + angle_coeff @angle:cc-na-sy harmonic 61.877 125.170 # SOURCE5 5 1.1548 + angle_coeff @angle:h1-cy-na harmonic 62.857 106.380 # SOURCE5 5 0.0918 + angle_coeff @angle:h4-cf-sy harmonic 42.563 115.000 # SOURCE5 20 1.1588 + angle_coeff @angle:c-p5-c3 harmonic 44.432 111.280 # SOURCE5 6 2.1227 + angle_coeff @angle:ca-c-nc harmonic 84.546 117.030 # SOURCE5 5 0.2959 + angle_coeff @angle:c3-os-sy harmonic 63.872 115.050 # SOURCE5 5 0.9975 + angle_coeff @angle:cd-ne-sy harmonic 65.441 120.780 # SOURCE5 5 1.2762 + angle_coeff @angle:cx-ca-nb harmonic 85.768 116.900 # SOURCE5 5 0.8439 + angle_coeff @angle:nc-ss-ss harmonic 93.760 97.440 # SOURCE5 6 0.0880 + angle_coeff @angle:hp-p5-os harmonic 45.642 103.080 # SOURCE5 5 0.8064 + angle_coeff @angle:ca-n-oh harmonic 84.294 115.620 # SOURCE5 5 1.0474 + angle_coeff @angle:c3-s6-ne harmonic 91.348 108.190 # SOURCE5 5 0.2914 + angle_coeff @angle:c1-cx-h1 harmonic 48.407 114.800 # SOURCE5 5 0.4789 + angle_coeff @angle:na-c3-oh harmonic 109.816 108.590 # SOURCE5 6 1.4542 + angle_coeff @angle:n-nc-nd harmonic 109.773 119.880 # SOURCE5 5 0.1982 + angle_coeff @angle:c3-na-nb harmonic 85.173 113.140 # SOURCE5 5 0.4557 + angle_coeff @angle:ne-c-os harmonic 113.522 112.010 # SOURCE5 5 1.9012 + angle_coeff @angle:br-ce-ce harmonic 64.975 115.220 # SOURCE5 6 0.2328 + angle_coeff @angle:cc-c2-oh harmonic 91.119 115.180 # SOURCE5 6 0.1517 + angle_coeff @angle:c1-cx-os harmonic 84.507 117.430 # SOURCE5 5 0.5408 + angle_coeff @angle:nc-cc-os harmonic 109.642 121.720 # SOURCE5 5 2.3919 + angle_coeff @angle:br-ce-cf harmonic 63.865 121.600 # SOURCE5 5 1.8246 + angle_coeff @angle:cy-c3-f harmonic 87.269 111.480 # SOURCE5 5 0.6981 + angle_coeff @angle:h5-ce-ne harmonic 62.727 113.650 # SOURCE5 5 0.5892 + angle_coeff @angle:n3-py-n3 harmonic 78.976 104.560 # SOURCE5 5 0.5659 + angle_coeff @angle:br-cc-ca harmonic 62.532 126.640 # SOURCE5 5 0.3204 + angle_coeff @angle:f-c3-na harmonic 113.041 110.410 # SOURCE5 5 0.7067 + angle_coeff @angle:cc-c3-s4 harmonic 63.350 112.000 # SOURCE5 5 0.1216 + angle_coeff @angle:ce-cf-sx harmonic 64.738 112.970 # SOURCE5 5 1.7021 + angle_coeff @angle:cc-cc-i harmonic 59.680 125.790 # SOURCE5 5 1.4784 + angle_coeff @angle:c-cg-ch harmonic 58.652 176.690 # SOURCE5 5 0.2913 + angle_coeff @angle:ce-c3-hx harmonic 47.212 110.880 # SOURCE5 5 0.3335 + angle_coeff @angle:cd-na-cy harmonic 64.047 126.730 # SOURCE5 13 0.8228 + angle_coeff @angle:br-c3-c2 harmonic 63.737 111.170 # SOURCE5 5 1.2445 + angle_coeff @angle:ce-ce-cg harmonic 68.210 114.640 # SOURCE5 5 0.4759 + angle_coeff @angle:cl-cd-nd harmonic 90.599 121.290 # SOURCE5 5 0.8123 + angle_coeff @angle:n-ca-na harmonic 109.145 117.170 # SOURCE5 5 0.3934 + angle_coeff @angle:cx-cd-nd harmonic 83.980 121.600 # SOURCE5 5 0.1341 + angle_coeff @angle:cl-p5-os harmonic 69.550 104.530 # SOURCE5 5 0.1303 + angle_coeff @angle:cx-ss-cy harmonic 73.867 91.640 # SOURCE5 5 0.0761 + angle_coeff @angle:cc-cg-ch harmonic 59.342 177.060 # SOURCE5 5 0.7516 + angle_coeff @angle:cc-sy-oh harmonic 92.772 104.120 # SOURCE5 5 0.3761 + angle_coeff @angle:cq-ca-os harmonic 87.894 116.910 # SOURCE5 38 1.2997 + angle_coeff @angle:ca-cd-ca harmonic 65.280 122.940 # SOURCE5 37 2.3284 + angle_coeff @angle:f-py-nf harmonic 83.682 108.600 # SOURCE5 47 0.7739 + angle_coeff @angle:ca-nh-cf harmonic 65.017 127.740 # SOURCE5 32 0.9569 + angle_coeff @angle:cf-cx-cx harmonic 64.347 118.620 # SOURCE5 40 1.7472 + angle_coeff @angle:py-nf-py harmonic 111.020 121.410 # SOURCE5 34 1.5196 + angle_coeff @angle:c-cc-ss harmonic 62.961 121.970 # SOURCE5 29 2.1476 + angle_coeff @angle:cc-na-cx harmonic 66.440 116.390 # SOURCE5 14 0.5535 + angle_coeff @angle:c2-cf-cx harmonic 66.366 122.740 # SOURCE5 23 1.5745 + angle_coeff @angle:ce-cd-os harmonic 87.197 123.070 # SOURCE5 15 1.3662 + angle_coeff @angle:cd-cc-cx harmonic 66.301 124.150 # SOURCE5 10 1.8770 + angle_coeff @angle:cf-n1-n1 harmonic 77.561 177.620 # SOURCE5 10 0.5740 + angle_coeff @angle:cf-n-hn harmonic 48.071 113.830 # SOURCE5 11 1.3642 + angle_coeff @angle:ce-ce-nf harmonic 86.585 120.790 # SOURCE5 9 1.8014 + angle_coeff @angle:cf-no-o harmonic 86.024 118.220 # SOURCE5 11 0.7792 + angle_coeff @angle:h4-cf-nh harmonic 62.318 115.580 # SOURCE5 10 0.8050 + angle_coeff @angle:nf-c-s harmonic 82.148 124.230 # SOURCE5 9 1.7990 + angle_coeff @angle:na-cd-sh harmonic 79.224 122.950 # SOURCE5 9 1.1542 + angle_coeff @angle:cc-cy-hc harmonic 48.302 107.200 # SOURCE5 8 0.5300 + angle_coeff @angle:cf-cc-na harmonic 85.967 124.930 # SOURCE5 9 0.9918 + angle_coeff @angle:c-cf-h4 harmonic 46.659 118.080 # SOURCE5 8 2.4522 + angle_coeff @angle:ce-cd-n harmonic 86.203 124.200 # SOURCE5 10 0.8706 + angle_coeff @angle:cf-c3-h2 harmonic 46.902 112.270 # SOURCE5 9 0.2011 + angle_coeff @angle:na-cc-na harmonic 115.931 106.600 # SOURCE5 10 1.3968 + angle_coeff @angle:ch-ca-nb harmonic 87.852 116.870 # SOURCE5 10 0.6088 + angle_coeff @angle:cf-c2-f harmonic 90.032 122.620 # SOURCE5 11 1.4117 + angle_coeff @angle:cg-cc-nc harmonic 85.036 123.030 # SOURCE5 7 0.2371 + angle_coeff @angle:h5-cd-n2 harmonic 63.978 123.280 # SOURCE5 5 1.2554 + angle_coeff @angle:cd-c3-cf harmonic 66.313 110.890 # SOURCE5 7 2.0183 + angle_coeff @angle:nf-cc-ss harmonic 79.536 126.000 # SOURCE5 6 1.6775 + angle_coeff @angle:na-cc-nf harmonic 111.251 122.470 # SOURCE5 7 2.4448 + angle_coeff @angle:nf-cf-ne harmonic 108.272 127.960 # SOURCE5 10 1.2321 + angle_coeff @angle:n-cd-os harmonic 110.414 119.020 # SOURCE5 8 1.4066 + angle_coeff @angle:ce-cf-os harmonic 88.396 120.230 # SOURCE5 8 2.3122 + angle_coeff @angle:br-cf-c2 harmonic 64.169 120.520 # SOURCE5 8 0.4148 + angle_coeff @angle:cq-nb-na harmonic 87.511 118.110 # SOURCE5 5 0.5760 + angle_coeff @angle:cc-ce-nf harmonic 86.147 122.390 # SOURCE5 7 1.4919 + angle_coeff @angle:cf-s4-ss harmonic 74.492 88.650 # SOURCE5 8 0.4156 + angle_coeff @angle:br-cd-ss harmonic 65.672 120.060 # SOURCE5 6 0.2609 + angle_coeff @angle:c-cf-ss harmonic 64.495 113.230 # SOURCE5 6 1.9344 + angle_coeff @angle:c2-cd-ss harmonic 62.687 127.480 # SOURCE5 6 0.3389 + angle_coeff @angle:n2-s4-nf harmonic 122.203 104.290 # SOURCE5 8 0.9503 + angle_coeff @angle:nd-c-s harmonic 82.136 124.470 # SOURCE5 7 1.3793 + angle_coeff @angle:c2-cf-ss harmonic 62.956 123.860 # SOURCE5 5 1.0553 + angle_coeff @angle:cd-cd-ne harmonic 87.342 121.680 # SOURCE5 7 1.9093 + angle_coeff @angle:ca-nc-cc harmonic 73.420 104.240 # SOURCE5 8 0.2625 + angle_coeff @angle:cd-n2-oh harmonic 89.258 113.250 # SOURCE5 7 1.6484 + angle_coeff @angle:ca-cf-n harmonic 83.340 118.990 # SOURCE5 8 0.3821 + angle_coeff @angle:h4-cf-sx harmonic 41.742 115.270 # SOURCE5 5 0.1053 + angle_coeff @angle:c3-cf-nf harmonic 83.812 116.230 # SOURCE5 5 1.2988 + angle_coeff @angle:c1-n1-cf harmonic 61.729 176.870 # SOURCE5 7 0.6686 + angle_coeff @angle:c3-n2-cc harmonic 67.858 117.010 # SOURCE5 6 1.8279 + angle_coeff @angle:ca-cf-ch harmonic 67.208 116.470 # SOURCE5 5 1.0847 + angle_coeff @angle:c2-cd-na harmonic 86.738 123.270 # SOURCE5 6 1.9888 + angle_coeff @angle:n2-ce-ne harmonic 111.801 120.690 # SOURCE5 6 1.4522 + angle_coeff @angle:nh-cf-nh harmonic 108.620 119.710 # SOURCE5 6 0.4946 + angle_coeff @angle:cc-c-nf harmonic 87.008 112.220 # SOURCE5 6 0.1806 + angle_coeff @angle:cf-cx-os harmonic 82.835 117.210 # SOURCE5 6 1.3466 + angle_coeff @angle:nb-ca-nf harmonic 109.027 121.410 # SOURCE5 6 1.6965 + angle_coeff @angle:br-ca-cq harmonic 63.564 121.390 # SOURCE5 7 0.3403 + angle_coeff @angle:cd-cf-cd harmonic 67.224 116.170 # SOURCE5 6 0.4089 + angle_coeff @angle:cf-ce-sy harmonic 62.892 123.190 # SOURCE5 5 0.3760 + angle_coeff @angle:cc-cc-no harmonic 82.299 125.950 # SOURCE5 5 2.2787 + angle_coeff @angle:cf-c3-f harmonic 88.340 110.310 # SOURCE5 6 0.9204 + angle_coeff @angle:cx-cd-na harmonic 81.840 127.210 # SOURCE5 7 2.0873 + angle_coeff @angle:c3-ce-cd harmonic 67.111 117.430 # SOURCE5 5 2.0116 + angle_coeff @angle:cf-cf-s4 harmonic 63.624 119.120 # SOURCE5 6 0.0093 + angle_coeff @angle:c-c-cf harmonic 64.646 115.440 # SOURCE5 5 1.0373 + angle_coeff @angle:cf-cy-h1 harmonic 46.242 115.490 # SOURCE5 5 0.2559 + angle_coeff @angle:ch-cf-ss harmonic 63.731 118.190 # SOURCE5 5 1.0760 + angle_coeff @angle:cf-cv-ss harmonic 61.912 130.090 # SOURCE5 7 2.1973 + angle_coeff @angle:c-cx-cf harmonic 64.969 116.840 # SOURCE5 7 1.2393 + angle_coeff @angle:c3-ss-ce harmonic 71.418 101.280 # SOURCE5 6 2.4411 + angle_coeff @angle:cf-cy-hc harmonic 46.374 114.840 # SOURCE5 5 0.4991 + angle_coeff @angle:br-cd-nd harmonic 82.466 116.250 # SOURCE5 5 0.0824 + angle_coeff @angle:ca-nf-cc harmonic 67.557 123.670 # SOURCE5 5 2.0742 + angle_coeff @angle:cd-cc-o harmonic 86.659 136.060 # SOURCE5 5 0.5251 + angle_coeff @angle:cd-na-sy harmonic 61.877 125.170 # SOURCE5 5 1.1548 + angle_coeff @angle:ca-c-nd harmonic 84.546 117.030 # SOURCE5 5 0.2959 + angle_coeff @angle:cc-nf-sy harmonic 65.441 120.780 # SOURCE5 5 1.2762 + angle_coeff @angle:nd-ss-ss harmonic 93.760 97.440 # SOURCE5 6 0.0880 + angle_coeff @angle:c3-s6-nf harmonic 91.348 108.190 # SOURCE5 5 0.2914 + angle_coeff @angle:n-nd-nc harmonic 109.773 119.880 # SOURCE5 5 0.1982 + angle_coeff @angle:nf-c-os harmonic 113.522 112.010 # SOURCE5 5 1.9012 + angle_coeff @angle:br-cf-cf harmonic 64.975 115.220 # SOURCE5 6 0.2328 + angle_coeff @angle:cd-c2-oh harmonic 91.119 115.180 # SOURCE5 6 0.1517 + angle_coeff @angle:nd-cd-os harmonic 109.642 121.720 # SOURCE5 5 2.3919 + angle_coeff @angle:br-cf-ce harmonic 63.865 121.600 # SOURCE5 5 1.8246 + angle_coeff @angle:h5-cf-nf harmonic 62.727 113.650 # SOURCE5 5 0.5892 + angle_coeff @angle:br-cd-ca harmonic 62.532 126.640 # SOURCE5 5 0.3204 + angle_coeff @angle:cd-c3-s4 harmonic 63.350 112.000 # SOURCE5 5 0.1216 + angle_coeff @angle:cf-ce-sx harmonic 64.738 112.970 # SOURCE5 5 1.7021 + angle_coeff @angle:cd-cd-i harmonic 59.818 125.790 # SOURCE5 5 1.4784 + angle_coeff @angle:c-ch-cg harmonic 58.652 176.690 # SOURCE5 5 0.2913 + angle_coeff @angle:cf-c3-hx harmonic 47.217 110.880 # SOURCE5 5 0.3335 + angle_coeff @angle:cf-cf-ch harmonic 68.210 114.640 # SOURCE5 5 0.4759 + angle_coeff @angle:cl-cc-nc harmonic 90.599 121.290 # SOURCE5 5 0.8123 + angle_coeff @angle:cx-cc-nc harmonic 83.980 121.600 # SOURCE5 5 0.1341 + angle_coeff @angle:cd-ch-cg harmonic 59.342 177.060 # SOURCE5 5 0.7516 + angle_coeff @angle:cd-sy-oh harmonic 92.772 104.120 # SOURCE5 5 0.3761 + } # (end of angle_coeffs) + + write_once("Data Angles By Type") { + @angle:hw-ow-hw @atom:hw @atom:ow @atom:hw + @angle:hw-hw-ow @atom:hw @atom:hw @atom:ow + @angle:br-c1-br @atom:br @atom:c1 @atom:br + @angle:br-c1-c1 @atom:br @atom:c1 @atom:c1 + @angle:c1-c1-c1 @atom:c1 @atom:c1 @atom:c1 + @angle:c1-c1-c2 @atom:c1 @atom:c1 @atom:c2 + @angle:c1-c1-c3 @atom:c1 @atom:c1 @atom:c3 + @angle:c1-c1-ca @atom:c1 @atom:c1 @atom:ca + @angle:c1-c1-cl @atom:c1 @atom:c1 @atom:cl + @angle:c1-c1-f @atom:c1 @atom:c1 @atom:f + @angle:c1-c1-ha @atom:c1 @atom:c1 @atom:ha + @angle:c1-c1-hc @atom:c1 @atom:c1 @atom:hc + @angle:c1-c1-i @atom:c1 @atom:c1 @atom:i + @angle:c1-c1-n1 @atom:c1 @atom:c1 @atom:n1 + @angle:c1-c1-n2 @atom:c1 @atom:c1 @atom:n2 + @angle:c1-c1-n3 @atom:c1 @atom:c1 @atom:n3 + @angle:c1-c1-n4 @atom:c1 @atom:c1 @atom:n4 + @angle:c1-c1-n @atom:c1 @atom:c1 @atom:n + @angle:c1-c1-na @atom:c1 @atom:c1 @atom:na + @angle:c1-c1-nh @atom:c1 @atom:c1 @atom:nh + @angle:c1-c1-no @atom:c1 @atom:c1 @atom:no + @angle:c1-c1-o @atom:c1 @atom:c1 @atom:o + @angle:c1-c1-oh @atom:c1 @atom:c1 @atom:oh + @angle:c1-c1-os @atom:c1 @atom:c1 @atom:os + @angle:c1-c1-p2 @atom:c1 @atom:c1 @atom:p2 + @angle:c1-c1-p3 @atom:c1 @atom:c1 @atom:p3 + @angle:c1-c1-p4 @atom:c1 @atom:c1 @atom:p4 + @angle:c1-c1-p5 @atom:c1 @atom:c1 @atom:p5 + @angle:c1-c1-s4 @atom:c1 @atom:c1 @atom:s4 + @angle:c1-c1-s6 @atom:c1 @atom:c1 @atom:s6 + @angle:c1-c1-s @atom:c1 @atom:c1 @atom:s + @angle:c1-c1-sh @atom:c1 @atom:c1 @atom:sh + @angle:c1-c1-ss @atom:c1 @atom:c1 @atom:ss + @angle:c2-c1-c2 @atom:c2 @atom:c1 @atom:c2 + @angle:c2-c1-ce @atom:c2 @atom:c1 @atom:ce + @angle:c2-c1-n1 @atom:c2 @atom:c1 @atom:n1 + @angle:c2-c1-o @atom:c2 @atom:c1 @atom:o + @angle:c2-c1-s2 @atom:c2 @atom:c1 @atom:s2 + @angle:c3-c1-c3 @atom:c3 @atom:c1 @atom:c3 + @angle:c3-c1-cg @atom:c3 @atom:c1 @atom:cg + @angle:c3-c1-n1 @atom:c3 @atom:c1 @atom:n1 + @angle:ca-c1-ca @atom:ca @atom:c1 @atom:ca + @angle:c-c1-c1 @atom:c @atom:c1 @atom:c1 + @angle:cg-c1-ha @atom:cg @atom:c1 @atom:ha + @angle:ch-c1-ha @atom:ch @atom:c1 @atom:ha + @angle:cl-c1-cl @atom:cl @atom:c1 @atom:cl + @angle:f-c1-f @atom:f @atom:c1 @atom:f + @angle:i-c1-i @atom:i @atom:c1 @atom:i + @angle:n1-c1-n1 @atom:n1 @atom:c1 @atom:n1 + @angle:n1-c1-n3 @atom:n1 @atom:c1 @atom:n3 + @angle:n1-c1-nh @atom:n1 @atom:c1 @atom:nh + @angle:n1-c1-os @atom:n1 @atom:c1 @atom:os + @angle:n1-c1-p3 @atom:n1 @atom:c1 @atom:p3 + @angle:n1-c1-ss @atom:n1 @atom:c1 @atom:ss + @angle:n2-c1-n2 @atom:n2 @atom:c1 @atom:n2 + @angle:n2-c1-o @atom:n2 @atom:c1 @atom:o + @angle:n2-c1-s @atom:n2 @atom:c1 @atom:s + @angle:n3-c1-n3 @atom:n3 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@atom:cx + @angle:ce-cd-os @atom:ce @atom:cd @atom:os + @angle:cd-cc-cx @atom:cd @atom:cc @atom:cx + @angle:cf-n1-n1 @atom:cf @atom:n1 @atom:n1 + @angle:cf-n-hn @atom:cf @atom:n @atom:hn + @angle:ce-ce-nf @atom:ce @atom:ce @atom:nf + @angle:cf-no-o @atom:cf @atom:no @atom:o + @angle:h4-cf-nh @atom:h4 @atom:cf @atom:nh + @angle:nf-c-s @atom:nf @atom:c @atom:s + @angle:na-cd-sh @atom:na @atom:cd @atom:sh + @angle:cc-cy-hc @atom:cc @atom:cy @atom:hc + @angle:cf-cc-na @atom:cf @atom:cc @atom:na + @angle:c-cf-h4 @atom:c @atom:cf @atom:h4 + @angle:ce-cd-n @atom:ce @atom:cd @atom:n + @angle:cf-c3-h2 @atom:cf @atom:c3 @atom:h2 + @angle:na-cc-na @atom:na @atom:cc @atom:na + @angle:ch-ca-nb @atom:ch @atom:ca @atom:nb + @angle:cf-c2-f @atom:cf @atom:c2 @atom:f + @angle:cg-cc-nc @atom:cg @atom:cc @atom:nc + @angle:h5-cd-n2 @atom:h5 @atom:cd @atom:n2 + @angle:cd-c3-cf @atom:cd @atom:c3 @atom:cf + @angle:nf-cc-ss @atom:nf @atom:cc @atom:ss + @angle:na-cc-nf @atom:na @atom:cc @atom:nf + @angle:nf-cf-ne @atom:nf @atom:cf @atom:ne + @angle:n-cd-os @atom:n @atom:cd @atom:os + @angle:ce-cf-os @atom:ce @atom:cf @atom:os + @angle:br-cf-c2 @atom:br @atom:cf @atom:c2 + @angle:cq-nb-na @atom:cq @atom:nb @atom:na + @angle:cc-ce-nf @atom:cc @atom:ce @atom:nf + @angle:cf-s4-ss @atom:cf @atom:s4 @atom:ss + @angle:br-cd-ss @atom:br @atom:cd @atom:ss + @angle:c-cf-ss @atom:c @atom:cf @atom:ss + @angle:c2-cd-ss @atom:c2 @atom:cd @atom:ss + @angle:n2-s4-nf @atom:n2 @atom:s4 @atom:nf + @angle:nd-c-s @atom:nd @atom:c @atom:s + @angle:c2-cf-ss @atom:c2 @atom:cf @atom:ss + @angle:cd-cd-ne @atom:cd @atom:cd @atom:ne + @angle:ca-nc-cc @atom:ca @atom:nc @atom:cc + @angle:cd-n2-oh @atom:cd @atom:n2 @atom:oh + @angle:ca-cf-n @atom:ca @atom:cf @atom:n + @angle:h4-cf-sx @atom:h4 @atom:cf @atom:sx + @angle:c3-cf-nf @atom:c3 @atom:cf @atom:nf + @angle:c1-n1-cf @atom:c1 @atom:n1 @atom:cf + @angle:c3-n2-cc @atom:c3 @atom:n2 @atom:cc + @angle:ca-cf-ch @atom:ca @atom:cf @atom:ch + @angle:c2-cd-na @atom:c2 @atom:cd @atom:na + @angle:n2-ce-ne @atom:n2 @atom:ce @atom:ne + @angle:nh-cf-nh @atom:nh @atom:cf @atom:nh + @angle:cc-c-nf @atom:cc @atom:c @atom:nf + @angle:cf-cx-os @atom:cf @atom:cx @atom:os + @angle:nb-ca-nf @atom:nb @atom:ca @atom:nf + @angle:br-ca-cq @atom:br @atom:ca @atom:cq + @angle:cd-cf-cd @atom:cd @atom:cf @atom:cd + @angle:cf-ce-sy @atom:cf @atom:ce @atom:sy + @angle:cc-cc-no @atom:cc @atom:cc @atom:no + @angle:cf-c3-f @atom:cf @atom:c3 @atom:f + @angle:cx-cd-na @atom:cx @atom:cd @atom:na + @angle:c3-ce-cd @atom:c3 @atom:ce @atom:cd + @angle:cf-cf-s4 @atom:cf @atom:cf @atom:s4 + @angle:c-c-cf @atom:c @atom:c @atom:cf + @angle:cf-cy-h1 @atom:cf @atom:cy @atom:h1 + @angle:ch-cf-ss @atom:ch @atom:cf @atom:ss + @angle:cf-cv-ss @atom:cf @atom:cv @atom:ss + @angle:c-cx-cf @atom:c @atom:cx @atom:cf + @angle:c3-ss-ce @atom:c3 @atom:ss @atom:ce + @angle:cf-cy-hc @atom:cf @atom:cy @atom:hc + @angle:br-cd-nd @atom:br @atom:cd @atom:nd + @angle:ca-nf-cc @atom:ca @atom:nf @atom:cc + @angle:cd-cc-o @atom:cd @atom:cc @atom:o + @angle:cd-na-sy @atom:cd @atom:na @atom:sy + @angle:ca-c-nd @atom:ca @atom:c @atom:nd + @angle:cc-nf-sy @atom:cc @atom:nf @atom:sy + @angle:nd-ss-ss @atom:nd @atom:ss @atom:ss + @angle:c3-s6-nf @atom:c3 @atom:s6 @atom:nf + @angle:n-nd-nc @atom:n @atom:nd @atom:nc + @angle:nf-c-os @atom:nf @atom:c @atom:os + @angle:br-cf-cf @atom:br @atom:cf @atom:cf + @angle:cd-c2-oh @atom:cd @atom:c2 @atom:oh + @angle:nd-cd-os @atom:nd @atom:cd @atom:os + @angle:br-cf-ce @atom:br @atom:cf @atom:ce + @angle:h5-cf-nf @atom:h5 @atom:cf @atom:nf + @angle:br-cd-ca @atom:br @atom:cd @atom:ca + @angle:cd-c3-s4 @atom:cd @atom:c3 @atom:s4 + @angle:cf-ce-sx @atom:cf @atom:ce @atom:sx + @angle:cd-cd-i @atom:cd @atom:cd @atom:i + @angle:c-ch-cg @atom:c @atom:ch @atom:cg + @angle:cf-c3-hx @atom:cf @atom:c3 @atom:hx + @angle:cf-cf-ch @atom:cf @atom:cf @atom:ch + @angle:cl-cc-nc @atom:cl @atom:cc @atom:nc + @angle:cx-cc-nc @atom:cx @atom:cc @atom:nc + @angle:cd-ch-cg @atom:cd @atom:ch @atom:cg + @angle:cd-sy-oh @atom:cd @atom:sy @atom:oh + } # (end of Angles By Type) + + write_once("In Settings") { + dihedral_coeff @dihedral:X-c-c-X fourier 1 0.3 2 180.0 + dihedral_coeff @dihedral:X-c-c1-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c-cg-X fourier 1 0.0 2 180.0 # same as X-c-c1-X + dihedral_coeff @dihedral:X-c-ch-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c-c2-X fourier 1 2.175 2 180.0 # intrpol.bsd.on C6H6 + dihedral_coeff @dihedral:X-c-cu-X fourier 1 2.175 2 180.0 # intrpol.bsd.on C6H6 + dihedral_coeff @dihedral:X-c-cv-X fourier 1 2.175 2 180.0 # intrpol.bsd.on C6H6 + dihedral_coeff @dihedral:X-c-ce-X fourier 1 2.175 2 180.0 # intrpol.bsd.on C6H6 + dihedral_coeff @dihedral:X-c-cf-X fourier 1 2.175 2 180.0 # intrpol.bsd.on C6H6 + dihedral_coeff @dihedral:X-c-c3-X fourier 1 0.0 2 180.0 # JCC, 7, (1986), 230 + dihedral_coeff @dihedral:X-c-cx-X fourier 1 0.0 2 180.0 # JCC, 7, (1986), 230 + dihedral_coeff @dihedral:X-c-cy-X fourier 1 0.0 2 180.0 # JCC, 7, (1986), 230 + dihedral_coeff @dihedral:X-c-ca-X fourier 1 1.0 2 180.0 # optimized by Junmei Wang, Jan-2013 + dihedral_coeff @dihedral:X-c-cc-X fourier 1 2.875 2 180.0 # statistic value + dihedral_coeff @dihedral:X-c-cd-X fourier 1 2.875 2 180.0 # statistic value + dihedral_coeff @dihedral:X-c-n-X fourier 1 2.5 2 180.0 # AA,NMA (no c-n3, c-n4, c-nh) + dihedral_coeff @dihedral:X-c-n2-X fourier 1 4.15 2 180.0 # double bond, same as X-c2-n2-X + dihedral_coeff @dihedral:X-c-nc-X fourier 1 4.0 2 180.0 # same as X-C-NC-X + dihedral_coeff @dihedral:X-c-nd-X fourier 1 4.0 2 180.0 # same as X-C-NC-X + dihedral_coeff @dihedral:X-c-ne-X fourier 1 0.2 2 180.0 # single bond + dihedral_coeff @dihedral:X-c-nf-X fourier 1 0.2 2 180.0 # single bond + dihedral_coeff @dihedral:X-c-na-X fourier 2 1.45 2 180.0 0.35 4 180.0 + dihedral_coeff @dihedral:X-c-no-X fourier 1 0.45 2 180.0 + dihedral_coeff @dihedral:X-c-oh-X fourier 1 2.3 2 180.0 # Junmei et al, 1999 + dihedral_coeff @dihedral:X-c-os-X fourier 1 2.7 2 180.0 # Junmei et al, 1999 + dihedral_coeff @dihedral:X-c-p2-X fourier 1 6.65 2 180.0 # double bond, same as X-c2-p2-X + dihedral_coeff @dihedral:X-c-pc-X fourier 1 2.0 2 180.0 # estimated + dihedral_coeff @dihedral:X-c-pd-X fourier 1 2.0 2 180.0 # estimated + dihedral_coeff @dihedral:X-c-pe-X fourier 1 0.0 2 180.0 # single bond + dihedral_coeff @dihedral:X-c-pf-X fourier 1 0.0 2 180.0 # single bond + dihedral_coeff @dihedral:X-c-p3-X fourier 1 1.55 2 180.0 + dihedral_coeff @dihedral:X-c-p4-X fourier 1 1.35 2 180.0 + dihedral_coeff @dihedral:X-c-px-X fourier 1 1.35 2 180.0 + dihedral_coeff @dihedral:X-c-p5-X fourier 1 1.0 2 0.0 + dihedral_coeff @dihedral:X-c-py-X fourier 1 1.0 2 0.0 + dihedral_coeff @dihedral:X-c-sh-X fourier 1 2.25 2 180.0 + dihedral_coeff @dihedral:X-c-ss-X fourier 1 3.1 2 180.0 + dihedral_coeff @dihedral:X-c-s4-X fourier 1 0.2 2 180.0 + dihedral_coeff @dihedral:X-c-sx-X fourier 1 0.2 2 180.0 + dihedral_coeff @dihedral:X-c-s6-X fourier 1 0.5 2 0.0 + dihedral_coeff @dihedral:X-c-sy-X fourier 1 0.5 2 0.0 + dihedral_coeff @dihedral:X-c1-c1-X fourier 1 0.0 2 180.0 # for both triple and single bonds + dihedral_coeff @dihedral:X-c1-cg-X fourier 1 0.0 2 180.0 # for both triple and single bonds + dihedral_coeff @dihedral:X-c1-ch-X fourier 1 0.0 2 180.0 # for both triple and single bonds + dihedral_coeff @dihedral:X-cg-cg-X fourier 1 0.0 2 180.0 # for both triple and single bonds + dihedral_coeff @dihedral:X-ch-ch-X fourier 1 0.0 2 180.0 # for both triple and single bonds + dihedral_coeff @dihedral:X-cg-ch-X fourier 1 0.0 2 180.0 # for both triple and single bonds + dihedral_coeff @dihedral:X-c1-c2-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-c3-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-ca-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-cc-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-cd-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-ce-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-cf-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-cu-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-cv-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-cx-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-cy-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-n-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-n2-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-n3-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-n4-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-na-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-nb-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-nc-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-nd-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-ne-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-nf-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-nh-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-no-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-oh-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-os-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-p2-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-pb-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-pc-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-pd-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-pe-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-pf-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-p3-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-p4-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-px-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-p5-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-py-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-s2-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-sh-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-ss-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-s4-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-sx-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-s6-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-sy-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c2-c2-X fourier 1 6.65 2 180.0 # c2=c2 double bond, intrpol.bsd.on C6H6 + dihedral_coeff @dihedral:X-c2-ce-X fourier 1 6.65 2 180.0 # c2=c2 double bond, intrpol.bsd.on C6H6 + dihedral_coeff @dihedral:X-c2-cf-X fourier 1 6.65 2 180.0 # c2=c2 double bond, intrpol.bsd.on C6H6 + dihedral_coeff @dihedral:X-ce-cf-X fourier 1 6.65 2 180.0 # c2=c2 double bond, intrpol.bsd.on C6H6 + dihedral_coeff @dihedral:X-ce-ce-X fourier 1 1.0 2 180.0 # c2-c2 single bond, parm99 + dihedral_coeff @dihedral:X-cf-cf-X fourier 1 1.0 2 180.0 # c2-c2 single bond, parm99 + dihedral_coeff @dihedral:X-cc-cd-X fourier 1 4.0 2 180.0 # statistic value of parm94 + dihedral_coeff @dihedral:X-cc-cc-X fourier 1 4.0 2 180.0 # statistic value of parm94 + dihedral_coeff @dihedral:X-cd-cd-X fourier 1 4.0 2 180.0 # statistic value of parm94 + dihedral_coeff @dihedral:X-c2-c3-X fourier 1 0.0 2 0.0 # JCC,7,(1986),230 + dihedral_coeff @dihedral:X-c2-ca-X fourier 1 0.7 2 180.0 # optimized by Junmei Wang, March 2013 + dihedral_coeff @dihedral:X-c2-n-X fourier 1 0.65 2 180.0 + dihedral_coeff @dihedral:X-c2-n2-X fourier 1 4.15 2 180.0 # double bond, parm99 + dihedral_coeff @dihedral:X-c2-ne-X fourier 1 4.15 2 180.0 # double bond, parm99 + dihedral_coeff @dihedral:X-c2-nf-X fourier 1 4.15 2 180.0 # double bond, parm99 + dihedral_coeff @dihedral:X-ce-ne-X fourier 1 0.8 2 180.0 # single bond + dihedral_coeff @dihedral:X-cf-nf-X fourier 1 0.8 2 180.0 # single bond + dihedral_coeff @dihedral:X-c2-nc-X fourier 1 4.75 2 180.0 # statistic value from parm94 + dihedral_coeff @dihedral:X-c2-nd-X fourier 1 4.75 2 180.0 # statistic value from parm94 + dihedral_coeff @dihedral:X-cc-nd-X fourier 1 4.75 2 180.0 # statistic value from parm94 + dihedral_coeff @dihedral:X-cd-nc-X fourier 1 4.75 2 180.0 # statistiv value from parm94 + dihedral_coeff @dihedral:X-cc-nc-X fourier 1 4.75 2 180.0 # statistic value from parm94 + dihedral_coeff @dihedral:X-cd-nd-X fourier 1 4.75 2 180.0 # statistiv value from parm94 + dihedral_coeff @dihedral:X-c2-n3-X fourier 1 0.3 2 180.0 # intrpol. + dihedral_coeff @dihedral:X-c2-n4-X fourier 1 0.0 3 180.0 # intrpol. + dihedral_coeff @dihedral:X-c2-na-X fourier 1 0.625 2 180.0 + dihedral_coeff @dihedral:X-cc-na-X fourier 1 1.7 2 180.0 # statistic value from parm94 + dihedral_coeff @dihedral:X-cd-na-X fourier 1 1.7 2 180.0 # statistic value from parm94 + dihedral_coeff @dihedral:X-c2-nh-X fourier 1 0.675 2 180.0 + dihedral_coeff @dihedral:X-c2-no-X fourier 1 0.75 2 180.0 + dihedral_coeff @dihedral:X-c2-oh-X fourier 1 1.05 2 180.0 # parm99 + dihedral_coeff @dihedral:X-c2-os-X fourier 1 1.05 2 180.0 # parm99 + dihedral_coeff @dihedral:X-c2-p2-X fourier 1 6.65 2 180.0 # double bond + dihedral_coeff @dihedral:X-c2-pe-X fourier 1 6.65 2 180.0 # double bond + dihedral_coeff @dihedral:X-c2-pf-X fourier 1 6.65 2 180.0 # double bond + dihedral_coeff @dihedral:X-ce-pf-X fourier 1 6.65 2 180.0 # double bond + dihedral_coeff @dihedral:X-ce-pe-X fourier 1 0.95 2 180.0 # single bond + dihedral_coeff @dihedral:X-cf-pf-X fourier 1 0.95 2 180.0 # single bond + dihedral_coeff @dihedral:X-c2-pc-X fourier 1 4.75 2 180.0 # estimated + dihedral_coeff @dihedral:X-c2-pd-X fourier 1 4.75 2 180.0 # estimated + dihedral_coeff @dihedral:X-cc-pc-X fourier 1 4.75 2 180.0 # estimated + dihedral_coeff @dihedral:X-cc-pd-X fourier 1 4.75 2 180.0 # estimated + dihedral_coeff @dihedral:X-cd-pc-X fourier 1 4.75 2 180.0 # estimated + dihedral_coeff @dihedral:X-cd-pd-X fourier 1 4.75 2 180.0 # estimated + dihedral_coeff @dihedral:X-c2-p3-X fourier 1 0.45 2 180.0 + dihedral_coeff @dihedral:X-c2-p4-X fourier 1 6.65 2 180.0 # c2=p4 double bond !!! + dihedral_coeff @dihedral:X-ce-p4-X fourier 1 6.65 2 180.0 # c2=p4 double bond !!! + dihedral_coeff @dihedral:X-cf-p4-X fourier 1 6.65 2 180.0 # c2=p4 double bond !!! + dihedral_coeff @dihedral:X-c2-px-X fourier 1 0.325 2 0.0 + dihedral_coeff @dihedral:X-ce-px-X fourier 1 0.325 2 0.0 + dihedral_coeff @dihedral:X-cf-px-X fourier 1 0.325 2 0.0 + dihedral_coeff @dihedral:X-c2-p5-X fourier 1 6.65 2 180.0 # c2=p5 double bond !!! + dihedral_coeff @dihedral:X-ce-p5-X fourier 1 6.65 2 180.0 # c2=p5 double bond !!! + dihedral_coeff @dihedral:X-cf-p5-X fourier 1 6.65 2 180.0 # c2=p5 double bond !!! + dihedral_coeff @dihedral:X-c2-py-X fourier 1 1.43333333333 2 180.0 + dihedral_coeff @dihedral:X-ce-py-X fourier 1 1.43333333333 2 180.0 + dihedral_coeff @dihedral:X-cf-py-X fourier 1 1.43333333333 2 180.0 + dihedral_coeff @dihedral:X-c2-sh-X fourier 1 0.5 2 180.0 + dihedral_coeff @dihedral:X-c2-ss-X fourier 1 1.1 2 180.0 + dihedral_coeff @dihedral:X-c2-s4-X fourier 1 6.65 2 180.0 # c2=s4 double bond !!! + dihedral_coeff @dihedral:X-ce-s4-X fourier 1 6.65 2 180.0 # c2=s4 double bond !!! + dihedral_coeff @dihedral:X-cf-s4-X fourier 1 6.65 2 180.0 # c2=s4 double bond !!! + dihedral_coeff @dihedral:X-c2-sx-X fourier 1 0.6 2 0.0 + dihedral_coeff @dihedral:X-ce-sx-X fourier 1 0.6 2 0.0 + dihedral_coeff @dihedral:X-cf-sx-X fourier 1 0.6 2 0.0 + dihedral_coeff @dihedral:X-c2-s6-X fourier 1 6.65 2 180.0 # c2=s6 double bond !!! + dihedral_coeff @dihedral:X-ce-s6-X fourier 1 6.65 2 180.0 # c2=s6 double bond !!! + dihedral_coeff @dihedral:X-cf-s6-X fourier 1 6.65 2 180.0 # c2=s6 double bond !!! + dihedral_coeff @dihedral:X-c2-sy-X fourier 1 1.26666666667 2 180.0 + dihedral_coeff @dihedral:X-ce-sy-X fourier 1 1.26666666667 2 180.0 + dihedral_coeff @dihedral:X-cf-sy-X fourier 1 1.26666666667 2 180.0 + dihedral_coeff @dihedral:X-c3-c3-X fourier 1 0.155555555556 3 0.0 # JCC,7,(1986),230 + dihedral_coeff @dihedral:X-cx-cx-X fourier 1 0.155555555556 3 0.0 # same as X-c3-c3-X + dihedral_coeff @dihedral:X-cy-cy-X fourier 1 0.155555555556 3 0.0 # same as X-c3-c3-X + dihedral_coeff @dihedral:X-c3-ca-X fourier 1 0.0 2 0.0 # JCC,7,(1986),230 + dihedral_coeff @dihedral:X-c3-n-X fourier 1 0.0 2 0.0 # JCC,7,(1986),230 + dihedral_coeff @dihedral:X-cx-n-X fourier 1 0.0 2 0.0 # same as X-c3-n-X + dihedral_coeff @dihedral:X-cy-n-X fourier 1 0.0 2 0.0 # same as X-c3-n-X + dihedral_coeff @dihedral:X-c3-n2-X fourier 1 0.0 3 0.0 # JCC,7,(1986),230 + dihedral_coeff @dihedral:X-c3-ne-X fourier 1 0.0 3 0.0 # JCC,7,(1986),230 + dihedral_coeff @dihedral:X-c3-nf-X fourier 1 0.0 3 0.0 # JCC,7,(1986),230 + dihedral_coeff @dihedral:X-c3-n3-X fourier 1 0.3 3 0.0 # Junmei et al, 1999 + dihedral_coeff @dihedral:X-c3-n4-X fourier 1 0.155555555556 3 0.0 # JCC,7,(1986),230 + dihedral_coeff @dihedral:X-c3-na-X fourier 1 0.0 2 0.0 # JCC,7,(1986),230 + dihedral_coeff @dihedral:X-c3-nh-X fourier 1 0.0 2 0.0 # JCC,7,(1986),230 + dihedral_coeff @dihedral:X-c3-no-X fourier 1 0.0 2 0.0 # JCC,7,(1986),230 + dihedral_coeff @dihedral:X-c3-oh-X fourier 1 0.166666666667 3 0.0 # JCC,7,(1986),230 + dihedral_coeff @dihedral:X-c3-os-X fourier 1 0.383333333333 3 0.0 # JCC,7,(1986),230 + dihedral_coeff @dihedral:X-c3-p2-X fourier 1 0.266666666667 2 180.0 + dihedral_coeff @dihedral:X-c3-pe-X fourier 1 0.266666666667 2 180.0 + dihedral_coeff @dihedral:X-c3-pf-X fourier 1 0.266666666667 2 180.0 + dihedral_coeff @dihedral:X-c3-p3-X fourier 1 0.133333333333 3 0.0 + dihedral_coeff @dihedral:X-c3-p4-X fourier 1 0.133333333333 3 0.0 + dihedral_coeff @dihedral:X-c3-px-X fourier 1 0.133333333333 3 0.0 + dihedral_coeff @dihedral:X-c3-p5-X fourier 1 0.0222222222222 3 0.0 + dihedral_coeff @dihedral:X-c3-py-X fourier 1 0.0222222222222 3 0.0 + dihedral_coeff @dihedral:X-c3-sh-X fourier 1 0.25 3 0.0 # JCC,7,(1986),230 + dihedral_coeff @dihedral:X-c3-ss-X fourier 1 0.333333333333 3 0.0 # JCC,7,(1986),230 + dihedral_coeff @dihedral:X-c3-s4-X fourier 1 0.2 3 0.0 + dihedral_coeff @dihedral:X-c3-sx-X fourier 1 0.2 3 0.0 + dihedral_coeff @dihedral:X-c3-s6-X fourier 1 0.144444444444 3 0.0 + dihedral_coeff @dihedral:X-c3-sy-X fourier 1 0.144444444444 3 0.0 + dihedral_coeff @dihedral:X-c3-cc-X fourier 1 0.0 3 0.0 # same as X-c3-ca-X + dihedral_coeff @dihedral:X-c3-cd-X fourier 1 0.0 3 0.0 # same as X-c3-ca-X + dihedral_coeff @dihedral:X-ca-ca-X fourier 1 3.625 2 180.0 # intrpol.bsd.on C6H6 + dihedral_coeff @dihedral:X-ca-cp-X fourier 1 3.625 2 180.0 # intrpol.bsd.on C6H6 + dihedral_coeff @dihedral:X-ca-cq-X fourier 1 3.625 2 180.0 # intrpol.bsd.on C6H6 + dihedral_coeff @dihedral:X-cp-cp-X fourier 1 1.0 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-cq-cq-X fourier 1 1.0 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-ca-n-X fourier 1 0.45 2 180.0 + dihedral_coeff @dihedral:X-ca-n2-X fourier 1 0.0 3 180.0 + dihedral_coeff @dihedral:X-ca-ne-X fourier 1 0.0 3 180.0 + dihedral_coeff @dihedral:X-ca-nf-X fourier 1 0.0 3 180.0 + dihedral_coeff @dihedral:X-ca-n4-X fourier 1 1.75 2 0.0 + dihedral_coeff @dihedral:X-ca-na-X fourier 1 0.3 2 180.0 + dihedral_coeff @dihedral:X-ca-nb-X fourier 1 4.8 2 180.0 # same as X-CA-NC-X + dihedral_coeff @dihedral:X-ca-nc-X fourier 1 4.8 2 180.0 # same as X-CA-NC-X + dihedral_coeff @dihedral:X-ca-nd-X fourier 1 4.8 2 180.0 # same as X-CA-NC-X + dihedral_coeff @dihedral:X-ca-nh-X fourier 1 1.05 2 180.0 + dihedral_coeff @dihedral:X-cc-nh-X fourier 1 1.05 2 180.0 # same as X-ca-nh-X + dihedral_coeff @dihedral:X-cd-nh-X fourier 1 1.05 2 180.0 # same as X-ca-nh-X + dihedral_coeff @dihedral:X-ca-no-X fourier 1 0.6 2 180.0 + dihedral_coeff @dihedral:X-ca-oh-X fourier 1 0.9 2 180.0 # Junmei et al, 99 + dihedral_coeff @dihedral:X-ca-os-X fourier 1 0.9 2 180.0 # same as X-ca-oh-X + dihedral_coeff @dihedral:X-ca-p2-X fourier 1 0.6 2 180.0 + dihedral_coeff @dihedral:X-ca-pe-X fourier 1 0.6 2 180.0 # same as X-ca-p2-X + dihedral_coeff @dihedral:X-ca-pf-X fourier 1 0.6 2 180.0 # same as X-ca-p2-X + dihedral_coeff @dihedral:X-ca-pc-X fourier 1 4.8 2 180.0 # estimated, intrpol + dihedral_coeff @dihedral:X-ca-pd-X fourier 1 4.8 2 180.0 # estimated, intrpol + dihedral_coeff @dihedral:X-ca-p3-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-ca-p4-X fourier 1 0.525 2 180.0 + dihedral_coeff @dihedral:X-ca-px-X fourier 1 0.525 2 180.0 # estimated, same as X-ca-p4-X + dihedral_coeff @dihedral:X-ca-p5-X fourier 1 1.46666666667 2 180.0 + dihedral_coeff @dihedral:X-ca-py-X fourier 1 1.46666666667 2 180.0 # estimated, same as X-ca-p5-X + dihedral_coeff @dihedral:X-ca-sh-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-ca-ss-X fourier 1 0.4 2 180.0 + dihedral_coeff @dihedral:X-ca-s4-X fourier 1 0.3 2 0.0 + dihedral_coeff @dihedral:X-ca-sx-X fourier 1 0.3 2 0.0 # estimated, same as X-ca-s4-X + dihedral_coeff @dihedral:X-ca-s6-X fourier 1 1.3 2 180.0 + dihedral_coeff @dihedral:X-ca-sy-X fourier 1 1.3 2 180.0 # estimated, same as X-ca-s6-X + dihedral_coeff @dihedral:X-n-cc-X fourier 1 1.65 2 180.0 # statistic value from parm94 + dihedral_coeff @dihedral:X-n-cd-X fourier 1 1.65 2 180.0 # statistic value from parm94 + dihedral_coeff @dihedral:X-n-n-X fourier 1 1.15 2 0.0 + dihedral_coeff @dihedral:X-n-n2-X fourier 1 0.4 2 0.0 + dihedral_coeff @dihedral:X-n-ne-X fourier 1 0.4 2 0.0 + dihedral_coeff @dihedral:X-n-nf-X fourier 1 0.4 2 0.0 + dihedral_coeff @dihedral:X-n-n3-X fourier 1 1.075 2 0.0 + dihedral_coeff @dihedral:X-n-n4-X fourier 1 0.95 2 0.0 + dihedral_coeff @dihedral:X-n-na-X fourier 1 0.7 2 0.0 + dihedral_coeff @dihedral:X-n-nc-X fourier 1 4.8 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-n-nd-X fourier 1 4.8 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-n-nh-X fourier 1 1.1 2 0.0 + dihedral_coeff @dihedral:X-n-no-X fourier 1 1.375 2 180.0 + dihedral_coeff @dihedral:X-n-oh-X fourier 1 1.5 2 0.0 + dihedral_coeff @dihedral:X-n-os-X fourier 1 1.1 2 0.0 + dihedral_coeff @dihedral:X-n-p2-X fourier 1 1.0 2 180.0 + dihedral_coeff @dihedral:X-n-pe-X fourier 1 1.0 2 180.0 + dihedral_coeff @dihedral:X-n-pf-X fourier 1 1.0 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-n-pc-X fourier 1 4.8 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-n-pd-X fourier 1 4.8 2 180.0 + dihedral_coeff @dihedral:X-n-p3-X fourier 1 2.25 2 0.0 + dihedral_coeff @dihedral:X-n-p4-X fourier 1 0.325 2 0.0 + dihedral_coeff @dihedral:X-n-px-X fourier 1 0.325 2 0.0 + dihedral_coeff @dihedral:X-n-p5-X fourier 1 2.2 2 180.0 + dihedral_coeff @dihedral:X-n-py-X fourier 1 2.2 2 180.0 + dihedral_coeff @dihedral:X-n-sh-X fourier 1 1.1 2 0.0 + dihedral_coeff @dihedral:X-n-ss-X fourier 1 1.5 2 0.0 + dihedral_coeff @dihedral:X-n-s4-X fourier 1 1.5 3 0.0 + dihedral_coeff @dihedral:X-n-sx-X fourier 1 1.5 3 0.0 + dihedral_coeff @dihedral:X-n-s6-X fourier 1 1.1 2 180.0 + dihedral_coeff @dihedral:X-n-sy-X fourier 1 1.1 2 180.0 + dihedral_coeff @dihedral:X-n1-c2-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-c3-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-ca-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-cc-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-cd-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-ce-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-cf-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-cu-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-cv-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-cx-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-cy-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-n-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-n1-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-n2-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-n3-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-n4-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-na-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-nb-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-nc-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-nd-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-ne-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-nf-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-nh-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-no-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-oh-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-os-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-p2-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-pb-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-pc-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-pd-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-pe-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-pf-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-p3-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-p4-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-px-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-p5-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-py-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-s2-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-sh-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-ss-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-s4-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-sx-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-s6-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-sy-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n2-n2-X fourier 2 3.0 2 180.0 2.8 1 0.0 # double bond + dihedral_coeff @dihedral:X-n2-ne-X fourier 2 3.0 2 180.0 2.8 1 0.0 # double bond + dihedral_coeff @dihedral:X-n2-nf-X fourier 2 3.0 2 180.0 2.8 1 0.0 # double bond + dihedral_coeff @dihedral:X-ne-nf-X fourier 2 3.0 2 180.0 2.8 1 0.0 # double bond + dihedral_coeff @dihedral:X-ne-ne-X fourier 1 1.2 2 180.0 # single bond, intrpol + dihedral_coeff @dihedral:X-nf-nf-X fourier 1 1.2 2 180.0 # single bond, intrpol + dihedral_coeff @dihedral:X-nc-nc-X fourier 1 4.0 2 180.0 # estimated, intrpol + dihedral_coeff @dihedral:X-nd-nd-X fourier 1 4.0 2 180.0 # estimated, intrpol + dihedral_coeff @dihedral:X-nc-nd-X fourier 1 4.0 2 180.0 # estimated, intrpol + dihedral_coeff @dihedral:X-n2-nc-X fourier 2 3.0 2 180.0 2.8 1 0.0 # same as X-n2-n2-X + dihedral_coeff @dihedral:X-n2-nd-X fourier 2 3.0 2 180.0 2.8 1 0.0 # same as X-n2-n2-X + dihedral_coeff @dihedral:X-n2-n3-X fourier 1 6.1 2 180.0 + dihedral_coeff @dihedral:X-ne-n3-X fourier 1 6.1 2 180.0 + dihedral_coeff @dihedral:X-nf-n3-X fourier 1 6.1 2 180.0 + dihedral_coeff @dihedral:X-n2-n4-X fourier 1 8.0 2 180.0 + dihedral_coeff @dihedral:X-ne-n4-X fourier 1 8.0 2 180.0 + dihedral_coeff @dihedral:X-nf-n4-X fourier 1 8.0 2 180.0 + dihedral_coeff @dihedral:X-n2-na-X fourier 1 1.7 2 180.0 + dihedral_coeff @dihedral:X-ne-na-X fourier 1 1.7 2 180.0 + dihedral_coeff @dihedral:X-nf-na-X fourier 1 1.7 2 180.0 + dihedral_coeff @dihedral:X-na-nc-X fourier 1 4.8 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-na-nd-X fourier 1 4.8 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-n2-nh-X fourier 1 2.8 2 180.0 + dihedral_coeff @dihedral:X-ne-nh-X fourier 1 2.8 2 180.0 + dihedral_coeff @dihedral:X-nf-nh-X fourier 1 2.8 2 180.0 + dihedral_coeff @dihedral:X-n2-no-X fourier 1 0.75 2 180.0 + dihedral_coeff @dihedral:X-ne-no-X fourier 1 0.75 2 180.0 + dihedral_coeff @dihedral:X-nf-no-X fourier 1 0.75 2 180.0 + dihedral_coeff @dihedral:X-n2-oh-X fourier 1 3.2 2 180.0 + dihedral_coeff @dihedral:X-ne-oh-X fourier 1 3.2 2 180.0 + dihedral_coeff @dihedral:X-nf-oh-X fourier 1 3.2 2 180.0 + dihedral_coeff @dihedral:X-n2-os-X fourier 1 3.0 2 180.0 + dihedral_coeff @dihedral:X-ne-os-X fourier 1 3.0 2 180.0 + dihedral_coeff @dihedral:X-nf-os-X fourier 1 3.0 2 180.0 + dihedral_coeff @dihedral:X-nc-os-X fourier 1 4.8 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-nc-ss-X fourier 1 4.8 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-n2-p2-X fourier 1 5.4 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-n2-pe-X fourier 1 5.4 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-n2-pf-X fourier 1 5.4 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-ne-pf-X fourier 1 5.4 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-n2-pc-X fourier 1 5.4 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-n2-pd-X fourier 1 5.4 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-nc-p2-X fourier 1 5.4 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-nd-p2-X fourier 1 5.4 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-nc-pc-X fourier 1 6.6 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-nd-pd-X fourier 1 6.6 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-nd-pc-X fourier 1 6.6 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-nc-pd-X fourier 1 6.6 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-ne-pe-X fourier 1 0.6 1 0.0 # single bond + dihedral_coeff @dihedral:X-nf-pf-X fourier 1 0.6 1 0.0 # single bond + dihedral_coeff @dihedral:X-n2-p3-X fourier 1 2.1 2 180.0 + dihedral_coeff @dihedral:X-n2-p4-X fourier 1 6.65 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-ne-p4-X fourier 1 6.65 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-nf-p4-X fourier 1 6.65 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-n2-p5-X fourier 1 6.66666666667 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-ne-p5-X fourier 1 1.0 3 180.0 + dihedral_coeff @dihedral:X-nf-p5-X fourier 1 1.0 3 180.0 + dihedral_coeff @dihedral:X-ne-px-X fourier 1 1.0 3 180.0 + dihedral_coeff @dihedral:X-nf-px-X fourier 1 1.0 3 180.0 + dihedral_coeff @dihedral:X-n2-sh-X fourier 1 2.1 2 180.0 + dihedral_coeff @dihedral:X-ne-sh-X fourier 1 2.1 2 180.0 + dihedral_coeff @dihedral:X-nf-sh-X fourier 1 2.1 2 180.0 + dihedral_coeff @dihedral:X-n2-ss-X fourier 2 2.8 2 180.0 1.3 1 180.0 + dihedral_coeff @dihedral:X-ne-ss-X fourier 2 2.8 2 180.0 1.3 1 180.0 + dihedral_coeff @dihedral:X-nf-ss-X fourier 2 2.8 2 180.0 1.3 1 180.0 + dihedral_coeff @dihedral:X-n2-s4-X fourier 1 6.65 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-ne-sx-X fourier 1 1.5 3 180.0 + dihedral_coeff @dihedral:X-nf-sx-X fourier 1 1.5 3 180.0 + dihedral_coeff @dihedral:X-n2-s6-X fourier 1 6.66666666667 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-ne-sy-X fourier 2 0.5 3 180.0 6.8 1 180.0 + dihedral_coeff @dihedral:X-nf-sy-X fourier 2 0.5 3 180.0 6.8 1 180.0 + dihedral_coeff @dihedral:X-n3-n3-X fourier 1 2.25 2 0.0 + dihedral_coeff @dihedral:X-n3-n4-X fourier 1 0.25 3 0.0 + dihedral_coeff @dihedral:X-n3-na-X fourier 1 1.6 2 0.0 + dihedral_coeff @dihedral:X-n3-nh-X fourier 1 1.9 2 0.0 + dihedral_coeff @dihedral:X-n3-no-X fourier 1 4.0 2 180.0 + dihedral_coeff @dihedral:X-n3-oh-X fourier 1 2.2 2 0.0 + dihedral_coeff @dihedral:X-n3-os-X fourier 1 1.8 2 0.0 + dihedral_coeff @dihedral:X-n3-p2-X fourier 1 3.2 2 180.0 + dihedral_coeff @dihedral:X-n3-pe-X fourier 1 3.2 2 180.0 + dihedral_coeff @dihedral:X-n3-pf-X fourier 1 3.2 2 180.0 + dihedral_coeff @dihedral:X-n3-p3-X fourier 1 2.35 2 0.0 + dihedral_coeff @dihedral:X-n3-p4-X fourier 1 2.1 2 180.0 + dihedral_coeff @dihedral:X-n3-px-X fourier 1 2.1 2 180.0 + dihedral_coeff @dihedral:X-n3-p5-X fourier 1 3.0 2 180.0 + dihedral_coeff @dihedral:X-n3-py-X fourier 1 3.0 2 180.0 + dihedral_coeff @dihedral:X-n3-sh-X fourier 1 3.1 2 0.0 + dihedral_coeff @dihedral:X-n3-ss-X fourier 1 2.6 2 0.0 + dihedral_coeff @dihedral:X-n3-s4-X fourier 1 3.75 2 0.0 + dihedral_coeff @dihedral:X-n3-sx-X fourier 1 3.75 2 0.0 + dihedral_coeff @dihedral:X-n3-s6-X fourier 1 3.13333333333 2 0.0 + dihedral_coeff @dihedral:X-n3-sy-X fourier 1 3.13333333333 2 0.0 + dihedral_coeff @dihedral:X-n4-n4-X fourier 1 0.188888888889 3 0.0 + dihedral_coeff @dihedral:X-n4-na-X fourier 1 0.233333333333 3 0.0 + dihedral_coeff @dihedral:X-n4-nh-X fourier 1 0.183333333333 3 0.0 + dihedral_coeff @dihedral:X-n4-no-X fourier 1 0.0833333333333 3 180.0 + dihedral_coeff @dihedral:X-n4-oh-X fourier 1 0.333333333333 3 0.0 + dihedral_coeff @dihedral:X-n4-os-X fourier 1 0.566666666667 3 0.0 + dihedral_coeff @dihedral:X-n4-p2-X fourier 1 0.166666666667 3 180.0 + dihedral_coeff @dihedral:X-n4-pe-X fourier 1 0.166666666667 3 180.0 + dihedral_coeff @dihedral:X-n4-pf-X fourier 1 0.166666666667 3 180.0 + dihedral_coeff @dihedral:X-n4-p3-X fourier 1 0.15 3 0.0 + dihedral_coeff @dihedral:X-n4-p4-X fourier 1 0.05 3 0.0 + dihedral_coeff @dihedral:X-n4-px-X fourier 1 0.05 3 0.0 + dihedral_coeff @dihedral:X-n4-p5-X fourier 1 0.0888888888889 3 0.0 + dihedral_coeff @dihedral:X-n4-py-X fourier 1 0.0888888888889 3 0.0 + dihedral_coeff @dihedral:X-n4-sh-X fourier 1 0.666666666667 3 0.0 + dihedral_coeff @dihedral:X-n4-ss-X fourier 1 0.333333333333 3 0.0 + dihedral_coeff @dihedral:X-n4-s4-X fourier 1 0.283333333333 3 0.0 + dihedral_coeff @dihedral:X-n4-sx-X fourier 1 0.283333333333 3 0.0 + dihedral_coeff @dihedral:X-n4-s6-X fourier 1 0.133333333333 3 0.0 + dihedral_coeff @dihedral:X-n4-sy-X fourier 1 0.133333333333 3 0.0 + dihedral_coeff @dihedral:X-na-na-X fourier 1 0.9 2 0.0 + dihedral_coeff @dihedral:X-na-nh-X fourier 1 1.2 2 0.0 + dihedral_coeff @dihedral:X-na-no-X fourier 1 6.0 2 180.0 + dihedral_coeff @dihedral:X-na-oh-X fourier 1 1.0 2 0.0 + dihedral_coeff @dihedral:X-na-os-X fourier 1 0.65 2 0.0 + dihedral_coeff @dihedral:X-na-p2-X fourier 1 1.0 2 180.0 + dihedral_coeff @dihedral:X-na-pe-X fourier 1 1.0 2 180.0 + dihedral_coeff @dihedral:X-na-pf-X fourier 1 1.0 2 180.0 + dihedral_coeff @dihedral:X-na-p3-X fourier 1 1.45 2 0.0 + dihedral_coeff @dihedral:X-na-p4-X fourier 1 1.1 3 0.0 + dihedral_coeff @dihedral:X-na-px-X fourier 1 1.1 3 0.0 + dihedral_coeff @dihedral:X-na-p5-X fourier 1 0.833333333333 2 180.0 + dihedral_coeff @dihedral:X-na-py-X fourier 1 0.833333333333 2 180.0 + dihedral_coeff @dihedral:X-na-sh-X fourier 1 1.8 2 0.0 + dihedral_coeff @dihedral:X-na-ss-X fourier 1 7.8 2 0.0 + dihedral_coeff @dihedral:X-na-s4-X fourier 1 1.05 2 0.0 + dihedral_coeff @dihedral:X-na-sx-X fourier 1 1.05 2 0.0 + dihedral_coeff @dihedral:X-na-s6-X fourier 1 3.66666666667 2 180.0 + dihedral_coeff @dihedral:X-na-sy-X fourier 1 3.66666666667 2 180.0 + dihedral_coeff @dihedral:X-nh-nh-X fourier 1 1.8 3 180.0 + dihedral_coeff @dihedral:X-nh-no-X fourier 1 2.55 2 180.0 + dihedral_coeff @dihedral:X-nh-oh-X fourier 1 1.5 2 0.0 + dihedral_coeff @dihedral:X-nh-os-X fourier 1 1.5 1 0.0 + dihedral_coeff @dihedral:X-nh-p2-X fourier 1 1.4 2 180.0 + dihedral_coeff @dihedral:X-nh-pe-X fourier 1 1.4 2 180.0 + dihedral_coeff @dihedral:X-nh-pf-X fourier 1 1.4 2 180.0 + dihedral_coeff @dihedral:X-nh-p3-X fourier 1 2.35 2 0.0 + dihedral_coeff @dihedral:X-nh-p4-X fourier 1 1.175 3 0.0 + dihedral_coeff @dihedral:X-nh-px-X fourier 1 1.175 3 0.0 + dihedral_coeff @dihedral:X-nh-p5-X fourier 1 0.8 2 0.0 + dihedral_coeff @dihedral:X-nh-py-X fourier 1 0.8 2 0.0 + dihedral_coeff @dihedral:X-nh-sh-X fourier 1 1.6 2 0.0 + dihedral_coeff @dihedral:X-nh-ss-X fourier 1 2.1 2 0.0 + dihedral_coeff @dihedral:X-nh-s4-X fourier 2 0.75 2 0.0 0.1 3 180.0 + dihedral_coeff @dihedral:X-nh-sx-X fourier 2 0.75 2 0.0 0.1 3 180.0 + dihedral_coeff @dihedral:X-nh-s6-X fourier 1 0.1 2 180.0 + dihedral_coeff @dihedral:X-nh-sy-X fourier 1 0.1 2 180.0 + dihedral_coeff @dihedral:X-no-no-X fourier 2 0.4 4 180.0 1.8 2 180.0 + dihedral_coeff @dihedral:X-no-oh-X fourier 1 3.9 2 180.0 + dihedral_coeff @dihedral:X-no-os-X fourier 1 3.0 2 180.0 + dihedral_coeff @dihedral:X-no-p2-X fourier 1 0.3 2 180.0 + dihedral_coeff @dihedral:X-no-pe-X fourier 1 0.3 2 180.0 + dihedral_coeff @dihedral:X-no-pf-X fourier 1 0.3 2 180.0 + dihedral_coeff @dihedral:X-no-p3-X fourier 1 1.9 2 180.0 + dihedral_coeff @dihedral:X-no-p4-X fourier 1 0.575 2 180.0 + dihedral_coeff @dihedral:X-no-px-X fourier 1 0.575 2 180.0 + dihedral_coeff @dihedral:X-no-p5-X fourier 2 2.4 2 0.0 0.4 3 0.0 + dihedral_coeff @dihedral:X-no-py-X fourier 2 2.4 2 0.0 0.4 3 0.0 + dihedral_coeff @dihedral:X-no-sh-X fourier 1 2.3 2 180.0 + dihedral_coeff @dihedral:X-no-ss-X fourier 1 2.7 2 180.0 + dihedral_coeff @dihedral:X-no-s4-X fourier 1 2.6 2 180.0 + dihedral_coeff @dihedral:X-no-sx-X fourier 1 2.6 2 180.0 + dihedral_coeff @dihedral:X-no-s6-X fourier 1 0.333333333333 2 0.0 + dihedral_coeff @dihedral:X-no-sy-X fourier 1 0.333333333333 2 0.0 + dihedral_coeff @dihedral:X-oh-oh-X fourier 1 1.6 2 0.0 + dihedral_coeff @dihedral:X-oh-os-X fourier 1 1.6 2 0.0 + dihedral_coeff @dihedral:X-oh-p2-X fourier 1 1.5 2 180.0 + dihedral_coeff @dihedral:X-oh-pe-X fourier 1 1.5 2 180.0 + dihedral_coeff @dihedral:X-oh-pf-X fourier 1 1.5 2 180.0 + dihedral_coeff @dihedral:X-oh-p3-X fourier 1 0.4 3 180.0 + dihedral_coeff @dihedral:X-oh-p4-X fourier 1 0.7 1 0.0 + dihedral_coeff @dihedral:X-oh-px-X fourier 1 0.7 1 0.0 + dihedral_coeff @dihedral:X-oh-p5-X fourier 1 0.533333333333 3 0.0 + dihedral_coeff @dihedral:X-oh-py-X fourier 1 0.533333333333 3 0.0 + dihedral_coeff @dihedral:X-oh-sh-X fourier 1 2.4 2 0.0 + dihedral_coeff @dihedral:X-oh-ss-X fourier 1 2.4 2 0.0 + dihedral_coeff @dihedral:X-oh-s4-X fourier 1 5.0 1 0.0 + dihedral_coeff @dihedral:X-oh-sx-X fourier 1 5.0 1 0.0 + dihedral_coeff @dihedral:X-oh-s6-X fourier 1 9.5 1 180.0 + dihedral_coeff @dihedral:X-oh-sy-X fourier 1 9.5 1 180.0 + dihedral_coeff @dihedral:X-os-os-X fourier 1 1.0 1 0.0 + dihedral_coeff @dihedral:X-os-ss-X fourier 1 2.2 2 0.0 + dihedral_coeff @dihedral:X-os-sh-X fourier 1 1.8 2 0.0 + dihedral_coeff @dihedral:X-os-s4-X fourier 1 1.65 3 0.0 + dihedral_coeff @dihedral:X-os-sx-X fourier 1 1.65 3 0.0 + dihedral_coeff @dihedral:X-os-s6-X fourier 1 1.2 2 180.0 + dihedral_coeff @dihedral:X-os-sy-X fourier 1 1.2 2 180.0 + dihedral_coeff @dihedral:X-os-p2-X fourier 2 3.0 2 180.0 2.0 1 180.0 + dihedral_coeff @dihedral:X-os-pe-X fourier 2 3.0 2 180.0 2.0 1 180.0 + dihedral_coeff @dihedral:X-os-pf-X fourier 2 3.0 2 180.0 2.0 1 180.0 + dihedral_coeff @dihedral:X-os-p3-X fourier 1 2.2 2 0.0 + dihedral_coeff @dihedral:X-os-p4-X fourier 1 1.05 2 180.0 + dihedral_coeff @dihedral:X-os-px-X fourier 1 1.05 2 180.0 + dihedral_coeff @dihedral:X-os-p5-X fourier 1 0.8 2 0.0 + dihedral_coeff @dihedral:X-os-py-X fourier 1 0.8 2 0.0 + dihedral_coeff @dihedral:X-p2-p2-X fourier 1 6.6 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-p2-pe-X fourier 1 6.6 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-p2-pf-X fourier 1 6.6 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-p2-pc-X fourier 1 6.6 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-p2-pd-X fourier 1 6.6 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-pe-pe-X fourier 1 1.2 2 180.0 # single bond + dihedral_coeff @dihedral:X-pf-pf-X fourier 1 1.2 2 180.0 # single bond + dihedral_coeff @dihedral:X-pc-pc-X fourier 1 7.2 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-pd-pd-X fourier 1 7.2 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-pc-pd-X fourier 1 7.2 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-p2-p3-X fourier 1 1.2 1 0.0 + dihedral_coeff @dihedral:X-pe-p3-X fourier 1 1.2 1 0.0 + dihedral_coeff @dihedral:X-pf-p3-X fourier 1 1.2 1 0.0 + dihedral_coeff @dihedral:X-p2-p4-X fourier 1 6.65 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-pe-px-X fourier 1 2.45 2 0.0 + dihedral_coeff @dihedral:X-pf-px-X fourier 1 2.45 2 0.0 + dihedral_coeff @dihedral:X-p2-p5-X fourier 1 6.66666666667 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-pe-py-X fourier 1 1.9 1 0.0 + dihedral_coeff @dihedral:X-pf-py-X fourier 1 1.9 1 0.0 + dihedral_coeff @dihedral:X-p2-sh-X fourier 1 1.4 2 180.0 + dihedral_coeff @dihedral:X-pe-sh-X fourier 1 1.4 2 180.0 + dihedral_coeff @dihedral:X-pf-sh-X fourier 1 1.4 2 180.0 + dihedral_coeff @dihedral:X-p2-ss-X fourier 1 1.4 2 180.0 + dihedral_coeff @dihedral:X-pe-ss-X fourier 1 1.4 2 180.0 + dihedral_coeff @dihedral:X-pf-ss-X fourier 1 1.4 2 180.0 + dihedral_coeff @dihedral:X-p2-s4-X fourier 1 6.65 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-pe-sx-X fourier 1 1.5 2 0.0 + dihedral_coeff @dihedral:X-pf-sx-X fourier 1 1.5 2 0.0 + dihedral_coeff @dihedral:X-p2-s6-X fourier 1 6.66666666667 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-pe-sy-X fourier 1 0.4 3 180.0 + dihedral_coeff @dihedral:X-pf-sy-X fourier 1 0.4 3 180.0 + dihedral_coeff @dihedral:X-p3-p3-X fourier 1 0.5 3 0.0 + dihedral_coeff @dihedral:X-p3-p4-X fourier 1 0.9 1 0.0 + dihedral_coeff @dihedral:X-p3-px-X fourier 1 0.9 1 0.0 + dihedral_coeff @dihedral:X-p3-p5-X fourier 1 1.83333333333 2 180.0 + dihedral_coeff @dihedral:X-p3-py-X fourier 1 1.83333333333 2 180.0 + dihedral_coeff @dihedral:X-p3-sh-X fourier 1 4.6 2 0.0 + dihedral_coeff @dihedral:X-p3-ss-X fourier 1 1.15 3 0.0 + dihedral_coeff @dihedral:X-p3-s4-X fourier 1 3.85 2 0.0 + dihedral_coeff @dihedral:X-p3-sx-X fourier 1 3.85 2 0.0 + dihedral_coeff @dihedral:X-p3-s6-X fourier 1 0.266666666667 3 0.0 + dihedral_coeff @dihedral:X-p3-sy-X fourier 1 0.266666666667 3 0.0 + dihedral_coeff @dihedral:X-p4-p4-X fourier 1 6.65 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-px-px-X fourier 1 1.45 2 180.0 + dihedral_coeff @dihedral:X-p4-p5-X fourier 1 6.65 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-px-py-X fourier 1 0.316666666667 2 180.0 + dihedral_coeff @dihedral:X-p4-s4-X fourier 1 6.65 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-px-sx-X fourier 1 0.85 1 0.0 + dihedral_coeff @dihedral:X-p4-s6-X fourier 1 6.65 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-px-sy-X fourier 1 0.116666666667 3 0.0 + dihedral_coeff @dihedral:X-p4-sh-X fourier 1 0.25 1 180.0 + dihedral_coeff @dihedral:X-px-sh-X fourier 1 0.25 1 180.0 + dihedral_coeff @dihedral:X-p4-ss-X fourier 1 0.6 2 180.0 + dihedral_coeff @dihedral:X-px-ss-X fourier 1 0.6 2 180.0 + dihedral_coeff @dihedral:X-p5-p5-X fourier 1 6.66666666667 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-py-py-X fourier 1 0.6 2 0.0 + dihedral_coeff @dihedral:X-p5-sh-X fourier 1 0.3 3 0.0 + dihedral_coeff @dihedral:X-py-sh-X fourier 1 0.3 3 0.0 + dihedral_coeff @dihedral:X-p5-ss-X fourier 1 3.8 2 180.0 + dihedral_coeff @dihedral:X-py-ss-X fourier 1 3.8 2 180.0 + dihedral_coeff @dihedral:X-p5-s4-X fourier 1 6.66666666667 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-py-sx-X fourier 1 0.266666666667 3 0.0 + dihedral_coeff @dihedral:X-p5-s6-X fourier 1 6.66666666667 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-py-sy-X fourier 1 0.277777777778 3 0.0 + dihedral_coeff @dihedral:X-sh-sh-X fourier 1 5.6 3 0.0 + dihedral_coeff @dihedral:X-sh-ss-X fourier 1 5.3 3 0.0 + dihedral_coeff @dihedral:X-sh-s4-X fourier 1 0.7 3 0.0 + dihedral_coeff @dihedral:X-sh-sx-X fourier 1 0.7 3 0.0 + dihedral_coeff @dihedral:X-sh-s6-X fourier 1 4.66666666667 2 180.0 + dihedral_coeff @dihedral:X-sh-sy-X fourier 1 4.66666666667 2 180.0 + dihedral_coeff @dihedral:X-ss-ss-X fourier 1 0.0 3 0.0 + dihedral_coeff @dihedral:X-ss-s4-X fourier 1 0.3 3 0.0 + dihedral_coeff @dihedral:X-ss-sx-X fourier 1 0.3 3 0.0 + dihedral_coeff @dihedral:X-ss-s6-X fourier 1 3.06666666667 2 180.0 + dihedral_coeff @dihedral:X-ss-sy-X fourier 1 3.06666666667 2 180.0 + dihedral_coeff @dihedral:X-s4-s4-X fourier 1 6.65 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-sx-sx-X fourier 1 0.625 3 0.0 + dihedral_coeff @dihedral:X-s4-s6-X fourier 1 6.66666666667 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-sx-sy-X fourier 1 4.33333333333 2 180.0 + dihedral_coeff @dihedral:X-s6-s6-X fourier 1 6.66666666667 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-sy-sy-X fourier 1 0.155555555556 2 180.0 + dihedral_coeff @dihedral:X-cf-pe-X fourier 1 6.65 2 180.0 # NEW + dihedral_coeff @dihedral:X-nd-os-X fourier 1 4.8 2 180.0 # NEW + dihedral_coeff @dihedral:X-nd-ss-X fourier 1 4.8 2 180.0 # NEW + dihedral_coeff @dihedral:X-nf-pe-X fourier 1 5.4 2 180.0 # NEW + dihedral_coeff @dihedral:c2-ne-p5-o fourier 2 0.0 3 0.0 2.3 1 0.0 # TorType=1 + dihedral_coeff @dihedral:c2-nf-p5-o fourier 2 0.0 3 0.0 2.3 1 0.0 # TorType=1 + dihedral_coeff @dihedral:ce-ne-p5-o fourier 2 0.0 3 0.0 2.3 1 0.0 # TorType=1 + dihedral_coeff @dihedral:ce-nf-p5-o fourier 2 0.0 3 0.0 2.3 1 0.0 # TorType=1 + dihedral_coeff @dihedral:cf-ne-p5-o fourier 2 0.0 3 0.0 2.3 1 0.0 # TorType=1 + dihedral_coeff @dihedral:cf-nf-p5-o fourier 2 0.0 3 0.0 2.3 1 0.0 # TorType=1 + dihedral_coeff @dihedral:hn-n-c-o fourier 2 2.5 2 180.0 2.0 1 0.0 # JCC,7,(1986),230 TorType=1 + dihedral_coeff @dihedral:c3-n3-p5-o fourier 2 3.0 2 180.0 2.3 3 0.0 # TorType=1 + dihedral_coeff @dihedral:oh-p5-os-c3 fourier 2 0.25 3 0.0 1.2 2 0.0 # JCC,7,(1986),230 TorType=1 + dihedral_coeff @dihedral:h1-c3-c-o fourier 2 0.8 1 0.0 0.08 3 180.0 # Junmei et al, 1999 TorType=1 + dihedral_coeff @dihedral:ho-oh-c-o fourier 2 2.3 2 180.0 1.9 1 0.0 # Junmei et al, 1999 TorType=1 + dihedral_coeff @dihedral:c2-c2-c-o fourier 2 2.175 2 180.0 0.3 3 0.0 # Junmei et al, 1999 TorType=1 + dihedral_coeff @dihedral:c3-c3-os-c fourier 2 0.383 3 0.0 0.8 1 180.0 # Junmei et al, 1999 TorType=1 + dihedral_coeff @dihedral:c3-os-c3-na fourier 2 0.383 3 0.0 0.65 2 0.0 # parm98.dat, TC,PC,PAK TorType=1 + dihedral_coeff @dihedral:o-c-os-c3 fourier 2 2.7 2 180.0 1.4 1 180.0 # Junmei et al, 1999 TorType=1 + dihedral_coeff @dihedral:os-c3-na-c2 fourier 2 0.0 2 0.0 2.5 1 0.0 # parm98, TC,PC,PAK TorType=1 + dihedral_coeff @dihedral:h1-c3-c3-os fourier 2 0.0 3 0.0 0.25 1 0.0 # Junmei et al, 1999 TorType=1 + dihedral_coeff @dihedral:h1-c3-c3-oh fourier 2 0.0 3 0.0 0.25 1 0.0 # Junmei et al, 1999 TorType=1 + dihedral_coeff @dihedral:h1-c3-c3-f fourier 2 0.0 3 0.0 0.19 1 0.0 # Junmei et al, 1999 TorType=1 + dihedral_coeff @dihedral:h1-c3-c3-cl fourier 2 0.0 3 0.0 0.25 1 0.0 # Junmei et al, 1999 TorType=1 + dihedral_coeff @dihedral:h1-c3-c3-br fourier 2 0.0 3 0.0 0.55 1 0.0 # Junmei et al, 1999 TorType=1 + dihedral_coeff @dihedral:hc-c3-c3-os fourier 2 0.0 3 0.0 0.25 1 0.0 # Junmei et al, 1999 TorType=1 + dihedral_coeff @dihedral:c3-n4-c3-ca fourier 2 0.156 3 0.0 0.7 2 0.0 # Junmei, 2015 TorType=1 + dihedral_coeff @dihedral:oh-c3-c3-n4 fourier 2 0.144 3 0.0 1.3 2 0.0 # Junmei, 2015 TorType=1 + dihedral_coeff @dihedral:c3-c3-n4-c3 fourier 1 0.156 3 0.0 # Junmei, 2015 TorType=1 + dihedral_coeff @dihedral:c3-c-os-p5 fourier 2 2.7 2 180.0 2.0 1 180.0 # Junmei, 2015 TorType=1 + dihedral_coeff @dihedral:c-os-p5-o fourier 3 0.8 2 0.0 1.1 1 0.0 0.5 3 180.0 # Junmei, 2015 TorType=1 + dihedral_coeff @dihedral:c3-c3-os-p5 fourier 2 0.383 3 0.0 3.95 1 180.0 # Junmei, 2015 TorType=1 + dihedral_coeff @dihedral:c3-os-p5-o fourier 2 0.8 2 0.0 0.55 3 0.0 # Junmei, 2015 TorType=1 + dihedral_coeff @dihedral:ca-ca-os-p5 fourier 1 1.75 2 180.0 # Junmei, 2015 TorType=1 + dihedral_coeff @dihedral:ca-os-p5-o fourier 2 0.8 2 180.0 0.1 3 0.0 # Junmei, 2015 TorType=1 + dihedral_coeff @dihedral:br-c3-c3-br fourier 2 0.5 3 0.0 1.82 1 0.0 # m9 GA AUE=0.9626 RMSE=1.1958 TorType=2 + dihedral_coeff @dihedral:c-n-c2-c2 fourier 2 1.57 2 180.0 1.53 1 180.0 # c25 GA AUE=0.3367 RMSE=0.3900 TorType=2 + dihedral_coeff @dihedral:c3-ss-c2-c2 fourier 2 1.28 2 180.0 1.2 3 180.0 # c39 GA AUE=0.3908 RMSE=0.4760 TorType=2 + dihedral_coeff @dihedral:c3-c2-c2-c3 fourier 2 5.29 2 180.0 0.4 1 180.0 # c22 GA AUE=2.0091 RMSE=3.0745 TorType=2 + dihedral_coeff @dihedral:c3-c3-c3-c3 fourier 3 0.13 3 0.0 0.29 2 180.0 0.11 1 0.0 # c42 GA AUE=0.2975 RMSE=0.3306 TorType=2 + dihedral_coeff @dihedral:n-c-c3-c3 fourier 2 0.0 4 180.0 0.71 2 180.0 # p20 GA AUE=0.5445 RMSE=0.7015 TorType=2 + dihedral_coeff @dihedral:c3-os-c3-c3 fourier 2 0.24 3 0.0 0.16 2 0.0 # p29 GA AUE=0.4256 RMSE=0.5201 TorType=2 + dihedral_coeff @dihedral:ca-nh-n3-c3 fourier 1 1.12 2 0.0 # c115 SS AUE=2.2848 RMSE=2.9445 TorType=2 + dihedral_coeff @dihedral:hs-sh-ss-c3 fourier 2 1.6 3 0.0 2.81 2 0.0 # c223 GA AUE=0.7163 RMSE=0.8348 TorType=2 + dihedral_coeff @dihedral:ho-oh-nh-ca fourier 2 1.43 1 0.0 0.5 2 0.0 # c156 GA AUE=0.4441 RMSE=0.5406 TorType=2 + dihedral_coeff @dihedral:cl-c3-c3-cl fourier 2 0.5 3 0.0 0.93 1 0.0 # m8 GA AUE=0.9322 RMSE=1.0556 TorType=2 + dihedral_coeff @dihedral:c-n-c3-c3 fourier 3 0.1 4 180.0 0.17 3 0.0 1.02 1 180.0 # p19 GA AUE=0.2882 RMSE=0.4031 TorType=2 + dihedral_coeff @dihedral:c2-p2-n-c fourier 2 1.48 2 180.0 2.15 1 180.0 # c88 GA AUE=0.5049 RMSE=0.6214 TorType=2 + dihedral_coeff @dihedral:f-c3-c3-f fourier 2 1.0 3 0.0 0.64 1 180.0 # m7 GA AUE=1.3130 RMSE=1.6963 TorType=2 + dihedral_coeff @dihedral:hc-c3-c2-c2 fourier 2 0.36 3 180.0 1.47 1 0.0 # c23 GA AUE=0.0738 RMSE=0.0893 TorType=2 + dihedral_coeff @dihedral:hc-c3-c3-br fourier 2 0.21 3 0.0 0.08 1 0.0 # m5 GA AUE=0.2036 RMSE=0.2389 TorType=2 + dihedral_coeff @dihedral:hc-c3-c3-c3 fourier 1 0.08 3 0.0 # m2 SS AUE=0.2468 RMSE=0.2989 TorType=2 + dihedral_coeff @dihedral:hc-c3-c3-cl fourier 2 0.22 3 0.0 0.25 1 180.0 # m4 GA AUE=0.1732 RMSE=0.2055 TorType=2 + dihedral_coeff @dihedral:hc-c3-c3-f fourier 2 0.22 3 0.0 1.97 1 180.0 # m3 GA AUE=0.0868 RMSE=0.1021 TorType=2 + dihedral_coeff @dihedral:hc-c3-c3-hc fourier 1 0.12 3 0.0 # m1 SS AUE=0.2420 RMSE=0.2944 TorType=2 + dihedral_coeff @dihedral:hc-c3-c3-oh fourier 2 0.18 3 0.0 0.51 1 0.0 # m11 GA AUE=0.1021 RMSE=0.1307 TorType=2 + dihedral_coeff @dihedral:n-c-c3-n fourier 2 0.1 1 180.0 2.12 2 180.0 # p17 GA AUE=0.9129 RMSE=1.0401 TorType=2 + dihedral_coeff @dihedral:oh-c3-c3-os fourier 3 1.01 3 0.0 0.0 2 0.0 0.02 1 180.0 # suger5ring,suger6ring GA AUE=0.6597 RMSE=0.8978 TorType=2 + dihedral_coeff @dihedral:os-p5-os-c3 fourier 2 0.0 3 0.0 2.61 2 0.0 # c191 GA AUE=0.2324 RMSE=0.3542 TorType=2 + dihedral_coeff @dihedral:c3-n-c-c3 fourier 2 0.26 2 180.0 0.5 1 0.0 # c5 GA AUE=0.9706 RMSE=1.2796 TorType=2 + dihedral_coeff @dihedral:c3-os-c-c3 fourier 3 1.58 1 180.0 3.18 2 180.0 0.73 3 0.0 # c13 GA AUE=0.2469 RMSE=0.2990 TorType=2 + dihedral_coeff @dihedral:hs-sh-c-c3 fourier 2 1.08 2 180.0 1.92 1 180.0 # c18 GA AUE=0.2126 RMSE=0.3029 TorType=2 + dihedral_coeff @dihedral:os-c3-os-c3 fourier 3 0.0 3 180.0 1.24 2 0.0 0.97 1 180.0 # cococ,lactose2,t12 GA AUE=0.8913 RMSE=1.4261 TorType=2 + dihedral_coeff @dihedral:c3-ss-ss-c3 fourier 2 3.15 2 0.0 0.89 3 0.0 # c226,p2 GA AUE=0.4785 RMSE=0.5249 TorType=2 + dihedral_coeff @dihedral:o-c-c3-hc fourier 2 0.83 1 0.0 0.04 3 180.0 # CH3COO,CH3COOH GA AUE=0.0144 RMSE=0.0193 TorType=2 + dihedral_coeff @dihedral:ho-oh-c3-c3 fourier 1 0.0 3 0.0 # m19 SS AUE=0.1539 RMSE=0.2110 TorType=2 + dihedral_coeff @dihedral:oh-c3-c3-oh fourier 2 0.9 3 0.0 1.13 2 0.0 # p5,ch2oh2 GA AUE=0.9894 RMSE=1.1930 TorType=2 + dihedral_coeff @dihedral:os-c3-c3-os fourier 3 0.0 3 0.0 0.0 2 180.0 0.17 1 180.0 # p28,suger5ring,suger6ring,coccoc GA AUE=1.1750 RMSE=1.6708 TorType=2 + dihedral_coeff @dihedral:c1-c1-c3-c1 fourier 1 0.0 2 0.0 # t5 SS AUE=0.0048 RMSE=0.0058 TorType=3 + dihedral_coeff @dihedral:c2-c2-c3-c2 fourier 1 0.112 2 0.0 # t4 SS AUE=0.5917 RMSE=0.7276 TorType=3 + dihedral_coeff @dihedral:c2-ce-ca-ca fourier 1 0.505 2 180.0 # add6f SS AUE=0.2273 RMSE=0.3302 TorType=3 + dihedral_coeff @dihedral:c2-ce-ce-c3 fourier 1 0.5 2 180.0 # set1_2 SS AUE=0.6541 RMSE=0.8643 TorType=3 + dihedral_coeff @dihedral:c2-cf-cd-cc fourier 1 0.5 2 180.0 # add6d SS AUE=0.3708 RMSE=0.4956 TorType=3 + dihedral_coeff @dihedral:c2-n2-c3-n2 fourier 2 1.57 2 180.0 2.73 1 180.0 # t14 GA AUE=1.3428 RMSE=1.6221 TorType=3 + dihedral_coeff @dihedral:c2-n2-na-cd fourier 1 1.575 2 180.0 # c99 SS AUE=0.2455 RMSE=0.3271 TorType=3 + dihedral_coeff @dihedral:c2-n2-n-c fourier 1 2.79 1 180.0 # c80 SS AUE=2.1704 RMSE=2.7351 TorType=3 + dihedral_coeff @dihedral:c2-n2-nh-c2 fourier 1 1.2 2 0.0 # set3_6 SS AUE=1.7161 RMSE=2.4147 TorType=3 + dihedral_coeff @dihedral:c2-ne-ca-ca fourier 1 0.495 3 0.0 # c63 SS AUE=1.1301 RMSE=1.4142 TorType=3 + dihedral_coeff @dihedral:c2-ne-ce-c2 fourier 1 0.17 2 180.0 # c26 SS AUE=0.7462 RMSE=0.9083 TorType=3 + dihedral_coeff @dihedral:c2-ne-ce-c3 fourier 1 0.82 2 0.0 # set1_6 SS AUE=0.2966 RMSE=0.4200 TorType=3 + dihedral_coeff @dihedral:c2-nh-c2-c2 fourier 1 0.98 2 180.0 # set3_2 SS AUE=0.5762 RMSE=0.7682 TorType=3 + dihedral_coeff @dihedral:c2-nh-c2-c3 fourier 1 3.14 2 180.0 # set3_26 SS AUE=0.5612 RMSE=0.7360 TorType=3 + dihedral_coeff @dihedral:c2-nh-c3-h1 fourier 1 0.4 3 0.0 # set3_3 SS AUE=0.2455 RMSE=0.3092 TorType=3 + dihedral_coeff @dihedral:c2-nh-ca-ca fourier 1 0.55 2 180.0 # set3_4 SS AUE=0.8992 RMSE=1.3720 TorType=3 + dihedral_coeff @dihedral:c2-nh-nh-c2 fourier 1 2.93 3 0.0 # set3_24 SS AUE=2.3906 RMSE=3.0117 TorType=3 + dihedral_coeff @dihedral:c2-p2-c3-p2 fourier 1 2.07 1 180.0 # t18 SS AUE=0.4761 RMSE=0.6635 TorType=3 + dihedral_coeff @dihedral:c2-p2-n4-hn fourier 1 0.0 3 180.0 # c133 SS AUE=0.2623 RMSE=0.3265 TorType=3 + dihedral_coeff @dihedral:c2-p2-na-cc fourier 1 1.83 2 180.0 # c146 SS AUE=0.3236 RMSE=0.3673 TorType=3 + dihedral_coeff @dihedral:c2-p2-nh-c2 fourier 1 1.33 2 180.0 # set3_14 SS AUE=0.4660 RMSE=0.7730 TorType=3 + dihedral_coeff @dihedral:c2-p2-nh-c3 fourier 1 2.4 2 180.0 # c119 SS AUE=1.0662 RMSE=1.4725 TorType=3 + dihedral_coeff @dihedral:c2-p2-nh-ca fourier 1 1.88 1 180.0 # c158 SS AUE=1.5854 RMSE=1.8810 TorType=3 + dihedral_coeff @dihedral:c2-pe-ca-ca fourier 1 1.065 2 180.0 # c71 SS AUE=0.2838 RMSE=0.3291 TorType=3 + dihedral_coeff @dihedral:c2-pe-ce-c2 fourier 1 0.825 2 180.0 # c34 SS AUE=0.3082 RMSE=0.3467 TorType=3 + dihedral_coeff @dihedral:c2-pe-ce-c3 fourier 1 3.64 1 180.0 # set1_14 SS AUE=0.2869 RMSE=0.3329 TorType=3 + dihedral_coeff @dihedral:c2-pe-ne-c2 fourier 1 0.29 1 0.0 # c104 SS AUE=0.4118 RMSE=0.5379 TorType=3 + dihedral_coeff @dihedral:c2-pe-pe-c2 fourier 1 0.68 2 180.0 # c196 SS AUE=0.2486 RMSE=0.3241 TorType=3 + dihedral_coeff @dihedral:c3-c2-nh-ca fourier 2 1.16 2 180.0 1.88 1 0.0 # set1_10 GA AUE=0.3625 RMSE=0.5970 TorType=3 + dihedral_coeff @dihedral:c3-c3-c3-hc fourier 1 0.08 3 0.0 # t2 SS AUE=0.2507 RMSE=0.3027 TorType=3 + dihedral_coeff @dihedral:c3-c3-cc-ca fourier 1 0.082 3 0.0 # p3 SS AUE=0.4586 RMSE=0.5633 TorType=3 + dihedral_coeff @dihedral:c3-c3-n-c fourier 3 0.65 4 180.0 0.03 3 180.0 2.26 1 0.0 # sialic2 GA AUE=1.1541 RMSE=1.2847 TorType=3 + dihedral_coeff @dihedral:c3-c-c3-c3 fourier 1 0.332 2 180.0 # p10 SS AUE=0.3226 RMSE=0.4401 TorType=3 + dihedral_coeff @dihedral:c3-c-ce-c3 fourier 1 4.11 2 0.0 # set3_25 SS AUE=0.6933 RMSE=1.1187 TorType=3 + dihedral_coeff @dihedral:c3-ce-ce-c3 fourier 1 0.5 2 180.0 # set3_22 SS AUE=1.0809 RMSE=1.3455 TorType=3 + dihedral_coeff @dihedral:c3-n2-c2-c3 fourier 1 10.37 2 180.0 # c7 SS AUE=1.1629 RMSE=1.3902 TorType=3 + dihedral_coeff @dihedral:c3-n3-n3-c3 fourier 1 2.31 2 0.0 # c112 SS AUE=0.8815 RMSE=1.0390 TorType=3 + dihedral_coeff @dihedral:c3-n3-nh-c2 fourier 1 1.355 2 0.0 # set3_7 SS AUE=1.4104 RMSE=1.6750 TorType=3 + dihedral_coeff @dihedral:c3-n4-ca-ca fourier 1 1.495 2 0.0 # c65 SS AUE=0.2872 RMSE=0.3575 TorType=3 + dihedral_coeff @dihedral:c3-n4-n4-c3 fourier 1 0.244 3 0.0 # c127 SS AUE=0.6207 RMSE=0.7993 TorType=3 + dihedral_coeff @dihedral:c3-nh-c2-c2 fourier 2 0.95 2 180.0 1.12 3 180.0 # c27 GA AUE=0.7690 RMSE=1.0440 TorType=3 + dihedral_coeff @dihedral:c3-nh-c2-c3 fourier 1 2.495 2 180.0 # set1_7 SS AUE=0.8853 RMSE=1.2321 TorType=3 + dihedral_coeff @dihedral:c3-os-c2-c2 fourier 2 2.52 2 180.0 2.0 1 180.0 # c33 GA AUE=0.9155 RMSE=1.0796 TorType=3 + dihedral_coeff @dihedral:c3-os-c2-c3 fourier 1 4.79 2 180.0 # set1_13 SS AUE=0.9973 RMSE=1.5097 TorType=3 + dihedral_coeff @dihedral:c3-os-c3-h1 fourier 1 0.337 3 0.0 # c52 SS AUE=0.2706 RMSE=0.3300 TorType=3 + dihedral_coeff @dihedral:c3-os-ca-ca fourier 1 1.61 2 180.0 # c70 SS AUE=0.3151 RMSE=0.3580 TorType=3 + dihedral_coeff @dihedral:c3-os-n2-c2 fourier 2 2.2 2 180.0 0.9 3 180.0 # c103 SS AUE=1.2430 RMSE=1.4817 TorType=3 + dihedral_coeff @dihedral:c3-os-n3-c3 fourier 1 0.84 2 0.0 # c118 SS AUE=0.7374 RMSE=0.9683 TorType=3 + dihedral_coeff @dihedral:c3-os-n4-c3 fourier 1 0.62 3 180.0 # c132 SS AUE=0.8090 RMSE=0.9444 TorType=3 + dihedral_coeff @dihedral:c3-os-na-cc fourier 1 0.19 2 0.0 # c145 SS AUE=0.2720 RMSE=0.3305 TorType=3 + dihedral_coeff @dihedral:c3-os-n-c fourier 1 0.42 2 0.0 # c87 SS AUE=0.3019 RMSE=0.3567 TorType=3 + dihedral_coeff @dihedral:c3-os-nh-c2 fourier 1 1.15 1 0.0 # set3_13 SS AUE=0.9655 RMSE=1.1845 TorType=3 + dihedral_coeff @dihedral:c3-os-nh-ca fourier 1 0.5 1 0.0 # c157 SS AUE=0.8647 RMSE=1.0585 TorType=3 + dihedral_coeff @dihedral:c3-os-no-o fourier 1 2.515 2 180.0 # c168 SS AUE=0.3706 RMSE=0.4248 TorType=3 + dihedral_coeff @dihedral:c3-os-oh-ho fourier 1 1.01 2 0.0 # c178 SS AUE=0.2810 RMSE=0.3796 TorType=3 + dihedral_coeff @dihedral:c3-os-os-c3 fourier 1 0.38 1 0.0 # c187 SS AUE=0.4838 RMSE=0.6593 TorType=3 + dihedral_coeff @dihedral:c3-os-p2-c2 fourier 2 2.94 2 180.0 1.85 1 180.0 # c188 GA AUE=0.3661 RMSE=0.4565 TorType=3 + dihedral_coeff @dihedral:c3-p3-c2-c2 fourier 1 0.297 2 0.0 # c35 SS AUE=1.0902 RMSE=1.4763 TorType=3 + dihedral_coeff @dihedral:c3-p3-c2-c3 fourier 1 0.95 2 180.0 # set1_15 SS AUE=0.4182 RMSE=0.4905 TorType=3 + dihedral_coeff @dihedral:c3-p3-ca-ca fourier 1 0.177 2 180.0 # c72 SS AUE=0.2797 RMSE=0.3319 TorType=3 + dihedral_coeff @dihedral:c3-p3-n2-c2 fourier 1 5.0 2 180.0 # c105 SS AUE=0.8649 RMSE=1.0889 TorType=3 + dihedral_coeff @dihedral:c3-p3-n3-c3 fourier 1 2.85 2 0.0 # c120 SS AUE=0.8776 RMSE=1.2067 TorType=3 + dihedral_coeff @dihedral:c3-p3-n4-c3 fourier 1 0.067 3 0.0 # c134 SS AUE=0.1760 RMSE=0.2433 TorType=3 + dihedral_coeff @dihedral:c3-p3-na-cc fourier 1 1.025 2 0.0 # c147 SS AUE=0.2741 RMSE=0.3331 TorType=3 + dihedral_coeff @dihedral:c3-p3-n-c fourier 1 1.83 2 0.0 # c89 SS AUE=0.9690 RMSE=1.3708 TorType=3 + dihedral_coeff @dihedral:c3-p3-nh-c2 fourier 1 1.85 2 0.0 # set3_15 SS AUE=0.8611 RMSE=0.9832 TorType=3 + dihedral_coeff @dihedral:c3-p3-no-o fourier 1 1.4 2 180.0 # c170 SS AUE=0.5082 RMSE=0.5728 TorType=3 + dihedral_coeff @dihedral:c3-p3-oh-ho fourier 1 0.24 3 180.0 # c180 SS AUE=0.9983 RMSE=1.2838 TorType=3 + dihedral_coeff @dihedral:c3-p3-p2-c2 fourier 1 0.2 1 0.0 # c197 SS AUE=0.5014 RMSE=0.7016 TorType=3 + dihedral_coeff @dihedral:c3-p3-p3-c3 fourier 1 0.375 3 0.0 # c204 SS AUE=0.8032 RMSE=0.9405 TorType=3 + dihedral_coeff @dihedral:c3-p4-n3-c3 fourier 1 1.778 2 180.0 # c121 SS AUE=1.1246 RMSE=1.4091 TorType=3 + dihedral_coeff @dihedral:c3-p4-n4-hn fourier 1 0.005 3 0.0 # c135 SS AUE=0.2627 RMSE=0.3254 TorType=3 + dihedral_coeff @dihedral:c3-p4-na-cc fourier 2 1.0 3 0.0 0.64 2 180.0 # c148 GA AUE=0.9954 RMSE=1.1119 TorType=3 + dihedral_coeff @dihedral:c3-p4-nh-c2 fourier 1 0.9 1 0.0 # set3_16 SS AUE=1.0315 RMSE=1.1976 TorType=3 + dihedral_coeff @dihedral:c3-p4-nh-ca fourier 2 0.0 3 180.0 0.84 2 180.0 # c160 GA AUE=1.0676 RMSE=1.4622 TorType=3 + dihedral_coeff @dihedral:c3-p4-os-c3 fourier 1 0.6 2 180.0 # c190 SS AUE=0.5663 RMSE=0.6640 TorType=3 + dihedral_coeff @dihedral:c3-p4-p3-c3 fourier 1 1.4 1 0.0 # c205 SS AUE=0.7593 RMSE=0.9141 TorType=3 + dihedral_coeff @dihedral:c3-px-ca-ca fourier 1 0.432 2 180.0 # c73 SS AUE=0.4755 RMSE=0.6108 TorType=3 + dihedral_coeff @dihedral:c3-px-c-c3 fourier 2 0.0 2 0.0 0.58 1 180.0 # c16 GA AUE=1.0361 RMSE=1.3175 TorType=3 + dihedral_coeff @dihedral:c3-px-ce-c2 fourier 1 1.13 2 0.0 # c36 SS AUE=1.2444 RMSE=1.6024 TorType=3 + dihedral_coeff @dihedral:c3-px-ce-c3 fourier 1 0.81 2 180.0 # set1_16 SS AUE=0.9969 RMSE=1.2788 TorType=3 + dihedral_coeff @dihedral:c3-px-ne-c2 fourier 2 0.61 3 0.0 1.44 1 0.0 # c106 GA AUE=1.6606 RMSE=2.1207 TorType=3 + dihedral_coeff @dihedral:c3-px-pe-c2 fourier 1 1.565 2 0.0 # c198 SS AUE=1.0967 RMSE=1.2917 TorType=3 + dihedral_coeff @dihedral:c3-s4-c3-h1 fourier 1 0.117 3 0.0 # c59 SS AUE=0.2210 RMSE=0.2792 TorType=3 + dihedral_coeff @dihedral:c3-s4-n3-c3 fourier 1 3.1 2 0.0 # c125 SS AUE=1.3654 RMSE=1.8896 TorType=3 + dihedral_coeff @dihedral:c3-s4-n4-c3 fourier 1 0.2 3 0.0 # c139 SS AUE=0.7713 RMSE=0.9400 TorType=3 + dihedral_coeff @dihedral:c3-s4-na-cc fourier 1 0.55 2 0.0 # c152 SS AUE=0.5159 RMSE=0.7408 TorType=3 + dihedral_coeff @dihedral:c3-s4-nh-c2 fourier 3 0.235 2 180.0 0.5 3 0.0 1.302 1 0.0 # set3_20 GA AUE=1.5742 RMSE=1.9736 TorType=3 + dihedral_coeff @dihedral:c3-s4-no-o fourier 1 1.13 2 180.0 # c175 SS AUE=0.7753 RMSE=0.8760 TorType=3 + dihedral_coeff @dihedral:c3-s4-oh-ho fourier 1 0.0 1 180.0 # c185 SS AUE=1.7272 RMSE=2.1061 TorType=3 + dihedral_coeff @dihedral:c3-s4-os-c3 fourier 1 1.31 1 180.0 # c194 SS AUE=0.9618 RMSE=1.1506 TorType=3 + dihedral_coeff @dihedral:c3-s4-p3-c3 fourier 1 2.22 2 0.0 # c209 SS AUE=1.9189 RMSE=2.5861 TorType=3 + dihedral_coeff @dihedral:c3-s4-sh-hs fourier 2 0.0 3 0.0 0.56 2 180.0 # c224 GA AUE=1.1511 RMSE=1.3863 TorType=3 + dihedral_coeff @dihedral:c3-s4-ss-c3 fourier 1 0.05 3 0.0 # c227 SS AUE=0.7707 RMSE=0.9378 TorType=3 + dihedral_coeff @dihedral:c3-s6-c3-h1 fourier 1 0.089 3 0.0 # c60 SS AUE=0.0648 RMSE=0.0808 TorType=3 + dihedral_coeff @dihedral:c3-s6-n3-c3 fourier 1 3.61 2 0.0 # c126 SS AUE=1.8933 RMSE=2.6424 TorType=3 + dihedral_coeff @dihedral:c3-s6-n4-c3 fourier 1 1.47 1 0.0 # c140 SS AUE=0.2994 RMSE=0.3260 TorType=3 + dihedral_coeff @dihedral:c3-s6-na-cc fourier 1 3.938 2 180.0 # c153 SS AUE=0.8118 RMSE=1.0393 TorType=3 + dihedral_coeff @dihedral:c3-s6-n-c fourier 1 0.768 2 180.0 # c95 SS AUE=0.4645 RMSE=0.6488 TorType=3 + dihedral_coeff @dihedral:c3-s6-nh-c2 fourier 1 0.667 2 0.0 # set3_21 SS AUE=1.6191 RMSE=2.2150 TorType=3 + dihedral_coeff @dihedral:c3-s6-no-o fourier 1 0.348 2 0.0 # c176 SS AUE=0.2701 RMSE=0.3306 TorType=3 + dihedral_coeff @dihedral:c3-s6-oh-ho fourier 1 11.69 1 180.0 # c186 SS AUE=0.6401 RMSE=0.8081 TorType=3 + dihedral_coeff @dihedral:c3-s6-os-c3 fourier 1 0.533 2 180.0 # c195 SS AUE=0.9691 RMSE=1.1571 TorType=3 + dihedral_coeff @dihedral:c3-s6-p3-c3 fourier 1 0.183 3 0.0 # c210 SS AUE=0.5556 RMSE=0.6476 TorType=3 + dihedral_coeff @dihedral:c3-s6-sh-hs fourier 1 4.317 2 180.0 # c225 SS AUE=1.0170 RMSE=1.0970 TorType=3 + dihedral_coeff @dihedral:c3-s6-ss-c3 fourier 1 2.4 2 180.0 # c228 SS AUE=0.8201 RMSE=1.0146 TorType=3 + dihedral_coeff @dihedral:c3-ss-c2-c3 fourier 1 2.025 2 180.0 # set1_19 SS AUE=0.5269 RMSE=0.6098 TorType=3 + dihedral_coeff @dihedral:c3-ss-c3-c3 fourier 1 0.167 3 0.0 # p9 SS AUE=0.4614 RMSE=0.5750 TorType=3 + dihedral_coeff @dihedral:c3-ss-c3-h1 fourier 1 0.22 3 0.0 # c58 SS AUE=0.2551 RMSE=0.3303 TorType=3 + dihedral_coeff @dihedral:c3-ss-ca-ca fourier 1 0.75 2 180.0 # c76 SS AUE=0.2509 RMSE=0.3297 TorType=3 + dihedral_coeff @dihedral:c3-ss-n2-c2 fourier 2 1.35 2 180.0 1.38 1 180.0 # c109 GA AUE=0.6324 RMSE=0.7825 TorType=3 + dihedral_coeff @dihedral:c3-ss-n3-c3 fourier 1 2.68 2 0.0 # c124 SS AUE=1.0072 RMSE=1.2488 TorType=3 + dihedral_coeff @dihedral:c3-ss-n4-c3 fourier 1 0.39 3 0.0 # c138 SS AUE=0.3868 RMSE=0.4909 TorType=3 + dihedral_coeff @dihedral:c3-ss-n-c fourier 1 0.5 2 0.0 # c93 SS AUE=0.5560 RMSE=0.7560 TorType=3 + dihedral_coeff @dihedral:c3-ss-nh-c2 fourier 1 1.1 2 0.0 # set3_19 SS AUE=0.9372 RMSE=1.1240 TorType=3 + dihedral_coeff @dihedral:c3-ss-no-o fourier 1 2.295 2 180.0 # c174 SS AUE=0.3406 RMSE=0.3839 TorType=3 + dihedral_coeff @dihedral:c3-ss-oh-ho fourier 1 2.13 2 0.0 # c184 SS AUE=0.2806 RMSE=0.3277 TorType=3 + dihedral_coeff @dihedral:c3-ss-os-c3 fourier 1 1.74 2 0.0 # c193 SS AUE=0.5504 RMSE=0.6616 TorType=3 + dihedral_coeff @dihedral:c3-ss-p2-c2 fourier 1 2.97 2 180.0 # c201 SS AUE=0.8463 RMSE=1.2678 TorType=3 + dihedral_coeff @dihedral:c3-ss-p3-c3 fourier 1 3.75 2 0.0 # c208 SS AUE=0.5096 RMSE=0.5972 TorType=3 + dihedral_coeff @dihedral:c3-ss-p4-c3 fourier 1 0.57 2 180.0 # c214 SS AUE=0.7214 RMSE=0.9325 TorType=3 + dihedral_coeff @dihedral:c3-sx-ca-ca fourier 1 0.64 2 0.0 # c77 SS AUE=0.6566 RMSE=0.8245 TorType=3 + dihedral_coeff @dihedral:c3-sx-ce-c2 fourier 2 1.46 2 0.0 1.5 3 180.0 # c40 GA AUE=1.8189 RMSE=2.2140 TorType=3 + dihedral_coeff @dihedral:c3-sx-ce-c3 fourier 3 1.5 3 0.0 4.16 2 0.0 3.1 1 180.0 # set1_20 GA AUE=2.1436 RMSE=3.2053 TorType=3 + dihedral_coeff @dihedral:c3-sx-ne-c2 fourier 2 1.0 3 180.0 1.9 1 180.0 # c110 GA AUE=1.5150 RMSE=1.7663 TorType=3 + dihedral_coeff @dihedral:c3-sx-pe-c2 fourier 1 4.19 2 0.0 # c202 SS AUE=2.6033 RMSE=3.2866 TorType=3 + dihedral_coeff @dihedral:c3-sx-px-c3 fourier 1 2.67 1 0.0 # c215 SS AUE=0.8306 RMSE=1.0179 TorType=3 + dihedral_coeff @dihedral:c3-sx-sx-c3 fourier 1 2.92 1 0.0 # c229 SS AUE=2.7179 RMSE=3.6787 TorType=3 + dihedral_coeff @dihedral:c3-sx-sy-c3 fourier 1 4.94 2 180.0 # c230 SS AUE=1.7022 RMSE=1.9951 TorType=3 + dihedral_coeff @dihedral:c3-sy-ca-ca fourier 1 1.22 2 180.0 # c78 SS AUE=0.2941 RMSE=0.3313 TorType=3 + dihedral_coeff @dihedral:c3-sy-ce-c2 fourier 1 0.935 2 180.0 # c41 SS AUE=0.9708 RMSE=1.2822 TorType=3 + dihedral_coeff @dihedral:c3-sy-ce-c3 fourier 3 0.64 3 0.0 0.333 2 180.0 1.04 1 180.0 # set1_21 GA AUE=0.6383 RMSE=0.7388 TorType=3 + dihedral_coeff @dihedral:c3-sy-ne-c2 fourier 2 0.34 3 180.0 7.467 1 180.0 # c111 GA AUE=0.2248 RMSE=0.3231 TorType=3 + dihedral_coeff @dihedral:c3-sy-pe-c2 fourier 1 0.237 3 180.0 # c203 SS AUE=0.3743 RMSE=0.4294 TorType=3 + dihedral_coeff @dihedral:c3-sy-px-c3 fourier 1 0.062 3 0.0 # c216 SS AUE=0.6353 RMSE=0.7537 TorType=3 + dihedral_coeff @dihedral:c3-sy-sy-c3 fourier 1 0.378 2 0.0 # c231 SS AUE=1.1799 RMSE=1.3634 TorType=3 + dihedral_coeff @dihedral:ca-c3-c3-c fourier 1 0.1 3 0.0 # p22 SS AUE=0.8008 RMSE=1.0051 TorType=3 + dihedral_coeff @dihedral:ca-c3-c3-n fourier 1 0.21 3 0.0 # p16 SS AUE=0.6330 RMSE=0.8053 TorType=3 + dihedral_coeff @dihedral:ca-ca-c3-ca fourier 1 0.0 2 180.0 # t1 SS AUE=0.1988 RMSE=0.2606 TorType=3 + dihedral_coeff @dihedral:ca-ca-ce-c2 fourier 1 0.618 2 180.0 # c24 SS AUE=0.2364 RMSE=0.3330 TorType=3 + dihedral_coeff @dihedral:ca-ca-ce-c3 fourier 1 0.54 2 180.0 # set1_4 SS AUE=0.2602 RMSE=0.3333 TorType=3 + dihedral_coeff @dihedral:ca-ca-os-c fourier 1 0.65 2 180.0 # t35b SS AUE=0.2491 RMSE=0.3333 TorType=3 + dihedral_coeff @dihedral:ca-cf-ce-ca fourier 1 8.51 2 180.0 # add6b SS AUE=4.0000 RMSE=5.4296 TorType=3 + dihedral_coeff @dihedral:ca-c-os-c3 fourier 1 2.685 2 180.0 # t36b SS AUE=1.2217 RMSE=1.4489 TorType=3 + dihedral_coeff @dihedral:ca-cp-cp-ca fourier 1 0.795 2 180.0 # c61 SS AUE=0.2914 RMSE=0.3303 TorType=3 + dihedral_coeff @dihedral:ca-nh-c2-c2 fourier 1 1.92 1 180.0 # c30 SS AUE=0.8599 RMSE=1.1406 TorType=3 + dihedral_coeff @dihedral:ca-nh-n2-c2 fourier 3 1.37 3 180.0 2.0 2 0.0 0.0 1 180.0 # c100 GA AUE=2.0208 RMSE=2.4869 TorType=3 + dihedral_coeff @dihedral:ca-nh-n4-c3 fourier 1 0.1 3 0.0 # c129 SS AUE=1.1901 RMSE=1.4071 TorType=3 + dihedral_coeff @dihedral:ca-nh-na-cd fourier 1 0.7 2 0.0 # c142 SS AUE=0.5118 RMSE=0.8838 TorType=3 + dihedral_coeff @dihedral:ca-nh-n-c fourier 1 0.605 2 0.0 # c84 SS AUE=1.2184 RMSE=1.3197 TorType=3 + dihedral_coeff @dihedral:ca-nh-nh-c2 fourier 1 1.49 3 0.0 # set3_10 SS AUE=2.7548 RMSE=3.5233 TorType=3 + dihedral_coeff @dihedral:ca-nh-nh-ca fourier 1 4.59 1 0.0 # c154 SS AUE=3.6427 RMSE=5.6136 TorType=3 + dihedral_coeff @dihedral:ca-nh-no-o fourier 1 0.62 2 180.0 # c155 SS AUE=1.3263 RMSE=1.9039 TorType=3 + dihedral_coeff @dihedral:ca-nh-p3-c3 fourier 2 1.94 2 180.0 0.54 3 0.0 # c159 GA AUE=0.8724 RMSE=1.1678 TorType=3 + dihedral_coeff @dihedral:ca-nh-p5-os fourier 1 0.467 2 0.0 # c161 SS AUE=0.8323 RMSE=0.9798 TorType=3 + dihedral_coeff @dihedral:ca-nh-s4-c3 fourier 2 1.245 2 0.0 0.225 3 0.0 # c164 GA AUE=1.5450 RMSE=1.8592 TorType=3 + dihedral_coeff @dihedral:ca-nh-s6-c3 fourier 1 1.93 3 0.0 # c165 SS AUE=0.7711 RMSE=0.9257 TorType=3 + dihedral_coeff @dihedral:ca-nh-ss-c3 fourier 2 1.29 2 180.0 1.19 1 180.0 # c163 GA AUE=0.9564 RMSE=1.5597 TorType=3 + dihedral_coeff @dihedral:ca-nh-sy-ca fourier 2 0.1 2 180.0 0.99 3 0.0 # add6a SS AUE=0.6854 RMSE=0.9512 TorType=3 + dihedral_coeff @dihedral:ca-os-c-o fourier 1 1.275 2 180.0 # t35a SS AUE=1.2481 RMSE=1.5211 TorType=3 + dihedral_coeff @dihedral:c-c3-c3-n fourier 1 0.21 3 0.0 # p26 SS AUE=1.0437 RMSE=1.3000 TorType=3 + dihedral_coeff @dihedral:c-c3-n-c fourier 2 0.39 2 180.0 0.64 1 0.0 # p18 GA AUE=0.4030 RMSE=0.5768 TorType=3 + dihedral_coeff @dihedral:cc-na-c2-c2 fourier 1 0.728 2 180.0 # c29 SS AUE=0.2592 RMSE=0.3329 TorType=3 + dihedral_coeff @dihedral:cc-na-c2-c3 fourier 1 1.125 2 180.0 # set1_9 SS AUE=0.3784 RMSE=0.4839 TorType=3 + dihedral_coeff @dihedral:cc-na-ca-ca fourier 1 0.603 2 180.0 # c66 SS AUE=0.2705 RMSE=0.3328 TorType=3 + dihedral_coeff @dihedral:cc-na-na-cd fourier 1 0.4 2 0.0 # c141 SS AUE=0.5320 RMSE=0.6402 TorType=3 + dihedral_coeff @dihedral:cc-na-nh-c2 fourier 1 0.7 2 0.0 # set3_9 SS AUE=0.7727 RMSE=0.9375 TorType=3 + dihedral_coeff @dihedral:cc-n-c-c3 fourier 1 0.5 2 180.0 # set2_9 SS AUE=0.2224 RMSE=0.3240 TorType=3 + dihedral_coeff @dihedral:cd-cc-c3-c3 fourier 1 0.157 3 180.0 # p1 SS AUE=0.2727 RMSE=0.3320 TorType=3 + dihedral_coeff @dihedral:cd-na-c3-na fourier 1 0.023 2 0.0 # t16 SS AUE=0.2606 RMSE=0.3332 TorType=3 + dihedral_coeff @dihedral:c-n-c2-c3 fourier 1 1.51 1 180.0 # set1_5 SS AUE=0.6699 RMSE=0.8754 TorType=3 + dihedral_coeff @dihedral:c-n-c3-n fourier 1 2.08 2 0.0 # t17 SS AUE=0.8425 RMSE=1.0798 TorType=3 + dihedral_coeff @dihedral:c-n-ca-ca fourier 1 0.95 2 180.0 # c62 SS AUE=0.8788 RMSE=0.9694 TorType=3 + dihedral_coeff @dihedral:c-n-n-c fourier 2 3.0 2 180.0 2.49 1 0.0 # c79 GA AUE=1.1290 RMSE=1.3734 TorType=3 + dihedral_coeff @dihedral:c-n-nh-c2 fourier 1 0.6 2 0.0 # set3_5 SS AUE=0.7968 RMSE=0.8909 TorType=3 + dihedral_coeff @dihedral:c-os-c-c3 fourier 1 1.98 1 180.0 # set3_29 SS AUE=0.2568 RMSE=0.3303 TorType=3 + dihedral_coeff @dihedral:cz-nh-c3-c3 fourier 1 0.248 2 180.0 # p11 SS AUE=0.2819 RMSE=0.3532 TorType=3 + dihedral_coeff @dihedral:h1-c3-n2-c2 fourier 1 0.165 3 180.0 # c45 SS AUE=0.6984 RMSE=0.9045 TorType=3 + dihedral_coeff @dihedral:h1-c3-n3-c3 fourier 1 0.225 3 0.0 # c46 SS AUE=0.2936 RMSE=0.3481 TorType=3 + dihedral_coeff @dihedral:h1-c3-na-cc fourier 1 0.0 2 180.0 # c48 SS AUE=0.0685 RMSE=0.0813 TorType=3 + dihedral_coeff @dihedral:h1-c3-n-c fourier 1 0.0 2 180.0 # c44 SS AUE=0.1670 RMSE=0.1874 TorType=3 + dihedral_coeff @dihedral:h1-c3-nh-ca fourier 1 0.332 2 0.0 # c49 SS AUE=1.0901 RMSE=1.3252 TorType=3 + dihedral_coeff @dihedral:h1-c3-no-o fourier 1 0.0 2 180.0 # c50 SS AUE=0.0210 RMSE=0.0225 TorType=3 + dihedral_coeff @dihedral:h1-c3-os-p5 fourier 1 0.217 3 0.0 # c56 SS AUE=0.3987 RMSE=0.4985 TorType=3 + dihedral_coeff @dihedral:hc-c3-c2-c3 fourier 1 0.31 2 0.0 # set1_3 SS AUE=0.6796 RMSE=0.8466 TorType=3 + dihedral_coeff @dihedral:hc-c3-c3-i fourier 1 0.21 3 0.0 # m6 SS AUE=0.3234 RMSE=0.3857 TorType=3 + dihedral_coeff @dihedral:hc-c3-c3-n3 fourier 1 0.1 3 0.0 # m12 SS AUE=0.1396 RMSE=0.1646 TorType=3 + dihedral_coeff @dihedral:hc-c3-ca-ca fourier 1 0.0 2 180.0 # c43 SS AUE=0.0203 RMSE=0.0347 TorType=3 + dihedral_coeff @dihedral:hc-c3-p2-c2 fourier 1 0.933 2 180.0 # c53 SS AUE=0.3657 RMSE=0.4529 TorType=3 + dihedral_coeff @dihedral:hc-c3-p3-c3 fourier 1 0.145 3 0.0 # c54 SS AUE=0.2605 RMSE=0.3289 TorType=3 + dihedral_coeff @dihedral:hc-c3-p4-c3 fourier 1 0.05 3 0.0 # c55 SS AUE=0.1589 RMSE=0.2005 TorType=3 + dihedral_coeff @dihedral:hn-n3-c3-c3 fourier 1 0.217 3 0.0 # m20 SS AUE=0.7039 RMSE=0.8271 TorType=3 + dihedral_coeff @dihedral:hn-n4-c2-c2 fourier 1 0.082 3 180.0 # c28 SS AUE=0.6341 RMSE=0.7948 TorType=3 + dihedral_coeff @dihedral:hn-n4-c2-c3 fourier 1 0.087 3 0.0 # set1_8 SS AUE=0.2828 RMSE=0.3296 TorType=3 + dihedral_coeff @dihedral:hn-n4-c3-hx fourier 1 0.109 3 0.0 # c47 SS AUE=0.2716 RMSE=0.3296 TorType=3 + dihedral_coeff @dihedral:hn-n4-n2-c2 fourier 1 8.663 2 180.0 # c98 SS AUE=0.3876 RMSE=0.4783 TorType=3 + dihedral_coeff @dihedral:hn-n4-n3-c3 fourier 1 0.188 3 0.0 # c113 SS AUE=0.3464 RMSE=0.4155 TorType=3 + dihedral_coeff @dihedral:hn-n4-na-cd fourier 1 0.15 3 0.0 # c128 SS AUE=0.1276 RMSE=0.1509 TorType=3 + dihedral_coeff @dihedral:hn-n4-n-c fourier 1 1.445 2 0.0 # c82 SS AUE=0.4066 RMSE=0.5885 TorType=3 + dihedral_coeff @dihedral:hn-n4-nh-c2 fourier 1 0.213 3 0.0 # set3_8 SS AUE=0.2620 RMSE=0.3316 TorType=3 + dihedral_coeff @dihedral:hn-nh-na-cd fourier 1 0.802 2 0.0 # c114 SS AUE=0.2869 RMSE=0.3676 TorType=3 + dihedral_coeff @dihedral:ho-oh-c2-c2 fourier 1 1.12 2 180.0 # c32 SS AUE=0.2661 RMSE=0.3303 TorType=3 + dihedral_coeff @dihedral:ho-oh-c2-c3 fourier 1 1.51 1 180.0 # set1_12 SS AUE=1.5331 RMSE=1.7625 TorType=3 + dihedral_coeff @dihedral:ho-oh-c3-h1 fourier 1 0.113 3 0.0 # c51 SS AUE=0.2631 RMSE=0.3230 TorType=3 + dihedral_coeff @dihedral:ho-oh-ca-ca fourier 1 0.835 2 180.0 # c69 SS AUE=0.2718 RMSE=0.3256 TorType=3 + dihedral_coeff @dihedral:ho-oh-n2-c2 fourier 1 2.37 2 180.0 # c102 SS AUE=0.3163 RMSE=0.3944 TorType=3 + dihedral_coeff @dihedral:ho-oh-n3-c3 fourier 1 1.23 2 0.0 # c117 SS AUE=0.7804 RMSE=0.9479 TorType=3 + dihedral_coeff @dihedral:ho-oh-n4-c3 fourier 1 0.34 3 0.0 # c131 SS AUE=0.4375 RMSE=0.5350 TorType=3 + dihedral_coeff @dihedral:ho-oh-na-cc fourier 1 0.44 2 0.0 # c144 SS AUE=0.2865 RMSE=0.3255 TorType=3 + dihedral_coeff @dihedral:ho-oh-nh-c2 fourier 1 0.85 2 0.0 # set3_12 SS AUE=0.6311 RMSE=0.7217 TorType=3 + dihedral_coeff @dihedral:ho-oh-no-o fourier 1 1.36 2 180.0 # c167 SS AUE=0.2872 RMSE=0.3226 TorType=3 + dihedral_coeff @dihedral:ho-oh-oh-ho fourier 1 1.21 2 0.0 # c177 SS AUE=0.6716 RMSE=0.7402 TorType=3 + dihedral_coeff @dihedral:ho-oh-p2-c2 fourier 1 1.41 2 180.0 # c179 SS AUE=0.6083 RMSE=0.8611 TorType=3 + dihedral_coeff @dihedral:ho-oh-p4-c3 fourier 1 0.83 1 180.0 # c181 SS AUE=0.8966 RMSE=1.0772 TorType=3 + dihedral_coeff @dihedral:ho-oh-p5-o fourier 1 0.367 3 0.0 # c182 SS AUE=0.8891 RMSE=1.0397 TorType=3 + dihedral_coeff @dihedral:hs-sh-c2-c2 fourier 1 0.64 2 180.0 # c38 SS AUE=0.5356 RMSE=0.6146 TorType=3 + dihedral_coeff @dihedral:hs-sh-c2-c3 fourier 1 1.46 1 180.0 # set1_18 SS AUE=1.6292 RMSE=1.8635 TorType=3 + dihedral_coeff @dihedral:hs-sh-c3-h1 fourier 1 0.143 3 0.0 # c57 SS AUE=0.2676 RMSE=0.3251 TorType=3 + dihedral_coeff @dihedral:hs-sh-ca-ca fourier 1 0.105 2 180.0 # c75 SS AUE=0.2588 RMSE=0.3299 TorType=3 + dihedral_coeff @dihedral:hs-sh-n2-c2 fourier 1 1.91 2 180.0 # c108 SS AUE=0.5066 RMSE=0.9568 TorType=3 + dihedral_coeff @dihedral:hs-sh-n3-c3 fourier 1 3.34 2 0.0 # c123 SS AUE=1.0521 RMSE=1.3809 TorType=3 + dihedral_coeff @dihedral:hs-sh-n4-c3 fourier 1 0.5 3 0.0 # c137 SS AUE=1.0514 RMSE=1.3202 TorType=3 + dihedral_coeff @dihedral:hs-sh-na-cc fourier 1 1.255 2 0.0 # c150 SS AUE=0.2920 RMSE=0.3622 TorType=3 + dihedral_coeff @dihedral:hs-sh-nh-c2 fourier 1 0.795 2 0.0 # set3_18 SS AUE=1.0130 RMSE=1.2554 TorType=3 + dihedral_coeff @dihedral:hs-sh-no-o fourier 1 1.3 2 180.0 # c173 SS AUE=0.2229 RMSE=0.2551 TorType=3 + dihedral_coeff @dihedral:hs-sh-oh-ho fourier 1 2.01 2 0.0 # c183 SS AUE=0.2853 RMSE=0.3308 TorType=3 + dihedral_coeff @dihedral:hs-sh-os-c3 fourier 1 1.85 2 0.0 # c192 SS AUE=0.4441 RMSE=0.5536 TorType=3 + dihedral_coeff @dihedral:hs-sh-p2-c2 fourier 1 0.89 2 180.0 # c200 SS AUE=0.2562 RMSE=0.3521 TorType=3 + dihedral_coeff @dihedral:hs-sh-p3-c3 fourier 1 3.6 2 0.0 # c207 SS AUE=0.5012 RMSE=0.6062 TorType=3 + dihedral_coeff @dihedral:hs-sh-p4-c3 fourier 1 0.585 1 180.0 # c213 SS AUE=1.2130 RMSE=1.4705 TorType=3 + dihedral_coeff @dihedral:hs-sh-p5-os fourier 2 2.89 2 0.0 1.29 1 0.0 # c218 GA AUE=0.8635 RMSE=1.2959 TorType=3 + dihedral_coeff @dihedral:hs-sh-sh-hs fourier 1 2.64 2 0.0 # c222 SS AUE=0.2962 RMSE=0.3759 TorType=3 + dihedral_coeff @dihedral:n2-c2-c3-c2 fourier 1 0.558 2 180.0 # t9 SS AUE=0.7685 RMSE=0.9760 TorType=3 + dihedral_coeff @dihedral:n3-c3-c3-c3 fourier 1 0.21 3 0.0 # p8 SS AUE=0.4096 RMSE=0.5005 TorType=3 + dihedral_coeff @dihedral:n3-c3-c3-ca fourier 1 0.1 3 0.0 # m16 SS AUE=0.8325 RMSE=1.0411 TorType=3 + dihedral_coeff @dihedral:n3-c3-n3-hn fourier 1 1.75 2 0.0 # t13 SS AUE=0.6939 RMSE=0.8306 TorType=3 + dihedral_coeff @dihedral:n4-c3-c3-c3 fourier 1 0.21 3 0.0 # p12 SS AUE=0.5399 RMSE=0.6216 TorType=3 + dihedral_coeff @dihedral:n4-c3-n4-hn fourier 1 0.1 3 0.0 # t26 SS AUE=0.0245 RMSE=0.0373 TorType=3 + dihedral_coeff @dihedral:n-c3-c3-c3 fourier 1 0.1 3 0.0 # p23 SS AUE=0.2641 RMSE=0.3317 TorType=3 + dihedral_coeff @dihedral:nh-c3-c3-c3 fourier 1 0.21 3 0.0 # p13 SS AUE=0.8361 RMSE=0.9491 TorType=3 + dihedral_coeff @dihedral:o-c-c3-c3 fourier 1 0.27 2 180.0 # p14 SS AUE=0.2361 RMSE=0.3321 TorType=3 + dihedral_coeff @dihedral:oh-c3-c3-c3 fourier 1 0.21 3 0.0 # p7 SS AUE=0.6517 RMSE=0.7713 TorType=3 + dihedral_coeff @dihedral:oh-c3-c3-c fourier 1 0.21 3 0.0 # p25 SS AUE=0.3653 RMSE=0.6406 TorType=3 + dihedral_coeff @dihedral:oh-c3-c3-n fourier 1 0.101 3 0.0 # p24 SS AUE=0.9998 RMSE=1.2475 TorType=3 + dihedral_coeff @dihedral:oh-c3-oh-ho fourier 1 1.57 2 0.0 # t11 SS AUE=0.6180 RMSE=0.8544 TorType=3 + dihedral_coeff @dihedral:o-no-c2-c2 fourier 1 0.398 2 180.0 # c31 SS AUE=0.2143 RMSE=0.3292 TorType=3 + dihedral_coeff @dihedral:o-no-c2-c3 fourier 1 0.66 2 180.0 # set1_11 SS AUE=0.2915 RMSE=0.3323 TorType=3 + dihedral_coeff @dihedral:o-no-c3-no fourier 1 5.02 2 180.0 # t15 SS AUE=0.7609 RMSE=0.9238 TorType=3 + dihedral_coeff @dihedral:o-no-ca-ca fourier 1 0.7 2 180.0 # c68 SS AUE=0.2638 RMSE=0.3293 TorType=3 + dihedral_coeff @dihedral:o-no-cd-cc fourier 1 1.075 2 180.0 # add6e SS AUE=0.2138 RMSE=0.3290 TorType=3 + dihedral_coeff @dihedral:o-no-n2-c2 fourier 1 1.03 2 180.0 # c101 SS AUE=0.3306 RMSE=0.4189 TorType=3 + dihedral_coeff @dihedral:o-no-n3-c3 fourier 1 2.17 2 180.0 # c116 SS AUE=2.5004 RMSE=3.2115 TorType=3 + dihedral_coeff @dihedral:o-no-n4-c3 fourier 1 1.25 2 180.0 # c130 SS AUE=0.1901 RMSE=0.4144 TorType=3 + dihedral_coeff @dihedral:o-no-na-cc fourier 1 1.09 2 180.0 # c143 SS AUE=0.5033 RMSE=0.6912 TorType=3 + dihedral_coeff @dihedral:o-no-nh-c2 fourier 1 0.0 2 180.0 # set3_11 SS AUE=2.0620 RMSE=2.8356 TorType=3 + dihedral_coeff @dihedral:o-no-no-o fourier 2 0.15 4 180.0 1.45 2 180.0 # c166 GA AUE=0.3903 RMSE=0.4419 TorType=3 + dihedral_coeff @dihedral:o-no-p2-c2 fourier 1 0.99 2 180.0 # c169 SS AUE=0.2765 RMSE=0.3321 TorType=3 + dihedral_coeff @dihedral:o-no-p4-c3 fourier 1 0.502 2 180.0 # c171 SS AUE=0.3449 RMSE=0.3960 TorType=3 + dihedral_coeff @dihedral:o-py-ne-c2 fourier 2 0.9 3 180.0 2.46 1 0.0 # c107 GA AUE=0.4990 RMSE=0.6000 TorType=3 + dihedral_coeff @dihedral:o-s4-c3-s4 fourier 1 1.34 1 180.0 # t25 SS AUE=1.1411 RMSE=1.4982 TorType=3 + dihedral_coeff @dihedral:o-s6-c3-s6 fourier 1 0.092 3 0.0 # t24 SS AUE=0.4257 RMSE=0.4949 TorType=3 + dihedral_coeff @dihedral:os-c-c3-c fourier 2 2.0 2 180.0 1.85 1 180.0 # t42 GA AUE=0.4321 RMSE=0.5299 TorType=3 + dihedral_coeff @dihedral:os-p3-os-c3 fourier 1 2.04 2 0.0 # c189 SS AUE=1.0926 RMSE=1.3514 TorType=3 + dihedral_coeff @dihedral:os-p5-n3-c3 fourier 1 5.0 2 180.0 # c122 SS AUE=2.8241 RMSE=3.6042 TorType=3 + dihedral_coeff @dihedral:os-p5-n4-c3 fourier 1 0.143 3 0.0 # c136 SS AUE=0.4630 RMSE=0.6433 TorType=3 + dihedral_coeff @dihedral:os-p5-na-cc fourier 1 2.18 2 180.0 # c149 SS AUE=0.6556 RMSE=0.9113 TorType=3 + dihedral_coeff @dihedral:os-p5-nh-c2 fourier 1 0.5 2 0.0 # set3_17 SS AUE=0.9578 RMSE=1.1771 TorType=3 + dihedral_coeff @dihedral:os-p5-no-o fourier 2 2.733 2 0.0 0.317 3 0.0 # c172 GA AUE=0.6484 RMSE=0.8206 TorType=3 + dihedral_coeff @dihedral:os-p5-p3-c3 fourier 1 2.005 2 180.0 # c206 SS AUE=1.1482 RMSE=1.4324 TorType=3 + dihedral_coeff @dihedral:os-p5-ss-c3 fourier 1 4.467 2 180.0 # c219 SS AUE=0.9050 RMSE=1.1227 TorType=3 + dihedral_coeff @dihedral:os-py-ca-ca fourier 1 1.8 2 180.0 # c74 SS AUE=0.8528 RMSE=1.0796 TorType=3 + dihedral_coeff @dihedral:os-py-ce-c2 fourier 1 1.767 2 180.0 # c37 SS AUE=0.8275 RMSE=1.0644 TorType=3 + dihedral_coeff @dihedral:os-py-ce-c3 fourier 1 4.2 2 180.0 # set1_17 SS AUE=0.9222 RMSE=1.1571 TorType=3 + dihedral_coeff @dihedral:os-py-pe-c2 fourier 1 2.567 1 0.0 # c199 SS AUE=0.6931 RMSE=0.8807 TorType=3 + dihedral_coeff @dihedral:os-py-py-c3 fourier 1 0.386 2 0.0 # c212 SS AUE=0.6618 RMSE=0.8385 TorType=3 + dihedral_coeff @dihedral:os-py-py-os fourier 1 0.387 2 0.0 # c217 SS AUE=0.6636 RMSE=1.0913 TorType=3 + dihedral_coeff @dihedral:os-py-sx-c3 fourier 1 0.348 3 0.0 # c220 SS AUE=0.6436 RMSE=0.8137 TorType=3 + dihedral_coeff @dihedral:os-py-sy-c3 fourier 2 2.86 2 0.0 0.38 1 0.0 # c221 GA AUE=1.1694 RMSE=1.4143 TorType=3 + dihedral_coeff @dihedral:p3-c3-p3-hp fourier 1 0.215 3 0.0 # t19 SS AUE=1.0811 RMSE=1.2418 TorType=3 + dihedral_coeff @dihedral:s-c-c3-c fourier 1 0.332 2 180.0 # t10 SS AUE=0.9021 RMSE=1.2368 TorType=3 + dihedral_coeff @dihedral:sh-c3-c3-n fourier 1 0.21 3 0.0 # p4 SS AUE=1.1296 RMSE=1.3941 TorType=3 + dihedral_coeff @dihedral:sh-c3-sh-hs fourier 1 0.083 3 0.0 # t22 SS AUE=0.4554 RMSE=0.5406 TorType=3 + dihedral_coeff @dihedral:ss-c3-ss-c3 fourier 1 0.497 3 0.0 # t23 SS AUE=0.5714 RMSE=0.8553 TorType=3 + dihedral_coeff @dihedral:c3-c3-ca-ca fourier 1 0.245 2 180.0 # m15,m17 SS AUE=0.2499 RMSE=0.3414 TorType=3 + dihedral_coeff @dihedral:c3-c3-c-o fourier 3 0.03 2 180.0 0.55 3 180.0 0.74 1 0.0 # sialic1,t37,t41 GA AUE=0.7374 RMSE=0.9897 TorType=3 + dihedral_coeff @dihedral:c3-c3-os-c3 fourier 3 0.91 3 0.0 1.0 2 0.0 0.0 1 0.0 # lactose1,ccoc GA AUE=1.5236 RMSE=2.4206 TorType=3 + dihedral_coeff @dihedral:ca-ca-c-o fourier 1 0.5225 2 180.0 # phcooh,t36a SS AUE=0.2702 RMSE=0.3317 TorType=3 + dihedral_coeff @dihedral:o-c-c3-c fourier 2 1.36 1 0.0 0.18 3 180.0 # t6,t7,t8 GA AUE=0.3790 RMSE=0.4991 TorType=3 + dihedral_coeff @dihedral:os-c3-c-o fourier 3 0.63 2 180.0 1.0 3 180.0 0.08 1 0.0 # iduronic2,t39,t40 GA AUE=1.0545 RMSE=1.4852 TorType=3 + dihedral_coeff @dihedral:c2-ce-cs-c3 fourier 1 2.18 2 0.0 # set2_2 SS AUE=0.8412 RMSE=1.0280 TorType=3 + dihedral_coeff @dihedral:c2-ce-c-c3 fourier 1 2.97 2 0.0 # c2 SS AUE=0.5377 RMSE=0.6518 TorType=3 + dihedral_coeff @dihedral:c2-ce-ce-c2 fourier 1 0.5 2 180.0 # c232,t3 SS AUE=0.7154 RMSE=0.9564 TorType=3 + dihedral_coeff @dihedral:c2-n-c-c3 fourier 1 0.77 1 180.0 # set3_1 SS AUE=1.1124 RMSE=1.4578 TorType=3 + dihedral_coeff @dihedral:c2-n-cs-c3 fourier 1 2.833 2 180.0 # set3_27 SS AUE=0.3805 RMSE=0.4661 TorType=3 + dihedral_coeff @dihedral:c2-ne-c-c3 fourier 1 2.08 1 180.0 # c6 SS AUE=0.4876 RMSE=0.8222 TorType=3 + dihedral_coeff @dihedral:c2-ne-cs-c3 fourier 1 4.67 1 180.0 # set2_6 SS AUE=1.2531 RMSE=1.5945 TorType=3 + dihedral_coeff @dihedral:c2-pe-c-c3 fourier 1 1.75 1 180.0 # c14 SS AUE=1.0447 RMSE=1.2490 TorType=3 + dihedral_coeff @dihedral:c2-pe-cs-c3 fourier 1 2.96 1 180.0 # set2_14 SS AUE=0.8598 RMSE=1.0604 TorType=3 + dihedral_coeff @dihedral:c3-cs-cs-c3 fourier 1 0.455 2 180.0 # set3_23 SS AUE=0.7278 RMSE=1.0389 TorType=3 + dihedral_coeff @dihedral:c3-c-c-c3 fourier 1 0.512 2 180.0 # c1 SS AUE=0.2443 RMSE=0.3313 TorType=3 + dihedral_coeff @dihedral:c3-c-cs-c3 fourier 1 0.8 2 180.0 # set2_1 SS AUE=1.0068 RMSE=1.3922 TorType=3 + dihedral_coeff @dihedral:c3-c-n-ca fourier 2 0.75 2 180.0 0.5 3 0.0 # c10 GA AUE=1.0418 RMSE=1.1578 TorType=3 + dihedral_coeff @dihedral:c3-cs-n-ca fourier 1 3.913 2 180.0 # set2_10 SS AUE=1.3234 RMSE=1.7703 TorType=3 + dihedral_coeff @dihedral:c3-n7-c3-c3 fourier 2 0.02 3 180.0 0.05 2 0.0 # m13 GA AUE=0.3404 RMSE=0.4405 TorType=3 + dihedral_coeff @dihedral:c3-n3-c3-c3 fourier 2 0.58 3 0.0 0.28 2 180.0 # m14 GA AUE=0.4298 RMSE=0.5205 TorType=3 + dihedral_coeff @dihedral:c3-n-cs-c3 fourier 2 2.0 2 180.0 2.31 1 0.0 # set2_7 GA AUE=0.7571 RMSE=0.9582 TorType=3 + dihedral_coeff @dihedral:c3-nu-ca-ca fourier 1 0.55 2 180.0 # c67 SS AUE=0.5825 RMSE=0.8345 TorType=3 + dihedral_coeff @dihedral:c3-nh-ca-ca fourier 1 0.733 2 180.0 # c64 SS AUE=0.6264 RMSE=0.7797 TorType=3 + dihedral_coeff @dihedral:c3-os-cs-c3 fourier 3 0.12 1 0.0 3.47 2 180.0 0.73 3 0.0 # set2_13 GA AUE=0.2180 RMSE=0.2948 TorType=3 + dihedral_coeff @dihedral:c3-p3-c-c3 fourier 1 1.538 2 180.0 # c15 SS AUE=0.3737 RMSE=0.4391 TorType=3 + dihedral_coeff @dihedral:c3-p3-cs-c3 fourier 1 2.05 2 180.0 # set2_15 SS AUE=0.4669 RMSE=0.6407 TorType=3 + dihedral_coeff @dihedral:c3-ss-c-c3 fourier 1 2.1 2 180.0 # c19 SS AUE=0.9147 RMSE=1.1012 TorType=3 + dihedral_coeff @dihedral:c3-ss-cs-c3 fourier 1 3.585 2 180.0 # set2_19 SS AUE=0.3546 RMSE=0.4561 TorType=3 + dihedral_coeff @dihedral:c3-sx-c-c3 fourier 2 0.95 2 0.0 1.46 1 180.0 # c20 GA AUE=1.4077 RMSE=1.8160 TorType=3 + dihedral_coeff @dihedral:c3-sx-cs-c3 fourier 2 0.0 2 180.0 0.82 1 180.0 # set2_20 GA AUE=1.3014 RMSE=1.5331 TorType=3 + dihedral_coeff @dihedral:c3-sy-cs-c3 fourier 1 0.167 2 0.0 # set2_21 SS AUE=0.4320 RMSE=0.5527 TorType=3 + dihedral_coeff @dihedral:c3-sy-c-c3 fourier 1 0.833 2 0.0 # c21 SS AUE=1.1437 RMSE=1.4496 TorType=3 + dihedral_coeff @dihedral:ca-ca-c-c3 fourier 1 0.552 2 180.0 # c4 SS AUE=0.2254 RMSE=0.3313 TorType=3 + dihedral_coeff @dihedral:ca-ca-cs-c3 fourier 1 0.63 2 180.0 # set2_4 SS AUE=0.2690 RMSE=0.3277 TorType=3 + dihedral_coeff @dihedral:c-c3-c3-c3 fourier 1 0.1 3 0.0 # p15,p21 SS AUE=0.6594 RMSE=0.8092 TorType=3 + dihedral_coeff @dihedral:c-n-cs-c3 fourier 1 0.57 2 0.0 # set2_5 SS AUE=1.0844 RMSE=1.5574 TorType=3 + dihedral_coeff @dihedral:c-n-c-c3 fourier 2 0.0 2 180.0 1.72 1 180.0 # set3_28 GA AUE=1.6503 RMSE=2.2241 TorType=3 + dihedral_coeff @dihedral:hc-c3-c-c3 fourier 1 0.0 2 0.0 # c3 SS AUE=0.0845 RMSE=0.1001 TorType=3 + dihedral_coeff @dihedral:hc-c3-cs-c3 fourier 1 0.665 2 0.0 # set2_3 SS AUE=0.5619 RMSE=0.7242 TorType=3 + dihedral_coeff @dihedral:hn-n4-c-c3 fourier 2 1.025 2 180.0 0.365 4 180.0 # c8 GA AUE=0.2852 RMSE=0.3192 TorType=3 + dihedral_coeff @dihedral:hn-n4-cs-c3 fourier 2 0.95 2 180.0 0.745 4 0.0 # set2_8 GA AUE=0.7027 RMSE=0.8556 TorType=3 + dihedral_coeff @dihedral:ho-oh-c-c3 fourier 1 1.78 2 180.0 # c12 SS AUE=0.3293 RMSE=0.3814 TorType=3 + dihedral_coeff @dihedral:ho-oh-cs-c3 fourier 1 2.92 2 180.0 # set2_12 SS AUE=0.3286 RMSE=0.4081 TorType=3 + dihedral_coeff @dihedral:hs-sh-cs-c3 fourier 2 2.69 2 180.0 1.39 1 180.0 # set2_18 GA AUE=0.2516 RMSE=0.2978 TorType=3 + dihedral_coeff @dihedral:o-n-c-c3 fourier 1 0.37 2 180.0 # c11 SS AUE=0.3392 RMSE=0.4173 TorType=3 + dihedral_coeff @dihedral:o-n-cs-c3 fourier 1 0.52 2 0.0 # set2_11 SS AUE=0.2859 RMSE=0.3263 TorType=3 + dihedral_coeff @dihedral:o-p5-c3-p5 fourier 2 2.59 2 180.0 3.17 1 0.0 # t20 GA AUE=1.4330 RMSE=1.6847 TorType=3 + dihedral_coeff @dihedral:os-py-c-c3 fourier 1 2.37 2 0.0 # c17 SS AUE=1.1966 RMSE=1.4736 TorType=3 + dihedral_coeff @dihedral:os-py-cs-c3 fourier 1 0.5 2 0.0 # set2_17 SS AUE=0.8458 RMSE=1.0943 TorType=3 + } # (end of dihedral_coeffs) + + write_once("Data Dihedrals By Type") { + @dihedral:X-c-c-X @atom:* @atom:c @atom:c @atom:* + @dihedral:X-c-c1-X @atom:* @atom:c @atom:c1 @atom:* + @dihedral:X-c-cg-X @atom:* @atom:c @atom:cg @atom:* + @dihedral:X-c-ch-X @atom:* @atom:c @atom:ch @atom:* + @dihedral:X-c-c2-X @atom:* @atom:c @atom:c2 @atom:* + @dihedral:X-c-cu-X @atom:* @atom:c @atom:cu @atom:* + @dihedral:X-c-cv-X @atom:* @atom:c @atom:cv @atom:* + @dihedral:X-c-ce-X @atom:* @atom:c @atom:ce @atom:* + @dihedral:X-c-cf-X @atom:* @atom:c @atom:cf @atom:* + @dihedral:X-c-c3-X @atom:* @atom:c @atom:c3 @atom:* + @dihedral:X-c-cx-X @atom:* @atom:c @atom:cx @atom:* + @dihedral:X-c-cy-X @atom:* @atom:c @atom:cy @atom:* + @dihedral:X-c-ca-X @atom:* @atom:c @atom:ca @atom:* + @dihedral:X-c-cc-X @atom:* @atom:c @atom:cc @atom:* + @dihedral:X-c-cd-X @atom:* @atom:c @atom:cd @atom:* + @dihedral:X-c-n-X @atom:* @atom:c @atom:n @atom:* + @dihedral:X-c-n2-X @atom:* @atom:c @atom:n2 @atom:* + @dihedral:X-c-nc-X @atom:* @atom:c @atom:nc @atom:* + @dihedral:X-c-nd-X @atom:* @atom:c @atom:nd @atom:* + @dihedral:X-c-ne-X @atom:* @atom:c @atom:ne @atom:* + @dihedral:X-c-nf-X @atom:* @atom:c @atom:nf @atom:* + @dihedral:X-c-na-X @atom:* @atom:c @atom:na @atom:* + @dihedral:X-c-na-X @atom:* @atom:c @atom:na @atom:* + @dihedral:X-c-no-X @atom:* @atom:c @atom:no @atom:* + @dihedral:X-c-oh-X @atom:* @atom:c @atom:oh @atom:* + @dihedral:X-c-os-X @atom:* @atom:c @atom:os @atom:* + @dihedral:X-c-p2-X @atom:* @atom:c @atom:p2 @atom:* + @dihedral:X-c-pc-X @atom:* @atom:c @atom:pc @atom:* + @dihedral:X-c-pd-X @atom:* @atom:c @atom:pd @atom:* + @dihedral:X-c-pe-X @atom:* @atom:c @atom:pe @atom:* + @dihedral:X-c-pf-X @atom:* @atom:c @atom:pf @atom:* + @dihedral:X-c-p3-X @atom:* @atom:c @atom:p3 @atom:* + @dihedral:X-c-p4-X @atom:* @atom:c @atom:p4 @atom:* + @dihedral:X-c-px-X @atom:* @atom:c @atom:px @atom:* + @dihedral:X-c-p5-X @atom:* @atom:c @atom:p5 @atom:* + @dihedral:X-c-py-X @atom:* @atom:c @atom:py @atom:* + @dihedral:X-c-sh-X @atom:* @atom:c @atom:sh @atom:* + @dihedral:X-c-ss-X @atom:* @atom:c @atom:ss @atom:* + @dihedral:X-c-s4-X @atom:* @atom:c @atom:s4 @atom:* + @dihedral:X-c-sx-X @atom:* @atom:c @atom:sx @atom:* + @dihedral:X-c-s6-X @atom:* @atom:c @atom:s6 @atom:* + @dihedral:X-c-sy-X @atom:* @atom:c @atom:sy @atom:* + @dihedral:X-c1-c1-X @atom:* @atom:c1 @atom:c1 @atom:* + @dihedral:X-c1-cg-X @atom:* @atom:c1 @atom:cg @atom:* + @dihedral:X-c1-ch-X @atom:* @atom:c1 @atom:ch @atom:* + @dihedral:X-cg-cg-X @atom:* @atom:cg @atom:cg @atom:* + @dihedral:X-ch-ch-X @atom:* @atom:ch @atom:ch @atom:* + @dihedral:X-cg-ch-X @atom:* @atom:cg @atom:ch @atom:* + @dihedral:X-c1-c2-X @atom:* @atom:c1 @atom:c2 @atom:* + @dihedral:X-c1-c3-X @atom:* @atom:c1 @atom:c3 @atom:* + @dihedral:X-c1-ca-X @atom:* @atom:c1 @atom:ca @atom:* + @dihedral:X-c1-cc-X @atom:* @atom:c1 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@atom:c3 + @dihedral:hn-n3-c3-c3 @atom:hn @atom:n3 @atom:c3 @atom:c3 + @dihedral:hn-n4-c2-c2 @atom:hn @atom:n4 @atom:c2 @atom:c2 + @dihedral:hn-n4-c2-c3 @atom:hn @atom:n4 @atom:c2 @atom:c3 + @dihedral:hn-n4-c3-hx @atom:hn @atom:n4 @atom:c3 @atom:hx + @dihedral:hn-n4-n2-c2 @atom:hn @atom:n4 @atom:n2 @atom:c2 + @dihedral:hn-n4-n3-c3 @atom:hn @atom:n4 @atom:n3 @atom:c3 + @dihedral:hn-n4-na-cd @atom:hn @atom:n4 @atom:na @atom:cd + @dihedral:hn-n4-n-c @atom:hn @atom:n4 @atom:n @atom:c + @dihedral:hn-n4-nh-c2 @atom:hn @atom:n4 @atom:nh @atom:c2 + @dihedral:hn-nh-na-cd @atom:hn @atom:nh @atom:na @atom:cd + @dihedral:ho-oh-c2-c2 @atom:ho @atom:oh @atom:c2 @atom:c2 + @dihedral:ho-oh-c2-c3 @atom:ho @atom:oh @atom:c2 @atom:c3 + @dihedral:ho-oh-c3-h1 @atom:ho @atom:oh @atom:c3 @atom:h1 + @dihedral:ho-oh-ca-ca @atom:ho @atom:oh @atom:ca @atom:ca + @dihedral:ho-oh-n2-c2 @atom:ho @atom:oh @atom:n2 @atom:c2 + @dihedral:ho-oh-n3-c3 @atom:ho @atom:oh @atom:n3 @atom:c3 + @dihedral:ho-oh-n4-c3 @atom:ho @atom:oh @atom:n4 @atom:c3 + @dihedral:ho-oh-na-cc @atom:ho @atom:oh @atom:na @atom:cc + @dihedral:ho-oh-nh-c2 @atom:ho @atom:oh @atom:nh @atom:c2 + @dihedral:ho-oh-no-o @atom:ho @atom:oh @atom:no @atom:o + @dihedral:ho-oh-oh-ho @atom:ho @atom:oh @atom:oh @atom:ho + @dihedral:ho-oh-p2-c2 @atom:ho @atom:oh @atom:p2 @atom:c2 + @dihedral:ho-oh-p4-c3 @atom:ho @atom:oh @atom:p4 @atom:c3 + @dihedral:ho-oh-p5-o @atom:ho @atom:oh @atom:p5 @atom:o + @dihedral:hs-sh-c2-c2 @atom:hs @atom:sh @atom:c2 @atom:c2 + @dihedral:hs-sh-c2-c3 @atom:hs @atom:sh @atom:c2 @atom:c3 + @dihedral:hs-sh-c3-h1 @atom:hs @atom:sh @atom:c3 @atom:h1 + @dihedral:hs-sh-ca-ca @atom:hs @atom:sh @atom:ca @atom:ca + @dihedral:hs-sh-n2-c2 @atom:hs @atom:sh @atom:n2 @atom:c2 + @dihedral:hs-sh-n3-c3 @atom:hs @atom:sh @atom:n3 @atom:c3 + @dihedral:hs-sh-n4-c3 @atom:hs @atom:sh @atom:n4 @atom:c3 + @dihedral:hs-sh-na-cc @atom:hs @atom:sh @atom:na @atom:cc + @dihedral:hs-sh-nh-c2 @atom:hs @atom:sh @atom:nh @atom:c2 + @dihedral:hs-sh-no-o @atom:hs @atom:sh @atom:no @atom:o + @dihedral:hs-sh-oh-ho @atom:hs @atom:sh @atom:oh @atom:ho + @dihedral:hs-sh-os-c3 @atom:hs @atom:sh @atom:os @atom:c3 + @dihedral:hs-sh-p2-c2 @atom:hs @atom:sh @atom:p2 @atom:c2 + @dihedral:hs-sh-p3-c3 @atom:hs @atom:sh @atom:p3 @atom:c3 + @dihedral:hs-sh-p4-c3 @atom:hs @atom:sh @atom:p4 @atom:c3 + @dihedral:hs-sh-p5-os @atom:hs @atom:sh @atom:p5 @atom:os + @dihedral:hs-sh-p5-os @atom:hs @atom:sh @atom:p5 @atom:os + @dihedral:hs-sh-sh-hs @atom:hs @atom:sh @atom:sh @atom:hs + @dihedral:n2-c2-c3-c2 @atom:n2 @atom:c2 @atom:c3 @atom:c2 + @dihedral:n3-c3-c3-c3 @atom:n3 @atom:c3 @atom:c3 @atom:c3 + @dihedral:n3-c3-c3-ca @atom:n3 @atom:c3 @atom:c3 @atom:ca + @dihedral:n3-c3-n3-hn @atom:n3 @atom:c3 @atom:n3 @atom:hn + @dihedral:n4-c3-c3-c3 @atom:n4 @atom:c3 @atom:c3 @atom:c3 + @dihedral:n4-c3-n4-hn @atom:n4 @atom:c3 @atom:n4 @atom:hn + @dihedral:n-c3-c3-c3 @atom:n @atom:c3 @atom:c3 @atom:c3 + @dihedral:nh-c3-c3-c3 @atom:nh @atom:c3 @atom:c3 @atom:c3 + @dihedral:o-c-c3-c3 @atom:o @atom:c @atom:c3 @atom:c3 + @dihedral:oh-c3-c3-c3 @atom:oh @atom:c3 @atom:c3 @atom:c3 + @dihedral:oh-c3-c3-c @atom:oh @atom:c3 @atom:c3 @atom:c + @dihedral:oh-c3-c3-n @atom:oh @atom:c3 @atom:c3 @atom:n + @dihedral:oh-c3-oh-ho @atom:oh @atom:c3 @atom:oh @atom:ho + @dihedral:o-no-c2-c2 @atom:o @atom:no @atom:c2 @atom:c2 + @dihedral:o-no-c2-c3 @atom:o @atom:no @atom:c2 @atom:c3 + @dihedral:o-no-c3-no @atom:o @atom:no @atom:c3 @atom:no + @dihedral:o-no-ca-ca @atom:o @atom:no @atom:ca @atom:ca + @dihedral:o-no-cd-cc @atom:o @atom:no @atom:cd @atom:cc + @dihedral:o-no-n2-c2 @atom:o @atom:no @atom:n2 @atom:c2 + @dihedral:o-no-n3-c3 @atom:o @atom:no @atom:n3 @atom:c3 + @dihedral:o-no-n4-c3 @atom:o @atom:no @atom:n4 @atom:c3 + @dihedral:o-no-na-cc @atom:o @atom:no @atom:na @atom:cc + @dihedral:o-no-nh-c2 @atom:o @atom:no @atom:nh @atom:c2 + @dihedral:o-no-no-o @atom:o @atom:no @atom:no @atom:o + @dihedral:o-no-no-o @atom:o @atom:no @atom:no @atom:o + @dihedral:o-no-p2-c2 @atom:o @atom:no @atom:p2 @atom:c2 + @dihedral:o-no-p4-c3 @atom:o @atom:no @atom:p4 @atom:c3 + @dihedral:o-py-ne-c2 @atom:o @atom:py @atom:ne @atom:c2 + @dihedral:o-py-ne-c2 @atom:o @atom:py @atom:ne @atom:c2 + @dihedral:o-s4-c3-s4 @atom:o @atom:s4 @atom:c3 @atom:s4 + @dihedral:o-s6-c3-s6 @atom:o @atom:s6 @atom:c3 @atom:s6 + @dihedral:os-c-c3-c @atom:os @atom:c @atom:c3 @atom:c + @dihedral:os-c-c3-c @atom:os @atom:c @atom:c3 @atom:c + @dihedral:os-p3-os-c3 @atom:os @atom:p3 @atom:os @atom:c3 + @dihedral:os-p5-n3-c3 @atom:os @atom:p5 @atom:n3 @atom:c3 + @dihedral:os-p5-n4-c3 @atom:os @atom:p5 @atom:n4 @atom:c3 + @dihedral:os-p5-na-cc @atom:os @atom:p5 @atom:na @atom:cc + @dihedral:os-p5-nh-c2 @atom:os @atom:p5 @atom:nh @atom:c2 + @dihedral:os-p5-no-o @atom:os @atom:p5 @atom:no @atom:o + @dihedral:os-p5-no-o @atom:os @atom:p5 @atom:no @atom:o + @dihedral:os-p5-p3-c3 @atom:os @atom:p5 @atom:p3 @atom:c3 + @dihedral:os-p5-ss-c3 @atom:os @atom:p5 @atom:ss @atom:c3 + @dihedral:os-py-ca-ca @atom:os @atom:py @atom:ca @atom:ca + @dihedral:os-py-ce-c2 @atom:os @atom:py @atom:ce @atom:c2 + @dihedral:os-py-ce-c3 @atom:os @atom:py @atom:ce @atom:c3 + @dihedral:os-py-pe-c2 @atom:os @atom:py @atom:pe @atom:c2 + @dihedral:os-py-py-c3 @atom:os @atom:py @atom:py @atom:c3 + @dihedral:os-py-py-os @atom:os @atom:py @atom:py @atom:os + @dihedral:os-py-sx-c3 @atom:os @atom:py @atom:sx @atom:c3 + @dihedral:os-py-sy-c3 @atom:os @atom:py @atom:sy @atom:c3 + @dihedral:os-py-sy-c3 @atom:os @atom:py @atom:sy @atom:c3 + @dihedral:p3-c3-p3-hp @atom:p3 @atom:c3 @atom:p3 @atom:hp + @dihedral:s-c-c3-c @atom:s @atom:c @atom:c3 @atom:c + @dihedral:sh-c3-c3-n @atom:sh @atom:c3 @atom:c3 @atom:n + @dihedral:sh-c3-sh-hs @atom:sh @atom:c3 @atom:sh @atom:hs + @dihedral:ss-c3-ss-c3 @atom:ss @atom:c3 @atom:ss @atom:c3 + @dihedral:c3-c3-ca-ca @atom:c3 @atom:c3 @atom:ca @atom:ca + @dihedral:c3-c3-c-o @atom:c3 @atom:c3 @atom:c @atom:o + @dihedral:c3-c3-c-o @atom:c3 @atom:c3 @atom:c @atom:o + @dihedral:c3-c3-c-o @atom:c3 @atom:c3 @atom:c @atom:o + @dihedral:c3-c3-os-c3 @atom:c3 @atom:c3 @atom:os @atom:c3 + @dihedral:c3-c3-os-c3 @atom:c3 @atom:c3 @atom:os @atom:c3 + @dihedral:c3-c3-os-c3 @atom:c3 @atom:c3 @atom:os @atom:c3 + @dihedral:ca-ca-c-o @atom:ca @atom:ca @atom:c @atom:o + @dihedral:o-c-c3-c @atom:o @atom:c @atom:c3 @atom:c + @dihedral:o-c-c3-c @atom:o @atom:c @atom:c3 @atom:c + @dihedral:os-c3-c-o @atom:os @atom:c3 @atom:c @atom:o + @dihedral:os-c3-c-o @atom:os @atom:c3 @atom:c @atom:o + @dihedral:os-c3-c-o @atom:os @atom:c3 @atom:c @atom:o + @dihedral:c2-ce-cs-c3 @atom:c2 @atom:ce @atom:cs @atom:c3 + @dihedral:c2-ce-c-c3 @atom:c2 @atom:ce @atom:c @atom:c3 + @dihedral:c2-ce-ce-c2 @atom:c2 @atom:ce @atom:ce @atom:c2 + @dihedral:c2-n-c-c3 @atom:c2 @atom:n @atom:c @atom:c3 + @dihedral:c2-n-cs-c3 @atom:c2 @atom:n @atom:cs @atom:c3 + @dihedral:c2-ne-c-c3 @atom:c2 @atom:ne @atom:c @atom:c3 + @dihedral:c2-ne-cs-c3 @atom:c2 @atom:ne @atom:cs @atom:c3 + @dihedral:c2-pe-c-c3 @atom:c2 @atom:pe @atom:c @atom:c3 + @dihedral:c2-pe-cs-c3 @atom:c2 @atom:pe @atom:cs @atom:c3 + @dihedral:c3-cs-cs-c3 @atom:c3 @atom:cs @atom:cs @atom:c3 + @dihedral:c3-c-c-c3 @atom:c3 @atom:c @atom:c @atom:c3 + @dihedral:c3-c-cs-c3 @atom:c3 @atom:c @atom:cs @atom:c3 + @dihedral:c3-c-n-ca @atom:c3 @atom:c @atom:n @atom:ca + @dihedral:c3-c-n-ca @atom:c3 @atom:c @atom:n @atom:ca + @dihedral:c3-cs-n-ca @atom:c3 @atom:cs @atom:n @atom:ca + @dihedral:c3-n7-c3-c3 @atom:c3 @atom:n7 @atom:c3 @atom:c3 + @dihedral:c3-n7-c3-c3 @atom:c3 @atom:n7 @atom:c3 @atom:c3 + @dihedral:c3-n3-c3-c3 @atom:c3 @atom:n3 @atom:c3 @atom:c3 + @dihedral:c3-n3-c3-c3 @atom:c3 @atom:n3 @atom:c3 @atom:c3 + @dihedral:c3-n-cs-c3 @atom:c3 @atom:n @atom:cs @atom:c3 + @dihedral:c3-n-cs-c3 @atom:c3 @atom:n @atom:cs @atom:c3 + @dihedral:c3-nu-ca-ca @atom:c3 @atom:nu @atom:ca @atom:ca + @dihedral:c3-nh-ca-ca @atom:c3 @atom:nh @atom:ca @atom:ca + @dihedral:c3-os-cs-c3 @atom:c3 @atom:os @atom:cs @atom:c3 + @dihedral:c3-os-cs-c3 @atom:c3 @atom:os @atom:cs @atom:c3 + @dihedral:c3-os-cs-c3 @atom:c3 @atom:os @atom:cs @atom:c3 + @dihedral:c3-p3-c-c3 @atom:c3 @atom:p3 @atom:c @atom:c3 + @dihedral:c3-p3-cs-c3 @atom:c3 @atom:p3 @atom:cs @atom:c3 + @dihedral:c3-ss-c-c3 @atom:c3 @atom:ss @atom:c @atom:c3 + @dihedral:c3-ss-cs-c3 @atom:c3 @atom:ss @atom:cs @atom:c3 + @dihedral:c3-sx-c-c3 @atom:c3 @atom:sx @atom:c @atom:c3 + @dihedral:c3-sx-c-c3 @atom:c3 @atom:sx @atom:c @atom:c3 + @dihedral:c3-sx-cs-c3 @atom:c3 @atom:sx @atom:cs @atom:c3 + @dihedral:c3-sx-cs-c3 @atom:c3 @atom:sx @atom:cs @atom:c3 + @dihedral:c3-sy-cs-c3 @atom:c3 @atom:sy @atom:cs @atom:c3 + @dihedral:c3-sy-c-c3 @atom:c3 @atom:sy @atom:c @atom:c3 + @dihedral:ca-ca-c-c3 @atom:ca @atom:ca @atom:c @atom:c3 + @dihedral:ca-ca-cs-c3 @atom:ca @atom:ca @atom:cs @atom:c3 + @dihedral:c-c3-c3-c3 @atom:c @atom:c3 @atom:c3 @atom:c3 + @dihedral:c-n-cs-c3 @atom:c @atom:n @atom:cs @atom:c3 + @dihedral:c-n-c-c3 @atom:c @atom:n @atom:c @atom:c3 + @dihedral:c-n-c-c3 @atom:c @atom:n @atom:c @atom:c3 + @dihedral:hc-c3-c-c3 @atom:hc @atom:c3 @atom:c @atom:c3 + @dihedral:hc-c3-cs-c3 @atom:hc @atom:c3 @atom:cs @atom:c3 + @dihedral:hn-n4-c-c3 @atom:hn @atom:n4 @atom:c @atom:c3 + @dihedral:hn-n4-c-c3 @atom:hn @atom:n4 @atom:c @atom:c3 + @dihedral:hn-n4-cs-c3 @atom:hn @atom:n4 @atom:cs @atom:c3 + @dihedral:hn-n4-cs-c3 @atom:hn @atom:n4 @atom:cs @atom:c3 + @dihedral:ho-oh-c-c3 @atom:ho @atom:oh @atom:c @atom:c3 + @dihedral:ho-oh-cs-c3 @atom:ho @atom:oh @atom:cs @atom:c3 + @dihedral:hs-sh-cs-c3 @atom:hs @atom:sh @atom:cs @atom:c3 + @dihedral:hs-sh-cs-c3 @atom:hs @atom:sh @atom:cs @atom:c3 + @dihedral:o-n-c-c3 @atom:o @atom:n @atom:c @atom:c3 + @dihedral:o-n-cs-c3 @atom:o @atom:n @atom:cs @atom:c3 + @dihedral:o-p5-c3-p5 @atom:o @atom:p5 @atom:c3 @atom:p5 + @dihedral:o-p5-c3-p5 @atom:o @atom:p5 @atom:c3 @atom:p5 + @dihedral:os-py-c-c3 @atom:os @atom:py @atom:c @atom:c3 + @dihedral:os-py-cs-c3 @atom:os @atom:py @atom:cs @atom:c3 + } # (end of Dihedrals By Type) + + write_once("In Settings") { + improper_coeff @improper:X-o-c-o cvff 1.1 -1 2 # JCC,7,(1986),230 + improper_coeff @improper:X-X-c-o cvff 10.5 -1 2 # JCC,7,(1986),230 + improper_coeff @improper:X-X-ca-ha cvff 1.1 -1 2 # bsd.on C6H6 nmodes + improper_coeff @improper:X-X-n-hn cvff 1.1 -1 2 # JCC,7,(1986),230 + improper_coeff @improper:X-X-n2-hn cvff 1.1 -1 2 # JCC,7,(1986),230 + improper_coeff @improper:X-X-na-hn cvff 1.1 -1 2 # JCC,7,(1986),230 + improper_coeff @improper:X-c3-n-c3 cvff 1.1 -1 2 # JCC,7,(1986),230 + improper_coeff @improper:X-n2-ca-n2 cvff 10.5 -1 2 # JCC,7,(1986),230 + improper_coeff @improper:c-c2-c2-c3 cvff 1.1 -1 2 # dac guess, 9/94 + improper_coeff @improper:c-ca-ca-c3 cvff 1.1 -1 2 # dac guess, 9/94 + improper_coeff @improper:c-c3-n-hn cvff 1.1 -1 2 # Junmei et al.1999 + improper_coeff @improper:c-c3-n-o cvff 1.1 -1 2 # Junmei et al.1999 + improper_coeff @improper:c2-c2-na-c3 cvff 1.1 -1 2 + improper_coeff @improper:c2-c-c2-c3 cvff 1.1 -1 2 + improper_coeff @improper:c2-c3-c2-hc cvff 1.1 -1 2 # Junmei et al.1999 + improper_coeff @improper:c2-c3-ca-hc cvff 1.1 -1 2 # Junmei et al.1999 + improper_coeff @improper:c2-hc-c-o cvff 1.1 -1 2 # Junmei et al.1999 + improper_coeff @improper:c3-o-c-oh cvff 1.1 -1 2 + improper_coeff @improper:c3-c2-c2-n2 cvff 1.1 -1 2 + improper_coeff @improper:c3-c2-c2-na cvff 1.1 -1 2 + improper_coeff @improper:c3-ca-ca-n2 cvff 1.1 -1 2 + improper_coeff @improper:c3-ca-ca-na cvff 1.1 -1 2 + improper_coeff @improper:ca-ca-ca-c2 cvff 1.1 -1 2 + improper_coeff @improper:ca-ca-ca-c3 cvff 1.1 -1 2 + improper_coeff @improper:ca-ca-ca-f cvff 1.1 -1 2 # Junmei et al.1999 + improper_coeff @improper:ca-ca-ca-cl cvff 1.1 -1 2 # Junmei et al.1999 + improper_coeff @improper:ca-ca-ca-br cvff 1.1 -1 2 # Junmei et al.1999 + improper_coeff @improper:ca-ca-ca-i cvff 1.1 -1 2 # Junmei et al.1999 + improper_coeff @improper:ca-ca-c-oh cvff 1.1 -1 2 # (not used in tyr!) + improper_coeff @improper:ca-ca-na-c3 cvff 1.1 -1 2 + improper_coeff @improper:ca-c-ca-c3 cvff 1.1 -1 2 + improper_coeff @improper:ca-hc-c-o cvff 1.1 -1 2 # Junmei et al.1999 + improper_coeff @improper:ca-n2-ca-n2 cvff 1.1 -1 2 # dac, 10/94 + improper_coeff @improper:hc-o-c-oh cvff 1.1 -1 2 # Junmei et al.1999 + improper_coeff @improper:hc-o-c-os cvff 1.1 -1 2 + improper_coeff @improper:n2-c2-ca-n2 cvff 1.1 -1 2 # dac guess, 9/94 + improper_coeff @improper:n2-ca-ca-n2 cvff 1.1 -1 2 # dac guess, 9/94 + improper_coeff @improper:na-n2-ca-n2 cvff 1.1 -1 2 # dac, 10/94 + } # (end of improper_coeffs) + + write_once("Data Impropers By Type (gaff_imp.py)") { + @improper:X-o-c-o @atom:* @atom:o @atom:c @atom:o + @improper:X-X-c-o @atom:* @atom:* @atom:c @atom:o + @improper:X-X-ca-ha @atom:* @atom:* @atom:ca @atom:ha + @improper:X-X-n-hn @atom:* @atom:* @atom:n @atom:hn + @improper:X-X-n2-hn @atom:* @atom:* @atom:n2 @atom:hn + @improper:X-X-na-hn @atom:* @atom:* @atom:na @atom:hn + @improper:X-c3-n-c3 @atom:* @atom:c3 @atom:n @atom:c3 + @improper:X-n2-ca-n2 @atom:* @atom:n2 @atom:ca @atom:n2 + @improper:c-c2-c2-c3 @atom:c @atom:c2 @atom:c2 @atom:c3 + @improper:c-ca-ca-c3 @atom:c @atom:ca @atom:ca @atom:c3 + @improper:c-c3-n-hn @atom:c @atom:c3 @atom:n @atom:hn + @improper:c-c3-n-o @atom:c @atom:c3 @atom:n @atom:o + @improper:c2-c2-na-c3 @atom:c2 @atom:c2 @atom:na @atom:c3 + @improper:c2-c-c2-c3 @atom:c2 @atom:c @atom:c2 @atom:c3 + @improper:c2-c3-c2-hc @atom:c2 @atom:c3 @atom:c2 @atom:hc + @improper:c2-c3-ca-hc @atom:c2 @atom:c3 @atom:ca @atom:hc + @improper:c2-hc-c-o @atom:c2 @atom:hc @atom:c @atom:o + @improper:c3-o-c-oh @atom:c3 @atom:o @atom:c @atom:oh + @improper:c3-c2-c2-n2 @atom:c3 @atom:c2 @atom:c2 @atom:n2 + @improper:c3-c2-c2-na @atom:c3 @atom:c2 @atom:c2 @atom:na + @improper:c3-ca-ca-n2 @atom:c3 @atom:ca @atom:ca @atom:n2 + @improper:c3-ca-ca-na @atom:c3 @atom:ca @atom:ca @atom:na + @improper:ca-ca-ca-c2 @atom:ca @atom:ca @atom:ca @atom:c2 + @improper:ca-ca-ca-c3 @atom:ca @atom:ca @atom:ca @atom:c3 + @improper:ca-ca-ca-f @atom:ca @atom:ca @atom:ca @atom:f + @improper:ca-ca-ca-cl @atom:ca @atom:ca @atom:ca @atom:cl + @improper:ca-ca-ca-br @atom:ca @atom:ca @atom:ca @atom:br + @improper:ca-ca-ca-i @atom:ca @atom:ca @atom:ca @atom:i + @improper:ca-ca-c-oh @atom:ca @atom:ca @atom:c @atom:oh + @improper:ca-ca-na-c3 @atom:ca @atom:ca @atom:na @atom:c3 + @improper:ca-c-ca-c3 @atom:ca @atom:c @atom:ca @atom:c3 + @improper:ca-hc-c-o @atom:ca @atom:hc @atom:c @atom:o + @improper:ca-n2-ca-n2 @atom:ca @atom:n2 @atom:ca @atom:n2 + @improper:hc-o-c-oh @atom:hc @atom:o @atom:c @atom:oh + @improper:hc-o-c-os @atom:hc @atom:o @atom:c @atom:os + @improper:n2-c2-ca-n2 @atom:n2 @atom:c2 @atom:ca @atom:n2 + @improper:n2-ca-ca-n2 @atom:n2 @atom:ca @atom:ca @atom:n2 + @improper:na-n2-ca-n2 @atom:na @atom:n2 @atom:ca @atom:n2 + } # (end of Impropers By Type) + + + write_once("In Init") { + # Default styles and settings for AMBER based force-fields: + units real + atom_style full + bond_style hybrid harmonic + angle_style hybrid harmonic + dihedral_style hybrid fourier + improper_style hybrid cvff + pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0 + kspace_style pppm 0.0001 + + # NOTE: If you do not want to use long-range coulombic forces, + # comment out the two lines above and uncomment this line: + # pair_style hybrid lj/charmm/coul/charmm 9.0 10.0 + + pair_modify mix arithmetic + special_bonds amber + } + +} + + diff --git a/tools/moltemplate/moltemplate/force_fields/loplsaa.lt b/tools/moltemplate/moltemplate/force_fields/loplsaa.lt index 0c9614632c..017411a75f 100644 --- a/tools/moltemplate/moltemplate/force_fields/loplsaa.lt +++ b/tools/moltemplate/moltemplate/force_fields/loplsaa.lt @@ -1,17 +1,17 @@ -########################################################################### -## Extra OPLSAA parameters and atom types for long hydrocarbon chains ## -## SOURCE: Sui, Pluhackova, Böckmann, J.Chem.Theory.Comp (2012), 8, 1459 ## -## CREDIT: Sebastian Echeverri (file format conversion) ## -########################################################################### +############################################################################ +## Extra OPLSAA parameters and atom types for long hydrocarbon chains ## +## SOURCES: Sui, Pluhackova, Böckmann, J.Chem.Theory.Comp (2012), 8(4), 1459 +## Pluhackova,...,Böckmann, J.Phys.Chem.B (2015), 119(49), 15287 ## +## CREDIT: Sebastian Echeverri (file format conversion) ## +############################################################################ # This file was generated using: -# tinkerparm2lt.py -name LOPLSAA -file loplsaa_ext.prm -dihedral-style opls -# (and then edited manually to make sure the -# bond, angle, and improper interactions for these atoms -# remain unchanged) +# tinkerparm2lt.py -name OPLSAA -file loplsaa_ext.prm -dihedral-style opls -zeropad 3 +# (...and then EDITED manually to make sure the default bond, angle, +# and improper interactions for these atoms remain unchanged) -import "oplsaa.lt" # <-- Load the ordinary OPLS parameters - # We will extend and override them below +import "oplsaa.lt" # <-- Load the ordinary OPLS parameters first + # We will augment and override them below @@ -22,12 +22,20 @@ OPLSAA { write_once("In Charges") { set type @atom:80L charge -0.222 # "Alkane CH3- (LOPLS CT_CH3)" set type @atom:81L charge -0.148 # "Alkane -CH2- (LOPLS CT_CH2)" + set type @atom:81LL charge 0.19 # "Alkane -CH2- (LOPLS ALT)" set type @atom:85LCH3 charge 0.074 # "Alkane H-C CH3 (LOPLS HC_CH3)" set type @atom:85LCH2 charge 0.074 # "Alkane H-C CH2 (LOPLS HC_CH2)" set type @atom:87L charge -0.16 # "Alkene RH-C= (LOPLS CM_CH)" set type @atom:89L charge 0.16 # "Alkene H-C= (LOPLS HC_CH)" set type @atom:86L charge 0.0 # "Alkene R2-C= (LOPLS)" set type @atom:88L charge -0.23 # "Alkene H2-C= (LOPLS)" + set type @atom:96L charge -0.683 # "Alcohol -OH (LOPLS)" + set type @atom:97L charge 0.418 # "Alcohol -OH (LOPLS)" + set type @atom:111L charge -0.7 # "Diol -OH (LOPLS)" + set type @atom:112L charge 0.435 # "Diol -OH (LOPLS)" + set type @atom:113L charge -0.73 # "Triol -OH (LOPLS)" + set type @atom:114L charge 0.465 # "Triol -OH (LOPLS)" + set type @atom:118L charge 0.06 # "Diol & Triol H-COH (LOPLS)" set type @atom:169L charge 0.005 # "Chloroalkene Cl-CH= (LOPLS)" set type @atom:266L charge -0.07 # "Uracil & Thymine C5 (LOPLS)" set type @atom:267L charge 0.08 # "Uracil & Thymine C6 (LOPLS)" @@ -37,9 +45,14 @@ OPLSAA { set type @atom:325L charge 0.1 # "CytosineH+ C6 (LOPLS)" set type @atom:340L charge 0.18 # "Trifluorothymine CF3- (LOPLS)" set type @atom:342L charge 0.12 # "Chloroalkene Cl2-C= (LOPLS)" + set type @atom:406L charge 0.75 # "Ester -COOR (LOPLS)" + set type @atom:407L charge -0.55 # "Ester C=O (LOPLS)" + set type @atom:408L charge -0.45 # "Ester CO-O-R (LOPLS)" set type @atom:458L charge -0.03 # "Vinyl Ether =CH-OR (LOPLS)" set type @atom:459L charge 0.085 # "Vinyl Ether =CR-OR (LOPLS)" set type @atom:649L charge -0.344 # "Cl..CH3..Cl- Sn2 TS (LOPLS)" + set type @atom:718L charge 0.06 # "Propylene Carbonate CH2 (LOPLS)" + set type @atom:718LL charge 0.03 # "Propylene Carbonate CH2 (LOPLS ALT)" set type @atom:900L charge -0.25 # "Allene/Ketene H2C=C=X (LOPLS)" set type @atom:901L charge -0.1 # "Allene/Ketene HRC=C=X (LOPLS)" set type @atom:902L charge 0.05 # "Allene/Ketene R2C=C=X (LOPLS)" @@ -49,12 +62,20 @@ OPLSAA { write_once("Data Masses") { @atom:80L 12.011 @atom:81L 12.011 + @atom:81LL 12.011 @atom:85LCH3 1.008 @atom:85LCH2 1.008 @atom:87L 12.011 @atom:89L 1.008 @atom:86L 12.011 @atom:88L 12.011 + @atom:96L 15.999 + @atom:97L 1.008 + @atom:111L 15.999 + @atom:112L 1.008 + @atom:113L 15.999 + @atom:114L 1.008 + @atom:118L 1.008 @atom:169L 12.011 @atom:266L 12.011 @atom:267L 12.011 @@ -64,66 +85,113 @@ OPLSAA { @atom:325L 12.011 @atom:340L 12.011 @atom:342L 12.011 + @atom:406L 12.011 + @atom:407L 15.999 + @atom:408L 15.999 @atom:458L 12.011 @atom:459L 12.011 @atom:649L 12.011 + @atom:718L 1.008 + @atom:718LL 1.008 @atom:900L 12.011 @atom:901L 12.011 @atom:902L 12.011 } #(end of atom masses) - # ------- force-field-IDs for bonded interaction lookup ------- - # (First append the "force-field-ID" to the atom type name. - # Later use these expanded names for force-field lookup.) - replace{ @atom:80L @atom:80L_b13_a13_d13L_i13 } - replace{ @atom:81L @atom:81L_b13_a13_d13L_i13 } - replace{ @atom:85LCH3 @atom:85LCH3_b46_a46_d46_i46 } - replace{ @atom:85LCH2 @atom:85LCH2_b46_a46_d46_i46 } - replace{ @atom:87L @atom:87L_b47_a47_d47L_i47 } - replace{ @atom:89L @atom:89L_b46_a46_d46_i46 } - replace{ @atom:86L @atom:86L_b47_a47_d47L_i47 } - replace{ @atom:88L @atom:88L_b47_a47_d47L_i47 } - replace{ @atom:169L @atom:169L_b47_a47_d47L_i47 } - replace{ @atom:266L @atom:266L_b47_a47_d47L_i47 } - replace{ @atom:267L @atom:267L_b47_a47_d47L_i47 } - replace{ @atom:280L @atom:280L_b47_a47_d47L_i47 } - replace{ @atom:281L @atom:281L_b47_a47_d47L_i47 } - replace{ @atom:324L @atom:324L_b47_a47_d47L_i47 } - replace{ @atom:325L @atom:325L_b47_a47_d47L_i47 } - replace{ @atom:340L @atom:340L_b47_a47_d47L_i47 } - replace{ @atom:342L @atom:342L_b47_a47_d47L_i47 } - replace{ @atom:458L @atom:458L_b47_a47_d47L_i47 } - replace{ @atom:459L @atom:459L_b47_a47_d47L_i47 } - replace{ @atom:649L @atom:649L_b47_a47_d47L_i47 } - replace{ @atom:900L @atom:900L_b47_a47_d47L_i47 } - replace{ @atom:901L @atom:901L_b47_a47_d47L_i47 } - replace{ @atom:902L @atom:902L_b47_a47_d47L_i47 } - #(end of force-field-IDs) + + # ---------- EQUIVALENCE CATEGORIES for bonded interaction lookup ---------- + # Each type of atom has a separate ID used for looking up bond parameters + # and a separate ID for looking up 3-body angle interaction parameters + # and a separate ID for looking up 4-body dihedral interaction parameters + # and a separate ID for looking up 4-body improper interaction parameters + # The complete @atom type name includes ALL of these ID numbers. There's + # no need to force the end-user to type the complete name of each atom. + # The "replace" command used below informs moltemplate that the short + # @atom names we have been using abovee are equivalent to the complete + # @atom names used below: + + replace{ @atom:80L @atom:80L_b013_a013_d013L_i013 } + replace{ @atom:81L @atom:81L_b013_a013_d013L_i013 } + replace{ @atom:81LL @atom:81LL_b013_a013_d013LL_i013 } + replace{ @atom:85LCH3 @atom:85LCH3_b046_a046_d046_i046 } + replace{ @atom:85LCH2 @atom:85LCH2_b046_a046_d046_i046 } + replace{ @atom:87L @atom:87L_b047_a047_d047L_i047 } + replace{ @atom:89L @atom:89L_b046_a046_d046_i046 } + replace{ @atom:86L @atom:86L_b047_a047_d047L_i047 } + replace{ @atom:88L @atom:88L_b047_a047_d047L_i047 } + replace{ @atom:96L @atom:96L_b005_a005_d005L_i005 } + replace{ @atom:97L @atom:97L_b007_a007_d007L_i007 } + replace{ @atom:111L @atom:111L_b005_a005_d005L_i005 } + replace{ @atom:112L @atom:112L_b007_a007_d007L_i007 } + replace{ @atom:113L @atom:113L_b005_a005_d005L_i005 } + replace{ @atom:114L @atom:114L_b007_a007_d007L_i007 } + replace{ @atom:118L @atom:118L_b046_a046_d046L_i046 } + replace{ @atom:169L @atom:169L_b047_a047_d047L_i047 } + replace{ @atom:266L @atom:266L_b047_a047_d047L_i047 } + replace{ @atom:267L @atom:267L_b047_a047_d047L_i047 } + replace{ @atom:280L @atom:280L_b047_a047_d047L_i047 } + replace{ @atom:281L @atom:281L_b047_a047_d047L_i047 } + replace{ @atom:324L @atom:324L_b047_a047_d047L_i047 } + replace{ @atom:325L @atom:325L_b047_a047_d047L_i047 } + replace{ @atom:340L @atom:340L_b047_a047_d047L_i047 } + replace{ @atom:342L @atom:342L_b047_a047_d047L_i047 } + replace{ @atom:406L @atom:406L_b003_a003_d003L_i003 } + replace{ @atom:407L @atom:407L_b004_a004_d004L_i004 } + replace{ @atom:408L @atom:408L_b020_a020_d020L_i020 } + replace{ @atom:458L @atom:458L_b047_a047_d047L_i047 } + replace{ @atom:459L @atom:459L_b047_a047_d047L_i047 } + replace{ @atom:649L @atom:649L_b047_a047_d047L_i047 } + replace{ @atom:718L @atom:718L_b046_a046_d046L_i046 } + replace{ @atom:718LL @atom:718LL_b046_a046_d046L_i046 } + replace{ @atom:900L @atom:900L_b047_a047_d047L_i047 } + replace{ @atom:901L @atom:901L_b047_a047_d047L_i047 } + replace{ @atom:902L @atom:902L_b047_a047_d047L_i047 } + + + + + # --------------- Non-Bonded interactions: --------------------- + # http://lammps.sandia.gov/doc/pair_lj.html + # Syntax: + # pair_coeff AtomType1 AtomType2 parameters... write_once("In Settings") { - pair_coeff @atom:80L_b13_a13_d13L_i13 @atom:80L_b13_a13_d13L_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:81L_b13_a13_d13L_i13 @atom:81L_b13_a13_d13L_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:85LCH3_b46_a46_d46_i46 @atom:85LCH3_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5 - pair_coeff @atom:85LCH2_b46_a46_d46_i46 @atom:85LCH2_b46_a46_d46_i46 lj/cut/coul/long 0.026290630975 2.5 - pair_coeff @atom:87L_b47_a47_d47L_i47 @atom:87L_b47_a47_d47L_i47 lj/cut/coul/long 0.076 3.55 - pair_coeff @atom:89L_b46_a46_d46_i46 @atom:89L_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:86L_b47_a47_d47L_i47 @atom:86L_b47_a47_d47L_i47 lj/cut/coul/long 0.076 3.55 - pair_coeff @atom:88L_b47_a47_d47L_i47 @atom:88L_b47_a47_d47L_i47 lj/cut/coul/long 0.076 3.55 - pair_coeff @atom:169L_b47_a47_d47L_i47 @atom:169L_b47_a47_d47L_i47 lj/cut/coul/long 0.076 3.55 - pair_coeff @atom:266L_b47_a47_d47L_i47 @atom:266L_b47_a47_d47L_i47 lj/cut/coul/long 0.08 3.5 - pair_coeff @atom:267L_b47_a47_d47L_i47 @atom:267L_b47_a47_d47L_i47 lj/cut/coul/long 0.08 3.5 - pair_coeff @atom:280L_b47_a47_d47L_i47 @atom:280L_b47_a47_d47L_i47 lj/cut/coul/long 0.08 3.5 - pair_coeff @atom:281L_b47_a47_d47L_i47 @atom:281L_b47_a47_d47L_i47 lj/cut/coul/long 0.08 3.5 - pair_coeff @atom:324L_b47_a47_d47L_i47 @atom:324L_b47_a47_d47L_i47 lj/cut/coul/long 0.08 3.5 - pair_coeff @atom:325L_b47_a47_d47L_i47 @atom:325L_b47_a47_d47L_i47 lj/cut/coul/long 0.08 3.5 - pair_coeff @atom:340L_b47_a47_d47L_i47 @atom:340L_b47_a47_d47L_i47 lj/cut/coul/long 0.08 3.5 - pair_coeff @atom:342L_b47_a47_d47L_i47 @atom:342L_b47_a47_d47L_i47 lj/cut/coul/long 0.076 3.55 - pair_coeff @atom:458L_b47_a47_d47L_i47 @atom:458L_b47_a47_d47L_i47 lj/cut/coul/long 0.076 3.55 - pair_coeff @atom:459L_b47_a47_d47L_i47 @atom:459L_b47_a47_d47L_i47 lj/cut/coul/long 0.076 3.55 - pair_coeff @atom:649L_b47_a47_d47L_i47 @atom:649L_b47_a47_d47L_i47 lj/cut/coul/long 0.076 3.55 - pair_coeff @atom:900L_b47_a47_d47L_i47 @atom:900L_b47_a47_d47L_i47 lj/cut/coul/long 0.086 3.3 - pair_coeff @atom:901L_b47_a47_d47L_i47 @atom:901L_b47_a47_d47L_i47 lj/cut/coul/long 0.086 3.3 - pair_coeff @atom:902L_b47_a47_d47L_i47 @atom:902L_b47_a47_d47L_i47 lj/cut/coul/long 0.086 3.3 + pair_coeff @atom:80L_b013_a013_d013L_i013 @atom:80L_b013_a013_d013L_i013 0.066 3.5 + pair_coeff @atom:81L_b013_a013_d013L_i013 @atom:81L_b013_a013_d013L_i013 0.066 3.5 + pair_coeff @atom:81LL_b013_a013_d013LL_i013 @atom:81LL_b013_a013_d013LL_i013 0.066 0.35 + pair_coeff @atom:85LCH3_b046_a046_d046_i046 @atom:85LCH3_b046_a046_d046_i046 0.03 2.5 + pair_coeff @atom:85LCH2_b046_a046_d046_i046 @atom:85LCH2_b046_a046_d046_i046 0.026290630975 2.5 + pair_coeff @atom:87L_b047_a047_d047L_i047 @atom:87L_b047_a047_d047L_i047 0.076 3.55 + pair_coeff @atom:89L_b046_a046_d046_i046 @atom:89L_b046_a046_d046_i046 0.03 2.42 + pair_coeff @atom:86L_b047_a047_d047L_i047 @atom:86L_b047_a047_d047L_i047 0.076 3.55 + pair_coeff @atom:88L_b047_a047_d047L_i047 @atom:88L_b047_a047_d047L_i047 0.076 3.55 + pair_coeff @atom:96L_b005_a005_d005L_i005 @atom:96L_b005_a005_d005L_i005 0.17 0.312 + pair_coeff @atom:97L_b007_a007_d007L_i007 @atom:97L_b007_a007_d007L_i007 0.0 0.0 + pair_coeff @atom:111L_b005_a005_d005L_i005 @atom:111L_b005_a005_d005L_i005 0.17 0.307 + pair_coeff @atom:112L_b007_a007_d007L_i007 @atom:112L_b007_a007_d007L_i007 0.0 0.0 + pair_coeff @atom:113L_b005_a005_d005L_i005 @atom:113L_b005_a005_d005L_i005 0.17 0.307 + pair_coeff @atom:114L_b007_a007_d007L_i007 @atom:114L_b007_a007_d007L_i007 0.0 0.0 + pair_coeff @atom:118L_b046_a046_d046L_i046 @atom:118L_b046_a046_d046L_i046 0.03 0.25 + pair_coeff @atom:169L_b047_a047_d047L_i047 @atom:169L_b047_a047_d047L_i047 0.076 3.55 + pair_coeff @atom:266L_b047_a047_d047L_i047 @atom:266L_b047_a047_d047L_i047 0.08 3.5 + pair_coeff @atom:267L_b047_a047_d047L_i047 @atom:267L_b047_a047_d047L_i047 0.08 3.5 + pair_coeff @atom:280L_b047_a047_d047L_i047 @atom:280L_b047_a047_d047L_i047 0.08 3.5 + pair_coeff @atom:281L_b047_a047_d047L_i047 @atom:281L_b047_a047_d047L_i047 0.08 3.5 + pair_coeff @atom:324L_b047_a047_d047L_i047 @atom:324L_b047_a047_d047L_i047 0.08 3.5 + pair_coeff @atom:325L_b047_a047_d047L_i047 @atom:325L_b047_a047_d047L_i047 0.08 3.5 + pair_coeff @atom:340L_b047_a047_d047L_i047 @atom:340L_b047_a047_d047L_i047 0.08 3.5 + pair_coeff @atom:342L_b047_a047_d047L_i047 @atom:342L_b047_a047_d047L_i047 0.076 3.55 + pair_coeff @atom:406L_b003_a003_d003L_i003 @atom:406L_b003_a003_d003L_i003 0.105 0.31875 + pair_coeff @atom:407L_b004_a004_d004L_i004 @atom:407L_b004_a004_d004L_i004 0.168 0.3108 + pair_coeff @atom:408L_b020_a020_d020L_i020 @atom:408L_b020_a020_d020L_i020 0.17 0.255 + pair_coeff @atom:458L_b047_a047_d047L_i047 @atom:458L_b047_a047_d047L_i047 0.076 3.55 + pair_coeff @atom:459L_b047_a047_d047L_i047 @atom:459L_b047_a047_d047L_i047 0.076 3.55 + pair_coeff @atom:649L_b047_a047_d047L_i047 @atom:649L_b047_a047_d047L_i047 0.076 3.55 + pair_coeff @atom:718L_b046_a046_d046L_i046 @atom:718L_b046_a046_d046L_i046 0.15 0.242 + pair_coeff @atom:718LL_b046_a046_d046L_i046 @atom:718LL_b046_a046_d046L_i046 0.15 0.242 + pair_coeff @atom:900L_b047_a047_d047L_i047 @atom:900L_b047_a047_d047L_i047 0.086 3.3 + pair_coeff @atom:901L_b047_a047_d047L_i047 @atom:901L_b047_a047_d047L_i047 0.086 3.3 + pair_coeff @atom:902L_b047_a047_d047L_i047 @atom:902L_b047_a047_d047L_i047 0.086 3.3 } #(end of pair_coeffs) @@ -135,499 +203,69 @@ OPLSAA { # Dihedral parameters for some of these atoms are modified: + # ----------- Dihedral Interactions: ------------ + # http://lammps.sandia.gov/doc/dihedral_opls.html + # Syntax: + # dihedral_coeff DihedralTypeName parameters... + write_once("In Settings") { - dihedral_coeff @dihedral:13L-13L-13L-13L opls 0.6446926386 -0.2143420172 0.1782194073 0.0 - dihedral_coeff @dihedral:X-47L-47L-X opls 0.0 12.2502629063 0.0 0.0 - dihedral_coeff @dihedral:47L-47L-13L-13L opls -0.8050121893 0.3218905354 -0.1032768881 0.0 - dihedral_coeff @dihedral:13L-13L-13L-47L opls 0.4821902486 0.1343683078 0.1777461759 0.0 + dihedral_coeff @dihedral:013L_013L_013L_013L 0.6446926386 -0.2143420172 0.1782194073 0.0 + dihedral_coeff @dihedral:X_047L_047L_X 0.0 12.2502629063 0.0 0.0 + dihedral_coeff @dihedral:047L_047L_013L_013L -0.8050121893 0.3218905354 -0.1032768881 0.0 + dihedral_coeff @dihedral:013L_013L_013L_047L 0.4821902486 0.1343683078 0.1777461759 0.0 + dihedral_coeff @dihedral:046L_013LL_005L_007L 0.00962596 -0.0145554 0.381091 0.0 + dihedral_coeff @dihedral:046L_013LL_013LL_005L 0.0143774 0.033021 0.26687 0.0 + dihedral_coeff @dihedral:013LL_013LL_005L_007L -0.675785 -0.0160421 0.373199 0.0 + dihedral_coeff @dihedral:013LL_013LL_013LL_005L 1.31261 -0.266307 0.637867 0.0 + dihedral_coeff @dihedral:005L_013LL_013LL_005L 2.69106 -0.849706 0.725731 0.0 + dihedral_coeff @dihedral:013LL_003L_020L_013LL 3.11923 5.73771 0.0 0.0 + dihedral_coeff @dihedral:013LL_020L_003L_004L 0.0 5.73772 0.0 0.0 + dihedral_coeff @dihedral:046L_013LL_003L_020L -0.00742471 0.00217734 0.111803 0.0 + dihedral_coeff @dihedral:003L_020L_013LL_013LL -1.7354 -1.24844 0.623897 0.0 + dihedral_coeff @dihedral:046L_013LL_013LL_020L 0.0113337 0.0236209 0.429747 0.0 + dihedral_coeff @dihedral:013LL_013LL_003L_020L 0.884988 -0.626905 -0.493344 0.0 + dihedral_coeff @dihedral:013LL_013LL_003L_004L -0.276019 1.23685 -0.670745 0.0 + dihedral_coeff @dihedral:003L_013LL_013LL_046L -0.0021152 0.0173542 -0.295208 0.0 + dihedral_coeff @dihedral:003L_013LL_013LL_013LL -2.30738 -0.627326 0.621951 0.0 + dihedral_coeff @dihedral:013LL_013LL_013LL_020L 2.25871 -1.02408 1.0071 0.0 + dihedral_coeff @dihedral:020L_013LL_013LL_020L 4.66787 -2.62698 1.3248 0.0 + dihedral_coeff @dihedral:005L_013LL_013LL_020L 5.03208 -2.37742 1.23809 0.0 } #(end of dihedral_coeffs) - - # First we must slightly loosen the requirements to generate dihedrals - # involving atom types d13 or d47. We want the same rules to apply - # for atoms of type d13L and d47L. To cover both of these cases, - # I replaced "d13_" with "d13*_" in the lines below: - # (Later I will add the custom dihedrals for these atom types.) + # Rules for creating dihedral interactions according to atom type: + # DihedralTypeName AtomType1 AtomType2 AtomType3 AtomType4 + # (* = wildcard) write_once("Data Dihedrals By Type") { - @dihedral:2-2-2-13 @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d13*_i* - @dihedral:2-2-13-2 @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d2_i* - @dihedral:4-3-3-13 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-3-3-13 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-3-3-24 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* - @dihedral:13-3-3-46 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d46_i* - @dihedral:13-3-5-7 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d7_i* - @dihedral:1-3-13-13 @atom:*_b*_a*_d1_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* - @dihedral:1-3-13-46 @atom:*_b*_a*_d1_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d46_i* - @dihedral:3-3-13-46 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d46_i* - @dihedral:4-3-13-X @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:* - @dihedral:4-3-13-13 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* - @dihedral:4-3-13-21 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d21_i* - @dihedral:4-3-13-44 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d44_i* - @dihedral:4-3-13-24 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d24_i* - @dihedral:4-3-13-46 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d46_i* - @dihedral:4-3-13-48 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d48_i* - @dihedral:5-3-13-13 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* - @dihedral:5-3-13-44 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d44_i* - @dihedral:5-3-13-46 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d46_i* - @dihedral:13-3-13-13 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-3-13-46 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d46_i* - @dihedral:20-3-13-13 @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* - @dihedral:20-3-13-46 @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d46_i* - @dihedral:21-3-13-13 @atom:*_b*_a*_d21_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* - @dihedral:21-3-13-46 @atom:*_b*_a*_d21_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d46_i* - @dihedral:24-3-13-13 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* - @dihedral:24-3-13-21 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d21_i* - @dihedral:24-3-13-24 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d24_i* - @dihedral:24-3-13-46 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d46_i* - @dihedral:46-3-13-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* - @dihedral:46-3-13-46 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d46_i* - @dihedral:48-3-13-46 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d46_i* - @dihedral:52-3-13-13 @atom:*_b*_a*_d52_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* - @dihedral:52-3-13-44 @atom:*_b*_a*_d52_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d44_i* - @dihedral:52-3-13-46 @atom:*_b*_a*_d52_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d46_i* - @dihedral:65-3-13-13 @atom:*_b*_a*_d65_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* - @dihedral:65-3-13-46 @atom:*_b*_a*_d65_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d46_i* - @dihedral:107-3-13-46 @atom:*_b*_a*_d107_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d46_i* - @dihedral:4-3-20-13 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-3-20-13 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-3-20-48 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d48_i* - @dihedral:24-3-20-13 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13*_i* - @dihedral:46-3-20-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13*_i* - @dihedral:48-3-20-13 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13*_i* - @dihedral:3-3-24-13 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13*_i* - @dihedral:4-3-24-13 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13*_i* - @dihedral:4-3-24-47 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d47*_i* - @dihedral:5-3-24-13 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-3-24-5 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d5_i* - @dihedral:13-3-24-13 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-3-24-45 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d45_i* - @dihedral:13-3-24-48 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d48_i* - @dihedral:20-3-24-13 @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13*_i* - @dihedral:24-3-24-13 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13*_i* - @dihedral:46-3-24-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13*_i* - @dihedral:47-3-24-45 @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d45_i* - @dihedral:X-3-47-13 @atom:* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d13*_i* - @dihedral:4-3-47-46 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d46_i* - @dihedral:4-3-47-47 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d47*_i* - @dihedral:5-3-47-47 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d47*_i* - @dihedral:24-3-47-46 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d46_i* - @dihedral:24-3-47-47 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d47*_i* - @dihedral:107-3-47-46 @atom:*_b*_a*_d107_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d46_i* - @dihedral:107-3-47-47 @atom:*_b*_a*_d107_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d47*_i* - @dihedral:13-3-48-48 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:X-3-50-13 @atom:* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d13*_i* - @dihedral:4-3-50-47 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d47*_i* - @dihedral:5-3-50-47 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d47*_i* - @dihedral:13-3-50-47 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d47*_i* - @dihedral:13-3-56-X @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d56_i* @atom:* - @dihedral:13-3-56-13 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d13*_i* - @dihedral:4-3-107-13 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d107_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-3-107-13 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d107_i* @atom:*_b*_a*_d13*_i* - @dihedral:7-5-13-2 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d2_i* - @dihedral:7-5-13-6 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d6_i* - @dihedral:7-5-13-13 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* - @dihedral:7-5-13-46 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d46_i* - @dihedral:7-5-13-47 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d47*_i* - @dihedral:7-5-13-48 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d48_i* - @dihedral:7-5-13-50 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d50_i* - @dihedral:7-5-44-13 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d13*_i* - @dihedral:7-5-47-47 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d47*_i* - @dihedral:7-5-79-13 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d13*_i* - @dihedral:X-13-13-3 @atom:* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d3_i* - @dihedral:X-13-13-13 @atom:* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* - @dihedral:X-13-13-24 @atom:* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d24_i* - @dihedral:1-13-13-1 @atom:*_b*_a*_d1_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d1_i* - @dihedral:1-13-13-5 @atom:*_b*_a*_d1_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d5_i* - @dihedral:1-13-13-13 @atom:*_b*_a*_d1_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* - @dihedral:1-13-13-46 @atom:*_b*_a*_d1_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d46_i* - @dihedral:3-13-13-3 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d3_i* - @dihedral:3-13-13-5 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d5_i* - @dihedral:3-13-13-13 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* - @dihedral:3-13-13-15 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d15_i* - @dihedral:3-13-13-16 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d16_i* - @dihedral:3-13-13-24 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d24_i* - @dihedral:3-13-13-46 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d46_i* - @dihedral:3-13-13-48 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d48_i* - @dihedral:3-13-13-80 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d80_i* - @dihedral:5-13-13-5 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d5_i* - @dihedral:5-13-13-13 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* - @dihedral:5-13-13-20 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d20_i* - @dihedral:5-13-13-44 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d44_i* - @dihedral:5-13-13-24 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d24_i* - @dihedral:5-13-13-46 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d46_i* - @dihedral:13-13-13-13 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-13-13-15 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d15_i* - @dihedral:13-13-13-16 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d16_i* - @dihedral:13-13-13-19 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d19_i* - @dihedral:13-13-13-21 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d21_i* - @dihedral:13-13-13-44 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d44_i* - @dihedral:13-13-13-24 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d24_i* - @dihedral:13-13-13-46 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d46_i* - @dihedral:13-13-13-51 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d51_i* - @dihedral:13-13-13-53 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d53_i* - @dihedral:13-13-13-65 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d65_i* - @dihedral:13-13-13-66 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d66_i* - @dihedral:13-13-13-79 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d79_i* - @dihedral:13-13-13-107 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d107_i* - @dihedral:13-13-13-108 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d108_i* - @dihedral:15-13-13-46 @atom:*_b*_a*_d15_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d46_i* - @dihedral:16-13-13-46 @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d46_i* - @dihedral:19-13-13-46 @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d46_i* - @dihedral:20-13-13-20 @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d20_i* - @dihedral:20-13-13-46 @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d46_i* - @dihedral:21-13-13-21 @atom:*_b*_a*_d21_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d21_i* - @dihedral:21-13-13-44 @atom:*_b*_a*_d21_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d44_i* - @dihedral:21-13-13-46 @atom:*_b*_a*_d21_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d46_i* - @dihedral:44-13-13-44 @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d44_i* - @dihedral:44-13-13-46 @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d46_i* - @dihedral:44-13-13-48 @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d48_i* - @dihedral:24-13-13-46 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d46_i* - @dihedral:24-13-13-48 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d48_i* - @dihedral:24-13-13-80 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d80_i* - @dihedral:46-13-13-46 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d46_i* - @dihedral:46-13-13-47 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d47*_i* - @dihedral:46-13-13-48 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d48_i* - @dihedral:46-13-13-51 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d51_i* - @dihedral:46-13-13-53 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d53_i* - @dihedral:46-13-13-55 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d55_i* - @dihedral:46-13-13-59 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d59_i* - @dihedral:46-13-13-62 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d62_i* - @dihedral:46-13-13-65 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d65_i* - @dihedral:46-13-13-66 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d66_i* - @dihedral:46-13-13-79 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d79_i* - @dihedral:46-13-13-80 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d80_i* - @dihedral:46-13-13-82 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d82_i* - @dihedral:46-13-13-83 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d83_i* - @dihedral:46-13-13-84 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d84_i* - @dihedral:46-13-13-87 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d87_i* - @dihedral:46-13-13-88 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d88_i* - @dihedral:46-13-13-102 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d102_i* - @dihedral:46-13-13-104 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d104_i* - @dihedral:46-13-13-107 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d107_i* - @dihedral:46-13-13-108 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d108_i* - @dihedral:46-13-13-109 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d109_i* - @dihedral:48-13-13-53 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d53_i* - @dihedral:108-13-13-108 @atom:*_b*_a*_d108_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d108_i* - @dihedral:13-13-15-17 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d15_i* @atom:*_b*_a*_d17_i* - @dihedral:46-13-15-17 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d15_i* @atom:*_b*_a*_d17_i* - @dihedral:13-13-16-13 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-13-16-16 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d16_i* - @dihedral:46-13-16-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d13*_i* - @dihedral:46-13-16-16 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d16_i* - @dihedral:46-13-16-48 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d48_i* - @dihedral:X-13-18-19 @atom:* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d18_i* @atom:*_b*_a*_d19_i* - @dihedral:46-13-18-19 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d18_i* @atom:*_b*_a*_d19_i* - @dihedral:X-13-19-18 @atom:* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d18_i* - @dihedral:X-13-19-19 @atom:* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d19_i* - @dihedral:13-13-19-19 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d19_i* - @dihedral:46-13-19-19 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d19_i* - @dihedral:X-13-20-13 @atom:* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13*_i* - @dihedral:56-13-20-13 @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13*_i* - @dihedral:57-13-20-13 @atom:*_b*_a*_d57_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-13-20-3 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d3_i* - @dihedral:13-13-20-13 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-13-20-64 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d64_i* - @dihedral:46-13-20-X @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d20_i* @atom:* - @dihedral:46-13-20-3 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d3_i* - @dihedral:46-13-20-47 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d47*_i* - @dihedral:46-13-20-48 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d48_i* - @dihedral:46-13-20-51 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d51_i* - @dihedral:46-13-20-64 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d64_i* - @dihedral:13-13-44-13 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-13-44-45 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d45_i* - @dihedral:46-13-44-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d13*_i* - @dihedral:46-13-44-45 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d45_i* - @dihedral:46-13-44-48 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d48_i* - @dihedral:X-13-24-45 @atom:* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d45_i* - @dihedral:3-13-24-3 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* - @dihedral:3-13-24-13 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13*_i* - @dihedral:3-13-24-45 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d45_i* - @dihedral:13-13-24-3 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* - @dihedral:13-13-24-13 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-13-24-45 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d45_i* - @dihedral:13-13-24-59 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d59_i* - @dihedral:13-13-24-79 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d79_i* - @dihedral:13-13-24-91 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d91_i* - @dihedral:46-13-24-3 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* - @dihedral:46-13-24-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13*_i* - @dihedral:46-13-24-45 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d45_i* - @dihedral:46-13-24-48 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d48_i* - @dihedral:46-13-24-79 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d79_i* - @dihedral:48-13-24-59 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d59_i* - @dihedral:X-13-47-13 @atom:* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d13*_i* - @dihedral:X-13-47-46 @atom:* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d46_i* - @dihedral:X-13-47-47 @atom:* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d47*_i* - @dihedral:X-13-47-50 @atom:* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d50_i* - @dihedral:1-13-47-47 @atom:*_b*_a*_d1_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d47*_i* - @dihedral:13-13-47-13 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-13-47-47 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d47*_i* - @dihedral:13-13-47-50 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d50_i* - @dihedral:46-13-47-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d13*_i* - @dihedral:46-13-47-46 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d46_i* - @dihedral:46-13-47-47 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d47*_i* - @dihedral:46-13-47-50 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d50_i* - @dihedral:46-13-47-110 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d110_i* - @dihedral:47-13-47-13 @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d13*_i* - @dihedral:47-13-47-46 @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d46_i* - @dihedral:X-13-48-48 @atom:* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:1-13-48-48 @atom:*_b*_a*_d1_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:13-13-48-48 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:13-13-48-56 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d56_i* - @dihedral:21-13-48-48 @atom:*_b*_a*_d21_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:46-13-48-48 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:64-13-48-48 @atom:*_b*_a*_d64_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:65-13-48-48 @atom:*_b*_a*_d65_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:X-13-50-47 @atom:* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d47*_i* - @dihedral:13-13-50-50 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d50_i* - @dihedral:46-13-50-47 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d47*_i* - @dihedral:46-13-50-50 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d50_i* - @dihedral:46-13-50-109 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d109_i* - @dihedral:13-13-51-X @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d51_i* @atom:* - @dihedral:13-13-51-46 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d51_i* @atom:*_b*_a*_d46_i* - @dihedral:46-13-51-20 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d51_i* @atom:*_b*_a*_d20_i* - @dihedral:13-13-53-13 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-13-53-45 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d45_i* - @dihedral:46-13-53-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d13*_i* - @dihedral:46-13-53-45 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d45_i* - @dihedral:46-13-53-48 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d48_i* - @dihedral:46-13-53-54 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d54_i* - @dihedral:13-13-55-45 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d55_i* @atom:*_b*_a*_d45_i* - @dihedral:13-13-55-48 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d55_i* @atom:*_b*_a*_d48_i* - @dihedral:13-13-55-54 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d55_i* @atom:*_b*_a*_d54_i* - @dihedral:46-13-55-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d55_i* @atom:*_b*_a*_d13*_i* - @dihedral:46-13-55-45 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d55_i* @atom:*_b*_a*_d45_i* - @dihedral:46-13-55-48 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d55_i* @atom:*_b*_a*_d48_i* - @dihedral:13-13-56-18 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d18_i* - @dihedral:X-13-57-X @atom:* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d57_i* @atom:* - @dihedral:13-13-57-X @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d57_i* @atom:* - @dihedral:13-13-57-62 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d57_i* @atom:*_b*_a*_d62_i* - @dihedral:13-13-57-82 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d57_i* @atom:*_b*_a*_d82_i* - @dihedral:20-13-57-X @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d57_i* @atom:* - @dihedral:20-13-57-62 @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d57_i* @atom:*_b*_a*_d62_i* - @dihedral:20-13-57-82 @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d57_i* @atom:*_b*_a*_d82_i* - @dihedral:13-13-59-X @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d59_i* @atom:* - @dihedral:13-13-59-56 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d59_i* @atom:*_b*_a*_d56_i* - @dihedral:46-13-59-X @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d59_i* @atom:* - @dihedral:13-13-62-X @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d62_i* @atom:* - @dihedral:46-13-62-X @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d62_i* @atom:* - @dihedral:46-13-64-20 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d64_i* @atom:*_b*_a*_d20_i* - @dihedral:46-13-64-52 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d64_i* @atom:*_b*_a*_d52_i* - @dihedral:48-13-64-20 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d64_i* @atom:*_b*_a*_d20_i* - @dihedral:48-13-64-52 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d64_i* @atom:*_b*_a*_d52_i* - @dihedral:X-13-79-23 @atom:* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d23_i* - @dihedral:X-13-79-24 @atom:* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d24_i* - @dihedral:13-13-79-13 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-13-79-23 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d23_i* - @dihedral:46-13-79-5 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d5_i* - @dihedral:46-13-79-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d13*_i* - @dihedral:46-13-79-23 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d23_i* - @dihedral:46-13-79-48 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d48_i* - @dihedral:13-13-80-X @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d80_i* @atom:* - @dihedral:13-13-80-60 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d80_i* @atom:*_b*_a*_d60_i* - @dihedral:13-13-80-84 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d80_i* @atom:*_b*_a*_d84_i* - @dihedral:46-13-80-X @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d80_i* @atom:* - @dihedral:46-13-80-60 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d80_i* @atom:*_b*_a*_d60_i* - @dihedral:46-13-80-84 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d80_i* @atom:*_b*_a*_d84_i* - @dihedral:13-13-82-X @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d82_i* @atom:* - @dihedral:46-13-82-X @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d82_i* @atom:* - @dihedral:13-13-83-X @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d83_i* @atom:* - @dihedral:46-13-83-X @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d83_i* @atom:* - @dihedral:1-13-84-X @atom:*_b*_a*_d1_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d84_i* @atom:* - @dihedral:13-13-84-X @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d84_i* @atom:* - @dihedral:13-13-84-57 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d57_i* - @dihedral:21-13-84-X @atom:*_b*_a*_d21_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d84_i* @atom:* - @dihedral:46-13-84-X @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d84_i* @atom:* - @dihedral:1-13-87-X @atom:*_b*_a*_d1_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d87_i* @atom:* - @dihedral:13-13-87-X @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d87_i* @atom:* - @dihedral:21-13-87-X @atom:*_b*_a*_d21_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d87_i* @atom:* - @dihedral:46-13-87-X @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d87_i* @atom:* - @dihedral:13-13-88-X @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d88_i* @atom:* - @dihedral:46-13-88-X @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d88_i* @atom:* - @dihedral:X-13-90-X @atom:* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d90_i* @atom:* - @dihedral:46-13-90-X @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d90_i* @atom:* - @dihedral:46-13-91-91 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d91_i* - @dihedral:13-13-95-13 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d95_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-13-95-46 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d95_i* @atom:*_b*_a*_d46_i* - @dihedral:13-13-102-103 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d102_i* @atom:*_b*_a*_d103_i* - @dihedral:46-13-102-103 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d102_i* @atom:*_b*_a*_d103_i* - @dihedral:13-13-104-13 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d104_i* @atom:*_b*_a*_d13*_i* - @dihedral:46-13-104-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d104_i* @atom:*_b*_a*_d13*_i* - @dihedral:X-13-105-X @atom:* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d105_i* @atom:* - @dihedral:13-13-105-X @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d105_i* @atom:* - @dihedral:13-13-105-62 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d105_i* @atom:*_b*_a*_d62_i* - @dihedral:13-13-105-82 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d105_i* @atom:*_b*_a*_d82_i* - @dihedral:20-13-105-X @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d105_i* @atom:* - @dihedral:20-13-105-62 @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d105_i* @atom:*_b*_a*_d62_i* - @dihedral:20-13-105-82 @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d105_i* @atom:*_b*_a*_d82_i* - @dihedral:3-13-107-13 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d107_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-13-107-3 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d107_i* @atom:*_b*_a*_d3_i* - @dihedral:13-13-107-13 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d107_i* @atom:*_b*_a*_d13*_i* - @dihedral:46-13-107-3 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d107_i* @atom:*_b*_a*_d3_i* - @dihedral:46-13-107-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d107_i* @atom:*_b*_a*_d13*_i* - @dihedral:46-13-107-48 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d107_i* @atom:*_b*_a*_d48_i* - @dihedral:13-13-108-13 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d108_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-13-108-45 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d108_i* @atom:*_b*_a*_d45_i* - @dihedral:46-13-108-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d108_i* @atom:*_b*_a*_d13*_i* - @dihedral:46-13-108-20 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d108_i* @atom:*_b*_a*_d20_i* - @dihedral:46-13-108-45 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d108_i* @atom:*_b*_a*_d45_i* - @dihedral:13-13-109-109 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* - @dihedral:46-13-109-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d13*_i* - @dihedral:46-13-109-46 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d46_i* - @dihedral:46-13-109-109 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* - @dihedral:13-16-16-13 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-16-48-48 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:13-16-48-56 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d56_i* - @dihedral:13-16-59-56 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d59_i* @atom:*_b*_a*_d56_i* - @dihedral:18-18-56-13 @atom:*_b*_a*_d18_i* @atom:*_b*_a*_d18_i* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-19-19-13 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-19-19-46 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d46_i* - @dihedral:13-19-19-47 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d47*_i* - @dihedral:13-19-19-109 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d109_i* - @dihedral:46-19-19-47 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d47*_i* - @dihedral:19-19-47-13 @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d13*_i* - @dihedral:19-19-47-46 @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d46_i* - @dihedral:19-19-47-47 @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d47*_i* - @dihedral:13-20-44-13 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-20-44-45 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d45_i* - @dihedral:13-20-47-13 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-20-47-46 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d46_i* - @dihedral:13-20-47-47 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d47*_i* - @dihedral:13-20-47-50 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d50_i* - @dihedral:13-20-48-48 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:13-20-48-56 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d56_i* - @dihedral:13-20-51-5 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d51_i* @atom:*_b*_a*_d5_i* - @dihedral:13-20-51-13 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d51_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-20-51-20 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d51_i* @atom:*_b*_a*_d20_i* - @dihedral:13-20-51-46 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d51_i* @atom:*_b*_a*_d46_i* - @dihedral:13-20-56-3 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d3_i* - @dihedral:13-20-59-56 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d59_i* @atom:*_b*_a*_d56_i* - @dihedral:13-20-64-13 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d64_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-20-64-52 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d64_i* @atom:*_b*_a*_d52_i* - @dihedral:108-20-108-13 @atom:*_b*_a*_d108_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d108_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-44-44-13 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-44-44-45 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d45_i* - @dihedral:13-44-48-48 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:13-24-48-48 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:13-24-79-48 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d48_i* - @dihedral:13-24-82-61 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d61_i* - @dihedral:47-24-86-48 @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d48_i* - @dihedral:47-24-86-56 @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d56_i* - @dihedral:47-46-47-13 @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d13*_i* - @dihedral:47-46-47-46 @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d46_i* - @dihedral:X-47-47-X @atom:* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d47*_i* @atom:* - @dihedral:X-47-47-19 @atom:* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d19_i* - @dihedral:3-47-47-24 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d24_i* - @dihedral:3-47-47-46 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d46_i* - @dihedral:5-47-47-13 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d13*_i* - @dihedral:5-47-47-46 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d46_i* - @dihedral:13-47-47-13 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-47-47-19 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d19_i* - @dihedral:13-47-47-20 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d20_i* - @dihedral:13-47-47-46 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d46_i* - @dihedral:19-47-47-46 @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d46_i* - @dihedral:20-47-47-46 @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d46_i* - @dihedral:21-47-47-21 @atom:*_b*_a*_d21_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d21_i* - @dihedral:21-47-47-46 @atom:*_b*_a*_d21_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d46_i* - @dihedral:46-47-47-46 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d46_i* - @dihedral:46-47-47-48 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d48_i* - @dihedral:13-47-48-48 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:46-47-48-48 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:46-47-48-56 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d56_i* - @dihedral:47-47-48-48 @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:13-47-50-13 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-47-50-46 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d46_i* - @dihedral:13-47-50-48 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d48_i* - @dihedral:13-47-50-50 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d50_i* - @dihedral:13-47-50-109 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d109_i* - @dihedral:24-47-50-3 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d3_i* - @dihedral:46-47-50-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d13*_i* - @dihedral:46-47-50-46 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d46_i* - @dihedral:46-47-50-48 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d48_i* - @dihedral:46-47-50-50 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d50_i* - @dihedral:46-47-50-109 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d109_i* - @dihedral:X-47-84-X @atom:* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d84_i* @atom:* - @dihedral:X-47-86-48 @atom:* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d48_i* - @dihedral:3-47-86-86 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d86_i* - @dihedral:49-47-86-X @atom:*_b*_a*_d49_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d86_i* @atom:* - @dihedral:49-47-86-24 @atom:*_b*_a*_d49_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d24_i* - @dihedral:X-47-87-X @atom:* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d87_i* @atom:* - @dihedral:X-47-88-X @atom:* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d88_i* @atom:* - @dihedral:13-47-110-47 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d110_i* @atom:*_b*_a*_d47*_i* - @dihedral:46-47-110-47 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d110_i* @atom:*_b*_a*_d47*_i* - @dihedral:X-48-48-13 @atom:* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-48-48-13 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-48-48-48 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:13-48-48-49 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d49_i* - @dihedral:13-48-48-50 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d50_i* - @dihedral:47-48-48-49 @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d49_i* - @dihedral:48-48-50-47 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d47*_i* - @dihedral:56-48-50-47 @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d47*_i* - @dihedral:48-48-53-13 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d13*_i* - @dihedral:55-48-55-13 @atom:*_b*_a*_d55_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d55_i* @atom:*_b*_a*_d13*_i* - @dihedral:48-48-79-13 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d13*_i* - @dihedral:56-48-101-13 @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d101_i* @atom:*_b*_a*_d13*_i* - @dihedral:48-48-109-13 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-50-50-13 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-50-50-46 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d46_i* - @dihedral:13-50-50-47 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d47*_i* - @dihedral:46-50-50-47 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d47*_i* - @dihedral:47-50-50-47 @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d47*_i* - @dihedral:13-50-109-13 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-50-109-109 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* - @dihedral:46-50-109-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d13*_i* - @dihedral:47-50-109-13 @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d13*_i* - @dihedral:47-50-109-46 @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d46_i* - @dihedral:47-50-109-109 @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* - @dihedral:13-53-82-61 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d61_i* - @dihedral:13-56-56-13 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-56-56-48 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d48_i* - @dihedral:4-89-90-13 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d89_i* @atom:*_b*_a*_d90_i* @atom:*_b*_a*_d13*_i* - @dihedral:91-89-90-13 @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d89_i* @atom:*_b*_a*_d90_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-91-91-13 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-91-91-46 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d46_i* - @dihedral:13-109-109-13 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-109-109-46 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d46_i* - @dihedral:13-109-109-48 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d48_i* - @dihedral:13-109-109-50 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d50_i* - @dihedral:13-109-109-109 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* - @dihedral:24-3-13-53 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d53_i* - @dihedral:52-3-13-24 @atom:*_b*_a*_d52_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d24_i* - @dihedral:3-13-13-53 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d53_i* - @dihedral:3-13-13-83 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d83_i* - @dihedral:3-13-13-84 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d84_i* - @dihedral:3-13-13-85 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d85_i* - @dihedral:5-13-13-53 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d53_i* - @dihedral:15-13-13-53 @atom:*_b*_a*_d15_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d53_i* - @dihedral:16-13-13-53 @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d53_i* - @dihedral:13-13-13-55 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d55_i* - @dihedral:24-13-13-83 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d83_i* - @dihedral:53-13-13-83 @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d83_i* - @dihedral:24-13-13-84 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d84_i* - @dihedral:53-13-13-84 @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d84_i* - @dihedral:24-13-13-85 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d85_i* - @dihedral:46-13-13-85 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d85_i* - @dihedral:53-13-13-85 @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d85_i* - @dihedral:3-13-53-13 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d13*_i* - @dihedral:3-13-53-54 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d54_i* - @dihedral:13-13-53-54 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d54_i* - @dihedral:46-13-55-54 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d55_i* @atom:*_b*_a*_d54_i* - @dihedral:13-13-85-X @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d85_i* @atom:* - @dihedral:13-13-85-57 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d85_i* @atom:*_b*_a*_d57_i* - @dihedral:46-13-85-X @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d85_i* @atom:* - @dihedral:13-13-13-20 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d20_i* - @dihedral:13-13-13-47 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d47*_i* + @dihedral:013L_013L_013L_013L @atom:*_b*_a*_d013L_i* @atom:*_b*_a*_d013L_i* @atom:*_b*_a*_d013L_i* @atom:*_b*_a*_d013L_i* + @dihedral:X_047L_047L_X @atom:* @atom:*_b*_a*_d047L_i* @atom:*_b*_a*_d047L_i* @atom:* + @dihedral:047L_047L_013L_013L @atom:*_b*_a*_d047L_i* @atom:*_b*_a*_d047L_i* @atom:*_b*_a*_d013L_i* @atom:*_b*_a*_d013L_i* + @dihedral:013L_013L_013L_047L @atom:*_b*_a*_d013L_i* @atom:*_b*_a*_d013L_i* @atom:*_b*_a*_d013L_i* @atom:*_b*_a*_d047L_i* + @dihedral:046L_013LL_005L_007L @atom:*_b*_a*_d046L_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d005L_i* @atom:*_b*_a*_d007L_i* + @dihedral:046L_013LL_013LL_005L @atom:*_b*_a*_d046L_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d005L_i* + @dihedral:013LL_013LL_005L_007L @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d005L_i* @atom:*_b*_a*_d007L_i* + @dihedral:013LL_013LL_013LL_005L @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d005L_i* + @dihedral:005L_013LL_013LL_005L @atom:*_b*_a*_d005L_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d005L_i* + @dihedral:013LL_003L_020L_013LL @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d003L_i* @atom:*_b*_a*_d020L_i* @atom:*_b*_a*_d013LL_i* + @dihedral:013LL_020L_003L_004L @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d020L_i* @atom:*_b*_a*_d003L_i* @atom:*_b*_a*_d004L_i* + @dihedral:046L_013LL_003L_020L @atom:*_b*_a*_d046L_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d003L_i* @atom:*_b*_a*_d020L_i* + @dihedral:003L_020L_013LL_013LL @atom:*_b*_a*_d003L_i* @atom:*_b*_a*_d020L_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d013LL_i* + @dihedral:046L_013LL_013LL_020L @atom:*_b*_a*_d046L_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d020L_i* + @dihedral:013LL_013LL_003L_020L @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d003L_i* @atom:*_b*_a*_d020L_i* + @dihedral:013LL_013LL_003L_004L @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d003L_i* @atom:*_b*_a*_d004L_i* + @dihedral:003L_013LL_013LL_046L @atom:*_b*_a*_d003L_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d046L_i* + @dihedral:003L_013LL_013LL_013LL @atom:*_b*_a*_d003L_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d013LL_i* + @dihedral:013LL_013LL_013LL_020L @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d020L_i* + @dihedral:020L_013LL_013LL_020L @atom:*_b*_a*_d020L_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d020L_i* + @dihedral:005L_013LL_013LL_020L @atom:*_b*_a*_d005L_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d020L_i* } #(end of dihedrals by type) - # New dihedrals which have been customized: - # (These will override the rules above) + # ----------- New Dihedral Interactions: ------------ + # http://lammps.sandia.gov/doc/dihedral_opls.html + # Syntax: + # dihedral_coeff DihedralTypeName parameters... - write_once("Data Dihedrals By Type") { - @dihedral:13L-13L-13L-13L @atom:*_b*_a*_d13L_i* @atom:*_b*_a*_d13L_i* @atom:*_b*_a*_d13L_i* @atom:*_b*_a*_d13L_i* - @dihedral:X-47L-47L-X @atom:* @atom:*_b*_a*_d47L_i* @atom:*_b*_a*_d47L_i* @atom:* - @dihedral:47L-47L-13L-13L @atom:*_b*_a*_d47L_i* @atom:*_b*_a*_d47L_i* @atom:*_b*_a*_d13L_i* @atom:*_b*_a*_d13L_i* - @dihedral:13L-13L-13L-47L @atom:*_b*_a*_d13L_i* @atom:*_b*_a*_d13L_i* @atom:*_b*_a*_d13L_i* @atom:*_b*_a*_d47L_i* - } #(end of dihedrals by type) -} # end of additional parameters appended to the "OPLSAA" object +} # OPLSAA + diff --git a/tools/moltemplate/moltemplate/force_fields/martini.lt b/tools/moltemplate/moltemplate/force_fields/martini.lt index 3279e55dbc..9304de004a 100644 --- a/tools/moltemplate/moltemplate/force_fields/martini.lt +++ b/tools/moltemplate/moltemplate/force_fields/martini.lt @@ -1,13 +1,25 @@ # Autogenerated by EMC 2 LT tool v0.1 on 2017-06-28 # # cd martini/ -# ./emcprm2lt.py martini.prm lipids.prm cholesterol.prm --bond-style=harmonic --angle-style=cosine/squared --pair-style=lj/gromacs/coul/gromacs --name=martini +# emcprm2lt.py martini.prm lipids.prm cholesterol.prm --bond-style=harmonic --angle-style=cosine/squared --pair-style=lj/gromacs/coul/gromacs --name=martini # mv -f martini.lt ../ # +# For details see the "README.txt" file (located in "force_fields/martini/") +# +# (Note: The rigid bond constraints used original MARTINI model for +# cholesterol have been replaced by stiff but flexible bonds. +# There is a trade-off between increasing the stiffness of the bonds, and +# using larger time steps. To alter the stiffness of the bonds, and edit +# the "ITEM BOND" section of the "cholesterol.prm", edit the "k" parameters +# (3rd column, for the "S..." entries), and run "emcprm2lt.py" again.) +# # Adapted from EMC by Pieter J. in 't Veld # Originally written as, FFNAME:MARTINI STYLE:COARSE VERSION:V2.0 on Feb 2014 +# "emcprm2lt.py" was written by David Stelter. + MARTINI { + write_once("Data Masses") { @atom:BP4 72.000000 # BP4 @atom:C1 72.000000 # C1 @@ -2210,4 +2222,6 @@ MARTINI { pair_style hybrid lj/gromacs/coul/gromacs 9.000000 12.000000 special_bonds lj/coul 0.0 0.0 0.0 } # end init + } # MARTINI + diff --git a/tools/moltemplate/moltemplate/force_fields/martini/emcprm2lt.py b/tools/moltemplate/moltemplate/force_fields/martini/emcprm2lt.py deleted file mode 100755 index 81ed2358aa..0000000000 --- a/tools/moltemplate/moltemplate/force_fields/martini/emcprm2lt.py +++ /dev/null @@ -1,580 +0,0 @@ -#!/usr/bin/python - -import os, sys, getopt -import datetime - -__version__ = 0.1 - -#################### UNITS #################### -# Only used with --units flag -econv = 1.0 # Additional Factor for unit conversion if needed (energies) -lconv = 1.0 # Additional Factor for unit conversion if neededa (lengths) -dconv = 1.0 # Additional Factor for unit conversion if neededa (densities) -############################################### - -print('\nEMC 2 LT conversion tool: v%s\n' % __version__) - -def helpme(): - print 'Help for the EMC 2 LT conversion tool\n' - print 'Input takes a list of files in EMC .prm format to be read.' - print 'Additional styles (bond, angle, etc) can be modified via the',\ - 'command line. Any valid LAMMPS style can be used.\n' - print 'Styles include:' - print '--pair-style=' - print '--bond-style=' - print '--angle-style=' - print '--dihedral-style=' - print '--improper-style=\n' - print 'Default styles are lj/cut/coul/long, harmonic, harmonic, harmonic,',\ - 'harmonic \n' - print 'Other commands:' - print '--name= provides basename for output file if desired\n' - print '--units flag for manual units (no parameter needed)\n' - print 'Usage example:' - print 'emcprm2lt.py file1 file2 --bond-style=harmonic --angle-style=harmonic' - print '' - -def Abort(): - print 'Aborting...' - sys.exit() - -def WriteInit(): -# Write generic LAMMPS settings, likely need additional on a per-ff basis - foutput.write(' write_once("In Init") {\n') - foutput.write(' # Warning: This is a very generic "In Init" section, further\n') - foutput.write(' # modification prior to any simulation is extremely likely\n') - foutput.write(' units real\n') - foutput.write(' atom_style full\n') - foutput.write(' bond_style hybrid %s\n' % bstyle) - if angle_flag: - foutput.write(' angle_style hybrid %s\n' % astyle) - if torsion_flag: - foutput.write(' dihedral_style hybrid %s\n' % dstyle) - if improp_flag: - foutput.write(' improper_style hybrid %s\n' % istyle) - foutput.write(' pair_style hybrid %s %f %f\n' % (pstyle, - float(inner[0])*lconv, float(cutoff[0])*lconv)) - if pair14[0] == 'OFF': - foutput.write(' special_bonds lj/coul 0.0 0.0 0.0\n') - else: - print 'Warning: special_bonds needed, add to "In Init" section\n' - foutput.write(' } # end init\n') - -def Units(length_flag, energy_flag, density_flag): -# Check flags for all units, determine what conversions are needed, hard-coded for LAMMPS 'real' - print 'Attempting to auto-convert units... This should always be double-checked',\ - ' especially for unique potential styles' - global lconv; global econv; global dconv - if length_flag: - print 'Warning: length scale does not match LAMMPS real units, attempting conversion to angstroms' - if length[0] == 'NANOMETER': - lconv = 10.0 - print ' nanometer -> angstrom' - elif length[0] == 'MICROMETER': - lconv = 10000.0 - print ' micrometer -> angstrom' - elif length[0] == 'METER': - lconv = 10000000000.0 - print ' meter -> angstrom' - else: - print 'Length units NOT converted' - if energy_flag: - print 'Warning: energy units do not match LAMMPS real units, attempting conversion to kcal/mol' - if energy[0] == 'KJ/MOL': - econv = 0.239006 - print ' kj/mol -> kcal/mol' - elif energy[0] == 'J/MOL': - econv = 0.000239006 - print ' j/mol -> kcal/mol' - elif energy[0] == 'CAL/MOL': - econv = 0.001 - print ' cal/mol -> kcal/mol' - else: - print 'Energy units NOT converted' - if density_flag: - print 'Warning: density units do not match LAMMPS real units, attempting conversion to gram/cm^3' - if density[0] == 'KG/M^3': - dconv = 0.001 - print ' kg/m^3 -> g/cm^3' - else: - print 'Density units NOT converted' - return lconv, econv, dconv - -def ChkPotential(manual_flag, angle_flag, torsion_flag, improp_flag): -# Check type of potential, determine type of unit conversion is necessary - global beconv - if angle_flag: - global aeconv - if torsion_flag: - global deconv - if improp_flag: - global ieconv - if manual_flag == False: - # Chk bond potential - if bstyle == '' or bstyle == 'harmonic': - beconv = econv / (2*pow(lconv,2)) - else: - print 'Cannot find bond potential type, use manual units' - Abort() - if angle_flag: - if astyle == '' or astyle == 'harmonic': - aeconv = econv - elif astyle == 'cosine/squared': - aeconv = econv / 2 - else: - print 'Cannot find angle potential type, use manual units' - Abort() - # torsion and improper not implemented fully - elif torsion_flag: - if dstyle == '' or dstyle == 'harmonic': - deconv = econv - else: - print 'Cannot find torsion potential type, use manual units' - Abort() - elif improp_flag: - if istyle == '' or istyle == 'harmonic': - ieconv = econv - else: - print 'Cannot find improper potential type, use manual units' - Abort() - else: - # Modify as needed - print 'Warning: Manual units used, set potential conversion units in script' - beconv = 1 - if angle_flag: - aeconv = 1 - if torsion_flag: - deconv = 1 - if improp_flag: - ieconv = 1 - - -### Parse input ### -if len(sys.argv) == 1: - helpme() - sys.exit() -manual_units = False # Turned on via command line -args = list(sys.argv[1:]) -myopts, args = getopt.gnu_getopt(args, 'fh', ['pair-style=', 'bond-style=', 'angle-style=', - 'dihedral-style=', 'improper-style=', 'name=', 'units']) -filenames = list(args) -pstyle = ''; bstyle = ''; astyle = ''; dstyle = ''; istyle = '' -name = '' -for opt, arg in myopts: - if opt in ('-f'): - filenames = arg - elif opt in ('--pair-style'): - pstyle = arg - elif opt in ('--bond-style'): - bstyle = arg - elif opt in ('--angle-style'): - astyle = arg - elif opt in ('--dihedral-style'): - dstyle = arg - elif opt in ('--improper-style'): - istyle = arg - elif opt in ('--name'): - name = arg - elif opt in ('--units'): - manual_units = True - print 'Manual units enabled, modify python script accordingly' - elif opt in ('-h', '--help'): - helpme() - sys.exit() - -### Check input filenames, make sure they exist ### -print 'Converting: ' -for i in range(len(filenames)): - if os.path.isfile(filenames[i]): - print '', filenames[i] - else: - print 'invalid filename:', filenames[i] - Abort() -print 'from EMC .prm to moltemplate .lt format\n' - -### Open all files ### -f = [open(fname, 'r') for fname in filenames] - -### All these settings from DEFINE should be list of fixed size ### -ffname = [[] for i in range(len(f))] -fftype = [[] for i in range(len(f))] -version = [[] for i in range(len(f))] -created1 = [[] for i in range(len(f))] -created2 = [[] for i in range(len(f))] -length = [[] for i in range(len(f))] -energy = [[] for i in range(len(f))] -density = [[] for i in range(len(f))] -mix = [[] for i in range(len(f))] -nbonded = [[] for i in range(len(f))] -inner = [[] for i in range(len(f))] -cutoff = [[] for i in range(len(f))] -pair14 = [[] for i in range(len(f))] -angle_def = [[] for i in range(len(f))] -torsion_def = [[] for i in range(len(f))] -improp_def = [[] for i in range(len(f))] # not all prm have this - -### Parse DEFINE section, save info for each file ### -for i in range(len(f)): - grab = False - for line in f[i]: - if line.strip() == 'ITEM DEFINE': - grab = True - elif line.strip() == 'ITEM END': - grab = False - elif grab: - if line.startswith('FFNAME'): - ffname[i] = line.split()[1].strip() - if line.startswith('FFTYPE'): - fftype[i] = line.split()[1].strip() - if line.startswith('VERSION'): - version[i] = line.split()[1].strip() - if line.startswith('CREATED'): - created1[i] = line.split()[1].strip() - created2[i] = line.split()[2].strip() - if line.startswith('LENGTH'): - length[i] = line.split()[1].strip() - if line.startswith('ENERGY'): - energy[i] = line.split()[1].strip() - if line.startswith('DENSITY'): - density[i] = line.split()[1].strip() - if line.startswith('MIX'): - mix[i] = line.split()[1].strip() - if line.startswith('NBONDED'): - nbonded[i] = line.split()[1].strip() - if line.startswith('INNER'): - inner[i] = line.split()[1].strip() - if line.startswith('CUTOFF'): - cutoff[i] = line.split()[1].strip() - if line.startswith('PAIR14'): - pair14[i] = line.split()[1].strip() - if line.startswith('ANGLE'): - angle_def[i] = line.split()[1].strip() - if line.startswith('TORSION'): - torsion_def[i] = line.split()[1].strip() - if line.startswith('IMPROP'): - improp_def[i] = line.split()[1].strip() - -### Sanity Checks ### -for i in range(len(f)): - for j in range(len(f)): - if ffname[j] != ffname[i]: - print 'force field files do not match' - Abort() - if length[j] != length[i]: - print 'units not identical between files' - Abort() - if energy[j] != energy[i]: - print 'units not identical between files' - Abort() - if density[j] != density[i]: - print 'units not identical between files' - Abort() - if inner[j] != inner[i]: - print 'inner cutoff not identical between files' - Abort() - if cutoff[j] != cutoff[i]: - print 'cutoff not identical between files' - Abort() - if pair14[j] != pair14[i]: - print '1-4 pair interaction not consistent between files' - Abort() - -### Check if sections exist in PRM file ### -angle_flag = False; torsion_flag = False; improp_flag = False -for i in range(len(f)): - if angle_def[i] == 'WARN': - angle_flag = True - if torsion_def[i] == 'WARN': - torsion_flag = True - if improp_def[i] == 'WARN': - improp_flag = True - -### Check which units to use, trip convert flags ### -length_flag = False; energy_flag = False; density_flag = False -if length[0] != 'ANGSTROM': - length_flag = True -if energy[0] != 'KCAL/MOL': - energy_flag = True -if density[0] != 'G/CC': - density_flag = True -if manual_units == True: - length_flag = False - energy_flag = False - density_flag = False -Units(length_flag, energy_flag, density_flag) - -### Read Whole File, save to lists ### -# Non-crucial sections include -# BONDS, ANGLE, TORSION, IMPROP, NONBOND -# Read all sections every time, only output sections when flags tripped -f = [open(fname, 'r') for fname in filenames] -masses = []; nonbond = []; bond = []; angle = []; torsion = []; improp = [] -equiv = [] -for i in range(len(f)): - MASS = False - NONBOND = False - BOND = False - ANGLE = False - TORSION = False - IMPROP = False - EQUIV = False - for line in f[i]: - if line.strip() == 'ITEM MASS': - MASS = True - elif line.strip() == 'ITEM END': - MASS = False - elif MASS: - if not line.startswith('#'): - if not line.startswith('\n'): - masses.append(line.strip().split()) - if line.strip() == 'ITEM NONBOND': - NONBOND = True - elif line.strip() == 'ITEM END': - NONBOND = False - elif NONBOND: - if not line.startswith('#'): - if not line.startswith('\n'): - nonbond.append(line.strip().split()) - if line.strip() == 'ITEM BOND': - BOND = True - elif line.strip() == 'ITEM END': - BOND = False - elif BOND: - if not line.startswith('#'): - if not line.startswith('\n'): - bond.append(line.strip().split()) - if line.strip() == 'ITEM ANGLE': - ANGLE = True - elif line.strip() == 'ITEM END': - ANGLE = False - elif ANGLE: - if not line.startswith('#'): - if not line.startswith('\n'): - angle.append(line.strip().split()) - if line.strip() == 'ITEM TORSION': - TORSION = True - elif line.strip() == 'ITEM END': - TORSION = False - elif TORSION: - if not line.startswith('#'): - if not line.startswith('\n'): - torsion.append(line.strip().split()) - if line.strip() == 'ITEM IMPROP': - IMPROP = True - elif line.strip() == 'ITEM END': - IMPROP = False - elif IMPROP: - if not line.startswith('#'): - if not line.startswith('\n'): - improp.append(line.strip().split()) - if line.strip() == 'ITEM EQUIVALENCE': - EQUIV = True - elif line.strip() == 'ITEM END': - EQUIV = False - elif EQUIV: - if not line.startswith('#'): - if not line.startswith('\n'): - equiv.append(line.strip().split()) -### Close prm files ### -for fname in f: - fname.close() - -### Sanity checks before writing LT files ### -# Check Equiv -for i in range(len(equiv)): - for j in range(len(equiv)): - if (equiv[i][0] == equiv[j][0]) and (equiv[i] != equiv[j]): - print 'Error: Identical atom types with different equivalences' - Abort() -# Check Masses -for i in range(len(masses)): - for j in range(len(masses)): - if (masses[i][0] == masses[j][0]) and (masses[i][1] != masses[j][1]): - print 'Error: Identical types with different mass' - Abort() -# Check Nonbond -for i in range(len(nonbond)): - for j in range(len(nonbond)): - if (nonbond[i][0] == nonbond[j][0]) and (nonbond[i][1] == nonbond[j][1]) and ((nonbond[i][2] != nonbond[j][2]) or (nonbond[i][3] != nonbond[j][3])): - print 'Error: Identical types with different pair-interactions' - Abort() - -### Remove double equivalences ### -for i in range(len(equiv)): - once = True - for j in range(len(equiv)): - if (equiv[i][0] == equiv[j][0]) and once: - once = False - elif (equiv[i][0] == equiv[j][0]): - equiv[j][1] = None - equiv[j][2] = 'duplicate' - if len(equiv[i]) != 6: - print 'Warning: Incorrect equivalence formatting for type %s' % equiv[i][0],\ - 'skipping type, topology may not be complete' - equiv[i][1] = None - equiv[i][2] = 'invalid_format' - -### Check Potential Styles and Set Units ### -ChkPotential(manual_units, angle_flag, torsion_flag, improp_flag) - -### Set output LT file ### -fname = 'ff_output.lt' -if name == '': - fname = ffname[0] + '.lt' -else: - fname = name + '.lt' -foutput = open(fname, 'w') - -### Output to LT format ### -foutput.write('# Autogenerated by EMC 2 LT tool v%s on %s\n' % (__version__, str(datetime.date.today()))) -foutput.write('#\n# ') -for i in range(len(sys.argv)): - foutput.write('%s ' % sys.argv[i]) -foutput.write('\n') -foutput.write('#\n') -foutput.write('# Adapted from EMC by Pieter J. in \'t Veld\n') -foutput.write('# Originally written as, FFNAME:%s STYLE:%s VERSION:%s on %s %s\n' % - (ffname[0], fftype[0], version[0], created1[0], created2[0])) -foutput.write('\n') -foutput.write('%s {\n' % ffname[0]) - -# Charges not necessary? emc file assign charges in smiles, which would -# be in the per-molecule files created by moltemplate user... not here - -### Mass Info ### -foutput.write(' write_once("Data Masses") {\n') -for i in range(len(masses)): - if equiv[i][1] != None: - foutput.write(' @atom:%s %f # %s\n' % - (masses[i][0], float(masses[i][1]), masses[i][0])) -foutput.write(' } # end of atom masses\n\n') - -### Equiv Info ### -# Write Equivalence -foutput.write(' # ----- EQUIVALENCE CATEGORIES for bonded interaction lookup -----\n') -for i in range(len(equiv)): - if equiv[i][1] != None: - foutput.write(' replace{ @atom:%s @atom:%s_b%s_a%s_d%s_i%s}\n' % - (equiv[i][0], equiv[i][0], equiv[i][2], equiv[i][3], equiv[i][4], equiv[i][5])) -foutput.write(' # END EQUIVALENCE\n\n') - -### Nonbonded Info ### -if pstyle == '': - print 'Warning: no non-bonded potential provided, assuming lj/cut/coul/long' - pstyle = 'lj/cut/coul/long' -foutput.write(' write_once("In Settings") {\n') -foutput.write(' # ----- Non-Bonded interactions -----\n') -# Add new types from equivalence -for i in range(len(equiv)): - once = True - for j in range(len(nonbond)): - # Get terms for new types - if (equiv[i][0] != equiv[i][1]) and (equiv[i][1] == nonbond[j][0]): - if not equiv[i][1] == nonbond[j][1]: - line = '%s %s %s %s' % (equiv[i][0], nonbond[j][1], nonbond[j][2], nonbond[j][3]) - nonbond.append(line.split()) - if once: - once = False - line = '%s %s %s %s' % (equiv[i][0], equiv[i][0], nonbond[j][2], nonbond[j][3]) - nonbond.append(line.split()) - if (equiv[i][0] != equiv[i][1]) and (equiv[i][1] == nonbond[j][1]): - line = '%s %s %s %s' % (equiv[i][0], nonbond[j][0], nonbond[j][2], nonbond[j][3]) - if line.split() != nonbond[-1]: - nonbond.append(line.split()) -for i in range(len(nonbond)): - atom1name = None - atom2name = None - # Cross Terms + Diagonal, normal - for j in range(len(equiv)): - if nonbond[i][0] == equiv[j][0]: - atom1name = '%s_b%s_a%s_d%s_i%s' % (nonbond[i][0], equiv[j][2], equiv[j][3], equiv[j][4], equiv[j][5]) - if nonbond[i][1] == equiv[j][0]: - atom2name = '%s_b%s_a%s_d%s_i%s' % (nonbond[i][1], equiv[j][2], equiv[j][3], equiv[j][4], equiv[j][5]) - #foutput.write(' pair_coeff @atom:%s @atom:%s %s %f %f' % - # (nonbond[i][0], nonbond[i][1], pstyle, float(nonbond[i][2])*econv, float(nonbond[i][2])*lconv)) - foutput.write(' pair_coeff @atom:%s @atom:%s %s %f %f' % - (atom1name, atom2name, pstyle, float(nonbond[i][3])*econv, float(nonbond[i][2])*lconv)) - foutput.write(' # %s-%s\n' % (nonbond[i][0], nonbond[i][1])) -foutput.write(' } # end of nonbonded parameters\n\n') - -### Bond Info ### -if bstyle == '': - print 'Warning: no bond potential provided, assuming harmonic' - bstyle == 'harmonic' -foutput.write(' write_once("In Settings") {\n') -foutput.write(' # ----- Bonds -----\n') -for i in range(len(bond)): - foutput.write(' bond_coeff @bond:%s-%s %s %f %f' % - (bond[i][0], bond[i][1], bstyle, float(bond[i][2])*beconv, float(bond[i][3])*lconv)) - foutput.write(' # %s-%s\n' % (bond[i][0], bond[i][1])) -foutput.write(' }\n\n') -foutput.write(' write_once("Data Bonds By Type") {\n') -for i in range(len(bond)): - foutput.write(' @bond:%s-%s @atom:*_b%s_a*_d*_i* @atom:*_b%s_a*_d*_i*\n' % - (bond[i][0], bond[i][1], bond[i][0], bond[i][1])) -foutput.write(' } # end of bonds\n\n') - -### Angle Info ### -if angle_flag: - if astyle == '': - print 'Warning: no angle potential provided, assuming harmonic' - astyle == 'harmonic' - foutput.write(' write_once("In Settings") {\n') - foutput.write(' # ----- Angles -----\n') - for i in range(len(angle)): - foutput.write(' angle_coeff @angle:%s-%s-%s %s %f %f' % - (angle[i][0], angle[i][1], angle[i][2], astyle, float(angle[i][3])*aeconv, float(angle[i][4]))) - foutput.write(' # %s-%s-%s\n' % (angle[i][0], angle[i][1], angle[i][2])) - foutput.write(' }\n\n') - foutput.write(' write_once("Data Angles By Type") {\n') - for i in range(len(angle)): - foutput.write(' @angle:%s-%s-%s @atom:*_b*_a%s_d*_i* @atom:*_b*_a%s_d*_i* @atom:*_b*_a%s_d*_i*\n' % - (angle[i][0], angle[i][1], angle[i][2], angle[i][0], angle[i][1], angle[i][2])) - foutput.write(' } # end of angles\n\n') - -### Torsion/Dihedral Info ###a -# Incomplete -if torsion_flag: - if dstyle == '': - print 'Warning: no dihedral/torsion potential provided, assuming harmonic' - dstyle == 'harmonic' - foutput.write(' write_once("In Settings") {\n') - foutput.write(' # ----- Dihedrals -----\n') - for i in range(len(torsion)): - foutput.write(' dihedral_coeff @dihedral:%s-%s-%s-%s %s %f %f %f %f\n' % - (torsion[i][0], torsion[i][1], torsion[i][2], torsion[i][3], dstyle, float(torsion[i][4])*deconv, float(torsion[i][5]), float(torsion[i][6]))) - foutput.write(' }\n\n') - foutput.write(' write_once("Data Dihedrals By Type") {\n') - for i in range(len(torsion)): - foutput.write(' @dihedral:%s-%s-%s-%s @atom:*_b*_a*_d%s_i* @atom:*_b*_a*_d%s_i* @atom:*_b*_a*_d%s_i* @atom:*_b*_a*_d%s_i*' % - (torsion[i][0], torsion[i][1], torsion[i][2], torsion[i][3], torsion[i][0], torsion[i][1], torsion[i][2], torsion[i][3])) - foutput.write(' } # end of dihedrals\n\n') - -### Improper Info ### -# Incomplete -ieconv = econv # improper coeff conversion -if improp_flag: - if istyle == '': - print 'Warning: no improper potential provided, assuming harmonic' - istyle == 'harmonic' - foutput.write(' write_once("In Settings") {\n') - foutput.write(' # ----- Impropers -----\n') - # As discussed, a check for convention of impropers is probably needed here - for i in range(len(improp)): - foutput.write(' improper_coeff @improper:%s-%s-%s-%s %s %f %f\n' % - (improp[i][0], improp[i][1], improp[i][2], improp[i][3], istyle, - float(improp[i][4]), float(improp[i][5]))) - foutput.write(' }\n\n') - foutput.write(' write_once("Data Impropers By Type") {\n') - for i in range(len(improp)): - foutput.write(' @improper:%s-%s-%s-%s @atom:*_b*_a*_d*_i%s @atom:*_b*_a*_d*_i%s @atom:*_b*_a*_d*_i%s @atom:*_b*_a*_d*_i%s' % - (improp[i][0], improp[i][1], improp[i][2], improp[i][3], improp[i][0], improp[i][1], improp[i][2], improp[i][3])) - foutput.write(' } # end of impropers\n\n') - -### Initialization Info ### -print 'Warning: Attempting to write generic "In Init" section,',\ - 'further modification after this script is extremely likely' -WriteInit() - -foutput.write('} # %s\n' % ffname[0]) -sys.exit() diff --git a/tools/moltemplate/moltemplate/force_fields/martini_original_format/README.txt b/tools/moltemplate/moltemplate/force_fields/martini_original_format/README.txt new file mode 100644 index 0000000000..2e20697a43 --- /dev/null +++ b/tools/moltemplate/moltemplate/force_fields/martini_original_format/README.txt @@ -0,0 +1,42 @@ +The files in this directory are used to create the "martini.lt" file +(containing MARTINI force field parameters for moltemplate). +These .PRM files are distributed with "EMC" written by Pieter J. in 't Veld. +The original MARTINI files are distributed at http://cgmartini.nl + +Conversion from EMC (.PRM) format to moltemplate (.LT) format was +done using the "emcprm2lt.py" script written by David Stelter. +Here is an example how to use the emcprm2lt.py script: + +emcprm2lt.py martini.prm lipids.prm cholesterol.prm --bond-style=harmonic --angle-style=cosine/squared --pair-style=lj/gromacs/coul/gromacs --name=martini + +This will generate a file named "martini.lt" which (in this example) +only includes the force field parameters for lipids and cholestrol. +Later you can define new molecules in moltemplate using: + +import "martini.lt" +NewMolecule inherits MARTINI { + write("Data Atoms") {...atom coordinates and types go here...} + write("Data Bond List") {...list of bonds goes here...} +} + +See "DOPC.lt" in /examples/coarse_grained/MARTINI_examples/ for more details. + +(Note: The rigid bond constraints used for cholesterol in the original MARTINI + model for cholesterol have been replaced by stiff but flexible bonds. + There is a trade-off between increasing the stiffness of the bonds + and using larger time steps. To alter the stiffness of the bonds + edit the "ITEM BOND" section of the "cholesterol.prm", edit the "k" + parameters (3rd column, for the "S..." entries, and run "emcprm2lt.py" again.) + +---- Credits: ---- +emcprm2lt.py was written by David Stelter +EMC was written by Pieter J. in 't Veld +MARTINI was created by S.J. Marrink and coworkers (http://cgmartini.nl) + +---- additional citation request ---- + +Since we borrowed force field parameters from files distributed with EMC, +if you use files generated by "emcprm2lt.py", please also cite the EMC paper: +P. J. in ‘t Veld and G. C. Rutledge, Macromolecules 2003, 36, 7358 + + diff --git a/tools/moltemplate/moltemplate/force_fields/martini/aminoacids.prm b/tools/moltemplate/moltemplate/force_fields/martini_original_format/aminoacids.prm similarity index 100% rename from tools/moltemplate/moltemplate/force_fields/martini/aminoacids.prm rename to tools/moltemplate/moltemplate/force_fields/martini_original_format/aminoacids.prm diff --git a/tools/moltemplate/moltemplate/force_fields/martini/cholesterol.prm b/tools/moltemplate/moltemplate/force_fields/martini_original_format/cholesterol.prm similarity index 98% rename from tools/moltemplate/moltemplate/force_fields/martini/cholesterol.prm rename to tools/moltemplate/moltemplate/force_fields/martini_original_format/cholesterol.prm index 7d78eed759..f9b4f7b8d0 100644 --- a/tools/moltemplate/moltemplate/force_fields/martini/cholesterol.prm +++ b/tools/moltemplate/moltemplate/force_fields/martini_original_format/cholesterol.prm @@ -78,6 +78,7 @@ SP12 SP1 SP12 SP12 SP12 SP12 ITEM END # Bond parameters +# To change the bond stiffness, edit the "k" parameter ITEM BOND diff --git a/tools/moltemplate/moltemplate/force_fields/martini/lipids.prm b/tools/moltemplate/moltemplate/force_fields/martini_original_format/lipids.prm similarity index 100% rename from tools/moltemplate/moltemplate/force_fields/martini/lipids.prm rename to tools/moltemplate/moltemplate/force_fields/martini_original_format/lipids.prm diff --git a/tools/moltemplate/moltemplate/force_fields/martini/martini.prm b/tools/moltemplate/moltemplate/force_fields/martini_original_format/martini.prm similarity index 100% rename from tools/moltemplate/moltemplate/force_fields/martini/martini.prm rename to tools/moltemplate/moltemplate/force_fields/martini_original_format/martini.prm diff --git a/tools/moltemplate/moltemplate/force_fields/martini/polymers.prm b/tools/moltemplate/moltemplate/force_fields/martini_original_format/polymers.prm similarity index 100% rename from tools/moltemplate/moltemplate/force_fields/martini/polymers.prm rename to tools/moltemplate/moltemplate/force_fields/martini_original_format/polymers.prm diff --git a/tools/moltemplate/moltemplate/force_fields/martini/sugars.prm b/tools/moltemplate/moltemplate/force_fields/martini_original_format/sugars.prm similarity index 100% rename from tools/moltemplate/moltemplate/force_fields/martini/sugars.prm rename to tools/moltemplate/moltemplate/force_fields/martini_original_format/sugars.prm diff --git a/tools/moltemplate/moltemplate/force_fields/oplsaa.lt b/tools/moltemplate/moltemplate/force_fields/oplsaa.lt index 92b2628df5..7bb69a7445 100644 --- a/tools/moltemplate/moltemplate/force_fields/oplsaa.lt +++ b/tools/moltemplate/moltemplate/force_fields/oplsaa.lt @@ -1,6 +1,18 @@ -# This file contains OPLSAA parameters and rules for creating -# angle, dihedral, and improper interactions according to OPLSAA conventions. -# These parameters are taken from those distributed with BOSS Version 4.8. +# This file contains OPLSAA parameters and rules for creating angle, dihedral, +# and improper interactions according to OPLSAA conventions, taken from +# "OPLS All-Atom Parameters for Organic Molecules, Ions, +# Peptides & Nucleic Acids, July 2008" and distributed with BOSS Version 4.8. +# This file was generated automatically using this script: +# +# tinkerparm2lt.py -name OPLSAA -file oplsaa.prm -dihedral-style opls -zeropad 3 +# +# The "oplsaa.prm" file was downloaded on 2018-6-15 from the TINKER website +# https://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm +# (Corrections to imrpopers were added by David Huang (adelaide.edu.au)) +# (Additional conversion details are explained at the end of this file.) +# Urey-Bradley parameters are not included, and a quadratic energy function +# is used (rather than a cosine) for the improper interactions (in order +# to take advantage of available GPU acceleration in LAMMPS at this time). # # USAGE: You can create molecules using this force-field this way: # @@ -13,6 +25,8 @@ # } # } # +# You can omit the atom charge in your molecule definition. +# (Partial charges will be assigned later according to the force field rules.) # Responsibility for choosing the atom types (eg "@atom:88", "@atom:89") falls # on the user. You must select the type of each atom in the molecule carefully # by looking at the description in the "In Charges" section of this file @@ -23,7 +37,6 @@ - OPLSAA { # Below we will use lammps "set" command to assign atom charges @@ -1860,912 +1873,912 @@ OPLSAA { # @atom names we have been using abovee are equivalent to the complete # @atom names used below: - replace{ @atom:1 @atom:1_b1_a1_d1_i1 } - replace{ @atom:2 @atom:2_b2_a2_d2_i2 } - replace{ @atom:3 @atom:3_b3_a3_d3_i3 } - replace{ @atom:4 @atom:4_b4_a4_d4_i4 } - replace{ @atom:5 @atom:5_b5_a5_d5_i5 } - replace{ @atom:6 @atom:6_b6_a6_d6_i6 } - replace{ @atom:7 @atom:7_b7_a7_d7_i7 } - replace{ @atom:8 @atom:8_b8_a8_d8_i8 } - replace{ @atom:9 @atom:9_b6_a6_d6_i6 } - replace{ @atom:10 @atom:10_b6_a6_d6_i6 } - replace{ @atom:11 @atom:11_b6_a6_d6_i6 } - replace{ @atom:12 @atom:12_b6_a6_d6_i6 } - replace{ @atom:13 @atom:13_b2_a2_d2_i2 } - replace{ @atom:14 @atom:14_b9_a9_d9_i9 } - replace{ @atom:15 @atom:15_b10_a10_d10_i10 } - replace{ @atom:16 @atom:16_b11_a11_d11_i11 } - replace{ @atom:17 @atom:17_b12_a12_d12_i12 } - replace{ @atom:18 @atom:18_b13_a13_d13_i13 } - replace{ @atom:19 @atom:19_b14_a14_d14_i14 } - replace{ @atom:20 @atom:20_b5_a5_d5_i5 } - replace{ @atom:21 @atom:21_b7_a7_d7_i7 } - replace{ @atom:22 @atom:22_b6_a6_d6_i6 } - replace{ @atom:23 @atom:23_b2_a2_d2_i2 } - replace{ @atom:24 @atom:24_b15_a15_d15_i15 } - replace{ @atom:25 @atom:25_b15_a15_d15_i15 } - replace{ @atom:26 @atom:26_b16_a16_d16_i16 } - replace{ @atom:27 @atom:27_b16_a16_d16_i16 } - replace{ @atom:28 @atom:28_b17_a17_d17_i17 } - replace{ @atom:29 @atom:29_b17_a17_d17_i17 } - replace{ @atom:30 @atom:30_b6_a6_d6_i6 } - replace{ @atom:31 @atom:31_b2_a2_d2_i2 } - replace{ @atom:32 @atom:32_b6_a6_d6_i6 } - replace{ @atom:33 @atom:33_b2_a2_d2_i2 } - replace{ @atom:34 @atom:34_b6_a6_d6_i6 } - replace{ @atom:35 @atom:35_b2_a2_d2_i2 } - replace{ @atom:36 @atom:36_b18_a18_d18_i18 } - replace{ @atom:37 @atom:37_b19_a19_d19_i19 } - replace{ @atom:38 @atom:38_b6_a6_d6_i6 } - replace{ @atom:39 @atom:39_b10_a10_d10_i10 } - replace{ @atom:40 @atom:40_b13_a13_d13_i13 } - replace{ @atom:41 @atom:41_b20_a20_d20_i20 } - replace{ @atom:42 @atom:42_b6_a6_d6_i6 } - replace{ @atom:43 @atom:43_b2_a2_d2_i2 } - replace{ @atom:44 @atom:44_b2_a2_d2_i2 } - replace{ @atom:45 @atom:45_b21_a21_d21_i21 } - replace{ @atom:46 @atom:46_b10_a10_d10_i10 } - replace{ @atom:47 @atom:47_b21_a21_d21_i21 } - replace{ @atom:48 @atom:48_b13_a13_d13_i13 } - replace{ @atom:49 @atom:49_b21_a21_d21_i21 } - replace{ @atom:50 @atom:50_b22_a22_d22_i22 } - replace{ @atom:51 @atom:51_b23_a23_d23_i23 } - replace{ @atom:52 @atom:52_b6_a6_d6_i6 } - replace{ @atom:53 @atom:53_b4_a4_d4_i4 } - replace{ @atom:54 @atom:54_b24_a24_d24_i24 } - replace{ @atom:55 @atom:55_b3_a3_d3_i3 } - replace{ @atom:56 @atom:56_b6_a6_d6_i6 } - replace{ @atom:57 @atom:57_b25_a25_d25_i25 } - replace{ @atom:58 @atom:58_b26_a26_d26_i26 } - replace{ @atom:59 @atom:59_b27_a27_d27_i27 } - replace{ @atom:60 @atom:60_b28_a28_d28_i28 } - replace{ @atom:61 @atom:61_b29_a29_d29_i29 } - replace{ @atom:62 @atom:62_b30_a30_d30_i30 } - replace{ @atom:63 @atom:63_b31_a31_d31_i31 } - replace{ @atom:64 @atom:64_b32_a32_d32_i32 } - replace{ @atom:65 @atom:65_b31_a31_d31_i31 } - replace{ @atom:66 @atom:66_b32_a32_d32_i32 } - replace{ @atom:67 @atom:67_b33_a33_d33_i33 } - replace{ @atom:68 @atom:68_b34_a34_d34_i34 } - replace{ @atom:69 @atom:69_b35_a35_d35_i35 } - replace{ @atom:70 @atom:70_b36_a36_d36_i36 } - replace{ @atom:71 @atom:71_b37_a37_d37_i37 } - replace{ @atom:72 @atom:72_b38_a38_d38_i38 } - replace{ @atom:73 @atom:73_b39_a39_d39_i39 } - replace{ @atom:74 @atom:74_b40_a40_d40_i40 } - replace{ @atom:75 @atom:75_b41_a41_d41_i41 } - replace{ @atom:76 @atom:76_b42_a42_d42_i42 } - replace{ @atom:77 @atom:77_b43_a43_d43_i43 } - replace{ @atom:78 @atom:78_b44_a44_d44_i44 } - replace{ @atom:79 @atom:79_b45_a45_d45_i45 } - replace{ @atom:80 @atom:80_b13_a13_d13_i13 } - replace{ @atom:81 @atom:81_b13_a13_d13_i13 } - replace{ @atom:82 @atom:82_b13_a13_d13_i13 } - replace{ @atom:83 @atom:83_b13_a13_d13_i13 } - replace{ @atom:84 @atom:84_b13_a13_d13_i13 } - replace{ @atom:85 @atom:85_b46_a46_d46_i46 } - replace{ @atom:86 @atom:86_b47_a47_d47_i47 } - replace{ @atom:87 @atom:87_b47_a47_d47_i47 } - replace{ @atom:88 @atom:88_b47_a47_d47_i47 } - replace{ @atom:89 @atom:89_b46_a46_d46_i46 } - replace{ @atom:90 @atom:90_b48_a48_d48_i48 } - replace{ @atom:91 @atom:91_b49_a49_d49_i49 } - replace{ @atom:92 @atom:92_b48_a48_d48_i48 } - replace{ @atom:93 @atom:93_b13_a13_d13_i13 } - replace{ @atom:94 @atom:94_b13_a13_d13_i13 } - replace{ @atom:95 @atom:95_b50_a50_d50_i50 } - replace{ @atom:96 @atom:96_b5_a5_d5_i5 } - replace{ @atom:97 @atom:97_b7_a7_d7_i7 } - replace{ @atom:98 @atom:98_b46_a46_d46_i46 } - replace{ @atom:99 @atom:99_b13_a13_d13_i13 } - replace{ @atom:100 @atom:100_b13_a13_d13_i13 } - replace{ @atom:101 @atom:101_b13_a13_d13_i13 } - replace{ @atom:102 @atom:102_b13_a13_d13_i13 } - replace{ @atom:103 @atom:103_b13_a13_d13_i13 } - replace{ @atom:104 @atom:104_b5_a5_d5_i5 } - replace{ @atom:105 @atom:105_b7_a7_d7_i7 } - replace{ @atom:106 @atom:106_b1_a1_d1_i1 } - replace{ @atom:107 @atom:107_b46_a46_d46_i46 } - replace{ @atom:108 @atom:108_b48_a48_d48_i48 } - replace{ @atom:109 @atom:109_b5_a5_d5_i5 } - replace{ @atom:110 @atom:110_b7_a7_d7_i7 } - replace{ @atom:111 @atom:111_b5_a5_d5_i5 } - replace{ @atom:112 @atom:112_b7_a7_d7_i7 } - replace{ @atom:113 @atom:113_b5_a5_d5_i5 } - replace{ @atom:114 @atom:114_b7_a7_d7_i7 } - replace{ @atom:115 @atom:115_b13_a13_d13_i13 } - replace{ @atom:116 @atom:116_b13_a13_d13_i13 } - replace{ @atom:117 @atom:117_b13_a13_d13_i13 } - replace{ @atom:118 @atom:118_b46_a46_d46_i46 } - replace{ @atom:119 @atom:119_b20_a20_d20_i20 } - replace{ @atom:120 @atom:120_b50_a50_d50_i50 } - replace{ @atom:121 @atom:121_b20_a20_d20_i20 } - replace{ @atom:122 @atom:122_b20_a20_d20_i20 } - replace{ @atom:123 @atom:123_b13_a13_d13_i13 } - replace{ @atom:124 @atom:124_b13_a13_d13_i13 } - replace{ @atom:125 @atom:125_b13_a13_d13_i13 } - replace{ @atom:126 @atom:126_b13_a13_d13_i13 } - replace{ @atom:127 @atom:127_b46_a46_d46_i46 } - replace{ @atom:128 @atom:128_b20_a20_d20_i20 } - replace{ @atom:129 @atom:129_b5_a5_d5_i5 } - replace{ @atom:130 @atom:130_b7_a7_d7_i7 } - replace{ @atom:131 @atom:131_b51_a51_d51_i51 } - replace{ @atom:132 @atom:132_b46_a46_d46_i46 } - replace{ @atom:133 @atom:133_b51_a51_d51_i51 } - replace{ @atom:134 @atom:134_b46_a46_d46_i46 } - replace{ @atom:135 @atom:135_b51_a51_d51_i51 } - replace{ @atom:136 @atom:136_b46_a46_d46_i46 } - replace{ @atom:137 @atom:137_b51_a51_d51_i51 } - replace{ @atom:138 @atom:138_b46_a46_d46_i46 } - replace{ @atom:139 @atom:139_b51_a51_d51_i51 } - replace{ @atom:140 @atom:140_b51_a51_d51_i51 } - replace{ @atom:141 @atom:141_b48_a48_d48_i48 } - replace{ @atom:142 @atom:142_b15_a15_d15_i15 } - replace{ @atom:143 @atom:143_b15_a15_d15_i15 } - replace{ @atom:144 @atom:144_b16_a16_d16_i16 } - replace{ @atom:145 @atom:145_b16_a16_d16_i16 } - replace{ @atom:146 @atom:146_b17_a17_d17_i17 } - replace{ @atom:147 @atom:147_b17_a17_d17_i17 } - replace{ @atom:148 @atom:148_b13_a13_d13_i13 } - replace{ @atom:149 @atom:149_b13_a13_d13_i13 } - replace{ @atom:150 @atom:150_b13_a13_d13_i13 } - replace{ @atom:151 @atom:151_b13_a13_d13_i13 } - replace{ @atom:152 @atom:152_b13_a13_d13_i13 } - replace{ @atom:153 @atom:153_b13_a13_d13_i13 } - replace{ @atom:154 @atom:154_b13_a13_d13_i13 } - replace{ @atom:155 @atom:155_b13_a13_d13_i13 } - replace{ @atom:156 @atom:156_b13_a13_d13_i13 } - replace{ @atom:157 @atom:157_b13_a13_d13_i13 } - replace{ @atom:158 @atom:158_b13_a13_d13_i13 } - replace{ @atom:159 @atom:159_b13_a13_d13_i13 } - replace{ @atom:160 @atom:160_b13_a13_d13_i13 } - replace{ @atom:161 @atom:161_b13_a13_d13_i13 } - replace{ @atom:162 @atom:162_b13_a13_d13_i13 } - replace{ @atom:163 @atom:163_b48_a48_d48_i48 } - replace{ @atom:164 @atom:164_b16_a16_d16_i16 } - replace{ @atom:165 @atom:165_b13_a13_d13_i13 } - replace{ @atom:166 @atom:166_b13_a13_d13_i13 } - replace{ @atom:167 @atom:167_b13_a13_d13_i13 } - replace{ @atom:168 @atom:168_b21_a21_d21_i21 } - replace{ @atom:169 @atom:169_b47_a47_d47_i47 } - replace{ @atom:170 @atom:170_b48_a48_d48_i48 } - replace{ @atom:171 @atom:171_b13_a13_d13_i13 } - replace{ @atom:172 @atom:172_b13_a13_d13_i13 } - replace{ @atom:173 @atom:173_b3_a3_d3_i3 } - replace{ @atom:174 @atom:174_b3_a3_d3_i3 } - replace{ @atom:175 @atom:175_b3_a3_d3_i3 } - replace{ @atom:176 @atom:176_b3_a3_d3_i3 } - replace{ @atom:177 @atom:177_b3_a3_d3_i3 } - replace{ @atom:178 @atom:178_b4_a4_d4_i4 } - replace{ @atom:179 @atom:179_b24_a24_d24_i24 } - replace{ @atom:180 @atom:180_b24_a24_d24_i24 } - replace{ @atom:181 @atom:181_b24_a24_d24_i24 } - replace{ @atom:182 @atom:182_b45_a45_d45_i45 } - replace{ @atom:183 @atom:183_b45_a45_d45_i45 } - replace{ @atom:184 @atom:184_b13_a13_d13_i13 } - replace{ @atom:185 @atom:185_b13_a13_d13_i13 } - replace{ @atom:186 @atom:186_b13_a13_d13_i13 } - replace{ @atom:187 @atom:187_b13_a13_d13_i13 } - replace{ @atom:188 @atom:188_b13_a13_d13_i13 } - replace{ @atom:189 @atom:189_b3_a3_d3_i3 } - replace{ @atom:190 @atom:190_b4_a4_d4_i4 } - replace{ @atom:191 @atom:191_b24_a24_d24_i24 } - replace{ @atom:192 @atom:192_b45_a45_d45_i45 } - replace{ @atom:193 @atom:193_b24_a24_d24_i24 } - replace{ @atom:194 @atom:194_b3_a3_d3_i3 } - replace{ @atom:195 @atom:195_b4_a4_d4_i4 } - replace{ @atom:196 @atom:196_b45_a45_d45_i45 } - replace{ @atom:197 @atom:197_b46_a46_d46_i46 } - replace{ @atom:198 @atom:198_b13_a13_d13_i13 } - replace{ @atom:199 @atom:199_b13_a13_d13_i13 } - replace{ @atom:200 @atom:200_b13_a13_d13_i13 } - replace{ @atom:201 @atom:201_b13_a13_d13_i13 } - replace{ @atom:202 @atom:202_b48_a48_d48_i48 } - replace{ @atom:203 @atom:203_b19_a19_d19_i19 } - replace{ @atom:204 @atom:204_b18_a18_d18_i18 } - replace{ @atom:205 @atom:205_b48_a48_d48_i48 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@atom:308_b60_a60_d60_i60 } - replace{ @atom:309 @atom:309_b3_a3_d3_i3 } - replace{ @atom:310 @atom:310_b45_a45_d45_i45 } - replace{ @atom:311 @atom:311_b55_a55_d55_i55 } - replace{ @atom:312 @atom:312_b45_a45_d45_i45 } - replace{ @atom:313 @atom:313_b4_a4_d4_i4 } - replace{ @atom:314 @atom:314_b13_a13_d13_i13 } - replace{ @atom:315 @atom:315_b46_a46_d46_i46 } - replace{ @atom:316 @atom:316_b13_a13_d13_i13 } - replace{ @atom:317 @atom:317_b46_a46_d46_i46 } - replace{ @atom:318 @atom:318_b13_a13_d13_i13 } - replace{ @atom:319 @atom:319_b46_a46_d46_i46 } - replace{ @atom:320 @atom:320_b57_a57_d57_i57 } - replace{ @atom:321 @atom:321_b3_a3_d3_i3 } - replace{ @atom:322 @atom:322_b57_a57_d57_i57 } - replace{ @atom:323 @atom:323_b48_a48_d48_i48 } - replace{ @atom:324 @atom:324_b47_a47_d47_i47 } - replace{ @atom:325 @atom:325_b47_a47_d47_i47 } - replace{ @atom:326 @atom:326_b45_a45_d45_i45 } - replace{ @atom:327 @atom:327_b4_a4_d4_i4 } - replace{ @atom:328 @atom:328_b45_a45_d45_i45 } - 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@atom:471_b56_a56_d56_i56 } - replace{ @atom:472 @atom:472_b59_a59_d59_i59 } - replace{ @atom:473 @atom:473_b48_a48_d48_i48 } - replace{ @atom:474 @atom:474_b48_a48_d48_i48 } - replace{ @atom:475 @atom:475_b49_a49_d49_i49 } - replace{ @atom:476 @atom:476_b49_a49_d49_i49 } - replace{ @atom:477 @atom:477_b49_a49_d49_i49 } - replace{ @atom:478 @atom:478_b56_a56_d56_i56 } - replace{ @atom:479 @atom:479_b48_a48_d48_i48 } - replace{ @atom:480 @atom:480_b48_a48_d48_i48 } - replace{ @atom:481 @atom:481_b49_a49_d49_i49 } - replace{ @atom:482 @atom:482_b49_a49_d49_i49 } - replace{ @atom:483 @atom:483_b57_a57_d57_i57 } - replace{ @atom:484 @atom:484_b84_a84_d84_i84 } - replace{ @atom:485 @atom:485_b87_a87_d87_i87 } - replace{ @atom:486 @atom:486_b45_a45_d45_i45 } - replace{ @atom:487 @atom:487_b49_a49_d49_i49 } - replace{ @atom:488 @atom:488_b49_a49_d49_i49 } - replace{ @atom:489 @atom:489_b57_a57_d57_i57 } - replace{ @atom:490 @atom:490_b61_a61_d61_i61 } - replace{ @atom:491 @atom:491_b88_a88_d88_i88 } - replace{ @atom:492 @atom:492_b87_a87_d87_i87 } - replace{ @atom:493 @atom:493_b84_a84_d84_i84 } - replace{ @atom:494 @atom:494_b45_a45_d45_i45 } - replace{ @atom:495 @atom:495_b49_a49_d49_i49 } - replace{ @atom:496 @atom:496_b49_a49_d49_i49 } - replace{ @atom:497 @atom:497_b49_a49_d49_i49 } - replace{ @atom:498 @atom:498_b57_a57_d57_i57 } - replace{ @atom:499 @atom:499_b82_a82_d82_i82 } - replace{ @atom:500 @atom:500_b61_a61_d61_i61 } - replace{ @atom:501 @atom:501_b83_a83_d83_i83 } - replace{ @atom:502 @atom:502_b84_a84_d84_i84 } - replace{ @atom:503 @atom:503_b45_a45_d45_i45 } - replace{ @atom:504 @atom:504_b49_a49_d49_i49 } - replace{ @atom:505 @atom:505_b49_a49_d49_i49 } - replace{ @atom:506 @atom:506_b49_a49_d49_i49 } - replace{ @atom:507 @atom:507_b20_a20_d20_i20 } - replace{ @atom:508 @atom:508_b84_a84_d84_i84 } - replace{ @atom:509 @atom:509_b87_a87_d87_i87 } - replace{ @atom:510 @atom:510_b49_a49_d49_i49 } - replace{ @atom:511 @atom:511_b49_a49_d49_i49 } - replace{ @atom:512 @atom:512_b20_a20_d20_i20 } - replace{ @atom:513 @atom:513_b82_a82_d82_i82 } - replace{ @atom:514 @atom:514_b61_a61_d61_i61 } - replace{ @atom:515 @atom:515_b83_a83_d83_i83 } - replace{ @atom:516 @atom:516_b84_a84_d84_i84 } - replace{ @atom:517 @atom:517_b49_a49_d49_i49 } - replace{ @atom:518 @atom:518_b49_a49_d49_i49 } - replace{ @atom:519 @atom:519_b49_a49_d49_i49 } - replace{ @atom:520 @atom:520_b20_a20_d20_i20 } - replace{ @atom:521 @atom:521_b61_a61_d61_i61 } - replace{ @atom:522 @atom:522_b88_a88_d88_i88 } - replace{ @atom:523 @atom:523_b87_a87_d87_i87 } - replace{ @atom:524 @atom:524_b84_a84_d84_i84 } - replace{ @atom:525 @atom:525_b49_a49_d49_i49 } - replace{ @atom:526 @atom:526_b49_a49_d49_i49 } - replace{ @atom:527 @atom:527_b49_a49_d49_i49 } - replace{ @atom:528 @atom:528_b57_a57_d57_i57 } - replace{ @atom:529 @atom:529_b84_a84_d84_i84 } - replace{ @atom:530 @atom:530_b87_a87_d87_i87 } - replace{ @atom:531 @atom:531_b48_a48_d48_i48 } - replace{ @atom:532 @atom:532_b48_a48_d48_i48 } - replace{ @atom:533 @atom:533_b48_a48_d48_i48 } - replace{ @atom:534 @atom:534_b48_a48_d48_i48 } - replace{ @atom:535 @atom:535_b81_a81_d81_i81 } - replace{ @atom:536 @atom:536_b60_a60_d60_i60 } - replace{ @atom:537 @atom:537_b45_a45_d45_i45 } - replace{ @atom:538 @atom:538_b49_a49_d49_i49 } - replace{ @atom:539 @atom:539_b49_a49_d49_i49 } - replace{ @atom:540 @atom:540_b49_a49_d49_i49 } - replace{ @atom:541 @atom:541_b49_a49_d49_i49 } - replace{ @atom:542 @atom:542_b49_a49_d49_i49 } - replace{ @atom:543 @atom:543_b49_a49_d49_i49 } - replace{ @atom:544 @atom:544_b56_a56_d56_i56 } - replace{ @atom:545 @atom:545_b48_a48_d48_i48 } - replace{ @atom:546 @atom:546_b48_a48_d48_i48 } - replace{ @atom:547 @atom:547_b48_a48_d48_i48 } - replace{ @atom:548 @atom:548_b48_a48_d48_i48 } - replace{ @atom:549 @atom:549_b48_a48_d48_i48 } - replace{ @atom:550 @atom:550_b48_a48_d48_i48 } - replace{ @atom:551 @atom:551_b48_a48_d48_i48 } - replace{ @atom:552 @atom:552_b48_a48_d48_i48 } - replace{ @atom:553 @atom:553_b48_a48_d48_i48 } - replace{ @atom:554 @atom:554_b49_a49_d49_i49 } - replace{ @atom:555 @atom:555_b49_a49_d49_i49 } - replace{ @atom:556 @atom:556_b49_a49_d49_i49 } - replace{ @atom:557 @atom:557_b49_a49_d49_i49 } - replace{ @atom:558 @atom:558_b49_a49_d49_i49 } - replace{ @atom:559 @atom:559_b49_a49_d49_i49 } - replace{ @atom:560 @atom:560_b49_a49_d49_i49 } - replace{ @atom:561 @atom:561_b56_a56_d56_i56 } - replace{ @atom:562 @atom:562_b59_a59_d59_i59 } - replace{ @atom:563 @atom:563_b56_a56_d56_i56 } - replace{ @atom:564 @atom:564_b60_a60_d60_i60 } - replace{ @atom:565 @atom:565_b60_a60_d60_i60 } - replace{ @atom:566 @atom:566_b48_a48_d48_i48 } - replace{ @atom:567 @atom:567_b61_a61_d61_i61 } - replace{ @atom:568 @atom:568_b62_a62_d62_i62 } - replace{ @atom:569 @atom:569_b57_a57_d57_i57 } - replace{ @atom:570 @atom:570_b49_a49_d49_i49 } - replace{ @atom:571 @atom:571_b49_a49_d49_i49 } - replace{ @atom:572 @atom:572_b49_a49_d49_i49 } - replace{ @atom:573 @atom:573_b45_a45_d45_i45 } - replace{ @atom:574 @atom:574_b16_a16_d16_i16 } - replace{ @atom:575 @atom:575_b82_a82_d82_i82 } - replace{ @atom:576 @atom:576_b61_a61_d61_i61 } - replace{ @atom:577 @atom:577_b83_a83_d83_i83 } - replace{ @atom:578 @atom:578_b84_a84_d84_i84 } - replace{ @atom:579 @atom:579_b49_a49_d49_i49 } - replace{ @atom:580 @atom:580_b49_a49_d49_i49 } - replace{ @atom:581 @atom:581_b49_a49_d49_i49 } - replace{ @atom:582 @atom:582_b56_a56_d56_i56 } - replace{ @atom:583 @atom:583_b59_a59_d59_i59 } - replace{ @atom:584 @atom:584_b49_a49_d49_i49 } - replace{ @atom:585 @atom:585_b48_a48_d48_i48 } - replace{ @atom:586 @atom:586_b13_a13_d13_i13 } - replace{ @atom:587 @atom:587_b56_a56_d56_i56 } - replace{ @atom:588 @atom:588_b48_a48_d48_i48 } - replace{ @atom:589 @atom:589_b48_a48_d48_i48 } - replace{ @atom:590 @atom:590_b48_a48_d48_i48 } - replace{ @atom:591 @atom:591_b48_a48_d48_i48 } - replace{ @atom:592 @atom:592_b48_a48_d48_i48 } - replace{ @atom:593 @atom:593_b48_a48_d48_i48 } - replace{ @atom:594 @atom:594_b49_a49_d49_i49 } - replace{ @atom:595 @atom:595_b49_a49_d49_i49 } - replace{ @atom:596 @atom:596_b49_a49_d49_i49 } - replace{ @atom:597 @atom:597_b49_a49_d49_i49 } - replace{ @atom:598 @atom:598_b57_a57_d57_i57 } - replace{ @atom:599 @atom:599_b82_a82_d82_i82 } - replace{ @atom:600 @atom:600_b61_a61_d61_i61 } - replace{ @atom:601 @atom:601_b83_a83_d83_i83 } - replace{ @atom:602 @atom:602_b84_a84_d84_i84 } - replace{ @atom:603 @atom:603_b13_a13_d13_i13 } - replace{ @atom:604 @atom:604_b49_a49_d49_i49 } - replace{ @atom:605 @atom:605_b49_a49_d49_i49 } - replace{ @atom:606 @atom:606_b49_a49_d49_i49 } - replace{ @atom:607 @atom:607_b46_a46_d46_i46 } - replace{ @atom:608 @atom:608_b13_a13_d13_i13 } - replace{ @atom:609 @atom:609_b13_a13_d13_i13 } - replace{ @atom:610 @atom:610_b13_a13_d13_i13 } - replace{ @atom:611 @atom:611_b13_a13_d13_i13 } - replace{ @atom:612 @atom:612_b13_a13_d13_i13 } - replace{ @atom:613 @atom:613_b13_a13_d13_i13 } - replace{ @atom:614 @atom:614_b13_a13_d13_i13 } - replace{ @atom:615 @atom:615_b13_a13_d13_i13 } - replace{ @atom:616 @atom:616_b13_a13_d13_i13 } - replace{ @atom:617 @atom:617_b13_a13_d13_i13 } - replace{ @atom:618 @atom:618_b13_a13_d13_i13 } - replace{ @atom:619 @atom:619_b13_a13_d13_i13 } - replace{ @atom:620 @atom:620_b13_a13_d13_i13 } - replace{ @atom:621 @atom:621_b13_a13_d13_i13 } - replace{ @atom:622 @atom:622_b13_a13_d13_i13 } - replace{ @atom:623 @atom:623_b15_a15_d15_i15 } - replace{ @atom:624 @atom:624_b17_a17_d17_i17 } - replace{ @atom:625 @atom:625_b48_a48_d48_i48 } - replace{ @atom:626 @atom:626_b89_a89_d89_i89 } - replace{ @atom:627 @atom:627_b90_a90_d90_i90 } - replace{ @atom:628 @atom:628_b91_a91_d91_i91 } - replace{ @atom:629 @atom:629_b91_a91_d91_i91 } - replace{ @atom:630 @atom:630_b13_a13_d13_i13 } - replace{ @atom:631 @atom:631_b86_a86_d86_i86 } - replace{ @atom:632 @atom:632_b86_a86_d86_i86 } - replace{ @atom:633 @atom:633_b86_a86_d86_i86 } - replace{ @atom:634 @atom:634_b86_a86_d86_i86 } - replace{ @atom:635 @atom:635_b86_a86_d86_i86 } - replace{ @atom:636 @atom:636_b86_a86_d86_i86 } - replace{ @atom:637 @atom:637_b16_a16_d16_i16 } - replace{ @atom:638 @atom:638_b92_a92_d92_i92 } - replace{ @atom:639 @atom:639_b93_a93_d93_i93 } - replace{ @atom:640 @atom:640_b94_a94_d94_i94 } - replace{ @atom:641 @atom:641_b95_a95_d95_i95 } - replace{ @atom:642 @atom:642_b13_a13_d13_i13 } - replace{ @atom:643 @atom:643_b46_a46_d46_i46 } - replace{ @atom:644 @atom:644_b96_a96_d96_i96 } - replace{ @atom:645 @atom:645_b97_a97_d97_i97 } - replace{ @atom:646 @atom:646_b98_a98_d98_i98 } - replace{ @atom:647 @atom:647_b99_a99_d99_i99 } + replace{ @atom:1 @atom:1_b001_a001_d001_i001 } + replace{ @atom:2 @atom:2_b002_a002_d002_i002 } + replace{ @atom:3 @atom:3_b003_a003_d003_i003 } + replace{ @atom:4 @atom:4_b004_a004_d004_i004 } + replace{ @atom:5 @atom:5_b005_a005_d005_i005 } + replace{ @atom:6 @atom:6_b006_a006_d006_i006 } + replace{ @atom:7 @atom:7_b007_a007_d007_i007 } + replace{ @atom:8 @atom:8_b008_a008_d008_i008 } + replace{ @atom:9 @atom:9_b006_a006_d006_i006 } + replace{ @atom:10 @atom:10_b006_a006_d006_i006 } + replace{ @atom:11 @atom:11_b006_a006_d006_i006 } + replace{ @atom:12 @atom:12_b006_a006_d006_i006 } + replace{ @atom:13 @atom:13_b002_a002_d002_i002 } + replace{ @atom:14 @atom:14_b009_a009_d009_i009 } + replace{ @atom:15 @atom:15_b010_a010_d010_i010 } + replace{ @atom:16 @atom:16_b011_a011_d011_i011 } + replace{ @atom:17 @atom:17_b012_a012_d012_i012 } + replace{ @atom:18 @atom:18_b013_a013_d013_i013 } + replace{ @atom:19 @atom:19_b014_a014_d014_i014 } + replace{ @atom:20 @atom:20_b005_a005_d005_i005 } + replace{ @atom:21 @atom:21_b007_a007_d007_i007 } + replace{ @atom:22 @atom:22_b006_a006_d006_i006 } + replace{ @atom:23 @atom:23_b002_a002_d002_i002 } + replace{ @atom:24 @atom:24_b015_a015_d015_i015 } + replace{ @atom:25 @atom:25_b015_a015_d015_i015 } + replace{ @atom:26 @atom:26_b016_a016_d016_i016 } + replace{ @atom:27 @atom:27_b016_a016_d016_i016 } + replace{ @atom:28 @atom:28_b017_a017_d017_i017 } + replace{ @atom:29 @atom:29_b017_a017_d017_i017 } + replace{ @atom:30 @atom:30_b006_a006_d006_i006 } + replace{ @atom:31 @atom:31_b002_a002_d002_i002 } + replace{ @atom:32 @atom:32_b006_a006_d006_i006 } + replace{ @atom:33 @atom:33_b002_a002_d002_i002 } + replace{ @atom:34 @atom:34_b006_a006_d006_i006 } + replace{ @atom:35 @atom:35_b002_a002_d002_i002 } + replace{ @atom:36 @atom:36_b018_a018_d018_i018 } + replace{ @atom:37 @atom:37_b019_a019_d019_i019 } + replace{ @atom:38 @atom:38_b006_a006_d006_i006 } + replace{ @atom:39 @atom:39_b010_a010_d010_i010 } + replace{ @atom:40 @atom:40_b013_a013_d013_i013 } + replace{ @atom:41 @atom:41_b020_a020_d020_i020 } + replace{ @atom:42 @atom:42_b006_a006_d006_i006 } + replace{ @atom:43 @atom:43_b002_a002_d002_i002 } + replace{ @atom:44 @atom:44_b002_a002_d002_i002 } + replace{ @atom:45 @atom:45_b021_a021_d021_i021 } + replace{ @atom:46 @atom:46_b010_a010_d010_i010 } + replace{ @atom:47 @atom:47_b021_a021_d021_i021 } + replace{ @atom:48 @atom:48_b013_a013_d013_i013 } + replace{ @atom:49 @atom:49_b021_a021_d021_i021 } + replace{ @atom:50 @atom:50_b022_a022_d022_i022 } + replace{ @atom:51 @atom:51_b023_a023_d023_i023 } + replace{ @atom:52 @atom:52_b006_a006_d006_i006 } + replace{ @atom:53 @atom:53_b004_a004_d004_i004 } + replace{ @atom:54 @atom:54_b024_a024_d024_i024 } + replace{ @atom:55 @atom:55_b003_a003_d003_i003 } + replace{ @atom:56 @atom:56_b006_a006_d006_i006 } + replace{ @atom:57 @atom:57_b025_a025_d025_i025 } + replace{ @atom:58 @atom:58_b026_a026_d026_i026 } + replace{ @atom:59 @atom:59_b027_a027_d027_i027 } + replace{ @atom:60 @atom:60_b028_a028_d028_i028 } + replace{ @atom:61 @atom:61_b029_a029_d029_i029 } + replace{ @atom:62 @atom:62_b030_a030_d030_i030 } + replace{ @atom:63 @atom:63_b031_a031_d031_i031 } + replace{ @atom:64 @atom:64_b032_a032_d032_i032 } + replace{ @atom:65 @atom:65_b031_a031_d031_i031 } + replace{ @atom:66 @atom:66_b032_a032_d032_i032 } + replace{ @atom:67 @atom:67_b033_a033_d033_i033 } + replace{ @atom:68 @atom:68_b034_a034_d034_i034 } + replace{ @atom:69 @atom:69_b035_a035_d035_i035 } + replace{ @atom:70 @atom:70_b036_a036_d036_i036 } + replace{ @atom:71 @atom:71_b037_a037_d037_i037 } + replace{ @atom:72 @atom:72_b038_a038_d038_i038 } + replace{ @atom:73 @atom:73_b039_a039_d039_i039 } + replace{ @atom:74 @atom:74_b040_a040_d040_i040 } + replace{ @atom:75 @atom:75_b041_a041_d041_i041 } + replace{ @atom:76 @atom:76_b042_a042_d042_i042 } + replace{ @atom:77 @atom:77_b043_a043_d043_i043 } + replace{ @atom:78 @atom:78_b044_a044_d044_i044 } + replace{ @atom:79 @atom:79_b045_a045_d045_i045 } + replace{ @atom:80 @atom:80_b013_a013_d013_i013 } + replace{ @atom:81 @atom:81_b013_a013_d013_i013 } + replace{ @atom:82 @atom:82_b013_a013_d013_i013 } + replace{ @atom:83 @atom:83_b013_a013_d013_i013 } + replace{ @atom:84 @atom:84_b013_a013_d013_i013 } + replace{ @atom:85 @atom:85_b046_a046_d046_i046 } + replace{ @atom:86 @atom:86_b047_a047_d047_i047 } + replace{ @atom:87 @atom:87_b047_a047_d047_i047 } + replace{ @atom:88 @atom:88_b047_a047_d047_i047 } + replace{ @atom:89 @atom:89_b046_a046_d046_i046 } + replace{ @atom:90 @atom:90_b048_a048_d048_i048 } + replace{ @atom:91 @atom:91_b049_a049_d049_i049 } + replace{ @atom:92 @atom:92_b048_a048_d048_i048 } + replace{ @atom:93 @atom:93_b013_a013_d013_i013 } + replace{ @atom:94 @atom:94_b013_a013_d013_i013 } + replace{ @atom:95 @atom:95_b050_a050_d050_i050 } + replace{ @atom:96 @atom:96_b005_a005_d005_i005 } + replace{ @atom:97 @atom:97_b007_a007_d007_i007 } + replace{ @atom:98 @atom:98_b046_a046_d046_i046 } + replace{ @atom:99 @atom:99_b013_a013_d013_i013 } + replace{ @atom:100 @atom:100_b013_a013_d013_i013 } + replace{ @atom:101 @atom:101_b013_a013_d013_i013 } + replace{ @atom:102 @atom:102_b013_a013_d013_i013 } + replace{ @atom:103 @atom:103_b013_a013_d013_i013 } + replace{ @atom:104 @atom:104_b005_a005_d005_i005 } + replace{ @atom:105 @atom:105_b007_a007_d007_i007 } + replace{ @atom:106 @atom:106_b001_a001_d001_i001 } + replace{ @atom:107 @atom:107_b046_a046_d046_i046 } + replace{ @atom:108 @atom:108_b048_a048_d048_i048 } + replace{ @atom:109 @atom:109_b005_a005_d005_i005 } + replace{ @atom:110 @atom:110_b007_a007_d007_i007 } + replace{ @atom:111 @atom:111_b005_a005_d005_i005 } + replace{ @atom:112 @atom:112_b007_a007_d007_i007 } + replace{ @atom:113 @atom:113_b005_a005_d005_i005 } + replace{ @atom:114 @atom:114_b007_a007_d007_i007 } + replace{ @atom:115 @atom:115_b013_a013_d013_i013 } + replace{ @atom:116 @atom:116_b013_a013_d013_i013 } + replace{ @atom:117 @atom:117_b013_a013_d013_i013 } + replace{ @atom:118 @atom:118_b046_a046_d046_i046 } + replace{ @atom:119 @atom:119_b020_a020_d020_i020 } + replace{ @atom:120 @atom:120_b050_a050_d050_i050 } + replace{ @atom:121 @atom:121_b020_a020_d020_i020 } + replace{ @atom:122 @atom:122_b020_a020_d020_i020 } + replace{ @atom:123 @atom:123_b013_a013_d013_i013 } + replace{ @atom:124 @atom:124_b013_a013_d013_i013 } + replace{ @atom:125 @atom:125_b013_a013_d013_i013 } + replace{ @atom:126 @atom:126_b013_a013_d013_i013 } + replace{ @atom:127 @atom:127_b046_a046_d046_i046 } + replace{ @atom:128 @atom:128_b020_a020_d020_i020 } + replace{ @atom:129 @atom:129_b005_a005_d005_i005 } + replace{ @atom:130 @atom:130_b007_a007_d007_i007 } + replace{ @atom:131 @atom:131_b051_a051_d051_i051 } + replace{ @atom:132 @atom:132_b046_a046_d046_i046 } + replace{ @atom:133 @atom:133_b051_a051_d051_i051 } + replace{ @atom:134 @atom:134_b046_a046_d046_i046 } + replace{ @atom:135 @atom:135_b051_a051_d051_i051 } + replace{ @atom:136 @atom:136_b046_a046_d046_i046 } + replace{ @atom:137 @atom:137_b051_a051_d051_i051 } + replace{ @atom:138 @atom:138_b046_a046_d046_i046 } + replace{ @atom:139 @atom:139_b051_a051_d051_i051 } + replace{ @atom:140 @atom:140_b051_a051_d051_i051 } + replace{ @atom:141 @atom:141_b048_a048_d048_i048 } + replace{ @atom:142 @atom:142_b015_a015_d015_i015 } + replace{ @atom:143 @atom:143_b015_a015_d015_i015 } + replace{ @atom:144 @atom:144_b016_a016_d016_i016 } + replace{ @atom:145 @atom:145_b016_a016_d016_i016 } + replace{ @atom:146 @atom:146_b017_a017_d017_i017 } + replace{ @atom:147 @atom:147_b017_a017_d017_i017 } + replace{ @atom:148 @atom:148_b013_a013_d013_i013 } + replace{ @atom:149 @atom:149_b013_a013_d013_i013 } + replace{ @atom:150 @atom:150_b013_a013_d013_i013 } + replace{ @atom:151 @atom:151_b013_a013_d013_i013 } + replace{ @atom:152 @atom:152_b013_a013_d013_i013 } + replace{ @atom:153 @atom:153_b013_a013_d013_i013 } + replace{ @atom:154 @atom:154_b013_a013_d013_i013 } + replace{ @atom:155 @atom:155_b013_a013_d013_i013 } + replace{ @atom:156 @atom:156_b013_a013_d013_i013 } + replace{ @atom:157 @atom:157_b013_a013_d013_i013 } + replace{ @atom:158 @atom:158_b013_a013_d013_i013 } + replace{ @atom:159 @atom:159_b013_a013_d013_i013 } + replace{ @atom:160 @atom:160_b013_a013_d013_i013 } + replace{ @atom:161 @atom:161_b013_a013_d013_i013 } + replace{ @atom:162 @atom:162_b013_a013_d013_i013 } + replace{ @atom:163 @atom:163_b048_a048_d048_i048 } + replace{ @atom:164 @atom:164_b016_a016_d016_i016 } + replace{ @atom:165 @atom:165_b013_a013_d013_i013 } + replace{ @atom:166 @atom:166_b013_a013_d013_i013 } + replace{ @atom:167 @atom:167_b013_a013_d013_i013 } + replace{ @atom:168 @atom:168_b021_a021_d021_i021 } + replace{ @atom:169 @atom:169_b047_a047_d047_i047 } + replace{ @atom:170 @atom:170_b048_a048_d048_i048 } + replace{ @atom:171 @atom:171_b013_a013_d013_i013 } + replace{ @atom:172 @atom:172_b013_a013_d013_i013 } + replace{ @atom:173 @atom:173_b003_a003_d003_i003 } + replace{ @atom:174 @atom:174_b003_a003_d003_i003 } + replace{ @atom:175 @atom:175_b003_a003_d003_i003 } + replace{ @atom:176 @atom:176_b003_a003_d003_i003 } + replace{ @atom:177 @atom:177_b003_a003_d003_i003 } + replace{ @atom:178 @atom:178_b004_a004_d004_i004 } + replace{ @atom:179 @atom:179_b024_a024_d024_i024 } + replace{ @atom:180 @atom:180_b024_a024_d024_i024 } + replace{ @atom:181 @atom:181_b024_a024_d024_i024 } + replace{ @atom:182 @atom:182_b045_a045_d045_i045 } + replace{ @atom:183 @atom:183_b045_a045_d045_i045 } + replace{ @atom:184 @atom:184_b013_a013_d013_i013 } + replace{ @atom:185 @atom:185_b013_a013_d013_i013 } + replace{ @atom:186 @atom:186_b013_a013_d013_i013 } + replace{ @atom:187 @atom:187_b013_a013_d013_i013 } + replace{ @atom:188 @atom:188_b013_a013_d013_i013 } + replace{ @atom:189 @atom:189_b003_a003_d003_i003 } + replace{ @atom:190 @atom:190_b004_a004_d004_i004 } + replace{ @atom:191 @atom:191_b024_a024_d024_i024 } + replace{ @atom:192 @atom:192_b045_a045_d045_i045 } + replace{ @atom:193 @atom:193_b024_a024_d024_i024 } + replace{ @atom:194 @atom:194_b003_a003_d003_i003 } + replace{ @atom:195 @atom:195_b004_a004_d004_i004 } + replace{ @atom:196 @atom:196_b045_a045_d045_i045 } + replace{ @atom:197 @atom:197_b046_a046_d046_i046 } + replace{ @atom:198 @atom:198_b013_a013_d013_i013 } + replace{ @atom:199 @atom:199_b013_a013_d013_i013 } + replace{ @atom:200 @atom:200_b013_a013_d013_i013 } + replace{ @atom:201 @atom:201_b013_a013_d013_i013 } + replace{ @atom:202 @atom:202_b048_a048_d048_i048 } + replace{ @atom:203 @atom:203_b019_a019_d019_i019 } + replace{ @atom:204 @atom:204_b018_a018_d018_i018 } + replace{ @atom:205 @atom:205_b048_a048_d048_i048 } + replace{ @atom:206 @atom:206_b021_a021_d021_i021 } + replace{ @atom:207 @atom:207_b024_a024_d024_i024 } + replace{ @atom:208 @atom:208_b048_a048_d048_i048 } + replace{ @atom:209 @atom:209_b003_a003_d003_i003 } + replace{ @atom:210 @atom:210_b004_a004_d004_i004 } + replace{ @atom:211 @atom:211_b005_a005_d005_i005 } + replace{ @atom:212 @atom:212_b007_a007_d007_i007 } + replace{ @atom:213 @atom:213_b003_a003_d003_i003 } + replace{ @atom:214 @atom:214_b052_a052_d052_i052 } + replace{ @atom:215 @atom:215_b013_a013_d013_i013 } + replace{ @atom:216 @atom:216_b013_a013_d013_i013 } + replace{ @atom:217 @atom:217_b013_a013_d013_i013 } + replace{ @atom:218 @atom:218_b013_a013_d013_i013 } + replace{ @atom:219 @atom:219_b003_a003_d003_i003 } + replace{ @atom:220 @atom:220_b004_a004_d004_i004 } + replace{ @atom:221 @atom:221_b046_a046_d046_i046 } + replace{ @atom:222 @atom:222_b003_a003_d003_i003 } + replace{ @atom:223 @atom:223_b004_a004_d004_i004 } + replace{ @atom:224 @atom:224_b046_a046_d046_i046 } + replace{ @atom:225 @atom:225_b013_a013_d013_i013 } + replace{ @atom:226 @atom:226_b013_a013_d013_i013 } + replace{ @atom:227 @atom:227_b013_a013_d013_i013 } + replace{ @atom:228 @atom:228_b013_a013_d013_i013 } + replace{ @atom:229 @atom:229_b053_a053_d053_i053 } + replace{ @atom:230 @atom:230_b053_a053_d053_i053 } + replace{ @atom:231 @atom:231_b053_a053_d053_i053 } + replace{ @atom:232 @atom:232_b054_a054_d054_i054 } + replace{ @atom:233 @atom:233_b054_a054_d054_i054 } + replace{ @atom:234 @atom:234_b013_a013_d013_i013 } + replace{ @atom:235 @atom:235_b013_a013_d013_i013 } + replace{ @atom:236 @atom:236_b013_a013_d013_i013 } + replace{ @atom:237 @atom:237_b013_a013_d013_i013 } + replace{ @atom:238 @atom:238_b013_a013_d013_i013 } + replace{ @atom:239 @atom:239_b013_a013_d013_i013 } + replace{ @atom:240 @atom:240_b013_a013_d013_i013 } + replace{ @atom:241 @atom:241_b013_a013_d013_i013 } + replace{ @atom:242 @atom:242_b013_a013_d013_i013 } + replace{ @atom:243 @atom:243_b055_a055_d055_i055 } + replace{ @atom:244 @atom:244_b054_a054_d054_i054 } + replace{ @atom:245 @atom:245_b048_a048_d048_i048 } + replace{ @atom:246 @atom:246_b055_a055_d055_i055 } + replace{ @atom:247 @atom:247_b054_a054_d054_i054 } + replace{ @atom:248 @atom:248_b013_a013_d013_i013 } + replace{ @atom:249 @atom:249_b013_a013_d013_i013 } + replace{ @atom:250 @atom:250_b013_a013_d013_i013 } + replace{ @atom:251 @atom:251_b013_a013_d013_i013 } + replace{ @atom:252 @atom:252_b053_a053_d053_i053 } + replace{ @atom:253 @atom:253_b054_a054_d054_i054 } + replace{ @atom:254 @atom:254_b056_a056_d056_i056 } + replace{ @atom:255 @atom:255_b048_a048_d048_i048 } + replace{ @atom:256 @atom:256_b055_a055_d055_i055 } + replace{ @atom:257 @atom:257_b045_a045_d045_i045 } + replace{ @atom:258 @atom:258_b048_a048_d048_i048 } + replace{ @atom:259 @atom:259_b049_a049_d049_i049 } + replace{ @atom:260 @atom:260_b048_a048_d048_i048 } + replace{ @atom:261 @atom:261_b049_a049_d049_i049 } + replace{ @atom:262 @atom:262_b057_a057_d057_i057 } + replace{ @atom:263 @atom:263_b003_a003_d003_i003 } + replace{ @atom:264 @atom:264_b057_a057_d057_i057 } + replace{ @atom:265 @atom:265_b003_a003_d003_i003 } + replace{ @atom:266 @atom:266_b047_a047_d047_i047 } + replace{ @atom:267 @atom:267_b047_a047_d047_i047 } + replace{ @atom:268 @atom:268_b045_a045_d045_i045 } + replace{ @atom:269 @atom:269_b004_a004_d004_i004 } + replace{ @atom:270 @atom:270_b045_a045_d045_i045 } + replace{ @atom:271 @atom:271_b004_a004_d004_i004 } + replace{ @atom:272 @atom:272_b046_a046_d046_i046 } + replace{ @atom:273 @atom:273_b046_a046_d046_i046 } + replace{ @atom:274 @atom:274_b013_a013_d013_i013 } + replace{ @atom:275 @atom:275_b046_a046_d046_i046 } + replace{ @atom:276 @atom:276_b057_a057_d057_i057 } + replace{ @atom:277 @atom:277_b003_a003_d003_i003 } + replace{ @atom:278 @atom:278_b056_a056_d056_i056 } + replace{ @atom:279 @atom:279_b048_a048_d048_i048 } + replace{ @atom:280 @atom:280_b047_a047_d047_i047 } + replace{ @atom:281 @atom:281_b047_a047_d047_i047 } + replace{ @atom:282 @atom:282_b045_a045_d045_i045 } + replace{ @atom:283 @atom:283_b004_a004_d004_i004 } + replace{ @atom:284 @atom:284_b055_a055_d055_i055 } + replace{ @atom:285 @atom:285_b045_a045_d045_i045 } + replace{ @atom:286 @atom:286_b045_a045_d045_i045 } + replace{ @atom:287 @atom:287_b046_a046_d046_i046 } + replace{ @atom:288 @atom:288_b058_a058_d058_i058 } + replace{ @atom:289 @atom:289_b056_a056_d056_i056 } + replace{ @atom:290 @atom:290_b059_a059_d059_i059 } + replace{ @atom:291 @atom:291_b056_a056_d056_i056 } + replace{ @atom:292 @atom:292_b060_a060_d060_i060 } + replace{ @atom:293 @atom:293_b060_a060_d060_i060 } + replace{ @atom:294 @atom:294_b048_a048_d048_i048 } + replace{ @atom:295 @atom:295_b061_a061_d061_i061 } + replace{ @atom:296 @atom:296_b062_a062_d062_i062 } + replace{ @atom:297 @atom:297_b057_a057_d057_i057 } + replace{ @atom:298 @atom:298_b063_a063_d063_i063 } + replace{ @atom:299 @atom:299_b055_a055_d055_i055 } + replace{ @atom:300 @atom:300_b045_a045_d045_i045 } + replace{ @atom:301 @atom:301_b045_a045_d045_i045 } + replace{ @atom:302 @atom:302_b063_a063_d063_i063 } + replace{ @atom:303 @atom:303_b045_a045_d045_i045 } + replace{ @atom:304 @atom:304_b057_a057_d057_i057 } + replace{ @atom:305 @atom:305_b048_a048_d048_i048 } + replace{ @atom:306 @atom:306_b056_a056_d056_i056 } + replace{ @atom:307 @atom:307_b060_a060_d060_i060 } + replace{ @atom:308 @atom:308_b060_a060_d060_i060 } + replace{ @atom:309 @atom:309_b003_a003_d003_i003 } + replace{ @atom:310 @atom:310_b045_a045_d045_i045 } + replace{ @atom:311 @atom:311_b055_a055_d055_i055 } + replace{ @atom:312 @atom:312_b045_a045_d045_i045 } + replace{ @atom:313 @atom:313_b004_a004_d004_i004 } + replace{ @atom:314 @atom:314_b013_a013_d013_i013 } + replace{ @atom:315 @atom:315_b046_a046_d046_i046 } + replace{ @atom:316 @atom:316_b013_a013_d013_i013 } + replace{ @atom:317 @atom:317_b046_a046_d046_i046 } + replace{ @atom:318 @atom:318_b013_a013_d013_i013 } + replace{ @atom:319 @atom:319_b046_a046_d046_i046 } + replace{ @atom:320 @atom:320_b057_a057_d057_i057 } + replace{ @atom:321 @atom:321_b003_a003_d003_i003 } + replace{ @atom:322 @atom:322_b057_a057_d057_i057 } + replace{ @atom:323 @atom:323_b048_a048_d048_i048 } + replace{ @atom:324 @atom:324_b047_a047_d047_i047 } + replace{ @atom:325 @atom:325_b047_a047_d047_i047 } + replace{ @atom:326 @atom:326_b045_a045_d045_i045 } + replace{ @atom:327 @atom:327_b004_a004_d004_i004 } + replace{ @atom:328 @atom:328_b045_a045_d045_i045 } + replace{ @atom:329 @atom:329_b055_a055_d055_i055 } + replace{ @atom:330 @atom:330_b045_a045_d045_i045 } + replace{ @atom:331 @atom:331_b045_a045_d045_i045 } + replace{ @atom:332 @atom:332_b049_a049_d049_i049 } + replace{ @atom:333 @atom:333_b058_a058_d058_i058 } + replace{ @atom:334 @atom:334_b013_a013_d013_i013 } + replace{ @atom:335 @atom:335_b046_a046_d046_i046 } + replace{ @atom:336 @atom:336_b064_a064_d064_i064 } + replace{ @atom:337 @atom:337_b052_a052_d052_i052 } + replace{ @atom:338 @atom:338_b020_a020_d020_i020 } + replace{ @atom:339 @atom:339_b013_a013_d013_i013 } + replace{ @atom:340 @atom:340_b047_a047_d047_i047 } + replace{ @atom:341 @atom:341_b021_a021_d021_i021 } + replace{ @atom:342 @atom:342_b047_a047_d047_i047 } + replace{ @atom:343 @atom:343_b001_a001_d001_i001 } + replace{ @atom:344 @atom:344_b021_a021_d021_i021 } + replace{ @atom:345 @atom:345_b065_a065_d065_i065 } + replace{ @atom:346 @atom:346_b066_a066_d066_i066 } + replace{ @atom:347 @atom:347_b067_a067_d067_i067 } + replace{ @atom:348 @atom:348_b068_a068_d068_i068 } + replace{ @atom:349 @atom:349_b069_a069_d069_i069 } + replace{ @atom:350 @atom:350_b070_a070_d070_i070 } + replace{ @atom:351 @atom:351_b071_a071_d071_i071 } + replace{ @atom:352 @atom:352_b072_a072_d072_i072 } + replace{ @atom:353 @atom:353_b073_a073_d073_i073 } + replace{ @atom:354 @atom:354_b074_a074_d074_i074 } + replace{ @atom:355 @atom:355_b075_a075_d075_i075 } + replace{ @atom:356 @atom:356_b076_a076_d076_i076 } + replace{ @atom:357 @atom:357_b006_a006_d006_i006 } + replace{ @atom:358 @atom:358_b046_a046_d046_i046 } + replace{ @atom:359 @atom:359_b015_a015_d015_i015 } + replace{ @atom:360 @atom:360_b006_a006_d006_i006 } + replace{ @atom:361 @atom:361_b046_a046_d046_i046 } + replace{ @atom:362 @atom:362_b005_a005_d005_i005 } + replace{ @atom:363 @atom:363_b013_a013_d013_i013 } + replace{ @atom:364 @atom:364_b046_a046_d046_i046 } + replace{ @atom:365 @atom:365_b019_a019_d019_i019 } + replace{ @atom:366 @atom:366_b018_a018_d018_i018 } + replace{ @atom:367 @atom:367_b006_a006_d006_i006 } + replace{ @atom:368 @atom:368_b046_a046_d046_i046 } + replace{ @atom:369 @atom:369_b053_a053_d053_i053 } + replace{ @atom:370 @atom:370_b045_a045_d045_i045 } + replace{ @atom:371 @atom:371_b006_a006_d006_i006 } + replace{ @atom:372 @atom:372_b046_a046_d046_i046 } + replace{ @atom:373 @atom:373_b013_a013_d013_i013 } + replace{ @atom:374 @atom:374_b046_a046_d046_i046 } + replace{ @atom:375 @atom:375_b033_a033_d033_i033 } + replace{ @atom:376 @atom:376_b005_a005_d005_i005 } + replace{ @atom:377 @atom:377_b007_a007_d007_i007 } + replace{ @atom:378 @atom:378_b077_a077_d077_i077 } + replace{ @atom:379 @atom:379_b078_a078_d078_i078 } + replace{ @atom:380 @atom:380_b020_a020_d020_i020 } + replace{ @atom:381 @atom:381_b064_a064_d064_i064 } + replace{ @atom:382 @atom:382_b052_a052_d052_i052 } + replace{ @atom:383 @atom:383_b020_a020_d020_i020 } + replace{ @atom:384 @atom:384_b013_a013_d013_i013 } + replace{ @atom:385 @atom:385_b046_a046_d046_i046 } + replace{ @atom:386 @atom:386_b064_a064_d064_i064 } + replace{ @atom:387 @atom:387_b052_a052_d052_i052 } + replace{ @atom:388 @atom:388_b020_a020_d020_i020 } + replace{ @atom:389 @atom:389_b013_a013_d013_i013 } + replace{ @atom:390 @atom:390_b046_a046_d046_i046 } + replace{ @atom:391 @atom:391_b064_a064_d064_i064 } + replace{ @atom:392 @atom:392_b052_a052_d052_i052 } + replace{ @atom:393 @atom:393_b020_a020_d020_i020 } + replace{ @atom:394 @atom:394_b013_a013_d013_i013 } + replace{ @atom:395 @atom:395_b046_a046_d046_i046 } + replace{ @atom:396 @atom:396_b013_a013_d013_i013 } + replace{ @atom:397 @atom:397_b046_a046_d046_i046 } + replace{ @atom:398 @atom:398_b048_a048_d048_i048 } + replace{ @atom:399 @atom:399_b013_a013_d013_i013 } + replace{ @atom:400 @atom:400_b046_a046_d046_i046 } + replace{ @atom:401 @atom:401_b048_a048_d048_i048 } + replace{ @atom:402 @atom:402_b013_a013_d013_i013 } + replace{ @atom:403 @atom:403_b046_a046_d046_i046 } + replace{ @atom:404 @atom:404_b048_a048_d048_i048 } + replace{ @atom:405 @atom:405_b013_a013_d013_i013 } + replace{ @atom:406 @atom:406_b003_a003_d003_i003 } + replace{ @atom:407 @atom:407_b004_a004_d004_i004 } + replace{ @atom:408 @atom:408_b020_a020_d020_i020 } + replace{ @atom:409 @atom:409_b013_a013_d013_i013 } + replace{ @atom:410 @atom:410_b046_a046_d046_i046 } + replace{ @atom:411 @atom:411_b003_a003_d003_i003 } + replace{ @atom:412 @atom:412_b003_a003_d003_i003 } + replace{ @atom:413 @atom:413_b048_a048_d048_i048 } + replace{ @atom:414 @atom:414_b020_a020_d020_i020 } + replace{ @atom:415 @atom:415_b079_a079_d079_i079 } + replace{ @atom:416 @atom:416_b023_a023_d023_i023 } + replace{ @atom:417 @atom:417_b013_a013_d013_i013 } + replace{ @atom:418 @atom:418_b046_a046_d046_i046 } + replace{ @atom:419 @atom:419_b024_a024_d024_i024 } + replace{ @atom:420 @atom:420_b045_a045_d045_i045 } + replace{ @atom:421 @atom:421_b024_a024_d024_i024 } + replace{ @atom:422 @atom:422_b045_a045_d045_i045 } + replace{ @atom:423 @atom:423_b013_a013_d013_i013 } + replace{ @atom:424 @atom:424_b046_a046_d046_i046 } + replace{ @atom:425 @atom:425_b013_a013_d013_i013 } + replace{ @atom:426 @atom:426_b046_a046_d046_i046 } + replace{ @atom:427 @atom:427_b013_a013_d013_i013 } + replace{ @atom:428 @atom:428_b046_a046_d046_i046 } + replace{ @atom:429 @atom:429_b048_a048_d048_i048 } + replace{ @atom:430 @atom:430_b048_a048_d048_i048 } + replace{ @atom:431 @atom:431_b013_a013_d013_i013 } + replace{ @atom:432 @atom:432_b013_a013_d013_i013 } + replace{ @atom:433 @atom:433_b013_a013_d013_i013 } + replace{ @atom:434 @atom:434_b079_a079_d079_i079 } + replace{ @atom:435 @atom:435_b023_a023_d023_i023 } + replace{ @atom:436 @atom:436_b022_a022_d022_i022 } + replace{ @atom:437 @atom:437_b022_a022_d022_i022 } + replace{ @atom:438 @atom:438_b023_a023_d023_i023 } + replace{ @atom:439 @atom:439_b013_a013_d013_i013 } + replace{ @atom:440 @atom:440_b013_a013_d013_i013 } + replace{ @atom:441 @atom:441_b080_a080_d080_i080 } + replace{ @atom:442 @atom:442_b060_a060_d060_i060 } + replace{ @atom:443 @atom:443_b081_a081_d081_i081 } + replace{ @atom:444 @atom:444_b057_a057_d057_i057 } + replace{ @atom:445 @atom:445_b045_a045_d045_i045 } + replace{ @atom:446 @atom:446_b013_a013_d013_i013 } + replace{ @atom:447 @atom:447_b082_a082_d082_i082 } + replace{ @atom:448 @atom:448_b083_a083_d083_i083 } + replace{ @atom:449 @atom:449_b084_a084_d084_i084 } + replace{ @atom:450 @atom:450_b082_a082_d082_i082 } + replace{ @atom:451 @atom:451_b085_a085_d085_i085 } + replace{ @atom:452 @atom:452_b061_a061_d061_i061 } + replace{ @atom:453 @atom:453_b057_a057_d057_i057 } + replace{ @atom:454 @atom:454_b045_a045_d045_i045 } + replace{ @atom:455 @atom:455_b084_a084_d084_i084 } + replace{ @atom:456 @atom:456_b013_a013_d013_i013 } + replace{ @atom:457 @atom:457_b013_a013_d013_i013 } + replace{ @atom:458 @atom:458_b047_a047_d047_i047 } + replace{ @atom:459 @atom:459_b047_a047_d047_i047 } + replace{ @atom:460 @atom:460_b086_a086_d086_i086 } + replace{ @atom:461 @atom:461_b056_a056_d056_i056 } + replace{ @atom:462 @atom:462_b048_a048_d048_i048 } + replace{ @atom:463 @atom:463_b048_a048_d048_i048 } + replace{ @atom:464 @atom:464_b048_a048_d048_i048 } + replace{ @atom:465 @atom:465_b049_a049_d049_i049 } + replace{ @atom:466 @atom:466_b049_a049_d049_i049 } + replace{ @atom:467 @atom:467_b049_a049_d049_i049 } + replace{ @atom:468 @atom:468_b056_a056_d056_i056 } + replace{ @atom:469 @atom:469_b048_a048_d048_i048 } + replace{ @atom:470 @atom:470_b049_a049_d049_i049 } + replace{ @atom:471 @atom:471_b056_a056_d056_i056 } + replace{ @atom:472 @atom:472_b059_a059_d059_i059 } + replace{ @atom:473 @atom:473_b048_a048_d048_i048 } + replace{ @atom:474 @atom:474_b048_a048_d048_i048 } + replace{ @atom:475 @atom:475_b049_a049_d049_i049 } + replace{ @atom:476 @atom:476_b049_a049_d049_i049 } + replace{ @atom:477 @atom:477_b049_a049_d049_i049 } + replace{ @atom:478 @atom:478_b056_a056_d056_i056 } + replace{ @atom:479 @atom:479_b048_a048_d048_i048 } + replace{ @atom:480 @atom:480_b048_a048_d048_i048 } + replace{ @atom:481 @atom:481_b049_a049_d049_i049 } + replace{ @atom:482 @atom:482_b049_a049_d049_i049 } + replace{ @atom:483 @atom:483_b057_a057_d057_i057 } + replace{ @atom:484 @atom:484_b084_a084_d084_i084 } + replace{ @atom:485 @atom:485_b087_a087_d087_i087 } + replace{ @atom:486 @atom:486_b045_a045_d045_i045 } + replace{ @atom:487 @atom:487_b049_a049_d049_i049 } + replace{ @atom:488 @atom:488_b049_a049_d049_i049 } + replace{ @atom:489 @atom:489_b057_a057_d057_i057 } + replace{ @atom:490 @atom:490_b061_a061_d061_i061 } + replace{ @atom:491 @atom:491_b088_a088_d088_i088 } + replace{ @atom:492 @atom:492_b087_a087_d087_i087 } + replace{ @atom:493 @atom:493_b084_a084_d084_i084 } + replace{ @atom:494 @atom:494_b045_a045_d045_i045 } + replace{ @atom:495 @atom:495_b049_a049_d049_i049 } + replace{ @atom:496 @atom:496_b049_a049_d049_i049 } + replace{ @atom:497 @atom:497_b049_a049_d049_i049 } + replace{ @atom:498 @atom:498_b057_a057_d057_i057 } + replace{ @atom:499 @atom:499_b082_a082_d082_i082 } + replace{ @atom:500 @atom:500_b061_a061_d061_i061 } + replace{ @atom:501 @atom:501_b083_a083_d083_i083 } + replace{ @atom:502 @atom:502_b084_a084_d084_i084 } + replace{ @atom:503 @atom:503_b045_a045_d045_i045 } + replace{ @atom:504 @atom:504_b049_a049_d049_i049 } + replace{ @atom:505 @atom:505_b049_a049_d049_i049 } + replace{ @atom:506 @atom:506_b049_a049_d049_i049 } + replace{ @atom:507 @atom:507_b020_a020_d020_i020 } + replace{ @atom:508 @atom:508_b084_a084_d084_i084 } + replace{ @atom:509 @atom:509_b087_a087_d087_i087 } + replace{ @atom:510 @atom:510_b049_a049_d049_i049 } + replace{ @atom:511 @atom:511_b049_a049_d049_i049 } + replace{ @atom:512 @atom:512_b020_a020_d020_i020 } + replace{ @atom:513 @atom:513_b082_a082_d082_i082 } + replace{ @atom:514 @atom:514_b061_a061_d061_i061 } + replace{ @atom:515 @atom:515_b083_a083_d083_i083 } + replace{ @atom:516 @atom:516_b084_a084_d084_i084 } + replace{ @atom:517 @atom:517_b049_a049_d049_i049 } + replace{ @atom:518 @atom:518_b049_a049_d049_i049 } + replace{ @atom:519 @atom:519_b049_a049_d049_i049 } + replace{ @atom:520 @atom:520_b020_a020_d020_i020 } + replace{ @atom:521 @atom:521_b061_a061_d061_i061 } + replace{ @atom:522 @atom:522_b088_a088_d088_i088 } + replace{ @atom:523 @atom:523_b087_a087_d087_i087 } + replace{ @atom:524 @atom:524_b084_a084_d084_i084 } + replace{ @atom:525 @atom:525_b049_a049_d049_i049 } + replace{ @atom:526 @atom:526_b049_a049_d049_i049 } + replace{ @atom:527 @atom:527_b049_a049_d049_i049 } + replace{ @atom:528 @atom:528_b057_a057_d057_i057 } + replace{ @atom:529 @atom:529_b084_a084_d084_i084 } + replace{ @atom:530 @atom:530_b087_a087_d087_i087 } + replace{ @atom:531 @atom:531_b048_a048_d048_i048 } + replace{ @atom:532 @atom:532_b048_a048_d048_i048 } + replace{ @atom:533 @atom:533_b048_a048_d048_i048 } + replace{ @atom:534 @atom:534_b048_a048_d048_i048 } + replace{ @atom:535 @atom:535_b081_a081_d081_i081 } + replace{ @atom:536 @atom:536_b060_a060_d060_i060 } + replace{ @atom:537 @atom:537_b045_a045_d045_i045 } + replace{ @atom:538 @atom:538_b049_a049_d049_i049 } + replace{ @atom:539 @atom:539_b049_a049_d049_i049 } + replace{ @atom:540 @atom:540_b049_a049_d049_i049 } + replace{ @atom:541 @atom:541_b049_a049_d049_i049 } + replace{ @atom:542 @atom:542_b049_a049_d049_i049 } + replace{ @atom:543 @atom:543_b049_a049_d049_i049 } + replace{ @atom:544 @atom:544_b056_a056_d056_i056 } + replace{ @atom:545 @atom:545_b048_a048_d048_i048 } + replace{ @atom:546 @atom:546_b048_a048_d048_i048 } + replace{ @atom:547 @atom:547_b048_a048_d048_i048 } + replace{ @atom:548 @atom:548_b048_a048_d048_i048 } + replace{ @atom:549 @atom:549_b048_a048_d048_i048 } + replace{ @atom:550 @atom:550_b048_a048_d048_i048 } + replace{ @atom:551 @atom:551_b048_a048_d048_i048 } + replace{ @atom:552 @atom:552_b048_a048_d048_i048 } + replace{ @atom:553 @atom:553_b048_a048_d048_i048 } + replace{ @atom:554 @atom:554_b049_a049_d049_i049 } + replace{ @atom:555 @atom:555_b049_a049_d049_i049 } + replace{ @atom:556 @atom:556_b049_a049_d049_i049 } + replace{ @atom:557 @atom:557_b049_a049_d049_i049 } + replace{ @atom:558 @atom:558_b049_a049_d049_i049 } + replace{ @atom:559 @atom:559_b049_a049_d049_i049 } + replace{ @atom:560 @atom:560_b049_a049_d049_i049 } + replace{ @atom:561 @atom:561_b056_a056_d056_i056 } + replace{ @atom:562 @atom:562_b059_a059_d059_i059 } + replace{ @atom:563 @atom:563_b056_a056_d056_i056 } + replace{ @atom:564 @atom:564_b060_a060_d060_i060 } + replace{ @atom:565 @atom:565_b060_a060_d060_i060 } + replace{ @atom:566 @atom:566_b048_a048_d048_i048 } + replace{ @atom:567 @atom:567_b061_a061_d061_i061 } + replace{ @atom:568 @atom:568_b062_a062_d062_i062 } + replace{ @atom:569 @atom:569_b057_a057_d057_i057 } + replace{ @atom:570 @atom:570_b049_a049_d049_i049 } + replace{ @atom:571 @atom:571_b049_a049_d049_i049 } + replace{ @atom:572 @atom:572_b049_a049_d049_i049 } + replace{ @atom:573 @atom:573_b045_a045_d045_i045 } + replace{ @atom:574 @atom:574_b016_a016_d016_i016 } + replace{ @atom:575 @atom:575_b082_a082_d082_i082 } + replace{ @atom:576 @atom:576_b061_a061_d061_i061 } + replace{ @atom:577 @atom:577_b083_a083_d083_i083 } + replace{ @atom:578 @atom:578_b084_a084_d084_i084 } + replace{ @atom:579 @atom:579_b049_a049_d049_i049 } + replace{ @atom:580 @atom:580_b049_a049_d049_i049 } + replace{ @atom:581 @atom:581_b049_a049_d049_i049 } + replace{ @atom:582 @atom:582_b056_a056_d056_i056 } + replace{ @atom:583 @atom:583_b059_a059_d059_i059 } + replace{ @atom:584 @atom:584_b049_a049_d049_i049 } + replace{ @atom:585 @atom:585_b048_a048_d048_i048 } + replace{ @atom:586 @atom:586_b013_a013_d013_i013 } + replace{ @atom:587 @atom:587_b056_a056_d056_i056 } + replace{ @atom:588 @atom:588_b048_a048_d048_i048 } + replace{ @atom:589 @atom:589_b048_a048_d048_i048 } + replace{ @atom:590 @atom:590_b048_a048_d048_i048 } + replace{ @atom:591 @atom:591_b048_a048_d048_i048 } + replace{ @atom:592 @atom:592_b048_a048_d048_i048 } + replace{ @atom:593 @atom:593_b048_a048_d048_i048 } + replace{ @atom:594 @atom:594_b049_a049_d049_i049 } + replace{ @atom:595 @atom:595_b049_a049_d049_i049 } + replace{ @atom:596 @atom:596_b049_a049_d049_i049 } + replace{ @atom:597 @atom:597_b049_a049_d049_i049 } + replace{ @atom:598 @atom:598_b057_a057_d057_i057 } + replace{ @atom:599 @atom:599_b082_a082_d082_i082 } + replace{ @atom:600 @atom:600_b061_a061_d061_i061 } + replace{ @atom:601 @atom:601_b083_a083_d083_i083 } + replace{ @atom:602 @atom:602_b084_a084_d084_i084 } + replace{ @atom:603 @atom:603_b013_a013_d013_i013 } + replace{ @atom:604 @atom:604_b049_a049_d049_i049 } + replace{ @atom:605 @atom:605_b049_a049_d049_i049 } + replace{ @atom:606 @atom:606_b049_a049_d049_i049 } + replace{ @atom:607 @atom:607_b046_a046_d046_i046 } + replace{ @atom:608 @atom:608_b013_a013_d013_i013 } + replace{ @atom:609 @atom:609_b013_a013_d013_i013 } + replace{ @atom:610 @atom:610_b013_a013_d013_i013 } + replace{ @atom:611 @atom:611_b013_a013_d013_i013 } + replace{ @atom:612 @atom:612_b013_a013_d013_i013 } + replace{ @atom:613 @atom:613_b013_a013_d013_i013 } + replace{ @atom:614 @atom:614_b013_a013_d013_i013 } + replace{ @atom:615 @atom:615_b013_a013_d013_i013 } + replace{ @atom:616 @atom:616_b013_a013_d013_i013 } + replace{ @atom:617 @atom:617_b013_a013_d013_i013 } + replace{ @atom:618 @atom:618_b013_a013_d013_i013 } + replace{ @atom:619 @atom:619_b013_a013_d013_i013 } + replace{ @atom:620 @atom:620_b013_a013_d013_i013 } + replace{ @atom:621 @atom:621_b013_a013_d013_i013 } + replace{ @atom:622 @atom:622_b013_a013_d013_i013 } + replace{ @atom:623 @atom:623_b015_a015_d015_i015 } + replace{ @atom:624 @atom:624_b017_a017_d017_i017 } + replace{ @atom:625 @atom:625_b048_a048_d048_i048 } + replace{ @atom:626 @atom:626_b089_a089_d089_i089 } + replace{ @atom:627 @atom:627_b090_a090_d090_i090 } + replace{ @atom:628 @atom:628_b091_a091_d091_i091 } + replace{ @atom:629 @atom:629_b091_a091_d091_i091 } + replace{ @atom:630 @atom:630_b013_a013_d013_i013 } + replace{ @atom:631 @atom:631_b086_a086_d086_i086 } + replace{ @atom:632 @atom:632_b086_a086_d086_i086 } + replace{ @atom:633 @atom:633_b086_a086_d086_i086 } + replace{ @atom:634 @atom:634_b086_a086_d086_i086 } + replace{ @atom:635 @atom:635_b086_a086_d086_i086 } + replace{ @atom:636 @atom:636_b086_a086_d086_i086 } + replace{ @atom:637 @atom:637_b016_a016_d016_i016 } + replace{ @atom:638 @atom:638_b092_a092_d092_i092 } + replace{ @atom:639 @atom:639_b093_a093_d093_i093 } + replace{ @atom:640 @atom:640_b094_a094_d094_i094 } + replace{ @atom:641 @atom:641_b095_a095_d095_i095 } + replace{ @atom:642 @atom:642_b013_a013_d013_i013 } + replace{ @atom:643 @atom:643_b046_a046_d046_i046 } + replace{ @atom:644 @atom:644_b096_a096_d096_i096 } + replace{ @atom:645 @atom:645_b097_a097_d097_i097 } + replace{ @atom:646 @atom:646_b098_a098_d098_i098 } + replace{ @atom:647 @atom:647_b099_a099_d099_i099 } replace{ @atom:648 @atom:648_b100_a100_d100_i100 } - replace{ @atom:649 @atom:649_b47_a47_d47_i47 } - replace{ @atom:650 @atom:650_b21_a21_d21_i21 } - replace{ @atom:651 @atom:651_b46_a46_d46_i46 } - replace{ @atom:652 @atom:652_b91_a91_d91_i91 } - replace{ @atom:653 @atom:653_b91_a91_d91_i91 } - replace{ @atom:654 @atom:654_b91_a91_d91_i91 } - replace{ @atom:655 @atom:655_b48_a48_d48_i48 } - replace{ @atom:656 @atom:656_b49_a49_d49_i49 } - replace{ @atom:657 @atom:657_b48_a48_d48_i48 } - replace{ @atom:658 @atom:658_b49_a49_d49_i49 } - replace{ @atom:659 @atom:659_b48_a48_d48_i48 } - replace{ @atom:660 @atom:660_b1_a1_d1_i1 } - replace{ @atom:661 @atom:661_b48_a48_d48_i48 } - replace{ @atom:662 @atom:662_b1_a1_d1_i1 } - replace{ @atom:663 @atom:663_b65_a65_d65_i65 } - replace{ @atom:664 @atom:664_b2_a2_d2_i2 } - replace{ @atom:665 @atom:665_b48_a48_d48_i48 } - replace{ @atom:666 @atom:666_b13_a13_d13_i13 } - replace{ @atom:667 @atom:667_b1_a1_d1_i1 } - replace{ @atom:668 @atom:668_b48_a48_d48_i48 } - replace{ @atom:669 @atom:669_b1_a1_d1_i1 } - replace{ @atom:670 @atom:670_b48_a48_d48_i48 } - replace{ @atom:671 @atom:671_b65_a65_d65_i65 } - replace{ @atom:672 @atom:672_b48_a48_d48_i48 } - replace{ @atom:673 @atom:673_b66_a66_d66_i66 } - replace{ @atom:674 @atom:674_b91_a91_d91_i91 } - replace{ @atom:675 @atom:675_b15_a15_d15_i15 } - replace{ @atom:676 @atom:676_b48_a48_d48_i48 } - replace{ @atom:677 @atom:677_b48_a48_d48_i48 } - replace{ @atom:678 @atom:678_b48_a48_d48_i48 } - replace{ @atom:679 @atom:679_b48_a48_d48_i48 } - replace{ @atom:680 @atom:680_b48_a48_d48_i48 } - replace{ @atom:681 @atom:681_b49_a49_d49_i49 } - replace{ @atom:682 @atom:682_b49_a49_d49_i49 } - replace{ @atom:683 @atom:683_b48_a48_d48_i48 } - replace{ @atom:684 @atom:684_b55_a55_d55_i55 } - replace{ @atom:685 @atom:685_b45_a45_d45_i45 } - replace{ @atom:686 @atom:686_b45_a45_d45_i45 } - replace{ @atom:687 @atom:687_b49_a49_d49_i49 } - replace{ @atom:688 @atom:688_b13_a13_d13_i13 } - replace{ @atom:689 @atom:689_b13_a13_d13_i13 } + replace{ @atom:649 @atom:649_b047_a047_d047_i047 } + replace{ @atom:650 @atom:650_b021_a021_d021_i021 } + replace{ @atom:651 @atom:651_b046_a046_d046_i046 } + replace{ @atom:652 @atom:652_b091_a091_d091_i091 } + replace{ @atom:653 @atom:653_b091_a091_d091_i091 } + replace{ @atom:654 @atom:654_b091_a091_d091_i091 } + replace{ @atom:655 @atom:655_b048_a048_d048_i048 } + replace{ @atom:656 @atom:656_b049_a049_d049_i049 } + replace{ @atom:657 @atom:657_b048_a048_d048_i048 } + replace{ @atom:658 @atom:658_b049_a049_d049_i049 } + replace{ @atom:659 @atom:659_b048_a048_d048_i048 } + replace{ @atom:660 @atom:660_b001_a001_d001_i001 } + replace{ @atom:661 @atom:661_b048_a048_d048_i048 } + replace{ @atom:662 @atom:662_b001_a001_d001_i001 } + replace{ @atom:663 @atom:663_b065_a065_d065_i065 } + replace{ @atom:664 @atom:664_b002_a002_d002_i002 } + replace{ @atom:665 @atom:665_b048_a048_d048_i048 } + replace{ @atom:666 @atom:666_b013_a013_d013_i013 } + replace{ @atom:667 @atom:667_b001_a001_d001_i001 } + replace{ @atom:668 @atom:668_b048_a048_d048_i048 } + replace{ @atom:669 @atom:669_b001_a001_d001_i001 } + replace{ @atom:670 @atom:670_b048_a048_d048_i048 } + replace{ @atom:671 @atom:671_b065_a065_d065_i065 } + replace{ @atom:672 @atom:672_b048_a048_d048_i048 } + replace{ @atom:673 @atom:673_b066_a066_d066_i066 } + replace{ @atom:674 @atom:674_b091_a091_d091_i091 } + replace{ @atom:675 @atom:675_b015_a015_d015_i015 } + replace{ @atom:676 @atom:676_b048_a048_d048_i048 } + replace{ @atom:677 @atom:677_b048_a048_d048_i048 } + replace{ @atom:678 @atom:678_b048_a048_d048_i048 } + replace{ @atom:679 @atom:679_b048_a048_d048_i048 } + replace{ @atom:680 @atom:680_b048_a048_d048_i048 } + replace{ @atom:681 @atom:681_b049_a049_d049_i049 } + replace{ @atom:682 @atom:682_b049_a049_d049_i049 } + replace{ @atom:683 @atom:683_b048_a048_d048_i048 } + replace{ @atom:684 @atom:684_b055_a055_d055_i055 } + replace{ @atom:685 @atom:685_b045_a045_d045_i045 } + replace{ @atom:686 @atom:686_b045_a045_d045_i045 } + replace{ @atom:687 @atom:687_b049_a049_d049_i049 } + replace{ @atom:688 @atom:688_b013_a013_d013_i013 } + replace{ @atom:689 @atom:689_b013_a013_d013_i013 } replace{ @atom:690 @atom:690_b101_a101_d101_i101 } - replace{ @atom:691 @atom:691_b56_a56_d56_i56 } + replace{ @atom:691 @atom:691_b056_a056_d056_i056 } replace{ @atom:692 @atom:692_b101_a101_d101_i101 } - replace{ @atom:693 @atom:693_b48_a48_d48_i48 } - replace{ @atom:694 @atom:694_b18_a18_d18_i18 } - replace{ @atom:695 @atom:695_b19_a19_d19_i19 } - replace{ @atom:696 @atom:696_b13_a13_d13_i13 } - replace{ @atom:697 @atom:697_b13_a13_d13_i13 } - replace{ @atom:698 @atom:698_b13_a13_d13_i13 } - replace{ @atom:699 @atom:699_b13_a13_d13_i13 } - replace{ @atom:700 @atom:700_b46_a46_d46_i46 } + replace{ @atom:693 @atom:693_b048_a048_d048_i048 } + replace{ @atom:694 @atom:694_b018_a018_d018_i018 } + replace{ @atom:695 @atom:695_b019_a019_d019_i019 } + replace{ @atom:696 @atom:696_b013_a013_d013_i013 } + replace{ @atom:697 @atom:697_b013_a013_d013_i013 } + replace{ @atom:698 @atom:698_b013_a013_d013_i013 } + replace{ @atom:699 @atom:699_b013_a013_d013_i013 } + replace{ @atom:700 @atom:700_b046_a046_d046_i046 } replace{ @atom:701 @atom:701_b102_a102_d102_i102 } replace{ @atom:702 @atom:702_b103_a103_d103_i103 } - replace{ @atom:703 @atom:703_b13_a13_d13_i13 } - replace{ @atom:704 @atom:704_b46_a46_d46_i46 } - replace{ @atom:705 @atom:705_b13_a13_d13_i13 } - replace{ @atom:706 @atom:706_b13_a13_d13_i13 } - replace{ @atom:707 @atom:707_b13_a13_d13_i13 } + replace{ @atom:703 @atom:703_b013_a013_d013_i013 } + replace{ @atom:704 @atom:704_b046_a046_d046_i046 } + replace{ @atom:705 @atom:705_b013_a013_d013_i013 } + replace{ @atom:706 @atom:706_b013_a013_d013_i013 } + replace{ @atom:707 @atom:707_b013_a013_d013_i013 } replace{ @atom:708 @atom:708_b102_a102_d102_i102 } - replace{ @atom:709 @atom:709_b48_a48_d48_i48 } - replace{ @atom:710 @atom:710_b13_a13_d13_i13 } - replace{ @atom:711 @atom:711_b56_a56_d56_i56 } - replace{ @atom:712 @atom:712_b4_a4_d4_i4 } - replace{ @atom:713 @atom:713_b3_a3_d3_i3 } - replace{ @atom:714 @atom:714_b20_a20_d20_i20 } - replace{ @atom:715 @atom:715_b13_a13_d13_i13 } - replace{ @atom:716 @atom:716_b13_a13_d13_i13 } - replace{ @atom:717 @atom:717_b13_a13_d13_i13 } - replace{ @atom:718 @atom:718_b46_a46_d46_i46 } - replace{ @atom:719 @atom:719_b46_a46_d46_i46 } - replace{ @atom:720 @atom:720_b46_a46_d46_i46 } - replace{ @atom:721 @atom:721_b20_a20_d20_i20 } + replace{ @atom:709 @atom:709_b048_a048_d048_i048 } + replace{ @atom:710 @atom:710_b013_a013_d013_i013 } + replace{ @atom:711 @atom:711_b056_a056_d056_i056 } + replace{ @atom:712 @atom:712_b004_a004_d004_i004 } + replace{ @atom:713 @atom:713_b003_a003_d003_i003 } + replace{ @atom:714 @atom:714_b020_a020_d020_i020 } + replace{ @atom:715 @atom:715_b013_a013_d013_i013 } + replace{ @atom:716 @atom:716_b013_a013_d013_i013 } + replace{ @atom:717 @atom:717_b013_a013_d013_i013 } + replace{ @atom:718 @atom:718_b046_a046_d046_i046 } + replace{ @atom:719 @atom:719_b046_a046_d046_i046 } + replace{ @atom:720 @atom:720_b046_a046_d046_i046 } + replace{ @atom:721 @atom:721_b020_a020_d020_i020 } replace{ @atom:722 @atom:722_b104_a104_d104_i104 } - replace{ @atom:723 @atom:723_b13_a13_d13_i13 } - replace{ @atom:724 @atom:724_b13_a13_d13_i13 } - replace{ @atom:725 @atom:725_b46_a46_d46_i46 } - replace{ @atom:726 @atom:726_b64_a64_d64_i64 } - replace{ @atom:727 @atom:727_b1_a1_d1_i1 } - replace{ @atom:728 @atom:728_b24_a24_d24_i24 } - replace{ @atom:729 @atom:729_b4_a4_d4_i4 } - replace{ @atom:730 @atom:730_b44_a44_d44_i44 } - replace{ @atom:731 @atom:731_b44_a44_d44_i44 } - replace{ @atom:732 @atom:732_b44_a44_d44_i44 } - replace{ @atom:733 @atom:733_b13_a13_d13_i13 } - replace{ @atom:734 @atom:734_b13_a13_d13_i13 } - replace{ @atom:735 @atom:735_b13_a13_d13_i13 } - replace{ @atom:736 @atom:736_b13_a13_d13_i13 } - replace{ @atom:737 @atom:737_b13_a13_d13_i13 } - replace{ @atom:738 @atom:738_b13_a13_d13_i13 } - replace{ @atom:739 @atom:739_b45_a45_d45_i45 } - replace{ @atom:740 @atom:740_b45_a45_d45_i45 } - replace{ @atom:741 @atom:741_b46_a46_d46_i46 } - replace{ @atom:742 @atom:742_b13_a13_d13_i13 } - replace{ @atom:743 @atom:743_b13_a13_d13_i13 } - replace{ @atom:744 @atom:744_b13_a13_d13_i13 } - replace{ @atom:745 @atom:745_b13_a13_d13_i13 } - replace{ @atom:746 @atom:746_b48_a48_d48_i48 } - replace{ @atom:747 @atom:747_b48_a48_d48_i48 } - replace{ @atom:748 @atom:748_b48_a48_d48_i48 } - replace{ @atom:749 @atom:749_b13_a13_d13_i13 } - replace{ @atom:750 @atom:750_b13_a13_d13_i13 } - replace{ @atom:751 @atom:751_b13_a13_d13_i13 } - replace{ @atom:752 @atom:752_b13_a13_d13_i13 } - replace{ @atom:753 @atom:753_b13_a13_d13_i13 } - replace{ @atom:754 @atom:754_b13_a13_d13_i13 } - replace{ @atom:755 @atom:755_b19_a19_d19_i19 } - replace{ @atom:756 @atom:756_b46_a46_d46_i46 } - replace{ @atom:757 @atom:757_b19_a19_d19_i19 } - replace{ @atom:758 @atom:758_b19_a19_d19_i19 } - replace{ @atom:759 @atom:759_b19_a19_d19_i19 } - replace{ @atom:760 @atom:760_b46_a46_d46_i46 } - replace{ @atom:761 @atom:761_b51_a51_d51_i51 } - replace{ @atom:762 @atom:762_b51_a51_d51_i51 } - replace{ @atom:763 @atom:763_b51_a51_d51_i51 } - replace{ @atom:764 @atom:764_b5_a5_d5_i5 } - replace{ @atom:765 @atom:765_b7_a7_d7_i7 } + replace{ @atom:723 @atom:723_b013_a013_d013_i013 } + replace{ @atom:724 @atom:724_b013_a013_d013_i013 } + replace{ @atom:725 @atom:725_b046_a046_d046_i046 } + replace{ @atom:726 @atom:726_b064_a064_d064_i064 } + replace{ @atom:727 @atom:727_b001_a001_d001_i001 } + replace{ @atom:728 @atom:728_b024_a024_d024_i024 } + replace{ @atom:729 @atom:729_b004_a004_d004_i004 } + replace{ @atom:730 @atom:730_b044_a044_d044_i044 } + replace{ @atom:731 @atom:731_b044_a044_d044_i044 } + replace{ @atom:732 @atom:732_b044_a044_d044_i044 } + replace{ @atom:733 @atom:733_b013_a013_d013_i013 } + replace{ @atom:734 @atom:734_b013_a013_d013_i013 } + replace{ @atom:735 @atom:735_b013_a013_d013_i013 } + replace{ @atom:736 @atom:736_b013_a013_d013_i013 } + replace{ @atom:737 @atom:737_b013_a013_d013_i013 } + replace{ @atom:738 @atom:738_b013_a013_d013_i013 } + replace{ @atom:739 @atom:739_b045_a045_d045_i045 } + replace{ @atom:740 @atom:740_b045_a045_d045_i045 } + replace{ @atom:741 @atom:741_b046_a046_d046_i046 } + replace{ @atom:742 @atom:742_b013_a013_d013_i013 } + replace{ @atom:743 @atom:743_b013_a013_d013_i013 } + replace{ @atom:744 @atom:744_b013_a013_d013_i013 } + replace{ @atom:745 @atom:745_b013_a013_d013_i013 } + replace{ @atom:746 @atom:746_b048_a048_d048_i048 } + replace{ @atom:747 @atom:747_b048_a048_d048_i048 } + replace{ @atom:748 @atom:748_b048_a048_d048_i048 } + replace{ @atom:749 @atom:749_b013_a013_d013_i013 } + replace{ @atom:750 @atom:750_b013_a013_d013_i013 } + replace{ @atom:751 @atom:751_b013_a013_d013_i013 } + replace{ @atom:752 @atom:752_b013_a013_d013_i013 } + replace{ @atom:753 @atom:753_b013_a013_d013_i013 } + replace{ @atom:754 @atom:754_b013_a013_d013_i013 } + replace{ @atom:755 @atom:755_b019_a019_d019_i019 } + replace{ @atom:756 @atom:756_b046_a046_d046_i046 } + replace{ @atom:757 @atom:757_b019_a019_d019_i019 } + replace{ @atom:758 @atom:758_b019_a019_d019_i019 } + replace{ @atom:759 @atom:759_b019_a019_d019_i019 } + replace{ @atom:760 @atom:760_b046_a046_d046_i046 } + replace{ @atom:761 @atom:761_b051_a051_d051_i051 } + replace{ @atom:762 @atom:762_b051_a051_d051_i051 } + replace{ @atom:763 @atom:763_b051_a051_d051_i051 } + replace{ @atom:764 @atom:764_b005_a005_d005_i005 } + replace{ @atom:765 @atom:765_b007_a007_d007_i007 } replace{ @atom:766 @atom:766_b105_a105_d105_i105 } replace{ @atom:767 @atom:767_b105_a105_d105_i105 } replace{ @atom:768 @atom:768_b105_a105_d105_i105 } - replace{ @atom:769 @atom:769_b19_a19_d19_i19 } - replace{ @atom:770 @atom:770_b53_a53_d53_i53 } - replace{ @atom:771 @atom:771_b54_a54_d54_i54 } - replace{ @atom:772 @atom:772_b13_a13_d13_i13 } - replace{ @atom:773 @atom:773_b13_a13_d13_i13 } - replace{ @atom:774 @atom:774_b13_a13_d13_i13 } - replace{ @atom:775 @atom:775_b13_a13_d13_i13 } - replace{ @atom:776 @atom:776_b84_a84_d84_i84 } - replace{ @atom:777 @atom:777_b87_a87_d87_i87 } - replace{ @atom:778 @atom:778_b86_a86_d86_i86 } - replace{ @atom:779 @atom:779_b86_a86_d86_i86 } - replace{ @atom:780 @atom:780_b46_a46_d46_i46 } - replace{ @atom:781 @atom:781_b13_a13_d13_i13 } - replace{ @atom:782 @atom:782_b3_a3_d3_i3 } - replace{ @atom:783 @atom:783_b53_a53_d53_i53 } - replace{ @atom:784 @atom:784_b52_a52_d52_i52 } - replace{ @atom:785 @atom:785_b54_a54_d54_i54 } - replace{ @atom:786 @atom:786_b1_a1_d1_i1 } - replace{ @atom:787 @atom:787_b13_a13_d13_i13 } - replace{ @atom:788 @atom:788_b46_a46_d46_i46 } - replace{ @atom:789 @atom:789_b13_a13_d13_i13 } - replace{ @atom:790 @atom:790_b13_a13_d13_i13 } - replace{ @atom:791 @atom:791_b13_a13_d13_i13 } - replace{ @atom:792 @atom:792_b13_a13_d13_i13 } - replace{ @atom:793 @atom:793_b13_a13_d13_i13 } - replace{ @atom:794 @atom:794_b13_a13_d13_i13 } - replace{ @atom:795 @atom:795_b1_a1_d1_i1 } - replace{ @atom:796 @atom:796_b13_a13_d13_i13 } - replace{ @atom:797 @atom:797_b46_a46_d46_i46 } - replace{ @atom:798 @atom:798_b13_a13_d13_i13 } - replace{ @atom:799 @atom:799_b13_a13_d13_i13 } - replace{ @atom:800 @atom:800_b21_a21_d21_i21 } - replace{ @atom:801 @atom:801_b13_a13_d13_i13 } - replace{ @atom:802 @atom:802_b46_a46_d46_i46 } - replace{ @atom:803 @atom:803_b13_a13_d13_i13 } - replace{ @atom:804 @atom:804_b13_a13_d13_i13 } - replace{ @atom:805 @atom:805_b65_a65_d65_i65 } - replace{ @atom:806 @atom:806_b13_a13_d13_i13 } - replace{ @atom:807 @atom:807_b46_a46_d46_i46 } - replace{ @atom:808 @atom:808_b13_a13_d13_i13 } - replace{ @atom:809 @atom:809_b13_a13_d13_i13 } - replace{ @atom:810 @atom:810_b1_a1_d1_i1 } - replace{ @atom:811 @atom:811_b21_a21_d21_i21 } - replace{ @atom:812 @atom:812_b65_a65_d65_i65 } - replace{ @atom:813 @atom:813_b48_a48_d48_i48 } - replace{ @atom:814 @atom:814_b20_a20_d20_i20 } - replace{ @atom:815 @atom:815_b13_a13_d13_i13 } - replace{ @atom:816 @atom:816_b1_a1_d1_i1 } - replace{ @atom:817 @atom:817_b24_a24_d24_i24 } - replace{ @atom:818 @atom:818_b48_a48_d48_i48 } - replace{ @atom:819 @atom:819_b13_a13_d13_i13 } - replace{ @atom:820 @atom:820_b3_a3_d3_i3 } - replace{ @atom:821 @atom:821_b3_a3_d3_i3 } - replace{ @atom:822 @atom:822_b4_a4_d4_i4 } - replace{ @atom:823 @atom:823_b24_a24_d24_i24 } - replace{ @atom:824 @atom:824_b45_a45_d45_i45 } - replace{ @atom:825 @atom:825_b5_a5_d5_i5 } - replace{ @atom:826 @atom:826_b7_a7_d7_i7 } - replace{ @atom:827 @atom:827_b13_a13_d13_i13 } - replace{ @atom:828 @atom:828_b13_a13_d13_i13 } - replace{ @atom:829 @atom:829_b86_a86_d86_i86 } - replace{ @atom:830 @atom:830_b86_a86_d86_i86 } - replace{ @atom:831 @atom:831_b86_a86_d86_i86 } - replace{ @atom:832 @atom:832_b86_a86_d86_i86 } - replace{ @atom:833 @atom:833_b48_a48_d48_i48 } + replace{ @atom:769 @atom:769_b019_a019_d019_i019 } + replace{ @atom:770 @atom:770_b053_a053_d053_i053 } + replace{ @atom:771 @atom:771_b054_a054_d054_i054 } + replace{ @atom:772 @atom:772_b013_a013_d013_i013 } + replace{ @atom:773 @atom:773_b013_a013_d013_i013 } + replace{ @atom:774 @atom:774_b013_a013_d013_i013 } + replace{ @atom:775 @atom:775_b013_a013_d013_i013 } + replace{ @atom:776 @atom:776_b084_a084_d084_i084 } + replace{ @atom:777 @atom:777_b087_a087_d087_i087 } + replace{ @atom:778 @atom:778_b086_a086_d086_i086 } + replace{ @atom:779 @atom:779_b086_a086_d086_i086 } + replace{ @atom:780 @atom:780_b046_a046_d046_i046 } + replace{ @atom:781 @atom:781_b013_a013_d013_i013 } + replace{ @atom:782 @atom:782_b003_a003_d003_i003 } + replace{ @atom:783 @atom:783_b053_a053_d053_i053 } + replace{ @atom:784 @atom:784_b052_a052_d052_i052 } + replace{ @atom:785 @atom:785_b054_a054_d054_i054 } + replace{ @atom:786 @atom:786_b001_a001_d001_i001 } + replace{ @atom:787 @atom:787_b013_a013_d013_i013 } + replace{ @atom:788 @atom:788_b046_a046_d046_i046 } + replace{ @atom:789 @atom:789_b013_a013_d013_i013 } + replace{ @atom:790 @atom:790_b013_a013_d013_i013 } + replace{ @atom:791 @atom:791_b013_a013_d013_i013 } + replace{ @atom:792 @atom:792_b013_a013_d013_i013 } + replace{ @atom:793 @atom:793_b013_a013_d013_i013 } + replace{ @atom:794 @atom:794_b013_a013_d013_i013 } + replace{ @atom:795 @atom:795_b001_a001_d001_i001 } + replace{ @atom:796 @atom:796_b013_a013_d013_i013 } + replace{ @atom:797 @atom:797_b046_a046_d046_i046 } + replace{ @atom:798 @atom:798_b013_a013_d013_i013 } + replace{ @atom:799 @atom:799_b013_a013_d013_i013 } + replace{ @atom:800 @atom:800_b021_a021_d021_i021 } + replace{ @atom:801 @atom:801_b013_a013_d013_i013 } + replace{ @atom:802 @atom:802_b046_a046_d046_i046 } + replace{ @atom:803 @atom:803_b013_a013_d013_i013 } + replace{ @atom:804 @atom:804_b013_a013_d013_i013 } + replace{ @atom:805 @atom:805_b065_a065_d065_i065 } + replace{ @atom:806 @atom:806_b013_a013_d013_i013 } + replace{ @atom:807 @atom:807_b046_a046_d046_i046 } + replace{ @atom:808 @atom:808_b013_a013_d013_i013 } + replace{ @atom:809 @atom:809_b013_a013_d013_i013 } + replace{ @atom:810 @atom:810_b001_a001_d001_i001 } + replace{ @atom:811 @atom:811_b021_a021_d021_i021 } + replace{ @atom:812 @atom:812_b065_a065_d065_i065 } + replace{ @atom:813 @atom:813_b048_a048_d048_i048 } + replace{ @atom:814 @atom:814_b020_a020_d020_i020 } + replace{ @atom:815 @atom:815_b013_a013_d013_i013 } + replace{ @atom:816 @atom:816_b001_a001_d001_i001 } + replace{ @atom:817 @atom:817_b024_a024_d024_i024 } + replace{ @atom:818 @atom:818_b048_a048_d048_i048 } + replace{ @atom:819 @atom:819_b013_a013_d013_i013 } + replace{ @atom:820 @atom:820_b003_a003_d003_i003 } + replace{ @atom:821 @atom:821_b003_a003_d003_i003 } + replace{ @atom:822 @atom:822_b004_a004_d004_i004 } + replace{ @atom:823 @atom:823_b024_a024_d024_i024 } + replace{ @atom:824 @atom:824_b045_a045_d045_i045 } + replace{ @atom:825 @atom:825_b005_a005_d005_i005 } + replace{ @atom:826 @atom:826_b007_a007_d007_i007 } + replace{ @atom:827 @atom:827_b013_a013_d013_i013 } + replace{ @atom:828 @atom:828_b013_a013_d013_i013 } + replace{ @atom:829 @atom:829_b086_a086_d086_i086 } + replace{ @atom:830 @atom:830_b086_a086_d086_i086 } + replace{ @atom:831 @atom:831_b086_a086_d086_i086 } + replace{ @atom:832 @atom:832_b086_a086_d086_i086 } + replace{ @atom:833 @atom:833_b048_a048_d048_i048 } replace{ @atom:834 @atom:834_b106_a106_d106_i106 } - replace{ @atom:835 @atom:835_b13_a13_d13_i13 } - replace{ @atom:836 @atom:836_b13_a13_d13_i13 } - replace{ @atom:837 @atom:837_b13_a13_d13_i13 } - replace{ @atom:838 @atom:838_b66_a66_d66_i66 } - replace{ @atom:839 @atom:839_b46_a46_d46_i46 } - replace{ @atom:840 @atom:840_b24_a24_d24_i24 } - replace{ @atom:841 @atom:841_b48_a48_d48_i48 } - replace{ @atom:842 @atom:842_b48_a48_d48_i48 } - replace{ @atom:843 @atom:843_b24_a24_d24_i24 } - replace{ @atom:844 @atom:844_b48_a48_d48_i48 } - replace{ @atom:845 @atom:845_b3_a3_d3_i3 } - replace{ @atom:846 @atom:846_b4_a4_d4_i4 } + replace{ @atom:835 @atom:835_b013_a013_d013_i013 } + replace{ @atom:836 @atom:836_b013_a013_d013_i013 } + replace{ @atom:837 @atom:837_b013_a013_d013_i013 } + replace{ @atom:838 @atom:838_b066_a066_d066_i066 } + replace{ @atom:839 @atom:839_b046_a046_d046_i046 } + replace{ @atom:840 @atom:840_b024_a024_d024_i024 } + replace{ @atom:841 @atom:841_b048_a048_d048_i048 } + replace{ @atom:842 @atom:842_b048_a048_d048_i048 } + replace{ @atom:843 @atom:843_b024_a024_d024_i024 } + replace{ @atom:844 @atom:844_b048_a048_d048_i048 } + replace{ @atom:845 @atom:845_b003_a003_d003_i003 } + replace{ @atom:846 @atom:846_b004_a004_d004_i004 } replace{ @atom:847 @atom:847_b107_a107_d107_i107 } - replace{ @atom:848 @atom:848_b13_a13_d13_i13 } - replace{ @atom:849 @atom:849_b13_a13_d13_i13 } - replace{ @atom:850 @atom:850_b13_a13_d13_i13 } - replace{ @atom:851 @atom:851_b13_a13_d13_i13 } - replace{ @atom:852 @atom:852_b46_a46_d46_i46 } - replace{ @atom:853 @atom:853_b3_a3_d3_i3 } - replace{ @atom:854 @atom:854_b4_a4_d4_i4 } - replace{ @atom:855 @atom:855_b46_a46_d46_i46 } - replace{ @atom:856 @atom:856_b13_a13_d13_i13 } - replace{ @atom:857 @atom:857_b13_a13_d13_i13 } - replace{ @atom:858 @atom:858_b13_a13_d13_i13 } - replace{ @atom:859 @atom:859_b13_a13_d13_i13 } - replace{ @atom:860 @atom:860_b13_a13_d13_i13 } - replace{ @atom:861 @atom:861_b13_a13_d13_i13 } - replace{ @atom:862 @atom:862_b13_a13_d13_i13 } - replace{ @atom:863 @atom:863_b13_a13_d13_i13 } - replace{ @atom:864 @atom:864_b13_a13_d13_i13 } - replace{ @atom:865 @atom:865_b13_a13_d13_i13 } + replace{ @atom:848 @atom:848_b013_a013_d013_i013 } + replace{ @atom:849 @atom:849_b013_a013_d013_i013 } + replace{ @atom:850 @atom:850_b013_a013_d013_i013 } + replace{ @atom:851 @atom:851_b013_a013_d013_i013 } + replace{ @atom:852 @atom:852_b046_a046_d046_i046 } + replace{ @atom:853 @atom:853_b003_a003_d003_i003 } + replace{ @atom:854 @atom:854_b004_a004_d004_i004 } + replace{ @atom:855 @atom:855_b046_a046_d046_i046 } + replace{ @atom:856 @atom:856_b013_a013_d013_i013 } + replace{ @atom:857 @atom:857_b013_a013_d013_i013 } + replace{ @atom:858 @atom:858_b013_a013_d013_i013 } + replace{ @atom:859 @atom:859_b013_a013_d013_i013 } + replace{ @atom:860 @atom:860_b013_a013_d013_i013 } + replace{ @atom:861 @atom:861_b013_a013_d013_i013 } + replace{ @atom:862 @atom:862_b013_a013_d013_i013 } + replace{ @atom:863 @atom:863_b013_a013_d013_i013 } + replace{ @atom:864 @atom:864_b013_a013_d013_i013 } + replace{ @atom:865 @atom:865_b013_a013_d013_i013 } replace{ @atom:866 @atom:866_b108_a108_d108_i108 } replace{ @atom:867 @atom:867_b108_a108_d108_i108 } replace{ @atom:868 @atom:868_b108_a108_d108_i108 } replace{ @atom:869 @atom:869_b108_a108_d108_i108 } - replace{ @atom:870 @atom:870_b45_a45_d45_i45 } - replace{ @atom:871 @atom:871_b13_a13_d13_i13 } - replace{ @atom:872 @atom:872_b13_a13_d13_i13 } - replace{ @atom:873 @atom:873_b13_a13_d13_i13 } - replace{ @atom:874 @atom:874_b13_a13_d13_i13 } - replace{ @atom:875 @atom:875_b1_a1_d1_i1 } - replace{ @atom:876 @atom:876_b21_a21_d21_i21 } - replace{ @atom:877 @atom:877_b65_a65_d65_i65 } - replace{ @atom:878 @atom:878_b66_a66_d66_i66 } - replace{ @atom:879 @atom:879_b68_a68_d68_i68 } - replace{ @atom:880 @atom:880_b69_a69_d69_i69 } - replace{ @atom:881 @atom:881_b70_a70_d70_i70 } - replace{ @atom:882 @atom:882_b71_a71_d71_i71 } - replace{ @atom:883 @atom:883_b72_a72_d72_i72 } - replace{ @atom:884 @atom:884_b73_a73_d73_i73 } - replace{ @atom:885 @atom:885_b74_a74_d74_i74 } - replace{ @atom:886 @atom:886_b75_a75_d75_i75 } - replace{ @atom:887 @atom:887_b76_a76_d76_i76 } - replace{ @atom:888 @atom:888_b13_a13_d13_i13 } - replace{ @atom:889 @atom:889_b13_a13_d13_i13 } - replace{ @atom:890 @atom:890_b13_a13_d13_i13 } - replace{ @atom:891 @atom:891_b13_a13_d13_i13 } - replace{ @atom:892 @atom:892_b46_a46_d46_i46 } - replace{ @atom:893 @atom:893_b53_a53_d53_i53 } - replace{ @atom:894 @atom:894_b48_a48_d48_i48 } - replace{ @atom:895 @atom:895_b53_a53_d53_i53 } - replace{ @atom:896 @atom:896_b48_a48_d48_i48 } + replace{ @atom:870 @atom:870_b045_a045_d045_i045 } + replace{ @atom:871 @atom:871_b013_a013_d013_i013 } + replace{ @atom:872 @atom:872_b013_a013_d013_i013 } + replace{ @atom:873 @atom:873_b013_a013_d013_i013 } + replace{ @atom:874 @atom:874_b013_a013_d013_i013 } + replace{ @atom:875 @atom:875_b001_a001_d001_i001 } + replace{ @atom:876 @atom:876_b021_a021_d021_i021 } + replace{ @atom:877 @atom:877_b065_a065_d065_i065 } + replace{ @atom:878 @atom:878_b066_a066_d066_i066 } + replace{ @atom:879 @atom:879_b068_a068_d068_i068 } + replace{ @atom:880 @atom:880_b069_a069_d069_i069 } + replace{ @atom:881 @atom:881_b070_a070_d070_i070 } + replace{ @atom:882 @atom:882_b071_a071_d071_i071 } + replace{ @atom:883 @atom:883_b072_a072_d072_i072 } + replace{ @atom:884 @atom:884_b073_a073_d073_i073 } + replace{ @atom:885 @atom:885_b074_a074_d074_i074 } + replace{ @atom:886 @atom:886_b075_a075_d075_i075 } + replace{ @atom:887 @atom:887_b076_a076_d076_i076 } + replace{ @atom:888 @atom:888_b013_a013_d013_i013 } + replace{ @atom:889 @atom:889_b013_a013_d013_i013 } + replace{ @atom:890 @atom:890_b013_a013_d013_i013 } + replace{ @atom:891 @atom:891_b013_a013_d013_i013 } + replace{ @atom:892 @atom:892_b046_a046_d046_i046 } + replace{ @atom:893 @atom:893_b053_a053_d053_i053 } + replace{ @atom:894 @atom:894_b048_a048_d048_i048 } + replace{ @atom:895 @atom:895_b053_a053_d053_i053 } + replace{ @atom:896 @atom:896_b048_a048_d048_i048 } replace{ @atom:897 @atom:897_b109_a109_d109_i109 } replace{ @atom:898 @atom:898_b109_a109_d109_i109 } - replace{ @atom:899 @atom:899_b46_a46_d46_i46 } - replace{ @atom:900 @atom:900_b47_a47_d47_i47 } - replace{ @atom:901 @atom:901_b47_a47_d47_i47 } - replace{ @atom:902 @atom:902_b47_a47_d47_i47 } + replace{ @atom:899 @atom:899_b046_a046_d046_i046 } + replace{ @atom:900 @atom:900_b047_a047_d047_i047 } + replace{ @atom:901 @atom:901_b047_a047_d047_i047 } + replace{ @atom:902 @atom:902_b047_a047_d047_i047 } replace{ @atom:903 @atom:903_b110_a110_d110_i110 } replace{ @atom:904 @atom:904_b110_a110_d110_i110 } - replace{ @atom:905 @atom:905_b4_a4_d4_i4 } - replace{ @atom:906 @atom:906_b13_a13_d13_i13 } + replace{ @atom:905 @atom:905_b004_a004_d004_i004 } + replace{ @atom:906 @atom:906_b013_a013_d013_i013 } @@ -2773,915 +2786,915 @@ OPLSAA { # --------------- Non-Bonded interactions: --------------------- # http://lammps.sandia.gov/doc/pair_lj.html # Syntax: - # pair_coeff AtomType1 AtomType2 pair_style_name parameters... + # pair_coeff AtomType1 AtomType2 parameters... write_once("In Settings") { - pair_coeff @atom:1_b1_a1_d1_i1 @atom:1_b1_a1_d1_i1 lj/cut/coul/long 0.061 2.94 - pair_coeff @atom:2_b2_a2_d2_i2 @atom:2_b2_a2_d2_i2 lj/cut/coul/long 0.118 3.905 - pair_coeff @atom:3_b3_a3_d3_i3 @atom:3_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75 - pair_coeff @atom:4_b4_a4_d4_i4 @atom:4_b4_a4_d4_i4 lj/cut/coul/long 0.21 2.96 - pair_coeff @atom:5_b5_a5_d5_i5 @atom:5_b5_a5_d5_i5 lj/cut/coul/long 0.17 3.0 - pair_coeff @atom:6_b6_a6_d6_i6 @atom:6_b6_a6_d6_i6 lj/cut/coul/long 0.16 3.91 - pair_coeff @atom:7_b7_a7_d7_i7 @atom:7_b7_a7_d7_i7 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:8_b8_a8_d8_i8 @atom:8_b8_a8_d8_i8 lj/cut/coul/long 0.294 3.73 - pair_coeff @atom:9_b6_a6_d6_i6 @atom:9_b6_a6_d6_i6 lj/cut/coul/long 0.207 3.775 - pair_coeff @atom:10_b6_a6_d6_i6 @atom:10_b6_a6_d6_i6 lj/cut/coul/long 0.175 3.905 - pair_coeff @atom:11_b6_a6_d6_i6 @atom:11_b6_a6_d6_i6 lj/cut/coul/long 0.16 3.91 - pair_coeff @atom:12_b6_a6_d6_i6 @atom:12_b6_a6_d6_i6 lj/cut/coul/long 0.145 3.96 - pair_coeff @atom:13_b2_a2_d2_i2 @atom:13_b2_a2_d2_i2 lj/cut/coul/long 0.118 3.905 - pair_coeff @atom:14_b9_a9_d9_i9 @atom:14_b9_a9_d9_i9 lj/cut/coul/long 0.14 3.85 - pair_coeff @atom:15_b10_a10_d10_i10 @atom:15_b10_a10_d10_i10 lj/cut/coul/long 0.08 3.85 - pair_coeff @atom:16_b11_a11_d11_i11 @atom:16_b11_a11_d11_i11 lj/cut/coul/long 0.115 3.8 - pair_coeff @atom:17_b12_a12_d12_i12 @atom:17_b12_a12_d12_i12 lj/cut/coul/long 0.11 3.75 - pair_coeff @atom:18_b13_a13_d13_i13 @atom:18_b13_a13_d13_i13 lj/cut/coul/long 0.05 3.8 - pair_coeff @atom:19_b14_a14_d14_i14 @atom:19_b14_a14_d14_i14 lj/cut/coul/long 0.105 3.75 - pair_coeff @atom:20_b5_a5_d5_i5 @atom:20_b5_a5_d5_i5 lj/cut/coul/long 0.17 3.07 - pair_coeff @atom:21_b7_a7_d7_i7 @atom:21_b7_a7_d7_i7 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:22_b6_a6_d6_i6 @atom:22_b6_a6_d6_i6 lj/cut/coul/long 0.207 3.775 - pair_coeff @atom:23_b2_a2_d2_i2 @atom:23_b2_a2_d2_i2 lj/cut/coul/long 0.118 3.905 - pair_coeff @atom:24_b15_a15_d15_i15 @atom:24_b15_a15_d15_i15 lj/cut/coul/long 0.25 3.7 - pair_coeff @atom:25_b15_a15_d15_i15 @atom:25_b15_a15_d15_i15 lj/cut/coul/long 0.25 3.55 - pair_coeff @atom:26_b16_a16_d16_i16 @atom:26_b16_a16_d16_i16 lj/cut/coul/long 0.25 3.55 - pair_coeff @atom:27_b16_a16_d16_i16 @atom:27_b16_a16_d16_i16 lj/cut/coul/long 0.25 3.55 - pair_coeff @atom:28_b17_a17_d17_i17 @atom:28_b17_a17_d17_i17 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:29_b17_a17_d17_i17 @atom:29_b17_a17_d17_i17 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:30_b6_a6_d6_i6 @atom:30_b6_a6_d6_i6 lj/cut/coul/long 0.207 3.775 - pair_coeff @atom:31_b2_a2_d2_i2 @atom:31_b2_a2_d2_i2 lj/cut/coul/long 0.118 3.905 - pair_coeff @atom:32_b6_a6_d6_i6 @atom:32_b6_a6_d6_i6 lj/cut/coul/long 0.17 3.8 - pair_coeff @atom:33_b2_a2_d2_i2 @atom:33_b2_a2_d2_i2 lj/cut/coul/long 0.118 3.8 - pair_coeff @atom:34_b6_a6_d6_i6 @atom:34_b6_a6_d6_i6 lj/cut/coul/long 0.17 3.8 - pair_coeff @atom:35_b2_a2_d2_i2 @atom:35_b2_a2_d2_i2 lj/cut/coul/long 0.118 3.8 - pair_coeff @atom:36_b18_a18_d18_i18 @atom:36_b18_a18_d18_i18 lj/cut/coul/long 0.17 3.2 - pair_coeff @atom:37_b19_a19_d19_i19 @atom:37_b19_a19_d19_i19 lj/cut/coul/long 0.15 3.65 - pair_coeff @atom:38_b6_a6_d6_i6 @atom:38_b6_a6_d6_i6 lj/cut/coul/long 0.207 3.775 - pair_coeff @atom:39_b10_a10_d10_i10 @atom:39_b10_a10_d10_i10 lj/cut/coul/long 0.08 3.85 - pair_coeff @atom:40_b13_a13_d13_i13 @atom:40_b13_a13_d13_i13 lj/cut/coul/long 0.05 3.8 - pair_coeff @atom:41_b20_a20_d20_i20 @atom:41_b20_a20_d20_i20 lj/cut/coul/long 0.17 3.0 - pair_coeff @atom:42_b6_a6_d6_i6 @atom:42_b6_a6_d6_i6 lj/cut/coul/long 0.17 3.8 - pair_coeff @atom:43_b2_a2_d2_i2 @atom:43_b2_a2_d2_i2 lj/cut/coul/long 0.118 3.8 - pair_coeff @atom:44_b2_a2_d2_i2 @atom:44_b2_a2_d2_i2 lj/cut/coul/long 0.118 3.8 - pair_coeff @atom:45_b21_a21_d21_i21 @atom:45_b21_a21_d21_i21 lj/cut/coul/long 0.3 3.4 - pair_coeff @atom:46_b10_a10_d10_i10 @atom:46_b10_a10_d10_i10 lj/cut/coul/long 0.08 3.8 - pair_coeff @atom:47_b21_a21_d21_i21 @atom:47_b21_a21_d21_i21 lj/cut/coul/long 0.3 3.47 - pair_coeff @atom:48_b13_a13_d13_i13 @atom:48_b13_a13_d13_i13 lj/cut/coul/long 0.05 3.8 - pair_coeff @atom:49_b21_a21_d21_i21 @atom:49_b21_a21_d21_i21 lj/cut/coul/long 0.266 3.47 - pair_coeff @atom:50_b22_a22_d22_i22 @atom:50_b22_a22_d22_i22 lj/cut/coul/long 0.395 3.56 - pair_coeff @atom:51_b23_a23_d23_i23 @atom:51_b23_a23_d23_i23 lj/cut/coul/long 0.28 2.93 - pair_coeff @atom:52_b6_a6_d6_i6 @atom:52_b6_a6_d6_i6 lj/cut/coul/long 0.16 3.81 - pair_coeff @atom:53_b4_a4_d4_i4 @atom:53_b4_a4_d4_i4 lj/cut/coul/long 0.21 2.96 - pair_coeff @atom:54_b24_a24_d24_i24 @atom:54_b24_a24_d24_i24 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:55_b3_a3_d3_i3 @atom:55_b3_a3_d3_i3 lj/cut/coul/long 0.115 3.8 - pair_coeff @atom:56_b6_a6_d6_i6 @atom:56_b6_a6_d6_i6 lj/cut/coul/long 0.17 3.8 - pair_coeff @atom:57_b25_a25_d25_i25 @atom:57_b25_a25_d25_i25 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:58_b26_a26_d26_i26 @atom:58_b26_a26_d26_i26 lj/cut/coul/long 0.02 2.556 - pair_coeff @atom:59_b27_a27_d27_i27 @atom:59_b27_a27_d27_i27 lj/cut/coul/long 0.069 2.78 - pair_coeff @atom:60_b28_a28_d28_i28 @atom:60_b28_a28_d28_i28 lj/cut/coul/long 0.2339 3.401 - pair_coeff @atom:61_b29_a29_d29_i29 @atom:61_b29_a29_d29_i29 lj/cut/coul/long 0.317 3.624 - pair_coeff @atom:62_b30_a30_d30_i30 @atom:62_b30_a30_d30_i30 lj/cut/coul/long 0.433 3.935 - pair_coeff @atom:63_b31_a31_d31_i31 @atom:63_b31_a31_d31_i31 lj/cut/coul/long 0.1521 3.15061 - pair_coeff @atom:64_b32_a32_d32_i32 @atom:64_b32_a32_d32_i32 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:65_b31_a31_d31_i31 @atom:65_b31_a31_d31_i31 lj/cut/coul/long 0.155 3.15365 - pair_coeff @atom:66_b32_a32_d32_i32 @atom:66_b32_a32_d32_i32 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:67_b33_a33_d33_i33 @atom:67_b33_a33_d33_i33 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:68_b34_a34_d34_i34 @atom:68_b34_a34_d34_i34 lj/cut/coul/long 0.15 3.176 - pair_coeff @atom:69_b35_a35_d35_i35 @atom:69_b35_a35_d35_i35 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:70_b36_a36_d36_i36 @atom:70_b36_a36_d36_i36 lj/cut/coul/long 0.1 3.27 - pair_coeff @atom:71_b37_a37_d37_i37 @atom:71_b37_a37_d37_i37 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:72_b38_a38_d38_i38 @atom:72_b38_a38_d38_i38 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:73_b39_a39_d39_i39 @atom:73_b39_a39_d39_i39 lj/cut/coul/long 0.16 3.12 - pair_coeff @atom:74_b40_a40_d40_i40 @atom:74_b40_a40_d40_i40 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:75_b41_a41_d41_i41 @atom:75_b41_a41_d41_i41 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:76_b42_a42_d42_i42 @atom:76_b42_a42_d42_i42 lj/cut/coul/long 0.1554 3.16557 - pair_coeff @atom:77_b43_a43_d43_i43 @atom:77_b43_a43_d43_i43 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:78_b44_a44_d44_i44 @atom:78_b44_a44_d44_i44 lj/cut/coul/long 0.17 3.42 - pair_coeff @atom:79_b45_a45_d45_i45 @atom:79_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:80_b13_a13_d13_i13 @atom:80_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:81_b13_a13_d13_i13 @atom:81_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:82_b13_a13_d13_i13 @atom:82_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:83_b13_a13_d13_i13 @atom:83_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:84_b13_a13_d13_i13 @atom:84_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:85_b46_a46_d46_i46 @atom:85_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5 - pair_coeff @atom:86_b47_a47_d47_i47 @atom:86_b47_a47_d47_i47 lj/cut/coul/long 0.076 3.55 - pair_coeff @atom:87_b47_a47_d47_i47 @atom:87_b47_a47_d47_i47 lj/cut/coul/long 0.076 3.55 - pair_coeff @atom:88_b47_a47_d47_i47 @atom:88_b47_a47_d47_i47 lj/cut/coul/long 0.076 3.55 - pair_coeff @atom:89_b46_a46_d46_i46 @atom:89_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:90_b48_a48_d48_i48 @atom:90_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:91_b49_a49_d49_i49 @atom:91_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:92_b48_a48_d48_i48 @atom:92_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:93_b13_a13_d13_i13 @atom:93_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:94_b13_a13_d13_i13 @atom:94_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:95_b50_a50_d50_i50 @atom:95_b50_a50_d50_i50 lj/cut/coul/long 0.076 3.55 - pair_coeff @atom:96_b5_a5_d5_i5 @atom:96_b5_a5_d5_i5 lj/cut/coul/long 0.17 3.12 - pair_coeff @atom:97_b7_a7_d7_i7 @atom:97_b7_a7_d7_i7 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:98_b46_a46_d46_i46 @atom:98_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5 - pair_coeff @atom:99_b13_a13_d13_i13 @atom:99_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:100_b13_a13_d13_i13 @atom:100_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:101_b13_a13_d13_i13 @atom:101_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:102_b13_a13_d13_i13 @atom:102_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:103_b13_a13_d13_i13 @atom:103_b13_a13_d13_i13 lj/cut/coul/long 0.062 3.25 - pair_coeff @atom:104_b5_a5_d5_i5 @atom:104_b5_a5_d5_i5 lj/cut/coul/long 0.17 3.07 - pair_coeff @atom:105_b7_a7_d7_i7 @atom:105_b7_a7_d7_i7 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:106_b1_a1_d1_i1 @atom:106_b1_a1_d1_i1 lj/cut/coul/long 0.061 2.94 - pair_coeff @atom:107_b46_a46_d46_i46 @atom:107_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5 - pair_coeff @atom:108_b48_a48_d48_i48 @atom:108_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:109_b5_a5_d5_i5 @atom:109_b5_a5_d5_i5 lj/cut/coul/long 0.17 3.07 - pair_coeff @atom:110_b7_a7_d7_i7 @atom:110_b7_a7_d7_i7 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:111_b5_a5_d5_i5 @atom:111_b5_a5_d5_i5 lj/cut/coul/long 0.17 3.07 - pair_coeff @atom:112_b7_a7_d7_i7 @atom:112_b7_a7_d7_i7 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:113_b5_a5_d5_i5 @atom:113_b5_a5_d5_i5 lj/cut/coul/long 0.17 3.07 - pair_coeff @atom:114_b7_a7_d7_i7 @atom:114_b7_a7_d7_i7 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:115_b13_a13_d13_i13 @atom:115_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:116_b13_a13_d13_i13 @atom:116_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:117_b13_a13_d13_i13 @atom:117_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:118_b46_a46_d46_i46 @atom:118_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5 - pair_coeff @atom:119_b20_a20_d20_i20 @atom:119_b20_a20_d20_i20 lj/cut/coul/long 0.14 2.9 - pair_coeff @atom:120_b50_a50_d50_i50 @atom:120_b50_a50_d50_i50 lj/cut/coul/long 0.076 3.55 - pair_coeff @atom:121_b20_a20_d20_i20 @atom:121_b20_a20_d20_i20 lj/cut/coul/long 0.14 2.9 - pair_coeff @atom:122_b20_a20_d20_i20 @atom:122_b20_a20_d20_i20 lj/cut/coul/long 0.14 2.9 - pair_coeff @atom:123_b13_a13_d13_i13 @atom:123_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:124_b13_a13_d13_i13 @atom:124_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:125_b13_a13_d13_i13 @atom:125_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:126_b13_a13_d13_i13 @atom:126_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:127_b46_a46_d46_i46 @atom:127_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5 - pair_coeff @atom:128_b20_a20_d20_i20 @atom:128_b20_a20_d20_i20 lj/cut/coul/long 0.14 2.9 - pair_coeff @atom:129_b5_a5_d5_i5 @atom:129_b5_a5_d5_i5 lj/cut/coul/long 0.17 3.07 - pair_coeff @atom:130_b7_a7_d7_i7 @atom:130_b7_a7_d7_i7 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:131_b51_a51_d51_i51 @atom:131_b51_a51_d51_i51 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:132_b46_a46_d46_i46 @atom:132_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5 - pair_coeff @atom:133_b51_a51_d51_i51 @atom:133_b51_a51_d51_i51 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:134_b46_a46_d46_i46 @atom:134_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5 - pair_coeff @atom:135_b51_a51_d51_i51 @atom:135_b51_a51_d51_i51 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:136_b46_a46_d46_i46 @atom:136_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5 - pair_coeff @atom:137_b51_a51_d51_i51 @atom:137_b51_a51_d51_i51 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:138_b46_a46_d46_i46 @atom:138_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5 - pair_coeff @atom:139_b51_a51_d51_i51 @atom:139_b51_a51_d51_i51 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:140_b51_a51_d51_i51 @atom:140_b51_a51_d51_i51 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:141_b48_a48_d48_i48 @atom:141_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:142_b15_a15_d15_i15 @atom:142_b15_a15_d15_i15 lj/cut/coul/long 0.25 3.55 - pair_coeff @atom:143_b15_a15_d15_i15 @atom:143_b15_a15_d15_i15 lj/cut/coul/long 0.25 3.7 - pair_coeff @atom:144_b16_a16_d16_i16 @atom:144_b16_a16_d16_i16 lj/cut/coul/long 0.25 3.55 - pair_coeff @atom:145_b16_a16_d16_i16 @atom:145_b16_a16_d16_i16 lj/cut/coul/long 0.25 3.55 - pair_coeff @atom:146_b17_a17_d17_i17 @atom:146_b17_a17_d17_i17 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:147_b17_a17_d17_i17 @atom:147_b17_a17_d17_i17 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:148_b13_a13_d13_i13 @atom:148_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:149_b13_a13_d13_i13 @atom:149_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:150_b13_a13_d13_i13 @atom:150_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:151_b13_a13_d13_i13 @atom:151_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:152_b13_a13_d13_i13 @atom:152_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:153_b13_a13_d13_i13 @atom:153_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:154_b13_a13_d13_i13 @atom:154_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:155_b13_a13_d13_i13 @atom:155_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:156_b13_a13_d13_i13 @atom:156_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:157_b13_a13_d13_i13 @atom:157_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:158_b13_a13_d13_i13 @atom:158_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:159_b13_a13_d13_i13 @atom:159_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:160_b13_a13_d13_i13 @atom:160_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:161_b13_a13_d13_i13 @atom:161_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:162_b13_a13_d13_i13 @atom:162_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:163_b48_a48_d48_i48 @atom:163_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:164_b16_a16_d16_i16 @atom:164_b16_a16_d16_i16 lj/cut/coul/long 0.25 3.55 - pair_coeff @atom:165_b13_a13_d13_i13 @atom:165_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:166_b13_a13_d13_i13 @atom:166_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:167_b13_a13_d13_i13 @atom:167_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:168_b21_a21_d21_i21 @atom:168_b21_a21_d21_i21 lj/cut/coul/long 0.3 3.4 - pair_coeff @atom:169_b47_a47_d47_i47 @atom:169_b47_a47_d47_i47 lj/cut/coul/long 0.076 3.55 - pair_coeff @atom:170_b48_a48_d48_i48 @atom:170_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:171_b13_a13_d13_i13 @atom:171_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:172_b13_a13_d13_i13 @atom:172_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:173_b3_a3_d3_i3 @atom:173_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75 - pair_coeff @atom:174_b3_a3_d3_i3 @atom:174_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75 - pair_coeff @atom:175_b3_a3_d3_i3 @atom:175_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75 - pair_coeff @atom:176_b3_a3_d3_i3 @atom:176_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75 - pair_coeff @atom:177_b3_a3_d3_i3 @atom:177_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75 - pair_coeff @atom:178_b4_a4_d4_i4 @atom:178_b4_a4_d4_i4 lj/cut/coul/long 0.21 2.96 - pair_coeff @atom:179_b24_a24_d24_i24 @atom:179_b24_a24_d24_i24 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:180_b24_a24_d24_i24 @atom:180_b24_a24_d24_i24 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:181_b24_a24_d24_i24 @atom:181_b24_a24_d24_i24 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:182_b45_a45_d45_i45 @atom:182_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:183_b45_a45_d45_i45 @atom:183_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:184_b13_a13_d13_i13 @atom:184_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:185_b13_a13_d13_i13 @atom:185_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:186_b13_a13_d13_i13 @atom:186_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:187_b13_a13_d13_i13 @atom:187_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:188_b13_a13_d13_i13 @atom:188_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:189_b3_a3_d3_i3 @atom:189_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75 - pair_coeff @atom:190_b4_a4_d4_i4 @atom:190_b4_a4_d4_i4 lj/cut/coul/long 0.21 2.96 - pair_coeff @atom:191_b24_a24_d24_i24 @atom:191_b24_a24_d24_i24 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:192_b45_a45_d45_i45 @atom:192_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:193_b24_a24_d24_i24 @atom:193_b24_a24_d24_i24 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:194_b3_a3_d3_i3 @atom:194_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75 - pair_coeff @atom:195_b4_a4_d4_i4 @atom:195_b4_a4_d4_i4 lj/cut/coul/long 0.21 2.96 - pair_coeff @atom:196_b45_a45_d45_i45 @atom:196_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:197_b46_a46_d46_i46 @atom:197_b46_a46_d46_i46 lj/cut/coul/long 0.02 2.5 - pair_coeff @atom:198_b13_a13_d13_i13 @atom:198_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:199_b13_a13_d13_i13 @atom:199_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:200_b13_a13_d13_i13 @atom:200_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:201_b13_a13_d13_i13 @atom:201_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:202_b48_a48_d48_i48 @atom:202_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:203_b19_a19_d19_i19 @atom:203_b19_a19_d19_i19 lj/cut/coul/long 0.15 3.65 - pair_coeff @atom:204_b18_a18_d18_i18 @atom:204_b18_a18_d18_i18 lj/cut/coul/long 0.17 3.2 - pair_coeff @atom:205_b48_a48_d48_i48 @atom:205_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:206_b21_a21_d21_i21 @atom:206_b21_a21_d21_i21 lj/cut/coul/long 0.3 3.4 - pair_coeff @atom:207_b24_a24_d24_i24 @atom:207_b24_a24_d24_i24 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:208_b48_a48_d48_i48 @atom:208_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:209_b3_a3_d3_i3 @atom:209_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75 - pair_coeff @atom:210_b4_a4_d4_i4 @atom:210_b4_a4_d4_i4 lj/cut/coul/long 0.21 2.96 - pair_coeff @atom:211_b5_a5_d5_i5 @atom:211_b5_a5_d5_i5 lj/cut/coul/long 0.17 3.0 - pair_coeff @atom:212_b7_a7_d7_i7 @atom:212_b7_a7_d7_i7 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:213_b3_a3_d3_i3 @atom:213_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75 - pair_coeff @atom:214_b52_a52_d52_i52 @atom:214_b52_a52_d52_i52 lj/cut/coul/long 0.21 2.96 - pair_coeff @atom:215_b13_a13_d13_i13 @atom:215_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:216_b13_a13_d13_i13 @atom:216_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:217_b13_a13_d13_i13 @atom:217_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:218_b13_a13_d13_i13 @atom:218_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:219_b3_a3_d3_i3 @atom:219_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75 - pair_coeff @atom:220_b4_a4_d4_i4 @atom:220_b4_a4_d4_i4 lj/cut/coul/long 0.21 2.96 - pair_coeff @atom:221_b46_a46_d46_i46 @atom:221_b46_a46_d46_i46 lj/cut/coul/long 0.015 2.42 - pair_coeff @atom:222_b3_a3_d3_i3 @atom:222_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75 - pair_coeff @atom:223_b4_a4_d4_i4 @atom:223_b4_a4_d4_i4 lj/cut/coul/long 0.21 2.96 - pair_coeff @atom:224_b46_a46_d46_i46 @atom:224_b46_a46_d46_i46 lj/cut/coul/long 0.015 2.42 - pair_coeff @atom:225_b13_a13_d13_i13 @atom:225_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:226_b13_a13_d13_i13 @atom:226_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:227_b13_a13_d13_i13 @atom:227_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:228_b13_a13_d13_i13 @atom:228_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:229_b53_a53_d53_i53 @atom:229_b53_a53_d53_i53 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:230_b53_a53_d53_i53 @atom:230_b53_a53_d53_i53 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:231_b53_a53_d53_i53 @atom:231_b53_a53_d53_i53 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:232_b54_a54_d54_i54 @atom:232_b54_a54_d54_i54 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:233_b54_a54_d54_i54 @atom:233_b54_a54_d54_i54 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:234_b13_a13_d13_i13 @atom:234_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:235_b13_a13_d13_i13 @atom:235_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:236_b13_a13_d13_i13 @atom:236_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:237_b13_a13_d13_i13 @atom:237_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:238_b13_a13_d13_i13 @atom:238_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:239_b13_a13_d13_i13 @atom:239_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:240_b13_a13_d13_i13 @atom:240_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:241_b13_a13_d13_i13 @atom:241_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:242_b13_a13_d13_i13 @atom:242_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:243_b55_a55_d55_i55 @atom:243_b55_a55_d55_i55 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:244_b54_a54_d54_i54 @atom:244_b54_a54_d54_i54 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:245_b48_a48_d48_i48 @atom:245_b48_a48_d48_i48 lj/cut/coul/long 0.05 3.55 - pair_coeff @atom:246_b55_a55_d55_i55 @atom:246_b55_a55_d55_i55 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:247_b54_a54_d54_i54 @atom:247_b54_a54_d54_i54 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:248_b13_a13_d13_i13 @atom:248_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:249_b13_a13_d13_i13 @atom:249_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:250_b13_a13_d13_i13 @atom:250_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:251_b13_a13_d13_i13 @atom:251_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:252_b53_a53_d53_i53 @atom:252_b53_a53_d53_i53 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:253_b54_a54_d54_i54 @atom:253_b54_a54_d54_i54 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:254_b56_a56_d56_i56 @atom:254_b56_a56_d56_i56 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:255_b48_a48_d48_i48 @atom:255_b48_a48_d48_i48 lj/cut/coul/long 0.08 3.5 - pair_coeff @atom:256_b55_a55_d55_i55 @atom:256_b55_a55_d55_i55 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:257_b45_a45_d45_i45 @atom:257_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:258_b48_a48_d48_i48 @atom:258_b48_a48_d48_i48 lj/cut/coul/long 0.08 3.5 - pair_coeff @atom:259_b49_a49_d49_i49 @atom:259_b49_a49_d49_i49 lj/cut/coul/long 0.05 2.5 - pair_coeff @atom:260_b48_a48_d48_i48 @atom:260_b48_a48_d48_i48 lj/cut/coul/long 0.08 3.5 - pair_coeff @atom:261_b49_a49_d49_i49 @atom:261_b49_a49_d49_i49 lj/cut/coul/long 0.05 2.5 - pair_coeff @atom:262_b57_a57_d57_i57 @atom:262_b57_a57_d57_i57 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:263_b3_a3_d3_i3 @atom:263_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75 - pair_coeff @atom:264_b57_a57_d57_i57 @atom:264_b57_a57_d57_i57 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:265_b3_a3_d3_i3 @atom:265_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75 - pair_coeff @atom:266_b47_a47_d47_i47 @atom:266_b47_a47_d47_i47 lj/cut/coul/long 0.08 3.5 - pair_coeff @atom:267_b47_a47_d47_i47 @atom:267_b47_a47_d47_i47 lj/cut/coul/long 0.08 3.5 - pair_coeff @atom:268_b45_a45_d45_i45 @atom:268_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:269_b4_a4_d4_i4 @atom:269_b4_a4_d4_i4 lj/cut/coul/long 0.21 2.96 - pair_coeff @atom:270_b45_a45_d45_i45 @atom:270_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:271_b4_a4_d4_i4 @atom:271_b4_a4_d4_i4 lj/cut/coul/long 0.21 2.96 - pair_coeff @atom:272_b46_a46_d46_i46 @atom:272_b46_a46_d46_i46 lj/cut/coul/long 0.05 2.5 - pair_coeff @atom:273_b46_a46_d46_i46 @atom:273_b46_a46_d46_i46 lj/cut/coul/long 0.05 2.5 - pair_coeff @atom:274_b13_a13_d13_i13 @atom:274_b13_a13_d13_i13 lj/cut/coul/long 0.08 3.5 - pair_coeff @atom:275_b46_a46_d46_i46 @atom:275_b46_a46_d46_i46 lj/cut/coul/long 0.05 2.5 - pair_coeff @atom:276_b57_a57_d57_i57 @atom:276_b57_a57_d57_i57 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:277_b3_a3_d3_i3 @atom:277_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75 - pair_coeff @atom:278_b56_a56_d56_i56 @atom:278_b56_a56_d56_i56 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:279_b48_a48_d48_i48 @atom:279_b48_a48_d48_i48 lj/cut/coul/long 0.08 3.5 - pair_coeff @atom:280_b47_a47_d47_i47 @atom:280_b47_a47_d47_i47 lj/cut/coul/long 0.08 3.5 - pair_coeff @atom:281_b47_a47_d47_i47 @atom:281_b47_a47_d47_i47 lj/cut/coul/long 0.08 3.5 - pair_coeff @atom:282_b45_a45_d45_i45 @atom:282_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:283_b4_a4_d4_i4 @atom:283_b4_a4_d4_i4 lj/cut/coul/long 0.21 2.96 - pair_coeff @atom:284_b55_a55_d55_i55 @atom:284_b55_a55_d55_i55 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:285_b45_a45_d45_i45 @atom:285_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:286_b45_a45_d45_i45 @atom:286_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:287_b46_a46_d46_i46 @atom:287_b46_a46_d46_i46 lj/cut/coul/long 0.05 2.5 - pair_coeff @atom:288_b58_a58_d58_i58 @atom:288_b58_a58_d58_i58 lj/cut/coul/long 0.05 2.5 - pair_coeff @atom:289_b56_a56_d56_i56 @atom:289_b56_a56_d56_i56 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:290_b59_a59_d59_i59 @atom:290_b59_a59_d59_i59 lj/cut/coul/long 0.08 3.5 - pair_coeff @atom:291_b56_a56_d56_i56 @atom:291_b56_a56_d56_i56 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:292_b60_a60_d60_i60 @atom:292_b60_a60_d60_i60 lj/cut/coul/long 0.08 3.5 - pair_coeff @atom:293_b60_a60_d60_i60 @atom:293_b60_a60_d60_i60 lj/cut/coul/long 0.08 3.5 - pair_coeff @atom:294_b48_a48_d48_i48 @atom:294_b48_a48_d48_i48 lj/cut/coul/long 0.08 3.5 - pair_coeff @atom:295_b61_a61_d61_i61 @atom:295_b61_a61_d61_i61 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:296_b62_a62_d62_i62 @atom:296_b62_a62_d62_i62 lj/cut/coul/long 0.08 3.5 - pair_coeff @atom:297_b57_a57_d57_i57 @atom:297_b57_a57_d57_i57 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:298_b63_a63_d63_i63 @atom:298_b63_a63_d63_i63 lj/cut/coul/long 0.05 2.5 - pair_coeff @atom:299_b55_a55_d55_i55 @atom:299_b55_a55_d55_i55 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:300_b45_a45_d45_i45 @atom:300_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:301_b45_a45_d45_i45 @atom:301_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:302_b63_a63_d63_i63 @atom:302_b63_a63_d63_i63 lj/cut/coul/long 0.05 2.5 - pair_coeff @atom:303_b45_a45_d45_i45 @atom:303_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:304_b57_a57_d57_i57 @atom:304_b57_a57_d57_i57 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:305_b48_a48_d48_i48 @atom:305_b48_a48_d48_i48 lj/cut/coul/long 0.08 3.5 - pair_coeff @atom:306_b56_a56_d56_i56 @atom:306_b56_a56_d56_i56 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:307_b60_a60_d60_i60 @atom:307_b60_a60_d60_i60 lj/cut/coul/long 0.08 3.5 - pair_coeff @atom:308_b60_a60_d60_i60 @atom:308_b60_a60_d60_i60 lj/cut/coul/long 0.08 3.5 - pair_coeff @atom:309_b3_a3_d3_i3 @atom:309_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75 - pair_coeff @atom:310_b45_a45_d45_i45 @atom:310_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:311_b55_a55_d55_i55 @atom:311_b55_a55_d55_i55 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:312_b45_a45_d45_i45 @atom:312_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:313_b4_a4_d4_i4 @atom:313_b4_a4_d4_i4 lj/cut/coul/long 0.21 2.96 - pair_coeff @atom:314_b13_a13_d13_i13 @atom:314_b13_a13_d13_i13 lj/cut/coul/long 0.08 3.5 - pair_coeff @atom:315_b46_a46_d46_i46 @atom:315_b46_a46_d46_i46 lj/cut/coul/long 0.05 2.5 - pair_coeff @atom:316_b13_a13_d13_i13 @atom:316_b13_a13_d13_i13 lj/cut/coul/long 0.08 3.5 - pair_coeff @atom:317_b46_a46_d46_i46 @atom:317_b46_a46_d46_i46 lj/cut/coul/long 0.05 2.5 - pair_coeff @atom:318_b13_a13_d13_i13 @atom:318_b13_a13_d13_i13 lj/cut/coul/long 0.08 3.5 - pair_coeff @atom:319_b46_a46_d46_i46 @atom:319_b46_a46_d46_i46 lj/cut/coul/long 0.05 2.5 - pair_coeff @atom:320_b57_a57_d57_i57 @atom:320_b57_a57_d57_i57 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:321_b3_a3_d3_i3 @atom:321_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75 - pair_coeff @atom:322_b57_a57_d57_i57 @atom:322_b57_a57_d57_i57 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:323_b48_a48_d48_i48 @atom:323_b48_a48_d48_i48 lj/cut/coul/long 0.08 3.5 - pair_coeff @atom:324_b47_a47_d47_i47 @atom:324_b47_a47_d47_i47 lj/cut/coul/long 0.08 3.5 - pair_coeff @atom:325_b47_a47_d47_i47 @atom:325_b47_a47_d47_i47 lj/cut/coul/long 0.08 3.5 - pair_coeff @atom:326_b45_a45_d45_i45 @atom:326_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:327_b4_a4_d4_i4 @atom:327_b4_a4_d4_i4 lj/cut/coul/long 0.21 2.96 - pair_coeff @atom:328_b45_a45_d45_i45 @atom:328_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:329_b55_a55_d55_i55 @atom:329_b55_a55_d55_i55 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:330_b45_a45_d45_i45 @atom:330_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:331_b45_a45_d45_i45 @atom:331_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:332_b49_a49_d49_i49 @atom:332_b49_a49_d49_i49 lj/cut/coul/long 0.05 2.5 - pair_coeff @atom:333_b58_a58_d58_i58 @atom:333_b58_a58_d58_i58 lj/cut/coul/long 0.05 2.5 - pair_coeff @atom:334_b13_a13_d13_i13 @atom:334_b13_a13_d13_i13 lj/cut/coul/long 0.08 3.5 - pair_coeff @atom:335_b46_a46_d46_i46 @atom:335_b46_a46_d46_i46 lj/cut/coul/long 0.05 2.5 - pair_coeff @atom:336_b64_a64_d64_i64 @atom:336_b64_a64_d64_i64 lj/cut/coul/long 0.2 3.74 - pair_coeff @atom:337_b52_a52_d52_i52 @atom:337_b52_a52_d52_i52 lj/cut/coul/long 0.21 2.96 - pair_coeff @atom:338_b20_a20_d20_i20 @atom:338_b20_a20_d20_i20 lj/cut/coul/long 0.17 3.0 - pair_coeff @atom:339_b13_a13_d13_i13 @atom:339_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.55 - pair_coeff @atom:340_b47_a47_d47_i47 @atom:340_b47_a47_d47_i47 lj/cut/coul/long 0.08 3.5 - pair_coeff @atom:341_b21_a21_d21_i21 @atom:341_b21_a21_d21_i21 lj/cut/coul/long 0.3 3.4 - pair_coeff @atom:342_b47_a47_d47_i47 @atom:342_b47_a47_d47_i47 lj/cut/coul/long 0.076 3.55 - pair_coeff @atom:343_b1_a1_d1_i1 @atom:343_b1_a1_d1_i1 lj/cut/coul/long 0.71 3.05 - pair_coeff @atom:344_b21_a21_d21_i21 @atom:344_b21_a21_d21_i21 lj/cut/coul/long 0.71 4.02 - pair_coeff @atom:345_b65_a65_d65_i65 @atom:345_b65_a65_d65_i65 lj/cut/coul/long 0.71 4.28 - pair_coeff @atom:346_b66_a66_d66_i66 @atom:346_b66_a66_d66_i66 lj/cut/coul/long 0.71 4.81 - pair_coeff @atom:347_b67_a67_d67_i67 @atom:347_b67_a67_d67_i67 lj/cut/coul/long 0.0005 5.34 - pair_coeff @atom:348_b68_a68_d68_i68 @atom:348_b68_a68_d68_i68 lj/cut/coul/long 0.0005 2.87 - pair_coeff @atom:349_b69_a69_d69_i69 @atom:349_b69_a69_d69_i69 lj/cut/coul/long 0.0005 4.07 - pair_coeff @atom:350_b70_a70_d70_i70 @atom:350_b70_a70_d70_i70 lj/cut/coul/long 0.0005 5.17 - pair_coeff @atom:351_b71_a71_d71_i71 @atom:351_b71_a71_d71_i71 lj/cut/coul/long 0.0005 5.6 - pair_coeff @atom:352_b72_a72_d72_i72 @atom:352_b72_a72_d72_i72 lj/cut/coul/long 0.0005 6.2 - pair_coeff @atom:353_b73_a73_d73_i73 @atom:353_b73_a73_d73_i73 lj/cut/coul/long 0.875044 1.644471 - pair_coeff @atom:354_b74_a74_d74_i74 @atom:354_b74_a74_d74_i74 lj/cut/coul/long 0.449657 2.412031 - pair_coeff @atom:355_b75_a75_d75_i75 @atom:355_b75_a75_d75_i75 lj/cut/coul/long 0.118226 3.102688 - pair_coeff @atom:356_b76_a76_d76_i76 @atom:356_b76_a76_d76_i76 lj/cut/coul/long 0.047096 3.81661 - pair_coeff @atom:357_b6_a6_d6_i6 @atom:357_b6_a6_d6_i6 lj/cut/coul/long 0.3 4.2 - pair_coeff @atom:358_b46_a46_d46_i46 @atom:358_b46_a46_d46_i46 lj/cut/coul/long 0.05 2.5 - pair_coeff @atom:359_b15_a15_d15_i15 @atom:359_b15_a15_d15_i15 lj/cut/coul/long 0.5 4.25 - pair_coeff @atom:360_b6_a6_d6_i6 @atom:360_b6_a6_d6_i6 lj/cut/coul/long 0.3 4.2 - pair_coeff @atom:361_b46_a46_d46_i46 @atom:361_b46_a46_d46_i46 lj/cut/coul/long 0.05 2.5 - pair_coeff @atom:362_b5_a5_d5_i5 @atom:362_b5_a5_d5_i5 lj/cut/coul/long 0.25 3.15 - pair_coeff @atom:363_b13_a13_d13_i13 @atom:363_b13_a13_d13_i13 lj/cut/coul/long 0.3 4.2 - pair_coeff @atom:364_b46_a46_d46_i46 @atom:364_b46_a46_d46_i46 lj/cut/coul/long 0.05 2.5 - pair_coeff @atom:365_b19_a19_d19_i19 @atom:365_b19_a19_d19_i19 lj/cut/coul/long 0.15 3.65 - pair_coeff @atom:366_b18_a18_d18_i18 @atom:366_b18_a18_d18_i18 lj/cut/coul/long 0.25 3.4 - pair_coeff @atom:367_b6_a6_d6_i6 @atom:367_b6_a6_d6_i6 lj/cut/coul/long 0.3 4.2 - pair_coeff @atom:368_b46_a46_d46_i46 @atom:368_b46_a46_d46_i46 lj/cut/coul/long 0.05 2.5 - pair_coeff @atom:369_b53_a53_d53_i53 @atom:369_b53_a53_d53_i53 lj/cut/coul/long 0.25 3.4 - pair_coeff @atom:370_b45_a45_d45_i45 @atom:370_b45_a45_d45_i45 lj/cut/coul/long 0.05 2.5 - pair_coeff @atom:371_b6_a6_d6_i6 @atom:371_b6_a6_d6_i6 lj/cut/coul/long 0.3 4.2 - pair_coeff @atom:372_b46_a46_d46_i46 @atom:372_b46_a46_d46_i46 lj/cut/coul/long 0.05 2.5 - pair_coeff @atom:373_b13_a13_d13_i13 @atom:373_b13_a13_d13_i13 lj/cut/coul/long 0.3 4.2 - pair_coeff @atom:374_b46_a46_d46_i46 @atom:374_b46_a46_d46_i46 lj/cut/coul/long 0.05 2.5 - pair_coeff @atom:375_b33_a33_d33_i33 @atom:375_b33_a33_d33_i33 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:376_b5_a5_d5_i5 @atom:376_b5_a5_d5_i5 lj/cut/coul/long 0.25 3.2 - pair_coeff @atom:377_b7_a7_d7_i7 @atom:377_b7_a7_d7_i7 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:378_b77_a77_d77_i77 @atom:378_b77_a77_d77_i77 lj/cut/coul/long 0.4 2.81524 - pair_coeff @atom:379_b78_a78_d78_i78 @atom:379_b78_a78_d78_i78 lj/cut/coul/long 0.2 3.11815 - pair_coeff @atom:380_b20_a20_d20_i20 @atom:380_b20_a20_d20_i20 lj/cut/coul/long 0.14 2.9 - pair_coeff @atom:381_b64_a64_d64_i64 @atom:381_b64_a64_d64_i64 lj/cut/coul/long 0.2 3.74 - pair_coeff @atom:382_b52_a52_d52_i52 @atom:382_b52_a52_d52_i52 lj/cut/coul/long 0.2 3.15 - pair_coeff @atom:383_b20_a20_d20_i20 @atom:383_b20_a20_d20_i20 lj/cut/coul/long 0.14 2.9 - pair_coeff @atom:384_b13_a13_d13_i13 @atom:384_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:385_b46_a46_d46_i46 @atom:385_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5 - pair_coeff @atom:386_b64_a64_d64_i64 @atom:386_b64_a64_d64_i64 lj/cut/coul/long 0.2 3.74 - pair_coeff @atom:387_b52_a52_d52_i52 @atom:387_b52_a52_d52_i52 lj/cut/coul/long 0.2 3.15 - pair_coeff @atom:388_b20_a20_d20_i20 @atom:388_b20_a20_d20_i20 lj/cut/coul/long 0.14 2.9 - pair_coeff @atom:389_b13_a13_d13_i13 @atom:389_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:390_b46_a46_d46_i46 @atom:390_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5 - pair_coeff @atom:391_b64_a64_d64_i64 @atom:391_b64_a64_d64_i64 lj/cut/coul/long 0.2 3.74 - pair_coeff @atom:392_b52_a52_d52_i52 @atom:392_b52_a52_d52_i52 lj/cut/coul/long 0.2 3.15 - pair_coeff @atom:393_b20_a20_d20_i20 @atom:393_b20_a20_d20_i20 lj/cut/coul/long 0.14 2.9 - pair_coeff @atom:394_b13_a13_d13_i13 @atom:394_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:395_b46_a46_d46_i46 @atom:395_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5 - pair_coeff @atom:396_b13_a13_d13_i13 @atom:396_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:397_b46_a46_d46_i46 @atom:397_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5 - pair_coeff @atom:398_b48_a48_d48_i48 @atom:398_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:399_b13_a13_d13_i13 @atom:399_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:400_b46_a46_d46_i46 @atom:400_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5 - pair_coeff @atom:401_b48_a48_d48_i48 @atom:401_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:402_b13_a13_d13_i13 @atom:402_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:403_b46_a46_d46_i46 @atom:403_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5 - pair_coeff @atom:404_b48_a48_d48_i48 @atom:404_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:405_b13_a13_d13_i13 @atom:405_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:406_b3_a3_d3_i3 @atom:406_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75 - pair_coeff @atom:407_b4_a4_d4_i4 @atom:407_b4_a4_d4_i4 lj/cut/coul/long 0.21 2.96 - pair_coeff @atom:408_b20_a20_d20_i20 @atom:408_b20_a20_d20_i20 lj/cut/coul/long 0.17 3.0 - pair_coeff @atom:409_b13_a13_d13_i13 @atom:409_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:410_b46_a46_d46_i46 @atom:410_b46_a46_d46_i46 lj/cut/coul/long 0.015 2.42 - pair_coeff @atom:411_b3_a3_d3_i3 @atom:411_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75 - pair_coeff @atom:412_b3_a3_d3_i3 @atom:412_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75 - pair_coeff @atom:413_b48_a48_d48_i48 @atom:413_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:414_b20_a20_d20_i20 @atom:414_b20_a20_d20_i20 lj/cut/coul/long 0.17 3.0 - pair_coeff @atom:415_b79_a79_d79_i79 @atom:415_b79_a79_d79_i79 lj/cut/coul/long 0.25 3.55 - pair_coeff @atom:416_b23_a23_d23_i23 @atom:416_b23_a23_d23_i23 lj/cut/coul/long 0.17 2.96 - pair_coeff @atom:417_b13_a13_d13_i13 @atom:417_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:418_b46_a46_d46_i46 @atom:418_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5 - pair_coeff @atom:419_b24_a24_d24_i24 @atom:419_b24_a24_d24_i24 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:420_b45_a45_d45_i45 @atom:420_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:421_b24_a24_d24_i24 @atom:421_b24_a24_d24_i24 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:422_b45_a45_d45_i45 @atom:422_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:423_b13_a13_d13_i13 @atom:423_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:424_b46_a46_d46_i46 @atom:424_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5 - pair_coeff @atom:425_b13_a13_d13_i13 @atom:425_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:426_b46_a46_d46_i46 @atom:426_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5 - pair_coeff @atom:427_b13_a13_d13_i13 @atom:427_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:428_b46_a46_d46_i46 @atom:428_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5 - pair_coeff @atom:429_b48_a48_d48_i48 @atom:429_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:430_b48_a48_d48_i48 @atom:430_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:431_b13_a13_d13_i13 @atom:431_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:432_b13_a13_d13_i13 @atom:432_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:433_b13_a13_d13_i13 @atom:433_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:434_b79_a79_d79_i79 @atom:434_b79_a79_d79_i79 lj/cut/coul/long 0.25 3.55 - pair_coeff @atom:435_b23_a23_d23_i23 @atom:435_b23_a23_d23_i23 lj/cut/coul/long 0.17 2.96 - pair_coeff @atom:436_b22_a22_d22_i22 @atom:436_b22_a22_d22_i22 lj/cut/coul/long 0.395 3.56 - pair_coeff @atom:437_b22_a22_d22_i22 @atom:437_b22_a22_d22_i22 lj/cut/coul/long 0.395 3.56 - pair_coeff @atom:438_b23_a23_d23_i23 @atom:438_b23_a23_d23_i23 lj/cut/coul/long 0.28 2.93 - pair_coeff @atom:439_b13_a13_d13_i13 @atom:439_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:440_b13_a13_d13_i13 @atom:440_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:441_b80_a80_d80_i80 @atom:441_b80_a80_d80_i80 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:442_b60_a60_d60_i60 @atom:442_b60_a60_d60_i60 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:443_b81_a81_d81_i81 @atom:443_b81_a81_d81_i81 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:444_b57_a57_d57_i57 @atom:444_b57_a57_d57_i57 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:445_b45_a45_d45_i45 @atom:445_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:446_b13_a13_d13_i13 @atom:446_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:447_b82_a82_d82_i82 @atom:447_b82_a82_d82_i82 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:448_b83_a83_d83_i83 @atom:448_b83_a83_d83_i83 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:449_b84_a84_d84_i84 @atom:449_b84_a84_d84_i84 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:450_b82_a82_d82_i82 @atom:450_b82_a82_d82_i82 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:451_b85_a85_d85_i85 @atom:451_b85_a85_d85_i85 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:452_b61_a61_d61_i61 @atom:452_b61_a61_d61_i61 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:453_b57_a57_d57_i57 @atom:453_b57_a57_d57_i57 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:454_b45_a45_d45_i45 @atom:454_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:455_b84_a84_d84_i84 @atom:455_b84_a84_d84_i84 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:456_b13_a13_d13_i13 @atom:456_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:457_b13_a13_d13_i13 @atom:457_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:458_b47_a47_d47_i47 @atom:458_b47_a47_d47_i47 lj/cut/coul/long 0.076 3.55 - pair_coeff @atom:459_b47_a47_d47_i47 @atom:459_b47_a47_d47_i47 lj/cut/coul/long 0.076 3.55 - pair_coeff @atom:460_b86_a86_d86_i86 @atom:460_b86_a86_d86_i86 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:461_b56_a56_d56_i56 @atom:461_b56_a56_d56_i56 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:462_b48_a48_d48_i48 @atom:462_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:463_b48_a48_d48_i48 @atom:463_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:464_b48_a48_d48_i48 @atom:464_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:465_b49_a49_d49_i49 @atom:465_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:466_b49_a49_d49_i49 @atom:466_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:467_b49_a49_d49_i49 @atom:467_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:468_b56_a56_d56_i56 @atom:468_b56_a56_d56_i56 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:469_b48_a48_d48_i48 @atom:469_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:470_b49_a49_d49_i49 @atom:470_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:471_b56_a56_d56_i56 @atom:471_b56_a56_d56_i56 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:472_b59_a59_d59_i59 @atom:472_b59_a59_d59_i59 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:473_b48_a48_d48_i48 @atom:473_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:474_b48_a48_d48_i48 @atom:474_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:475_b49_a49_d49_i49 @atom:475_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:476_b49_a49_d49_i49 @atom:476_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:477_b49_a49_d49_i49 @atom:477_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:478_b56_a56_d56_i56 @atom:478_b56_a56_d56_i56 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:479_b48_a48_d48_i48 @atom:479_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:480_b48_a48_d48_i48 @atom:480_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:481_b49_a49_d49_i49 @atom:481_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:482_b49_a49_d49_i49 @atom:482_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:483_b57_a57_d57_i57 @atom:483_b57_a57_d57_i57 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:484_b84_a84_d84_i84 @atom:484_b84_a84_d84_i84 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:485_b87_a87_d87_i87 @atom:485_b87_a87_d87_i87 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:486_b45_a45_d45_i45 @atom:486_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:487_b49_a49_d49_i49 @atom:487_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:488_b49_a49_d49_i49 @atom:488_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:489_b57_a57_d57_i57 @atom:489_b57_a57_d57_i57 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:490_b61_a61_d61_i61 @atom:490_b61_a61_d61_i61 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:491_b88_a88_d88_i88 @atom:491_b88_a88_d88_i88 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:492_b87_a87_d87_i87 @atom:492_b87_a87_d87_i87 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:493_b84_a84_d84_i84 @atom:493_b84_a84_d84_i84 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:494_b45_a45_d45_i45 @atom:494_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:495_b49_a49_d49_i49 @atom:495_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:496_b49_a49_d49_i49 @atom:496_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:497_b49_a49_d49_i49 @atom:497_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:498_b57_a57_d57_i57 @atom:498_b57_a57_d57_i57 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:499_b82_a82_d82_i82 @atom:499_b82_a82_d82_i82 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:500_b61_a61_d61_i61 @atom:500_b61_a61_d61_i61 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:501_b83_a83_d83_i83 @atom:501_b83_a83_d83_i83 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:502_b84_a84_d84_i84 @atom:502_b84_a84_d84_i84 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:503_b45_a45_d45_i45 @atom:503_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:504_b49_a49_d49_i49 @atom:504_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:505_b49_a49_d49_i49 @atom:505_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:506_b49_a49_d49_i49 @atom:506_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:507_b20_a20_d20_i20 @atom:507_b20_a20_d20_i20 lj/cut/coul/long 0.14 2.9 - pair_coeff @atom:508_b84_a84_d84_i84 @atom:508_b84_a84_d84_i84 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:509_b87_a87_d87_i87 @atom:509_b87_a87_d87_i87 lj/cut/coul/long 0.076 3.55 - pair_coeff @atom:510_b49_a49_d49_i49 @atom:510_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:511_b49_a49_d49_i49 @atom:511_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:512_b20_a20_d20_i20 @atom:512_b20_a20_d20_i20 lj/cut/coul/long 0.14 2.9 - pair_coeff @atom:513_b82_a82_d82_i82 @atom:513_b82_a82_d82_i82 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:514_b61_a61_d61_i61 @atom:514_b61_a61_d61_i61 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:515_b83_a83_d83_i83 @atom:515_b83_a83_d83_i83 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:516_b84_a84_d84_i84 @atom:516_b84_a84_d84_i84 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:517_b49_a49_d49_i49 @atom:517_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:518_b49_a49_d49_i49 @atom:518_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:519_b49_a49_d49_i49 @atom:519_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:520_b20_a20_d20_i20 @atom:520_b20_a20_d20_i20 lj/cut/coul/long 0.14 2.9 - pair_coeff @atom:521_b61_a61_d61_i61 @atom:521_b61_a61_d61_i61 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:522_b88_a88_d88_i88 @atom:522_b88_a88_d88_i88 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:523_b87_a87_d87_i87 @atom:523_b87_a87_d87_i87 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:524_b84_a84_d84_i84 @atom:524_b84_a84_d84_i84 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:525_b49_a49_d49_i49 @atom:525_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:526_b49_a49_d49_i49 @atom:526_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:527_b49_a49_d49_i49 @atom:527_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:528_b57_a57_d57_i57 @atom:528_b57_a57_d57_i57 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:529_b84_a84_d84_i84 @atom:529_b84_a84_d84_i84 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:530_b87_a87_d87_i87 @atom:530_b87_a87_d87_i87 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:531_b48_a48_d48_i48 @atom:531_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:532_b48_a48_d48_i48 @atom:532_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:533_b48_a48_d48_i48 @atom:533_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:534_b48_a48_d48_i48 @atom:534_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:535_b81_a81_d81_i81 @atom:535_b81_a81_d81_i81 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:536_b60_a60_d60_i60 @atom:536_b60_a60_d60_i60 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:537_b45_a45_d45_i45 @atom:537_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:538_b49_a49_d49_i49 @atom:538_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:539_b49_a49_d49_i49 @atom:539_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:540_b49_a49_d49_i49 @atom:540_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:541_b49_a49_d49_i49 @atom:541_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:542_b49_a49_d49_i49 @atom:542_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:543_b49_a49_d49_i49 @atom:543_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:544_b56_a56_d56_i56 @atom:544_b56_a56_d56_i56 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:545_b48_a48_d48_i48 @atom:545_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:546_b48_a48_d48_i48 @atom:546_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:547_b48_a48_d48_i48 @atom:547_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:548_b48_a48_d48_i48 @atom:548_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:549_b48_a48_d48_i48 @atom:549_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:550_b48_a48_d48_i48 @atom:550_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:551_b48_a48_d48_i48 @atom:551_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:552_b48_a48_d48_i48 @atom:552_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:553_b48_a48_d48_i48 @atom:553_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:554_b49_a49_d49_i49 @atom:554_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:555_b49_a49_d49_i49 @atom:555_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:556_b49_a49_d49_i49 @atom:556_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:557_b49_a49_d49_i49 @atom:557_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:558_b49_a49_d49_i49 @atom:558_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:559_b49_a49_d49_i49 @atom:559_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:560_b49_a49_d49_i49 @atom:560_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:561_b56_a56_d56_i56 @atom:561_b56_a56_d56_i56 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:562_b59_a59_d59_i59 @atom:562_b59_a59_d59_i59 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:563_b56_a56_d56_i56 @atom:563_b56_a56_d56_i56 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:564_b60_a60_d60_i60 @atom:564_b60_a60_d60_i60 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:565_b60_a60_d60_i60 @atom:565_b60_a60_d60_i60 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:566_b48_a48_d48_i48 @atom:566_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:567_b61_a61_d61_i61 @atom:567_b61_a61_d61_i61 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:568_b62_a62_d62_i62 @atom:568_b62_a62_d62_i62 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:569_b57_a57_d57_i57 @atom:569_b57_a57_d57_i57 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:570_b49_a49_d49_i49 @atom:570_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:571_b49_a49_d49_i49 @atom:571_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:572_b49_a49_d49_i49 @atom:572_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:573_b45_a45_d45_i45 @atom:573_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:574_b16_a16_d16_i16 @atom:574_b16_a16_d16_i16 lj/cut/coul/long 0.25 3.55 - pair_coeff @atom:575_b82_a82_d82_i82 @atom:575_b82_a82_d82_i82 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:576_b61_a61_d61_i61 @atom:576_b61_a61_d61_i61 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:577_b83_a83_d83_i83 @atom:577_b83_a83_d83_i83 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:578_b84_a84_d84_i84 @atom:578_b84_a84_d84_i84 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:579_b49_a49_d49_i49 @atom:579_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:580_b49_a49_d49_i49 @atom:580_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:581_b49_a49_d49_i49 @atom:581_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:582_b56_a56_d56_i56 @atom:582_b56_a56_d56_i56 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:583_b59_a59_d59_i59 @atom:583_b59_a59_d59_i59 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:584_b49_a49_d49_i49 @atom:584_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:585_b48_a48_d48_i48 @atom:585_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:586_b13_a13_d13_i13 @atom:586_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:587_b56_a56_d56_i56 @atom:587_b56_a56_d56_i56 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:588_b48_a48_d48_i48 @atom:588_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:589_b48_a48_d48_i48 @atom:589_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:590_b48_a48_d48_i48 @atom:590_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:591_b48_a48_d48_i48 @atom:591_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:592_b48_a48_d48_i48 @atom:592_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:593_b48_a48_d48_i48 @atom:593_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:594_b49_a49_d49_i49 @atom:594_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:595_b49_a49_d49_i49 @atom:595_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:596_b49_a49_d49_i49 @atom:596_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:597_b49_a49_d49_i49 @atom:597_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:598_b57_a57_d57_i57 @atom:598_b57_a57_d57_i57 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:599_b82_a82_d82_i82 @atom:599_b82_a82_d82_i82 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:600_b61_a61_d61_i61 @atom:600_b61_a61_d61_i61 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:601_b83_a83_d83_i83 @atom:601_b83_a83_d83_i83 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:602_b84_a84_d84_i84 @atom:602_b84_a84_d84_i84 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:603_b13_a13_d13_i13 @atom:603_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:604_b49_a49_d49_i49 @atom:604_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:605_b49_a49_d49_i49 @atom:605_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:606_b49_a49_d49_i49 @atom:606_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:607_b46_a46_d46_i46 @atom:607_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5 - pair_coeff @atom:608_b13_a13_d13_i13 @atom:608_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:609_b13_a13_d13_i13 @atom:609_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:610_b13_a13_d13_i13 @atom:610_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:611_b13_a13_d13_i13 @atom:611_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:612_b13_a13_d13_i13 @atom:612_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:613_b13_a13_d13_i13 @atom:613_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:614_b13_a13_d13_i13 @atom:614_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:615_b13_a13_d13_i13 @atom:615_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:616_b13_a13_d13_i13 @atom:616_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:617_b13_a13_d13_i13 @atom:617_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:618_b13_a13_d13_i13 @atom:618_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:619_b13_a13_d13_i13 @atom:619_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:620_b13_a13_d13_i13 @atom:620_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:621_b13_a13_d13_i13 @atom:621_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:622_b13_a13_d13_i13 @atom:622_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:623_b15_a15_d15_i15 @atom:623_b15_a15_d15_i15 lj/cut/coul/long 0.25 3.55 - pair_coeff @atom:624_b17_a17_d17_i17 @atom:624_b17_a17_d17_i17 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:625_b48_a48_d48_i48 @atom:625_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:626_b89_a89_d89_i89 @atom:626_b89_a89_d89_i89 lj/cut/coul/long 0.105 3.75 - pair_coeff @atom:627_b90_a90_d90_i90 @atom:627_b90_a90_d90_i90 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:628_b91_a91_d91_i91 @atom:628_b91_a91_d91_i91 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:629_b91_a91_d91_i91 @atom:629_b91_a91_d91_i91 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:630_b13_a13_d13_i13 @atom:630_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:631_b86_a86_d86_i86 @atom:631_b86_a86_d86_i86 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:632_b86_a86_d86_i86 @atom:632_b86_a86_d86_i86 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:633_b86_a86_d86_i86 @atom:633_b86_a86_d86_i86 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:634_b86_a86_d86_i86 @atom:634_b86_a86_d86_i86 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:635_b86_a86_d86_i86 @atom:635_b86_a86_d86_i86 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:636_b86_a86_d86_i86 @atom:636_b86_a86_d86_i86 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:637_b16_a16_d16_i16 @atom:637_b16_a16_d16_i16 lj/cut/coul/long 0.25 3.55 - pair_coeff @atom:638_b92_a92_d92_i92 @atom:638_b92_a92_d92_i92 lj/cut/coul/long 0.054 3.473 - pair_coeff @atom:639_b93_a93_d93_i93 @atom:639_b93_a93_d93_i93 lj/cut/coul/long 0.05 3.3 - pair_coeff @atom:640_b94_a94_d94_i94 @atom:640_b94_a94_d94_i94 lj/cut/coul/long 0.05 3.3 - pair_coeff @atom:641_b95_a95_d95_i95 @atom:641_b95_a95_d95_i95 lj/cut/coul/long 0.076 3.55 - pair_coeff @atom:642_b13_a13_d13_i13 @atom:642_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:643_b46_a46_d46_i46 @atom:643_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5 - pair_coeff @atom:644_b96_a96_d96_i96 @atom:644_b96_a96_d96_i96 lj/cut/coul/long 0.06 3.75 - pair_coeff @atom:645_b97_a97_d97_i97 @atom:645_b97_a97_d97_i97 lj/cut/coul/long 0.054 3.473 - pair_coeff @atom:646_b98_a98_d98_i98 @atom:646_b98_a98_d98_i98 lj/cut/coul/long 0.05 3.3 - pair_coeff @atom:647_b99_a99_d99_i99 @atom:647_b99_a99_d99_i99 lj/cut/coul/long 0.05 3.3 - pair_coeff @atom:648_b100_a100_d100_i100 @atom:648_b100_a100_d100_i100 lj/cut/coul/long 0.04 2.95 - pair_coeff @atom:649_b47_a47_d47_i47 @atom:649_b47_a47_d47_i47 lj/cut/coul/long 0.076 3.55 - pair_coeff @atom:650_b21_a21_d21_i21 @atom:650_b21_a21_d21_i21 lj/cut/coul/long 0.3 3.4 - pair_coeff @atom:651_b46_a46_d46_i46 @atom:651_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:652_b91_a91_d91_i91 @atom:652_b91_a91_d91_i91 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:653_b91_a91_d91_i91 @atom:653_b91_a91_d91_i91 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:654_b91_a91_d91_i91 @atom:654_b91_a91_d91_i91 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:655_b48_a48_d48_i48 @atom:655_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:656_b49_a49_d49_i49 @atom:656_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:657_b48_a48_d48_i48 @atom:657_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:658_b49_a49_d49_i49 @atom:658_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:659_b48_a48_d48_i48 @atom:659_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:660_b1_a1_d1_i1 @atom:660_b1_a1_d1_i1 lj/cut/coul/long 0.061 2.85 - pair_coeff @atom:661_b48_a48_d48_i48 @atom:661_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:662_b1_a1_d1_i1 @atom:662_b1_a1_d1_i1 lj/cut/coul/long 0.061 2.85 - pair_coeff @atom:663_b65_a65_d65_i65 @atom:663_b65_a65_d65_i65 lj/cut/coul/long 0.47 3.47 - pair_coeff @atom:664_b2_a2_d2_i2 @atom:664_b2_a2_d2_i2 lj/cut/coul/long 0.118 3.905 - pair_coeff @atom:665_b48_a48_d48_i48 @atom:665_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:666_b13_a13_d13_i13 @atom:666_b13_a13_d13_i13 lj/cut/coul/long 0.062 3.25 - pair_coeff @atom:667_b1_a1_d1_i1 @atom:667_b1_a1_d1_i1 lj/cut/coul/long 0.061 2.94 - pair_coeff @atom:668_b48_a48_d48_i48 @atom:668_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:669_b1_a1_d1_i1 @atom:669_b1_a1_d1_i1 lj/cut/coul/long 0.061 2.85 - pair_coeff @atom:670_b48_a48_d48_i48 @atom:670_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:671_b65_a65_d65_i65 @atom:671_b65_a65_d65_i65 lj/cut/coul/long 0.47 3.47 - pair_coeff @atom:672_b48_a48_d48_i48 @atom:672_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:673_b66_a66_d66_i66 @atom:673_b66_a66_d66_i66 lj/cut/coul/long 0.6 3.75 - pair_coeff @atom:674_b91_a91_d91_i91 @atom:674_b91_a91_d91_i91 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:675_b15_a15_d15_i15 @atom:675_b15_a15_d15_i15 lj/cut/coul/long 0.25 3.55 - pair_coeff @atom:676_b48_a48_d48_i48 @atom:676_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:677_b48_a48_d48_i48 @atom:677_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:678_b48_a48_d48_i48 @atom:678_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:679_b48_a48_d48_i48 @atom:679_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:680_b48_a48_d48_i48 @atom:680_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:681_b49_a49_d49_i49 @atom:681_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:682_b49_a49_d49_i49 @atom:682_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:683_b48_a48_d48_i48 @atom:683_b48_a48_d48_i48 lj/cut/coul/long 0.05 3.55 - pair_coeff @atom:684_b55_a55_d55_i55 @atom:684_b55_a55_d55_i55 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:685_b45_a45_d45_i45 @atom:685_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:686_b45_a45_d45_i45 @atom:686_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:687_b49_a49_d49_i49 @atom:687_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:688_b13_a13_d13_i13 @atom:688_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:689_b13_a13_d13_i13 @atom:689_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:690_b101_a101_d101_i101 @atom:690_b101_a101_d101_i101 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:691_b56_a56_d56_i56 @atom:691_b56_a56_d56_i56 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:692_b101_a101_d101_i101 @atom:692_b101_a101_d101_i101 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:693_b48_a48_d48_i48 @atom:693_b48_a48_d48_i48 lj/cut/coul/long 0.05 3.55 - pair_coeff @atom:694_b18_a18_d18_i18 @atom:694_b18_a18_d18_i18 lj/cut/coul/long 0.17 3.2 - pair_coeff @atom:695_b19_a19_d19_i19 @atom:695_b19_a19_d19_i19 lj/cut/coul/long 0.066 3.3 - pair_coeff @atom:696_b13_a13_d13_i13 @atom:696_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.3 - pair_coeff @atom:697_b13_a13_d13_i13 @atom:697_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.3 - pair_coeff @atom:698_b13_a13_d13_i13 @atom:698_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.3 - pair_coeff @atom:699_b13_a13_d13_i13 @atom:699_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.3 - pair_coeff @atom:700_b46_a46_d46_i46 @atom:700_b46_a46_d46_i46 lj/cut/coul/long 0.015 2.5 - pair_coeff @atom:701_b102_a102_d102_i102 @atom:701_b102_a102_d102_i102 lj/cut/coul/long 0.12 3.25 - pair_coeff @atom:702_b103_a103_d103_i103 @atom:702_b103_a103_d103_i103 lj/cut/coul/long 0.17 2.96 - pair_coeff @atom:703_b13_a13_d13_i13 @atom:703_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:704_b46_a46_d46_i46 @atom:704_b46_a46_d46_i46 lj/cut/coul/long 0.015 2.5 - pair_coeff @atom:705_b13_a13_d13_i13 @atom:705_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:706_b13_a13_d13_i13 @atom:706_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:707_b13_a13_d13_i13 @atom:707_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:708_b102_a102_d102_i102 @atom:708_b102_a102_d102_i102 lj/cut/coul/long 0.12 3.25 - pair_coeff @atom:709_b48_a48_d48_i48 @atom:709_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:710_b13_a13_d13_i13 @atom:710_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.3 - pair_coeff @atom:711_b56_a56_d56_i56 @atom:711_b56_a56_d56_i56 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:712_b4_a4_d4_i4 @atom:712_b4_a4_d4_i4 lj/cut/coul/long 0.21 2.96 - pair_coeff @atom:713_b3_a3_d3_i3 @atom:713_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75 - pair_coeff @atom:714_b20_a20_d20_i20 @atom:714_b20_a20_d20_i20 lj/cut/coul/long 0.17 3.0 - pair_coeff @atom:715_b13_a13_d13_i13 @atom:715_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:716_b13_a13_d13_i13 @atom:716_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:717_b13_a13_d13_i13 @atom:717_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:718_b46_a46_d46_i46 @atom:718_b46_a46_d46_i46 lj/cut/coul/long 0.015 2.42 - pair_coeff @atom:719_b46_a46_d46_i46 @atom:719_b46_a46_d46_i46 lj/cut/coul/long 0.015 2.42 - pair_coeff @atom:720_b46_a46_d46_i46 @atom:720_b46_a46_d46_i46 lj/cut/coul/long 0.015 2.42 - pair_coeff @atom:721_b20_a20_d20_i20 @atom:721_b20_a20_d20_i20 lj/cut/coul/long 0.14 2.9 - pair_coeff @atom:722_b104_a104_d104_i104 @atom:722_b104_a104_d104_i104 lj/cut/coul/long 0.2 3.74 - pair_coeff @atom:723_b13_a13_d13_i13 @atom:723_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:724_b13_a13_d13_i13 @atom:724_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:725_b46_a46_d46_i46 @atom:725_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5 - pair_coeff @atom:726_b64_a64_d64_i64 @atom:726_b64_a64_d64_i64 lj/cut/coul/long 0.2 3.74 - pair_coeff @atom:727_b1_a1_d1_i1 @atom:727_b1_a1_d1_i1 lj/cut/coul/long 0.061 3.1181 - pair_coeff @atom:728_b24_a24_d24_i24 @atom:728_b24_a24_d24_i24 lj/cut/coul/long 0.17 3.15 - pair_coeff @atom:729_b4_a4_d4_i4 @atom:729_b4_a4_d4_i4 lj/cut/coul/long 0.21 2.86 - pair_coeff @atom:730_b44_a44_d44_i44 @atom:730_b44_a44_d44_i44 lj/cut/coul/long 0.17 3.3 - pair_coeff @atom:731_b44_a44_d44_i44 @atom:731_b44_a44_d44_i44 lj/cut/coul/long 0.17 3.3 - pair_coeff @atom:732_b44_a44_d44_i44 @atom:732_b44_a44_d44_i44 lj/cut/coul/long 0.17 3.3 - pair_coeff @atom:733_b13_a13_d13_i13 @atom:733_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:734_b13_a13_d13_i13 @atom:734_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:735_b13_a13_d13_i13 @atom:735_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:736_b13_a13_d13_i13 @atom:736_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:737_b13_a13_d13_i13 @atom:737_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:738_b13_a13_d13_i13 @atom:738_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:739_b45_a45_d45_i45 @atom:739_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:740_b45_a45_d45_i45 @atom:740_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:741_b46_a46_d46_i46 @atom:741_b46_a46_d46_i46 lj/cut/coul/long 0.015 2.5 - pair_coeff @atom:742_b13_a13_d13_i13 @atom:742_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:743_b13_a13_d13_i13 @atom:743_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:744_b13_a13_d13_i13 @atom:744_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:745_b13_a13_d13_i13 @atom:745_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:746_b48_a48_d48_i48 @atom:746_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:747_b48_a48_d48_i48 @atom:747_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:748_b48_a48_d48_i48 @atom:748_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:749_b13_a13_d13_i13 @atom:749_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:750_b13_a13_d13_i13 @atom:750_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:751_b13_a13_d13_i13 @atom:751_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:752_b13_a13_d13_i13 @atom:752_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:753_b13_a13_d13_i13 @atom:753_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:754_b13_a13_d13_i13 @atom:754_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:755_b19_a19_d19_i19 @atom:755_b19_a19_d19_i19 lj/cut/coul/long 0.086 3.3 - pair_coeff @atom:756_b46_a46_d46_i46 @atom:756_b46_a46_d46_i46 lj/cut/coul/long 0.015 2.42 - pair_coeff @atom:757_b19_a19_d19_i19 @atom:757_b19_a19_d19_i19 lj/cut/coul/long 0.21 3.3 - pair_coeff @atom:758_b19_a19_d19_i19 @atom:758_b19_a19_d19_i19 lj/cut/coul/long 0.135 3.3 - pair_coeff @atom:759_b19_a19_d19_i19 @atom:759_b19_a19_d19_i19 lj/cut/coul/long 0.1 3.3 - pair_coeff @atom:760_b46_a46_d46_i46 @atom:760_b46_a46_d46_i46 lj/cut/coul/long 0.015 2.5 - pair_coeff @atom:761_b51_a51_d51_i51 @atom:761_b51_a51_d51_i51 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:762_b51_a51_d51_i51 @atom:762_b51_a51_d51_i51 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:763_b51_a51_d51_i51 @atom:763_b51_a51_d51_i51 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:764_b5_a5_d5_i5 @atom:764_b5_a5_d5_i5 lj/cut/coul/long 0.17 3.12 - pair_coeff @atom:765_b7_a7_d7_i7 @atom:765_b7_a7_d7_i7 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:766_b105_a105_d105_i105 @atom:766_b105_a105_d105_i105 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:767_b105_a105_d105_i105 @atom:767_b105_a105_d105_i105 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:768_b105_a105_d105_i105 @atom:768_b105_a105_d105_i105 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:769_b19_a19_d19_i19 @atom:769_b19_a19_d19_i19 lj/cut/coul/long 0.21 3.3 - pair_coeff @atom:770_b53_a53_d53_i53 @atom:770_b53_a53_d53_i53 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:771_b54_a54_d54_i54 @atom:771_b54_a54_d54_i54 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:772_b13_a13_d13_i13 @atom:772_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:773_b13_a13_d13_i13 @atom:773_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:774_b13_a13_d13_i13 @atom:774_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:775_b13_a13_d13_i13 @atom:775_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:776_b84_a84_d84_i84 @atom:776_b84_a84_d84_i84 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:777_b87_a87_d87_i87 @atom:777_b87_a87_d87_i87 lj/cut/coul/long 0.076 3.55 - pair_coeff @atom:778_b86_a86_d86_i86 @atom:778_b86_a86_d86_i86 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:779_b86_a86_d86_i86 @atom:779_b86_a86_d86_i86 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:780_b46_a46_d46_i46 @atom:780_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5 - pair_coeff @atom:781_b13_a13_d13_i13 @atom:781_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:782_b3_a3_d3_i3 @atom:782_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75 - pair_coeff @atom:783_b53_a53_d53_i53 @atom:783_b53_a53_d53_i53 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:784_b52_a52_d52_i52 @atom:784_b52_a52_d52_i52 lj/cut/coul/long 0.21 2.96 - pair_coeff @atom:785_b54_a54_d54_i54 @atom:785_b54_a54_d54_i54 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:786_b1_a1_d1_i1 @atom:786_b1_a1_d1_i1 lj/cut/coul/long 0.061 2.94 - pair_coeff @atom:787_b13_a13_d13_i13 @atom:787_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:788_b46_a46_d46_i46 @atom:788_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5 - pair_coeff @atom:789_b13_a13_d13_i13 @atom:789_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:790_b13_a13_d13_i13 @atom:790_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:791_b13_a13_d13_i13 @atom:791_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:792_b13_a13_d13_i13 @atom:792_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:793_b13_a13_d13_i13 @atom:793_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:794_b13_a13_d13_i13 @atom:794_b13_a13_d13_i13 lj/cut/coul/long 0.097 3.5 - pair_coeff @atom:795_b1_a1_d1_i1 @atom:795_b1_a1_d1_i1 lj/cut/coul/long 0.053 2.95 - pair_coeff @atom:796_b13_a13_d13_i13 @atom:796_b13_a13_d13_i13 lj/cut/coul/long 0.062 3.25 - pair_coeff @atom:797_b46_a46_d46_i46 @atom:797_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5 - pair_coeff @atom:798_b13_a13_d13_i13 @atom:798_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:799_b13_a13_d13_i13 @atom:799_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:800_b21_a21_d21_i21 @atom:800_b21_a21_d21_i21 lj/cut/coul/long 0.3 3.4 - pair_coeff @atom:801_b13_a13_d13_i13 @atom:801_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:802_b46_a46_d46_i46 @atom:802_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5 - pair_coeff @atom:803_b13_a13_d13_i13 @atom:803_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:804_b13_a13_d13_i13 @atom:804_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:805_b65_a65_d65_i65 @atom:805_b65_a65_d65_i65 lj/cut/coul/long 0.47 3.47 - pair_coeff @atom:806_b13_a13_d13_i13 @atom:806_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:807_b46_a46_d46_i46 @atom:807_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5 - pair_coeff @atom:808_b13_a13_d13_i13 @atom:808_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:809_b13_a13_d13_i13 @atom:809_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:810_b1_a1_d1_i1 @atom:810_b1_a1_d1_i1 lj/cut/coul/long 0.061 2.94 - pair_coeff @atom:811_b21_a21_d21_i21 @atom:811_b21_a21_d21_i21 lj/cut/coul/long 0.3 3.4 - pair_coeff @atom:812_b65_a65_d65_i65 @atom:812_b65_a65_d65_i65 lj/cut/coul/long 0.47 3.47 - pair_coeff @atom:813_b48_a48_d48_i48 @atom:813_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:814_b20_a20_d20_i20 @atom:814_b20_a20_d20_i20 lj/cut/coul/long 0.14 2.9 - pair_coeff @atom:815_b13_a13_d13_i13 @atom:815_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:816_b1_a1_d1_i1 @atom:816_b1_a1_d1_i1 lj/cut/coul/long 0.06 2.9 - pair_coeff @atom:817_b24_a24_d24_i24 @atom:817_b24_a24_d24_i24 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:818_b48_a48_d48_i48 @atom:818_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:819_b13_a13_d13_i13 @atom:819_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:820_b3_a3_d3_i3 @atom:820_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75 - pair_coeff @atom:821_b3_a3_d3_i3 @atom:821_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75 - pair_coeff @atom:822_b4_a4_d4_i4 @atom:822_b4_a4_d4_i4 lj/cut/coul/long 0.21 2.96 - pair_coeff @atom:823_b24_a24_d24_i24 @atom:823_b24_a24_d24_i24 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:824_b45_a45_d45_i45 @atom:824_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:825_b5_a5_d5_i5 @atom:825_b5_a5_d5_i5 lj/cut/coul/long 0.17 3.12 - pair_coeff @atom:826_b7_a7_d7_i7 @atom:826_b7_a7_d7_i7 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:827_b13_a13_d13_i13 @atom:827_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:828_b13_a13_d13_i13 @atom:828_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:829_b86_a86_d86_i86 @atom:829_b86_a86_d86_i86 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:830_b86_a86_d86_i86 @atom:830_b86_a86_d86_i86 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:831_b86_a86_d86_i86 @atom:831_b86_a86_d86_i86 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:832_b86_a86_d86_i86 @atom:832_b86_a86_d86_i86 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:833_b48_a48_d48_i48 @atom:833_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:834_b106_a106_d106_i106 @atom:834_b106_a106_d106_i106 lj/cut/coul/long 0.0125 1.96 - pair_coeff @atom:835_b13_a13_d13_i13 @atom:835_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:836_b13_a13_d13_i13 @atom:836_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:837_b13_a13_d13_i13 @atom:837_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:838_b66_a66_d66_i66 @atom:838_b66_a66_d66_i66 lj/cut/coul/long 0.6 3.75 - pair_coeff @atom:839_b46_a46_d46_i46 @atom:839_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5 - pair_coeff @atom:840_b24_a24_d24_i24 @atom:840_b24_a24_d24_i24 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:841_b48_a48_d48_i48 @atom:841_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:842_b48_a48_d48_i48 @atom:842_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:843_b24_a24_d24_i24 @atom:843_b24_a24_d24_i24 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:844_b48_a48_d48_i48 @atom:844_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:845_b3_a3_d3_i3 @atom:845_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75 - pair_coeff @atom:846_b4_a4_d4_i4 @atom:846_b4_a4_d4_i4 lj/cut/coul/long 0.21 2.96 - pair_coeff @atom:847_b107_a107_d107_i107 @atom:847_b107_a107_d107_i107 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:848_b13_a13_d13_i13 @atom:848_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:849_b13_a13_d13_i13 @atom:849_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:850_b13_a13_d13_i13 @atom:850_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:851_b13_a13_d13_i13 @atom:851_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:852_b46_a46_d46_i46 @atom:852_b46_a46_d46_i46 lj/cut/coul/long 0.015 2.42 - pair_coeff @atom:853_b3_a3_d3_i3 @atom:853_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75 - pair_coeff @atom:854_b4_a4_d4_i4 @atom:854_b4_a4_d4_i4 lj/cut/coul/long 0.21 2.96 - pair_coeff @atom:855_b46_a46_d46_i46 @atom:855_b46_a46_d46_i46 lj/cut/coul/long 0.015 2.42 - pair_coeff @atom:856_b13_a13_d13_i13 @atom:856_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:857_b13_a13_d13_i13 @atom:857_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:858_b13_a13_d13_i13 @atom:858_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:859_b13_a13_d13_i13 @atom:859_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:860_b13_a13_d13_i13 @atom:860_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:861_b13_a13_d13_i13 @atom:861_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:862_b13_a13_d13_i13 @atom:862_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:863_b13_a13_d13_i13 @atom:863_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:864_b13_a13_d13_i13 @atom:864_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:865_b13_a13_d13_i13 @atom:865_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:866_b108_a108_d108_i108 @atom:866_b108_a108_d108_i108 lj/cut/coul/long 0.1 4.0 - pair_coeff @atom:867_b108_a108_d108_i108 @atom:867_b108_a108_d108_i108 lj/cut/coul/long 0.1 4.0 - pair_coeff @atom:868_b108_a108_d108_i108 @atom:868_b108_a108_d108_i108 lj/cut/coul/long 0.1 4.0 - pair_coeff @atom:869_b108_a108_d108_i108 @atom:869_b108_a108_d108_i108 lj/cut/coul/long 0.1 4.0 - pair_coeff @atom:870_b45_a45_d45_i45 @atom:870_b45_a45_d45_i45 lj/cut/coul/long 0.03 2.5 - pair_coeff @atom:871_b13_a13_d13_i13 @atom:871_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:872_b13_a13_d13_i13 @atom:872_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:873_b13_a13_d13_i13 @atom:873_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:874_b13_a13_d13_i13 @atom:874_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:875_b1_a1_d1_i1 @atom:875_b1_a1_d1_i1 lj/cut/coul/long 0.72 3.08 - pair_coeff @atom:876_b21_a21_d21_i21 @atom:876_b21_a21_d21_i21 lj/cut/coul/long 0.11779 4.18 - pair_coeff @atom:877_b65_a65_d65_i65 @atom:877_b65_a65_d65_i65 lj/cut/coul/long 0.09 4.51 - pair_coeff @atom:878_b66_a66_d66_i66 @atom:878_b66_a66_d66_i66 lj/cut/coul/long 0.07 5.15 - pair_coeff @atom:879_b68_a68_d68_i68 @atom:879_b68_a68_d68_i68 lj/cut/coul/long 0.018279 2.7 - pair_coeff @atom:880_b69_a69_d69_i69 @atom:880_b69_a69_d69_i69 lj/cut/coul/long 0.002772 3.35 - pair_coeff @atom:881_b70_a70_d70_i70 @atom:881_b70_a70_d70_i70 lj/cut/coul/long 0.000328 4.06 - pair_coeff @atom:882_b71_a71_d71_i71 @atom:882_b71_a71_d71_i71 lj/cut/coul/long 0.000171 4.32 - pair_coeff @atom:883_b72_a72_d72_i72 @atom:883_b72_a72_d72_i72 lj/cut/coul/long 8.1e-05 4.82 - pair_coeff @atom:884_b73_a73_d73_i73 @atom:884_b73_a73_d73_i73 lj/cut/coul/long 0.875044 2.91 - pair_coeff @atom:885_b74_a74_d74_i74 @atom:885_b74_a74_d74_i74 lj/cut/coul/long 0.449657 3.47 - pair_coeff @atom:886_b75_a75_d75_i75 @atom:886_b75_a75_d75_i75 lj/cut/coul/long 0.118226 3.82 - pair_coeff @atom:887_b76_a76_d76_i76 @atom:887_b76_a76_d76_i76 lj/cut/coul/long 0.047096 4.18 - pair_coeff @atom:888_b13_a13_d13_i13 @atom:888_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:889_b13_a13_d13_i13 @atom:889_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:890_b13_a13_d13_i13 @atom:890_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:891_b13_a13_d13_i13 @atom:891_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:892_b46_a46_d46_i46 @atom:892_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5 - pair_coeff @atom:893_b53_a53_d53_i53 @atom:893_b53_a53_d53_i53 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:894_b48_a48_d48_i48 @atom:894_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:895_b53_a53_d53_i53 @atom:895_b53_a53_d53_i53 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:896_b48_a48_d48_i48 @atom:896_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:897_b109_a109_d109_i109 @atom:897_b109_a109_d109_i109 lj/cut/coul/long 0.076 3.55 - pair_coeff @atom:898_b109_a109_d109_i109 @atom:898_b109_a109_d109_i109 lj/cut/coul/long 0.076 3.55 - pair_coeff @atom:899_b46_a46_d46_i46 @atom:899_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:900_b47_a47_d47_i47 @atom:900_b47_a47_d47_i47 lj/cut/coul/long 0.086 3.3 - pair_coeff @atom:901_b47_a47_d47_i47 @atom:901_b47_a47_d47_i47 lj/cut/coul/long 0.086 3.3 - pair_coeff @atom:902_b47_a47_d47_i47 @atom:902_b47_a47_d47_i47 lj/cut/coul/long 0.086 3.3 - pair_coeff @atom:903_b110_a110_d110_i110 @atom:903_b110_a110_d110_i110 lj/cut/coul/long 0.086 3.3 - pair_coeff @atom:904_b110_a110_d110_i110 @atom:904_b110_a110_d110_i110 lj/cut/coul/long 0.086 3.3 - pair_coeff @atom:905_b4_a4_d4_i4 @atom:905_b4_a4_d4_i4 lj/cut/coul/long 0.21 2.96 - pair_coeff @atom:906_b13_a13_d13_i13 @atom:906_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 + pair_coeff @atom:1_b001_a001_d001_i001 @atom:1_b001_a001_d001_i001 0.061 2.94 + pair_coeff @atom:2_b002_a002_d002_i002 @atom:2_b002_a002_d002_i002 0.118 3.905 + pair_coeff @atom:3_b003_a003_d003_i003 @atom:3_b003_a003_d003_i003 0.105 3.75 + pair_coeff @atom:4_b004_a004_d004_i004 @atom:4_b004_a004_d004_i004 0.21 2.96 + pair_coeff @atom:5_b005_a005_d005_i005 @atom:5_b005_a005_d005_i005 0.17 3.0 + pair_coeff @atom:6_b006_a006_d006_i006 @atom:6_b006_a006_d006_i006 0.16 3.91 + pair_coeff @atom:7_b007_a007_d007_i007 @atom:7_b007_a007_d007_i007 0.0 0.0 + pair_coeff @atom:8_b008_a008_d008_i008 @atom:8_b008_a008_d008_i008 0.294 3.73 + pair_coeff @atom:9_b006_a006_d006_i006 @atom:9_b006_a006_d006_i006 0.207 3.775 + pair_coeff @atom:10_b006_a006_d006_i006 @atom:10_b006_a006_d006_i006 0.175 3.905 + pair_coeff @atom:11_b006_a006_d006_i006 @atom:11_b006_a006_d006_i006 0.16 3.91 + pair_coeff @atom:12_b006_a006_d006_i006 @atom:12_b006_a006_d006_i006 0.145 3.96 + pair_coeff @atom:13_b002_a002_d002_i002 @atom:13_b002_a002_d002_i002 0.118 3.905 + pair_coeff @atom:14_b009_a009_d009_i009 @atom:14_b009_a009_d009_i009 0.14 3.85 + pair_coeff @atom:15_b010_a010_d010_i010 @atom:15_b010_a010_d010_i010 0.08 3.85 + pair_coeff @atom:16_b011_a011_d011_i011 @atom:16_b011_a011_d011_i011 0.115 3.8 + pair_coeff @atom:17_b012_a012_d012_i012 @atom:17_b012_a012_d012_i012 0.11 3.75 + pair_coeff @atom:18_b013_a013_d013_i013 @atom:18_b013_a013_d013_i013 0.05 3.8 + pair_coeff @atom:19_b014_a014_d014_i014 @atom:19_b014_a014_d014_i014 0.105 3.75 + pair_coeff @atom:20_b005_a005_d005_i005 @atom:20_b005_a005_d005_i005 0.17 3.07 + pair_coeff @atom:21_b007_a007_d007_i007 @atom:21_b007_a007_d007_i007 0.0 0.0 + pair_coeff @atom:22_b006_a006_d006_i006 @atom:22_b006_a006_d006_i006 0.207 3.775 + pair_coeff @atom:23_b002_a002_d002_i002 @atom:23_b002_a002_d002_i002 0.118 3.905 + pair_coeff @atom:24_b015_a015_d015_i015 @atom:24_b015_a015_d015_i015 0.25 3.7 + pair_coeff @atom:25_b015_a015_d015_i015 @atom:25_b015_a015_d015_i015 0.25 3.55 + pair_coeff @atom:26_b016_a016_d016_i016 @atom:26_b016_a016_d016_i016 0.25 3.55 + pair_coeff @atom:27_b016_a016_d016_i016 @atom:27_b016_a016_d016_i016 0.25 3.55 + pair_coeff @atom:28_b017_a017_d017_i017 @atom:28_b017_a017_d017_i017 0.0 0.0 + pair_coeff @atom:29_b017_a017_d017_i017 @atom:29_b017_a017_d017_i017 0.0 0.0 + pair_coeff @atom:30_b006_a006_d006_i006 @atom:30_b006_a006_d006_i006 0.207 3.775 + pair_coeff @atom:31_b002_a002_d002_i002 @atom:31_b002_a002_d002_i002 0.118 3.905 + pair_coeff @atom:32_b006_a006_d006_i006 @atom:32_b006_a006_d006_i006 0.17 3.8 + pair_coeff @atom:33_b002_a002_d002_i002 @atom:33_b002_a002_d002_i002 0.118 3.8 + pair_coeff @atom:34_b006_a006_d006_i006 @atom:34_b006_a006_d006_i006 0.17 3.8 + pair_coeff @atom:35_b002_a002_d002_i002 @atom:35_b002_a002_d002_i002 0.118 3.8 + pair_coeff @atom:36_b018_a018_d018_i018 @atom:36_b018_a018_d018_i018 0.17 3.2 + pair_coeff @atom:37_b019_a019_d019_i019 @atom:37_b019_a019_d019_i019 0.15 3.65 + pair_coeff @atom:38_b006_a006_d006_i006 @atom:38_b006_a006_d006_i006 0.207 3.775 + pair_coeff @atom:39_b010_a010_d010_i010 @atom:39_b010_a010_d010_i010 0.08 3.85 + pair_coeff @atom:40_b013_a013_d013_i013 @atom:40_b013_a013_d013_i013 0.05 3.8 + pair_coeff @atom:41_b020_a020_d020_i020 @atom:41_b020_a020_d020_i020 0.17 3.0 + pair_coeff @atom:42_b006_a006_d006_i006 @atom:42_b006_a006_d006_i006 0.17 3.8 + pair_coeff @atom:43_b002_a002_d002_i002 @atom:43_b002_a002_d002_i002 0.118 3.8 + pair_coeff @atom:44_b002_a002_d002_i002 @atom:44_b002_a002_d002_i002 0.118 3.8 + pair_coeff @atom:45_b021_a021_d021_i021 @atom:45_b021_a021_d021_i021 0.3 3.4 + pair_coeff @atom:46_b010_a010_d010_i010 @atom:46_b010_a010_d010_i010 0.08 3.8 + pair_coeff @atom:47_b021_a021_d021_i021 @atom:47_b021_a021_d021_i021 0.3 3.47 + pair_coeff @atom:48_b013_a013_d013_i013 @atom:48_b013_a013_d013_i013 0.05 3.8 + pair_coeff @atom:49_b021_a021_d021_i021 @atom:49_b021_a021_d021_i021 0.266 3.47 + pair_coeff @atom:50_b022_a022_d022_i022 @atom:50_b022_a022_d022_i022 0.395 3.56 + pair_coeff @atom:51_b023_a023_d023_i023 @atom:51_b023_a023_d023_i023 0.28 2.93 + pair_coeff @atom:52_b006_a006_d006_i006 @atom:52_b006_a006_d006_i006 0.16 3.81 + pair_coeff @atom:53_b004_a004_d004_i004 @atom:53_b004_a004_d004_i004 0.21 2.96 + pair_coeff @atom:54_b024_a024_d024_i024 @atom:54_b024_a024_d024_i024 0.17 3.25 + pair_coeff @atom:55_b003_a003_d003_i003 @atom:55_b003_a003_d003_i003 0.115 3.8 + pair_coeff @atom:56_b006_a006_d006_i006 @atom:56_b006_a006_d006_i006 0.17 3.8 + pair_coeff @atom:57_b025_a025_d025_i025 @atom:57_b025_a025_d025_i025 0.0 0.0 + pair_coeff @atom:58_b026_a026_d026_i026 @atom:58_b026_a026_d026_i026 0.02 2.556 + pair_coeff @atom:59_b027_a027_d027_i027 @atom:59_b027_a027_d027_i027 0.069 2.78 + pair_coeff @atom:60_b028_a028_d028_i028 @atom:60_b028_a028_d028_i028 0.2339 3.401 + pair_coeff @atom:61_b029_a029_d029_i029 @atom:61_b029_a029_d029_i029 0.317 3.624 + pair_coeff @atom:62_b030_a030_d030_i030 @atom:62_b030_a030_d030_i030 0.433 3.935 + pair_coeff @atom:63_b031_a031_d031_i031 @atom:63_b031_a031_d031_i031 0.1521 3.15061 + pair_coeff @atom:64_b032_a032_d032_i032 @atom:64_b032_a032_d032_i032 0.0 0.0 + pair_coeff @atom:65_b031_a031_d031_i031 @atom:65_b031_a031_d031_i031 0.155 3.15365 + pair_coeff @atom:66_b032_a032_d032_i032 @atom:66_b032_a032_d032_i032 0.0 0.0 + pair_coeff @atom:67_b033_a033_d033_i033 @atom:67_b033_a033_d033_i033 0.0 0.0 + pair_coeff @atom:68_b034_a034_d034_i034 @atom:68_b034_a034_d034_i034 0.15 3.176 + pair_coeff @atom:69_b035_a035_d035_i035 @atom:69_b035_a035_d035_i035 0.0 0.0 + pair_coeff @atom:70_b036_a036_d036_i036 @atom:70_b036_a036_d036_i036 0.1 3.27 + pair_coeff @atom:71_b037_a037_d037_i037 @atom:71_b037_a037_d037_i037 0.0 0.0 + pair_coeff @atom:72_b038_a038_d038_i038 @atom:72_b038_a038_d038_i038 0.0 0.0 + pair_coeff @atom:73_b039_a039_d039_i039 @atom:73_b039_a039_d039_i039 0.16 3.12 + pair_coeff @atom:74_b040_a040_d040_i040 @atom:74_b040_a040_d040_i040 0.0 0.0 + pair_coeff @atom:75_b041_a041_d041_i041 @atom:75_b041_a041_d041_i041 0.0 0.0 + pair_coeff @atom:76_b042_a042_d042_i042 @atom:76_b042_a042_d042_i042 0.1554 3.16557 + pair_coeff @atom:77_b043_a043_d043_i043 @atom:77_b043_a043_d043_i043 0.0 0.0 + pair_coeff @atom:78_b044_a044_d044_i044 @atom:78_b044_a044_d044_i044 0.17 3.42 + pair_coeff @atom:79_b045_a045_d045_i045 @atom:79_b045_a045_d045_i045 0.0 0.0 + pair_coeff @atom:80_b013_a013_d013_i013 @atom:80_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:81_b013_a013_d013_i013 @atom:81_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:82_b013_a013_d013_i013 @atom:82_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:83_b013_a013_d013_i013 @atom:83_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:84_b013_a013_d013_i013 @atom:84_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:85_b046_a046_d046_i046 @atom:85_b046_a046_d046_i046 0.03 2.5 + pair_coeff @atom:86_b047_a047_d047_i047 @atom:86_b047_a047_d047_i047 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@atom:135_b051_a051_d051_i051 @atom:135_b051_a051_d051_i051 0.066 3.5 + pair_coeff @atom:136_b046_a046_d046_i046 @atom:136_b046_a046_d046_i046 0.03 2.5 + pair_coeff @atom:137_b051_a051_d051_i051 @atom:137_b051_a051_d051_i051 0.066 3.5 + pair_coeff @atom:138_b046_a046_d046_i046 @atom:138_b046_a046_d046_i046 0.03 2.5 + pair_coeff @atom:139_b051_a051_d051_i051 @atom:139_b051_a051_d051_i051 0.066 3.5 + pair_coeff @atom:140_b051_a051_d051_i051 @atom:140_b051_a051_d051_i051 0.066 3.5 + pair_coeff @atom:141_b048_a048_d048_i048 @atom:141_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:142_b015_a015_d015_i015 @atom:142_b015_a015_d015_i015 0.25 3.55 + pair_coeff @atom:143_b015_a015_d015_i015 @atom:143_b015_a015_d015_i015 0.25 3.7 + pair_coeff @atom:144_b016_a016_d016_i016 @atom:144_b016_a016_d016_i016 0.25 3.55 + pair_coeff @atom:145_b016_a016_d016_i016 @atom:145_b016_a016_d016_i016 0.25 3.55 + pair_coeff @atom:146_b017_a017_d017_i017 @atom:146_b017_a017_d017_i017 0.0 0.0 + pair_coeff @atom:147_b017_a017_d017_i017 @atom:147_b017_a017_d017_i017 0.0 0.0 + pair_coeff @atom:148_b013_a013_d013_i013 @atom:148_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:149_b013_a013_d013_i013 @atom:149_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:150_b013_a013_d013_i013 @atom:150_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:151_b013_a013_d013_i013 @atom:151_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:152_b013_a013_d013_i013 @atom:152_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:153_b013_a013_d013_i013 @atom:153_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:154_b013_a013_d013_i013 @atom:154_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:155_b013_a013_d013_i013 @atom:155_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:156_b013_a013_d013_i013 @atom:156_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:157_b013_a013_d013_i013 @atom:157_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:158_b013_a013_d013_i013 @atom:158_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:159_b013_a013_d013_i013 @atom:159_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:160_b013_a013_d013_i013 @atom:160_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:161_b013_a013_d013_i013 @atom:161_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:162_b013_a013_d013_i013 @atom:162_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:163_b048_a048_d048_i048 @atom:163_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:164_b016_a016_d016_i016 @atom:164_b016_a016_d016_i016 0.25 3.55 + pair_coeff @atom:165_b013_a013_d013_i013 @atom:165_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:166_b013_a013_d013_i013 @atom:166_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:167_b013_a013_d013_i013 @atom:167_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:168_b021_a021_d021_i021 @atom:168_b021_a021_d021_i021 0.3 3.4 + pair_coeff @atom:169_b047_a047_d047_i047 @atom:169_b047_a047_d047_i047 0.076 3.55 + pair_coeff @atom:170_b048_a048_d048_i048 @atom:170_b048_a048_d048_i048 0.07 3.55 + pair_coeff 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@atom:183_b045_a045_d045_i045 @atom:183_b045_a045_d045_i045 0.0 0.0 + pair_coeff @atom:184_b013_a013_d013_i013 @atom:184_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:185_b013_a013_d013_i013 @atom:185_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:186_b013_a013_d013_i013 @atom:186_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:187_b013_a013_d013_i013 @atom:187_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:188_b013_a013_d013_i013 @atom:188_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:189_b003_a003_d003_i003 @atom:189_b003_a003_d003_i003 0.105 3.75 + pair_coeff @atom:190_b004_a004_d004_i004 @atom:190_b004_a004_d004_i004 0.21 2.96 + pair_coeff @atom:191_b024_a024_d024_i024 @atom:191_b024_a024_d024_i024 0.17 3.25 + pair_coeff @atom:192_b045_a045_d045_i045 @atom:192_b045_a045_d045_i045 0.0 0.0 + pair_coeff @atom:193_b024_a024_d024_i024 @atom:193_b024_a024_d024_i024 0.17 3.25 + pair_coeff @atom:194_b003_a003_d003_i003 @atom:194_b003_a003_d003_i003 0.105 3.75 + pair_coeff @atom:195_b004_a004_d004_i004 @atom:195_b004_a004_d004_i004 0.21 2.96 + pair_coeff @atom:196_b045_a045_d045_i045 @atom:196_b045_a045_d045_i045 0.0 0.0 + pair_coeff @atom:197_b046_a046_d046_i046 @atom:197_b046_a046_d046_i046 0.02 2.5 + pair_coeff @atom:198_b013_a013_d013_i013 @atom:198_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:199_b013_a013_d013_i013 @atom:199_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:200_b013_a013_d013_i013 @atom:200_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:201_b013_a013_d013_i013 @atom:201_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:202_b048_a048_d048_i048 @atom:202_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:203_b019_a019_d019_i019 @atom:203_b019_a019_d019_i019 0.15 3.65 + pair_coeff @atom:204_b018_a018_d018_i018 @atom:204_b018_a018_d018_i018 0.17 3.2 + pair_coeff @atom:205_b048_a048_d048_i048 @atom:205_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:206_b021_a021_d021_i021 @atom:206_b021_a021_d021_i021 0.3 3.4 + pair_coeff 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@atom:231_b053_a053_d053_i053 @atom:231_b053_a053_d053_i053 0.17 3.25 + pair_coeff @atom:232_b054_a054_d054_i054 @atom:232_b054_a054_d054_i054 0.0 0.0 + pair_coeff @atom:233_b054_a054_d054_i054 @atom:233_b054_a054_d054_i054 0.0 0.0 + pair_coeff @atom:234_b013_a013_d013_i013 @atom:234_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:235_b013_a013_d013_i013 @atom:235_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:236_b013_a013_d013_i013 @atom:236_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:237_b013_a013_d013_i013 @atom:237_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:238_b013_a013_d013_i013 @atom:238_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:239_b013_a013_d013_i013 @atom:239_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:240_b013_a013_d013_i013 @atom:240_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:241_b013_a013_d013_i013 @atom:241_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:242_b013_a013_d013_i013 @atom:242_b013_a013_d013_i013 0.066 3.5 + pair_coeff 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@atom:255_b048_a048_d048_i048 @atom:255_b048_a048_d048_i048 0.08 3.5 + pair_coeff @atom:256_b055_a055_d055_i055 @atom:256_b055_a055_d055_i055 0.17 3.25 + pair_coeff @atom:257_b045_a045_d045_i045 @atom:257_b045_a045_d045_i045 0.0 0.0 + pair_coeff @atom:258_b048_a048_d048_i048 @atom:258_b048_a048_d048_i048 0.08 3.5 + pair_coeff @atom:259_b049_a049_d049_i049 @atom:259_b049_a049_d049_i049 0.05 2.5 + pair_coeff @atom:260_b048_a048_d048_i048 @atom:260_b048_a048_d048_i048 0.08 3.5 + pair_coeff @atom:261_b049_a049_d049_i049 @atom:261_b049_a049_d049_i049 0.05 2.5 + pair_coeff @atom:262_b057_a057_d057_i057 @atom:262_b057_a057_d057_i057 0.17 3.25 + pair_coeff @atom:263_b003_a003_d003_i003 @atom:263_b003_a003_d003_i003 0.105 3.75 + pair_coeff @atom:264_b057_a057_d057_i057 @atom:264_b057_a057_d057_i057 0.17 3.25 + pair_coeff @atom:265_b003_a003_d003_i003 @atom:265_b003_a003_d003_i003 0.105 3.75 + pair_coeff @atom:266_b047_a047_d047_i047 @atom:266_b047_a047_d047_i047 0.08 3.5 + pair_coeff @atom:267_b047_a047_d047_i047 @atom:267_b047_a047_d047_i047 0.08 3.5 + pair_coeff @atom:268_b045_a045_d045_i045 @atom:268_b045_a045_d045_i045 0.0 0.0 + pair_coeff @atom:269_b004_a004_d004_i004 @atom:269_b004_a004_d004_i004 0.21 2.96 + pair_coeff @atom:270_b045_a045_d045_i045 @atom:270_b045_a045_d045_i045 0.0 0.0 + pair_coeff @atom:271_b004_a004_d004_i004 @atom:271_b004_a004_d004_i004 0.21 2.96 + pair_coeff @atom:272_b046_a046_d046_i046 @atom:272_b046_a046_d046_i046 0.05 2.5 + pair_coeff @atom:273_b046_a046_d046_i046 @atom:273_b046_a046_d046_i046 0.05 2.5 + pair_coeff @atom:274_b013_a013_d013_i013 @atom:274_b013_a013_d013_i013 0.08 3.5 + pair_coeff @atom:275_b046_a046_d046_i046 @atom:275_b046_a046_d046_i046 0.05 2.5 + pair_coeff @atom:276_b057_a057_d057_i057 @atom:276_b057_a057_d057_i057 0.17 3.25 + pair_coeff @atom:277_b003_a003_d003_i003 @atom:277_b003_a003_d003_i003 0.105 3.75 + pair_coeff @atom:278_b056_a056_d056_i056 @atom:278_b056_a056_d056_i056 0.17 3.25 + pair_coeff @atom:279_b048_a048_d048_i048 @atom:279_b048_a048_d048_i048 0.08 3.5 + pair_coeff @atom:280_b047_a047_d047_i047 @atom:280_b047_a047_d047_i047 0.08 3.5 + pair_coeff @atom:281_b047_a047_d047_i047 @atom:281_b047_a047_d047_i047 0.08 3.5 + pair_coeff @atom:282_b045_a045_d045_i045 @atom:282_b045_a045_d045_i045 0.0 0.0 + pair_coeff @atom:283_b004_a004_d004_i004 @atom:283_b004_a004_d004_i004 0.21 2.96 + pair_coeff @atom:284_b055_a055_d055_i055 @atom:284_b055_a055_d055_i055 0.17 3.25 + pair_coeff @atom:285_b045_a045_d045_i045 @atom:285_b045_a045_d045_i045 0.0 0.0 + pair_coeff @atom:286_b045_a045_d045_i045 @atom:286_b045_a045_d045_i045 0.0 0.0 + pair_coeff @atom:287_b046_a046_d046_i046 @atom:287_b046_a046_d046_i046 0.05 2.5 + pair_coeff @atom:288_b058_a058_d058_i058 @atom:288_b058_a058_d058_i058 0.05 2.5 + pair_coeff @atom:289_b056_a056_d056_i056 @atom:289_b056_a056_d056_i056 0.17 3.25 + pair_coeff @atom:290_b059_a059_d059_i059 @atom:290_b059_a059_d059_i059 0.08 3.5 + pair_coeff @atom:291_b056_a056_d056_i056 @atom:291_b056_a056_d056_i056 0.17 3.25 + pair_coeff @atom:292_b060_a060_d060_i060 @atom:292_b060_a060_d060_i060 0.08 3.5 + pair_coeff @atom:293_b060_a060_d060_i060 @atom:293_b060_a060_d060_i060 0.08 3.5 + pair_coeff @atom:294_b048_a048_d048_i048 @atom:294_b048_a048_d048_i048 0.08 3.5 + pair_coeff @atom:295_b061_a061_d061_i061 @atom:295_b061_a061_d061_i061 0.17 3.25 + pair_coeff @atom:296_b062_a062_d062_i062 @atom:296_b062_a062_d062_i062 0.08 3.5 + pair_coeff @atom:297_b057_a057_d057_i057 @atom:297_b057_a057_d057_i057 0.17 3.25 + pair_coeff @atom:298_b063_a063_d063_i063 @atom:298_b063_a063_d063_i063 0.05 2.5 + pair_coeff @atom:299_b055_a055_d055_i055 @atom:299_b055_a055_d055_i055 0.17 3.25 + pair_coeff @atom:300_b045_a045_d045_i045 @atom:300_b045_a045_d045_i045 0.0 0.0 + pair_coeff @atom:301_b045_a045_d045_i045 @atom:301_b045_a045_d045_i045 0.0 0.0 + pair_coeff @atom:302_b063_a063_d063_i063 @atom:302_b063_a063_d063_i063 0.05 2.5 + pair_coeff @atom:303_b045_a045_d045_i045 @atom:303_b045_a045_d045_i045 0.0 0.0 + pair_coeff @atom:304_b057_a057_d057_i057 @atom:304_b057_a057_d057_i057 0.17 3.25 + pair_coeff @atom:305_b048_a048_d048_i048 @atom:305_b048_a048_d048_i048 0.08 3.5 + pair_coeff @atom:306_b056_a056_d056_i056 @atom:306_b056_a056_d056_i056 0.17 3.25 + pair_coeff @atom:307_b060_a060_d060_i060 @atom:307_b060_a060_d060_i060 0.08 3.5 + pair_coeff @atom:308_b060_a060_d060_i060 @atom:308_b060_a060_d060_i060 0.08 3.5 + pair_coeff @atom:309_b003_a003_d003_i003 @atom:309_b003_a003_d003_i003 0.105 3.75 + pair_coeff @atom:310_b045_a045_d045_i045 @atom:310_b045_a045_d045_i045 0.0 0.0 + pair_coeff @atom:311_b055_a055_d055_i055 @atom:311_b055_a055_d055_i055 0.17 3.25 + pair_coeff @atom:312_b045_a045_d045_i045 @atom:312_b045_a045_d045_i045 0.0 0.0 + pair_coeff @atom:313_b004_a004_d004_i004 @atom:313_b004_a004_d004_i004 0.21 2.96 + pair_coeff @atom:314_b013_a013_d013_i013 @atom:314_b013_a013_d013_i013 0.08 3.5 + pair_coeff @atom:315_b046_a046_d046_i046 @atom:315_b046_a046_d046_i046 0.05 2.5 + pair_coeff @atom:316_b013_a013_d013_i013 @atom:316_b013_a013_d013_i013 0.08 3.5 + pair_coeff @atom:317_b046_a046_d046_i046 @atom:317_b046_a046_d046_i046 0.05 2.5 + pair_coeff @atom:318_b013_a013_d013_i013 @atom:318_b013_a013_d013_i013 0.08 3.5 + pair_coeff @atom:319_b046_a046_d046_i046 @atom:319_b046_a046_d046_i046 0.05 2.5 + pair_coeff @atom:320_b057_a057_d057_i057 @atom:320_b057_a057_d057_i057 0.17 3.25 + pair_coeff @atom:321_b003_a003_d003_i003 @atom:321_b003_a003_d003_i003 0.105 3.75 + pair_coeff @atom:322_b057_a057_d057_i057 @atom:322_b057_a057_d057_i057 0.17 3.25 + pair_coeff @atom:323_b048_a048_d048_i048 @atom:323_b048_a048_d048_i048 0.08 3.5 + pair_coeff @atom:324_b047_a047_d047_i047 @atom:324_b047_a047_d047_i047 0.08 3.5 + pair_coeff @atom:325_b047_a047_d047_i047 @atom:325_b047_a047_d047_i047 0.08 3.5 + pair_coeff @atom:326_b045_a045_d045_i045 @atom:326_b045_a045_d045_i045 0.0 0.0 + pair_coeff @atom:327_b004_a004_d004_i004 @atom:327_b004_a004_d004_i004 0.21 2.96 + pair_coeff @atom:328_b045_a045_d045_i045 @atom:328_b045_a045_d045_i045 0.0 0.0 + pair_coeff @atom:329_b055_a055_d055_i055 @atom:329_b055_a055_d055_i055 0.17 3.25 + pair_coeff @atom:330_b045_a045_d045_i045 @atom:330_b045_a045_d045_i045 0.0 0.0 + pair_coeff @atom:331_b045_a045_d045_i045 @atom:331_b045_a045_d045_i045 0.0 0.0 + pair_coeff @atom:332_b049_a049_d049_i049 @atom:332_b049_a049_d049_i049 0.05 2.5 + pair_coeff @atom:333_b058_a058_d058_i058 @atom:333_b058_a058_d058_i058 0.05 2.5 + pair_coeff @atom:334_b013_a013_d013_i013 @atom:334_b013_a013_d013_i013 0.08 3.5 + pair_coeff @atom:335_b046_a046_d046_i046 @atom:335_b046_a046_d046_i046 0.05 2.5 + pair_coeff @atom:336_b064_a064_d064_i064 @atom:336_b064_a064_d064_i064 0.2 3.74 + pair_coeff @atom:337_b052_a052_d052_i052 @atom:337_b052_a052_d052_i052 0.21 2.96 + pair_coeff @atom:338_b020_a020_d020_i020 @atom:338_b020_a020_d020_i020 0.17 3.0 + pair_coeff @atom:339_b013_a013_d013_i013 @atom:339_b013_a013_d013_i013 0.066 3.55 + pair_coeff @atom:340_b047_a047_d047_i047 @atom:340_b047_a047_d047_i047 0.08 3.5 + pair_coeff @atom:341_b021_a021_d021_i021 @atom:341_b021_a021_d021_i021 0.3 3.4 + pair_coeff @atom:342_b047_a047_d047_i047 @atom:342_b047_a047_d047_i047 0.076 3.55 + pair_coeff @atom:343_b001_a001_d001_i001 @atom:343_b001_a001_d001_i001 0.71 3.05 + pair_coeff @atom:344_b021_a021_d021_i021 @atom:344_b021_a021_d021_i021 0.71 4.02 + pair_coeff @atom:345_b065_a065_d065_i065 @atom:345_b065_a065_d065_i065 0.71 4.28 + pair_coeff @atom:346_b066_a066_d066_i066 @atom:346_b066_a066_d066_i066 0.71 4.81 + pair_coeff @atom:347_b067_a067_d067_i067 @atom:347_b067_a067_d067_i067 0.0005 5.34 + pair_coeff @atom:348_b068_a068_d068_i068 @atom:348_b068_a068_d068_i068 0.0005 2.87 + pair_coeff @atom:349_b069_a069_d069_i069 @atom:349_b069_a069_d069_i069 0.0005 4.07 + pair_coeff @atom:350_b070_a070_d070_i070 @atom:350_b070_a070_d070_i070 0.0005 5.17 + pair_coeff @atom:351_b071_a071_d071_i071 @atom:351_b071_a071_d071_i071 0.0005 5.6 + pair_coeff @atom:352_b072_a072_d072_i072 @atom:352_b072_a072_d072_i072 0.0005 6.2 + pair_coeff @atom:353_b073_a073_d073_i073 @atom:353_b073_a073_d073_i073 0.875044 1.644471 + pair_coeff @atom:354_b074_a074_d074_i074 @atom:354_b074_a074_d074_i074 0.449657 2.412031 + pair_coeff @atom:355_b075_a075_d075_i075 @atom:355_b075_a075_d075_i075 0.118226 3.102688 + pair_coeff @atom:356_b076_a076_d076_i076 @atom:356_b076_a076_d076_i076 0.047096 3.81661 + pair_coeff @atom:357_b006_a006_d006_i006 @atom:357_b006_a006_d006_i006 0.3 4.2 + pair_coeff @atom:358_b046_a046_d046_i046 @atom:358_b046_a046_d046_i046 0.05 2.5 + pair_coeff @atom:359_b015_a015_d015_i015 @atom:359_b015_a015_d015_i015 0.5 4.25 + pair_coeff @atom:360_b006_a006_d006_i006 @atom:360_b006_a006_d006_i006 0.3 4.2 + pair_coeff @atom:361_b046_a046_d046_i046 @atom:361_b046_a046_d046_i046 0.05 2.5 + pair_coeff @atom:362_b005_a005_d005_i005 @atom:362_b005_a005_d005_i005 0.25 3.15 + pair_coeff @atom:363_b013_a013_d013_i013 @atom:363_b013_a013_d013_i013 0.3 4.2 + pair_coeff @atom:364_b046_a046_d046_i046 @atom:364_b046_a046_d046_i046 0.05 2.5 + pair_coeff @atom:365_b019_a019_d019_i019 @atom:365_b019_a019_d019_i019 0.15 3.65 + pair_coeff @atom:366_b018_a018_d018_i018 @atom:366_b018_a018_d018_i018 0.25 3.4 + pair_coeff @atom:367_b006_a006_d006_i006 @atom:367_b006_a006_d006_i006 0.3 4.2 + pair_coeff @atom:368_b046_a046_d046_i046 @atom:368_b046_a046_d046_i046 0.05 2.5 + pair_coeff @atom:369_b053_a053_d053_i053 @atom:369_b053_a053_d053_i053 0.25 3.4 + pair_coeff @atom:370_b045_a045_d045_i045 @atom:370_b045_a045_d045_i045 0.05 2.5 + pair_coeff @atom:371_b006_a006_d006_i006 @atom:371_b006_a006_d006_i006 0.3 4.2 + pair_coeff @atom:372_b046_a046_d046_i046 @atom:372_b046_a046_d046_i046 0.05 2.5 + pair_coeff @atom:373_b013_a013_d013_i013 @atom:373_b013_a013_d013_i013 0.3 4.2 + pair_coeff @atom:374_b046_a046_d046_i046 @atom:374_b046_a046_d046_i046 0.05 2.5 + pair_coeff @atom:375_b033_a033_d033_i033 @atom:375_b033_a033_d033_i033 0.0 0.0 + pair_coeff @atom:376_b005_a005_d005_i005 @atom:376_b005_a005_d005_i005 0.25 3.2 + pair_coeff @atom:377_b007_a007_d007_i007 @atom:377_b007_a007_d007_i007 0.0 0.0 + pair_coeff @atom:378_b077_a077_d077_i077 @atom:378_b077_a077_d077_i077 0.4 2.81524 + pair_coeff @atom:379_b078_a078_d078_i078 @atom:379_b078_a078_d078_i078 0.2 3.11815 + pair_coeff @atom:380_b020_a020_d020_i020 @atom:380_b020_a020_d020_i020 0.14 2.9 + pair_coeff @atom:381_b064_a064_d064_i064 @atom:381_b064_a064_d064_i064 0.2 3.74 + pair_coeff @atom:382_b052_a052_d052_i052 @atom:382_b052_a052_d052_i052 0.2 3.15 + pair_coeff @atom:383_b020_a020_d020_i020 @atom:383_b020_a020_d020_i020 0.14 2.9 + pair_coeff @atom:384_b013_a013_d013_i013 @atom:384_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:385_b046_a046_d046_i046 @atom:385_b046_a046_d046_i046 0.03 2.5 + pair_coeff @atom:386_b064_a064_d064_i064 @atom:386_b064_a064_d064_i064 0.2 3.74 + pair_coeff @atom:387_b052_a052_d052_i052 @atom:387_b052_a052_d052_i052 0.2 3.15 + pair_coeff @atom:388_b020_a020_d020_i020 @atom:388_b020_a020_d020_i020 0.14 2.9 + pair_coeff @atom:389_b013_a013_d013_i013 @atom:389_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:390_b046_a046_d046_i046 @atom:390_b046_a046_d046_i046 0.03 2.5 + pair_coeff @atom:391_b064_a064_d064_i064 @atom:391_b064_a064_d064_i064 0.2 3.74 + pair_coeff @atom:392_b052_a052_d052_i052 @atom:392_b052_a052_d052_i052 0.2 3.15 + pair_coeff @atom:393_b020_a020_d020_i020 @atom:393_b020_a020_d020_i020 0.14 2.9 + pair_coeff @atom:394_b013_a013_d013_i013 @atom:394_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:395_b046_a046_d046_i046 @atom:395_b046_a046_d046_i046 0.03 2.5 + pair_coeff @atom:396_b013_a013_d013_i013 @atom:396_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:397_b046_a046_d046_i046 @atom:397_b046_a046_d046_i046 0.03 2.5 + pair_coeff @atom:398_b048_a048_d048_i048 @atom:398_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:399_b013_a013_d013_i013 @atom:399_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:400_b046_a046_d046_i046 @atom:400_b046_a046_d046_i046 0.03 2.5 + pair_coeff @atom:401_b048_a048_d048_i048 @atom:401_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:402_b013_a013_d013_i013 @atom:402_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:403_b046_a046_d046_i046 @atom:403_b046_a046_d046_i046 0.03 2.5 + pair_coeff @atom:404_b048_a048_d048_i048 @atom:404_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:405_b013_a013_d013_i013 @atom:405_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:406_b003_a003_d003_i003 @atom:406_b003_a003_d003_i003 0.105 3.75 + pair_coeff @atom:407_b004_a004_d004_i004 @atom:407_b004_a004_d004_i004 0.21 2.96 + pair_coeff @atom:408_b020_a020_d020_i020 @atom:408_b020_a020_d020_i020 0.17 3.0 + pair_coeff @atom:409_b013_a013_d013_i013 @atom:409_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:410_b046_a046_d046_i046 @atom:410_b046_a046_d046_i046 0.015 2.42 + pair_coeff @atom:411_b003_a003_d003_i003 @atom:411_b003_a003_d003_i003 0.105 3.75 + pair_coeff @atom:412_b003_a003_d003_i003 @atom:412_b003_a003_d003_i003 0.105 3.75 + pair_coeff @atom:413_b048_a048_d048_i048 @atom:413_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:414_b020_a020_d020_i020 @atom:414_b020_a020_d020_i020 0.17 3.0 + pair_coeff @atom:415_b079_a079_d079_i079 @atom:415_b079_a079_d079_i079 0.25 3.55 + pair_coeff @atom:416_b023_a023_d023_i023 @atom:416_b023_a023_d023_i023 0.17 2.96 + pair_coeff @atom:417_b013_a013_d013_i013 @atom:417_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:418_b046_a046_d046_i046 @atom:418_b046_a046_d046_i046 0.03 2.5 + pair_coeff @atom:419_b024_a024_d024_i024 @atom:419_b024_a024_d024_i024 0.17 3.25 + pair_coeff @atom:420_b045_a045_d045_i045 @atom:420_b045_a045_d045_i045 0.0 0.0 + pair_coeff @atom:421_b024_a024_d024_i024 @atom:421_b024_a024_d024_i024 0.17 3.25 + pair_coeff @atom:422_b045_a045_d045_i045 @atom:422_b045_a045_d045_i045 0.0 0.0 + pair_coeff @atom:423_b013_a013_d013_i013 @atom:423_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:424_b046_a046_d046_i046 @atom:424_b046_a046_d046_i046 0.03 2.5 + pair_coeff @atom:425_b013_a013_d013_i013 @atom:425_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:426_b046_a046_d046_i046 @atom:426_b046_a046_d046_i046 0.03 2.5 + pair_coeff @atom:427_b013_a013_d013_i013 @atom:427_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:428_b046_a046_d046_i046 @atom:428_b046_a046_d046_i046 0.03 2.5 + pair_coeff @atom:429_b048_a048_d048_i048 @atom:429_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:430_b048_a048_d048_i048 @atom:430_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:431_b013_a013_d013_i013 @atom:431_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:432_b013_a013_d013_i013 @atom:432_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:433_b013_a013_d013_i013 @atom:433_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:434_b079_a079_d079_i079 @atom:434_b079_a079_d079_i079 0.25 3.55 + pair_coeff @atom:435_b023_a023_d023_i023 @atom:435_b023_a023_d023_i023 0.17 2.96 + pair_coeff @atom:436_b022_a022_d022_i022 @atom:436_b022_a022_d022_i022 0.395 3.56 + pair_coeff @atom:437_b022_a022_d022_i022 @atom:437_b022_a022_d022_i022 0.395 3.56 + pair_coeff @atom:438_b023_a023_d023_i023 @atom:438_b023_a023_d023_i023 0.28 2.93 + pair_coeff @atom:439_b013_a013_d013_i013 @atom:439_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:440_b013_a013_d013_i013 @atom:440_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:441_b080_a080_d080_i080 @atom:441_b080_a080_d080_i080 0.07 3.55 + pair_coeff @atom:442_b060_a060_d060_i060 @atom:442_b060_a060_d060_i060 0.07 3.55 + pair_coeff @atom:443_b081_a081_d081_i081 @atom:443_b081_a081_d081_i081 0.07 3.55 + pair_coeff @atom:444_b057_a057_d057_i057 @atom:444_b057_a057_d057_i057 0.17 3.25 + pair_coeff @atom:445_b045_a045_d045_i045 @atom:445_b045_a045_d045_i045 0.0 0.0 + pair_coeff @atom:446_b013_a013_d013_i013 @atom:446_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:447_b082_a082_d082_i082 @atom:447_b082_a082_d082_i082 0.07 3.55 + pair_coeff @atom:448_b083_a083_d083_i083 @atom:448_b083_a083_d083_i083 0.07 3.55 + pair_coeff @atom:449_b084_a084_d084_i084 @atom:449_b084_a084_d084_i084 0.07 3.55 + pair_coeff @atom:450_b082_a082_d082_i082 @atom:450_b082_a082_d082_i082 0.07 3.55 + pair_coeff @atom:451_b085_a085_d085_i085 @atom:451_b085_a085_d085_i085 0.07 3.55 + pair_coeff @atom:452_b061_a061_d061_i061 @atom:452_b061_a061_d061_i061 0.17 3.25 + pair_coeff @atom:453_b057_a057_d057_i057 @atom:453_b057_a057_d057_i057 0.17 3.25 + pair_coeff @atom:454_b045_a045_d045_i045 @atom:454_b045_a045_d045_i045 0.0 0.0 + pair_coeff @atom:455_b084_a084_d084_i084 @atom:455_b084_a084_d084_i084 0.07 3.55 + pair_coeff @atom:456_b013_a013_d013_i013 @atom:456_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:457_b013_a013_d013_i013 @atom:457_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:458_b047_a047_d047_i047 @atom:458_b047_a047_d047_i047 0.076 3.55 + pair_coeff @atom:459_b047_a047_d047_i047 @atom:459_b047_a047_d047_i047 0.076 3.55 + pair_coeff @atom:460_b086_a086_d086_i086 @atom:460_b086_a086_d086_i086 0.07 3.55 + pair_coeff @atom:461_b056_a056_d056_i056 @atom:461_b056_a056_d056_i056 0.17 3.25 + pair_coeff @atom:462_b048_a048_d048_i048 @atom:462_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:463_b048_a048_d048_i048 @atom:463_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:464_b048_a048_d048_i048 @atom:464_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:465_b049_a049_d049_i049 @atom:465_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:466_b049_a049_d049_i049 @atom:466_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:467_b049_a049_d049_i049 @atom:467_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:468_b056_a056_d056_i056 @atom:468_b056_a056_d056_i056 0.17 3.25 + pair_coeff @atom:469_b048_a048_d048_i048 @atom:469_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:470_b049_a049_d049_i049 @atom:470_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:471_b056_a056_d056_i056 @atom:471_b056_a056_d056_i056 0.17 3.25 + pair_coeff @atom:472_b059_a059_d059_i059 @atom:472_b059_a059_d059_i059 0.07 3.55 + pair_coeff @atom:473_b048_a048_d048_i048 @atom:473_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:474_b048_a048_d048_i048 @atom:474_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:475_b049_a049_d049_i049 @atom:475_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:476_b049_a049_d049_i049 @atom:476_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:477_b049_a049_d049_i049 @atom:477_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:478_b056_a056_d056_i056 @atom:478_b056_a056_d056_i056 0.17 3.25 + pair_coeff @atom:479_b048_a048_d048_i048 @atom:479_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:480_b048_a048_d048_i048 @atom:480_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:481_b049_a049_d049_i049 @atom:481_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:482_b049_a049_d049_i049 @atom:482_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:483_b057_a057_d057_i057 @atom:483_b057_a057_d057_i057 0.17 3.25 + pair_coeff @atom:484_b084_a084_d084_i084 @atom:484_b084_a084_d084_i084 0.07 3.55 + pair_coeff @atom:485_b087_a087_d087_i087 @atom:485_b087_a087_d087_i087 0.07 3.55 + pair_coeff @atom:486_b045_a045_d045_i045 @atom:486_b045_a045_d045_i045 0.0 0.0 + pair_coeff @atom:487_b049_a049_d049_i049 @atom:487_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:488_b049_a049_d049_i049 @atom:488_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:489_b057_a057_d057_i057 @atom:489_b057_a057_d057_i057 0.17 3.25 + pair_coeff @atom:490_b061_a061_d061_i061 @atom:490_b061_a061_d061_i061 0.17 3.25 + pair_coeff @atom:491_b088_a088_d088_i088 @atom:491_b088_a088_d088_i088 0.07 3.55 + pair_coeff @atom:492_b087_a087_d087_i087 @atom:492_b087_a087_d087_i087 0.07 3.55 + pair_coeff @atom:493_b084_a084_d084_i084 @atom:493_b084_a084_d084_i084 0.07 3.55 + pair_coeff @atom:494_b045_a045_d045_i045 @atom:494_b045_a045_d045_i045 0.0 0.0 + pair_coeff @atom:495_b049_a049_d049_i049 @atom:495_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:496_b049_a049_d049_i049 @atom:496_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:497_b049_a049_d049_i049 @atom:497_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:498_b057_a057_d057_i057 @atom:498_b057_a057_d057_i057 0.17 3.25 + pair_coeff @atom:499_b082_a082_d082_i082 @atom:499_b082_a082_d082_i082 0.07 3.55 + pair_coeff @atom:500_b061_a061_d061_i061 @atom:500_b061_a061_d061_i061 0.17 3.25 + pair_coeff @atom:501_b083_a083_d083_i083 @atom:501_b083_a083_d083_i083 0.07 3.55 + pair_coeff @atom:502_b084_a084_d084_i084 @atom:502_b084_a084_d084_i084 0.07 3.55 + pair_coeff @atom:503_b045_a045_d045_i045 @atom:503_b045_a045_d045_i045 0.0 0.0 + pair_coeff @atom:504_b049_a049_d049_i049 @atom:504_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:505_b049_a049_d049_i049 @atom:505_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:506_b049_a049_d049_i049 @atom:506_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:507_b020_a020_d020_i020 @atom:507_b020_a020_d020_i020 0.14 2.9 + pair_coeff @atom:508_b084_a084_d084_i084 @atom:508_b084_a084_d084_i084 0.07 3.55 + pair_coeff @atom:509_b087_a087_d087_i087 @atom:509_b087_a087_d087_i087 0.076 3.55 + pair_coeff @atom:510_b049_a049_d049_i049 @atom:510_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:511_b049_a049_d049_i049 @atom:511_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:512_b020_a020_d020_i020 @atom:512_b020_a020_d020_i020 0.14 2.9 + pair_coeff @atom:513_b082_a082_d082_i082 @atom:513_b082_a082_d082_i082 0.07 3.55 + pair_coeff @atom:514_b061_a061_d061_i061 @atom:514_b061_a061_d061_i061 0.17 3.25 + pair_coeff @atom:515_b083_a083_d083_i083 @atom:515_b083_a083_d083_i083 0.07 3.55 + pair_coeff @atom:516_b084_a084_d084_i084 @atom:516_b084_a084_d084_i084 0.07 3.55 + pair_coeff @atom:517_b049_a049_d049_i049 @atom:517_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:518_b049_a049_d049_i049 @atom:518_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:519_b049_a049_d049_i049 @atom:519_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:520_b020_a020_d020_i020 @atom:520_b020_a020_d020_i020 0.14 2.9 + pair_coeff @atom:521_b061_a061_d061_i061 @atom:521_b061_a061_d061_i061 0.17 3.25 + pair_coeff @atom:522_b088_a088_d088_i088 @atom:522_b088_a088_d088_i088 0.07 3.55 + pair_coeff @atom:523_b087_a087_d087_i087 @atom:523_b087_a087_d087_i087 0.07 3.55 + pair_coeff @atom:524_b084_a084_d084_i084 @atom:524_b084_a084_d084_i084 0.07 3.55 + pair_coeff @atom:525_b049_a049_d049_i049 @atom:525_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:526_b049_a049_d049_i049 @atom:526_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:527_b049_a049_d049_i049 @atom:527_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:528_b057_a057_d057_i057 @atom:528_b057_a057_d057_i057 0.17 3.25 + pair_coeff @atom:529_b084_a084_d084_i084 @atom:529_b084_a084_d084_i084 0.07 3.55 + pair_coeff @atom:530_b087_a087_d087_i087 @atom:530_b087_a087_d087_i087 0.07 3.55 + pair_coeff @atom:531_b048_a048_d048_i048 @atom:531_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:532_b048_a048_d048_i048 @atom:532_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:533_b048_a048_d048_i048 @atom:533_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:534_b048_a048_d048_i048 @atom:534_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:535_b081_a081_d081_i081 @atom:535_b081_a081_d081_i081 0.07 3.55 + pair_coeff @atom:536_b060_a060_d060_i060 @atom:536_b060_a060_d060_i060 0.07 3.55 + pair_coeff @atom:537_b045_a045_d045_i045 @atom:537_b045_a045_d045_i045 0.0 0.0 + pair_coeff @atom:538_b049_a049_d049_i049 @atom:538_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:539_b049_a049_d049_i049 @atom:539_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:540_b049_a049_d049_i049 @atom:540_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:541_b049_a049_d049_i049 @atom:541_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:542_b049_a049_d049_i049 @atom:542_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:543_b049_a049_d049_i049 @atom:543_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:544_b056_a056_d056_i056 @atom:544_b056_a056_d056_i056 0.17 3.25 + pair_coeff @atom:545_b048_a048_d048_i048 @atom:545_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:546_b048_a048_d048_i048 @atom:546_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:547_b048_a048_d048_i048 @atom:547_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:548_b048_a048_d048_i048 @atom:548_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:549_b048_a048_d048_i048 @atom:549_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:550_b048_a048_d048_i048 @atom:550_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:551_b048_a048_d048_i048 @atom:551_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:552_b048_a048_d048_i048 @atom:552_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:553_b048_a048_d048_i048 @atom:553_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:554_b049_a049_d049_i049 @atom:554_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:555_b049_a049_d049_i049 @atom:555_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:556_b049_a049_d049_i049 @atom:556_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:557_b049_a049_d049_i049 @atom:557_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:558_b049_a049_d049_i049 @atom:558_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:559_b049_a049_d049_i049 @atom:559_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:560_b049_a049_d049_i049 @atom:560_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:561_b056_a056_d056_i056 @atom:561_b056_a056_d056_i056 0.17 3.25 + pair_coeff @atom:562_b059_a059_d059_i059 @atom:562_b059_a059_d059_i059 0.07 3.55 + pair_coeff @atom:563_b056_a056_d056_i056 @atom:563_b056_a056_d056_i056 0.17 3.25 + pair_coeff @atom:564_b060_a060_d060_i060 @atom:564_b060_a060_d060_i060 0.07 3.55 + pair_coeff @atom:565_b060_a060_d060_i060 @atom:565_b060_a060_d060_i060 0.07 3.55 + pair_coeff @atom:566_b048_a048_d048_i048 @atom:566_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:567_b061_a061_d061_i061 @atom:567_b061_a061_d061_i061 0.17 3.25 + pair_coeff @atom:568_b062_a062_d062_i062 @atom:568_b062_a062_d062_i062 0.07 3.55 + pair_coeff @atom:569_b057_a057_d057_i057 @atom:569_b057_a057_d057_i057 0.17 3.25 + pair_coeff @atom:570_b049_a049_d049_i049 @atom:570_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:571_b049_a049_d049_i049 @atom:571_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:572_b049_a049_d049_i049 @atom:572_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:573_b045_a045_d045_i045 @atom:573_b045_a045_d045_i045 0.0 0.0 + pair_coeff @atom:574_b016_a016_d016_i016 @atom:574_b016_a016_d016_i016 0.25 3.55 + pair_coeff @atom:575_b082_a082_d082_i082 @atom:575_b082_a082_d082_i082 0.07 3.55 + pair_coeff @atom:576_b061_a061_d061_i061 @atom:576_b061_a061_d061_i061 0.17 3.25 + pair_coeff @atom:577_b083_a083_d083_i083 @atom:577_b083_a083_d083_i083 0.07 3.55 + pair_coeff @atom:578_b084_a084_d084_i084 @atom:578_b084_a084_d084_i084 0.07 3.55 + pair_coeff @atom:579_b049_a049_d049_i049 @atom:579_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:580_b049_a049_d049_i049 @atom:580_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:581_b049_a049_d049_i049 @atom:581_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:582_b056_a056_d056_i056 @atom:582_b056_a056_d056_i056 0.17 3.25 + pair_coeff @atom:583_b059_a059_d059_i059 @atom:583_b059_a059_d059_i059 0.07 3.55 + pair_coeff @atom:584_b049_a049_d049_i049 @atom:584_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:585_b048_a048_d048_i048 @atom:585_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:586_b013_a013_d013_i013 @atom:586_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:587_b056_a056_d056_i056 @atom:587_b056_a056_d056_i056 0.17 3.25 + pair_coeff @atom:588_b048_a048_d048_i048 @atom:588_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:589_b048_a048_d048_i048 @atom:589_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:590_b048_a048_d048_i048 @atom:590_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:591_b048_a048_d048_i048 @atom:591_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:592_b048_a048_d048_i048 @atom:592_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:593_b048_a048_d048_i048 @atom:593_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:594_b049_a049_d049_i049 @atom:594_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:595_b049_a049_d049_i049 @atom:595_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:596_b049_a049_d049_i049 @atom:596_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:597_b049_a049_d049_i049 @atom:597_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:598_b057_a057_d057_i057 @atom:598_b057_a057_d057_i057 0.17 3.25 + pair_coeff @atom:599_b082_a082_d082_i082 @atom:599_b082_a082_d082_i082 0.07 3.55 + pair_coeff @atom:600_b061_a061_d061_i061 @atom:600_b061_a061_d061_i061 0.17 3.25 + pair_coeff @atom:601_b083_a083_d083_i083 @atom:601_b083_a083_d083_i083 0.07 3.55 + pair_coeff @atom:602_b084_a084_d084_i084 @atom:602_b084_a084_d084_i084 0.07 3.55 + pair_coeff @atom:603_b013_a013_d013_i013 @atom:603_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:604_b049_a049_d049_i049 @atom:604_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:605_b049_a049_d049_i049 @atom:605_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:606_b049_a049_d049_i049 @atom:606_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:607_b046_a046_d046_i046 @atom:607_b046_a046_d046_i046 0.03 2.5 + pair_coeff @atom:608_b013_a013_d013_i013 @atom:608_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:609_b013_a013_d013_i013 @atom:609_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:610_b013_a013_d013_i013 @atom:610_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:611_b013_a013_d013_i013 @atom:611_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:612_b013_a013_d013_i013 @atom:612_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:613_b013_a013_d013_i013 @atom:613_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:614_b013_a013_d013_i013 @atom:614_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:615_b013_a013_d013_i013 @atom:615_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:616_b013_a013_d013_i013 @atom:616_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:617_b013_a013_d013_i013 @atom:617_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:618_b013_a013_d013_i013 @atom:618_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:619_b013_a013_d013_i013 @atom:619_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:620_b013_a013_d013_i013 @atom:620_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:621_b013_a013_d013_i013 @atom:621_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:622_b013_a013_d013_i013 @atom:622_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:623_b015_a015_d015_i015 @atom:623_b015_a015_d015_i015 0.25 3.55 + pair_coeff @atom:624_b017_a017_d017_i017 @atom:624_b017_a017_d017_i017 0.0 0.0 + pair_coeff @atom:625_b048_a048_d048_i048 @atom:625_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:626_b089_a089_d089_i089 @atom:626_b089_a089_d089_i089 0.105 3.75 + pair_coeff @atom:627_b090_a090_d090_i090 @atom:627_b090_a090_d090_i090 0.17 3.25 + pair_coeff @atom:628_b091_a091_d091_i091 @atom:628_b091_a091_d091_i091 0.066 3.5 + pair_coeff @atom:629_b091_a091_d091_i091 @atom:629_b091_a091_d091_i091 0.066 3.5 + pair_coeff @atom:630_b013_a013_d013_i013 @atom:630_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:631_b086_a086_d086_i086 @atom:631_b086_a086_d086_i086 0.07 3.55 + pair_coeff @atom:632_b086_a086_d086_i086 @atom:632_b086_a086_d086_i086 0.07 3.55 + pair_coeff @atom:633_b086_a086_d086_i086 @atom:633_b086_a086_d086_i086 0.07 3.55 + pair_coeff @atom:634_b086_a086_d086_i086 @atom:634_b086_a086_d086_i086 0.07 3.55 + pair_coeff @atom:635_b086_a086_d086_i086 @atom:635_b086_a086_d086_i086 0.07 3.55 + pair_coeff @atom:636_b086_a086_d086_i086 @atom:636_b086_a086_d086_i086 0.07 3.55 + pair_coeff @atom:637_b016_a016_d016_i016 @atom:637_b016_a016_d016_i016 0.25 3.55 + pair_coeff @atom:638_b092_a092_d092_i092 @atom:638_b092_a092_d092_i092 0.054 3.473 + pair_coeff @atom:639_b093_a093_d093_i093 @atom:639_b093_a093_d093_i093 0.05 3.3 + pair_coeff @atom:640_b094_a094_d094_i094 @atom:640_b094_a094_d094_i094 0.05 3.3 + pair_coeff @atom:641_b095_a095_d095_i095 @atom:641_b095_a095_d095_i095 0.076 3.55 + pair_coeff @atom:642_b013_a013_d013_i013 @atom:642_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:643_b046_a046_d046_i046 @atom:643_b046_a046_d046_i046 0.03 2.5 + pair_coeff @atom:644_b096_a096_d096_i096 @atom:644_b096_a096_d096_i096 0.06 3.75 + pair_coeff @atom:645_b097_a097_d097_i097 @atom:645_b097_a097_d097_i097 0.054 3.473 + pair_coeff @atom:646_b098_a098_d098_i098 @atom:646_b098_a098_d098_i098 0.05 3.3 + pair_coeff @atom:647_b099_a099_d099_i099 @atom:647_b099_a099_d099_i099 0.05 3.3 + pair_coeff @atom:648_b100_a100_d100_i100 @atom:648_b100_a100_d100_i100 0.04 2.95 + pair_coeff @atom:649_b047_a047_d047_i047 @atom:649_b047_a047_d047_i047 0.076 3.55 + pair_coeff @atom:650_b021_a021_d021_i021 @atom:650_b021_a021_d021_i021 0.3 3.4 + pair_coeff @atom:651_b046_a046_d046_i046 @atom:651_b046_a046_d046_i046 0.03 2.42 + pair_coeff @atom:652_b091_a091_d091_i091 @atom:652_b091_a091_d091_i091 0.066 3.5 + pair_coeff @atom:653_b091_a091_d091_i091 @atom:653_b091_a091_d091_i091 0.066 3.5 + pair_coeff @atom:654_b091_a091_d091_i091 @atom:654_b091_a091_d091_i091 0.066 3.5 + pair_coeff @atom:655_b048_a048_d048_i048 @atom:655_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:656_b049_a049_d049_i049 @atom:656_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:657_b048_a048_d048_i048 @atom:657_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:658_b049_a049_d049_i049 @atom:658_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:659_b048_a048_d048_i048 @atom:659_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:660_b001_a001_d001_i001 @atom:660_b001_a001_d001_i001 0.061 2.85 + pair_coeff @atom:661_b048_a048_d048_i048 @atom:661_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:662_b001_a001_d001_i001 @atom:662_b001_a001_d001_i001 0.061 2.85 + pair_coeff @atom:663_b065_a065_d065_i065 @atom:663_b065_a065_d065_i065 0.47 3.47 + pair_coeff @atom:664_b002_a002_d002_i002 @atom:664_b002_a002_d002_i002 0.118 3.905 + pair_coeff @atom:665_b048_a048_d048_i048 @atom:665_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:666_b013_a013_d013_i013 @atom:666_b013_a013_d013_i013 0.062 3.25 + pair_coeff @atom:667_b001_a001_d001_i001 @atom:667_b001_a001_d001_i001 0.061 2.94 + pair_coeff @atom:668_b048_a048_d048_i048 @atom:668_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:669_b001_a001_d001_i001 @atom:669_b001_a001_d001_i001 0.061 2.85 + pair_coeff @atom:670_b048_a048_d048_i048 @atom:670_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:671_b065_a065_d065_i065 @atom:671_b065_a065_d065_i065 0.47 3.47 + pair_coeff @atom:672_b048_a048_d048_i048 @atom:672_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:673_b066_a066_d066_i066 @atom:673_b066_a066_d066_i066 0.6 3.75 + pair_coeff @atom:674_b091_a091_d091_i091 @atom:674_b091_a091_d091_i091 0.066 3.5 + pair_coeff @atom:675_b015_a015_d015_i015 @atom:675_b015_a015_d015_i015 0.25 3.55 + pair_coeff @atom:676_b048_a048_d048_i048 @atom:676_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:677_b048_a048_d048_i048 @atom:677_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:678_b048_a048_d048_i048 @atom:678_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:679_b048_a048_d048_i048 @atom:679_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:680_b048_a048_d048_i048 @atom:680_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:681_b049_a049_d049_i049 @atom:681_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:682_b049_a049_d049_i049 @atom:682_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:683_b048_a048_d048_i048 @atom:683_b048_a048_d048_i048 0.05 3.55 + pair_coeff @atom:684_b055_a055_d055_i055 @atom:684_b055_a055_d055_i055 0.17 3.25 + pair_coeff @atom:685_b045_a045_d045_i045 @atom:685_b045_a045_d045_i045 0.0 0.0 + pair_coeff @atom:686_b045_a045_d045_i045 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@atom:698_b013_a013_d013_i013 0.066 3.3 + pair_coeff @atom:699_b013_a013_d013_i013 @atom:699_b013_a013_d013_i013 0.066 3.3 + pair_coeff @atom:700_b046_a046_d046_i046 @atom:700_b046_a046_d046_i046 0.015 2.5 + pair_coeff @atom:701_b102_a102_d102_i102 @atom:701_b102_a102_d102_i102 0.12 3.25 + pair_coeff @atom:702_b103_a103_d103_i103 @atom:702_b103_a103_d103_i103 0.17 2.96 + pair_coeff @atom:703_b013_a013_d013_i013 @atom:703_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:704_b046_a046_d046_i046 @atom:704_b046_a046_d046_i046 0.015 2.5 + pair_coeff @atom:705_b013_a013_d013_i013 @atom:705_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:706_b013_a013_d013_i013 @atom:706_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:707_b013_a013_d013_i013 @atom:707_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:708_b102_a102_d102_i102 @atom:708_b102_a102_d102_i102 0.12 3.25 + pair_coeff @atom:709_b048_a048_d048_i048 @atom:709_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:710_b013_a013_d013_i013 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@atom:842_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:843_b024_a024_d024_i024 @atom:843_b024_a024_d024_i024 0.17 3.25 + pair_coeff @atom:844_b048_a048_d048_i048 @atom:844_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:845_b003_a003_d003_i003 @atom:845_b003_a003_d003_i003 0.105 3.75 + pair_coeff @atom:846_b004_a004_d004_i004 @atom:846_b004_a004_d004_i004 0.21 2.96 + pair_coeff @atom:847_b107_a107_d107_i107 @atom:847_b107_a107_d107_i107 0.17 3.25 + pair_coeff @atom:848_b013_a013_d013_i013 @atom:848_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:849_b013_a013_d013_i013 @atom:849_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:850_b013_a013_d013_i013 @atom:850_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:851_b013_a013_d013_i013 @atom:851_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:852_b046_a046_d046_i046 @atom:852_b046_a046_d046_i046 0.015 2.42 + pair_coeff @atom:853_b003_a003_d003_i003 @atom:853_b003_a003_d003_i003 0.105 3.75 + pair_coeff @atom:854_b004_a004_d004_i004 @atom:854_b004_a004_d004_i004 0.21 2.96 + pair_coeff @atom:855_b046_a046_d046_i046 @atom:855_b046_a046_d046_i046 0.015 2.42 + pair_coeff @atom:856_b013_a013_d013_i013 @atom:856_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:857_b013_a013_d013_i013 @atom:857_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:858_b013_a013_d013_i013 @atom:858_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:859_b013_a013_d013_i013 @atom:859_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:860_b013_a013_d013_i013 @atom:860_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:861_b013_a013_d013_i013 @atom:861_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:862_b013_a013_d013_i013 @atom:862_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:863_b013_a013_d013_i013 @atom:863_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:864_b013_a013_d013_i013 @atom:864_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:865_b013_a013_d013_i013 @atom:865_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:866_b108_a108_d108_i108 @atom:866_b108_a108_d108_i108 0.1 4.0 + pair_coeff @atom:867_b108_a108_d108_i108 @atom:867_b108_a108_d108_i108 0.1 4.0 + pair_coeff @atom:868_b108_a108_d108_i108 @atom:868_b108_a108_d108_i108 0.1 4.0 + pair_coeff @atom:869_b108_a108_d108_i108 @atom:869_b108_a108_d108_i108 0.1 4.0 + pair_coeff @atom:870_b045_a045_d045_i045 @atom:870_b045_a045_d045_i045 0.03 2.5 + pair_coeff @atom:871_b013_a013_d013_i013 @atom:871_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:872_b013_a013_d013_i013 @atom:872_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:873_b013_a013_d013_i013 @atom:873_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:874_b013_a013_d013_i013 @atom:874_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:875_b001_a001_d001_i001 @atom:875_b001_a001_d001_i001 0.72 3.08 + pair_coeff @atom:876_b021_a021_d021_i021 @atom:876_b021_a021_d021_i021 0.11779 4.18 + pair_coeff @atom:877_b065_a065_d065_i065 @atom:877_b065_a065_d065_i065 0.09 4.51 + pair_coeff @atom:878_b066_a066_d066_i066 @atom:878_b066_a066_d066_i066 0.07 5.15 + pair_coeff @atom:879_b068_a068_d068_i068 @atom:879_b068_a068_d068_i068 0.018279 2.7 + pair_coeff @atom:880_b069_a069_d069_i069 @atom:880_b069_a069_d069_i069 0.002772 3.35 + pair_coeff @atom:881_b070_a070_d070_i070 @atom:881_b070_a070_d070_i070 0.000328 4.06 + pair_coeff @atom:882_b071_a071_d071_i071 @atom:882_b071_a071_d071_i071 0.000171 4.32 + pair_coeff @atom:883_b072_a072_d072_i072 @atom:883_b072_a072_d072_i072 8.1e-05 4.82 + pair_coeff @atom:884_b073_a073_d073_i073 @atom:884_b073_a073_d073_i073 0.875044 2.91 + pair_coeff @atom:885_b074_a074_d074_i074 @atom:885_b074_a074_d074_i074 0.449657 3.47 + pair_coeff @atom:886_b075_a075_d075_i075 @atom:886_b075_a075_d075_i075 0.118226 3.82 + pair_coeff @atom:887_b076_a076_d076_i076 @atom:887_b076_a076_d076_i076 0.047096 4.18 + pair_coeff @atom:888_b013_a013_d013_i013 @atom:888_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:889_b013_a013_d013_i013 @atom:889_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:890_b013_a013_d013_i013 @atom:890_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:891_b013_a013_d013_i013 @atom:891_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:892_b046_a046_d046_i046 @atom:892_b046_a046_d046_i046 0.03 2.5 + pair_coeff @atom:893_b053_a053_d053_i053 @atom:893_b053_a053_d053_i053 0.17 3.25 + pair_coeff @atom:894_b048_a048_d048_i048 @atom:894_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:895_b053_a053_d053_i053 @atom:895_b053_a053_d053_i053 0.17 3.25 + pair_coeff @atom:896_b048_a048_d048_i048 @atom:896_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:897_b109_a109_d109_i109 @atom:897_b109_a109_d109_i109 0.076 3.55 + pair_coeff @atom:898_b109_a109_d109_i109 @atom:898_b109_a109_d109_i109 0.076 3.55 + pair_coeff @atom:899_b046_a046_d046_i046 @atom:899_b046_a046_d046_i046 0.03 2.42 + pair_coeff @atom:900_b047_a047_d047_i047 @atom:900_b047_a047_d047_i047 0.086 3.3 + pair_coeff @atom:901_b047_a047_d047_i047 @atom:901_b047_a047_d047_i047 0.086 3.3 + pair_coeff @atom:902_b047_a047_d047_i047 @atom:902_b047_a047_d047_i047 0.086 3.3 + pair_coeff @atom:903_b110_a110_d110_i110 @atom:903_b110_a110_d110_i110 0.086 3.3 + pair_coeff @atom:904_b110_a110_d110_i110 @atom:904_b110_a110_d110_i110 0.086 3.3 + pair_coeff @atom:905_b004_a004_d004_i004 @atom:905_b004_a004_d004_i004 0.21 2.96 + pair_coeff @atom:906_b013_a013_d013_i013 @atom:906_b013_a013_d013_i013 0.066 3.5 } #(end of pair_coeffs) @@ -3689,388 +3702,388 @@ OPLSAA { # ------- Bonded Interactions: ------- # http://lammps.sandia.gov/doc/bond_harmonic.html # Syntax: - # bond_coeff BondTypeName BondStyle parameters... + # bond_coeff BondTypeName parameters... write_once("In Settings") { - bond_coeff @bond:1-2 harmonic 367.0 1.38 - bond_coeff @bond:1-3 harmonic 420.0 1.357 - bond_coeff @bond:1-13 harmonic 367.0 1.36 - bond_coeff @bond:1-19 harmonic 450.0 1.279 - bond_coeff @bond:1-25 harmonic 300.0 0.3 - bond_coeff @bond:1-47 harmonic 420.0 1.34 - bond_coeff @bond:1-48 harmonic 420.0 1.354 - bond_coeff @bond:1-82 harmonic 420.0 1.354 - bond_coeff @bond:1-83 harmonic 420.0 1.354 - bond_coeff @bond:1-84 harmonic 420.0 1.354 - bond_coeff @bond:1-87 harmonic 420.0 1.354 - bond_coeff @bond:1-88 harmonic 420.0 1.354 - bond_coeff @bond:1-108 harmonic 461.0 1.57 - bond_coeff @bond:2-2 harmonic 260.0 1.526 - bond_coeff @bond:2-3 harmonic 317.0 1.522 - bond_coeff @bond:2-5 harmonic 386.0 1.425 - bond_coeff @bond:2-6 harmonic 260.0 1.526 - bond_coeff @bond:2-10 harmonic 260.0 1.526 - bond_coeff @bond:2-11 harmonic 317.0 1.5 - bond_coeff @bond:2-12 harmonic 317.0 1.51 - bond_coeff @bond:2-13 harmonic 260.0 1.526 - bond_coeff @bond:2-14 harmonic 317.0 1.5 - bond_coeff @bond:2-15 harmonic 222.0 1.81 - bond_coeff @bond:2-16 harmonic 222.0 1.81 - bond_coeff @bond:2-20 harmonic 320.0 1.425 - bond_coeff @bond:2-24 harmonic 337.0 1.449 - bond_coeff @bond:2-44 harmonic 382.0 1.448 - bond_coeff @bond:2-48 harmonic 317.0 1.51 - bond_coeff @bond:2-51 harmonic 260.0 1.526 - bond_coeff @bond:2-53 harmonic 367.0 1.471 - bond_coeff @bond:2-55 harmonic 337.0 1.463 - bond_coeff @bond:2-80 harmonic 317.0 1.495 - bond_coeff @bond:3-3 harmonic 350.0 1.51 - bond_coeff @bond:3-4 harmonic 570.0 1.229 - bond_coeff @bond:3-5 harmonic 450.0 1.364 - bond_coeff @bond:3-6 harmonic 317.0 1.522 - bond_coeff @bond:3-10 harmonic 317.0 1.522 - bond_coeff @bond:3-12 harmonic 469.0 1.4 - bond_coeff @bond:3-13 harmonic 317.0 1.522 - bond_coeff @bond:3-19 harmonic 400.0 1.444 - bond_coeff @bond:3-20 harmonic 214.0 1.327 - bond_coeff @bond:3-21 harmonic 300.0 1.79 - bond_coeff @bond:3-24 harmonic 490.0 1.335 - bond_coeff @bond:3-44 harmonic 317.0 1.522 - bond_coeff @bond:3-46 harmonic 340.0 1.09 - bond_coeff @bond:3-47 harmonic 410.0 1.444 - bond_coeff @bond:3-48 harmonic 400.0 1.49 - bond_coeff @bond:3-50 harmonic 385.0 1.46 - bond_coeff @bond:3-52 harmonic 656.0 1.25 - bond_coeff @bond:3-56 harmonic 457.0 1.358 - bond_coeff @bond:3-57 harmonic 418.0 1.388 - bond_coeff @bond:3-60 harmonic 447.0 1.419 - bond_coeff @bond:3-65 harmonic 300.0 1.98 - bond_coeff @bond:3-84 harmonic 400.0 1.49 - bond_coeff @bond:3-86 harmonic 385.0 1.46 - bond_coeff @bond:3-105 harmonic 424.0 1.383 - bond_coeff @bond:3-107 harmonic 490.0 1.335 - bond_coeff @bond:4-25 harmonic 553.0 0.3 - bond_coeff @bond:4-64 harmonic 525.0 1.48 - bond_coeff @bond:4-89 harmonic 570.0 1.229 - bond_coeff @bond:4-110 harmonic 700.0 1.171 - bond_coeff @bond:5-6 harmonic 386.0 1.425 - bond_coeff @bond:5-7 harmonic 553.0 0.945 - bond_coeff @bond:5-10 harmonic 386.0 1.425 - bond_coeff @bond:5-13 harmonic 320.0 1.41 - bond_coeff @bond:5-20 harmonic 250.0 1.47 - bond_coeff @bond:5-24 harmonic 400.0 1.38 - bond_coeff @bond:5-25 harmonic 340.0 0.3 - bond_coeff @bond:5-44 harmonic 320.0 1.45 - bond_coeff @bond:5-47 harmonic 450.0 1.37 - bond_coeff @bond:5-48 harmonic 450.0 1.364 - bond_coeff @bond:5-51 harmonic 320.0 1.38 - bond_coeff @bond:5-64 harmonic 230.0 1.61 - bond_coeff @bond:5-79 harmonic 450.0 1.67 - bond_coeff @bond:5-106 harmonic 94.0 1.8 - bond_coeff @bond:5-108 harmonic 374.0 1.64 - bond_coeff @bond:6-6 harmonic 260.0 1.526 - bond_coeff @bond:6-10 harmonic 260.0 1.526 - bond_coeff @bond:6-11 harmonic 317.0 1.5 - bond_coeff @bond:6-13 harmonic 260.0 1.526 - bond_coeff @bond:6-14 harmonic 317.0 1.5 - bond_coeff @bond:6-15 harmonic 222.0 1.81 - bond_coeff @bond:6-16 harmonic 222.0 1.81 - bond_coeff @bond:6-20 harmonic 320.0 1.425 - bond_coeff @bond:6-24 harmonic 337.0 1.449 - bond_coeff @bond:6-44 harmonic 382.0 1.448 - bond_coeff @bond:6-47 harmonic 317.0 1.51 - bond_coeff @bond:6-51 harmonic 260.0 1.526 - bond_coeff @bond:6-53 harmonic 367.0 1.471 - bond_coeff @bond:6-55 harmonic 337.0 1.463 - bond_coeff @bond:6-79 harmonic 222.0 1.81 - bond_coeff @bond:6-105 harmonic 337.0 1.475 - bond_coeff @bond:7-20 harmonic 553.0 0.945 - bond_coeff @bond:7-25 harmonic 340.0 0.1 - bond_coeff @bond:9-9 harmonic 530.0 1.34 - bond_coeff @bond:9-11 harmonic 530.0 1.34 - bond_coeff @bond:9-14 harmonic 530.0 1.34 - bond_coeff @bond:10-10 harmonic 260.0 1.526 - bond_coeff @bond:10-11 harmonic 317.0 1.5 - bond_coeff @bond:10-14 harmonic 317.0 1.5 - bond_coeff @bond:10-20 harmonic 320.0 1.425 - bond_coeff @bond:10-24 harmonic 337.0 1.449 - bond_coeff @bond:10-44 harmonic 382.0 1.448 - bond_coeff @bond:10-105 harmonic 337.0 1.475 - bond_coeff @bond:11-11 harmonic 530.0 1.34 - bond_coeff @bond:11-13 harmonic 317.0 1.5 - bond_coeff @bond:11-14 harmonic 530.0 1.34 - bond_coeff @bond:11-79 harmonic 222.0 1.76 - bond_coeff @bond:12-12 harmonic 469.0 1.4 - bond_coeff @bond:12-48 harmonic 469.0 1.4 - bond_coeff @bond:12-60 harmonic 469.0 1.4 - bond_coeff @bond:12-81 harmonic 469.0 1.4 - bond_coeff @bond:13-13 harmonic 268.0 1.529 - bond_coeff @bond:13-14 harmonic 317.0 1.5 - bond_coeff @bond:13-15 harmonic 222.0 1.81 - bond_coeff @bond:13-16 harmonic 222.0 1.81 - bond_coeff @bond:13-18 harmonic 390.0 1.43 - bond_coeff @bond:13-19 harmonic 390.0 1.47 - bond_coeff @bond:13-20 harmonic 320.0 1.41 - bond_coeff @bond:13-21 harmonic 245.0 1.781 - bond_coeff @bond:13-22 harmonic 340.0 1.79 - bond_coeff @bond:13-24 harmonic 337.0 1.449 - bond_coeff @bond:13-25 harmonic 340.0 0.3 - bond_coeff @bond:13-44 harmonic 382.0 1.448 - bond_coeff @bond:13-46 harmonic 340.0 1.09 - bond_coeff @bond:13-47 harmonic 317.0 1.51 - bond_coeff @bond:13-48 harmonic 317.0 1.51 - bond_coeff @bond:13-50 harmonic 317.0 1.51 - bond_coeff @bond:13-51 harmonic 268.0 1.529 - bond_coeff @bond:13-53 harmonic 367.0 1.471 - bond_coeff @bond:13-55 harmonic 337.0 1.463 - bond_coeff @bond:13-56 harmonic 337.0 1.449 - bond_coeff @bond:13-57 harmonic 337.0 1.475 - bond_coeff @bond:13-60 harmonic 317.0 1.51 - bond_coeff @bond:13-64 harmonic 212.0 1.843 - bond_coeff @bond:13-65 harmonic 245.0 1.945 - bond_coeff @bond:13-66 harmonic 200.0 2.19 - bond_coeff @bond:13-79 harmonic 340.0 1.77 - bond_coeff @bond:13-80 harmonic 317.0 1.495 - bond_coeff @bond:13-83 harmonic 317.0 1.504 - bond_coeff @bond:13-84 harmonic 317.0 1.504 - bond_coeff @bond:13-85 harmonic 317.0 1.504 - bond_coeff @bond:13-87 harmonic 317.0 1.495 - bond_coeff @bond:13-90 harmonic 337.0 1.449 - bond_coeff @bond:13-91 harmonic 280.0 1.51 - bond_coeff @bond:13-95 harmonic 532.8 1.46 - bond_coeff @bond:13-101 harmonic 382.0 1.448 - bond_coeff @bond:13-102 harmonic 375.0 1.49 - bond_coeff @bond:13-104 harmonic 212.0 1.82 - bond_coeff @bond:13-105 harmonic 337.0 1.475 - bond_coeff @bond:13-107 harmonic 337.0 1.449 - bond_coeff @bond:13-108 harmonic 187.0 1.86 - bond_coeff @bond:13-109 harmonic 317.0 1.51 - bond_coeff @bond:14-14 harmonic 530.0 1.34 - bond_coeff @bond:15-17 harmonic 274.0 1.336 - bond_coeff @bond:15-48 harmonic 250.0 1.74 - bond_coeff @bond:16-16 harmonic 166.0 2.038 - bond_coeff @bond:16-19 harmonic 300.0 1.685 - bond_coeff @bond:16-24 harmonic 250.0 1.73 - bond_coeff @bond:16-25 harmonic 340.0 0.5 - bond_coeff @bond:16-47 harmonic 250.0 1.76 - bond_coeff @bond:16-48 harmonic 250.0 1.76 - bond_coeff @bond:16-61 harmonic 250.0 1.73 - bond_coeff @bond:16-82 harmonic 250.0 1.76 - bond_coeff @bond:16-84 harmonic 250.0 1.74 - bond_coeff @bond:16-91 harmonic 222.0 1.81 - bond_coeff @bond:16-108 harmonic 144.0 2.15 - bond_coeff @bond:17-25 harmonic 340.0 0.1 - bond_coeff @bond:18-18 harmonic 550.0 1.12 - bond_coeff @bond:18-19 harmonic 650.0 1.157 - bond_coeff @bond:18-48 harmonic 400.0 1.41 - bond_coeff @bond:18-56 harmonic 550.0 1.24 - bond_coeff @bond:19-19 harmonic 1150.0 1.21 - bond_coeff @bond:19-21 harmonic 330.0 1.637 - bond_coeff @bond:19-46 harmonic 420.0 1.08 - bond_coeff @bond:19-47 harmonic 400.0 1.426 - bond_coeff @bond:19-48 harmonic 400.0 1.451 - bond_coeff @bond:19-50 harmonic 400.0 1.426 - bond_coeff @bond:19-65 harmonic 330.0 1.784 - bond_coeff @bond:19-88 harmonic 400.0 1.451 - bond_coeff @bond:19-91 harmonic 400.0 1.451 - bond_coeff @bond:20-20 harmonic 250.0 1.47 - bond_coeff @bond:20-21 harmonic 200.0 1.69 - bond_coeff @bond:20-24 harmonic 320.0 1.45 - bond_coeff @bond:20-25 harmonic 340.0 0.3 - bond_coeff @bond:20-44 harmonic 320.0 1.45 - bond_coeff @bond:20-47 harmonic 450.0 1.37 - bond_coeff @bond:20-48 harmonic 450.0 1.364 - bond_coeff @bond:20-51 harmonic 320.0 1.38 - bond_coeff @bond:20-60 harmonic 340.0 1.36 - bond_coeff @bond:20-61 harmonic 462.0 1.399 - bond_coeff @bond:20-64 harmonic 230.0 1.61 - bond_coeff @bond:20-82 harmonic 462.0 1.357 - bond_coeff @bond:20-84 harmonic 340.0 1.36 - bond_coeff @bond:20-108 harmonic 374.0 1.64 - bond_coeff @bond:21-25 harmonic 300.0 0.3 - bond_coeff @bond:21-47 harmonic 300.0 1.725 - bond_coeff @bond:21-48 harmonic 300.0 1.725 - bond_coeff @bond:21-82 harmonic 300.0 1.725 - bond_coeff @bond:21-83 harmonic 300.0 1.725 - bond_coeff @bond:21-84 harmonic 300.0 1.725 - bond_coeff @bond:21-87 harmonic 300.0 1.725 - bond_coeff @bond:21-88 harmonic 300.0 1.725 - bond_coeff @bond:21-108 harmonic 223.0 2.02 - bond_coeff @bond:22-23 harmonic 700.0 1.53 - bond_coeff @bond:22-25 harmonic 340.0 0.5 - bond_coeff @bond:23-25 harmonic 340.0 0.3 - bond_coeff @bond:23-79 harmonic 700.0 1.44 - bond_coeff @bond:24-25 harmonic 367.0 0.3 - bond_coeff @bond:24-45 harmonic 434.0 1.01 - bond_coeff @bond:24-48 harmonic 427.0 1.381 - bond_coeff @bond:24-59 harmonic 427.0 1.381 - bond_coeff @bond:24-79 harmonic 434.0 1.67 - bond_coeff @bond:24-84 harmonic 427.0 1.381 - bond_coeff @bond:24-88 harmonic 427.0 1.381 - bond_coeff @bond:24-91 harmonic 337.0 1.449 - bond_coeff @bond:24-103 harmonic 500.0 1.27 - bond_coeff @bond:24-106 harmonic 40.0 2.05 - bond_coeff @bond:25-25 harmonic 340.0 0.3 - bond_coeff @bond:25-44 harmonic 340.0 0.3 - bond_coeff @bond:25-45 harmonic 340.0 0.1 - bond_coeff @bond:25-46 harmonic 340.0 0.3 - bond_coeff @bond:25-47 harmonic 340.0 0.3 - bond_coeff @bond:25-48 harmonic 367.0 0.3 - bond_coeff @bond:25-49 harmonic 340.0 0.3 - bond_coeff @bond:25-53 harmonic 340.0 0.3 - bond_coeff @bond:25-56 harmonic 367.0 0.3 - bond_coeff @bond:25-61 harmonic 367.0 0.3 - bond_coeff @bond:25-65 harmonic 300.0 0.3 - bond_coeff @bond:25-103 harmonic 340.0 0.1 - bond_coeff @bond:31-32 harmonic 600.0 0.9572 - bond_coeff @bond:31-33 harmonic 900.0 0.15 - bond_coeff @bond:31-106 harmonic 40.0 2.05 - bond_coeff @bond:34-35 harmonic 529.6 0.9572 - bond_coeff @bond:36-37 harmonic 600.0 0.9572 - bond_coeff @bond:36-38 harmonic 900.0 0.175 - bond_coeff @bond:39-40 harmonic 600.0 0.9572 - bond_coeff @bond:39-41 harmonic 900.0 0.7 - bond_coeff @bond:42-43 harmonic 600.0 1.0 - bond_coeff @bond:44-44 harmonic 350.0 1.445 - bond_coeff @bond:44-45 harmonic 434.0 1.01 - bond_coeff @bond:44-48 harmonic 481.0 1.34 - bond_coeff @bond:44-79 harmonic 340.0 1.77 - bond_coeff @bond:44-91 harmonic 382.0 1.448 - bond_coeff @bond:44-108 harmonic 266.0 1.74 - bond_coeff @bond:45-53 harmonic 434.0 1.01 - bond_coeff @bond:45-55 harmonic 434.0 1.01 - bond_coeff @bond:45-56 harmonic 434.0 1.01 - bond_coeff @bond:45-57 harmonic 434.0 1.01 - bond_coeff @bond:45-101 harmonic 434.0 1.01 - bond_coeff @bond:45-105 harmonic 434.0 1.01 - bond_coeff @bond:45-108 harmonic 166.0 1.48 - bond_coeff @bond:46-47 harmonic 340.0 1.08 - bond_coeff @bond:46-50 harmonic 340.0 1.08 - bond_coeff @bond:46-51 harmonic 340.0 1.09 - bond_coeff @bond:46-80 harmonic 340.0 1.08 - bond_coeff @bond:46-91 harmonic 340.0 1.088 - bond_coeff @bond:46-95 harmonic 532.8 1.084 - bond_coeff @bond:46-108 harmonic 166.0 1.48 - bond_coeff @bond:46-109 harmonic 340.0 1.08 - bond_coeff @bond:47-47 harmonic 549.0 1.34 - bond_coeff @bond:47-48 harmonic 427.0 1.433 - bond_coeff @bond:47-50 harmonic 549.0 1.34 - bond_coeff @bond:47-57 harmonic 448.0 1.365 - bond_coeff @bond:47-58 harmonic 367.0 1.08 - bond_coeff @bond:47-65 harmonic 300.0 1.9 - bond_coeff @bond:47-66 harmonic 250.0 2.08 - bond_coeff @bond:47-86 harmonic 385.0 1.46 - bond_coeff @bond:47-91 harmonic 317.0 1.51 - bond_coeff @bond:47-105 harmonic 448.0 1.365 - bond_coeff @bond:47-110 harmonic 700.0 1.305 - bond_coeff @bond:48-48 harmonic 469.0 1.4 - bond_coeff @bond:48-49 harmonic 367.0 1.08 - 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1.394 - bond_coeff @bond:61-88 harmonic 410.0 1.32 - bond_coeff @bond:62-63 harmonic 367.0 1.08 - bond_coeff @bond:62-105 harmonic 440.0 1.371 - bond_coeff @bond:63-82 harmonic 367.0 1.08 - bond_coeff @bond:64-108 harmonic 108.0 2.25 - bond_coeff @bond:65-82 harmonic 300.0 1.87 - bond_coeff @bond:65-83 harmonic 300.0 1.87 - bond_coeff @bond:65-84 harmonic 300.0 1.87 - bond_coeff @bond:65-87 harmonic 300.0 1.87 - bond_coeff @bond:65-88 harmonic 300.0 1.87 - bond_coeff @bond:65-108 harmonic 151.0 2.19 - bond_coeff @bond:66-82 harmonic 250.0 2.08 - bond_coeff @bond:66-83 harmonic 250.0 2.08 - bond_coeff @bond:66-84 harmonic 250.0 2.08 - bond_coeff @bond:66-87 harmonic 250.0 2.08 - bond_coeff @bond:66-88 harmonic 250.0 2.08 - bond_coeff @bond:66-108 harmonic 108.0 2.44 - bond_coeff @bond:77-78 harmonic 500.0 1.8 - bond_coeff @bond:80-84 harmonic 546.0 1.352 - bond_coeff @bond:82-86 harmonic 385.0 1.46 - bond_coeff @bond:82-87 harmonic 520.0 1.37 - bond_coeff @bond:83-84 harmonic 520.0 1.37 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@bond:047_058 367.0 1.08 + bond_coeff @bond:047_065 300.0 1.9 + bond_coeff @bond:047_066 250.0 2.08 + bond_coeff @bond:047_086 385.0 1.46 + bond_coeff @bond:047_091 317.0 1.51 + bond_coeff @bond:047_105 448.0 1.365 + bond_coeff @bond:047_110 700.0 1.305 + bond_coeff @bond:048_048 469.0 1.4 + bond_coeff @bond:048_049 367.0 1.08 + bond_coeff @bond:048_050 427.0 1.433 + bond_coeff @bond:048_053 400.0 1.45 + bond_coeff @bond:048_055 481.0 1.34 + bond_coeff @bond:048_056 483.0 1.339 + bond_coeff @bond:048_057 427.0 1.381 + bond_coeff @bond:048_060 469.0 1.404 + bond_coeff @bond:048_061 414.0 1.391 + bond_coeff @bond:048_064 220.0 1.78 + bond_coeff @bond:048_065 300.0 1.87 + bond_coeff @bond:048_066 250.0 2.08 + bond_coeff @bond:048_079 340.0 1.77 + bond_coeff @bond:048_081 469.0 1.4 + bond_coeff @bond:048_084 546.0 1.367 + bond_coeff @bond:048_086 469.0 1.4 + bond_coeff @bond:048_088 469.0 1.421 + bond_coeff @bond:048_091 317.0 1.49 + bond_coeff @bond:048_101 382.0 1.385 + bond_coeff @bond:048_102 400.0 1.46 + bond_coeff @bond:048_109 427.0 1.433 + bond_coeff @bond:049_059 367.0 1.08 + bond_coeff @bond:049_062 340.0 1.08 + bond_coeff @bond:049_082 367.0 1.08 + bond_coeff @bond:049_083 367.0 1.08 + bond_coeff @bond:049_084 367.0 1.08 + bond_coeff @bond:049_085 367.0 1.08 + bond_coeff @bond:049_087 367.0 1.08 + bond_coeff @bond:049_088 367.0 1.08 + bond_coeff @bond:050_050 385.0 1.46 + bond_coeff @bond:050_056 457.0 1.29 + bond_coeff @bond:050_084 549.0 1.365 + bond_coeff @bond:050_109 385.0 1.46 + bond_coeff @bond:051_105 337.0 1.475 + bond_coeff @bond:052_064 525.0 1.48 + bond_coeff @bond:053_054 434.0 1.01 + bond_coeff @bond:054_055 434.0 1.01 + bond_coeff @bond:055_059 481.0 1.34 + bond_coeff @bond:055_082 481.0 1.34 + bond_coeff @bond:056_056 500.0 1.32 + bond_coeff @bond:056_059 502.0 1.324 + bond_coeff @bond:056_060 461.0 1.354 + bond_coeff @bond:056_082 461.0 1.354 + bond_coeff @bond:056_086 483.0 1.339 + bond_coeff @bond:056_103 550.0 1.21 + bond_coeff @bond:056_109 457.0 1.29 + bond_coeff @bond:057_060 436.0 1.374 + bond_coeff @bond:057_061 400.0 1.349 + bond_coeff @bond:057_062 440.0 1.371 + bond_coeff @bond:057_081 428.0 1.38 + bond_coeff @bond:057_082 477.0 1.343 + bond_coeff @bond:057_084 427.0 1.381 + bond_coeff @bond:057_085 427.0 1.381 + bond_coeff @bond:057_086 385.0 1.44 + bond_coeff @bond:058_083 367.0 1.08 + bond_coeff @bond:058_084 367.0 1.08 + bond_coeff @bond:059_063 367.0 1.08 + bond_coeff @bond:060_060 520.0 1.37 + bond_coeff @bond:060_061 414.0 1.391 + bond_coeff @bond:060_080 388.0 1.459 + bond_coeff @bond:060_081 447.0 1.419 + bond_coeff @bond:060_087 469.0 1.424 + bond_coeff @bond:060_105 436.0 1.374 + bond_coeff @bond:061_061 400.0 1.28 + bond_coeff @bond:061_062 529.0 1.304 + bond_coeff @bond:061_082 488.0 1.335 + bond_coeff @bond:061_083 410.0 1.394 + bond_coeff @bond:061_084 410.0 1.394 + bond_coeff @bond:061_088 410.0 1.32 + bond_coeff @bond:062_063 367.0 1.08 + bond_coeff @bond:062_105 440.0 1.371 + bond_coeff @bond:063_082 367.0 1.08 + bond_coeff @bond:064_108 108.0 2.25 + bond_coeff @bond:065_082 300.0 1.87 + bond_coeff @bond:065_083 300.0 1.87 + bond_coeff @bond:065_084 300.0 1.87 + bond_coeff @bond:065_087 300.0 1.87 + bond_coeff @bond:065_088 300.0 1.87 + bond_coeff @bond:065_108 151.0 2.19 + bond_coeff @bond:066_082 250.0 2.08 + bond_coeff @bond:066_083 250.0 2.08 + bond_coeff @bond:066_084 250.0 2.08 + bond_coeff @bond:066_087 250.0 2.08 + bond_coeff @bond:066_088 250.0 2.08 + bond_coeff @bond:066_108 108.0 2.44 + bond_coeff @bond:077_078 500.0 1.8 + bond_coeff @bond:080_084 546.0 1.352 + bond_coeff @bond:082_086 385.0 1.46 + bond_coeff @bond:082_087 520.0 1.37 + bond_coeff @bond:083_084 520.0 1.37 + bond_coeff @bond:083_086 385.0 1.46 + bond_coeff @bond:084_084 512.0 1.375 + bond_coeff @bond:084_086 385.0 1.46 + bond_coeff @bond:084_087 546.0 1.367 + bond_coeff @bond:084_088 520.0 1.37 + bond_coeff @bond:085_085 520.0 1.37 + bond_coeff @bond:086_086 385.0 1.46 + bond_coeff @bond:086_087 385.0 1.46 + bond_coeff @bond:086_088 385.0 1.46 + bond_coeff @bond:087_087 469.0 1.424 + bond_coeff @bond:087_088 469.0 1.424 + bond_coeff @bond:089_090 490.0 1.335 + bond_coeff @bond:089_091 317.0 1.522 + bond_coeff @bond:090_091 337.0 1.449 + bond_coeff @bond:091_091 260.0 1.52 + bond_coeff @bond:102_103 550.0 1.225 + bond_coeff @bond:108_108 94.0 2.32 + bond_coeff @bond:109_109 549.0 1.345 } #(end of bond_coeffs) # Rules for assigning bond types by atom type: @@ -4078,385 +4091,385 @@ OPLSAA { # (* = wildcard) write_once("Data Bonds By Type") { - @bond:1-2 @atom:*_b1_a*_d*_i* @atom:*_b2_a*_d*_i* - @bond:1-3 @atom:*_b1_a*_d*_i* @atom:*_b3_a*_d*_i* - @bond:1-13 @atom:*_b1_a*_d*_i* @atom:*_b13_a*_d*_i* - @bond:1-19 @atom:*_b1_a*_d*_i* @atom:*_b19_a*_d*_i* - @bond:1-25 @atom:*_b1_a*_d*_i* @atom:*_b25_a*_d*_i* - @bond:1-47 @atom:*_b1_a*_d*_i* @atom:*_b47_a*_d*_i* - @bond:1-48 @atom:*_b1_a*_d*_i* @atom:*_b48_a*_d*_i* - @bond:1-82 @atom:*_b1_a*_d*_i* @atom:*_b82_a*_d*_i* - @bond:1-83 @atom:*_b1_a*_d*_i* @atom:*_b83_a*_d*_i* - @bond:1-84 @atom:*_b1_a*_d*_i* @atom:*_b84_a*_d*_i* - @bond:1-87 @atom:*_b1_a*_d*_i* @atom:*_b87_a*_d*_i* - @bond:1-88 @atom:*_b1_a*_d*_i* @atom:*_b88_a*_d*_i* - @bond:1-108 @atom:*_b1_a*_d*_i* @atom:*_b108_a*_d*_i* - @bond:2-2 @atom:*_b2_a*_d*_i* @atom:*_b2_a*_d*_i* - @bond:2-3 @atom:*_b2_a*_d*_i* @atom:*_b3_a*_d*_i* - @bond:2-5 @atom:*_b2_a*_d*_i* @atom:*_b5_a*_d*_i* - @bond:2-6 @atom:*_b2_a*_d*_i* @atom:*_b6_a*_d*_i* - @bond:2-10 @atom:*_b2_a*_d*_i* @atom:*_b10_a*_d*_i* - @bond:2-11 @atom:*_b2_a*_d*_i* @atom:*_b11_a*_d*_i* - @bond:2-12 @atom:*_b2_a*_d*_i* @atom:*_b12_a*_d*_i* - @bond:2-13 @atom:*_b2_a*_d*_i* @atom:*_b13_a*_d*_i* - @bond:2-14 @atom:*_b2_a*_d*_i* @atom:*_b14_a*_d*_i* - @bond:2-15 @atom:*_b2_a*_d*_i* @atom:*_b15_a*_d*_i* - @bond:2-16 @atom:*_b2_a*_d*_i* @atom:*_b16_a*_d*_i* - @bond:2-20 @atom:*_b2_a*_d*_i* @atom:*_b20_a*_d*_i* - @bond:2-24 @atom:*_b2_a*_d*_i* @atom:*_b24_a*_d*_i* - @bond:2-44 @atom:*_b2_a*_d*_i* @atom:*_b44_a*_d*_i* - @bond:2-48 @atom:*_b2_a*_d*_i* @atom:*_b48_a*_d*_i* - @bond:2-51 @atom:*_b2_a*_d*_i* @atom:*_b51_a*_d*_i* - @bond:2-53 @atom:*_b2_a*_d*_i* @atom:*_b53_a*_d*_i* - @bond:2-55 @atom:*_b2_a*_d*_i* @atom:*_b55_a*_d*_i* - @bond:2-80 @atom:*_b2_a*_d*_i* @atom:*_b80_a*_d*_i* - @bond:3-3 @atom:*_b3_a*_d*_i* @atom:*_b3_a*_d*_i* - @bond:3-4 @atom:*_b3_a*_d*_i* @atom:*_b4_a*_d*_i* - @bond:3-5 @atom:*_b3_a*_d*_i* @atom:*_b5_a*_d*_i* - @bond:3-6 @atom:*_b3_a*_d*_i* @atom:*_b6_a*_d*_i* - @bond:3-10 @atom:*_b3_a*_d*_i* @atom:*_b10_a*_d*_i* - @bond:3-12 @atom:*_b3_a*_d*_i* @atom:*_b12_a*_d*_i* - @bond:3-13 @atom:*_b3_a*_d*_i* @atom:*_b13_a*_d*_i* - @bond:3-19 @atom:*_b3_a*_d*_i* @atom:*_b19_a*_d*_i* - @bond:3-20 @atom:*_b3_a*_d*_i* @atom:*_b20_a*_d*_i* - @bond:3-21 @atom:*_b3_a*_d*_i* @atom:*_b21_a*_d*_i* - @bond:3-24 @atom:*_b3_a*_d*_i* @atom:*_b24_a*_d*_i* - @bond:3-44 @atom:*_b3_a*_d*_i* @atom:*_b44_a*_d*_i* - @bond:3-46 @atom:*_b3_a*_d*_i* @atom:*_b46_a*_d*_i* - @bond:3-47 @atom:*_b3_a*_d*_i* @atom:*_b47_a*_d*_i* - @bond:3-48 @atom:*_b3_a*_d*_i* @atom:*_b48_a*_d*_i* - @bond:3-50 @atom:*_b3_a*_d*_i* @atom:*_b50_a*_d*_i* - @bond:3-52 @atom:*_b3_a*_d*_i* @atom:*_b52_a*_d*_i* - @bond:3-56 @atom:*_b3_a*_d*_i* @atom:*_b56_a*_d*_i* - @bond:3-57 @atom:*_b3_a*_d*_i* @atom:*_b57_a*_d*_i* - @bond:3-60 @atom:*_b3_a*_d*_i* @atom:*_b60_a*_d*_i* - @bond:3-65 @atom:*_b3_a*_d*_i* @atom:*_b65_a*_d*_i* - @bond:3-84 @atom:*_b3_a*_d*_i* @atom:*_b84_a*_d*_i* - @bond:3-86 @atom:*_b3_a*_d*_i* @atom:*_b86_a*_d*_i* - @bond:3-105 @atom:*_b3_a*_d*_i* @atom:*_b105_a*_d*_i* - @bond:3-107 @atom:*_b3_a*_d*_i* @atom:*_b107_a*_d*_i* - @bond:4-25 @atom:*_b4_a*_d*_i* @atom:*_b25_a*_d*_i* - @bond:4-64 @atom:*_b4_a*_d*_i* @atom:*_b64_a*_d*_i* - @bond:4-89 @atom:*_b4_a*_d*_i* @atom:*_b89_a*_d*_i* - @bond:4-110 @atom:*_b4_a*_d*_i* @atom:*_b110_a*_d*_i* - @bond:5-6 @atom:*_b5_a*_d*_i* @atom:*_b6_a*_d*_i* - @bond:5-7 @atom:*_b5_a*_d*_i* @atom:*_b7_a*_d*_i* - @bond:5-10 @atom:*_b5_a*_d*_i* @atom:*_b10_a*_d*_i* - @bond:5-13 @atom:*_b5_a*_d*_i* @atom:*_b13_a*_d*_i* - @bond:5-20 @atom:*_b5_a*_d*_i* @atom:*_b20_a*_d*_i* - @bond:5-24 @atom:*_b5_a*_d*_i* @atom:*_b24_a*_d*_i* - @bond:5-25 @atom:*_b5_a*_d*_i* @atom:*_b25_a*_d*_i* - @bond:5-44 @atom:*_b5_a*_d*_i* @atom:*_b44_a*_d*_i* - @bond:5-47 @atom:*_b5_a*_d*_i* @atom:*_b47_a*_d*_i* - @bond:5-48 @atom:*_b5_a*_d*_i* @atom:*_b48_a*_d*_i* - @bond:5-51 @atom:*_b5_a*_d*_i* @atom:*_b51_a*_d*_i* - @bond:5-64 @atom:*_b5_a*_d*_i* @atom:*_b64_a*_d*_i* - @bond:5-79 @atom:*_b5_a*_d*_i* @atom:*_b79_a*_d*_i* - @bond:5-106 @atom:*_b5_a*_d*_i* @atom:*_b106_a*_d*_i* - @bond:5-108 @atom:*_b5_a*_d*_i* @atom:*_b108_a*_d*_i* - @bond:6-6 @atom:*_b6_a*_d*_i* @atom:*_b6_a*_d*_i* - @bond:6-10 @atom:*_b6_a*_d*_i* @atom:*_b10_a*_d*_i* - @bond:6-11 @atom:*_b6_a*_d*_i* @atom:*_b11_a*_d*_i* - @bond:6-13 @atom:*_b6_a*_d*_i* @atom:*_b13_a*_d*_i* - @bond:6-14 @atom:*_b6_a*_d*_i* @atom:*_b14_a*_d*_i* - @bond:6-15 @atom:*_b6_a*_d*_i* @atom:*_b15_a*_d*_i* - @bond:6-16 @atom:*_b6_a*_d*_i* @atom:*_b16_a*_d*_i* - @bond:6-20 @atom:*_b6_a*_d*_i* @atom:*_b20_a*_d*_i* - @bond:6-24 @atom:*_b6_a*_d*_i* @atom:*_b24_a*_d*_i* - @bond:6-44 @atom:*_b6_a*_d*_i* @atom:*_b44_a*_d*_i* - @bond:6-47 @atom:*_b6_a*_d*_i* @atom:*_b47_a*_d*_i* - @bond:6-51 @atom:*_b6_a*_d*_i* @atom:*_b51_a*_d*_i* - @bond:6-53 @atom:*_b6_a*_d*_i* @atom:*_b53_a*_d*_i* - @bond:6-55 @atom:*_b6_a*_d*_i* @atom:*_b55_a*_d*_i* - @bond:6-79 @atom:*_b6_a*_d*_i* @atom:*_b79_a*_d*_i* - @bond:6-105 @atom:*_b6_a*_d*_i* @atom:*_b105_a*_d*_i* - @bond:7-20 @atom:*_b7_a*_d*_i* @atom:*_b20_a*_d*_i* - @bond:7-25 @atom:*_b7_a*_d*_i* @atom:*_b25_a*_d*_i* - @bond:9-9 @atom:*_b9_a*_d*_i* @atom:*_b9_a*_d*_i* - @bond:9-11 @atom:*_b9_a*_d*_i* @atom:*_b11_a*_d*_i* - @bond:9-14 @atom:*_b9_a*_d*_i* @atom:*_b14_a*_d*_i* - @bond:10-10 @atom:*_b10_a*_d*_i* @atom:*_b10_a*_d*_i* - @bond:10-11 @atom:*_b10_a*_d*_i* @atom:*_b11_a*_d*_i* - @bond:10-14 @atom:*_b10_a*_d*_i* @atom:*_b14_a*_d*_i* - @bond:10-20 @atom:*_b10_a*_d*_i* @atom:*_b20_a*_d*_i* - @bond:10-24 @atom:*_b10_a*_d*_i* @atom:*_b24_a*_d*_i* - @bond:10-44 @atom:*_b10_a*_d*_i* @atom:*_b44_a*_d*_i* - @bond:10-105 @atom:*_b10_a*_d*_i* @atom:*_b105_a*_d*_i* - @bond:11-11 @atom:*_b11_a*_d*_i* @atom:*_b11_a*_d*_i* - @bond:11-13 @atom:*_b11_a*_d*_i* @atom:*_b13_a*_d*_i* - @bond:11-14 @atom:*_b11_a*_d*_i* @atom:*_b14_a*_d*_i* - @bond:11-79 @atom:*_b11_a*_d*_i* @atom:*_b79_a*_d*_i* - @bond:12-12 @atom:*_b12_a*_d*_i* @atom:*_b12_a*_d*_i* - @bond:12-48 @atom:*_b12_a*_d*_i* @atom:*_b48_a*_d*_i* - @bond:12-60 @atom:*_b12_a*_d*_i* @atom:*_b60_a*_d*_i* - @bond:12-81 @atom:*_b12_a*_d*_i* @atom:*_b81_a*_d*_i* - @bond:13-13 @atom:*_b13_a*_d*_i* @atom:*_b13_a*_d*_i* - @bond:13-14 @atom:*_b13_a*_d*_i* @atom:*_b14_a*_d*_i* - @bond:13-15 @atom:*_b13_a*_d*_i* @atom:*_b15_a*_d*_i* - @bond:13-16 @atom:*_b13_a*_d*_i* @atom:*_b16_a*_d*_i* - @bond:13-18 @atom:*_b13_a*_d*_i* @atom:*_b18_a*_d*_i* - @bond:13-19 @atom:*_b13_a*_d*_i* @atom:*_b19_a*_d*_i* - @bond:13-20 @atom:*_b13_a*_d*_i* @atom:*_b20_a*_d*_i* - @bond:13-21 @atom:*_b13_a*_d*_i* @atom:*_b21_a*_d*_i* - @bond:13-22 @atom:*_b13_a*_d*_i* @atom:*_b22_a*_d*_i* - @bond:13-24 @atom:*_b13_a*_d*_i* @atom:*_b24_a*_d*_i* - @bond:13-25 @atom:*_b13_a*_d*_i* @atom:*_b25_a*_d*_i* - @bond:13-44 @atom:*_b13_a*_d*_i* @atom:*_b44_a*_d*_i* - @bond:13-46 @atom:*_b13_a*_d*_i* @atom:*_b46_a*_d*_i* - @bond:13-47 @atom:*_b13_a*_d*_i* @atom:*_b47_a*_d*_i* - @bond:13-48 @atom:*_b13_a*_d*_i* @atom:*_b48_a*_d*_i* - @bond:13-50 @atom:*_b13_a*_d*_i* @atom:*_b50_a*_d*_i* - @bond:13-51 @atom:*_b13_a*_d*_i* @atom:*_b51_a*_d*_i* - @bond:13-53 @atom:*_b13_a*_d*_i* @atom:*_b53_a*_d*_i* - @bond:13-55 @atom:*_b13_a*_d*_i* @atom:*_b55_a*_d*_i* - @bond:13-56 @atom:*_b13_a*_d*_i* @atom:*_b56_a*_d*_i* - @bond:13-57 @atom:*_b13_a*_d*_i* @atom:*_b57_a*_d*_i* - @bond:13-60 @atom:*_b13_a*_d*_i* @atom:*_b60_a*_d*_i* - @bond:13-64 @atom:*_b13_a*_d*_i* @atom:*_b64_a*_d*_i* - @bond:13-65 @atom:*_b13_a*_d*_i* @atom:*_b65_a*_d*_i* - @bond:13-66 @atom:*_b13_a*_d*_i* @atom:*_b66_a*_d*_i* - @bond:13-79 @atom:*_b13_a*_d*_i* @atom:*_b79_a*_d*_i* - @bond:13-80 @atom:*_b13_a*_d*_i* @atom:*_b80_a*_d*_i* - @bond:13-83 @atom:*_b13_a*_d*_i* @atom:*_b83_a*_d*_i* - @bond:13-84 @atom:*_b13_a*_d*_i* @atom:*_b84_a*_d*_i* - @bond:13-85 @atom:*_b13_a*_d*_i* @atom:*_b85_a*_d*_i* - @bond:13-87 @atom:*_b13_a*_d*_i* @atom:*_b87_a*_d*_i* - @bond:13-90 @atom:*_b13_a*_d*_i* @atom:*_b90_a*_d*_i* - @bond:13-91 @atom:*_b13_a*_d*_i* @atom:*_b91_a*_d*_i* - @bond:13-95 @atom:*_b13_a*_d*_i* @atom:*_b95_a*_d*_i* - @bond:13-101 @atom:*_b13_a*_d*_i* @atom:*_b101_a*_d*_i* - @bond:13-102 @atom:*_b13_a*_d*_i* @atom:*_b102_a*_d*_i* - @bond:13-104 @atom:*_b13_a*_d*_i* @atom:*_b104_a*_d*_i* - @bond:13-105 @atom:*_b13_a*_d*_i* @atom:*_b105_a*_d*_i* - @bond:13-107 @atom:*_b13_a*_d*_i* @atom:*_b107_a*_d*_i* - @bond:13-108 @atom:*_b13_a*_d*_i* @atom:*_b108_a*_d*_i* - @bond:13-109 @atom:*_b13_a*_d*_i* @atom:*_b109_a*_d*_i* - @bond:14-14 @atom:*_b14_a*_d*_i* @atom:*_b14_a*_d*_i* - @bond:15-17 @atom:*_b15_a*_d*_i* @atom:*_b17_a*_d*_i* - @bond:15-48 @atom:*_b15_a*_d*_i* @atom:*_b48_a*_d*_i* - @bond:16-16 @atom:*_b16_a*_d*_i* @atom:*_b16_a*_d*_i* - @bond:16-19 @atom:*_b16_a*_d*_i* @atom:*_b19_a*_d*_i* - @bond:16-24 @atom:*_b16_a*_d*_i* @atom:*_b24_a*_d*_i* - @bond:16-25 @atom:*_b16_a*_d*_i* @atom:*_b25_a*_d*_i* - @bond:16-47 @atom:*_b16_a*_d*_i* @atom:*_b47_a*_d*_i* - @bond:16-48 @atom:*_b16_a*_d*_i* @atom:*_b48_a*_d*_i* - @bond:16-61 @atom:*_b16_a*_d*_i* @atom:*_b61_a*_d*_i* - @bond:16-82 @atom:*_b16_a*_d*_i* @atom:*_b82_a*_d*_i* - @bond:16-84 @atom:*_b16_a*_d*_i* @atom:*_b84_a*_d*_i* - @bond:16-91 @atom:*_b16_a*_d*_i* @atom:*_b91_a*_d*_i* - @bond:16-108 @atom:*_b16_a*_d*_i* @atom:*_b108_a*_d*_i* - @bond:17-25 @atom:*_b17_a*_d*_i* @atom:*_b25_a*_d*_i* - @bond:18-18 @atom:*_b18_a*_d*_i* @atom:*_b18_a*_d*_i* - @bond:18-19 @atom:*_b18_a*_d*_i* @atom:*_b19_a*_d*_i* - @bond:18-48 @atom:*_b18_a*_d*_i* @atom:*_b48_a*_d*_i* - @bond:18-56 @atom:*_b18_a*_d*_i* @atom:*_b56_a*_d*_i* - @bond:19-19 @atom:*_b19_a*_d*_i* @atom:*_b19_a*_d*_i* - @bond:19-21 @atom:*_b19_a*_d*_i* @atom:*_b21_a*_d*_i* - @bond:19-46 @atom:*_b19_a*_d*_i* @atom:*_b46_a*_d*_i* - @bond:19-47 @atom:*_b19_a*_d*_i* @atom:*_b47_a*_d*_i* - @bond:19-48 @atom:*_b19_a*_d*_i* @atom:*_b48_a*_d*_i* - @bond:19-50 @atom:*_b19_a*_d*_i* @atom:*_b50_a*_d*_i* - @bond:19-65 @atom:*_b19_a*_d*_i* @atom:*_b65_a*_d*_i* - @bond:19-88 @atom:*_b19_a*_d*_i* @atom:*_b88_a*_d*_i* - @bond:19-91 @atom:*_b19_a*_d*_i* @atom:*_b91_a*_d*_i* - @bond:20-20 @atom:*_b20_a*_d*_i* @atom:*_b20_a*_d*_i* - @bond:20-21 @atom:*_b20_a*_d*_i* @atom:*_b21_a*_d*_i* - @bond:20-24 @atom:*_b20_a*_d*_i* @atom:*_b24_a*_d*_i* - @bond:20-25 @atom:*_b20_a*_d*_i* @atom:*_b25_a*_d*_i* - @bond:20-44 @atom:*_b20_a*_d*_i* @atom:*_b44_a*_d*_i* - @bond:20-47 @atom:*_b20_a*_d*_i* @atom:*_b47_a*_d*_i* - @bond:20-48 @atom:*_b20_a*_d*_i* @atom:*_b48_a*_d*_i* - @bond:20-51 @atom:*_b20_a*_d*_i* @atom:*_b51_a*_d*_i* - @bond:20-60 @atom:*_b20_a*_d*_i* @atom:*_b60_a*_d*_i* - @bond:20-61 @atom:*_b20_a*_d*_i* @atom:*_b61_a*_d*_i* - @bond:20-64 @atom:*_b20_a*_d*_i* @atom:*_b64_a*_d*_i* - @bond:20-82 @atom:*_b20_a*_d*_i* @atom:*_b82_a*_d*_i* - @bond:20-84 @atom:*_b20_a*_d*_i* @atom:*_b84_a*_d*_i* - @bond:20-108 @atom:*_b20_a*_d*_i* @atom:*_b108_a*_d*_i* - @bond:21-25 @atom:*_b21_a*_d*_i* @atom:*_b25_a*_d*_i* - @bond:21-47 @atom:*_b21_a*_d*_i* @atom:*_b47_a*_d*_i* - @bond:21-48 @atom:*_b21_a*_d*_i* @atom:*_b48_a*_d*_i* - @bond:21-82 @atom:*_b21_a*_d*_i* @atom:*_b82_a*_d*_i* - @bond:21-83 @atom:*_b21_a*_d*_i* @atom:*_b83_a*_d*_i* - @bond:21-84 @atom:*_b21_a*_d*_i* @atom:*_b84_a*_d*_i* - @bond:21-87 @atom:*_b21_a*_d*_i* @atom:*_b87_a*_d*_i* - @bond:21-88 @atom:*_b21_a*_d*_i* @atom:*_b88_a*_d*_i* - @bond:21-108 @atom:*_b21_a*_d*_i* @atom:*_b108_a*_d*_i* - @bond:22-23 @atom:*_b22_a*_d*_i* @atom:*_b23_a*_d*_i* - @bond:22-25 @atom:*_b22_a*_d*_i* @atom:*_b25_a*_d*_i* - @bond:23-25 @atom:*_b23_a*_d*_i* @atom:*_b25_a*_d*_i* - @bond:23-79 @atom:*_b23_a*_d*_i* @atom:*_b79_a*_d*_i* - @bond:24-25 @atom:*_b24_a*_d*_i* @atom:*_b25_a*_d*_i* - @bond:24-45 @atom:*_b24_a*_d*_i* @atom:*_b45_a*_d*_i* - @bond:24-48 @atom:*_b24_a*_d*_i* @atom:*_b48_a*_d*_i* - @bond:24-59 @atom:*_b24_a*_d*_i* @atom:*_b59_a*_d*_i* - @bond:24-79 @atom:*_b24_a*_d*_i* @atom:*_b79_a*_d*_i* - @bond:24-84 @atom:*_b24_a*_d*_i* @atom:*_b84_a*_d*_i* - @bond:24-88 @atom:*_b24_a*_d*_i* @atom:*_b88_a*_d*_i* - @bond:24-91 @atom:*_b24_a*_d*_i* @atom:*_b91_a*_d*_i* - @bond:24-103 @atom:*_b24_a*_d*_i* @atom:*_b103_a*_d*_i* - @bond:24-106 @atom:*_b24_a*_d*_i* @atom:*_b106_a*_d*_i* - @bond:25-25 @atom:*_b25_a*_d*_i* @atom:*_b25_a*_d*_i* - @bond:25-44 @atom:*_b25_a*_d*_i* @atom:*_b44_a*_d*_i* - @bond:25-45 @atom:*_b25_a*_d*_i* @atom:*_b45_a*_d*_i* - @bond:25-46 @atom:*_b25_a*_d*_i* @atom:*_b46_a*_d*_i* - @bond:25-47 @atom:*_b25_a*_d*_i* @atom:*_b47_a*_d*_i* - @bond:25-48 @atom:*_b25_a*_d*_i* @atom:*_b48_a*_d*_i* - @bond:25-49 @atom:*_b25_a*_d*_i* @atom:*_b49_a*_d*_i* - @bond:25-53 @atom:*_b25_a*_d*_i* @atom:*_b53_a*_d*_i* - @bond:25-56 @atom:*_b25_a*_d*_i* @atom:*_b56_a*_d*_i* - @bond:25-61 @atom:*_b25_a*_d*_i* @atom:*_b61_a*_d*_i* - @bond:25-65 @atom:*_b25_a*_d*_i* @atom:*_b65_a*_d*_i* - @bond:25-103 @atom:*_b25_a*_d*_i* @atom:*_b103_a*_d*_i* - @bond:31-32 @atom:*_b31_a*_d*_i* @atom:*_b32_a*_d*_i* - @bond:31-33 @atom:*_b31_a*_d*_i* @atom:*_b33_a*_d*_i* - @bond:31-106 @atom:*_b31_a*_d*_i* @atom:*_b106_a*_d*_i* - @bond:34-35 @atom:*_b34_a*_d*_i* @atom:*_b35_a*_d*_i* - @bond:36-37 @atom:*_b36_a*_d*_i* @atom:*_b37_a*_d*_i* - @bond:36-38 @atom:*_b36_a*_d*_i* @atom:*_b38_a*_d*_i* - @bond:39-40 @atom:*_b39_a*_d*_i* @atom:*_b40_a*_d*_i* - @bond:39-41 @atom:*_b39_a*_d*_i* @atom:*_b41_a*_d*_i* - @bond:42-43 @atom:*_b42_a*_d*_i* @atom:*_b43_a*_d*_i* - @bond:44-44 @atom:*_b44_a*_d*_i* @atom:*_b44_a*_d*_i* - @bond:44-45 @atom:*_b44_a*_d*_i* @atom:*_b45_a*_d*_i* - @bond:44-48 @atom:*_b44_a*_d*_i* @atom:*_b48_a*_d*_i* - @bond:44-79 @atom:*_b44_a*_d*_i* @atom:*_b79_a*_d*_i* - @bond:44-91 @atom:*_b44_a*_d*_i* @atom:*_b91_a*_d*_i* - @bond:44-108 @atom:*_b44_a*_d*_i* @atom:*_b108_a*_d*_i* - @bond:45-53 @atom:*_b45_a*_d*_i* @atom:*_b53_a*_d*_i* - @bond:45-55 @atom:*_b45_a*_d*_i* @atom:*_b55_a*_d*_i* - @bond:45-56 @atom:*_b45_a*_d*_i* @atom:*_b56_a*_d*_i* - @bond:45-57 @atom:*_b45_a*_d*_i* @atom:*_b57_a*_d*_i* - @bond:45-101 @atom:*_b45_a*_d*_i* @atom:*_b101_a*_d*_i* - @bond:45-105 @atom:*_b45_a*_d*_i* @atom:*_b105_a*_d*_i* - @bond:45-108 @atom:*_b45_a*_d*_i* @atom:*_b108_a*_d*_i* - @bond:46-47 @atom:*_b46_a*_d*_i* @atom:*_b47_a*_d*_i* - @bond:46-50 @atom:*_b46_a*_d*_i* @atom:*_b50_a*_d*_i* - @bond:46-51 @atom:*_b46_a*_d*_i* @atom:*_b51_a*_d*_i* - @bond:46-80 @atom:*_b46_a*_d*_i* @atom:*_b80_a*_d*_i* - @bond:46-91 @atom:*_b46_a*_d*_i* @atom:*_b91_a*_d*_i* - @bond:46-95 @atom:*_b46_a*_d*_i* @atom:*_b95_a*_d*_i* - @bond:46-108 @atom:*_b46_a*_d*_i* @atom:*_b108_a*_d*_i* - @bond:46-109 @atom:*_b46_a*_d*_i* @atom:*_b109_a*_d*_i* - @bond:47-47 @atom:*_b47_a*_d*_i* @atom:*_b47_a*_d*_i* - @bond:47-48 @atom:*_b47_a*_d*_i* @atom:*_b48_a*_d*_i* - @bond:47-50 @atom:*_b47_a*_d*_i* @atom:*_b50_a*_d*_i* - @bond:47-57 @atom:*_b47_a*_d*_i* @atom:*_b57_a*_d*_i* - @bond:47-58 @atom:*_b47_a*_d*_i* @atom:*_b58_a*_d*_i* - @bond:47-65 @atom:*_b47_a*_d*_i* @atom:*_b65_a*_d*_i* - @bond:47-66 @atom:*_b47_a*_d*_i* @atom:*_b66_a*_d*_i* - @bond:47-86 @atom:*_b47_a*_d*_i* @atom:*_b86_a*_d*_i* - @bond:47-91 @atom:*_b47_a*_d*_i* @atom:*_b91_a*_d*_i* - @bond:47-105 @atom:*_b47_a*_d*_i* @atom:*_b105_a*_d*_i* - @bond:47-110 @atom:*_b47_a*_d*_i* @atom:*_b110_a*_d*_i* - @bond:48-48 @atom:*_b48_a*_d*_i* @atom:*_b48_a*_d*_i* - @bond:48-49 @atom:*_b48_a*_d*_i* @atom:*_b49_a*_d*_i* - @bond:48-50 @atom:*_b48_a*_d*_i* @atom:*_b50_a*_d*_i* - @bond:48-53 @atom:*_b48_a*_d*_i* @atom:*_b53_a*_d*_i* - @bond:48-55 @atom:*_b48_a*_d*_i* @atom:*_b55_a*_d*_i* - @bond:48-56 @atom:*_b48_a*_d*_i* @atom:*_b56_a*_d*_i* - @bond:48-57 @atom:*_b48_a*_d*_i* @atom:*_b57_a*_d*_i* - @bond:48-60 @atom:*_b48_a*_d*_i* @atom:*_b60_a*_d*_i* - @bond:48-61 @atom:*_b48_a*_d*_i* @atom:*_b61_a*_d*_i* - @bond:48-64 @atom:*_b48_a*_d*_i* @atom:*_b64_a*_d*_i* - @bond:48-65 @atom:*_b48_a*_d*_i* @atom:*_b65_a*_d*_i* - @bond:48-66 @atom:*_b48_a*_d*_i* @atom:*_b66_a*_d*_i* - @bond:48-79 @atom:*_b48_a*_d*_i* @atom:*_b79_a*_d*_i* - @bond:48-81 @atom:*_b48_a*_d*_i* @atom:*_b81_a*_d*_i* - @bond:48-84 @atom:*_b48_a*_d*_i* @atom:*_b84_a*_d*_i* - @bond:48-86 @atom:*_b48_a*_d*_i* @atom:*_b86_a*_d*_i* - @bond:48-88 @atom:*_b48_a*_d*_i* @atom:*_b88_a*_d*_i* - @bond:48-91 @atom:*_b48_a*_d*_i* @atom:*_b91_a*_d*_i* - @bond:48-101 @atom:*_b48_a*_d*_i* @atom:*_b101_a*_d*_i* - @bond:48-102 @atom:*_b48_a*_d*_i* @atom:*_b102_a*_d*_i* - @bond:48-109 @atom:*_b48_a*_d*_i* @atom:*_b109_a*_d*_i* - @bond:49-59 @atom:*_b49_a*_d*_i* @atom:*_b59_a*_d*_i* - @bond:49-62 @atom:*_b49_a*_d*_i* @atom:*_b62_a*_d*_i* - @bond:49-82 @atom:*_b49_a*_d*_i* @atom:*_b82_a*_d*_i* - @bond:49-83 @atom:*_b49_a*_d*_i* @atom:*_b83_a*_d*_i* - @bond:49-84 @atom:*_b49_a*_d*_i* @atom:*_b84_a*_d*_i* - @bond:49-85 @atom:*_b49_a*_d*_i* @atom:*_b85_a*_d*_i* - @bond:49-87 @atom:*_b49_a*_d*_i* @atom:*_b87_a*_d*_i* - @bond:49-88 @atom:*_b49_a*_d*_i* @atom:*_b88_a*_d*_i* - @bond:50-50 @atom:*_b50_a*_d*_i* @atom:*_b50_a*_d*_i* - @bond:50-56 @atom:*_b50_a*_d*_i* @atom:*_b56_a*_d*_i* - @bond:50-84 @atom:*_b50_a*_d*_i* @atom:*_b84_a*_d*_i* - @bond:50-109 @atom:*_b50_a*_d*_i* @atom:*_b109_a*_d*_i* - @bond:51-105 @atom:*_b51_a*_d*_i* @atom:*_b105_a*_d*_i* - @bond:52-64 @atom:*_b52_a*_d*_i* @atom:*_b64_a*_d*_i* - @bond:53-54 @atom:*_b53_a*_d*_i* @atom:*_b54_a*_d*_i* - @bond:54-55 @atom:*_b54_a*_d*_i* @atom:*_b55_a*_d*_i* - @bond:55-59 @atom:*_b55_a*_d*_i* @atom:*_b59_a*_d*_i* - @bond:55-82 @atom:*_b55_a*_d*_i* @atom:*_b82_a*_d*_i* - @bond:56-56 @atom:*_b56_a*_d*_i* @atom:*_b56_a*_d*_i* - @bond:56-59 @atom:*_b56_a*_d*_i* @atom:*_b59_a*_d*_i* - @bond:56-60 @atom:*_b56_a*_d*_i* @atom:*_b60_a*_d*_i* - @bond:56-82 @atom:*_b56_a*_d*_i* @atom:*_b82_a*_d*_i* - @bond:56-86 @atom:*_b56_a*_d*_i* @atom:*_b86_a*_d*_i* - @bond:56-103 @atom:*_b56_a*_d*_i* @atom:*_b103_a*_d*_i* - @bond:56-109 @atom:*_b56_a*_d*_i* @atom:*_b109_a*_d*_i* - @bond:57-60 @atom:*_b57_a*_d*_i* @atom:*_b60_a*_d*_i* - @bond:57-61 @atom:*_b57_a*_d*_i* @atom:*_b61_a*_d*_i* - @bond:57-62 @atom:*_b57_a*_d*_i* @atom:*_b62_a*_d*_i* - @bond:57-81 @atom:*_b57_a*_d*_i* @atom:*_b81_a*_d*_i* - @bond:57-82 @atom:*_b57_a*_d*_i* @atom:*_b82_a*_d*_i* - @bond:57-84 @atom:*_b57_a*_d*_i* @atom:*_b84_a*_d*_i* - @bond:57-85 @atom:*_b57_a*_d*_i* @atom:*_b85_a*_d*_i* - @bond:57-86 @atom:*_b57_a*_d*_i* @atom:*_b86_a*_d*_i* - @bond:58-83 @atom:*_b58_a*_d*_i* @atom:*_b83_a*_d*_i* - @bond:58-84 @atom:*_b58_a*_d*_i* @atom:*_b84_a*_d*_i* - @bond:59-63 @atom:*_b59_a*_d*_i* @atom:*_b63_a*_d*_i* - @bond:60-60 @atom:*_b60_a*_d*_i* @atom:*_b60_a*_d*_i* - @bond:60-61 @atom:*_b60_a*_d*_i* @atom:*_b61_a*_d*_i* - @bond:60-80 @atom:*_b60_a*_d*_i* @atom:*_b80_a*_d*_i* - @bond:60-81 @atom:*_b60_a*_d*_i* @atom:*_b81_a*_d*_i* - @bond:60-87 @atom:*_b60_a*_d*_i* @atom:*_b87_a*_d*_i* - @bond:60-105 @atom:*_b60_a*_d*_i* @atom:*_b105_a*_d*_i* - @bond:61-61 @atom:*_b61_a*_d*_i* @atom:*_b61_a*_d*_i* - @bond:61-62 @atom:*_b61_a*_d*_i* @atom:*_b62_a*_d*_i* - @bond:61-82 @atom:*_b61_a*_d*_i* @atom:*_b82_a*_d*_i* - @bond:61-83 @atom:*_b61_a*_d*_i* @atom:*_b83_a*_d*_i* - @bond:61-84 @atom:*_b61_a*_d*_i* @atom:*_b84_a*_d*_i* - @bond:61-88 @atom:*_b61_a*_d*_i* @atom:*_b88_a*_d*_i* - @bond:62-63 @atom:*_b62_a*_d*_i* @atom:*_b63_a*_d*_i* - @bond:62-105 @atom:*_b62_a*_d*_i* @atom:*_b105_a*_d*_i* - @bond:63-82 @atom:*_b63_a*_d*_i* @atom:*_b82_a*_d*_i* - @bond:64-108 @atom:*_b64_a*_d*_i* @atom:*_b108_a*_d*_i* - @bond:65-82 @atom:*_b65_a*_d*_i* @atom:*_b82_a*_d*_i* - @bond:65-83 @atom:*_b65_a*_d*_i* @atom:*_b83_a*_d*_i* - @bond:65-84 @atom:*_b65_a*_d*_i* @atom:*_b84_a*_d*_i* - @bond:65-87 @atom:*_b65_a*_d*_i* @atom:*_b87_a*_d*_i* - @bond:65-88 @atom:*_b65_a*_d*_i* @atom:*_b88_a*_d*_i* - @bond:65-108 @atom:*_b65_a*_d*_i* @atom:*_b108_a*_d*_i* - @bond:66-82 @atom:*_b66_a*_d*_i* @atom:*_b82_a*_d*_i* - @bond:66-83 @atom:*_b66_a*_d*_i* @atom:*_b83_a*_d*_i* - @bond:66-84 @atom:*_b66_a*_d*_i* @atom:*_b84_a*_d*_i* - @bond:66-87 @atom:*_b66_a*_d*_i* @atom:*_b87_a*_d*_i* - @bond:66-88 @atom:*_b66_a*_d*_i* @atom:*_b88_a*_d*_i* - @bond:66-108 @atom:*_b66_a*_d*_i* @atom:*_b108_a*_d*_i* - @bond:77-78 @atom:*_b77_a*_d*_i* @atom:*_b78_a*_d*_i* - @bond:80-84 @atom:*_b80_a*_d*_i* @atom:*_b84_a*_d*_i* - @bond:82-86 @atom:*_b82_a*_d*_i* @atom:*_b86_a*_d*_i* - @bond:82-87 @atom:*_b82_a*_d*_i* @atom:*_b87_a*_d*_i* - @bond:83-84 @atom:*_b83_a*_d*_i* @atom:*_b84_a*_d*_i* - @bond:83-86 @atom:*_b83_a*_d*_i* @atom:*_b86_a*_d*_i* - @bond:84-84 @atom:*_b84_a*_d*_i* @atom:*_b84_a*_d*_i* - @bond:84-86 @atom:*_b84_a*_d*_i* @atom:*_b86_a*_d*_i* - @bond:84-87 @atom:*_b84_a*_d*_i* @atom:*_b87_a*_d*_i* - @bond:84-88 @atom:*_b84_a*_d*_i* @atom:*_b88_a*_d*_i* - @bond:85-85 @atom:*_b85_a*_d*_i* @atom:*_b85_a*_d*_i* - @bond:86-86 @atom:*_b86_a*_d*_i* @atom:*_b86_a*_d*_i* - @bond:86-87 @atom:*_b86_a*_d*_i* @atom:*_b87_a*_d*_i* - @bond:86-88 @atom:*_b86_a*_d*_i* @atom:*_b88_a*_d*_i* - @bond:87-87 @atom:*_b87_a*_d*_i* @atom:*_b87_a*_d*_i* - @bond:87-88 @atom:*_b87_a*_d*_i* @atom:*_b88_a*_d*_i* - @bond:89-90 @atom:*_b89_a*_d*_i* @atom:*_b90_a*_d*_i* - @bond:89-91 @atom:*_b89_a*_d*_i* @atom:*_b91_a*_d*_i* - @bond:90-91 @atom:*_b90_a*_d*_i* @atom:*_b91_a*_d*_i* - @bond:91-91 @atom:*_b91_a*_d*_i* @atom:*_b91_a*_d*_i* - @bond:102-103 @atom:*_b102_a*_d*_i* @atom:*_b103_a*_d*_i* - @bond:108-108 @atom:*_b108_a*_d*_i* @atom:*_b108_a*_d*_i* - @bond:109-109 @atom:*_b109_a*_d*_i* @atom:*_b109_a*_d*_i* + @bond:001_002 @atom:*_b001*_a*_d*_i* @atom:*_b002*_a*_d*_i* + @bond:001_003 @atom:*_b001*_a*_d*_i* @atom:*_b003*_a*_d*_i* + @bond:001_013 @atom:*_b001*_a*_d*_i* @atom:*_b013*_a*_d*_i* + @bond:001_019 @atom:*_b001*_a*_d*_i* @atom:*_b019*_a*_d*_i* + @bond:001_025 @atom:*_b001*_a*_d*_i* @atom:*_b025*_a*_d*_i* + @bond:001_047 @atom:*_b001*_a*_d*_i* @atom:*_b047*_a*_d*_i* + @bond:001_048 @atom:*_b001*_a*_d*_i* @atom:*_b048*_a*_d*_i* + @bond:001_082 @atom:*_b001*_a*_d*_i* @atom:*_b082*_a*_d*_i* + @bond:001_083 @atom:*_b001*_a*_d*_i* @atom:*_b083*_a*_d*_i* + @bond:001_084 @atom:*_b001*_a*_d*_i* @atom:*_b084*_a*_d*_i* + @bond:001_087 @atom:*_b001*_a*_d*_i* @atom:*_b087*_a*_d*_i* + @bond:001_088 @atom:*_b001*_a*_d*_i* @atom:*_b088*_a*_d*_i* + @bond:001_108 @atom:*_b001*_a*_d*_i* @atom:*_b108*_a*_d*_i* + @bond:002_002 @atom:*_b002*_a*_d*_i* @atom:*_b002*_a*_d*_i* + @bond:002_003 @atom:*_b002*_a*_d*_i* @atom:*_b003*_a*_d*_i* + @bond:002_005 @atom:*_b002*_a*_d*_i* @atom:*_b005*_a*_d*_i* + @bond:002_006 @atom:*_b002*_a*_d*_i* @atom:*_b006*_a*_d*_i* + @bond:002_010 @atom:*_b002*_a*_d*_i* @atom:*_b010*_a*_d*_i* + @bond:002_011 @atom:*_b002*_a*_d*_i* @atom:*_b011*_a*_d*_i* + @bond:002_012 @atom:*_b002*_a*_d*_i* @atom:*_b012*_a*_d*_i* + @bond:002_013 @atom:*_b002*_a*_d*_i* @atom:*_b013*_a*_d*_i* + @bond:002_014 @atom:*_b002*_a*_d*_i* @atom:*_b014*_a*_d*_i* + @bond:002_015 @atom:*_b002*_a*_d*_i* @atom:*_b015*_a*_d*_i* + @bond:002_016 @atom:*_b002*_a*_d*_i* @atom:*_b016*_a*_d*_i* + @bond:002_020 @atom:*_b002*_a*_d*_i* @atom:*_b020*_a*_d*_i* + @bond:002_024 @atom:*_b002*_a*_d*_i* @atom:*_b024*_a*_d*_i* + @bond:002_044 @atom:*_b002*_a*_d*_i* @atom:*_b044*_a*_d*_i* + @bond:002_048 @atom:*_b002*_a*_d*_i* @atom:*_b048*_a*_d*_i* + @bond:002_051 @atom:*_b002*_a*_d*_i* @atom:*_b051*_a*_d*_i* + @bond:002_053 @atom:*_b002*_a*_d*_i* @atom:*_b053*_a*_d*_i* + @bond:002_055 @atom:*_b002*_a*_d*_i* @atom:*_b055*_a*_d*_i* + @bond:002_080 @atom:*_b002*_a*_d*_i* @atom:*_b080*_a*_d*_i* + @bond:003_003 @atom:*_b003*_a*_d*_i* @atom:*_b003*_a*_d*_i* + @bond:003_004 @atom:*_b003*_a*_d*_i* @atom:*_b004*_a*_d*_i* + @bond:003_005 @atom:*_b003*_a*_d*_i* @atom:*_b005*_a*_d*_i* + @bond:003_006 @atom:*_b003*_a*_d*_i* @atom:*_b006*_a*_d*_i* + @bond:003_010 @atom:*_b003*_a*_d*_i* @atom:*_b010*_a*_d*_i* + @bond:003_012 @atom:*_b003*_a*_d*_i* @atom:*_b012*_a*_d*_i* + @bond:003_013 @atom:*_b003*_a*_d*_i* @atom:*_b013*_a*_d*_i* + @bond:003_019 @atom:*_b003*_a*_d*_i* @atom:*_b019*_a*_d*_i* + @bond:003_020 @atom:*_b003*_a*_d*_i* @atom:*_b020*_a*_d*_i* + @bond:003_021 @atom:*_b003*_a*_d*_i* @atom:*_b021*_a*_d*_i* + @bond:003_024 @atom:*_b003*_a*_d*_i* @atom:*_b024*_a*_d*_i* + @bond:003_044 @atom:*_b003*_a*_d*_i* @atom:*_b044*_a*_d*_i* + @bond:003_046 @atom:*_b003*_a*_d*_i* @atom:*_b046*_a*_d*_i* + @bond:003_047 @atom:*_b003*_a*_d*_i* @atom:*_b047*_a*_d*_i* + @bond:003_048 @atom:*_b003*_a*_d*_i* @atom:*_b048*_a*_d*_i* + @bond:003_050 @atom:*_b003*_a*_d*_i* @atom:*_b050*_a*_d*_i* + @bond:003_052 @atom:*_b003*_a*_d*_i* @atom:*_b052*_a*_d*_i* + @bond:003_056 @atom:*_b003*_a*_d*_i* @atom:*_b056*_a*_d*_i* + @bond:003_057 @atom:*_b003*_a*_d*_i* @atom:*_b057*_a*_d*_i* + @bond:003_060 @atom:*_b003*_a*_d*_i* @atom:*_b060*_a*_d*_i* + @bond:003_065 @atom:*_b003*_a*_d*_i* @atom:*_b065*_a*_d*_i* + @bond:003_084 @atom:*_b003*_a*_d*_i* @atom:*_b084*_a*_d*_i* + @bond:003_086 @atom:*_b003*_a*_d*_i* @atom:*_b086*_a*_d*_i* + @bond:003_105 @atom:*_b003*_a*_d*_i* @atom:*_b105*_a*_d*_i* + @bond:003_107 @atom:*_b003*_a*_d*_i* @atom:*_b107*_a*_d*_i* + @bond:004_025 @atom:*_b004*_a*_d*_i* @atom:*_b025*_a*_d*_i* + @bond:004_064 @atom:*_b004*_a*_d*_i* @atom:*_b064*_a*_d*_i* + @bond:004_089 @atom:*_b004*_a*_d*_i* @atom:*_b089*_a*_d*_i* + @bond:004_110 @atom:*_b004*_a*_d*_i* @atom:*_b110*_a*_d*_i* + @bond:005_006 @atom:*_b005*_a*_d*_i* @atom:*_b006*_a*_d*_i* + @bond:005_007 @atom:*_b005*_a*_d*_i* @atom:*_b007*_a*_d*_i* + @bond:005_010 @atom:*_b005*_a*_d*_i* @atom:*_b010*_a*_d*_i* + @bond:005_013 @atom:*_b005*_a*_d*_i* @atom:*_b013*_a*_d*_i* + @bond:005_020 @atom:*_b005*_a*_d*_i* @atom:*_b020*_a*_d*_i* + @bond:005_024 @atom:*_b005*_a*_d*_i* @atom:*_b024*_a*_d*_i* + @bond:005_025 @atom:*_b005*_a*_d*_i* @atom:*_b025*_a*_d*_i* + @bond:005_044 @atom:*_b005*_a*_d*_i* @atom:*_b044*_a*_d*_i* + @bond:005_047 @atom:*_b005*_a*_d*_i* @atom:*_b047*_a*_d*_i* + @bond:005_048 @atom:*_b005*_a*_d*_i* @atom:*_b048*_a*_d*_i* + @bond:005_051 @atom:*_b005*_a*_d*_i* @atom:*_b051*_a*_d*_i* + @bond:005_064 @atom:*_b005*_a*_d*_i* @atom:*_b064*_a*_d*_i* + @bond:005_079 @atom:*_b005*_a*_d*_i* @atom:*_b079*_a*_d*_i* + @bond:005_106 @atom:*_b005*_a*_d*_i* @atom:*_b106*_a*_d*_i* + @bond:005_108 @atom:*_b005*_a*_d*_i* @atom:*_b108*_a*_d*_i* + @bond:006_006 @atom:*_b006*_a*_d*_i* @atom:*_b006*_a*_d*_i* + @bond:006_010 @atom:*_b006*_a*_d*_i* @atom:*_b010*_a*_d*_i* + @bond:006_011 @atom:*_b006*_a*_d*_i* @atom:*_b011*_a*_d*_i* + @bond:006_013 @atom:*_b006*_a*_d*_i* @atom:*_b013*_a*_d*_i* + @bond:006_014 @atom:*_b006*_a*_d*_i* @atom:*_b014*_a*_d*_i* + @bond:006_015 @atom:*_b006*_a*_d*_i* @atom:*_b015*_a*_d*_i* + @bond:006_016 @atom:*_b006*_a*_d*_i* @atom:*_b016*_a*_d*_i* + @bond:006_020 @atom:*_b006*_a*_d*_i* @atom:*_b020*_a*_d*_i* + @bond:006_024 @atom:*_b006*_a*_d*_i* @atom:*_b024*_a*_d*_i* + @bond:006_044 @atom:*_b006*_a*_d*_i* @atom:*_b044*_a*_d*_i* + @bond:006_047 @atom:*_b006*_a*_d*_i* @atom:*_b047*_a*_d*_i* + @bond:006_051 @atom:*_b006*_a*_d*_i* @atom:*_b051*_a*_d*_i* + @bond:006_053 @atom:*_b006*_a*_d*_i* @atom:*_b053*_a*_d*_i* + @bond:006_055 @atom:*_b006*_a*_d*_i* @atom:*_b055*_a*_d*_i* + @bond:006_079 @atom:*_b006*_a*_d*_i* @atom:*_b079*_a*_d*_i* + @bond:006_105 @atom:*_b006*_a*_d*_i* @atom:*_b105*_a*_d*_i* + @bond:007_020 @atom:*_b007*_a*_d*_i* @atom:*_b020*_a*_d*_i* + @bond:007_025 @atom:*_b007*_a*_d*_i* @atom:*_b025*_a*_d*_i* + @bond:009_009 @atom:*_b009*_a*_d*_i* @atom:*_b009*_a*_d*_i* + @bond:009_011 @atom:*_b009*_a*_d*_i* @atom:*_b011*_a*_d*_i* + @bond:009_014 @atom:*_b009*_a*_d*_i* @atom:*_b014*_a*_d*_i* + @bond:010_010 @atom:*_b010*_a*_d*_i* @atom:*_b010*_a*_d*_i* + @bond:010_011 @atom:*_b010*_a*_d*_i* @atom:*_b011*_a*_d*_i* + @bond:010_014 @atom:*_b010*_a*_d*_i* @atom:*_b014*_a*_d*_i* + @bond:010_020 @atom:*_b010*_a*_d*_i* @atom:*_b020*_a*_d*_i* + @bond:010_024 @atom:*_b010*_a*_d*_i* @atom:*_b024*_a*_d*_i* + @bond:010_044 @atom:*_b010*_a*_d*_i* @atom:*_b044*_a*_d*_i* + @bond:010_105 @atom:*_b010*_a*_d*_i* @atom:*_b105*_a*_d*_i* + @bond:011_011 @atom:*_b011*_a*_d*_i* @atom:*_b011*_a*_d*_i* + @bond:011_013 @atom:*_b011*_a*_d*_i* @atom:*_b013*_a*_d*_i* + @bond:011_014 @atom:*_b011*_a*_d*_i* @atom:*_b014*_a*_d*_i* + @bond:011_079 @atom:*_b011*_a*_d*_i* @atom:*_b079*_a*_d*_i* + @bond:012_012 @atom:*_b012*_a*_d*_i* @atom:*_b012*_a*_d*_i* + @bond:012_048 @atom:*_b012*_a*_d*_i* @atom:*_b048*_a*_d*_i* + @bond:012_060 @atom:*_b012*_a*_d*_i* @atom:*_b060*_a*_d*_i* + @bond:012_081 @atom:*_b012*_a*_d*_i* @atom:*_b081*_a*_d*_i* + @bond:013_013 @atom:*_b013*_a*_d*_i* @atom:*_b013*_a*_d*_i* + @bond:013_014 @atom:*_b013*_a*_d*_i* @atom:*_b014*_a*_d*_i* + @bond:013_015 @atom:*_b013*_a*_d*_i* @atom:*_b015*_a*_d*_i* + @bond:013_016 @atom:*_b013*_a*_d*_i* @atom:*_b016*_a*_d*_i* + @bond:013_018 @atom:*_b013*_a*_d*_i* @atom:*_b018*_a*_d*_i* + @bond:013_019 @atom:*_b013*_a*_d*_i* @atom:*_b019*_a*_d*_i* + @bond:013_020 @atom:*_b013*_a*_d*_i* @atom:*_b020*_a*_d*_i* + @bond:013_021 @atom:*_b013*_a*_d*_i* @atom:*_b021*_a*_d*_i* + @bond:013_022 @atom:*_b013*_a*_d*_i* @atom:*_b022*_a*_d*_i* + @bond:013_024 @atom:*_b013*_a*_d*_i* @atom:*_b024*_a*_d*_i* + @bond:013_025 @atom:*_b013*_a*_d*_i* @atom:*_b025*_a*_d*_i* + @bond:013_044 @atom:*_b013*_a*_d*_i* @atom:*_b044*_a*_d*_i* + @bond:013_046 @atom:*_b013*_a*_d*_i* @atom:*_b046*_a*_d*_i* + @bond:013_047 @atom:*_b013*_a*_d*_i* @atom:*_b047*_a*_d*_i* + @bond:013_048 @atom:*_b013*_a*_d*_i* @atom:*_b048*_a*_d*_i* + @bond:013_050 @atom:*_b013*_a*_d*_i* @atom:*_b050*_a*_d*_i* + @bond:013_051 @atom:*_b013*_a*_d*_i* @atom:*_b051*_a*_d*_i* + @bond:013_053 @atom:*_b013*_a*_d*_i* @atom:*_b053*_a*_d*_i* + @bond:013_055 @atom:*_b013*_a*_d*_i* @atom:*_b055*_a*_d*_i* + @bond:013_056 @atom:*_b013*_a*_d*_i* @atom:*_b056*_a*_d*_i* + @bond:013_057 @atom:*_b013*_a*_d*_i* @atom:*_b057*_a*_d*_i* + @bond:013_060 @atom:*_b013*_a*_d*_i* @atom:*_b060*_a*_d*_i* + @bond:013_064 @atom:*_b013*_a*_d*_i* @atom:*_b064*_a*_d*_i* + @bond:013_065 @atom:*_b013*_a*_d*_i* @atom:*_b065*_a*_d*_i* + @bond:013_066 @atom:*_b013*_a*_d*_i* @atom:*_b066*_a*_d*_i* + @bond:013_079 @atom:*_b013*_a*_d*_i* @atom:*_b079*_a*_d*_i* + @bond:013_080 @atom:*_b013*_a*_d*_i* @atom:*_b080*_a*_d*_i* + @bond:013_083 @atom:*_b013*_a*_d*_i* @atom:*_b083*_a*_d*_i* + @bond:013_084 @atom:*_b013*_a*_d*_i* @atom:*_b084*_a*_d*_i* + @bond:013_085 @atom:*_b013*_a*_d*_i* @atom:*_b085*_a*_d*_i* + @bond:013_087 @atom:*_b013*_a*_d*_i* @atom:*_b087*_a*_d*_i* + @bond:013_090 @atom:*_b013*_a*_d*_i* @atom:*_b090*_a*_d*_i* + @bond:013_091 @atom:*_b013*_a*_d*_i* @atom:*_b091*_a*_d*_i* + @bond:013_095 @atom:*_b013*_a*_d*_i* @atom:*_b095*_a*_d*_i* + @bond:013_101 @atom:*_b013*_a*_d*_i* @atom:*_b101*_a*_d*_i* + @bond:013_102 @atom:*_b013*_a*_d*_i* @atom:*_b102*_a*_d*_i* + @bond:013_104 @atom:*_b013*_a*_d*_i* @atom:*_b104*_a*_d*_i* + @bond:013_105 @atom:*_b013*_a*_d*_i* @atom:*_b105*_a*_d*_i* + @bond:013_107 @atom:*_b013*_a*_d*_i* @atom:*_b107*_a*_d*_i* + @bond:013_108 @atom:*_b013*_a*_d*_i* @atom:*_b108*_a*_d*_i* + @bond:013_109 @atom:*_b013*_a*_d*_i* @atom:*_b109*_a*_d*_i* + @bond:014_014 @atom:*_b014*_a*_d*_i* @atom:*_b014*_a*_d*_i* + @bond:015_017 @atom:*_b015*_a*_d*_i* @atom:*_b017*_a*_d*_i* + @bond:015_048 @atom:*_b015*_a*_d*_i* @atom:*_b048*_a*_d*_i* + @bond:016_016 @atom:*_b016*_a*_d*_i* @atom:*_b016*_a*_d*_i* + @bond:016_019 @atom:*_b016*_a*_d*_i* @atom:*_b019*_a*_d*_i* + @bond:016_024 @atom:*_b016*_a*_d*_i* @atom:*_b024*_a*_d*_i* + @bond:016_025 @atom:*_b016*_a*_d*_i* @atom:*_b025*_a*_d*_i* + @bond:016_047 @atom:*_b016*_a*_d*_i* @atom:*_b047*_a*_d*_i* + @bond:016_048 @atom:*_b016*_a*_d*_i* @atom:*_b048*_a*_d*_i* + @bond:016_061 @atom:*_b016*_a*_d*_i* @atom:*_b061*_a*_d*_i* + @bond:016_082 @atom:*_b016*_a*_d*_i* @atom:*_b082*_a*_d*_i* + @bond:016_084 @atom:*_b016*_a*_d*_i* @atom:*_b084*_a*_d*_i* + @bond:016_091 @atom:*_b016*_a*_d*_i* @atom:*_b091*_a*_d*_i* + @bond:016_108 @atom:*_b016*_a*_d*_i* @atom:*_b108*_a*_d*_i* + @bond:017_025 @atom:*_b017*_a*_d*_i* @atom:*_b025*_a*_d*_i* + @bond:018_018 @atom:*_b018*_a*_d*_i* @atom:*_b018*_a*_d*_i* + @bond:018_019 @atom:*_b018*_a*_d*_i* @atom:*_b019*_a*_d*_i* + @bond:018_048 @atom:*_b018*_a*_d*_i* @atom:*_b048*_a*_d*_i* + @bond:018_056 @atom:*_b018*_a*_d*_i* @atom:*_b056*_a*_d*_i* + @bond:019_019 @atom:*_b019*_a*_d*_i* @atom:*_b019*_a*_d*_i* + @bond:019_021 @atom:*_b019*_a*_d*_i* @atom:*_b021*_a*_d*_i* + @bond:019_046 @atom:*_b019*_a*_d*_i* @atom:*_b046*_a*_d*_i* + @bond:019_047 @atom:*_b019*_a*_d*_i* @atom:*_b047*_a*_d*_i* + @bond:019_048 @atom:*_b019*_a*_d*_i* @atom:*_b048*_a*_d*_i* + @bond:019_050 @atom:*_b019*_a*_d*_i* @atom:*_b050*_a*_d*_i* + @bond:019_065 @atom:*_b019*_a*_d*_i* @atom:*_b065*_a*_d*_i* + @bond:019_088 @atom:*_b019*_a*_d*_i* @atom:*_b088*_a*_d*_i* + @bond:019_091 @atom:*_b019*_a*_d*_i* @atom:*_b091*_a*_d*_i* + @bond:020_020 @atom:*_b020*_a*_d*_i* @atom:*_b020*_a*_d*_i* + @bond:020_021 @atom:*_b020*_a*_d*_i* @atom:*_b021*_a*_d*_i* + @bond:020_024 @atom:*_b020*_a*_d*_i* @atom:*_b024*_a*_d*_i* + @bond:020_025 @atom:*_b020*_a*_d*_i* @atom:*_b025*_a*_d*_i* + @bond:020_044 @atom:*_b020*_a*_d*_i* @atom:*_b044*_a*_d*_i* + @bond:020_047 @atom:*_b020*_a*_d*_i* @atom:*_b047*_a*_d*_i* + @bond:020_048 @atom:*_b020*_a*_d*_i* @atom:*_b048*_a*_d*_i* + @bond:020_051 @atom:*_b020*_a*_d*_i* @atom:*_b051*_a*_d*_i* + @bond:020_060 @atom:*_b020*_a*_d*_i* @atom:*_b060*_a*_d*_i* + @bond:020_061 @atom:*_b020*_a*_d*_i* @atom:*_b061*_a*_d*_i* + @bond:020_064 @atom:*_b020*_a*_d*_i* @atom:*_b064*_a*_d*_i* + @bond:020_082 @atom:*_b020*_a*_d*_i* @atom:*_b082*_a*_d*_i* + @bond:020_084 @atom:*_b020*_a*_d*_i* @atom:*_b084*_a*_d*_i* + @bond:020_108 @atom:*_b020*_a*_d*_i* @atom:*_b108*_a*_d*_i* + @bond:021_025 @atom:*_b021*_a*_d*_i* @atom:*_b025*_a*_d*_i* + @bond:021_047 @atom:*_b021*_a*_d*_i* @atom:*_b047*_a*_d*_i* + @bond:021_048 @atom:*_b021*_a*_d*_i* @atom:*_b048*_a*_d*_i* + @bond:021_082 @atom:*_b021*_a*_d*_i* @atom:*_b082*_a*_d*_i* + @bond:021_083 @atom:*_b021*_a*_d*_i* @atom:*_b083*_a*_d*_i* + @bond:021_084 @atom:*_b021*_a*_d*_i* @atom:*_b084*_a*_d*_i* + @bond:021_087 @atom:*_b021*_a*_d*_i* @atom:*_b087*_a*_d*_i* + @bond:021_088 @atom:*_b021*_a*_d*_i* @atom:*_b088*_a*_d*_i* + @bond:021_108 @atom:*_b021*_a*_d*_i* @atom:*_b108*_a*_d*_i* + @bond:022_023 @atom:*_b022*_a*_d*_i* @atom:*_b023*_a*_d*_i* + @bond:022_025 @atom:*_b022*_a*_d*_i* @atom:*_b025*_a*_d*_i* + @bond:023_025 @atom:*_b023*_a*_d*_i* @atom:*_b025*_a*_d*_i* + @bond:023_079 @atom:*_b023*_a*_d*_i* @atom:*_b079*_a*_d*_i* + @bond:024_025 @atom:*_b024*_a*_d*_i* @atom:*_b025*_a*_d*_i* + @bond:024_045 @atom:*_b024*_a*_d*_i* @atom:*_b045*_a*_d*_i* + @bond:024_048 @atom:*_b024*_a*_d*_i* @atom:*_b048*_a*_d*_i* + @bond:024_059 @atom:*_b024*_a*_d*_i* @atom:*_b059*_a*_d*_i* + @bond:024_079 @atom:*_b024*_a*_d*_i* @atom:*_b079*_a*_d*_i* + @bond:024_084 @atom:*_b024*_a*_d*_i* @atom:*_b084*_a*_d*_i* + @bond:024_088 @atom:*_b024*_a*_d*_i* @atom:*_b088*_a*_d*_i* + @bond:024_091 @atom:*_b024*_a*_d*_i* @atom:*_b091*_a*_d*_i* + @bond:024_103 @atom:*_b024*_a*_d*_i* @atom:*_b103*_a*_d*_i* + @bond:024_106 @atom:*_b024*_a*_d*_i* @atom:*_b106*_a*_d*_i* + @bond:025_025 @atom:*_b025*_a*_d*_i* @atom:*_b025*_a*_d*_i* + @bond:025_044 @atom:*_b025*_a*_d*_i* @atom:*_b044*_a*_d*_i* + @bond:025_045 @atom:*_b025*_a*_d*_i* @atom:*_b045*_a*_d*_i* + @bond:025_046 @atom:*_b025*_a*_d*_i* @atom:*_b046*_a*_d*_i* + @bond:025_047 @atom:*_b025*_a*_d*_i* @atom:*_b047*_a*_d*_i* + @bond:025_048 @atom:*_b025*_a*_d*_i* @atom:*_b048*_a*_d*_i* + @bond:025_049 @atom:*_b025*_a*_d*_i* @atom:*_b049*_a*_d*_i* + @bond:025_053 @atom:*_b025*_a*_d*_i* @atom:*_b053*_a*_d*_i* + @bond:025_056 @atom:*_b025*_a*_d*_i* @atom:*_b056*_a*_d*_i* + @bond:025_061 @atom:*_b025*_a*_d*_i* @atom:*_b061*_a*_d*_i* + @bond:025_065 @atom:*_b025*_a*_d*_i* @atom:*_b065*_a*_d*_i* + @bond:025_103 @atom:*_b025*_a*_d*_i* @atom:*_b103*_a*_d*_i* + @bond:031_032 @atom:*_b031*_a*_d*_i* @atom:*_b032*_a*_d*_i* + @bond:031_033 @atom:*_b031*_a*_d*_i* @atom:*_b033*_a*_d*_i* + @bond:031_106 @atom:*_b031*_a*_d*_i* @atom:*_b106*_a*_d*_i* + @bond:034_035 @atom:*_b034*_a*_d*_i* @atom:*_b035*_a*_d*_i* + @bond:036_037 @atom:*_b036*_a*_d*_i* @atom:*_b037*_a*_d*_i* + @bond:036_038 @atom:*_b036*_a*_d*_i* @atom:*_b038*_a*_d*_i* + @bond:039_040 @atom:*_b039*_a*_d*_i* @atom:*_b040*_a*_d*_i* + @bond:039_041 @atom:*_b039*_a*_d*_i* @atom:*_b041*_a*_d*_i* + @bond:042_043 @atom:*_b042*_a*_d*_i* @atom:*_b043*_a*_d*_i* + @bond:044_044 @atom:*_b044*_a*_d*_i* @atom:*_b044*_a*_d*_i* + @bond:044_045 @atom:*_b044*_a*_d*_i* @atom:*_b045*_a*_d*_i* + @bond:044_048 @atom:*_b044*_a*_d*_i* @atom:*_b048*_a*_d*_i* + @bond:044_079 @atom:*_b044*_a*_d*_i* @atom:*_b079*_a*_d*_i* + @bond:044_091 @atom:*_b044*_a*_d*_i* @atom:*_b091*_a*_d*_i* + @bond:044_108 @atom:*_b044*_a*_d*_i* @atom:*_b108*_a*_d*_i* + @bond:045_053 @atom:*_b045*_a*_d*_i* @atom:*_b053*_a*_d*_i* + @bond:045_055 @atom:*_b045*_a*_d*_i* @atom:*_b055*_a*_d*_i* + @bond:045_056 @atom:*_b045*_a*_d*_i* @atom:*_b056*_a*_d*_i* + @bond:045_057 @atom:*_b045*_a*_d*_i* @atom:*_b057*_a*_d*_i* + @bond:045_101 @atom:*_b045*_a*_d*_i* @atom:*_b101*_a*_d*_i* + @bond:045_105 @atom:*_b045*_a*_d*_i* @atom:*_b105*_a*_d*_i* + @bond:045_108 @atom:*_b045*_a*_d*_i* @atom:*_b108*_a*_d*_i* + @bond:046_047 @atom:*_b046*_a*_d*_i* @atom:*_b047*_a*_d*_i* + @bond:046_050 @atom:*_b046*_a*_d*_i* @atom:*_b050*_a*_d*_i* + @bond:046_051 @atom:*_b046*_a*_d*_i* @atom:*_b051*_a*_d*_i* + @bond:046_080 @atom:*_b046*_a*_d*_i* @atom:*_b080*_a*_d*_i* + @bond:046_091 @atom:*_b046*_a*_d*_i* @atom:*_b091*_a*_d*_i* + @bond:046_095 @atom:*_b046*_a*_d*_i* @atom:*_b095*_a*_d*_i* + @bond:046_108 @atom:*_b046*_a*_d*_i* @atom:*_b108*_a*_d*_i* + @bond:046_109 @atom:*_b046*_a*_d*_i* @atom:*_b109*_a*_d*_i* + @bond:047_047 @atom:*_b047*_a*_d*_i* @atom:*_b047*_a*_d*_i* + @bond:047_048 @atom:*_b047*_a*_d*_i* @atom:*_b048*_a*_d*_i* + @bond:047_050 @atom:*_b047*_a*_d*_i* @atom:*_b050*_a*_d*_i* + @bond:047_057 @atom:*_b047*_a*_d*_i* @atom:*_b057*_a*_d*_i* + @bond:047_058 @atom:*_b047*_a*_d*_i* @atom:*_b058*_a*_d*_i* + @bond:047_065 @atom:*_b047*_a*_d*_i* @atom:*_b065*_a*_d*_i* + @bond:047_066 @atom:*_b047*_a*_d*_i* @atom:*_b066*_a*_d*_i* + @bond:047_086 @atom:*_b047*_a*_d*_i* @atom:*_b086*_a*_d*_i* + @bond:047_091 @atom:*_b047*_a*_d*_i* @atom:*_b091*_a*_d*_i* + @bond:047_105 @atom:*_b047*_a*_d*_i* @atom:*_b105*_a*_d*_i* + @bond:047_110 @atom:*_b047*_a*_d*_i* @atom:*_b110*_a*_d*_i* + @bond:048_048 @atom:*_b048*_a*_d*_i* @atom:*_b048*_a*_d*_i* + @bond:048_049 @atom:*_b048*_a*_d*_i* @atom:*_b049*_a*_d*_i* + @bond:048_050 @atom:*_b048*_a*_d*_i* @atom:*_b050*_a*_d*_i* + @bond:048_053 @atom:*_b048*_a*_d*_i* @atom:*_b053*_a*_d*_i* + @bond:048_055 @atom:*_b048*_a*_d*_i* @atom:*_b055*_a*_d*_i* + @bond:048_056 @atom:*_b048*_a*_d*_i* @atom:*_b056*_a*_d*_i* + @bond:048_057 @atom:*_b048*_a*_d*_i* @atom:*_b057*_a*_d*_i* + @bond:048_060 @atom:*_b048*_a*_d*_i* @atom:*_b060*_a*_d*_i* + @bond:048_061 @atom:*_b048*_a*_d*_i* @atom:*_b061*_a*_d*_i* + @bond:048_064 @atom:*_b048*_a*_d*_i* @atom:*_b064*_a*_d*_i* + @bond:048_065 @atom:*_b048*_a*_d*_i* @atom:*_b065*_a*_d*_i* + @bond:048_066 @atom:*_b048*_a*_d*_i* @atom:*_b066*_a*_d*_i* + @bond:048_079 @atom:*_b048*_a*_d*_i* @atom:*_b079*_a*_d*_i* + @bond:048_081 @atom:*_b048*_a*_d*_i* @atom:*_b081*_a*_d*_i* + @bond:048_084 @atom:*_b048*_a*_d*_i* @atom:*_b084*_a*_d*_i* + @bond:048_086 @atom:*_b048*_a*_d*_i* @atom:*_b086*_a*_d*_i* + @bond:048_088 @atom:*_b048*_a*_d*_i* @atom:*_b088*_a*_d*_i* + @bond:048_091 @atom:*_b048*_a*_d*_i* @atom:*_b091*_a*_d*_i* + @bond:048_101 @atom:*_b048*_a*_d*_i* @atom:*_b101*_a*_d*_i* + @bond:048_102 @atom:*_b048*_a*_d*_i* @atom:*_b102*_a*_d*_i* + @bond:048_109 @atom:*_b048*_a*_d*_i* @atom:*_b109*_a*_d*_i* + @bond:049_059 @atom:*_b049*_a*_d*_i* @atom:*_b059*_a*_d*_i* + @bond:049_062 @atom:*_b049*_a*_d*_i* @atom:*_b062*_a*_d*_i* + @bond:049_082 @atom:*_b049*_a*_d*_i* @atom:*_b082*_a*_d*_i* + @bond:049_083 @atom:*_b049*_a*_d*_i* @atom:*_b083*_a*_d*_i* + @bond:049_084 @atom:*_b049*_a*_d*_i* @atom:*_b084*_a*_d*_i* + @bond:049_085 @atom:*_b049*_a*_d*_i* @atom:*_b085*_a*_d*_i* + @bond:049_087 @atom:*_b049*_a*_d*_i* @atom:*_b087*_a*_d*_i* + @bond:049_088 @atom:*_b049*_a*_d*_i* @atom:*_b088*_a*_d*_i* + @bond:050_050 @atom:*_b050*_a*_d*_i* @atom:*_b050*_a*_d*_i* + @bond:050_056 @atom:*_b050*_a*_d*_i* @atom:*_b056*_a*_d*_i* + @bond:050_084 @atom:*_b050*_a*_d*_i* @atom:*_b084*_a*_d*_i* + @bond:050_109 @atom:*_b050*_a*_d*_i* @atom:*_b109*_a*_d*_i* + @bond:051_105 @atom:*_b051*_a*_d*_i* @atom:*_b105*_a*_d*_i* + @bond:052_064 @atom:*_b052*_a*_d*_i* @atom:*_b064*_a*_d*_i* + @bond:053_054 @atom:*_b053*_a*_d*_i* @atom:*_b054*_a*_d*_i* + @bond:054_055 @atom:*_b054*_a*_d*_i* @atom:*_b055*_a*_d*_i* + @bond:055_059 @atom:*_b055*_a*_d*_i* @atom:*_b059*_a*_d*_i* + @bond:055_082 @atom:*_b055*_a*_d*_i* @atom:*_b082*_a*_d*_i* + @bond:056_056 @atom:*_b056*_a*_d*_i* @atom:*_b056*_a*_d*_i* + @bond:056_059 @atom:*_b056*_a*_d*_i* @atom:*_b059*_a*_d*_i* + @bond:056_060 @atom:*_b056*_a*_d*_i* @atom:*_b060*_a*_d*_i* + @bond:056_082 @atom:*_b056*_a*_d*_i* @atom:*_b082*_a*_d*_i* + @bond:056_086 @atom:*_b056*_a*_d*_i* @atom:*_b086*_a*_d*_i* + @bond:056_103 @atom:*_b056*_a*_d*_i* @atom:*_b103*_a*_d*_i* + @bond:056_109 @atom:*_b056*_a*_d*_i* @atom:*_b109*_a*_d*_i* + @bond:057_060 @atom:*_b057*_a*_d*_i* @atom:*_b060*_a*_d*_i* + @bond:057_061 @atom:*_b057*_a*_d*_i* @atom:*_b061*_a*_d*_i* + @bond:057_062 @atom:*_b057*_a*_d*_i* @atom:*_b062*_a*_d*_i* + @bond:057_081 @atom:*_b057*_a*_d*_i* @atom:*_b081*_a*_d*_i* + @bond:057_082 @atom:*_b057*_a*_d*_i* @atom:*_b082*_a*_d*_i* + @bond:057_084 @atom:*_b057*_a*_d*_i* @atom:*_b084*_a*_d*_i* + @bond:057_085 @atom:*_b057*_a*_d*_i* @atom:*_b085*_a*_d*_i* + @bond:057_086 @atom:*_b057*_a*_d*_i* @atom:*_b086*_a*_d*_i* + @bond:058_083 @atom:*_b058*_a*_d*_i* @atom:*_b083*_a*_d*_i* + @bond:058_084 @atom:*_b058*_a*_d*_i* @atom:*_b084*_a*_d*_i* + @bond:059_063 @atom:*_b059*_a*_d*_i* @atom:*_b063*_a*_d*_i* + @bond:060_060 @atom:*_b060*_a*_d*_i* @atom:*_b060*_a*_d*_i* + @bond:060_061 @atom:*_b060*_a*_d*_i* @atom:*_b061*_a*_d*_i* + @bond:060_080 @atom:*_b060*_a*_d*_i* @atom:*_b080*_a*_d*_i* + @bond:060_081 @atom:*_b060*_a*_d*_i* @atom:*_b081*_a*_d*_i* + @bond:060_087 @atom:*_b060*_a*_d*_i* @atom:*_b087*_a*_d*_i* + @bond:060_105 @atom:*_b060*_a*_d*_i* @atom:*_b105*_a*_d*_i* + @bond:061_061 @atom:*_b061*_a*_d*_i* @atom:*_b061*_a*_d*_i* + @bond:061_062 @atom:*_b061*_a*_d*_i* @atom:*_b062*_a*_d*_i* + @bond:061_082 @atom:*_b061*_a*_d*_i* @atom:*_b082*_a*_d*_i* + @bond:061_083 @atom:*_b061*_a*_d*_i* @atom:*_b083*_a*_d*_i* + @bond:061_084 @atom:*_b061*_a*_d*_i* @atom:*_b084*_a*_d*_i* + @bond:061_088 @atom:*_b061*_a*_d*_i* @atom:*_b088*_a*_d*_i* + @bond:062_063 @atom:*_b062*_a*_d*_i* @atom:*_b063*_a*_d*_i* + @bond:062_105 @atom:*_b062*_a*_d*_i* @atom:*_b105*_a*_d*_i* + @bond:063_082 @atom:*_b063*_a*_d*_i* @atom:*_b082*_a*_d*_i* + @bond:064_108 @atom:*_b064*_a*_d*_i* @atom:*_b108*_a*_d*_i* + @bond:065_082 @atom:*_b065*_a*_d*_i* @atom:*_b082*_a*_d*_i* + @bond:065_083 @atom:*_b065*_a*_d*_i* @atom:*_b083*_a*_d*_i* + @bond:065_084 @atom:*_b065*_a*_d*_i* @atom:*_b084*_a*_d*_i* + @bond:065_087 @atom:*_b065*_a*_d*_i* @atom:*_b087*_a*_d*_i* + @bond:065_088 @atom:*_b065*_a*_d*_i* @atom:*_b088*_a*_d*_i* + @bond:065_108 @atom:*_b065*_a*_d*_i* @atom:*_b108*_a*_d*_i* + @bond:066_082 @atom:*_b066*_a*_d*_i* @atom:*_b082*_a*_d*_i* + @bond:066_083 @atom:*_b066*_a*_d*_i* @atom:*_b083*_a*_d*_i* + @bond:066_084 @atom:*_b066*_a*_d*_i* @atom:*_b084*_a*_d*_i* + @bond:066_087 @atom:*_b066*_a*_d*_i* @atom:*_b087*_a*_d*_i* + @bond:066_088 @atom:*_b066*_a*_d*_i* @atom:*_b088*_a*_d*_i* + @bond:066_108 @atom:*_b066*_a*_d*_i* @atom:*_b108*_a*_d*_i* + @bond:077_078 @atom:*_b077*_a*_d*_i* @atom:*_b078*_a*_d*_i* + @bond:080_084 @atom:*_b080*_a*_d*_i* @atom:*_b084*_a*_d*_i* + @bond:082_086 @atom:*_b082*_a*_d*_i* @atom:*_b086*_a*_d*_i* + @bond:082_087 @atom:*_b082*_a*_d*_i* @atom:*_b087*_a*_d*_i* + @bond:083_084 @atom:*_b083*_a*_d*_i* @atom:*_b084*_a*_d*_i* + @bond:083_086 @atom:*_b083*_a*_d*_i* @atom:*_b086*_a*_d*_i* + @bond:084_084 @atom:*_b084*_a*_d*_i* @atom:*_b084*_a*_d*_i* + @bond:084_086 @atom:*_b084*_a*_d*_i* @atom:*_b086*_a*_d*_i* + @bond:084_087 @atom:*_b084*_a*_d*_i* @atom:*_b087*_a*_d*_i* + @bond:084_088 @atom:*_b084*_a*_d*_i* @atom:*_b088*_a*_d*_i* + @bond:085_085 @atom:*_b085*_a*_d*_i* @atom:*_b085*_a*_d*_i* + @bond:086_086 @atom:*_b086*_a*_d*_i* @atom:*_b086*_a*_d*_i* + @bond:086_087 @atom:*_b086*_a*_d*_i* @atom:*_b087*_a*_d*_i* + @bond:086_088 @atom:*_b086*_a*_d*_i* @atom:*_b088*_a*_d*_i* + @bond:087_087 @atom:*_b087*_a*_d*_i* @atom:*_b087*_a*_d*_i* + @bond:087_088 @atom:*_b087*_a*_d*_i* @atom:*_b088*_a*_d*_i* + @bond:089_090 @atom:*_b089*_a*_d*_i* @atom:*_b090*_a*_d*_i* + @bond:089_091 @atom:*_b089*_a*_d*_i* @atom:*_b091*_a*_d*_i* + @bond:090_091 @atom:*_b090*_a*_d*_i* @atom:*_b091*_a*_d*_i* + @bond:091_091 @atom:*_b091*_a*_d*_i* @atom:*_b091*_a*_d*_i* + @bond:102_103 @atom:*_b102*_a*_d*_i* @atom:*_b103*_a*_d*_i* + @bond:108_108 @atom:*_b108*_a*_d*_i* @atom:*_b108*_a*_d*_i* + @bond:109_109 @atom:*_b109*_a*_d*_i* @atom:*_b109*_a*_d*_i* } #(end of bonds by type) @@ -4465,1026 +4478,1026 @@ OPLSAA { # ------- Angle Interactions: ------- # http://lammps.sandia.gov/doc/angle_harmonic.html # Syntax: - # angle_coeff AngleTypeName AngleStyle parameters... + # angle_coeff AngleTypeName parameters... write_once("In Settings") { - angle_coeff @angle:25-1-25 harmonic 33.0 109.47 - angle_coeff @angle:1-2-2 harmonic 50.0 109.5 - angle_coeff @angle:2-2-2 harmonic 63.0 112.4 - angle_coeff @angle:2-2-3 harmonic 63.0 112.4 - angle_coeff @angle:2-2-5 harmonic 80.0 109.5 - angle_coeff @angle:2-2-6 harmonic 63.0 112.4 - angle_coeff @angle:6-2-6 harmonic 63.0 112.4 - angle_coeff @angle:5-2-6 harmonic 80.0 109.5 - angle_coeff @angle:2-2-10 harmonic 63.0 112.4 - angle_coeff @angle:3-2-10 harmonic 63.0 112.4 - angle_coeff @angle:6-2-10 harmonic 63.0 112.4 - angle_coeff @angle:10-2-10 harmonic 63.0 112.4 - angle_coeff @angle:5-2-10 harmonic 80.0 109.5 - angle_coeff @angle:10-2-12 harmonic 63.0 114.0 - angle_coeff @angle:6-2-13 harmonic 63.0 112.4 - angle_coeff @angle:10-2-15 harmonic 50.0 108.6 - angle_coeff @angle:2-2-16 harmonic 50.0 114.7 - angle_coeff @angle:10-2-16 harmonic 50.0 114.7 - angle_coeff @angle:2-2-20 harmonic 80.0 109.5 - angle_coeff @angle:6-2-20 harmonic 80.0 109.5 - angle_coeff @angle:10-2-20 harmonic 80.0 109.5 - angle_coeff @angle:3-2-24 harmonic 80.0 110.3 - angle_coeff @angle:2-2-24 harmonic 80.0 111.2 - angle_coeff @angle:2-2-44 harmonic 56.2 109.47 - angle_coeff @angle:6-2-44 harmonic 56.2 109.47 - angle_coeff @angle:10-2-44 harmonic 56.2 109.47 - angle_coeff @angle:13-2-44 harmonic 56.2 109.47 - angle_coeff @angle:3-2-44 harmonic 80.0 111.2 - angle_coeff @angle:2-2-48 harmonic 63.0 112.4 - angle_coeff @angle:10-2-48 harmonic 63.0 114.0 - angle_coeff @angle:2-2-51 harmonic 63.0 112.4 - angle_coeff @angle:6-2-51 harmonic 63.0 112.4 - angle_coeff @angle:2-2-53 harmonic 80.0 111.2 - angle_coeff @angle:2-2-55 harmonic 80.0 111.2 - angle_coeff @angle:10-2-80 harmonic 63.0 115.6 - angle_coeff @angle:2-3-4 harmonic 80.0 120.4 - angle_coeff @angle:1-3-4 harmonic 80.0 121.0 - angle_coeff @angle:3-3-4 harmonic 80.0 121.4 - angle_coeff @angle:4-3-4 harmonic 80.0 126.0 - angle_coeff @angle:4-3-5 harmonic 80.0 121.0 - angle_coeff @angle:4-3-6 harmonic 80.0 120.4 - angle_coeff @angle:5-3-10 harmonic 70.0 115.0 - angle_coeff @angle:4-3-10 harmonic 80.0 120.4 - angle_coeff @angle:5-3-12 harmonic 70.0 120.0 - angle_coeff @angle:12-3-12 harmonic 85.0 120.0 - angle_coeff @angle:5-3-13 harmonic 70.0 108.0 - angle_coeff @angle:13-3-13 harmonic 70.0 116.0 - angle_coeff @angle:1-3-13 harmonic 80.0 111.0 - angle_coeff @angle:3-3-13 harmonic 80.0 117.2 - angle_coeff @angle:4-3-13 harmonic 80.0 120.4 - angle_coeff @angle:10-3-20 harmonic 81.0 111.4 - angle_coeff @angle:13-3-20 harmonic 81.0 111.4 - angle_coeff @angle:4-3-20 harmonic 83.0 123.4 - angle_coeff @angle:13-3-21 harmonic 75.0 109.0 - angle_coeff @angle:4-3-21 harmonic 75.0 119.0 - angle_coeff @angle:24-3-24 harmonic 70.0 114.2 - angle_coeff @angle:2-3-24 harmonic 70.0 116.6 - angle_coeff @angle:3-3-24 harmonic 70.0 116.6 - angle_coeff @angle:6-3-24 harmonic 70.0 116.6 - angle_coeff @angle:10-3-24 harmonic 70.0 116.6 - angle_coeff @angle:13-3-24 harmonic 70.0 116.6 - angle_coeff @angle:4-3-24 harmonic 80.0 122.9 - angle_coeff @angle:20-3-24 harmonic 81.0 111.4 - angle_coeff @angle:13-3-44 harmonic 70.0 116.0 - angle_coeff @angle:4-3-44 harmonic 80.0 120.4 - angle_coeff @angle:13-3-46 harmonic 35.0 115.0 - angle_coeff @angle:46-3-46 harmonic 35.0 115.0 - angle_coeff @angle:4-3-46 harmonic 35.0 123.0 - angle_coeff @angle:24-3-46 harmonic 40.0 114.0 - angle_coeff @angle:5-3-46 harmonic 40.0 115.0 - angle_coeff @angle:20-3-46 harmonic 40.0 115.0 - angle_coeff @angle:24-3-47 harmonic 70.0 115.5 - angle_coeff @angle:4-3-47 harmonic 80.0 125.3 - angle_coeff @angle:46-3-48 harmonic 35.0 115.0 - angle_coeff @angle:24-3-48 harmonic 70.0 115.5 - angle_coeff @angle:13-3-48 harmonic 70.0 116.0 - angle_coeff @angle:5-3-48 harmonic 70.0 120.0 - angle_coeff @angle:4-3-48 harmonic 80.0 120.4 - angle_coeff @angle:20-3-48 harmonic 81.0 111.4 - angle_coeff @angle:48-3-48 harmonic 85.0 120.0 - angle_coeff @angle:13-3-50 harmonic 70.0 116.0 - angle_coeff @angle:46-3-50 harmonic 80.0 116.0 - angle_coeff @angle:4-3-50 harmonic 80.0 124.0 - angle_coeff @angle:10-3-52 harmonic 65.0 117.0 - angle_coeff @angle:2-3-52 harmonic 70.0 117.0 - angle_coeff @angle:6-3-52 harmonic 70.0 117.0 - angle_coeff @angle:13-3-52 harmonic 70.0 117.0 - angle_coeff @angle:48-3-52 harmonic 70.0 117.0 - angle_coeff @angle:4-3-52 harmonic 80.0 126.0 - angle_coeff @angle:52-3-52 harmonic 80.0 126.0 - angle_coeff @angle:46-3-56 harmonic 35.0 122.0 - angle_coeff @angle:4-3-56 harmonic 80.0 122.5 - angle_coeff @angle:47-3-57 harmonic 70.0 114.1 - angle_coeff @angle:56-3-57 harmonic 70.0 118.6 - angle_coeff @angle:57-3-57 harmonic 70.0 118.6 - angle_coeff @angle:4-3-57 harmonic 80.0 120.6 - angle_coeff @angle:24-3-60 harmonic 70.0 111.3 - angle_coeff @angle:57-3-60 harmonic 70.0 111.3 - angle_coeff @angle:4-3-60 harmonic 80.0 128.8 - angle_coeff @angle:13-3-65 harmonic 75.0 109.0 - angle_coeff @angle:4-3-65 harmonic 75.0 119.0 - angle_coeff @angle:44-3-84 harmonic 70.0 116.0 - angle_coeff @angle:4-3-84 harmonic 80.0 120.4 - angle_coeff @angle:4-3-87 harmonic 80.0 128.2 - angle_coeff @angle:57-3-105 harmonic 70.0 115.4 - angle_coeff @angle:56-3-105 harmonic 70.0 118.6 - angle_coeff @angle:4-3-105 harmonic 80.0 120.9 - angle_coeff @angle:13-3-107 harmonic 70.0 116.6 - angle_coeff @angle:4-3-107 harmonic 80.0 122.9 - angle_coeff @angle:25-4-25 harmonic 10.0 117.0 - angle_coeff @angle:3-4-25 harmonic 35.0 113.0 - angle_coeff @angle:3-5-7 harmonic 35.0 113.0 - angle_coeff @angle:2-5-7 harmonic 55.0 108.5 - angle_coeff @angle:6-5-7 harmonic 55.0 108.5 - angle_coeff @angle:7-5-10 harmonic 55.0 108.5 - angle_coeff @angle:7-5-13 harmonic 55.0 108.5 - angle_coeff @angle:7-5-24 harmonic 49.0 105.4 - angle_coeff @angle:25-5-25 harmonic 5.0 109.47 - angle_coeff @angle:7-5-25 harmonic 10.0 109.47 - angle_coeff @angle:13-5-25 harmonic 10.0 109.47 - angle_coeff @angle:7-5-47 harmonic 35.0 109.0 - angle_coeff @angle:25-5-48 harmonic 10.0 109.47 - angle_coeff @angle:7-5-48 harmonic 35.0 113.0 - angle_coeff @angle:7-5-51 harmonic 55.0 108.5 - angle_coeff @angle:7-5-64 harmonic 55.0 108.5 - angle_coeff @angle:13-5-64 harmonic 100.0 120.5 - angle_coeff @angle:7-5-79 harmonic 74.0 110.0 - angle_coeff @angle:7-5-106 harmonic 100.0 126.0 - angle_coeff @angle:5-7-25 harmonic 10.0 109.47 - angle_coeff @angle:25-7-25 harmonic 33.0 109.47 - angle_coeff @angle:2-10-2 harmonic 63.0 112.4 - angle_coeff @angle:2-10-3 harmonic 63.0 111.1 - angle_coeff @angle:2-10-5 harmonic 80.0 109.5 - angle_coeff @angle:3-10-6 harmonic 63.0 111.1 - angle_coeff @angle:6-10-6 harmonic 63.0 111.5 - angle_coeff @angle:2-10-6 harmonic 63.0 112.4 - angle_coeff @angle:5-10-6 harmonic 80.0 109.5 - angle_coeff @angle:3-10-10 harmonic 63.0 111.1 - angle_coeff @angle:2-10-10 harmonic 63.0 111.5 - angle_coeff @angle:6-10-10 harmonic 63.0 111.5 - angle_coeff @angle:10-10-10 harmonic 63.0 111.5 - angle_coeff @angle:5-10-10 harmonic 80.0 109.5 - angle_coeff @angle:2-10-20 harmonic 80.0 109.5 - angle_coeff @angle:6-10-20 harmonic 80.0 109.5 - angle_coeff @angle:10-10-20 harmonic 80.0 109.5 - angle_coeff @angle:3-10-24 harmonic 63.0 110.1 - angle_coeff @angle:6-10-24 harmonic 80.0 109.5 - angle_coeff @angle:2-10-24 harmonic 80.0 109.7 - angle_coeff @angle:10-10-24 harmonic 80.0 109.7 - angle_coeff @angle:2-10-44 harmonic 56.2 109.47 - angle_coeff @angle:6-10-44 harmonic 56.2 109.47 - angle_coeff @angle:10-10-44 harmonic 56.2 109.47 - angle_coeff @angle:13-10-44 harmonic 56.2 109.47 - angle_coeff @angle:3-10-44 harmonic 80.0 109.7 - angle_coeff @angle:2-10-48 harmonic 63.0 112.4 - angle_coeff @angle:20-10-48 harmonic 80.0 109.5 - angle_coeff @angle:2-10-105 harmonic 80.0 109.5 - angle_coeff @angle:10-10-105 harmonic 80.0 109.5 - angle_coeff @angle:20-10-105 harmonic 80.0 109.5 - angle_coeff @angle:2-11-2 harmonic 70.0 124.0 - angle_coeff @angle:2-11-6 harmonic 70.0 124.0 - angle_coeff @angle:6-11-6 harmonic 70.0 124.0 - angle_coeff @angle:2-11-9 harmonic 70.0 118.0 - angle_coeff @angle:6-11-9 harmonic 70.0 118.0 - angle_coeff @angle:9-11-10 harmonic 70.0 118.0 - angle_coeff @angle:2-11-10 harmonic 70.0 124.0 - angle_coeff @angle:6-11-10 harmonic 70.0 124.0 - angle_coeff @angle:10-11-10 harmonic 70.0 124.0 - angle_coeff @angle:2-11-11 harmonic 70.0 118.0 - angle_coeff @angle:6-11-11 harmonic 70.0 118.0 - angle_coeff @angle:9-11-11 harmonic 70.0 118.0 - angle_coeff @angle:10-11-11 harmonic 70.0 118.0 - angle_coeff @angle:11-11-11 harmonic 70.0 118.0 - angle_coeff @angle:9-11-13 harmonic 70.0 118.0 - angle_coeff @angle:11-11-13 harmonic 70.0 118.0 - angle_coeff @angle:2-11-13 harmonic 70.0 124.0 - angle_coeff @angle:6-11-13 harmonic 70.0 124.0 - angle_coeff @angle:10-11-13 harmonic 70.0 124.0 - angle_coeff @angle:13-11-13 harmonic 70.0 124.0 - angle_coeff @angle:9-11-14 harmonic 70.0 118.0 - angle_coeff @angle:11-11-14 harmonic 70.0 118.0 - angle_coeff @angle:9-11-79 harmonic 70.0 118.0 - angle_coeff @angle:2-12-12 harmonic 70.0 120.0 - angle_coeff @angle:3-12-12 harmonic 85.0 120.0 - angle_coeff @angle:12-12-12 harmonic 85.0 120.0 - angle_coeff @angle:12-12-48 harmonic 85.0 120.0 - angle_coeff @angle:12-12-60 harmonic 85.0 120.0 - angle_coeff @angle:12-12-81 harmonic 85.0 120.0 - angle_coeff @angle:1-13-1 harmonic 77.0 109.1 - angle_coeff @angle:2-13-2 harmonic 40.0 109.5 - angle_coeff @angle:1-13-3 harmonic 50.0 109.5 - angle_coeff @angle:2-13-3 harmonic 63.0 111.1 - angle_coeff @angle:3-13-3 harmonic 63.0 111.1 - angle_coeff @angle:2-13-6 harmonic 40.0 109.5 - angle_coeff @angle:6-13-6 harmonic 40.0 109.5 - angle_coeff @angle:3-13-6 harmonic 63.0 109.5 - angle_coeff @angle:1-13-13 harmonic 50.0 109.5 - angle_coeff @angle:5-13-13 harmonic 50.0 109.5 - angle_coeff @angle:13-13-13 harmonic 58.35 112.7 - angle_coeff @angle:3-13-13 harmonic 63.0 111.1 - angle_coeff @angle:13-13-15 harmonic 50.0 108.6 - angle_coeff @angle:13-13-16 harmonic 50.0 114.7 - angle_coeff @angle:13-13-19 harmonic 58.35 112.7 - angle_coeff @angle:3-13-20 harmonic 50.0 109.5 - angle_coeff @angle:13-13-20 harmonic 50.0 109.5 - angle_coeff @angle:3-13-21 harmonic 69.0 109.8 - angle_coeff @angle:13-13-21 harmonic 69.0 109.8 - angle_coeff @angle:21-13-21 harmonic 78.0 111.7 - angle_coeff @angle:13-13-22 harmonic 50.0 108.6 - angle_coeff @angle:20-13-24 harmonic 50.0 109.5 - angle_coeff @angle:3-13-24 harmonic 63.0 110.1 - angle_coeff @angle:2-13-24 harmonic 80.0 109.7 - angle_coeff @angle:13-13-24 harmonic 80.0 109.7 - angle_coeff @angle:16-13-44 harmonic 50.0 114.7 - angle_coeff @angle:2-13-44 harmonic 56.2 109.47 - angle_coeff @angle:6-13-44 harmonic 56.2 109.47 - angle_coeff @angle:10-13-44 harmonic 56.2 109.47 - angle_coeff @angle:13-13-44 harmonic 56.2 109.47 - angle_coeff @angle:3-13-44 harmonic 80.0 111.2 - angle_coeff @angle:46-13-46 harmonic 33.0 107.8 - angle_coeff @angle:18-13-46 harmonic 35.0 108.5 - angle_coeff @angle:19-13-46 harmonic 35.0 108.5 - angle_coeff @angle:2-13-46 harmonic 35.0 109.5 - angle_coeff @angle:3-13-46 harmonic 35.0 109.5 - angle_coeff @angle:5-13-46 harmonic 35.0 109.5 - angle_coeff @angle:15-13-46 harmonic 35.0 109.5 - angle_coeff @angle:16-13-46 harmonic 35.0 109.5 - angle_coeff @angle:20-13-46 harmonic 35.0 109.5 - angle_coeff @angle:22-13-46 harmonic 35.0 109.5 - angle_coeff @angle:24-13-46 harmonic 35.0 109.5 - angle_coeff @angle:44-13-46 harmonic 35.0 109.5 - angle_coeff @angle:13-13-46 harmonic 37.5 110.7 - angle_coeff @angle:1-13-46 harmonic 40.0 107.0 - angle_coeff @angle:21-13-46 harmonic 51.0 107.6 - angle_coeff @angle:46-13-47 harmonic 35.0 109.5 - angle_coeff @angle:1-13-47 harmonic 50.0 109.5 - angle_coeff @angle:13-13-47 harmonic 63.0 111.1 - angle_coeff @angle:47-13-47 harmonic 63.0 112.4 - angle_coeff @angle:46-13-48 harmonic 35.0 109.5 - angle_coeff @angle:47-13-48 harmonic 40.0 109.5 - angle_coeff @angle:48-13-48 harmonic 40.0 109.5 - angle_coeff @angle:1-13-48 harmonic 50.0 109.5 - angle_coeff @angle:5-13-48 harmonic 50.0 109.5 - angle_coeff @angle:20-13-48 harmonic 50.0 109.5 - angle_coeff @angle:16-13-48 harmonic 50.0 114.7 - angle_coeff @angle:3-13-48 harmonic 63.0 112.0 - angle_coeff @angle:2-13-48 harmonic 63.0 114.0 - angle_coeff @angle:13-13-48 harmonic 63.0 114.0 - angle_coeff @angle:44-13-48 harmonic 80.0 111.2 - angle_coeff @angle:46-13-50 harmonic 35.0 109.5 - angle_coeff @angle:46-13-51 harmonic 37.5 110.7 - angle_coeff @angle:5-13-51 harmonic 50.0 109.5 - angle_coeff @angle:13-13-51 harmonic 58.35 112.7 - angle_coeff @angle:46-13-53 harmonic 35.0 109.5 - angle_coeff @angle:3-13-53 harmonic 80.0 111.2 - angle_coeff @angle:13-13-53 harmonic 80.0 111.2 - angle_coeff @angle:46-13-55 harmonic 35.0 109.5 - angle_coeff @angle:13-13-55 harmonic 80.0 111.2 - angle_coeff @angle:46-13-56 harmonic 35.0 109.5 - angle_coeff @angle:3-13-56 harmonic 63.0 110.1 - angle_coeff @angle:13-13-56 harmonic 65.0 109.0 - angle_coeff @angle:46-13-57 harmonic 35.0 109.5 - angle_coeff @angle:48-13-57 harmonic 80.0 111.2 - angle_coeff @angle:46-13-60 harmonic 35.0 109.5 - angle_coeff @angle:13-13-60 harmonic 63.0 114.0 - angle_coeff @angle:46-13-64 harmonic 41.0 109.5 - angle_coeff @angle:13-13-64 harmonic 43.0 109.5 - angle_coeff @angle:48-13-64 harmonic 43.0 109.5 - angle_coeff @angle:46-13-65 harmonic 51.0 107.6 - angle_coeff @angle:3-13-65 harmonic 69.0 109.8 - angle_coeff @angle:13-13-65 harmonic 69.0 110.0 - angle_coeff @angle:48-13-65 harmonic 69.0 110.0 - angle_coeff @angle:65-13-65 harmonic 78.0 111.7 - angle_coeff @angle:46-13-66 harmonic 75.0 111.0 - angle_coeff @angle:13-13-66 harmonic 75.0 112.0 - angle_coeff @angle:46-13-79 harmonic 35.0 109.5 - angle_coeff @angle:13-13-79 harmonic 50.0 108.6 - angle_coeff @angle:1-13-79 harmonic 50.0 109.5 - angle_coeff @angle:46-13-80 harmonic 35.0 109.5 - angle_coeff @angle:13-13-80 harmonic 63.0 115.6 - angle_coeff @angle:46-13-83 harmonic 35.0 109.5 - angle_coeff @angle:13-13-83 harmonic 63.0 114.0 - angle_coeff @angle:46-13-84 harmonic 35.0 109.5 - angle_coeff @angle:16-13-84 harmonic 50.0 114.7 - angle_coeff @angle:13-13-84 harmonic 63.0 114.0 - angle_coeff @angle:46-13-85 harmonic 35.0 109.5 - angle_coeff @angle:13-13-85 harmonic 63.0 114.0 - angle_coeff @angle:46-13-87 harmonic 35.0 109.5 - angle_coeff @angle:13-13-87 harmonic 63.0 115.6 - angle_coeff @angle:46-13-90 harmonic 35.0 109.5 - angle_coeff @angle:13-13-90 harmonic 80.0 110.0 - angle_coeff @angle:3-13-90 harmonic 80.0 113.0 - angle_coeff @angle:46-13-91 harmonic 37.5 110.7 - angle_coeff @angle:46-13-95 harmonic 35.0 105.0 - angle_coeff @angle:13-13-95 harmonic 63.0 105.0 - angle_coeff @angle:46-13-101 harmonic 35.0 109.5 - angle_coeff @angle:13-13-101 harmonic 80.0 111.2 - angle_coeff @angle:46-13-102 harmonic 35.0 105.0 - angle_coeff @angle:13-13-102 harmonic 63.0 111.1 - angle_coeff @angle:46-13-104 harmonic 41.0 109.5 - angle_coeff @angle:13-13-104 harmonic 43.0 109.5 - angle_coeff @angle:46-13-105 harmonic 35.0 109.5 - angle_coeff @angle:13-13-105 harmonic 50.0 109.5 - angle_coeff @angle:20-13-105 harmonic 50.0 109.5 - angle_coeff @angle:46-13-107 harmonic 35.0 109.5 - angle_coeff @angle:13-13-107 harmonic 80.0 109.7 - angle_coeff @angle:46-13-108 harmonic 35.0 109.5 - angle_coeff @angle:13-13-108 harmonic 60.0 112.0 - angle_coeff @angle:2-14-2 harmonic 70.0 124.0 - angle_coeff @angle:2-14-6 harmonic 70.0 124.0 - angle_coeff @angle:6-14-6 harmonic 70.0 124.0 - angle_coeff @angle:2-14-9 harmonic 70.0 118.0 - angle_coeff @angle:6-14-9 harmonic 70.0 118.0 - angle_coeff @angle:9-14-10 harmonic 70.0 118.0 - angle_coeff @angle:2-14-10 harmonic 70.0 124.0 - angle_coeff @angle:6-14-10 harmonic 70.0 124.0 - angle_coeff @angle:10-14-10 harmonic 70.0 124.0 - angle_coeff @angle:2-14-11 harmonic 70.0 118.0 - angle_coeff @angle:6-14-11 harmonic 70.0 118.0 - angle_coeff @angle:9-14-11 harmonic 70.0 118.0 - angle_coeff @angle:10-14-11 harmonic 70.0 118.0 - angle_coeff @angle:11-14-11 harmonic 70.0 118.0 - angle_coeff @angle:9-14-13 harmonic 70.0 118.0 - angle_coeff @angle:11-14-13 harmonic 70.0 118.0 - angle_coeff @angle:2-14-13 harmonic 70.0 124.0 - angle_coeff @angle:6-14-13 harmonic 70.0 124.0 - angle_coeff @angle:10-14-13 harmonic 70.0 124.0 - angle_coeff @angle:13-14-13 harmonic 70.0 124.0 - angle_coeff @angle:2-14-14 harmonic 70.0 118.0 - angle_coeff @angle:6-14-14 harmonic 70.0 118.0 - angle_coeff @angle:9-14-14 harmonic 70.0 118.0 - angle_coeff @angle:10-14-14 harmonic 70.0 118.0 - angle_coeff @angle:11-14-14 harmonic 70.0 118.0 - angle_coeff @angle:13-14-14 harmonic 70.0 118.0 - angle_coeff @angle:14-14-14 harmonic 70.0 118.0 - angle_coeff @angle:17-15-17 harmonic 35.0 92.07 - angle_coeff @angle:2-15-17 harmonic 44.0 96.0 - angle_coeff @angle:6-15-17 harmonic 44.0 96.0 - angle_coeff @angle:13-15-17 harmonic 44.0 96.0 - angle_coeff @angle:25-15-25 harmonic 5.0 109.47 - angle_coeff @angle:13-15-25 harmonic 10.0 109.47 - angle_coeff @angle:33-15-33 harmonic 10.0 160.0 - angle_coeff @angle:2-15-33 harmonic 150.0 96.7 - angle_coeff @angle:6-15-33 harmonic 150.0 96.7 - angle_coeff @angle:13-15-33 harmonic 150.0 96.7 - angle_coeff @angle:17-15-33 harmonic 150.0 96.7 - angle_coeff @angle:17-15-48 harmonic 50.0 96.0 - angle_coeff @angle:2-16-6 harmonic 62.0 98.9 - angle_coeff @angle:13-16-13 harmonic 62.0 98.9 - angle_coeff @angle:2-16-16 harmonic 68.0 103.7 - angle_coeff @angle:6-16-16 harmonic 68.0 103.7 - angle_coeff @angle:13-16-16 harmonic 68.0 103.7 - angle_coeff @angle:13-16-19 harmonic 65.0 100.0 - angle_coeff @angle:25-16-25 harmonic 5.0 109.47 - angle_coeff @angle:13-16-25 harmonic 10.0 109.47 - angle_coeff @angle:33-16-33 harmonic 10.0 160.0 - angle_coeff @angle:2-16-33 harmonic 150.0 96.7 - angle_coeff @angle:6-16-33 harmonic 150.0 96.7 - angle_coeff @angle:13-16-33 harmonic 150.0 96.7 - angle_coeff @angle:16-16-33 harmonic 150.0 96.7 - angle_coeff @angle:13-16-48 harmonic 62.0 104.2 - angle_coeff @angle:47-16-48 harmonic 62.0 104.2 - angle_coeff @angle:24-16-60 harmonic 74.0 92.4 - angle_coeff @angle:25-16-61 harmonic 10.0 130.0 - angle_coeff @angle:25-16-82 harmonic 10.0 130.0 - angle_coeff @angle:60-16-82 harmonic 74.0 97.0 - angle_coeff @angle:25-16-84 harmonic 10.0 130.0 - angle_coeff @angle:82-16-84 harmonic 74.0 90.0 - angle_coeff @angle:60-16-84 harmonic 74.0 97.0 - angle_coeff @angle:84-16-84 harmonic 74.0 97.0 - angle_coeff @angle:13-16-91 harmonic 62.0 94.0 - angle_coeff @angle:15-17-25 harmonic 10.0 109.47 - angle_coeff @angle:25-17-25 harmonic 33.0 109.47 - angle_coeff @angle:13-18-19 harmonic 150.0 180.0 - angle_coeff @angle:19-18-48 harmonic 170.0 180.0 - angle_coeff @angle:18-18-56 harmonic 100.0 180.0 - angle_coeff @angle:13-19-18 harmonic 150.0 180.0 - angle_coeff @angle:16-19-19 harmonic 140.0 180.0 - angle_coeff @angle:13-19-19 harmonic 150.0 180.0 - angle_coeff @angle:18-19-25 harmonic 10.0 90.0 - angle_coeff @angle:19-19-46 harmonic 112.0 180.0 - angle_coeff @angle:18-19-47 harmonic 150.0 180.0 - angle_coeff @angle:19-19-47 harmonic 160.0 180.0 - angle_coeff @angle:18-19-48 harmonic 150.0 180.0 - angle_coeff @angle:19-19-48 harmonic 160.0 180.0 - angle_coeff @angle:19-19-50 harmonic 160.0 180.0 - angle_coeff @angle:18-19-55 harmonic 150.0 180.0 - angle_coeff @angle:18-19-88 harmonic 150.0 180.0 - angle_coeff @angle:2-20-2 harmonic 100.0 111.8 - angle_coeff @angle:2-20-3 harmonic 83.0 116.9 - angle_coeff @angle:3-20-6 harmonic 83.0 116.9 - angle_coeff @angle:2-20-6 harmonic 100.0 111.8 - angle_coeff @angle:2-20-7 harmonic 55.0 108.5 - angle_coeff @angle:7-20-10 harmonic 55.0 108.5 - angle_coeff @angle:3-20-10 harmonic 83.0 116.9 - angle_coeff @angle:10-20-10 harmonic 100.0 111.8 - angle_coeff @angle:13-20-13 harmonic 60.0 109.5 - angle_coeff @angle:3-20-13 harmonic 83.0 116.9 - angle_coeff @angle:25-20-25 harmonic 5.0 109.47 - angle_coeff @angle:13-20-25 harmonic 10.0 109.47 - angle_coeff @angle:13-20-47 harmonic 75.0 111.0 - angle_coeff @angle:25-20-48 harmonic 10.0 109.47 - angle_coeff @angle:13-20-48 harmonic 75.0 111.0 - angle_coeff @angle:47-20-48 harmonic 75.0 111.0 - angle_coeff @angle:48-20-48 harmonic 75.0 111.0 - angle_coeff @angle:3-20-48 harmonic 83.0 116.9 - angle_coeff @angle:2-20-48 harmonic 100.0 111.8 - angle_coeff @angle:13-20-51 harmonic 60.0 109.5 - angle_coeff @angle:2-20-51 harmonic 100.0 113.0 - angle_coeff @angle:6-20-51 harmonic 100.0 113.0 - angle_coeff @angle:10-20-51 harmonic 100.0 113.0 - angle_coeff @angle:24-20-60 harmonic 70.0 104.5 - angle_coeff @angle:25-20-61 harmonic 10.0 125.0 - angle_coeff @angle:2-20-64 harmonic 100.0 120.5 - angle_coeff @angle:6-20-64 harmonic 100.0 120.5 - angle_coeff @angle:10-20-64 harmonic 100.0 120.5 - angle_coeff @angle:13-20-64 harmonic 100.0 120.5 - angle_coeff @angle:48-20-64 harmonic 100.0 120.5 - angle_coeff @angle:64-20-64 harmonic 100.0 120.5 - angle_coeff @angle:25-20-82 harmonic 10.0 125.0 - angle_coeff @angle:60-20-82 harmonic 70.0 106.5 - angle_coeff @angle:82-20-82 harmonic 70.0 107.0 - angle_coeff @angle:25-20-84 harmonic 10.0 125.0 - angle_coeff @angle:82-20-84 harmonic 70.0 104.0 - angle_coeff @angle:60-20-84 harmonic 70.0 106.5 - angle_coeff @angle:84-20-84 harmonic 70.0 106.5 - angle_coeff @angle:61-20-84 harmonic 70.0 108.9 - angle_coeff @angle:108-20-108 harmonic 20.0 145.0 - angle_coeff @angle:13-20-108 harmonic 40.0 130.0 - angle_coeff @angle:25-21-25 harmonic 33.0 109.47 - angle_coeff @angle:13-22-13 harmonic 62.0 96.0 - angle_coeff @angle:13-22-23 harmonic 74.0 107.0 - angle_coeff @angle:23-22-25 harmonic 10.0 90.0 - angle_coeff @angle:2-24-3 harmonic 50.0 121.9 - angle_coeff @angle:3-24-3 harmonic 70.0 126.4 - angle_coeff @angle:3-24-5 harmonic 46.0 115.7 - angle_coeff @angle:2-24-6 harmonic 50.0 121.9 - angle_coeff @angle:3-24-6 harmonic 50.0 121.9 - angle_coeff @angle:2-24-10 harmonic 50.0 118.0 - angle_coeff @angle:3-24-10 harmonic 50.0 121.9 - angle_coeff @angle:13-24-13 harmonic 50.0 118.0 - angle_coeff @angle:3-24-13 harmonic 50.0 121.9 - angle_coeff @angle:3-24-16 harmonic 70.0 112.0 - angle_coeff @angle:3-24-20 harmonic 70.0 108.6 - angle_coeff @angle:3-24-25 harmonic 10.0 109.5 - angle_coeff @angle:25-24-45 harmonic 10.0 100.0 - angle_coeff @angle:5-24-45 harmonic 35.0 110.2 - angle_coeff @angle:3-24-45 harmonic 35.0 119.8 - angle_coeff @angle:45-24-45 harmonic 35.0 120.0 - angle_coeff @angle:2-24-45 harmonic 38.0 118.4 - angle_coeff @angle:6-24-45 harmonic 38.0 118.4 - angle_coeff @angle:10-24-45 harmonic 38.0 118.4 - angle_coeff @angle:13-24-45 harmonic 38.0 118.4 - angle_coeff @angle:45-24-48 harmonic 35.0 119.8 - angle_coeff @angle:13-24-48 harmonic 50.0 118.0 - angle_coeff @angle:3-24-48 harmonic 50.0 121.9 - angle_coeff @angle:48-24-48 harmonic 70.0 118.0 - angle_coeff @angle:54-24-54 harmonic 35.0 120.0 - angle_coeff @angle:45-24-59 harmonic 35.0 118.0 - angle_coeff @angle:3-24-59 harmonic 70.0 125.2 - angle_coeff @angle:13-24-79 harmonic 50.0 120.0 - angle_coeff @angle:45-24-79 harmonic 100.0 111.0 - angle_coeff @angle:45-24-84 harmonic 35.0 119.8 - angle_coeff @angle:48-24-84 harmonic 70.0 118.0 - angle_coeff @angle:16-24-86 harmonic 70.0 117.0 - angle_coeff @angle:45-24-87 harmonic 35.0 119.8 - angle_coeff @angle:48-24-87 harmonic 70.0 118.0 - angle_coeff @angle:45-24-88 harmonic 35.0 119.8 - angle_coeff @angle:48-24-88 harmonic 70.0 118.0 - angle_coeff @angle:45-24-91 harmonic 40.0 113.0 - angle_coeff @angle:3-24-91 harmonic 55.0 128.0 - angle_coeff @angle:48-24-103 harmonic 70.0 121.0 - angle_coeff @angle:3-24-106 harmonic 20.0 126.0 - angle_coeff @angle:25-25-25 harmonic 33.0 109.47 - angle_coeff @angle:32-31-32 harmonic 75.0 104.52 - angle_coeff @angle:32-31-33 harmonic 50.0 52.26 - angle_coeff @angle:35-34-35 harmonic 34.05 104.52 - angle_coeff @angle:37-36-37 harmonic 75.0 109.5 - angle_coeff @angle:37-36-38 harmonic 50.0 54.75 - angle_coeff @angle:40-39-40 harmonic 75.0 104.52 - angle_coeff @angle:41-39-41 harmonic 50.0 109.47 - angle_coeff @angle:40-39-41 harmonic 50.0 110.6948 - angle_coeff @angle:43-42-43 harmonic 75.0 109.47 - angle_coeff @angle:2-44-2 harmonic 51.8 107.2 - angle_coeff @angle:2-44-6 harmonic 51.8 107.2 - angle_coeff @angle:6-44-6 harmonic 51.8 107.2 - angle_coeff @angle:2-44-10 harmonic 51.8 107.2 - angle_coeff @angle:6-44-10 harmonic 51.8 107.2 - angle_coeff @angle:10-44-10 harmonic 51.8 107.2 - angle_coeff @angle:2-44-13 harmonic 51.8 107.2 - 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angle_coeff @angle:25-45-44 harmonic 10.0 109.5 - angle_coeff @angle:25-46-25 harmonic 33.0 109.47 - angle_coeff @angle:13-46-25 harmonic 37.5 109.47 - angle_coeff @angle:1-47-1 harmonic 80.0 108.0 - angle_coeff @angle:1-47-3 harmonic 80.0 121.5 - angle_coeff @angle:3-47-6 harmonic 85.0 119.7 - angle_coeff @angle:3-47-13 harmonic 70.0 119.7 - angle_coeff @angle:13-47-13 harmonic 70.0 130.0 - angle_coeff @angle:25-47-46 harmonic 10.0 90.0 - angle_coeff @angle:20-47-46 harmonic 35.0 114.5 - angle_coeff @angle:13-47-46 harmonic 35.0 117.0 - angle_coeff @angle:46-47-46 harmonic 35.0 117.0 - angle_coeff @angle:3-47-46 harmonic 35.0 119.7 - angle_coeff @angle:19-47-46 harmonic 35.0 120.0 - angle_coeff @angle:1-47-46 harmonic 50.0 112.0 - angle_coeff @angle:21-47-46 harmonic 60.0 114.0 - angle_coeff @angle:25-47-47 harmonic 2.0 90.0 - angle_coeff @angle:46-47-47 harmonic 35.0 120.0 - angle_coeff @angle:5-47-47 harmonic 70.0 123.0 - angle_coeff @angle:20-47-47 harmonic 70.0 123.0 - angle_coeff @angle:13-47-47 harmonic 70.0 124.0 - angle_coeff @angle:19-47-47 harmonic 70.0 124.0 - angle_coeff @angle:21-47-47 harmonic 75.0 121.5 - angle_coeff @angle:1-47-47 harmonic 80.0 121.5 - angle_coeff @angle:16-47-47 harmonic 85.0 119.4 - angle_coeff @angle:3-47-47 harmonic 85.0 120.7 - angle_coeff @angle:46-47-48 harmonic 35.0 123.3 - angle_coeff @angle:47-47-48 harmonic 85.0 117.0 - angle_coeff @angle:13-47-48 harmonic 85.0 119.7 - angle_coeff @angle:25-47-50 harmonic 2.0 90.0 - angle_coeff @angle:46-47-50 harmonic 35.0 120.0 - angle_coeff @angle:5-47-50 harmonic 70.0 123.0 - angle_coeff @angle:20-47-50 harmonic 70.0 123.0 - angle_coeff @angle:13-47-50 harmonic 70.0 124.0 - angle_coeff @angle:46-47-57 harmonic 35.0 119.1 - angle_coeff @angle:13-47-57 harmonic 70.0 120.0 - angle_coeff @angle:20-47-57 harmonic 70.0 120.0 - angle_coeff @angle:47-47-57 harmonic 70.0 121.2 - angle_coeff @angle:16-47-57 harmonic 85.0 119.4 - angle_coeff @angle:57-47-58 harmonic 35.0 119.1 - angle_coeff @angle:47-47-58 harmonic 35.0 119.7 - angle_coeff @angle:46-47-65 harmonic 60.0 114.0 - angle_coeff @angle:47-47-65 harmonic 75.0 120.0 - angle_coeff @angle:46-47-91 harmonic 35.0 135.0 - angle_coeff @angle:3-47-91 harmonic 70.0 119.7 - angle_coeff @angle:47-47-91 harmonic 70.0 124.0 - angle_coeff @angle:46-47-105 harmonic 35.0 119.1 - angle_coeff @angle:58-47-105 harmonic 35.0 119.1 - angle_coeff @angle:13-47-105 harmonic 70.0 120.0 - angle_coeff @angle:20-47-105 harmonic 70.0 120.0 - angle_coeff @angle:47-47-105 harmonic 70.0 121.2 - angle_coeff @angle:16-47-105 harmonic 85.0 119.4 - angle_coeff @angle:46-47-110 harmonic 40.0 121.0 - angle_coeff @angle:13-47-110 harmonic 80.0 122.0 - angle_coeff @angle:48-47-110 harmonic 80.0 122.0 - angle_coeff @angle:1-47-110 harmonic 80.0 125.0 - angle_coeff @angle:2-48-12 harmonic 70.0 120.0 - angle_coeff @angle:12-48-12 harmonic 85.0 120.0 - angle_coeff @angle:3-48-13 harmonic 70.0 119.7 - angle_coeff @angle:25-48-48 harmonic 10.0 90.0 - angle_coeff @angle:48-48-48 harmonic 63.0 120.0 - angle_coeff @angle:2-48-48 harmonic 70.0 120.0 - angle_coeff @angle:5-48-48 harmonic 70.0 120.0 - angle_coeff @angle:10-48-48 harmonic 70.0 120.0 - angle_coeff @angle:13-48-48 harmonic 70.0 120.0 - angle_coeff @angle:15-48-48 harmonic 70.0 120.0 - angle_coeff @angle:19-48-48 harmonic 70.0 120.0 - angle_coeff @angle:20-48-48 harmonic 70.0 120.0 - angle_coeff @angle:24-48-48 harmonic 70.0 120.0 - angle_coeff @angle:44-48-48 harmonic 70.0 120.0 - angle_coeff @angle:47-48-48 harmonic 70.0 124.0 - angle_coeff @angle:21-48-48 harmonic 75.0 120.0 - angle_coeff @angle:1-48-48 harmonic 80.0 120.0 - angle_coeff @angle:18-48-48 harmonic 80.0 120.0 - angle_coeff @angle:16-48-48 harmonic 85.0 119.4 - angle_coeff @angle:3-48-48 harmonic 85.0 120.0 - angle_coeff @angle:25-48-49 harmonic 2.0 90.0 - angle_coeff @angle:24-48-49 harmonic 35.0 119.1 - angle_coeff @angle:3-48-49 harmonic 35.0 120.0 - angle_coeff @angle:48-48-49 harmonic 35.0 120.0 - angle_coeff @angle:48-48-50 harmonic 70.0 124.0 - angle_coeff @angle:48-48-53 harmonic 70.0 120.0 - angle_coeff @angle:55-48-55 harmonic 70.0 120.0 - angle_coeff @angle:47-48-55 harmonic 70.0 120.1 - angle_coeff @angle:48-48-55 harmonic 70.0 120.1 - angle_coeff @angle:49-48-56 harmonic 35.0 116.0 - angle_coeff @angle:13-48-56 harmonic 70.0 116.0 - angle_coeff @angle:44-48-56 harmonic 70.0 116.0 - angle_coeff @angle:55-48-56 harmonic 70.0 119.3 - angle_coeff @angle:5-48-56 harmonic 70.0 120.0 - angle_coeff @angle:47-48-56 harmonic 70.0 121.5 - angle_coeff @angle:50-48-56 harmonic 70.0 121.5 - angle_coeff @angle:48-48-56 harmonic 70.0 124.0 - angle_coeff @angle:21-48-56 harmonic 75.0 120.0 - angle_coeff @angle:49-48-57 harmonic 35.0 120.0 - angle_coeff @angle:48-48-57 harmonic 70.0 108.7 - angle_coeff @angle:55-48-57 harmonic 70.0 116.0 - angle_coeff @angle:13-48-57 harmonic 70.0 120.0 - angle_coeff @angle:47-48-57 harmonic 70.0 121.5 - angle_coeff @angle:56-48-57 harmonic 70.0 123.3 - angle_coeff @angle:49-48-60 harmonic 35.0 120.0 - angle_coeff @angle:48-48-60 harmonic 63.0 120.0 - angle_coeff @angle:57-48-60 harmonic 70.0 108.7 - angle_coeff @angle:56-48-60 harmonic 70.0 117.3 - angle_coeff @angle:55-48-60 harmonic 70.0 123.5 - angle_coeff @angle:2-48-60 harmonic 70.0 128.6 - angle_coeff @angle:13-48-60 harmonic 70.0 128.6 - angle_coeff @angle:49-48-61 harmonic 35.0 119.1 - angle_coeff @angle:48-48-61 harmonic 70.0 108.7 - angle_coeff @angle:57-48-61 harmonic 70.0 123.3 - angle_coeff @angle:48-48-64 harmonic 85.0 119.4 - angle_coeff @angle:48-48-65 harmonic 75.0 120.0 - angle_coeff @angle:48-48-66 harmonic 75.0 120.0 - angle_coeff @angle:48-48-79 harmonic 85.0 119.4 - angle_coeff @angle:49-48-81 harmonic 35.0 120.0 - angle_coeff @angle:48-48-81 harmonic 85.0 120.0 - angle_coeff @angle:49-48-84 harmonic 35.0 126.9 - angle_coeff @angle:60-48-84 harmonic 63.0 106.4 - angle_coeff @angle:48-48-84 harmonic 70.0 107.4 - angle_coeff @angle:49-48-86 harmonic 35.0 120.0 - angle_coeff @angle:48-48-86 harmonic 63.0 120.0 - angle_coeff @angle:56-48-86 harmonic 70.0 124.0 - angle_coeff @angle:49-48-88 harmonic 35.0 128.2 - angle_coeff @angle:101-48-101 harmonic 70.0 111.8 - angle_coeff @angle:56-48-101 harmonic 70.0 124.1 - angle_coeff @angle:48-48-102 harmonic 85.0 120.0 - angle_coeff @angle:48-48-109 harmonic 70.0 124.0 - angle_coeff @angle:25-50-46 harmonic 10.0 90.0 - angle_coeff @angle:19-50-46 harmonic 35.0 120.0 - angle_coeff @angle:25-50-47 harmonic 2.0 90.0 - angle_coeff @angle:46-50-47 harmonic 35.0 120.0 - angle_coeff @angle:3-50-47 harmonic 70.0 118.7 - angle_coeff @angle:13-50-47 harmonic 70.0 124.0 - angle_coeff @angle:46-50-48 harmonic 35.0 123.3 - angle_coeff @angle:47-50-48 harmonic 85.0 117.0 - angle_coeff @angle:25-50-50 harmonic 2.0 90.0 - angle_coeff @angle:46-50-50 harmonic 35.0 120.0 - angle_coeff @angle:13-50-50 harmonic 70.0 124.0 - angle_coeff @angle:47-50-50 harmonic 70.0 124.0 - angle_coeff @angle:50-50-84 harmonic 35.0 106.0 - angle_coeff @angle:46-50-84 harmonic 35.0 122.0 - angle_coeff @angle:46-50-109 harmonic 35.0 120.0 - angle_coeff @angle:13-50-109 harmonic 70.0 124.0 - angle_coeff @angle:47-50-109 harmonic 70.0 124.0 - angle_coeff @angle:6-51-6 harmonic 40.0 109.5 - angle_coeff @angle:5-51-13 harmonic 50.0 109.5 - angle_coeff @angle:13-51-20 harmonic 50.0 109.5 - angle_coeff @angle:2-51-20 harmonic 80.0 109.5 - angle_coeff @angle:6-51-20 harmonic 80.0 109.5 - angle_coeff @angle:5-51-20 harmonic 92.6 111.55 - angle_coeff @angle:20-51-20 harmonic 92.6 111.55 - angle_coeff @angle:46-51-46 harmonic 33.0 109.5 - angle_coeff @angle:5-51-46 harmonic 35.0 109.5 - angle_coeff @angle:20-51-46 harmonic 35.0 109.5 - angle_coeff @angle:13-51-46 harmonic 37.5 110.7 - angle_coeff @angle:46-51-105 harmonic 35.0 109.5 - angle_coeff @angle:13-51-105 harmonic 50.0 109.5 - angle_coeff @angle:20-51-105 harmonic 50.0 109.5 - angle_coeff @angle:13-53-13 harmonic 50.0 113.0 - angle_coeff @angle:13-53-25 harmonic 10.0 100.0 - angle_coeff @angle:45-53-45 harmonic 43.6 109.5 - angle_coeff @angle:25-53-48 harmonic 10.0 100.0 - angle_coeff @angle:13-53-48 harmonic 55.0 114.0 - angle_coeff @angle:2-53-54 harmonic 35.0 109.5 - angle_coeff @angle:6-53-54 harmonic 35.0 109.5 - angle_coeff @angle:13-53-54 harmonic 35.0 109.5 - angle_coeff @angle:48-53-54 harmonic 35.0 109.5 - angle_coeff @angle:54-53-54 harmonic 35.0 109.5 - angle_coeff @angle:25-53-82 harmonic 10.0 100.0 - angle_coeff @angle:13-55-13 harmonic 50.0 118.0 - angle_coeff @angle:45-55-45 harmonic 35.0 113.0 - angle_coeff @angle:13-55-45 harmonic 35.0 118.4 - angle_coeff @angle:45-55-48 harmonic 35.0 120.0 - angle_coeff @angle:2-55-48 harmonic 50.0 123.2 - angle_coeff @angle:6-55-48 harmonic 50.0 123.2 - angle_coeff @angle:13-55-48 harmonic 50.0 123.2 - angle_coeff @angle:2-55-54 harmonic 35.0 118.4 - angle_coeff @angle:13-55-54 harmonic 35.0 118.4 - angle_coeff @angle:48-55-54 harmonic 35.0 120.0 - angle_coeff @angle:54-55-54 harmonic 35.0 120.0 - angle_coeff @angle:45-55-59 harmonic 35.0 120.0 - angle_coeff @angle:3-56-13 harmonic 70.0 120.5 - angle_coeff @angle:13-56-18 harmonic 70.0 120.0 - angle_coeff @angle:25-56-48 harmonic 5.0 120.0 - angle_coeff @angle:45-56-48 harmonic 35.0 113.0 - angle_coeff @angle:13-56-48 harmonic 50.0 118.0 - angle_coeff @angle:48-56-48 harmonic 70.0 117.0 - angle_coeff @angle:3-56-48 harmonic 70.0 120.5 - angle_coeff @angle:13-56-56 harmonic 70.0 117.0 - angle_coeff @angle:48-56-56 harmonic 70.0 117.0 - angle_coeff @angle:25-56-59 harmonic 5.0 119.8 - angle_coeff @angle:48-56-59 harmonic 70.0 118.6 - angle_coeff @angle:59-56-59 harmonic 70.0 118.6 - angle_coeff @angle:59-56-60 harmonic 70.0 111.0 - angle_coeff @angle:48-56-60 harmonic 70.0 112.2 - angle_coeff @angle:59-56-82 harmonic 70.0 111.0 - angle_coeff @angle:48-56-86 harmonic 70.0 117.0 - angle_coeff @angle:13-56-103 harmonic 70.0 114.0 - angle_coeff @angle:3-57-3 harmonic 70.0 126.4 - angle_coeff @angle:3-57-45 harmonic 35.0 116.8 - angle_coeff @angle:45-57-47 harmonic 35.0 119.2 - angle_coeff @angle:3-57-47 harmonic 70.0 121.6 - angle_coeff @angle:45-57-48 harmonic 35.0 118.0 - angle_coeff @angle:3-57-48 harmonic 70.0 125.2 - angle_coeff @angle:48-57-48 harmonic 70.0 125.2 - angle_coeff @angle:45-57-60 harmonic 30.0 125.8 - angle_coeff @angle:13-57-60 harmonic 70.0 125.8 - angle_coeff @angle:60-57-61 harmonic 56.0 113.1 - angle_coeff @angle:45-57-61 harmonic 56.0 118.4 - angle_coeff @angle:13-57-61 harmonic 70.0 118.4 - angle_coeff @angle:48-57-61 harmonic 70.0 118.4 - angle_coeff @angle:45-57-62 harmonic 30.0 128.8 - angle_coeff @angle:60-57-62 harmonic 70.0 105.4 - angle_coeff @angle:48-57-62 harmonic 70.0 109.8 - angle_coeff @angle:13-57-62 harmonic 70.0 128.8 - angle_coeff @angle:45-57-81 harmonic 35.0 123.1 - angle_coeff @angle:45-57-82 harmonic 35.0 120.0 - angle_coeff @angle:61-57-82 harmonic 56.0 113.1 - angle_coeff @angle:60-57-82 harmonic 70.0 109.8 - angle_coeff @angle:45-57-84 harmonic 35.0 120.0 - angle_coeff @angle:61-57-84 harmonic 56.0 113.1 - angle_coeff @angle:60-57-84 harmonic 70.0 109.8 - angle_coeff @angle:82-57-84 harmonic 70.0 109.8 - angle_coeff @angle:84-57-84 harmonic 70.0 109.8 - angle_coeff @angle:81-57-84 harmonic 70.0 111.6 - angle_coeff @angle:45-57-85 harmonic 35.0 120.0 - angle_coeff @angle:82-57-85 harmonic 70.0 109.8 - angle_coeff @angle:24-59-55 harmonic 70.0 116.0 - angle_coeff @angle:49-59-56 harmonic 35.0 115.45 - angle_coeff @angle:13-59-56 harmonic 70.0 115.5 - angle_coeff @angle:55-59-56 harmonic 70.0 119.3 - angle_coeff @angle:24-59-56 harmonic 70.0 123.3 - angle_coeff @angle:56-59-56 harmonic 70.0 129.1 - angle_coeff @angle:56-59-63 harmonic 35.0 115.45 - angle_coeff @angle:13-60-48 harmonic 70.0 120.0 - angle_coeff @angle:48-60-48 harmonic 85.0 134.9 - angle_coeff @angle:56-60-57 harmonic 70.0 126.2 - angle_coeff @angle:57-60-60 harmonic 70.0 106.2 - angle_coeff @angle:20-60-60 harmonic 70.0 110.6 - angle_coeff @angle:16-60-60 harmonic 70.0 111.0 - angle_coeff @angle:13-60-60 harmonic 70.0 120.0 - angle_coeff @angle:24-60-60 harmonic 70.0 127.7 - angle_coeff @angle:56-60-60 harmonic 70.0 127.7 - angle_coeff @angle:48-60-60 harmonic 85.0 117.3 - angle_coeff @angle:3-60-60 harmonic 85.0 119.2 - angle_coeff @angle:60-60-61 harmonic 70.0 111.0 - angle_coeff @angle:24-60-61 harmonic 70.0 126.2 - angle_coeff @angle:3-60-61 harmonic 70.0 130.0 - angle_coeff @angle:48-60-61 harmonic 70.0 132.4 - angle_coeff @angle:12-60-80 harmonic 85.0 134.9 - angle_coeff @angle:48-60-80 harmonic 85.0 134.9 - angle_coeff @angle:80-60-81 harmonic 85.0 108.8 - angle_coeff @angle:12-60-81 harmonic 85.0 116.2 - angle_coeff @angle:48-60-81 harmonic 85.0 116.2 - angle_coeff @angle:3-60-84 harmonic 70.0 130.0 - angle_coeff @angle:60-60-87 harmonic 70.0 107.3 - angle_coeff @angle:57-60-87 harmonic 70.0 107.7 - angle_coeff @angle:81-60-87 harmonic 85.0 108.8 - angle_coeff @angle:12-60-87 harmonic 85.0 134.9 - angle_coeff @angle:48-60-87 harmonic 85.0 134.9 - angle_coeff @angle:60-60-105 harmonic 70.0 106.2 - angle_coeff @angle:56-60-105 harmonic 70.0 126.2 - angle_coeff @angle:48-61-48 harmonic 70.0 125.2 - angle_coeff @angle:25-61-57 harmonic 10.0 125.0 - angle_coeff @angle:25-61-61 harmonic 10.0 125.0 - angle_coeff @angle:60-61-62 harmonic 70.0 103.8 - angle_coeff @angle:25-61-82 harmonic 10.0 125.0 - angle_coeff @angle:61-61-82 harmonic 70.0 109.0 - angle_coeff @angle:60-61-82 harmonic 70.0 110.0 - angle_coeff @angle:82-61-83 harmonic 70.0 110.0 - angle_coeff @angle:57-61-84 harmonic 70.0 104.1 - angle_coeff @angle:82-61-84 harmonic 70.0 110.0 - angle_coeff @angle:57-61-88 harmonic 70.0 104.1 - angle_coeff @angle:20-61-88 harmonic 70.0 105.3 - angle_coeff @angle:49-62-57 harmonic 35.0 120.0 - angle_coeff @angle:49-62-61 harmonic 35.0 120.0 - angle_coeff @angle:57-62-61 harmonic 70.0 113.9 - angle_coeff @angle:57-62-63 harmonic 35.0 123.05 - angle_coeff @angle:61-62-63 harmonic 35.0 123.05 - angle_coeff @angle:49-62-105 harmonic 35.0 120.0 - angle_coeff @angle:63-62-105 harmonic 35.0 123.05 - angle_coeff @angle:61-62-105 harmonic 70.0 113.9 - angle_coeff @angle:5-64-5 harmonic 45.0 102.6 - angle_coeff @angle:4-64-5 harmonic 100.0 108.23 - angle_coeff @angle:4-64-13 harmonic 45.0 109.5 - angle_coeff @angle:5-64-20 harmonic 45.0 102.6 - angle_coeff @angle:20-64-20 harmonic 45.0 102.6 - angle_coeff @angle:13-64-20 harmonic 45.0 109.5 - angle_coeff @angle:4-64-20 harmonic 100.0 108.23 - angle_coeff @angle:4-64-48 harmonic 45.0 109.5 - angle_coeff @angle:5-64-48 harmonic 45.0 109.5 - angle_coeff @angle:20-64-48 harmonic 45.0 109.5 - angle_coeff @angle:5-64-52 harmonic 45.0 108.23 - angle_coeff @angle:13-64-52 harmonic 45.0 109.5 - angle_coeff @angle:20-64-52 harmonic 100.0 108.23 - angle_coeff @angle:52-64-52 harmonic 140.0 119.9 - angle_coeff @angle:25-65-25 harmonic 33.0 109.47 - angle_coeff @angle:25-66-25 harmonic 33.0 109.47 - angle_coeff @angle:78-77-78 harmonic 150.0 180.0 - angle_coeff @angle:6-79-11 harmonic 62.0 98.9 - angle_coeff @angle:13-79-13 harmonic 62.0 102.0 - angle_coeff @angle:5-79-13 harmonic 75.0 96.4 - angle_coeff @angle:5-79-23 harmonic 74.0 108.7 - angle_coeff @angle:13-79-23 harmonic 74.0 108.9 - angle_coeff @angle:23-79-23 harmonic 104.0 119.0 - angle_coeff @angle:13-79-24 harmonic 100.0 103.0 - angle_coeff @angle:23-79-24 harmonic 120.0 107.0 - angle_coeff @angle:13-79-44 harmonic 62.0 102.0 - angle_coeff @angle:23-79-44 harmonic 74.0 108.9 - angle_coeff @angle:13-79-48 harmonic 62.0 102.0 - angle_coeff @angle:23-79-48 harmonic 74.0 107.2 - angle_coeff @angle:5-79-48 harmonic 75.0 96.4 - angle_coeff @angle:24-79-48 harmonic 100.0 103.0 - angle_coeff @angle:13-79-82 harmonic 62.0 102.0 - angle_coeff @angle:46-80-60 harmonic 35.0 126.8 - angle_coeff @angle:2-80-60 harmonic 70.0 128.6 - angle_coeff @angle:13-80-60 harmonic 70.0 128.6 - angle_coeff @angle:46-80-84 harmonic 35.0 126.8 - angle_coeff @angle:2-80-84 harmonic 70.0 125.0 - angle_coeff @angle:13-80-84 harmonic 70.0 125.0 - angle_coeff @angle:60-80-84 harmonic 85.0 106.4 - angle_coeff @angle:12-81-57 harmonic 70.0 132.8 - angle_coeff @angle:48-81-57 harmonic 70.0 132.8 - angle_coeff @angle:57-81-60 harmonic 70.0 104.4 - angle_coeff @angle:12-81-60 harmonic 85.0 122.7 - angle_coeff @angle:48-81-60 harmonic 85.0 122.7 - angle_coeff @angle:13-82-16 harmonic 70.0 125.0 - angle_coeff @angle:16-82-24 harmonic 70.0 125.0 - angle_coeff @angle:16-82-44 harmonic 70.0 120.2 - angle_coeff @angle:20-82-49 harmonic 35.0 117.0 - angle_coeff @angle:16-82-49 harmonic 35.0 125.0 - angle_coeff @angle:49-82-57 harmonic 35.0 120.0 - angle_coeff @angle:57-82-57 harmonic 70.0 120.0 - angle_coeff @angle:13-82-57 harmonic 70.0 125.0 - angle_coeff @angle:48-82-57 harmonic 70.0 125.0 - angle_coeff @angle:56-82-57 harmonic 70.0 126.2 - angle_coeff @angle:49-82-61 harmonic 35.0 120.0 - angle_coeff @angle:16-82-61 harmonic 70.0 115.0 - angle_coeff @angle:20-82-61 harmonic 70.0 115.0 - angle_coeff @angle:57-82-61 harmonic 70.0 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@angle:004_003_087 80.0 128.2 + angle_coeff @angle:057_003_105 70.0 115.4 + angle_coeff @angle:056_003_105 70.0 118.6 + angle_coeff @angle:004_003_105 80.0 120.9 + angle_coeff @angle:013_003_107 70.0 116.6 + angle_coeff @angle:004_003_107 80.0 122.9 + angle_coeff @angle:025_004_025 10.0 117.0 + angle_coeff @angle:003_004_025 35.0 113.0 + angle_coeff @angle:003_005_007 35.0 113.0 + angle_coeff @angle:002_005_007 55.0 108.5 + angle_coeff @angle:006_005_007 55.0 108.5 + angle_coeff @angle:007_005_010 55.0 108.5 + angle_coeff @angle:007_005_013 55.0 108.5 + angle_coeff @angle:007_005_024 49.0 105.4 + angle_coeff @angle:025_005_025 5.0 109.47 + angle_coeff @angle:007_005_025 10.0 109.47 + angle_coeff @angle:013_005_025 10.0 109.47 + angle_coeff @angle:007_005_047 35.0 109.0 + angle_coeff @angle:025_005_048 10.0 109.47 + angle_coeff @angle:007_005_048 35.0 113.0 + angle_coeff @angle:007_005_051 55.0 108.5 + angle_coeff @angle:007_005_064 55.0 108.5 + angle_coeff @angle:013_005_064 100.0 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angle_coeff @angle:013_090_089 55.0 127.0 + angle_coeff @angle:089_090_091 50.0 94.0 + angle_coeff @angle:013_090_091 50.0 126.0 + angle_coeff @angle:024_091_046 35.0 108.0 + angle_coeff @angle:013_091_046 35.0 114.3 + angle_coeff @angle:044_091_046 35.0 114.3 + angle_coeff @angle:046_091_046 35.0 114.3 + angle_coeff @angle:016_091_046 37.5 108.0 + angle_coeff @angle:046_091_047 35.0 109.5 + angle_coeff @angle:046_091_089 37.5 110.0 + angle_coeff @angle:024_091_089 70.0 117.0 + angle_coeff @angle:046_091_090 35.0 111.0 + angle_coeff @angle:016_091_090 55.0 109.0 + angle_coeff @angle:091_091_091 30.0 79.2 + angle_coeff @angle:013_091_091 37.5 117.2 + angle_coeff @angle:044_091_091 37.5 117.2 + angle_coeff @angle:046_091_091 37.5 117.2 + angle_coeff @angle:024_091_091 37.5 126.0 + angle_coeff @angle:016_091_091 55.0 128.0 + angle_coeff @angle:089_091_091 63.0 85.0 + angle_coeff @angle:047_091_091 63.0 114.0 + angle_coeff @angle:090_091_091 80.0 89.0 + angle_coeff @angle:013_095_013 172.8 120.0 + angle_coeff @angle:013_095_046 144.0 120.0 + angle_coeff @angle:013_101_045 35.0 109.5 + angle_coeff @angle:045_101_045 43.6 106.4 + angle_coeff @angle:045_101_048 50.0 112.5 + angle_coeff @angle:013_101_048 50.0 120.5 + angle_coeff @angle:013_102_103 80.0 117.5 + angle_coeff @angle:048_102_103 80.0 117.5 + angle_coeff @angle:103_102_103 80.0 125.0 + angle_coeff @angle:025_103_025 10.0 109.5 + angle_coeff @angle:025_103_102 10.0 109.5 + angle_coeff @angle:013_104_013 45.0 109.5 + angle_coeff @angle:003_105_010 70.0 117.6 + angle_coeff @angle:003_105_013 70.0 117.6 + angle_coeff @angle:003_105_045 35.0 119.2 + angle_coeff @angle:045_105_047 35.0 119.2 + angle_coeff @angle:013_105_047 70.0 121.2 + angle_coeff @angle:003_105_047 70.0 121.6 + angle_coeff @angle:003_105_051 70.0 117.6 + angle_coeff @angle:047_105_051 70.0 121.2 + angle_coeff @angle:045_105_060 30.0 125.8 + angle_coeff @angle:006_105_060 70.0 125.8 + angle_coeff @angle:010_105_060 70.0 125.8 + angle_coeff @angle:013_105_060 70.0 125.8 + angle_coeff @angle:051_105_060 70.0 125.8 + angle_coeff @angle:045_105_062 30.0 128.8 + angle_coeff @angle:060_105_062 70.0 105.4 + angle_coeff @angle:006_105_062 70.0 128.8 + angle_coeff @angle:010_105_062 70.0 128.8 + angle_coeff @angle:013_105_062 70.0 128.8 + angle_coeff @angle:051_105_062 70.0 128.8 + angle_coeff @angle:004_106_024 20.0 109.5 + angle_coeff @angle:024_106_024 20.0 109.5 + angle_coeff @angle:013_107_013 50.0 118.0 + angle_coeff @angle:003_107_013 50.0 121.9 + angle_coeff @angle:001_108_013 35.0 110.5 + angle_coeff @angle:013_108_013 60.0 110.0 + angle_coeff @angle:013_108_020 60.0 100.0 + angle_coeff @angle:020_108_020 60.0 110.0 + angle_coeff @angle:013_108_021 35.0 110.5 + angle_coeff @angle:045_108_045 35.0 109.5 + angle_coeff @angle:013_108_045 35.0 110.5 + angle_coeff @angle:046_108_046 35.0 109.5 + angle_coeff @angle:013_108_046 35.0 110.5 + angle_coeff @angle:013_108_065 35.0 110.5 + angle_coeff @angle:013_108_066 35.0 110.5 + angle_coeff @angle:013_108_108 50.0 112.0 + angle_coeff @angle:046_109_048 35.0 123.3 + angle_coeff @angle:046_109_050 35.0 120.0 + angle_coeff @angle:013_109_050 70.0 124.0 + angle_coeff @angle:046_109_109 35.0 120.0 + angle_coeff @angle:013_109_109 70.0 124.0 + angle_coeff @angle:050_109_109 70.0 124.0 + angle_coeff @angle:048_109_109 85.0 117.0 + angle_coeff @angle:004_110_047 160.0 180.0 + angle_coeff @angle:047_110_047 160.0 180.0 } #(end of angle_coeffs) # Rules for creating angle interactions according to atom type: @@ -5492,1023 +5505,1023 @@ OPLSAA { # (* = wildcard) write_once("Data Angles By Type") { - @angle:25-1-25 @atom:*_b*_a25_d*_i* @atom:*_b*_a1_d*_i* @atom:*_b*_a25_d*_i* - @angle:1-2-2 @atom:*_b*_a1_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a2_d*_i* - @angle:2-2-2 @atom:*_b*_a2_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a2_d*_i* - @angle:2-2-3 @atom:*_b*_a2_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a3_d*_i* - @angle:2-2-5 @atom:*_b*_a2_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a5_d*_i* - @angle:2-2-6 @atom:*_b*_a2_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a6_d*_i* - @angle:6-2-6 @atom:*_b*_a6_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a6_d*_i* - @angle:5-2-6 @atom:*_b*_a5_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a6_d*_i* - @angle:2-2-10 @atom:*_b*_a2_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a10_d*_i* - @angle:3-2-10 @atom:*_b*_a3_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a10_d*_i* - @angle:6-2-10 @atom:*_b*_a6_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a10_d*_i* - @angle:10-2-10 @atom:*_b*_a10_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a10_d*_i* - @angle:5-2-10 @atom:*_b*_a5_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a10_d*_i* - @angle:10-2-12 @atom:*_b*_a10_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a12_d*_i* - @angle:6-2-13 @atom:*_b*_a6_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a13_d*_i* - @angle:10-2-15 @atom:*_b*_a10_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a15_d*_i* - @angle:2-2-16 @atom:*_b*_a2_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a16_d*_i* - @angle:10-2-16 @atom:*_b*_a10_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a16_d*_i* - @angle:2-2-20 @atom:*_b*_a2_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a20_d*_i* - @angle:6-2-20 @atom:*_b*_a6_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a20_d*_i* - @angle:10-2-20 @atom:*_b*_a10_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a20_d*_i* - @angle:3-2-24 @atom:*_b*_a3_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a24_d*_i* - @angle:2-2-24 @atom:*_b*_a2_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a24_d*_i* - @angle:2-2-44 @atom:*_b*_a2_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a44_d*_i* - @angle:6-2-44 @atom:*_b*_a6_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a44_d*_i* - @angle:10-2-44 @atom:*_b*_a10_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a44_d*_i* - @angle:13-2-44 @atom:*_b*_a13_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a44_d*_i* - @angle:3-2-44 @atom:*_b*_a3_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a44_d*_i* - @angle:2-2-48 @atom:*_b*_a2_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a48_d*_i* - @angle:10-2-48 @atom:*_b*_a10_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a48_d*_i* - @angle:2-2-51 @atom:*_b*_a2_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a51_d*_i* - @angle:6-2-51 @atom:*_b*_a6_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a51_d*_i* - @angle:2-2-53 @atom:*_b*_a2_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a53_d*_i* - @angle:2-2-55 @atom:*_b*_a2_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a55_d*_i* - @angle:10-2-80 @atom:*_b*_a10_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a80_d*_i* - @angle:2-3-4 @atom:*_b*_a2_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a4_d*_i* - @angle:1-3-4 @atom:*_b*_a1_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a4_d*_i* - @angle:3-3-4 @atom:*_b*_a3_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a4_d*_i* - @angle:4-3-4 @atom:*_b*_a4_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a4_d*_i* - @angle:4-3-5 @atom:*_b*_a4_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a5_d*_i* - @angle:4-3-6 @atom:*_b*_a4_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a6_d*_i* - @angle:5-3-10 @atom:*_b*_a5_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a10_d*_i* - @angle:4-3-10 @atom:*_b*_a4_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a10_d*_i* - @angle:5-3-12 @atom:*_b*_a5_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a12_d*_i* - @angle:12-3-12 @atom:*_b*_a12_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a12_d*_i* - @angle:5-3-13 @atom:*_b*_a5_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a13_d*_i* - @angle:13-3-13 @atom:*_b*_a13_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a13_d*_i* - @angle:1-3-13 @atom:*_b*_a1_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a13_d*_i* - @angle:3-3-13 @atom:*_b*_a3_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a13_d*_i* - @angle:4-3-13 @atom:*_b*_a4_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a13_d*_i* - @angle:10-3-20 @atom:*_b*_a10_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a20_d*_i* - @angle:13-3-20 @atom:*_b*_a13_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a20_d*_i* - @angle:4-3-20 @atom:*_b*_a4_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a20_d*_i* - @angle:13-3-21 @atom:*_b*_a13_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a21_d*_i* - @angle:4-3-21 @atom:*_b*_a4_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a21_d*_i* - @angle:24-3-24 @atom:*_b*_a24_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a24_d*_i* - @angle:2-3-24 @atom:*_b*_a2_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a24_d*_i* - @angle:3-3-24 @atom:*_b*_a3_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a24_d*_i* - @angle:6-3-24 @atom:*_b*_a6_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a24_d*_i* - @angle:10-3-24 @atom:*_b*_a10_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a24_d*_i* - @angle:13-3-24 @atom:*_b*_a13_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a24_d*_i* - @angle:4-3-24 @atom:*_b*_a4_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a24_d*_i* - @angle:20-3-24 @atom:*_b*_a20_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a24_d*_i* - @angle:13-3-44 @atom:*_b*_a13_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a44_d*_i* - @angle:4-3-44 @atom:*_b*_a4_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a44_d*_i* - @angle:13-3-46 @atom:*_b*_a13_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a46_d*_i* - @angle:46-3-46 @atom:*_b*_a46_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a46_d*_i* - @angle:4-3-46 @atom:*_b*_a4_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a46_d*_i* - @angle:24-3-46 @atom:*_b*_a24_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a46_d*_i* - @angle:5-3-46 @atom:*_b*_a5_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a46_d*_i* - @angle:20-3-46 @atom:*_b*_a20_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a46_d*_i* - @angle:24-3-47 @atom:*_b*_a24_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a47_d*_i* - @angle:4-3-47 @atom:*_b*_a4_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a47_d*_i* - @angle:46-3-48 @atom:*_b*_a46_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a48_d*_i* - @angle:24-3-48 @atom:*_b*_a24_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a48_d*_i* - @angle:13-3-48 @atom:*_b*_a13_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a48_d*_i* - @angle:5-3-48 @atom:*_b*_a5_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a48_d*_i* - @angle:4-3-48 @atom:*_b*_a4_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a48_d*_i* - @angle:20-3-48 @atom:*_b*_a20_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a48_d*_i* - @angle:48-3-48 @atom:*_b*_a48_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a48_d*_i* - @angle:13-3-50 @atom:*_b*_a13_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a50_d*_i* - @angle:46-3-50 @atom:*_b*_a46_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a50_d*_i* - @angle:4-3-50 @atom:*_b*_a4_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a50_d*_i* - @angle:10-3-52 @atom:*_b*_a10_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a52_d*_i* - @angle:2-3-52 @atom:*_b*_a2_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a52_d*_i* - @angle:6-3-52 @atom:*_b*_a6_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a52_d*_i* - @angle:13-3-52 @atom:*_b*_a13_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a52_d*_i* - @angle:48-3-52 @atom:*_b*_a48_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a52_d*_i* - @angle:4-3-52 @atom:*_b*_a4_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a52_d*_i* - @angle:52-3-52 @atom:*_b*_a52_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a52_d*_i* - @angle:46-3-56 @atom:*_b*_a46_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a56_d*_i* - @angle:4-3-56 @atom:*_b*_a4_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a56_d*_i* - @angle:47-3-57 @atom:*_b*_a47_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a57_d*_i* - @angle:56-3-57 @atom:*_b*_a56_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a57_d*_i* - @angle:57-3-57 @atom:*_b*_a57_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a57_d*_i* - @angle:4-3-57 @atom:*_b*_a4_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a57_d*_i* - @angle:24-3-60 @atom:*_b*_a24_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a60_d*_i* - @angle:57-3-60 @atom:*_b*_a57_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a60_d*_i* - @angle:4-3-60 @atom:*_b*_a4_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a60_d*_i* - @angle:13-3-65 @atom:*_b*_a13_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a65_d*_i* - @angle:4-3-65 @atom:*_b*_a4_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a65_d*_i* - @angle:44-3-84 @atom:*_b*_a44_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a84_d*_i* - @angle:4-3-84 @atom:*_b*_a4_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a84_d*_i* - @angle:4-3-87 @atom:*_b*_a4_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a87_d*_i* - @angle:57-3-105 @atom:*_b*_a57_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a105_d*_i* - @angle:56-3-105 @atom:*_b*_a56_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a105_d*_i* - @angle:4-3-105 @atom:*_b*_a4_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a105_d*_i* - @angle:13-3-107 @atom:*_b*_a13_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a107_d*_i* - @angle:4-3-107 @atom:*_b*_a4_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a107_d*_i* - @angle:25-4-25 @atom:*_b*_a25_d*_i* @atom:*_b*_a4_d*_i* @atom:*_b*_a25_d*_i* - @angle:3-4-25 @atom:*_b*_a3_d*_i* @atom:*_b*_a4_d*_i* @atom:*_b*_a25_d*_i* - @angle:3-5-7 @atom:*_b*_a3_d*_i* @atom:*_b*_a5_d*_i* @atom:*_b*_a7_d*_i* - @angle:2-5-7 @atom:*_b*_a2_d*_i* @atom:*_b*_a5_d*_i* @atom:*_b*_a7_d*_i* - @angle:6-5-7 @atom:*_b*_a6_d*_i* @atom:*_b*_a5_d*_i* @atom:*_b*_a7_d*_i* - @angle:7-5-10 @atom:*_b*_a7_d*_i* @atom:*_b*_a5_d*_i* @atom:*_b*_a10_d*_i* - @angle:7-5-13 @atom:*_b*_a7_d*_i* @atom:*_b*_a5_d*_i* @atom:*_b*_a13_d*_i* - @angle:7-5-24 @atom:*_b*_a7_d*_i* @atom:*_b*_a5_d*_i* @atom:*_b*_a24_d*_i* - @angle:25-5-25 @atom:*_b*_a25_d*_i* @atom:*_b*_a5_d*_i* @atom:*_b*_a25_d*_i* - @angle:7-5-25 @atom:*_b*_a7_d*_i* @atom:*_b*_a5_d*_i* @atom:*_b*_a25_d*_i* - @angle:13-5-25 @atom:*_b*_a13_d*_i* @atom:*_b*_a5_d*_i* @atom:*_b*_a25_d*_i* - 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@atom:*_b*_a13_d*_i* @atom:*_b*_a108_d*_i* @atom:*_b*_a65_d*_i* - @angle:13-108-66 @atom:*_b*_a13_d*_i* @atom:*_b*_a108_d*_i* @atom:*_b*_a66_d*_i* - @angle:13-108-108 @atom:*_b*_a13_d*_i* @atom:*_b*_a108_d*_i* @atom:*_b*_a108_d*_i* - @angle:46-109-48 @atom:*_b*_a46_d*_i* @atom:*_b*_a109_d*_i* @atom:*_b*_a48_d*_i* - @angle:46-109-50 @atom:*_b*_a46_d*_i* @atom:*_b*_a109_d*_i* @atom:*_b*_a50_d*_i* - @angle:13-109-50 @atom:*_b*_a13_d*_i* @atom:*_b*_a109_d*_i* @atom:*_b*_a50_d*_i* - @angle:46-109-109 @atom:*_b*_a46_d*_i* @atom:*_b*_a109_d*_i* @atom:*_b*_a109_d*_i* - @angle:13-109-109 @atom:*_b*_a13_d*_i* @atom:*_b*_a109_d*_i* @atom:*_b*_a109_d*_i* - @angle:50-109-109 @atom:*_b*_a50_d*_i* @atom:*_b*_a109_d*_i* @atom:*_b*_a109_d*_i* - @angle:48-109-109 @atom:*_b*_a48_d*_i* @atom:*_b*_a109_d*_i* @atom:*_b*_a109_d*_i* - @angle:4-110-47 @atom:*_b*_a4_d*_i* @atom:*_b*_a110_d*_i* @atom:*_b*_a47_d*_i* - @angle:47-110-47 @atom:*_b*_a47_d*_i* @atom:*_b*_a110_d*_i* @atom:*_b*_a47_d*_i* + 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@angle:002_002_055 @atom:*_b*_a002*_d*_i* @atom:*_b*_a002*_d*_i* @atom:*_b*_a055*_d*_i* + @angle:010_002_080 @atom:*_b*_a010*_d*_i* @atom:*_b*_a002*_d*_i* @atom:*_b*_a080*_d*_i* + @angle:002_003_004 @atom:*_b*_a002*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a004*_d*_i* + @angle:001_003_004 @atom:*_b*_a001*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a004*_d*_i* + @angle:003_003_004 @atom:*_b*_a003*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a004*_d*_i* + @angle:004_003_004 @atom:*_b*_a004*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a004*_d*_i* + @angle:004_003_005 @atom:*_b*_a004*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a005*_d*_i* + @angle:004_003_006 @atom:*_b*_a004*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a006*_d*_i* + @angle:005_003_010 @atom:*_b*_a005*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a010*_d*_i* + @angle:004_003_010 @atom:*_b*_a004*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a010*_d*_i* + @angle:005_003_012 @atom:*_b*_a005*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a012*_d*_i* + @angle:012_003_012 @atom:*_b*_a012*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a012*_d*_i* + @angle:005_003_013 @atom:*_b*_a005*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:013_003_013 @atom:*_b*_a013*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:001_003_013 @atom:*_b*_a001*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:003_003_013 @atom:*_b*_a003*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:004_003_013 @atom:*_b*_a004*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:010_003_020 @atom:*_b*_a010*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a020*_d*_i* + @angle:013_003_020 @atom:*_b*_a013*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a020*_d*_i* + @angle:004_003_020 @atom:*_b*_a004*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a020*_d*_i* + @angle:013_003_021 @atom:*_b*_a013*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a021*_d*_i* + @angle:004_003_021 @atom:*_b*_a004*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a021*_d*_i* + 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@angle:004_003_048 @atom:*_b*_a004*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:020_003_048 @atom:*_b*_a020*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:048_003_048 @atom:*_b*_a048*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:013_003_050 @atom:*_b*_a013*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a050*_d*_i* + @angle:046_003_050 @atom:*_b*_a046*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a050*_d*_i* + @angle:004_003_050 @atom:*_b*_a004*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a050*_d*_i* + @angle:010_003_052 @atom:*_b*_a010*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a052*_d*_i* + @angle:002_003_052 @atom:*_b*_a002*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a052*_d*_i* + @angle:006_003_052 @atom:*_b*_a006*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a052*_d*_i* + @angle:013_003_052 @atom:*_b*_a013*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a052*_d*_i* + @angle:048_003_052 @atom:*_b*_a048*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a052*_d*_i* + @angle:004_003_052 @atom:*_b*_a004*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a052*_d*_i* + @angle:052_003_052 @atom:*_b*_a052*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a052*_d*_i* + @angle:046_003_056 @atom:*_b*_a046*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a056*_d*_i* + @angle:004_003_056 @atom:*_b*_a004*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a056*_d*_i* + @angle:047_003_057 @atom:*_b*_a047*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a057*_d*_i* + @angle:056_003_057 @atom:*_b*_a056*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a057*_d*_i* + @angle:057_003_057 @atom:*_b*_a057*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a057*_d*_i* + @angle:004_003_057 @atom:*_b*_a004*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a057*_d*_i* + @angle:024_003_060 @atom:*_b*_a024*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a060*_d*_i* + @angle:057_003_060 @atom:*_b*_a057*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a060*_d*_i* + @angle:004_003_060 @atom:*_b*_a004*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a060*_d*_i* + @angle:013_003_065 @atom:*_b*_a013*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a065*_d*_i* + @angle:004_003_065 @atom:*_b*_a004*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a065*_d*_i* + @angle:044_003_084 @atom:*_b*_a044*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a084*_d*_i* + @angle:004_003_084 @atom:*_b*_a004*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a084*_d*_i* + @angle:004_003_087 @atom:*_b*_a004*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a087*_d*_i* + @angle:057_003_105 @atom:*_b*_a057*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a105*_d*_i* + @angle:056_003_105 @atom:*_b*_a056*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a105*_d*_i* + @angle:004_003_105 @atom:*_b*_a004*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a105*_d*_i* + @angle:013_003_107 @atom:*_b*_a013*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a107*_d*_i* + @angle:004_003_107 @atom:*_b*_a004*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a107*_d*_i* + @angle:025_004_025 @atom:*_b*_a025*_d*_i* @atom:*_b*_a004*_d*_i* @atom:*_b*_a025*_d*_i* + @angle:003_004_025 @atom:*_b*_a003*_d*_i* @atom:*_b*_a004*_d*_i* @atom:*_b*_a025*_d*_i* + @angle:003_005_007 @atom:*_b*_a003*_d*_i* @atom:*_b*_a005*_d*_i* @atom:*_b*_a007*_d*_i* + @angle:002_005_007 @atom:*_b*_a002*_d*_i* @atom:*_b*_a005*_d*_i* @atom:*_b*_a007*_d*_i* + @angle:006_005_007 @atom:*_b*_a006*_d*_i* @atom:*_b*_a005*_d*_i* @atom:*_b*_a007*_d*_i* + @angle:007_005_010 @atom:*_b*_a007*_d*_i* @atom:*_b*_a005*_d*_i* @atom:*_b*_a010*_d*_i* + @angle:007_005_013 @atom:*_b*_a007*_d*_i* @atom:*_b*_a005*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:007_005_024 @atom:*_b*_a007*_d*_i* @atom:*_b*_a005*_d*_i* @atom:*_b*_a024*_d*_i* + @angle:025_005_025 @atom:*_b*_a025*_d*_i* @atom:*_b*_a005*_d*_i* @atom:*_b*_a025*_d*_i* + @angle:007_005_025 @atom:*_b*_a007*_d*_i* @atom:*_b*_a005*_d*_i* @atom:*_b*_a025*_d*_i* + @angle:013_005_025 @atom:*_b*_a013*_d*_i* @atom:*_b*_a005*_d*_i* @atom:*_b*_a025*_d*_i* + @angle:007_005_047 @atom:*_b*_a007*_d*_i* @atom:*_b*_a005*_d*_i* @atom:*_b*_a047*_d*_i* + @angle:025_005_048 @atom:*_b*_a025*_d*_i* @atom:*_b*_a005*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:007_005_048 @atom:*_b*_a007*_d*_i* @atom:*_b*_a005*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:007_005_051 @atom:*_b*_a007*_d*_i* @atom:*_b*_a005*_d*_i* @atom:*_b*_a051*_d*_i* + @angle:007_005_064 @atom:*_b*_a007*_d*_i* @atom:*_b*_a005*_d*_i* @atom:*_b*_a064*_d*_i* + @angle:013_005_064 @atom:*_b*_a013*_d*_i* @atom:*_b*_a005*_d*_i* @atom:*_b*_a064*_d*_i* + @angle:007_005_079 @atom:*_b*_a007*_d*_i* @atom:*_b*_a005*_d*_i* @atom:*_b*_a079*_d*_i* + @angle:007_005_106 @atom:*_b*_a007*_d*_i* @atom:*_b*_a005*_d*_i* @atom:*_b*_a106*_d*_i* + @angle:005_007_025 @atom:*_b*_a005*_d*_i* @atom:*_b*_a007*_d*_i* @atom:*_b*_a025*_d*_i* + @angle:025_007_025 @atom:*_b*_a025*_d*_i* @atom:*_b*_a007*_d*_i* @atom:*_b*_a025*_d*_i* + @angle:002_010_002 @atom:*_b*_a002*_d*_i* @atom:*_b*_a010*_d*_i* @atom:*_b*_a002*_d*_i* + @angle:002_010_003 @atom:*_b*_a002*_d*_i* @atom:*_b*_a010*_d*_i* @atom:*_b*_a003*_d*_i* + @angle:002_010_005 @atom:*_b*_a002*_d*_i* @atom:*_b*_a010*_d*_i* @atom:*_b*_a005*_d*_i* + @angle:003_010_006 @atom:*_b*_a003*_d*_i* @atom:*_b*_a010*_d*_i* @atom:*_b*_a006*_d*_i* + @angle:006_010_006 @atom:*_b*_a006*_d*_i* @atom:*_b*_a010*_d*_i* @atom:*_b*_a006*_d*_i* + @angle:002_010_006 @atom:*_b*_a002*_d*_i* @atom:*_b*_a010*_d*_i* @atom:*_b*_a006*_d*_i* + @angle:005_010_006 @atom:*_b*_a005*_d*_i* @atom:*_b*_a010*_d*_i* @atom:*_b*_a006*_d*_i* + @angle:003_010_010 @atom:*_b*_a003*_d*_i* @atom:*_b*_a010*_d*_i* @atom:*_b*_a010*_d*_i* + @angle:002_010_010 @atom:*_b*_a002*_d*_i* @atom:*_b*_a010*_d*_i* @atom:*_b*_a010*_d*_i* + @angle:006_010_010 @atom:*_b*_a006*_d*_i* @atom:*_b*_a010*_d*_i* @atom:*_b*_a010*_d*_i* + @angle:010_010_010 @atom:*_b*_a010*_d*_i* @atom:*_b*_a010*_d*_i* @atom:*_b*_a010*_d*_i* + @angle:005_010_010 @atom:*_b*_a005*_d*_i* @atom:*_b*_a010*_d*_i* @atom:*_b*_a010*_d*_i* + @angle:002_010_020 @atom:*_b*_a002*_d*_i* @atom:*_b*_a010*_d*_i* @atom:*_b*_a020*_d*_i* + @angle:006_010_020 @atom:*_b*_a006*_d*_i* @atom:*_b*_a010*_d*_i* @atom:*_b*_a020*_d*_i* + @angle:010_010_020 @atom:*_b*_a010*_d*_i* @atom:*_b*_a010*_d*_i* @atom:*_b*_a020*_d*_i* + @angle:003_010_024 @atom:*_b*_a003*_d*_i* @atom:*_b*_a010*_d*_i* @atom:*_b*_a024*_d*_i* + @angle:006_010_024 @atom:*_b*_a006*_d*_i* @atom:*_b*_a010*_d*_i* @atom:*_b*_a024*_d*_i* + @angle:002_010_024 @atom:*_b*_a002*_d*_i* @atom:*_b*_a010*_d*_i* @atom:*_b*_a024*_d*_i* + @angle:010_010_024 @atom:*_b*_a010*_d*_i* @atom:*_b*_a010*_d*_i* @atom:*_b*_a024*_d*_i* + @angle:002_010_044 @atom:*_b*_a002*_d*_i* @atom:*_b*_a010*_d*_i* @atom:*_b*_a044*_d*_i* + @angle:006_010_044 @atom:*_b*_a006*_d*_i* @atom:*_b*_a010*_d*_i* @atom:*_b*_a044*_d*_i* + @angle:010_010_044 @atom:*_b*_a010*_d*_i* @atom:*_b*_a010*_d*_i* @atom:*_b*_a044*_d*_i* + @angle:013_010_044 @atom:*_b*_a013*_d*_i* @atom:*_b*_a010*_d*_i* @atom:*_b*_a044*_d*_i* + @angle:003_010_044 @atom:*_b*_a003*_d*_i* @atom:*_b*_a010*_d*_i* @atom:*_b*_a044*_d*_i* + @angle:002_010_048 @atom:*_b*_a002*_d*_i* @atom:*_b*_a010*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:020_010_048 @atom:*_b*_a020*_d*_i* @atom:*_b*_a010*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:002_010_105 @atom:*_b*_a002*_d*_i* @atom:*_b*_a010*_d*_i* @atom:*_b*_a105*_d*_i* + @angle:010_010_105 @atom:*_b*_a010*_d*_i* @atom:*_b*_a010*_d*_i* @atom:*_b*_a105*_d*_i* + @angle:020_010_105 @atom:*_b*_a020*_d*_i* @atom:*_b*_a010*_d*_i* @atom:*_b*_a105*_d*_i* + @angle:002_011_002 @atom:*_b*_a002*_d*_i* @atom:*_b*_a011*_d*_i* @atom:*_b*_a002*_d*_i* + @angle:002_011_006 @atom:*_b*_a002*_d*_i* @atom:*_b*_a011*_d*_i* @atom:*_b*_a006*_d*_i* + @angle:006_011_006 @atom:*_b*_a006*_d*_i* @atom:*_b*_a011*_d*_i* @atom:*_b*_a006*_d*_i* + @angle:002_011_009 @atom:*_b*_a002*_d*_i* @atom:*_b*_a011*_d*_i* @atom:*_b*_a009*_d*_i* + @angle:006_011_009 @atom:*_b*_a006*_d*_i* @atom:*_b*_a011*_d*_i* @atom:*_b*_a009*_d*_i* + @angle:009_011_010 @atom:*_b*_a009*_d*_i* @atom:*_b*_a011*_d*_i* @atom:*_b*_a010*_d*_i* + @angle:002_011_010 @atom:*_b*_a002*_d*_i* @atom:*_b*_a011*_d*_i* @atom:*_b*_a010*_d*_i* + @angle:006_011_010 @atom:*_b*_a006*_d*_i* @atom:*_b*_a011*_d*_i* @atom:*_b*_a010*_d*_i* + @angle:010_011_010 @atom:*_b*_a010*_d*_i* @atom:*_b*_a011*_d*_i* @atom:*_b*_a010*_d*_i* + @angle:002_011_011 @atom:*_b*_a002*_d*_i* @atom:*_b*_a011*_d*_i* @atom:*_b*_a011*_d*_i* + @angle:006_011_011 @atom:*_b*_a006*_d*_i* @atom:*_b*_a011*_d*_i* @atom:*_b*_a011*_d*_i* + @angle:009_011_011 @atom:*_b*_a009*_d*_i* @atom:*_b*_a011*_d*_i* @atom:*_b*_a011*_d*_i* + @angle:010_011_011 @atom:*_b*_a010*_d*_i* @atom:*_b*_a011*_d*_i* @atom:*_b*_a011*_d*_i* + @angle:011_011_011 @atom:*_b*_a011*_d*_i* @atom:*_b*_a011*_d*_i* @atom:*_b*_a011*_d*_i* + @angle:009_011_013 @atom:*_b*_a009*_d*_i* @atom:*_b*_a011*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:011_011_013 @atom:*_b*_a011*_d*_i* @atom:*_b*_a011*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:002_011_013 @atom:*_b*_a002*_d*_i* @atom:*_b*_a011*_d*_i* @atom:*_b*_a013*_d*_i* + 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@angle:012_012_081 @atom:*_b*_a012*_d*_i* @atom:*_b*_a012*_d*_i* @atom:*_b*_a081*_d*_i* + @angle:001_013_001 @atom:*_b*_a001*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a001*_d*_i* + @angle:002_013_002 @atom:*_b*_a002*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a002*_d*_i* + @angle:001_013_003 @atom:*_b*_a001*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a003*_d*_i* + @angle:002_013_003 @atom:*_b*_a002*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a003*_d*_i* + @angle:003_013_003 @atom:*_b*_a003*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a003*_d*_i* + @angle:002_013_006 @atom:*_b*_a002*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a006*_d*_i* + @angle:006_013_006 @atom:*_b*_a006*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a006*_d*_i* + @angle:003_013_006 @atom:*_b*_a003*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a006*_d*_i* + @angle:001_013_013 @atom:*_b*_a001*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:005_013_013 @atom:*_b*_a005*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* + 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@angle:013_013_046 @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a046*_d*_i* + @angle:001_013_046 @atom:*_b*_a001*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a046*_d*_i* + @angle:021_013_046 @atom:*_b*_a021*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a046*_d*_i* + @angle:046_013_047 @atom:*_b*_a046*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a047*_d*_i* + @angle:001_013_047 @atom:*_b*_a001*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a047*_d*_i* + @angle:013_013_047 @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a047*_d*_i* + @angle:047_013_047 @atom:*_b*_a047*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a047*_d*_i* + @angle:046_013_048 @atom:*_b*_a046*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:047_013_048 @atom:*_b*_a047*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:048_013_048 @atom:*_b*_a048*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:001_013_048 @atom:*_b*_a001*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:005_013_048 @atom:*_b*_a005*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:020_013_048 @atom:*_b*_a020*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:016_013_048 @atom:*_b*_a016*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:003_013_048 @atom:*_b*_a003*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:002_013_048 @atom:*_b*_a002*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:013_013_048 @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:044_013_048 @atom:*_b*_a044*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:046_013_050 @atom:*_b*_a046*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a050*_d*_i* + @angle:046_013_051 @atom:*_b*_a046*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a051*_d*_i* + @angle:005_013_051 @atom:*_b*_a005*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a051*_d*_i* + @angle:013_013_051 @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a051*_d*_i* + @angle:046_013_053 @atom:*_b*_a046*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a053*_d*_i* + @angle:003_013_053 @atom:*_b*_a003*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a053*_d*_i* + @angle:013_013_053 @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a053*_d*_i* + @angle:046_013_055 @atom:*_b*_a046*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a055*_d*_i* + @angle:013_013_055 @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a055*_d*_i* + @angle:046_013_056 @atom:*_b*_a046*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a056*_d*_i* + @angle:003_013_056 @atom:*_b*_a003*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a056*_d*_i* + @angle:013_013_056 @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a056*_d*_i* + @angle:046_013_057 @atom:*_b*_a046*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a057*_d*_i* + @angle:048_013_057 @atom:*_b*_a048*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a057*_d*_i* + @angle:046_013_060 @atom:*_b*_a046*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a060*_d*_i* + 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@angle:046_013_079 @atom:*_b*_a046*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a079*_d*_i* + @angle:013_013_079 @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a079*_d*_i* + @angle:001_013_079 @atom:*_b*_a001*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a079*_d*_i* + @angle:046_013_080 @atom:*_b*_a046*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a080*_d*_i* + @angle:013_013_080 @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a080*_d*_i* + @angle:046_013_083 @atom:*_b*_a046*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a083*_d*_i* + @angle:013_013_083 @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a083*_d*_i* + @angle:046_013_084 @atom:*_b*_a046*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a084*_d*_i* + @angle:016_013_084 @atom:*_b*_a016*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a084*_d*_i* + @angle:013_013_084 @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a084*_d*_i* + @angle:046_013_085 @atom:*_b*_a046*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a085*_d*_i* + @angle:013_013_085 @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a085*_d*_i* + @angle:046_013_087 @atom:*_b*_a046*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a087*_d*_i* + @angle:013_013_087 @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a087*_d*_i* + @angle:046_013_090 @atom:*_b*_a046*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a090*_d*_i* + @angle:013_013_090 @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a090*_d*_i* + @angle:003_013_090 @atom:*_b*_a003*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a090*_d*_i* + @angle:046_013_091 @atom:*_b*_a046*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a091*_d*_i* + @angle:046_013_095 @atom:*_b*_a046*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a095*_d*_i* + @angle:013_013_095 @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a095*_d*_i* + @angle:046_013_101 @atom:*_b*_a046*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a101*_d*_i* + @angle:013_013_101 @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a101*_d*_i* + 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@angle:013_016_019 @atom:*_b*_a013*_d*_i* @atom:*_b*_a016*_d*_i* @atom:*_b*_a019*_d*_i* + @angle:025_016_025 @atom:*_b*_a025*_d*_i* @atom:*_b*_a016*_d*_i* @atom:*_b*_a025*_d*_i* + @angle:013_016_025 @atom:*_b*_a013*_d*_i* @atom:*_b*_a016*_d*_i* @atom:*_b*_a025*_d*_i* + @angle:033_016_033 @atom:*_b*_a033*_d*_i* @atom:*_b*_a016*_d*_i* @atom:*_b*_a033*_d*_i* + @angle:002_016_033 @atom:*_b*_a002*_d*_i* @atom:*_b*_a016*_d*_i* @atom:*_b*_a033*_d*_i* + @angle:006_016_033 @atom:*_b*_a006*_d*_i* @atom:*_b*_a016*_d*_i* @atom:*_b*_a033*_d*_i* + @angle:013_016_033 @atom:*_b*_a013*_d*_i* @atom:*_b*_a016*_d*_i* @atom:*_b*_a033*_d*_i* + @angle:016_016_033 @atom:*_b*_a016*_d*_i* @atom:*_b*_a016*_d*_i* @atom:*_b*_a033*_d*_i* + @angle:013_016_048 @atom:*_b*_a013*_d*_i* @atom:*_b*_a016*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:047_016_048 @atom:*_b*_a047*_d*_i* @atom:*_b*_a016*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:024_016_060 @atom:*_b*_a024*_d*_i* @atom:*_b*_a016*_d*_i* @atom:*_b*_a060*_d*_i* + @angle:025_016_061 @atom:*_b*_a025*_d*_i* @atom:*_b*_a016*_d*_i* @atom:*_b*_a061*_d*_i* + @angle:025_016_082 @atom:*_b*_a025*_d*_i* @atom:*_b*_a016*_d*_i* @atom:*_b*_a082*_d*_i* + @angle:060_016_082 @atom:*_b*_a060*_d*_i* @atom:*_b*_a016*_d*_i* @atom:*_b*_a082*_d*_i* + @angle:025_016_084 @atom:*_b*_a025*_d*_i* @atom:*_b*_a016*_d*_i* @atom:*_b*_a084*_d*_i* + @angle:082_016_084 @atom:*_b*_a082*_d*_i* @atom:*_b*_a016*_d*_i* @atom:*_b*_a084*_d*_i* + @angle:060_016_084 @atom:*_b*_a060*_d*_i* @atom:*_b*_a016*_d*_i* @atom:*_b*_a084*_d*_i* + @angle:084_016_084 @atom:*_b*_a084*_d*_i* @atom:*_b*_a016*_d*_i* @atom:*_b*_a084*_d*_i* + @angle:013_016_091 @atom:*_b*_a013*_d*_i* @atom:*_b*_a016*_d*_i* @atom:*_b*_a091*_d*_i* + @angle:015_017_025 @atom:*_b*_a015*_d*_i* @atom:*_b*_a017*_d*_i* @atom:*_b*_a025*_d*_i* + @angle:025_017_025 @atom:*_b*_a025*_d*_i* @atom:*_b*_a017*_d*_i* @atom:*_b*_a025*_d*_i* + @angle:013_018_019 @atom:*_b*_a013*_d*_i* @atom:*_b*_a018*_d*_i* @atom:*_b*_a019*_d*_i* + @angle:019_018_048 @atom:*_b*_a019*_d*_i* @atom:*_b*_a018*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:018_018_056 @atom:*_b*_a018*_d*_i* @atom:*_b*_a018*_d*_i* @atom:*_b*_a056*_d*_i* + @angle:013_019_018 @atom:*_b*_a013*_d*_i* @atom:*_b*_a019*_d*_i* @atom:*_b*_a018*_d*_i* + @angle:016_019_019 @atom:*_b*_a016*_d*_i* @atom:*_b*_a019*_d*_i* @atom:*_b*_a019*_d*_i* + @angle:013_019_019 @atom:*_b*_a013*_d*_i* @atom:*_b*_a019*_d*_i* @atom:*_b*_a019*_d*_i* + @angle:018_019_025 @atom:*_b*_a018*_d*_i* @atom:*_b*_a019*_d*_i* @atom:*_b*_a025*_d*_i* + @angle:019_019_046 @atom:*_b*_a019*_d*_i* @atom:*_b*_a019*_d*_i* @atom:*_b*_a046*_d*_i* + @angle:018_019_047 @atom:*_b*_a018*_d*_i* @atom:*_b*_a019*_d*_i* @atom:*_b*_a047*_d*_i* + @angle:019_019_047 @atom:*_b*_a019*_d*_i* @atom:*_b*_a019*_d*_i* @atom:*_b*_a047*_d*_i* + @angle:018_019_048 @atom:*_b*_a018*_d*_i* @atom:*_b*_a019*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:019_019_048 @atom:*_b*_a019*_d*_i* @atom:*_b*_a019*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:019_019_050 @atom:*_b*_a019*_d*_i* @atom:*_b*_a019*_d*_i* @atom:*_b*_a050*_d*_i* + @angle:018_019_055 @atom:*_b*_a018*_d*_i* @atom:*_b*_a019*_d*_i* @atom:*_b*_a055*_d*_i* + @angle:018_019_088 @atom:*_b*_a018*_d*_i* @atom:*_b*_a019*_d*_i* @atom:*_b*_a088*_d*_i* + @angle:002_020_002 @atom:*_b*_a002*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a002*_d*_i* + @angle:002_020_003 @atom:*_b*_a002*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a003*_d*_i* + @angle:003_020_006 @atom:*_b*_a003*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a006*_d*_i* + @angle:002_020_006 @atom:*_b*_a002*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a006*_d*_i* + @angle:002_020_007 @atom:*_b*_a002*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a007*_d*_i* + @angle:007_020_010 @atom:*_b*_a007*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a010*_d*_i* + @angle:003_020_010 @atom:*_b*_a003*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a010*_d*_i* + @angle:010_020_010 @atom:*_b*_a010*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a010*_d*_i* + @angle:013_020_013 @atom:*_b*_a013*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:003_020_013 @atom:*_b*_a003*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:025_020_025 @atom:*_b*_a025*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a025*_d*_i* + @angle:013_020_025 @atom:*_b*_a013*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a025*_d*_i* + @angle:013_020_047 @atom:*_b*_a013*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a047*_d*_i* + @angle:025_020_048 @atom:*_b*_a025*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:013_020_048 @atom:*_b*_a013*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:047_020_048 @atom:*_b*_a047*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:048_020_048 @atom:*_b*_a048*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:003_020_048 @atom:*_b*_a003*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:002_020_048 @atom:*_b*_a002*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a048*_d*_i* + 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@angle:013_024_013 @atom:*_b*_a013*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:003_024_013 @atom:*_b*_a003*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:003_024_016 @atom:*_b*_a003*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a016*_d*_i* + @angle:003_024_020 @atom:*_b*_a003*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a020*_d*_i* + @angle:003_024_025 @atom:*_b*_a003*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a025*_d*_i* + @angle:025_024_045 @atom:*_b*_a025*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a045*_d*_i* + @angle:005_024_045 @atom:*_b*_a005*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a045*_d*_i* + @angle:003_024_045 @atom:*_b*_a003*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a045*_d*_i* + @angle:045_024_045 @atom:*_b*_a045*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a045*_d*_i* + @angle:002_024_045 @atom:*_b*_a002*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a045*_d*_i* + @angle:006_024_045 @atom:*_b*_a006*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a045*_d*_i* + @angle:010_024_045 @atom:*_b*_a010*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a045*_d*_i* + @angle:013_024_045 @atom:*_b*_a013*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a045*_d*_i* + @angle:045_024_048 @atom:*_b*_a045*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:013_024_048 @atom:*_b*_a013*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:003_024_048 @atom:*_b*_a003*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:048_024_048 @atom:*_b*_a048*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:054_024_054 @atom:*_b*_a054*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a054*_d*_i* + @angle:045_024_059 @atom:*_b*_a045*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a059*_d*_i* + @angle:003_024_059 @atom:*_b*_a003*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a059*_d*_i* + @angle:013_024_079 @atom:*_b*_a013*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a079*_d*_i* + @angle:045_024_079 @atom:*_b*_a045*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a079*_d*_i* + @angle:045_024_084 @atom:*_b*_a045*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a084*_d*_i* + @angle:048_024_084 @atom:*_b*_a048*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a084*_d*_i* + @angle:016_024_086 @atom:*_b*_a016*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a086*_d*_i* + @angle:045_024_087 @atom:*_b*_a045*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a087*_d*_i* + @angle:048_024_087 @atom:*_b*_a048*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a087*_d*_i* + @angle:045_024_088 @atom:*_b*_a045*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a088*_d*_i* + @angle:048_024_088 @atom:*_b*_a048*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a088*_d*_i* + @angle:045_024_091 @atom:*_b*_a045*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a091*_d*_i* + @angle:003_024_091 @atom:*_b*_a003*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a091*_d*_i* + @angle:048_024_103 @atom:*_b*_a048*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a103*_d*_i* + @angle:003_024_106 @atom:*_b*_a003*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a106*_d*_i* + @angle:025_025_025 @atom:*_b*_a025*_d*_i* @atom:*_b*_a025*_d*_i* @atom:*_b*_a025*_d*_i* + @angle:032_031_032 @atom:*_b*_a032*_d*_i* @atom:*_b*_a031*_d*_i* @atom:*_b*_a032*_d*_i* + @angle:032_031_033 @atom:*_b*_a032*_d*_i* @atom:*_b*_a031*_d*_i* @atom:*_b*_a033*_d*_i* + @angle:035_034_035 @atom:*_b*_a035*_d*_i* @atom:*_b*_a034*_d*_i* @atom:*_b*_a035*_d*_i* + @angle:037_036_037 @atom:*_b*_a037*_d*_i* @atom:*_b*_a036*_d*_i* @atom:*_b*_a037*_d*_i* + @angle:037_036_038 @atom:*_b*_a037*_d*_i* @atom:*_b*_a036*_d*_i* @atom:*_b*_a038*_d*_i* + @angle:040_039_040 @atom:*_b*_a040*_d*_i* @atom:*_b*_a039*_d*_i* @atom:*_b*_a040*_d*_i* + @angle:041_039_041 @atom:*_b*_a041*_d*_i* @atom:*_b*_a039*_d*_i* @atom:*_b*_a041*_d*_i* + @angle:040_039_041 @atom:*_b*_a040*_d*_i* @atom:*_b*_a039*_d*_i* @atom:*_b*_a041*_d*_i* + @angle:043_042_043 @atom:*_b*_a043*_d*_i* @atom:*_b*_a042*_d*_i* @atom:*_b*_a043*_d*_i* + @angle:002_044_002 @atom:*_b*_a002*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a002*_d*_i* + @angle:002_044_006 @atom:*_b*_a002*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a006*_d*_i* + @angle:006_044_006 @atom:*_b*_a006*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a006*_d*_i* + @angle:002_044_010 @atom:*_b*_a002*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a010*_d*_i* + @angle:006_044_010 @atom:*_b*_a006*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a010*_d*_i* + @angle:010_044_010 @atom:*_b*_a010*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a010*_d*_i* + @angle:002_044_013 @atom:*_b*_a002*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:006_044_013 @atom:*_b*_a006*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:010_044_013 @atom:*_b*_a010*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:013_044_013 @atom:*_b*_a013*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:003_044_013 @atom:*_b*_a003*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:025_044_045 @atom:*_b*_a025*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a045*_d*_i* + @angle:013_044_045 @atom:*_b*_a013*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a045*_d*_i* + @angle:002_044_045 @atom:*_b*_a002*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a045*_d*_i* + @angle:006_044_045 @atom:*_b*_a006*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a045*_d*_i* + @angle:010_044_045 @atom:*_b*_a010*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a045*_d*_i* + @angle:045_044_045 @atom:*_b*_a045*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a045*_d*_i* + @angle:025_044_048 @atom:*_b*_a025*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:045_044_048 @atom:*_b*_a045*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:013_044_048 @atom:*_b*_a013*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:048_044_048 @atom:*_b*_a048*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:003_044_048 @atom:*_b*_a003*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:045_044_079 @atom:*_b*_a045*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a079*_d*_i* + @angle:013_044_079 @atom:*_b*_a013*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a079*_d*_i* + @angle:048_044_079 @atom:*_b*_a048*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a079*_d*_i* + @angle:048_044_091 @atom:*_b*_a048*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a091*_d*_i* + @angle:025_045_025 @atom:*_b*_a025*_d*_i* @atom:*_b*_a045*_d*_i* @atom:*_b*_a025*_d*_i* + @angle:025_045_044 @atom:*_b*_a025*_d*_i* @atom:*_b*_a045*_d*_i* @atom:*_b*_a044*_d*_i* + @angle:025_046_025 @atom:*_b*_a025*_d*_i* @atom:*_b*_a046*_d*_i* @atom:*_b*_a025*_d*_i* + @angle:013_046_025 @atom:*_b*_a013*_d*_i* @atom:*_b*_a046*_d*_i* @atom:*_b*_a025*_d*_i* + @angle:001_047_001 @atom:*_b*_a001*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a001*_d*_i* + @angle:001_047_003 @atom:*_b*_a001*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a003*_d*_i* + @angle:003_047_006 @atom:*_b*_a003*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a006*_d*_i* + @angle:003_047_013 @atom:*_b*_a003*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:013_047_013 @atom:*_b*_a013*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:025_047_046 @atom:*_b*_a025*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a046*_d*_i* + @angle:020_047_046 @atom:*_b*_a020*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a046*_d*_i* + @angle:013_047_046 @atom:*_b*_a013*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a046*_d*_i* + @angle:046_047_046 @atom:*_b*_a046*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a046*_d*_i* + @angle:003_047_046 @atom:*_b*_a003*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a046*_d*_i* + @angle:019_047_046 @atom:*_b*_a019*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a046*_d*_i* + @angle:001_047_046 @atom:*_b*_a001*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a046*_d*_i* + @angle:021_047_046 @atom:*_b*_a021*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a046*_d*_i* + @angle:025_047_047 @atom:*_b*_a025*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a047*_d*_i* + @angle:046_047_047 @atom:*_b*_a046*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a047*_d*_i* + @angle:005_047_047 @atom:*_b*_a005*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a047*_d*_i* + @angle:020_047_047 @atom:*_b*_a020*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a047*_d*_i* + @angle:013_047_047 @atom:*_b*_a013*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a047*_d*_i* + @angle:019_047_047 @atom:*_b*_a019*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a047*_d*_i* + @angle:021_047_047 @atom:*_b*_a021*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a047*_d*_i* + @angle:001_047_047 @atom:*_b*_a001*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a047*_d*_i* + @angle:016_047_047 @atom:*_b*_a016*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a047*_d*_i* + @angle:003_047_047 @atom:*_b*_a003*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a047*_d*_i* + @angle:046_047_048 @atom:*_b*_a046*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:047_047_048 @atom:*_b*_a047*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:013_047_048 @atom:*_b*_a013*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:025_047_050 @atom:*_b*_a025*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a050*_d*_i* + @angle:046_047_050 @atom:*_b*_a046*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a050*_d*_i* + @angle:005_047_050 @atom:*_b*_a005*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a050*_d*_i* + @angle:020_047_050 @atom:*_b*_a020*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a050*_d*_i* + @angle:013_047_050 @atom:*_b*_a013*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a050*_d*_i* + @angle:046_047_057 @atom:*_b*_a046*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a057*_d*_i* + @angle:013_047_057 @atom:*_b*_a013*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a057*_d*_i* + @angle:020_047_057 @atom:*_b*_a020*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a057*_d*_i* + @angle:047_047_057 @atom:*_b*_a047*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a057*_d*_i* + @angle:016_047_057 @atom:*_b*_a016*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a057*_d*_i* + @angle:057_047_058 @atom:*_b*_a057*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a058*_d*_i* + @angle:047_047_058 @atom:*_b*_a047*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a058*_d*_i* + @angle:046_047_065 @atom:*_b*_a046*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a065*_d*_i* + @angle:047_047_065 @atom:*_b*_a047*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a065*_d*_i* + @angle:046_047_091 @atom:*_b*_a046*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a091*_d*_i* + @angle:003_047_091 @atom:*_b*_a003*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a091*_d*_i* + @angle:047_047_091 @atom:*_b*_a047*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a091*_d*_i* + @angle:046_047_105 @atom:*_b*_a046*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a105*_d*_i* + @angle:058_047_105 @atom:*_b*_a058*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a105*_d*_i* + @angle:013_047_105 @atom:*_b*_a013*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a105*_d*_i* + @angle:020_047_105 @atom:*_b*_a020*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a105*_d*_i* + @angle:047_047_105 @atom:*_b*_a047*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a105*_d*_i* + @angle:016_047_105 @atom:*_b*_a016*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a105*_d*_i* + @angle:046_047_110 @atom:*_b*_a046*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a110*_d*_i* + @angle:013_047_110 @atom:*_b*_a013*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a110*_d*_i* + @angle:048_047_110 @atom:*_b*_a048*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a110*_d*_i* + @angle:001_047_110 @atom:*_b*_a001*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a110*_d*_i* + @angle:002_048_012 @atom:*_b*_a002*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a012*_d*_i* + @angle:012_048_012 @atom:*_b*_a012*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a012*_d*_i* + @angle:003_048_013 @atom:*_b*_a003*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:025_048_048 @atom:*_b*_a025*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:048_048_048 @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:002_048_048 @atom:*_b*_a002*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:005_048_048 @atom:*_b*_a005*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:010_048_048 @atom:*_b*_a010*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:013_048_048 @atom:*_b*_a013*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:015_048_048 @atom:*_b*_a015*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:019_048_048 @atom:*_b*_a019*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:020_048_048 @atom:*_b*_a020*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:024_048_048 @atom:*_b*_a024*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:044_048_048 @atom:*_b*_a044*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:047_048_048 @atom:*_b*_a047*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:021_048_048 @atom:*_b*_a021*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:001_048_048 @atom:*_b*_a001*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:018_048_048 @atom:*_b*_a018*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:016_048_048 @atom:*_b*_a016*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:003_048_048 @atom:*_b*_a003*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:025_048_049 @atom:*_b*_a025*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a049*_d*_i* + @angle:024_048_049 @atom:*_b*_a024*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a049*_d*_i* + @angle:003_048_049 @atom:*_b*_a003*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a049*_d*_i* + @angle:048_048_049 @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a049*_d*_i* + @angle:048_048_050 @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a050*_d*_i* + @angle:048_048_053 @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a053*_d*_i* + @angle:055_048_055 @atom:*_b*_a055*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a055*_d*_i* + @angle:047_048_055 @atom:*_b*_a047*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a055*_d*_i* + @angle:048_048_055 @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a055*_d*_i* + @angle:049_048_056 @atom:*_b*_a049*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a056*_d*_i* + @angle:013_048_056 @atom:*_b*_a013*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a056*_d*_i* + @angle:044_048_056 @atom:*_b*_a044*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a056*_d*_i* + @angle:055_048_056 @atom:*_b*_a055*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a056*_d*_i* + @angle:005_048_056 @atom:*_b*_a005*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a056*_d*_i* + @angle:047_048_056 @atom:*_b*_a047*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a056*_d*_i* + @angle:050_048_056 @atom:*_b*_a050*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a056*_d*_i* + @angle:048_048_056 @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a056*_d*_i* + @angle:021_048_056 @atom:*_b*_a021*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a056*_d*_i* + @angle:049_048_057 @atom:*_b*_a049*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a057*_d*_i* + @angle:048_048_057 @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a057*_d*_i* + @angle:055_048_057 @atom:*_b*_a055*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a057*_d*_i* + @angle:013_048_057 @atom:*_b*_a013*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a057*_d*_i* + @angle:047_048_057 @atom:*_b*_a047*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a057*_d*_i* + @angle:056_048_057 @atom:*_b*_a056*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a057*_d*_i* + @angle:049_048_060 @atom:*_b*_a049*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a060*_d*_i* + @angle:048_048_060 @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a060*_d*_i* + @angle:057_048_060 @atom:*_b*_a057*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a060*_d*_i* + @angle:056_048_060 @atom:*_b*_a056*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a060*_d*_i* + @angle:055_048_060 @atom:*_b*_a055*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a060*_d*_i* + @angle:002_048_060 @atom:*_b*_a002*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a060*_d*_i* + @angle:013_048_060 @atom:*_b*_a013*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a060*_d*_i* + @angle:049_048_061 @atom:*_b*_a049*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a061*_d*_i* + @angle:048_048_061 @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a061*_d*_i* + @angle:057_048_061 @atom:*_b*_a057*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a061*_d*_i* + @angle:048_048_064 @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a064*_d*_i* + @angle:048_048_065 @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a065*_d*_i* + @angle:048_048_066 @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a066*_d*_i* + @angle:048_048_079 @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a079*_d*_i* + @angle:049_048_081 @atom:*_b*_a049*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a081*_d*_i* + @angle:048_048_081 @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a081*_d*_i* + @angle:049_048_084 @atom:*_b*_a049*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a084*_d*_i* + @angle:060_048_084 @atom:*_b*_a060*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a084*_d*_i* + @angle:048_048_084 @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a084*_d*_i* + @angle:049_048_086 @atom:*_b*_a049*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a086*_d*_i* + @angle:048_048_086 @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a086*_d*_i* + @angle:056_048_086 @atom:*_b*_a056*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a086*_d*_i* + @angle:049_048_088 @atom:*_b*_a049*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a088*_d*_i* + @angle:101_048_101 @atom:*_b*_a101*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a101*_d*_i* + @angle:056_048_101 @atom:*_b*_a056*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a101*_d*_i* + @angle:048_048_102 @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a102*_d*_i* + @angle:048_048_109 @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a109*_d*_i* + @angle:025_050_046 @atom:*_b*_a025*_d*_i* @atom:*_b*_a050*_d*_i* @atom:*_b*_a046*_d*_i* + @angle:019_050_046 @atom:*_b*_a019*_d*_i* @atom:*_b*_a050*_d*_i* @atom:*_b*_a046*_d*_i* + @angle:025_050_047 @atom:*_b*_a025*_d*_i* @atom:*_b*_a050*_d*_i* @atom:*_b*_a047*_d*_i* + @angle:046_050_047 @atom:*_b*_a046*_d*_i* @atom:*_b*_a050*_d*_i* @atom:*_b*_a047*_d*_i* + @angle:003_050_047 @atom:*_b*_a003*_d*_i* @atom:*_b*_a050*_d*_i* @atom:*_b*_a047*_d*_i* + @angle:013_050_047 @atom:*_b*_a013*_d*_i* @atom:*_b*_a050*_d*_i* @atom:*_b*_a047*_d*_i* + @angle:046_050_048 @atom:*_b*_a046*_d*_i* @atom:*_b*_a050*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:047_050_048 @atom:*_b*_a047*_d*_i* @atom:*_b*_a050*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:025_050_050 @atom:*_b*_a025*_d*_i* @atom:*_b*_a050*_d*_i* @atom:*_b*_a050*_d*_i* + @angle:046_050_050 @atom:*_b*_a046*_d*_i* @atom:*_b*_a050*_d*_i* @atom:*_b*_a050*_d*_i* + @angle:013_050_050 @atom:*_b*_a013*_d*_i* @atom:*_b*_a050*_d*_i* @atom:*_b*_a050*_d*_i* + @angle:047_050_050 @atom:*_b*_a047*_d*_i* @atom:*_b*_a050*_d*_i* @atom:*_b*_a050*_d*_i* + @angle:050_050_084 @atom:*_b*_a050*_d*_i* @atom:*_b*_a050*_d*_i* @atom:*_b*_a084*_d*_i* + @angle:046_050_084 @atom:*_b*_a046*_d*_i* @atom:*_b*_a050*_d*_i* @atom:*_b*_a084*_d*_i* + @angle:046_050_109 @atom:*_b*_a046*_d*_i* @atom:*_b*_a050*_d*_i* @atom:*_b*_a109*_d*_i* + @angle:013_050_109 @atom:*_b*_a013*_d*_i* @atom:*_b*_a050*_d*_i* @atom:*_b*_a109*_d*_i* + @angle:047_050_109 @atom:*_b*_a047*_d*_i* @atom:*_b*_a050*_d*_i* @atom:*_b*_a109*_d*_i* + @angle:006_051_006 @atom:*_b*_a006*_d*_i* @atom:*_b*_a051*_d*_i* @atom:*_b*_a006*_d*_i* + @angle:005_051_013 @atom:*_b*_a005*_d*_i* @atom:*_b*_a051*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:013_051_020 @atom:*_b*_a013*_d*_i* @atom:*_b*_a051*_d*_i* @atom:*_b*_a020*_d*_i* + @angle:002_051_020 @atom:*_b*_a002*_d*_i* @atom:*_b*_a051*_d*_i* @atom:*_b*_a020*_d*_i* + @angle:006_051_020 @atom:*_b*_a006*_d*_i* @atom:*_b*_a051*_d*_i* @atom:*_b*_a020*_d*_i* + @angle:005_051_020 @atom:*_b*_a005*_d*_i* @atom:*_b*_a051*_d*_i* @atom:*_b*_a020*_d*_i* + @angle:020_051_020 @atom:*_b*_a020*_d*_i* @atom:*_b*_a051*_d*_i* @atom:*_b*_a020*_d*_i* + @angle:046_051_046 @atom:*_b*_a046*_d*_i* @atom:*_b*_a051*_d*_i* @atom:*_b*_a046*_d*_i* + @angle:005_051_046 @atom:*_b*_a005*_d*_i* @atom:*_b*_a051*_d*_i* @atom:*_b*_a046*_d*_i* + @angle:020_051_046 @atom:*_b*_a020*_d*_i* @atom:*_b*_a051*_d*_i* @atom:*_b*_a046*_d*_i* + @angle:013_051_046 @atom:*_b*_a013*_d*_i* @atom:*_b*_a051*_d*_i* @atom:*_b*_a046*_d*_i* + @angle:046_051_105 @atom:*_b*_a046*_d*_i* @atom:*_b*_a051*_d*_i* @atom:*_b*_a105*_d*_i* + @angle:013_051_105 @atom:*_b*_a013*_d*_i* @atom:*_b*_a051*_d*_i* @atom:*_b*_a105*_d*_i* + @angle:020_051_105 @atom:*_b*_a020*_d*_i* @atom:*_b*_a051*_d*_i* @atom:*_b*_a105*_d*_i* + @angle:013_053_013 @atom:*_b*_a013*_d*_i* @atom:*_b*_a053*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:013_053_025 @atom:*_b*_a013*_d*_i* @atom:*_b*_a053*_d*_i* @atom:*_b*_a025*_d*_i* + @angle:045_053_045 @atom:*_b*_a045*_d*_i* @atom:*_b*_a053*_d*_i* @atom:*_b*_a045*_d*_i* + @angle:025_053_048 @atom:*_b*_a025*_d*_i* @atom:*_b*_a053*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:013_053_048 @atom:*_b*_a013*_d*_i* @atom:*_b*_a053*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:002_053_054 @atom:*_b*_a002*_d*_i* @atom:*_b*_a053*_d*_i* @atom:*_b*_a054*_d*_i* + @angle:006_053_054 @atom:*_b*_a006*_d*_i* @atom:*_b*_a053*_d*_i* @atom:*_b*_a054*_d*_i* + @angle:013_053_054 @atom:*_b*_a013*_d*_i* @atom:*_b*_a053*_d*_i* @atom:*_b*_a054*_d*_i* + @angle:048_053_054 @atom:*_b*_a048*_d*_i* @atom:*_b*_a053*_d*_i* @atom:*_b*_a054*_d*_i* + @angle:054_053_054 @atom:*_b*_a054*_d*_i* @atom:*_b*_a053*_d*_i* @atom:*_b*_a054*_d*_i* + @angle:025_053_082 @atom:*_b*_a025*_d*_i* @atom:*_b*_a053*_d*_i* @atom:*_b*_a082*_d*_i* + @angle:013_055_013 @atom:*_b*_a013*_d*_i* @atom:*_b*_a055*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:045_055_045 @atom:*_b*_a045*_d*_i* @atom:*_b*_a055*_d*_i* @atom:*_b*_a045*_d*_i* + @angle:013_055_045 @atom:*_b*_a013*_d*_i* @atom:*_b*_a055*_d*_i* @atom:*_b*_a045*_d*_i* + @angle:045_055_048 @atom:*_b*_a045*_d*_i* @atom:*_b*_a055*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:002_055_048 @atom:*_b*_a002*_d*_i* @atom:*_b*_a055*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:006_055_048 @atom:*_b*_a006*_d*_i* @atom:*_b*_a055*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:013_055_048 @atom:*_b*_a013*_d*_i* @atom:*_b*_a055*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:002_055_054 @atom:*_b*_a002*_d*_i* @atom:*_b*_a055*_d*_i* @atom:*_b*_a054*_d*_i* + @angle:013_055_054 @atom:*_b*_a013*_d*_i* @atom:*_b*_a055*_d*_i* @atom:*_b*_a054*_d*_i* + @angle:048_055_054 @atom:*_b*_a048*_d*_i* @atom:*_b*_a055*_d*_i* @atom:*_b*_a054*_d*_i* + @angle:054_055_054 @atom:*_b*_a054*_d*_i* @atom:*_b*_a055*_d*_i* @atom:*_b*_a054*_d*_i* + @angle:045_055_059 @atom:*_b*_a045*_d*_i* @atom:*_b*_a055*_d*_i* @atom:*_b*_a059*_d*_i* + @angle:003_056_013 @atom:*_b*_a003*_d*_i* @atom:*_b*_a056*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:013_056_018 @atom:*_b*_a013*_d*_i* @atom:*_b*_a056*_d*_i* @atom:*_b*_a018*_d*_i* + @angle:025_056_048 @atom:*_b*_a025*_d*_i* @atom:*_b*_a056*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:045_056_048 @atom:*_b*_a045*_d*_i* @atom:*_b*_a056*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:013_056_048 @atom:*_b*_a013*_d*_i* @atom:*_b*_a056*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:048_056_048 @atom:*_b*_a048*_d*_i* @atom:*_b*_a056*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:003_056_048 @atom:*_b*_a003*_d*_i* @atom:*_b*_a056*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:013_056_056 @atom:*_b*_a013*_d*_i* @atom:*_b*_a056*_d*_i* @atom:*_b*_a056*_d*_i* + @angle:048_056_056 @atom:*_b*_a048*_d*_i* @atom:*_b*_a056*_d*_i* @atom:*_b*_a056*_d*_i* + @angle:025_056_059 @atom:*_b*_a025*_d*_i* @atom:*_b*_a056*_d*_i* @atom:*_b*_a059*_d*_i* + @angle:048_056_059 @atom:*_b*_a048*_d*_i* @atom:*_b*_a056*_d*_i* @atom:*_b*_a059*_d*_i* + @angle:059_056_059 @atom:*_b*_a059*_d*_i* @atom:*_b*_a056*_d*_i* @atom:*_b*_a059*_d*_i* + @angle:059_056_060 @atom:*_b*_a059*_d*_i* @atom:*_b*_a056*_d*_i* @atom:*_b*_a060*_d*_i* + @angle:048_056_060 @atom:*_b*_a048*_d*_i* @atom:*_b*_a056*_d*_i* @atom:*_b*_a060*_d*_i* + @angle:059_056_082 @atom:*_b*_a059*_d*_i* @atom:*_b*_a056*_d*_i* @atom:*_b*_a082*_d*_i* + @angle:048_056_086 @atom:*_b*_a048*_d*_i* @atom:*_b*_a056*_d*_i* @atom:*_b*_a086*_d*_i* + @angle:013_056_103 @atom:*_b*_a013*_d*_i* @atom:*_b*_a056*_d*_i* @atom:*_b*_a103*_d*_i* + @angle:003_057_003 @atom:*_b*_a003*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a003*_d*_i* + @angle:003_057_045 @atom:*_b*_a003*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a045*_d*_i* + @angle:045_057_047 @atom:*_b*_a045*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a047*_d*_i* + @angle:003_057_047 @atom:*_b*_a003*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a047*_d*_i* + @angle:045_057_048 @atom:*_b*_a045*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:003_057_048 @atom:*_b*_a003*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:048_057_048 @atom:*_b*_a048*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:045_057_060 @atom:*_b*_a045*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a060*_d*_i* + @angle:013_057_060 @atom:*_b*_a013*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a060*_d*_i* + @angle:060_057_061 @atom:*_b*_a060*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a061*_d*_i* + @angle:045_057_061 @atom:*_b*_a045*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a061*_d*_i* + @angle:013_057_061 @atom:*_b*_a013*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a061*_d*_i* + @angle:048_057_061 @atom:*_b*_a048*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a061*_d*_i* + @angle:045_057_062 @atom:*_b*_a045*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a062*_d*_i* + @angle:060_057_062 @atom:*_b*_a060*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a062*_d*_i* + @angle:048_057_062 @atom:*_b*_a048*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a062*_d*_i* + @angle:013_057_062 @atom:*_b*_a013*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a062*_d*_i* + @angle:045_057_081 @atom:*_b*_a045*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a081*_d*_i* + @angle:045_057_082 @atom:*_b*_a045*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a082*_d*_i* + @angle:061_057_082 @atom:*_b*_a061*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a082*_d*_i* + @angle:060_057_082 @atom:*_b*_a060*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a082*_d*_i* + @angle:045_057_084 @atom:*_b*_a045*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a084*_d*_i* + @angle:061_057_084 @atom:*_b*_a061*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a084*_d*_i* + @angle:060_057_084 @atom:*_b*_a060*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a084*_d*_i* + @angle:082_057_084 @atom:*_b*_a082*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a084*_d*_i* + @angle:084_057_084 @atom:*_b*_a084*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a084*_d*_i* + @angle:081_057_084 @atom:*_b*_a081*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a084*_d*_i* + @angle:045_057_085 @atom:*_b*_a045*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a085*_d*_i* + @angle:082_057_085 @atom:*_b*_a082*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a085*_d*_i* + @angle:024_059_055 @atom:*_b*_a024*_d*_i* @atom:*_b*_a059*_d*_i* @atom:*_b*_a055*_d*_i* + @angle:049_059_056 @atom:*_b*_a049*_d*_i* @atom:*_b*_a059*_d*_i* @atom:*_b*_a056*_d*_i* + @angle:013_059_056 @atom:*_b*_a013*_d*_i* @atom:*_b*_a059*_d*_i* @atom:*_b*_a056*_d*_i* + @angle:055_059_056 @atom:*_b*_a055*_d*_i* @atom:*_b*_a059*_d*_i* @atom:*_b*_a056*_d*_i* + @angle:024_059_056 @atom:*_b*_a024*_d*_i* @atom:*_b*_a059*_d*_i* @atom:*_b*_a056*_d*_i* + @angle:056_059_056 @atom:*_b*_a056*_d*_i* @atom:*_b*_a059*_d*_i* @atom:*_b*_a056*_d*_i* + @angle:056_059_063 @atom:*_b*_a056*_d*_i* @atom:*_b*_a059*_d*_i* @atom:*_b*_a063*_d*_i* + @angle:013_060_048 @atom:*_b*_a013*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:048_060_048 @atom:*_b*_a048*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:056_060_057 @atom:*_b*_a056*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a057*_d*_i* + @angle:057_060_060 @atom:*_b*_a057*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a060*_d*_i* + @angle:020_060_060 @atom:*_b*_a020*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a060*_d*_i* + @angle:016_060_060 @atom:*_b*_a016*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a060*_d*_i* + @angle:013_060_060 @atom:*_b*_a013*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a060*_d*_i* + @angle:024_060_060 @atom:*_b*_a024*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a060*_d*_i* + @angle:056_060_060 @atom:*_b*_a056*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a060*_d*_i* + @angle:048_060_060 @atom:*_b*_a048*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a060*_d*_i* + @angle:003_060_060 @atom:*_b*_a003*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a060*_d*_i* + @angle:060_060_061 @atom:*_b*_a060*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a061*_d*_i* + @angle:024_060_061 @atom:*_b*_a024*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a061*_d*_i* + @angle:003_060_061 @atom:*_b*_a003*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a061*_d*_i* + @angle:048_060_061 @atom:*_b*_a048*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a061*_d*_i* + @angle:012_060_080 @atom:*_b*_a012*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a080*_d*_i* + @angle:048_060_080 @atom:*_b*_a048*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a080*_d*_i* + @angle:080_060_081 @atom:*_b*_a080*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a081*_d*_i* + @angle:012_060_081 @atom:*_b*_a012*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a081*_d*_i* + @angle:048_060_081 @atom:*_b*_a048*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a081*_d*_i* + @angle:003_060_084 @atom:*_b*_a003*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a084*_d*_i* + @angle:060_060_087 @atom:*_b*_a060*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a087*_d*_i* + @angle:057_060_087 @atom:*_b*_a057*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a087*_d*_i* + @angle:081_060_087 @atom:*_b*_a081*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a087*_d*_i* + @angle:012_060_087 @atom:*_b*_a012*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a087*_d*_i* + @angle:048_060_087 @atom:*_b*_a048*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a087*_d*_i* + @angle:060_060_105 @atom:*_b*_a060*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a105*_d*_i* + @angle:056_060_105 @atom:*_b*_a056*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a105*_d*_i* + @angle:048_061_048 @atom:*_b*_a048*_d*_i* @atom:*_b*_a061*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:025_061_057 @atom:*_b*_a025*_d*_i* @atom:*_b*_a061*_d*_i* @atom:*_b*_a057*_d*_i* + @angle:025_061_061 @atom:*_b*_a025*_d*_i* @atom:*_b*_a061*_d*_i* @atom:*_b*_a061*_d*_i* + @angle:060_061_062 @atom:*_b*_a060*_d*_i* @atom:*_b*_a061*_d*_i* @atom:*_b*_a062*_d*_i* + @angle:025_061_082 @atom:*_b*_a025*_d*_i* @atom:*_b*_a061*_d*_i* @atom:*_b*_a082*_d*_i* + @angle:061_061_082 @atom:*_b*_a061*_d*_i* @atom:*_b*_a061*_d*_i* @atom:*_b*_a082*_d*_i* + @angle:060_061_082 @atom:*_b*_a060*_d*_i* @atom:*_b*_a061*_d*_i* @atom:*_b*_a082*_d*_i* + @angle:082_061_083 @atom:*_b*_a082*_d*_i* @atom:*_b*_a061*_d*_i* @atom:*_b*_a083*_d*_i* + @angle:057_061_084 @atom:*_b*_a057*_d*_i* @atom:*_b*_a061*_d*_i* @atom:*_b*_a084*_d*_i* + 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@angle:005_064_005 @atom:*_b*_a005*_d*_i* @atom:*_b*_a064*_d*_i* @atom:*_b*_a005*_d*_i* + @angle:004_064_005 @atom:*_b*_a004*_d*_i* @atom:*_b*_a064*_d*_i* @atom:*_b*_a005*_d*_i* + @angle:004_064_013 @atom:*_b*_a004*_d*_i* @atom:*_b*_a064*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:005_064_020 @atom:*_b*_a005*_d*_i* @atom:*_b*_a064*_d*_i* @atom:*_b*_a020*_d*_i* + @angle:020_064_020 @atom:*_b*_a020*_d*_i* @atom:*_b*_a064*_d*_i* @atom:*_b*_a020*_d*_i* + @angle:013_064_020 @atom:*_b*_a013*_d*_i* @atom:*_b*_a064*_d*_i* @atom:*_b*_a020*_d*_i* + @angle:004_064_020 @atom:*_b*_a004*_d*_i* @atom:*_b*_a064*_d*_i* @atom:*_b*_a020*_d*_i* + @angle:004_064_048 @atom:*_b*_a004*_d*_i* @atom:*_b*_a064*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:005_064_048 @atom:*_b*_a005*_d*_i* @atom:*_b*_a064*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:020_064_048 @atom:*_b*_a020*_d*_i* @atom:*_b*_a064*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:005_064_052 @atom:*_b*_a005*_d*_i* @atom:*_b*_a064*_d*_i* @atom:*_b*_a052*_d*_i* + 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@angle:013_082_016 @atom:*_b*_a013*_d*_i* @atom:*_b*_a082*_d*_i* @atom:*_b*_a016*_d*_i* + @angle:016_082_024 @atom:*_b*_a016*_d*_i* @atom:*_b*_a082*_d*_i* @atom:*_b*_a024*_d*_i* + @angle:016_082_044 @atom:*_b*_a016*_d*_i* @atom:*_b*_a082*_d*_i* @atom:*_b*_a044*_d*_i* + @angle:020_082_049 @atom:*_b*_a020*_d*_i* @atom:*_b*_a082*_d*_i* @atom:*_b*_a049*_d*_i* + @angle:016_082_049 @atom:*_b*_a016*_d*_i* @atom:*_b*_a082*_d*_i* @atom:*_b*_a049*_d*_i* + @angle:049_082_057 @atom:*_b*_a049*_d*_i* @atom:*_b*_a082*_d*_i* @atom:*_b*_a057*_d*_i* + @angle:057_082_057 @atom:*_b*_a057*_d*_i* @atom:*_b*_a082*_d*_i* @atom:*_b*_a057*_d*_i* + @angle:013_082_057 @atom:*_b*_a013*_d*_i* @atom:*_b*_a082*_d*_i* @atom:*_b*_a057*_d*_i* + @angle:048_082_057 @atom:*_b*_a048*_d*_i* @atom:*_b*_a082*_d*_i* @atom:*_b*_a057*_d*_i* + @angle:056_082_057 @atom:*_b*_a056*_d*_i* @atom:*_b*_a082*_d*_i* @atom:*_b*_a057*_d*_i* + @angle:049_082_061 @atom:*_b*_a049*_d*_i* @atom:*_b*_a082*_d*_i* @atom:*_b*_a061*_d*_i* + @angle:016_082_061 @atom:*_b*_a016*_d*_i* @atom:*_b*_a082*_d*_i* @atom:*_b*_a061*_d*_i* + @angle:020_082_061 @atom:*_b*_a020*_d*_i* @atom:*_b*_a082*_d*_i* @atom:*_b*_a061*_d*_i* + @angle:057_082_061 @atom:*_b*_a057*_d*_i* @atom:*_b*_a082*_d*_i* @atom:*_b*_a061*_d*_i* + @angle:013_082_061 @atom:*_b*_a013*_d*_i* @atom:*_b*_a082*_d*_i* @atom:*_b*_a061*_d*_i* + @angle:044_082_061 @atom:*_b*_a044*_d*_i* @atom:*_b*_a082*_d*_i* @atom:*_b*_a061*_d*_i* + @angle:024_082_061 @atom:*_b*_a024*_d*_i* @atom:*_b*_a082*_d*_i* @atom:*_b*_a061*_d*_i* + @angle:057_082_079 @atom:*_b*_a057*_d*_i* @atom:*_b*_a082*_d*_i* @atom:*_b*_a079*_d*_i* + @angle:061_082_079 @atom:*_b*_a061*_d*_i* @atom:*_b*_a082*_d*_i* @atom:*_b*_a079*_d*_i* + @angle:020_082_086 @atom:*_b*_a020*_d*_i* @atom:*_b*_a082*_d*_i* @atom:*_b*_a086*_d*_i* + @angle:061_082_086 @atom:*_b*_a061*_d*_i* @atom:*_b*_a082*_d*_i* @atom:*_b*_a086*_d*_i* + @angle:057_082_087 @atom:*_b*_a057*_d*_i* @atom:*_b*_a082*_d*_i* @atom:*_b*_a087*_d*_i* + @angle:056_082_087 @atom:*_b*_a056*_d*_i* @atom:*_b*_a082*_d*_i* @atom:*_b*_a087*_d*_i* + @angle:049_083_061 @atom:*_b*_a049*_d*_i* @atom:*_b*_a083*_d*_i* @atom:*_b*_a061*_d*_i* + @angle:048_083_061 @atom:*_b*_a048*_d*_i* @atom:*_b*_a083*_d*_i* @atom:*_b*_a061*_d*_i* + @angle:013_083_061 @atom:*_b*_a013*_d*_i* @atom:*_b*_a083*_d*_i* @atom:*_b*_a061*_d*_i* + @angle:049_083_084 @atom:*_b*_a049*_d*_i* @atom:*_b*_a083*_d*_i* @atom:*_b*_a084*_d*_i* + @angle:061_083_084 @atom:*_b*_a061*_d*_i* @atom:*_b*_a083*_d*_i* @atom:*_b*_a084*_d*_i* + @angle:013_083_084 @atom:*_b*_a013*_d*_i* @atom:*_b*_a083*_d*_i* @atom:*_b*_a084*_d*_i* + @angle:013_084_016 @atom:*_b*_a013*_d*_i* @atom:*_b*_a084*_d*_i* @atom:*_b*_a016*_d*_i* + @angle:013_084_020 @atom:*_b*_a013*_d*_i* @atom:*_b*_a084*_d*_i* @atom:*_b*_a020*_d*_i* + @angle:016_084_024 @atom:*_b*_a016*_d*_i* @atom:*_b*_a084*_d*_i* @atom:*_b*_a024*_d*_i* + @angle:020_084_049 @atom:*_b*_a020*_d*_i* @atom:*_b*_a084*_d*_i* @atom:*_b*_a049*_d*_i* + @angle:016_084_049 @atom:*_b*_a016*_d*_i* @atom:*_b*_a084*_d*_i* @atom:*_b*_a049*_d*_i* + @angle:048_084_049 @atom:*_b*_a048*_d*_i* @atom:*_b*_a084*_d*_i* @atom:*_b*_a049*_d*_i* + @angle:049_084_050 @atom:*_b*_a049*_d*_i* @atom:*_b*_a084*_d*_i* @atom:*_b*_a050*_d*_i* + @angle:020_084_050 @atom:*_b*_a020*_d*_i* @atom:*_b*_a084*_d*_i* @atom:*_b*_a050*_d*_i* + @angle:049_084_057 @atom:*_b*_a049*_d*_i* @atom:*_b*_a084*_d*_i* @atom:*_b*_a057*_d*_i* + @angle:013_084_057 @atom:*_b*_a013*_d*_i* @atom:*_b*_a084*_d*_i* @atom:*_b*_a057*_d*_i* + @angle:048_084_057 @atom:*_b*_a048*_d*_i* @atom:*_b*_a084*_d*_i* @atom:*_b*_a057*_d*_i* + @angle:003_084_057 @atom:*_b*_a003*_d*_i* @atom:*_b*_a084*_d*_i* @atom:*_b*_a057*_d*_i* + @angle:057_084_058 @atom:*_b*_a057*_d*_i* @atom:*_b*_a084*_d*_i* @atom:*_b*_a058*_d*_i* + @angle:013_084_061 @atom:*_b*_a013*_d*_i* @atom:*_b*_a084*_d*_i* @atom:*_b*_a061*_d*_i* + @angle:049_084_080 @atom:*_b*_a049*_d*_i* @atom:*_b*_a084*_d*_i* @atom:*_b*_a080*_d*_i* + 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@angle:049_085_085 @atom:*_b*_a049*_d*_i* @atom:*_b*_a085*_d*_i* @atom:*_b*_a085*_d*_i* + @angle:057_085_085 @atom:*_b*_a057*_d*_i* @atom:*_b*_a085*_d*_i* @atom:*_b*_a085*_d*_i* + @angle:013_085_085 @atom:*_b*_a013*_d*_i* @atom:*_b*_a085*_d*_i* @atom:*_b*_a085*_d*_i* + @angle:048_086_048 @atom:*_b*_a048*_d*_i* @atom:*_b*_a086*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:048_086_056 @atom:*_b*_a048*_d*_i* @atom:*_b*_a086*_d*_i* @atom:*_b*_a056*_d*_i* + @angle:048_086_082 @atom:*_b*_a048*_d*_i* @atom:*_b*_a086*_d*_i* @atom:*_b*_a082*_d*_i* + @angle:048_086_083 @atom:*_b*_a048*_d*_i* @atom:*_b*_a086*_d*_i* @atom:*_b*_a083*_d*_i* + @angle:048_086_084 @atom:*_b*_a048*_d*_i* @atom:*_b*_a086*_d*_i* @atom:*_b*_a084*_d*_i* + @angle:048_086_086 @atom:*_b*_a048*_d*_i* @atom:*_b*_a086*_d*_i* @atom:*_b*_a086*_d*_i* + @angle:056_086_086 @atom:*_b*_a056*_d*_i* @atom:*_b*_a086*_d*_i* @atom:*_b*_a086*_d*_i* + @angle:048_086_087 @atom:*_b*_a048*_d*_i* @atom:*_b*_a086*_d*_i* @atom:*_b*_a087*_d*_i* + @angle:048_086_088 @atom:*_b*_a048*_d*_i* @atom:*_b*_a086*_d*_i* @atom:*_b*_a088*_d*_i* + @angle:049_087_060 @atom:*_b*_a049*_d*_i* @atom:*_b*_a087*_d*_i* @atom:*_b*_a060*_d*_i* + @angle:046_087_060 @atom:*_b*_a046*_d*_i* @atom:*_b*_a087*_d*_i* @atom:*_b*_a060*_d*_i* + @angle:013_087_060 @atom:*_b*_a013*_d*_i* @atom:*_b*_a087*_d*_i* @atom:*_b*_a060*_d*_i* + @angle:049_087_084 @atom:*_b*_a049*_d*_i* @atom:*_b*_a087*_d*_i* @atom:*_b*_a084*_d*_i* + @angle:046_087_084 @atom:*_b*_a046*_d*_i* @atom:*_b*_a087*_d*_i* @atom:*_b*_a084*_d*_i* + @angle:084_087_084 @atom:*_b*_a084*_d*_i* @atom:*_b*_a087*_d*_i* @atom:*_b*_a084*_d*_i* + @angle:082_087_084 @atom:*_b*_a082*_d*_i* @atom:*_b*_a087*_d*_i* @atom:*_b*_a084*_d*_i* + @angle:002_087_084 @atom:*_b*_a002*_d*_i* @atom:*_b*_a087*_d*_i* @atom:*_b*_a084*_d*_i* + @angle:013_087_084 @atom:*_b*_a013*_d*_i* @atom:*_b*_a087*_d*_i* @atom:*_b*_a084*_d*_i* + @angle:003_087_084 @atom:*_b*_a003*_d*_i* @atom:*_b*_a087*_d*_i* @atom:*_b*_a084*_d*_i* + @angle:060_087_084 @atom:*_b*_a060*_d*_i* @atom:*_b*_a087*_d*_i* @atom:*_b*_a084*_d*_i* + @angle:084_087_086 @atom:*_b*_a084*_d*_i* @atom:*_b*_a087*_d*_i* @atom:*_b*_a086*_d*_i* + @angle:049_087_087 @atom:*_b*_a049*_d*_i* @atom:*_b*_a087*_d*_i* @atom:*_b*_a087*_d*_i* + @angle:060_087_087 @atom:*_b*_a060*_d*_i* @atom:*_b*_a087*_d*_i* @atom:*_b*_a087*_d*_i* + @angle:084_087_087 @atom:*_b*_a084*_d*_i* @atom:*_b*_a087*_d*_i* @atom:*_b*_a087*_d*_i* + @angle:086_087_087 @atom:*_b*_a086*_d*_i* @atom:*_b*_a087*_d*_i* @atom:*_b*_a087*_d*_i* + @angle:084_087_088 @atom:*_b*_a084*_d*_i* @atom:*_b*_a087*_d*_i* @atom:*_b*_a088*_d*_i* + @angle:048_088_049 @atom:*_b*_a048*_d*_i* @atom:*_b*_a088*_d*_i* @atom:*_b*_a049*_d*_i* + @angle:049_088_061 @atom:*_b*_a049*_d*_i* @atom:*_b*_a088*_d*_i* @atom:*_b*_a061*_d*_i* + @angle:013_088_061 @atom:*_b*_a013*_d*_i* @atom:*_b*_a088*_d*_i* @atom:*_b*_a061*_d*_i* + @angle:019_088_061 @atom:*_b*_a019*_d*_i* @atom:*_b*_a088*_d*_i* @atom:*_b*_a061*_d*_i* + @angle:061_088_087 @atom:*_b*_a061*_d*_i* @atom:*_b*_a088*_d*_i* @atom:*_b*_a087*_d*_i* + @angle:004_089_090 @atom:*_b*_a004*_d*_i* @atom:*_b*_a089*_d*_i* @atom:*_b*_a090*_d*_i* + @angle:090_089_091 @atom:*_b*_a090*_d*_i* @atom:*_b*_a089*_d*_i* @atom:*_b*_a091*_d*_i* + @angle:004_089_091 @atom:*_b*_a004*_d*_i* @atom:*_b*_a089*_d*_i* @atom:*_b*_a091*_d*_i* + @angle:013_090_089 @atom:*_b*_a013*_d*_i* @atom:*_b*_a090*_d*_i* @atom:*_b*_a089*_d*_i* + @angle:089_090_091 @atom:*_b*_a089*_d*_i* @atom:*_b*_a090*_d*_i* @atom:*_b*_a091*_d*_i* + @angle:013_090_091 @atom:*_b*_a013*_d*_i* @atom:*_b*_a090*_d*_i* @atom:*_b*_a091*_d*_i* + @angle:024_091_046 @atom:*_b*_a024*_d*_i* @atom:*_b*_a091*_d*_i* @atom:*_b*_a046*_d*_i* + @angle:013_091_046 @atom:*_b*_a013*_d*_i* @atom:*_b*_a091*_d*_i* @atom:*_b*_a046*_d*_i* + @angle:044_091_046 @atom:*_b*_a044*_d*_i* @atom:*_b*_a091*_d*_i* @atom:*_b*_a046*_d*_i* + @angle:046_091_046 @atom:*_b*_a046*_d*_i* @atom:*_b*_a091*_d*_i* @atom:*_b*_a046*_d*_i* + @angle:016_091_046 @atom:*_b*_a016*_d*_i* @atom:*_b*_a091*_d*_i* @atom:*_b*_a046*_d*_i* + @angle:046_091_047 @atom:*_b*_a046*_d*_i* @atom:*_b*_a091*_d*_i* @atom:*_b*_a047*_d*_i* + @angle:046_091_089 @atom:*_b*_a046*_d*_i* @atom:*_b*_a091*_d*_i* @atom:*_b*_a089*_d*_i* + @angle:024_091_089 @atom:*_b*_a024*_d*_i* @atom:*_b*_a091*_d*_i* @atom:*_b*_a089*_d*_i* + @angle:046_091_090 @atom:*_b*_a046*_d*_i* @atom:*_b*_a091*_d*_i* @atom:*_b*_a090*_d*_i* + @angle:016_091_090 @atom:*_b*_a016*_d*_i* @atom:*_b*_a091*_d*_i* @atom:*_b*_a090*_d*_i* + @angle:091_091_091 @atom:*_b*_a091*_d*_i* @atom:*_b*_a091*_d*_i* @atom:*_b*_a091*_d*_i* + @angle:013_091_091 @atom:*_b*_a013*_d*_i* @atom:*_b*_a091*_d*_i* @atom:*_b*_a091*_d*_i* + @angle:044_091_091 @atom:*_b*_a044*_d*_i* @atom:*_b*_a091*_d*_i* @atom:*_b*_a091*_d*_i* + @angle:046_091_091 @atom:*_b*_a046*_d*_i* @atom:*_b*_a091*_d*_i* @atom:*_b*_a091*_d*_i* + @angle:024_091_091 @atom:*_b*_a024*_d*_i* @atom:*_b*_a091*_d*_i* @atom:*_b*_a091*_d*_i* + @angle:016_091_091 @atom:*_b*_a016*_d*_i* @atom:*_b*_a091*_d*_i* @atom:*_b*_a091*_d*_i* + @angle:089_091_091 @atom:*_b*_a089*_d*_i* @atom:*_b*_a091*_d*_i* @atom:*_b*_a091*_d*_i* + @angle:047_091_091 @atom:*_b*_a047*_d*_i* @atom:*_b*_a091*_d*_i* @atom:*_b*_a091*_d*_i* + @angle:090_091_091 @atom:*_b*_a090*_d*_i* @atom:*_b*_a091*_d*_i* @atom:*_b*_a091*_d*_i* + @angle:013_095_013 @atom:*_b*_a013*_d*_i* @atom:*_b*_a095*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:013_095_046 @atom:*_b*_a013*_d*_i* @atom:*_b*_a095*_d*_i* @atom:*_b*_a046*_d*_i* + @angle:013_101_045 @atom:*_b*_a013*_d*_i* @atom:*_b*_a101*_d*_i* @atom:*_b*_a045*_d*_i* + @angle:045_101_045 @atom:*_b*_a045*_d*_i* @atom:*_b*_a101*_d*_i* @atom:*_b*_a045*_d*_i* + @angle:045_101_048 @atom:*_b*_a045*_d*_i* @atom:*_b*_a101*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:013_101_048 @atom:*_b*_a013*_d*_i* @atom:*_b*_a101*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:013_102_103 @atom:*_b*_a013*_d*_i* @atom:*_b*_a102*_d*_i* @atom:*_b*_a103*_d*_i* + @angle:048_102_103 @atom:*_b*_a048*_d*_i* @atom:*_b*_a102*_d*_i* @atom:*_b*_a103*_d*_i* + @angle:103_102_103 @atom:*_b*_a103*_d*_i* @atom:*_b*_a102*_d*_i* @atom:*_b*_a103*_d*_i* + @angle:025_103_025 @atom:*_b*_a025*_d*_i* @atom:*_b*_a103*_d*_i* @atom:*_b*_a025*_d*_i* + @angle:025_103_102 @atom:*_b*_a025*_d*_i* @atom:*_b*_a103*_d*_i* @atom:*_b*_a102*_d*_i* + @angle:013_104_013 @atom:*_b*_a013*_d*_i* @atom:*_b*_a104*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:003_105_010 @atom:*_b*_a003*_d*_i* @atom:*_b*_a105*_d*_i* @atom:*_b*_a010*_d*_i* + @angle:003_105_013 @atom:*_b*_a003*_d*_i* @atom:*_b*_a105*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:003_105_045 @atom:*_b*_a003*_d*_i* @atom:*_b*_a105*_d*_i* @atom:*_b*_a045*_d*_i* + @angle:045_105_047 @atom:*_b*_a045*_d*_i* @atom:*_b*_a105*_d*_i* @atom:*_b*_a047*_d*_i* + @angle:013_105_047 @atom:*_b*_a013*_d*_i* @atom:*_b*_a105*_d*_i* @atom:*_b*_a047*_d*_i* + @angle:003_105_047 @atom:*_b*_a003*_d*_i* @atom:*_b*_a105*_d*_i* @atom:*_b*_a047*_d*_i* + @angle:003_105_051 @atom:*_b*_a003*_d*_i* @atom:*_b*_a105*_d*_i* @atom:*_b*_a051*_d*_i* + @angle:047_105_051 @atom:*_b*_a047*_d*_i* @atom:*_b*_a105*_d*_i* @atom:*_b*_a051*_d*_i* + @angle:045_105_060 @atom:*_b*_a045*_d*_i* @atom:*_b*_a105*_d*_i* @atom:*_b*_a060*_d*_i* + @angle:006_105_060 @atom:*_b*_a006*_d*_i* @atom:*_b*_a105*_d*_i* @atom:*_b*_a060*_d*_i* + @angle:010_105_060 @atom:*_b*_a010*_d*_i* @atom:*_b*_a105*_d*_i* @atom:*_b*_a060*_d*_i* + @angle:013_105_060 @atom:*_b*_a013*_d*_i* @atom:*_b*_a105*_d*_i* @atom:*_b*_a060*_d*_i* + @angle:051_105_060 @atom:*_b*_a051*_d*_i* @atom:*_b*_a105*_d*_i* @atom:*_b*_a060*_d*_i* + @angle:045_105_062 @atom:*_b*_a045*_d*_i* @atom:*_b*_a105*_d*_i* @atom:*_b*_a062*_d*_i* + @angle:060_105_062 @atom:*_b*_a060*_d*_i* @atom:*_b*_a105*_d*_i* @atom:*_b*_a062*_d*_i* + @angle:006_105_062 @atom:*_b*_a006*_d*_i* @atom:*_b*_a105*_d*_i* @atom:*_b*_a062*_d*_i* + @angle:010_105_062 @atom:*_b*_a010*_d*_i* @atom:*_b*_a105*_d*_i* @atom:*_b*_a062*_d*_i* + @angle:013_105_062 @atom:*_b*_a013*_d*_i* @atom:*_b*_a105*_d*_i* @atom:*_b*_a062*_d*_i* + @angle:051_105_062 @atom:*_b*_a051*_d*_i* @atom:*_b*_a105*_d*_i* @atom:*_b*_a062*_d*_i* + @angle:004_106_024 @atom:*_b*_a004*_d*_i* @atom:*_b*_a106*_d*_i* @atom:*_b*_a024*_d*_i* + @angle:024_106_024 @atom:*_b*_a024*_d*_i* @atom:*_b*_a106*_d*_i* @atom:*_b*_a024*_d*_i* + @angle:013_107_013 @atom:*_b*_a013*_d*_i* @atom:*_b*_a107*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:003_107_013 @atom:*_b*_a003*_d*_i* @atom:*_b*_a107*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:001_108_013 @atom:*_b*_a001*_d*_i* @atom:*_b*_a108*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:013_108_013 @atom:*_b*_a013*_d*_i* @atom:*_b*_a108*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:013_108_020 @atom:*_b*_a013*_d*_i* @atom:*_b*_a108*_d*_i* @atom:*_b*_a020*_d*_i* + @angle:020_108_020 @atom:*_b*_a020*_d*_i* @atom:*_b*_a108*_d*_i* @atom:*_b*_a020*_d*_i* + @angle:013_108_021 @atom:*_b*_a013*_d*_i* @atom:*_b*_a108*_d*_i* @atom:*_b*_a021*_d*_i* + @angle:045_108_045 @atom:*_b*_a045*_d*_i* @atom:*_b*_a108*_d*_i* @atom:*_b*_a045*_d*_i* + @angle:013_108_045 @atom:*_b*_a013*_d*_i* @atom:*_b*_a108*_d*_i* @atom:*_b*_a045*_d*_i* + @angle:046_108_046 @atom:*_b*_a046*_d*_i* @atom:*_b*_a108*_d*_i* @atom:*_b*_a046*_d*_i* + @angle:013_108_046 @atom:*_b*_a013*_d*_i* @atom:*_b*_a108*_d*_i* @atom:*_b*_a046*_d*_i* + @angle:013_108_065 @atom:*_b*_a013*_d*_i* @atom:*_b*_a108*_d*_i* @atom:*_b*_a065*_d*_i* + @angle:013_108_066 @atom:*_b*_a013*_d*_i* @atom:*_b*_a108*_d*_i* @atom:*_b*_a066*_d*_i* + @angle:013_108_108 @atom:*_b*_a013*_d*_i* @atom:*_b*_a108*_d*_i* @atom:*_b*_a108*_d*_i* + @angle:046_109_048 @atom:*_b*_a046*_d*_i* @atom:*_b*_a109*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:046_109_050 @atom:*_b*_a046*_d*_i* @atom:*_b*_a109*_d*_i* @atom:*_b*_a050*_d*_i* + @angle:013_109_050 @atom:*_b*_a013*_d*_i* @atom:*_b*_a109*_d*_i* @atom:*_b*_a050*_d*_i* + @angle:046_109_109 @atom:*_b*_a046*_d*_i* @atom:*_b*_a109*_d*_i* @atom:*_b*_a109*_d*_i* + @angle:013_109_109 @atom:*_b*_a013*_d*_i* @atom:*_b*_a109*_d*_i* @atom:*_b*_a109*_d*_i* + @angle:050_109_109 @atom:*_b*_a050*_d*_i* @atom:*_b*_a109*_d*_i* @atom:*_b*_a109*_d*_i* + @angle:048_109_109 @atom:*_b*_a048*_d*_i* @atom:*_b*_a109*_d*_i* @atom:*_b*_a109*_d*_i* + @angle:004_110_047 @atom:*_b*_a004*_d*_i* @atom:*_b*_a110*_d*_i* @atom:*_b*_a047*_d*_i* + @angle:047_110_047 @atom:*_b*_a047*_d*_i* @atom:*_b*_a110*_d*_i* @atom:*_b*_a047*_d*_i* } #(end of angles by type) @@ -6517,809 +6530,809 @@ OPLSAA { # ----------- Dihedral Interactions: ------------ # http://lammps.sandia.gov/doc/dihedral_opls.html # Syntax: - # dihedral_coeff DihedralTypeName DihedralStyle parameters... + # dihedral_coeff DihedralTypeName parameters... write_once("In Settings") { - dihedral_coeff @dihedral:X-2-2-2 opls -2.5 1.25 3.1 0.0 - dihedral_coeff @dihedral:X-2-2-6 opls -2.5 1.25 3.1 0.0 - dihedral_coeff @dihedral:1-2-2-2 opls -2.0 0.7 3.0 0.0 - dihedral_coeff @dihedral:1-2-2-6 opls -2.0 0.7 3.0 0.0 - dihedral_coeff @dihedral:2-2-2-2 opls -3.4 1.25 3.1 0.0 - dihedral_coeff @dihedral:2-2-2-6 opls -3.4 1.25 3.1 0.0 - dihedral_coeff @dihedral:2-2-2-10 opls -3.4 1.25 3.1 0.0 - dihedral_coeff @dihedral:2-2-2-13 opls -3.4 1.25 3.1 0.0 - dihedral_coeff @dihedral:2-2-2-65 opls -2.0 0.5 3.25 0.0 - dihedral_coeff @dihedral:6-2-2-6 opls -3.4 1.25 3.1 0.0 - dihedral_coeff @dihedral:6-2-2-65 opls -2.0 0.5 3.25 0.0 - dihedral_coeff @dihedral:10-2-2-10 opls -3.4 1.25 3.1 0.0 - dihedral_coeff @dihedral:2-2-5-7 opls 0.3 0.0 1.3 0.0 - dihedral_coeff @dihedral:6-2-5-7 opls 0.3 0.0 1.3 0.0 - dihedral_coeff @dihedral:10-2-5-7 opls 0.3 0.0 1.3 0.0 - dihedral_coeff @dihedral:X-2-10-2 opls -2.5 1.25 3.1 0.0 - dihedral_coeff @dihedral:2-2-10-2 opls -3.4 1.25 3.1 0.0 - dihedral_coeff @dihedral:2-2-13-2 opls -3.4 1.25 3.1 0.0 - dihedral_coeff @dihedral:6-2-20-2 opls -7.4 3.0 1.8 0.0 - dihedral_coeff @dihedral:6-2-20-6 opls -8.4 3.0 1.8 0.0 - dihedral_coeff @dihedral:4-3-3-4 opls 1.6 3.2 0.0 0.0 - dihedral_coeff @dihedral:4-3-3-13 opls 0.0 0.5 0.0 0.0 - dihedral_coeff @dihedral:4-3-3-24 opls 0.0 0.0 0.0 0.0 - dihedral_coeff @dihedral:4-3-3-46 opls 0.0 0.0 0.0 0.0 - dihedral_coeff @dihedral:13-3-3-13 opls 0.7 -1.5 0.0 0.0 - dihedral_coeff @dihedral:13-3-3-24 opls -0.5 0.2 0.0 0.0 - dihedral_coeff @dihedral:13-3-3-46 opls 0.8 -0.76 0.0 0.0 - dihedral_coeff @dihedral:24-3-3-46 opls -0.9 0.3 0.0 0.0 - dihedral_coeff @dihedral:46-3-3-46 opls 0.0 0.0 0.3 0.0 - dihedral_coeff @dihedral:3-3-5-7 opls 3.0 5.5 0.0 0.0 - dihedral_coeff @dihedral:4-3-5-7 opls 0.0 5.0 0.0 0.0 - dihedral_coeff @dihedral:13-3-5-7 opls 1.5 5.5 0.0 0.0 - dihedral_coeff @dihedral:24-3-5-7 opls -2.0 5.0 0.0 0.0 - dihedral_coeff @dihedral:46-3-5-7 opls 1.5 5.5 0.0 0.0 - dihedral_coeff @dihedral:48-3-5-7 opls 4.0 5.0 0.0 0.0 - dihedral_coeff @dihedral:1-3-13-13 opls 0.0 0.0 0.0 0.0 - dihedral_coeff @dihedral:1-3-13-46 opls 0.0 0.0 0.36 0.0 - dihedral_coeff @dihedral:3-3-13-46 opls 0.0 0.0 0.085 0.0 - dihedral_coeff 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@dihedral:087_003_024_045 0.0 4.9 0.0 0.0 + dihedral_coeff @dihedral:087_003_024_048 2.3 6.089 0.0 0.0 + dihedral_coeff @dihedral:087_003_024_084 2.3 6.089 0.0 0.0 + dihedral_coeff @dihedral:087_003_024_087 2.3 6.089 0.0 0.0 + dihedral_coeff @dihedral:X_003_047_013 0.9 0.23 -0.505 0.0 + dihedral_coeff @dihedral:004_003_047_046 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:004_003_047_047 2.5 6.0 0.0 0.0 + dihedral_coeff @dihedral:005_003_047_047 3.2 -3.0 0.0 0.0 + dihedral_coeff @dihedral:024_003_047_046 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:024_003_047_047 2.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:107_003_047_046 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:107_003_047_047 2.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:004_003_048_048 0.0 2.1 0.0 0.0 + dihedral_coeff @dihedral:005_003_048_048 0.0 2.1 0.0 0.0 + dihedral_coeff @dihedral:013_003_048_048 0.0 0.2 0.0 0.0 + dihedral_coeff @dihedral:020_003_048_048 0.0 2.1 0.0 0.0 + dihedral_coeff @dihedral:024_003_048_048 0.0 1.1 0.0 0.0 + dihedral_coeff @dihedral:046_003_048_048 0.0 0.2 0.0 0.0 + dihedral_coeff @dihedral:X_003_050_013 0.9 0.23 -0.505 0.0 + dihedral_coeff @dihedral:004_003_050_047 2.5 6.0 0.0 0.0 + dihedral_coeff @dihedral:005_003_050_047 3.2 -3.0 0.0 0.0 + dihedral_coeff @dihedral:013_003_050_047 0.8 -3.0 0.0 0.0 + dihedral_coeff @dihedral:013_003_056_X 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:013_003_056_013 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:046_003_056_X 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:046_003_056_045 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:X_003_060_X 0.0 7.0 0.0 0.0 + dihedral_coeff @dihedral:004_003_060_X 0.0 7.0 0.0 0.0 + dihedral_coeff @dihedral:004_003_082_X 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:004_003_082_057 2.0 1.0 0.0 0.0 + dihedral_coeff @dihedral:004_003_082_061 0.0 1.0 0.0 0.0 + dihedral_coeff @dihedral:082_003_082_057 -2.0 1.0 0.0 0.0 + dihedral_coeff @dihedral:082_003_082_061 0.0 1.0 0.0 0.0 + dihedral_coeff @dihedral:004_003_084_020 -0.75 1.5 0.0 0.0 + dihedral_coeff @dihedral:004_003_084_087 0.75 1.5 0.0 0.0 + dihedral_coeff @dihedral:084_003_084_020 0.0 1.5 0.0 0.0 + dihedral_coeff @dihedral:084_003_084_087 0.0 1.5 0.0 0.0 + dihedral_coeff @dihedral:048_003_086_048 0.0 2.17 0.0 0.0 + dihedral_coeff @dihedral:X_003_087_X 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:004_003_087_084 0.0 2.1 0.0 0.0 + dihedral_coeff @dihedral:004_003_087_087 0.0 2.1 0.0 0.0 + dihedral_coeff @dihedral:024_003_087_084 0.0 1.1 0.0 0.0 + dihedral_coeff @dihedral:024_003_087_087 0.0 1.1 0.0 0.0 + dihedral_coeff @dihedral:004_003_107_013 0.0 4.9 0.0 0.0 + dihedral_coeff @dihedral:013_003_107_013 0.0 4.9 0.0 0.0 + dihedral_coeff @dihedral:004_003_109_109 2.5 6.0 0.0 0.0 + dihedral_coeff @dihedral:005_003_109_109 3.2 -3.0 0.0 0.0 + dihedral_coeff @dihedral:X_004_106_X 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:007_005_010_002 0.3 0.0 0.5 0.0 + dihedral_coeff @dihedral:007_005_010_006 0.3 0.0 0.5 0.0 + dihedral_coeff @dihedral:007_005_013_002 0.0 0.0 0.2 0.0 + dihedral_coeff @dihedral:007_005_013_006 0.0 0.0 0.2 0.0 + dihedral_coeff @dihedral:007_005_013_013 -0.356 -0.174 0.492 0.0 + dihedral_coeff @dihedral:007_005_013_046 0.0 0.0 0.352 0.0 + dihedral_coeff @dihedral:007_005_013_047 -0.9 0.0 0.0 0.0 + dihedral_coeff @dihedral:007_005_013_048 -0.9 0.0 0.0 0.0 + dihedral_coeff @dihedral:007_005_013_050 -0.9 0.0 0.0 0.0 + dihedral_coeff @dihedral:007_005_044_013 0.0 0.0 0.3 0.0 + dihedral_coeff @dihedral:007_005_044_045 0.0 0.0 0.3 0.0 + dihedral_coeff @dihedral:007_005_024_003 5.519 -6.7 0.581 0.0 + dihedral_coeff @dihedral:007_005_024_045 2.722 -5.154 0.0 0.0 + dihedral_coeff @dihedral:007_005_047_047 0.0 1.682 0.0 0.0 + dihedral_coeff @dihedral:007_005_048_048 0.0 1.682 0.0 0.0 + dihedral_coeff @dihedral:007_005_051_020 -1.257 -1.806 0.003 0.0 + dihedral_coeff @dihedral:007_005_056_003 3.0 3.0 0.0 0.0 + dihedral_coeff @dihedral:007_005_064_004 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:007_005_064_005 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:007_005_079_013 -0.75 0.0 0.0 0.0 + dihedral_coeff @dihedral:007_005_079_023 0.75 0.0 0.0 0.0 + dihedral_coeff @dihedral:007_005_079_048 2.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:X_013_013_003 -4.344 -1.714 0.0 0.0 + dihedral_coeff @dihedral:X_013_013_013 1.711 -0.5 0.663 0.0 + dihedral_coeff @dihedral:X_013_013_024 1.428 0.086 0.029 0.0 + dihedral_coeff @dihedral:001_013_013_001 -2.5 0.0 0.25 0.0 + dihedral_coeff @dihedral:001_013_013_005 0.0 0.0 0.54 0.0 + dihedral_coeff @dihedral:001_013_013_013 0.3 -0.4 0.4 0.0 + dihedral_coeff @dihedral:001_013_013_046 0.0 0.0 0.4 0.0 + dihedral_coeff @dihedral:003_013_013_003 -0.55 0.0 1.0 0.0 + dihedral_coeff @dihedral:003_013_013_005 -6.18 0.0 0.0 0.0 + dihedral_coeff @dihedral:003_013_013_013 -2.06 -0.313 0.315 0.0 + dihedral_coeff @dihedral:003_013_013_015 -4.344 -1.714 0.0 0.0 + dihedral_coeff @dihedral:003_013_013_016 -4.344 -1.714 0.0 0.0 + dihedral_coeff @dihedral:003_013_013_024 -9.0 2.0 0.8 0.0 + dihedral_coeff @dihedral:003_013_013_046 0.0 0.0 -0.1 0.0 + dihedral_coeff @dihedral:003_013_013_048 -1.697 -0.456 0.585 0.0 + dihedral_coeff @dihedral:003_013_013_080 -1.697 -0.456 0.585 0.0 + dihedral_coeff @dihedral:005_013_013_005 9.508 0.0 0.0 0.0 + dihedral_coeff @dihedral:005_013_013_013 -1.552 0.0 0.0 0.0 + dihedral_coeff @dihedral:005_013_013_020 4.319 0.0 0.0 0.0 + dihedral_coeff @dihedral:005_013_013_044 8.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:005_013_013_024 6.28 -1.467 2.03 0.0 + dihedral_coeff @dihedral:005_013_013_046 0.0 0.0 0.468 0.0 + dihedral_coeff @dihedral:013_013_013_013 1.3 -0.05 0.2 0.0 + dihedral_coeff @dihedral:013_013_013_015 1.262 -0.198 0.465 0.0 + dihedral_coeff @dihedral:013_013_013_016 2.619 -0.62 0.258 0.0 + dihedral_coeff @dihedral:013_013_013_019 0.0 -0.65 0.0 0.0 + dihedral_coeff @dihedral:013_013_013_021 0.0 0.0 0.4 0.0 + dihedral_coeff @dihedral:013_013_013_044 2.392 -0.674 0.55 0.0 + dihedral_coeff @dihedral:013_013_013_024 0.845 -0.962 0.713 0.0 + dihedral_coeff @dihedral:013_013_013_046 0.0 0.0 0.3 0.0 + dihedral_coeff @dihedral:013_013_013_051 1.3 -0.05 0.2 0.0 + dihedral_coeff @dihedral:013_013_013_053 2.732 -0.229 0.485 0.0 + dihedral_coeff @dihedral:013_013_013_065 0.0 0.0 0.4 0.0 + dihedral_coeff @dihedral:013_013_013_066 0.0 0.0 0.4 0.0 + dihedral_coeff @dihedral:013_013_013_079 1.262 -0.198 0.465 0.0 + dihedral_coeff @dihedral:013_013_013_107 1.964 0.0 0.659 0.0 + dihedral_coeff @dihedral:013_013_013_108 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:015_013_013_046 0.0 0.0 0.452 0.0 + dihedral_coeff @dihedral:016_013_013_046 0.0 0.0 0.452 0.0 + dihedral_coeff @dihedral:019_013_013_046 0.0 0.0 0.366 0.0 + dihedral_coeff @dihedral:020_013_013_020 -0.55 0.0 0.0 0.0 + dihedral_coeff @dihedral:020_013_013_046 0.0 0.0 0.468 0.0 + dihedral_coeff @dihedral:021_013_013_021 -0.25 0.0 0.0 0.0 + dihedral_coeff @dihedral:021_013_013_044 2.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:021_013_013_046 0.0 0.0 0.4 0.0 + dihedral_coeff @dihedral:044_013_013_044 11.035 -0.968 0.27 0.0 + dihedral_coeff @dihedral:044_013_013_046 -1.013 -0.709 0.473 0.0 + dihedral_coeff @dihedral:044_013_013_048 -0.8 0.0 0.0 0.0 + dihedral_coeff @dihedral:024_013_013_046 0.0 0.0 0.464 0.0 + dihedral_coeff @dihedral:024_013_013_048 0.845 -0.962 0.713 0.0 + dihedral_coeff @dihedral:024_013_013_080 0.845 -0.962 0.713 0.0 + dihedral_coeff @dihedral:046_013_013_046 0.0 0.0 0.3 0.0 + dihedral_coeff @dihedral:046_013_013_047 0.0 0.0 0.366 0.0 + dihedral_coeff @dihedral:046_013_013_048 0.0 0.0 0.462 0.0 + dihedral_coeff @dihedral:046_013_013_051 0.0 0.0 0.3 0.0 + dihedral_coeff @dihedral:046_013_013_053 0.0 0.0 0.384 0.0 + dihedral_coeff @dihedral:046_013_013_055 0.0 0.0 -0.582 0.0 + dihedral_coeff @dihedral:046_013_013_059 0.0 0.0 0.462 0.0 + dihedral_coeff @dihedral:046_013_013_062 0.0 0.0 0.462 0.0 + dihedral_coeff @dihedral:046_013_013_065 0.0 0.0 0.4 0.0 + dihedral_coeff @dihedral:046_013_013_066 0.0 0.0 0.4 0.0 + dihedral_coeff @dihedral:046_013_013_079 0.0 0.0 0.452 0.0 + dihedral_coeff @dihedral:046_013_013_080 0.0 0.0 0.462 0.0 + dihedral_coeff @dihedral:046_013_013_082 0.0 0.0 0.462 0.0 + dihedral_coeff @dihedral:046_013_013_083 0.0 0.0 0.462 0.0 + dihedral_coeff @dihedral:046_013_013_084 0.0 0.0 0.462 0.0 + dihedral_coeff @dihedral:046_013_013_087 0.0 0.0 0.462 0.0 + dihedral_coeff @dihedral:046_013_013_088 0.0 0.0 0.462 0.0 + dihedral_coeff @dihedral:046_013_013_102 0.0 0.0 -0.225 0.0 + dihedral_coeff @dihedral:046_013_013_104 0.0 0.0 0.3 0.0 + dihedral_coeff @dihedral:046_013_013_107 0.0 0.0 0.464 0.0 + dihedral_coeff @dihedral:046_013_013_108 0.0 0.0 0.45 0.0 + dihedral_coeff @dihedral:046_013_013_109 0.0 0.0 0.366 0.0 + dihedral_coeff @dihedral:048_013_013_053 1.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:108_013_013_108 5.2 -0.5 0.0 0.0 + dihedral_coeff @dihedral:013_013_015_017 -0.759 -0.282 0.68 0.0 + dihedral_coeff @dihedral:046_013_015_017 0.0 0.0 0.48 0.0 + dihedral_coeff @dihedral:013_013_016_013 0.925 -0.576 0.677 0.0 + dihedral_coeff @dihedral:013_013_016_016 1.941 -0.836 0.935 0.0 + dihedral_coeff @dihedral:046_013_016_013 0.0 0.0 0.647 0.0 + dihedral_coeff @dihedral:046_013_016_016 0.0 0.0 0.558 0.0 + dihedral_coeff @dihedral:046_013_016_048 0.0 0.0 0.647 0.0 + dihedral_coeff @dihedral:X_013_018_019 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:046_013_018_019 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:X_013_019_018 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:X_013_019_019 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:013_013_019_019 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:046_013_019_019 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:X_013_020_013 -0.521 -2.018 1.996 0.0 + dihedral_coeff @dihedral:056_013_020_013 -0.5 -1.5 1.0 0.0 + dihedral_coeff @dihedral:057_013_020_013 -0.5 -1.5 1.0 0.0 + dihedral_coeff @dihedral:013_013_020_003 -1.22 -0.126 0.422 0.0 + dihedral_coeff @dihedral:013_013_020_013 0.65 -0.25 0.67 0.0 + dihedral_coeff @dihedral:013_013_020_064 -1.42 -0.62 0.1 0.0 + dihedral_coeff @dihedral:046_013_020_X 0.0 0.0 0.76 0.0 + dihedral_coeff @dihedral:046_013_020_003 0.0 0.0 0.198 0.0 + dihedral_coeff @dihedral:046_013_020_047 0.0 0.0 0.76 0.0 + dihedral_coeff @dihedral:046_013_020_048 0.0 0.0 0.76 0.0 + dihedral_coeff @dihedral:046_013_020_051 0.0 0.0 0.76 0.0 + dihedral_coeff @dihedral:046_013_020_064 0.0 0.0 0.3 0.0 + dihedral_coeff @dihedral:X_013_024_045 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:003_013_024_003 -2.365 0.912 -0.85 0.0 + dihedral_coeff @dihedral:003_013_024_013 -1.737 1.251 -3.501 0.0 + dihedral_coeff @dihedral:003_013_024_045 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:013_013_024_003 0.0 0.462 0.0 0.0 + dihedral_coeff @dihedral:013_013_024_013 4.753 -0.734 0.0 0.0 + dihedral_coeff @dihedral:013_013_024_045 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:013_013_024_059 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:013_013_024_079 2.929 -2.533 0.497 0.0 + dihedral_coeff @dihedral:013_013_024_091 2.3 6.089 0.0 0.0 + dihedral_coeff @dihedral:046_013_024_003 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:046_013_024_013 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:046_013_024_045 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:046_013_024_048 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:046_013_024_079 1.362 -1.457 0.149 0.0 + dihedral_coeff @dihedral:048_013_024_059 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:013_013_044_013 0.416 -0.128 0.695 0.0 + dihedral_coeff @dihedral:013_013_044_045 -0.19 -0.417 0.418 0.0 + dihedral_coeff @dihedral:046_013_044_013 0.0 0.0 0.56 0.0 + dihedral_coeff @dihedral:046_013_044_045 0.0 0.0 0.4 0.0 + dihedral_coeff @dihedral:046_013_044_048 0.0 0.0 0.56 0.0 + dihedral_coeff @dihedral:X_013_047_013 1.711 -0.5 0.663 0.0 + dihedral_coeff @dihedral:X_013_047_046 0.0 0.0 0.468 0.0 + dihedral_coeff @dihedral:X_013_047_047 0.5 0.0 0.0 0.0 + dihedral_coeff @dihedral:X_013_047_050 0.5 0.0 0.0 0.0 + dihedral_coeff @dihedral:001_013_047_047 0.5 0.0 0.0 0.0 + dihedral_coeff @dihedral:013_013_047_013 2.817 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dihedral_coeff @dihedral:065_013_048_048 0.0 0.0 0.4 0.0 + dihedral_coeff @dihedral:X_013_050_047 0.5 0.0 0.0 0.0 + dihedral_coeff @dihedral:013_013_050_050 0.346 0.405 -0.904 0.0 + dihedral_coeff @dihedral:046_013_050_047 0.0 0.0 -0.372 0.0 + dihedral_coeff @dihedral:046_013_050_050 0.0 0.0 -0.372 0.0 + dihedral_coeff @dihedral:046_013_050_109 0.0 0.0 -0.372 0.0 + dihedral_coeff @dihedral:013_013_051_X 1.711 -0.5 0.663 0.0 + dihedral_coeff @dihedral:013_013_051_046 0.0 0.0 0.3 0.0 + dihedral_coeff @dihedral:046_013_051_020 0.0 0.0 0.468 0.0 + dihedral_coeff @dihedral:013_013_053_013 1.438 -0.124 0.264 0.0 + dihedral_coeff @dihedral:013_013_053_045 0.0 0.0 0.347 0.0 + dihedral_coeff @dihedral:046_013_053_013 0.0 0.0 0.302 0.0 + dihedral_coeff @dihedral:046_013_053_045 0.0 0.0 0.261 0.0 + dihedral_coeff @dihedral:046_013_053_048 0.0 0.0 0.462 0.0 + dihedral_coeff @dihedral:046_013_053_054 0.0 0.0 0.3 0.0 + dihedral_coeff @dihedral:013_013_055_045 -0.19 -0.417 0.418 0.0 + dihedral_coeff 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0.0 0.0 0.0 + dihedral_coeff @dihedral:046_013_080_060 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:046_013_080_084 0.0 0.0 -0.48 0.0 + dihedral_coeff @dihedral:013_013_082_X 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:046_013_082_X 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:013_013_083_X 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:046_013_083_X 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:001_013_084_X 0.0 0.45 0.0 0.0 + dihedral_coeff @dihedral:013_013_084_X 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:013_013_084_057 1.7 -0.6 0.0 0.0 + dihedral_coeff @dihedral:021_013_084_X 0.0 -0.4 0.0 0.0 + dihedral_coeff @dihedral:046_013_084_X 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:001_013_087_X 0.0 0.45 0.0 0.0 + dihedral_coeff @dihedral:013_013_087_X 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:021_013_087_X 0.0 -0.4 0.0 0.0 + dihedral_coeff @dihedral:046_013_087_X 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:013_013_088_X 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:046_013_088_X 0.0 0.0 0.0 0.0 + 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0.0 0.0 + dihedral_coeff @dihedral:013_020_051_005 -0.375 -1.358 0.004 0.0 + dihedral_coeff @dihedral:013_020_051_013 0.65 -0.25 0.67 0.0 + dihedral_coeff @dihedral:013_020_051_020 -0.375 -1.358 0.004 0.0 + dihedral_coeff @dihedral:013_020_051_046 0.0 0.0 0.76 0.0 + dihedral_coeff @dihedral:013_020_056_003 3.0 3.0 0.0 0.0 + dihedral_coeff @dihedral:013_020_059_056 0.0 5.2 0.0 0.0 + dihedral_coeff @dihedral:X_020_064_052 0.0 0.0 0.562 0.0 + dihedral_coeff @dihedral:013_020_064_013 3.5 -3.3 1.5 0.0 + dihedral_coeff @dihedral:013_020_064_052 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:048_020_064_004 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:084_020_082_061 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:082_020_084_088 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:084_020_084_049 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:084_020_084_087 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:108_020_108_013 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:108_020_108_020 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:X_024_048_048 0.0 2.1 0.0 0.0 + dihedral_coeff @dihedral:003_024_048_048 0.0 2.1 0.0 0.0 + dihedral_coeff @dihedral:013_024_048_048 0.0 2.1 0.0 0.0 + dihedral_coeff @dihedral:045_024_048_048 0.0 2.1 0.0 0.0 + dihedral_coeff @dihedral:059_024_048_048 0.0 2.1 0.0 0.0 + dihedral_coeff @dihedral:082_024_048_048 0.0 2.1 0.0 0.0 + dihedral_coeff @dihedral:084_024_048_048 0.0 2.1 0.0 0.0 + dihedral_coeff @dihedral:X_024_059_X 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:X_024_059_049 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:045_024_059_X 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:X_024_060_X 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:X_024_079_023 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:013_024_079_048 2.074 -2.966 2.473 0.0 + dihedral_coeff @dihedral:045_024_079_048 1.671 -4.901 0.669 0.0 + dihedral_coeff @dihedral:013_024_082_061 0.0 2.1 0.0 0.0 + dihedral_coeff @dihedral:045_024_082_016 0.0 2.1 0.0 0.0 + dihedral_coeff @dihedral:045_024_082_020 0.0 2.1 0.0 0.0 + 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dihedral_coeff @dihedral:003_024_091_046 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:003_024_091_089 -1.396 -0.427 0.0 0.0 + dihedral_coeff @dihedral:003_024_091_091 -1.396 -0.427 0.0 0.0 + dihedral_coeff @dihedral:045_024_091_046 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:045_024_091_089 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:045_024_091_091 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:X_024_106_X 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:013_044_044_013 0.0 0.0 0.3 0.0 + dihedral_coeff @dihedral:013_044_044_045 0.0 0.0 0.3 0.0 + dihedral_coeff @dihedral:045_044_044_045 0.0 0.0 0.3 0.0 + dihedral_coeff @dihedral:013_044_048_048 -7.582 3.431 3.198 0.0 + dihedral_coeff @dihedral:045_044_048_048 0.0 2.03 0.0 0.0 + dihedral_coeff @dihedral:059_044_048_048 0.0 2.1 0.0 0.0 + dihedral_coeff @dihedral:082_044_048_048 0.0 2.1 0.0 0.0 + dihedral_coeff @dihedral:084_044_048_048 0.0 2.1 0.0 0.0 + dihedral_coeff @dihedral:045_044_082_016 0.0 2.1 0.0 0.0 + dihedral_coeff @dihedral:045_044_082_061 0.0 2.1 0.0 0.0 + dihedral_coeff @dihedral:048_044_082_016 0.0 2.1 0.0 0.0 + dihedral_coeff @dihedral:048_044_082_061 0.0 2.1 0.0 0.0 + dihedral_coeff @dihedral:047_046_047_013 0.0 -8.0 0.0 0.0 + dihedral_coeff @dihedral:047_046_047_046 0.0 -8.0 0.0 0.0 + dihedral_coeff @dihedral:X_047_047_X 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:X_047_047_019 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:003_047_047_024 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:003_047_047_046 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:005_047_047_013 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:005_047_047_046 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:013_047_047_013 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:013_047_047_019 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:013_047_047_020 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:013_047_047_046 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:019_047_047_046 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:020_047_047_046 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:021_047_047_021 -1.6 14.0 0.0 0.0 + dihedral_coeff @dihedral:021_047_047_046 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:046_047_047_046 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:046_047_047_048 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:013_047_048_048 0.205 -0.531 0.0 0.0 + dihedral_coeff @dihedral:046_047_048_048 0.0 0.0 -0.372 0.0 + dihedral_coeff @dihedral:046_047_048_056 0.0 0.0 -0.372 0.0 + dihedral_coeff @dihedral:047_047_048_048 1.241 3.353 -0.286 0.0 + dihedral_coeff @dihedral:013_047_050_013 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:013_047_050_046 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:013_047_050_048 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:013_047_050_050 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:013_047_050_109 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:024_047_050_003 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:046_047_050_013 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:046_047_050_046 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:046_047_050_048 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:046_047_050_050 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:046_047_050_109 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:X_047_084_X 0.0 2.17 0.0 0.0 + dihedral_coeff @dihedral:X_047_086_048 0.0 2.17 0.0 0.0 + dihedral_coeff @dihedral:003_047_086_086 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:049_047_086_X 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:049_047_086_024 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:X_047_087_X 0.0 2.17 0.0 0.0 + dihedral_coeff @dihedral:X_047_088_X 0.0 2.17 0.0 0.0 + dihedral_coeff @dihedral:013_047_110_047 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:046_047_110_047 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:X_048_048_X 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:X_048_048_013 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:X_048_048_048 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:X_048_048_049 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:001_048_048_048 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:001_048_048_049 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:013_048_048_013 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:013_048_048_048 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:013_048_048_049 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:013_048_048_050 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:021_048_048_048 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:021_048_048_049 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:044_048_048_049 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:047_048_048_049 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:048_048_048_048 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:048_048_048_049 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:048_048_048_050 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:048_048_048_055 0.0 1.62 0.0 -0.44 + dihedral_coeff @dihedral:048_048_048_060 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:048_048_048_065 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:048_048_048_066 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:048_048_048_086 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:048_048_048_109 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:049_048_048_049 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:049_048_048_050 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:049_048_048_060 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:049_048_048_065 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:049_048_048_066 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:049_048_048_086 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:049_048_048_109 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:056_048_048_086 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:048_048_050_046 0.0 0.0 -0.372 0.0 + dihedral_coeff @dihedral:048_048_050_047 1.241 3.353 -0.286 0.0 + dihedral_coeff @dihedral:056_048_050_046 0.0 0.0 -0.372 0.0 + dihedral_coeff @dihedral:056_048_050_047 1.241 3.353 -0.286 0.0 + dihedral_coeff @dihedral:048_048_053_013 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:048_048_053_054 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:X_048_055_045 0.0 2.03 0.0 0.0 + dihedral_coeff @dihedral:048_048_055_045 0.0 3.9 0.0 0.0 + dihedral_coeff @dihedral:055_048_055_013 0.0 7.936 0.0 0.0 + dihedral_coeff @dihedral:055_048_055_045 0.0 3.9 0.0 0.0 + dihedral_coeff @dihedral:060_048_055_045 0.0 2.03 0.0 0.0 + dihedral_coeff @dihedral:X_048_056_X 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:048_048_056_048 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:049_048_056_048 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:X_048_060_X 0.0 7.0 0.0 0.0 + dihedral_coeff @dihedral:X_048_079_023 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:048_048_079_013 0.0 -0.9 0.0 0.0 + dihedral_coeff @dihedral:048_048_079_024 1.656 -0.768 -0.117 0.0 + dihedral_coeff @dihedral:048_048_086_048 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:048_048_086_056 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:048_048_086_086 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:049_048_086_048 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:049_048_086_056 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:049_048_086_086 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:056_048_086_048 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:056_048_086_086 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:049_048_088_049 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:056_048_101_013 0.0 3.651 0.0 0.0 + dihedral_coeff @dihedral:048_048_102_103 0.0 1.15 0.0 0.0 + dihedral_coeff @dihedral:048_048_109_013 0.205 -0.531 0.0 0.0 + dihedral_coeff @dihedral:048_048_109_046 0.0 0.0 -0.372 0.0 + dihedral_coeff @dihedral:048_048_109_109 1.241 3.353 -0.286 0.0 + dihedral_coeff @dihedral:X_050_050_049 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:003_050_050_003 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:013_050_050_013 0.0 0.0 0.3 0.0 + dihedral_coeff @dihedral:013_050_050_046 0.0 0.0 0.3 0.0 + dihedral_coeff @dihedral:013_050_050_047 0.0 0.0 -0.372 0.0 + dihedral_coeff @dihedral:046_050_050_046 0.0 0.0 0.3 0.0 + dihedral_coeff @dihedral:046_050_050_047 0.0 0.0 -0.372 0.0 + dihedral_coeff @dihedral:047_050_050_047 1.423 4.055 0.858 0.0 + dihedral_coeff @dihedral:013_050_109_013 0.0 0.0 0.3 0.0 + dihedral_coeff @dihedral:013_050_109_109 0.0 0.0 -0.372 0.0 + dihedral_coeff @dihedral:046_050_109_013 0.0 0.0 0.3 0.0 + dihedral_coeff @dihedral:046_050_109_046 0.0 0.0 0.3 0.0 + dihedral_coeff @dihedral:046_050_109_109 0.0 0.0 -0.372 0.0 + dihedral_coeff @dihedral:047_050_109_013 0.0 0.0 -0.372 0.0 + dihedral_coeff @dihedral:047_050_109_046 0.0 0.0 -0.372 0.0 + dihedral_coeff @dihedral:047_050_109_109 1.423 4.055 0.858 0.0 + dihedral_coeff @dihedral:013_053_082_061 0.0 2.1 0.0 0.0 + dihedral_coeff @dihedral:048_053_082_061 0.0 2.1 0.0 0.0 + dihedral_coeff @dihedral:045_055_059_X 0.0 2.03 0.0 0.0 + dihedral_coeff @dihedral:013_056_056_013 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:013_056_056_048 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:048_056_056_048 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:X_056_059_X 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:X_056_059_049 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:X_056_060_X 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:X_056_062_X 0.0 10.0 0.0 0.0 + dihedral_coeff @dihedral:X_056_082_X 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:048_056_086_048 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:048_056_086_086 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:X_057_060_X 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:045_057_060_X 0.0 5.0 0.0 0.0 + dihedral_coeff @dihedral:X_057_061_X 0.0 10.0 0.0 0.0 + dihedral_coeff @dihedral:X_057_062_X 0.0 10.0 0.0 0.0 + dihedral_coeff @dihedral:X_057_081_X 0.0 3.05 0.0 0.0 + dihedral_coeff @dihedral:X_057_082_X 0.0 4.65 0.0 0.0 + dihedral_coeff @dihedral:X_057_082_049 0.0 10.0 0.0 0.0 + dihedral_coeff @dihedral:045_057_082_X 0.0 5.0 0.0 0.0 + dihedral_coeff @dihedral:X_057_084_X 0.0 2.8 0.0 0.0 + dihedral_coeff @dihedral:045_057_084_X 0.0 5.0 0.0 0.0 + dihedral_coeff @dihedral:061_057_086_048 0.0 2.17 0.0 0.0 + dihedral_coeff @dihedral:084_057_086_048 0.0 2.17 0.0 0.0 + dihedral_coeff @dihedral:X_060_060_X 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:X_060_061_X 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:X_060_080_X 0.0 3.35 0.0 0.0 + dihedral_coeff @dihedral:X_060_081_X 0.0 6.0 0.0 0.0 + dihedral_coeff @dihedral:X_060_087_X 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:048_060_087_084 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:060_060_087_084 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:X_061_061_X 0.0 10.0 0.0 0.0 + dihedral_coeff @dihedral:X_061_062_X 0.0 10.0 0.0 0.0 + dihedral_coeff @dihedral:X_061_082_X 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:X_061_082_049 0.0 10.0 0.0 0.0 + dihedral_coeff @dihedral:083_061_082_016 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:088_061_082_016 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:088_061_082_020 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:X_061_083_X 0.0 4.8 0.0 0.0 + dihedral_coeff @dihedral:082_061_083_049 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:082_061_083_084 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:X_061_084_X 0.0 10.0 0.0 0.0 + dihedral_coeff @dihedral:X_061_088_X 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:082_061_088_084 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:X_080_084_X 0.0 13.05 0.0 0.0 + dihedral_coeff @dihedral:X_082_084_X 0.0 2.17 0.0 0.0 + dihedral_coeff @dihedral:016_082_086_048 0.0 2.17 0.0 0.0 + dihedral_coeff @dihedral:020_082_086_048 0.0 2.17 0.0 0.0 + dihedral_coeff @dihedral:057_082_086_048 0.0 2.17 0.0 0.0 + dihedral_coeff @dihedral:061_082_086_048 0.0 2.17 0.0 0.0 + dihedral_coeff @dihedral:X_082_087_X 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:X_083_084_X 0.0 10.75 0.0 0.0 + dihedral_coeff @dihedral:X_083_084_049 0.0 10.75 0.0 0.0 + dihedral_coeff @dihedral:049_083_084_X 0.0 10.75 0.0 0.0 + dihedral_coeff @dihedral:049_083_084_016 0.0 10.75 0.0 0.0 + dihedral_coeff @dihedral:049_083_084_049 0.0 10.75 0.0 0.0 + dihedral_coeff @dihedral:061_083_084_016 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:061_083_084_020 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:061_083_084_049 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:X_083_086_048 0.0 2.17 0.0 0.0 + dihedral_coeff @dihedral:061_083_086_048 0.0 2.17 0.0 0.0 + dihedral_coeff @dihedral:061_083_087_X 0.0 2.17 0.0 0.0 + dihedral_coeff @dihedral:084_083_087_X 0.0 2.17 0.0 0.0 + dihedral_coeff @dihedral:X_084_084_X 0.0 10.75 0.0 0.0 + dihedral_coeff @dihedral:X_084_084_049 0.0 10.75 0.0 0.0 + dihedral_coeff @dihedral:016_084_084_049 0.0 10.75 0.0 0.0 + dihedral_coeff @dihedral:049_084_084_049 0.0 10.75 0.0 0.0 + dihedral_coeff @dihedral:X_084_086_048 0.0 2.17 0.0 0.0 + dihedral_coeff @dihedral:016_084_086_048 0.0 2.17 0.0 0.0 + dihedral_coeff @dihedral:020_084_086_048 0.0 2.17 0.0 0.0 + dihedral_coeff @dihedral:057_084_086_048 0.0 2.17 0.0 0.0 + dihedral_coeff @dihedral:X_084_087_X 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:X_084_087_049 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:049_084_087_049 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:X_084_088_049 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:016_084_088_049 0.0 10.75 0.0 0.0 + dihedral_coeff @dihedral:016_084_088_061 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:020_084_088_061 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:049_084_088_X 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:049_084_088_061 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:048_086_086_048 0.0 2.17 0.0 0.0 + dihedral_coeff @dihedral:048_086_086_056 0.0 2.17 0.0 0.0 + dihedral_coeff @dihedral:048_086_087_X 0.0 2.17 0.0 0.0 + dihedral_coeff @dihedral:048_086_088_X 0.0 2.17 0.0 0.0 + dihedral_coeff @dihedral:048_086_088_061 0.0 2.17 0.0 0.0 + dihedral_coeff @dihedral:056_086_088_X 0.0 2.17 0.0 0.0 + dihedral_coeff @dihedral:X_087_087_020 0.0 2.17 0.0 0.0 + dihedral_coeff @dihedral:X_087_087_057 0.0 2.17 0.0 0.0 + dihedral_coeff @dihedral:X_087_087_087 0.0 2.17 0.0 0.0 + dihedral_coeff @dihedral:049_087_087_049 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:004_089_090_013 0.0 6.089 0.0 0.0 + dihedral_coeff @dihedral:004_089_090_045 0.0 4.9 0.0 0.0 + dihedral_coeff @dihedral:004_089_090_048 0.0 6.089 0.0 0.0 + dihedral_coeff @dihedral:004_089_090_091 0.0 20.0 0.0 0.0 + dihedral_coeff @dihedral:091_089_090_013 2.3 6.089 0.0 0.0 + dihedral_coeff @dihedral:091_089_090_045 0.0 4.9 0.0 0.0 + dihedral_coeff @dihedral:091_089_090_048 2.3 6.089 0.0 0.0 + dihedral_coeff @dihedral:091_089_090_091 2.3 6.089 0.0 0.0 + dihedral_coeff @dihedral:X_089_091_X 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:004_089_091_046 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:004_089_091_091 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:090_089_091_046 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:090_089_091_091 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:X_090_091_X 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:X_090_091_046 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:X_090_091_091 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:X_091_091_X 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:X_091_091_024 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:013_091_091_013 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:013_091_091_046 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:046_091_091_046 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:046_091_091_091 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:091_091_091_091 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:X_109_109_X 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:013_109_109_013 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:013_109_109_046 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:013_109_109_048 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:013_109_109_050 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:013_109_109_109 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:046_109_109_046 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:046_109_109_048 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:046_109_109_050 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:046_109_109_109 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:048_109_109_048 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:048_109_109_050 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:048_109_109_109 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:050_109_109_050 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:050_109_109_109 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:109_109_109_109 1.423 4.055 0.858 0.0 + dihedral_coeff @dihedral:024_003_013_053 1.816 1.222 1.581 0.0 + dihedral_coeff @dihedral:052_003_013_024 0.0 0.82 0.0 0.0 + dihedral_coeff @dihedral:003_013_013_053 1.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:003_013_013_083 -1.697 -0.456 0.585 0.0 + dihedral_coeff @dihedral:003_013_013_084 -1.697 -0.456 0.585 0.0 + dihedral_coeff @dihedral:003_013_013_085 -1.697 -0.456 0.585 0.0 + dihedral_coeff @dihedral:005_013_013_053 6.28 -1.467 2.03 0.0 + dihedral_coeff @dihedral:015_013_013_053 1.428 0.086 0.029 0.0 + dihedral_coeff @dihedral:016_013_013_053 1.428 0.086 0.029 0.0 + dihedral_coeff @dihedral:013_013_013_055 2.732 -0.229 0.485 0.0 + dihedral_coeff @dihedral:024_013_013_083 0.845 -0.962 0.713 0.0 + dihedral_coeff @dihedral:053_013_013_083 1.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:024_013_013_084 0.845 -0.962 0.713 0.0 + dihedral_coeff @dihedral:053_013_013_084 1.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:024_013_013_085 0.845 -0.962 0.713 0.0 + dihedral_coeff @dihedral:046_013_013_085 0.0 0.0 0.462 0.0 + dihedral_coeff @dihedral:053_013_013_085 1.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:003_013_053_013 1.438 -0.124 0.264 0.0 + dihedral_coeff @dihedral:003_013_053_054 0.0 0.0 0.347 0.0 + dihedral_coeff @dihedral:013_013_053_054 0.0 0.0 0.347 0.0 + dihedral_coeff @dihedral:046_013_055_054 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:013_013_085_X 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:013_013_085_057 1.7 -0.6 0.0 0.0 + dihedral_coeff @dihedral:046_013_085_X 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:055_048_055_054 0.0 3.9 0.0 0.0 + dihedral_coeff @dihedral:X_048_081_X 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:X_057_085_X 0.0 5.0 0.0 0.0 + dihedral_coeff @dihedral:X_085_085_X 0.0 10.75 0.0 0.0 + dihedral_coeff @dihedral:013_013_013_020 1.3 -0.05 0.2 0.0 + dihedral_coeff @dihedral:013_013_013_047 1.3 -0.05 0.2 0.0 } #(end of dihedral_coeffs) # Rules for creating dihedral interactions according to atom type: @@ -7327,806 +7340,806 @@ OPLSAA { # (* = wildcard) write_once("Data Dihedrals By Type") { - @dihedral:X-2-2-2 @atom:* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* - @dihedral:X-2-2-6 @atom:* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d6_i* - @dihedral:1-2-2-2 @atom:*_b*_a*_d1_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* - @dihedral:1-2-2-6 @atom:*_b*_a*_d1_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d6_i* - @dihedral:2-2-2-2 @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* - @dihedral:2-2-2-6 @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d6_i* - @dihedral:2-2-2-10 @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d10_i* - @dihedral:2-2-2-13 @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d13_i* - @dihedral:2-2-2-65 @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d65_i* - @dihedral:6-2-2-6 @atom:*_b*_a*_d6_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d6_i* - @dihedral:6-2-2-65 @atom:*_b*_a*_d6_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d65_i* - @dihedral:10-2-2-10 @atom:*_b*_a*_d10_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d10_i* - @dihedral:2-2-5-7 @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d7_i* - @dihedral:6-2-5-7 @atom:*_b*_a*_d6_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d7_i* - @dihedral:10-2-5-7 @atom:*_b*_a*_d10_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d7_i* - @dihedral:X-2-10-2 @atom:* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d10_i* @atom:*_b*_a*_d2_i* - @dihedral:2-2-10-2 @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d10_i* @atom:*_b*_a*_d2_i* - @dihedral:2-2-13-2 @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d2_i* - @dihedral:6-2-20-2 @atom:*_b*_a*_d6_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d2_i* - @dihedral:6-2-20-6 @atom:*_b*_a*_d6_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d6_i* - @dihedral:4-3-3-4 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d4_i* - @dihedral:4-3-3-13 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* - @dihedral:4-3-3-24 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* - @dihedral:4-3-3-46 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d46_i* - @dihedral:13-3-3-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* - @dihedral:13-3-3-24 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* - @dihedral:13-3-3-46 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d46_i* - @dihedral:24-3-3-46 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d46_i* - @dihedral:46-3-3-46 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d46_i* - @dihedral:3-3-5-7 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d7_i* - @dihedral:4-3-5-7 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d7_i* - @dihedral:13-3-5-7 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d7_i* - @dihedral:24-3-5-7 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d7_i* - @dihedral:46-3-5-7 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d7_i* - @dihedral:48-3-5-7 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d7_i* - @dihedral:1-3-13-13 @atom:*_b*_a*_d1_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* - @dihedral:1-3-13-46 @atom:*_b*_a*_d1_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i* - @dihedral:3-3-13-46 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i* - @dihedral:4-3-13-X @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:* - @dihedral:4-3-13-13 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* - @dihedral:4-3-13-21 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d21_i* - @dihedral:4-3-13-44 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d44_i* - @dihedral:4-3-13-24 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i* - @dihedral:4-3-13-46 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i* - @dihedral:4-3-13-48 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d48_i* - @dihedral:5-3-13-13 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* - @dihedral:5-3-13-44 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d44_i* - @dihedral:5-3-13-46 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i* - @dihedral:13-3-13-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* - @dihedral:13-3-13-46 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i* - @dihedral:20-3-13-13 @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* - @dihedral:20-3-13-46 @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i* - @dihedral:21-3-13-13 @atom:*_b*_a*_d21_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* - @dihedral:21-3-13-46 @atom:*_b*_a*_d21_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i* - @dihedral:24-3-13-13 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* - @dihedral:24-3-13-21 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d21_i* - @dihedral:24-3-13-24 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i* - @dihedral:24-3-13-46 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i* - @dihedral:46-3-13-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* - @dihedral:46-3-13-46 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i* - @dihedral:48-3-13-46 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i* - @dihedral:52-3-13-13 @atom:*_b*_a*_d52_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* - @dihedral:52-3-13-44 @atom:*_b*_a*_d52_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d44_i* - @dihedral:52-3-13-46 @atom:*_b*_a*_d52_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i* - @dihedral:65-3-13-13 @atom:*_b*_a*_d65_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* - @dihedral:65-3-13-46 @atom:*_b*_a*_d65_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i* - @dihedral:107-3-13-46 @atom:*_b*_a*_d107_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i* - @dihedral:4-3-20-13 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13_i* - @dihedral:4-3-20-48 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d48_i* - @dihedral:13-3-20-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13_i* - @dihedral:13-3-20-48 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d48_i* - @dihedral:24-3-20-13 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13_i* - @dihedral:46-3-20-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13_i* - @dihedral:48-3-20-13 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13_i* - @dihedral:3-3-24-13 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13_i* - @dihedral:3-3-24-45 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d45_i* - @dihedral:4-3-24-5 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d5_i* - @dihedral:4-3-24-13 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13_i* - @dihedral:4-3-24-45 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d45_i* - @dihedral:4-3-24-47 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d47_i* - @dihedral:4-3-24-48 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d48_i* - @dihedral:4-3-24-91 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d91_i* - @dihedral:5-3-24-13 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13_i* - @dihedral:5-3-24-45 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d45_i* - @dihedral:13-3-24-5 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d5_i* - @dihedral:13-3-24-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13_i* - @dihedral:13-3-24-45 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d45_i* - @dihedral:13-3-24-48 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d48_i* - @dihedral:20-3-24-13 @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13_i* - @dihedral:20-3-24-45 @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d45_i* - @dihedral:24-3-24-3 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* - @dihedral:24-3-24-13 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13_i* - @dihedral:24-3-24-45 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d45_i* - @dihedral:46-3-24-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13_i* - @dihedral:46-3-24-45 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d45_i* - @dihedral:47-3-24-45 @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d45_i* - @dihedral:48-3-24-45 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d45_i* - @dihedral:48-3-24-48 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d48_i* - @dihedral:48-3-24-84 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d84_i* - @dihedral:48-3-24-87 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d87_i* - @dihedral:84-3-24-48 @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d48_i* - @dihedral:84-3-24-84 @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d84_i* - @dihedral:84-3-24-87 @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d87_i* - @dihedral:87-3-24-45 @atom:*_b*_a*_d87_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d45_i* - @dihedral:87-3-24-48 @atom:*_b*_a*_d87_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d48_i* - @dihedral:87-3-24-84 @atom:*_b*_a*_d87_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d84_i* - @dihedral:87-3-24-87 @atom:*_b*_a*_d87_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d87_i* - @dihedral:X-3-47-13 @atom:* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d13_i* - @dihedral:4-3-47-46 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d46_i* - @dihedral:4-3-47-47 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i* - @dihedral:5-3-47-47 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i* - @dihedral:24-3-47-46 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d46_i* - @dihedral:24-3-47-47 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i* - @dihedral:107-3-47-46 @atom:*_b*_a*_d107_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d46_i* - @dihedral:107-3-47-47 @atom:*_b*_a*_d107_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i* - @dihedral:4-3-48-48 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:5-3-48-48 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:13-3-48-48 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:20-3-48-48 @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:24-3-48-48 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:46-3-48-48 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:X-3-50-13 @atom:* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d13_i* - @dihedral:4-3-50-47 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d47_i* - @dihedral:5-3-50-47 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d47_i* - @dihedral:13-3-50-47 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d47_i* - @dihedral:13-3-56-X @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d56_i* @atom:* - @dihedral:13-3-56-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d13_i* - @dihedral:46-3-56-X @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d56_i* @atom:* - @dihedral:46-3-56-45 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d45_i* - @dihedral:X-3-60-X @atom:* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d60_i* @atom:* - @dihedral:4-3-60-X @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d60_i* @atom:* - @dihedral:4-3-82-X @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d82_i* @atom:* - @dihedral:4-3-82-57 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d57_i* - @dihedral:4-3-82-61 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d61_i* - @dihedral:82-3-82-57 @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d57_i* - @dihedral:82-3-82-61 @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d61_i* - @dihedral:4-3-84-20 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d20_i* - @dihedral:4-3-84-87 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d87_i* - @dihedral:84-3-84-20 @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d20_i* - @dihedral:84-3-84-87 @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d87_i* - @dihedral:48-3-86-48 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d48_i* - @dihedral:X-3-87-X @atom:* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d87_i* @atom:* - @dihedral:4-3-87-84 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d87_i* @atom:*_b*_a*_d84_i* - @dihedral:4-3-87-87 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d87_i* @atom:*_b*_a*_d87_i* - @dihedral:24-3-87-84 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d87_i* @atom:*_b*_a*_d84_i* - @dihedral:24-3-87-87 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d87_i* @atom:*_b*_a*_d87_i* - @dihedral:4-3-107-13 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d107_i* @atom:*_b*_a*_d13_i* - @dihedral:13-3-107-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d107_i* @atom:*_b*_a*_d13_i* - @dihedral:4-3-109-109 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* - @dihedral:5-3-109-109 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* - @dihedral:X-4-106-X @atom:* @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d106_i* @atom:* - @dihedral:7-5-10-2 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d10_i* @atom:*_b*_a*_d2_i* - @dihedral:7-5-10-6 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d10_i* @atom:*_b*_a*_d6_i* - @dihedral:7-5-13-2 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d2_i* - @dihedral:7-5-13-6 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d6_i* - @dihedral:7-5-13-13 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* - @dihedral:7-5-13-46 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i* - @dihedral:7-5-13-47 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* - @dihedral:7-5-13-48 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d48_i* - @dihedral:7-5-13-50 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d50_i* - @dihedral:7-5-44-13 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d13_i* - @dihedral:7-5-44-45 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d45_i* - @dihedral:7-5-24-3 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* - @dihedral:7-5-24-45 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d45_i* - @dihedral:7-5-47-47 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i* - @dihedral:7-5-48-48 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:7-5-51-20 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d51_i* @atom:*_b*_a*_d20_i* - @dihedral:7-5-56-3 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d3_i* - @dihedral:7-5-64-4 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d64_i* @atom:*_b*_a*_d4_i* - @dihedral:7-5-64-5 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d64_i* @atom:*_b*_a*_d5_i* - @dihedral:7-5-79-13 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d13_i* - @dihedral:7-5-79-23 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d23_i* - @dihedral:7-5-79-48 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d48_i* - @dihedral:X-13-13-3 @atom:* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d3_i* - @dihedral:X-13-13-13 @atom:* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* - @dihedral:X-13-13-24 @atom:* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i* - @dihedral:1-13-13-1 @atom:*_b*_a*_d1_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d1_i* - @dihedral:1-13-13-5 @atom:*_b*_a*_d1_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d5_i* - @dihedral:1-13-13-13 @atom:*_b*_a*_d1_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* - @dihedral:1-13-13-46 @atom:*_b*_a*_d1_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i* - @dihedral:3-13-13-3 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d3_i* - @dihedral:3-13-13-5 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d5_i* - @dihedral:3-13-13-13 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* - @dihedral:3-13-13-15 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d15_i* - @dihedral:3-13-13-16 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d16_i* - @dihedral:3-13-13-24 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i* - @dihedral:3-13-13-46 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i* - @dihedral:3-13-13-48 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d48_i* - @dihedral:3-13-13-80 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d80_i* - @dihedral:5-13-13-5 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d5_i* - @dihedral:5-13-13-13 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* - @dihedral:5-13-13-20 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* - @dihedral:5-13-13-44 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d44_i* - @dihedral:5-13-13-24 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i* - @dihedral:5-13-13-46 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i* - @dihedral:13-13-13-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* - @dihedral:13-13-13-15 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d15_i* - @dihedral:13-13-13-16 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d16_i* - @dihedral:13-13-13-19 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d19_i* - @dihedral:13-13-13-21 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d21_i* - @dihedral:13-13-13-44 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d44_i* - @dihedral:13-13-13-24 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i* - @dihedral:13-13-13-46 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i* - @dihedral:13-13-13-51 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d51_i* - @dihedral:13-13-13-53 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d53_i* - @dihedral:13-13-13-65 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d65_i* - @dihedral:13-13-13-66 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d66_i* - @dihedral:13-13-13-79 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d79_i* - @dihedral:13-13-13-107 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d107_i* - @dihedral:13-13-13-108 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d108_i* - @dihedral:15-13-13-46 @atom:*_b*_a*_d15_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i* - @dihedral:16-13-13-46 @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i* - @dihedral:19-13-13-46 @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i* - @dihedral:20-13-13-20 @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* - @dihedral:20-13-13-46 @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i* - @dihedral:21-13-13-21 @atom:*_b*_a*_d21_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d21_i* - @dihedral:21-13-13-44 @atom:*_b*_a*_d21_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d44_i* - @dihedral:21-13-13-46 @atom:*_b*_a*_d21_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i* - @dihedral:44-13-13-44 @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d44_i* - @dihedral:44-13-13-46 @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i* - @dihedral:44-13-13-48 @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d48_i* - @dihedral:24-13-13-46 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i* - @dihedral:24-13-13-48 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d48_i* - @dihedral:24-13-13-80 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d80_i* - @dihedral:46-13-13-46 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i* - @dihedral:46-13-13-47 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* - @dihedral:46-13-13-48 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d48_i* - @dihedral:46-13-13-51 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d51_i* - @dihedral:46-13-13-53 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d53_i* - @dihedral:46-13-13-55 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d55_i* - @dihedral:46-13-13-59 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d59_i* - @dihedral:46-13-13-62 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d62_i* - @dihedral:46-13-13-65 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d65_i* - @dihedral:46-13-13-66 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d66_i* - @dihedral:46-13-13-79 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d79_i* - @dihedral:46-13-13-80 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d80_i* - @dihedral:46-13-13-82 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d82_i* - @dihedral:46-13-13-83 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d83_i* - @dihedral:46-13-13-84 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d84_i* - @dihedral:46-13-13-87 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d87_i* - @dihedral:46-13-13-88 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d88_i* - @dihedral:46-13-13-102 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d102_i* - @dihedral:46-13-13-104 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d104_i* - @dihedral:46-13-13-107 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d107_i* - @dihedral:46-13-13-108 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d108_i* - @dihedral:46-13-13-109 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d109_i* - @dihedral:48-13-13-53 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d53_i* - @dihedral:108-13-13-108 @atom:*_b*_a*_d108_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d108_i* - @dihedral:13-13-15-17 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d15_i* @atom:*_b*_a*_d17_i* - @dihedral:46-13-15-17 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d15_i* @atom:*_b*_a*_d17_i* - @dihedral:13-13-16-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d13_i* - @dihedral:13-13-16-16 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d16_i* - @dihedral:46-13-16-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d13_i* - @dihedral:46-13-16-16 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d16_i* - @dihedral:46-13-16-48 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d48_i* - @dihedral:X-13-18-19 @atom:* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d18_i* @atom:*_b*_a*_d19_i* - @dihedral:46-13-18-19 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d18_i* @atom:*_b*_a*_d19_i* - @dihedral:X-13-19-18 @atom:* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d18_i* - @dihedral:X-13-19-19 @atom:* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d19_i* - @dihedral:13-13-19-19 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d19_i* - @dihedral:46-13-19-19 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d19_i* - @dihedral:X-13-20-13 @atom:* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13_i* - @dihedral:56-13-20-13 @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13_i* - @dihedral:57-13-20-13 @atom:*_b*_a*_d57_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13_i* - @dihedral:13-13-20-3 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d3_i* - @dihedral:13-13-20-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13_i* - @dihedral:13-13-20-64 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d64_i* - @dihedral:46-13-20-X @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:* - @dihedral:46-13-20-3 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d3_i* - @dihedral:46-13-20-47 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d47_i* - @dihedral:46-13-20-48 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d48_i* - @dihedral:46-13-20-51 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d51_i* - @dihedral:46-13-20-64 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d64_i* - @dihedral:X-13-24-45 @atom:* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d45_i* - @dihedral:3-13-24-3 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* - @dihedral:3-13-24-13 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13_i* - @dihedral:3-13-24-45 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d45_i* - @dihedral:13-13-24-3 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* - @dihedral:13-13-24-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13_i* - @dihedral:13-13-24-45 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d45_i* - @dihedral:13-13-24-59 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d59_i* - @dihedral:13-13-24-79 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d79_i* - @dihedral:13-13-24-91 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d91_i* - @dihedral:46-13-24-3 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* - @dihedral:46-13-24-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13_i* - @dihedral:46-13-24-45 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d45_i* - @dihedral:46-13-24-48 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d48_i* - @dihedral:46-13-24-79 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d79_i* - @dihedral:48-13-24-59 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d59_i* - @dihedral:13-13-44-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d13_i* - @dihedral:13-13-44-45 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d45_i* - @dihedral:46-13-44-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d13_i* - @dihedral:46-13-44-45 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d45_i* - @dihedral:46-13-44-48 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d48_i* - @dihedral:X-13-47-13 @atom:* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d13_i* - @dihedral:X-13-47-46 @atom:* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d46_i* - @dihedral:X-13-47-47 @atom:* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i* - @dihedral:X-13-47-50 @atom:* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d50_i* - @dihedral:1-13-47-47 @atom:*_b*_a*_d1_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i* - @dihedral:13-13-47-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d13_i* - @dihedral:13-13-47-47 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i* - @dihedral:13-13-47-50 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d50_i* - @dihedral:46-13-47-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d13_i* - @dihedral:46-13-47-46 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d46_i* - @dihedral:46-13-47-47 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i* - @dihedral:46-13-47-50 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d50_i* - @dihedral:46-13-47-110 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d110_i* - @dihedral:47-13-47-13 @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d13_i* - @dihedral:47-13-47-46 @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d46_i* - @dihedral:X-13-48-48 @atom:* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:1-13-48-48 @atom:*_b*_a*_d1_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:13-13-48-48 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:13-13-48-56 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d56_i* - @dihedral:21-13-48-48 @atom:*_b*_a*_d21_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:46-13-48-48 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:64-13-48-48 @atom:*_b*_a*_d64_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:65-13-48-48 @atom:*_b*_a*_d65_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:X-13-50-47 @atom:* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d47_i* - @dihedral:13-13-50-50 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d50_i* - @dihedral:46-13-50-47 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d47_i* - @dihedral:46-13-50-50 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d50_i* - @dihedral:46-13-50-109 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d109_i* - @dihedral:13-13-51-X @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d51_i* @atom:* - @dihedral:13-13-51-46 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d51_i* @atom:*_b*_a*_d46_i* - @dihedral:46-13-51-20 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d51_i* @atom:*_b*_a*_d20_i* - @dihedral:13-13-53-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d13_i* - @dihedral:13-13-53-45 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d45_i* - @dihedral:46-13-53-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d13_i* - @dihedral:46-13-53-45 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d45_i* - @dihedral:46-13-53-48 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d48_i* - @dihedral:46-13-53-54 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d54_i* - @dihedral:13-13-55-45 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d55_i* @atom:*_b*_a*_d45_i* - @dihedral:13-13-55-48 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d55_i* @atom:*_b*_a*_d48_i* - @dihedral:13-13-55-54 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d55_i* @atom:*_b*_a*_d54_i* - @dihedral:46-13-55-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d55_i* @atom:*_b*_a*_d13_i* - @dihedral:46-13-55-45 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d55_i* @atom:*_b*_a*_d45_i* - @dihedral:46-13-55-48 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d55_i* @atom:*_b*_a*_d48_i* - @dihedral:13-13-56-18 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d18_i* - @dihedral:X-13-57-X @atom:* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d57_i* @atom:* - @dihedral:13-13-57-X @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d57_i* @atom:* - @dihedral:13-13-57-62 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d57_i* @atom:*_b*_a*_d62_i* - @dihedral:13-13-57-82 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d57_i* @atom:*_b*_a*_d82_i* - @dihedral:20-13-57-X @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d57_i* @atom:* - @dihedral:20-13-57-62 @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d57_i* @atom:*_b*_a*_d62_i* - @dihedral:20-13-57-82 @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d57_i* @atom:*_b*_a*_d82_i* - @dihedral:13-13-59-X @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d59_i* @atom:* - @dihedral:13-13-59-56 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d59_i* @atom:*_b*_a*_d56_i* - @dihedral:46-13-59-X @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d59_i* @atom:* - @dihedral:13-13-62-X @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d62_i* @atom:* - @dihedral:46-13-62-X @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d62_i* @atom:* - @dihedral:46-13-64-20 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d64_i* @atom:*_b*_a*_d20_i* - @dihedral:46-13-64-52 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d64_i* @atom:*_b*_a*_d52_i* - @dihedral:48-13-64-20 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d64_i* @atom:*_b*_a*_d20_i* - @dihedral:48-13-64-52 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d64_i* @atom:*_b*_a*_d52_i* - @dihedral:X-13-79-23 @atom:* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d23_i* - @dihedral:X-13-79-24 @atom:* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d24_i* - @dihedral:13-13-79-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d13_i* - @dihedral:13-13-79-23 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d23_i* - @dihedral:46-13-79-5 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d5_i* - @dihedral:46-13-79-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d13_i* - @dihedral:46-13-79-23 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d23_i* - @dihedral:46-13-79-48 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d48_i* - @dihedral:13-13-80-X @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d80_i* @atom:* - @dihedral:13-13-80-60 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d80_i* @atom:*_b*_a*_d60_i* - @dihedral:13-13-80-84 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d80_i* @atom:*_b*_a*_d84_i* - @dihedral:46-13-80-X @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d80_i* @atom:* - @dihedral:46-13-80-60 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d80_i* @atom:*_b*_a*_d60_i* - @dihedral:46-13-80-84 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d80_i* @atom:*_b*_a*_d84_i* - @dihedral:13-13-82-X @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d82_i* @atom:* - @dihedral:46-13-82-X @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d82_i* @atom:* - @dihedral:13-13-83-X @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d83_i* @atom:* - @dihedral:46-13-83-X @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d83_i* @atom:* - @dihedral:1-13-84-X @atom:*_b*_a*_d1_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d84_i* @atom:* - @dihedral:13-13-84-X @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d84_i* @atom:* - @dihedral:13-13-84-57 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d57_i* - @dihedral:21-13-84-X @atom:*_b*_a*_d21_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d84_i* @atom:* - @dihedral:46-13-84-X @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d84_i* @atom:* - @dihedral:1-13-87-X @atom:*_b*_a*_d1_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d87_i* @atom:* - @dihedral:13-13-87-X @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d87_i* @atom:* - @dihedral:21-13-87-X @atom:*_b*_a*_d21_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d87_i* @atom:* - @dihedral:46-13-87-X @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d87_i* @atom:* - @dihedral:13-13-88-X @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d88_i* @atom:* - @dihedral:46-13-88-X @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d88_i* @atom:* - @dihedral:X-13-90-X @atom:* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d90_i* @atom:* - @dihedral:46-13-90-X @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d90_i* @atom:* - @dihedral:46-13-91-91 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d91_i* - @dihedral:13-13-95-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d95_i* @atom:*_b*_a*_d13_i* - @dihedral:13-13-95-46 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d95_i* @atom:*_b*_a*_d46_i* - @dihedral:13-13-102-103 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d102_i* @atom:*_b*_a*_d103_i* - @dihedral:46-13-102-103 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d102_i* @atom:*_b*_a*_d103_i* - @dihedral:13-13-104-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d104_i* @atom:*_b*_a*_d13_i* - @dihedral:46-13-104-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d104_i* @atom:*_b*_a*_d13_i* - @dihedral:X-13-105-X @atom:* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d105_i* @atom:* - @dihedral:13-13-105-X @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d105_i* @atom:* - @dihedral:13-13-105-62 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d105_i* @atom:*_b*_a*_d62_i* - @dihedral:13-13-105-82 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d105_i* @atom:*_b*_a*_d82_i* - @dihedral:20-13-105-X @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d105_i* @atom:* - @dihedral:20-13-105-62 @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d105_i* @atom:*_b*_a*_d62_i* - @dihedral:20-13-105-82 @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d105_i* @atom:*_b*_a*_d82_i* - @dihedral:3-13-107-13 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d107_i* @atom:*_b*_a*_d13_i* - @dihedral:13-13-107-3 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d107_i* @atom:*_b*_a*_d3_i* - @dihedral:13-13-107-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d107_i* @atom:*_b*_a*_d13_i* - @dihedral:46-13-107-3 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d107_i* @atom:*_b*_a*_d3_i* - @dihedral:46-13-107-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d107_i* @atom:*_b*_a*_d13_i* - @dihedral:46-13-107-48 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d107_i* @atom:*_b*_a*_d48_i* - @dihedral:13-13-108-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d108_i* @atom:*_b*_a*_d13_i* - @dihedral:13-13-108-45 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d108_i* @atom:*_b*_a*_d45_i* - @dihedral:46-13-108-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d108_i* @atom:*_b*_a*_d13_i* - @dihedral:46-13-108-20 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d108_i* @atom:*_b*_a*_d20_i* - @dihedral:46-13-108-45 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d108_i* @atom:*_b*_a*_d45_i* - @dihedral:13-13-109-109 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* - @dihedral:46-13-109-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d13_i* - @dihedral:46-13-109-46 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d46_i* - @dihedral:46-13-109-109 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* - @dihedral:17-15-48-X @atom:*_b*_a*_d17_i* @atom:*_b*_a*_d15_i* @atom:*_b*_a*_d48_i* @atom:* - @dihedral:17-15-48-48 @atom:*_b*_a*_d17_i* @atom:*_b*_a*_d15_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:13-16-16-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d13_i* - @dihedral:13-16-48-48 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:13-16-48-56 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d56_i* - @dihedral:13-16-59-56 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d59_i* @atom:*_b*_a*_d56_i* - @dihedral:84-16-82-X @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d82_i* @atom:* - @dihedral:84-16-82-61 @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d61_i* - @dihedral:82-16-84-49 @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d49_i* - @dihedral:82-16-84-83 @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d83_i* - @dihedral:82-16-84-88 @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d88_i* - @dihedral:X-16-91-X @atom:* @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d91_i* @atom:* - @dihedral:19-18-48-X @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d18_i* @atom:*_b*_a*_d48_i* @atom:* - @dihedral:19-18-48-48 @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d18_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:18-18-56-13 @atom:*_b*_a*_d18_i* @atom:*_b*_a*_d18_i* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d13_i* - @dihedral:18-18-56-46 @atom:*_b*_a*_d18_i* @atom:*_b*_a*_d18_i* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d46_i* - @dihedral:X-19-19-X @atom:* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d19_i* @atom:* - @dihedral:13-19-19-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d13_i* - @dihedral:13-19-19-46 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d46_i* - @dihedral:13-19-19-47 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d47_i* - @dihedral:13-19-19-109 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d109_i* - @dihedral:46-19-19-47 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d47_i* - @dihedral:46-19-19-109 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d109_i* - @dihedral:19-19-47-13 @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d13_i* - @dihedral:19-19-47-46 @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d46_i* - @dihedral:19-19-47-47 @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i* - @dihedral:13-20-44-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d13_i* - @dihedral:13-20-44-45 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d45_i* - @dihedral:13-20-47-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d13_i* - @dihedral:13-20-47-46 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d46_i* - @dihedral:13-20-47-47 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i* - @dihedral:13-20-47-50 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d50_i* - @dihedral:3-20-48-48 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:13-20-48-48 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:13-20-48-56 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d56_i* - @dihedral:64-20-48-48 @atom:*_b*_a*_d64_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:13-20-51-5 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d51_i* @atom:*_b*_a*_d5_i* - @dihedral:13-20-51-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d51_i* @atom:*_b*_a*_d13_i* - @dihedral:13-20-51-20 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d51_i* @atom:*_b*_a*_d20_i* - @dihedral:13-20-51-46 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d51_i* @atom:*_b*_a*_d46_i* - @dihedral:13-20-56-3 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d3_i* - @dihedral:13-20-59-56 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d59_i* @atom:*_b*_a*_d56_i* - @dihedral:X-20-64-52 @atom:* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d64_i* @atom:*_b*_a*_d52_i* - @dihedral:13-20-64-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d64_i* @atom:*_b*_a*_d13_i* - @dihedral:13-20-64-52 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d64_i* @atom:*_b*_a*_d52_i* - @dihedral:48-20-64-4 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d64_i* @atom:*_b*_a*_d4_i* - @dihedral:84-20-82-61 @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d61_i* - @dihedral:82-20-84-88 @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d88_i* - @dihedral:84-20-84-49 @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d49_i* - @dihedral:84-20-84-87 @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d87_i* - @dihedral:108-20-108-13 @atom:*_b*_a*_d108_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d108_i* @atom:*_b*_a*_d13_i* - @dihedral:108-20-108-20 @atom:*_b*_a*_d108_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d108_i* @atom:*_b*_a*_d20_i* - @dihedral:X-24-48-48 @atom:* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:3-24-48-48 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:13-24-48-48 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:45-24-48-48 @atom:*_b*_a*_d45_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:59-24-48-48 @atom:*_b*_a*_d59_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:82-24-48-48 @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:84-24-48-48 @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:X-24-59-X @atom:* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d59_i* @atom:* - @dihedral:X-24-59-49 @atom:* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d59_i* @atom:*_b*_a*_d49_i* - @dihedral:45-24-59-X @atom:*_b*_a*_d45_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d59_i* @atom:* - @dihedral:X-24-60-X @atom:* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d60_i* @atom:* - @dihedral:X-24-79-23 @atom:* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d23_i* - @dihedral:13-24-79-48 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d48_i* - @dihedral:45-24-79-48 @atom:*_b*_a*_d45_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d48_i* - @dihedral:13-24-82-61 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d61_i* - @dihedral:45-24-82-16 @atom:*_b*_a*_d45_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d16_i* - @dihedral:45-24-82-20 @atom:*_b*_a*_d45_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d20_i* - @dihedral:45-24-82-61 @atom:*_b*_a*_d45_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d61_i* - @dihedral:48-24-82-16 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d16_i* - @dihedral:48-24-82-20 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d20_i* - @dihedral:48-24-82-61 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d61_i* - @dihedral:X-24-84-X @atom:* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d84_i* @atom:* - @dihedral:3-24-84-84 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d84_i* - @dihedral:45-24-84-16 @atom:*_b*_a*_d45_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d16_i* - @dihedral:45-24-84-20 @atom:*_b*_a*_d45_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d20_i* - @dihedral:48-24-84-16 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d16_i* - @dihedral:48-24-84-20 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d20_i* - @dihedral:3-24-86-48 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d48_i* - @dihedral:3-24-86-56 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d56_i* - @dihedral:3-24-86-86 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d86_i* - @dihedral:47-24-86-48 @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d48_i* - @dihedral:47-24-86-56 @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d56_i* - @dihedral:X-24-87-X @atom:* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d87_i* @atom:* - @dihedral:X-24-88-X @atom:* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d88_i* @atom:* - @dihedral:3-24-91-46 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d46_i* - @dihedral:3-24-91-89 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d89_i* - @dihedral:3-24-91-91 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d91_i* - @dihedral:45-24-91-46 @atom:*_b*_a*_d45_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d46_i* - @dihedral:45-24-91-89 @atom:*_b*_a*_d45_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d89_i* - @dihedral:45-24-91-91 @atom:*_b*_a*_d45_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d91_i* - @dihedral:X-24-106-X @atom:* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d106_i* @atom:* - @dihedral:13-44-44-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d13_i* - @dihedral:13-44-44-45 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d45_i* - @dihedral:45-44-44-45 @atom:*_b*_a*_d45_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d45_i* - @dihedral:13-44-48-48 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:45-44-48-48 @atom:*_b*_a*_d45_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:59-44-48-48 @atom:*_b*_a*_d59_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:82-44-48-48 @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:84-44-48-48 @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:45-44-82-16 @atom:*_b*_a*_d45_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d16_i* - @dihedral:45-44-82-61 @atom:*_b*_a*_d45_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d61_i* - @dihedral:48-44-82-16 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d16_i* - @dihedral:48-44-82-61 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d61_i* - @dihedral:47-46-47-13 @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d13_i* - 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@atom:*_b*_a*_d47_i* @atom:*_b*_a*_d20_i* - @dihedral:13-47-47-46 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d46_i* - @dihedral:19-47-47-46 @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d46_i* - @dihedral:20-47-47-46 @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d46_i* - @dihedral:21-47-47-21 @atom:*_b*_a*_d21_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d21_i* - @dihedral:21-47-47-46 @atom:*_b*_a*_d21_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d46_i* - @dihedral:46-47-47-46 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d46_i* - @dihedral:46-47-47-48 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d48_i* - @dihedral:13-47-48-48 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:46-47-48-48 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:46-47-48-56 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d56_i* - @dihedral:47-47-48-48 @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:13-47-50-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d13_i* - @dihedral:13-47-50-46 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d46_i* - @dihedral:13-47-50-48 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d48_i* - @dihedral:13-47-50-50 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d50_i* - @dihedral:13-47-50-109 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d109_i* - @dihedral:24-47-50-3 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d3_i* - @dihedral:46-47-50-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d13_i* - @dihedral:46-47-50-46 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d46_i* - @dihedral:46-47-50-48 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d48_i* - @dihedral:46-47-50-50 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d50_i* - @dihedral:46-47-50-109 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d109_i* - @dihedral:X-47-84-X @atom:* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d84_i* @atom:* - @dihedral:X-47-86-48 @atom:* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d48_i* - @dihedral:3-47-86-86 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d86_i* - @dihedral:49-47-86-X @atom:*_b*_a*_d49_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d86_i* @atom:* - @dihedral:49-47-86-24 @atom:*_b*_a*_d49_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d24_i* - @dihedral:X-47-87-X @atom:* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d87_i* @atom:* - @dihedral:X-47-88-X @atom:* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d88_i* @atom:* - @dihedral:13-47-110-47 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d110_i* @atom:*_b*_a*_d47_i* - @dihedral:46-47-110-47 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d110_i* @atom:*_b*_a*_d47_i* - @dihedral:X-48-48-X @atom:* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:* - @dihedral:X-48-48-13 @atom:* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d13_i* - @dihedral:X-48-48-48 @atom:* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:X-48-48-49 @atom:* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d49_i* - @dihedral:1-48-48-48 @atom:*_b*_a*_d1_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:1-48-48-49 @atom:*_b*_a*_d1_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d49_i* - @dihedral:13-48-48-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d13_i* - @dihedral:13-48-48-48 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:13-48-48-49 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d49_i* - @dihedral:13-48-48-50 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d50_i* - @dihedral:21-48-48-48 @atom:*_b*_a*_d21_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:21-48-48-49 @atom:*_b*_a*_d21_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d49_i* - @dihedral:44-48-48-49 @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d49_i* - @dihedral:47-48-48-49 @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d49_i* - @dihedral:48-48-48-48 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:48-48-48-49 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d49_i* - @dihedral:48-48-48-50 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d50_i* - @dihedral:48-48-48-55 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d55_i* - @dihedral:48-48-48-60 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d60_i* - @dihedral:48-48-48-65 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d65_i* - @dihedral:48-48-48-66 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d66_i* - @dihedral:48-48-48-86 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d86_i* - @dihedral:48-48-48-109 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d109_i* - @dihedral:49-48-48-49 @atom:*_b*_a*_d49_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d49_i* - @dihedral:49-48-48-50 @atom:*_b*_a*_d49_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d50_i* - @dihedral:49-48-48-60 @atom:*_b*_a*_d49_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d60_i* - @dihedral:49-48-48-65 @atom:*_b*_a*_d49_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d65_i* - @dihedral:49-48-48-66 @atom:*_b*_a*_d49_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d66_i* - @dihedral:49-48-48-86 @atom:*_b*_a*_d49_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d86_i* - @dihedral:49-48-48-109 @atom:*_b*_a*_d49_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d109_i* - @dihedral:56-48-48-86 @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d86_i* - @dihedral:48-48-50-46 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d46_i* - @dihedral:48-48-50-47 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d47_i* - @dihedral:56-48-50-46 @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d46_i* - @dihedral:56-48-50-47 @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d47_i* - @dihedral:48-48-53-13 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d13_i* - @dihedral:48-48-53-54 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d54_i* - @dihedral:X-48-55-45 @atom:* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d55_i* @atom:*_b*_a*_d45_i* - @dihedral:48-48-55-45 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d55_i* @atom:*_b*_a*_d45_i* - @dihedral:55-48-55-13 @atom:*_b*_a*_d55_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d55_i* @atom:*_b*_a*_d13_i* - @dihedral:55-48-55-45 @atom:*_b*_a*_d55_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d55_i* @atom:*_b*_a*_d45_i* - @dihedral:60-48-55-45 @atom:*_b*_a*_d60_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d55_i* @atom:*_b*_a*_d45_i* - @dihedral:X-48-56-X @atom:* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d56_i* @atom:* - @dihedral:48-48-56-48 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d48_i* - @dihedral:49-48-56-48 @atom:*_b*_a*_d49_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d48_i* - @dihedral:X-48-60-X @atom:* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d60_i* @atom:* - @dihedral:X-48-79-23 @atom:* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d23_i* - @dihedral:48-48-79-13 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d13_i* - @dihedral:48-48-79-24 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d24_i* - @dihedral:48-48-86-48 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d48_i* - @dihedral:48-48-86-56 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d56_i* - @dihedral:48-48-86-86 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d86_i* - @dihedral:49-48-86-48 @atom:*_b*_a*_d49_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d48_i* - @dihedral:49-48-86-56 @atom:*_b*_a*_d49_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d56_i* - @dihedral:49-48-86-86 @atom:*_b*_a*_d49_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d86_i* - @dihedral:56-48-86-48 @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d48_i* - @dihedral:56-48-86-86 @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d86_i* - @dihedral:49-48-88-49 @atom:*_b*_a*_d49_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d88_i* @atom:*_b*_a*_d49_i* - @dihedral:56-48-101-13 @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d101_i* @atom:*_b*_a*_d13_i* - @dihedral:48-48-102-103 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d102_i* @atom:*_b*_a*_d103_i* - @dihedral:48-48-109-13 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d13_i* - @dihedral:48-48-109-46 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d46_i* - @dihedral:48-48-109-109 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* - @dihedral:X-50-50-49 @atom:* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d49_i* - @dihedral:3-50-50-3 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d3_i* - @dihedral:13-50-50-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d13_i* - @dihedral:13-50-50-46 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d46_i* - @dihedral:13-50-50-47 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d47_i* - @dihedral:46-50-50-46 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d46_i* - @dihedral:46-50-50-47 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d47_i* - @dihedral:47-50-50-47 @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d47_i* - @dihedral:13-50-109-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d13_i* - @dihedral:13-50-109-109 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* - @dihedral:46-50-109-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d13_i* - @dihedral:46-50-109-46 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d46_i* - @dihedral:46-50-109-109 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* - @dihedral:47-50-109-13 @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d13_i* - @dihedral:47-50-109-46 @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d46_i* - @dihedral:47-50-109-109 @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* - @dihedral:13-53-82-61 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d61_i* - @dihedral:48-53-82-61 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d61_i* - @dihedral:45-55-59-X @atom:*_b*_a*_d45_i* @atom:*_b*_a*_d55_i* @atom:*_b*_a*_d59_i* @atom:* - @dihedral:13-56-56-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d13_i* - @dihedral:13-56-56-48 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d48_i* - @dihedral:48-56-56-48 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d48_i* - @dihedral:X-56-59-X @atom:* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d59_i* @atom:* - @dihedral:X-56-59-49 @atom:* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d59_i* @atom:*_b*_a*_d49_i* - @dihedral:X-56-60-X @atom:* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d60_i* @atom:* - @dihedral:X-56-62-X @atom:* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d62_i* @atom:* - @dihedral:X-56-82-X @atom:* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d82_i* @atom:* - @dihedral:48-56-86-48 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d48_i* - @dihedral:48-56-86-86 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d86_i* - @dihedral:X-57-60-X @atom:* @atom:*_b*_a*_d57_i* @atom:*_b*_a*_d60_i* @atom:* - @dihedral:45-57-60-X @atom:*_b*_a*_d45_i* @atom:*_b*_a*_d57_i* @atom:*_b*_a*_d60_i* @atom:* - @dihedral:X-57-61-X @atom:* @atom:*_b*_a*_d57_i* @atom:*_b*_a*_d61_i* @atom:* - @dihedral:X-57-62-X @atom:* @atom:*_b*_a*_d57_i* @atom:*_b*_a*_d62_i* @atom:* - @dihedral:X-57-81-X @atom:* @atom:*_b*_a*_d57_i* @atom:*_b*_a*_d81_i* @atom:* - @dihedral:X-57-82-X @atom:* @atom:*_b*_a*_d57_i* @atom:*_b*_a*_d82_i* @atom:* - @dihedral:X-57-82-49 @atom:* @atom:*_b*_a*_d57_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d49_i* - @dihedral:45-57-82-X @atom:*_b*_a*_d45_i* @atom:*_b*_a*_d57_i* @atom:*_b*_a*_d82_i* @atom:* - @dihedral:X-57-84-X @atom:* @atom:*_b*_a*_d57_i* @atom:*_b*_a*_d84_i* @atom:* - @dihedral:45-57-84-X @atom:*_b*_a*_d45_i* @atom:*_b*_a*_d57_i* @atom:*_b*_a*_d84_i* @atom:* - @dihedral:61-57-86-48 @atom:*_b*_a*_d61_i* @atom:*_b*_a*_d57_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d48_i* - @dihedral:84-57-86-48 @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d57_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d48_i* - @dihedral:X-60-60-X @atom:* @atom:*_b*_a*_d60_i* @atom:*_b*_a*_d60_i* @atom:* - @dihedral:X-60-61-X @atom:* @atom:*_b*_a*_d60_i* @atom:*_b*_a*_d61_i* @atom:* - @dihedral:X-60-80-X @atom:* @atom:*_b*_a*_d60_i* @atom:*_b*_a*_d80_i* @atom:* - @dihedral:X-60-81-X @atom:* @atom:*_b*_a*_d60_i* @atom:*_b*_a*_d81_i* @atom:* - @dihedral:X-60-87-X @atom:* @atom:*_b*_a*_d60_i* @atom:*_b*_a*_d87_i* @atom:* - @dihedral:48-60-87-84 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d60_i* @atom:*_b*_a*_d87_i* @atom:*_b*_a*_d84_i* - @dihedral:60-60-87-84 @atom:*_b*_a*_d60_i* @atom:*_b*_a*_d60_i* @atom:*_b*_a*_d87_i* @atom:*_b*_a*_d84_i* - @dihedral:X-61-61-X @atom:* @atom:*_b*_a*_d61_i* @atom:*_b*_a*_d61_i* @atom:* - @dihedral:X-61-62-X @atom:* @atom:*_b*_a*_d61_i* @atom:*_b*_a*_d62_i* @atom:* - @dihedral:X-61-82-X @atom:* @atom:*_b*_a*_d61_i* @atom:*_b*_a*_d82_i* @atom:* - @dihedral:X-61-82-49 @atom:* @atom:*_b*_a*_d61_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d49_i* - @dihedral:83-61-82-16 @atom:*_b*_a*_d83_i* @atom:*_b*_a*_d61_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d16_i* - @dihedral:88-61-82-16 @atom:*_b*_a*_d88_i* @atom:*_b*_a*_d61_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d16_i* - @dihedral:88-61-82-20 @atom:*_b*_a*_d88_i* @atom:*_b*_a*_d61_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d20_i* - @dihedral:X-61-83-X @atom:* @atom:*_b*_a*_d61_i* @atom:*_b*_a*_d83_i* @atom:* - @dihedral:82-61-83-49 @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d61_i* @atom:*_b*_a*_d83_i* @atom:*_b*_a*_d49_i* - @dihedral:82-61-83-84 @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d61_i* @atom:*_b*_a*_d83_i* @atom:*_b*_a*_d84_i* - @dihedral:X-61-84-X @atom:* @atom:*_b*_a*_d61_i* @atom:*_b*_a*_d84_i* @atom:* - @dihedral:X-61-88-X @atom:* @atom:*_b*_a*_d61_i* @atom:*_b*_a*_d88_i* @atom:* - @dihedral:82-61-88-84 @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d61_i* @atom:*_b*_a*_d88_i* @atom:*_b*_a*_d84_i* - @dihedral:X-80-84-X @atom:* @atom:*_b*_a*_d80_i* @atom:*_b*_a*_d84_i* @atom:* - @dihedral:X-82-84-X @atom:* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d84_i* @atom:* - @dihedral:16-82-86-48 @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d48_i* - @dihedral:20-82-86-48 @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d48_i* - @dihedral:57-82-86-48 @atom:*_b*_a*_d57_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d48_i* - @dihedral:61-82-86-48 @atom:*_b*_a*_d61_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d48_i* - @dihedral:X-82-87-X @atom:* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d87_i* @atom:* - @dihedral:X-83-84-X @atom:* @atom:*_b*_a*_d83_i* @atom:*_b*_a*_d84_i* @atom:* - @dihedral:X-83-84-49 @atom:* @atom:*_b*_a*_d83_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d49_i* - @dihedral:49-83-84-X @atom:*_b*_a*_d49_i* @atom:*_b*_a*_d83_i* @atom:*_b*_a*_d84_i* @atom:* - @dihedral:49-83-84-16 @atom:*_b*_a*_d49_i* @atom:*_b*_a*_d83_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d16_i* - @dihedral:49-83-84-49 @atom:*_b*_a*_d49_i* @atom:*_b*_a*_d83_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d49_i* - @dihedral:61-83-84-16 @atom:*_b*_a*_d61_i* @atom:*_b*_a*_d83_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d16_i* - @dihedral:61-83-84-20 @atom:*_b*_a*_d61_i* @atom:*_b*_a*_d83_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d20_i* - @dihedral:61-83-84-49 @atom:*_b*_a*_d61_i* @atom:*_b*_a*_d83_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d49_i* - @dihedral:X-83-86-48 @atom:* @atom:*_b*_a*_d83_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d48_i* - @dihedral:61-83-86-48 @atom:*_b*_a*_d61_i* @atom:*_b*_a*_d83_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d48_i* - @dihedral:61-83-87-X @atom:*_b*_a*_d61_i* @atom:*_b*_a*_d83_i* @atom:*_b*_a*_d87_i* @atom:* - @dihedral:84-83-87-X @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d83_i* @atom:*_b*_a*_d87_i* @atom:* - @dihedral:X-84-84-X @atom:* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d84_i* @atom:* - @dihedral:X-84-84-49 @atom:* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d49_i* - @dihedral:16-84-84-49 @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d49_i* - @dihedral:49-84-84-49 @atom:*_b*_a*_d49_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d49_i* - @dihedral:X-84-86-48 @atom:* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d48_i* - @dihedral:16-84-86-48 @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d48_i* - @dihedral:20-84-86-48 @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d48_i* - @dihedral:57-84-86-48 @atom:*_b*_a*_d57_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d48_i* - @dihedral:X-84-87-X @atom:* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d87_i* @atom:* - @dihedral:X-84-87-49 @atom:* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d87_i* @atom:*_b*_a*_d49_i* - @dihedral:49-84-87-49 @atom:*_b*_a*_d49_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d87_i* @atom:*_b*_a*_d49_i* - @dihedral:X-84-88-49 @atom:* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d88_i* @atom:*_b*_a*_d49_i* - @dihedral:16-84-88-49 @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d88_i* @atom:*_b*_a*_d49_i* - @dihedral:16-84-88-61 @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d88_i* @atom:*_b*_a*_d61_i* - @dihedral:20-84-88-61 @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d88_i* @atom:*_b*_a*_d61_i* - @dihedral:49-84-88-X @atom:*_b*_a*_d49_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d88_i* @atom:* - @dihedral:49-84-88-61 @atom:*_b*_a*_d49_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d88_i* @atom:*_b*_a*_d61_i* - @dihedral:48-86-86-48 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d48_i* - @dihedral:48-86-86-56 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d56_i* - @dihedral:48-86-87-X @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d87_i* @atom:* - @dihedral:48-86-88-X @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d88_i* @atom:* - @dihedral:48-86-88-61 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d88_i* @atom:*_b*_a*_d61_i* - @dihedral:56-86-88-X @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d88_i* @atom:* - @dihedral:X-87-87-20 @atom:* @atom:*_b*_a*_d87_i* @atom:*_b*_a*_d87_i* @atom:*_b*_a*_d20_i* - @dihedral:X-87-87-57 @atom:* @atom:*_b*_a*_d87_i* @atom:*_b*_a*_d87_i* @atom:*_b*_a*_d57_i* - @dihedral:X-87-87-87 @atom:* @atom:*_b*_a*_d87_i* @atom:*_b*_a*_d87_i* @atom:*_b*_a*_d87_i* - @dihedral:49-87-87-49 @atom:*_b*_a*_d49_i* @atom:*_b*_a*_d87_i* @atom:*_b*_a*_d87_i* @atom:*_b*_a*_d49_i* - @dihedral:4-89-90-13 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d89_i* @atom:*_b*_a*_d90_i* @atom:*_b*_a*_d13_i* - @dihedral:4-89-90-45 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d89_i* @atom:*_b*_a*_d90_i* @atom:*_b*_a*_d45_i* - @dihedral:4-89-90-48 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d89_i* @atom:*_b*_a*_d90_i* @atom:*_b*_a*_d48_i* - @dihedral:4-89-90-91 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d89_i* @atom:*_b*_a*_d90_i* @atom:*_b*_a*_d91_i* - @dihedral:91-89-90-13 @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d89_i* @atom:*_b*_a*_d90_i* @atom:*_b*_a*_d13_i* - @dihedral:91-89-90-45 @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d89_i* @atom:*_b*_a*_d90_i* @atom:*_b*_a*_d45_i* - @dihedral:91-89-90-48 @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d89_i* @atom:*_b*_a*_d90_i* @atom:*_b*_a*_d48_i* - @dihedral:91-89-90-91 @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d89_i* @atom:*_b*_a*_d90_i* @atom:*_b*_a*_d91_i* - @dihedral:X-89-91-X @atom:* @atom:*_b*_a*_d89_i* @atom:*_b*_a*_d91_i* @atom:* - @dihedral:4-89-91-46 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d89_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d46_i* - @dihedral:4-89-91-91 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d89_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d91_i* - @dihedral:90-89-91-46 @atom:*_b*_a*_d90_i* @atom:*_b*_a*_d89_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d46_i* - @dihedral:90-89-91-91 @atom:*_b*_a*_d90_i* @atom:*_b*_a*_d89_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d91_i* - @dihedral:X-90-91-X @atom:* @atom:*_b*_a*_d90_i* @atom:*_b*_a*_d91_i* @atom:* - @dihedral:X-90-91-46 @atom:* @atom:*_b*_a*_d90_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d46_i* - @dihedral:X-90-91-91 @atom:* @atom:*_b*_a*_d90_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d91_i* - @dihedral:X-91-91-X @atom:* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d91_i* @atom:* - @dihedral:X-91-91-24 @atom:* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d24_i* - @dihedral:13-91-91-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d13_i* - @dihedral:13-91-91-46 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d46_i* - @dihedral:46-91-91-46 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d46_i* - @dihedral:46-91-91-91 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d91_i* - @dihedral:91-91-91-91 @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d91_i* - @dihedral:X-109-109-X @atom:* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* @atom:* - @dihedral:13-109-109-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d13_i* - @dihedral:13-109-109-46 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d46_i* - @dihedral:13-109-109-48 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d48_i* - @dihedral:13-109-109-50 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d50_i* - @dihedral:13-109-109-109 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* - @dihedral:46-109-109-46 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d46_i* - @dihedral:46-109-109-48 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d48_i* - @dihedral:46-109-109-50 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d50_i* - @dihedral:46-109-109-109 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* - @dihedral:48-109-109-48 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d48_i* - @dihedral:48-109-109-50 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d50_i* - @dihedral:48-109-109-109 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* - @dihedral:50-109-109-50 @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d50_i* - @dihedral:50-109-109-109 @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* - @dihedral:109-109-109-109 @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* - @dihedral:24-3-13-53 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d53_i* - @dihedral:52-3-13-24 @atom:*_b*_a*_d52_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i* - @dihedral:3-13-13-53 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d53_i* - @dihedral:3-13-13-83 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d83_i* - @dihedral:3-13-13-84 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d84_i* - @dihedral:3-13-13-85 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d85_i* - @dihedral:5-13-13-53 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d53_i* - @dihedral:15-13-13-53 @atom:*_b*_a*_d15_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d53_i* - @dihedral:16-13-13-53 @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d53_i* - @dihedral:13-13-13-55 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d55_i* - @dihedral:24-13-13-83 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d83_i* - @dihedral:53-13-13-83 @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d83_i* - @dihedral:24-13-13-84 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d84_i* - @dihedral:53-13-13-84 @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d84_i* - @dihedral:24-13-13-85 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d85_i* - @dihedral:46-13-13-85 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d85_i* - @dihedral:53-13-13-85 @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d85_i* - @dihedral:3-13-53-13 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d13_i* - @dihedral:3-13-53-54 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d54_i* - @dihedral:13-13-53-54 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d54_i* - @dihedral:46-13-55-54 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d55_i* @atom:*_b*_a*_d54_i* - @dihedral:13-13-85-X @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d85_i* @atom:* - @dihedral:13-13-85-57 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d85_i* @atom:*_b*_a*_d57_i* - @dihedral:46-13-85-X @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d85_i* @atom:* - @dihedral:55-48-55-54 @atom:*_b*_a*_d55_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d55_i* @atom:*_b*_a*_d54_i* - @dihedral:X-48-81-X @atom:* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d81_i* @atom:* - @dihedral:X-57-85-X @atom:* @atom:*_b*_a*_d57_i* @atom:*_b*_a*_d85_i* @atom:* - @dihedral:X-85-85-X @atom:* @atom:*_b*_a*_d85_i* @atom:*_b*_a*_d85_i* @atom:* - @dihedral:13-13-13-20 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* - @dihedral:13-13-13-47 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* + @dihedral:X_002_002_002 @atom:* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d002*_i* + @dihedral:X_002_002_006 @atom:* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d006*_i* + @dihedral:001_002_002_002 @atom:*_b*_a*_d001*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d002*_i* + @dihedral:001_002_002_006 @atom:*_b*_a*_d001*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d006*_i* + @dihedral:002_002_002_002 @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d002*_i* + @dihedral:002_002_002_006 @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d006*_i* + @dihedral:002_002_002_010 @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d010*_i* + @dihedral:002_002_002_013 @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d013*_i* + @dihedral:002_002_002_065 @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d065*_i* + @dihedral:006_002_002_006 @atom:*_b*_a*_d006*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d006*_i* + @dihedral:006_002_002_065 @atom:*_b*_a*_d006*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d065*_i* + @dihedral:010_002_002_010 @atom:*_b*_a*_d010*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d010*_i* + @dihedral:002_002_005_007 @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d007*_i* + @dihedral:006_002_005_007 @atom:*_b*_a*_d006*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d007*_i* + @dihedral:010_002_005_007 @atom:*_b*_a*_d010*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d007*_i* + @dihedral:X_002_010_002 @atom:* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d010*_i* @atom:*_b*_a*_d002*_i* + @dihedral:002_002_010_002 @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d010*_i* @atom:*_b*_a*_d002*_i* + @dihedral:002_002_013_002 @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d002*_i* + @dihedral:006_002_020_002 @atom:*_b*_a*_d006*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d002*_i* + @dihedral:006_002_020_006 @atom:*_b*_a*_d006*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d006*_i* + @dihedral:004_003_003_004 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d004*_i* + @dihedral:004_003_003_013 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* + @dihedral:004_003_003_024 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* + @dihedral:004_003_003_046 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d046*_i* + @dihedral:013_003_003_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* + @dihedral:013_003_003_024 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* + @dihedral:013_003_003_046 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d046*_i* + @dihedral:024_003_003_046 @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d046*_i* + @dihedral:046_003_003_046 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d046*_i* + @dihedral:003_003_005_007 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d007*_i* + @dihedral:004_003_005_007 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d007*_i* + @dihedral:013_003_005_007 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d007*_i* + @dihedral:024_003_005_007 @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d007*_i* + @dihedral:046_003_005_007 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d007*_i* + @dihedral:048_003_005_007 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d007*_i* + @dihedral:001_003_013_013 @atom:*_b*_a*_d001*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* + @dihedral:001_003_013_046 @atom:*_b*_a*_d001*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* + @dihedral:003_003_013_046 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* + @dihedral:004_003_013_X @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:* + @dihedral:004_003_013_013 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* + @dihedral:004_003_013_021 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d021*_i* + @dihedral:004_003_013_044 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d044*_i* + @dihedral:004_003_013_024 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* + @dihedral:004_003_013_046 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* + @dihedral:004_003_013_048 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d048*_i* + @dihedral:005_003_013_013 @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* + @dihedral:005_003_013_044 @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d044*_i* + @dihedral:005_003_013_046 @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* + @dihedral:013_003_013_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* + @dihedral:013_003_013_046 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* + @dihedral:020_003_013_013 @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* + @dihedral:020_003_013_046 @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* + @dihedral:021_003_013_013 @atom:*_b*_a*_d021*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* + @dihedral:021_003_013_046 @atom:*_b*_a*_d021*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* + @dihedral:024_003_013_013 @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* + @dihedral:024_003_013_021 @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d021*_i* + @dihedral:024_003_013_024 @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* + @dihedral:024_003_013_046 @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* + @dihedral:046_003_013_013 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* + @dihedral:046_003_013_046 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* + @dihedral:048_003_013_046 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* + @dihedral:052_003_013_013 @atom:*_b*_a*_d052*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* + @dihedral:052_003_013_044 @atom:*_b*_a*_d052*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d044*_i* + @dihedral:052_003_013_046 @atom:*_b*_a*_d052*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* + @dihedral:065_003_013_013 @atom:*_b*_a*_d065*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* + @dihedral:065_003_013_046 @atom:*_b*_a*_d065*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* + @dihedral:107_003_013_046 @atom:*_b*_a*_d107*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* + @dihedral:004_003_020_013 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d013*_i* + @dihedral:004_003_020_048 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d048*_i* + @dihedral:013_003_020_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d013*_i* + @dihedral:013_003_020_048 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d048*_i* + @dihedral:024_003_020_013 @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d013*_i* + @dihedral:046_003_020_013 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d013*_i* + @dihedral:048_003_020_013 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d013*_i* + @dihedral:003_003_024_013 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d013*_i* + @dihedral:003_003_024_045 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d045*_i* + @dihedral:004_003_024_005 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d005*_i* + @dihedral:004_003_024_013 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d013*_i* + @dihedral:004_003_024_045 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d045*_i* + @dihedral:004_003_024_047 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d047*_i* + @dihedral:004_003_024_048 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d048*_i* + @dihedral:004_003_024_091 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d091*_i* + @dihedral:005_003_024_013 @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d013*_i* + @dihedral:005_003_024_045 @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d045*_i* + @dihedral:013_003_024_005 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d005*_i* + @dihedral:013_003_024_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d013*_i* + @dihedral:013_003_024_045 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d045*_i* + @dihedral:013_003_024_048 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d048*_i* + @dihedral:020_003_024_013 @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d013*_i* + @dihedral:020_003_024_045 @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d045*_i* + @dihedral:024_003_024_003 @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d003*_i* + @dihedral:024_003_024_013 @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d013*_i* + @dihedral:024_003_024_045 @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d045*_i* + @dihedral:046_003_024_013 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d013*_i* + @dihedral:046_003_024_045 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d045*_i* + @dihedral:047_003_024_045 @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d045*_i* + @dihedral:048_003_024_045 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d045*_i* + @dihedral:048_003_024_048 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d048*_i* + @dihedral:048_003_024_084 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d084*_i* + @dihedral:048_003_024_087 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d087*_i* + @dihedral:084_003_024_048 @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d048*_i* + @dihedral:084_003_024_084 @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d084*_i* + @dihedral:084_003_024_087 @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d087*_i* + @dihedral:087_003_024_045 @atom:*_b*_a*_d087*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d045*_i* + @dihedral:087_003_024_048 @atom:*_b*_a*_d087*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d048*_i* + @dihedral:087_003_024_084 @atom:*_b*_a*_d087*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d084*_i* + @dihedral:087_003_024_087 @atom:*_b*_a*_d087*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d087*_i* + @dihedral:X_003_047_013 @atom:* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d013*_i* + @dihedral:004_003_047_046 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d046*_i* + @dihedral:004_003_047_047 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* + @dihedral:005_003_047_047 @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* + @dihedral:024_003_047_046 @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d046*_i* + @dihedral:024_003_047_047 @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* + @dihedral:107_003_047_046 @atom:*_b*_a*_d107*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d046*_i* + @dihedral:107_003_047_047 @atom:*_b*_a*_d107*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* + @dihedral:004_003_048_048 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:005_003_048_048 @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:013_003_048_048 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:020_003_048_048 @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:024_003_048_048 @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:046_003_048_048 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:X_003_050_013 @atom:* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d013*_i* + @dihedral:004_003_050_047 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d047*_i* + @dihedral:005_003_050_047 @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d047*_i* + @dihedral:013_003_050_047 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d047*_i* + @dihedral:013_003_056_X @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d056*_i* @atom:* + @dihedral:013_003_056_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d013*_i* + @dihedral:046_003_056_X @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d056*_i* @atom:* + @dihedral:046_003_056_045 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d045*_i* + @dihedral:X_003_060_X @atom:* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d060*_i* @atom:* + @dihedral:004_003_060_X @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d060*_i* @atom:* + @dihedral:004_003_082_X @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d082*_i* @atom:* + @dihedral:004_003_082_057 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d057*_i* + @dihedral:004_003_082_061 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d061*_i* + @dihedral:082_003_082_057 @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d057*_i* + @dihedral:082_003_082_061 @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d061*_i* + @dihedral:004_003_084_020 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d020*_i* + @dihedral:004_003_084_087 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d087*_i* + @dihedral:084_003_084_020 @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d020*_i* + @dihedral:084_003_084_087 @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d087*_i* + @dihedral:048_003_086_048 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d048*_i* + @dihedral:X_003_087_X @atom:* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d087*_i* @atom:* + @dihedral:004_003_087_084 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d087*_i* @atom:*_b*_a*_d084*_i* + @dihedral:004_003_087_087 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d087*_i* @atom:*_b*_a*_d087*_i* + @dihedral:024_003_087_084 @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d087*_i* @atom:*_b*_a*_d084*_i* + @dihedral:024_003_087_087 @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d087*_i* @atom:*_b*_a*_d087*_i* + @dihedral:004_003_107_013 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d107*_i* @atom:*_b*_a*_d013*_i* + @dihedral:013_003_107_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d107*_i* @atom:*_b*_a*_d013*_i* + @dihedral:004_003_109_109 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* + @dihedral:005_003_109_109 @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* + @dihedral:X_004_106_X @atom:* @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d106*_i* @atom:* + @dihedral:007_005_010_002 @atom:*_b*_a*_d007*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d010*_i* @atom:*_b*_a*_d002*_i* + @dihedral:007_005_010_006 @atom:*_b*_a*_d007*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d010*_i* @atom:*_b*_a*_d006*_i* + @dihedral:007_005_013_002 @atom:*_b*_a*_d007*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d002*_i* + @dihedral:007_005_013_006 @atom:*_b*_a*_d007*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d006*_i* + @dihedral:007_005_013_013 @atom:*_b*_a*_d007*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* + @dihedral:007_005_013_046 @atom:*_b*_a*_d007*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* + @dihedral:007_005_013_047 @atom:*_b*_a*_d007*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* + @dihedral:007_005_013_048 @atom:*_b*_a*_d007*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d048*_i* + @dihedral:007_005_013_050 @atom:*_b*_a*_d007*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d050*_i* + @dihedral:007_005_044_013 @atom:*_b*_a*_d007*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d013*_i* + @dihedral:007_005_044_045 @atom:*_b*_a*_d007*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d045*_i* + @dihedral:007_005_024_003 @atom:*_b*_a*_d007*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d003*_i* + @dihedral:007_005_024_045 @atom:*_b*_a*_d007*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d045*_i* + @dihedral:007_005_047_047 @atom:*_b*_a*_d007*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* + @dihedral:007_005_048_048 @atom:*_b*_a*_d007*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:007_005_051_020 @atom:*_b*_a*_d007*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d051*_i* @atom:*_b*_a*_d020*_i* + @dihedral:007_005_056_003 @atom:*_b*_a*_d007*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d003*_i* + @dihedral:007_005_064_004 @atom:*_b*_a*_d007*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d064*_i* @atom:*_b*_a*_d004*_i* + @dihedral:007_005_064_005 @atom:*_b*_a*_d007*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d064*_i* @atom:*_b*_a*_d005*_i* + @dihedral:007_005_079_013 @atom:*_b*_a*_d007*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d079*_i* @atom:*_b*_a*_d013*_i* + @dihedral:007_005_079_023 @atom:*_b*_a*_d007*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d079*_i* @atom:*_b*_a*_d023*_i* + @dihedral:007_005_079_048 @atom:*_b*_a*_d007*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d079*_i* @atom:*_b*_a*_d048*_i* + @dihedral:X_013_013_003 @atom:* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d003*_i* + @dihedral:X_013_013_013 @atom:* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* + @dihedral:X_013_013_024 @atom:* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* + @dihedral:001_013_013_001 @atom:*_b*_a*_d001*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d001*_i* + @dihedral:001_013_013_005 @atom:*_b*_a*_d001*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d005*_i* + @dihedral:001_013_013_013 @atom:*_b*_a*_d001*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* + @dihedral:001_013_013_046 @atom:*_b*_a*_d001*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* + @dihedral:003_013_013_003 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d003*_i* + @dihedral:003_013_013_005 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d005*_i* + @dihedral:003_013_013_013 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* + @dihedral:003_013_013_015 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d015*_i* + @dihedral:003_013_013_016 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d016*_i* + @dihedral:003_013_013_024 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* + @dihedral:003_013_013_046 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* + @dihedral:003_013_013_048 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d048*_i* + @dihedral:003_013_013_080 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d080*_i* + @dihedral:005_013_013_005 @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d005*_i* + @dihedral:005_013_013_013 @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* + @dihedral:005_013_013_020 @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* + @dihedral:005_013_013_044 @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d044*_i* + @dihedral:005_013_013_024 @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* + @dihedral:005_013_013_046 @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* + @dihedral:013_013_013_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* + @dihedral:013_013_013_015 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d015*_i* + @dihedral:013_013_013_016 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d016*_i* + @dihedral:013_013_013_019 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d019*_i* + @dihedral:013_013_013_021 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d021*_i* + @dihedral:013_013_013_044 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d044*_i* + @dihedral:013_013_013_024 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* + @dihedral:013_013_013_046 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* + @dihedral:013_013_013_051 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d051*_i* + @dihedral:013_013_013_053 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d053*_i* + @dihedral:013_013_013_065 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d065*_i* + @dihedral:013_013_013_066 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d066*_i* + @dihedral:013_013_013_079 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d079*_i* + @dihedral:013_013_013_107 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d107*_i* + @dihedral:013_013_013_108 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d108*_i* + @dihedral:015_013_013_046 @atom:*_b*_a*_d015*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* + @dihedral:016_013_013_046 @atom:*_b*_a*_d016*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* + @dihedral:019_013_013_046 @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* + @dihedral:020_013_013_020 @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* + @dihedral:020_013_013_046 @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* + @dihedral:021_013_013_021 @atom:*_b*_a*_d021*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d021*_i* + @dihedral:021_013_013_044 @atom:*_b*_a*_d021*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d044*_i* + @dihedral:021_013_013_046 @atom:*_b*_a*_d021*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* + @dihedral:044_013_013_044 @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d044*_i* + @dihedral:044_013_013_046 @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* + @dihedral:044_013_013_048 @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d048*_i* + @dihedral:024_013_013_046 @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* + @dihedral:024_013_013_048 @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d048*_i* + @dihedral:024_013_013_080 @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d080*_i* + @dihedral:046_013_013_046 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* + @dihedral:046_013_013_047 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* + @dihedral:046_013_013_048 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d048*_i* + @dihedral:046_013_013_051 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d051*_i* + @dihedral:046_013_013_053 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d053*_i* + @dihedral:046_013_013_055 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d055*_i* + @dihedral:046_013_013_059 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d059*_i* + @dihedral:046_013_013_062 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d062*_i* + @dihedral:046_013_013_065 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d065*_i* + @dihedral:046_013_013_066 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d066*_i* + @dihedral:046_013_013_079 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d079*_i* + @dihedral:046_013_013_080 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d080*_i* + @dihedral:046_013_013_082 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d082*_i* + @dihedral:046_013_013_083 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d083*_i* + @dihedral:046_013_013_084 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d084*_i* + @dihedral:046_013_013_087 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d087*_i* + @dihedral:046_013_013_088 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d088*_i* + @dihedral:046_013_013_102 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d102*_i* + @dihedral:046_013_013_104 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d104*_i* + @dihedral:046_013_013_107 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d107*_i* + @dihedral:046_013_013_108 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d108*_i* + @dihedral:046_013_013_109 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d109*_i* + @dihedral:048_013_013_053 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d053*_i* + @dihedral:108_013_013_108 @atom:*_b*_a*_d108*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d108*_i* + @dihedral:013_013_015_017 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d015*_i* @atom:*_b*_a*_d017*_i* + @dihedral:046_013_015_017 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d015*_i* @atom:*_b*_a*_d017*_i* + @dihedral:013_013_016_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d016*_i* @atom:*_b*_a*_d013*_i* + @dihedral:013_013_016_016 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d016*_i* @atom:*_b*_a*_d016*_i* + @dihedral:046_013_016_013 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d016*_i* @atom:*_b*_a*_d013*_i* + @dihedral:046_013_016_016 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d016*_i* @atom:*_b*_a*_d016*_i* + @dihedral:046_013_016_048 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d016*_i* @atom:*_b*_a*_d048*_i* + @dihedral:X_013_018_019 @atom:* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d018*_i* @atom:*_b*_a*_d019*_i* + @dihedral:046_013_018_019 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d018*_i* @atom:*_b*_a*_d019*_i* + @dihedral:X_013_019_018 @atom:* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d018*_i* + @dihedral:X_013_019_019 @atom:* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d019*_i* + @dihedral:013_013_019_019 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d019*_i* + @dihedral:046_013_019_019 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d019*_i* + @dihedral:X_013_020_013 @atom:* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d013*_i* + @dihedral:056_013_020_013 @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d013*_i* + @dihedral:057_013_020_013 @atom:*_b*_a*_d057*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d013*_i* + @dihedral:013_013_020_003 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d003*_i* + @dihedral:013_013_020_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d013*_i* + @dihedral:013_013_020_064 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d064*_i* + @dihedral:046_013_020_X @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:* + @dihedral:046_013_020_003 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d003*_i* + @dihedral:046_013_020_047 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d047*_i* + @dihedral:046_013_020_048 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d048*_i* + @dihedral:046_013_020_051 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d051*_i* + @dihedral:046_013_020_064 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d064*_i* + @dihedral:X_013_024_045 @atom:* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d045*_i* + @dihedral:003_013_024_003 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d003*_i* + @dihedral:003_013_024_013 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d013*_i* + @dihedral:003_013_024_045 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d045*_i* + @dihedral:013_013_024_003 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d003*_i* + @dihedral:013_013_024_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d013*_i* + @dihedral:013_013_024_045 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d045*_i* + @dihedral:013_013_024_059 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d059*_i* + @dihedral:013_013_024_079 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d079*_i* + @dihedral:013_013_024_091 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d091*_i* + @dihedral:046_013_024_003 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d003*_i* + @dihedral:046_013_024_013 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d013*_i* + @dihedral:046_013_024_045 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d045*_i* + @dihedral:046_013_024_048 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d048*_i* + @dihedral:046_013_024_079 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d079*_i* + @dihedral:048_013_024_059 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d059*_i* + @dihedral:013_013_044_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d013*_i* + @dihedral:013_013_044_045 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d045*_i* + @dihedral:046_013_044_013 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d013*_i* + @dihedral:046_013_044_045 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d045*_i* + @dihedral:046_013_044_048 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d048*_i* + @dihedral:X_013_047_013 @atom:* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d013*_i* + @dihedral:X_013_047_046 @atom:* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d046*_i* + @dihedral:X_013_047_047 @atom:* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* + @dihedral:X_013_047_050 @atom:* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d050*_i* + @dihedral:001_013_047_047 @atom:*_b*_a*_d001*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* + @dihedral:013_013_047_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d013*_i* + @dihedral:013_013_047_047 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* + @dihedral:013_013_047_050 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d050*_i* + @dihedral:046_013_047_013 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d013*_i* + @dihedral:046_013_047_046 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d046*_i* + @dihedral:046_013_047_047 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* + @dihedral:046_013_047_050 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d050*_i* + @dihedral:046_013_047_110 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d110*_i* + @dihedral:047_013_047_013 @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d013*_i* + @dihedral:047_013_047_046 @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d046*_i* + @dihedral:X_013_048_048 @atom:* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:001_013_048_048 @atom:*_b*_a*_d001*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:013_013_048_048 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:013_013_048_056 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d056*_i* + @dihedral:021_013_048_048 @atom:*_b*_a*_d021*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:046_013_048_048 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:064_013_048_048 @atom:*_b*_a*_d064*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:065_013_048_048 @atom:*_b*_a*_d065*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:X_013_050_047 @atom:* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d047*_i* + @dihedral:013_013_050_050 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d050*_i* + @dihedral:046_013_050_047 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d047*_i* + @dihedral:046_013_050_050 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d050*_i* + @dihedral:046_013_050_109 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d109*_i* + @dihedral:013_013_051_X @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d051*_i* @atom:* + @dihedral:013_013_051_046 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d051*_i* @atom:*_b*_a*_d046*_i* + @dihedral:046_013_051_020 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d051*_i* @atom:*_b*_a*_d020*_i* + @dihedral:013_013_053_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d053*_i* @atom:*_b*_a*_d013*_i* + @dihedral:013_013_053_045 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d053*_i* @atom:*_b*_a*_d045*_i* + @dihedral:046_013_053_013 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d053*_i* @atom:*_b*_a*_d013*_i* + @dihedral:046_013_053_045 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d053*_i* @atom:*_b*_a*_d045*_i* + @dihedral:046_013_053_048 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d053*_i* @atom:*_b*_a*_d048*_i* + @dihedral:046_013_053_054 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d053*_i* @atom:*_b*_a*_d054*_i* + @dihedral:013_013_055_045 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d055*_i* @atom:*_b*_a*_d045*_i* + @dihedral:013_013_055_048 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d055*_i* @atom:*_b*_a*_d048*_i* + @dihedral:013_013_055_054 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d055*_i* @atom:*_b*_a*_d054*_i* + @dihedral:046_013_055_013 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d055*_i* @atom:*_b*_a*_d013*_i* + @dihedral:046_013_055_045 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d055*_i* @atom:*_b*_a*_d045*_i* + @dihedral:046_013_055_048 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d055*_i* @atom:*_b*_a*_d048*_i* + @dihedral:013_013_056_018 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d018*_i* + @dihedral:X_013_057_X @atom:* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d057*_i* @atom:* + @dihedral:013_013_057_X @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d057*_i* @atom:* + @dihedral:013_013_057_062 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d057*_i* @atom:*_b*_a*_d062*_i* + @dihedral:013_013_057_082 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d057*_i* @atom:*_b*_a*_d082*_i* + @dihedral:020_013_057_X @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d057*_i* @atom:* + @dihedral:020_013_057_062 @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d057*_i* @atom:*_b*_a*_d062*_i* + @dihedral:020_013_057_082 @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d057*_i* @atom:*_b*_a*_d082*_i* + @dihedral:013_013_059_X @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d059*_i* @atom:* + @dihedral:013_013_059_056 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d059*_i* @atom:*_b*_a*_d056*_i* + @dihedral:046_013_059_X @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d059*_i* @atom:* + @dihedral:013_013_062_X @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d062*_i* @atom:* + @dihedral:046_013_062_X @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d062*_i* @atom:* + @dihedral:046_013_064_020 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d064*_i* @atom:*_b*_a*_d020*_i* + @dihedral:046_013_064_052 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d064*_i* @atom:*_b*_a*_d052*_i* + @dihedral:048_013_064_020 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d064*_i* @atom:*_b*_a*_d020*_i* + @dihedral:048_013_064_052 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d064*_i* @atom:*_b*_a*_d052*_i* + @dihedral:X_013_079_023 @atom:* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d079*_i* @atom:*_b*_a*_d023*_i* + @dihedral:X_013_079_024 @atom:* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d079*_i* @atom:*_b*_a*_d024*_i* + @dihedral:013_013_079_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d079*_i* @atom:*_b*_a*_d013*_i* + @dihedral:013_013_079_023 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d079*_i* @atom:*_b*_a*_d023*_i* + @dihedral:046_013_079_005 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d079*_i* @atom:*_b*_a*_d005*_i* + @dihedral:046_013_079_013 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d079*_i* @atom:*_b*_a*_d013*_i* + @dihedral:046_013_079_023 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d079*_i* @atom:*_b*_a*_d023*_i* + @dihedral:046_013_079_048 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d079*_i* @atom:*_b*_a*_d048*_i* + @dihedral:013_013_080_X @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d080*_i* @atom:* + @dihedral:013_013_080_060 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d080*_i* @atom:*_b*_a*_d060*_i* + @dihedral:013_013_080_084 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d080*_i* @atom:*_b*_a*_d084*_i* + @dihedral:046_013_080_X @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d080*_i* @atom:* + @dihedral:046_013_080_060 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d080*_i* @atom:*_b*_a*_d060*_i* + @dihedral:046_013_080_084 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d080*_i* @atom:*_b*_a*_d084*_i* + @dihedral:013_013_082_X @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d082*_i* @atom:* + @dihedral:046_013_082_X @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d082*_i* @atom:* + @dihedral:013_013_083_X @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d083*_i* @atom:* + @dihedral:046_013_083_X @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d083*_i* @atom:* + @dihedral:001_013_084_X @atom:*_b*_a*_d001*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d084*_i* @atom:* + @dihedral:013_013_084_X @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d084*_i* @atom:* + @dihedral:013_013_084_057 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d057*_i* + @dihedral:021_013_084_X @atom:*_b*_a*_d021*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d084*_i* @atom:* + @dihedral:046_013_084_X @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d084*_i* @atom:* + @dihedral:001_013_087_X @atom:*_b*_a*_d001*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d087*_i* @atom:* + @dihedral:013_013_087_X @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d087*_i* @atom:* + @dihedral:021_013_087_X @atom:*_b*_a*_d021*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d087*_i* @atom:* + @dihedral:046_013_087_X @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d087*_i* @atom:* + @dihedral:013_013_088_X @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d088*_i* @atom:* + @dihedral:046_013_088_X @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d088*_i* @atom:* + @dihedral:X_013_090_X @atom:* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d090*_i* @atom:* + @dihedral:046_013_090_X @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d090*_i* @atom:* + @dihedral:046_013_091_091 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d091*_i* + @dihedral:013_013_095_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d095*_i* @atom:*_b*_a*_d013*_i* + @dihedral:013_013_095_046 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d095*_i* @atom:*_b*_a*_d046*_i* + @dihedral:013_013_102_103 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d102*_i* @atom:*_b*_a*_d103*_i* + @dihedral:046_013_102_103 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d102*_i* @atom:*_b*_a*_d103*_i* + @dihedral:013_013_104_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d104*_i* @atom:*_b*_a*_d013*_i* + @dihedral:046_013_104_013 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d104*_i* @atom:*_b*_a*_d013*_i* + @dihedral:X_013_105_X @atom:* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d105*_i* @atom:* + @dihedral:013_013_105_X @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d105*_i* @atom:* + @dihedral:013_013_105_062 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d105*_i* @atom:*_b*_a*_d062*_i* + @dihedral:013_013_105_082 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d105*_i* @atom:*_b*_a*_d082*_i* + @dihedral:020_013_105_X @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d105*_i* @atom:* + @dihedral:020_013_105_062 @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d105*_i* @atom:*_b*_a*_d062*_i* + @dihedral:020_013_105_082 @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d105*_i* @atom:*_b*_a*_d082*_i* + @dihedral:003_013_107_013 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d107*_i* @atom:*_b*_a*_d013*_i* + @dihedral:013_013_107_003 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d107*_i* @atom:*_b*_a*_d003*_i* + @dihedral:013_013_107_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d107*_i* @atom:*_b*_a*_d013*_i* + @dihedral:046_013_107_003 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d107*_i* @atom:*_b*_a*_d003*_i* + @dihedral:046_013_107_013 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d107*_i* @atom:*_b*_a*_d013*_i* + @dihedral:046_013_107_048 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d107*_i* @atom:*_b*_a*_d048*_i* + @dihedral:013_013_108_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d108*_i* @atom:*_b*_a*_d013*_i* + @dihedral:013_013_108_045 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d108*_i* @atom:*_b*_a*_d045*_i* + @dihedral:046_013_108_013 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d108*_i* @atom:*_b*_a*_d013*_i* + @dihedral:046_013_108_020 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d108*_i* @atom:*_b*_a*_d020*_i* + @dihedral:046_013_108_045 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d108*_i* @atom:*_b*_a*_d045*_i* + @dihedral:013_013_109_109 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* + @dihedral:046_013_109_013 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d013*_i* + @dihedral:046_013_109_046 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d046*_i* + @dihedral:046_013_109_109 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* + @dihedral:017_015_048_X @atom:*_b*_a*_d017*_i* @atom:*_b*_a*_d015*_i* @atom:*_b*_a*_d048*_i* @atom:* + @dihedral:017_015_048_048 @atom:*_b*_a*_d017*_i* @atom:*_b*_a*_d015*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:013_016_016_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d016*_i* @atom:*_b*_a*_d016*_i* @atom:*_b*_a*_d013*_i* + @dihedral:013_016_048_048 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d016*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:013_016_048_056 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d016*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d056*_i* + @dihedral:013_016_059_056 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d016*_i* @atom:*_b*_a*_d059*_i* @atom:*_b*_a*_d056*_i* + @dihedral:084_016_082_X @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d016*_i* @atom:*_b*_a*_d082*_i* @atom:* + @dihedral:084_016_082_061 @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d016*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d061*_i* + @dihedral:082_016_084_049 @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d016*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d049*_i* + @dihedral:082_016_084_083 @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d016*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d083*_i* + @dihedral:082_016_084_088 @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d016*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d088*_i* + @dihedral:X_016_091_X @atom:* @atom:*_b*_a*_d016*_i* @atom:*_b*_a*_d091*_i* @atom:* + @dihedral:019_018_048_X @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d018*_i* @atom:*_b*_a*_d048*_i* @atom:* + @dihedral:019_018_048_048 @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d018*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:018_018_056_013 @atom:*_b*_a*_d018*_i* @atom:*_b*_a*_d018*_i* @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d013*_i* + @dihedral:018_018_056_046 @atom:*_b*_a*_d018*_i* @atom:*_b*_a*_d018*_i* @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d046*_i* + @dihedral:X_019_019_X @atom:* @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d019*_i* @atom:* + @dihedral:013_019_019_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d013*_i* + @dihedral:013_019_019_046 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d046*_i* + @dihedral:013_019_019_047 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d047*_i* + @dihedral:013_019_019_109 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d109*_i* + @dihedral:046_019_019_047 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d047*_i* + @dihedral:046_019_019_109 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d109*_i* + @dihedral:019_019_047_013 @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d013*_i* + @dihedral:019_019_047_046 @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d046*_i* + @dihedral:019_019_047_047 @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* + @dihedral:013_020_044_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d013*_i* + @dihedral:013_020_044_045 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d045*_i* + @dihedral:013_020_047_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d013*_i* + @dihedral:013_020_047_046 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d046*_i* + @dihedral:013_020_047_047 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* + @dihedral:013_020_047_050 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d050*_i* + @dihedral:003_020_048_048 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:013_020_048_048 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:013_020_048_056 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d056*_i* + @dihedral:064_020_048_048 @atom:*_b*_a*_d064*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:013_020_051_005 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d051*_i* @atom:*_b*_a*_d005*_i* + @dihedral:013_020_051_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d051*_i* @atom:*_b*_a*_d013*_i* + @dihedral:013_020_051_020 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d051*_i* @atom:*_b*_a*_d020*_i* + @dihedral:013_020_051_046 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d051*_i* @atom:*_b*_a*_d046*_i* + @dihedral:013_020_056_003 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d003*_i* + @dihedral:013_020_059_056 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d059*_i* @atom:*_b*_a*_d056*_i* + @dihedral:X_020_064_052 @atom:* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d064*_i* @atom:*_b*_a*_d052*_i* + @dihedral:013_020_064_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d064*_i* @atom:*_b*_a*_d013*_i* + @dihedral:013_020_064_052 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d064*_i* @atom:*_b*_a*_d052*_i* + @dihedral:048_020_064_004 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d064*_i* @atom:*_b*_a*_d004*_i* + @dihedral:084_020_082_061 @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d061*_i* + @dihedral:082_020_084_088 @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d088*_i* + @dihedral:084_020_084_049 @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d049*_i* + @dihedral:084_020_084_087 @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d087*_i* + @dihedral:108_020_108_013 @atom:*_b*_a*_d108*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d108*_i* @atom:*_b*_a*_d013*_i* + @dihedral:108_020_108_020 @atom:*_b*_a*_d108*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d108*_i* @atom:*_b*_a*_d020*_i* + @dihedral:X_024_048_048 @atom:* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:003_024_048_048 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:013_024_048_048 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:045_024_048_048 @atom:*_b*_a*_d045*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:059_024_048_048 @atom:*_b*_a*_d059*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:082_024_048_048 @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:084_024_048_048 @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:X_024_059_X @atom:* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d059*_i* @atom:* + @dihedral:X_024_059_049 @atom:* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d059*_i* @atom:*_b*_a*_d049*_i* + @dihedral:045_024_059_X @atom:*_b*_a*_d045*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d059*_i* @atom:* + @dihedral:X_024_060_X @atom:* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d060*_i* @atom:* + @dihedral:X_024_079_023 @atom:* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d079*_i* @atom:*_b*_a*_d023*_i* + @dihedral:013_024_079_048 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d079*_i* @atom:*_b*_a*_d048*_i* + @dihedral:045_024_079_048 @atom:*_b*_a*_d045*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d079*_i* @atom:*_b*_a*_d048*_i* + @dihedral:013_024_082_061 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d061*_i* + @dihedral:045_024_082_016 @atom:*_b*_a*_d045*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d016*_i* + @dihedral:045_024_082_020 @atom:*_b*_a*_d045*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d020*_i* + @dihedral:045_024_082_061 @atom:*_b*_a*_d045*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d061*_i* + @dihedral:048_024_082_016 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d016*_i* + @dihedral:048_024_082_020 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d020*_i* + @dihedral:048_024_082_061 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d061*_i* + @dihedral:X_024_084_X @atom:* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d084*_i* @atom:* + @dihedral:003_024_084_084 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d084*_i* + @dihedral:045_024_084_016 @atom:*_b*_a*_d045*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d016*_i* + @dihedral:045_024_084_020 @atom:*_b*_a*_d045*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d020*_i* + @dihedral:048_024_084_016 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d016*_i* + @dihedral:048_024_084_020 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d020*_i* + @dihedral:003_024_086_048 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d048*_i* + @dihedral:003_024_086_056 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d056*_i* + @dihedral:003_024_086_086 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d086*_i* + @dihedral:047_024_086_048 @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d048*_i* + @dihedral:047_024_086_056 @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d056*_i* + @dihedral:X_024_087_X @atom:* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d087*_i* @atom:* + @dihedral:X_024_088_X @atom:* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d088*_i* @atom:* + @dihedral:003_024_091_046 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d046*_i* + @dihedral:003_024_091_089 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d089*_i* + @dihedral:003_024_091_091 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d091*_i* + @dihedral:045_024_091_046 @atom:*_b*_a*_d045*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d046*_i* + @dihedral:045_024_091_089 @atom:*_b*_a*_d045*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d089*_i* + @dihedral:045_024_091_091 @atom:*_b*_a*_d045*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d091*_i* + @dihedral:X_024_106_X @atom:* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d106*_i* @atom:* + @dihedral:013_044_044_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d013*_i* + @dihedral:013_044_044_045 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d045*_i* + @dihedral:045_044_044_045 @atom:*_b*_a*_d045*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d045*_i* + @dihedral:013_044_048_048 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:045_044_048_048 @atom:*_b*_a*_d045*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:059_044_048_048 @atom:*_b*_a*_d059*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:082_044_048_048 @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:084_044_048_048 @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:045_044_082_016 @atom:*_b*_a*_d045*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d016*_i* + @dihedral:045_044_082_061 @atom:*_b*_a*_d045*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d061*_i* + @dihedral:048_044_082_016 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d016*_i* + @dihedral:048_044_082_061 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d061*_i* + @dihedral:047_046_047_013 @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d013*_i* + @dihedral:047_046_047_046 @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d046*_i* + @dihedral:X_047_047_X @atom:* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* @atom:* + @dihedral:X_047_047_019 @atom:* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d019*_i* + @dihedral:003_047_047_024 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d024*_i* + @dihedral:003_047_047_046 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d046*_i* + @dihedral:005_047_047_013 @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d013*_i* + @dihedral:005_047_047_046 @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d046*_i* + @dihedral:013_047_047_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d013*_i* + @dihedral:013_047_047_019 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d019*_i* + @dihedral:013_047_047_020 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d020*_i* + @dihedral:013_047_047_046 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d046*_i* + @dihedral:019_047_047_046 @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d046*_i* + @dihedral:020_047_047_046 @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d046*_i* + @dihedral:021_047_047_021 @atom:*_b*_a*_d021*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d021*_i* + @dihedral:021_047_047_046 @atom:*_b*_a*_d021*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d046*_i* + @dihedral:046_047_047_046 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d046*_i* + @dihedral:046_047_047_048 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d048*_i* + @dihedral:013_047_048_048 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:046_047_048_048 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:046_047_048_056 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d056*_i* + @dihedral:047_047_048_048 @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:013_047_050_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d013*_i* + @dihedral:013_047_050_046 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d046*_i* + @dihedral:013_047_050_048 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d048*_i* + @dihedral:013_047_050_050 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d050*_i* + @dihedral:013_047_050_109 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d109*_i* + @dihedral:024_047_050_003 @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d003*_i* + @dihedral:046_047_050_013 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d013*_i* + @dihedral:046_047_050_046 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d046*_i* + @dihedral:046_047_050_048 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d048*_i* + @dihedral:046_047_050_050 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d050*_i* + @dihedral:046_047_050_109 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d109*_i* + @dihedral:X_047_084_X @atom:* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d084*_i* @atom:* + @dihedral:X_047_086_048 @atom:* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d048*_i* + @dihedral:003_047_086_086 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d086*_i* + @dihedral:049_047_086_X @atom:*_b*_a*_d049*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d086*_i* @atom:* + @dihedral:049_047_086_024 @atom:*_b*_a*_d049*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d024*_i* + @dihedral:X_047_087_X @atom:* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d087*_i* @atom:* + @dihedral:X_047_088_X @atom:* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d088*_i* @atom:* + @dihedral:013_047_110_047 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d110*_i* @atom:*_b*_a*_d047*_i* + @dihedral:046_047_110_047 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d110*_i* @atom:*_b*_a*_d047*_i* + @dihedral:X_048_048_X @atom:* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:* + @dihedral:X_048_048_013 @atom:* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d013*_i* + @dihedral:X_048_048_048 @atom:* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:X_048_048_049 @atom:* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d049*_i* + @dihedral:001_048_048_048 @atom:*_b*_a*_d001*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:001_048_048_049 @atom:*_b*_a*_d001*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d049*_i* + @dihedral:013_048_048_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d013*_i* + @dihedral:013_048_048_048 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:013_048_048_049 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d049*_i* + @dihedral:013_048_048_050 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d050*_i* + @dihedral:021_048_048_048 @atom:*_b*_a*_d021*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:021_048_048_049 @atom:*_b*_a*_d021*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d049*_i* + @dihedral:044_048_048_049 @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d049*_i* + @dihedral:047_048_048_049 @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d049*_i* + @dihedral:048_048_048_048 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:048_048_048_049 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d049*_i* + @dihedral:048_048_048_050 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d050*_i* + @dihedral:048_048_048_055 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d055*_i* + @dihedral:048_048_048_060 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d060*_i* + @dihedral:048_048_048_065 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d065*_i* + @dihedral:048_048_048_066 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d066*_i* + @dihedral:048_048_048_086 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d086*_i* + @dihedral:048_048_048_109 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d109*_i* + @dihedral:049_048_048_049 @atom:*_b*_a*_d049*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d049*_i* + @dihedral:049_048_048_050 @atom:*_b*_a*_d049*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d050*_i* + @dihedral:049_048_048_060 @atom:*_b*_a*_d049*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d060*_i* + @dihedral:049_048_048_065 @atom:*_b*_a*_d049*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d065*_i* + @dihedral:049_048_048_066 @atom:*_b*_a*_d049*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d066*_i* + @dihedral:049_048_048_086 @atom:*_b*_a*_d049*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d086*_i* + @dihedral:049_048_048_109 @atom:*_b*_a*_d049*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d109*_i* + @dihedral:056_048_048_086 @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d086*_i* + @dihedral:048_048_050_046 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d046*_i* + @dihedral:048_048_050_047 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d047*_i* + @dihedral:056_048_050_046 @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d046*_i* + @dihedral:056_048_050_047 @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d047*_i* + @dihedral:048_048_053_013 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d053*_i* @atom:*_b*_a*_d013*_i* + @dihedral:048_048_053_054 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d053*_i* @atom:*_b*_a*_d054*_i* + @dihedral:X_048_055_045 @atom:* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d055*_i* @atom:*_b*_a*_d045*_i* + @dihedral:048_048_055_045 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d055*_i* @atom:*_b*_a*_d045*_i* + @dihedral:055_048_055_013 @atom:*_b*_a*_d055*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d055*_i* @atom:*_b*_a*_d013*_i* + @dihedral:055_048_055_045 @atom:*_b*_a*_d055*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d055*_i* @atom:*_b*_a*_d045*_i* + @dihedral:060_048_055_045 @atom:*_b*_a*_d060*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d055*_i* @atom:*_b*_a*_d045*_i* + @dihedral:X_048_056_X @atom:* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d056*_i* @atom:* + @dihedral:048_048_056_048 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d048*_i* + @dihedral:049_048_056_048 @atom:*_b*_a*_d049*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d048*_i* + @dihedral:X_048_060_X @atom:* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d060*_i* @atom:* + @dihedral:X_048_079_023 @atom:* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d079*_i* @atom:*_b*_a*_d023*_i* + @dihedral:048_048_079_013 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d079*_i* @atom:*_b*_a*_d013*_i* + @dihedral:048_048_079_024 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d079*_i* @atom:*_b*_a*_d024*_i* + @dihedral:048_048_086_048 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d048*_i* + @dihedral:048_048_086_056 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d056*_i* + @dihedral:048_048_086_086 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d086*_i* + @dihedral:049_048_086_048 @atom:*_b*_a*_d049*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d048*_i* + @dihedral:049_048_086_056 @atom:*_b*_a*_d049*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d056*_i* + @dihedral:049_048_086_086 @atom:*_b*_a*_d049*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d086*_i* + @dihedral:056_048_086_048 @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d048*_i* + @dihedral:056_048_086_086 @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d086*_i* + @dihedral:049_048_088_049 @atom:*_b*_a*_d049*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d088*_i* @atom:*_b*_a*_d049*_i* + @dihedral:056_048_101_013 @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d101*_i* @atom:*_b*_a*_d013*_i* + @dihedral:048_048_102_103 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d102*_i* @atom:*_b*_a*_d103*_i* + @dihedral:048_048_109_013 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d013*_i* + @dihedral:048_048_109_046 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d046*_i* + @dihedral:048_048_109_109 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* + @dihedral:X_050_050_049 @atom:* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d049*_i* + @dihedral:003_050_050_003 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d003*_i* + @dihedral:013_050_050_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d013*_i* + @dihedral:013_050_050_046 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d046*_i* + @dihedral:013_050_050_047 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d047*_i* + @dihedral:046_050_050_046 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d046*_i* + @dihedral:046_050_050_047 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d047*_i* + @dihedral:047_050_050_047 @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d047*_i* + @dihedral:013_050_109_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d013*_i* + @dihedral:013_050_109_109 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* + @dihedral:046_050_109_013 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d013*_i* + @dihedral:046_050_109_046 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d046*_i* + @dihedral:046_050_109_109 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* + @dihedral:047_050_109_013 @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d013*_i* + @dihedral:047_050_109_046 @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d046*_i* + @dihedral:047_050_109_109 @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* + @dihedral:013_053_082_061 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d053*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d061*_i* + @dihedral:048_053_082_061 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d053*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d061*_i* + @dihedral:045_055_059_X @atom:*_b*_a*_d045*_i* @atom:*_b*_a*_d055*_i* @atom:*_b*_a*_d059*_i* @atom:* + @dihedral:013_056_056_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d013*_i* + @dihedral:013_056_056_048 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d048*_i* + @dihedral:048_056_056_048 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d048*_i* + @dihedral:X_056_059_X @atom:* @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d059*_i* @atom:* + @dihedral:X_056_059_049 @atom:* @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d059*_i* @atom:*_b*_a*_d049*_i* + @dihedral:X_056_060_X @atom:* @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d060*_i* @atom:* + @dihedral:X_056_062_X @atom:* @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d062*_i* @atom:* + @dihedral:X_056_082_X @atom:* @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d082*_i* @atom:* + @dihedral:048_056_086_048 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d048*_i* + @dihedral:048_056_086_086 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d086*_i* + @dihedral:X_057_060_X @atom:* @atom:*_b*_a*_d057*_i* @atom:*_b*_a*_d060*_i* @atom:* + @dihedral:045_057_060_X @atom:*_b*_a*_d045*_i* @atom:*_b*_a*_d057*_i* @atom:*_b*_a*_d060*_i* @atom:* + @dihedral:X_057_061_X @atom:* @atom:*_b*_a*_d057*_i* @atom:*_b*_a*_d061*_i* @atom:* + @dihedral:X_057_062_X @atom:* @atom:*_b*_a*_d057*_i* @atom:*_b*_a*_d062*_i* @atom:* + @dihedral:X_057_081_X @atom:* @atom:*_b*_a*_d057*_i* @atom:*_b*_a*_d081*_i* @atom:* + @dihedral:X_057_082_X @atom:* @atom:*_b*_a*_d057*_i* @atom:*_b*_a*_d082*_i* @atom:* + @dihedral:X_057_082_049 @atom:* @atom:*_b*_a*_d057*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d049*_i* + @dihedral:045_057_082_X @atom:*_b*_a*_d045*_i* @atom:*_b*_a*_d057*_i* @atom:*_b*_a*_d082*_i* @atom:* + @dihedral:X_057_084_X @atom:* @atom:*_b*_a*_d057*_i* @atom:*_b*_a*_d084*_i* @atom:* + @dihedral:045_057_084_X @atom:*_b*_a*_d045*_i* @atom:*_b*_a*_d057*_i* @atom:*_b*_a*_d084*_i* @atom:* + @dihedral:061_057_086_048 @atom:*_b*_a*_d061*_i* @atom:*_b*_a*_d057*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d048*_i* + @dihedral:084_057_086_048 @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d057*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d048*_i* + @dihedral:X_060_060_X @atom:* @atom:*_b*_a*_d060*_i* @atom:*_b*_a*_d060*_i* @atom:* + @dihedral:X_060_061_X @atom:* @atom:*_b*_a*_d060*_i* @atom:*_b*_a*_d061*_i* @atom:* + @dihedral:X_060_080_X @atom:* @atom:*_b*_a*_d060*_i* @atom:*_b*_a*_d080*_i* @atom:* + @dihedral:X_060_081_X @atom:* @atom:*_b*_a*_d060*_i* @atom:*_b*_a*_d081*_i* @atom:* + @dihedral:X_060_087_X @atom:* @atom:*_b*_a*_d060*_i* @atom:*_b*_a*_d087*_i* @atom:* + @dihedral:048_060_087_084 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d060*_i* @atom:*_b*_a*_d087*_i* @atom:*_b*_a*_d084*_i* + @dihedral:060_060_087_084 @atom:*_b*_a*_d060*_i* @atom:*_b*_a*_d060*_i* @atom:*_b*_a*_d087*_i* @atom:*_b*_a*_d084*_i* + @dihedral:X_061_061_X @atom:* @atom:*_b*_a*_d061*_i* @atom:*_b*_a*_d061*_i* @atom:* + @dihedral:X_061_062_X @atom:* @atom:*_b*_a*_d061*_i* @atom:*_b*_a*_d062*_i* @atom:* + @dihedral:X_061_082_X @atom:* @atom:*_b*_a*_d061*_i* @atom:*_b*_a*_d082*_i* @atom:* + @dihedral:X_061_082_049 @atom:* @atom:*_b*_a*_d061*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d049*_i* + @dihedral:083_061_082_016 @atom:*_b*_a*_d083*_i* @atom:*_b*_a*_d061*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d016*_i* + @dihedral:088_061_082_016 @atom:*_b*_a*_d088*_i* @atom:*_b*_a*_d061*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d016*_i* + @dihedral:088_061_082_020 @atom:*_b*_a*_d088*_i* @atom:*_b*_a*_d061*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d020*_i* + @dihedral:X_061_083_X @atom:* @atom:*_b*_a*_d061*_i* @atom:*_b*_a*_d083*_i* @atom:* + @dihedral:082_061_083_049 @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d061*_i* @atom:*_b*_a*_d083*_i* @atom:*_b*_a*_d049*_i* + @dihedral:082_061_083_084 @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d061*_i* @atom:*_b*_a*_d083*_i* @atom:*_b*_a*_d084*_i* + @dihedral:X_061_084_X @atom:* @atom:*_b*_a*_d061*_i* @atom:*_b*_a*_d084*_i* @atom:* + @dihedral:X_061_088_X @atom:* @atom:*_b*_a*_d061*_i* @atom:*_b*_a*_d088*_i* @atom:* + @dihedral:082_061_088_084 @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d061*_i* @atom:*_b*_a*_d088*_i* @atom:*_b*_a*_d084*_i* + @dihedral:X_080_084_X @atom:* @atom:*_b*_a*_d080*_i* @atom:*_b*_a*_d084*_i* @atom:* + @dihedral:X_082_084_X @atom:* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d084*_i* @atom:* + @dihedral:016_082_086_048 @atom:*_b*_a*_d016*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d048*_i* + @dihedral:020_082_086_048 @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d048*_i* + @dihedral:057_082_086_048 @atom:*_b*_a*_d057*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d048*_i* + @dihedral:061_082_086_048 @atom:*_b*_a*_d061*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d048*_i* + @dihedral:X_082_087_X @atom:* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d087*_i* @atom:* + @dihedral:X_083_084_X @atom:* @atom:*_b*_a*_d083*_i* @atom:*_b*_a*_d084*_i* @atom:* + @dihedral:X_083_084_049 @atom:* @atom:*_b*_a*_d083*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d049*_i* + @dihedral:049_083_084_X @atom:*_b*_a*_d049*_i* @atom:*_b*_a*_d083*_i* @atom:*_b*_a*_d084*_i* @atom:* + @dihedral:049_083_084_016 @atom:*_b*_a*_d049*_i* @atom:*_b*_a*_d083*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d016*_i* + @dihedral:049_083_084_049 @atom:*_b*_a*_d049*_i* @atom:*_b*_a*_d083*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d049*_i* + @dihedral:061_083_084_016 @atom:*_b*_a*_d061*_i* @atom:*_b*_a*_d083*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d016*_i* + @dihedral:061_083_084_020 @atom:*_b*_a*_d061*_i* @atom:*_b*_a*_d083*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d020*_i* + @dihedral:061_083_084_049 @atom:*_b*_a*_d061*_i* @atom:*_b*_a*_d083*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d049*_i* + @dihedral:X_083_086_048 @atom:* @atom:*_b*_a*_d083*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d048*_i* + @dihedral:061_083_086_048 @atom:*_b*_a*_d061*_i* @atom:*_b*_a*_d083*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d048*_i* + @dihedral:061_083_087_X @atom:*_b*_a*_d061*_i* @atom:*_b*_a*_d083*_i* @atom:*_b*_a*_d087*_i* @atom:* + @dihedral:084_083_087_X @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d083*_i* @atom:*_b*_a*_d087*_i* @atom:* + @dihedral:X_084_084_X @atom:* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d084*_i* @atom:* + @dihedral:X_084_084_049 @atom:* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d049*_i* + @dihedral:016_084_084_049 @atom:*_b*_a*_d016*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d049*_i* + @dihedral:049_084_084_049 @atom:*_b*_a*_d049*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d049*_i* + @dihedral:X_084_086_048 @atom:* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d048*_i* + @dihedral:016_084_086_048 @atom:*_b*_a*_d016*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d048*_i* + @dihedral:020_084_086_048 @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d048*_i* + @dihedral:057_084_086_048 @atom:*_b*_a*_d057*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d048*_i* + @dihedral:X_084_087_X @atom:* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d087*_i* @atom:* + @dihedral:X_084_087_049 @atom:* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d087*_i* @atom:*_b*_a*_d049*_i* + @dihedral:049_084_087_049 @atom:*_b*_a*_d049*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d087*_i* @atom:*_b*_a*_d049*_i* + @dihedral:X_084_088_049 @atom:* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d088*_i* @atom:*_b*_a*_d049*_i* + @dihedral:016_084_088_049 @atom:*_b*_a*_d016*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d088*_i* @atom:*_b*_a*_d049*_i* + @dihedral:016_084_088_061 @atom:*_b*_a*_d016*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d088*_i* @atom:*_b*_a*_d061*_i* + @dihedral:020_084_088_061 @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d088*_i* @atom:*_b*_a*_d061*_i* + @dihedral:049_084_088_X @atom:*_b*_a*_d049*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d088*_i* @atom:* + @dihedral:049_084_088_061 @atom:*_b*_a*_d049*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d088*_i* @atom:*_b*_a*_d061*_i* + @dihedral:048_086_086_048 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d048*_i* + @dihedral:048_086_086_056 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d056*_i* + @dihedral:048_086_087_X @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d087*_i* @atom:* + @dihedral:048_086_088_X @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d088*_i* @atom:* + @dihedral:048_086_088_061 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d088*_i* @atom:*_b*_a*_d061*_i* + @dihedral:056_086_088_X @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d088*_i* @atom:* + @dihedral:X_087_087_020 @atom:* @atom:*_b*_a*_d087*_i* @atom:*_b*_a*_d087*_i* @atom:*_b*_a*_d020*_i* + @dihedral:X_087_087_057 @atom:* @atom:*_b*_a*_d087*_i* @atom:*_b*_a*_d087*_i* @atom:*_b*_a*_d057*_i* + @dihedral:X_087_087_087 @atom:* @atom:*_b*_a*_d087*_i* @atom:*_b*_a*_d087*_i* @atom:*_b*_a*_d087*_i* + @dihedral:049_087_087_049 @atom:*_b*_a*_d049*_i* @atom:*_b*_a*_d087*_i* @atom:*_b*_a*_d087*_i* @atom:*_b*_a*_d049*_i* + @dihedral:004_089_090_013 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d089*_i* @atom:*_b*_a*_d090*_i* @atom:*_b*_a*_d013*_i* + @dihedral:004_089_090_045 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d089*_i* @atom:*_b*_a*_d090*_i* @atom:*_b*_a*_d045*_i* + @dihedral:004_089_090_048 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d089*_i* @atom:*_b*_a*_d090*_i* @atom:*_b*_a*_d048*_i* + @dihedral:004_089_090_091 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d089*_i* @atom:*_b*_a*_d090*_i* @atom:*_b*_a*_d091*_i* + @dihedral:091_089_090_013 @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d089*_i* @atom:*_b*_a*_d090*_i* @atom:*_b*_a*_d013*_i* + @dihedral:091_089_090_045 @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d089*_i* @atom:*_b*_a*_d090*_i* @atom:*_b*_a*_d045*_i* + @dihedral:091_089_090_048 @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d089*_i* @atom:*_b*_a*_d090*_i* @atom:*_b*_a*_d048*_i* + @dihedral:091_089_090_091 @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d089*_i* @atom:*_b*_a*_d090*_i* @atom:*_b*_a*_d091*_i* + @dihedral:X_089_091_X @atom:* @atom:*_b*_a*_d089*_i* @atom:*_b*_a*_d091*_i* @atom:* + @dihedral:004_089_091_046 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d089*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d046*_i* + @dihedral:004_089_091_091 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d089*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d091*_i* + @dihedral:090_089_091_046 @atom:*_b*_a*_d090*_i* @atom:*_b*_a*_d089*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d046*_i* + @dihedral:090_089_091_091 @atom:*_b*_a*_d090*_i* @atom:*_b*_a*_d089*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d091*_i* + @dihedral:X_090_091_X @atom:* @atom:*_b*_a*_d090*_i* @atom:*_b*_a*_d091*_i* @atom:* + @dihedral:X_090_091_046 @atom:* @atom:*_b*_a*_d090*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d046*_i* + @dihedral:X_090_091_091 @atom:* @atom:*_b*_a*_d090*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d091*_i* + @dihedral:X_091_091_X @atom:* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d091*_i* @atom:* + @dihedral:X_091_091_024 @atom:* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d024*_i* + @dihedral:013_091_091_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d013*_i* + @dihedral:013_091_091_046 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d046*_i* + @dihedral:046_091_091_046 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d046*_i* + @dihedral:046_091_091_091 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d091*_i* + @dihedral:091_091_091_091 @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d091*_i* + @dihedral:X_109_109_X @atom:* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* @atom:* + @dihedral:013_109_109_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d013*_i* + @dihedral:013_109_109_046 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d046*_i* + @dihedral:013_109_109_048 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d048*_i* + @dihedral:013_109_109_050 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d050*_i* + @dihedral:013_109_109_109 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* + @dihedral:046_109_109_046 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d046*_i* + @dihedral:046_109_109_048 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d048*_i* + @dihedral:046_109_109_050 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d050*_i* + @dihedral:046_109_109_109 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* + @dihedral:048_109_109_048 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d048*_i* + @dihedral:048_109_109_050 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d050*_i* + @dihedral:048_109_109_109 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* + @dihedral:050_109_109_050 @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d050*_i* + @dihedral:050_109_109_109 @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* + @dihedral:109_109_109_109 @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* + @dihedral:024_003_013_053 @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d053*_i* + @dihedral:052_003_013_024 @atom:*_b*_a*_d052*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* + @dihedral:003_013_013_053 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d053*_i* + @dihedral:003_013_013_083 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d083*_i* + @dihedral:003_013_013_084 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d084*_i* + @dihedral:003_013_013_085 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d085*_i* + @dihedral:005_013_013_053 @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d053*_i* + @dihedral:015_013_013_053 @atom:*_b*_a*_d015*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d053*_i* + @dihedral:016_013_013_053 @atom:*_b*_a*_d016*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d053*_i* + @dihedral:013_013_013_055 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d055*_i* + @dihedral:024_013_013_083 @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d083*_i* + @dihedral:053_013_013_083 @atom:*_b*_a*_d053*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d083*_i* + @dihedral:024_013_013_084 @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d084*_i* + @dihedral:053_013_013_084 @atom:*_b*_a*_d053*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d084*_i* + @dihedral:024_013_013_085 @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d085*_i* + @dihedral:046_013_013_085 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d085*_i* + @dihedral:053_013_013_085 @atom:*_b*_a*_d053*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d085*_i* + @dihedral:003_013_053_013 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d053*_i* @atom:*_b*_a*_d013*_i* + @dihedral:003_013_053_054 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d053*_i* @atom:*_b*_a*_d054*_i* + @dihedral:013_013_053_054 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d053*_i* @atom:*_b*_a*_d054*_i* + @dihedral:046_013_055_054 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d055*_i* @atom:*_b*_a*_d054*_i* + @dihedral:013_013_085_X @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d085*_i* @atom:* + @dihedral:013_013_085_057 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d085*_i* @atom:*_b*_a*_d057*_i* + @dihedral:046_013_085_X @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d085*_i* @atom:* + @dihedral:055_048_055_054 @atom:*_b*_a*_d055*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d055*_i* @atom:*_b*_a*_d054*_i* + @dihedral:X_048_081_X @atom:* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d081*_i* @atom:* + @dihedral:X_057_085_X @atom:* @atom:*_b*_a*_d057*_i* @atom:*_b*_a*_d085*_i* @atom:* + @dihedral:X_085_085_X @atom:* @atom:*_b*_a*_d085*_i* @atom:*_b*_a*_d085*_i* @atom:* + @dihedral:013_013_013_020 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* + @dihedral:013_013_013_047 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* } #(end of dihedrals by type) @@ -8135,25 +8148,61 @@ OPLSAA { # ---------- Improper Interactions: ---------- # http://lammps.sandia.gov/doc/improper_harmonic.html # Syntax: - # improper_coeff ImproperTypeName ImproperStyle parameters + # improper_coeff ImproperTypeName parameters write_once("In Settings") { - improper_coeff @improper:X-X-3-4 harmonic 10.5 180.0 - improper_coeff @improper:X-X-3-52 harmonic 10.5 180.0 - improper_coeff @improper:X-X-24-X harmonic 2.5 180.0 - improper_coeff @improper:X-X-47-X harmonic 15.0 180.0 - improper_coeff @improper:X-X-48-X harmonic 2.5 180.0 + # The following force field parameters were converted from + # the tinker parameter file (oplsaa.prm) and then edited by hand: + # Thanks to David Huang (adelaide.edu.au) for the corrections: + + improper_coeff @improper:X_X_003_004 10.5 180.0 # (moltemplate) + # <==> "imptors 0 0 3 4 21.000 180.0 2" in oplsaa.prm (tinker) + # <==> "define improper_O_C_X_Y 180.0 43.93200 2" in oplsaa.ff (gromacs) + + improper_coeff @improper:X_X_003_052 10.5 180.0 # (moltemplate) + # <==> "imptors 0 0 3 52 21.000 180.0 2" in oplsaa.prm (tinker) + # <==> "define improper_O_C_X_Y 180.0 43.93200 2" in oplsaa.ff (gromacs) + + improper_coeff @improper:X_X_024_X 1.0 180.0 # (moltemplate) + # <==> "imptors 0 0 24 0 5.000 180.0 2" in oplsaa.prm (tinker) - INCORRECT? + # <==> "define improper_Z_N_X_Y 180.0 4.18400 2" in oplsaa.ff (gromacs) + + improper_coeff @improper:X_X_047_X 15.0 180.0 # (moltemplate) + # <==> "imptors 0 0 47 0 30.000 180.0 2" in oplsaa.prm (tinker) + # <==> "define improper_Z_CM_X_Y 180.0 62.76000 2" in oplsaa.ff (gromacs) + + improper_coeff @improper:X_X_048_X 1.1 180.0 # (moltemplate) + # <==> "imptors 0 0 48 0 5.000 180.0 2" in oplsaa.prm (tinker) - INCORRECT? + # <==> "define improper_Z_CA_X_Y 180.0 4.60240 2" in oplsaa.ff (gromacs) + + improper_coeff @improper:055_055_X_055 10.5 180.0 + # <==> "define improper_N2_X_N2_N2 180.0 43.93200" in oplsaa.ff (gromacs) + # <==> no corresponding line found in oplsaa.prm (tinker) + + # --- As of 2017-9-13, I am unsure if I should add this rule: ---- + # The gromacs file for oplsaa include the following line: + # "define improper_X_NO_ON_NO 180.0 43.93200" in oplsaa.ff (gromacs) + # but there is no corresponding line found in oplsaa.prm (tinker) + # and there is no corresponding line from opls-a.prm (emc (BASF)) + # I'm not sure what the "NO" and "ON" correspond to. If I had to guess, + # the corresponding moltemplate line might be one of these two choices: + # improper_coeff @improper:X_103_102_102 10.5 180.0 ? + # improper_coeff @improper:X_102_103_103 10.5 180.0 ? + # but I'd prefer to leave this out. + } #(end of improper_coeffs) - # Rules for creating dihedral interactions according to atom type: + + # Rules for creating improper interactions according to atom type: # ImproperTypeName AtomType1 AtomType2 AtomType3 AtomType4 # (* = wildcard) write_once("Data Impropers By Type (opls_imp.py)") { - @improper:X-X-3-4 @atom:* @atom:* @atom:*_b*_a*_d*_i3 @atom:*_b*_a*_d*_i4 - @improper:X-X-3-52 @atom:* @atom:* @atom:*_b*_a*_d*_i3 @atom:*_b*_a*_d*_i52 - @improper:X-X-24-X @atom:* @atom:* @atom:*_b*_a*_d*_i24 @atom:* - @improper:X-X-47-X @atom:* @atom:* @atom:*_b*_a*_d*_i47 @atom:* - @improper:X-X-48-X @atom:* @atom:* @atom:*_b*_a*_d*_i48 @atom:* + @improper:X_X_003_004 @atom:* @atom:* @atom:*_b*_a*_d*_i003* @atom:*_b*_a*_d*_i004* + @improper:X_X_003_052 @atom:* @atom:* @atom:*_b*_a*_d*_i003* @atom:*_b*_a*_d*_i052* + @improper:X_X_024_X @atom:* @atom:* @atom:*_b*_a*_d*_i024* @atom:* + @improper:X_X_047_X @atom:* @atom:* @atom:*_b*_a*_d*_i047* @atom:* + @improper:X_X_048_X @atom:* @atom:* @atom:*_b*_a*_d*_i048* @atom:* + @improper:055_055_X_055 @atom:*_b*_a*_d*_i55 @atom:*_b*_a*_d*_i55 @atom:* @atom:*_b*_a*_d*_i55 } #(end of impropers by type) @@ -8961,11 +9010,11 @@ OPLSAA { write_once("In Init") { units real atom_style full - bond_style hybrid harmonic - angle_style hybrid harmonic - dihedral_style hybrid opls - improper_style hybrid harmonic - pair_style hybrid lj/cut/coul/long 10.0 10.0 + bond_style harmonic + angle_style harmonic + dihedral_style opls + improper_style harmonic + pair_style lj/cut/coul/long 10.0 10.0 pair_modify mix geometric special_bonds lj/coul 0.0 0.0 0.5 kspace_style pppm 0.0001 @@ -8985,34 +9034,3 @@ OPLSAA { } # OPLSAA - - - - -############################### NOTES #################################### -# -# This file was generated (on 2017-7-18) using this script: -# -# tinkerparm2lt.py -name OPLSAA -file oplsaa.prm -dihedral-style opls -# -# The oplsaa.prm file was downloaded from the TINKER website -# https://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm -# (You can build a smaller version of this file by editing the oplsaa.prm -# file and deleting the lines beginning with "atom" that you don't need, -# and subsequently running tinkerparm2lt.py on the new file. This can -# help reduce the number of atom types, which can help with visualization, -# and in some cases may also improve performance.) -# -# The following 1-2, 1-3, and 1-4 weighting parameters were ASSUMED: -# special_bonds lj/coul 0.0 0.0 0.5 -# (See http://lammps.sandia.gov/doc/special_bonds.html for details) -# -# WARNING: All Urey-Bradley interactions have been IGNORED including: -# ffid1 ffid2 ffid3 K r0 -# ureybrad 35 34 35 38.25 1.5537 -# -# WARNING: Many of these atoms are UNITED-ATOM (UA) atoms (#1-56). This means -# the hydrogen atoms have been absorbed into the heavy atoms, and the -# force-field modified accordingly. (Hopefully, moltemplate will -# complain if you attempt to bond these atoms to hydrogen atoms.) -########################################################################## diff --git a/tools/moltemplate/moltemplate/force_fields/oplsaa/AUTHOR.txt b/tools/moltemplate/moltemplate/force_fields/oplsaa/AUTHOR.txt deleted file mode 100644 index a3e9f3ee78..0000000000 --- a/tools/moltemplate/moltemplate/force_fields/oplsaa/AUTHOR.txt +++ /dev/null @@ -1,2 +0,0 @@ -OPLSAA force-field conversion tools provided by -Jason Lambert, Sebastian Echeverri, and Andrew Jewett diff --git a/tools/moltemplate/moltemplate/force_fields/oplsaa_original_format/AUTHOR.txt b/tools/moltemplate/moltemplate/force_fields/oplsaa_original_format/AUTHOR.txt new file mode 100644 index 0000000000..5874b5926b --- /dev/null +++ b/tools/moltemplate/moltemplate/force_fields/oplsaa_original_format/AUTHOR.txt @@ -0,0 +1,7 @@ + +OPLSAA force-field conversion tools provided by +Jason Lambert and Andrew Jewett. + +LOPLSAA force-field conversion provided by Sebastian Echeverri. + + diff --git a/tools/moltemplate/moltemplate/force_fields/oplsaa_original_format/README.txt b/tools/moltemplate/moltemplate/force_fields/oplsaa_original_format/README.txt new file mode 100644 index 0000000000..2412c4aa7d --- /dev/null +++ b/tools/moltemplate/moltemplate/force_fields/oplsaa_original_format/README.txt @@ -0,0 +1,10 @@ +The "oplsaa.lt" file contains force field parameters which we found in the +"oplsaa.prm" file which is distributed with TINKER. +Jay Ponder, (the author of TINKER) preferred that we do not distribute +that file with moltemplate. However you can download that file here: + +https://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm + +This directory does contain other files ("loplsaa.prm") containing additional +force field parameters that modify the original OPLSAA force field. + diff --git a/tools/moltemplate/moltemplate/force_fields/oplsaa/loplsaa_ext.prm b/tools/moltemplate/moltemplate/force_fields/oplsaa_original_format/loplsaa_ext.prm similarity index 52% rename from tools/moltemplate/moltemplate/force_fields/oplsaa/loplsaa_ext.prm rename to tools/moltemplate/moltemplate/force_fields/oplsaa_original_format/loplsaa_ext.prm index ff0e3e445c..bf89d9a341 100644 --- a/tools/moltemplate/moltemplate/force_fields/oplsaa/loplsaa_ext.prm +++ b/tools/moltemplate/moltemplate/force_fields/oplsaa_original_format/loplsaa_ext.prm @@ -1,19 +1,28 @@ - ########################################################################### - ## Extra OPLSAA parameters and atom types for long hydrocarbon chains ## - ## SOURCE: Sui, Pluhackova, Böckmann, J.Chem.Theory.Comp (2012), 8, 1459 ## - ## CREDIT: Sebastian Echeverri (file format conversion) ## - ########################################################################### - ## This file was used with "tinkerparm2lt.py" to create "loplsaa.lt" ## - ########################################################################### + ############################################################################ + ## Extra OPLSAA parameters and atom types for long hydrocarbon chains ## + ## SOURCES: Sui, Pluhackova, Böckmann, J.Chem.Theory.Comp (2012), 8(4), 1459 + ## Pluhackova,...,Böckmann, J.Phys.Chem.B (2015), 119(49), 15287 ## + ## CREDIT: Sebastian Echeverri (file format conversion) ## + ############################################################################ + ## This file was used with "tinkerparm2lt.py" to create "loplsaa.lt" ## + ############################################################################ atom 80L 13L CT "Alkane CH3- (LOPLS CT_CH3)" 6 12.011 4 atom 81L 13L CT "Alkane -CH2- (LOPLS CT_CH2)" 6 12.011 4 +atom 81LL 13LL CT "Alkane -CH2- (LOPLS ALT)" 6 12.011 4 atom 85LCH3 46 HC "Alkane H-C CH3 (LOPLS HC_CH3)" 1 1.008 1 atom 85LCH2 46 HC "Alkane H-C CH2 (LOPLS HC_CH2)" 1 1.008 1 atom 87L 47L CM "Alkene RH-C= (LOPLS CM_CH)" 6 12.011 3 atom 89L 46 HC "Alkene H-C= (LOPLS HC_CH)" 1 1.008 1 atom 86L 47L CM "Alkene R2-C= (LOPLS)" 6 12.011 3 atom 88L 47L CM "Alkene H2-C= (LOPLS)" 6 12.011 3 +atom 96L 5L OH "Alcohol -OH (LOPLS)" 8 15.999 2 +atom 97L 7L HO "Alcohol -OH (LOPLS)" 1 1.008 1 +atom 111L 5L OH "Diol -OH (LOPLS)" 8 15.999 2 +atom 112L 7L HO "Diol -OH (LOPLS)" 1 1.008 1 +atom 113L 5L OH "Triol -OH (LOPLS)" 8 15.999 2 +atom 114L 7L HO "Triol -OH (LOPLS)" 1 1.008 1 +atom 118L 46L HC "Diol & Triol H-COH (LOPLS)" 1 1.008 1 atom 169L 47L CM "Chloroalkene Cl-CH= (LOPLS)" 6 12.011 3 atom 266L 47L CM "Uracil & Thymine C5 (LOPLS)" 6 12.011 3 atom 267L 47L CM "Uracil & Thymine C6 (LOPLS)" 6 12.011 3 @@ -23,21 +32,36 @@ atom 324L 47L CM "CytosineH+ C5 (LOPLS)" 6 12.011 3 atom 325L 47L CM "CytosineH+ C6 (LOPLS)" 6 12.011 3 atom 340L 47L CM "Trifluorothymine CF3- (LOPLS)" 6 12.011 4 atom 342L 47L CM "Chloroalkene Cl2-C= (LOPLS)" 6 12.011 3 +atom 406L 3L C_2 "Ester -COOR (LOPLS)" 6 12.011 3 +atom 407L 4L O_2 "Ester C=O (LOPLS)" 8 15.999 1 +atom 408L 20L OS "Ester CO-O-R (LOPLS)" 8 15.999 2 atom 458L 47L CM "Vinyl Ether =CH-OR (LOPLS)" 6 12.011 3 atom 459L 47L CM "Vinyl Ether =CR-OR (LOPLS)" 6 12.011 3 atom 649L 47L CM "Cl..CH3..Cl- Sn2 TS (LOPLS)" 6 12.011 5 +atom 718L 46L HC "Propylene Carbonate CH2 (LOPLS)" 1 1.008 1 +atom 718LL 46L HC "Propylene Carbonate CH2 (LOPLS ALT)" 1 1.008 1 atom 900L 47L CM "Allene/Ketene H2C=C=X (LOPLS)" 6 12.011 3 atom 901L 47L CM "Allene/Ketene HRC=C=X (LOPLS)" 6 12.011 3 atom 902L 47L CM "Allene/Ketene R2C=C=X (LOPLS)" 6 12.011 3 +###################### + vdw 80L 3.5000 0.0660 vdw 81L 3.5000 0.0660 +vdw 81LL 0.3500 0.0660 vdw 85LCH3 2.5000 0.0300 vdw 85LCH2 2.5000 0.026290630975 vdw 87L 3.5500 0.0760 vdw 89L 2.4200 0.0300 vdw 86L 3.5500 0.0760 vdw 88L 3.5500 0.0760 +vdw 96L 0.3120 0.1700 +vdw 97L 0.0000 0.0000 +vdw 111L 0.3070 0.1700 +vdw 112L 0.0000 0.0000 +vdw 113L 0.3070 0.1700 +vdw 114L 0.0000 0.0000 +vdw 118L 0.2500 0.0300 vdw 169L 3.5500 0.0760 vdw 266L 3.5000 0.0800 vdw 267L 3.5000 0.0800 @@ -47,13 +71,21 @@ vdw 324L 3.5000 0.0800 vdw 325L 3.5000 0.0800 vdw 340L 3.5000 0.0800 vdw 342L 3.5500 0.0760 +vdw 406L 0.31875 0.1050 +vdw 407L 0.3108 0.1680 +vdw 408L 0.2550 0.1700 vdw 458L 3.5500 0.0760 vdw 459L 3.5500 0.0760 vdw 649L 3.5500 0.0760 +vdw 718L 0.2420 0.1500 +vdw 718LL 0.2420 0.1500 vdw 900L 3.3000 0.0860 vdw 901L 3.3000 0.0860 vdw 902L 3.3000 0.0860 +###################### + + # New torsion angle parameters # Taken from table 2 of # Sui, Pluhackova, Böckmann, J.Chem.Theory.Comp (2012), 8, 1459 @@ -62,14 +94,42 @@ torsion 0 47L 47L 0 0.0 0 1 12.2502629063 180 2 0.0 torsion 47L 47L 13L 13L -0.8050121893 0 1 0.3218905354 180 2 -0.1032768881 0 3 0 180 4 # offset V0=-0.3574832696 torsion 13L 13L 13L 47L 0.4821902486 0 1 0.1343683078 180 2 0.1777461759 0 3 0 180 4 # offset V0=0.4405726577 +###################### +torsion 46L 13LL 5L 7L 0.00962596 0 1 -0.0145554 180 2 0.381091 0 3 0 180 4 # offset V0=0.00133126 +torsion 46L 13LL 13LL 5L 0.0143774 0 1 0.033021 180 2 0.26687 0 3 0 180 4 # offset V0=-0.0291993 +torsion 13LL 13LL 5L 7L -0.675785 0 1 -0.0160421 180 2 0.373199 0 3 0 180 4 # offset V0=-0.0225884 +torsion 13LL 13LL 13LL 5L 1.31261 0 1 -0.266307 180 2 0.637867 0 3 0 180 4 # offset V0=0.00224187 +torsion 5L 13LL 13LL 5L 2.69106 0 1 -0.849706 180 2 0.725731 0 3 0 180 4 # offset V0=-0.3326 +torsion 13LL 3L 20L 13LL 3.11923 0 1 5.73771 180 2 0.0 0 3 0 180 4 # offset V0=0.493475 +torsion 13LL 20L 3L 4L 0.0 0 1 5.73772 180 2 0.0 0 3 0 180 4 # offset V0=-0.28142 +torsion 46L 13LL 3L 20L -0.00742471 0 1 0.00217734 180 2 0.111803 0 3 0 180 4 # offset V0=-0.012512 +torsion 3L 20L 13LL 13LL -1.7354 0 1 -1.24844 180 2 0.623897 0 3 0 180 4 # offset V0=0.11706 +torsion 46L 13LL 13LL 20L 0.0113337 0 1 0.0236209 180 2 0.429747 0 3 0 180 4 # offset V0=-0.0255306 +torsion 13LL 13LL 3L 20L 0.884988 0 1 -0.626905 180 2 -0.493344 0 3 0 180 4 # offset V0=-0.0195172 +torsion 13LL 13LL 3L 4L -0.276019 0 1 1.23685 180 2 -0.670745 0 3 0 180 4 # offset V0=-0.0322467 +torsion 3L 13LL 13LL 46L -0.0021152 0 1 0.0173542 180 2 -0.295208 0 3 0 180 4 # offset V0=-0.0433963 +torsion 3L 13LL 13LL 13LL -2.30738 0 1 -0.627326 180 2 0.621951 0 3 0 180 4 # offset V0=0.0323566 +torsion 13LL 13LL 13LL 20L 2.25871 0 1 -1.02408 180 2 1.0071 0 3 0 180 4 # offset V0=0.0297084 +torsion 20L 13LL 13LL 20L 4.66787 0 1 -2.62698 180 2 1.3248 0 3 0 180 4 # offset V0=-1.48385 +torsion 5L 13LL 13LL 20L 5.03208 0 1 -2.37742 180 2 1.23809 0 3 0 180 4 # offset V0=0.223141 +###################### + charge 80L -0.222 #"Alkane CH3- (LOPLS)" "CT_CH3" 3.50 0.0660 charge 81L -0.148 #"Alkane -CH2- (LOPLS)" "CT_CH2" 3.50 0.0660 +charge 81LL 0.19 charge 85LCH3 0.074 #"Alkane H-C CH3 (LOPLS)" "HC_CH3" 2.50 0.0300 charge 85LCH2 0.074 #"Alkane H-C CH2 (LOPLS)" "HC_CH2" 2.50 0.0263 charge 87L -0.160 #"Alkene RH-C= (LOPLS)" "CM_CH" 3.55 0.0760 charge 89L 0.160 #"Alkene H-C= (LOPLS)" "HC_CH" 2.42 0.0300 charge 86L 0.0000 charge 88L -0.2300 +charge 96L -0.683 +charge 97L 0.418 +charge 111L -0.7 +charge 112L 0.435 +charge 113L -0.73 +charge 114L 0.465 +charge 118L 0.06 charge 169L 0.0050 charge 266L -0.0700 charge 267L 0.0800 @@ -79,9 +139,15 @@ charge 324L -0.0600 charge 325L 0.1000 charge 340L 0.1800 charge 342L 0.1200 +charge 406L 0.75 +charge 407L -0.55 +charge 408L -0.45 charge 458L -0.0300 charge 459L 0.0850 charge 649L -0.3440 +charge 718L 0.06 +charge 718LL 0.03 charge 900L -0.2500 charge 901L -0.1000 charge 902L 0.0500 + diff --git a/tools/moltemplate/moltemplate/force_fields/sdk/SDK_lipid+chol.lt b/tools/moltemplate/moltemplate/force_fields/sdk.lt similarity index 98% rename from tools/moltemplate/moltemplate/force_fields/sdk/SDK_lipid+chol.lt rename to tools/moltemplate/moltemplate/force_fields/sdk.lt index f610085113..8207614282 100644 --- a/tools/moltemplate/moltemplate/force_fields/sdk/SDK_lipid+chol.lt +++ b/tools/moltemplate/moltemplate/force_fields/sdk.lt @@ -1,11 +1,21 @@ # Autogenerated by EMC 2 LT tool v0.2 on 2017-06-29 # -# ./emcprm2lt.py --pair-style=lj/sdk/coul/long --bond-style=harmonic --angle-style=sdk sdk_lipids.prm sdk_cholesterol.prm --name=SDK_lipid+chol --units +# cd sdk/ +# emcprm2lt.py --pair-style=lj/sdk/coul/long --bond-style=harmonic --angle-style=sdk sdk_lipids.prm sdk_cholesterol.prm --name=sdk --units +# mv -f sdk.lt ../ +# +# This file contains force field parameters for lipids and cholesterol from: +# Shinoda et al. J. Phys. Chem. B, Vol. 114, No. 20, 2010 +# MacDermaid et al. J. Chem. Phys, 143(24), 243144, 2015 +# For details see the "README.txt" file (located in "force_fields/sdk/") # # Adapted from EMC by Pieter J. in 't Veld # Originally written as, FFNAME:SDK STYLE:COARSE VERSION:1.0 on Oct 2014 +# "emcprm2lt.py" was written by David Stelter. + SDK { + write_once("Data Masses") { @atom:CM 42.080400 # CM @atom:CMD2 26.037800 # CMD2 @@ -420,4 +430,6 @@ SDK { pair_style hybrid lj/sdk/coul/long 9.000000 12.000000 special_bonds lj/coul 0.0 0.0 0.0 } # end init + } # SDK + diff --git a/tools/moltemplate/moltemplate/force_fields/sdk/README.txt b/tools/moltemplate/moltemplate/force_fields/sdk/README.txt deleted file mode 100644 index 6ca9e8f98f..0000000000 --- a/tools/moltemplate/moltemplate/force_fields/sdk/README.txt +++ /dev/null @@ -1,63 +0,0 @@ -README! - -v0.2 - -This is only part of the SDK force field and is to be used for lipids only. Only parameters from: - -Shinoda et al. J. Phys. Chem. B, Vol. 114, No. 20, 2010 -http://dx.doi.org/10.1021/jp9107206 - -are used. - -NOTE: We extracted the parameters from that publication from the files -distributed with the "EMC" tool. If you use these files, please also cite: -P. J. in ‘t Veld and G. C. Rutledge, Macromolecules 2003, 36, 7358. - - -This works for any topology built using the following types: - -Name Structure Charge -NC -CH2CH2-N-(CH3)3 +1 -NH -CH2CH2-NH3 +1 -PH -PO4- -1 -PHE -PO4- (PE lipid) -1 -GL -CH2CH-CH2- -EST1 -CH2CO2- -EST2 -H2CO2- -CMD2 -HC=CH- (cis) -CM -CH2CH2CH2- -CT CH3CH2CH2- -CT2 CH3CH2- -W (H2O)3 - -This coarse-grainng allows for design of a wide variety of lipids. - -NEW! in v0.2: - SDK Cholesterol model has been added! Using parameters from: - -MacDermaid et al. J. Chem. Phys, 143(24), 243144, 2015 -http://dx.doi.org/10.1063/1.4937153 - -are used. The following types are defined specifically for cholesterol: - -Name Structure Location -C2T -CH-(CH3)2 Tail -CM2 -CH2-CH2- Tail -CM2R -CH2-CH2- Ring A -CMDB -CH2-C=CH- Ring A/B -CMB -CH2-CH-CH- Ring B/C -CMR -CH-CH2-CH2- Ring B/C -CMR5 -CH2-CH2-CH- Ring D -CTB -CH2-CH-CH3- Tail -CTBA -C-CH3 Ring A/B -CTBB -C-CH3 Ring C/D -OAB -CH-OH Ring A - -See the provided reference for details on the CG cholesterol topology. -A 5-10 timestep is used when using cholesterol. - -Several limiations, due to missing parameters: --use of cholesterol with type "NH" is not possible. --use of cholesterol with type "PHE" is not possible. - ---- diff --git a/tools/moltemplate/moltemplate/force_fields/sdk_original_format/README.txt b/tools/moltemplate/moltemplate/force_fields/sdk_original_format/README.txt new file mode 100644 index 0000000000..eb2eed836d --- /dev/null +++ b/tools/moltemplate/moltemplate/force_fields/sdk_original_format/README.txt @@ -0,0 +1,84 @@ +The files in this directory are used to create the "sdk.lt" file +(containing SDK force field parameters for moltemplate). +These .PRM files are distributed with "EMC" written by Pieter J. in 't Veld. + +Conversion from EMC (.PRM) format to moltemplate (.LT) format was +done using the "emcprm2lt.py" script written by David Stelter. +Here is an example how to use the emcprm2lt.py script: + +emcprm2lt.py --pair-style=lj/sdk/coul/long --bond-style=harmonic --angle-style=sdk sdk_lipids.prm sdk_cholesterol.prm --name=SDK_lipid+chol --units + +This will generate a file named "sdk.lt" which (in this example) +only includes the force field parameters for lipids and cholestrol. +Later you can define new molecules in moltemplate using: + +import "sdk.lt" +NewMolecule inherits SDK { + write("Data Atoms") {...atom coordinates and types go here...} + write("Data Bond List") {...list of bonds goes here...} +} + +This is only part of the SDK force field and is to be used for lipids +and cholesterol only. Lipid parameters were taken from: + +Shinoda et al. J. Phys. Chem. B, Vol. 114, No. 20, 2010 +http://dx.doi.org/10.1021/jp9107206 + +Cholesterol parameters were taken from: +MacDermaid et al. J. Chem. Phys, 143(24), 243144, 2015 +http://dx.doi.org/10.1063/1.4937153 + +You can define lipids with any topology built using the following types: + +Name Structure Charge +NC -CH2CH2-N-(CH3)3 +1 +NH -CH2CH2-NH3 +1 +PH -PO4- -1 +PHE -PO4- (PE lipid) -1 +GL -CH2CH-CH2- +EST1 -CH2CO2- +EST2 -H2CO2- +CMD2 -HC=CH- (cis) +CM -CH2CH2CH2- +CT CH3CH2CH2- +CT2 CH3CH2- +W (H2O)3 + +This coarse-grainng allows for design of a wide variety of lipids. + +The following types are defined specifically for cholesterol: + +Name Structure Location +C2T -CH-(CH3)2 Tail +CM2 -CH2-CH2- Tail +CM2R -CH2-CH2- Ring A +CMDB -CH2-C=CH- Ring A/B +CMB -CH2-CH-CH- Ring B/C +CMR -CH-CH2-CH2- Ring B/C +CMR5 -CH2-CH2-CH- Ring D +CTB -CH2-CH-CH3- Tail +CTBA -C-CH3 Ring A/B +CTBB -C-CH3 Ring C/D +OAB -CH-OH Ring A + +See the provided reference for details on the CG cholesterol topology. +A 5.0-10.0 timestep is used when using cholesterol. + +Several limiations, due to missing parameters: +-use of cholesterol with type "NH" is not possible. +-use of cholesterol with type "PHE" is not possible. + +---- Credits: ---- + +emcprm2lt.py was written by David Stelter +EMC was written by Pieter J. in 't Veld +SDK was created by Shinoda, DeVane, Klein, J.Phys.Chem.B, Vol. 114, No. 20, 2010 + +---- additional citation request ---- + +Since we borrowed force field parameters from files distributed with EMC, +if you use files generated by "emcprm2lt.py", please also cite the EMC paper: +P. J. in ‘t Veld and G. C. Rutledge, Macromolecules 2003, 36, 7358 + + + diff --git a/tools/moltemplate/moltemplate/force_fields/sdk/SDK_lipidONLY.lt b/tools/moltemplate/moltemplate/force_fields/sdk_original_format/SDK_lipidONLY.lt similarity index 100% rename from tools/moltemplate/moltemplate/force_fields/sdk/SDK_lipidONLY.lt rename to tools/moltemplate/moltemplate/force_fields/sdk_original_format/SDK_lipidONLY.lt diff --git a/tools/moltemplate/moltemplate/force_fields/sdk/sdk_cholesterol.prm b/tools/moltemplate/moltemplate/force_fields/sdk_original_format/sdk_cholesterol.prm similarity index 100% rename from tools/moltemplate/moltemplate/force_fields/sdk/sdk_cholesterol.prm rename to tools/moltemplate/moltemplate/force_fields/sdk_original_format/sdk_cholesterol.prm diff --git a/tools/moltemplate/moltemplate/force_fields/sdk/sdk_lipids.prm b/tools/moltemplate/moltemplate/force_fields/sdk_original_format/sdk_lipids.prm similarity index 100% rename from tools/moltemplate/moltemplate/force_fields/sdk/sdk_lipids.prm rename to tools/moltemplate/moltemplate/force_fields/sdk_original_format/sdk_lipids.prm diff --git a/tools/moltemplate/moltemplate/genpoly_lt.py b/tools/moltemplate/moltemplate/genpoly_lt.py index 2c4014e5db..9d8ec84608 100755 --- a/tools/moltemplate/moltemplate/genpoly_lt.py +++ b/tools/moltemplate/moltemplate/genpoly_lt.py @@ -256,7 +256,7 @@ class GPSettings(object): if i + 1 >= len(argv): raise InputError('Error: ' + argv[i] + ' flag should be followed ' + 'by 3 numbers separated by commas (no spaces)\n') - self.direction_orig = map(float, argv[i + 1].split(',')) + self.direction_orig = list(map(float, argv[i + 1].split(','))) del(argv[i:i + 2]) elif argv[i].lower() == '-circular': if i + 1 >= len(argv): @@ -294,7 +294,7 @@ class GPSettings(object): if i + 1 >= len(argv): raise InputError('Error: ' + argv[i] + ' flag should be followed ' + 'by 3 numbers separated by commas (no spaces)\n') - self.box_padding = map(float, argv[i + 1].split(',')) + self.box_padding = list(map(float, argv[i + 1].split(','))) if len(self.box_padding) == 1: self.box_padding = self.box_padding * 3 del(argv[i:i + 2]) @@ -340,7 +340,7 @@ class WrapPeriodic(object): @classmethod def Wrap(obj, i, N): - if i / N != 0: + if i // N != 0: obj.bounds_err = True return i % N @@ -384,7 +384,7 @@ class GenPoly(object): for i in range(0, len(lines)): tokens = lines[i].strip().split() if (len(tokens) == 3): - coords.append(map(float, tokens)) + coords.append(list(map(float, tokens))) self.N = len(coords) if self.N < 2: diff --git a/tools/moltemplate/moltemplate/ltemplify.py b/tools/moltemplate/moltemplate/ltemplify.py index 753d9b3ad0..2fa20b0d05 100755 --- a/tools/moltemplate/moltemplate/ltemplify.py +++ b/tools/moltemplate/moltemplate/ltemplify.py @@ -2,7 +2,6 @@ # -*- coding: utf-8 -*- # Author: Andrew Jewett (jewett.aij at g mail) -# http://www.chem.ucsb.edu/~sheagroup # License: 3-clause BSD License (See LICENSE.TXT) # Copyright (c) 2012, Regents of the University of California # All rights reserved. @@ -31,14 +30,14 @@ import sys try: from .ttree_lex import * from .lttree_styles import * -except (SystemError, ValueError): +except (ImportError, SystemError, ValueError): # not installed as a package from ttree_lex import * from lttree_styles import * g_program_name = __file__.split('/')[-1] # = 'ltemplify.py' -g_version_str = '0.53.1' -g_date_str = '2017-6-08' +g_version_str = '0.54.0' +g_date_str = '2017-10-03' def Intify(s): if s.isdigit(): @@ -1279,7 +1278,7 @@ def main(): atomtype_i_str = tokens[0] if '*' in atomtype_i_str: raise InputError('PROBLEM near or before ' + ErrorLeader(infile, lineno) + '\n' - ' As of 2015-8, moltemplate forbids use of the "\*\" wildcard\n' + ' As of 2017-10, moltemplate forbids use of the "\*\" wildcard\n' ' character in the \"Pair Coeffs\" section.\n') else: i = int(atomtype_i_str) @@ -1308,7 +1307,7 @@ def main(): atomtype_j_str = tokens[1] if (('*' in atomtype_i_str) or ('*' in atomtype_j_str)): raise InputError('PROBLEM near or before ' + ErrorLeader(infile, lineno) + '\n' - ' As of 2015-8, moltemplate forbids use of the "\*\" wildcard\n' + ' As of 2017-10, moltemplate forbids use of the "\*\" wildcard\n' ' character in the \"PairIJ Coeffs\" section.\n') else: i = int(atomtype_i_str) @@ -1828,8 +1827,11 @@ def main(): else: i_a = i_b = Intify(atomtype_i_str) + assert((type(i_a) is int) and (type(i_b) is int)) + i_a_final = None i_b_final = None + for i in range(i_a, i_b + 1): if ((i in needed_atomtypes) or (min_sel_atomtype <= i)): i_a_final = i @@ -2615,7 +2617,7 @@ def main(): # ' --groups-- Attempting to parse \"group\" commands.\n' # ' This may cause '+g_program_name+' to crash.\n' # ' If so, comment out all group commands in your input script(s), and\n' - # ' try again. (And please report the error. -Andrew 2014-10-30)\n') + # ' try again. (And please report the error. -Andrew 2017-10)\n') i_line = 0 groups_needed = set(['all']) @@ -2885,9 +2887,9 @@ def main(): for i in range(atomids_lo, atomids_hi+1): if i in needed_atomids: l_new_set_commands.append((' ' * indent) + - tokens[0:2].join(' ')+' '+ + ' '.join(tokens[0:2])+' '+ str(i) + ' ' + - tokens[3:].join(' ')) + ' '.join(tokens[3:])) elif tokens[1] == 'mol': pattern = tokens[2].split('*') if pattern[0] == '': @@ -2903,9 +2905,9 @@ def main(): molids_hi = min(int(pattern[1]), max_needed_molid) for i in range(molids_lo, molids_hi+1): if i in needed_molids: - l_new_set_commands.append(tokens[0:2].join(' ')+' '+ + l_new_set_commands.append(' '.join(tokens[0:2])+' '+ str(i) + ' ' + - tokens[3:].join(' ')) + ' '.join(tokens[3:])) elif tokens[0] == 'group': group_name = tokens[2] if group_name in groups_needed: @@ -3480,7 +3482,7 @@ def main(): # sys.stderr.write('######################################################\n' # 'WARNING: One or more \"group\" commands appear to refer to relevant atoms.\n' # ' Please check to make sure that the group(s) generated by\n' - # ' '+g_program_name+' contain the correct atoms. (-Andrew 2014-10-30)\n' + # ' '+g_program_name+' contain the correct atoms. (-Andrew 2017-10)\n' # '######################################################\n') assert(non_empty_output) @@ -3575,7 +3577,7 @@ def main(): ' Please look over the resulting LT file and check for errors.\n' ' Convert any remaining atom, bond, angle, dihedral, or improper id\n' ' or type numbers to the corresponding $ or @-style counter variables.\n' - ' Feel free to report any bugs you find. (-Andrew Jewett 2015-8-02)\n') + ' Feel free to report any bugs you find. (-Andrew Jewett 2017-10)\n') except (ValueError, InputError) as err: diff --git a/tools/moltemplate/moltemplate/lttree.py b/tools/moltemplate/moltemplate/lttree.py index 168a60ecc3..9d5ee07ac2 100755 --- a/tools/moltemplate/moltemplate/lttree.py +++ b/tools/moltemplate/moltemplate/lttree.py @@ -1,6 +1,7 @@ #!/usr/bin/env python # Author: Andrew Jewett (jewett.aij at g mail) +# http://www.moltemplate.org # http://www.chem.ucsb.edu/~sheagroup # License: 3-clause BSD License (See LICENSE.TXT) # Copyright (c) 2011, Regents of the University of California @@ -28,8 +29,8 @@ Additional LAMMPS-specific features may be added in the future. """ g_program_name = __file__.split('/')[-1] # ='lttree.py' -g_date_str = '2017-4-11' -g_version_str = '0.76.0' +g_date_str = '2018-3-15' +g_version_str = '0.77.0' import sys @@ -45,10 +46,22 @@ try: from .ttree_lex import InputError, TextBlock, DeleteLinesWithBadVars, \ TemplateLexer from .lttree_styles import AtomStyle2ColNames, ColNames2AidAtypeMolid, \ - ColNames2Coords, ColNames2Vects, data_atoms, data_masses + ColNames2Coords, ColNames2Vects, \ + data_atoms, data_prefix, data_masses, \ + data_velocities, data_ellipsoids, data_triangles, data_lines, \ + data_pair_coeffs, data_bond_coeffs, data_angle_coeffs, \ + data_dihedral_coeffs, data_improper_coeffs, data_bondbond_coeffs, \ + data_bondangle_coeffs, data_middlebondtorsion_coeffs, \ + data_endbondtorsion_coeffs, data_angletorsion_coeffs, \ + data_angleangletorsion_coeffs, data_bondbond13_coeffs, \ + data_angleangle_coeffs, data_bonds_by_type, data_angles_by_type, \ + data_dihedrals_by_type, data_impropers_by_type, \ + data_bonds, data_bond_list, data_angles, data_dihedrals, data_impropers, \ + data_boundary, data_pbc, data_prefix_no_space, in_init, in_settings, \ + in_prefix from .ttree_matrix_stack import AffineTransform, MultiAffineStack, \ LinTransform -except (SystemError, ValueError): +except (ImportError, SystemError, ValueError): # not installed as a package from ttree import * from ttree_lex import * @@ -332,6 +345,60 @@ def TransformAtomText(text, matrix, settings): return '\n'.join(lines) + +def TransformEllipsoidText(text, matrix, settings): + """ Apply the transformation matrix to the quaternions represented + by the last four numbers on each line. + The \"matrix\" stores the aggregate sum of combined transformations + to be applied and the rotational part of this matrix + must be converted to a quaternion. + + """ + + #sys.stderr.write('matrix_stack.M = \n'+ MatToStr(matrix) + '\n') + + lines = text.split('\n') + + for i in range(0, len(lines)): + line_orig = lines[i] + ic = line_orig.find('#') + if ic != -1: + line = line_orig[:ic] + comment = ' ' + line_orig[ic:].rstrip('\n') + else: + line = line_orig.rstrip('\n') + comment = '' + + columns = line.split() + + if len(columns) != 0: + if len(columns) != 8: + raise InputError('Error (lttree.py): Expected 7 numbers' + + ' instead of ' + + str(len(columns)) + + '\nline:\n' + + line + + ' in each line of the ellipsoids\" section.\n"') + q_orig = [float(columns[-4]), + float(columns[-3]), + float(columns[-2]), + float(columns[-1])] + + qRot = [0.0, 0.0, 0.0, 0.0] + Matrix2Quaternion(matrix, qRot) + + q_new = [0.0, 0.0, 0.0, 0.0] + MultQuat(q_new, qRot, q_orig) + + columns[-4] = str(q_new[0]) + columns[-3] = str(q_new[1]) + columns[-2] = str(q_new[2]) + columns[-1] = str(q_new[3]) + lines[i] = ' '.join(columns) + comment + return '\n'.join(lines) + + + def CalcCM(text_Atoms, text_Masses=None, settings=None): @@ -487,8 +554,8 @@ def _ExecCommands(command_list, transform_block += '.' + transform transform = transform.split('(')[0] if ((transform == 'movecm') or - (transform == 'rotcm') or - (transform == 'scalecm')): + (transform == 'rotcm') or + (transform == 'scalecm')): break transform_blocks.append(transform_block) @@ -553,6 +620,8 @@ def _ExecCommands(command_list, # before passing them on to the caller. if command.filename == data_atoms: text = TransformAtomText(text, matrix_stack.M, settings) + if command.filename == data_ellipsoids: + text = TransformEllipsoidText(text, matrix_stack.M, settings) files_content[command.filename].append(text) @@ -599,6 +668,9 @@ def _ExecCommands(command_list, files_content[data_atoms] = \ TransformAtomText(files_content[data_atoms], matrix_stack.M, settings) + files_content[data_ellipsoids] = \ + TransformEllipsoidText(files_content[data_ellipsoids], + matrix_stack.M, settings) for ppcommand in postprocessing_commands: matrix_stack.Pop(which_stack=command.context_node) diff --git a/tools/moltemplate/moltemplate/lttree_check.py b/tools/moltemplate/moltemplate/lttree_check.py index 10daa89be2..5fb5b6f6ce 100755 --- a/tools/moltemplate/moltemplate/lttree_check.py +++ b/tools/moltemplate/moltemplate/lttree_check.py @@ -1,6 +1,7 @@ #!/usr/bin/env python # Author: Andrew Jewett (jewett.aij at g mail) +# http://www.moltemplate.org # http://www.chem.ucsb.edu/~sheagroup # License: 3-clause BSD License (See LICENSE.TXT) # Copyright (c) 2011, Regents of the University of California @@ -45,7 +46,7 @@ the files generated by lttree.py or moltemplate.sh. import sys try: - from .ttree_lex import RemoveOuterQuotes, HasWildCard, InputError, \ + from .ttree_lex import RemoveOuterQuotes, HasWildcard, InputError, \ ErrorLeader, TextBlock, VarRef, TemplateLexer, \ ExtractCatName, TableFromTemplate from .ttree import BasicUISettings, BasicUIParseArgs, EraseTemplateFiles, \ @@ -68,7 +69,7 @@ try: from .lttree import LttreeSettings, LttreeParseArgs from .ttree_matrix_stack import AffineTransform, MultiAffineStack, \ LinTransform -except (SystemError, ValueError): +except (ImportError, SystemError, ValueError): # not installed as a package from ttree_lex import * from ttree import * @@ -80,7 +81,7 @@ except (SystemError, ValueError): try: from .ttree import StaticObj, WriteFileCommand, DescrToCatLeafPtkns, \ AssignStaticVarPtrs, FindReplacementVarPairs, ReplaceVars -except (SystemError, ValueError): +except (ImportError, SystemError, ValueError): # not installed as a package from ttree import * from lttree import * @@ -93,8 +94,8 @@ if sys.version < '2.6': g_program_name = __file__.split('/')[-1] # = 'lttree_check.py' -g_version_str = '0.78.0' -g_date_str = '2017-4-11' +g_version_str = '0.80.1' +g_date_str = '2017-10-01' # g_no_check_msg = \ @@ -904,6 +905,7 @@ def CheckSyntaxCheap(lex): def CheckSyntaxStatic(context_node, root_node, atom_column_names, + allow_wildcards, data_pair_coeffs_defined, data_bond_coeffs_defined, data_angle_coeffs_defined, @@ -936,6 +938,7 @@ def CheckSyntaxStatic(context_node, elif (filename.find(in_prefix) == 0): # if filename begins with "In " CheckInFileSyntax(command.tmpl_list, root_node, + allow_wildcards, in_pair_coeffs_defined, in_bond_coeffs_defined, in_angle_coeffs_defined, @@ -1337,15 +1340,18 @@ def CheckSyntaxStatic(context_node, elif (isinstance(entry, VarRef) and ('*' in entry.descr_str)): compound_wildcard = True - if compound_wildcard: + if compound_wildcard and (not allow_wildcards): raise InputError('--- Paranoid checking: ---\n' ' Possible error near ' + ErrorLeader(entry.srcloc.infile, entry.srcloc.lineno) + '\n' 'The wildcard symbol, \"*\", is not recommended within \"' + filename + '\".\n' 'It is safer to specify the parameters for each type explicitly.\n' - 'You CAN use \"*\" wildcards, but you must disable syntax checking. To get\n' - 'past this error message, run moltemplate.sh using the \"-nocheck\" option.\n') + 'To get past this error message, run moltemplate.sh with the \"-allow-wildcards\"\n' + 'argument. If not all of the @atom,@bond,@angle,@dihedral,@improper types are\n' + 'included in the a*b range of values, then MAKE SURE that these types are\n' + 'assigned to connsecutively increasing integer values by first defining them in\n' + 'that order, or if that fails, by using the \"-a\" to assign the values manually\n') if filename == 'Data Bond Coeffs': # Commenting the next line out. We did this already: @@ -1641,6 +1647,7 @@ def CheckSyntaxStatic(context_node, CheckSyntaxStatic(child, root_node, atom_column_names, + allow_wildcards, data_pair_coeffs_defined, data_bond_coeffs_defined, data_angle_coeffs_defined, @@ -1656,6 +1663,7 @@ def CheckSyntaxStatic(context_node, def CheckInFileSyntax(tmpl_list, root_node, + allow_wildcards, pair_coeffs_defined, bond_coeffs_defined, angle_coeffs_defined, @@ -1700,7 +1708,7 @@ def CheckInFileSyntax(tmpl_list, elif (isinstance(entry, VarRef) and ('*' in entry.descr_str)): compound_wildcard = True - if compound_wildcard: + if compound_wildcard and (not allow_wildcards): raise InputError('---- Paranoid checking: ---\n' ' Possible error near ' + ErrorLeader(entry.srcloc.infile, @@ -1708,8 +1716,11 @@ def CheckInFileSyntax(tmpl_list, 'The wildcard symbol, \"*\", is not recommended within a \"' + table[i][0].text + '\".\n' 'command. It is safer to specify the parameters for each bond type explicitly.\n' - 'You CAN use \"*\" wildcards, but you must disable syntax checking. To get\n' - 'past this error message, run moltemplate.sh using the \"-nocheck\" option.\n') + 'To get past this error message, run moltemplate.sh with the \"-allow-wildcards\"\n' + 'argument. If not all of the @bond,@angle,@dihedral,@improper types are included\n' + 'in the range, then MAKE SURE these @bond,@angle,@dihedral,@improper types are\n' + 'assigned to connsecutively increasing integer values by first defining them in\n' + 'that order, or if that fails, by using the \"-a\" to assign the values manually\n') if ((isinstance(table[i][0], TextBlock)) and ((table[i][0].text.lower() == 'bondcoeff') or @@ -1857,9 +1868,9 @@ def CheckInFileSyntax(tmpl_list, if len(table[i]) > 2: # if not, deal with error later if ((isinstance(table[i][1], TextBlock) and - (table[i][1].text == '*')) and - (isinstance(table[i][1], TextBlock) and - (table[i][1].text == '*'))): + (table[i][1].text == '*')) and #'* *' <--BUG? + (isinstance(table[i][1], TextBlock) and # <--BUG? + (table[i][1].text == '*'))): # <--BUG? pair_coeffs_defined.add(('*', '*')) else: compound_wildcard = False @@ -1889,21 +1900,24 @@ def CheckInFileSyntax(tmpl_list, ('*' in entry.descr_str)): compound_wildcard = True - if compound_wildcard: + if compound_wildcard and (not allow_wildcards): raise InputError('---- Paranoid checking: ---\n' ' Possible error near ' + ErrorLeader(entry.srcloc.infile, entry.srcloc.lineno) + '\n' 'The wildcard symbol, \"*\", is not recommended within a \"pair_coeff\" command.\n' 'It is safer to specify the parameters for each bond type explicitly.\n' - 'You CAN use \"*\" wildcards, but you must disable syntax checking. To get\n' - 'past this error message, run moltemplate.sh using the \"-nocheck\" option.\n') + 'To get past this error message, run moltemplate.sh with the \"-allow-wildcards\"\n' + 'argument. If not all of the @atom types are included in the range, then\n' + 'MAKE SURE the relevant @atom types in the * range are assigned to\n' + 'connsecutively increasing integer values by first defining them in that\n' + 'order, or if that fails, by using the \"-a\" to assign the values manually.\n') if ((len(table[i]) > 2) and - (isinstance(table[i][1], TextBlock) and - (table[i][1].text == '*')) and - (isinstance(table[i][2], TextBlock) and - (table[i][2].text == '*'))): + ((isinstance(table[i][1], TextBlock) and + (table[i][1].text == '*')) or + (isinstance(table[i][2], TextBlock) and + (table[i][2].text == '*')))): pass # we dealt with this case earlier elif (not ((len(table[i]) > 2) and @@ -1941,7 +1955,21 @@ def LttreeCheckParseArgs(argv, settings, main=False, show_warnings=True): if len(argv) == 1: raise InputError('Error: This program requires at least one argument\n' ' the name of a file containing ttree template commands\n') - elif len(argv) == 2: + settings.allow_wildcards = True + i = 1 + while i < len(argv): + if argv[i].lower() in ('-allow-wildcards', '-allowwildcards'): + settings.allow_wildcards = True + del argv[i:i+1] + elif argv[i].lower() in ('-forbid-wildcards', '-forbidwildcards'): + settings.allow_wildcards = False + del argv[i:i+1] + else: + i += 1 + #(perhaps later I'll add some additional argumets) + + # The only argument left should be the system.lt file we want to read: + if len(argv) == 2: try: # Parse text from the file named argv[1] settings.lex.infile = argv[1] @@ -1951,8 +1979,6 @@ def LttreeCheckParseArgs(argv, settings, main=False, show_warnings=True): ' \"' + argv[1] + '\"\n' ' for reading.\n') sys.exit(1) - del(argv[1:2]) - else: # if there are more than 2 remaining arguments, problem_args = ['\"' + arg + '\"' for arg in argv[1:]] @@ -2045,6 +2071,7 @@ def main(): CheckSyntaxStatic(static_tree_root, static_tree_root, settings.column_names, + settings.allow_wildcards, data_pair_coeffs_defined, data_bond_coeffs_defined, data_angle_coeffs_defined, @@ -2060,6 +2087,7 @@ def main(): CheckSyntaxStatic(static_tree_root, static_tree_root, settings.column_names, + settings.allow_wildcards, data_pair_coeffs_defined, data_bond_coeffs_defined, data_angle_coeffs_defined, @@ -2089,12 +2117,20 @@ def main(): else: bond_coeffs_defined = in_bond_coeffs_defined + bond_types_have_wildcards = False bond_bindings = static_tree_root.categories['bond'].bindings for nd, bond_binding in bond_bindings.items(): if not nd.IsDeleted(): + has_wildcard = HasWildcard(bond_binding.full_name) + if has_wildcard: + bond_types_have_wildcards = True + for nd, bond_binding in bond_bindings.items(): + if not nd.IsDeleted(): + #has_wildcard = HasWildcard(bond_binding.full_name) if ((not (bond_binding in bond_coeffs_defined)) and - (not HasWildCard(bond_binding.full_name)) and - (not ('*' in bond_coeffs_defined))): + #(not has_wildcard) and + (not bond_types_have_wildcards) and + (not ('*' in bond_coeffs_defined))): raise InputError('---------------------------------------------------------------------\n' + ' Syntax error: Missing bond coeff.\n\n' + ' No coeffs for the \"' + bond_binding.full_name + '\" bond type have been\n' + @@ -2108,7 +2144,7 @@ def main(): if 'angle' in static_tree_root.categories: if ((len(data_angle_coeffs_defined) > 0) and - (len(in_angle_coeffs_defined) > 0)): + (len(in_angle_coeffs_defined) > 0)): raise InputError('---------------------------------------------------------------------\n' + ' Syntax error: You can EITHER use \"angle_coeff\" commands\n' + ' OR you can have a \"Data Angle Coeffs\" section.\n' + @@ -2122,12 +2158,20 @@ def main(): else: angle_coeffs_defined = in_angle_coeffs_defined + angle_types_have_wildcards = False angle_bindings = static_tree_root.categories['angle'].bindings for nd, angle_binding in angle_bindings.items(): if not nd.IsDeleted(): + has_wildcard = HasWildcard(angle_binding.full_name) + if has_wildcard: + angle_types_have_wildcards = True + for nd, angle_binding in angle_bindings.items(): + if not nd.IsDeleted(): + #has_wildcard = HasWildcard(angle_binding.full_name) if ((not (angle_binding in angle_coeffs_defined)) and - #(not HasWildCard(angle_binding.full_name)) and - (not ('*' in angle_coeffs_defined))): + #(not has_wildcard)) and + (not angle_types_have_wildcards) and + (not ('*' in angle_coeffs_defined))): raise InputError('---------------------------------------------------------------------\n' + ' Syntax error: Missing angle coeff.\n\n' + ' No coeffs for the \"' + angle_binding.full_name + '\" angle type have been\n' + @@ -2142,7 +2186,7 @@ def main(): #sys.stderr.write('dihedral_bindings = '+str(dihedral_bindings)+'\n') if ((len(data_dihedral_coeffs_defined) > 0) and - (len(in_dihedral_coeffs_defined) > 0)): + (len(in_dihedral_coeffs_defined) > 0)): raise InputError('---------------------------------------------------------------------\n' + ' Syntax error: You can EITHER use \"dihedral_coeff\" commands\n' + ' OR you can have a \"Data Dihedral Coeffs\" section.\n' + @@ -2156,13 +2200,21 @@ def main(): else: dihedral_coeffs_defined = in_dihedral_coeffs_defined + dihedral_types_have_wildcards = False dihedral_bindings = static_tree_root.categories[ 'dihedral'].bindings for nd, dihedral_binding in dihedral_bindings.items(): if not nd.IsDeleted(): + has_wildcard = HasWildcard(dihedral_binding.full_name) + if has_wildcard: + dihedral_types_have_wildcards = True + for nd, dihedral_binding in dihedral_bindings.items(): + if not nd.IsDeleted(): + #has_wildcard = HasWildcard(dihedral_binding.full_name) if ((not (dihedral_binding in dihedral_coeffs_defined)) and - #(not HasWildCard(dihedral_binding.full_name)) and - (not ('*' in dihedral_coeffs_defined))): + #(not has_wildcard) and + (not dihedral_types_have_wildcards) and + (not ('*' in dihedral_coeffs_defined))): raise InputError('---------------------------------------------------------------------\n' + ' Syntax error: Missing dihedral coeff.\n\n' + ' No coeffs for the \"' + dihedral_binding.full_name + '\" dihedral type have been\n' + @@ -2190,13 +2242,21 @@ def main(): else: improper_coeffs_defined = in_improper_coeffs_defined + improper_types_have_wildcards = False improper_bindings = static_tree_root.categories[ 'improper'].bindings for nd, improper_binding in improper_bindings.items(): if not nd.IsDeleted(): + has_wildcard = HasWildcard(improper_binding.full_name) + if has_wildcard: + improper_types_have_wildcards = True + for nd, improper_binding in improper_bindings.items(): + if not nd.IsDeleted(): + #has_wildcard = HasWildcard(improper_binding.full_name) if ((not (improper_binding in improper_coeffs_defined)) and - #(not HasWildCard(improper_binding.full_name)) and - (not ('*' in improper_coeffs_defined))): + #(not has_wildcard) and + (not improper_types_have_wildcards) and + (not ('*' in improper_coeffs_defined))): raise InputError('---------------------------------------------------------------------\n' + ' Syntax error: Missing improper coeff.\n\n' + ' No coeffs for the \"' + improper_binding.full_name + '\" improper type have been\n' + @@ -2210,7 +2270,7 @@ def main(): if 'atom' in static_tree_root.categories: if ((len(data_pair_coeffs_defined) > 0) and - (len(in_pair_coeffs_defined) > 0)): + (len(in_pair_coeffs_defined) > 0)): raise InputError('---------------------------------------------------------------------\n' + ' Syntax error: You can EITHER use \"pair_coeff\" commands\n' + ' OR you can have a \"Data Pair Coeffs\" section.\n' + @@ -2225,13 +2285,21 @@ def main(): else: pair_coeffs_defined = in_pair_coeffs_defined + atom_types_have_wildcards = False atom_bindings = static_tree_root.categories['atom'].bindings for nd, atom_binding in atom_bindings.items(): if not nd.IsDeleted(): + has_wildcard = HasWildcard(atom_binding.full_name) + if has_wildcard: + atom_types_have_wildcards = True + for nd, atom_binding in atom_bindings.items(): + if not nd.IsDeleted(): + #has_wildcard = HasWildcard(atom_binding.full_name) if ((not ((atom_binding, atom_binding) in pair_coeffs_defined)) and - (not HasWildCard(atom_binding.full_name)) and + #(not has_wildcard) and + (not atom_types_have_wildcards) and (not (('*', '*') in pair_coeffs_defined)) and (not (atom_binding.nptr.cat_name, atom_binding.nptr.cat_node, diff --git a/tools/moltemplate/moltemplate/lttree_postprocess.py b/tools/moltemplate/moltemplate/lttree_postprocess.py index 1bb985361f..41eb8ed858 100755 --- a/tools/moltemplate/moltemplate/lttree_postprocess.py +++ b/tools/moltemplate/moltemplate/lttree_postprocess.py @@ -16,14 +16,14 @@ import sys try: from .lttree_styles import * from .ttree_lex import ExtractCatName -except (SystemError, ValueError): +except (ImportError, SystemError, ValueError): # not installed as a package from lttree_styles import * from ttree_lex import ExtractCatName g_program_name = __file__.split('/')[-1] # = 'lttree_postprocess.py' -g_version_str = '0.5.0' -g_date_str = '2016-12-21' +g_version_str = '0.5.1' +g_date_str = '2017-8-23' def main(): atom_style = 'full' diff --git a/tools/moltemplate/moltemplate/lttree_styles.py b/tools/moltemplate/moltemplate/lttree_styles.py index adeb1de749..5691aaddf6 100644 --- a/tools/moltemplate/moltemplate/lttree_styles.py +++ b/tools/moltemplate/moltemplate/lttree_styles.py @@ -2,6 +2,7 @@ # -*- coding: utf-8 -*- # Author: Andrew Jewett (jewett.aij at g mail) +# http://www.moltemplate.org # http://www.chem.ucsb.edu/~sheagroup # License: 3-clause BSD License (See LICENSE.TXT) # Copyright (c) 2012, Regents of the University of California @@ -9,7 +10,7 @@ try: from .ttree_lex import InputError -except (SystemError, ValueError): +except (ImportError, SystemError, ValueError): # not installed as a package from ttree_lex import InputError diff --git a/tools/moltemplate/moltemplate/nbody_Angles.py b/tools/moltemplate/moltemplate/nbody_Angles.py index e6b2fbff1f..9cc5456b01 100644 --- a/tools/moltemplate/moltemplate/nbody_Angles.py +++ b/tools/moltemplate/moltemplate/nbody_Angles.py @@ -1,6 +1,6 @@ try: from .nbody_graph_search import Ugraph -except (SystemError, ValueError): +except (ImportError, SystemError, ValueError): # not installed as a package from nbody_graph_search import Ugraph diff --git a/tools/moltemplate/moltemplate/nbody_Bonds.py b/tools/moltemplate/moltemplate/nbody_Bonds.py index c11c3e60e2..64c82700b7 100644 --- a/tools/moltemplate/moltemplate/nbody_Bonds.py +++ b/tools/moltemplate/moltemplate/nbody_Bonds.py @@ -1,6 +1,6 @@ try: from .nbody_graph_search import Ugraph -except (SystemError, ValueError): +except (ImportError, SystemError, ValueError): # not installed as a package from nbody_graph_search import Ugraph diff --git a/tools/moltemplate/moltemplate/nbody_Dihedrals.py b/tools/moltemplate/moltemplate/nbody_Dihedrals.py index 9197db9143..86fbdd3414 100644 --- a/tools/moltemplate/moltemplate/nbody_Dihedrals.py +++ b/tools/moltemplate/moltemplate/nbody_Dihedrals.py @@ -1,6 +1,6 @@ try: from .nbody_graph_search import Ugraph -except (SystemError, ValueError): +except (ImportError, SystemError, ValueError): # not installed as a package from nbody_graph_search import Ugraph diff --git a/tools/moltemplate/moltemplate/nbody_Impropers.py b/tools/moltemplate/moltemplate/nbody_Impropers.py index 6b48d9aa19..bbb88bd37f 100644 --- a/tools/moltemplate/moltemplate/nbody_Impropers.py +++ b/tools/moltemplate/moltemplate/nbody_Impropers.py @@ -1,6 +1,6 @@ try: from .nbody_graph_search import Ugraph -except (SystemError, ValueError): +except (ImportError, SystemError, ValueError): # not installed as a package from nbody_graph_search import Ugraph diff --git a/tools/moltemplate/moltemplate/nbody_alt_symmetry/cenIflipJK.py b/tools/moltemplate/moltemplate/nbody_alt_symmetry/cenIflipJK.py new file mode 100644 index 0000000000..d4b7d22b2e --- /dev/null +++ b/tools/moltemplate/moltemplate/nbody_alt_symmetry/cenIflipJK.py @@ -0,0 +1,61 @@ +try: + from ..nbody_graph_search import Ugraph +except: + # not installed as a module + from nbody_graph_search import Ugraph + +# To find 4-body "improper" interactions, +# (by default, most of the time), we would use this subgraph: +# 3 +# * 1st bond connects atoms 0 and 1 +# | => 2nd bond connects atoms 0 and 2 +# _.*._ 3rd bond connects atoms 0 and 3 +# *' 0 `* +# 1 2 +# + +bond_pattern = Ugraph([(0,1), (0,2), (0,3)]) +# (Ugraph atom indices begin at 0, not 1) + + +def canonical_order(match): + """ + When searching for atoms with matching bond patterns GraphMatcher + often returns redundant results. We must define a "canonical_order" + function which sorts the atoms and bonds in a way which is consistent + with the type of N-body interaction being considered. + The atoms (and bonds) in a candidate match are rearranged by the + canonical_order(). Then the re-ordered list of atom and bond ids is + tested against the list of atom/bond ids in the matches-found-so-far, + before it is added to the list of interactions found so far. + (For example, it does not make sense to define a separate 4-body improper- + angle interaction between atoms 0, 1, 2, 3 AND 0, 2, 1, 3. + The "improper angle" is often defined as the angle between planes formed + by atoms 0,1,2 & 1,2,3. Alternately, it may instead be defined as the + angle between the 0,1,2 plane and atom 3. Either way, this angle does + not change when swapping the middle pair of atoms (1 and 2) + (except for a change of sign, which does not matter since the energy functions + used are typically sign invariant. Furthermore, neither of OUTER pair of atoms + are the central atom. There are 3!=6 ways of ordering the remaining 3 atoms.) + Consequently it does not make sense to define a separate 4-body improper- + interaction between atoms 0,1,2,3 AS WELL AS between 0,2,1,3. + So we sort the atoms and bonds so that the first atom has a always has + a lower atomID than the last atom. (Later we will check to see if we + have already defined an interaction between these 4 atoms. If not then + we create a new one.) + + """ + atom0 = match[0][0] + atom1 = match[0][1] + atom2 = match[0][2] + atom3 = match[0][3] + # match[1][0:2] contains the ID numbers for the 3 bonds + bond0 = match[1][0] + bond1 = match[1][1] + bond2 = match[1][2] + if atom1 <= atom2: + #return ((atom0,atom1,atom2,atom3), (bond0, bond1, bond2)) + # But this is the same thing as: + return match + else: + return ((atom0,atom2,atom1,atom3), (bond1, bond0, bond2)) diff --git a/tools/moltemplate/moltemplate/nbody_alt_symmetry/cenJflipIL.py b/tools/moltemplate/moltemplate/nbody_alt_symmetry/cenJflipIL.py new file mode 100644 index 0000000000..b00a2afda8 --- /dev/null +++ b/tools/moltemplate/moltemplate/nbody_alt_symmetry/cenJflipIL.py @@ -0,0 +1,68 @@ +try: + from ..nbody_graph_search import Ugraph +except: + # not installed as a module + from nbody_graph_search import Ugraph + +# To find 4-body "improper" interactions, +# (by default, most of the time), we would use this subgraph: +# 0 +# * 1st bond connects atoms 1 and 0 +# | => 2nd bond connects atoms 1 and 2 +# _.*._ 3rd bond connects atoms 1 and 3 +# *' 1 `* +# 2 3 +# +# In OPLS, the central atom is the second atom ("1"). +# This differs from other force-fields. +# We take this detail into account in the line below: + +bond_pattern = Ugraph([(1,0), (1,2), (1,3)]) + +# As with other force-fields, the improper-angle is the angle between the planes +# defined by the first three atoms (0,1,2) and last three atoms (1,2,3). +# (This is implemented in LAMMPS using an improper_style which requires +# that the atoms in the interaction will be listed in this order: 0,1,2,3.) + +def canonical_order(match): + """ + Before defining a new interaction, we must check to see if an + interaction between these same 4 atoms has already been created + (perhaps listed in a different, but equivalent order). + If we don't check for this this, we will create many unnecessary redundant + interactions (which can slow down he simulation). + To avoid this, I define a "canonical_order" function which sorts the atoms + and bonds in a way which is consistent with the symmetry of the interaction + being generated... Later the re-ordered list of atom and bond ids will be + tested against the list of atom/bond ids in the matches-found-so-far, + before it is added to the list of interactions found so far. Note that + the energy of an improper interactions is a function of the improper angle. + The "improper angle" is often defined as the angle between planes formed + by atoms 0,1,2 & 1,2,3. (Alternately, it is sometimes defined as the + angle between the 0,1,2 plane and atom 3.) + This angle does not change when swapping the OUTER pair of atoms (0 and 3) + (except for a change of sign, which does not matter since the energy functions + used are typically sign invariant. Furthermore, neither of OUTER pair of atoms + are the central atom. There are 3!=6 ways of ordering the remaining 3 atoms.) + Consequently it does not make sense to define a separate 4-body improper- + interaction between atoms 0,1,2,3 AS WELL AS between 3,1,2,0. + So we sort the atoms and bonds so that the first atom has a always has + a lower atomID than the last atom. (Later we will check to see if we + have already defined an interaction between these 4 atoms. If not then + we create a new one.) + + """ + atom0 = match[0][0] + atom1 = match[0][1] + atom2 = match[0][2] + atom3 = match[0][3] + # match[1][0:2] contains the ID numbers for the 3 bonds + bond0 = match[1][0] + bond1 = match[1][1] + bond2 = match[1][2] + if atom0 <= atom3: + #return ((atom0,atom1,atom2,atom3), (bond0, bond1, bond2)) + # But this is the same thing as: + return match + else: + return ((atom3,atom1,atom2,atom0), (bond2,bond1,bond0)) diff --git a/tools/moltemplate/moltemplate/nbody_by_type.py b/tools/moltemplate/moltemplate/nbody_by_type.py index 65b51064c8..1d73b23fb9 100755 --- a/tools/moltemplate/moltemplate/nbody_by_type.py +++ b/tools/moltemplate/moltemplate/nbody_by_type.py @@ -169,7 +169,7 @@ try: from .nbody_by_type_lib import GenInteractions_str from .ttree_lex import * from .lttree_styles import AtomStyle2ColNames, ColNames2AidAtypeMolid -except (SystemError, ValueError): +except (ImportError, SystemError, ValueError): from extract_lammps_data import * from nbody_by_type_lib import GenInteractions_str from ttree_lex import * @@ -373,7 +373,7 @@ def GenInteractions_files(lines_data, try: g = importlib.import_module(name, pkg) break - except (SystemError, ImportError): + except (ImportError, SystemError, ValueError): pass if g is None: @@ -513,7 +513,7 @@ def main(): ' (See nbody_Dihedrals.py for example.)\n') bond_pattern_module_name = argv[i + 1] # If the file name ends in ".py", then strip off this suffix. - # For some reason, the next line does not work: + # The next line does not work. Too lazy to care why. # bond_pattern_module_name=bond_pattern_module_name.rstrip('.py') # Do this instead pc = bond_pattern_module_name.rfind('.py') @@ -578,8 +578,8 @@ def main(): ' (The actual problem may be earlier in the argument list.)\n') if ((section_name == '') or - (section_name_bytype == '') or - (bond_pattern_module_name == '')): + (section_name_bytype == '') or + (bond_pattern_module_name == '')): raise InputError('Syntax Error(' + g_program_name + '):\n\n' ' You have not defined the following arguments:\n' ' -section name\n' diff --git a/tools/moltemplate/moltemplate/nbody_by_type_lib.py b/tools/moltemplate/moltemplate/nbody_by_type_lib.py index b8011a80d5..da5a3b0452 100644 --- a/tools/moltemplate/moltemplate/nbody_by_type_lib.py +++ b/tools/moltemplate/moltemplate/nbody_by_type_lib.py @@ -30,7 +30,7 @@ from collections import defaultdict try: from .nbody_graph_search import Ugraph, GraphMatcher from .ttree_lex import MatchesPattern, MatchesAll, InputError -except (SystemError, ValueError): +except (ImportError, SystemError, ValueError): # not installed as a package from nbody_graph_search import Ugraph, GraphMatcher from ttree_lex import MatchesPattern, MatchesAll, InputError diff --git a/tools/moltemplate/moltemplate/nbody_fix_ttree_assignments.py b/tools/moltemplate/moltemplate/nbody_fix_ttree_assignments.py index a975eb1b79..d92cc87904 100755 --- a/tools/moltemplate/moltemplate/nbody_fix_ttree_assignments.py +++ b/tools/moltemplate/moltemplate/nbody_fix_ttree_assignments.py @@ -46,7 +46,7 @@ import sys try: from .ttree_lex import SplitQuotedString, InputError -except (SystemError, ValueError): +except (ImportError, SystemError, ValueError): # not installed as a package from ttree_lex import * diff --git a/tools/moltemplate/moltemplate/nbody_reorder_atoms.py b/tools/moltemplate/moltemplate/nbody_reorder_atoms.py index 53a51a38c4..85b8b4e510 100755 --- a/tools/moltemplate/moltemplate/nbody_reorder_atoms.py +++ b/tools/moltemplate/moltemplate/nbody_reorder_atoms.py @@ -63,7 +63,7 @@ def main(): # defines g.bond_pattern, g.canonical_order g = importlib.import_module(name, pkg) break - except (SystemError, ImportError): + except (ImportError, SystemError, ValueError): pass if g is None: diff --git a/tools/moltemplate/moltemplate/postprocess_coeffs.py b/tools/moltemplate/moltemplate/postprocess_coeffs.py new file mode 100755 index 0000000000..439f6dc9c1 --- /dev/null +++ b/tools/moltemplate/moltemplate/postprocess_coeffs.py @@ -0,0 +1,287 @@ +#!/usr/bin/env python + +man_page_text = """ +Usage (example): + +postprocess_coeffs.py ttree_assignments.txt < file.template > file_new.template + +Moltemplate users would like to be able to use commands with wildcards like: + bond_coeff @bond:*/A/* harmonic 533.7 120.0 + pair_coeff @atom:A* @atom:B* lj/cut 0.35 2.7 +as shorthand for specifying force field parameters for multiple atom&bond types: + bond_coeff @bond:a/A/c harmonic 533.7 120.0 + bond_coeff @bond:b/A/d harmonic 533.7 120.0 + pair_coeff @atom:A* @atom:B* lj/cut 0.35 2.7 + pair_coeff @atom:A @atom:B lj/cut 0.35 2.7 + pair_coeff @atom:A1 @atom:B1 lj/cut 0.35 2.7 + pair_coeff @atom:A1 @atom:B2 lj/cut 0.35 2.7 + pair_coeff @atom:A2 @atom:B1 lj/cut 0.35 2.7 + pair_coeff @atom:A2 @atom:B2 lj/cut 0.35 2.7 + : : : : : : +However LAMMPS does not interpret the * character this way. +Hence, this script will replace the line with the * wildcards above with the +lines text that follow above. This script also works for bond_coeff, +angle_coeff, dihedral_coeff, and improper_coeff commands (expanding wildcard +characters appearing in @bond, @angle, @dihedral, and @improper variables). + +This program expects an argument (ttree_assignments.txt) which has a list of all +of the atom types (and bond_types, and angle_types...) which have been defined +and it will substitute those variable names in place of the wildcard expressions +(The ttree_assignments.txt file is a 2-column file variables in the 1st column, + and their integer values in the 2nd column. The 2nd column is ignored.) + +The resulting list of commands with explicit variable names will be +printed to the standard-out. + +""" + + +import sys +import gc + +try: + from .ttree import ExtractFormattingCommands + from .ttree_lex import * + +except (ImportError, SystemError, ValueError): + # not installed as a package + from ttree import ExtractFormattingCommands + from ttree_lex import * + + +g_filename = __file__.split('/')[-1] +g_module_name = g_filename +if g_filename.rfind('.py') != -1: + g_module_name = g_filename[:g_filename.rfind('.py')] +g_date_str = '2018-6-09' +g_version_str = '0.2.0' +g_program_name = g_filename +#sys.stderr.write(g_program_name+' v'+g_version_str+' '+g_date_str+' ') + + +def ExtractVarName(text): + """ Read a string like 'atom:A ' or '{/atom:A B/C/../D }ABC ' + and return ('','@atom:A',' ') or ('{','atom:A B/C/../D ','}ABC') + These are 3-tuples containing the portion of the text containing + only the variable's name (assumed to be within the text), + ...in addition to the text on either side of the variable name. + """ + i_begin = 0 + escape = '\'' + lparen = '{' + rparen = '}' + escaped = False + commenters = '#' + whitespace = ' \t\r\f\n' + terminators = whitespace + commenters + # Ideally, perhaps I should lookup these values from ttree_lex.TtreeLex to + # make sure I am being consistent, instead of re-defining them in this file. + #while ((i_begin < len(text)) and + # (text[i_begin] in whitespace)): + # i_begin += 1 + in_paren = text[i_begin:i_begin+1] == lparen + if in_paren: + terminators = rparen + i_begin += 1 + i_end = i_begin + while ((i_end < len(text)) and + (text[i_end] not in terminators)): + i_end += 1 + return (text[0: i_begin], + text[i_begin:i_end], + text[i_end:]) + + + +def main(): + try: + if (len(sys.argv) != 2): + raise InputError('Error running \"' + g_program_name + '\"\n' + ' Typical usage:\n' + ' postprocess_coeffs.py ttree_assignments.txt < file.template > file.rendered\n' + '\n' + ' Missing argument.\n' + ' Expected the name of a 2-column file containing\n' + ' variable names and their bindings (values).\n' + ' (This is likely a programmer error.\n' + ' This script was not intended to be run by end users.)\n') + + bindings_filename = sys.argv[1] + f = open(bindings_filename) + atom_types = set([]) + bond_types = set([]) + angle_types = set([]) + dihedral_types = set([]) + improper_types = set([]) + + #BasicUIReadBindingsStream(assignments, f, bindings_filename) + + # The line above is robust but it uses far too much memory. + # This for loop below works for most cases. + for line in f: + #tokens = lines.strip().split() + # like split but handles quotes + tokens = SplitQuotedString(line.strip()) + if len(tokens) < 2: + continue + if tokens[0].find('@') != 0: + continue + if tokens[0][2:].find('atom') == 0: + atom_types.add(tokens[0][1:]) + elif tokens[0][2:].find('bond') == 0: + bond_types.add(tokens[0][1:]) + elif tokens[0][2:].find('angle') == 0: + angle_types.add(tokens[0][1:]) + elif tokens[0][2:].find('dihedral') == 0: + dihedral_types.add(tokens[0][1:]) + elif tokens[0][2:].find('improper') == 0: + improper_types.add(tokens[0][1:]) + + f.close() + gc.collect() + + lex = LineLex(sys.stdin, '__standard_input_for_postprocess_coeffs__') + #lex = LineLex(open('deleteme.template', 'r'), '__standard_input_for_postprocess_coeffs_') + lex.commenters = '' #(don't attempt to skip over comments) + lex.line_extend_chars += '&' #(because LAMMPS interprets '&' as '\') + + while True: + line_orig = lex.ReadLine() + #sys.stderr.write('line_orig = \"'+str(line_orig)+'\"\n') + if (not line_orig) or (line_orig == ''): + break + tokens = line_orig.strip().split('@') + + if ((len(tokens) >= 2) and + (tokens[0].find('bond_coeff') == 0) and + #does this token contain '*' or '?' + HasWildcard(tokens[1]) and + (tokens[1][0:1] != '{')): #(don't pattern match * in {})?' + left_paren, typepattern, text_after = ExtractVarName(tokens[1]) + for btype in bond_types: + if MatchesPattern(btype, typepattern): + #assert(left_paren == '') + tokens[1] = btype + text_after + sys.stdout.write('@'.join(tokens) + '\n') + + elif ((len(tokens) >= 2) and + (tokens[0].find('angle_coeff') == 0) and + #does this token contain '*' or '?' + HasWildcard(tokens[1]) and + (tokens[1][0:1] != '{')): + left_paren, typepattern, text_after = ExtractVarName(tokens[1]) + for antype in angle_types: + if MatchesPattern(antype, typepattern): + #assert(left_paren == '') + tokens[1] = antype + text_after + sys.stdout.write('@'.join(tokens) + '\n') + + elif ((len(tokens) >= 2) and + (tokens[0].find('dihedral_coeff') == 0) and + #does this token contain '*' or '?' + HasWildcard(tokens[1]) and + (tokens[1][0:1] != '{')): #(don't pattern match * in {}) + left_paren, typepattern, text_after = ExtractVarName(tokens[1]) + for dtype in dihedral_types: + if MatchesPattern(dtype, typepattern): + #assert(left_paren == '') + tokens[1] = dtype + text_after + sys.stdout.write('@'.join(tokens) + '\n') + + elif ((len(tokens) >= 2) and + (tokens[0].find('improper_coeff') == 0) and + #does this token contain '*' or '?' + HasWildcard(tokens[1]) and + (tokens[1][0:1] != '{')): #(don't pattern match * in {}) + left_paren, typepattern, text_after = ExtractVarName(tokens[1]) + for itype in improper_types: + if MatchesPattern(itype, typepattern): + #assert(left_paren == '') + tokens[1] = itype + text_after + sys.stdout.write('@'.join(tokens) + '\n') + + #elif ((len(tokens) >= 3) and + # (tokens[0].find('pair_coeff') == 0) and + # (HasWildcard(tokens[1]) or HasWildcard(tokens[2]))): + elif ((len(tokens) >= 2) and + (tokens[0].find('pair_coeff') == 0)): + # First deal with cases with only one @variable, such as: + # pair_coeff @atom:A* * ... + # pair_coeff * @atom:A* ... + # (We don't deal with cases like "* *" because LAMMPS interprets + # these in a special way: manybody pair_styles use "* *") + if len(tokens) == 2: + if tokens[0].rstrip()[-1:] == '*': + tokens[0] = tokens[0].rstrip()[:-1] + tokens.insert(1, '/atom:* ') + else: + ic = tokens[1].find(' * ') + tokens.append('/atom:* '+tokens[1][ic+3:]) + tokens[1] = tokens[1][:ic]+' ' + + assert(len(tokens) >= 3) + left_paren1,typepattern1,text_after1=ExtractVarName(tokens[1]) + + # Then deal with cases like this: + # pair_coeff @{/atom:r1}*@{/atom:r3} @{/atom:r4}*@{/atom:r6} + # In this case we should be using ' ' as the delimeter, not '@' + # to separate the two arguments from eachother, since + # @{/atom:r1}*@{/atom:r3} is the first argument, and + # @{/atom:r4}*@{/atom:r6} is the second argument + + # Check: Were there any whitespace characters in the text + # separating token[1] from token[2]? + if ((left_paren1 == '{') and + (len(SplitQuotedString(text_after1)) == 1)): + # If not, then tokens[1] and tokens[2] are both part of + # the 1st argument. + tokens[1] = tokens[1]+'@'+tokens[2] + left_paren1 = '' + text_after1 = '' + typepattern1 = tokens[1] + del tokens[2] + + left_paren2,typepattern2,text_after2=ExtractVarName(tokens[2]) + # Check: Were there any whitespace characters in the text + # separating token[2] from what follows? + if ((len(tokens) > 3) and + (len(SplitQuotedString(text_after2)) == 1)): + # If not, then tokens[2] and tokens[3] are both part of + # the 2nd argument. + tokens[2] = tokens[2]+'@'+tokens[3] + left_paren2 = '' + text_after2 = '' + typepattern2 = tokens[2] + del tokens[3] + if (HasWildcard(tokens[1]) and + (tokens[1][0:1] != '{')): #(don't pattern match * in {}) + atom_types1 = atom_types + else: + atom_types1 = set([typepattern1]) + if (HasWildcard(tokens[2]) and + (tokens[2][0:1] != '{')): #(don't pattern match * in {}) + atom_types2 = atom_types + else: + atom_types2 = set([typepattern2]) + for atype1 in atom_types1: + #sys.stderr.write('atype1 = \"'+str(atype1)+'\"\n') + if MatchesPattern(atype1, typepattern1): + #assert(left_paren1 == '') + tokens[1] = left_paren1 + atype1 + text_after1 + for atype2 in atom_types2: + #sys.stderr.write(' atype2 = \"'+str(atype2)+'\"\n') + if MatchesPattern(atype2, typepattern2): + #assert(left_paren2 == '') + tokens[2] = left_paren2 + atype2 + text_after2 + sys.stdout.write('@'.join(tokens) + '\n') + else: + sys.stdout.write(line_orig) + + except (ValueError, InputError) as err: + sys.stderr.write('\n' + str(err) + '\n') + sys.exit(-1) + + return + +if __name__ == '__main__': + main() diff --git a/tools/moltemplate/moltemplate/postprocess_input_script.py b/tools/moltemplate/moltemplate/postprocess_input_script.py index b23f4e955f..f237502e57 100755 --- a/tools/moltemplate/moltemplate/postprocess_input_script.py +++ b/tools/moltemplate/moltemplate/postprocess_input_script.py @@ -1,4 +1,8 @@ #!/usr/bin/env python +# Author: Andrew Jewett (jewett.aij at g mail) +# License: 3-clause BSD License (See LICENSE.TXT) +# Copyright (c) 2017, California Institute of Technology +# All rights reserved. """ Reorder the integer arguments to the commands in a LAMMPS input diff --git a/tools/moltemplate/moltemplate/raw2data.py b/tools/moltemplate/moltemplate/raw2data.py index 8f029ee018..b39208a33f 100755 --- a/tools/moltemplate/moltemplate/raw2data.py +++ b/tools/moltemplate/moltemplate/raw2data.py @@ -1,17 +1,21 @@ #!/usr/bin/env python # -*- coding: utf-8 -*- +import sys, io + try: from .dump2data import * -except: + from .extract_lammps_data import lammps_data_sections +except (ImportError, SystemError, ValueError): # not installed as a package from dump2data import * + from extract_lammps_data import lammps_data_sections g_program_name = 'raw2data.py' g_date_str = '2016-12-21' g_version_str = 'v0.44.0' -####### Main Code Below: ####### + ####### Main Code Below: ####### def main(): sys.stderr.write(g_program_name + ' ' + g_version_str + ' ' + g_date_str) sys.stderr.write('\n') @@ -21,12 +25,64 @@ def main(): misc_settings = MiscSettings() misc_settings.multi = False + # First process any arguments which are specific to "raw2data.py" + # (and remove them before passing them to dump2data.ParseArgs()) + sort_data_file_by_atom_id = False + argv = [arg for arg in sys.argv] + i = 1 + while i < len(argv): + if argv[i].lower() == '-ignore-atom-id': + sort_data_file_by_atom_id = True + del argv[i:i+1] + if argv[i].lower() == '-sort': + sort_data_file_by_atom_id = False + del argv[i:i+1] + else: + i += 1 + #(perhaps later I'll add some additional argumets) + warning_strings = [] - ParseArgs(sys.argv, + ParseArgs(argv, misc_settings, data_settings, warning_strings) + frame_atom_order = [] + + # The atoms in the "Atoms" section of the data file might be out + # of order. Extract the text from that section, and figure out the + # atom-ID assigned to each atom (number in the first column). + # Then assign the these atom-ID numbers to entries in the + # coordinates list (frame_coords) in the same order. We want the + # lines of text in the coordinate file to pasted to the end of + # the lines of text in the "Atoms" section of the data file + # in the same order, regardless of the atom-ID numbers in that file. + # Counterintuitively, the only way to do that is to assign the same + # atom-ID numbers to the coordinate list in frame_coords". So we + # have to extract those numbers from the data file. + in_atoms_section = False + num_blank_lines = 0 + for line in data_settings.contents: + ic = line.find('#') + line = line[:ic] #(this also removes the newline character) + tokens = line.strip().split() + if line.strip() == 'Atoms': + in_atoms_section = True + elif line.strip() in lammps_data_sections: + in_atoms_section = False + elif in_atoms_section: + if len(tokens) > 0: + if sort_data_file_by_atom_id: + atomid = tokens[0] + frame_atom_order.append(atomid) + #sys.stderr.write('atomid=\"'+str(atomid)+'\"\n') + else: + frame_atom_order.append(str(len(frame_atom_order)+1)) + else: + num_blank_lines += 1 + if num_blank_lines > 1: + in_atoms_section = False + frame_coords = defaultdict(list) frame_coords_ixiyiz = defaultdict(list) frame_vects = defaultdict(list) @@ -48,8 +104,8 @@ def main(): finished_reading_frame = False read_last_frame = False - #in_coord_file = open('tmp_atom_coords.dat','r') in_coord_file = sys.stdin + #in_coord_file = open('tmp_atom_coords.dat','r') read_last_frame = False while True: @@ -61,11 +117,13 @@ def main(): if line == '': # if EOF break + #frame_vects = defaultdict(list) frame_coords = defaultdict(list) while line.strip() != '': n_crds = len(frame_coords) #sys.stdout.write("n_crds="+str(n_crds)+": \""+line.strip()+"\"\n") - frame_coords[str(n_crds + 1)] = line.split() + frame_coords[frame_atom_order[n_crds]] = line.split() + #frame_vects[frame_atom_order[n_crds]] = ['0.0','0.0','0.0'] line = in_coord_file.readline() # Check to see if there are any blank lines at this location in the file @@ -91,6 +149,7 @@ def main(): None, misc_settings, data_settings, + None, frame_natoms, frame_coords, frame_coords_ixiyiz, diff --git a/tools/moltemplate/moltemplate/scripts/cleanup_moltemplate.sh b/tools/moltemplate/moltemplate/scripts/cleanup_moltemplate.sh index e5375674ae..5ffce30739 100755 --- a/tools/moltemplate/moltemplate/scripts/cleanup_moltemplate.sh +++ b/tools/moltemplate/moltemplate/scripts/cleanup_moltemplate.sh @@ -1,3 +1,5 @@ +#!/usr/bin/env bash + # cleanup_moltemplate.sh # This script attempts to remove irrelevant information from LAMMPS # input scripts and data files (such as extra, unneeded atom types @@ -71,16 +73,29 @@ moltemplate.sh system.lt # This will create: "system.data" "system.in.init" "system.in.settings." - # That's it. The new "system.data" and system.in.* files should + # That's it. The new "system.data" and system.in.settings files should # be ready to run in LAMMPS. + # Special case: "set" commands + # Typically "set type" or "set atom" commands are used to assign atom charge + # If there is a "system.in.charges" file, then it contains these commands + # however the atom type numbers will be wrong, so we must rewrite it. + # Replace it with the corresponding commands from the system.in.settings + # (whose atom type numbers are correct) + if [ -f "../system.in.charges" ]; then + awk '{ if ((NF >= 5) && ($1 == "set") && ($4 == "charge")) print $0}' \ + < system.in.settings > system.in.charges + # There is no need to remove these lines from "system.in.settings", + # (because there's no harm to invoke the "set" command twice) + # ...but if you want to do that, try using a command similar to: + #sed '/set type/,+1 d' < system.in.settings > system.in.settings.tmp + #mv -f system.in.settings.tmp system.in.settings + fi + + # Now move the system.data and system.in.* files to their original location: mv -f system.data system.in.* ../ cd ../ - grep "set type" system.in.settings > system.in.charges - # now remove these lines from system.in.settings - sed '/set type/,+1 d' < system.in.settings > system.in.settings.tmp - mv -f system.in.settings.tmp system.in.settings # Finally, delete all of the temporary files we generated rm -rf new_lt_file_TMP diff --git a/tools/moltemplate/moltemplate/scripts/emoltemplate.sh b/tools/moltemplate/moltemplate/scripts/emoltemplate.sh index eaba9c4960..e72d2d9e29 100755 --- a/tools/moltemplate/moltemplate/scripts/emoltemplate.sh +++ b/tools/moltemplate/moltemplate/scripts/emoltemplate.sh @@ -10,8 +10,8 @@ # All rights reserved. G_PROGRAM_NAME="emoltemplate.sh" -G_VERSION="1.0.5" -G_DATE="2017-2-01" +G_VERSION="1.1.0" +G_DATE="2018-6-26" echo "${G_PROGRAM_NAME} v${G_VERSION} ${G_DATE}" >&2 echo "" >&2 @@ -37,7 +37,6 @@ PY_SCR_DIR=`dirname "$0"` if [ ! -s "${PY_SCR_DIR}/ttree.py" ]; then PY_SCR_DIR="$PY_SCR_DIR/.." fi -MOLTEMPLATE_SCRIPT_DIR="$SCRIPT_DIR/../moltemplate/src" MSG_BAD_INSTALL=$(cat < "${data_atoms}.template.minimal"; then exit 4 @@ -599,7 +598,7 @@ if [ -s "${data_bond_list}.template" ]; then echo "Looking up bond types according to atom type" >&2 #-- Generate a file containing bondid bondtype atomid1 atomid2 -- - if ! $PYTHON_COMMAND "${MOLTEMPLATE_SCRIPT_DIR}/bonds_by_type.py" \ + if ! $PYTHON_COMMAND "${PY_SCR_DIR}/bonds_by_type.py" \ -atom-style "id type" \ -atoms "${data_atoms}.template.minimal" \ -bond-list "${data_bond_list}.template.minimal" \ @@ -641,7 +640,7 @@ if [ -s "${data_bond_list}.template" ]; then ## The next 2 lines extract the variable names from data_new.template.tmp ## and instert them into the appropriate place in ttree_assignments.txt ## (renumbering the relevant variable-assignments to avoid clashes). - #if ! $PYTHON_COMMAND "${MOLTEMPLATE_SCRIPT_DIR}/nbody_fix_ttree_assignments.py" \ + #if ! $PYTHON_COMMAND "${PY_SCR_DIR}/nbody_fix_ttree_assignments.py" \ # '/bond' gen_bonds.template.tmp \ # < ttree_assignments.txt \ # > ttree_assignments.tmp; then @@ -659,7 +658,7 @@ if [ -s "${data_bond_list}.template" ]; then # names present in the .template file. (We want to convert the file from # a .template format into an ordinary (numeric) LAMMPS data-section format.) - if ! $PYTHON_COMMAND "${MOLTEMPLATE_SCRIPT_DIR}/ttree_render.py" \ + if ! $PYTHON_COMMAND "${PY_SCR_DIR}/ttree_render.py" \ ttree_assignments.txt \ < "${data_bonds}.template" \ > "$data_bonds"; then @@ -695,10 +694,10 @@ for FILE in "$data_angles_by_type"*.template; do SUBGRAPH_SCRIPT="nbody_Angles.py" else echo "(using the rules in \"$SUBGRAPH_SCRIPT\")" >&2 - #if [ ! -s "${MOLTEMPLATE_SCRIPT_DIR}/nbody_alt_symmetry/$SUBGRAPH_SCRIPT" ]; then + #if [ ! -s "${PY_SCR_DIR}/nbody_alt_symmetry/$SUBGRAPH_SCRIPT" ]; then # echo "Error: File \"$SUBGRAPH_SCRIPT\" not found.\n" >&2 # echo " It should be located in this directory:\n" >&2 - # echo " ${MOLTEMPLATE_SCRIPT_DIR}/nbody_alt_symmetry/\n" >&2 + # echo " ${PY_SCR_DIR}/nbody_alt_symmetry/\n" >&2 # exit 4 #fi fi @@ -708,7 +707,7 @@ for FILE in "$data_angles_by_type"*.template; do # The first step is to strip out the espresso-specific junk from each # section so we end up with a simple multi-column file containing only # the symbols we care about (which identify atom ids, atom and bond types) - if ! $PYTHON_COMMAND "${SCRIPT_DIR}/extract_espresso_atom_types.py" \ + if ! $PYTHON_COMMAND "${PY_SCR_DIR}/extract_espresso_atom_types.py" \ < "${data_atoms}.template" \ > "${data_atoms}.template.minimal"; then exit 4 @@ -721,7 +720,7 @@ for FILE in "$data_angles_by_type"*.template; do < "${data_bonds}.template" \ > "${data_bonds}.template.minimal" - if ! $PYTHON_COMMAND "${MOLTEMPLATE_SCRIPT_DIR}/nbody_by_type.py" \ + if ! $PYTHON_COMMAND "${PY_SCR_DIR}/nbody_by_type.py" \ -subgraph "${SUBGRAPH_SCRIPT}" \ -section "Angles" \ -sectionbytype "Angles By Type" \ @@ -767,7 +766,7 @@ for FILE in "$data_angles_by_type"*.template; do ## The next 2 lines extract the variable names from data_new.template.tmp ## and instert them into the appropriate place in ttree_assignments.txt ## (renumbering the relevant variable-assignments to avoid clashes). - #if ! $PYTHON_COMMAND "${MOLTEMPLATE_SCRIPT_DIR}/nbody_fix_ttree_assignments.py" \ + #if ! $PYTHON_COMMAND "${PY_SCR_DIR}/nbody_fix_ttree_assignments.py" \ # '/angle' gen_angles.template.tmp \ # < ttree_assignments.txt \ # > ttree_assignments.tmp; then @@ -781,7 +780,7 @@ for FILE in "$data_angles_by_type"*.template; do # names present in the .template file. (We want to convert the file from # a .template format into an ordinary (numeric) LAMMPS data-section format) - if ! $PYTHON_COMMAND "${MOLTEMPLATE_SCRIPT_DIR}/ttree_render.py" \ + if ! $PYTHON_COMMAND "${PY_SCR_DIR}/ttree_render.py" \ ttree_assignments.txt \ < "$data_angles.template" \ > "$data_angles"; then @@ -815,10 +814,10 @@ for FILE in "$data_dihedrals_by_type"*.template; do SUBGRAPH_SCRIPT="nbody_Dihedrals.py" else echo "(using the rules in \"$SUBGRAPH_SCRIPT\")" >&2 - #if [ ! -s "${MOLTEMPLATE_SCRIPT_DIR}/nbody_alt_symmetry/$SUBGRAPH_SCRIPT" ]; then + #if [ ! -s "${PY_SCR_DIR}/nbody_alt_symmetry/$SUBGRAPH_SCRIPT" ]; then # echo "Error: File \"$SUBGRAPH_SCRIPT\" not found.\n" >&2 # echo " It should be located in this directory:\n" >&2 - # echo " ${MOLTEMPLATE_SCRIPT_DIR}/nbody_alt_symmetry/\n" >&2 + # echo " ${PY_SCR_DIR}/nbody_alt_symmetry/\n" >&2 # exit 4 #fi fi @@ -828,7 +827,7 @@ for FILE in "$data_dihedrals_by_type"*.template; do # The first step is to strip out the espresso-specific junk from each # section so we end up with a simple multi-column file containing only # the symbols we care about (which identify atom ids, atom and bond types) - if ! $PYTHON_COMMAND "${SCRIPT_DIR}/extract_espresso_atom_types.py" \ + if ! $PYTHON_COMMAND "${PY_SCR_DIR}/extract_espresso_atom_types.py" \ < "${data_atoms}.template" \ > "${data_atoms}.template.minimal"; then exit 4 @@ -841,7 +840,7 @@ for FILE in "$data_dihedrals_by_type"*.template; do < "${data_bonds}.template" \ > "${data_bonds}.template.minimal" - if ! $PYTHON_COMMAND "${MOLTEMPLATE_SCRIPT_DIR}/nbody_by_type.py" \ + if ! $PYTHON_COMMAND "${PY_SCR_DIR}/nbody_by_type.py" \ -subgraph "${SUBGRAPH_SCRIPT}" \ -section "Dihedrals" \ -sectionbytype "Dihedrals By Type" \ @@ -887,7 +886,7 @@ for FILE in "$data_dihedrals_by_type"*.template; do ## The next 2 lines extract the variable names from data_new.template.tmp ## and instert them into the appropriate place in ttree_assignments.txt ## (renumbering the relevant variable-assignments to avoid clashes). - #if ! $PYTHON_COMMAND "${MOLTEMPLATE_SCRIPT_DIR}/nbody_fix_ttree_assignments.py" \ + #if ! $PYTHON_COMMAND "${PY_SCR_DIR}/nbody_fix_ttree_assignments.py" \ # '/dihedral' gen_dihedrals.template.tmp \ # < ttree_assignments.txt \ # > ttree_assignments.tmp; then @@ -901,7 +900,7 @@ for FILE in "$data_dihedrals_by_type"*.template; do # names present in the .template file. (We want to convert the file from # a .template format into an ordinary (numeric) LAMMPS data-section format) - if ! $PYTHON_COMMAND "${MOLTEMPLATE_SCRIPT_DIR}/ttree_render.py" \ + if ! $PYTHON_COMMAND "${PY_SCR_DIR}/ttree_render.py" \ ttree_assignments.txt \ < "$data_dihedrals.template" \ > "$data_dihedrals"; then @@ -938,10 +937,10 @@ for FILE in "$data_impropers_by_type"*.template; do SUBGRAPH_SCRIPT="nbody_Impropers.py" else echo "(using the rules in \"$SUBGRAPH_SCRIPT\")" >&2 - #if [ ! -s "${MOLTEMPLATE_SCRIPT_DIR}/nbody_alt_symmetry/$SUBGRAPH_SCRIPT" ]; then + #if [ ! -s "${PY_SCR_DIR}/nbody_alt_symmetry/$SUBGRAPH_SCRIPT" ]; then # echo "Error: File \"$SUBGRAPH_SCRIPT\" not found.\n" >&2 # echo " It should be located in this directory:\n" >&2 - # echo " ${MOLTEMPLATE_SCRIPT_DIR}/nbody_alt_symmetry/\n" >&2 + # echo " ${PY_SCR_DIR}/nbody_alt_symmetry/\n" >&2 # exit 4 #fi fi @@ -951,7 +950,7 @@ for FILE in "$data_impropers_by_type"*.template; do # The first step is to strip out the espresso-specific junk from each # section so we end up with a simple multi-column file containing only # the symbols we care about (which identify atom ids, atom and bond types) - if ! $PYTHON_COMMAND "${SCRIPT_DIR}/extract_espresso_atom_types.py" \ + if ! $PYTHON_COMMAND "${PY_SCR_DIR}/extract_espresso_atom_types.py" \ < "${data_atoms}.template" \ > "${data_atoms}.template.minimal"; then exit 4 @@ -964,7 +963,7 @@ for FILE in "$data_impropers_by_type"*.template; do < "${data_bonds}.template" \ > "${data_bonds}.template.minimal" - if ! $PYTHON_COMMAND "${MOLTEMPLATE_SCRIPT_DIR}/nbody_by_type.py" \ + if ! $PYTHON_COMMAND "${PY_SCR_DIR}/nbody_by_type.py" \ -subgraph "${SUBGRAPH_SCRIPT}" \ -section "Impropers" \ -sectionbytype "Impropers By Type" \ @@ -1012,7 +1011,7 @@ for FILE in "$data_impropers_by_type"*.template; do ## The next 2 lines extract the variable names from data_new.template.tmp ## and instert them into the appropriate place in ttree_assignments.txt ## (renumbering the relevant variable-assignments to avoid clashes). - #if ! $PYTHON_COMMAND "${MOLTEMPLATE_SCRIPT_DIR}/nbody_fix_ttree_assignments.py" \ + #if ! $PYTHON_COMMAND "${PY_SCR_DIR}/nbody_fix_ttree_assignments.py" \ # '/improper' gen_impropers.template.tmp \ # < ttree_assignments.txt \ # > ttree_assignments.tmp; then @@ -1026,7 +1025,7 @@ for FILE in "$data_impropers_by_type"*.template; do # names present in the .template file. (We want to convert the file from # a .template format into an ordinary (numeric) LAMMPS data-section format) - if ! $PYTHON_COMMAND "${MOLTEMPLATE_SCRIPT_DIR}/ttree_render.py" \ + if ! $PYTHON_COMMAND "${PY_SCR_DIR}/ttree_render.py" \ ttree_assignments.txt \ < "$data_impropers.template" \ > "$data_impropers"; then @@ -1216,7 +1215,6 @@ if [ -s "$data_atoms" ]; then cat "$data_atoms" >> "$OUT_FILE_TCL" fi - if [ -s "$tmp_atom_coords" ]; then rm -f "$OUT_FILE_COORDS" awk 'BEGIN{natom=0} {if (NF>=3) {print "part " natom " pos " $1 " " $2 " " $3; natom++}}' < "$tmp_atom_coords" >> "$OUT_FILE_TCL" diff --git a/tools/moltemplate/moltemplate/scripts/moltemplate.sh b/tools/moltemplate/moltemplate/scripts/moltemplate.sh index 870ab9c8cc..5e7fd2321c 100755 --- a/tools/moltemplate/moltemplate/scripts/moltemplate.sh +++ b/tools/moltemplate/moltemplate/scripts/moltemplate.sh @@ -3,15 +3,14 @@ # # Author: Andrew Jewett (jewett.aij at g mail) # http://www.moltemplate.org -# http://jensenlab.caltech.edu # http://www.chem.ucsb.edu/~sheagroup # License: 3-clause BSD License (See LICENSE.txt) # Copyright (c) 2012, Regents of the University of California # All rights reserved. G_PROGRAM_NAME="moltemplate.sh" -G_VERSION="2.3.7" -G_DATE="2017-8-22" +G_VERSION="2.8.6" +G_DATE="2018-6-27" echo "${G_PROGRAM_NAME} v${G_VERSION} ${G_DATE}" >&2 echo "" >&2 @@ -223,6 +222,7 @@ $data_bonds_by_type* ${data_angles_by_type}* ${data_dihedrals_by_type}* ${data_impropers_by_type}* +$data_charge_by_bond $in_init $in_settings EOF @@ -395,6 +395,20 @@ while [ "$i" -lt "$ARGC" ]; do # Disable syntax checking by undefining LTTREE_CHECK_COMMAND unset LTTREE_CHECK_COMMAND unset LTTREE_POSTPROCESS_COMMAND + elif [ "$A" = "-allow-wildcards" ]; then + # Disable syntax checking by undefining LTTREE_CHECK_COMMAND + if [ -z "$LTTREE_CHECK_ARGS" ]; then + LTTREE_CHECK_ARGS="\"$A\"" + else + LTTREE_CHECK_ARGS="${LTTREE_CHECK_ARGS} \"$A\"" + fi + elif [ "$A" = "-forbid-wildcards" ]; then + # Disable syntax checking by undefining LTTREE_CHECK_COMMAND + if [ -z "$LTTREE_CHECK_ARGS" ]; then + LTTREE_CHECK_ARGS="\"$A\"" + else + LTTREE_CHECK_ARGS="${LTTREE_CHECK_ARGS} \"$A\"" + fi elif [ "$A" = "-checkff" ]; then # Disable syntax checking by undefining LTTREE_CHECK_COMMAND CHECKFF="$A" @@ -529,11 +543,23 @@ while [ "$i" -lt "$ARGC" ]; do fi #echo " (extracting coordinates from \"$PDB_FILE\")" >&2 if grep -q '^ATOM \|^HETATM' "$PDB_FILE"; then + # Extract the coordinates from the PDB file: + + # COMMENTING OUT ("pdbsort.py") + # I used to sort the PDB file by (ChainID,SeqNum,InsertCode) + # and then extract the coordinates from the file. + # This turned out to be inconvenient for users. Instead + # just read the coordinates in the order they appear in the file. + # OLD CODE: # Extract the coords from the "ATOM" records in the PDB file - if ! $PYTHON_COMMAND "${PY_SCR_DIR}/pdbsort.py" < "$PDB_FILE" \ - | awk '/^ATOM |^HETATM/{print substr($0,31,8)" "substr($0,39,8)" "substr($0,47,8)}' > "$tmp_atom_coords"; then - ERR_INTERNAL - fi + #if ! $PYTHON_COMMAND "${PY_SCR_DIR}/pdbsort.py" < "$PDB_FILE" \ + # | awk '/^ATOM |^HETATM/{print substr($0,31,8)" "substr($0,39,8)" "substr($0,47,8)}' > "$tmp_atom_coords"; then + # ERR_INTERNAL + #fi + # NEW CODE (USE THIS INSTEAD): + awk '/^ATOM |^HETATM/{print substr($0,31,8)" "substr($0,39,8)" "substr($0,47,8)}' \ + < "$PDB_FILE" \ + > "$tmp_atom_coords" else echo "$SYNTAX_MSG" >&2 echo "-----------------------" >&2 @@ -681,6 +707,7 @@ fi + OUT_FILE_INPUT_SCRIPT="${OUT_FILE_BASE}.in" OUT_FILE_INIT="${OUT_FILE_BASE}.in.init" OUT_FILE_SETTINGS="${OUT_FILE_BASE}.in.settings" @@ -701,16 +728,14 @@ rm -f "$OUT_FILE_INPUT_SCRIPT" "$OUT_FILE_INIT" "$OUT_FILE_SETTINGS" "$OUT_FILE_ - # If checking is not disabled, then first check for common spelling errors. if [ -n "$LTTREE_CHECK_COMMAND" ]; then - if ! eval $LTTREE_CHECK_COMMAND $TTREE_ARGS; then + if ! eval $LTTREE_CHECK_COMMAND $TTREE_ARGS $LTTREE_CHECK_ARGS; then exit 1 fi fi - # --- Run ttree. --- # # 3, 2, 1, ... @@ -926,11 +951,12 @@ fi - +FILE_angles_by_type1="" +FILE_angles_by_type2="" #for FILE in "$data_angles_by_type"*.template; do IFS_BACKUP="$IFS" IFS=$(echo -en "\n\b") -for FILE in `ls -v "$data_angles_by_type"*.template`; do +for FILE in `ls -v "$data_angles_by_type"*.template 2> /dev/null`; do if [ ! -s "$FILE" ] || [ ! -s "$data_bonds" ]; then break; # This handles with the special cases that occur when @@ -964,6 +990,9 @@ for FILE in `ls -v "$data_angles_by_type"*.template`; do # fi fi + FILE_angles_by_type2="$FILE_angles_by_type1" + FILE_angles_by_type1="$FILE" + #-- Generate a file containing the list of interactions on separate lines -- if ! $PYTHON_COMMAND "${PY_SCR_DIR}/nbody_by_type.py" \ -subgraph "${SUBGRAPH_SCRIPT}" \ @@ -1033,7 +1062,7 @@ FILE_dihedrals_by_type2="" #for FILE in "$data_dihedrals_by_type"*.template; do IFS_BACKUP="$IFS" IFS=$(echo -en "\n\b") -for FILE in `ls -v "$data_dihedrals_by_type"*.template`; do +for FILE in `ls -v "$data_dihedrals_by_type"*.template 2> /dev/null`; do if [ ! -s "$FILE" ] || [ ! -s "$data_bonds" ]; then break; # This handles with the special cases that occur when @@ -1067,7 +1096,7 @@ for FILE in `ls -v "$data_dihedrals_by_type"*.template`; do # fi fi - FILE_dihedrals_by_type2="$FILE_impropers_by_type1" + FILE_dihedrals_by_type2="$FILE_dihedrals_by_type1" FILE_dihedrals_by_type1="$FILE" #-- Generate a file containing the list of interactions on separate lines -- @@ -1138,7 +1167,7 @@ FILE_impropers_by_type2="" #for FILE in "$data_impropers_by_type"*.template; do IFS_BACKUP="$IFS" IFS=$(echo -en "\n\b") -for FILE in `ls -v "$data_impropers_by_type"*.template`; do +for FILE in `ls -v "$data_impropers_by_type"*.template 2> /dev/null`; do if [ ! -s "$FILE" ] || [ ! -s "$data_bonds" ]; then break; # This handles with the special cases that occur when @@ -1238,6 +1267,39 @@ IFS="$IFS_BACKUP" +# Deal with wildcard characters ('*', '?') in "_coeff" commands +# appearing in any LAMMPS input scripts generated by moltemplate. +# Replace them with explicit variable names. Do this before rendering +#if [ -s "${in_settings}.template" ]; then +echo "expanding wildcards in \"_coeff\" commands" >&2 +#ls "${in_prefix}"*.template 2> /dev/null | while read file_name; do +for file_name in "${in_prefix}"*.template; do + + # invoking "postprocess_coeffs.py" can be very slow, so only do it if the + # file contains both _coeff commands and wildcards *,? on the same line: + if ! awk '{if (match($1,/'_coeff/') && match($0,/'[*,?]/')) exit 1}' < "$file_name"; then + + echo "expanding wildcards in \"_coeff\" commands in \"$file_name\"" >&2 + if ! eval $PYTHON_COMMAND "${PY_SCR_DIR}/postprocess_coeffs.py" ttree_assignments.txt < "$file_name" > "${file_name}.tmp"; then + ERR_INTERNAL + fi + + mv -f "${file_name}.tmp" "$file_name" + # Now reassign integers to these variables + bn=`basename "$file_name" .template` + if ! $PYTHON_COMMAND "${PY_SCR_DIR}/ttree_render.py" \ + ttree_assignments.txt \ + < "$file_name" \ + > "$bn"; then + exit 6 + fi + fi +done +#fi + + + + if [ -n "$LTTREE_POSTPROCESS_COMMAND" ]; then echo "" >&2 @@ -1335,9 +1397,34 @@ if [ -s "${data_angles}" ]; then ERR_INTERNAL fi mv -f "${data_angles}.tmp" "${data_angles}" + + if [ ! -z $FILE_angles_by_type2 ]; then + MSG_MULTIPLE_ANGLE_RULES=$(cat <&2 + fi fi + + if [ -s "${data_dihedrals}" ]; then SUBGRAPH_SCRIPT="nbody_Dihedrals.py" if [ -n "$SUBGRAPH_SCRIPT_DIHEDRALS" ]; then @@ -1460,7 +1547,6 @@ fi - # ------------------ Charge By Bond ---------------------- # Assign atom partial charges according to who they are bonded to @@ -1508,7 +1594,6 @@ fi - # ------------------------------------------------------- rm -f "$OUT_FILE_DATA" @@ -1528,6 +1613,9 @@ NIMPROPERS="0" if [ -s "${data_atoms}" ]; then NATOMS=`awk 'END{print NR}' < "${data_atoms}"` fi +if [ -s "${data_ellipsoids}" ]; then + NELLIPSOIDS=`awk 'END{print NR}' < "${data_ellipsoids}"` +fi if [ -s "${data_bonds}" ]; then NBONDS=`awk 'END{print NR}' < "${data_bonds}"` fi @@ -1545,6 +1633,9 @@ fi echo "LAMMPS Description" > "$OUT_FILE_DATA" echo "" >> "$OUT_FILE_DATA" echo " $NATOMS atoms" >> "$OUT_FILE_DATA" +if [ -n "$NELLIPSOIDS" ]; then + echo " $NATOMS ellipsoids" >> "$OUT_FILE_DATA" +fi if [ -n "$NBONDS" ]; then echo " $NBONDS bonds" >> "$OUT_FILE_DATA" fi @@ -1716,6 +1807,9 @@ fi echo "" >> "$OUT_FILE_DATA" + + + if [ -s "$data_masses" ]; then echo "Masses" >> "$OUT_FILE_DATA" echo "" >> "$OUT_FILE_DATA" @@ -1746,6 +1840,7 @@ if [ -n "$PAIR_COEFFS_IN_DATA" ]; then fi + if [ -s "$data_bond_coeffs" ]; then echo "Bond Coeffs" >> "$OUT_FILE_DATA" echo "" >> "$OUT_FILE_DATA" @@ -1992,7 +2087,7 @@ if [ -s "$tmp_atom_coords" ]; then # Copy the coordinates in $tmp_atom_coords into $OUT_FILE_DATA rm -f "$OUT_FILE_COORDS" - if ! eval $PYTHON_COMMAND "${PY_SCR_DIR}/raw2data.py" $ATOM_STYLE_ARG "$OUT_FILE_DATA" < "$tmp_atom_coords" > "$OUT_FILE_COORDS"; then + if ! eval $PYTHON_COMMAND "${PY_SCR_DIR}/raw2data.py -ignore-atom-id " $ATOM_STYLE_ARG "$OUT_FILE_DATA" < "$tmp_atom_coords" > "$OUT_FILE_COORDS"; then ERR_INTERNAL fi mv -f "$OUT_FILE_COORDS" "$OUT_FILE_DATA" @@ -2022,6 +2117,7 @@ fi + # ############## CLEAN UP ################ # A lot of files have been created along the way. @@ -2058,11 +2154,13 @@ IFS=$OIFS + # ############## DEAL WITH CUSTOM NON-STANDARD SECTIONS ################ # N_data_prefix=`expr length "$data_prefix"` <-- not posix compliant. AVOID N_data_prefix=${#data_prefix} #<-- works even if $data_prefix contains spaces +#for file_name in "${data_prefix}"*; do ls "${data_prefix}"* 2> /dev/null | while read file_name; do #If using bash: #SECTION_NAME="${file_name:$N_data_prefix}" @@ -2080,6 +2178,7 @@ ls "${data_prefix}"* 2> /dev/null | while read file_name; do mv -f "$file_name" output_ttree/ done + if [ -e "$data_prefix_no_space" ]; then echo "" >> "$OUT_FILE_DATA" @@ -2098,33 +2197,37 @@ if [ -e "$OUT_FILE_DATA" ]; then fi + + + #N_in_prefix=`expr length "$in_prefix"` <-- not posix compliant. AVOID. N_in_prefix=${#in_prefix} #<-- works even if $in_prefix contains spaces +#for file_name in "${in_prefix}"*; do ls "${in_prefix}"* 2> /dev/null | while read file_name; do #If using bash: #SECTION_NAME="${file_name:$N_in_prefix}" #If using sh: #SECTION_NAME=`expr substr "$file_name" $(($N_in_prefix+1)) 1000000` <-- not posix compliant. AVOID SECTION_NAME=`echo "" | awk "END{print substr(\"$file_name\",$((N_in_prefix+1)),1000000)}"` - FILE_SUFFIX=`echo "$SECTION_NAME" | awk '{print tolower($0)}'` + #FILE_SUFFIX=`echo "$SECTION_NAME" | awk '{print tolower($0)}'` + FILE_SUFFIX=`echo "$SECTION_NAME" | awk '{print tolower($0)}'|sed 's/ /./g'` # Create a new section in the lammps input script # matching the portion of the name of # the file after the in_prefix. - echo "" >> $OUT_FILE_INPUT_SCRIPT + echo "" >> "$OUT_FILE_INPUT_SCRIPT" echo "# ----------------- $SECTION_NAME Section -----------------" >> $OUT_FILE_INPUT_SCRIPT - cp -f "$file_name" ${OUT_FILE_INPUT_SCRIPT}.${FILE_SUFFIX} + cp -f "$file_name" "${OUT_FILE_INPUT_SCRIPT}.${FILE_SUFFIX}" - echo "" >> $OUT_FILE_INPUT_SCRIPT + echo "" >> "$OUT_FILE_INPUT_SCRIPT" echo "include \"${OUT_FILE_INPUT_SCRIPT}.${FILE_SUFFIX}\"" >> $OUT_FILE_INPUT_SCRIPT - echo "" >> $OUT_FILE_INPUT_SCRIPT - + echo "" >> "$OUT_FILE_INPUT_SCRIPT" mv -f "$file_name" output_ttree/ done if [ -e "$in_prefix_no_space" ]; then - echo "" >> $OUT_FILE_INPUT_SCRIPT - cat "$in_prefix_no_space" >> $OUT_FILE_INPUT_SCRIPT - echo "" >> $OUT_FILE_INPUT_SCRIPT + echo "" >> "$OUT_FILE_INPUT_SCRIPT" + cat "$in_prefix_no_space" >> "$OUT_FILE_INPUT_SCRIPT" + echo "" >> "$OUT_FILE_INPUT_SCRIPT" mv -f "$in_prefix_no_space" output_ttree/ fi @@ -2145,6 +2248,7 @@ for file_name in "$OUT_FILE_INIT" "$OUT_FILE_INPUT_SCRIPT" "$OUT_FILE_SETTINGS"; ERR_INTERNAL fi echo "" >&2 + mv -f "$file_name.tmp" "$file_name" #cat "$file_name" >> input_scripts_so_far.tmp #dos2unix < "$file_name" >> input_scripts_so_far.tmp @@ -2174,13 +2278,24 @@ for file_name in "$OUT_FILE_INIT" "$OUT_FILE_INPUT_SCRIPT" "$OUT_FILE_SETTINGS"; done -ls "${in_prefix}"* 2> /dev/null | while read file_name; do +# Process any custom input script files created by the user afterwards +#ls "${OUT_FILE_INPUT_SCRIPT}"* 2> /dev/null | while read file_name; do +for file_name in "${OUT_FILE_INPUT_SCRIPT}."*; do + if [ "$file_name" = "$OUT_FILE_INIT" ] || [ $file_name = "$OUT_FILE_INPUT_SCRIPT" ] || [ $file_name = "$OUT_FILE_SETTINGS" ]; then + continue + fi + if [[ "$file_name" == *.tmp ]]; then + continue + fi + if [[ "$file_name" == *.template ]]; then + continue + fi echo "postprocessing file \"$file_name\"" >&2 - if ! $PYTHON_COMMAND "${PY_SCR_DIR}/postprocess_input_script.py" input_scripts_so_far.tmp < "$file_name" > "$file_name".tmp; then + if ! $PYTHON_COMMAND "${PY_SCR_DIR}/postprocess_input_script.py" input_scripts_so_far.tmp < "$file_name" > "$file_name.tmp"; then ERR_INTERNAL fi echo "" >&2 - mv "$file_name".tmp "$file_name" + mv "$file_name.tmp" "$file_name" cat "$file_name" >> input_scripts_so_far.tmp done @@ -2188,6 +2303,7 @@ rm -f input_scripts_so_far.tmp + # ############ Optional: Add a fake run section as an example ############ diff --git a/tools/moltemplate/moltemplate/ttree.py b/tools/moltemplate/moltemplate/ttree.py index a68ada9f75..89777f3bdc 100755 --- a/tools/moltemplate/moltemplate/ttree.py +++ b/tools/moltemplate/moltemplate/ttree.py @@ -1,6 +1,6 @@ #!/usr/bin/env python -# Authors: Andrew Jewett (jewett.aij at g mail) +# Author: Andrew Jewett (jewett.aij at g mail) # http://www.moltemplate.org # http://www.chem.ucsb.edu/~sheagroup # License: 3-clause BSD License (See LICENSE.TXT) @@ -64,10 +64,10 @@ except NameError: # in words or tokens parsed by TtreeShlex. Otherwise it is identical to shlex. try: from .ttree_lex import TtreeShlex, SplitQuotedString, EscCharStrToChar, \ - SafelyEncodeString, RemoveOuterQuotes, MaxLenStr, HasWildCard, \ + SafelyEncodeString, RemoveOuterQuotes, MaxLenStr, HasWildcard, \ InputError, ErrorLeader, OSrcLoc, TextBlock, VarRef, VarBinding, \ TemplateLexer -except (SystemError, ValueError): +except (ImportError, SystemError, ValueError): # not installed as a package from ttree_lex import * @@ -1519,7 +1519,7 @@ def DescrToCatLeafNodes(descr_str, elif (create_missing_nodes and ((i_last_ptkn == len(leaf_ptkns) - 1) or - HasWildCard('/'.join(leaf_ptkns)))): + HasWildcard('/'.join(leaf_ptkns)))): # elif (create_missing_nodes and # (i_last_ptkn == len(leaf_ptkns)-1)): @@ -1951,9 +1951,9 @@ class StaticObj(object): break if ((cmd_token == 'write') or - (cmd_token == 'write_once') or - (cmd_token == 'create_var') or - (cmd_token == 'replace')): + (cmd_token == 'write_once') or + (cmd_token == 'create_var') or + (cmd_token == 'replace')): open_paren = lex.get_token() #print('Parse(): open_paren=\"'+open_paren+'\"') @@ -1980,7 +1980,14 @@ class StaticObj(object): tmpl_filename = None # This means: define the template without attaching # a file name to it. (IE., don't write the contents - # of what's enclosed in the curly brackets { } to a file.) + # of what's enclosed in the curly brackets { } to a file. + # Why? + # "create_var" commands are implemented as "write() {...}" + # commands (containing one or more variables) which + # never get written to a file or the terminal. Parsing + # the contents of the curly brackets defines the variables + # inside in the same way as parsing the text inside an + # ordinary "write() {...}" command. if (cmd_token == 'replace'): tmpl_filename = "ttree_replacements.txt" @@ -4259,7 +4266,7 @@ def AutoAssignVals(cat_node, # category counter without incrementing it. var_binding.value = str(cat.counter.query()) - elif HasWildCard(var_binding.full_name): + elif HasWildcard(var_binding.full_name): # -- The wildcard hack --- # Variables containing * or ? characters in their names # are not allowed. These are not variables, but patterns @@ -4634,7 +4641,7 @@ def WriteVarBindingsFile(node): # Now omit variables whos names contain "*" or "?" # (these are actually not variables, but wildcard patterns) - if not HasWildCard(var_binding.full_name): + if not HasWildcard(var_binding.full_name): if len(var_binding.refs) > 0: usage_example = ' #' +\ ErrorLeader(var_binding.refs[0].srcloc.infile, diff --git a/tools/moltemplate/moltemplate/ttree_lex.py b/tools/moltemplate/moltemplate/ttree_lex.py index e29d4bc35b..e93ca5bbd2 100644 --- a/tools/moltemplate/moltemplate/ttree_lex.py +++ b/tools/moltemplate/moltemplate/ttree_lex.py @@ -1,6 +1,7 @@ # -*- coding: iso-8859-1 -*- - +### -*- coding: utf-8 -*- # Author: Andrew Jewett (jewett.aij at g mail) +# http://www.moltemplate.org # http://www.chem.ucsb.edu/~sheagroup # License: 3-clause BSD License (See LICENSE.TXT) # Copyright (c) 2012, Regents of the University of California @@ -43,7 +44,8 @@ __all__ = ["TtreeShlex", "SafelyEncodeString", "RemoveOuterQuotes", "MaxLenStr", - "HasWildCard", + "HasWildcard", + "MatchesPattern", #"IsRegex", "InputError", "ErrorLeader", @@ -93,6 +95,10 @@ class TtreeShlex(object): self.commenters = '#' self.wordchars = ('abcdfeghijklmnopqrstuvwxyz' 'ABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789_') + #if self.posix: + # self.wordchars += ('ßàáâãäåæçèéêëìíîïðñòóôõöøùúûüýþÿ' + # 'ÀÁÂÃÄÅÆÇÈÉÊËÌÍÎÏÐÑÒÓÔÕÖØÙÚÛÜÝÞ') + if self.posix: self.wordchars += ('��������������������������������' '������������������������������') @@ -650,7 +656,7 @@ def MaxLenStr(s1, s2): # """ # return (len(pat)>=2) and (pat[0]=='/') and (pat[-1] == '/') -def HasWildCard(pat): +def HasWildcard(pat): """ Returns true if a string (pat) contains a '*' or '?' character. @@ -658,7 +664,7 @@ def HasWildCard(pat): return (pat.find('*') != -1) or (pat.find('?') != -1) -# def HasWildCard(pat): +# def HasWildcard(pat): # """ # Returns true if a string (pat) contains a non-backslash-protected # * or ? character. @@ -693,7 +699,7 @@ def MatchesPattern(s, pattern): # return False # new code: # uses precompiled regular expressions (See "pattern.search" below) - if HasWildCard(pattern): + if HasWildcard(pattern): if not fnmatch.fnmatchcase(s, pattern): return False elif s != pattern: @@ -1194,7 +1200,10 @@ def SplitTemplate(ltmpl, delim, delete_blanks=False): token_ltmpl = [] i = 0 while i < len(ltmpl): + entry = ltmpl[i] + #sys.stderr.write('ltmpl['+str(i)+'] = '+str(entry)+'\n') + if isinstance(entry, TextBlock): # if hasattr(entry, 'text'): prev_src_loc = entry.srcloc diff --git a/tools/moltemplate/moltemplate/ttree_matrix_stack.py b/tools/moltemplate/moltemplate/ttree_matrix_stack.py index 9c45fdc480..ba69cf7de7 100644 --- a/tools/moltemplate/moltemplate/ttree_matrix_stack.py +++ b/tools/moltemplate/moltemplate/ttree_matrix_stack.py @@ -1,4 +1,5 @@ # Author: Andrew Jewett (jewett.aij@gmail.com) +# http://www.moltemplate.org # http://www.chem.ucsb.edu/~sheagroup # License: 3-clause BSD License (See LICENSE.TXT) # Copyright (c) 2012, Regents of the University of California @@ -8,12 +9,19 @@ import random, math from collections import deque from array import array +#try: +# from StringIO import StringIO +#except ImportError: +# from io import StringIO + try: from .ttree_lex import InputError, ErrorLeader, OSrcLoc -except (SystemError, ValueError): +except (ImportError, SystemError, ValueError): # not installed as a package from ttree_lex import InputError, ErrorLeader, OSrcLoc + + def MultMat(dest, A, B): """ Multiply two matrices together. Store result in "dest". @@ -27,6 +35,21 @@ def MultMat(dest, A, B): for k in range(0, K): dest[i][j] += A[i][k] * B[k][j] +def Transpose(M): + return [ [M[j][i] for j in range(0, len(M))] + for i in range(0, len(M[0])) ] + + +def TransposeInPlace(M): + N = len(M) + for i in range(0, N): + for j in range(0, i): + M_ij = M[i][j] + M_ji = M[j][i] + M[i][j] = M_ji + M[j][i] = M_ij + + def MatToStr(M): strs = [] @@ -381,6 +404,51 @@ class AffineStack(object): AffineCompose(Mtmp, moveCentBack, Mdest) CopyMat(Mdest, Mtmp) + elif ((transform_str.find('quat(') == 0) or + (transform_str.find('quatT(') == 0)): + i_paren_close = transform_str.find(')') + if i_paren_close == -1: + i_paren_close = len(transform_str) + args = transform_str[5:i_paren_close].split(',') + center_v = None + if (len(args) == 7): + center_v = [float(args[4]), float(args[5]), float(args[6])] + elif (len(args) != 4): + raise InputError('Error near ' + ErrorLeader(src_loc.infile, src_loc.lineno) + ':\n' + ' Invalid command: \"' + transform_str + '\"\n' + ' This command requires either 4 or 7 numerical arguments. Either:\n' + ' rot(angle, axisX, axisY, axiZ) or \n' + ' rot(angle, axisX, axisY, axiZ, centerX, centerY, centerZ)') + M[0][3] = 0.0 # RotMatAXYZ() only modifies 3x3 submatrix of M + M[1][3] = 0.0 # The remaining final column must be zeroed by hand + M[2][3] = 0.0 + q = (float(args[0]), + float(args[1]), + float(args[2]), + float(args[3])) + Quaternion2Matrix(q, M) + if (transform_str.find('quatT(') == 0): + TransposeInPlace(M) + if (center_v == None): + AffineCompose(Mtmp, M, Mdest) + CopyMat(Mdest, Mtmp) + else: + # Move "center_v" to the origin + moveCentToOrig = [[1.0, 0.0, 0.0, -center_v[0]], + [0.0, 1.0, 0.0, -center_v[1]], + [0.0, 0.0, 1.0, -center_v[2]]] + AffineCompose(Mtmp, moveCentToOrig, Mdest) + CopyMat(Mdest, Mtmp) + # Rotate the coordinates (relative to the origin) + AffineCompose(Mtmp, M, Mdest) # M is the rotation matrix + CopyMat(Mdest, Mtmp) + # Move the origin back to center_v + moveCentBack = [[1.0, 0.0, 0.0, center_v[0]], + [0.0, 1.0, 0.0, center_v[1]], + [0.0, 0.0, 1.0, center_v[2]]] + AffineCompose(Mtmp, moveCentBack, Mdest) + CopyMat(Mdest, Mtmp) + # # elif transform_str.find('rotcm(') == 0: # # assert(xcm != None) # # i_paren_close = transform_str.find(')') @@ -585,6 +653,34 @@ class AffineStack(object): # # AffineCompose(Mtmp, moveCmBack, Mdest) # # CopyMat(Mdest, Mtmp) + #elif transform_str.find('read_xyz(') == 0: + # i_paren_close = transform_str.find(')') + # if i_paren_close == -1: + # i_paren_close = len(transform_str) + # args = transform_str[4:i_paren_close].split(',') + # if (len(args) != 1): + # raise InputError('Error near ' + ErrorLeader(src_loc.infile, src_loc.lineno) + ':\n' + # ' Invalid command: \"' + transform_str + '\"\n' + # ' This command expects the name of a file in XYZ format.\n') + # file_name = args[0] + # if (not file_name in coord_files): + # f = open(file_name, 'r') + # f.close() + # f.readline() # skip the first 2 lines + # f.readline() # of an .xyz file (header) + # for line in f: + # tokens = line.split() + # if (len(tokens) != 3) and (len(tokens) != 0): + # raise InputError('Error near ' + ErrorLeader(src_loc.infile, src_loc.lineno) + ':\n' + # ' Invalid command: \"' + transform_str + '\"\n' + # ' This command expects the name of a file in XYZ format.\n') + # crds.append((float(tokens[0]), + # float(tokens[1]), + # float(tokens[2])) + # self.coord_files[file_name] = crds + # else: + # crds = self.coord_files[file_name] + else: raise InputError('Error near ' + ErrorLeader(src_loc.infile, src_loc.lineno) + ':\n' ' Unknown transformation command: \"' + transform_str + '\"\n') @@ -601,6 +697,7 @@ class MultiAffineStack(object): self.stacks = None self.M = None self.error_if_substack_empty = False + self.coord_files = {} self.Clear() def Clear(self): @@ -610,6 +707,7 @@ class MultiAffineStack(object): self.stacks = deque([]) self.M = self.tot_stack.M self.error_if_substack_empty = False + self.coord_files = {} def _Update(self): self.tot_stack.Clear() @@ -793,6 +891,70 @@ def RotMatAXYZ(dest, angle, axis_x, axis_y, axis_z): # RotMatAXYZ(r, 90.0, 0.0, 0.0, 1.0) +def Quaternion2Matrix(q, M): + "convert a quaternion (q) to a 3x3 rotation matrix (M)""" + + M[0][0] = (q[0]*q[0])-(q[1]*q[1])-(q[2]*q[2])+(q[3]*q[3]) + M[1][1] = -(q[0]*q[0])+(q[1]*q[1])-(q[2]*q[2])+(q[3]*q[3]) + M[2][2] = -(q[0]*q[0])-(q[1]*q[1])+(q[2]*q[2])+(q[3]*q[3]) + M[0][1] = 2*(q[0]*q[1] - q[2]*q[3]); + M[1][0] = 2*(q[0]*q[1] + q[2]*q[3]); + M[1][2] = 2*(q[1]*q[2] - q[0]*q[3]); + M[2][1] = 2*(q[1]*q[2] + q[0]*q[3]); + M[0][2] = 2*(q[0]*q[2] + q[1]*q[3]); + M[2][0] = 2*(q[0]*q[2] - q[1]*q[3]); + + + +def Matrix2Quaternion(M, q): + """convert a 3x3 rotation matrix (M) to a quaternion (q) + http://www.euclideanspace.com/maths/geometry/rotations/conversions/matrixToQuaternion/ + """ + tr = M[0][0] + M[1][1] + M[2][2] + if tr > 0: + S = math.sqrt(tr+1.0) * 2 # S=4*qw + qw = 0.25 * S + qx = (M[2][1] - M[1][2]) / S + qy = (M[0][2] - M[2][0]) / S + qz = (M[1][0] - M[0][1]) / S + elif (M[0][0] > M[1][1]) and (M[0][0] > M[2][2]): + S = math.sqrt(1.0 + M[0][0] - M[1][1] - M[2][2]) * 2 # S=4*qx + qw = (M[2][1] - M[1][2]) / S + qx = 0.25 * S + qy = (M[0][1] + M[1][0]) / S + qz = (M[0][2] + M[2][0]) / S + elif (M[1][1] > M[2][2]): + S = math.sqrt(1.0 + M[1][1] - M[0][0] - M[2][2]) * 2 # S=4*qy + qw = (M[0][2] - M[2][0]) / S + qx = (M[0][1] + M[1][0]) / S + qy = 0.25 * S + qz = (M[1][2] + M[2][1]) / S + else: + S = math.sqrt(1.0 + M[2][2] - M[0][0] - M[1][1]) * 2 # S=4*qz + qw = (M[1][0] - M[0][1]) / S + qx = (M[0][2] + M[2][0]) / S + qy = (M[1][2] + M[2][1]) / S + qz = 0.25 * S + q[0] = qw + q[1] = qx + q[2] = qy + q[3] = qz + + +def MultQuat(dest, q1, q2): + """ multiply 2 quaternions and store the result in "qdest" + (q1[0] + i*q1[1] + j*q1[2] + k*q1[3]) + * + (q2[0] + i*q2[1] + j*q3[2] + k*q3[3]) + https://en.wikipedia.org/wiki/Quaternion#Hamilton_product + """ + dest[0] = q1[0]*q2[0] - q1[1]*q2[1] - q1[2]*q2[2] - q1[3]*q2[3] + dest[1] = q1[0]*q2[1] + q1[1]*q2[0] + q1[2]*q2[3] - q1[3]*q2[2] + dest[2] = q1[0]*q2[2] - q1[1]*q2[3] + q1[2]*q2[0] + q1[3]*q2[1] + dest[3] = q1[0]*q2[3] + q1[1]*q2[2] - q1[2]*q2[1] + q1[3]*q2[0] + + + def CrossProd(dest, A, B): dest[0] = (A[1] * B[2] - B[1] * A[2]) dest[1] = (A[2] * B[0] - B[2] * A[0]) diff --git a/tools/moltemplate/moltemplate/ttree_render.py b/tools/moltemplate/moltemplate/ttree_render.py index f59a04aeb5..15b26a2e70 100755 --- a/tools/moltemplate/moltemplate/ttree_render.py +++ b/tools/moltemplate/moltemplate/ttree_render.py @@ -21,7 +21,7 @@ import gc try: from .ttree import ExtractFormattingCommands from .ttree_lex import SplitQuotedString, InputError, TemplateLexer -except (SystemError, ValueError): +except (ImportError, SystemError, ValueError): # not installed as a package from ttree import ExtractFormattingCommands from ttree_lex import SplitQuotedString, InputError, TemplateLexer @@ -31,11 +31,14 @@ g_filename = __file__.split('/')[-1] g_module_name = g_filename if g_filename.rfind('.py') != -1: g_module_name = g_filename[:g_filename.rfind('.py')] -g_date_str = '2016-12-21' -g_version_str = '0.2.0' +g_date_str = '2017-11-04' +g_version_str = '0.2.2' g_program_name = g_filename #sys.stderr.write(g_program_name+' v'+g_version_str+' '+g_date_str+' ') + + + def main(): try: if (len(sys.argv) != 2): @@ -79,21 +82,43 @@ def main(): assert(isinstance(entry, str)) if ((len(entry) > 1) and (entry[0] in lex.var_delim)): + + if ((len(entry) >= 3) and + (entry[1] == '{') and + (entry[-1] == '}')): + entry = entry[0] + entry[2:-1] + if '.' in entry: ic = entry.find('.') var_name = entry[:ic] var_suffix = entry[ic:] + if not var_suffix[0:7] in ('.ljust(', '.rjust('): + var_name = entry + var_suffix = '' else: var_name = entry var_suffix = '' - var_name = entry if var_name not in assignments: - raise(InputError('Error(' + g_program_name + ')' - #' at '+ErrorLeader(var_ref.src_loc.infile, - # var_ref.src_loc.lineno)+ - ' unknown variable:\n' - ' \"' + var_name + '\"\n')) + #COMMENTING OUT: + #raise(InputError('Error(' + g_program_name + ')' + # #' at '+ErrorLeader(var_ref.src_loc.infile, + # # var_ref.src_loc.lineno)+ + # ' unknown variable:\n' + # ' \"' + var_name + '\"\n')) + # ...actually don't raise an error message: + # Actually there are some legitimate reaons this could occur. + # Some users want to put LAMMPS-style variables in the + # write_once() {...} text blocks in their moltemplate files. + # Variables in both LAMMPS and moltemplate contain $ characters, + # and this script gets confused. Better to just ignore it + # when this happens instead of printing an error message. + # Just leave the text alone and print the variable name. + # + # Do this by substituting the variable's name as it's value: + + var_value = var_name + else: var_value = assignments[var_name] diff --git a/tools/moltemplate/setup.py b/tools/moltemplate/setup.py index 30e835de0c..925850a49e 100644 --- a/tools/moltemplate/setup.py +++ b/tools/moltemplate/setup.py @@ -4,7 +4,12 @@ setup( name='moltemplate', - packages=['moltemplate', 'moltemplate/nbody_alt_symmetry'], + packages=['moltemplate', + 'moltemplate.nbody_alt_symmetry'], + + package_dir={'moltemplate': 'moltemplate'}, #.py files are in "moltemplate/" + + package_data={'moltemplate': ['force_fields/*.lt']}, #.lt files are in "moltemplate/force_fields/" description='A general cross-platform text-based molecule builder for LAMMPS', @@ -14,9 +19,9 @@ setup( url='https://github.com/jewettaij/moltemplate', - download_url='https://github.com/jewettaij/moltemplate/archive/v2.3.7.zip', + download_url='https://github.com/jewettaij/moltemplate/archive/v2.8.6.zip', - version='2.3.7', + version='2.8.6', keywords=['simulation', 'LAMMPS', 'molecule editor', 'molecule builder', 'ESPResSo'], @@ -32,7 +37,13 @@ setup( 'License :: OSI Approved :: BSD License', 'Operating System :: MacOS :: MacOS X', 'Operating System :: POSIX :: Linux', - 'Operating System :: Microsoft :: Windows'], + 'Operating System :: Microsoft :: Windows', + 'Programming Language :: Python', + 'Programming Language :: Unix Shell', + 'Topic :: Scientific/Engineering :: Chemistry', + 'Topic :: Scientific/Engineering :: Physics', + 'Topic :: Multimedia :: Graphics :: 3D Modeling', + 'Intended Audience :: Science/Research'], scripts=['moltemplate/scripts/moltemplate.sh', 'moltemplate/scripts/cleanup_moltemplate.sh', @@ -58,13 +69,13 @@ setup( 'nbody_reorder_atoms.py=moltemplate.nbody_reorder_atoms:main', 'pdbsort.py=moltemplate.pdbsort:main', 'postprocess_input_script.py=moltemplate.postprocess_input_script:main', + 'postprocess_coeffs.py=moltemplate.postprocess_coeffs:main', 'raw2data.py=moltemplate.raw2data:main', 'remove_duplicate_atoms.py=moltemplate.remove_duplicate_atoms:main', 'remove_duplicates_nbody.py=moltemplate.remove_duplicates_nbody:main', 'renumber_DATA_first_column.py=moltemplate.renumber_DATA_first_column:main']}, - package_data={'moltemplate': ['force_fields/*.lt']}, - # install_requires=['numpy', 'scipy', 'biopython'], + # install_requires=['numpy', 'scipy'], setup_requires=['pytest-runner'], tests_require=['pytest'], zip_safe=True,